The NLRP3 inflammasome is an important susceptibility factor in inflammatory bowel disease (IBD), yet its specific mechanisms in modulating gut microbiota during intestinal inflammation remain unclear. This study observed significant upregulation of NLRP3 inflammasome in colonic tissues from patients with active ulcerative colitis and a murine dextran sulfate sodium (DSS)-induced colitis model. Nlrp3 deletion markedly attenuated disease severity, evidenced by improved histopathology, reduced pro-inflammatory cytokines, and increased microbial alpha diversity. Notably, Nlrp3 deficiency mitigated the depletion of beneficial SCFA-producing taxa, specifically enriching Dubosiella and Rikenellaceae_RC9_gut_group, which was associated with the restoration of fecal propionate and butyrate levels. Furthermore, treatment with the SCFA-producing probiotic Clostridium butyricum alleviated colitis in wild-type mice but provided no additional benefit in Nlrp3 - deficient mice and failed to reduce inflammation in mice treated with the NLRP3 activator nigericin. Collectively, these results suggest that the therapeutic efficacy of C. butyricum may be influenced by the activation status of host NLRP3, underscoring the complex relationship between NLRP3 signaling and microbiota-mediated regulation in IBD pathogenesis.

The gut microbiota contributes to inflammatory bowel disease (IBD) pathogenesis, yet the functional impact of specific bacterial species remains unclear. Here, Odoribacter splanchnicus (O. splanchnicus) is indentified as a taxon depleted in human IBD cohorts and demonstrated its protective effects in acute and chronic murine colitis models. In mice, O. splanchnicus administration alleviated colonic inflammation and preserved barrier integrity, accompanied by a restructured mucosal immune landscape and reduced neutrophil extracellular traps (NETs) formation. This inhibitory effect on NETs is lost in Pad4-/- mice, highlighting its dependence on NETs formation machinery. Metabolomic profiling showed that O. splanchnicus treatment elevated the secondary bile acid lithocholic acid (LCA). This increase is lost following antibiotic cocktail treatment and restored by fecal microbiota transplantation from O. splanchnicus-treated donors, demonstrating a requirement for an intact gut microbiota. Mechanistically, LCA supplementation recapitulated the anti-NETs formation phenotype and suppressed colonic inflamation by inhibiting the NLRP3-GSDMD signaling pathway. Together, these findings define a gut microbiota-metabolite-neutrophil axis in IBD pathogenesis, highlighting the microbiota-dependent regulation of LCA as a key protective mechanism of O. splanchnicus.

BACKGROUND AND AIM:Peroxisome proliferator-activated receptors (PPARs), as nuclear receptors, modulate both lipid metabolism and inflammatory/immune processes. This study examines the impact of modulating the activities of the PPAR subtypes PPARβ/ð and PPARγ on the gut microbiota in inflammatory bowel disease (IBD). METHODS:Mice with dextran sulfate sodium (DSS)-induced acute colitis were treated with the PPARγ agonist pioglitazone, PPARβ/δ agonist GW0742, or their respective antagonists (GW9662, GSK3787). Weight loss, diarrhea severity, hematochezia, and disease activity index were assessed daily. Upon study completion, colon length, histopathology, and mRNA levels of the intestinal barrier and inflammatory markers were measured. Occludin and E-cadherin levels were assessed via immunofluorescence analysis, and cecal samples underwent 16S rRNA sequencing for gut microbiota analysis. RESULTS:Our findings revealed that the agonists pioglitazone and GW0742 effectively suppressed DSS-induced colitis, improved clinical symptoms, reversed colon shortening, and mitigated histological damage. Conversely, their antagonists, GW9662 and GSK3787, failed to alleviate inflammation and sometimes exacerbated disease indicators. Both agonists modulated DSS-induced dysbiosis by reducing the abundance of proinflammatory cytokine-associated microbiota, including Bacteroides, Enterococcus, and Escherichia-Shigella, while enhancing both α-diversity and β-diversity of the gut microbiome, to restore equilibrium. CONCLUSION:Our findings reveal that activation of PPARγ and PPARβ/δ can balance the gut microbiota in mice and ameliorate experimental colitis in mice. Thus, PPARγ and PPARβ/δ have protective effects against IBD and could serve as novel therapeutic targets for its treatment.

Background:Ulcerative colitis (UC), a chronic inflammatory bowel disease, is characterized by a multifactorial etiology and limited therapeutic options. Recent advancements in plant-derived exosome-like nanoparticles (PDENs) have demonstrated promising potential for UC treatment. This study explored the therapeutic efficacy of Andrographis paniculata-derived exosome-like nanoparticles (APELNs) in alleviating dextran sodium sulfate (DSS)-induced colitis.Methods:APELNs were isolated and purified using sucrose gradient centrifugation and subsequently characterized through visualization techniques. Their stability was assessed under simulated stomach-like and intestine-like conditions. The therapeutic potential of APELNs was evaluated through both in vivo and in vitro experiments. In addition, the biosafety of APELNs was comprehensively analyzed in these settings.Results:APELNs exhibited excellent stability and biosafety, with a targeted accumulation in inflamed colonic tissues under gastrointestinal conditions. The nanoparticles displayed a desirable size (about 180 nm) and a negative zeta potential (-40 mV). Treatment with APELNs significantly ameliorated colonic pathologies in vivo and suppressed the expression of pro-inflammatory cytokines in vitro. Mechanistically, APELNs enhanced gut microbiota richness and diversity, fostering the growth of the probiotic Lactobacillus murinus. Moreover, APELNs reduced intestinal permeability and preserved intestinal barrier integrity by upregulating tight junction proteins, including Claudin-1, zonula occludens-1, Mucin2, and anti-occludin. Importantly, oral administration of APELNs shifted macrophage polarization in the colon, inhibiting the pro-inflammatory M1 subset while promoting the anti-inflammatory M2 subset. This polarization was mediated through the activation of the phosphatidylinositol 3 kinase-protein kinase B (PI3K-AKT) and Janus tyrosine kinase-signal transducer and activator of transcription (JAK-STAT) signaling pathways and the upregulation of interleukin-4 receptor expression.Conclusion:These findings highlighted the potential of APELNs as a novel therapeutic strategy for UC, offering a promising alternative for effective disease management.

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.

Faecalibacterium prausnitzii is a major commensal bacterium that plays a crucial role in intestinal homeostasis. Its secretes an microbial anti-inflammatory molecule (MAM) that functions as a potential therapeutic agent in inflammatory bowel disease (IBD). However, the molecular mechanisms through which MAM exerts its beneficial effects remain incompletely understood. Here, we investigate whether MAM modulates autophagy and to evaluate its therapeutic potential in a murine model of colitis. A genetically engineered Lactococcus lactis strain expressing MAM was administered to mice with dextran sulfate sodium (DSS)-induced or 2,4,6-trinitrobenzene sulfonic acid (TNBS)-induced colitis. The therapeutic effects of MAM were evaluated using clinical scoring, histopathological analysis, and inflammatory cytokines measurement. Intestinal barrier function was assessed based on tight junction protein expression. Autophagy-related signaling pathways were analyzed using western blotting and immunohistochemistry. To determine how autophagy affects MAM, DSS-treated mice were treated with the autophagy inhibitor hydroxychloroquine (HCQ) and bafilomycin A1 (BafA1). Gut microbiota composition was profiled 16 S rRNA gene amplicon sequencing. Fecal short-chain fatty acid (SCFA) levels were quantified by gas chromatography–mass spectrometry (GC-MS). MAM treatment significantly alleviated colitis in both DSS- and TNBS-induced models, as evidenced by reduced disease activity, improved colon length, attenuated histopathological damage, and decreased pro-inflammatory cytokine production. MAM enhanced intestinal barrier integrity by upregulating ZO-1 and occludin. Notably, MAM counteracted the inhibitory effect of HCQ/BafA1 on autophagy, enhancing autophagic flux despite autophagy suppression. Furthermore, MAM treatment significantly increased the fecal concentrations of acetate, propionate, and butyrate. 16 S sequencing revealed the enrichment of beneficial taxa, including Lactobacillus and Lachnospiraceae_NK4A136_group, The abundance of these taxa was positively correlated with SCFA levels and improvement of colitis symptoms. We identified MAM as a multifunctional microbial effector with potent anti-inflammatory properties. MAM improves intestinal barrier function and attenuates experimental colitis through dual mechanisms involving the modulation of autophagy and gut microbiota composition. These findings highlight the translational potential of MAM and support further investigation into its use as a novel therapeutic strategy for IBD.

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.

Colorectal cancer (CRC) is a prevalent global malignancy where gut microbiota plays a key role. Streptococcus gallolyticus (Sg), a gut commensal and opportunistic pathogen, is associated with CRC. This study investigates the impact of the supernatant derived from Sg cultures (hereafter referred to as Sgsup) on CRC progression and examines the underlying mechanisms. Quantitative PCR (qPCR) was employed to assess Sg colonization in paired tumors and adjacent normal tissues from 46 CRC patients. CRC cell lines (HCT116, HT29) were treated with Sgsup, and cell proliferation was measured using the CCK-8 assay. Non-targeted metabolomic profiling of Sgsup was performed via liquid chromatography-mass spectrometry (LC-MS). An azoxymethane/dextran sulfate sodium (AOM/DSS)-induced mouse model of CRC was used to evaluate in vivo tumor burden, inflammation, and macrophage polarization (flow cytometry). Transcriptomic analysis via RNA-seq was conducted to identify enriched signaling pathways. The detection rate of Sg was significantly higher in tumor tissues compared to adjacent tissues (47.8

Probiotics have been proposed as a potential strategy for managing ulcerative colitis (UC). However, the underlying mechanisms mediating microbiota-host crosstalk remain largely elusive. Here, we report that Limosilactobacillus reuteri (L. reuteri), as a probiotic, secretes cytoplasmic membrane vesicles (CMVs) that communicate with host cells, alter host physiology, and alleviate dextran sulfate sodium (DSS)-induced colitis. First, L. reuteri-CMVs selectively promoted the proliferation of the beneficial bacterium Akkermansia muciniphila (AKK) by upregulating the expression of glycosidases (beta-N-acetylhexosaminidase and alpha-N-acetylglucosaminidase) involved in glycan degradation and metabolic pathways and restored the disrupted gut microbiota balance. Second, L. reuteri-CMVs were taken up by intestinal epithelial cells (IECs), elevated the expression of ZO-1, E-cadherin (Cdh1), and Occludin (Ocln), decreased intestinal permeability, and exerted protective effects on epithelial tight junction functionality. RNA sequencing analysis demonstrated that L. reuteri-CMVs repaired intestinal barrier by activating the HIF-1 signaling pathway and upregulating HMOX1 expression. Third, L. reuteri-CMVs increased the population of double positive (DP) CD4+CD8+ T cells in the intestinal epithelial layer, suppressing gut inflammation and maintaining gut mucosal homeostasis. Finally, L. reuteri-CMVs exhibited satisfactory stability and safety in the gastrointestinal tract and specifically targeted the desired sites in colitis mice. Collectively, these findings shed light on how L. reuteri interact with the host in colitis, and provide new insights into potential strategies for alleviating colitis.

Inflammatory bowel disease (IBD), including Crohn’s disease and ulcerative colitis, is considered significant global health concerns worldwide. Many studies have demonstrated that environmental and dietary factors influence the gut microbiota, which in turn orchestrates the host immune responses. These interactions are also involved in complex metabolic processes that contribute to the pathogenesis of IBD. Furthermore, recent studies in genomics and metabolomics have unveiled the intricate relationship between microbial influencers and host epigenetics. The dynamics of gut microbiota and its metabolites intricately align with DNA methylation, histone methylation, lactylation, glycosylation, and non-coding RNAs, which are key players in epigenetics. Here, we summarize and discuss the complex interplay among gut microbiota, epigenetics, and environmental and dietary factors, and their impact on the pathogenesis of IBD. Furthermore, we highlight the importance of multi-omics technologies in dissecting the host-microbe interactions in IBD, potentially offering a framework for developing effective treatment strategies.

Aberrant mucosal immune responses to gut microbiota contribute to inflammatory bowel disease (IBD), yet the mechanisms linking immunoglobulin-coated bacteria to mucosal inflammation remain unclear. Microbial extracellular vesicles (EVs) have emerged as potential modulators of host–microbiota interactions, metabolism, and immunity. This study examined how Lactobacillus johnsonii-derived EVs influence gut microbiota, amino acid metabolism, mucosal T cell polarization—particularly the Th17/Treg balance—and immunoglobulin transport in experimental colitis. Flow cytometry of fecal samples from IBD patients revealed increased IgA-, IgG-, and IgM-coated bacteria. Colonic expression of PIGR and FcRn was also elevated. L. johnsonii was depleted in ulcerative colitis, whereas Proteobacteria and Escherichia_Shigella were enriched. EVs displayed high structural integrity, gastrointestinal stability, and enhanced accumulation in inflamed colon. In DSS-induced colitis mice, both L. johnsonii and EVs alleviated inflammation, improved histology, reduced pro-inflammatory cytokines, decreased Th17 cells, increased Treg cells, and restored the Th17/Treg balance. These interventions also reduced IgA-, IgG-, and IgM-coated bacteria, lowered fecal immunoglobulins without affecting systemic levels, and downregulated PIGR and FcRn. Multi-omics analyses showed that EVs reshaped gut microbiota, enriched taurine-associated taxa (Lactobacillales, Lactobacillaceae, Lactobacillus murinus), and elevated the immunoregulatory metabolite taurine, which was linked to sulfur metabolism and epithelial homeostasis. Taurine supplementation reproduced EV effects, including reduced inflammation, improved barrier integrity, Th17/Treg rebalancing, and suppression of PIGR and FcRn. L. johnsonii-derived EVs restore mucosal immune balance in colitis through a coordinated EV–taurine–Th17/Treg–PIGR/FcRn–IgA/IgG axis. By integrating microbiota remodeling, metabolic regulation, and immune modulation—and outperforming the parent bacterium in stability, colonic enrichment, and breadth of effect—these EVs represent promising next-generation biologics for IBD therapy.

Background Different experimental techniques were used to search for evidence of bacteria in HCC. LPS/TLR4/CCL2/CCR2/M-MDSCs hypothesis was proposed using TCGA and transcriptome sequencing data. Combined with cells, animal models and clinical samples confirmed that Gram's negative bacteria and endotoxins affect the immune microenvironment of HCC and promote the development of HCC through this mechanism. Methods (1) The presence of bacteria was verified in HCC by different experimental techniques. (2) LPSLow and LPSHigh groups were distinguished according to the strength of LPS staining. Kaplan-Meier was used to analyze the survival difference between the two groups, and 16S rDNA sequencing was used to analyze the difference in bacterial community. (3) Differences of CD33 and CD8 expression between LPSLow and LPSHigh groups were verified by WB and IF in 30 fresh HCC tissues. FCM was used to verify the difference of MDSCs between LPSLow and LPSHigh. (5) Results (1) LPS were found in 93 HCC pathological sections (IDDF2024-ABS-0281 Figure 1) and were located in the cytoplasm of immune cells and non-immune cells. 16S rRNA signal was found in HCC (IDDF2024-ABS-0281 Figure 2). 40956 OTUs were obtained by 16S rDNA sequencing for HCC and paracancer. Culture omics found that 57% of the HCC samples were positive (IDDF2024-ABS-0281 Figure 3). (2) The prognosis of HCC patients in the LPSHigh group was poor. The EUB338 probe signal of the LPSHigh group was strong. Combined with TCGA data, TLR4 was positively correlated with CCL2, CCR2, and CD33 expression (IDDF2024-ABS-0281 Figure 4). IHC (IDDF2024-ABS-0281 Figure 5) and WB(Fig. 6) verified the relation of CD33 and CD8. The abundance of Proteobacteria in the LPSHigh group increased, while the abundance of Lactobacillus decreased. FCM showed that MDSCs in the LPSHigh group were higher (IDDF2024-ABS-0281 Figure 6). Conclusions Gram-negative bacteria and endotoxins in HCC affect the growth and prognosis of HCC through LPS/TLR4/CCL2/CCR2/M-MDSCs. The relative abundance of Proteobacteria in the LPSHigh group increased, and Lactobacillus decreased in human HCC. In the HCC model constructed by DEN combined with CCL4, neomycin treatment decreased the relative abundance of Proteobacteria and increased the relative abundance of Lactobacillus. Targeting this path becomes a new method for HCC.

Background Plant-derived exosome-like nanoparticles (PELNs) have been considered to have great prospects in the treatment of ulcerative colitis (UC) as they serve as a natural nano-drug carrier that can improve drug stability and cellular uptake. In this study, we isolated Houttuynia cordata-derived exosome-like nanoparticles (HELNs) from Houttuynia cordata and preliminarily explored the protective effect of HELNs on sodium dextran sulfate (DSS) induced colitis model. Methods HELNs were isolated from Houttuynia cordata using sucrose density gradient centrifugation.18 BALB/c mice were randomly divided into Ctrl (regular water), DSS (3.0% DSS water), and DSS+HELNs (DSS water + HELNs) groups. The mice were monitored daily for their body weights, stool consistency, and the presence of blood in the anus or stool. At the end of the experiment, their colon tissue was dissected. The colon lengths were measured, and the dissected tissues were collected for qPCR and pathology. Results After HELNs intervention, diarrhea, bloody stool and weight loss in colitis mice were alleviated (p<0.01). Disease activity index (DAI) score (p=0.0229) decreased, and colon length (p<0.01) improved. Compared with the DSS group, the pathological damage to the colon in the DSS+HELNs group was milder, which was mainly manifested by intact colonic mucosal structure and crypt structure, less inflammatory cell infiltration, and more goblet cells. Compared with the DSS group, the relative mRNA expression of pro-inflammatory cytokines (TNF-α and IL-6) was decreased (p<0.0001; p<0.0001), the relative expression level of anti-inflammatory cytokine IL-10 increased (p=0.0386), while the expression of tight junction protein of occlusion band protein-1 (ZO-1), occlusin-1 and mucin-2 (MUC2) increased (p=0.0341; p=0.0267). (IDDF2024-ABS-0118 Figure 1. Oral administration of HELNs protects mice from DSS-induced colitis, IDDF2024-ABS-0118 Figure 2. Transmission electron microscopy (TEM) images of HELNs and characterization of HELNs.; p<0.0001) Conclusions We first explored the use of HELNs in experimental colitis and found that HELNs play a therapeutic role by reducing the expression of inflammatory cytokines and promoting the restoration of intestinal barrier function.

Background Patients with inflammatory bowel disease (IBD), dysbiosis, and immunosuppression who receive fecal microbiota transplantation (FMT) from healthy donors are at an increased risk of developing bacteremia. This study investigates the efficacy of a mixture of seven short-chain fatty acid (SCFA)-producing bacterial strains (7-mix), the resulting culture supernatant mixture (mix-sup), and FMT for treating experimental ulcerative colitis (UC) and evaluates underlying mechanisms.Methods Utilizing culturomics, we isolated and cultured SCFA-producing bacteria from the stool of healthy donors. We used a mouse model of acute UC induced by dextran sulfate sodium (DSS) to assess the effects of 7-mix, mix-sup, and FMT on intestinal inflammation and barrier function, microbial abundance and diversity, and gut macrophage polarization by flow cytometry, immunohistochemistry, 16S rRNA gene sequencing, and transwell assays.Results The abundance of several SCFA-producing bacterial taxa decreased in patients with UC. Seven-mix and mix-sup suppressed the inflammatory response and enhanced intestinal mucosal barrier function in the mouse model of UC to an extent similar to or superior to that of FMT. Moreover, 7-mix and mix-sup increased the abundance of SCFA-producing bacteria and SCFA concentrations in colitic mice. The effects of these interventions on the inflammatory response and gut barrier function were mediated by JAK/STAT3/FOXO3 axis inactivation in macrophages by inducing M2 macrophage polarization in vivo and in vitro.Conclusions Our approach provides new opportunities to rationally harness live gut probiotic strains and metabolites to reduce intestinal inflammation, restore gut microbial composition, and expedite the development of safe and effective treatments for IBD.