Inducible Foxp3+ regulatory T-cell development by a commensal bacterium of the intestinal microbiota. Proc Natl Acad Sci U S A. 2010;107:12204-12209. [PMID: 20566854 DOI: 10.1073/pnas.0909122107]

Bacteriophage-driven DNA inversions shape bacterial functionality and long-term co-existence in Bacteroides fragilis

Bacterial genomic DNA inversions, which govern molecular phase-variations, provide the bacteria with functional plasticity and phenotypic diversity. These targeted rearrangements enable bacteria to respond to environmental challenges, such as bacteriophage predation, evading immune detection or gut colonization. This study investigated the short- and long-term effects of the lytic phage Barc2635 on the functional plasticity of Bacteroides fragilis, a gut commensal. Germ-free mice were colonized with B. fragilis and exposed to Barc2635 to identify genomic alterations driving phenotypic changes. Phage exposure triggered dynamic and prolonged bacterial responses, including significant shifts in phase-variable regions (PVRs), particularly in promoter orientations of polysaccharide biosynthesis loci. These shifts coincided with increased entropy in PVR inversion ratios, reflecting heightened genomic variability. In contrast, B. fragilis in control mice exhibited stable genomic configurations after gut adaptation. The phase-variable Type 1 restriction-modification system, which affects broad gene expression patterns, showed variability in both groups. However, phage-exposed bacteria displayed more restrained variability, suggesting phage-derived selection pressures. Our findings reveal that B. fragilis employs DNA inversions to adapt rapidly to phage exposure and colonization, highlighting a potential mechanism by which genomic variability contributes to its response to phage. This study demonstrates gut bacterial genomic and phenotypic plasticity upon exposure to the mammalian host and to bacteriophages.

Interplay of m6A RNA methylation and gut microbiota in modulating gut injury

The gut microbiota undergoes continuous variations among individuals and across their lifespan, shaped by diverse factors encompassing diet, age, lifestyle choices, medication intake, and disease states. These microbial inhabitants play a pivotal role in orchestrating physiological metabolic pathways through the production of metabolites like bile acids, choline, short-chain fatty acids, and neurotransmitters, thereby establishing a dynamic "gut-organ axis" with the host. The intricate interplay between the gut microbiota and the host is indispensable for gut health, and RNA N6-methyladenosine modification, a pivotal epigenetic mark on RNA, emerges as a key player in this process. M6A modification, the most prevalent internal modification of eukaryotic RNA, has garnered significant attention in the realm of RNA epigenetics. Recent findings underscore its potential to influence gut microbiota diversity and intestinal barrier function by modulating host gene expression patterns. Conversely, the gut microbiota, through its impact on the epigenetic landscape of host cells, may indirectly regulate the recruitment and activity of RNA m6A-modifying enzymes. This review endeavors to delve into the biological functions of m6A modification and its consequences on intestinal injury and disease pathogenesis, elucidating the partial possible mechanisms by which the gut microbiota and its metabolites maintain host intestinal health and homeostasis. Furthermore, it also explores the intricate crosstalk between them in intestinal injury, offering a novel perspective that deepens our understanding of the mechanisms underlying intestinal diseases.

Gut microbiota in hepatocellular carcinoma immunotherapy: immune microenvironment remodeling and gut microbiota modification

Hepatocellular carcinoma (HCC) remains a leading cause of cancer-related mortality, with limited treatment options at advanced stages. The gut microbiota, a diverse community of microorganisms residing in the gastrointestinal tract, plays a pivotal role in regulating immune responses through the gut-liver axis. Emerging evidence underscores its impact on HCC progression and the efficacy of immunotherapy. This review explores the intricate interactions between gut microbiota and the immune system in HCC, with a focus on key immune cells and pathways involved in tumor immunity. Additionally, it highlights strategies for modulating the gut microbiota - such as fecal microbiota transplantation, dietary interventions, and probiotics - as potential approaches to enhancing immunotherapy outcomes. A deeper understanding of these mechanisms could pave the way for novel therapeutic strategies aimed at improving patient prognosis.

The gut-skin axis: a bi-directional, microbiota-driven relationship with therapeutic potential

This review explores the emerging term "gut-skin axis" (GSA), describing the bidirectional signaling that occurs between the skin and the gastrointestinal tract under both homeostatic and disease conditions. Central to GSA communication are the gut and skin microbiota, the microbial communities that colonize these barrier surfaces. By influencing diverse host pathways, including innate immune, vitamin D receptor, and Aryl hydrocarbon receptor signaling, a balanced microbiota contributes to both tissue homeostasis and host defense. In contrast, microbiota imbalance, or dysbiosis at one site, can lead to local barrier dysfunction, resulting in the activation of signaling pathways that can disrupt tissue homeostasis at the other site, potentially leading to inflammatory skin conditions such as atopic dermatitis and psoriasis, or gut diseases like Inflammatory Bowel Disease. To date, most research on the GSA has examined the impact of the gut microbiota and diet on skin health, but recent studies show that exposing the skin to ultraviolet B-light can beneficially modulate both the gut microbiome and intestinal health. Thus, despite the traditional focus of clinicians and researchers on these organ systems as distinct, the GSA offers new opportunities to better understand the pathogenesis of cutaneous and gastrointestinal diseases and promote health at both sites.

New thoughts on the intestinal microbiome-B cell-IgA axis and therapies in IgA nephropathy

IgA nephropathy (IgAN), as the most common chronic glomerulonephritis worldwide, is often triggered by mucosal infections and follows a chronic progression, with the majority of patients ultimately progressing to end-stage renal disease (ESRD) during their lifetimes. Since the mystery of its complete pathogenesis has not been fully solved, the resulting lack of effective early diagnosis and treatment greatly affects the prognosis of patients. Given the well-defined pathological feature of IgA deposition in the mesangial region, the source and role of pathogenic IgA has been focused on. Starting from the microbiology and immunity of the gut, we systematically review both the physiological and the pathological process of microbiome-B cell-IgA axis, from microbial-induced IgA production to the role of IgA in the intestinal immune milieu, and ultimately end up with the various aspects of microbiome-B cell-IgA axis in the pathogenesis of IgAN as well as the corresponding therapeutic initiatives available. Our retrospective review helps researchers to systematically understand the complex role between intestinal flora dysbiosis and pathogenic IgA in IgAN. This understanding provides a foundation for in-depth explorations to uncover more detailed pathogenic mechanisms and to develop more precise and effective diagnostic and therapeutic approaches.

The Critical Role of Regulatory T Cells in Immune Tolerance and Rejection Following Liver Transplantation: Interactions With the Gut Microbiome

Liver transplantation (LT) is the ultimate treatment for patients with end-stage liver disease or early hepatocellular carcinoma. In the context of LT, because of the unique immunological characteristics of human liver allograft, 5%-20% of selected LT recipients can achieve operational tolerance. Nonetheless, there remains a risk of rejection in LT patients. Maintaining immune homeostasis is thus crucial for improving clinical outcomes in these patients. In mechanism, several immune cells, including dendritic cells, Kupffer cells, myeloid-derived suppressor cells, hepatic stellate cells, regulatory B cells, and CD4 + regulatory T cells (Treg), contribute to achieving tolerance following LT. In terms of Treg, it plays a role in successfully minimizing immunosuppression or achieving tolerance post-LT while also reducing the risk of rejection. Furthermore, the gut microbiome modulates systemic immune functions along the gut-liver axis. Recent studies have explored changes in the microbiome and its metabolites under various conditions, including post-LT, acute rejection, and tolerance. Certain functional microbiomes and metabolites exhibit immunomodulatory functions, such as the augmentation of Treg, influencing immune homeostasis. Therefore, understanding the mechanisms of tolerance in LT, the role of Treg in tolerance and rejection, as well as their interactions with gut microbiome, is vital for the management of LT patients.

Gut microbiota reshapes the TNBC immune microenvironment: Emerging immunotherapeutic strategies

Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer with limited treatment options and poor prognosis. The gut microbiota, a diverse community of microorganisms in the gastrointestinal tract, plays a crucial role in regulating immune responses through the gut-immune axis. Recent studies have highlighted its significant impact on TNBC progression and the efficacy of immunotherapies. This review examines the interactions between gut microbiota and the immune system in TNBC, focusing on key immune cells and pathways involved in tumor immunity. It also explores microbiota modulation strategies, including probiotics, prebiotics, dietary interventions, and fecal microbiota transplantation, as potential methods to enhance immunotherapeutic outcomes. Understanding these mechanisms offers promising avenues for improving treatment efficacy and patient prognosis in TNBC.

Exploring and evaluating microbiome resilience in the gut

The gut ecosystem is closely related to human gastrointestinal health and overall wellness. Microbiome resilience refers to the capability of a microbial community to resist or recover from perturbations to its original state of balance. So far, there is no consensus on the criteria for assessing microbiome resilience. This article provides new insights into the metrics and techniques for resilience assessment. We discussed several potential parameters, such as microbiome structure, keystone species, biomarkers, persistence degree, recovery rate, and various research techniques in microbiology, metagenomics, biochemistry, and dynamic modeling. The article further explores the factors that influence the gut microbiome resilience. The microbiome structure (i.e. abundance and diversity), keystone species, and microbe-microbe interplays determine microbiome resilience. Microorganisms employ a variety of mechanisms to achieve the microbiome resilience, including flexible metabolism, quorum sensing, functional redundancy, microbial cooperation, and competition. Host-microbe interactions play a crucial role in maintaining microbiome stability and functionality. Unlike other articles, we focus on the regulation of host immune system on microbiome resilience. The immune system facilitates bacterial preservation and colonization, community construction, probiotic protection, and pathogen elimination through the mechanisms of immunological tolerance, immune-driven microbial compartmentalization, and immune inclusion and exclusion. Microbial immunomodulation indirectly modulates microbiome resilience.

Microbiome alterations in primary Sjögren's syndrome: Regional dysbiosis and microbiome-targeted therapeutic strategies

Primary Sjögren's syndrome (pSS) is a complex autoimmune disease characterized by diverse clinical manifestations. While xerophthalmia and xerostomia are hallmark symptoms, the disease often involves multiple organ systems, including the kidneys, lungs, nervous system, and gastrointestinal tract, leading to systemic morbidity in severe cases. Despite extensive research, the precise pathogenesis of pSS remains unclear, likely involving infectious, hormonal, and genetic factors. Emerging evidence highlights the microbiome as a key contributor to autoimmune diseases, including pSS. Dysbiosis in the oral, ocular, gut, and genital microbiomes plays a critical role in disease onset, progression, and variability. This review summarizes current findings on microbiome alterations in pSS, emphasizing their role in pathogenesis and clinical features, and explores microbiome-targeted therapies. Understanding the role of the microbiome in pSS pathophysiology could advance disease management and inspire targeted therapeutic strategies.

Ketogenic diet and cancer: multidimensional exploration and research

The ketogenic diet (KD) has attracted attention in recent years for its potential anticancer effects. KD is a dietary structure of high fat, moderate protein, and extremely low carbohydrate content. Originally introduced as a treatment for epilepsy, KD has been widely applied in weight loss programs and the management of metabolic diseases. Previous studies have shown that KD can potentially inhibit the growth and spread of cancer by limiting energy supply to tumor cells, thereby inhibiting tumor angiogenesis, reducing oxidative stress in normal cells, and affecting cancer cell signaling and other processes. Moreover, KD has been shown to influence T-cell-mediated immune responses and inflammation by modulating the gut microbiota, enhance the efficacy of standard cancer treatments, and mitigate the complications of chemotherapy. However, controversies and uncertainties remain regarding the specific mechanisms and clinical effects of KD as an adjunctive therapy for cancer. Therefore, this review summarizes the existing research and explores the intricate relationships between KD and cancer treatment.

The gut-organ axis: Clinical aspects and immune mechanisms

The gut-brain axis exemplifies the bidirectional connection between the intestines and the brain, as evidenced by the impact of severe stress on gastrointestinal symptoms including abdominal pain and diarrhea, and conversely, the influence of abdominal discomfort on mood. Clinical observations support the notion of the gut-brain connection, including an increased prevalence of inflammatory bowel disease (IBD) in patients with depression and anxiety, as well as the association of changes in the gut microbiota with neurological disorders such as multiple sclerosis, Parkinson's disease, stroke and Alzheimer's disease. The gut and brain communicate via complex mechanisms involving inflammatory cytokines, immune cells, autonomic nerves, and gut microbiota, which contribute to the pathogenesis in certain gut and brain diseases. Two primary pathways mediate the bidirectional information exchange between the intestinal tract and the brain: signal transduction through bloodstream factors, such as bacterial metabolites and inflammatory cytokines, and neural pathways, such as neurotransmitters and inflammatory cytokines within the autonomic nervous system through the interaction between the nerve cells and beyond. In recent years, the basic mechanisms of the pathophysiology of the gut-brain axis have been gradually elucidated. Beyond the gut-brain interaction, emerging evidence suggests the influence of the gut extends to other organs, such as the liver and lungs, through intricate inter-organ communication pathways. An increasing number of reports on this clinical and basic cross-organ interactions underscore the potential for better understanding and novel therapeutic strategies targeting inter-organs networks. Further clarification of interactions between multiorgans premises transformative insights into cross-organ therapeutic strategies.

Thalidomide mitigates Crohn's disease colitis by modulating gut microbiota, metabolites, and regulatory T cell immunity

Thalidomide (THA) is renowned for its potent anti-inflammatory properties. This study aimed to elucidate its underlying mechanisms in the context of Crohn's disease (CD) development. Mouse colitis models were established by dextran sulfate sodium (DSS) treatment. Fecal microbiota and metabolites were analyzed by metagenomic sequencing and mass spectrometry, respectively. Antibiotic-treated mice served as models for microbiota depletion and transplantation. The expression of forkhead box P3+ (FOXP3+) regulatory T cells (Tregs) was measured by flow cytometry and immunohistochemical assay in colitis model and patient cohort. THA inhibited colitis in DSS-treated mice by altering the gut microbiota profile, with an increased abundance of probiotics Bacteroides fragilis, while pathogenic bacteria were depleted. In addition, THA increased beneficial metabolites bile acids and significantly restored gut barrier function. Transcriptomic profiling revealed that THA inhibited interleukin-17 (IL-17), IL-1β and cell cycle signaling. Fecal microbiota transplantation from THA-treated mice to microbiota-depleted mice partly recapitulated the effects of THA. Specifically, increased level of gut commensal B. fragilis was observed, correlated with elevated levels of the microbial metabolite 3alpha-hydroxy-7-oxo-5beta-cholanic acid (7-ketolithocholic acid, 7-KA) following THA treatment. This microbial metabolite may stable FOXP3 expression by targeting the receptor FMR1 autosomal homolog 1 (FXR1) to inhibit autophagy. An interaction between FOXP3 and FXR1 was identified, with binding regions localized to the FOXP3 domain (aa238-335) and the FXR1 domain (aa82-222), respectively. Conclusively, THA modulates the gut microbiota and metabolite profiles towards a more beneficial composition, enhances gut barrier function, promotes the differentiation of FOXP3+ Tregs and curbs pro-inflammatory pathways.

Outer membrane vesicles in gram-negative bacteria and its correlation with pathogenesis

There is a widespread distribution of gram-negative bacteria worldwide, which are responsible for the deaths of numerous patients each year. The illnesses they cause can be localized and systemic, and these bacteria possess several key virulence factors that contribute to their pathogenicity. In recent years, several distinct mechanisms of pathogenesis have evolved that remain largely unknown to scientists and medical experts. Among these, outer membrane vesicles (OMVs) are undoubtedly one of the most significant factors influencing virulence. OMVs contain various bacterial compounds and can have diverse effects on host organisms and the immune system, potentially exacerbating disease and inflammation while evading immune responses. This review comprehensively examines the role of OMVs in bacterial pathogenesis, their interaction with host cells, and their potential biomedical applications. Understanding the molecular mechanisms governing OMV biogenesis and function could pave the way for novel antimicrobial strategies and therapeutic interventions.

Colonic goblet cell-associated antigen passages mediate physiologic and beneficial translocation of live gut bacteria in preweaning mice

Gut-resident microorganisms have time-limited effects in distant tissues during early life. However, the reasons behind this phenomenon are largely unknown. Here, using bacterial culture techniques, we show that a subset of live gut-resident bacteria translocate and disseminate to extraintestinal tissues (mesenteric lymph nodes and spleen) in preweaning (day of life 17), but not adult (day of life 35), mice. Translocation and dissemination in preweaning mice appeared physiologic as it did not induce an inflammatory response and required host goblet cells, the formation of goblet cell-associated antigen passages, sphingosine-1-phosphate receptor-dependent leukocyte trafficking and phagocytic cells. One translocating strain, Lactobacillus animalisWU, showed antimicrobial activity against the late-onset sepsis pathogen Escherichia coli ST69 in vitro, and its translocation was associated with protection from systemic sepsis in vivo. While limited in context, these findings challenge the idea that translocation of gut microbiota is pathological and show physiologic and beneficial translocation during early life.

Modulation of Host Immunity by Microbiome-Derived Indole-3-Propionic Acid and Other Bacterial Metabolites

In recent years, we have witnessed a rapidly growing interest in the intricate communications between intestinal microorganisms and the host immune system. Research on the human microbiome is evolving from merely descriptive and correlative studies to a deeper mechanistic understanding of the bidirectional interactions between gut microbiota and the mucosal immune system. Despite numerous challenges, it has become increasingly evident that an imbalance in gut microbiota composition, known as dysbiosis, is associated with the development and progression of various metabolic, immune, cancer, and neurodegenerative disorders. A growing body of evidence highlights the importance of small molecules produced by intestinal commensal bacteria, collectively referred to as gut microbial metabolites. These metabolites serve as crucial diffusible messengers, translating the microbial language to host cells. This review aims to explore the complex and not yet fully understood molecular mechanisms through which microbiota-derived metabolites influence the activity of the immune cells and shape immune reactions in the gut and other organs. Specifically, we will discuss recent research that reveals the close relationship between microbial indole-3-propionic acid (IPA) and mucosal immunity. Furthermore, we will emphasize the beneficial effects of IPA on intestinal inflammation and discuss its potential clinical implications.

Immune tolerance to foreign antigens in the intestine: mechanisms mediated by CD4＋ T cells

The immune system encounters a diverse array of antigens, both self and foreign, necessitating mechanisms to maintain tolerance and prevent harmful inflammatory responses. CD4＋ T cells, crucial in orchestrating immune responses, play a critical role in mediating tolerance to both self and foreign antigens. While the mechanisms of CD4＋ T cell-mediated tolerance to self-antigens are well-documented, the understanding of tolerance to foreign antigens, including those from commensal microbes and food, remains incomplete. This review discusses recent progress in the mechanisms underlying immune tolerance to foreign antigens, with a focus on the role of CD4＋ T cells. We explore how inflammatory and tolerogenic CD4＋ T cell subsets are developed and maintained. Moreover, we delve into the complexities of immune responses to commensal microbes and food antigens by reviewing recent findings, highlighting the immunological contexts that shape immune tolerance. Understanding these mechanisms enhances our comprehension of how immune tolerance is established and sustained, providing insights into potential therapeutic approaches for managing chronic inflammatory diseases resulting from a loss of immune tolerance to foreign antigens. [BMB Reports 2025; 58(4): 158-168].

Effect of Bacteroides on Crohn's disease

Crohn's disease (CD), also known as cicatrizing enteritis, is an inflammatory bowel disease that occurs in the distal ileum and right colon of unknown cause and is also called inflammatory bowel disease (IBD) with ulcerative colitis (UC). In recent years, intestinal biota have been confirmed to play a significant role in various gastrointestinal diseases. Studies have found that intestinal microbiota disorders are closely associated with the onset and progression of Crohn's disease. Bacteroidetes, the second largest microbiota in the intestine, are crucial for equilibrium in the microbiota and intestinal environment. Certain Bacteroides can induce the development of Crohn's disease and aggravate intestinal inflammation directly or through their metabolites. Conversely, certain Bacteroides can reduce intestinal inflammation and symptoms of Crohn's disease. This article reviews the effect of several intestinal Bacteroides in the onset and progression of Crohn's disease and their impact on its treatment.

Microbiota-dependent modulation of intestinal anti-inflammatory CD4+ T cell responses

Barrier organs such as the gastrointestinal tract, lungs, and skin are colonized by diverse microbial strains, including bacteria, viruses, and fungi. These microorganisms, collectively known as the commensal microbiota, play critical roles in maintaining health by defending against pathogens, metabolizing nutrients, and providing essential metabolites. In the gut, commensal-derived antigens are frequently sensed by the intestinal immune system. Maintaining tolerance toward these beneficial microbial species is crucial, as failure to do so can lead to chronic inflammatory conditions like inflammatory bowel disease (IBD) and can even affect systemic immune or metabolic health. The immune system carefully regulates responses to commensals through various mechanisms, including the induction of anti-inflammatory CD4⁺ T cell responses. Foxp3⁺ regulatory T cells (Foxp3+ Tregs) and Type 1 regulatory T cells (Tr1) play a major role in promoting tolerance, as both cell types can produce the anti-inflammatory cytokine IL-10. In addition to these regulatory T cells, effector T cell subsets, such as Th17 cells, also adopt anti-inflammatory functions within the intestine in response to the microbiota. This process of anti-inflammatory CD4+ T cell induction is heavily influenced by the microbiota and their metabolites. Microbial metabolites affect intestinal epithelial cells, promoting the secretion of anti-inflammatory mediators that create a tolerogenic environment. They also modulate intestinal dendritic cells (DCs) and macrophages, inducing a tolerogenic state, and can interact directly with T cells to drive anti-inflammatory CD4⁺ T cell functionality. The disrupted balance of these signals may result in chronic inflammation, with broader implications for systemic health. In this review, we highlight the intricate interplays between commensal microorganisms and the immune system in the gut. We discuss how the microbiota influences the differentiation of commensal-specific anti-inflammatory CD4⁺ T cells, such as Foxp3⁺ Tregs, Tr1 cells, and Th17 cells, and explore the mechanisms through which microbial metabolites modulate these processes. We further discuss the innate signals that prime and commit these cells to an anti-inflammatory fate.

Akkermansia mono-colonization modulates microglia and astrocytes in a strain specific manner

Microglia and astrocytes are the primary glial cells in the central nervous system (CNS) and their function is shaped by multiple factors. Regulation of CNS glia by the microbiota have been reported, although the role of specific bacteria has not been identified. We colonized germ-free mice with the type strain Akkermansia muciniphila (AmT) and a novel A. muciniphila strain BWH-H3 (Am-H3) isolated from a subject with multiple sclerosis and compared to mice colonized with Bacteroides cellulosilyticus strain BWH-E5 (Bc) isolated from a healthy control subject. We then investigated the effect of these bacteria on microglia and astrocyte gene expression by RNA sequencing. We found altered gene expression profiles in brain microglia, with Akkermansia downregulating genes related to antigen presentation and cell migration. Furthermore, we observed strain specific effects, with Akkermansia H3 upregulating histone and protein binding associated genes and downregulating channel and ion transport genes. Astrocyte pathways that were altered by Akkermansia H3 mono-colonization included upregulation of proliferation pathways and downregulation in cytoskeletal associated genes. Furthermore, animals colonized with type strain Akkermansia and strain H3 had effects on the immune system including elevated splenic γδ-T cells and increased IFNγ production in CD4 + T cells. We also measured intestinal short chain fatty acids and found that both A. muciniphila strains produced proprionate while B. cellulosilyticus produced acetate, proprionate, and isovalerate. Taken together, our study shows that specific members of the intestinal microbiota influence both microglial and astroyctes which may be mediated by changes in short chain fatty acids and peripheral immune signaling.

Intestinal Microbiota and Vaccinations: A Systematic Review of the Literature

Background: Vaccination constitutes a low-cost, safe, and efficient public health measure that can help prevent the spread of infectious diseases and benefit the community. The fact that vaccination effectiveness varies among populations, and that the causes of this are still unclear, indicates that several factors are involved and should be thoroughly examined. The "intestinal microbiota" is the most crucial of these elements. Numerous clinical studies demonstrate the intestinal microbiota's significance in determining the alleged "immunogenicity" and efficacy of vaccines. This systematic review aimed to review all relevant scientific literature and highlight the role of intestinal microbiota in COVID-19, Salmonella typhi, Vibrio cholerae, and rotavirus vaccinations. Materials and Methods: The MESH terms "vaccines" and "microbiota" were used to search the major scientific databases PubMed, SciVerse Scopus, Web of Knowledge, and the Cochrane Central Register of Controlled Clinical Trials. Results: Between February 2024 and October 2024, the analysis was conducted using electronic databases, yielding a total of 235 references. Finally, 24 RCTs were chosen after meeting all inclusion criteria: eight studies of COVID-19, two studies of Salmonella typhi, three studies of Vibrio cholerae, and eleven studies of rotavirus. Only six of these demonstrated good study quality with a Jadad score of three or four. Conclusions: According to the review's results, the intestinal microbiota surely plays a role in vaccinations' enhanced immunogenicity, especially in younger people. As it is still unclear what mechanisms underlie this effect, more research is needed to better understand the role of the intestinal microbiota.

Exploring effects of gut microbiota on tertiary lymphoid structure formation for tumor immunotherapy

Anti-tumor immunity, including innate and adaptive immunity is critical in inhibiting tumorigenesis and development of tumor. The adaptive immunity needs specific lymph organs such as tertiary lymphoid structures (TLSs), which are highly correlated with improved survival outcomes in many cancers. In recent years, with increasing attention on the TLS in tumor microenvironment, TLSs have emerged as a novel target for anti-tumor therapy. Excitingly, studies have shown the contribution of TLSs to the adaptive immune responses. However, it is unclear how TLSs to form and how to more effectively defense against tumor through TLS formation. Recent studies have shown that the inflammation plays a critical role in TLS formation. Interestingly, studies have also found that gut microbiota can regulate the occurrence and development of inflammation. Therefore, we here summarize the potential effects of gut microbiota- mediated inflammation or immunosuppression on the TLS formation in tumor environments. Meanwhile, this review also explores how to manipulate mature TLS formation through regulating gut microbiota/metabolites or gut microbiota associated signal pathways for anti-tumor immunity, which potentially lead to a next-generation cancer immunotherapy.

BT1549 coordinates the in vitro IL-10 inducing activity of Bacteroides thetaiotaomicron

The intestine is home to a complex immune system that is engaged in mutualistic interactions with the microbiome that maintain intestinal homeostasis. A variety of immune-derived anti-inflammatory mediators have been uncovered and shown to be critical for maintaining these beneficial immune-microbiome relationships. Notably, the gut microbiome actively invokes the induction of anti-inflammatory pathways that limit the development of microbiome-targeted inflammatory immune responses. Despite the importance of this microbiome-driven immunomodulation, detailed knowledge of the microbial factors that promote these responses remains limited. We have previously established that the gut symbiont Bacteroides thetaiotaomicron stimulates the production of the anti-inflammatory cytokine IL-10 via soluble factors in a Toll-like receptor 2 (TLR2)-MyD88-dependent manner. Here, using TLR2 activity reporter cell lines, we show that the capacity of B. thetaiotaomicron to stimulate TLR2 activity was not critically dependent on either of the canonical heterodimeric forms of TLR2, TLR2/TLR1, or TLR2/TLR6, that typically mediate its function. Furthermore, biochemical manipulation of B. thetaiotaomicron-conditioned media suggests that IL-10 induction is mediated by a protease-resistant or non-proteogenic factor. We next uncovered that deletion of gene BT1549, a predicted secreted lipoprotein, significantly impaired the capacity of B. thetaiotaomicron to induce IL-10, while complementation in trans restored IL-10 induction, suggesting a role for BT1549 in the immunomodulatory function of B. thetaiotaomicron. Collectively, these data provide molecular insight into the pathways through which B. thetaiotaomicron operates to promote intestinal immune tolerance and symbiosis.

IMPORTANCE

Intestinal homeostasis requires the establishment of peaceful interactions between the gut microbiome and the intestinal immune system. Members of the gut microbiome, like the symbiont Bacteroides thetaiotaomicron, actively induce anti-inflammatory immune responses to maintain mutualistic relationships with the host. Despite the importance of such interactions, the specific microbial factors responsible remain largely unknown. Here, we show that B. thetaiotaomicron, which stimulates Toll-like receptor 2 (TLR2) to drive IL-10 production, can stimulate TLR2 independently of TLR1 or TLR6, the two known TLR that can form heterodimers with TLR2 to mediate TLR2-dependent responses. Furthermore, we show that IL-10 induction is likely mediated by a protease-resistant or non-proteogenic factor, and that this requires gene BT1549, a predicted secreted lipoprotein and peptidase. Collectively, our work provides insight into the molecular dialog through which B. thetaiotaomicron coordinates anti-inflammatory immune responses. This knowledge may facilitate future strategies to promote such responses for therapeutic purposes.

Targeting CD4+ T cells through gut microbiota: therapeutic potential of traditional Chinese medicine in inflammatory bowel disease

Inflammatory Bowel Disease (IBD) is an autoimmune disease characterized by chronic relapsing inflammation of the intestinal tract. Gut microbiota (GM) and CD4+T cells are important in the development of IBD. A lot of studies have shown that GM and their metabolites like short-chain fatty acids, bile acids and tryptophan can be involved in the differentiation of CD4+T cells through various mechanisms, which in turn regulate the immune homeostasis of the IBD patients. Therefore, regulating CD4+T cells through GM may be a potential therapeutic direction for the treatment of IBD. Many studies have shown that Traditional Chinese Medicine (TCM) formulas and some herbal extracts can affect CD4+T cell differentiation by regulating GM and its metabolites. In this review, we mainly focus on the role of GM and their metabolites in regulating the differentiation of CD4+T cells and their correlation with IBD. We also summarize the current research progress on the regulation of this process by TCM.

Exploring the pathogenesis of RA through the gut-articular axis-dysbiosis a potential factor

Rheumatoid arthritis (RA) is a chronic autoimmune disease with a complex etiology. It has been suggested that the pathogenesis of RA begins in the mucosa and then transitions to the joints when many factors interact, including microbial dysbiosis, inflammatory responses, and immune abnormalities at the mucosal site. Data from RA animals and patients suggest there are changes in the mucosal microflora before the onset of RA, and that dysbiosis of the mucosal ecology continues to play a role in the development of arthritis. Microbial dysbiosis of the mucosa reduces the normal barrier function of the intestinal tract, promotes inflammatory reactions in the mucosal areas of the intestines, and then activates the intestinal immune cells abnormally to produce a large number of auto-reactive antibodies that exacerbate arthritis. Current findings do not clarify whether dysbiosis is only a potential trigger for the development of RA. If it is possible to intervene in such microbial changes before the onset of RA, could the clinical symptoms of arthritis be prevented or reduced? Finding new ways to regulate gut flora composition to maintain gut barrier function is an ongoing challenge for the prevention and treatment of RA.

Association Between Altered Microbiota Composition and Immune System-Related Genes in COVID-19 Infection

Microbiota and immunity affect the host's susceptibility to SARS-CoV-2 infection and the severity of COVID-19. This study aimed to identify significant alterations in the microbiota composition, immune signaling pathways, their potential association, and candidate microRNA in COVID-19 patients using an in silico study model. Enrichment online databases and Python programming were utilized to analyze GSE164805, GSE180594, and GSE182279, as well as NGS data of microbiota composition (PRJNA650244 and PRJNA660302) associated with COVID-19, employing amplicon-based/marker gene sequencing methods. C1, TNF, C2, IL1, and CFH genes were found to have a significant impact on immune signaling pathways. Additionally, we observed a notable decrease in Bacteroides spp. and Faecalibacterium sp., while Escherichia coli, Streptococcus spp., and Akkermansia muciniphila showed increased abundance in COVID-19. Notably, A. muciniphila demonstrated an association with immunity through C1 and TNF, while Faecalibacterium sp. was linked to C2 and IL1. The correlation between E. coli and CFH, as well as IL1 and Streptococcus spp. with C2, was identified. hsa-let-7b-5p was identified as a potential candidate that may be involved in the interaction between the microbiota composition, immune response, and COVID-19. In conclusion, integrative in silico analysis shows that these microbiota members are potentially crucial in the immune responses against COVID-19.

Gut Microbiota Mediates Neuroinflammation in Alzheimer's Disease: Unraveling Key Factors and Mechanistic Insights

The gut microbiota, the complex community of microorganisms that inhabit the gastrointestinal tract, has emerged as a key player in the pathogenesis of neurodegenerative disorders, including Alzheimer's disease (AD). AD is characterized by progressive cognitive decline and neuronal loss, associated with the accumulation of amyloid-β plaques, neurofibrillary tangles, and neuroinflammation in the brain. Increasing evidence suggests that alterations in the composition and function of the gut microbiota, known as dysbiosis, may contribute to the development and progression of AD by modulating neuroinflammation, a chronic and maladaptive immune response in the central nervous system. This review aims to comprehensively analyze the current role of the gut microbiota in regulating neuroinflammation and glial cell function in AD. Its objective is to deepen our understanding of the pathogenesis of AD and to discuss the potential advantages and challenges of using gut microbiota modulation as a novel approach for the diagnosis, treatment, and prevention of AD.

The microbiome and acute organ injury: focus on kidneys

The microbiome of critically ill patients is significantly altered by both effects of the illnesses and clinical interventions provided during intensive care. Studies have shown that manipulating the microbiome can prevent or modulate complications of critical illness in experimental models and preliminary clinical trials. This review aims to discuss general concepts about the microbiome, including mechanisms of modifying acute organ dysfunction. The focus will be on the effects of microbiome modulation during experimental acute kidney injury (excluding septic acute kidney injury) and comparison with other experimental acute organ injuries commonly seen in critically ill patients.

Enterocloster clostridioformis protects against Salmonella pathogenesis and modulates epithelial and mucosal immune function

BACKGROUND

Promoting resistance to enteric pathogen infection is a core function of the gut microbiota; however, many of the specific host-commensal interactions that mediate this protection remain uncharacterised. To address this knowledge gap, we monocolonised germ-free mice with mouse-derived commensal microbes to screen for microbiota-induced resistance to Salmonella Typhimurium infection.

RESULTS

We identified Enterocloster clostridioformis as a protective species against S. Typhimurium infection. E. clostridioformis selectively upregulates resistin-like molecule β and cell cycle pathway expression at the level of caecal epithelial cells and increases T-regulatory cells in the underlying mucosal immune system, potentially contributing to reduced infection-induced pathology.

CONCLUSIONS

We highlight novel mechanisms of host-microbe interactions that can mediate microbiota-induced resistance to acute salmonellosis. In the backdrop of increasing antibiotic resistance, this study identifies novel potential avenues for further research into protective host responses against enteric infections and could lead to new therapeutic approaches. Video Abstract.

Microbial succession at weaning is guided by microbial metabolism of host glycans

The weaning transition from a milk-based to a solid-food diet supports critical developmental changes to the intestinal microbiome and immune system. However, the specific microbial and host features that influence microbial succession at weaning are not well understood. Here, we developed a simple approach to investigate the complex dynamics of microbial succession during weaning by co-housing gnotobiotic mice colonized with the defined pre-weaning community PedsCom and the adult-derived consortium OMM12. As expected, co-housing PedsCom mice with OMM12 recapitulated microbial succession at weaning and induced immune system maturation in PedsCom mice. Unexpectedly, we found that the OMM12 microbes with the highest host glycan utilization profiles were the most adept colonizers of PedsCom mice. Genomic analysis confirmed that PedsCom is deficient in the carbohydrate-active enzymes responsible for degrading host-derived glycans, including mucins, compared to adult-derived consortia. We validated a role for glycan utilization in vivo by demonstrating that the mucus-degrading commensal microbe Akkermansia muciniphila critically depends on the metabolism of mucin glycans for colonization of PedsCom mice. These findings highlight the importance of host-derived glycans in shaping microbial communities during the weaning transition and suggest host glycans as novel targets to modulate intestinal microbial populations, introduce beneficial probiotics, and enhance immune system development during weaning.

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.

Long-read 16S rRNA amplicon sequencing reveals microbial characteristics in patients with colorectal adenomas and carcinoma lesions in Egypt

BACKGROUND

Colorectal cancer (CRC) is among the five leading causes of cancer incidence and mortality. During the past decade, the role of the gut microbiota and its dysbiosis in colorectal tumorigenesis has been emphasized. Metagenomics and amplicon-based microbiome profiling provided insights into the potential role of microbial dysbiosis in the development of CRC.

AIM

To address the scarcity of information on differential microbiome composition of tumor tissue in comparison to adenomas and the lack of such data from Egyptian patients with CRC.

MATERIALS AND METHODS

Long-read nanopore sequencing of 16S rRNA amplicons was used to profile the colonic microbiota from fresh colonoscopic biopsy samples of Egyptian patients with CRC and patients with colonic polyps.

RESULTS

Species richness of CRC lesions was significantly higher than that in colonic polyps (p-value = 0.0078), while evenness of the CRC group was significantly lower than the colonic polyps group (p-value = 0.0055). Both species richness and Shannon diversity index of the late onset CRC samples were significantly higher than those of the early onset ones. The Firmicutes-to-Bacteroidetes (F/B) ratio was significantly higher in the CRC group than in the colonic polyps group (p-value = 0.0054), and significantly higher in samples from early-onset CRC. The Enterococcus spp. were significantly overabundant in patients with rectal cancer and early-onset CRC, while Staphylococcus spp. were significantly higher in patients with sigmoid cancer and late-onset CRC. In addition, the relative abundance of Fusobacterium nucleatum was significantly higher in CRC patients.

CONCLUSION

Differentiating trends were identified at phylum, genus, and species levels, despite the inter-individual differences. In summary, this study addressed the microbial dysbiosis associated with CRC and colonic polyps groups, paving the way for a better understanding of the pathogenesis of early and late-onset CRC in Egyptian patients.

Antimicrobial peptide DP7 alleviates dextran sulfate sodium (DSS)-induced colitis via modifying gut microbiota and regulating intestinal barrier function

Inflammatory bowel diseases (IBDs), such as Crohn's disease (CD) and ulcerative colitis (UC), represent a growing global health concern. Restoring the balance of the gut microbiota, a crucial factor in intestinal health, offers potential for treating IBD. DP7, a novel antimicrobial peptide with potent antibacterial activity, was investigated for its anti-inflammatory effects in a dextran sulfate sodium (DSS)-induced UC mouse model. DP7 significantly ameliorated key disease parameters, including disease activity index, weight loss, and shortened colon length, while preserving colonic epithelial integrity and reducing inflammatory infiltration. Further analysis revealed potential targets of DP7, highlighting the significant role of Muribaculaceae bacteria during inflammatory states. To further explore the role of the gut microbiota in DP7's efficacy, fecal microbiota transplantation (FMT) was performed using feces from DP7-treated mice. FMT successfully ameliorated colitis in recipient mice, providing further evidence for the crucial role of the gut microbiome in IBD treatment and DP7's ability to modulate the gut microbiota for therapeutic benefit. Moreover, our findings suggest that DP7's modulation of the immune system is intricately linked to the complex microbial environment. Our findings demonstrate that DP7 effectively mitigates inflammation, attenuates barrier dysfunction, and shapes the gut microbiota, suggesting its potential as a therapeutic agent for UC.

Targeting gut microbiota to regulate the adaptive immune response in atherosclerosis

Atherosclerosis, the leading cause of death worldwide, is a chronic inflammatory disease leading to the accumulation of lipid-rich plaques in the intima of large and medium-sized arteries. Accumulating evidence indicates the important regulatory role of the adaptive immune system in atherosclerosis during all stages of the disease. The gut microbiome has also become a key regulator of atherosclerosis and immunomodulation. Whilst existing research extensively explores the impact of the microbiome on the innate immune system, only a handful of studies have explored the regulatory capacity of the microbiome on the adaptive immune system to modulate atherogenesis. Building on these concepts and the pitfalls on the gut microbiota and adaptive immune response interaction, this review explores potential strategies to therapeutically target the microbiome, including the use of prebiotics and vaccinations, which could influence the adaptive immune response and consequently plaque composition and development.

Oral and Gut Microbial Hubs Associated With Reaction Threshold Interact With Circulating Immune Factors in Peanut Allergy

BACKGROUND

Among peanut-allergic individuals, there is high variability in the amount of peanut that triggers reactions (i.e., reaction threshold) that is not predictable or well-understood. We conducted this study to characterize relationships between the oral and gut microbiomes and systemic processes associated with reaction threshold in peanut allergy (PA).

METHODS

In a cohort of 120 children with suspected PA who underwent double-blind, placebo-controlled food challenges, we generated and analyzed parallel profiles of the oral microbiome, gut microbiome, peripheral blood transcriptome, peripheral blood cytometry, and serum antibody levels to identify threshold-associated markers and their inter-relationships.

RESULTS

The 120 participants included 23 children with no PA, 74 with high-threshold PA (reacting to ≥ 443 mg cumulative peanut protein), and 23 with low-threshold PA (reacting to < 443 mg cumulative peanut protein). Ten hub microbes were each identified in saliva and stool microbiome networks that were constructed, including the hub microbes Rothia aeria in saliva and Bacteroides sp. in stool that were associated with reaction threshold. These hub microbes were also associated with peripheral blood transcript levels for threshold-associated key drivers of FcγR-mediated phagocytosis and TLR signaling. Correlation network construction with additional data on threshold-associated peripheral blood neutrophil abundance and peanut-specific serum IgE and Ara h 2 antibody levels revealed central roles for saliva Rothia aeria and stool Bacteroides sp. in local-systemic networks for IgE- and IgG-mediated peanut allergy.

CONCLUSIONS

This integrated study of oral and stool microbiomes, blood transcriptome, cellular profiles, and peanut-specific serum antibodies revealed new relationships between local microbiota and systemic measures associated with reaction threshold in peanut allergy.

Warm and humid environment induces gut microbiota dysbiosis and bacterial translocation leading to inflammatory state and promotes proliferation and biofilm formation of certain bacteria, potentially causing sticky stool

BACKGROUND AND AIMS OF THE STUDY

Fluctuations in environmental temperature and humidity significantly affect human physiology and disease manifestation. In the Lingnan region of China, high summer temperatures and humidity often cause symptoms like diminished appetite, sticky tongue coating, sticky stool, unsatisfactory defecation, lethargy, and joint heaviness. These are referred to as "Dampness Syndrome" in Traditional Chinese Medicine (TCM). Thick and greasy tongue fur and sticky feces are characteristic symptoms of "Dampness Syndrome" and serve as crucial diagnostic indicators in TCM for assessing health conditions. However, the specific mechanisms that lead to these symptoms, such as sticky feces and thick and greasy tongue fur, have not been fully elucidated. Understanding these external symptoms is essential, as they reflect internal health status. Warm, humid environments favor microorganism growth, potentially disrupting gut microbiota and bacterial translocation, which could induce an immune-inflammatory response. The primary objective of this study is to explore the potential significant role of immune response products in influencing the proliferation and biofilm formation of gut microbiota, which may subsequently lead to changes in fecal characteristics.

METHODS

In this study, mice were exposed to a controlled warm and humid environment (25 ± 3 °C with 95% humidity) for 16 days to simulate conditions associated with "Dampness Syndrome." After this period, Huoxiang Zhengqi Water, a traditional remedy, has been administrated for four days. On the one hand saliva and tongue coating samples were also taken from human subjects with "Dampness Syndrome" for microorganism culturing and to assess biofilm formation, on the other hand the co-culture products of a macrophage cell line RAW264.7 and Candida albicans and the effect of tumor necrosis factor-α (TNF-α) were evaluated for their impact on the proliferation and biofilm-forming abilities of different bacterial strains.

RESULTS

Compared to a control group, the treatment group exhibited significant changes in gut microbiota, including increased biofilm formation, which was mitigated by Huoxiang Zhengqi Water. In the model group, fungal translocation was observed, potentially triggering an inflammatory response. Intraperitoneal injections of various bacterial strains in mice reproduced the sticky stool characteristics. Both mice and human subjects with "Dampness Syndrome" displayed elevated serum levels of inflammatory cytokines TNF-α and interleukin-17 A (IL-17A). Interestingly, Saliva samples from individuals with "Dampness Syndrome" showed elevated TNF-α levels, accompanied by thick and greasy tongue fur. Culturing samples from the tongue coating of individuals in the "Dampness Syndrome" group revealed an increased biofilm formation capability. C. albicans co-cultured with RAW264.7 cells increased TNF-α secretion, and the supernatant promoted pathogenic bacterial proliferation and biofilm formation. TNF-α specifically enhanced biofilm formation in microorganism like C. albicans and Staphylococcus aureus, with minimal effect on beneficial bacteria like Lacticaseibacillus paracasei and Lactiplantibacillus plantarum in the tested conditions.

CONCLUSIONS

These findings provided new insights into the biological mechanisms of 'Dampness Syndrome' and support the therapeutic role of Huoxiang Zhengqi Water in treating symptoms associated with microbial dysbiosis and inflammation. Additionally, they indicate that TNF-α seems to have selective effects in promoting the proliferation and biofilm formation of different microbial species.

A human oral commensal-mediated protection against Sjögren's syndrome with maintenance of T cell immune homeostasis and improved oral microbiota

Sjögren's syndrome (SS) is a prevalent systemic autoimmune disease with substantial impacts on women's health worldwide. Although oral Haemophilus parainfluenzae is reduced in SS, its significance remains unclear. This study aimed to elucidate the pathophysiological role of H. parainfluenzae in SS. Reduced salivary H. parainfluenzae levels in SS patients were confirmed through quantitative PCR. Oral H. parainfluenzae inoculation in NOD mice alleviated focal sialadenitis, improved salivary function, and reduced IFN-γ+CD3+ and IFN-γ+CD8+ T cells in salivary gland-draining lymph nodes, maintaining immune homeostasis against a biased type 1 response. Inoculation also enhanced salivary microbiota diversity, balanced the Firmicutes-to-Proteobacteria ratio, and reduced the overwhelming presence of Pseudomonas mendocina. In vitro, H. parainfluenzae-preconditioned A253 cells limited CD8 T cell expansion with reduced IFN-γ production. These findings suggest that H. parainfluenzae improves oral microbial diversity, promotes homeostatic T-cell immunity, and protects against SS, supporting its potential as a next-generation probiotic.

Impact of gut microbiota on cardiac aging

Recent research has suggested imbalances in gut microbiota composition as contributors to cardiac aging. An individual's physical condition, along with lifestyle-associated factors, including diet and medication, are significant determinants of gut microbiota composition. This review discusses evidence of bidirectional associations between aging and gut microbiota, identifying gut microbiota-derived metabolites as potential regulators of cardiac aging. It summarizes the effects of gut microbiota on cardiac aging diseases, including cardiac hypertrophy and fibrosis, heart failure, and atrial fibrillation. Furthermore, this review discusses the potential anti-aging effects of modifying gut microbiota composition through dietary and pharmacological interventions. Lastly, it underscores critical knowledge gaps and outlines future research directions. Given the current limited understanding of the direct relationship between gut microbiota and cardiac aging, there is an urgent need for preclinical and clinical investigations into the mechanistic interactions between gut microbiota and cardiac aging. Such endeavors hold promise for shedding light on the pathophysiology of cardiac aging and uncovering new therapeutic targets for cardiac aging diseases.

Characteristics of skin microbiome associated with disease severity in systemic sclerosis

Systemic sclerosis (SSc) is a chronic autoimmune disorder characterised by skin fibrosis and internal organ involvement. Disruptions in the microbial communities on the skin may contribute to the onset of autoimmune diseases that affect the skin. However, current research on the skin microbiome in SSc is lacking. This study aimed to investigate skin microbiome associated with disease severity in SSc. Skin swabs were collected from the upper limbs of 46 healthy controls (HCs) and 36 patients with SSc. Metagenomic analysis based on the 16S rRNA gene was conducted and stratified by cutaneous subtype and modified Rodnan skin score (mRSS) severity. Significant differences in skin bacterial communities were observed between the HCs and patients with SSc, with further significant variations based on subtype and mRSS severity. The identified biomarkers were Bacteroides and Faecalibacterium for patients with diffuse cutaneous SSc with high mRSS (≥ 10) and Mycobacterium and Parabacteroides for those with low mRSS (< 10). Gardnerella, Abies, Lactobacillus, and Roseburia were the biomarkers in patients with limited cutaneous SSc (lcSS) and high mRSS, whereas Coprococcus predominated in patients with lcSS and low mRSS. Cutaneous subtype analysis identified Pediococcus as a biomarker in the HCs, whereas mRSS analysis revealed the presence of Pseudomonas in conjunction with Pediococcus. In conclusion, patients with SSc exhibit distinct skin microbiota compared with healthy controls. Bacterial composition varies by systemic sclerosis cutaneous subtype and skin thickness.

Gut microbiota contributes to the intestinal and extraintestinal immune homeostasis by balancing Th17/Treg cells

Gut microbiota is generally considered to play an important role in host health due to its extensive immunomodulatory activities. Th17 and Treg cells are two important CD4+ T cell subsets involved in immune regulation, and their imbalance is closely tied to many immune diseases. Recently, abundant researches have highlighted the importance of gut microbiota in supporting intestinal and extraintestinal immunity through the balance of Th17 and Treg cells. Here, we presented a comprehensive review of these findings. This review first provided an overview of gut microbiota, along with Th17/Treg cell differentiation and cytokine production. Subsequently, the review summarized the regulatory effects of gut microbiota (in terms of species, components, and metabolites) on the Th17/Treg cell balance in the local intestines and extraintestinal organs, such as lung, liver, brain, kidney, and bone. Specifically, the Th17 and Treg cells that can be modulated by gut microbiota originate not only from the gut and extraintestinal organs, but also from peripheral blood and spleen. Then, the microbial therapeutics, including probiotics, prebiotics, postbiotics, and fecal microbiota transplantation (FMT), were also reviewed because of their therapeutic potentials in addressing intestinal and extraintestinal diseases via the Th17/Treg axis. Finally, the review discussed the clinical applications and future study prospects of microbial therapeutics by targeting the Th17/Treg cell balance. In conclusion, this review focused on elucidating the regulatory effects of gut microbiota in balancing Th17/Treg cells to maintain intestinal and extraintestinal immune homeostasis, contributing to the further development and promotion of microbial therapeutics.

Gut Microbiota Modulation: A Novel Strategy for Rheumatoid Arthritis Therapy

Rheumatoid arthritis (RA) is a chronic autoimmune disease that leads to joint inflammation, progressive tissue damage and significant disability, severely impacting patients' quality of life. While the exact mechanisms underlying RA remain elusive, growing evidence suggests a strong link between intestinal microbiota dysbiosis and the disease's development and progression. Differences in microbial composition between healthy individuals and RA patients point to the role of gut microbiota in modulating immune responses and promoting inflammation. Therapies targeting microbiota restoration have demonstrated promise in improving treatment efficacy, enhancing patient outcomes and slowing disease progression. However, the complex interplay between gut microbiota and autoimmune pathways in RA requires further investigation to establish causative relationships and mechanisms. Here, we review the current understanding of the gut microbiota's role in RA pathogenesis and its potential as a therapeutic target.

Pyroptosis the Emerging Link Between Gut Microbiota and Multiple Sclerosis

This review elucidates the pivotal role of pyroptosis, triggered by gut microbiota, in the development of multiple sclerosis (MS), emphasizing its significance within the gut-brain axis. Our comprehensive analysis of recent literature reveals how dysbiosis in the gut microbiota of MS patients-characterized by reduced microbial diversity and shifts in bacterial populations-profoundly impacts immune regulation and the integrity of the central nervous system (CNS). Pyroptosis, an inflammatory form of programmed cell death, significantly exacerbates MS by promoting the release of inflammatory cytokines and causing substantial damage to CNS tissues. The gut microbiota facilitates this detrimental process through metabolites such as short-chain fatty acids and neuroactive compounds, or self-structural products like lipopolysaccharides (LPS), which modulate immune responses and influence neuronal survival. This review highlights the potential of modulating gut microbiota to regulate pyroptosis, thereby suggesting that targeting this pathway could be a promising therapeutic strategy to mitigate inflammatory responses and preserve neuronal integrity in patients with MS.

Gut microbiota mediated T cells regulation and autoimmune diseases

Gut microbiota regulates the immune system, the development and progression of autoimmune diseases (AIDs) and overall health. Recent studies have played a crucial part in understanding the specific role of different gut bacterial strains and their metabolites in different AIDs. Microbial signatures in AIDs are revealed by advanced sequencing and metabolomics studies. Microbes such as Faecalibacterium prausnitzii, Akkermansia muciniphila, Anaerostipes caccae, Bacteroides sp., Roseburia sp., Blautia sp., Blautia faecis, Clostridium lavalense, Christensenellaceae sp., Coprococcus sp., Firmicutes sp., Ruminococcaceae sp., Lachnospiraceae sp., Megamonas sp., Monoglobus sp., Streptococcus pneumoniae and Bifidobacterium sp. help maintain immune homeostasis; whereas, Prevotella copri, Ruminococcus gnavus, Lactobacillus salivarius, Enterococcus gallinarum, Elizabeth menigoseptica, Collinsella sp., Escherichia sp., Fusobacterium sp., Enterobacter ludwigii, Enterobacteriaceae sp., Proteobacteria, Porphyromonas gingivalis, Porphyromonas nigrescens, Dorea sp., and Clostridium sp. cause immuno-pathogenesis. A complex web of interactions is revealed by understanding the influence of gut microbiota on immune cells and various T cell subsets such as CD4+ T cells, CD8+ T cells, natural killer T cells, γδ T cells, etc. Certain AIDs, including rheumatoid arthritis, diabetes mellitus, atopic asthma, inflammatory bowel disease and non-alcoholic fatty liver disease exhibit a state of dysbiosis, characterized by alterations in microbial diversity and relative abundance of specific taxa. This review summarizes recent developments in understanding the role of certain microbiota composition in specific AIDs, and the factors affecting specific regulatory T cells through certain microbial metabolites and also focuses the potential application and therapeutic significance of gut microbiota-based interventions as novel adjunctive therapies for AIDs. Further research to determine the precise association of each gut bacterial strain in specific diseases is required.

Sex-dependent modulation of T and NK cells and gut microbiome by low sodium diet in patients with primary aldosteronism

Background

High dietary sodium intake is a major cardiovascular risk factor and adversely affects blood pressure control. Patients with primary aldosteronism (PA) are at increased cardiovascular risk, even after medical treatment, and high dietary sodium intake is common in these patients. Here, we analyze the impact of a moderate dietary sodium restriction on microbiome composition and immunophenotype in patients with PA.

Methods

Prospective two-stage clinical trial including two subgroups: 15 treatment-naive PA patients compared to matched normotensive controls; and 31 PA patients on mineralocorticoid receptor antagonist treatment before and three months after sodium restriction. Patients underwent blood pressure measurements, laboratory tests, analysis of peripheral blood mononuclear cells via flow cytometry and microbiome analysis.

Results

We observed a higher percentage of Tregs in treatment-naive PA patients (p = 0.0303), while the abundance of Bacteroides uniformis was higher in PA patients compared to normotensive controls (p = 0.00027) and the abundance of Lactobacillus species however was higher in the subgroup of normotensive controls (p = 0.0290). Sodium restriction was accompanied by a decrease in pro-inflammatory Tc17 cells in male patients (p = 0.0081, females p = 0.3274). Bacteroides uniformis abundance was higher in female patients (0.01230, p = 0.0016) and decreased upon sodium restriction (0.002309, p = 0.0068).

Conclusion

Dietary sodium restriction in patients with PA modulates the peripheral immune cell composition toward a less inflammatory phenotype. This suggests a potential mechanism by which sodium reduction modulates immune cell composition, leading to blood pressure reduction and positively impacting cardiovascular risk.

Lysate of Parabacteroides distasonis prevents severe forms of experimental autoimmune encephalomyelitis by modulating the priming of T cell response

The gut microbiota influences the reactivity of the immune system, and Parabacteroides distasonis has emerged as an anti-inflammatory commensal. Here, we investigated whether its lysate could prevent severe forms of neuroinflammation in experimental autoimmune encephalomyelitis (EAE) in mice and how this preventive strategy affects the gut microbiota and immune response. Lysate of anaerobically cultured P. distasonis (Pd lysate) was orally administered to C57BL/6 mice in four weekly doses. One week later, EAE was induced and disease severity was assessed three weeks after induction. Fecal microbiota changes in both vehicle- and Pd lysate-treated animals was analyzed by 16S V3-V4 amplicon sequencing and qPCR, antimicrobial peptide expression in the intestinal mucosa was measured by qPCR, and immune cell composition in the mesenteric and inguinal lymph nodes was measured by multicolor flow cytometry. Pd lysate significantly delayed the development of EAE and reduced its severity when administered prior to disease induction. EAE induction was the main factor in altering the gut microbiota, decreasing the abundance of lactobacilli and segmented filamentous bacteria. Pd lysate significantly increased the intestinal abundance of the genera Anaerostipes, Parabacteroides and Prevotella, and altered the expression of antimicrobial peptides in the intestinal mucosa. It significantly increased the frequency of regulatory T cells, induced an anti-inflammatory milieu in mesenteric lymph nodes, and reduced the activation of T cells at the priming site. Pd lysate prevents severe forms of EAE by triggering a T regulatory response and modulating T cell priming to autoantigens. Pd lysate could thus be a future modulator of neuroinflammation that increases the resistance to multiple sclerosis.

Gut Microbial Dysbiosis and Implications in Solid Organ Transplantation

The gut microbiome has been shown to play a significant role in solid organ transplantation, potentially influencing graft function and patient outcomes. Dysbiosis, characterized by reduced microbial diversity and an increase in pathogenic taxa, has been linked to higher incidences of allograft rejection, graft dysfunction, and post-transplant mortality. Several studies suggest that the gut microbiome might be able to serve as both a biomarker and a therapeutic target, potentially guiding personalized immunosuppressive therapies and other interventions to improve outcomes after solid organ transplantation. As summarized in this review, clinical studies have shown that specific microbial shifts correlate with adverse outcomes, including acute rejection and chronic allograft dysfunction. As research surrounding the relationship between the gut microbiome and solid organ transplant progresses, the integration of microbial analysis into clinical practice has the potential to revolutionize post-transplant care, offering new avenues to improve graft survival and patient quality of life. This review aims to provide a comprehensive overview of the relationship between gut microbial dysbiosis and transplantation outcomes, emphasizing the impact on kidney, liver, lung, and heart transplant recipients.

Cohabiting with ulcerative colitis patients decreases differences of gut microbiome between healthy individuals and the patients

Background: Ulcerative colitis (UC), which is characterized by chronic relapsing inflammation of the colon, results from a complex interaction of factors involving the host, environment, and microbiome. The present study aimed to investigate the gut microbial composition and metabolic variations in patients with UC and their spouses. Materials and Methods: Fecal samples were collected from 13 healthy spouses and couples with UC. 16S rRNA gene amplicon sequencing and metagenomics sequencing were used to analyze gut microbiota composition, pathways, gene expression, and enzyme activity, followed by the Kyoto Encyclopedia of Genes and Genomes. Results: We found that the microbiome diversity of couples with UC decreased, especially that of UC patients. Bacterial composition, such as Firmicutes, was altered between UC patients and healthy controls, but was not significantly different between UC patients and their spouses. This has also been observed in pathways, such as metabolism, genetic information processing, organismal systems, and human diseases. However, the genes and enzymes of spouses with UC were not significantly different from those of healthy individuals. Furthermore, the presence of Faecalibacterium correlated with oxidative phosphorylation, starch and sucrose metabolism, amino sugar and nucleotide sugar metabolism, and the bacterial secretion system, showed a marked decline in the UC group compared with their spouses, but did not vary between healthy couples. Conclusion: Our study revealed that cohabitation with UC patients decreased differences in the gut microbiome between healthy individuals and patients. Not only was the composition and diversity of the microbiota diminished, but active pathways also showed some decline. Furthermore, Firmicutes, Faecalibacterium, and the four related pathways may be associated with the pathological state of the host rather than with human behavior.

Multi-Drug Resistance and Breast Cancer Progression via Toll-Like Receptors (TLRs) Signaling

Toll-like receptors (TLRs) are essential receptors involved in inflammation and innate immunity. Various types of cancer cells, as well as innate immune cells, express TLRs. There is mounting proof that TLRs are critical to the development and spread of cancer as well as metabolism. In breast cancer, up-regulated levels of TLRs have been linked to the aggressiveness of the diseases, worse treatment outcomes, and the emergence of therapeutic resistance. Patients with advanced non-resectable, recurring, and metastatic breast cancer currently have few available treatment choices. An intriguing new strategy is an innate immunity-mediated anticancer immunotherapy, either used alone or in conjunction with existing treatments. In fact, several TLR agonists and antagonists have been used in clinical studies for anti-cancer immunotherapy. Consequently, TLRs serve as critical targets for controlling the course of breast cancer and treatment resistance in addition to being implicated in immune responses against pathogen infection and cancer immunology. In this review, we deliver an overview of the most current findings on TLR involvement in the development of breast cancer and treatment resistance.

Dynamic Changes in the Intraepithelial Lymphocyte Numbers Following Salmonella Typhimurium Infection in Broiler Chickens

At day 21 of age, Ross-308 broilers were orally gavaged with 7.5 × 106 CFU/mL S. Typhimurium (n = 30), and another 30 birds were kept as the control. The body weight of birds was recorded on days 0, 2, 7, and 14 days post-infection (dpi) to calculate body weight gains (BWGs). At each time point, seven birds per group were euthanized for sample collection to acquire IELs and lymphocytes from the ileum and spleen for flow cytometric analysis. A reduction in BWGs of the infected groups compared to the control group was observed only at 2 dpi. Additionally, there were no changes in the expression of IFN-γ, IL-1β, and TNF-α in the ileum at 2 and 7 dpi. The number of IELs increased significantly following Salmonella infection in the ileum at 2 and 7 dpi without any changes in spleen lymphocytes. The increase in the total number of IELs was derived from the elevated numbers of conventional CD8αβ+TCRαβ+ and natural IEL populations (CD4-CD8-TCRαβ+, CD8αα+TCRαβ+, TCRγδ+, non-T cells (TCRneg, and iCD8α cells)). The increase in regulatory IELs and the stable expression of proinflammatory cytokine genes during the first week of infection suggests the potential role of IELs in modulating intestinal inflammation.

Back to Roots: Dysbiosis, Obesity, Metabolic Syndrome, Type 2 Diabetes Mellitus, and Obstructive Sleep Apnea-Is There an Objective Connection? A Narrative Review

In recent decades, it has become clear that the gut is more than just a digestive organ; it also functions as an immune organ with regulatory capabilities and acts as a "second brain" that influences brain function due to the presence and regulatory roles of the gut microbiota (GM). The GM is a crucial component of its host and significantly impacts human health. Dysbiosis, or microbial imbalance, has been closely linked to various diseases, including gastrointestinal, neurological, psychiatric, and metabolic disorders. The aim of this narrative review is to highlight the roles of the GM in maintaining metabolic health. Sleep is a vital biological necessity, with living organisms having evolved an internal sleep-wake rhythm that aligns with a roughly 24 h light/dark cycle, and this is known as the circadian rhythm. This cycle is essential for tissue repair, restoration, and overall optimal body functioning. Sleep irregularities have become more prevalent in modern society, with fast-paced lifestyles often disrupting normal sleep patterns. Urban living factors, such as fast food consumption, shift work, exposure to artificial light and nighttime noise, medications, and social activities, can adversely affect circadian rhythms, with dysbiosis being one of the many factors incriminated in the etiology of sleep disorders.

Diverse roles of dendritic cell and regulatory T cell crosstalk in controlling health and disease

Dendritic cells (DCs) are specialized antigen-presenting cells for lymphocytes, including regulatory T (Treg) cells, a subset of CD4+ T cells expressing CD25 and Foxp3, a transcription factor. Treg cells maintain immunological self-tolerance in mice and humans, and suppress autoimmunity and other various immune responses such as tumor immunity, transplant rejection, allergy, responses to microbes, and inflammation. Treg-cell proliferation is controlled by antigen-presenting DCs. On the other hand, Treg cells suppress the function of DCs by restraining DC maturation. Therefore, the interaction between DCs and Treg cells, DC-Treg crosstalk, could contribute to controlling health and disease. We recently found that unique DC-Treg crosstalk plays a role in several conditions. First, Treg cells are expanded in ultraviolet B (UVB)-exposed skin by interacting with DCs, and the UVB-expanded Treg cells have a healing function. Second, manipulating DC-Treg crosstalk can induce effective acquired immune responses against severe acute respiratory syndrome coronavirus 2 antigens without adjuvants. Third, Treg cells with a special feature interact with DCs in the tumor microenvironment of human head and neck cancer, which may contribute to the prognosis. Understanding the underlying mechanisms of DC-Treg crosstalk may provide a novel strategy to control health and disease.