The microbiota in adaptive immune homeostasis and disease

Short-term antiretroviral therapy may not correct the dysregulations of plasma virome and cytokines induced by HIV-1 infection

An expansion of plasma anelloviruses and dysregulation of inflammation was associated with HIV-1 infection. However, how antiretroviral therapy (ART) affects the dynamics of plasma virome and cytokine profile remains largely unknown. To characterize the dynamics of plasma virome and cytokines in HIV-1-infected individuals before and during the first year of ART, a cohort of 26 HIV-1-infected individuals and 19 healthy controls was recruited. Blood samples were collected and subjected to metagenomic analysis and the measurement of 27 cytokines. Metagenomic analysis revealed an increased abundance and prevalence of human pegivirus type 1 (HPgV-1) and a slightly decreased diversity and abundance of anellovirus in plasma of HIV-1-infected individuals after ART. No obvious impact was observed on other plasma commensal viruses. Increased abundance and prevalence of HPgV-1 were further confirmed by RT-qPCR assay in a larger cohort of 114 HIV-1-infected individuals. Notably, most dysregulated cytokines were not fully restored by ART, with extremely abnormal levels of IL-10, GM-CSF, VEGF, and eotaxin, and a significantly increased level of plasma I-FABP. Anelloviruses showed significantly negative correlations with other commensal viruses except HPgV-1 but had positive correlations with several anti-inflammatory and Th1 cytokines. These results suggest that short-term ART may not significantly correct the virome and cytokine dysregulations induced by HIV-1 infection. The results highlight a need for further investigation into the long-term effects of ART on virome and cytokine profiles in HIV-1-infected individuals.

Research progress on the interaction between intestinal flora and microRNA in pelvic inflammatory diseases

Pelvic inflammatory disease (PID) is a common infectious disease of the female upper reproductive tract, and its pathological basis is immune inflammatory response. The imbalance of gut microflora (GM) may lead to the development of inflammatory process. A large number of studies have shown that fecal microbiota transplantation, probiotics, bacteria, prebiotics, and dietary intervention may play a potential role in remodeling GM and treating diseases. MicroRNAs (miRNAs) are involved in cell development, proliferation, apoptosis and other physiological processes. In addition, they play an important role in the inflammatory process, participating in the regulation of proinflammatory and anti-inflammatory pathways. Differences in miRNA profiles may be PID diagnostic tools and serve as prognostic markers of the disease. The relationship between miRNA and GM has not been fully elucidated. Recent studies have shown the role of miRNA in the regulation and induction of GM dysbiosis. In turn, microbiota can regulate the expression of miRNA and improve the immune status of the body. Therefore, this review aims to describe the interaction between GM and miRNA in PID, and to find potential precise targeted therapy for PID.

Butyrate Ameliorates Graves' Orbitopathy Through Regulating Orbital Fibroblast Phenotypes and Gut Microbiota

Purpose

Graves' orbitopathy (GO), the common extrathyroidal complication of Graves' disease (GD), is characterized by orbital fibroblast stimulation, adipogenesis, and hyaluronan production. Recently, gut microbiota and its metabolites have garnered attention for their possible involvement in GO.

Methods

This study utilized an animal model of GO and examined the effects of butyrate treatment on orbital fibroblast cells and gut microbiota. Ex vivo experiments were performed using orbital fibroblasts derived from healthy patients' and patients' with GO orbital tissue to evaluate vitality, activation, and adipogenesis in response to butyrate treatment. Gut microbiota diversity was also analyzed in butyrate-treated and untreated GO mice.

Results

In human orbital fibroblasts, butyrate treatment dramatically decreased the vitality of GO-derived fibroblasts without harming normal fibroblasts. Butyrate prevented activation and fibrotic processes induced by transforming growth factor beta 1 (TGF-β1) in GO and normal fibroblasts. Additionally, butyrate reduced lipid droplet formation and downregulated lipogenic markers in GO and normal orbital fibroblasts, inhibiting adipogenesis. In the GO mouse model, butyrate therapy improved orbital histological abnormalities and normalized serum thyroid hormone and antibody levels. The intestinal microbiome of butyrate-treated GO mice also changed significantly, with a reduction in certain bacteria (Bifidobacterium, GCA-900066575, and Parabacteroides) and an increase in others (Bacteroides and Rikenellaceae_RC9).

Conclusions

Butyrate ameliorates several of the symptoms of GO, lowering GO orbital fibroblast viability, adipogenesis, and TGF-β1-induced fibrosis without damaging normal fibroblasts. Butyrate normalizes thyroid function in a GO mouse model, improves histopathological alterations, and transforms gut microbiota populations, proving its potential in treating GO through the gut-thyroid axis.

Gut Microbiota and Metabolic Biomarkers Associated With Longevity

The dynamic balance between pro- and anti-inflammatory networks decreases as individuals age, and intestinal dysbiosis can initiate and maintain low-grade systemic inflammation. Interactions between the microbiota and humans occur from the beginning of life and, in general, the diversity of microbiota decreases with aging. The microbiome produces different metabolites with systemic effects, including immune system regulation. This understanding will be useful in controlling inflammation and preventing metabolic changes. Therefore, this review aims to identify the main metabolites synthesized by the intestinal microbiota to be used as biomarkers associated with longevity. This is a narrative review using scientific articles published in the last 10 years in the following databases: PubMed, Scielo, and Lilacs, using the Boolean operators "and" or "or." For this review, we identified 5 articles. The main metabolites described in the literature to date are organic acids, bile acids (BAs), short-chain fatty acids, branched-chain amino acids, trimethylamine N-oxide (TMAO), and derivatives of tryptophan and indole. Among these, the only ones not yet well characterized in studies on longevity were BAs and TMAO. Glutamate and p-cresol were also highlighted in the literature, with a negative association with longevity. The others showed an association, mostly positive, and can be used as potential biomarkers correlated with healthy aging and, if better studied, as targets for intervention to promote health and well-being.

Gut microbiota metabolites, secretory immunoglobulin A and Bayley-III cognitive scores in children from the CHILD Cohort Study

Background

Dysbiosis of the gut microbiota has been demonstrated in neurodevelopmental disorders but the underlying mechanisms that may explain these associations are poorly understood. Gut secretory immunoglobulin A (SIgA) binds pathogenic microbes, preventing mucosal penetration. Gut microbes also influence SIgA production and its binding characteristics through short-chain fatty acid (SCFA) metabolites, allowing them to regulate the immune response. Serum IgA deficiency has been noted in children with autism spectrum disorders (ASD). In this study, we aimed to determine whether SIgA level in infancy is associated with gut microbiota taxonomy and metabolites, and neurodevelopmental outcomes in preschool children.

Methods

For a subsample of 178 children from the Canadian CHILD Cohort Study, gut microbiota of fecal samples collected at 3-4 months and 12 months was profiled using 16S rRNA sequencing. Gut bacterial metabolites levels and SIgA level were measured by nuclear magnetic resonance (NMR) based metabolomics and SIgA enzyme-linked immunosorbent assay at 3-4 months, respectively. Bayley-III Scale of Infant Development was assessed at 12 and 24 months. We evaluated direct relationships in multiple linear regression models and putative causal relationships in statistical mediation models.

Results

Propionate and butyrate levels at 3-4 months were associated with decreased Bayley cognitive score at 24 months (p-values: 0.01 and 0.02, respectively) in adjusted multiple linear regression models, but when we investigated an indirect relationship mediated by decreased SIgA level at 3-4 months, it did not reach statistical significance (p-values: 0.18 and 0.20, respectively). Lactate level at 3-4 months was associated with increased Bayley cognitive score at 24 months in adjusted multiple linear regression models (p-value: 0.01), but the statistical model mediated by increased SIgA level at 3-4 months did not reach statistical significance neither (p-value: 0.20).

Conclusions

Our study contributes to growing evidence that neurodevelopment is influenced by the infant gut microbiota and that it might involve SIgA level, but larger studies are required.

Friends close, enemies closer: the complex role of the microbiome in antitumor immunity

Immunotherapy has achieved remarkable advances in cancer treatment by harnessing the immune system to combat tumors, yet its effectiveness remains inconsistent across patients and tumor types. The microbiota, a diverse assemblage of microorganisms residing at host barrier surfaces, is pivotal in shaping immune responses. This review explores the direct and indirect mechanisms via which the microbiota modulates antitumor immune responses both locally within the tumor microenvironment and systemically by affecting distant tumors. We discuss recent findings linking microbiota-derived metabolites and microbiota-derived antigens with antitumor immunity and immunotherapy response. Additionally, we discuss recent advances in microbiome-based therapies, including fecal microbiota transplantation. We propose the use and development of new analytical techniques to further characterize the complex functions and interactions between the microbiome and immune system. To conclude, we outline recommendations for future research and therapeutic approaches to leverage the microbiome to improve current immunotherapies.

Bidirectional Interplay Among Non-Coding RNAs, the Microbiome, and the Host During Development and Diseases

It is widely known that the dysregulation of non-coding RNAs (ncRNAs) and dysbiosis of the gut microbiome play significant roles in host development and the progression of various diseases. Emerging evidence has highlighted the bidirectional interplay between ncRNAs and the gut microbiome. This article aims to review the current understanding of the molecular mechanisms underlying the crosstalk between ncRNAs, especially microRNA (miRNA), and the gut microbiome in the context of development and diseases, such as colorectal cancer, inflammatory bowel diseases, neurological disorders, obesity, and cardiovascular disease. Ultimately, this review seeks to provide a foundation for exploring the potential roles of ncRNAs and gut microbiome interactions as biomarkers and therapeutic targets for clinical diagnosis and treatment, such as ncRNA mimics, antisense oligonucleotides, and small-molecule compounds, as well as probiotics, prebiotics, and diets.

[Physiology of aging: An update and genetic point of view]

Aging is a physiological process resulting from the accumulation of molecular and cellular damage over time, leading to a gradual decline in overall physical and mental health. Throughout this temporal continuum, various physiological alterations occur in the organism, modifying the individual's response to multiple stimuli and adverse factors. At the same time, an increasingly significant manifestation of genetic modifications is observed, which are intrinsically interconnected with the dynamics of these adaptive processes. The geriatric population is characterized by its high prevalence in hospital settings, particularly in critical care units, where admissions from this group account for nearly 50% of total admissions. Thus, acquiring and updating knowledge is relevant and necessary to ensure a more effective therapeutic approach for geriatric patients.

Antimicrobial peptide AP2 ameliorates Salmonella Typhimurium infection by modulating gut microbiota

BACKGROUND

Endogenous antimicrobial peptides and proteins are essential for shaping and maintaining a healthy gut microbiota, contributing to anti-inflammatory responses and resistance to pathogen colonization. Salmonella enterica subsp. enterica serovar Typhimurium (ST) infection is one of the most frequently reported bacterial diseases worldwide. Manipulation of the gut microbiota through exogenous antimicrobial peptides may protect against ST colonization and improve clinical outcomes.

RESULTS

This study demonstrated that oral administration of the antimicrobial peptide AP2 (2 µg /mouse), an optimized version of native apidaecin IB (AP IB), provided protective effects against ST infection in mice. These effects were evidenced by reduced ST-induced body weight loss and lower levels of serum inflammatory cytokines. A 16 S rRNA-based analysis of the cecal microbiota revealed that AP2 significantly modulated the gut microbiota, increasing the relative abundance of Bifidobacterium while decreasing that of Akkermansia at the genus level. Furthermore, the transplantation of fecal microbiota from AP2-treated donor mice, rather than from Control mice, significantly reduced cecal damage caused by ST and decreased the concentration of ST by one order of magnitude after infection.

CONCLUSIONS

These findings reveal a novel mechanism by which exogenous antimicrobial peptides mitigate Salmonella Typhimurium infection through the modulation of gut microbiota.

Immunomodulatory and anti-inflammatory potential of botanicals bioactive product (PHYTO AX'CELL™) for an improvement of the well-being of laying hens at the peak of production

This study was designed to assess the effectiveness of an authorized commercial standardized mixture of Artepillin-C, methyl-salicylates, flavonoids and curcuminoids (PHYTO AX'CELL™) provided intermittently during 8 weeks (wk) of trial to laying hens raised in enriched cages during the peak of the production, in the reduction of inflammation status, improving the immune response, and egg quality. In this study, 764 Lohmann LSL-White hens on the first day (d) of the 26th wk of age (T0), were randomly assigned to 2 replicated experimental groups, control and treated (n=382 each). The treatment was supplied in drinking water, as follows: 26th to 27th wk (T1, 14 d) first treatment administration at a dose of 1 mL/L (0.5 mL/L only the first d of the treatment); 28th to the 31st wk (T2, 4 wk of withdrawal period); 32nd to 33rd wk (T3, 14 d) second treatment at a dose of 1 mL/L, until the end of the trial (T4). At T0, mid-T3 and T4, 13 hens per group were sampled for serum biochemical analyses (metabolic profile, H/L ratio) and weighed, and 60 eggs per group were analyzed for quality parameters. At T4, 13 hens per group were sacrificed for histological investigations and gut IgA quantification. The treatment reduced the mortality rate in the treated group (0.00%) compared to the control (2.61%). An improvement in intestinal IgA production and immune reactivity in the treated hens was observed with a significant fluctuating trend of the heterophil, lymphocyte and their ratio (P < 0.05). The egg quality was improved by the treatment, with positive effects in the Haugh unit, shell weight and thickness (P < 0.05). A T4, significant reduction in duodenal and rectal pH was observed in the treated group (P < 0.05), without intestinal inflammation score changes, body weight, serum biochemistry, interleukin levels, and infectious bronchitis virus titers (P > 0.05). From the results, PHYTO AX'CELL™ improved the well-being and physical condition of laying hens raised in cages, modulating the immune system with a positive production of intestinal IgA, and egg quality parameters important for commercial purposes.

CRAmed: a conditional randomization test for high-dimensional mediation analysis in sparse microbiome data

MOTIVATION

Numerous microbiome studies have revealed significant associations between the microbiome and human health and disease. These findings have motivated researchers to explore the causal role of the microbiome in human complex traits and diseases. However, the complexities of microbiome data pose challenges for statistical analysis and interpretation of causal effects.

RESULTS

We introduced a novel statistical framework, CRAmed, for inferring the mediating role of the microbiome between treatment and outcome. CRAmed improved the interpretability of the mediation analysis by decomposing the natural indirect effect into two parts, corresponding to the presence-absence and abundance of a microbe, respectively. Comprehensive simulations demonstrated the superior performance of CRAmed in Recall, precision, and F1 score, with a notable level of robustness, compared to existing mediation analysis methods. Furthermore, two real data applications illustrated the effectiveness and interpretability of CRAmed. Our research revealed that CRAmed holds promise for uncovering the mediating role of the microbiome and understanding of the factors influencing host health.

AVAILABILITY AND IMPLEMENTATION

The R package CRAmed implementing the proposed methods is available online at https://github.com/liudoubletian/CRAmed.

The phospholipid kinase PIKFYVE is essential for Th17 differentiation

T helper 17 (Th17) cells are effector cells that mediate inflammatory responses to bacterial and fungal pathogens. While the cytokine signaling inputs required to generate Th17s are established, less is known about intracellular pathways that drive Th17 differentiation. Our previously published phosphoproteomic screen identifies that PIKFYVE, a lipid kinase that generates the phosphatidylinositol PtdIns(3,5)P2, is activated during Th17 differentiation. Herein, we discovered that PIKFYVE regulates kinase and transcription factor networks to promote Th17 differentiation. As a specific example, PtdIns(3,5)P2 directly stimulates mTORC1 kinase activity to promote cell division and differentiation pathways. Furthermore, PIKFYVE promotes STAT3 phosphorylation, which is required for Th17 differentiation. Chemical inhibition or CD4-specific deletion of PIKFYVE reduces Th17 differentiation and autoimmune pathology in the experimental autoimmune encephalomyelitis murine model of multiple sclerosis. Our findings identify molecular mechanisms by which PIKFYVE promotes Th17 differentiation and suggest that PIKFYVE is a potential therapeutic target in Th17-driven autoimmune diseases.

Zebrafish as a model for human epithelial pathology

Zebrafish (Danio rerio) have emerged as an influential model for studying human epithelial pathology, particularly because of their genetic similarity to humans and their unique physiological traits. This review explores the structural and functional homology between zebrafish and human epithelial tissues in organs, such as the gastrointestinal system, liver, and kidneys. Zebrafish possess significant cellular and functional homology with mammals, which facilitates the investigation of various diseases, including inflammatory bowel disease, nonalcoholic fatty liver disease, and polycystic kidney disease. The advantages of using zebrafish as a model organism include rapid external development, ease of genetic manipulation, and advanced imaging capabilities, allowing for the real-time observation of disease processes. However, limitations exist, particularly concerning the lack of organs in zebrafish and the potential for incomplete phenocopy of human conditions. Despite these challenges, ongoing research in adult zebrafish promises to enhance our understanding of the disease mechanisms and regenerative processes. By revealing the similarities and differences in epithelial cell function and disease pathways, this review highlights the value of zebrafish as a translational model for advancing our knowledge of human health and developing targeted therapies.

Bifidobacterium animalis ssp. lactis BX-245-fermented milk alleviates tumor burden in mice with colorectal cancer

Colorectal cancer (CRC) arises from the accumulation of abnormal mutations in colorectal cells during prolonged inflammation. This study aimed to investigate the potential of probiotic fermented milk containing the probiotic strain, Bifidobacterium animalis ssp. lactis BX-245 (BX-245), in alleviating tumor burden in CRC mice induced by azoxymethane and dextran sodium sulfate. The study monitored changes in tumor size and number, gut microbiota, metabolomics, and inflammation levels before and after the intervention. Our findings indicate that intragastric administration of BX245-fermented milk effectively modulated the intratumor microbiota, as well as the gut microbiota and its metabolism. We also observed a decreased relative abundance of intratumor Akkermansia in the CRC mice, while the intratumor Parabacteroides exhibited a significant positive correlation with tumor number and weight. Moreover, administering BX245-fermented milk significantly reduced gut barrier permeability, alleviated gut barrier damage, and increased serum IL-2 and IFN-γ levels compared with the ordinary fermented milk group. Collectively, our data suggest that administering probiotic fermented milk containing specific functional strains such as BX245 could result in a reduction in tumor burden in CRC mice. Conversely, ordinary fermented milk did not show the same tumor-inhibiting effects. The current results are preliminary, and further confirmation is necessary to establish the causal relationship among probiotic milk, changes in gut microbiota, and disease alleviation.

Helicobacter pylori and rheumatoid arthritis: Investigation of relation from traditional Chinese medicine

Rheumatoid arthritis (RA) is an autoimmune condition that predominantly affects synovial joints, manifesting with joint swelling, pain, and stiffness. In advanced stages, unchecked inflammation can inflict damage on bone and cartilage, resulting in disabilities and deformities of the joints. Additionally, systemic and extra-articular complications may arise due to the consequences of uncontrolled inflammation. Helicobacter pylori (H. pylori) is one of the most prevalent chronic bacterial infections in humans. This microorganism is a spiral-shaped, flagellated, microaerophilic gram-negative bacterium. Prolonged exposure leads to the activation of the immune system, with infected gastric mucosa epithelial cells continuously producing cytokines. This production, in turn, triggers the generation of antibodies as well as T Helper 1 and T Helper 2 effector T cells. The persistent antigenic stimulation resulting from H. pylori infection could lead to the progression of autoimmune diseases. Numerous clinical and pharmacological trials have illustrated the efficacy of traditional Chinese medicine against H. pylori. This review aims to delve into the connection between H. pylori and rheumatoid arthritis so as understand the pathogenesis. The concluding section of this review explores the interplay of Chinese medicine and Helicobacter pylori concerning rheumatoid arthritis.

Selenium-Enriched Lactiplantibacillus plantarum ZZU 8-12 Regulates Intestinal Microbiota and Inhibits Acute Liver Injury

Intake of certain Lactiplantibacillus strains was recognized as a potential strategy for acute liver injury (ALI) prevention. This study is aimed at developing a selenium-enriched Lactiplantibacillus strain-based ALI prevention strategy. L. plantarum ZZU 8-12 was isolated from human fecal sample and screened out based on its adaption to intestinal microenvironment, inhibitive capability against pathogenic bacteria, and in vivo anti-inflammation response in DSS-induced colitis mice model. The strain was applied as a producer of nano selenium particles to produce selenium-enriched L. plantarum ZZU 8-12. Intake of selenium-enriched L. plantarum ZZU 8-12 upregulated the abundance of short-chain fatty acid-producing genera including Lactiplantibacillus, Phascolarctobacterium, Butyricicoccus, and Clostridiales bacterium in fecal microbiota and thus inhibited ALI induced by CCL4 injection in mice. This study drew the potential for selenium-enriched L. plantarum ZZU 8-12 as an ingredient for ALI protection.

Cellular mechanisms underlying beneficial versus detrimental effects of bacterial antitumor immunotherapy

Bacteria engineered to express tumor antigens as a cancer vaccine have yielded mixed results. Here, we utilized an attenuated strain of Listeria monocytogenes ( ΔactA, Lm ) that does not express tumor antigen to explore the immunological response to Listeria itself in the context of intravenous (IV), intratumoral (IT), or a combination of IV+IT administration into tumor-bearing mice. Unexpectedly, we found that Lm persisted in tumors of immune competent mice, regardless of the administration route. While IT Lm alone led to the recruitment of immunosuppressive immune cells that promoted tumor growth, IV Lm followed by IT Lm controlled tumor growth. IV Lm vaccination generated a pool of anti- Lm cytotoxic CD8 T cells that killed Lm -infected non-tumor cells to control tumor growth both indirectly, by limiting cancer cell proliferation, and directly, by enhancing tumor-specific T cell responses. Our findings reveal a differential impact of IT Lm administration on tumor progression that depends on the presence of anti- Lm CD8 T cells, which alone are sufficient to promote therapeutic efficacy.

British Association of Dermatologists living guideline for managing people with alopecia areata 2024

Alopecia areata (AA) is a long-term condition that can occur in both children and adults. AA can appear as patches of baldness on the scalp. Sometimes, nail growth is also affected. Hair on other parts of the body may also fall out, such as the beard, eyebrows and eyelashes. Total loss of scalp hair is called alopecia totalis (AT). Complete loss of scalp, facial and body hair is called alopecia universalis (AU).

The British Association of Dermatologists gathered a group of experts in managing people of all ages with AA. The group consisted of 11 dermatologists, 1 psychologist, 2 people with AA and a team with expertise in preparing guidelines. This group of experts reviewed relevant studies published until 19 October 2023. Using the evidence, the group produced recommendations using rigorous standards for guideline development.

The guideline development group produced 49 recommendations for management of people with AA. They also made 7 recommendations for future research and suggested 11 audit points for hospitals.

Based on the guideline, the group prepared an updated patient information leaflet. The leaflet is available on the British Association of Dermatologists’ website (https://www.skinhealthinfo.org.uk/condition/alopecia-areata).

Harnessing Gut Microbiota for Biomimetic Innovations in Health and Biotechnology

The gut microbiota is a complex and dynamic ecosystem that plays a fundamental role in human health by regulating immunity, metabolism, and the gut-brain axis. Beyond its critical physiological functions, it has emerged as a rich source of inspiration for biomimetic innovations in healthcare and biotechnology. This review explores the transformative potential of microbiota-based biomimetics, focusing on key biological mechanisms such as resilience, self-regulation, and quorum sensing. These mechanisms have inspired the development of innovative applications, including personalized probiotics, synbiotics, artificial microbiomes, bioinspired biosensors, and bioremediation systems. Such technologies aim to emulate and optimize the intricate functions of microbial ecosystems, addressing challenges in healthcare and environmental sustainability. The integration of advanced technologies, such as artificial intelligence, bioengineering, and multi-omics approaches, has further accelerated the potential of microbiota biomimetics. These tools enable the development of precision therapies tailored to individual microbiota profiles, enhance the efficacy of diagnostic systems, and facilitate the design of environmentally sustainable solutions, such as waste-to-energy systems and bioremediation platforms. Emerging areas of innovation, including gut-on-chip models and synthetic biology, offer unprecedented opportunities for studying and applying microbiota principles in controlled environments. Despite these advancements, challenges remain. The replication of microbial complexity in artificial environments, ethical concerns regarding genetically engineered microorganisms, and equitable access to advanced therapies are critical hurdles that must be addressed. This review underscores the importance of interdisciplinary collaboration and public awareness in overcoming these barriers and ensuring the responsible development of microbiota-based solutions. By leveraging the principles of microbial ecosystems, microbiota biomimetics represents a promising frontier in healthcare and sustainability. This approach has the potential to revolutionize therapeutic strategies, redefine diagnostic tools, and address global challenges, paving the way for a more personalized, efficient, and sustainable future in medicine and biotechnology.

Bifidobacterium animalis BD400 protects from collagen-induced arthritis through histidine metabolism

Background

Rheumatoid arthritis (RA) is a common chronic and systemic autoimmune disease. Numerous clinical studies have indicated a correlation between alterations in gut microbiota and the onset and progression of RA. This research aims to restore intestinal microbiota to a healthy state through the oral administration of Bifidobacterium in the early stages with the goal of delaying the onset and progression of RA.

Methods

Collagen-induced arthritis (CIA) rat model was constructed to assess the development of RA using arthritis clinical scores, paw thickness, pathological analysis of knee joint. The immune response was evaluated by determinating specific antibodies and cytokines in serum and synovial fluid. The expression of intestinal barrier protein was analyzed by qPCR to evaluate the intestinal barrier function. Alterations in gut microbiota and metabolites were assessed by 16S rDNA and non-targeted metabolomics.

Results

The findings reveal that administering Bifidobacterium animalis BD400 orally led to a significant reduction in arthritis clinical scores and paw swelling thickness in CIA rats. Additionally, there was a decrease in osteo-facial fusion and calcified cartilage thickening in the knee joint. Furthermore, the oral administration of B. animalis BD400 resulted in the down-regulation of inflammatory factors TNF-α and collagenase MMP-13 in the knee joint. Levels of specific antibodies (anti-CII IgG, anti-CII IgG1, and anti-CII IgG2a) and cytokine IL-17A in serum, as well as cytokines (TNF-α and IL-1β) in the synovial fluid of B. animalis BD400-treated CIA rats, were significantly reduced (p < 0.05). The gene expression levels of intestinal barrier proteins (occludin-1, MUC-2, and ZO-1) showed a significant increase (p < 0.05) in B. animalis BD400-treated CIA rats. The oral administration of B. animalis BD400 altered the composition of intestinal microorganisms in CIA rats at the phylum and genus levels, particularly affecting the genus HT002. B. animalis BD400 alleviates RA by down-regulating 1-methyl-L-histidine and urocanate in the histidine metabolism, laying a foundation for the RA prevention.

Conclusion

By affecting genus HT002 and histidine metabolism in the gut microbiota of CIA rats, B. animalis BD400 restored intestinal permeability, inhibited systemic inflammatory response, and ultimately slowed down the development of RA.

The role of interleukin-17 in inflammation-related cancers

Emerging evidence indicates a correlation between inflammation and the development and progression of cancer. Among the various inflammatory signals, interleukin-17 (IL-17) family cytokines serve as a critical link between inflammation and cancer. IL-17 is a highly versatile pro-inflammatory cytokine that plays a pivotal role in host defense, tissue repair, the pathogenesis of inflammatory diseases, and cancer progression. During the early stages of tumorigenesis, IL-17 signaling directly promotes the proliferation of tumor cells. Conversely, IL-17 has been shown to exhibit antitumor immunity in several models of grafted subcutaneous tumors. Additionally, dynamic changes in the microbiome can influence the secretion of IL-17, thereby affecting tumor development. The specific role of IL-17 is contingent upon its functional classification, spatiotemporal characteristics, and the stage of tumor development. In this review, we introduce the fundamental biology of IL-17 and the expression profile of its receptors in cancer, while also reviewing and discussing recent advancements regarding the pleiotropic effects and mechanisms of IL-17 in inflammation-related cancers. Furthermore, we supplement our discussion with insights into the mechanisms by which IL-17 impacts cancer progression through interactions with the microbiota, and we explore the implications of IL-17 in cancer therapy. This comprehensive analysis aims to enhance our understanding of IL-17 and its potential role in cancer treatment.

Impact of dysregulated microbiota-derived C18 polyunsaturated fatty acid metabolites on arthritis severity in mice with collagen-induced arthritis

Objective

We aimed to evaluate microbiome and microbiota-derived C18 dietary polyunsaturated fatty acids (PUFAs), such as conjugated linoleic acid (CLA), and to investigate their differences that correlate with arthritis severity in collagen-induced arthritis (CIA) mice.

Methods

On day 84 after induction, during the chronic phase of arthritis, cecal samples were analyzed using 16S rRNA sequencing, and plasma and cecal digesta were evaluated using liquid chromatography-tandem mass spectrometry. Differences in microbial composition between 10 control (Ctrl) and 29 CIA mice or between the mild and severe subgroups based on arthritis scores were identified. The cecal metabolite profile and its correlation with the microbiome were evaluated with respect to arthritis severity.

Results

The hydroxy and oxo metabolite levels were higher in CIA mice than in Ctrl mice, some of which, including 10-hydroxy-cis-6-18:1, were positively correlated with arthritis scores. The 9-trans,11-trans CLA levels in CIA mice had a negative linear correlation with arthritis scores. Microbial diversity was lower in severe CIA mice than in mild CIA or Ctrl mice. The abundance of Lactobacillus relatively increased in the severe subgroup of CIA mice compared with that in the mild subgroup and was positively correlated with arthritis severity.

Conclusion

Alterations in gut microbiota and microbiota-derived C18 PUFA metabolites are associated in CIA mice and correlated with arthritis scores, indicating that plasma or fecal C18 PUFA metabolites can be potential biomarkers for arthritis severity and dysbiosis.

Fecal microbial load is a major determinant of gut microbiome variation and a confounder for disease associations

The microbiota in individual habitats differ in both relative composition and absolute abundance. While sequencing approaches determine the relative abundances of taxa and genes, they do not provide information on their absolute abundances. Here, we developed a machine-learning approach to predict fecal microbial loads (microbial cells per gram) solely from relative abundance data. Applying our prediction model to a large-scale metagenomic dataset (n = 34,539), we demonstrated that microbial load is the major determinant of gut microbiome variation and is associated with numerous host factors, including age, diet, and medication. We further found that for several diseases, changes in microbial load, rather than the disease condition itself, more strongly explained alterations in patients' gut microbiome. Adjusting for this effect substantially reduced the statistical significance of the majority of disease-associated species. Our analysis reveals that the fecal microbial load is a major confounder in microbiome studies, highlighting its importance for understanding microbiome variation in health and disease.

Mucosal immune response in biology, disease prevention and treatment

The mucosal immune system, as the most extensive peripheral immune network, serves as the frontline defense against a myriad of microbial and dietary antigens. It is crucial in preventing pathogen invasion and establishing immune tolerance. A comprehensive understanding of mucosal immunity is essential for developing treatments that can effectively target diseases at their entry points, thereby minimizing the overall impact on the body. Despite its importance, our knowledge of mucosal immunity remains incomplete, necessitating further research. The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has underscored the critical role of mucosal immunity in disease prevention and treatment. This systematic review focuses on the dynamic interactions between mucosa-associated lymphoid structures and related diseases. We delve into the basic structures and functions of these lymphoid tissues during disease processes and explore the intricate regulatory networks and mechanisms involved. Additionally, we summarize novel therapies and clinical research advances in the prevention of mucosal immunity-related diseases. The review also addresses the challenges in developing mucosal vaccines, which aim to induce specific immune responses while maintaining tolerance to non-pathogenic microbes. Innovative therapies, such as nanoparticle vaccines and inhalable antibodies, show promise in enhancing mucosal immunity and offer potential for improved disease prevention and treatment.

Altered gut microbial profiles in drug-treated rats with alcoholic heart disease

Introduction. Alcohol abuse can lead to significant cardiac injury, resulting in Alcoholic heart disease (AHD). The interplay between cardiac health and gut microbiota composition in the context of alcohol consumption is not well understood.Hypothesis. Shen Song Yang Xin (SSYX) capsule and amiodarone are common drugs used to treat alcoholic heart disease, but little is known about their microbial regulatory mechanisms in alcoholic heart disease.Aim. To investigate the effects of SSYX and amiodarone on cardiac injury and gut microbiota composition in a rat model of AHD induced by alcohol consumption.Methodology. We evaluated body weight, cardiac function, changes in gut morphology, and gut microbiota composition to assess the effects of SSYX and amiodarone on AHD.Results. Alcohol consumption significantly reduced body weight and aggravated cardiac fibrosis. However, SSYX attenuated fibrosis and improved cardiac function. SSYX also improved intestinal morphological changes caused by chronic alcoholism and activated the expression of ZO-1 and occludin, which are important in maintaining intestinal barrier function. The gut microbiota composition was altered in rats with AHD, with an increase in Actinobacteria abundance. Both SSYX and amiodarone affected the gut microbiota composition, and their effects were positively correlated. SSYX plays a protective role against heart injury caused by alcohol consumption. It improves cardiac function, intestinal morphological changes and gut microbiota composition.Conclusion. SSYX and amiodarone may have potential therapeutic options for AHD. Actinobacteria/Firmicutes ratio and the abundance of Christensenellaceae R7 group, norank_flachnospiraceae and Roseburia may serve as potential biomarkers for detecting alcoholic heart disease.

Associations of gut microbiota with disease development, disease activity, and therapeutic effects in patients with systemic lupus erythematosus

Altered gut microbiota is linked to systemic lupus erythematosus (SLE), but its association with disease development, disease activity, and post-intervention changes remains unclear. We compared new-onset SLE (NOSLE, n = 25), SLE in remission (RemSLE, n = 30), and healthy controls (HC, n = 30) cross-sectionally and conducted the first longitudinal analysis of NOSLE patients (n = 22) from pre-intervention to remission over 12 months. Significant β-diversity differences were observed in both NOSLE and RemSLE compared to HC, but not between NOSLE and RemSLE. Only four operational taxonomic units (OTUs) were enriched in NOSLE versus HC. However, 26 OTUs, including butyrate-producing bacteria (BPB), were depleted, and seven (including five BPBs) remained depleted in RemSLE compared to HC. OTUs positively and negatively correlated with disease activity were also identified. Longitudinal analysis revealed a reversal of several OTUs altered at onset and an increase in Streptococci, unrelated to the disease. Significant β-diversity differences were observed in patients with anti-SSA or anti-RNP antibodies and those with complement reduction compared to their counterparts. Our study identified gut microbiota alterations, including BPB depletion, in SLE regardless of onset or remission status, bacteria linked to disease activity, and a reversal of disease-associated bacteria along with the enrichment of Streptococci through intervention.

Role of Increasing Body Mass Index in Gut Barrier Dysfunction, Systemic Inflammation, and Metabolic Dysregulation in Obesity

AIMS

This study explores the link between body mass index (BMI), intestinal permeability, and associated changes in anthropometric and impedance parameters, lipid profiles, inflammatory markers, fecal metabolites, and gut microbiota taxa composition in participants having excessive body mass.

METHODS

A cohort of 58 obese individuals with comparable diet, age, and height was divided into three groups based on a priori clustering analyses that fit with BMI class ranges: Group I (25-29.9), Group II (30-39.9), and Group III (>40). Anthropometric and clinical parameters were assessed, including plasma C-reactive protein and cytokine profiles as inflammation markers. Intestinal permeability was measured using a multisaccharide assay, with fecal/serum zonulin and serum claudin-5 and claudin-15 levels. Fecal microbiota composition and metabolomic profiles were analyzed using a phylogenetic microarray and GC-MS techniques.

RESULTS

The statistical analyses of the clinical parameters were based on the full sample set, whereas a subset composed of 37 randomized patients was inspected for the GC/MS metabolite profiling of fecal specimens. An increase in potentially pro-inflammatory bacterial genera (e.g., Slackia, Dorea, Granulicatella) and a reduction in beneficial genera (e.g., Adlercreutzia, Clostridia UCG-014, Roseburia) were measured. The gas chromatography/mass spectrometry analysis of urine samples evidenced a statistically significant increase in m-cymen-8-ol, 1,3,5-Undecatriene, (E, Z) and a decreased concentration of p-cresol, carvone, p-cresol, and nonane.

CONCLUSIONS

Together, these data demonstrated how an increased BMI led to significant changes in inflammatory markers, intestinal barrier metabolites, glucose metabolism, endocrine indicators, and fecal metabolomic profiles that can indicate a different metabolite production from gut microbiota. Our findings suggest that targeting intestinal permeability may offer a therapeutic approach to prevent and manage obesity and related metabolic complications, reinforcing the link between gut barrier function and obesity.

Crosstalk between gut microbiota and cancer chemotherapy: current status and trends

BACKGROUND

Chemotherapy is crucial in the management of tumors, but challenges such as chemoresistance and adverse reactions frequently lead to therapeutic delays or even premature cessation. A growing body of research underscores a profound connection between the gut microbiota (GM) and cancer chemotherapy (CC). This paper aims to pinpoint highly influential publications and monitor the current landscape and evolving trends within the realm of GM/CC research.

METHODS

On October 1st, 2024, a comprehensive search for GM/CC publications spanning the past 20 years from 2004 to 2023 was conducted utilizing the Web of Science Core Collection (WoSCC). The scope encompassed both articles and reviews, and the data was subsequently extracted. To gain insights into the evolution and dynamics of this research field, we employed bibliometric analysis tools such as the Bibliometrix R package, VOSviewer, and Microsoft Excel to visualize and analyze various dimensions, including prominent journals, leading authors, esteemed institutions, contributing countries/regions, highly cited papers, and frequently occurring keywords.

RESULTS

A total of 888 papers were obtained. The number of publications about GM/CC studies has increased gradually. China and the United States published the largest number of papers. The INSERM was in the leading position in publishers. The most productive authors were Zitvogel L from France. Cancers had the largest number of papers. Citation analysis explained the historical evolution and breakthroughs in GM/CC research. Highly cited papers and common keywords illustrated the status and trends of GM/CC research. Four clusters were identified, and the hot topics included the role of the GM in the efficacy and toxicity of CC, the targeting of the GM to improve the outcome of CC, the mechanism by which the GM affects CC, and the correlation of the GM with carcinogenesis and cancer therapy. Metabolism, GM-derived metabolites, tumor microenvironment, immunity, intestinal barrier, tumor microbiota and Fusobacterium nucleatum may become the new hotspots and trends of GM/CC research.

CONCLUSION

This study analyzed global publications and bibliometric characteristics of the links between GM and CC, identified highly cited papers in GM/CC, provided insight into the status, hotspots, and trends of global GM/CC research, and showed that the GM can be used to predict the efficacy and toxicity of CC and modifying the GM can improve the outcomes of chemotherapeutics, which may inform clinical researchers of future directions.

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.

Gut microbiota has important roles in the obstructive sleep apnea-induced inflammation and consequent neurocognitive impairment

Obstructive sleep apnea (OSA) is a state of sleep disorder, characterized by repetitive episodes of apnea and chronic intermittent hypoxia. OSA has an extremely high prevalence worldwide and represents a serious challenge to public health, yet its severity is frequently underestimated. It is now well established that neurocognitive dysfunction, manifested as deficits in attention, memory, and executive functions, is a common complication observed in patients with OSA, whereas the specific pathogenesis remains poorly understood, despite the likelihood of involvement of inflammation. Here, we provide an overview of the current state of the art, demonstrating the intimacy of OSA with inflammation and cognitive impairment. Subsequently, we present the recent findings on the investigation of gut microbiota alteration in the OSA conditions, based on both patients-based clinical studies and animal models of OSA. We present an insightful discussion on the role of changes in the abundance of specific gut microbial members, including short-chain fatty acid (SCFA)-producers and/or microbes with pathogenic potential, in the pathogenesis of inflammation and further cognitive dysfunction. The transplantation of fecal microbiota from the mouse model of OSA can elicit inflammation and neurobehavioral disorders in naïve mice, thereby validating the causal relationship to inflammation and cognitive abnormality. This work calls for greater attention on OSA and the associated inflammation, which require timely and effective therapy to protect the brain from irreversible damage. This work also suggests that modification of the gut microbiota using prebiotics, probiotics or fecal microbiota transplantation may represent a potential adjuvant therapy for OSA.

Emerging Role of Gut Microbiota in Breast Cancer Development and Its Implications in Treatment

Background: The human digestive system contains approximately 100 trillion bacteria. The gut microbiota is an emerging field of research that is associated with specific biological processes in many diseases, including cardiovascular disease, obesity, diabetes, brain disease, rheumatoid arthritis, and cancer. Emerging evidence indicates that the gut microbiota affects the response to anticancer therapies by modulating the host immune system. Recent studies have explained a high correlation between the gut microbiota and breast cancer: dysbiosis in breast cancer may regulate the systemic inflammatory response, hormone metabolism, immune response, and the tumor microenvironment. Some of the gut bacteria are related to estrogen metabolism, which may increase or decrease the risk of breast cancer by changing the number of hormones. Further, the gut microbiota has been seen to modulate the immune system in respect of its ability to protect against and treat cancers, with a specific focus on hormone receptor-positive breast cancer. Probiotics and other therapies claiming to control the gut microbiome by bacterial means might be useful in the prevention, or even in the treatment, of breast cancer. Conclusions: The present review underlines the various aspects of gut microbiota in breast cancer risk and its clinical application, warranting research on individualized microbiome-modulated therapeutic approaches to breast cancer treatment.

Perspectives on Microbiome Therapeutics in Infectious Diseases: A Comprehensive Approach Beyond Immunology and Microbiology

Although global life expectancy has increased over the past 20 years due to advancements in managing infectious diseases, one-fifth of people still die from infections. In response to this ongoing threat, significant efforts are underway to develop vaccines and antimicrobial agents. However, pathogens evolve resistance mechanisms, complicating their control. The COVID-19 pandemic has underscored the limitations of focusing solely on the pathogen-killing strategies of immunology and microbiology to address complex, multisystemic infectious diseases. This highlights the urgent need for practical advancements, such as microbiome therapeutics, that address these limitations while complementing traditional approaches. Our review emphasizes key outcomes in the field, including evidence of probiotics reducing disease severity and insights into host-microbiome crosstalk that have informed novel therapeutic strategies. These findings underscore the potential of microbiome-based interventions to promote physiological function alongside existing strategies aimed at enhancing host immune responses and pathogen destruction. This narrative review explores microbiome therapeutics as next-generation treatments for infectious diseases, focusing on the application of probiotics and their role in host-microbiome interactions. While offering a novel perspective grounded in a cooperative defense system, this review also addresses the practical challenges and limitations in translating these advancements into clinical settings.

The oral-gut microbiome axis in health and disease

The human body hosts trillions of microorganisms throughout many diverse habitats with different physico-chemical characteristics. Among them, the oral cavity and the gut harbour some of the most dense and diverse microbial communities. Although these two sites are physiologically distinct, they are directly connected and can influence each other in several ways. For example, oral microorganisms can reach and colonize the gastrointestinal tract, particularly in the context of gut dysbiosis. However, the mechanisms of colonization and the role that the oral microbiome plays in causing or exacerbating diseases in other organs have not yet been fully elucidated. Here, we describe recent advances in our understanding of how the oral and intestinal microbiota interplay in relation to their impact on human health and disease.

Tanshinone IIA Exerts Cardioprotective Effects Through Improving Gut-Brain Axis Post-Myocardial Infarction

Myocardial infarction (MI) is a lethal cardiovascular disease worldwide. Emerging evidence has revealed the critical role of gut dysbiosis and impaired gut-brain axis in the pathological progression of MI. Tanshinone IIA (Tan IIA), a traditional Chinese medicine, has been demonstrated to exert therapeutic effects for MI. However, the effects of Tan IIA on gut-brain communication and its potential mechanisms post-MI are still unclear. In this study, we initially found that Tan IIA significantly reduced myocardial inflammation, apoptosis and fibrosis, therefore alleviating hypertrophy and improving cardiac function following MI, suggesting the cardioprotective effect of Tan IIA against MI. Additionally, we observed that Tan IIA improved the gut microbiota as evidenced by changing the α-diversity and β-diversity, and reduced histopathological impairments by decreasing inflammation and permeability in the intestinal tissues, indicating the substantial improvement of Tan IIA in gut function post-MI. Lastly, Tan IIA notably reduced lipopolysaccharides (LPS) level in serum, inflammation responses in paraventricular nucleus (PVN) and sympathetic hyperexcitability following MI, suggesting that restoration of Tan IIA on MI-induced brain alterations. Collectively, these results indicated that the cardioprotective effects of Tan IIA against MI might be associated with improvement in gut-brain axis, and LPS might be the critical factor linking gut and brain. Mechanically, Tan IIA-induced decreased intestinal damage reduced LPS release into serum, and reduced serum LPS contributes to decreased neuroinflammation with PVN and sympathetic inactivation, therefore protecting the myocardium against MI-induced injury.

Potential of Synbiotics and Probiotics as Chemopreventive Agent

Cancer remains a global problem, with millions of new cases diagnosed yearly and countless lives lost. The financial burden of cancer therapy, along with worries about the long-term safety of existing medicines, necessitates the investigation of alternative approaches to cancer prevention. Probiotics generate chemopreventive compounds such as bacteriocins, short-chain fatty acids (SCFA), and extracellular polymeric substances (EPS), which have demonstrated the ability to impede cancer cell proliferation, induce apoptosis, and bolster the expression of pro-apoptotic genes. On the other hand, prebiotics, classified as non-digestible food ingredients, promote the proliferation of probiotics within the colon, thereby ensuring sustained functionality of the gut microbiota. Consequently, the synergistic effect of combining prebiotics with probiotics, known as the synbiotic effect, in dietary interventions holds promise for potentially mitigating cancer risk and augmenting preventive measures. The utilization of gut microbiota in cancer treatment has shown promise in alleviating adverse health effects. This review explored the potential and the role of probiotics and synbiotics in enhancing health and contributing to cancer prevention efforts. In this review, the applications of functional probiotics and synbiotics, the mechanisms of action of probiotics in cancer, and the relationship of probiotics with various drugs were discussed, shedding light on the potential of probiotics and synbiotics to alleviate the burdens of cancer treatment.

Dietary fiber promotes antigen presentation on intestinal epithelial cells and development of small intestinal CD4+CD8αα+ intraepithelial T cells

The impact of dietary fiber on intestinal T cell development is poorly understood. Here we show that a low fiber diet reduces MHC-II antigen presentation by small intestinal epithelial cells (IECs) and consequently impairs development of CD4+CD8αα+ intraepithelial lymphocytes (DP IELs) through changes to the microbiota. Dietary fiber supports colonization by Segmented Filamentous Bacteria (SFB), which induces the secretion of IFNγ by type 1 innate lymphoid cells (ILC1s) that lead to MHC-II upregulation on IECs. IEC MHC-II expression caused either by SFB colonization or exogenous IFNγ administration induced differentiation of DP IELs. Finally, we show that a low fiber diet promotes overgrowth of Bifidobacterium pseudolongum, and that oral administration of B. pseudolongum reduces SFB abundance in the small intestine. Collectively we highlight the importance of dietary fiber in maintaining the balance among microbiota members that allow IEC MHC-II antigen presentation and define a mechanism of microbiota-ILC-IEC interactions participating in the development of intestinal intraepithelial T cells.

Mendelian randomization reveals predictive, preventive, and personalized insights into inflammatory bowel disease: the role of gut microbiome and circulating inflammatory proteins

Background

A chronic illness with increasing global frequency, inflammatory bowel disease (IBD), which includes ulcerative colitis (UC) and Crohn's disease (CD), profoundly affects patients' quality of life and healthcare systems. IBD pathogenesis consists of changes in gut microbiota, immune system dysregulation, and genetic predisposition. Although emerging data suggests that gut microbiota and circulating inflammatory proteins play critical roles in IBD, their utility as biomarkers for predictive, preventive, and personalized medicine (PPPM) remains incompletely understood.

Working hypothesis and methods

We hypothesized that specific gut microbiota and inflammatory proteins causally influence IBD risk and mediate pathways between gut microbiota and IBD development. We employed Mendelian randomization (MR) using genome-wide association studies (GWAS) to explore these causal relationships, including further analyses on UC and CD subtypes.

Results

We identified eight gut microbiota species linked to IBD, with four protective and four increasing risk. Nine inflammatory proteins were also associated, six increasing risk and three protective. MMP-10 and IL-10Rα mediated the effects of Clostridiaceae1 on IBD risk. For UC, five microbiota species were protective, five were risk factors, and two proteins increased risk while three were protective. IL-10Rα mediated the effects of Clostridiaceae1 on UC risk. For CD, eight microbiota species were protective, four increased risk, and nine proteins were implicated. However, no mediation pathways were supported by multivariable MR.

Conclusions

This study highlights specific gut microbiota and inflammatory proteins that may serve as therapeutic targets for PPPM in IBD, UC, and CD. These findings offer new insights into IBD pathogenesis and suggest potential avenues for improved prevention, early detection, and personalized treatment strategies.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13167-024-00384-2.

Technical note: A biological anthropologist's guide for applying microbiome science to studies of human and non-human primates

A central goal of biological anthropology is connecting environmental variation to differences in host physiology, biology, health, and evolution. The microbiome represents a valuable pathway for studying how variation in host environments impacts health outcomes. While there are many resources for learning about methods related to microbiome sample collection, laboratory analyses, and genetic sequencing, there are fewer dedicated to helping researchers navigate the dense portfolio of bioinformatics and statistical approaches for analyzing microbiome data. Those that do exist are rarely related to questions in biological anthropology and instead are often focused on human biomedicine. To address this gap, we expand on existing tutorials and provide a "road map" to aid biological anthropologists in understanding, selecting, and deploying the data analysis and visualization methods that are most appropriate for their specific research questions. Leveraging an existing dataset of fecal samples and survey data collected from wild geladas living in Simien Mountains National Park in Ethiopia (Baniel et al., 2021), this paper guides researchers toward answering three questions related to variation in the gut microbiome across host and environmental factors. By providing explanations, examples, and a reproducible workflow for different analytic methods, we move beyond the theoretical benefits of considering the microbiome within anthropological research and instead present researchers with a guide for applying microbiome science to their work. This paper makes microbiome science more accessible to biological anthropologists and paves the way for continued research into the microbiome's role in the ecology, evolution, and health of human and non-human primates.

Causal relationships between gut microbiome and aplastic anemia: a Mendelian randomization analysis

BACKGROUND

Previous observational studies have hinted at a potential correlation between aplastic anemia (AA) and the gut microbiome. However, the precise nature of this bidirectional causal relationship remains uncertain.

METHODS

We conducted a bidirectional two-sample Mendelian randomization (MR) study to investigate the potential causal link between the gut microbiome and AA. Statistical analysis of the gut microbiome was based on data from an extensive meta-analysis (genome-wide association study) conducted by the MiBioGen Alliance, involving 18,340 samples. Summary statistical data for AA were obtained from the Integrative Epidemiology Unit database. Single -nucleotide polymorphisms (SNPs) were estimated and summarized using inverse variance weighted (IVW), MR Egger, and weighted median methods in the bidirectional MR analysis. Cochran's Q test, MR Egger intercept test, and sensitivity analysis were employed to assess SNP heterogeneity, horizontal pleiotropy, and stability.

RESULTS

The IVW analysis revealed a significant correlation between AA and 10 bacterial taxa. However, there is currently insufficient evidence to support a causal relationship between AA and the composition of gut microbiome.

CONCLUSION

This study suggests a causal connection between the prevalence of specific gut microbiome and AA. Further investigation into the interaction between particular bacterial communities and AA could enhance efforts in prevention, monitoring, and treatment of the condition.

Control of T-cell immunity by fatty acid metabolism

Fatty acids play critical roles in maintaining the cellular functions of T cells and regulating T-cell immunity. This review synthesizes current research on the influence of fatty acids on T-cell subsets, including CD8+ T cells, TH1, TH17, Treg (regulatory T cells), and TFH (T follicular helper) cells. Fatty acids impact T cells by modulating signaling pathways, inducing metabolic changes, altering cellular structures, and regulating gene expression epigenetically. These processes affect T-cell activation, differentiation, and function, with implications for diseases such as autoimmune disease and cancer. Based on these insights, fatty acid pathways can potentially be modulated by novel therapeutics, paving the way for novel treatment approaches for immune-mediated disorders and cancer immunotherapy.

Factors of faecal microbiota transplantation applied to cancer management

The homeostasis of the microbiota is essential for human health. In particular, the gut microbiota plays a critical role in the regulation of the immune system. Thus, faecal microbiota transplantation (FMT), a technology that has rapidly developed in the last decade, has specifically been utilised for the treatment of intestinal inflammation and has recently been found to be able to treat tumours in combination with immunotherapy. FMT has become a breakthrough in enhancing the response rate to immunotherapy in cancer patients by altering the composition of the patient's gut microbiota. This review discusses the mechanisms of faecal microorganism effects on tumour development, drug treatment efficacy, and adverse effects and describes the recent clinical research trials on FMT. Moreover, the factors influencing the efficacy and safety of FMT are described. We summarise the possibilities of faecal transplantation in the treatment of tumours and its complications and propose directions to explore the development of FMT.

Exploring the role of gut microbiome in autoimmune diseases: A comprehensive review

As the industrialized society advances, there has been a gradual increase in the prevalence of autoimmune disorders. A probe into the fundamental causes has disclosed several factors in modern society that have an influence on the gut microbiome. These dramatic shifts in the gut microbiome are likely to be one of the reasons for the disarray in the immune system, and the relationship between the immune system and the gut microbiome emerging as a perennial hot topic of research. This review enumerates the findings from sequencing studies of gut microbiota on seven autoimmune diseases (ADs): Rheumatoid Arthritis (RA), Systemic Lupus Erythematosus (SLE), Ankylosing Spondylitis (AS), Systemic Sclerosis (SSc), Sjögren's Syndrome (SjS), Juvenile Idiopathic Arthritis (JIA), and Behçet's Disease (BD). It aims to identify commonalities in changes in the gut microbiome within the autoimmune disease cohort and characteristics specific to each disease. The dysregulation of the gut microbiome involves a disruption of the internal balance and the balance between the external environment and the host. This dysregulation impacts the host's immune system, potentially playing a role in the development of ADs. Damage to the gut epithelial barrier allows potential pathogens to translocate to the mucosal layer, contacting epithelial cells, disrupting tight junctions, and being recognized by antigen-presenting cells, which triggers an immune response. Primed T-cells assist B-cells in producing antibodies against pathogens; if antigen mimicry occurs, an immune response is generated in extraintestinal organs during immune cell circulation, clinically manifesting as ADs. However, current research is limited; advancements in sequencing technology, large-scale cohort studies, and fecal microbiota transplantation (FMT) research are expected to propel this field to new peaks.

The Oral Microbiota, Microbial Metabolites, and Immuno-Inflammatory Mechanisms in Cardiovascular Disease

Cardiovascular diseases (CVDs) remain a leading cause of global morbidity and mortality. Recent advancements in high-throughput omics techniques have enhanced our understanding of the human microbiome's role in the development of CVDs. Although the relationship between the gut microbiome and CVDs has attracted considerable research attention and has been rapidly evolving in recent years, the role of the oral microbiome remains less understood, with most prior studies focusing on periodontitis-related pathogens. In this review, we summarized previously reported associations between the oral microbiome and CVD, highlighting known CVD-associated taxa such as Porphyromonas gingivalis, Fusobacterium nucleatum, and Aggregatibacter actinomycetemcomitans. We also discussed the interactions between the oral and gut microbes. The potential mechanisms by which the oral microbiota can influence CVD development include oral and systemic inflammation, immune responses, cytokine release, translocation of oral bacteria into the bloodstream, and the impact of microbial-related products such as microbial metabolites (e.g., short-chain fatty acids [SCFAs], trimethylamine oxide [TMAO], hydrogen sulfide [H2S], nitric oxide [NO]) and specific toxins (e.g., lipopolysaccharide [LPS], leukotoxin [LtxA]). The processes driven by these mechanisms may contribute to atherosclerosis, endothelial dysfunction, and other cardiovascular pathologies. Integrated multi-omics methodologies, along with large-scale longitudinal population studies and intervention studies, will facilitate a deeper understanding of the metabolic and functional roles of the oral microbiome in cardiovascular health. This fundamental knowledge will support the development of targeted interventions and effective therapies to prevent or reduce the progression from cardiovascular risk to clinical CVD events.

Oat β-(1 → 3, 1 → 4)-d-glucan alleviates food allergy-induced colonic injury in mice by increasing Lachnospiraceae abundance and butyrate production

Oat β-(1 → 3, 1 → 4)-d-glucan (OBG), a linear polysaccharide primarily found in oat bran, has been demonstrated to possess immunomodulatory properties and regulate gut microbiota. This study aimed to investigate the impact of low molecular weight (Mw) OBG (155.2 kDa) on colonic injury and allergic symptoms induced by food allergy (FA), and to explore its potential mechanism. In Experiment 1, results indicated that oral OBG improved colonic inflammation and epithelial barrier, and significantly relieved allergy symptoms. Importantly, the OBG supplement altered the gut microbiota composition, particularly increasing the abundance of Lachnospiraceae and its genera, and promoted the production of short-chain fatty acids, especially butyrate. However, in Experiment 2, the gut microbial depletion eliminated these protective effects of OBG on the colon in allergic mice. Further, in Experiment 3, fecal microbiota transplantation and sterile fecal filtrate transfer directly validated the role of OBG-mediated gut microbiota and its metabolites in relieving FA and its induced colonic injury. Our findings suggest that low Mw OBG can alleviate FA-induced colonic damage by increasing Lachnospiraceae abundance and butyrate production, and provide novel insights into the health benefits and mechanisms of dietary polysaccharide intervention for FA.

Bacillus coagulans BACO-17 ameliorates in vitro and in vivo progression of Rheumatoid arthritis

Rheumatoid arthritis (RA) is an autoimmune disease that causes persistent inflammation involving the joints, cartilage, and synovium. In individuals with RA, alterations in the composition of intestinal bacteria suggest the vital role of gut microbiota in immune dysfunction. Multiple therapies commonly used to treat RA can also alter the diversity of gut microbiota, further suggesting the modulation of gut microbiota as a prevention or treatment for RA. Therefore, a better understanding of the changes in the gut microbiota that accompany RA should facilitate the development of novel therapeutic approaches. In this study, B. coagulans BACO-17 not only significantly reduced paw swelling, arthritis scores, and hind paw and forepaw thicknesses but also protected articular cartilage and the synovium against RA degeneration, with a corresponding downregulation of TNF-α expression. The inhibition or even reversing of RA progression highlights B. coagulans BACO-17 as a novel therapeutic for RA worth investigating.

Gut microbiota and skin pathologies: Mechanism of the gut-skin axis in atopic dermatitis and psoriasis

Atopic dermatitis (AD) and psoriasis are chronic skin diseases with a global impact, posing significant challenges to public health systems and severely affecting patients' quality of life. This review delves into the key role of the gut microbiota in these diseases, emphasizing the importance of the gut-skin axis in inflammatory mediators and immune regulation and revealing a complex bidirectional communication system. We comprehensively assessed the pathogenesis, clinical manifestations, and treatment strategies for AD and psoriasis, with a particular focus on how the gut microbiota and their metabolites influence disease progression via the gut-skin axis. In addition, personalized treatment plans based on individual patient microbiome characteristics have been proposed, offering new perspectives for future treatment approaches. We call for enhanced interdisciplinary cooperation to further explore the interactions between gut microbiota and skin diseases and to assess the potential of drugs and natural products in modulating the gut-skin axis, aiming to advance the treatment of skin diseases.

Preliminary Functional Analysis of the Gut Microbiome in Colic Horses

The gut microbiome plays a critical role in maintaining horse health, influencing digestion, immunity, and overall well-being. However, in certain conditions like colic, there is evidence of significant alterations in the microbial community. To analyze the composition of the fecal microbiome and the enriched predicted metabolic functions of horses with colic compared to a control group, 14 horses with colic and 14 control horses were recruited. From a stool sample, DNA extraction was carried out for subsequent 16S rRNA metagenomic analysis. The composition of the microbiome was analyzed from the sequences of each sample using the QIIME version 1.8.0 and DADA2 version 1.22 programs. PICRUSt2 was used to predict metabolic functions. Statistical analyses were performed with the Mann-Whitney U test from the Python scipy v1 package. The gut microbiomes of both groups were dominated by Firmicuteota, Bacteroidota, and Pseudomonadota phyla. Colic in horses was associated with reduced diversity, reduced abundance of Fibrobacter, and an increase in Streptococcus. The abundance of Firmicuteota was negatively correlated with Pseudomonadota and Actinobacteriota. The equine colic microbiome was predicted to be enriched in aerobic respiration pathways and fatty acid and amino acid degradation. These observations indicate discrete but important differences in the gut microbiome of colic horses.

The Rational Engineered Bacteria Based Biohybrid Living System for Tumor Therapy

Living therapy based on bacterial cells has gained increasing attention for their applications in tumor treatments. Bacterial cells can naturally target to tumor sites and active the innate immunological responses. The intrinsic advantages of bacteria attribute to the development of biohybrid living carriers for targeting delivery toward hypoxic environments. The rationally engineered bacterial cells integrate various functions to enhance the tumor therapy and reduce toxic side effects. In this review, the antitumor effects of bacteria and their application are discussed as living therapeutic agents across multiple antitumor platforms. The various kinds of bacteria used for cancer therapy are first introduced and demonstrated the mechanism of antitumor effects as well as the immunological effects. Additionally, this study focused on the genetically modified bacteria for the production of antitumor agents as living delivery system to treat cancer. The combination of living bacterial cells with functional nanomaterials is then discussed in the cancer treatments. In brief, the rational design of living therapy based on bacterial cells highlighted a rapid development in tumor therapy and pointed out the potentials in clinical applications.