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

Microbiota-derived IPA alleviates intestinal mucosal inflammation through upregulating Th1/Th17 cell apoptosis in inflammatory bowel disease

The gut microbiota-derived metabolite indole-3-propionic acid (IPA) plays an important role in maintaining intestinal mucosal homeostasis, while the molecular mechanisms underlying IPA regulation on mucosal CD4+ T cell functions in inflammatory bowel disease (IBD) remain elusive. Here we investigated the roles of IPA in modulating mucosal CD4+ T cells and its therapeutic potential in treatment of human IBD. Leveraging metabolomics and microbial community analyses, we observed that the levels of IPA-producing microbiota (e.g. Peptostreptococcus, Clostridium, and Fournierella) and IPA were decreased, while the IPA-consuming microbiota (e.g. Parabacteroides, Erysipelatoclostridium, and Lachnoclostridium) were increased in the feces of IBD patients than those in healthy donors. Dextran sulfate sodium (DSS)-induced acute colitis and CD45RBhighCD4+ T cell transfer-induced chronic colitis models were then established in mice and treated orally with IPA to study its role in intestinal mucosal inflammation in vivo. We found that oral administration of IPA attenuated mucosal inflammation in both acute and chronic colitis models in mice, as characterized by increased body weight, and reduced levels of pro-inflammatory cytokines (e.g. TNF-α, IFN-γ, and IL-17A) and histological scores in the colon. We further utilized RNA sequencing, molecular docking simulations, and surface plasmon resonance analyses and identified that IPA exerts its biological effects by interacting with heat shock protein 70 (HSP70), leading to inducing Th1/Th17 cell apoptosis. Consistently, ectopic expression of HSP70 in CD4+ T cells conferred resistance to IPA-induced Th1/Th17 cell apoptosis. Therefore, these findings identify a previously unrecognized pathway by which IPA modulates intestinal inflammation and provide a promising avenue for the treatment of IBD.

Interplay of gut microbiota in Kawasaki disease: role of gut microbiota and potential treatment strategies

Kawasaki disease (KD) is an acute systemic immune vasculitis with predominant involvement of the medium and small arteries. It mostly affects pediatric patients, representing the most common form of pediatric vasculitis in children less than 5 years old. Numerous diseases, especially those related to the immune system, have established links with the intestinal flora. Recent studies have investigated the intestinal flora changes throughout the management of KD. There was gut microbiota dysbiosis in pediatric KD at the acute phase, particularly the downregulation of short-chain fat acids-producing microbiota and the over-proliferation of opportunistic pathogens. The relationship between the response to therapies in individuals with KD and specific microbiota remains uncertain. Targeted microbial supplements and dietary regulation may serve as potential measures to alleviate KD complications and thus improve prognosis. This review provides an overview of the current understanding of the interplay of the gut microbiota and KD. Furthermore, it discusses the possibility of altering the gut microbiota to reinstate a healthy condition.

Bile acid receptor FXR promotes intestinal epithelial ferroptosis and subsequent ILC3 dysfunction in neonatal necrotizing enterocolitis

Necrotizing enterocolitis (NEC) is a common pediatric emergency primarily afflicting preterm infants, yet its mechanisms remain to be fully understood. Here, we report that plasma fibroblast growth factor (FGF)19, a target of farnesoid X receptor (FXR), was positively correlated with the clinical parameters of NEC. NEC patients and the NEC murine model displayed abundant FXR in intestinal epithelial cells (IECs), which was restricted by microbiota-derived short-chain fatty acids (SCFAs) under homeostasis. Genetic deficiency of FXR in IECs caused remission of NEC. Mechanistically, FXR facilitated ferroptosis of IECs via targeting acyl-coenzyme A synthetase long-chain family member 4 (Acsl4). Lipid peroxides released by ferroptotic IECs suppressed interleukin (IL)-22 secretion from type 3 innate lymphoid cells (ILC3s), thereby exacerbating NEC. Intestinal FXR antagonist, ACSL4 inhibitor, and ferroptosis inhibitor ameliorated murine NEC. Furthermore, the elevated lipid peroxides in NEC patients were positively correlated with FGF19 and disease parameters. These observations demonstrate the therapeutic value of targeting intestinal FXR and ferroptosis in NEC treatment.

Effect of prenatal antibiotics on breast milk and neonatal IgA and microbiome: a case-control translational study protocol

BACKGROUND

Up to 25-35% of women receive antibiotics (ABX) during pregnancy, but little is known about the consequences on a key mucosal interface such as the mammary gland, and on the development of the neonatal gut's microbiota and IgA. We hypothesize that prenatal ABX negatively affect the immune functionality of mammary gland, the composition of breast milk microbiota, the development of neonatal fecal microbiota and the abundance of neonatal fecal IgA.

METHODS

Case-control translational cohort study on women and neonates in the presence or absence (N = 41 + 41 pairs) of exposure to prenatal ABX for at least 7 consecutive days after 32 weeks of gestation.

RESULTS

We will evaluate IgA concentration in breast milk and in neonatal feces up to one year after delivery. We will also evaluate clinical parameters, neurodevelopment and the composition of the IgA-coated and uncoated fractions of breast milk and fecal microbiota by means of magnetic-activated cell sorting (MACS) coupled with shotgun metagenomics. Finally, we will measure the concentration of the chemokine CCL28 on maternal serum and breast milk, as a marker of activity of the entero-mammary pathway.

CONCLUSIONS

Our results might support a data-driven evaluation of breast milk immune function in women exposed to prenatal ABX.

IMPACT

Breast milk IgA and microbiota are critical to determine the positive effects of breastfeeding in infants. This research protocol will investigate breast milk IgA, microbiota, and the IgA+ / IgA- fractions of neonatal fecal microbiota upon exposure to prenatal antibiotics. Fecal IgA and microbiota in infants exposed or not exposed to prenatal antibiotics will be analyzed up to 1 year after birth. This research will clarify the impact of prenatal antibiotics on the immune function of breast milk. This, in turn, might support the selective evaluation of breast milk IgA/microbiota in mothers exposed to prenatal antibiotics, or in donor human milk.

Identification of disease-specific gut microbial markers in vitiligo

There is a potential correlation between vitiligo and gut microbiota, although research in this area is currently limited. The research employed high-throughput sequencing of 16S rRNA to examine the gut microbiome in the stool samples of 49 individuals with vitiligo and 49 without the condition. The study encompassed four comparison groups: (1) DI (disease) group vs. HC (healthy control) group; (2) DI_m group (disease group of minors) vs. HC_m group (healthy control group of minors); (3) DI_a group (adult disease group) vs. HC_a group (adult healthy control group); (4) DI_m group vs. DI_a group. Research findings have indicated the presence of spatial heterogeneity in the gut microbiota composition between individuals with vitiligo and healthy controls. A significant reduction in gut microbiota diversity has been observed in vitiligo patients across both minors and adult groups. However, variations have been noted in the composition of disease-related differential microbial markers among different age groups. Specifically, Bacteroides and Parabacteroides have been identified as specific markers of the intestinal microbiota of vitiligo patients in both minor and adult groups. Correlative analyses have revealed a positive correlation of these two genera with the Vitiligo Area Scoring Index (VASI) and disease duration. It is noteworthy that there are no significant differences in diversity between the DI_m group and the DI_a group, with similarities in microbiota composition and functional characteristics. Nevertheless, correlative analyses suggest a declining trend in Bacteroides and Parabacteroides with increasing age. Individuals with vitiligo exhibit distinct features in their gut microbiome when contrasted with those in the healthy control group. Additionally, the microbial marker genera that show variances between patients and healthy controls vary among different age groups. Disease-specific microbial marker genera (Bacteroides and Parabacteroides) are associated with VASI, duration of the condition, and age. These findings are essential for improving early diagnosis and developing potential treatment strategies for individuals with vitiligo.

Gut microbiota and atrial cardiomyopathy

Atrial cardiomyopathy is a multifaceted heart disease characterized by structural and functional abnormalities of the atria and is closely associated with atrial fibrillation and its complications. Its etiology involves a number of factors, including genetic, infectious, immunologic, and metabolic factors. Recent research has highlighted the critical role of the gut microbiota in the pathogenesis of atrial cardiomyopathy, and this is consistent with the gut-heart axis having major implications for cardiac health. The aim of this work is to bridge the knowledge gap regarding the interactions between the gut microbiota and atrial cardiomyopathy, with a particular focus on elucidating the mechanisms by which gut dysbiosis may induce atrial remodeling and dysfunction. This article provides an overview of the role of the gut microbiota in the pathogenesis of atrial cardiomyopathy, including changes in the composition of the gut microbiota and the effects of its metabolites. We also discuss how diet and exercise affect atrial cardiomyopathy by influencing the gut microbiota, as well as possible future therapeutic approaches targeting the gut-heart axis. A healthy gut microbiota can prevent disease, but ecological dysbiosis can lead to a variety of symptoms, including the induction of heart disease. We focus on the pathophysiological aspects of atrial cardiomyopathy, the impact of gut microbiota dysbiosis on atrial structure and function, and therapeutic strategies exploring modulation of the microbiota for the treatment of atrial cardiomyopathy. Finally, we discuss the role of gut microbiota in the treatment of atrial cardiomyopathy, including fecal microbiota transplantation and oral probiotics or prebiotics. Our study highlights the importance of gut microbiota homeostasis for cardiovascular health and suggests that targeted interventions on the gut microbiota may pave the way for innovative preventive and therapeutic strategies targeting atrial cardiomyopathy.

Alzheimer's disease and gut-brain axis: Drosophila melanogaster as a model

Research indicates that by 2050, more than 150 million people will be living with Alzheimer's disease (AD), a condition associated with neurodegeneration due to the accumulation of amyloid-beta and tau proteins. In addition to genetic background, endocrine disruption, and cellular senescence, management of the gut microbiota has emerged as a key element in the diagnosis, progression, and treatment of AD, as certain bacterial metabolites can travel through the bloodstream and cross the blood-brain barrier. This mini-review explores the relationship between tau protein accumulation and gut dysbiosis in Drosophila melanogaster. This model facilitates the investigation of how gut-derived metabolites contribute to neurocognitive impairment and dementia. Understanding the role of direct and indirect bacterial by-products, such as lactate and acetate, in glial cell activation and tau protein dynamics may provide insights into the mechanisms of AD progression and contribute to more effective treatments. Here we discuss how the simplicity and extensive genetic tools of Drosophila make it a valuable model for studying these interactions and testing potential therapeutics, including probiotics. Integrating Drosophila studies with other established models may reveal conserved pathways and accelerate the translation of findings into clinical applications.

The microbiota-gut-brain axis: a potential target in the small-molecule compounds and gene therapeutic strategies for Parkinson's disease

BACKGROUNDS

Parkinson's disease (PD) is a common neurodegenerative disorder characterized by motor symptoms and non-motor symptoms. It has been found that intestinal issues usually precede motor symptoms. Microorganisms in the gastrointestinal tract can affect central nervous system through the microbiota-gut-brain axis. Accumulating evidence has shown that disturbances in the microbiota-gut-brain axis are linked with PD. Thus, this pathway appears to be a promising therapeutic target for treatment of PD.

OBJECTIVES

In this review, we mainly described gut dysbiosis in PD and their underlying mechanisms for mediating neuroinflammation and peripheral immune response in PD pathology and futher discussed the potential small-molecule compounds and genic therapeutic strategies targeting the microbiota-gut-brain axis and their applications in PD.

CONCLUSIONS

Studies have found that some small molecule compounds and alterations of inflammation-related genes can improve the motor and non-motor symptoms of PD by improving the microbiota-gut-brain axis, which may provide potentially beneficial drugs and molecular targets for the therapies of PD.

How the early life microbiome shapes immune programming in childhood asthma and allergies

Despite advances in our understanding of their diagnosis and treatment, pediatric allergies impose substantial burdens on affected children, families, and healthcare systems. Further, the prevalence of allergic diseases has dramatically increased over the past half-century, leading to additional concerns and concerted efforts to identify the origins, potential predictors and preventions, and therapies of allergic diseases. Together with the increase in allergic diseases, changes in lifestyle and early-life environmental influences have corresponded with changes in colonization patterns of the infant gut microbiome. The gut microbiome plays a key role in developing the immune system, thus greatly influencing the development of allergic disease. In this review, we specifically highlight the importance of the proper maturation and composition of the gut microbiome as an essential step in healthy child development or disease progression. By exploring the intertwined development of the immune system and microbiome across pediatric allergic diseases, we provide insights into potential novel strategies for their prevention and management.

Aspartate Metabolism-Driven Gut Microbiota Dynamics and RIP-Dependent Mitochondrial Function Counteract Oxidative Stress

Aspartate (Asp) metabolism-mediated antioxidant functions have important implications for neonatal growth and intestinal health; however, the antioxidant mechanisms through which Asp regulates the gut microbiota and influences RIP activation remain elusive. This study reports that chronic oxidative stress disrupts gut microbiota and metabolite balance and that such imbalance is intricately tied to the perturbation of Asp metabolism. Under normal conditions, in vivo and in vitro studies reveal that exogenous Asp improves intestinal health by regulating epithelial cell proliferation, nutrient uptake, and apoptosis. During oxidative stress, Asp reduces Megasphaera abundance while increasing Ruminococcaceae. This reversal effect depends on the enhanced production of the antioxidant eicosapentaenoic acid mediated through Asp metabolism and microbiota. Mechanistically, the application of exogenous Asp orchestrates the antioxidant responses in enterocytes via the modulation of the RIP3-MLKL and RIP1-Nrf2-NF-κB pathways to eliminate excessive reactive oxygen species and maintain mitochondrial functionality and cellular survival. These results demonstrate that Asp signaling alleviates oxidative stress by dynamically modulating the gut microbiota and RIP-dependent mitochondrial function, providing a potential therapeutic strategy for oxidative stress disease treatment.

Gut Microbes as the Major Drivers of Rheumatoid Arthritis: Our Microbes Are Our Fortune!

Rheumatoid arthritis (RA) is an autoimmune disease with an unknown etiology. While certain genes provide strong susceptibility factors, the role of environmental factors is becoming increasingly recognized. Among genetic factors, human leukocyte antigen (HLA) genes, encoded within the major histocompatibility complex (MHC), have been linked to predisposition to RA, while among environmental factors, smoking, infections and diet are the major contributors. Genetic and environmental factors impact microbial composition in the host. Based on the dysbiosis observed in the gut and lung microbiome, a mucosal origin of RA has been suggested. However, proving whether genes or microbes provide a stronger risk factor has been difficult. Studies from RA patients and various mouse models, specifically humanized mice expressing HLA class II genes, have been instrumental in defining the role of environmental factors such as smoking and endogenous small intestinal microbes in modulating arthritis severity. The consensus based on most studies support an interaction between host genetic and environmental factors in the onset and severity of disease. However, until now, no microbial markers for disease prognosis or treatment efficacy have been available. Here, the role of gut microbes as markers of disease severity, and the potential for using endogenous commensals for modulating immune responses to suppress inflammation in the context of genetic factors, are discussed.

The success of the tumor immunotherapy: neutrophils from bench to beside

The present immune therapy was focused on the immune checkpoint blockade or Chimeric Antigen Receptor T-Cell Immunotherapy (CART) transfer, but how to activate the innate immune system to antitumor still lags out. Neutrophils are the most abundant circulating leukocytes in human, and heterogeneous neutrophils have been increasingly recognized as important players in tumor progression. They play double "edge-sward" by either supporting or suppressing the tumor growth, including driving angiogenesis, extracellular matrix remodeling to promote tumor growth, participating in antitumor adaptive immunity, or killing tumor cells directly to inhibit the tumor growth. The complex role of neutrophils in various tumors depends on the tumor microenvironment (TME) they are located, and emerging evidence has suggested that neutrophils may determine the success of tumor immunotherapy in the context of the immune checkpoint blockade, innate immune training, or drug-loaded extracellular microvesicles therapy, which makes them become an exciting target for tumor immunotherapy, but still with challenges. Here, we summarize the latest insights on how to activate neutrophils in antitumor immunity and discuss the advances of neutrophil-targeted immunotherapy strategies.

The right tool for the job: Chemical biology and microbiome science

Microbiomes exist in ecological niches ranging from the ocean and soil to inside of larger organisms like plants and animals. Within these niches, microbes play key roles in biochemical processes that impact larger phenomena, such as biogeochemical cycling or health. By understanding of how these processes occur at the molecular level, it may be possible to develop new interventions to address global problems. The complexity of these systems poses challenges to more traditional techniques. Chemical biology can help overcome these challenges by providing tools that are broadly applicable and can obtain molecular-level information about complex systems. This primer is intended to serve as a brief introduction to chemical biology and microbiome science, to highlight some of the ways that these two disciplines complement each other, and to encourage dialog and collaboration between these fields.

Dynamics of Bacterial and Viral Transmission in Experimental Microbiota Transplantation

Mouse models are vital tools for discerning the relative contributions of host and microbial genetics to disease, often requiring the transplantation of microbiota between different mouse strains. Transfer methods include antibiotic treatment of recipients and colonization using either co-housing with donors or the transplantation of fecal or cecal donor material. However, the efficiency and dynamics of these methods in reconstituting recipients with donor microbes is not well understood. We thus directly compared co-housing, fecal transplantation, and cecal transplantation methods. Donor mice from Taconic Biosciences, possessing distinct microbial communities, served as the microbial source for recipient mice from Jackson Laboratories, which were treated with antibiotics to disrupt their native microbiota. We monitored microbial populations longitudinally over the course of antibiotics treatment and reconstitution using 16S rRNA gene sequencing, quantitative PCR, and shotgun sequencing of viral-like particles. As expected, antibiotic treatment rapidly depleted microbial biomass and diversity, with slow and incomplete natural recovery of the microbiota in non-transplanted control mice. While all transfer methods reconstituted recipient mice with donor microbiota, co-housing achieved this more rapidly for both bacterial and viral communities. This study provides valuable insights into microbial transfer methods, enhancing reproducibility and informing best practices for microbiota transplantation in mouse models.

Establishment and maturation of gut microbiota in White King pigeon squabs: role of pigeon milk

Background

Pigeons are significant economic animals in China; however, research regarding the establishment and influencing factors of gut microbiota in squabs remains limited. Understanding how the gut microbiota develops in pigeons, particularly in relation to pigeon milk, is importance in pigeon production. This study aims to elucidate the establishment characteristics of the gut microbiota in White King pigeon squabs and explore the role of pigeon milk in this process.

Methods

This study employed 16S rRNA sequencing technology to investigate the dynamics of microbial composition in feces and pigeon milk at various growth stages of White King pigeon. Functional prediction analysis was performed to assess the metabolic pathways involved, and correlation analysis was used to explore the relationships between microbial communities in different sample types.

Results

The findings revealed a diverse microbiome present in the meconium of newborn pigeons, with a microbial composition that significantly differed from that of other feces groups. In contrast, the microbial composition of feces (FN) from pigeons aged 7 to 21 days exhibited less variability. At the phylum level, the predominant microbial taxa identified in the feces of FN were Firmicutes, Actinobacteriota, and Proteobacteria. At the genus level, the main dominant bacterial groups included Lactobacillus, Limosilactobacillus, and Turicibacter. Functional prediction analysis indicated that the gut microbiota of pigeons primarily participate in metabolic pathways related to carbohydrates, amino acids, lipids, cofactors, and vitamins. Furthermore, the dominant bacteria found in pigeon milk (MN) were identified as probiotics, including Limosilactobacillus, Ligilactobacillus, Lactobacillus, Bifidobacterium, and Aeriscardovia, which collectively accounted for over 90% of the total abundance. Correlation analysis of the abundance of shared microbes revealed that the association between meconium and feces at the other stages was extremely low. In contrast, the correlation between colostrum and feces at the post-feeding stage were found to be the highest.

Conclusion

This study indicates that prenatal colonization occurs in White King pigeons. Notably, within the first week after birth, the gut microbial composition of young pigeons becomes stable. Furthermore, the colostrum serves as the most significant driver for the establishment of intestinal microbiota in squab post-birth. The findings of this study suggest that microorganisms can be added to artificial pigeon milk based on the predominant microbial composition of colostrum. This approach could facilitate the establishment of gut microbiota in young pigeons, thereby promoting their growth and development and providing production benefits.

Impact of Early-Life Microbiota on Immune System Development and Allergic Disorders

Introduction: The shaping of the human intestinal microbiota starts during the intrauterine period and continues through the subsequent stages of extrauterine life. The microbiota plays a significant role in the predisposition and development of immune diseases, as well as various inflammatory processes. Importantly, the proper colonization of the fetal digestive system is influenced by maternal microbiota, the method of pregnancy completion and the further formation of the microbiota. In the subsequent stages of a child's life, breastfeeding, diet and the use of antibiotics influence the state of eubiosis, which determines proper growth and development from the neonatal period to adulthood. The literature data suggest that there is evidence to confirm that the intestinal microbiota of the infant plays an important role in regulating the immune response associated with the development of allergic diseases. However, the identification of specific bacterial species in relation to specific types of reactions in allergic diseases is the basic problem. Background: The main aim of the review was to demonstrate the influence of the microbiota of the mother, fetus and newborn on the functioning of the immune system in the context of allergies and asthma. Methods: We reviewed and thoroughly analyzed the content of over 1000 articles and abstracts between the beginning of June and the end of August 2024. Over 150 articles were selected for the detailed study. Results: The selection was based on the PubMed National Library of Medicine search engine, using selected keywords: "the impact of intestinal microbiota on the development of immune diseases and asthma", "intestinal microbiota and allergic diseases", "the impact of intrauterine microbiota on the development of asthma", "intrauterine microbiota and immune diseases", "intrauterine microbiota and atopic dermatitis", "intrauterine microbiota and food allergies", "maternal microbiota", "fetal microbiota" and "neonatal microbiota". The above relationships constituted the main criteria for including articles in the analysis. Conclusions: In the present review, we showed a relationship between the proper maternal microbiota and the normal functioning of the fetal and neonatal immune system. The state of eubiosis with an adequate amount and diversity of microbiota is essential in preventing the development of immune and allergic diseases. The way the microbiota is shaped, resulting from the health-promoting behavior of pregnant women, the rational conduct of the medical staff and the proper performance of the diagnostic and therapeutic process, is necessary to maintain the health of the mother and the child. Therefore, an appropriate lifestyle, rational antibiotic therapy as well as the way of completing the pregnancy are indispensable in the prevention of the above conditions. At the same time, considering the intestinal microbiota of the newborn in relation to the genera and phyla of bacteria that have a potentially protective effect, it is worth noting that the use of suitable probiotics and prebiotics seems to contribute to the protective effect.

The relationship between prenatal drought exposure and the diversity and composition of gut microbiome in pregnant women and neonates

Drought induced by climate change poses a serious threat to human health. The gut microbiome also plays a critical role in human health. However, no studies have explored the effect of drought on the human gut microbiome. Therefore, our study aimed to investigate the relationship between drought and gut microbiome. Our study included 59 mothers and 38 neonates in our study. 16S rRNA V3-V4 sequencing was used to profile the gut microbiome. The Standardized Precipitation Evapotranspiration Index (SPEI) was used to represent drought characteristics. KEGG pathway level 3 was employed for functional analysis. Generalized linear models were used to explore the effect of drought on the gut microbiome. Mothers and neonates were divided into the LSPEI (Lower SPEI) group or HSPEI (Higher SPEI) group by calculating the average levels of prenatal SPEI levels. The maternal and neonatal gut microbiome exhibited similar diversities in terms of alpha and beta diversity between the LSPEI and HSPEI groups. However, notable differences were observed in their composition. We found that in the neonatal gut microbiome, Sediminibacterium and Thermovirga were positively associated with SPEI after controlling for PM2.5 in linear regression models. Additionally, SPEI was significantly associated with phenylpropanoid biosynthesis and cyanoamino acid metabolism in neonates. This study identified that prenatal SPEI levels were correlated with specific maternal and neonatal gut microbial taxa, as well as neonatal gut microbial functional pathways. Future studies should further investigate the mechanisms by which drought exposure influences maternal and neonatal gut microbial diversities, composition, and functional pathways.

How maternal factors shape the immune system of breastfed infants to alleviate food allergy: A systematic and updated review

What infants eat early in life may shape the immune system and have long-standing consequences on the health of the host during later life. In the early months post-birth, breast milk serves as the exclusive and optimal nourishment for infants, facilitating crucial molecular exchanges between mother and infant. Recent advances have uncovered that some maternal factors influence breastfed infant outcomes, including the risk of food allergy (FA). To date, accumulated data show that breastfed infants have a lower risk of FA. However, the issue remains disputed, some reported preventive allergy effects, while others did not confirm such effects, or if identified, protective effects were limited to early childhood. The disputed outcomes may be attributed to the maternal status, as it determines the compounds of the breast milk that breastfed infants are exposed to. In this review, we first detail the compounds in breast milk and their roles in infant FA. Then, we present maternal factors resulting in alterations in breast milk compounds, such as maternal health status, maternal diet intake, and maternal food allergen intake, which subsequently impact FA in breastfed infants. Finally, we analyze how these compounds in breast milk alleviated the infant FA by mother-to-infant transmission. Altogether, the mechanisms are primarily linked to the synergetic and direct effects of compounds in breast milk, via promoting the colonization of gut microbiota and the development of the immune system in infants.

The renaissance of oral tolerance: merging tradition and new insights

Oral tolerance is the process by which feeding of soluble proteins induces antigen-specific systemic immune unresponsiveness. Oral tolerance is thought to have a central role in suppressing immune responses to 'harmless' food antigens, and its failure can lead to development of pathologies such as food allergies or coeliac disease. However, on the basis of long-standing experimental observations, the relevance of oral tolerance in human health has achieved new prominence recently following the discovery that oral administration of peanut proteins prevents the development of peanut allergy in at-risk human infants. In this Review, we summarize the new mechanistic insights into three key processes necessary for the induction of tolerance to oral antigens: antigen uptake and transport across the small intestinal epithelial barrier to the underlying immune cells; the processing, transport and presentation of fed antigen by different populations of antigen-presenting cells; and the development of immunosuppressive T cell populations that mediate antigen-specific tolerance. In addition, we consider how related but distinct processes maintain tolerance to bacterial antigens in the large intestine. Finally, we outline the molecular mechanisms and functional consequences of failure of oral tolerance and how these may be modulated to enhance clinical outcomes and prevent disease.

Influence of gut flora on diabetes management after kidney transplantation

Post-transplant diabetes mellitus (PTDM) is a common complication following renal transplantation, and its incidence has been gradually increasing in recent years, posing a significant public health challenge. Managing PTDM is complex, as studies suggest that it involves changes in the microbial flora across multiple organs. Recent research highlights the critical role of gut flora metabolism in the development of diabetes among post-renal transplant patients. This paper reviews the alterations in gut flora observed in PTDM patients and explores how gut flora influences PTDM. These findings may offer new perspectives on targeting gut flora metabolites for the prevention and treatment of PTDM.

Enzymatic Regulation of the Gut Microbiota: Mechanisms and Implications for Host Health

The gut microbiota, a complex ecosystem, is vital to host health as it aids digestion, modulates the immune system, influences metabolism, and interacts with the brain-gut axis. Various factors influence the composition of this microbiota. Enzymes, as essential catalysts, actively participate in biochemical reactions that have an impact on the gut microbial community, affecting both the microorganisms and the gut environment. Enzymes play an important role in the regulation of the intestinal microbiota, but the interactions between enzymes and microbial communities, as well as the precise mechanisms of enzymes, remain a challenge in scientific research. Enzymes serve both traditional nutritional functions, such as the breakdown of complex substrates into absorbable small molecules, and non-nutritional roles, which encompass antibacterial function, immunomodulation, intestinal health maintenance, and stress reduction, among others. This study categorizes enzymes according to their source and explores the mechanistic principles by which enzymes drive gut microbial activity, including the promotion of microbial proliferation, the direct elimination of harmful microbes, the modulation of bacterial interaction networks, and the reduction in immune stress. A systematic understanding of enzymes in regulating the gut microbiota and the study of their associated molecular mechanisms will facilitate the application of enzymes to precisely regulate the gut microbiota in the future and suggest new therapeutic strategies and dietary recommendations. In conclusion, this review provides a comprehensive overview of the role of enzymes in modulating the gut microbiota. It explores the underlying molecular and cellular mechanisms and discusses the potential applications of enzyme-mediated microbiota regulation for host gut health.

Gestational diabetes-combined excess weight gain exacerbates gut microbiota dysbiosis in newborns, associated with reduced abundance of Clostridium, Coriobacteriaceae, and Collinsella

Background

Existing literature indicates that Gestational diabetes mellitus (GDM) and maternal obesity disrupt the normal colonization of the neonatal gut microbiota alone. Still, the combined impact of GDM and excessive gestational weight gain (EGWG) on this process remains under explored. The association between gestational weight gain before/after GDM diagnosis and neonatal gut microbiota characteristics is also unclear.The purpose of this study is to conduct investigation and analysis on the above-mentioned issues, providing a basis for optimizing clinical management plans.

Methods

This study involved 98 mother-infant pairs categorized into GDM and non-GDM groups. The GDM group was further subdivided based on gestational weight gain (GWG) into normal (GDM+NGWG) and excessive (GDM+EGWG) weight gain groups. Neonatal stool samples were collected within 24 hours post-delivery for gut microbiota profiling through 16S rRNA gene sequencing. Statistical analyses explored correlations between total GWG/BMI gain and those before/after GDM diagnosis (t-GWG/GBG; b-GWG/GBG; a-GWG/GBG) with key bacterial taxa.

Results

Notable genus-level changes included enrichment of Escherichia and Klebsiella, and depletion of Bacteroides, Bifidobacterium, Coprococcus, Ruminococcus among GDM-Total and GDM+EGWG groups compared to non-GDM. Further,LEfSe analysis identified 30 differential bacteria taxa between GDM-Total and healthy control groups, which increased to 38 between GDM+EGWG and non-GDM groups, highlighting more pronounced microbial shifts associated with EGWG. Clostridium was negatively correlated with t-GWG and newborn birth weight; The Coriobacteriaceae showed a negative correlation with t-GWG, t-GBG, and a-GBG. Additionally,Collinsella exhibited negative correlations with t-GBG and a-GBG.

Conclusion

This study has identified that the presence of EGWG in GDM mothers further exacerbated neonatal gut microbial perturbations. Total GWG/GBG and those after the diagnosis of GDM were negatively correlated with the abundance of neonatal gut Clostridium, Coriobacteriaceae, and Collinsella. These findings provide new insights for precise prevention and management of GDM.

Age-stratification reveals age-specific intestinal microbiota signatures in juvenile idiopathic arthritis

OBJECTIVE

Juvenile Idiopathic Arthritis (JIA) comprises diverse chronic inflammatory conditions driven by malfunction of the immune system. The intestinal microbiota is considered a crucial environmental factor correlating with chronic inflammatory diseases, and for JIA certain alterations in the microbiota have already been described.

METHODS

Here, we have characterized intestinal microbiota samples from 54 JIA patients and 38 pediatric healthy controls by conventional 16S rRNA sequencing and by single-cell analysis for phenotypic features by multi-parameter microbiota flow cytometry (mMFC), which complements the population-based taxonomic profiling with the characterization of individual bacterial cells.

RESULTS

We found age to be a crucial confounder in microbiota analyses of JIA patients. Age stratification revealed specific microbiota alterations neglected by the general comparison of JIA patients and pediatric controls.

CONCLUSION

Age groups presented distinct taxonomic profiles and microbiota phenotypic signatures which transitioned with age, highlighting changes in the microbiota-immune system interaction with age.

Impacts of Helicobacter pylori infection and eradication on gastrointestinal microbiota: An up-to-date critical review and future perspectives

ABSTRACT

Helicobacter pylori ( H. pylori ) infects approximately half of the population worldwide and causes chronic gastritis, peptic ulcers, and gastric cancer. Test-and-treat strategies have been recommended for the prevention of H. pylori -associated diseases. Advancements in high-throughput sequencing technologies have broadened our understanding of the complex gastrointestinal (GI) microbiota and its role in maintaining host homeostasis. Recently, an increasing number of studies have indicated that the colonization of H. pylori induces dramatic alterations in the gastric microbiota, with a predominance of H. pylori and a reduction in microbial diversity. Dysbiosis of the gut microbiome has also been observed after H. pylori infection, which may play a role in the development of colorectal cancer. However, there is concern regarding the impact of antibiotics on the gut microbiota during H. pylori eradication. In this review, we summarize the current literature concerning how H. pylori infection reshapes the GI microbiota and the underlying mechanisms, including changes in the gastric environment, immune responses, and persistent inflammation. Additionally, the impacts of H. pylori eradication on GI microbial homeostasis and the use of probiotics as adjuvant therapy are also discussed. The shifts in the GI microbiota and their crosstalk with H. pylori  may provide potential targets for H. pylori -related gastric diseases and extragastric manifestations.

Gut microbiota and Parkinson's disease: potential links and the role of fecal microbiota transplantation

Parkinson's disease (PD) is the second most common neurodegenerative disease worldwide and seriously affects the quality of life of elderly patients. PD is characterized by the loss of dopaminergic neurons in the substantia nigra as well as abnormal accumulation of α-synuclein in neurons. Recent research has deepened our understanding of the gut microbiota, revealing that it participates in the pathological process of PD through the gut-brain axis, suggesting that the gut may be the source of PD. Therefore, studying the relationship between gut microbiota and PD is crucial for improving our understanding of the disease's prevention, diagnosis, and treatment. In this review, we first describe the bidirectional regulation of the gut-brain axis by the gut microbiota and the mechanisms underlying the involvement of gut microbiota and their metabolites in PD. We then summarize the different species of gut microbiota found in patients with PD and their correlations with clinical symptoms. Finally, we review the most comprehensive animal and human studies on treating PD through fecal microbiota transplantation (FMT), discussing the challenges and considerations associated with this treatment approach.

Göttingen Minipigs as a Model for Assessing the Impact of Drugs on the Gut and Milk Microbiota-A Preliminary Study

BACKGROUND

Early gut microbiota (GM) dysbiosis can affect a child's health and has been linked to the onset of pathologies later in life. Breast milk is recognized as a major driver of the structure and dynamics of an infant's GM. In addition to nutritious and prebiotic compounds, milk contains a microbiota that is shaped by several maternal factors, including gut microorganisms and medications. However, the impact of the latter on the milk microbiota is still largely unknown. Here, we investigated the effects of amoxicillin on the milk microbiota and GM of lactating Göttingen Minipigs sows, a promising model for studying medication transfer during lactation.

METHODS

Three sows were given amoxicillin (7 mg/kg/day) for three weeks starting from the second week after farrowing. Fecal and milk samples were collected before and after treatment and profiled by 16S rRNA amplicon sequencing.

RESULTS

Göttingen Minipigs' milk microbiota showed similarities to that of humans and conventional sows, with minor compositional shifts after treatment. At the genus level, we observed a decrease in Staphylococcus and o_Bacteroidales;Other;Other, and an increasing trend in the abundance of Streptococcus, Stenotrophomonas, f_Rhodobacteraceae;Other, Proteiniclasticum, f_Propionibacteriaceae;Other and Gemella. In contrast, as expected, the GM was strongly affected by amoxicillin, even at the phylum level.

CONCLUSIONS

In addition to demonstrating the relevance of Göttingen Minipigs as a valid model for studying the impact of medications on maternal milk and GM, our findings suggest that the milk microbiota may be more stable during antibiotic treatment than the GM.

Research focus and emerging trends of the gut microbiome and infant: a bibliometric analysis from 2004 to 2024

Background

Over the past two decades, gut microbiota has demonstrated unprecedented potential in human diseases and health. The gut microbiota in early life is crucial for later health outcomes. This study aims to reveal the knowledge collaboration network, research hotspots, and explore the emerging trends in the fields of infant and gut microbiome using bibliometric analysis.

Method

We searched the literature on infant and gut microbiome in the Web of Science Core Collection (WOSCC) database from 2004 to 2024. CiteSpace V (version: 6.3.R1) and VOSview (version: 1.6.20) were used to display the top authors, journals, institutions, countries, authors, keywords, co-cited articles, and potential trends.

Results

A total of 9,899 documents were retrieved from the Web of Science Core Collection. The United States, China, and Italy were the three most productive countries with 3,163, 1,510, and 660 publications. The University of California System was the most prolific institution (524 publications). Van Sinderen, Douwe from University College Cork of Ireland was the most impactful author. Many studies have focused on atopic dermatitis (AD), necrotizing enterocolitis (NEC), as well as the immune mechanisms and microbial treatments for these diseases, such as probiotic strains mixtures and human milk oligosaccharides (HMOs). The mother-to-infant microbiome transmission, chain fatty acids, and butyrate maybe the emerging trends.

Conclusion

This study provided an overview of the knowledge structure of infant and gut microbiome, as well as a reference for future research.

Correlation Between Regulation of Intestinal Flora by Danggui-Shaoyao-San and Improvement of Cognitive Impairment in Mice With Alzheimer's Disease

PURPOSE

The abnormal central glucose metabolism in Alzheimer's disease (AD) is related to the brain-gut axis. This study aims to explore the target of Danggui-Shaoyao-San (DSS) in improving cognitive impairment.

METHOD

This study analyzed the differences in mice intestinal flora by 16S rRNA sequencing. The cognitive protective effects of DSS were observed through the Morris water maze and the new object recognition. The mitigation effects of DSS on Aβ and p-tau, regulatory effects on glucose metabolism targets, and intestinal structure effects were observed through brain and colon slices staining. The differences in neural ultrastructure were compared by transmission electron microscopy.

FINDING

The results showed that DSS affected the composition of intestinal dominant bacteria and bacteria genera and regulated the abundance of intestinal bacteria in AD mice. DSS improved the behavior of AD mice, alleviated the deposition of AD pathological products in the brain and colon, regulated the expression of glycometabolism-related proteins, and improved the colon barrier structure and neural ultrastructure in the brain of mice with AD.

CONCLUSION

Our findings suggest that DSS may affect AD central glucose metabolism and improve cognition by regulating the gut-brain axis.

Time-varying ambient air pollution exposure is associated with gut microbiome variation in the first 2 years of life

The infant gut microbiome matures greatly in the first year of life. Ambient air pollution (AAP) exposure is associated with the infant gut microbiome. However, whether time-varying AAP influences infant gut microbiome variation is rarely investigated. This study aimed to investigate the effects of PM2.5, PM10, and O3 on infant gut microbiome variation longitudinally. Demographic information, stool samples, and AAP exposure concentrations were collected at 6, 12, 24 months from infants. Gut microbiome was processed and analyzed using 16S rRNA V3-V4 gene regions. AAP exposure concentrations were calculated using the China High Air Pollutants (CHAP) database. Multiple pollutant models were used to assess the mixed effects of PM2.5, PM10, and O3 on infant gut microbiome variation. Infants' gut microbiomes at 6, 12, 24 months old had significant differences in alpha diversity, beta diversity, and community composition. PM2.5 and O3 respectively explained 6.3% and 5.3% of the differences in community composition for 24-month-old infants. Single pollutant exposure and multiple pollutant exposure in different periods were both associated with alpha diversity indices and specific gut microbial phyla and genera. AAP was more associated with infant gut microbial alpha diversity indices, phyla variations, and genera variations at 12-24 months than 6-12 months. Multiple pollutant exposure in 0-2 lag months showed negative correlations with 12-24 months variation in Escherichia-Shigella (β = -0.854, 95%CI: 1.398 to -0.310) and Enterococcus (β = -0.979, 95%CI: 1.429 to -0.530). This study highlighted that time-varying PM2.5, PM10, and O3 synergistically influenced the variation of alpha diversity and abundance of gut microbial taxa in infants. Further research is needed to explore the effects and mechanisms of other environmental exposures on infant gut microbiome variation.

Selenium Attenuates Radiation Colitis by Regulating cGAS-STING Signaling

Radiation colitis is one of the most common complications in patients undergoing pelvic radiotherapy and there is no effective treatment in the clinic. Therefore, searching for effective agents for the treatment of radiation colitis is urgently needed. Herein, it is found that the essential element selenium (Se) is protective against radiation colitis through inhibiting X-ray-induced apoptosis, cell cycle arrest, and inflammation with the involvement of balancing the generation of reactive oxygen species after the irradiation. Mechanistically, Se, especially for selenium nanoparticles (SeNPs), induced selenoprotein expression and then functioned to effectively restrain DNA damage response, which reduced X-ray-induced intestinal injury. Additionally, SeNPs treatment also restrained the cyclic GMP-AMP synthas (cGAS)- stimulator of interferon genes (STING)-TBK1-IRF3 signaling pathway cascade, thereby blocking the transcription of inflammatory cytokine gene, IL-6 and TNF-α, and thus alleviating inflammation. Moreover, inducing selenoprotein expression, such as GPX4, with SeNPs in vivo can regulate intestinal microenvironment immunity and gut microbiota to attenuate radiation-induced colitis by inhibiting oxidative stress and maintaining microenvironment immunity homeostasis. Together, these results unravel a previously unidentified modulation role that SeNPs restrained radiation colitis with the involvement of inducing selenoprotein expression but suppressing cGAS-STING-TBK1-IRF3 cascade.

Chronic nasal inflammation early in life induces transient and long-term dysbiosis of gut microbiota in mice

The gut microbiota begins to colonize the host body following birth, develops during the suckling period and changes to the adult type after weaning. The early gut microbiota during the suckling period is thought to have profound effects on the host physiology throughout life but it is still unclear whether early dysbiosis is retained lifelong. Our previous study indicated that chronic nasal inflammation induces dysbiosis of gut microbiota in adult mice. In the present study, we addressed the question as to whether early exposure to chronic nasal inflammation induces dysbiosis, and if so, whether the dysbiosis is retained until adulthood and the sex differences in this effect. Male and female mice received repeated intranasal administration of lipopolysaccharide (LPS) or saline twice a week from P7 to P24 and were weaned at P24. The cecal contents were obtained for 16S rRNA analysis at 2 time points: at 4 weeks (wks), just after weaning, and at maturation to adulthood at 10 wks. The body weight did not differ between saline- and LPS-treated mice till around weaning, suggesting that the mothers' milk was given similarly to all mice. At 4 wks, the beta diversity was significantly different between saline- and LPS-treated male and female mice and the composition of the gut microbiota changed in LPS-treated mice. The abundance of phylum Bacteroidota tended to decrease and that of Firmicutes increased in LPS-treated male mice, while the abundance of Deferribacterota increased in LPS-treated female mice. At 10 wks, the beta diversity was not different between saline- and LPS-treated mice, but the abundance of family Lachnospiraceae significantly decreased in LPS-treated male and female mice by LEfSe analysis. Together, chronic nasal inflammation early in life caused transient and long-term dysbiosis of gut microbiota, which may contribute to the onset and progress of metabolic and neuropsychiatric disorders.

Traditionally produced tempeh harbors more diverse bacteria with more putative health-promoting properties than industrially produced tempeh

In recent years, there has been a significant shift towards industrialization in food production, resulting in the implementation of higher hygiene standards globally. Our study focused on examining the impact of hygiene standards on tempeh, a popular Rhizopus-based fermented soybean product native to Indonesia, and now famous around the world. We observed that tempeh produced with standardized hygiene measures exhibited a microbiome with comparable bacterial abundances but a markedly different community structure and function than traditionally produced tempeh. In detail, we found a decreased bacterial abundance of lactobacilli and enterobacteria, bacterial diversity, different indicator taxa, and significantly changed community structure in industrial tempeh. A similar picture was found for functional analysis: the quantity of bacterial genes was similar but qualitative changes were found for genes associated with human health. The resistome of tempeh varied based on its microbiome composition. The higher number of antimicrobial resistance genes in tempeh produced without standardized hygiene measures mainly belong to multidrug efflux pumps known to occur in plant-based food. Our findings were confirmed by functional insights into genomes and metagenome-assembled genomes from the dominant bacteria, e.g. Leuconostoc, Limosilactobacillus, Lactobacillus, Enterococcus, Paenibacillus, Azotobacter and Enterobacter. They harboured an impressive spectrum of genes important for human health, e.g. for production of vitamin B1, B7, B12, and K, iron and zinc transport systems and short chain fatty acid production. In conclusion, industrially produced tempeh harbours a less diverse microbiome than the traditional one. Although this ensures production at large scales as well as biosafety, in the long-term it can lead to potential effects for human gut health.

Unlocking the potential for microbiome-based therapeutics to address the sustainable development goal of good health and wellbeing

Recent years have witnessed major advances and an ever-growing list of healthcare applications for microbiome-based therapeutics. However, these advances have disproportionately targeted diseases common in high-income countries (HICs). Within low- to middle-income countries (LMIC), opportunities for microbiome-based therapeutics include sexual health epidemics, maternal health, early life mortality, malnutrition, vaccine response and infectious diseases. In this review we detail the advances that have been achieved in microbiome-based therapeutics for these areas of healthcare and identify where further work is required. Current efforts to characterise microbiomes from LMICs will aid in targeting and optimisation of therapeutics and preventative strategies specifically suited to the unmet needs within these populations. Once achieved, opportunities from disease treatment and improved treatment efficacy through to disease prevention and vector control can be effectively addressed using probiotics and live biotherapeutics. Together these strategies have the potential to increase individual health, overcome logistical challenges and reduce overall medical, individual, societal and economic costs.

Holistic Evaluation of the Gut Microbiota through Data Envelopment Analysis: A Cross-Sectional Study

Background

The gut microbiome plays a crucial role in human health, but maintaining a healthy gut microbiome remains challenging. Current approaches often focus on individual components rather than providing a holistic assessment.

Objectives

To introduce and evaluate a novel approach using data envelopment analysis (DEA) for assessing gut microbiota efficiency and identifying potential targets for personalized interventions.

Methods

We conducted a cross-sectional analysis of 577 participants from the Kanagawa "ME-BYO" Prospective Cohort Study. Lifestyle factors and gut microbiota composition were assessed. DEA was employed to calculate an efficiency score for each participant, incorporating multiple inputs (lifestyle factors) and outputs (gut microbiotas). This score represents how efficiently an individual's lifestyle factors contribute to their gut microbiota composition. Tobit regression analysis was used to assess associations between efficiency scores and demographic and health-related factors.

Results

The mean efficiency score was 0.86, with 14.2% of participants classified as efficient. Efficiency scores showed positive correlations with alcohol intake and Faith's phylogenetic diversity. Tobit regression analysis revealed significant associations between efficiency scores and sex, fat intake, and yogurt consumption. DEA identified specific targets for improving gut microbiota composition in inefficient individuals.

Conclusions

This study demonstrates the potential of DEA as a tool for evaluating gut microbiota efficiency and providing personalized recommendations for microbiota optimization. This approach could lead to more effective strategies for optimizing gut health across diverse populations.

Experimental models of antibiotic exposure and atopic disease

In addition to numerous clinical studies, research using experimental models have contributed extensive evidence to the link between antibiotic exposure and atopic disease. A number of mouse models of allergy have been developed and used to uncover the specific effects of various microbiota members and perturbations on allergy development. Studies in mice that lack microbes entirely have also demonstrated the various components of the immune system that require microbial exposure. The importance of the early-life period and the mechanisms by which atopy "protective" species identified in human cohorts promote immune development have been elucidated in mice. Finally, non-animal models involving human-derived cells shed light on specific effects of bacteria on human epithelial and immune responses. When considered alongside clinical cohort studies, experimental model systems have provided crucial evidence for the link between the neonatal gut microbiota and allergic disease, immensely supporting the stewardship of antibiotic administration in infants. The following review aims to describe the range of experimental models used for studying factors that affect the relationship between the gut microbiota and allergic disease and summarize key findings that have come from research in animal and in vitro models.

Exploring the Frontier: The Human Microbiome's Role in Rare Childhood Neurological Diseases and Epilepsy

Emerging research into the human microbiome, an intricate ecosystem of microorganisms residing in and on our bodies, reveals that it plays a pivotal role in maintaining our health, highlighting the potential for microbiome-based interventions to prevent, diagnose, treat, and manage a myriad of diseases. The objective of this review is to highlight the importance of microbiome studies in enhancing our understanding of rare genetic epilepsy and related neurological disorders. Studies suggest that the gut microbiome, acting through the gut-brain axis, impacts the development and severity of epileptic conditions in children. Disruptions in microbial composition can affect neurotransmitter systems, inflammatory responses, and immune regulation, which are all critical factors in the pathogenesis of epilepsy. This growing body of evidence points to the potential of microbiome-targeted therapies, such as probiotics or dietary modifications, as innovative approaches to managing epilepsy. By harnessing the power of the microbiome, we stand to develop more effective and personalized treatment strategies for children affected by this disease and other rare neurological diseases.

Reduce, reinforce, and replenish: safeguarding the early-life microbiota to reduce intergenerational health disparities

Socioeconomic (SE) disparity and health inequity are closely intertwined and associated with cross-generational increases in the rates of multiple chronic non-communicable diseases (NCDs) in North America and beyond. Coinciding with this social trend is an observed loss of biodiversity within the community of colonizing microbes that live in and on our bodies. Researchers have rightfully pointed to the microbiota as a key modifiable factor with the potential to ease existing health inequities. Although a number of studies have connected the adult microbiome to socioeconomic determinants and health outcomes, few studies have investigated the role of the infant microbiome in perpetuating these outcomes across generations. It is an essential and important question as the infant microbiota is highly sensitive to external forces, and observed shifts during this critical window often portend long-term outcomes of health and disease. While this is often studied in the context of direct modulators, such as delivery mode, family size, antibiotic exposure, and breastfeeding, many of these factors are tied to underlying socioeconomic and/or cross-generational factors. Exploring cross-generational socioeconomic and health inequities through the lens of the infant microbiome may provide valuable avenues to break these intergenerational cycles. In this review, we will focus on the impact of social inequality in infant microbiome development and discuss the benefits of prioritizing and restoring early-life microbiota maturation for reducing intergenerational health disparities.

Secretory IgA in breast milk protects against asthma through modulation of the gut microbiota

Asthma susceptibility is linked to dysbiosis in early-life gut microbiota, and the antibody secretory immunoglobulin (Ig)A (SIgA) is a key determinant of gut microbiota composition. SIgA is obtained through breast milk during the critical early-life window. We use a mouse model of SIgA deficiency and the house dust mite (HDM) model of asthma to elucidate the role of maternal SIgA in modulating the early-life gut microbiota and asthma protection. Mice that do not receive maternal SIgA display a transient bloom of segmented filamentous bacteria (SFB) in the small intestine during the early post-weaning period. Mice that do not receive maternal SIgA also display elevated T helper type 17 (Th17) cell activation in the intestine, which persists into adulthood and is associated with more severe inflammation in response to the HDM model of asthma. This study demonstrates a mechanism by which breast-milk-derived SIgA influences immune development and asthma susceptibility by modulating the early-life gut microbiota.

Mechanisms of microbe-mediated immune development in the context of antibiotics and asthma

The gut houses 70%-80% of the body's immune cells and represents the main point of contact between the immune system and the outside world. Immune maturation occurs largely after birth and is guided by the gut microbiota. In addition to the many human clinical studies that have identified relationships between gut microbiota composition and disease outcomes, experimental research has demonstrated a plethora of mechanisms by which specific microbes and microbial metabolites train the developing immune system. The healthy maturation of the gut microbiota has been well-characterized and discreet stages marked by changes in abundance of specific microbes have been identified. Building on Chapter 8, which discusses experimental models used to study the relationship between the gut microbiota and asthma, the present review aims to dive deeper into the specific microbes and metabolites that drive key processes in immune development. The implications of microbiota maturation patterns in the context of asthma and allergies, as well as the effects of antibiotics on microbe-immune crosstalk, will also be discussed.

Effects of parental care on skin microbial community composition in poison frogs

Parent-offspring interactions constitute the first contact of many newborns with their environment, priming community assembly of microbes through priority effects. Early exposure to microbes can have lasting influences on the assembly and functionality of the host's microbiota, leaving a life-long imprint on host health and disease. Studies of the role played by parental care in microbial acquisition have primarily focused on humans and hosts with agricultural relevance. Anuran vertebrates offer the opportunity to examine microbial community composition across life stages as a function of parental investment. In this study, we investigate vertical transmission of microbiota during parental care in a poison frog (Family Dendrobatidae), where fathers transport their offspring piggyback-style from terrestrial clutches to aquatic nurseries. We found that substantial bacterial colonization of the embryo begins after hatching from the vitelline envelope, emphasizing its potential role as microbial barrier during early development. Using a laboratory cross-foster experiment, we demonstrated that poison frogs performing tadpole transport serve as a source of skin microbes for tadpoles on their back. To study how transport impacts the microbial skin communities of tadpoles in an ecologically relevant setting, we sampled frogs and tadpoles of sympatric species that do or do not exhibit tadpole transport in their natural habitat. We found more diverse microbial communities associated with tadpoles of transporting species compared to a non-transporting frog. However, we detected no difference in the degree of similarity between adult and tadpole skin microbiotas, based on whether the frog species exhibits transporting behavior or not. Using a field experiment, we confirmed that tadpole transport can result in the persistent colonization of tadpoles by isolated microbial taxa associated with the caregiver's skin, albeit often at low prevalence. This is the first study to describe vertical transmission of skin microbes in anuran amphibians, showing that offspring transport may serve as a mechanism for transmission of parental skin microbes. Overall, these findings provide a foundation for further research on how vertical transmission in this order impacts host-associated microbiota and physiology.

Association between Turbot (Scophthalmus maximus) Fish Phenotype and the Post-Larval Bacteriome

Over the past decade, an increasing number of studies have emphasized the importance of the host microbiome in influencing organismal health and development. Aligned with this understanding, our study aimed to investigate the potential association between the turbot (Scophthalmus maximus) phenotypic traits and the post-larval bacteriome. Turbot post-larvae were sampled from twenty randomly selected production cycles thirty days after hatching (DAH) across multiple post-larval production batches over a three-month period (April to June). Fish were selectively sampled based on five phenotypic traits, namely, normal, large, small, malformed, and depigmented. Our results showed that small-sized post-larvae had significantly higher bacterial phylogenetic diversity in their bacterial communities than all other phenotypes. A more in-depth compositional analysis also revealed specific associations between certain bacterial taxa and fish phenotypes. For example, the genera Aliivibrio and Sulfitobacter were enriched in small-sized post-larvae, while the family Micrococcaceae were predominantly found in larger post-larvae. Furthermore, genus Exiguobacterium was linked to depigmented larvae, and genus Pantoea was more prevalent in normal post-larvae. These observations underscore the importance of further research to understand the roles of these bacterial taxa in larval growth and phenotypic differentiation. Such insights could contribute to developing microbiome modulation strategies, which may enhance turbot post-larval health and quality and improve larviculture production.

Chinese expert consensus on standard technical specifications for a gut microecomics laboratory (Review)

The intestinal microbiota is a complex ecosystem that not only affects various physiological functions, such as metabolism, inflammation and the immune response, but also has an important effect on the development of tumors and response to treatment. The detection of intestinal flora enables the timely identification of disease-related flora abnormalities, which has significant implications for both disease prevention and treatment. In the field of basic and clinical research targeting gut microbiome, there is a need to recognize and understand the laboratory assays for gut microbiomics. Currently, there is no unified standard for the experimental procedure, quality management and report interpretation of intestinal microbiome assay technology. In order to clarify the process, the Tumor and Microecology Committee of China Anti-Cancer Association and the Tumor and Microecology Committee of Hubei Provincial Immunology Society organized relevant experts to discuss and put forward the standard technical specifications for gut microecomics laboratories, which provides a basis for further in-depth research in the field of intestinal microecomics.

Intergenerational neurotoxicity of polystyrene nanoplastics in offspring mice is mediated by dysfunctional microbe-gut-brain axis

Nanoplastics (NPs) are ubiquitous in daily life, posing potential risks to the environment and human. While their negative effects on parental organisms have been extensively studied, intergenerational effects are still in the early stages of investigation. Here, we aimed to investigate the impact of maternal exposure to an environmentally relevant level of polystyrene NPs (PSNPs, 100 nm) during gestation and lactation (∼32 days, 50 μg/mouse/day) on neurotoxicity mediated by the microbe-gut-brain axis in offspring mice. Maternal PSNPs exposure significantly increased brain TNF-α level and microglia by 1.43 and 1.48 folds respectively, compared to control, accompanied by nuclear pyknosis and cell vacuolization in cortex and hippocampus. Targeted neurotransmitter metabolomics analysis revealed dysregulation in dopamine and serotonin metabolism. Specifically, dopamine levels increased significantly from 0.007 ng/L to 0.015 ng/L, while N-acetylseroton and 3,4-dihydroxyphenylacetic acid decreased significantly from 0.002 and 0.929 ng/L to 0.001 and 0.680 ng/L, respectively. Through a combination of 16S rRNA sequencing and biochemical analysis, we discovered that maternal PSNPs exposure led to a depletion of anti-inflammatory bacteria and an enrichment of pro-inflammatory bacteria resulting in intestinal barrier damage, elevated levels of lipopolysaccharide in blood, and subsequent activation of neuroinflammation. Meanwhile, gut bacteria dysbiosis interfered with communication between gut and brain by dysregulating neurotransmitter synthesis, as evidenced by significant associations between neurotransmitter-related bacteria (Akkermansia, Family_XIII_AD3011_group, Lachnoclostridium) and dopamine/serotonin related metabolites. Furthermore, transcriptional alterations in dopamine and serotonin related pathways were observed in the enteric nervous system, suggesting abnormal signal transduction from gut to brain contributes to neurotoxicity. This study provides new insights into NPs-induced neurotoxicity within the context of microbe-gut-brain axis and highlights the risk of cerebral dysfunction in offspring with maternal NPs exposure.

Fecal microbiota transplantation alleviates food allergy in neonatal mice via the PD-1/PD-L1 pathway and change of the microbiota composition

BACKGROUND

Food allergy (FA) is a common disorder in children and affects the health of children worldwide. The gut microbiota is closely related to the occurrence and development of FA. Fecal microbiota transplantation (FMT) is a way to treat diseases by reconstituting the microbiota; however, the role and mechanisms of FA have not been validated.

METHODS

In this study, we established an ovalbumin (OVA)-induced juvenile mouse model and used 16S RNA sequencing, pathological histological staining, molecular biology, and flow-through techniques to evaluate the protective effects of FMT treatment on FA and to explore the mechanisms.

RESULTS

OVA-induced dysregulation of the gut microbiota led to impaired intestinal function and immune dysregulation in FA mice. FMT treatment improved the structure, diversity, and composition of the gut microbiota and restored it to a near-donor state. FMT treatment reduced levels of Th2-associated inflammatory factors, decreased intestinal tissue inflammation, and reduced IgE production. In addition, FMT reduced the number of mast cells and eosinophils and suppressed OVA-specific antibodies. Further mechanistic studies revealed that FMT treatment induced immune tolerance by inducing the expression of CD103+DCs and programmed cell death ligand 1 (PD-L1) in mesenteric lymph nodes and promoting the production of Treg through the programmed cell death protein 1 (PD-1)/PD-L1 pathway. Meanwhile, Th2 cytokines, OVA-specific antibodies, and PD-1/PD-L1 showed a significant correlation with the gut microbiota.

CONCLUSIONS

FMT could regulate the gut microbiota and Th1/Th2 immune balance and might inhibit FA through the PD-1/PD-L1 pathway, which would provide a new idea for the treatment of FA.

Navigating the evolving landscape of atopic dermatitis: Challenges and future opportunities: The 4th Davos declaration

The 4th Davos Declaration was developed during the Global Allergy Forum in Davos which aimed to elevate the care of patients with atopic dermatitis (AD) by uniting experts and stakeholders. The forum addressed the high prevalence of AD, with a strategic focus on advancing research, treatment, and management to meet the evolving challenges in the field. This multidisciplinary forum brought together top leaders from research, clinical practice, policy, and patient advocacy to discuss the critical aspects of AD, including neuroimmunology, environmental factors, comorbidities, and breakthroughs in prevention, diagnosis, and treatment. The discussions were geared towards fostering a collaborative approach to integrate these advancements into practical, patient-centric care. The forum underlined the mounting burden of AD, attributing it to significant environmental and lifestyle changes. It acknowledged the progress in understanding AD and in developing targeted therapies but recognized a gap in translating these innovations into clinical practice. Emphasis was placed on the need for enhanced awareness, education, and stakeholder engagement to address this gap effectively and to consider environmental and lifestyle factors in a comprehensive disease management strategy. The 4th Davos Declaration marks a significant milestone in the journey to improve care for people with AD. By promoting a holistic approach that combines research, education, and clinical application, the Forum sets a roadmap for stakeholders to collaborate to improve patient outcomes in AD, reflecting a commitment to adapt and respond to the dynamic challenges of AD in a changing world.

Investigating Causal Associations between the Gut Microbiota and Dementia: A Mendelian Randomization Study

Background: The causal association of specific gut microbiota with dementia remains incompletely understood. We aimed to access the causal relationships in which one or more gut microbiota account for dementia. Method: Using data from the MiBioGen and FinnGen consortia, we employed multiple Mendelian randomization (MR) approaches including two-sample MR (TSMR), multivariable MR (MVMR), and Bayesian model averaging MR to comprehensively evaluate the causal associations between 119 genera and dementia, and to prioritize the predominant bacterium. Result: We identified 21 genera that had causal effects on dementia and suggested Barnesiella (OR = 0.827, 95%CI = 0.722-0.948, marginal inclusion probability [MIP] = 0.464; model-averaged causal estimate [MACE] = -0.068) and Allisonella (OR = 0.770, 95%CI = 0.693-0.855, MIP = 0.898, MACE = -0.204) as the predominant genera for AD and all-cause dementia. Conclusions: These findings confirm the causal relationships between specific gut microbiota and dementia, highlighting the necessity of multiple MR approaches in gut microbiota analysis, and provides promising genera as potential novel biomarkers for dementia risk.

A systematic framework for understanding the microbiome in human health and disease: from basic principles to clinical translation

The human microbiome is a complex and dynamic system that plays important roles in human health and disease. However, there remain limitations and theoretical gaps in our current understanding of the intricate relationship between microbes and humans. In this narrative review, we integrate the knowledge and insights from various fields, including anatomy, physiology, immunology, histology, genetics, and evolution, to propose a systematic framework. It introduces key concepts such as the 'innate and adaptive genomes', which enhance genetic and evolutionary comprehension of the human genome. The 'germ-free syndrome' challenges the traditional 'microbes as pathogens' view, advocating for the necessity of microbes for health. The 'slave tissue' concept underscores the symbiotic intricacies between human tissues and their microbial counterparts, highlighting the dynamic health implications of microbial interactions. 'Acquired microbial immunity' positions the microbiome as an adjunct to human immune systems, providing a rationale for probiotic therapies and prudent antibiotic use. The 'homeostatic reprogramming hypothesis' integrates the microbiome into the internal environment theory, potentially explaining the change in homeostatic indicators post-industrialization. The 'cell-microbe co-ecology model' elucidates the symbiotic regulation affecting cellular balance, while the 'meta-host model' broadens the host definition to include symbiotic microbes. The 'health-illness conversion model' encapsulates the innate and adaptive genomes' interplay and dysbiosis patterns. The aim here is to provide a more focused and coherent understanding of microbiome and highlight future research avenues that could lead to a more effective and efficient healthcare system.

Impact of Extreme Prematurity, Chorioamnionitis, and Sepsis on Neonatal Monocyte Characteristics and Functions

INTRODUCTION

The innate branch of the immune system is important in early life, in particular for infants born preterm.

METHODS

We performed a longitudinal analysis of the peripheral monocyte compartment in extremely preterm children from a randomized, placebo-controlled study of probiotic supplementation. PBMCs and fecal samples were collected at several timepoints during the first months of life. Monocyte characteristics were analyzed by flow cytometry, and LPS-stimulated PBMC culture supernatants were analyzed by Luminex or ELISA. Plasma cytokines and gut microbiota composition were analyzed by ELISA and 16S rRNA-sequencing, respectively.

RESULTS

The extremely preterm infants had persistent alterations in their monocyte characteristics that were further aggravated in chorioamnionitis cases. They showed a markedly reduced TLR4 expression and hampered LPS-stimulated cytokine responses 14 days after birth. Notably, at later timepoints, TLR4 expression and LPS responses no longer correlated. Sepsis during the first weeks of life strongly associated with increased pro-inflammatory, and reduced IL-10, responses also at postmenstrual week 36. Further, we report a correlation between gut microbiota features and monocyte phenotype and responses, but also that probiotic supplementation associated with distinct monocyte phenotypic characteristics, without significantly influencing their responsiveness.

CONCLUSION

Extremely preterm infants have monocyte characteristics and functional features that deviate from infants born full-term. Some of these differences persist until they reach an age corresponding to full-term, potentially making them more vulnerable to microbial exposures during the first months of life.

Integrating functional metagenomics to decipher microbiome-immune interactions

Microbial metabolites can be viewed as the cytokines of the microbiome, transmitting information about the microbial and metabolic environment of the gut to orchestrate and modulate local and systemic immune responses. Still, many immunology studies focus solely on the taxonomy and community structure of the gut microbiota rather than its functions. Early sequencing-based microbiota profiling approaches relied on PCR amplification of small regions of bacterial and fungal genomes to facilitate identification of the microbes present. However, recent microbiome analysis methods, particularly shotgun metagenomic sequencing, now enable culture-independent profiling of microbiome functions and metabolites in addition to taxonomic characterization. In this review, we showcase recent advances in functional metagenomics methods and applications and discuss the current limitations and potential avenues for future development. Importantly, we highlight a few examples of key areas of opportunity in immunology research where integrating functional metagenomic analyses of the microbiome can substantially enhance a mechanistic understanding of microbiome-immune interactions and their contributions to health and disease states.

From vacant to vivid: The nutritional landscape drives infant gut microbiota establishment

From the moment of birth, the newborn gastrointestinal tract is infiltrated by various bacteria originating from both maternal and environmental sources. These colonizing bacteria form a complex microbiota community that undergoes continuous changes until adulthood and plays an important role in infant health. The maturation of the infant gut microbiota is driven by many factors and follows a distinct patterned trajectory, with specific bacterial taxa establish in the intestine in accordance with developmental milestones as the infant grows. In this review, we highlight how elements such as diet and host physiology select for specific microbial functions and shape the composition of the bacterial community in the large intestine.