Transferable Immunoglobulin A-Coated Odoribacter splanchnicus in Responders to Fecal Microbiota Transplantation for Ulcerative Colitis Limits Colonic Inflammation

Precision microbiota therapy for IBD: premise and promise

Inflammatory Bowel Disease (IBD) is a spectrum of chronic inflammatory diseases of the intestine that includes subtypes of ulcerative colitis (UC) and Crohn's Disease (CD) and currently has no cure. While IBD results from a complex interplay between genetic, environmental, and immunological factors, sequencing advances over the last 10-15 years revealed signature changes in gut microbiota that contribute to the pathogenesis of IBD. These findings highlight IBD as a disease target for microbiome-based therapies, with the potential to treat the underlying microbial pathogenesis and provide adjuvant therapy to the emerging spectrum of advanced therapies for IBD. Building on the success of fecal microbiota transplantation (FMT) for Clostridioides difficile infection, therapies targeting gut microbiota have emerged as promising approaches for treating IBD; however, unique aspects of IBD pathogenesis highlight the need for more precision in the approach to microbiome therapeutics that leverage aspects of recipient and donor selection, diet and xenobiotics, and strain-specific interactions to enhance the efficacy and safety of IBD therapy. This review focuses on both pre-clinical and clinical studies that support the premise for microbial therapeutics for IBD and aims to provide a framework for the development of precision microbiome therapeutics to optimize clinical outcomes for patients with IBD.

Bifidobacterium inhibits the progression of colorectal tumorigenesis in mice through fatty acid isomerization and gut microbiota modulation

Colorectal cancer (CRC) represents the third most common cancer worldwide. Consequently, there is an urgent need to identify novel preventive and therapeutic strategies for CRC. This study aimed to screen for beneficial bacteria that have a preventive effect on CRC and to elucidate the potential mechanisms. Initially, we compared gut bacteria and bacterial metabolites of healthy volunteers and CRC patients, which demonstrated that intestinal conjugated linoleic acid (CLA), butyric acid, and Bifidobacterium in CRC patients were significantly lower than those in healthy volunteers, and these indicators were significantly negatively correlated with CRC. Next, spontaneous CRC mouse model were conducted to explore the effect of supplemental CLA-producing Bifidobacterium on CRC. Supplementation of mice with CLA-producing Bifidobacterium breve CCFM683 and B. pseudocatenulatum MY40C significantly prevented CRC. Moreover, molecular approaches demonstrated that CLA and the CLA-producing gene, bbi, were the key metabolites and genes for CCFM683 to prevent CRC. Inhibitor intervention results showed that PPAR-γ was the key receptor for preventing CRC. CCFM683 inhibited the NF-κB signaling pathway, up-regulated MUC2, Claudin-1, and ZO-1, and promoted tumor cell apoptosis via the CLA-PPAR-γ axis. Additionally, fecal microbiota transplantation (FMT) and metagenomic analysis showed that CCFM683 up-regulated Odoribacter splanchnicus through CLA production, which then prevented CRC by producing butyric acid, up-regulating TJ proteins, regulating cytokines, and regulating gut microbiota. These results will contribute to the clinical trials of Bifidobacterium and the theoretical research and development of CRC dietary products.

Orally-deliverable liposome-microgel complexes dynamically remodel intestinal environment to enhance probiotic ulcerative colitis therapy via TLR4 inhibition and tryptophan metabolic crosstalk

Probiotics emerges as a promising option for ulcerative colitis (UC) treatment, but its application remains challenging due to insufficient colon-targeted delivery efficiency and survival against the inflammation-associated intestinal oxidative stress. To address these issues, here we report a supramolecular liposome-microgel complex (SLMC) incorporated with Bacillus subtilis spores (BSSs) and dexamethasone (DEX) for orally-deliverable probiotic UC therapy. Specifically, BSSs and cholesterols were conjugated with gelatin via diselenide ligation to prepare microgels, followed by supramolecular complexation with UC-targeted DEX-loaded liposome via microfluidic engineering. The orally-administered SLMC efficiently accumulated in UC-affected colonic sites to release BSSs and DEX. DEX elicited rapid anti-inflammatory effect to reduce ROS generation, which cooperated with the ROS consumption by spore germination and diselenide cleavage to orchestrate an anaerobic intestinal microenvironment, thus promoting Bacillus subtilis colonization to restore gut homeostasis and initiate anti-inflammatory microbiota-macrophage metabolic crosstalk. Indeed, in vivo analysis showed that the SLMC treatment markedly inhibited pro-inflammatory TLR4-NF-κB signaling activities in mucosal macrophages through localized DEX delivery and boosting tryptophan metabolite production, leading to robust and durable UC abolishment. This study offers a practical approach for improving UC treatment in the clinic.

Optimizing Therapeutic Potential of Fecal Transplant in Inflammatory Bowel Disease

Inflammatory bowel disease (IBD) is a chronic inflammatory condition of the gastrointestinal tract influenced by genetic, environmental, immune, and microbial factors. Reduced gut microbial diversity and elevated proinflammatory bacteria levels in IBD disrupt mucosal immunity, barrier function, and inflammatory pathways. Fecal microbiota transplantation (FMT) is a potential therapy to restore microbial balance. Studies suggest that FMT may induce remission in mild-to-moderate ulcerative colitis but show limited efficacy in Crohn's disease and pouchitis. Donor microbiota colonization correlates with remission, but varied study designs challenge findings. Further research is required to standardize FMT protocols, optimize donor selection, and ensure long-term safety.

Exploiting regulatory T cells (Tregs): Cutting-edge therapy for autoimmune diseases

Regulatory T cells (Tregs) are a specialized subset of suppressive T cells that are essential for maintaining self-tolerance, regulating effector T cells, managing microbial infections, preventing tumors, allergies, and autoimmune disorders, and facilitating allograft transplantation. Disruptions in Treg function or abundance contribute to an imbalance between pathogenic and protective immune cells in autoimmune diseases. Recently, one promising treatment strategy to restore immune balance involves the selective expansion or manipulation of Tregs using low-dose IL-2 therapy, adoptive Treg cell transfer, and chimeric antigen receptor (CAR)-Treg approaches. Tregs have been shown in an increasing number of research studies to prevent or even treat a variety of disorders, such as tumors, autoimmune and allergic diseases, transplant rejection, and graft-versus-host disease. A thorough comprehension of Treg function is anticipated to provide clear prospects for effective Treg immunotherapy in the treatment of a wide range of diseases. This review provides an overview of Tregs biology, including their functions, suppressive mechanisms, phenotypic markers, as well as their involvement in disease settings. Furthermore, we discuss the therapeutic potential of different Treg subpopulations and their translational applications in the treatment of autoimmune diseases.

Glycyrrhiza pallidiflora Polysaccharide Ameliorates DSS-Induced Colitis by Protecting Intestinal Barrier Integrity

Ulcerative colitis (UC) is an idiopathic inflammatory bowel disease. Glycyrrhiza pallidiflora polysaccharide (GPP) is an important constituent of a species of Glycyrrhiza pallidiflora, but its therapeutic mechanism in UC mice is not clear. A dextran sulphate sodium salt (DSS)-induced mouse model of UC was established, and GPP was extracted by ultrasound-assisted extraction, optimised to a GPP content of 25.66% by one-factor optimisation. The effects of different doses (100, 200, 300 mg/kg) of GPP on UC were investigated. The results showed that GPP could delay the trend of weight loss, reduce the DAI score and decrease colon damage in mice, and GPP had a better ameliorative effect on enteritis, which provided a theoretical basis for studying the effect of natural products on UC.

Clostridium butyricum-induced balance in colonic retinol metabolism and short-chain fatty acid levels inhibit IgA-related mucosal immunity and relieve colitis developments

Gut microbiota and their metabolites play a significant role in inflammatory bowel disease. Here, we attempted to determine the anti-inflammatory role of the probiotic Clostridium. butyricum (CB) in inflammatory bowel disease and identify the exact immune mechanism. The clinical significance of Clostridiales and CB was explored in patients with ulcerative colitis. The inflammation-suppressive role of CB was evaluated in mice with DSS-induced colitis. 16S rRNA sequencing was performed to assess changes in the gut microbiota. Altered transcription levels were detected by RNA sequencing. Flow cytometry was performed to assess the frequency of IgA responses to gut microbiota. Clostridiales and CB were depleted in ulcerative colitis. Oral gavage with CB significantly suppressed weight loss and colon shortening in the dextran sulfate sodium-induced colitis mouse model. Intestinal barrier injury was reversed and the gut microbiota was restored upon treatment with CB administration. The mucosal immune response to gut microbiota was reversed upon treatment with CB. CB conditional medium was more effective than heat-killed CB in alleviating inflammation. Mechanistically, retinol metabolism and retinoic acid levels were higher in groups treated with CB and butyrate. CB and the metabolite butyrate exerted a suppressive role on the abundance of Immunoglobulin A-coated gut microbiota by inhibiting retinoic acid synthesis. In summary, CB protects against inflammation and intestinal barrier injury by producing anti-inflammatory metabolites that can regulate the mucosal immune response to gut microbiota by increasing retinoic acid levels in the colon.

Exploring the Mucosal Immune Response in Axial Spondyloarthritis Through Immunoglobulin A-Coated Microbiota

In this review, we focus on the mucosal immune response through Immunoglobulin A (IgA)-coated microbes and their role in gut dysbiosis in axial spondyloarthritis (axSpA) and associated inflammatory bowel disease. IgA-coated microbes contribute significantly to the microbial dysbiosis observed in axSpA, potentially driving gut inflammation and translocating outside of the gut and initiating systemic immune activation, thus contributing to disease pathogenesis. These insights will provide new avenues for understanding and treating axSpA and other immune-mediated inflammatory disorders by targeting specific host immune-microbe interactions.

Intestinal luminal anion transporters and their interplay with gut microbiome and inflammation

The intestine, as a critical interface between the external environment and the internal body, plays a central role in nutrient absorption, immune regulation, and maintaining homeostasis. The intestinal epithelium, composed of specialized epithelial cells, harbors apical anion transporters that primarily mediate the transport of chloride and bicarbonate ions, essential for maintaining electrolyte balance, pH homeostasis, and fluid absorption/secretion. In addition, the intestine hosts a diverse population of gut microbiota that plays a pivotal role in various physiological processes including nutrient metabolism, immune regulation, and maintenance of intestinal barrier integrity, all of which are critical for host gut homeostasis and health. The anion transporters and gut microbiome are intricately interconnected, where alterations in one can trigger changes in the other, leading to compromised barrier integrity and increasing susceptibility to pathophysiological states including gut inflammation. This review focuses on the interplay of key apical anion transporters including Down-Regulated in Adenoma (DRA, SLC26A3), Putative Anion Transporter-1 (PAT1, SLC26A6), and Cystic Fibrosis Transmembrane Conductance Regulator [CFTR, ATP-binding cassette subfamily C member 7 (ABCC7)] with the gut microbiome, barrier integrity, and their relationship to gut inflammation.

Dietary resistant starch protects against post-antibiotic intestinal damage by restoring microbial homeostasis and preserving intestinal barrier function in meat duck

Resistant starch (RS) is recognized as a nutritional strategy that supports gut and overall host health by modulating gut microbiota. To directly assess the effects of RS on gut microbiota and its role in improving intestinal barrier function in meat ducks, this study first established an antibiotic-induced microbial dysbiosis model, which was characterized by reduced gut microbial diversity, intestinal dysfunction, and an inflammatory outburst following antibiotic exposure. Whereafter, in addition to the control group, ducks treated with antibiotics for 7 consecutive days were further allocated to two groups and fed the basal diet and RS diet that derived from 12 % raw potato starch until 21 d. The results demonstrated that dietary RS supplementation reversed the antibiotic-induced reduction in microbial diversity and restored the Firmicutes-to-Bacteroidetes ratio. Additionally, RS inclusion enriched beneficial bacterial genera, including Coprobacter, Odoribacter, and Faecalibacterium (LDA score > 3). Post-antibiotic intervention led to a reduction in villus density and muscular thickness, accompanied by a significant downregulation (P < 0.05) of zonula occludens-1 and mucin-2 expression, along with increased serum pro-inflammatory cytokine levels (P < 0.05). Notably, dietary RS supplementation significantly enhanced (P < 0.05) the expression of glucagon-like peptide receptor and the anti-apoptotic factor Bcl-2, while suppressing caspase transcription. This resulted in increased villus height and muscular thickness in the ileum (P < 0.05). Furthermore, RS intervention remarkably reduced (P < 0.05) pro-inflammatory cytokine levels, particularly interleukin-1β and tumor necrosis factor-α, in both the ileum and serum. These effects were likely linked to alterations in cecal microbiota, including increased abundances of Barnesiella, Ruminiclostridium 9, Megamonas, Faecalitalea, Adlercreutzia, Coprobacter and Collinsella. In conclusion, dietary RS supplementation mitigated antibiotic-induced cecal microbial dysbiosis and restored intestinal structure by promoting enterocyte proliferation and reducing apoptosis. Consequently, RS supplementation helped alleviate systemic inflammation in meat ducks following antibiotic treatment.

Metagenomics for IgA-coated gut microbiota: from taxonomy to function

Immunoglobulin A (IgA) establishes intricate interactions with human gut microbiota, thereby forming IgA-coated microbiota. This forum first explores state-of-the-art metagenomic techniques for characterizing IgA-coated microbiota. Thereafter, metagenomic insights into its taxonomic diversity and microbial genomic functions that mediate IgA coating are provided. Finally, clinical implications for human health are highlighted.

Gut microbiota and blood metabolites: unveiling their roles in hippocampal volume changes through Mendelian randomization and mediation analysis

Changes in hippocampal volume (HV) are linked to various neuropsychiatric disorders. Observational studies suggest associations of gut microbiota (GM) and blood metabolites (BM) with changes in HV; however, their causal relationships remain unclear. We aimed to use Mendelian randomization (MR) to investigate the causal associations of GM and BM with changes in HV and to explore the potential mediating role of BM. Using two-sample MR (TSMR) analysis, we examined 412 GM traits and 1,400 BM traits with a focus on their causal relationships with age-independent/dependent longitudinal changes in HV, primarily using the inverse variance weighted method. Furthermore, we explored the mediating role of BM through a two-step MR design. We identified 44 GM traits and 175 BM traits having nominally significant causal associations with age-independent/dependent longitudinal changes in HV. In addition, the glycine-to-pyridoxal ratio (mediation proportion: 7.38%) and the phosphate-to-citrate ratio (mediation proportion: 12.55%) mediated the effect of the pathway of L-arginine degradation II on the reduction of age-independent longitudinal changes in HV. Our study reveals the causal effects of GM and BM on longitudinal changes in HV and identifies BM traits with mediating roles. These findings offer valuable insights for the prevention and treatment of the related neuropsychiatric disorders.

Exploring dried ginger essential oil as a therapeutic strategy for 5-FU-induced mucositis: Gut microbiota and tryptophan metabolite IAA-AHR/IL-22/STAT3 signaling axis

ETHNOPHARMACOLOGICAL RELEVANCE

5-Fluorouracil (5-FU) commonly induces severe mucositis, causing pain, inflammation, and gastrointestinal dysfunction, which significantly increases patient morbidity and reduces quality of life. In Ayurveda, Traditional Chinese Medicine, and other ethnopharmacological practices, dried ginger has been widely used to alleviate symptoms such as nausea, vomiting, diarrhea, and inflammation, highlighting its important role in traditional medicine.

AIM OF THE STUDY

This study explored the potential of dried ginger essential oil (DGEO) in mitigating intestinal epithelial barrier damage in mice with mucositis induced by 5-FU.

METHODS

The therapeutic effects of DGEO were evaluated by measurements of weight changes, diarrhea scores, ELISA, and H&E. Further investigations included 16S rRNA sequencing, untargeted metabolomics, molecular docking, and HPLC-MS/MS to explore its underlying mechanisms, with validation performed using western blotting and ELISA.

RESULTS

The results demonstrated that DGEO was effective in alleviating mucositis symptoms. It also improved the gut microbiota, enhanced the biotransformation of tryptophan to indole-3-acetic acid (IAA), and elevated the protein expressions of the AHR, CYP1A1, and p-STAT3, as well as level of IL-22. Moreover, DGEO improved the expressions of tight junction (TJ) proteins and anti-apoptotic proteins, enhancing intestinal barrier integrity.

CONCLUSION

These findings indicated that DGEO ameliorated 5-FU-induced mucositis by modulating gut microbiota and the tryptophan metabolite IAA-AHR/IL-22/STAT3 signaling axis, providing new insights into its therapeutic applications, particularly its ability to regulate gut microbiota and related signaling pathways.

Patient-donor similarity and donor-derived species contribute to the outcome of fecal microbiota transplantation for ulcerative colitis

BACKGROUND AND AIMS

Clinical applications of fecal microbiota transplantation (FMT) for treating ulcerative colitis (UC) have shown promising results. However, whether the beneficial effects of FMT are due to the transfer and colonization of donor-derived species in patients remains unclear. Here, we investigated the factors affecting the efficacy of the administration of triple antibiotics (A-FMT) and the criteria for appropriate donor and patient-donor matching.

METHODS

Ninety-seven patients with active UC who were enrolled between March 2014 and October 2019 underwent FMT. The clinical features were assessed based on a reduction in Lichtiger's clinical activity index 4 weeks after A-FMT, with long-term responders (LTR) defined as those with no increase or intensification within 12 months after A-FMT. Microbiome analysis was performed on 147 fecal samples (pre-A-FMT, post-A-FMT, and donor) from 49 patient-donor combinations that were assigned using the one-patient-to-one-donor strategy.

RESULTS

Of the 97 patients, 61 achieved a clinical response, and of those, 35 were classified as having clinical remission. The efficacy of A-FMT was affected by UC severity and previous administration of steroids (P = .027), immunosuppressants (P = .049), and biologics (P = .029). Effective donors were rich in taxa such as Bacteroidota, which are lost in UC, and the abundances of "patient-origin" and "new-amplicon sequence variant" taxa were significantly lower in Responders compared to Nonresponders (Remission; P = .03, LTR; P = .05). "Donor-derived" amplicon sequence variant sequences, Oscillospiraceae UCG-002 and Alistipes, were significantly enriched in Responders (P < .05). Our results showed that the taxonomic composition of patients and the similarity of Bacteroides and butyric-acid-producing bacteria in the patient-donor microbiota significantly influenced A-FMT efficacy (P < .05).

CONCLUSIONS

This study provides important insights for developing patient-tailored FMT-based therapies for UC.

Odoribacter splanchnicus-A Next-Generation Probiotic Candidate

As an important intestinal microorganism, Odoribacter splanchnicus frequently appears in high-throughput sequencing analyses, although pure culture research on this microorganism is not as advanced. It is widely present in the mammalian gut and is closely associated with the health status of the host and the incidence of various diseases. In recent years, changes in the abundance of O. splanchnicus have been found to be positively or negatively correlated with health issues, such as obesity, metabolic syndrome, diabetes, and intestinal inflammation. It may exhibit a dual protective or promotional role in specific diseases. Thus, it may play an important role in regulating host metabolism, immune response, and intestinal homeostasis. Additional research has revealed that O. splanchnicus can synthesize various metabolites, especially short-chain fatty acids (SCFAs), which play a key role in promoting intestinal health, enhancing energy metabolism, improving insulin resistance, and regulating immune responses in the host. Therefore, O. splanchnicus is a strong candidate for "next-generation probiotics", and its potential probiotic function provides novel ideas for the development of functional foods and the prevention and treatment of metabolic and intestinal inflammatory diseases. These findings can help develop new biological treatment strategies and optimize health management plans.

Intermittent fasting driven different adaptive strategies in Eothenomys miletus (Red-backed vole) at different altitudes: based on the patterns of variations in intestinal microbiota

In the face of global warming, the Eothenomys miletus (Red - backed vole), a species dwelling in highland mountainous regions, is likely to encounter difficulties. Given its restricted mobility, it may struggle with the uncertainty of food resources. In such circumstances, it becomes increasingly crucial for this species to adjust its diverse responses to fulfill its energy requirements. E. miletus specimens were gathered from different altitudes for intermittent fasting (IF) experiments. In these experiments, the specimens underwent random fasting for 3 days within a seven - day cycle. 16 S rDNA sequencing technology, combined with physiological and biochemical assessment methods, was employed to analyze the impacts of IF on gut microorganisms, physiological and biochemical indicators, and the interactions among them. By exploring the adaptive responses of E. miletus to uncertain food resources, which provides novel perspectives on the adaptive strategies of small rodents in the wild during food-scarce periods. The results showed that IF significantly reduced the body mass of E. miletus. Significant correlations were found between various gut microbes and physiological indicators. Under IF conditions, E. miletus at high altitudes experienced a smaller reduction in body mass compared to those at low altitudes. Moreover, the diversity of gut microbes and endemic bacteria in E. miletus at high altitudes varied more than that of low altitudes. The differential response in body mass reduction between high-altitude and low-altitude E. miletus under IF conditions indicated that altitude is an important factor influencing the physiological adaptation of this species to dietary changes. High-altitude E. miletus showed a relatively smaller decrease in body mass, potentially reflecting their better adaptation to environmental stressors over time. Additionally, the greater variation in gut microbe diversity and endemic bacteria in high-altitude E. miletus implied that altitude may shape the gut microbiota, which in turn could be related to their unique physiological adaptations at high altitudes. Overall, E. miletus at high altitude may possess more stable regulatory mechanisms, demonstrating better adaptation under IF conditions. These findings provide valuable insights into the complex interplay between diet, altitude, and gut microbiota in the context of E. miletus physiology, highlighting the importance of considering both environmental and microbial factors in understanding the species' responses to nutritional challenges.​.

Blood metabolites mediate causal inference studies on the effect of gut microbiota on the risk of vascular calcification

BACKGROUND

Emerging evidence indicates a notable connection between gut microbiota and Vascular Calcification (VC). Gut microbiota influences various disease processes through host metabolic pathways; however, the causative link between gut microbiota and VC, along with the potential mediating role of metabolites, is still not well understood.

METHODS

We leveraged data from the largest Genome-Wide Association Studies (GWAS) concerning gut microbiota, blood metabolites, and VC. To explore the causal relationships among these variables, we conducted two-sample bidirectional Mendelian Randomization (MR) analyses. Furthermore, mediation analyses were conducted to determine if metabolites act as an intermediary in the impact of gut microbiota on VC. In addition, we recruited CKD patients for mass spectrometry and CT examination, and performed a correlation analysis between the expression of blood metabolites and VC score. Finally, we experimentally validated the effects of intermediate metabolites on VC.

RESULTS

We identified 19 positive gut microbiota species and 52 positive blood metabolites with causal effects on VC. Additionally, the onset of VC was found to induce changes in the abundance of 24 gut microbiota species and 56 metabolites. Further analyses revealed that up to 13 positive gut microbiota species regulate the expression of 20 positive metabolites. Mediation analysis suggests that the gut microbiota g_KLE1615 promotes VC by downregulating the methionine-to-phosphate ratio. Mass spectrometry results indicate that over half of the metabolites identified through MR analysis show altered expression during CKD progression. Among them, 7 metabolites were significantly associated with the progression of VC. Further in vitro experiments confirmed the inhibitory effect of the intermediate metabolite methionine on VC.

CONCLUSION

Gut microbiota and blood metabolites are causally linked to VC. These findings provide a theoretical basis for microbiome- and metabolome-based therapeutic strategies for targeting VC and enhances our comprehension of the gut-vascular axis.

Exploring Causal Relationships Between Gut Microbiota, Inflammatory Cytokines, and Inflammatory Dermatoses: A Mendelian Randomization Study

Background

Some studies have established a link between gut microbiota, inflammatory proteins, and inflammatory dermatoses. However, the mediating role of inflammatory proteins in the gut-skin axis remains unclear.

Methods

Data on inflammatory proteins and gut microbiota were drawn from the GWAS catalog and MiBioGen consortium, with inflammatory skin disease data provided by the FinnGen consortium. Using genome-wide association studies (GWAS), we performed linkage disequilibrium score regression (LDSC) to assess genetic correlations and conducted a two-step Mendelian Randomization (MR) analysis to investigate circulating inflammatory proteins as potential mediators between gut microbiota and inflammatory dermatoses.

Results

MR analysis identified 38 gut microbiota and 23 inflammatory proteins associated with inflammatory skin diseases. After false discovery rate (FDR) correction, four gut microbiota taxa-Eubacterium fissicatena, Bacteroidaceae, Allisonella, and Bacteroides, remained statistically significant (OR = 1.32, 95% CI: 1.16-1.50, adjusted P = 0.007; OR = 2.25, 95% CI: 1.48-3.42, adjusted P = 0.026; OR = 1.42, 95% CI: 1.18-1.70, adjusted P = 0.014; OR = 2.25, 95% CI: 1.48-3.42, adjusted P = 0.013), with only IL-18R1 significantly associated with eczema (OR = 1.05, 95% CI: 1.03-1.08, adjusted P = 0.017). Further mediation analysis showed that IL-15RA mediated 11% of the pathway between Veillonellaceae and eczema, while FGF19 mediated 6% of the pathway between genus LachnospiraceaeUCG001 and psoriatic arthritis.

Conclusion

These findings provide potential targets for therapeutic interventions in inflammatory skin diseases.

Impact of Anaerobic Fermentation Liquid on Bok Choy and Mechanism of Combined Vitamin C from Bok Choy and Allicin in Treatment of DSS Colitis

In the context of pollution-free waste treatment, anaerobic fermentation liquid (AFL), a prominent by-product of biogas engineering, has emerged as a focal point in contemporary research. Concurrently, vitamin C, an active compound abundant in fruits and vegetables, possesses extensive application potential. The development of efficient extraction processes and the utilization of its biological activities have garnered significant attention from researchers. This study investigated the impact of AFL on the growth and vitamin C content of Bok choy through field trials of varying concentrations of AFL. The results indicated that the growth characteristics of Bok choy exhibited a concentration-dependent trend with increasing AFL dosage, with the highest yield observed in the AFL-2 group (8.43 kg/m2). Additionally, with the increase in the concentration of the AFL application, the vitamin C content in Bok choy exhibited a trend of initially increasing and then decreasing, reaching its highest value (70.83 mg/100 g) in the AFL-1 group. Furthermore, response surface methodology was employed to optimize the microwave-assisted organic solvent extraction process of vitamin C, revealing that the optimal conditions for microwave-assisted extraction using a 2% citric acid solution were as follows: a microwave power of 313 W, a microwave time of 1.3 min, and a liquid-to-solid ratio of 16.4:1 v/w, achieving a vitamin C extraction rate of 90.77%. Subsequent mechanistic studies on colitis repair demonstrated that the combination of vitamin C and allicin significantly enhanced the ability of intestinal microorganisms to ferment and degrade complex carbohydrates in colitis-afflicted mice, thereby alleviating intestinal inflammation, markedly reducing bacterial invasion signals on intestinal epithelial cells, and decreasing the risk of intestinal infection. This study provides a valuable perspective for the harmless utilization of agricultural waste, and provides a theoretical basis and technical support for the high-value utilization of natural active ingredients.

HDAC inhibitors and IBD: Charting new approaches in disease management

Inflammatory bowel disease (IBD) represents a group of chronic inflammatory disorders of the gastrointestinal tract. Despite substantial advances in our understanding of IBD pathogenesis, the currently available therapeutic options remain limited in their efficacy and often come with significant side effects. Therefore, there is an urgent need to explore novel approaches for the management of IBD. One promising avenue of investigation revolves around the use of histone deacetylase (HDAC) inhibitors, which have garnered considerable attention for their potential in modulating gene expression and curbing inflammatory responses. This review emphasizes the pressing need for innovative drugs in the treatment of IBD, and drawing from a wealth of preclinical studies and clinical trials, we underscore the multifaceted roles and the therapeutic effects of HDAC inhibitors in IBD models and patients. This review aims to contribute significantly to the understanding of HDAC inhibitors' importance and prospects in the management of IBD, ultimately paving the way for improved therapeutic strategies in this challenging clinical landscape.

Effect of fecal microbiota transplantation on ulcerative colitis model in rats: The gut-brain axis

Study objectives

The impact of fecal microbiota transplantation (FMT) on the TLR4/MYD88/NF-kB signaling pathway in the colon in the ulcerative colitis model, as well as the incidence of anxiety behaviors caused by the colitis model was investigated.

Methods

Twenthy four ats were induced with ulcerative colitis using a 4 % acetic acid solution administered intrarectally and were subsequently treated with prednisolone and FMT. The study examined several indicators, such as TLR4, MYD88, and NF-κB mRNA expression, along with oxidative stress factors. Additionally, it examined the relationship between anxiety-related behaviors and colitis and assessed the pro-inflammatory cytokines in the hippocampus.

Results

FMT led to lower disease score index and improved colon tissue pathology findings. This was associated with reduced mRNA expression of TLR4, MYD88, and NF-κB, as well as lower levels of TOS, and higher levels of TAC, GSH, and GSSG in colon tissues. FMT was found to reduce anxiety in both the open field and elevated plus maze tests. Additionally, levels of IL-6 and TNF-a were decreased in the hippocampus.

Conclusions

FMT suppressed acetic acid-induced colitis by inhibiting the TLR4/MYD88/NF-kB signaling pathway. FMT reduced anxiety in open field and plus maze tests, and resulted in decreased levels of IL-6 and TNF-a in the hippocampus.

Treatment of Acute Ulcerative Colitis with Zinc Hyaluronate in Mice

Ulcerative colitis (UC) is a type of inflammatory bowel disease arising from numerous factors, while UC patients face insufficient treatment options and a high incidence of adverse reactions to the current therapies. As a functional food additive, hyaluronic acid plays a certain role in intestinal repair. In this study, we constructed a mouse model of dextran sulfate sodium (DSS)-induced UC to examine the effects and underlying mechanisms of action of zinc hyaluronate (ZnHA) on the pathogenesis of UC. ZnHA effectively alleviated key clinical UC symptoms, such as weight loss, loose stools, and bloody stools. Mechanistically, ZnHA attenuated the expression of inflammatory factors, such as tumor necrosis factor-α, interleukin (IL)-6, and myeloperoxidase while upregulating the expression of IL-10. Furthermore, through intestinal flora and short-chain fatty acid analyses, ZnHA was found to promote propionic acid production by enriching beneficial bacteria. ZnHA simultaneously enhanced the expression of tight junction proteins, specifically ZO-1 and occludin, thereby restoring intestinal barrier function. Overall, our findings elucidate the therapeutic potential of ZnHA in treating acute UC by inhibiting intestinal inflammation and regulating flora, while also providing further theoretical support for development of hyaluronic acid to treat this disease.

Odoribacter splanchnicus-derived extracellular vesicles alleviate inflammatory bowel disease by modulating gastrointestinal inflammation and intestinal barrier function via the NLRP3 inflammasome suppression

BACKGROUND

Extracellular vesicles (EVs) derived from specific bacteria exert therapeutic potential on inflammatory diseases. Previous reports suggest the protective role of Odoribacter splanchnicus (O.splanchnicus) in inflammatory bowel disease (IBD). The effect of EVs derived from O.splanchnicus (Os-EVs) and the underlying mechanism on IBD were surveyed here.

METHODS

Os-EVs were derived with ultracentrifugation before characterization by transmission electron microscopy and nanoparticle tracking analysis. Based on IBD model mice induced by dextran sulfate sodium (DSS), the effects of Os-EVs on IBD symptoms, intestinal barrier dysfunction, and colonic apoptosis, inflammation as well as NLRP3 inflammasome activation were analyzed. NLRP3 knockout mice were exploited to judge the role of NLRP3 in Os-EVs against IBD.

RESULTS

Os-EVs were typically shaped as a double concave disc (average diameter = 95 nm). The administration of Os-EVs attenuated DSS-induced body weight loss, colon shortening, disease activity index score, and histological injury in mice. Os-EVs could also relieve intestinal barrier dysfunction and colonic apoptosis, as evidenced by the up-regulation of zona occludens-1 and Occludin and the decrease of TUNEL-positive staining in colonic tissues of IBD mice. Os-EVs downregulated the expression of the interleukin-1β (IL-1β), tumor necrosis factor-α, and IL-6, and elevated IL-10, accompanied by blockage of the NLRP3 inflammasome activation in DSS-induced mice. Furthermore, NLRP3 knockout mice experiments revealed that the protective role of Os-EVs in IBD relies on regulating NLRP3.

CONCLUSION

Our finding indicated that Os-EVs effectively ameliorated IBD through repressing NLRP3, strongly supporting the potential of probiotic-derived EVs for alleviating IBD.

The intestinal microbiome and metabolome discern disease severity in cytotoxic T-lymphocyte-associated protein 4 deficiency

BACKGROUND

Cytotoxic T-lymphocyte-associated protein 4 deficiency (CTLA4-D) is an inborn error of immunity (IEI) caused by heterozygous mutations, and characterized by immune cell infiltration into the gut and other organs, leading to intestinal disease, immune dysregulation and autoimmunity. While regulatory T-cell dysfunction remains central to CTLA4-D immunopathogenesis, mechanisms driving disease severity and intestinal pathology are unknown but likely involve intestinal dysbiosis. We determined whether the intestinal microbiome and metabolome could distinguish individuals with severe CTLA4-D and identify biomarkers of disease severity.

RESULTS

The genera Veillonella and Streptococcus emerged as biomarkers that distinguished CTLA4-D from healthy cohorts from both the National Institutes of Health (NIH) Clinical Center, USA (NIH; CTLA-D, n = 32; healthy controls, n = 16), and a geographically distinct cohort from the Center for Chronic Immunodeficiency (CCI) of the Medical Center - University of Freiburg, Germany (CCI; CTLA4-D, n = 25; healthy controls, n = 24). Since IEIs in general may be associated with perturbations of the microbiota, a disease control cohort of individuals with common variable immunodeficiency (CVID, n = 20) was included to evaluate for a CTLA4-D-specific microbial signature. Despite common IEI-associated microbiome changes, the two bacterial genera retained their specificity as biomarkers for CTLA4-D. We further identified intestinal microbiome and metabolomic signatures that distinguished patients with CTLA4-D having severe vs. mild disease. Microbiome changes were associated with distinct stool metabolomic profiles and predicted changes in metabolic pathways. These differences were impacted by the presence of gastrointestinal manifestations and were partially reversed by treatment with abatacept and/or sirolimus.

CONCLUSIONS

Loss of intestinal microbial diversity and dysbiosis causing metabolomic changes was observed in CTLA4-D. Albeit some of these features were shared with CVID, the distinct changes associated with CTLA4-D highlight the fact that IEI-associated microbiome changes likely reflect the underlying immune dysregulation. Identified candidate intestinal microbial and metabolic biomarkers distinguishing individuals with CTLA4-D based on severity should be studied prospectively to determine their predictive value, and investigated as potential therapeutic ta. Video Abstract.

Fecal microbiota changes associated with pathogenic and non-pathogenic diarrheas in foals

OBJECTIVES

Diarrhea is a common disease that could threaten the welfare of newborn foals. While there are several forms of foal diarrhea, the etiologies can be considered known pathogenic or non-pathogenic in nature. Moreover, there are likely differences in the composition of microbial populations in the gastrointestinal tracts of foals depending upon the etiology of diarrhea. Our study aims to examine the microbial population in the feces of foals with both pathogenic and non-pathogenic diarrheas to discern differences in their microbial compositions.

RESULTS

Foal diarrhea samples tested positive or negative for common equine neonatal diarrhea pathogens by diagnostic polymerase chain reaction (PCR), which allowed for samples to be segregated as pathogenic or non-pathogenic. Pathogenic samples tested positive for combinations of Clostridium perfringens and/or Clostridioides difficile toxins. As a result, significantly higher alpha diversity was seen in the non-pathogenic samples than in pathogenic ones. Sequencing of the V4 domains of bacterial 16 S rRNA genes demonstrated that non-pathogenic samples had more alpha diversity. Furthermore, eight microbial families and eleven genera showed significant differences in their abundances between pathogenic and non-pathogenic diarrhea samples.

Ulva lactuca polysaccharides combined with fecal microbiota transplantation ameliorated dextran sodium sulfate-induced colitis in C57BL/6J mice

BACKGROUND

Fecal microbiota transplantation (FMT) of healthy donors improves ulcerative colitis (UC) patients by restoring the balance of the gut microbiota. However, donors vary in microbial diversity and composition, often resulting in weak or even ineffective FMT. Improving the efficacy of FMT through combination treatment has become a promising strategy. Ulva lactuca polysaccharides (ULP) have been found to benefit host health by regulating gut microbiota. The effect of the combination of ULP and FMT in ameliorating UC has not yet been evaluated.

RESULTS

The present study found that supplementation with ULP combined with FMT showed better effects in ameliorating UC than supplementation with FMT alone. Results suggested that FMT or ULP combined with FMT alleviated the symptoms of UC in mice, as evidenced by prevention of body weight loss, improvement of disease activity index and protection of the intestinal mucus. Notably, ULP in combination with FMT was more effective than FMT in reducing levels of cytokines and related inflammatory enzymes. In addition, ULP combined with FMT effectively restored the dysbiosis induced by dextran sulfate sodium (DSS) and further enriched probiotics (such as Bifidobacterium). The production of short-chain fatty acids, especially acetic acid, was also significantly enriched by ULP combined with FMT.

CONCLUSION

Supplementation of ULP combined with FMT could significantly ameliorate DSS-induced colitis in mice by inhibiting inflammation and restoring dysbiosis of gut microbiota. These results suggested that ULP combined with FMT has potential application in ameliorating UC. © 2024 Society of Chemical Industry.

Therapeutic Potential of Cajanus cajan (L.) Millsp. Leaf Extract in Modulating Gut Microbiota and Immune Response for the Treatment of Inflammatory Bowel Disease

Background/Objectives: Inflammatory bowel disease (IBD) is a persistent inflammatory condition affecting the gastrointestinal tract, distinguished by the impairment of the intestinal epithelial barrier, dysregulation of the gut microbiota, and abnormal immune responses. Cajanus cajan (L.) Millsp., traditionally used in Chinese herbal medicine for gastrointestinal issues such as bleeding and dysentery, has garnered attention for its potential therapeutic benefits. However, its effects on IBD remain largely unexplored. Methods: In this study, the major compounds from Cajanus cajan leaf extract (CCLE) were initially characterized by LCMS-IT-TOF. The IBD model was developed in C57BL/6 mice by administering continuous 4% (w/v) dextran sodium sulfate (DSS) aqueous solution over a period of seven days. The body weight, colon length, disease activity index (DAI), and histopathological examination using hematoxylin and eosin (H&E) staining were performed in the IBD model. The levels of the main inflammatory factors, specifically TNF-α, IL-1β, IL-6, and myeloperoxidase (MPO), were quantified by employing enzyme-linked immunosorbent assay (ELISA) kits. Additionally, the levels of tight junction proteins (ZO-1, Occludin) and oxidative stress enzymes (iNOS, SOD1, CAT) were investigated by qPCR. Subsequently, flow cytometry was employed to analyze the populations of various immune cells within the spleen, thereby assessing the impact of the CCLE on the systemic immune homeostasis of IBD mice. Finally, 16S rDNA sequencing was conducted to examine the composition and relative abundance of gut microbiota across different experimental groups. In addition, molecular docking analysis was performed to assess the interaction between the principal components of CCLE and the aryl hydrocarbon receptor (AHR). Results: We identified seven bioactive compounds in CCLE: catechin, cajachalcone, 2-hydroxy-4-methoxy-6-(2-phenylcinyl)-benzoic acid, longistylin A, longistylin C, pinostrobin, amorfrutin A, and cajaninstilbene acid. Our results demonstrated that oral administration of CCLE significantly alleviates gastrointestinal symptoms in DSS-induced IBD mice by modulating the balance of gut-derived pro- and anti-inflammatory cytokines. This modulation is associated with a functional correction in M1/M2 macrophage polarization and the Th17/Treg cell balance in splenic immune cells, as well as shifts in the populations of harmful bacteria (Erysipelatoclostridium and Staphylococcus) and beneficial bacteria (Odoribacter, unidentified Oscillospiraceae, Lachnoclostridium, and Oscillibacter) in the gut. Furthermore, cajaninstilbene acid, longistylin A, and longistylin C were identified as potential AhR agonists. Conclusions: The present results suggested that CCLE, comprising stilbenes like cajaninstilbene acid, longistylin A, and longistylin C, protects the epithelial barrier's structure and function against DSS-induced acute IBD by restoring gut microbiota balance and systemic immune response as AhR agonists. Overall, CCLE represents a promising natural product-based therapeutic strategy for treating IBD by restoring gut microbiota balance and modulating systemic immune responses.

Bacterial and viral assemblages in ulcerative colitis patients following fecal microbiota and fecal filtrate transfer

Fecal microbiota filtrate transfer is discussed as a safe alternative to fecal microbiota transfer (FMT) to treat ulcerative colitis. We investigated modulation of viral and bacterial composition during fecal microbiota filtrate transfer followed by FMT in six patients with active ulcerative colitis (where clinical activity improved in three patients after filtrate transfer) and combined 16S ribosomal RNA gene amplicon sequencing with a virome analysis pipeline including fast viral particle enrichment and metagenome mapping to detect frequencies of 45,033 reference bacteriophage genomes. We showed that after antibiotic treatment and during filtrate transfer, the bacterial community typically adopted a stable composition distinct to that before antibiotic treatment, with no change toward a donor community. FMT in contrast typically changed the bacterial community to a community with similarity to donor(s). There were no indications of an establishment of predominant donor viruses during filtrate transfer but a remodeling of the virome. In contrast, the establishment of donor viruses during FMT correlated with the predicted hosts established during such transfer. Our approach warrants further investigation in a randomized trial to evaluate larger therapeutic interventions in a comparable and efficient manner.

Xanthohumol ameliorates dextran sodium sulfate-induced colitis in mice by inhibiting of NF-κB signaling pathways and modulating intestinal microbiota

ETHNOPHARMACOLOGICAL RELEVANCE

Xanthohumol (XN), an isoprenylated flavonoid natural product found only in hops, possesses a variety of biological activities such as anticancer, anti-inflammatory, hepatoprotective, and anti-obesity.

AIM OF THE STUDY

The aim of this study was to investigate the effects and mechanisms of XN on the treatment of colitis.

MATERIALS AND METHODS

First, acute colitis was induced by using distilled water containing 3% DSS for 10 consecutive days. The therapeutic efficacy of XN was assessed by an established DSS-induced mouse colitis model. Subsequently, disease activity index (DAI) and colon length of mice were assessed. The health of the intestines was assessed by histopathological analysis. Inflammatory factors, IL-1β, IL-6, and TNF-α, were detected in colon tissues by ELISA.Finally, mouse intestinal contents were extracted and subjected to 16 S rRNA Sequencing, and the gut microbiota was analysed for Alpha-diversity and Beta-diversity.

RESULTS

The results showed that XN ameliorated DSS-induced colitis. Furthermore, XN reduced pro-inflammatory cytokine levels such as IL-1β, IL-6, and TNF-α, as well as inhibited the activation of the TLR4/NF-κB pathway, all of which helped to mitigate the inflammatory response. Finally, we also found that XN alleviated intestinal dysbiosis in colitis mice.

CONCLUSION

In conclusion, our study demonstrated that XN provides protective effects against colitis, and has the potential to be further explored as a lead compound for the treatment of inflammatory bowel disease (IBD).

Biosynthetic enzyme analysis identifies a protective role for TLR4-acting gut microbial sulfonolipids in inflammatory bowel disease

The trillions of microorganisms inhabiting the human gut are intricately linked to human health. While specific microbes have been associated with diseases, microbial abundance alone cannot reveal the molecular mechanisms involved. One such important mechanism is the biosynthesis of functional metabolites. Here, we develop a biosynthetic enzyme-guided disease correlation approach to uncover microbial functional metabolites linked to disease. Applying this approach, we negatively correlate the expression of gut microbial sulfonolipid (SoL) biosynthetic enzymes to inflammatory bowel disease (IBD). Targeted chemoinformatics and metabolomics then confirm that SoL abundance is significantly decreased in IBD patient data and samples. In a mouse model of IBD, we further validate that SoL abundance is decreased while inflammation is increased in diseased mice. We show that SoLs consistently contribute to the immunoregulatory activity of different SoL-producing human microbes. We further reveal that sulfobacins A and B, representative SoLs, act on Toll-like receptor 4 (TLR4) and block lipopolysaccharide (LPS) binding, suppressing both LPS-induced inflammation and macrophage M1 polarization. Together, these results suggest that SoLs mediate a protective effect against IBD through TLR4 signaling and showcase a widely applicable biosynthetic enzyme-guided disease correlation approach to directly link the biosynthesis of gut microbial functional metabolites to human health.

Gastrointestinal germinal center B cell depletion and reduction in IgA+ plasma cells in HIV-1 infection

Gastrointestinal (GI) B cells and plasma cells (PCs) are critical to mucosal homeostasis and the host response to HIV-1 infection. Here, high-resolution mapping of human B cells and PCs sampled from the colon and ileum during both viremic and suppressed HIV-1 infection identified a reduction in germinal center (GC) B cells and follicular dendritic cells (FDCs) during HIV-1 viremia. Immunoglobulin A-positive (IgA+) PCs are the major cellular output of intestinal GCs and were significantly reduced during viremic HIV-1 infection. PC-associated transcriptional perturbations, including type I interferon signaling, persisted in antiretroviral therapy (ART)-treated individuals, suggesting ongoing disruption of the intestinal immune milieu during ART. GI humoral immune perturbations were associated with changes in the intestinal microbiome composition and systemic inflammation. These findings highlight a key immune defect in the GI mucosa due to HIV-1 viremia.

Causal effect of gut microbiota on occurrence of herpes zoster and postherpetic neuralgia, and role of Tyzzerella 3

BACKGROUND

Previous research has established connections between gut microbiota, immune modulation, and several virus-related diseases. However, no study has explored the relationships between gut microbiota and herpes zoster and postherpetic neuralgia (PHN).

METHODS

A total of 205 taxa of gut microbiota were regarded as exposures. The occurrences of herpes zoster and PHN were selected as outcomes. The causal effects of gut microbiota on herpes zoster and PHN were estimated with multiple methods for two-sample Mendelian randomization, such as inverse variance weighted (IVW), MR-Egger, and weighted median. All results were subjected to FDR correction to prevent from possibility of multiple comparison.

RESULTS

Among the significant findings, four taxa and one genus were identified as facilitators of herpes zoster and PHN, respectively. Conversely, six genera and eleven taxa were found to inhibit herpes zoster and PHN, respectively. The causal effect of the Tyzzerella 3 was confirmed through FDR correction, making it a key focus in this study. Specifically, it was found to causally facilitate herpes zoster primarily with IVW (OR 1.420, 95% CI 1.174-1.718, p < 0.001, q = 0.039), as there is no heterogeneity or horizontal pleiotropy found.

CONCLUSIONS

With investigation of the causal association between gut microbiota, and herpes zoster/PHN, significant findings were identified in 22 different taxa. Among them, Tyzzerella 3 keeps significant after multiple comparison correction, and displays potential to facilitate the occurrence of herpes zoster.

Gut Microbiota Features in Relation to Fecal Microbiota Transplantation Outcome in Ulcerative Colitis: A Systematic Review and Meta-Analysis

BACKGROUND & AIMS

Fecal microbiota transplantation (FMT) can induce remission in patients with ulcerative colitis, yet its efficacy needs improvement. We conducted a comprehensive evaluation of the current literature on microbial factors affecting outcome, as well as a meta-analysis on some of the largest datasets regarding composition.

METHODS

MEDLINE, Embase, and Cochrane were systematically searched through August 2024 for relevant studies. The quality of studies was analyzed with JBI tools and a composite critical appraisal score. Additionally, species-level data from 2 landmark FMT trials (the Transplantation of Feces in Ulcerative Colitis; Returning Nature's Homeostasis [TURN] and Fecal Microbiota Transplantation for Chronic Active Ulcerative Colitis [FOCUS] trials) were reanalyzed from a compositional perspective.

RESULTS

Out of 3755 citations identified, 56 met the inclusion criteria, of which 29 fulfilled quality standards. Higher microbial α-diversity, either in donors or recipients (at baseline or following FMT treatment), was associated with better clinical response rates. Engraftment of the donors' microbiota could not be clearly linked with clinical response, possibly because not every donor has an ideal microbiome. Butyrate-producing species from the Lachnospiraceae and Oscillospiraceae families were often related with response, whereas the reverse was true for Fusobacteria, many Proteobacteria, and Ruminococcus gnavus. Compositional analyses showed that clinical response is associated with a shift from a low-diversity, often Bacteroides-dominant composition to one with higher diversity, either dominated by various butyrate producers, the Christensenellaceae-Methanobrevibacter trophic network, or a moderate/high-diversity composition with abundant but not excessive levels of Prevotella copri.

CONCLUSIONS

This systematic review/meta-analysis yielded a coherent picture from a compositional perspective, which may help identify beneficial donor profiles and guide personalized FMT approaches.

Gastrointestinal germinal center B cell depletion and reduction in IgA + plasma cells in HIV-1 infection

Gastrointestinal (GI) B cells and plasma cells (PCs) are critical to mucosal homeostasis and the host response to HIV-1 infection. Here, high resolution mapping of human B cells and PCs sampled from the colon and ileum during both viremic and suppressed HIV-1 infection identified a reduction in germinal center (GC) B cells and follicular dendritic cells (FDCs) during HIV-1 viremia. IgA + PCs are the major cellular output of intestinal GCs and were significantly reduced during viremic HIV-1 infection. PC-associated transcriptional perturbations, including type I interferon signaling, persisted in antiretroviral therapy (ART)-treated individuals, suggesting ongoing disruption of the intestinal immune milieu during ART. GI humoral immune perturbations were associated with changes in the intestinal microbiome composition and systemic inflammation. These findings highlight a key immune defect in the GI mucosa due to HIV-1 viremia.

One Sentence Summary

Intestinal germinal center B cell reduction in HIV-1 infection linked to reduced IgA + plasma cells and systemic inflammation.

Ursolic Acid Regulates Immune Balance, Modulates Gut Microbial Metabolism, and Improves Liver Health in Mice

Ursolic acid (UA) has demonstrated significant immunomodulatory and hepatoprotective effects; however, the underlying mechanisms remain unclear. This study aims to analyze the impact of UA on the gut microbiome, metabolome, and liver transcriptome, investigate UA's role in maintaining gut immune homeostasis and liver health, and evaluate the potential contributions of gut microbes and their metabolites to these beneficial effects. Our findings indicate that UA enhances immune balance in the jejunum, fortifies intestinal barrier function, and promotes overall gut health. UA modulates the intestinal microbiota and its metabolic processes, notably increasing the abundance of beneficial bacteria such as Odoribacter and Parabacteroides, along with their metabolites, including ornithine and lactucin. Additionally, UA inhibits the expression of interleukin-1 receptor 1 (IL1R1) and calcium (Ca2+) voltage-gated channel auxiliary subunit beta 2 (CACNB2) while enhancing the synthesis pathways of retinol and ascorbic acid, thereby exerting a protective influence on liver function. In summary, UA enhances intestinal immune homeostasis and promotes liver health, with these advantageous effects potentially mediated by beneficial bacteria (Odoribacter and Parabacteroides) and their metabolites (ornithine and lactucin).

MicroHDF: predicting host phenotypes with metagenomic data using a deep forest-based framework

The gut microbiota plays a vital role in human health, and significant effort has been made to predict human phenotypes, especially diseases, with the microbiota as a promising indicator or predictor with machine learning (ML) methods. However, the accuracy is impacted by a lot of factors when predicting host phenotypes with the metagenomic data, e.g. small sample size, class imbalance, high-dimensional features, etc. To address these challenges, we propose MicroHDF, an interpretable deep learning framework to predict host phenotypes, where a cascade layers of deep forest units is designed for handling sample class imbalance and high dimensional features. The experimental results show that the performance of MicroHDF is competitive with that of existing state-of-the-art methods on 13 publicly available datasets of six different diseases. In particular, it performs best with the area under the receiver operating characteristic curve of 0.9182 ± 0.0098 and 0.9469 ± 0.0076 for inflammatory bowel disease (IBD) and liver cirrhosis, respectively. Our MicroHDF also shows better performance and robustness in cross-study validation. Furthermore, MicroHDF is applied to two high-risk diseases, IBD and autism spectrum disorder, as case studies to identify potential biomarkers. In conclusion, our method provides an effective and reliable prediction of the host phenotype and discovers informative features with biological insights.

Characteristics of Mucosa-Associated Microbiota in Ulcerative Colitis Patients with 5-Aminosalicylic Acid Intolerance

BACKGROUND/OBJECTIVES

5-Aminosalicylic acid (5-ASA) is a first-line therapy for ulcerative colitis (UC). This study examined the mucosa-associated microbiota (MAM) in UC patients, distinguishing between those who were 5-ASA tolerant and intolerant.

METHODS

Brushing samples were collected from the sigmoid and ileal end of patients with UC during endoscopic procedures. The samples were profiled by using the Illumina MiSeq platform. The V3-V4 regions of the 16S rRNA gene (460 bp) were amplified by using tailed PCR.

RESULTS

A total of 15 patients with 5-ASA intolerance, 38 patients with 5-ASA tolerance, and 19 healthy controls were recruited in this study. The α-diversity indices were remarkably different among the three groups in the ileum mucosa but not in the sigmoid colon. In the ileum mucosa, Alistipes, Ruminococcaceae, and Odoribacter were less abundant in the 5-ASA-intolerant group than in the control and 5-ASA-tolerant groups. On the contrary, Merdibacter, Brevundimonas, and Porphyromonas were more abundant in the 5-ASA-intolerant group than in other groups.

CONCLUSIONS

The present study showed that the changes in MAM were characterized by a decrease in mucoprotective bacteria rather than an increase in harmful bacteria.

Protection against DSS-induced colitis in mice through FcεRIα deficiency: the role of altered Lactobacillus

The role of mast cells (MCs) in ulcerative colitis (UC) development is controversial. FcεRI, the IgE high-affinity receptor, is known to activate MCs. However, its role in UC remains unclear. In our study, Anti-FcεRI showed highly diagnostic value for UC. FcεRIα knockout in mice ameliorated DSS-induced colitis in a gut microbiota-dependent manner. Increased Lactobacillus abundance in FcεRIα deficient mice showed strongly correlation with the remission of colitis. RNA sequencing indicated activation of the NLRP6 inflammasome pathway in FcεRIα knockout mice. Additionally, Lactobacillus plantarum supplementation protected against inflammatory injury and goblet cell loss, with activation of the NLRP6 inflammasome during colitis. Notably, this effect was absent when the strain is unable to produce lactic acid. In summary, colitis was mitigated in FcεRIα deficient mice, which may be attributed to the increased abundance of Lactobacillus. These findings contribute to a better understanding of the relationship between allergic reactions, microbiota, and colitis.

Lactobacillus plantarum Ameliorates Colorectal Cancer by Ameliorating the Intestinal Barrier through the CLA-PPAR-γ Axis

Colorectal cancer (CRC) is the third-largest cancer worldwide. Lactobacillus can regulate the intestinal barrier and gut microbiota. However, the mechanisms of Lactobacillus that alleviate CRC remained unknown. This study aimed to explore the regulatory effect of Lactobacillus plantarum on CRC and its potential mechanism. CCFM8661 treatment significantly ameliorated CRC compared with phosphate-buffered solution (PBS) treatment in ApcMin/+ mice. In addition, conjugated linoleic acid (CLA) was proved to be the key metabolite for CCFM8661 in ameliorating CRC by molecular biology techniques. Peroxisome proliferator-activated receptor γ (PPAR-γ) was proved to be the key receptor in ameliorating CRC by inhibitor intervention experiments. Moreover, supplementation with CCFM8661 ameliorated CRC by producing CLA to inhibit NF-κB pathway and pro-inflammatory cytokines, up-regulate ZO-1, Claudin-1, and MUC2, and promote tumor cell apoptosis in a PPAR-γ-dependent manner. Metagenomic analysis showed that CCFM8661 treatment significantly increased Odoribacter splanchnicus, which could ameliorate CRC by repairing the intestinal barrier. Clinical results showed that intestinal CLA, butyric acid, PPAR-γ, and Lactobacillus were significantly decreased in CRC patients, and these indicators were significantly negatively correlated with CRC. CCFM8661 alleviated CRC by ameliorating the intestinal barrier through the CLA-PPAR-γ axis. These results will promote the development of dietary probiotic supplements for CRC.

Baseline Serum and Stool Microbiome Biomarkers Predict Clinical Efficacy and Tissue Molecular Response After Ritlecitinib Induction Therapy in Ulcerative Colitis

BACKGROUND AND AIMS

Ritlecitinib, an oral JAK3/TEC family kinase inhibitor, was well-tolerated and efficacious in the phase 2b VIBRATO study in participants with moderate-to-severe ulcerative colitis [UC]. The aim of this study was to identify baseline serum and microbiome markers that predict subsequent clinical efficacy and to develop noninvasive serum signatures as potential real-time noninvasive surrogates of clinical efficacy after ritlecitinib.

METHODS

Tissue and peripheral blood proteomics, transcriptomics, and faecal metagenomics were performed on samples before and after 8 weeks of oral ritlecitinib induction therapy [20 mg, 70 mg, 200 mg, or placebo once daily, N = 39, 41, 33, and 18, respectively]. Linear mixed models were used to identify baseline and longitudinal protein markers associated with efficacy. The combined predictivity of these proteins was evaluated using a logistic model with permuted efficacy data. Differential expression of faecal metagenomics was used to differentiate responders and nonresponders.

RESULTS

Peripheral blood serum proteomics identified four baseline serum markers [LTA, CCL21, HLA-E, MEGF10] predictive of modified clinical remission [MR], endoscopic improvement [EI], histological remission [HR], and integrative score of tissue molecular improvement. In responders, 37 serum proteins significantly changed at Week 8 compared with baseline [false discovery rate of <0.05]; of these, changes in four [IL4R, TNFRSF4, SPINK4, and LAIR-1] predicted concurrent EI and HR responses. Faecal metagenomics analysis revealed baseline and treatment response signatures that correlated with EI, MR, and tissue molecular improvement.

CONCLUSIONS

Blood and microbiome biomarkers stratify endoscopic, histological, and tissue molecular responses to ritlecitinib, which may help guide future precision medicine approaches to UC treatment. ClinicalTrials.gov NCT02958865.

Phenylethanol Glycoside from Cistanche tubulosa Attenuates BSA-Induced Liver Fibrosis in Rats by Modulating the Gut Microbiota-Liver Axis

This study aimed to investigate the effect of phenylethanol glycoside from Cistanche tubulosa (CPhGs) on the prevention of bovine serum albumin (BSA)-induced hepatic fibrosis in rats. Investigation of the mechanisms of the anti-hepatic fibrosis effect was focused on CPhGs' influence on the "gut-liver" regulation, including the gut microbiota, intestinal barrier, systemic lipopolysaccharide (LPS) concentration, and LPS-related signaling pathway. The results show that CPhGs restored the diversity of gut microbiota, increased the relative abundance of Bacteroidetes, and decreased the relative abundance of Firmicutes and Proteobacteria in the fibrotic rats. In addition, CPhGs promoted the enrichment of probiotics such as Blautia, Oscillospira, Ruminococcus, Odoribacter, Bacteroides, and Parabacteroides in intestines of these rats. Furthermore, CPhGs reduced histopathological injury in the intestine and restored the tight junctions of the intestine by increasing the expression of ZO-1, occludin, and E-cadherin. CPhGs efficiently reduced serum LPS and liver lipopolysaccharide-binding protein (LBP) levels and inhibited the LPS-TLR4/MyD88/NF-κB pathway, which is related to protein expression in the liver. Correlation analysis confirmed that these beneficial bacteria were negatively associated with pathological damage, while LPS and harmful bacteria were positively associated with liver injury. Our fecal microbiota transplantation (FMT) experiment confirmed that gut microbiota is an important part of disease progression and that CPhGs is useful for the prevention and treatment of hepatic fibrosis. Our data demonstrate that the anti-hepatic fibrosis mechanism of CPhGs was mediated by regulation of the "gut-liver" axis. These results can stimulate consideration for its use in clinical practices.

Aggravated Ulcerative Colitis via circNlgn-Mediated Suppression of Nuclear Actin Polymerization

Colitis is a chronic bowel disease characterized by damage to the lining of the large intestine, with its precise underlying causes remaining incompletely understood. In this study, we provide evidence that circular RNA circNlgn plays a pivotal role in promoting the development of colitis. Colitis patients produce significant higher levels of circNlgn. Transgenic mice expressing circNlgn exhibit heightened susceptibility to colitis development and progression, primarily attributed to the presence of the protein isoform Nlgn173 encoded by circNlgn. Nlgn173 undergoes translocation into cell nuclei, where it interacts with actin, impeding the binding of actin-related protein 2 and 3 (Arp2/3) complex to actin molecules. Consequently, this leads to a reduction in actin polymerization. Mechanistically, Nlgn173 enhances tyrosine-53 phosphorylation of nuclear actin, diminishing its capacity to interact with the Arp2/3 complex and causing a decrease in filamentous actin levels. These alterations in actin dynamics result in inhibited cell cycle progression, increased apoptosis, and decreased proliferation of colonic epithelial cells, thereby exacerbating colitis development and progression. In contrast, the silencing of circNlgn or the targeted inhibition of Nlgn173 translation and nuclear translocation leads to the promotion of nuclear actin polymerization, enhanced cell survival, and reduced apoptosis and ultimately improves the outcome of colitis in vivo. Interestingly, nuclear actin polymerization is highly related with expression of PIAS3, which modulates signal transducer and activator of transcription 3 and NF-κB activity in colitis. Strategies such as circNlgn knockdown and targeting nuclear actin polymerization of the colonic epithelium may explore a novel avenue for acute ulcerative colitis clinical intervention.

Effects of hydroxychloroquine on the mucosal barrier and gut microbiota during healing of mice colitis

OBJECTIVES

The present study aimed to evaluate the impact of hydroxychloroquine (HCQ) on the mucosal barrier and gut microbiota during the healing of mice colitis.

METHODS

The body weight, colon length, colon Hematoxylin-Eosin (H&E) staining, occult blood in feces and serum inflammatory factor levels were measured to evaluate the function of HCQ on inflammatory process in colitis mice. The Alcian blue staining, immunohistochemistry, immunofluorescence and serum FITC-Dextran assay were performed to assess the intestinal mucosal permeability. And the composition and expression differences of intestinal microorganisms in feces were analyzed with 16S rDNA sequencing for exploration of HCQ impact on gut microbiota in colitis.

RESULTS

The results showed that the administration of HCQ did not significantly alter the body weight, colon length, or fecal occult blood of the mice. However, HCQ treatment did lead to recovery of the structure and morphology of the intestinal mucosa, increased expression of tight junction proteins (E-cadherin and Occludin), decreased permeability of the intestinal mucosal barrier, increased serum IL-10, and decreased level of tumor necrosis factor-alpha (TNF-α). Additionally, HCQ was found to increase the abundance of Euryarchaeota, Lactobacillus_murinus and Clostridium_fusiformis, while decreasing the abundance of Oscillibacter, uncultured_Odoribacter, Bacterioidetes and Muribaculum.

CONCLUSIONS

These findings support that HCQ plays a role in the treatment of mice colitis possibly by altering the gut microbiota.

Microbiota-associated mechanisms in colorectal cancer

Colorectal cancer (CRC) is one of the most common cancers worldwide, ranking third in terms of incidence and second as a cause of cancer-related death. There is growing scientific evidence that the gut microbiota plays a key role in the initiation and development of CRC. Specific bacterial species and complex microbial communities contribute directly to CRC pathogenesis by promoting the neoplastic transformation of intestinal epithelial cells or indirectly through their interaction with the host immune system. As a result, a protumoural and immunosuppressive environment is created conducive to CRC development. On the other hand, certain bacteria in the gut microbiota contribute to protection against CRC. In this chapter, we analysed the relationship of the gut microbiota to CRC and the associations identified with specific bacteria. Microbiota plays a key role in CRC through various mechanisms, such as increased intestinal permeability, inflammation and immune system dysregulation, biofilm formation, genotoxin production, virulence factors and oxidative stress. Exploring the interaction between gut microbiota and tumourigenesis is essential for developing innovative therapeutic approaches in the fight against CRC.

Deciphering Microbial Composition in Patients with Inflammatory Bowel Disease: Implications for Therapeutic Response to Biologic Agents

Growing evidence suggests that alterations in the gut microbiome impact the development of inflammatory bowel diseases (IBDs), including Crohn's disease (CD) and ulcerative colitis (UC). Although IBD often requires the use of immunosuppressant drugs and biologic therapies to facilitate clinical remission and mucosal healing, some patients do not benefit from these drugs, and the reasons for this remain poorly understood. Despite advancements, there is still a need to develop biomarkers to help predict prognosis and guide treatment decisions. The aim of this study was to investigate the gut microbiome of IBD patients using biologics to identify microbial signatures associated with responses, following standard accepted criteria. Microbiomes in 66 stool samples from 39 IBD patients, comprising 20 CD and 19 UC patients starting biologic therapies, and 29 samples from healthy controls (HCs) were prospectively analyzed via NGS and an ensemble of metagenomics analysis tools. At baseline, differences were observed in alpha and beta metrics among patients with CD, UC and HC, as well as between the CD and UC groups. The degree of dysbiosis was more pronounced in CD patients, and those with dysbiosis exhibited a limited response to biological drugs. Pairwise differential abundance analyses revealed an increasing trend in the abundance of an unannotated genus from the Clostridiales order, Gemmiger genus and an unannotated genus from the Rikenellaceae family, which were consistently identified in greater abundance in HC. The Clostridium genus was more abundant in CD patients. At baseline, a greater abundance of the Odoribacter and Ruminococcus genera was found in IBD patients who responded to biologics at 14 weeks, whereas a genus identified as SMB53 was more enriched at 52 weeks. The Collinsella genus showed a higher prevalence among non-responder IBD patients. Additionally, a greater abundance of an unclassified genus from the Barnesiellaceae family and one from Lachnospiraceae was observed in IBD patients responding to Vedolizumab at 14 weeks. Our analyses showed global microbial diversity, mainly in CD. This indicated the absence or depletion of key taxa responsible for producing short-chain fatty acids (SCFAs). We also identified an abundance of pathobiont microbes in IBD patients at baseline, particularly in non-responders to biologic therapies. Furthermore, specific bacteria-producing SCFAs were abundant in patients responding to biologics and in those responding to Vedolizumab.

The Non-Denatured Processing of Brasenia schreberi Mucilage-Characteristics of Hydrodynamic Properties and the Effect on In Vivo Functions

Food non-denatured processes, such as freeze-drying and grinding, are commonly applied to raw materials with good bioactive functions. Although the functional components are maintained, whether structural and physical changes impact the in vivo function is often ignored in practical situations. Brasenia schreberi mucilage (BSM) has a significant alleviation effect on DSS-induced colitis. This work focused on the influence of non-denatured manufacture on the colonic benefits of BSM-based products. First, three forms of products including fresh mucilage (FM), freeze-dried products (FS), and freeze-dried powder (FP) were prepared. Then, their in vitro physiochemical properties were compared, analyzing their influence on the gut inflammation degree, microbial composition, and SCFA production in mice. The results suggested that the water retention rate of FS and FP was decreased to 34.59 ± 3.85%, and 9.93 ± 1.76%. The viscosity of FM, FS, and FP was 20.14 Pa∙s, 4.92 Pa∙s, and 0.41 Pa∙s, respectively. The freeze-drying and grinding process also damaged the lamellar microstructure of BSM. Then, animal tests showed that colitis mice intervened with FM, FS, and FP had disease activity scores of 2.03, 3.95, and 4.62. Meanwhile, FM notably changed the gut microbial composition and significantly increased propionate and butyrate levels. It seemed that the distinct colitis alleviation efficacy of BSM-based products is attributed to different hydrodynamic properties in the gut. FM had relatively higher viscosity and correspondingly high nutritional density in the gut lumen, which stimulates Firmicutes growth and promotes butyrate production, and thereby exhibited the best efficiency on protecting from colitis.

The Importance of Microbiota and Fecal Microbiota Transplantation in Pancreatic Disorders

The role of the intestinal microbiota in the diagnosis and treatment of pancreatic diseases is increasingly significant. Consequently, fecal microbiota transplantation (FMT) is emerging as a promising therapeutic avenue for various pancreatic disorders, including cancer, pancreatitis, and type 1 diabetes (T1D). This innovative procedure entails transferring gut microbiota from healthy donors to individuals affected by pancreatic ailments with the potential to restore intestinal balance and alleviate associated symptoms. FMT represents a pioneering approach to improve patient outcomes in pancreatic diseases, offering tailored treatments customized to individual microbiomes and specific conditions. Recent research highlights the therapeutic benefits of targeting the gut microbiota for personalized interventions in pancreatic disorders. However, a comprehensive understanding of the intricate interplay between gut microbiota and pancreatic physiology warrants further investigation. The necessity for additional studies and research endeavors remains crucial, especially in elucidating both adult and pediatric cases affected by pathological pancreatic conditions.

Lycium barbarum arabinogalactan alleviates intestinal mucosal damage in mice by restoring intestinal microbes and mucin O-glycans

Structurally defined arabinogalactan (LBP-3) from Lycium barbarum have effect on improving intestinal barrier function. However, whether its intestinal barrier function depended on the changes of intestinal mucin O-glycans have not been investigated. A dextran sodium sulfate-induced acute colitis mouse model was employed to test prevention and treatment with LBP-3. The intestinal microbiota as well as colonic mucin O-glycan profiles were analyzed. Supplementation with LBP-3 inhibited harmful bacteria, including Desulfovibrionaceae, Enterobacteriaceae, and Helicobacteraceae while significantly increased the abundance of beneficial bacteria (e.g., Lachnospiraceae, Ruminococcaceae, and Lactobacillaceae). Notably, LBP-3 augmented the content of neutral O-glycans by stimulating the fucosylation glycoforms (F1H1N2 and F1H2N2), short-chain sulfated O-glycans (S1F1H1N2, S1H1N2, and S1H2N3), and sialylated medium- and long-chain O-glycans (F1H2N2A1, H2N3A1, and F1H3N2A1). In summary, we report that supplement LBP-3 significantly reduced pathological symptoms, restored the bacterial community, and promoted the expression of O-glycans to successfully prevent and alleviate colitis in a mouse model, especially in the LBP-3 prevention testing group. The underlying mechanism of action was investigated using glycomics to better clarify which the structurally defined LBP-3 were responsible for its beneficial effect against ulcerative colitis and assess its use as a functional food or pharmaceutical supplement.