Targeted delivery of the probiotic Saccharomyces boulardii to the extracellular matrix enhances gut residence time and recovery in murine colitis

Advanced microbiome therapeutics for oral delivery of peptides and proteins: Advances, challenges, and opportunities

Peptide and protein medicines have changed the therapeutic landscape for many diseases, yet oral delivery remains a significant challenge due to enzymatic degradation, instability, and poor permeability in the gastrointestinal tract. Advanced Microbiome Therapeutics (AMTs) could overcome some of these barriers by producing and releasing therapeutic peptides directly in the gastrointestinal tract. AMTs can localize peptide production at the site of absorption, providing either sustained or controlled release while potentially reducing side effects associated with systemic administration. Here, this review assesses the status of AMTs for oral peptide delivery and discusses the potential integration of permeation enhancers, mucoadhesive systems, and receptor-mediated transport strategies to improve oral bioavailability further. Combining these approaches could pave the way for more widespread oral delivery strategies for peptide and protein medicines.

Inflammation-targeted delivery of probiotics for alleviation of colitis and associated cognitive disorders through improved vitality and colonization

Oral probiotic biotherapies hold significant promise for addressing intestinal inflammatory disorders. Nonetheless, due to the challenging pathological microenvironment of the gastrointestinal tract, it is difficult to achieve deliver probiotics in an inflammation-targeted manner while improving their intestinal colonization and minimizing the impact of gastrointestinal environment on their vitality. To address this, an innovative probiotics oral delivery system (EcN-Apt@HG) against ulcerative colitis (UC) was developed by conjugating IL-6 aptamer to the surface of EcN and subsequently encapsulating the probiotics in a hydrogel consisting of aldehyde-functionalized chondroitin sulfate (CS) and Poly(amidoamine) (PAMAM). As expected, the encapsulated EcN demonstrated resistance to gastrointestinal conditions, and the colonization duration of probiotics in the colon was enhanced via the preferential adhesion effect of IL-6 aptamer on the inflammatory site. The EcN-Apt@HG system restored the damaged mucosal layer, suppressed hyperactive immune responses, and reshaped the dysbiosis of intestinal microflora, thereby synergistically alleviating dextran sulfate sodium (DSS)-induced colitis. Notably, EcN-Apt@HG significantly alleviated depression-like behaviors and cognitive impairment in colitis mice through gut-brain axis interaction. This approach provides a simple and promising strategy for inflammation-targeted delivery of probiotics to the intestine and shows great potential for UC therapy and associated cognitive disorders.

Surface-functionalized bacteria: Frontier explorations in next-generation live biotherapeutics

Screening robust living bacteria to produce living biotherapeutic products (LBPs) represents a burgeoning research field in biomedical applications. Despite their natural abilities to colonize bio-interfaces and proliferate, harnessing bacteria for such applications is hindered by considerable challenges in unsatisfied functionalities and safety concerns. Leveraging the high degree of customization and adaptability on the surface of bacteria demonstrates significant potential to improve therapeutic outcomes and achieve tailored functionalities of LBPs. This review focuses on the recent laboratory strategies of bacterial surface functionalization, which aims to address these challenges and potentiate the therapeutic effects in biomedicine. Firstly, we introduce various functional materials that are used for bacterial surface functionalization involving organic, inorganic, and biological materials. Secondly, the methodologies for achieving bacterial surface functionalization are categorized into three primary approaches including covalent bonding, non-covalent interactions, and hybrid techniques, while various advantages and limitations of different modification strategies are compared from multiple perspectives. Subsequently, the current status of the applications of surface-functionalized bacteria in bioimaging and disease treatments, especially in the treatment of inflammatory bowel disease (IBD) and cancer is summarized. Finally, challenges and pressing issues in the development of surface-functionalized bacteria as LBPs are presented.

Enabling technologies for in situ biomanufacturing using probiotic yeast

Saccharomyces boulardii (Sb) is a Generally Regarded As Safe (GRAS) probiotic yeast currently used to alleviate symptoms from various gastrointestinal diseases. Sb is a promising platform for probiotic and biotherapeutic engineering as it is the only probiotic eukaryote and carries with it a unique set of advantages compared to bacterial strains, including resistance to phage, high protein secretion abilities, and intrinsic resistance to antibiotics. While engineered Sb has not been studied as extensively as its close relative Saccharomyces cerevisiae (Sc), many genetic engineering tools developed for Sc have also shown promise in Sb. In this review, we address recent research to develop tools for genetic engineering, colonization modulation, biomarker sensing, and drug production in Sb. Ongoing efforts, especially those that overcome gut-specific challenges to engineered performance, are highlighted as they advance this chassis as a scalable platform for treating gastrointestinal diseases.

Engineering advanced bacterial therapy for tumor and inflammatory diseases

Bacteria have emerged as a promising living medicine for diseases in recent years. With rapid advancements in synthetic biology and materials science, engineered bacterial therapy has encountered new opportunities. Leveraging inherent genetic reprogramming capabilities and surface chemistry modification advantages, engineered bacterial therapy enables selective functional recombination and precise spatiotemporal control, thereby enhancing therapeutic efficacy against diseases. This review summarizes the advantages of engineered bacterial therapy and various engineering strategies employed. Moreover, it outlines representative studies of engineered bacterial therapy in the treatment of tumors and inflammatory diseases, summarizing diverse engineered approaches that enhance the efficacy for these conditions, offering novel avenues for efficient disease management. In addition, current limitations and challenges in utilizing engineered bacterial therapy are discussed, providing insights for further innovation in biomedicine. Specifically, the potential and prospects of oral engineered bacteria in treating gastrointestinal tumors and inflammatory diseases have been explored.

Effects of Saccharomyces boulardii cell wall polysaccharide supplementation on growth performance, serum immunity, and fecal microorganisms in newborn calves

Background

Xinjiang is characterized by extremely cold weather and significant seasonal temperature variations, and these harsh climatic conditions have led to a high incidence of diarrhea and increased mortality rates among newborn calves, resulting in substantial economic losses for the local cattle industry. Saccharomyces boulardii cell wall polysaccharide (SBWP) is a natural prebiotic that has emerged as a promising alternative to conventional antibiotics for the mitigation of systemic inflammation, diarrhea, and mortality in livestock production. Therefore, this study aimed to investigate the effects of SBWP supplementation on growth performance, diarrhea frequency, serum immunity, and intestinal microbiota in newborn calves.

Methods

In this study, a one-way experimental design was employed. A total of 45 newborn calves (Simmental♂ × Yili brown cattle♀, male, average body weight (BW) 35.58 ± 5.79 kg) were randomly allocated into five experimental groups. Each group consisted of three pens, with three calves per pen, and this allocation was carried out based on the percentage of SBWP used as a feed supplement. The diet for the five groups were as follows: group I received milk + basal diet without additives, group II received milk + basal diet + 0.005% gentamicin, group III received milk + basal diet + 250 mg/day/calf SBWP, group IV received milk + basal diet + 500 mg/day/calf SBWP, and group V received milk + basal diet + 1,000 mg/day/calf SBWP. Daily feed consumption was recorded, and BW was measured on days 1, 14, and 28 to calculate average daily gain (ADG), average daily feed intake, and feed-to-gain (F/G) ratio. Fecal samples were collected on days 1, 7, 14, 21, and 28 for microbiological analysis, and fecal scores were subjectively monitored and recorded daily by the same individual. In addition, blood samples were collected from each calf at the end of the trial for immune analysis.

Results

In comparison to group I, group IV showed a significant increase in both BW and ADG. Specifically, on the 14th and 28th trial days, BW of group IV showed a significant increase of 3.95 and 4.90%, respectively (p < 0.05). Similarly, during the 1-28 trial day period, ADG of group IV showed a significant increase of 28.49% (p < 0.05), whereas their F/G ratio decreased significantly by 22.89% (p < 0.05). No statistically significant difference was observed in BW, ADG, dry matter intake, and F/G ratio (p > 0.05) between groups IV and II. In addition, the fecal score and the diarrhea rate in group IV were significantly reduced by 31.62 and 18.54%, respectively (p < 0.05). No statistically significant difference was observed between groups IV and II (p > 0.05). Moreover, in group IV, IgG and IL-10 levels were significantly increased by 51.97 and 45.45%, respectively (p < 0.05), while IL-1, IL-6, and TNF-α levels were significantly decreased by 30.47, 28.17, and 25.49%, respectively (p < 0.05). Furthermore, a decreasing trend in the number of Escherichia coli and Clostridium perfringens was observed in the fecal microbiota samples obtained from group IV, whereas an increasing trend was observed in the growth of Lactobacillus and Bifidobacterium. Supplementing newborn calves with 500 mg of SBWP per day significantly enhanced the β-diversity indices and demonstrated a trend toward increasing α-diversity in their fecal microbiota, in contrast to the detrimental effects caused by 0.005% gentamicin. Furthermore, 500 mg/day/calf SBWP significantly increased the relative abundance of Lactobacillus and decreased the relative abundance of Escherichia-Shigella. However, no significant difference was observed in the relative abundance of Escherichia-Shigella between the groups receiving 500 mg/day/calf SBWP and 0.005% gentamicin.

Conclusion

The findings of this study show that the supplementation of 500 mg/day/calf SBWP to newborn calves significantly improves their growth performance, serum immunity, and intestinal microbiota structure while significantly reducing diarrhea frequency and inflammation. These findings indicate that the supplementation of 500 mg/day/calf SBWP can most effectively enhance the growth performance and reduce the diarrhea frequency in newborn calves.

Mulberry-derived postbiotics alleviate LPS-induced intestinal inflammation and modulate gut microbiota dysbiosis

Mulberry-derived postbiotics (MDP) have demonstrated promising bioactive properties, including antioxidant and anti-inflammatory effects; however, their specific role in modulating gut inflammation and microbiota composition remains underexplored. Given the growing interest in functional food ingredients for gut health and managing inflammatory disorders, this study aims to evaluate the effects of MDP in alleviating intestinal inflammation and altering the gut microbiota in an LPS-induced mouse model of systemic inflammation. MDP administration significantly mitigated LPS-induced pathological changes in the intestine, liver, spleen, and kidneys, thereby improving systemic health and immune function. Histological analysis revealed reduced inflammation and tissue damage in the intestinal epithelium, supporting the potential of MDP to improve gut barrier integrity. An antioxidant assay revealed that MDP decreased the malonaldehyde (MDA) levels and increased the enzymatic activities of CAT, SOD, and GSH in response to LPS administration, indicating enhanced cellular antioxidant defenses. Inflammatory cytokine analysis showed that MDP downregulated proinflammatory markers such as TNF-α, IL-1β, IL-6, MYD88, Nrf2 COX-2, and HO1, while upregulating TLR4, resulting in potential anti-inflammatory effects by modulating the TLR4-NF-κb pathway. Moreover, MDP promoted beneficial alterations in gut microbiota composition by increasing the abundance of Firmicutes and Bacteroidetes, which are linked to gut health and inflammation regulation. The changes in gut microbiota composition suggest a potential mechanism by which MDP may help restore gut homeostasis and reduce systemic inflammation. These findings suggest that MDP may serve as promising functional food ingredients that support immune health, reduce inflammation, and promote gut microbiota balance, offering potential applications in fortified foods and nutraceuticals aimed at mitigating inflammatory and metabolic disorders.

Polyphyllin Ⅵ modulates macrophage polarization through autophagy-NLRP3 inflammasome to alleviate inflammatory bowel disease

BACKGROUND

Inflammatory bowel disease (IBD) is a chronic inflammatory condition of the gastrointestinal tract with a rising global prevalence. If left untreated, it can result in severe complications, including colon cancer. Key factors in IBD pathogenesis include macrophages, NOD-like receptor thermal protein domain associated protein 3 (NLRP3), and autophagy. Polyphyllin Ⅵ (PPⅥ), a metanoidal saponin derived from the traditional Chinese herb Chonglou, exhibits significant anti-inflammatory and anti-cancer properties, making it a compound of considerable therapeutic interest.

PURPOSE

The present study investigated the relevant mechanism of PPⅥ on protecting IBD from the perspective of NLRP3 as well as macrophage immunomodulation and laid a theoretical foundation for the development of novel IBD therapeutic drugs.

METHODS

The IBD mice were prepared by dextran sodium sulfate, and RAW 264.7 inflammatory cells were established through LPS and ATP stimulation. The indicators of macrophage polarization, NLRP3, and autophagy were detected using Western Blot, RT-qPCR, H&E staining, immunofluorescence, and flow cytometry.

RESULTS

PPⅥ can enhance the inflammatory state of LPS-induced RAW264.7 macrophages, which can reduce weight loss, decrease DAI score, increase colon length, reduce oxidative stress, and decrease intestinal epithelial barrier damage, and thus diminish inflammatory injury in DSS-induced IBD mice. PPⅥ can modify intestinal inflammation and injury by modulating macrophage function. The administration of PPⅥ can maintain the balance between M1-type macrophages and M2-type macrophages while regulating the intestinal macrophage polarization via the NLRP3 inflammasome and autophagy through wildtype mice, cells, and Nlrp3-/- mice.

CONCLUSION

PPⅥ can regulate macrophage polarization through autophagic modulation of NLRP3 inflammasome to promote the repair of intestinal epithelial damage and maintain the integrity of the mucosal barrier, which contributes to the attenuation of inflammatory injury in DSS-induced IBD mice and provides a database for the development of novel clinical drugs.

INNOVATIONS

1. This subject discovered the protective effect of PPⅥ on IBD mice. 2. This subject proved that macrophages have an important role in the intestinal protection of PPⅥ in IBD mice, and PPⅥ can inhibit the polarization of M1-type macrophages and promote the polarization of M2-type macrophages. 3. This subject demonstrated that PPⅥ could regulate macrophage polarization through NLRP3 inflammasome and ameliorate intestinal inflammation in vitro, in vivo, and in Nlrp3-/- mice. 4. This subject confirmed that PPⅥ could regulate macrophage polarization to alleviate inflammatory injury by inhibiting NLRP3 inflammasome through modulating autophagy in vitro, in vivo, and the application of inhibitors. 5. This study explored the developmental value of PPⅥ and laid the theoretical foundation for the development of novel therapeutic drugs as well as therapeutic strategies for IBD.

Multifunctional Double-Loaded Oral Nanoplatform for Computed Tomography Imaging-Guided and Integrated Treatment of Inflammatory Bowel Disease

Excessive reactive oxygen species, disruption of the epithelial barrier, immune dysregulation, and gut microbiota imbalance are key factors driving the onset of inflammatory bowel disease (IBD) and complicating its treatment. Prompt diagnosis of diseases and precise delivery of therapeutic agents to inflamed intestinal sites offer promising targeted strategies for effectively treating IBD. Here, a barium sulfate-based nanoplatform (BaSO4@PDA@CeO2/DSP, BPCD) for synergistic delivery of nanozymes and drugs was developed. With enhanced colonic retention after oral drug delivery, this nanoplatform enables precise and effective targeting of inflammatory sites and CT imaging guidance to address multiple factors contributing to IBD. A comprehensive therapeutic effect was achieved through the synergistic action of cerium oxide with the optimized Ce3+/Ce4+ ratio and sustained release of dexamethasone sodium phosphate. Benefiting from superior gastrointestinal stability, the nanoplatform is highly effective in treating IBD by alleviating oxidative stress, modulating macrophage polarization balance, gut flora composition, and repairing the epithelial barrier. BPCD inhibits the development of IBD through multiple mechanisms and has superior biocompatibility, emerging as a practical alternative to traditional IBD therapies.

Magnetically targeted delivery of probiotics for controlled residence and accumulation in the intestine

The effectiveness of orally delivered probiotics in treating gastrointestinal diseases is restricted by inadequate gut retention. In this study, we present a magnetically controlled strategy for probiotic delivery, which enables controlled accumulation and residence of probiotics in the intestine. The magnetically controlled probiotic is established by attaching amino-modified iron oxide (Fe3O4-NH3+ NPs) to polydopamine-coated Lacticaseibacillus rhamnosus GG (LGG@P) through electrostatic self-assembly and named as LGG@P@Fe3O4. In a simulated gastrointestinal environment, LGG@P@Fe3O4 maintains both structural stability and probiotic viability. Furthermore, the LGG@P@Fe3O4 clusters can be easily manipulated by an external magnetic field, inducing directional movement and aggregation. In vitro simulations demonstrated significant accumulation and retention of LGG@P@Fe3O4 under a magnetic field, with the optical density (OD) value of the suspension decreasing from ∼1.17 to ∼0.29. In contrast, the OD value of the suspension without a magnetic field remained at its original level (∼1.15). In a mouse model with intragastrically administered LGG@P@Fe3O4, the group exposed to a magnet exhibited stronger gut fluorescence after 24 h. The magnetically controlled probiotic delivery strategy offers an easy manufacturing and feasible method to enhance the effectiveness of probiotics in treating gastrointestinal diseases.

Engineering Saccharomyces boulardii for enhanced surface display capacity

Saccharomyces boulardii (Sb) has gained significant attention for its potential therapeutic application as a probiotic yeast strain. Current approaches often leverage its secretion and display capabilities to deliver therapeutic agents aimed at alleviating intestinal disorders. However, relatively few studies have focused on optimizing its display efficiency. In this study, we evaluated two surface display systems, Aga2- and Sed1-based, for use in Sb by systematically modifying display cassette components and the host strain. Initially, both systems were tested in Saccharomyces cerevisiae (Sc) and Sb to validate their design. Sc consistently outperformed Sb in both display expression and efficiency, highlighting the need for further optimization in Sb. To enhance the display efficiency in Sb, we investigated specific modifications to the display cassette, including the use of linker sequences for Aga2 and variations in anchor length for Sed1. These experiments identified key factors influencing display performance. Subsequently, we engineered a modified Sb strain, LIP02, by overexpressing AGA1 and deleting cell wall-related genes (CCW12, CCW14, and FYV5). These modifications were expected to expand the available docking sites for the protein of interest (POI) and improve overall protein secretion and display efficiency. As a result, the modified strain exhibited a significant enhancement in display capacity compared to the wild-type Sb strain. Furthermore, genome integration of the display cassette in LIP02 enhanced both stability and expression compared to plasmid-based systems. Importantly, the functionality of β-glucosidase displayed on LIP02 was preserved, as demonstrated by improved enzymatic activity and robust growth on cellobiose as the sole carbon source. These findings establish LIP02 as a superior host for surface display applications in Sb, offering a more stable and efficient platform for the expression of therapeutic proteins and other functional biomolecules.

Iota-carrageenan oligosaccharide ameliorates DSS-induced colitis in mice by mediating gut microbiota dysbiosis and modulating SCFAs-PI3K-AKT pathway

Iota-carrageenan oligosaccharides (iCOs), derived from marine red algae, are traditionally used as antithrombotic and anti-inflammatory agents in folk medicinal practice. Despite the prevailing emphasis on these aspects in their applications, the potential of iCOs as a prebiotic agent for gut health and its subsequent impact on intestinal disorders such as colitis remains largely unexplored. A DSS-induced colitis model was employed in C57BL/6 male mice to analyze the gut microbiota via 16S rRNA sequencing. Fecal microbiota transplantation (FMT) was used to assess the therapeutic effects of iCOs on colitis. RNA sequencing (RNA-Seq) identified pathways and genes affected by iCOs. ELISA measured inflammatory cytokines, while western blot and RT-qPCR evaluated protein and gene expressions, respectively. The iCOs increased beneficial bacteria, such as Lactobacillus, Bifidobacterium, and Akkermansia. They enhanced short-chain fatty acid production and upregulated GPR41, GPR43, and GPR109A mRNA, influencing cytokine secretion. The iCOs reduced mRNA of SPHK1, BDKRB1, LCN2, and so on, potentially through PI3K-Akt pathway inhibition, and promoted tight junction protein expression. Our findings highlight the novel therapeutic potential of iCOs in colitis, indicating a multifaceted approach to treatment that includes gut microbiota modulation, intestinal barrier restoration, and the suppression of inflammatory responses.

Engineered Probiotic Saccharomyces boulardii Reduces Colitis-Associated Colorectal Cancer Burden in Mice

BACKGROUND

Individuals with inflammatory bowel diseases experience an elevated risk of colorectal cancer driven by chronic inflammation. Current systemic immunosuppressive therapies often cause severe side effects. Live oral biotherapeutics are an emerging treatment modality that directly target the intestines. We have engineered a probiotic Saccharomyces boulardii strain that expresses targeting ligands to bind fibronectin on inflamed mucosa and secretes anti-tumor necrosis factor nanobodies locally to reduce inflammation. We previously demonstrated that engineering S. boulardii to bind fibronectin enhanced colonization and reduced inflammation in a DSS colitis model.

AIMS

Here, we tested the anti-cancer potential of engineered S. boulardii using a well-established model of IBD-associated CRC, azoxymethane-treated interleukin 10-deficient (AOM/Il10-/-) mice. These mice develop inflammation and invasive tumors that model those found in inflammatory bowel disease.

METHODS

Mice were orally administered engineered S. boulardii at two dosing frequencies, unmodified S. boulardii, or placebo throughout the 18-week model. Colons were harvested for gross, histological, and molecular evaluation for inflammation and tumorigenesis.

RESULTS

Histological colon inflammation was reduced by twice weekly dosing of engineered and unmodified S. boulardii. Engineered S. boulardii reduced gross tumor number in a dose-dependent manner, with median tumor counts reduced from 7.5 to 2 per mouse (p < 0.0002 vs. placebo). Unmodified S. boulardii similarly reduced gross tumor number. Colonization studies revealed that engineered S. boulardii failed to colonize for greater time or density vs. unmodified S. boulardii.

CONCLUSION

Together our data indicate that engineering S. boulardii does not reduce its ability to decrease inflammation-associated tumorigenesis, and that further host-binding target optimization is required to enhance colonization and anti-cancer effects.

Probiotic Saccharomyces boulardii Against Cronobacter sakazakii Infection: In Vitro and In Vivo Studies

Cronobacter sakazakii is an opportunistic foodborne pathogen causing intestinal and extra-intestinal diseases in humans, especially young children, and is regarded as one of the main concerns in public health. Saccharomyces boulardii is a well-known probiotic yeast widely used to treat and prevent antibiotic-associated diarrheal infections in infants and neonates. This study evaluated the preventive effects and potential of probiotic S. boulardii against C. sakazakii intestinal infections in humans. Viability, bacterial virulence factor, cellular pro-inflammatory gene expression, and nanomechanical properties of the cytoplasmic membrane of caco-2 cells were evaluated using MTT, real-time PCR, and AFM methods, respectively. Using histopathological analysis, S. boulardii treatment was evaluated on infected newborn C57 BL/6 mice. We found that S. boulardii inoculation significantly (P < 0.05) increased the viability and downregulated the cellular pro-inflammatory genes (IL-8 and NFkB) and bacterial virulence factor genes (ompA and hfq) in infected intestinal cells while also decreasing the morphological alterations. We also observed that S. boulardii treatment reduced the intestinal damage induced by C. sakazakii infection. In conclusion, our findings demonstrate that S. boulardii effectively protects against C. sakazakii infections. This probiotic yeast holds promise as a potential preventive and therapeutic agent for intestinal diseases associated with C. sakazakii.

Development of a Dihydrofolate Reductase Selection System for Saccharomyces boulardii

Saccharomyces boulardii, the only commercially available probiotic yeast, has gained attention as a recombinant live biotherapeutic product (rLBP) empowered with the expression of heterologous therapeutic proteins for treating gastrointestinal diseases. However, the genetic modification of S. boulardii intended for clinical use is hindered by regulatory and technical challenges. In this study, we developed a dihydrofolate reductase (DHFR)-based selection system as an innovative alternative to traditional auxotrophic selection strategies for engineering S. boulardii. The DHFR selection system overcame inherent resistance of the yeast to methotrexate (MTX) by incorporating sulfanilamide, a dihydrofolate synthesis inhibitor, to enhance selection efficiency. The system demonstrated robust functionality, enabling the efficient screening of high-expression clones and tunable expression of therapeutic proteins, such as cytokines and antibodies, by modulating MTX concentrations. Furthermore, the yeast's endogenous DHFR homolog, DFR1, was shown to be a viable selection marker, providing greater host compatibility while maintaining functionality compared to DHFR. This selection system avoids reliance on foreign antibiotic selection markers and the construction of auxotrophic strains, thus simplifying engineering and allowing for a tunable protein expression. These advancements establish the DHFR/DFR1 selection system as a robust and versatile platform for developing S. boulardii-based live biotherapeutics.

Dental problems and oral microbiome alterations in ulcerative colitis

Ulcerative colitis is a chronic disease that has not well-established etiology. The role of microbial dysregulation in its pathogenesis has been recently highlighted. Overall, microbiome alterations concern the reduction of bacterial abundance and diversity, resulting in gut microbiome imbalance negatively affecting immunological aspects. There is a link between ulcerative colitis and the oral microbiome. The changes of oral microbiome are found at many levels, from gently dysbiotic composition to the presence of the main periodontal microbes. The analysis of oral microbiome can be a part of personalized medicine due to the fact that it is a potential biomarker. Patients with ulcerative colitis may manifest dental symptoms/problems, such as periodontitis (strongly related to the red-complex pathogens-Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, and bacteria belonging to the other complexes, such as Fusobacterium nucleatum and Aggregatibacter actinomycetecomitans), dental caries, oral ulcerations, leukoplakia, halitosis, and others. Notably, the DMFT (Decayed, Missing, Filled Teeth) index is higher in these patients compared to healthy subjects. According to some data, oral lichen planus (which is a disease with an immunological background) can also be observed in ulcerative colitis patients. It seems that deep understanding of ulcerative colitis in association with oral microbiome, immunology, and dental manifestations may be crucial to provide complex treatment from a dental point of view.

Classification of Nanomaterial Drug Delivery Systems for Inflammatory Bowel Disease

Inflammatory bowel disease (IBD), including Crohn's disease and ulcerative colitis, primarily arises from defects in the colonic barrier, imbalances of the gut microbiota, and immune response issues. These complex causes make it difficult to achieve a complete cure. Patients with IBD frequently experience recurrent abdominal pain and bloody diarrhea, while severe cases may result in intestinal obstruction, perforation, and cancer. Lifelong maintenance therapy may thus be needed to manage these symptoms; however, traditional IBD drugs, such as 5-aminosalicylic acid, glucocorticoids, immunosuppressants, and biological agents, are often associated with problems including poor solubility, instability, and ineffective targeting, as well as causing serious side effects in non-target tissues. Nanomaterial drug delivery systems (NDDS) have recently shown great promise in optimizing drug distribution, solubility through biocompatible coatings, enhancing bioavailability via PEGylation and reducing side effects. These formulations can enhance a drug's pharmacokinetics by modifying its properties, improve its ability to cross barriers, and boost bioavailability. In addition, NDDS can enable targeted delivery, increase local drug concentrations, improve efficacy, and reduce side effects, as well as protecting active drug molecules from immune recognition and protease degradation. The clinical use of these systems for treating IBD, however, requires further research. This review summarizes the classification of NDDS for IBD, and concludes that, despite ongoing challenges, NDDS may represent an effective treatment approach for IBD. In summary, NDDS enhance the targeted delivery of therapeutic agents to specific cells or tissues, thereby improving drug bioavailability and therapeutic efficacy. These systems effectively surmount biological barriers, facilitating efficient drug delivery to targeted sites, which is crucial for attaining optimal therapeutic outcomes. This review contributes to a deeper understanding of how the physicochemical properties of NDDS influence pharmacological behavior in vivo and can expedite their clinical translation.

A yeast-based oral therapeutic delivers immune checkpoint inhibitors to reduce intestinal tumor burden

Engineered probiotics are an emerging platform for in situ delivery of therapeutics to the gut. Herein, we developed an orally administered, yeast-based therapeutic delivery system to deliver next-generation immune checkpoint inhibitor (ICI) proteins directly to gastrointestinal tumors. We engineered Saccharomyces cerevisiae var. boulardii (Sb), a probiotic yeast with high genetic tractability and innate anticancer activity, to secrete "miniature" antibody variants that target programmed death ligand 1 (Sb_haPD-1). When tested in an ICI-refractory colorectal cancer (CRC) mouse model, Sb_haPD-1 significantly reduced intestinal tumor burden and resulted in significant shifts to the immune cell profile and microbiome composition. This oral therapeutic platform is modular and highly customizable, opening new avenues of targeted drug delivery that can be applied to treat a myriad of gastrointestinal malignancies.

Rewiring Tryptophan Metabolism via Programmable Probiotic Integrated by Dual-Layered Microcapsule Protects against Inflammatory Bowel Disease in Mice

Intestinal dysbiosis and the associated l-tryptophan metabolic disorder are pivotal in inflammatory bowel disease progression, leading to a compromised intestinal barrier integrity. Remedying the dysfunction in tryptophan metabolism has emerged as a promising therapeutic strategy. Herein, we reprogram the tryptophan metabolism in situ by EcN-TRP@A/G, encapsulating the engineered probiotic, EcN-TRP, with enhanced tryptophan synthesis capacity, for sustained modulation, thereby restoring intestinal barrier function and microbial homeostasis. The pH-responsive dual-layered EcN-TRP@A/G microcapsule developed via high-voltage electrospraying and liquid interface self-assembly, preserved probiotic viability in the harsh gastrointestinal milieu, and facilitated targeted colon release. Bioluminescent tracking in mice reveals a 22.84-fold increase in EcN-TRP@A/G viability and distribution compared to naked EcN-TRP. Targeted metabolomics highlights EcN-TRP@A/G's modulation of the tryptophan-indole pathway. Oral administration of EcN-TRP@A/G sustained elevates indole metabolites, particularly indole-3-acetic acid and indole-3-propionic acid, in colon tissue for up to 7 days. In IBD mice, EcN-TRP@A/G improves intestinal permeability, reduces inflammation, and recovers the gut microbiome by enhancing beneficial bacteria abundance like Prevotellaceae_UCG-001 and Anaerostipes while suppressing pathogenic strains like Escherichia-Shigella. Our findings offer a cost-effective approach, harnessing the probiotic metabolic potential in situ through engineered modifications for effective IBD treatment.

From probiotic chassis to modification strategies, control and improvement of genetically engineered probiotics for inflammatory bowel disease

With the rising morbidity of inflammatory bowel disease (IBD) year by year, conventional therapeutic drugs with systemic side effects are no longer able to meet the requirements of patients. Probiotics can improve gut microbiota, enhance intestinal barrier function, and regulate mucosal immunity, making them a potential complementary or alternative therapy for IBD. To compensate for the low potency of probiotics, genetic engineering technology has been widely used to improve their therapeutic function. In this review, we systematically summarize the genetically engineered probiotics used for IBD treatment, including probiotic chassis, genetic modification strategies, methods for controlling probiotics, and means of improving efficacy. Finally, we provide prospects on how genetically engineered probiotics can be extended to clinical applications.

Novel selenium-enriched Pichia kudriavzevii as a dietary supplement to alleviate dextran sulfate sodium-induced colitis in mice by modulating the gut microbiota and host metabolism

Inflammatory bowel disease (IBD) poses persistent challenges due to its chronic and recurrent nature, exacerbated by the unsatisfactory outcomes of the traditional treatment approaches. In this study, we developed a dietary supplement, selenium-enriched Pichia kudriavzevii (SeY), to alleviate dextran sulfate sodium-induced colitis in mice. The newly developed functional food shows dual-functional activity, acting both as a probiotic and a reliable source of organic selenium. This study aimed to investigate the preventive effects of SeY against dextran sulfate sodium-induced colitis in mice and elucidate the underlying mechanisms. Results showed that SeY, especially at high doses (HSeY), significantly ameliorated colitis symptoms, reduced colonic damage, attenuated inflammatory responses, and mitigated oxidative stress. Furthermore, HSeY strengthened intestinal barrier function by increasing goblet cell numbers, upregulating MUC2 expression, and enhancing tight junction proteins (ZO-1, claudin-1, and occludin). Additionally, HSeY alleviated gut microbiota dysbiosis by promoting the colonization of beneficial bacteria such as norank-f-Muribaculaceae and Bacteroides, while suppressing harmful microorganisms such as norank-f-norank-o-Clostridia-UCG-014. The altered gut microbiota also affected gut metabolism, with differential metabolites primarily associated with amino acids, such as tryptophan metabolism, contributing to the mitigation of oxidative stress and inflammatory responses. Further studies involving antibiotic-mediated depletion of gut flora and fecal microbiota transfer trials corroborated that the preventive effect of HSeY against IBD relied on the gut microbiota. This study provides vital insights into colitis prevention and advances selenium-enriched fortified food-targeted nutritional interventions.

Advances in the research of intestinal fungi in Crohn's disease

This article reviews of the original research published by Wu et al in the World Journal of Gastroenterology, delving into the pivotal role of the gut microbiota in the pathogenesis of Crohn's disease (CD). Insights were gained from fecal microbiota transplantation (FMT) in mouse models, revealing the intricate interplay between the gut microbiota, mesenteric adipose tissue (MAT), and creeping fat. The study uncovered the characteristics of inflammation and fibrosis in the MAT and intestinal tissues of patients with CD; moreover, through the FMT mouse model, it observed the impact of samples from healthy patients and those with CD on symptoms. The pathogenesis of CD is complex, and its etiology remains unclear; however, it is widely believed that gut microbiota dysbiosis plays a significant role. Recently, with the development and application of next-generation sequencing technology, research on the role of fungi in the pathogenesis and chronicity of CD has deepened. This editorial serves as a supplement to the research by Wu et al who discussed advances related to the study of fungi in CD.

The Gut Microbiome Advances Precision Medicine and Diagnostics for Inflammatory Bowel Diseases

The gut microbiome emerges as an integral component of precision medicine because of its signature variability among individuals and its plasticity, which enables personalized therapeutic interventions, especially when integrated with other multiomics data. This promise is further fueled by advances in next-generation sequencing and metabolomics, which allow in-depth high-precision profiling of microbiome communities, their genetic contents, and secreted chemistry. This knowledge has advanced our understanding of our microbial partners, their interaction with cellular targets, and their implication in human conditions such as inflammatory bowel disease (IBD). This explosion of microbiome data inspired the development of next-generation therapeutics for treating IBD that depend on manipulating the gut microbiome by diet modulation or using live products as therapeutics. The current landscape of artificial microbiome therapeutics is not limited to probiotics and fecal transplants but has expanded to include community consortia, engineered probiotics, and defined metabolites, bypassing several limitations that hindered rapid progress in this field such as safety and regulatory issues. More integrated research will reveal new therapeutic targets such as enzymes or receptors mediating interactions between microbiota-secreted molecules that drive or modulate diseases. With the shift toward precision medicine and the enhanced integration of host genetics and polymorphism in treatment regimes, the following key questions emerge: How can we effectively implement microbiomics to further personalize the treatment of diseases like IBD, leveraging proven and validated microbiome links? Can we modulate the microbiome to manage IBD by altering the host immune response? In this review, we discuss recent advances in understanding the mechanism underpinning the role of gut microbes in driving or preventing IBD. We highlight developed targeted approaches to reverse dysbiosis through precision editing of the microbiome. We analyze limitations and opportunities while defining the specific clinical niche for this innovative therapeutic modality for the treatment, prevention, and diagnosis of IBD and its potential implication in precision medicine.

Controlled release of microorganisms from engineered living materials

Probiotics offer therapeutic benefits by modulating the local microbiome, the host immune response, and the proliferation of pathogens. Probiotics have the potential to treat complex diseases, but their persistence or colonization is required at the target site for effective treatment. Although probiotic persistence can be achieved by repeated delivery, no biomaterial that releases clinically relevant doses of metabolically active probiotics in a sustained manner has been previously described. Here, we encapsulate stiff probiotic microorganisms within relatively less stiff hydrogels and show a generic mechanism where these microorganisms proliferate and induce hydrogel fracture, resulting in microbial release. Importantly, this fracture-based mechanism leads to microorganism release with zero-order release kinetics. Using this mechanism, small (∼1 μL) engineered living materials (ELMs) release >10 8 colony-forming-units (CFUs) of E. coli in 2 h. This release is sustained for at least 10 days. Cell release can be varied by more than three orders of magnitude by varying initial cell loading and modulating the mechanical properties of encapsulating matrix. As the governing mechanism of microbial release is entirely mechanical, we demonstrate controlled release of model Gram-negative, Gram-positive, and fungal probiotics from multiple hydrogel matrices.

SIGNIFICANCE

Probiotics offer therapeutic benefits and have the potential to treat complex diseases, but their persistence at the target site is often required for effective treatment. Although probiotic persistence can be achieved by repeated delivery, no biomaterial that releases metabolically active probiotics in a sustained manner has been developed yet. This work demonstrates a generic mechanism where stiff probiotics encapsulated within relatively less stiff hydrogels proliferate and induce hydrogel fracture. This allows a zero-order release of probiotics which can be easily controlled by adjusting the properties of the encapsulating matrices. This generic mechanism is applicable for a wide range of probiotics with different synthetic matrices and has the potential to be used in the treatment of a broad range of diseases.