Crohn's disease (CD) and ulcerative colitis (UC) are chronic relapsing inflammatory bowel disorders (IBD), the pathogenesis of which is uncertain but includes genetic susceptibility factors, immune-mediated tissue injury and environmental influences, most of which appear to act via the gut microbiome. We hypothesized that host-microbe alterations could be used to prognostically stratify patients experiencing relapses up to four years after endoscopy. We therefore examined multiple omics data, including published and new datasets, generated from paired inflamed and non-inflamed mucosal biopsies from 142 patients with IBD (54 CD; 88 UC) and from 34 control (non-diseased) biopsies. The relapse-predictive potential of 16S rRNA gene and transcript amplicons (standing and active microbiota) were investigated along with host transcriptomics, epigenomics and genetics. While standard single-omics analysis could not distinguish between patients who relapsed and those that remained in remission within four years of colonoscopy, we did find an association between the number of flares and a patient's succinotype. Our multi-omics machine learning approach was also able to predict relapse when combining features from the microbiome and human host. Therefore multi-omics, rather than single omics, better predicts relapse within 4 years of colonoscopy, while a patient's succinotype is associated with a higher frequency of relapses.

The establishment and maintenance of immune homeostasis rely on a dynamic, bidirectional exchange of information between commensal microorganisms and the host immune system. At the center of this process are CD4+Foxp3+ regulatory T cells (Tregs), which have emerged as pivotal mediators to ensure immunological equilibrium. This review explores the sophisticated mechanisms by which the gut microbiota modulates the differentiation, expansion, and functional specialization of Tregs, orchestrating intestinal immune tolerance to support host-microbiota mutualism. We discuss the role of microbial-derived structural components and metabolites in shaping the immunoregulatory fitness of Tregs. Additionally, we explore the impact of gut microbial dysbiosis, where disrupted microbial-immune crosstalk compromises immune tolerance, contributing to the development of inflammatory and autoimmune disorders. Finally, we highlight the potential of microbiota-based strategies to recalibrate intestinal immunity and restore immune tolerance.

The most common extra-intestinal manifestation (EIM) of inflammatory bowel disease (IBD), IBD-associated arthritis (IAA), occurs in 25-40% of patients and can be debilitating. In IBD, mucosal and stool microbiota richness is decreased, and compositional changes can precede or accompany disease onset. Likewise, spondyloarthritides are associated with altered gut microbiota, with overlapping bacterial signatures observed in IBD, suggesting key shared microbial factors are involved in both conditions. Much has been learned about the role of the intestinal microbiome in IBD, but less is known regarding its role in IAA. To address this knowledge gap, we analyzed the mucosa-associated intestinal microbiota of participants enrolled in the LOCATION-IBD cohort. Microbiota composition was established using 16S rRNA gene amplicon sequencing of intestinal biopsy samples taken from participants with IBD, with or without arthropathy. Microbiota samples clustered predominantly by participant, and similar taxa were present across the colon. The mucosal intestinal microbiota of females with IAA displayed a lower relative abundance of R. intestinalis, while males with IAA had a higher relative abundance of Corynebacterium, even when controlling for IBD-type, whether samples were taken from a site of inflammation and intestinal location. These findings indicate the mucosa-associated intestinal microbiota is associated with IAA in a sex-specific manner.

Crohn's disease and ulcerative colitis in humans and experimental immune-mediated colitis in mice are likely due in part to overactive immune responses to resident intestinal bacteria, including certain strains of adherent-invasive Escherichia coli (E. coli) such as E. coli NC101. We have previously shown that specific E. coli NC101 stress responses are upregulated during experimental colitis and attenuate inflammation. However, the roles of broader stress response pathways in E. coli NC101 during experimental colitis are unknown. We hypothesize that the global stress response regulator in E. coli, oxyS, also reduces experimental colitis. We show that intestinal E. coli NC101 upregulate oxyS expression during colitis in monocolonized interleukin-10 deficient mice. Furthermore, we demonstrate that oxyS-sufficient E. coli NC101 have decreased motility and biofilm formation in vitro and attenuated intestinal translocation and colitogenic potential in vivo compared with oxyS-deficient E. coli. These data suggest that activation of a generalized E. coli stress response, oxyS, reduces experimental colitis and may be a potential therapeutic target.

Fecal calprotectin (FCP) has limited specificity as diagnostic biomarker of pediatric inflammatory bowel disease (IBD), leading to unnecessary invasive endoscopies. This study aimed to develop and validate a fecal microbiota and amino acid (AA)-based diagnostic model.

Fecal samples from a discovery cohort (de novo IBD and healthy controls [HC]) were used to develop the diagnostic model. This model was applied in a validation cohort (de novo IBD and controls with gastrointestinal symptoms [CGI]). Microbiota and AAs were analyzed using interspace profiling and liquid chromatography-mass spectrometry techniques, respectively. Machine learning techniques were used to build the diagnostic model.

In the discovery cohort (58 IBD, 59 hC), two microbial species (Escherichia coli and Alistipes finegoldii) and four AAs (leucine, ornithine, taurine, and alpha-aminoadipic acid [AAD]) combined allowed for discrimination between both subgroups (AUC 0.94, 95% CI [0.89, 0.98]). In the validation cohort (43 IBD, 38 CGI), this panel of six markers could differentiate patients with IBD from CGI with an AUC of 0.84, 95% CI [0.67, 0.95]). Leucine showed the best diagnostic performance (AUC 0.89, 95% CI [0.81, 0.95]).

Leucine might serve as adjuvant noninvasive biomarker in the diagnostic work-up of pediatric IBD. Future research should investigate whether the combination of leucine with FCP could improve specificity and may help tailor the course of diagnostics.

Numerous studies have accelerated the knowledge expansion on the role of gut microbiota in inflammatory bowel disease (IBD). However, the precise mechanisms behind host-microbe cross-talk remain largely undefined, due to the complexity of the human intestinal ecosystem and multiple external factors. In this review, we introduce the interactome concept to systematically summarize how intestinal dysbiosis is involved in IBD pathogenesis in terms of microbial composition, functionality, genomic structure, transcriptional activity, and downstream proteins and metabolites. Meanwhile, this review also aims to present an updated overview of the relevant mechanisms, high-throughput multi-omics methodologies, different types of multi-omics cohort resources, and computational methods used to understand host-microbiota interactions in the context of IBD. Finally, we discuss the challenges pertaining to the integration of multi-omics data in order to reveal host-microbiota cross-talk and offer insights into relevant future research directions.

The gut microbiota produces short-chain fatty acids (SCFA) and acidifies the proximal colon which inhibits enteric pathogens. However, for many microbiota constituents, how they themselves resist these stresses is unknown. The anaerobic Lachnospiraceae family, which includes the acetogenic genus Blautia, produce SCFA, are genomically diverse, and vary in their capacity to acidify culture media. Here, we investigated how Lachnospiraceae tolerate pH stress and found that subunits of urease were associated with acidification in a random forest model. Urease cleaves urea into ammonia and carbon dioxide, however the role of urease in the physiology of Lachnospiraceae is unknown. We demonstrate that urease-encoding Blautia show urea-dependent changes in SCFA production, acidification, growth, and, strikingly, urease encoding Blautia directly incorporate the carbon from urea into SCFAs. In contrast, ureolytic Klebsiella pneumoniae or Proteus mirabilis do not show the same urea-dependency or carbon salvage. In agreement, the combination of urease and acetogenesis functions is rare in gut taxa. We find that Lachnospiraceae urease and acetogenesis genes can be co-expressed in healthy individuals and colonization of mice with a ureolytic Blautia reduces urea availability in colon contents demonstrating Blautia urease activity in vivo. In human and mouse microbial communities, the acetogenic recycling of urea carbon into acetate by Blautia leads to the incorporation of urea carbon into butyrate indicating carbon salvage into broader metabolite pools. Altogether, this shows that urea plays a central role in the physiology of health-associated Lachnospiraceae which use urea in a distinct manner that is different from that of ureolytic pathogens.

IgA-coated fractions of the intestinal microbiota of Crohn's disease (CD) patients have been shown to contain taxa that hallmark the compositional dysbiosis in CD microbiomes. However, the correlation between other cellular properties of intestinal bacteria and disease has not been explored further, especially for features that are not directly driven by the host immune-system, e.g. the expression of surface sugars by bacteria. By sorting and sequencing IgA-coated and lectin-stained fractions from CD patients microbiota and healthy controls, we found that lectin-stained bacteria were distinct from IgA-coated bacteria, but still displayed specific differences between CD and healthy controls. To exploit the discriminatory potential of both, immunoglobulin coated bacteria and the altered surface sugar expression of bacteria in CD, we developed a multiplexed single cell-based analysis approach for intestinal microbiota. By multi-parameter microbiota flow cytometry (mMFC) we characterized the intestinal microbiota of 55 CD patients and 44 healthy controls for 11-parameters in total, comprising host-immunoglobulin coating and the presence of distinct surface sugar moieties. The data were analyzed by machine-learning to assess disease-specific marker patterns in the microbiota phenotype. mMFC captured detailed characteristics of CD microbiota and identified patterns to classify CD patients. In addition, we identified phenotypic signatures in the CD microbiota which not only reflected remission after 6 weeks of anti-TNF treatment, but were also able to predict remission before the start of an adalimumab treatment course in a pilot study. We here present the proof-of-concept demonstrating that multi-parameter single-cell bacterial phenotyping by mMFC could be a novel tool with high translational potential to expand current microbiome investigations by phenotyping of bacteria to identify disease- and therapy-associated cellular alterations and to reveal novel target properties of bacteria for functional assays and therapeutic approaches.

Polyamines are important gut microbial metabolites known to affect host physiology, yet the mechanisms behind their microbial production remain incompletely understood. In this study, we developed a stable isotope-resolved metabolomic (SIRM) approach to track polyamine biosynthesis in the gut microbiome. Viable microbial cells were extracted from fresh human and mouse feces and incubated anaerobically with [U-13C]-labeled inulin (tracer). Liquid chromatography-high resolution mass spectrometry analysis revealed distinct 13C enrichment profiles for spermidine (SPD) and putrescine (PUT), indicating that the arginine-agmatine-SPD pathway contributes to SPD biosynthesis in addition to the well-known spermidine synthase pathway (PUT aminopropylation). Species differences were observed in the 13C enrichments of polyamines and related metabolites between the human and mouse microbiome. By analyzing the fecal metabolomics and metatranscriptomic data from an inflammatory bowel disease (IBD) cohort, we found significantly higher polyamine levels in IBD patients compared to healthy controls. Further investigations using single-strain SIRM and in silico analyses identified Bacteroides spp. as key contributors to polyamine biosynthesis, harboring essential genes for this process and potentially driving the upregulation of polyamines in IBD. Taken together, this study expands our understanding of polyamine biosynthesis in the gut microbiome and will facilitate the development of precision therapies to target polyamine-associated diseases.

Tryptophan-derived indoles produced by the gut microbiota, particularly indole-3-propionate (IPA), are key compounds associated with gastrointestinal balance and overall health. Reduced levels of IPA have been associated with inflammatory bowel disease, type 2 diabetes, and colorectal cancer. Since fiber-rich diets have been shown to promote IPA, we aimed to decipher fiber-specific effects and identify associated IPA-producing taxa in a range of healthy individuals. We cultured fecal microbiota from 16 adults with tryptophan and eight different dietary fibers and monitored community shifts by 16S rRNA gene amplicon sequencing and tryptophan-derived indoles using targeted liquid chromatography with diode array detection. The concentrations and types of indoles produced were donor-specific, with pectin strongly promoting IPA production in certain donors. IPA production was not associated with any known IPA producer but with the pectin-utilizing species Lachnospira eligens, which produced indole-3-lactate (ILA) in vitro, the IPA precursor. Supplementation of ILA in additional fecal microbiota cultures (n = 6) revealed its effective use as a substrate for IPA production. We identified a novel IPA producer, Enterocloster aldenensis, which produced IPA exclusively from ILA but not from tryptophan. Co-culture of L. eligens and E. aldenensis resulted in IPA production, providing new evidence for an ILA cross-feeding mechanism that may contribute to the IPA-promoting effects observed with pectin. Overall, we highlight the potential for targeted dietary interventions to promote beneficial gut taxa and metabolites.

The gut-brain axis (GBA) denotes the dynamic and bidirectional communication system that connects the gastrointestinal tract and the central nervous system (CNS). This review explored this axis, focusing on the role of microbial diversity and fitness in maintaining gastrointestinal health and preventing neurodegeneration, particularly in Alzheimer's disease (AD). Gut dysbiosis, characterized by the imbalance in populations of beneficial and harmful bacteria, has been associated with increased systemic inflammation, neuroinflammation, and the progression of AD through pathogenic mechanisms involving amyloid deposition, tauopathy, and increased blood-brain barrier (BBB) permeability. Emerging evidence highlighted the therapeutic potential of probiotics, dietary interventions, and intermittent fasting in restoring microbial balance, reducing inflammation, and minimizing neurodegenerative risks. Probiotics and synbiotics are promising in helping improve cognitive function and metabolic health, while dietary patterns like the Mediterranean diet were linked to decreased neuroinflammation and enhanced gut-brain communication. Despite significant advancement, further research is needed to elucidate the specific microbial strains, metabolites, and mechanisms influencing brain health. Future studies employing longitudinal designs and advanced omics technologies are essential to developing targeted microbiome-based therapies for managing AD-related disorders.

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.

As biodegradable food contact materials (FCMs), polylactic acid (PLA) and poly(butylene adipate-co-terephthalate) (PBAT) may release oligomers into food and raise potential health concerns. This study investigated the migration characteristics and digestive behaviors of oligomers by combining migration experiments, an in vitro digestion model, and high-resolution mass spectrometry. Moreover, the effects of the migrants from both materials on gut microbiota were evaluated following in vitro colonic fermentation for 48 h. The results indicated that 51 PLA oligomers and 45 PBAT oligomers were released into food simulants, with the migration increasing with ethanol concentration. Cyclic oligomers exhibited higher migration than linear oligomers. During digestion, PLA oligomers were almost completely degraded, whereas PBAT oligomers increased, additionally, cyclic oligomers were more susceptible to degradation. Migrants from both materials exhibited cytotoxicity effect on Caco-2 cells, disrupted the gut microbiota homeostasis, affecting multiple metabolic pathways. Especially, the migrants from PBAT inhibited the production of acetic, butyric, and isobutyric acids, while reducing the degradation of propionic acid. Overall, PBAT may pose a greater hazard than PLA. In conclusion, based on a new perspective of "lifecycle", this systematic study will contribute to a deeper understanding of the safety of PLA and PBAT when utilized as FCMs.

As an ecological disturbance, salinity changes substantially impact aquatic organism health. Gut microbiota plays a pivotal role in host health and exhibits heightened sensitivity to environmental salinity stress; however, the potential correlative mechanisms between gut microbiota dysbiosis triggered by salinity changes and host health remain unclear. The present study conducted a 4-week stress experiment to investigate the precise impact of gut microbiota on the inflammatory response in Scatophagus argus under different salinities (0 ‰ [hyposaline group, HO], 25 ‰ [control group, CT], and 40 ‰ [hypersaline group, HE]). Our results revealed that both HO and HE stress significantly changed the relative abundances of Gram-negative bacteria and the impairment of intestinal barrier function. Subsequently, the levels of lipopolysaccharide (LPS) in the serum exhibited a significant increase, and the expression levels of genes (tlrs, myd88, irak1, irak4, and traf6) involving TLRs/MyD88/NF-κB signaling pathway and pro-inflammatory cytokines (il-6, il-8, il-1β, and tnf-α) in the representative immune organs were significantly upregulated. Conversely, the abundance of the anti-inflammatory gene (tgf-β1) and its protein contents in serum were decreased. Transplantation of the gut microbiota from S. argus exposed to varying salinities into germ-free Oryzias latipes resulted in an enhanced inflammatory response. Our results suggested that both HO and HE stress increased the presence of Gram-negative bacteria and disrupted the intestinal barrier, leading to elevated serum LPS and subsequent systemic inflammation in fish. These findings provide innovative insights into the influence of salinity manipulation strategies on the health of aquatic organisms, contributing to the mariculture management in coastal areas.

Oral administration is a convenient way to deliver bioactive nutrients. However, the complex and dynamic environment of the gastrointestinal (GI) tract poses distinct challenges. These include the acidic environment of the stomach, limited transport across the GI mucosa, and the risk of enzymatic degradation, all of which can compromise the nutritional effectiveness of orally delivered nutrients. In response to these challenges, various GI tract delivery systems have been developed to target specific regions, such as the stomach, small intestine, or colon, to precisely control the release of bioactive nutrients and enhance their health-promoting benefits. This review critically examines the principles underlying stomach-, small intestine-, and colon-targeted delivery systems, highlighting the selection of appropriate wall materials and the interactions between delivery systems and the mucosal epithelial barrier. Moreover, we describe relevant biological models and quantitative analyses to measure these interactions. In particular, we emphasize the significant advantages offered by colon-targeted delivery systems in maintaining a healthy colonic microenvironment. This review aims to inspire novel concepts and stimulate further research into GI tract delivery systems, offering promising avenues for maximizing the therapeutic effects of bioactive nutrients in practical applications.

The composition of the intestinal microbiota influences the outcomes of patients receiving cancer treatment, although the best way to use this knowledge to improve cancer care remains unclear. In this Review, I synthesize the current understanding of host-microbiota dynamics in patients with cancer, and propose the integration of microbiota management guided by ecological principles in cancer care. Ecological management of the microbiota emphasizes the preservation of microbial populations - and the benefits they provide to the host - from the disruption caused by treatments such as chemotherapy and prophylactic antibiotics. The microbiota can be routinely and longitudinally monitored in patients using proven non-invasive methods, such as 16S ribosomal RNA amplicon sequencing. Longitudinal microbiome data can be processed with innovative computational tools based on principles of mathematical ecology to predict the risk of microbiota-related complications, guide treatment choices that minimize disturbance to the microbiota and restore microbial populations damaged by cancer treatment. Routine microbiome monitoring could also generate extensive datasets for human-based research, which could inform new microbiota-targeted interventions that improve responses to cancer treatments, including immune-checkpoint inhibitors. Applying ecological approaches to manage microbiota could enhance cancer care and improve patient outcomes.

Chronic granulomatous disease (CGD) is an inborn error of immunity that is caused by defects in any 1 of the 5 subunits (gp91phox, p47phox, p22phox, p67phox, p40phox) that form the NAD phosphate oxidase complex 2 (NOX2) or in the chaperone protein essential for reactive oxygen species (ROS) that supports its assembly. These defects lead to severely reduced phagocyte-derived ROS production. Almost 50% of patients with CGD have inflammatory bowel disease (IBD) associated with dysbiosis, and the age of IBD onset may vary according to the CGD genotype. Although we previously demonstrated that the intestinal microbiota determines colitis susceptibility in CGD mice, the underlying mechanisms remain unknown. We hypothesized that NOX2 defects are associated with distinct intestinal microbiome signatures and immune responses, which impact colitis severity. Chemical colitis susceptibility was evaluated in 2 strains of CGD mice (gp91phox-/- and p47phox-/-) with distinct microbiotas from 2 different animal facilities, while also evaluating the impact of microbiota standardization and colitogenic microbiota transfer on mucosal immune responses at the intestinal barrier. Although p47phox-/- and gp91phox-/- mice that harbored a colitogenic microbiota had increased colitis severity, the intestinal epithelial cells from p47phox-/- mice produced more ROS, which was associated with increased NOX isoform gene expression. In contrast, gp91phox-/- mice had decreased mucin production and a mucosal immune response profile suggestive of increased inflammasome activation at the intestinal barrier when compared with control and p47phox-/- mice. Our findings suggest that the microbiota impacts colitis susceptibility in a CGD genotype-specific manner, thereby potentially explaining differences in the timing of IBD onset in patients with different CGD genotypes and identifying potential novel and personalized therapeutic targets.

The gut microbiota of mammals possess distinctive metabolic pathways with untapped therapeutic potential. Using molecular insights into dietary fiber metabolism by the human gut microbiota, we designed a targeted drug delivery system, called GlycoCaging, that is based on bespoke glycoconjugates of a complex plant oligosaccharide. GlycoCaging of exemplar anti-inflammatory drugs enabled release of active molecules triggered by specific glycosidases of autochthonous gut bacteria. GlycoCaging ensured that drug efficacy was potentiated, and off-target effects were eliminated in murine models of inflammatory bowel disease. Biochemical and metagenomic analyses of gut microbiota of individual humans confirmed the broad applicability of this strategy.

Studies investigating microbial temporal dynamics are increasingly common, leveraging longitudinal designs that collect microbial abundance data across multiple time points from the same subjects. Traditional exploratory approaches like principal component analysis fail to fully utilize this structure. By organizing data as a three-way array-subjects as rows, microbial abundances as columns, and time points as the third dimension-multi-way methods such as parallel factor analysis (PARAFAC) can better capture temporal and structural patterns. This study demonstrates PARAFAC as a method to explore longitudinal microbiome data using three exemplary studies. In the first example, a long-time series of in vitro microbiomes, PARAFAC identifies primary time-resolved variations. The second example, a longitudinal infant gut microbiome study, shows that PARAFAC can distinguish subject groups and enhance comparative analysis, even with moderate missing data. In the third example, a gingivitis intervention study of the oral microbiome, PARAFAC enables the identification of microbial subcommunities of interest through post-hoc clustering. These examples highlight PARAFAC's broad applicability for analyzing longitudinal microbiome data across diverse environments. The approach is implemented in the R package parafac4microbiome, available on the Comprehensive R Archive Network (CRAN), providing researchers with accessible tools for similar analyses.IMPORTANCEUnderstanding how microbiomes change over time can give us valuable insights into their role in health and disease. Many traditional methods like principal component analysis miss important patterns in data collected over time, but parallel factor analysis (PARAFAC) helps uncover these trends in a much clearer way. Using this approach, we were able to identify key changes in microbiomes across different settings, like lab experiments, the infant gut, and the mouth. PARAFAC also works well even when some data is missing, which is a common issue. To make this tool accessible, we have included it in a user-friendly R package, enabling other researchers to analyze microbiome dynamics in their own studies and explore how these changes might influence health and treatments.

The gut microbiome plays a key role in the development of inflammatory bowel disease (IBD), as imbalances in microbial composition are associated with immune dysfunction. However, the specific mechanisms by which certain microorganisms contribute to this process remain unclear.

Here, we employed a multi-omics approach on fecal samples to identify novel microbiome markers and elucidate mechanisms underlying IBD. Shotgun metagenomics was applied to 212 samples (850 in total with validation cohort), shotgun metatranscriptomics to 103 samples and metabolomics to 105 samples. Machine learning techniques were used to predict disease and the three omics data were integrated to propose a mechanistic role of the microbiota.

Metagenomic analysis identified Crohn's disease (CD)-specific microbiome signatures, including a panel of 20 species that achieved a high diagnostic performance, with an area under the ROC curve (AUC) of 0.94 in an external validation set. Metatranscriptomic analysis revealed significant alterations in microbial fermentation pathways in CD, but not in ulcerative colitis (UC), highlighting disruptions that explain the depletion of butyrate-a key anti-inflammatory metabolite-observed in metabolomics analysis. Integrative multi-omics analyses further identified active virulence factor genes in CD, predominantly originating from the adherent-invasive Escherichia coli (AIEC). Notably, these findings unveiled novel mechanisms, including E. coli-mediated aspartate depletion and the utilization of propionate, which drives the expression of the ompA virulence gene, critical for bacterial adherence and invasion of the host's macrophages. Interestingly, these microbiome alterations were absent in UC, underscoring distinct mechanisms of disease development between the two IBD subtypes.

In conclusion, our study not only identifies promising novel biomarkers with strong diagnostic potential, which could be valuable in challenging clinical scenarios, but also offers an integrated multi-omics perspective on the microbial mechanisms underlying inflammation and virulence in Crohn's disease.

The complement system is a highly conserved and essential immune component with pivotal roles in innate and adaptive immunity. It is increasingly recognized that the complement system has a profound impact on disease. Current complement-targeting therapeutics for clinical use almost exclusively target the complement system in circulation. However, recent discoveries have demonstrated that complement is not only liver derived and plasma operative, but also synthesized and activated inside many cells locally within tissues, performing noncanonical, cell-autonomous intracellular functions, collectively referred to as the complosome. These intracellular complement pathways are distinct from the classical plasma-based system and critical for regulating fundamental cellular processes, including metabolism, gene transcription, autophagy, and the activation and resolution of inflammation. This Review explores the emerging roles of the complosome and current knowledge regarding its relation to human diseases, highlighting evidence across organ systems and disease states, including the kidneys, digestive tract, lungs, heart, CNS, musculoskeletal system, skin, and cancer. We also review current scientific approaches for detecting and functionally investigating the complosome, addressing challenges such as technological limitations and the need for advanced experimental models to delineate its tissue-specific roles. Finally, we discuss central unanswered questions critical for developing innovative therapeutic strategies targeting intracellular complement pathways. These strategies hold potential to modulate disease-specific mechanisms while preserving systemic complement activity.

Despite the availability of numerous new immune-directed therapeutics, the major constituents of inflammatory bowel disease (IBD)-ulcerative colitis (UC) and Crohn's disease (CD)-continue to afflict millions worldwide, resulting in significant morbidity and long-term health risks. IBD results from a triad of immune, environmental (eg, gut microbiome), and genetic (including epigenetic) mechanisms, and therefore has been subject to a wide variety of therapeutic strategies. Among these, the administration of probiotics, particularly Gram-positive lactic acid bacteria (LAB), targeting both immune and environmental factors, has shown promising potential for efficacy in selected populations in early clinical trials. However, knowledge gaps and inconsistent efficacy currently prevent recommendations for the use of probiotics in larger IBD patient populations. The inconsistent efficacy of probiotics is likely due to variable cell viability and potency after administration, further exacerbated by IBD patient heterogeneity. Thus, an alternative to live probiotics for IBD has emerged in the form of bacterial extracellular vesicles (BEVs)-cell-secreted nanovesicles containing abundant bioactive cargo that, like live probiotics, can regulate immune and environmental factors but with fewer viability limitations and safety concerns. In this review, we summarize the work done to date establishing the potential of BEVs to provide the therapeutic benefits in IBD and discuss the hurdles BEVs must overcome to achieve clinical translation. We also consider future directions for BEV therapeutics, especially treatment potential for necrotizing enterocolitis (NEC), which shares similarities in pathophysiology with IBD.

Inflammatory bowel disease (IBD) is characterized by recurring gastrointestinal inflammation, accompanied by a significant rise in global prevalence and disease severity. The overaccumulation of reactive oxygen and nitrogen species (RONS) in the intestinal environment disrupts redox homeostasis and drives pathological overgrowth of Escherichia coli, which are central to IBD pathogenesis. Herein, we designed a multifunctional nanozyme (W-PB) to enable sustained and targeted regulation of intestinal homeostasis through dual mechanisms: specific inhibition of E. coli overgrowth during colitis and efficient RONS clearance. To ensure colon-specific delivery, W-PB was encapsulated in an electrostatically crosslinked hydrogel composed of alginate and chitosan. This formulation protects W-PB from degradation in harsh gastrointestinal conditions and releases the nanoparticles selectively under weakly alkaline intestinal pH. The released tungsten ions suppress E. coli growth via competitive displacement of molybdenum in the molybdopterin cofactor, while W-PB simultaneously neutralizes excess RONS to shield intestinal cells from oxidative damage. In DSS-induced colitis models, the W-PB gel demonstrated significant therapeutic efficacy, achieved through intestinal microbiota remodeling and oxidative stress mitigation.

Ulcerative colitis (UC) is a chronic inflammatory bowel disease (IBD) characterized primarily by immune dysregulation. Its pathogenesis involves multiple factors, including dysregulation of T-cell subsets, hypersecretion of pro-inflammatory cytokines, imbalance in the gut microbiota, and disruption of the intestinal barrier. Among T-cell subsets, abnormal activation of Th1 and Th17 cells, in conjunction with Treg dysfunction, significantly amplifies local pro-inflammatory signals. Pro-inflammatory cytokines, such as TNF-α, IL-6, and IL-17, exacerbate apoptosis and disrupt tight junctions (TJs) in intestinal epithelial cells (IECs), thereby creating favorable conditions for invasion by pathogenic bacteria and their metabolites. Intestinal microecological imbalance not only leads to significant alterations in the structure of the bacterial flora but also involves abnormal fluctuations in its metabolites that directly regulate intestinal immune homeostasis, a factor closely associated with the severity of inflammation and prognosis of ulcerative colitis. Recent studies have demonstrated that in the treatment of UC, traditional Chinese medicine (TCM) achieves a multi-target, multi-pathway integrated intervention by regulating immune cell differentiation, balancing inflammatory factor levels, repairing the intestinal epithelial barrier, and remodeling the structure of the bacterial flora. This article reviews the pathogenic mechanisms underlying immune dysregulation in UC and the advances in research on TCM's role in immune regulation, anti-inflammatory repair, and flora modulation, encompassing the mechanisms of action of individual active ingredients and classic TCM compound formulas. Although some studies have preliminarily confirmed TCM's potential to modulate immunity and repair the intestinal barrier, breakthroughs in mechanism analysis, herb standardization, and large-scale validation remain forthcoming. It is anticipated that the unique advantages of TCM will be translated into a more precise therapeutic strategy for UC through modern molecular and systems biology approaches.

Intestinal microbiota possess a plethora of biotransformation capabilities, which can modify medications, including their Phase I or II metabolites in a process termed "Phase IV" metabolism. Phase IV metabolism is emerging as a significant contributor to interindividual variability in drug responses. Here we present examples of gastrointestinal-relevant medications that are known to be subject to bacterial Phase IV metabolism and propose avenues to improve precision medicine by modulating these bacterial functions.

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.

This review and commentary outline the strong rationale for normalizing the abnormal microbiota of patients with ulcerative colitis, Crohn's disease, and pouchitis and focus on strategies to improve current variable outcomes of fecal microbial transplant (FMT) in ulcerative colitis. Applying lessons from successful FMT therapy of recurrent Clostridioides difficile and insights from basic scientific understanding of host/microbial interactions provide strategies to enhance clinical outcomes in IBD. We outline promising approaches to develop novel-defined consortia of live biotherapeutic products and combination treatments to improve current results and to optimize and personalize treatment approaches in individual patients and disease subsets.

Metabolites generated from the intestinal microbiota regulate local and distant tissues. One important metabolite generated from l-tryptophan is indole-3-propionic acid (IPA), which has been shown previously to regulate intestinal mucosal homeostasis in specific pathogen-free (SPF)-colonized animals through distinct receptor-mediated events. Interestingly, IPA levels are reduced in patients with inflammatory bowel disease (IBD). In the current study, we assessed whether IPA could improve colitis outcomes in the absence of its production by the microbiota. To do this, colitis was induced by dextran sulfate sodium (DSS) in gnotobiotic mice colonized with the 12-member stable defined moderately diverse microbiota mouse 2 (sDMDMm2) microbial consortium, which lacks the genes required for IPA generation. We found that these mice were exquisitely sensitive to DSS compared with SPF-colonized mice. However, IPA treatment significantly increased survival. Infiltrating immune cells in the colon were not altered by IPA treatment nor were there any remarkable changes in local and systemic inflammatory mediator levels. Nevertheless, IPA treatment changed the composition of the fecal microbiota and enhanced intestinal barrier function, demonstrated by a reduction in FITC-dextran flux and retainment of a bioluminescent Escherichia coli within the lumen of colitic mice. Together, our data suggest that IPA treatment in the context of its systemic depletion enhances barrier function and enhances survival in the presence of established inflammation. These data support continued assessment of IPA as a potential treatment for IBD.NEW & NOTEWORTHY Indole-3-propionic acid (IPA) is a metabolite produced by the intestinal microbiota that has been shown to elicit beneficial effects in the gastrointestinal (GI) tract that include regulating intestinal barrier function, reducing inflammation, and controlling immune responses that lead to fibrosis. In patients with inflammatory bowel disease (IBD), IPA levels are reduced. In the current study, we found that treating mice with IPA at the peak of intestinal inflammation improved clinical outcomes and disease.

Food hydrogels targeting respiration of microorganisms via changing the micro-ecological environment in gut were prepared through the self-assembly of polyphenols extracted from tea leaves harvested in summer and autumn and the protein fibrils originating from egg white lysozyme. Oral administration with the hydrogels effectively inhibited the over-expansion of the facultative anaerobic bacterium indicated by E. coli Nissle 1917 (EcN) and alleviated the clinic symptoms of chronic intestinal inflammation in mice. Importantly, the hypoxia of epithelial cells was elevated significantly and the overexpression of the inducible NO synthase (INOs)-related NOS2 gene was inhibited substantially in colons of the colitis mice, which accounted for prevention of the abnormal expansion of E. coli via blocking respiration. The treatment with the hydrogels preserved normal mitochondrial function in colonic epithelial cells under oxidative stress, which could serve as the mechanism to maintain the capability to consume oxygen.

Ulcerative colitis (UC) is defined as a chronic intestinal inflammation with an unknown cause. During its occurrence and development, oxidative stress and intestinal microbiota dysbiosis play important roles. Nevertheless, the treatment of UC continues to pose significant challenges due to the intricate nature of physiological barriers and the suboptimal targeting efficacy of traditional therapeutic strategies. To solve the dilemma facing UC treatment, in this study, we developed a metal-phenolic nanozyme, designated as DHM-Zn, which exhibits anti-inflammatory and antioxidant properties via metal coordination between dihydromyricetin (DHM) and Zn2+. Furthermore, we engineered yeast microcapsules (YM) encapsulating the metal-phenolic nanozymes (DZ@YM), leveraging the inherent biosafety and tolerability advantages offered by natural microorganisms. Following oral administration, the intestinal retention characteristics of YM facilitated the efficient aggregation of DHM-Zn nanozymes at the inflammation site, thereby extending their therapeutic efficacy. In addition to augmenting anti-inflammatory and antioxidant effects, DZ@YM contributed to the restoration of intestinal microbial balance by increasing the abundance of beneficial bacteria such as Parabacteroides and Muribaculaceae, while regulating potentially harmful bacteria like Clostridium-sensu-stricto and Escherichia-Shigella, thereby achieving a synergistic multi-pathway therapeutic approach. Collectively, with excellent biocompatibility, this novel therapeutic approach demonstrates extensive potential for clinical application in the treatment of UC and offers new directions and insights for UC therapy.

The human gut microbiome is intricately linked to systemic and organ-specific immune responses and is highly responsive to dietary modulation. As metagenomic techniques enable in-depth study of an ever-growing number of gut microbial species, it has become increasingly feasible to decipher the specific functions of the gut microbiome and how they may be modulated by diet. Diet exerts both supportive and selective pressures on the gut microbiome by regulating a multitude of factors, including energy density, macronutrient and micronutrient content, and circadian rhythm. The microbiome, in turn, contributes to local and systemic immune responses by providing colonization resistance against pathogens, shaping immune cell activity and differentiation, and facilitating the production of bioactive metabolites. Emerging research has strengthened the connections between the gut microbiome and cardiometabolic disorders (e.g., cardiovascular disease, obesity, type-2 diabetes), autoimmune conditions (e.g., type-1 diabetes, rheumatoid arthritis, celiac disease), respiratory disease, chronic kidney and liver disease, inflammatory bowel disease, and neurological disorders (e.g., Alzheimer's, Parkinson's disease, depressive disorders). Here, we outline ways in which dietary factors impact host response in diseases through alterations of gut microbiome functionality and composition. Consideration of diet-mediated microbial effects within the context of the diseases discussed highlights the potential of microbiome-targeted treatment strategies as alternative or adjunct therapies to improve patient outcomes.