An engineered probiotic secreting Sj16 ameliorates colitis via Ruminococcaceae/butyrate/retinoic acid axis

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

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

Exploring the role of gut microbiota in intervertebral disc degeneration: insights from bidirectional Mendelian randomization analysis

OBJECTIVE

Although previous studies have indicated a potential association between the gut microbiota and intervertebral disc degeneration (IVDD), the precise nature of this relationship remains unclear. The objective of this study is to further explore the potential causal relationship between gut microbiota and IVDD using a bidirectional Mendelian randomization approach, with the aim of identifying potential microbial characteristics associated with IVDD.

METHODS

Using the data from genome-wide association studies (GWAS) involving 412 gut microbiota species and 227,388 controls and 29,508 cases of IVDD. Inverse variance weighted (IVW) was used as the primary Mendelian randomization (MR) analysis, complemented by weighted median, MR-Egger regression, weighted mode and simple mode methods. Extensive sensitivity analyses were performed to confirm the robustness of the results and to assess heterogeneity and horizontal pleiotropy.

RESULTS

This study revealed a positive genetic predisposition between 6 types of gut microbiota and IVDD through the IVW method, indicating that increased levels of these microbiota may lead to a higher risk of IVDD. Conversely, 6 types of gut microbiota were found to have negative effects on IVDD, suggesting that increased levels of these microbiota may have a protective effect against IVDD. Reverse MR analysis results revealed such possibilities as 1 positive and 5 negative causal relationships between IVDD and gut microbiota. The results of Cochran's Q test, MR-Egger regression, and MR-PRESSO analysis from the bidirectional Mendelian randomization all yielded p-values greater than 0.05, indicating that there is no significant heterogeneity or pleiotropy in the genetic effect analysis between gut microbiota and IVDD.

CONCLUSION

We used a bidirectional Mendelian randomization approach to identify various gut microbiota associated with IVDD. Our findings lay the foundation for further exploration of the pathogenesis and treatment strategies of gut microbiota and IVDD, and provide new possibilities for research on biomarkers of IVDD-related metabolic microbiota.

Probiotics and prebiotics: new treatment strategies for oral potentially malignant disorders and gastrointestinal precancerous lesions

Oral potentially malignant disorders (OPMDs) and gastrointestinal precancerous lesions (GPLs) are major public health concerns because of their potential to progress to cancer. Probiotics, prebiotics, and engineered probiotics can positively influence the prevention and management of OPMDs and GPLs. This review aims to comprehensively review the application status of probiotics, prebiotics and engineered probiotics in OPMDs and GPLs, explore their potential mechanisms of action, and anticipate their future clinical use.

Enhancing colonic health with encapsulated grape seed anthocyanins: Oral capsule for Colon-targeted delivery

Grape seed anthocyanins (GSA) offer health benefits and protect against diseases, including colitis. Its unpleasant smell and instability prevent widespread application. Antisolvent pretreatment GSA was encapsulated in chitosan-phytic acid 3D gel network. SEM and X-ray diffraction results demonstrate that pretreatment reduces GSA particle size and exhibits amorphous structure. FTIR confirmed they were physically encapsulated and not covalently bound. Its subsequent simulations digestion and fermentation showed only 26.69 % upper digestive tract leakage and altered gut microbiota and metabolites profile. In DSS-induced colitis model, it ameliorated the symptoms, including diarrhea, bloody stools, weight loss, and DAI score. Additionally, it regulates colitis mice pro- and anti-inflammatory cytokines, modifies cecum and colon SCFA profile, improves intestinal barrier, and restores colonic cell redox equilibrium. Collectively, GSA ameliorates experimental colitis via inhibiting TRL4/NF-κB and activating Nrf2 signaling pathway. In conclusion, we propose our GSA capsule can effectively deliver an intact parent form of GSA to the colon and has the potential to be a colonic health strategy.

Gut Microbiota Modulation in IBD: From the Old Paradigm to Revolutionary Tools

Inflammatory bowel diseases (IBDs) are chronic inflammatory disorders primarily comprising two main conditions: ulcerative colitis and Crohn's disease. The gut microbiota's role in driving inflammation in IBD has garnered significant attention, yet the precise mechanisms through which the microbiota influences IBD pathogenesis remain largely unclear. Given the limited therapeutic options for IBD, alternative microbiota-targeted therapies-including prebiotics, probiotics, postbiotics, and symbiotics-have been proposed. While these approaches have shown promising results, microbiota modulation is still mainly considered an adjunct therapy to conventional treatments, with a demonstrated impact on patients' quality of life. Fecal microbiota transplantation (FMT), already approved for treating Clostridioides difficile infection, represents the first in a series of innovative microbiota-based therapies under investigation. Microbial biotherapeutics are emerging as personalized and cutting-edge tools for IBD management, encompassing next-generation probiotics, bacterial consortia, bacteriophages, engineered probiotics, direct metabolic pathway modulation, and nanotherapeutics. This review explores microbial modulation as a therapeutic strategy for IBDs, highlighting current approaches and examining promising tools under development to better understand their potential clinical applications in managing intestinal inflammatory disorders.

Gut Microbiota Influences Developmental Anesthetic Neurotoxicity in Neonatal Rats

BACKGROUND

Anesthetic exposure during childhood is significantly associated with impairment of neurodevelopmental outcomes; however, the causal relationship and detailed mechanism of developmental anesthetic neurotoxicity remain unclear. Gut microbiota produces various metabolites and influences the brain function and development of the host. This relationship is referred to as the gut-brain axis. Gut microbiota may influence developmental anesthetic neurotoxicity caused by sevoflurane exposure. This study investigated the effect of changes in the composition of gut microbiota after fecal microbiota transplantation on spatial learning disability caused by developmental anesthetic neurotoxicity in neonatal rats.

METHODS

Neonatal rats were allocated into the Control (n = 10) and Sevo (n = 10) groups in Experiment 1 and the Sevo (n = 20) and Sevo+FMT (n = 20) groups in Experiment 2, according to the randomly allocated mothers' group. The rats in Sevo and Sevo+FMT groups were exposed to 2.1% sevoflurane for 2 hours on postnatal days 7 to 13. Neonatal rats in the Sevo+FMT group received fecal microbiota transplantation immediately after sevoflurane exposure on postnatal days 7 to 13. The samples for fecal microbiota transplantation were obtained from nonanesthetized healthy adult rats. Behavioral tests, including Open field, Y-maze, Morris water maze, and reversal Morris water maze tests, were performed to evaluate spatial learning ability on postnatal days 26 to 39.

RESULTS

Experiment 1 revealed that sevoflurane exposure significantly altered the gut microbiota composition. The relative abundance of Roseburia (effect value: 1.01) and Bacteroides genus (effect value: 1.03) increased significantly after sevoflurane exposure, whereas that of Lactobacillus (effect value: -1.20) decreased significantly. Experiment 2 revealed that fecal microbiota transplantation improved latency to target (mean ± SEM; Sevo group: 9.7 ± 8.2 seconds vs, Sevo+FMT group: 2.7 ± 2.4 seconds, d=1.16, 95% confidence interval: -12.7 to -1.3 seconds, P = .019) and target zone crossing times (Sevo group: 2.4 ± 1.6 vs, Sevo+FMT group: 5.4 ± 1.4, d=1.99, 95% confidence interval: 2.0-5.0, P < .001) in the reversal Morris water maze test. Microbiota analysis revealed that the α-diversity of gut microbiota increased after fecal microbiota transplantation. Similarly, the relative abundance of the Firmicutes phylum (effect value: 1.44), Ruminococcus genus (effect value: 1.69), and butyrate-producing bacteria increased after fecal microbiota transplantation. Furthermore, fecal microbiota transplantation increased the fecal concentration of butyrate and induced histone acetylation and the mRNA expression of brain-derived neurotrophic factor in the hippocampus, thereby suppressing neuroinflammation and neuronal apoptosis.

CONCLUSIONS

The alternation of gut microbiota after fecal microbiota transplantation influenced spatial learning ability in neonatal rats with developmental anesthetic neurotoxicity. Modulation of the gut microbiota may be an effective prophylaxis for developmental anesthetic neurotoxicity in children.

Administration of a Next-Generation Probiotic Escherichia coli Nissle 1917-GLP-1 Alleviates Diabetes in Mice With Type 1 and Type 2 Diabetes

Diabetes mellitus (DM) is a persistent and steadily progressing metabolic condition distinguished by unregulated high levels of blood glucose. GLP1 receptor agonists have recently gained recognition as first-line therapies in selected instances, as per the updated ADA guidelines, highlighting their efficacy not only in glycemic control but also in their broader health benefits. Nonetheless, the efficacy of GLP-1 is limited by its brief duration of action, rapid clearance from the body, and challenges associated with subcutaneous administration. In this study, we examined the potential diabetes-mitigating effects of a genetically engineered strain of Escherichia coli Nissle 1917 (EcN)-GLP-1, previously developed by our group. We utilized mouse models for both Type 1 diabetes mellitus (T1DM) and Type 2 diabetes mellitus (T2DM) to assess its efficacy. In the case of T1DM mice, the results revealed that EcN-GLP-1 resulted in a notable decrease in blood glucose levels. Furthermore, it exhibited a protective influence on the structural integrity of islet β-cells; downregulated the expressions of key inflammatory markers such as TLR-4, p-NF-κB/NF-κB, and Bax/Bcl-2; promoted the insulin secretion; and reinstated the perturbed diversity of microbial species to a normal state. Similarly, EcN-GLP-1 had a pronounced impact on T2DM mice, manifesting increased presence of islet β-cells, decreased inflammatory response and apoptosis, and regulation of lipid metabolism in the liver. In summary, the genetically modified EcN-GLP-1 strain demonstrates the ability to alleviate diabetes by enhancing the islet β-cell population, mitigating inflammatory reactions and apoptosis, optimizing liver lipid metabolism, and reinstating a balanced microbial diversity. These findings hold promise as a potential avenue for treating DM.

Genetically Encoded Biosensors for Constrained Biological Functions in Probiotic Escherichia coli Nissle

The probiotic Escherichia coli Nissle (EcN) is an exceptional strain that has attracted significant attention not only for its clinical efficacy in the treatment and prevention of gastrointestinal disorders but also as a burgeoning microbial chassis for living therapeutic applications. However, there is an immediate necessity to develop conditional expression systems that confine the activity of EcN specifically in the gastrointestinal tract, to avoid influencing the environment. Here, we constructed two genetically encoded interchangeable sensors responsive to body temperature at 37 °C, and small molecules such as protocatechuic acid (PCA), a metabolite found in green tea. By employing dCpf1 targeted deactivation of the LacI gene, we thereby coupled the above sensing modules with the Ptrc-lacO system and achieved improved signal outputs and relatively high ON/OFF ratios. Subsequently, we validated the biological function of engineering EcN using the enhanced green fluorescent protein (eGFP) in an animal model of mice. Taken together, the construction of genetically encoded sensors to restrict the biological functions of EcN would be applicable for the real-world implementation of living therapeutics or drug delivery.

Differential Gut Microbiome Profiles in Long-Distance Endurance Cyclists and Runners

We recently have shown that the gut microbiota composition in female and male runners positively correlates with sports, and female runners show similar gut microbiome diversity to male runners. However, gut microbiota composition has not yet been fully investigated in other endurance athletes, such as cyclists. Therefore, in the current study, we investigated the gut microbiome profiles in competitive, non-professional female and male cyclists compared to what we have shown in runners. We aim to understand (1) whether the gut microbiome signature is sport-specific; (2) whether there is a microbiome difference between female and male cyclists and runners; and (3) whether the gut bacteria expressed in cyclists and runners correlates with exercise performance. Our study included 58 subjects: 18 cyclists (9 males), 22 runners (13 males), and 18 control subjects (9 males). Fecal samples were obtained and subjected to taxonomic analysis to assess the relative abundances of species across subjects based on 16S rRNA sequencing results. Both alpha and beta diversity of the bacterial communities were evaluated to identify compositional variations between the groups. Each participant completed a maximal oxygen consumption test and a time-to-exhaustion test at 85% of the measured VO2max. Cyclists performed the test on an SRM ergometer, while runners used a motorized treadmill. Blood lactate levels were measured at 5 min intervals throughout the time-to-exhaustion trials. Alpha diversity demonstrated a significant difference (p-adj < 0.001) between cyclists and runners. Male cyclists showed significantly lower alpha diversity than runners (p-adj < 0.001). The taxonomic analysis of gut microbiota composition between cyclists, runners, and controls showed a lower or higher abundance of fifteen different bacteria. In cyclists, there was a significant positive correlation between six bacteria, and in runners, there was a significant positive correlation between eight bacteria, with weekly training volume, time-to-exhaustion, VO2max, and blood lactate levels. This study suggests potential sport-specific characteristics in long-distance cyclists' and runners' gut microbiome signatures. These findings emphasize the differences in gut microbiota between cyclists and runners, probably due to the difference in physiological and biomechanical conditions related to the activity mode during each sport.

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.

Genetically engineered bacteria as inflammatory bowel disease therapeutics

Inflammatory bowel disease (IBD) is a chronic and recurrent disease caused by immune response disorders that disrupt the intestinal lumen symbiotic ecosystem and dysregulate mucosal immune functions. Current therapies available for IBD primarily focus on symptom management, making early diagnosis and prompt intervention challenging. The development of genetically engineered bacteria using synthetic biology presents a new strategy for addressing these challenges. In this review, we present recent breakthroughs in the field of engineered bacteria for the treatment and detection of IBD and describe how bacteria can be genetically modified to produce therapeutic molecules or execute diagnostic functions. In particular, we discuss the challenges faced in translating live bacterial therapeutics from bacterial design to delivery strategies for further clinical applications.

Unveiling the therapeutic potential and mechanism of inulin in DSS-induced colitis mice

Inulin has been reported to alleviate colitis. In this study, colitis patients' feces were used to simulate fermentation to demonstrate changes in the microbiota profile in the presence of inulin. We found inulin can reshape the gut microbiota profile of colitis patients, especially by altering the abundance of Faecalibacterium and Blautia. Interestingly, the subsequent co-culture with inulin demonstrated that inulin promoted the growth of these two strains of bacteria. The dextran sodium sulfate (DSS)-induced mouse model was used to examine the effect of inulin and its combination with two probiotics on colitis. Results showed that all three treatments can alleviate the clinical symptoms, including weight-losing, colon-shortening, and the Disease Activity Index (DAI) score. Further investigations showed that the administrations regulate colitis mice's pro- and anti-inflammatory cytokines, such as TNF-α, IL-1β, IL-6, IL-10, and IL-17. Also, they alter the relative abundance of Faecalibacterium and Blautia, change the short-chain fatty acids (SCFAs) profile in the cecum and colon, and improve the intestinal barrier; specifically, the intervention increased the expressions of Claudin, Occludin, Zonula Occludens (ZO)-1, and Mucin (MUC)-2 in colonic tissues, thus restoring the colonic tissue structure and morphology of colitis mice. Collectively, our results confirm that inulin can alter the colitis patients' characteristic microbial community, and they can ameliorate experimental colitis by inhibiting the TRL4/MyD88/NF-κB signaling pathway-improving the inflammatory response and enhancing the intestinal barrier. In conclusion, we propose that inulin may hold promise as a functional food therapeutic approach for the treatment of colitis.

Engineering probiotic Escherichia coli Nissle 1917 to block transfer of multiple antibiotic resistance genes by exploiting a type I CRISPR-Cas system

Many multidrug-resistant (MDR) bacteria have evolved through the accumulation of antibiotic resistance genes (ARGs). Although the potential risk of probiotics as reservoirs of ARGs has been recognized, strategies for blocking the transfer of ARGs while using probiotics have rarely been explored. The probiotic Escherichia coli Nissle 1917 (EcN) has long been used for treating intestinal diseases. Here, we demonstrate frequent transfer of ARGs into EcN both in vitro and in vivo, raising concerns about its potential risk of accumulating antibiotic resistance. Given that no CRISPR-Cas system was found in natural EcN, we integrated the type I-E CRISPR-Cas3 system derived from E. coli BW25113 into EcN. The engineered EcN was able to efficiently cleave multiple ARGs [i.e., mcr-1, blaNDM-1, and tet(X)] encoding enzymes for degrading last-resort antibiotics. Through co-incubation of EcN expressing Cas3-Cascade and that expressing Cas9, we showed that the growth of the former strain outcompeted the latter strain, demonstrating a better clinical application prospect of EcN expressing the type I-E CRISPR-Cas3 system. In the intestine of a model animal (i.e., zebrafish), the engineered EcN exhibited immunity against the transfer of CRISPR-targeted ARGs. Our work equips EcN with immunity against the transfer of multiple ARGs by exploiting the exogenous type I-E CRISPR-Cas3 system, thereby reducing the risk of the spread of ARGs while using it as a probiotic chassis for generating living therapeutics.

IMPORTANCE

To reduce the development of antibiotic resistance, probiotics have been considered as a substitute for antibiotics. However, probiotics themselves are reservoirs of antibiotic resistance genes (ARGs). This study introduces a new strategy for limiting the spread of ARGs by engineering the typical probiotic strain Escherichia coli Nissle 1917 (EcN), which has been used for treating intestinal diseases and developed as living therapeutics. We also demonstrate that the type I CRISPR-Cas system imposes a lower growth burden than the type II CRISPR-Cas system, highlighting its promising clinical application potential. Our work not only provides a new strategy for restricting the transfer of ARGs while using probiotics but also enriches the genetic engineering toolbox of EcN, paving the way for the safe use and development of probiotics as living therapeutics.

Escherichia coli on colorectal cancer: A two-edged sword

Escherichia coli (E. coli) is a ubiquitous symbiotic bacterium in the gut, and the diversity of E. coli genes determines the diversity of its functions. In this review, the two-edged sword theory was innovatively proposed. For the question 'how can we harness the ambivalent nature of E. coli to screen and treat CRC?', in terms of CRC screening, the variations in the abundance and subtypes of E. coli across different populations present an opportunity to utilise it as a biomarker, while in terms of CRC treatment, the natural beneficial effect of E. coli on CRC may be limited, and engineered E. coli, particularly certain subtypes with probiotic potential, can indeed play a significant role in CRC treatment. It seems that the favourable role of E. coli as a genetic tool lies not in its direct impact on CRC but its potential as a research platform that can be integrated with various technologies such as nanoparticles, imaging methods, and synthetic biology modification. The relationship between gut microflora and CRC remains unclear due to the complex diversity and interaction of gut microflora. Therefore, the application of E. coli should be based on the 'One Health' view and take the interactions between E. coli and other microorganisms, host, and environmental factors, as well as its own changes into account. In this paper, the two-edged sword role of E. coli in CRC is emphasised to realise the great potential of E. coli in CRC screening and treatment.

Recent advances in bacteria-based platforms for inflammatory bowel diseases treatment

Inflammatory bowel disease (IBD) is a recurring chronic inflammatory disease. Current treatment strategies are aimed at alleviating clinical symptoms and are associated with gastrointestinal or systemic adverse effects. New delivery strategies are needed for the treatment of IBD. Bacteria are promising biocarriers, which can produce drugs in situ and sense the gut in real time. Herein, we focus on recent studies of engineered bacteria used for IBD treatment and introduce the application of engineered bacteria in the diagnosis. On this basis, the current dilemmas and future developments of bacterial delivery systems are discussed.

Probiotics: an alternative anti-parasite therapy

This paper review about probiotic effects and mechanism of action against the gut and non-gut helminths and protozoan parasites. Gastrointestinal parasitic infections are considered a serious health problem and are widely distributed globally. The disease process which emanates from this parasite infection provides some of the many public and veterinary health problems in the tropical and sub-tropical countries. Prevention and control of the parasite disease is through antihelmintic and anti-protozoan drugs, but, due to the increasing emergence of such drug resistance, eradication of parasite infestation in human and livestock still lingers a challenge, which requires the development of new alternative strategies. The use of beneficial microorganisms i.e. probiotics is becoming interesting due to their prophylactic application against several diseases including parasite infections. Recent studies on the interactions between probiotics, parasites and host immune cells using animal models and in vitro culture systems has increased considerably and draw much attention, yet the mechanisms of actions mediating the positive effects of these beneficial microorganisms on the hosts remain unexplored. Therefore, the aim of the present review is to summarize the latest findings on the probiotic research against the gut and non-gut parasites of significance.

Propionate-producing engineered probiotics ameliorated murine ulcerative colitis by restoring anti-inflammatory macrophage via the GPR43/HDAC1/IL-10 axis

Inflammatory bowel disease (IBD) is a chronic and unspecific inflammatory disorder of the gastrointestinal tract, and current treatment options often fail to maintain long-term remission. Studies have shown that propionate level is reduced in fecal samples from patients with IBD. Propionate can ameliorate IBD through intestinal epithelial cells and immune regulation, but its effects on the inflammatory microenvironment and macrophage differentiation have not been widely studied. To address this, we constructed an engineered propionate-producing probiotic (EcNP3) to achieve sustained restoration of propionate levels in the gut and increase its bioavailability. DSS-induced experimental intestinal inflammation model was used to evaluate the effect of EcNP3 on improving the intestinal mucosal barrier and increasing the proportion of anti-inflammatory macrophages. It was found that EcNP3 exhibited a restorative effect on the depletion of peritoneal anti-inflammatory macrophages (F4/80hiCD11bhi) and significantly improved the expression level of IL-10. Simultaneously, the expression of IL-1β, IL-6, and CXCL1 was downregulated while inhibiting apoptosis of tissue-resident macrophages ex vivo. Further investigation revealed that EcNP3 regulates IL-10 expression through G protein-coupled receptor 43 and histone deacetylase. Furthermore, EcNP3 significantly inhibited the protein expression of HDAC1 and promoted the histone acetylation level of cells. Finally, EcNP3 significantly improved DSS-induced colitis in mice by increasing mucus production and reducing inflammatory infiltration. Our results suggest that the engineered live biotherapeutic product EcNP3 is a safe and potently efficacious treatment for IBD, which defines a novel strategy in IBD therapy through macrophage IL-10 signaling.

Causal relationship between gut microbiota and thyroid nodules: a bidirectional two-sample Mendelian randomization study

Objective

Emerging evidence suggests alterations in gut microbiota (GM) composition following thyroid nodules (TNs) development, yet the causal relationship remains unclear. Utilizing Mendelian Randomization (MR), this study aims to elucidate the causal dynamics between GM and TNs.

Methods

Employing summary statistics from the MiBioGen consortium (n=18,340) and FinnGen consortium (1,634 TNs cases, 263,704 controls), we conducted univariable and multivariable MR analyses to explore the GM-TNs association. Techniques including inverse variance weighted, MR-Egger regression, weighted median, and MR-PRESSO were utilized for causal inference. Instrumental variable heterogeneity was assessed through Cochran's Q statistic and leave-one-out analysis. Reverse MR was applied for taxa showing significant forward MR associations, with multivariate adjustments for confounders.

Results

Our findings suggest that certain microbiota, identified as Ruminococcaceae_NK4A214_group (OR, 1.89; 95%CI, 0.47-7.64; p = 0.040), Senegalimassilia (OR, 1.72; 95%CI, 1.03-2.87; p =0.037), Lachnospiraceae (OR,0.64; 95%CI,0.41-0.99; p =0.045), exhibit a protective influence against TNs' development, indicated by negative causal associations. In contrast, microbiota categorized as Desulfovibrionales (OR, 0.63; 95%CI, 0.41-0.95; p =0.028), Prevotella_7 (OR, 0.79; 95%CI, 0.63-1.00; p =0.049), Faecalibacterium (OR, 0.66; 95%CI, 0.44-1.00; p =0.050), Desulfovibrionaceae (OR, 0.55; 95%CI, 0.35-0.86; p =0.008), Deltaproteobacteria (OR, 0.65; 95%CI, 0.43-0.97; p =0.036) are have a positive correlation with with TNs, suggesting they may serve as risk factors. Reverse MR analyses did not establish significant causal links. After comprehensive adjustment for confounders, taxa Desulfovibrionales (Order), Desulfovibrionaceae (Family), Deltaproteobacteria (Class) remain implicated as potential contributors to TNs' risk.

Discussion

This study substantiates a significant causal link between GM composition and TNs development, underscoring the thyroid-gut axis's relevance. The findings advocate for the integration of GM profiles in TNs' prevention and management, offering a foundation for future research in this domain.

Intestinal Delivery of Probiotics: Materials, Strategies, and Applications

Probiotics with diverse and crucial properties and functions have attracted broad interest from many researchers, who adopt intestinal delivery of probiotics to modulate the gut microbiota. However, the major problems faced for the therapeutic applications of probiotics are the viability and colonization of probiotics during their processing, oral intake, and subsequent delivery to the gut. The challenges of simple oral delivery (stability, controllability, targeting, etc.) have greatly limited the use of probiotics in clinical therapies. Nanotechnology can endow the probiotics to be delivered to the intestine with improved survival rate and increased resistance to the adverse environment. Additionally, the progress in synthetic biology has created new opportunities for efficiently and purposefully designing and manipulating the probiotics. In this article, a brief overview of the types of probiotics for intestinal delivery, the current progress of different probiotic encapsulation strategies, including the chemical, physical, and genetic strategies and their combinations, and the emerging single-cell encapsulation strategies using nanocoating methods, is presented. The action mechanisms of probiotics that are responsible for eliciting beneficial effects are also briefly discussed. Finally, the therapeutic applications of engineered probiotics are discussed, and the future trends toward developing engineered probiotics with advanced features and improved health benefits are proposed.

The Role of the Gut Microbiome in Inflammatory Bowel Disease: The Middle East Perspective

The gut microbiome is of paramount importance in preserving internal balance in the gastrointestinal tract; therefore, disruptions in its regulation have been linked to the development of inflammatory bowel disease (IBD). This article explores the intricate details of the gastrointestinal microbiome as it pertains to inflammatory bowel disease (IBD), with an emphasis on the Middle East. The study reviews the typical gut microbiome, modifications in inflammatory bowel disease (IBD), determinants impacting the gut microbiome of the Middle East, and prospective therapeutic interventions.

Cilostazol Attenuates Hepatic Steatosis and Intestinal Disorders in Nonalcoholic Fatty Liver Disease

Nonalcoholic fatty liver disease (NAFLD) is one of the most common chronic liver diseases in the world, which begins with liver lipid accumulation and is associated with metabolic syndrome. Also, the name chosen to replace NAFLD was metabolic dysfunction-associated steatotic liver disease (MASLD). We performed focused drug screening and found that Cilostazol effectively ameliorated hepatic steatosis and might offer potential for NAFLD treatment. Our aim was to investigate the therapeutic effects of Cilostazol on the glycolipid metabolism and intestinal flora in NAFLD mice and explore the specific mechanism. In this study, 7-week-old male C57BL/6J mice were fed a high-fat diet (HFD) for 8 weeks to induce NAFLD, and then treated with intragastric administration for 12 weeks. The results showed that Cilostazol inhibited liver lipid de novo synthesis by regulating the AMPK-ACC1/SCD1 pathway and inhibited liver gluconeogenesis by the AMPK-PGC1α-G6P/PEPCK pathway. Cilostazol improved the intestinal flora diversity and intestinal microbial composition in the NAFLD mice, and specifically regulated Desulfovibrio and Akkermansia. In addition, Cilostazol increased the level of short-chain fatty acids in the NAFLD mice to a level similar to that in the blank Control group. Cilostazol reduces liver lipid accumulation in NAFLD mice by improving glucose and lipid metabolism disorders and intestinal dysfunction, thereby achieving the purpose of treating NAFLD.

CXCR2, as a key regulatory gene of HDP-PG-1, maintains intestinal mucosal homeostasis

The intestine defends against pathogenic microbial invasion via the secretion of host defense peptides (HDPs). Nutritional immunomodulation can stimulate the expression of endogenous HDPs and enhance the body's immune defense, representing a novel non-antibiotic strategy for disease prevention. The project aims to explore the regulatory mechanism of protegrin-1 (PG-1) expression using sodium phenylbutyrate (PBA) by omics sequencing technology and further investigate the role of key regulatory genes on intestinal health. The results showed that PBA promoted PG-1 expression in intestinal epithelial cells based on cell density through epidermal growth factor receptor (EGFR) and G protein-coupled receptor (GPR43). Transcriptome sequencing and microRNA sequencing revealed that C-X-C motif chemokine receptor 2 (CXCR2) exhibited interactions with PG-1. Pre-treatment cells with a CXCR2 inhibitor (SB225002) effectively suppressed the induction of PG-1 by PBA. Furthermore, SB225002 significantly suppressed the gene expression of HDPs in the jejunum of mice without influencing on the morphology, number of goblet cells, and proliferation of the intestine. CXCR2 inhibition significantly reduced the expression of HDPs during E. coli infection, and resulted in the edema of jejunal epithelial cells. The 16S rDNA analysis of cecal contents showed that the E. coli and SB225002 treatments changed gut microbiota diversity and composition at different taxonomic levels. Correlation analysis suggested a potential regulatory relationship between gut microbiota and HDPs. To that end, a gene involved in the HDP expression, CXCR2, has been identified in the study, which contributes to improving intestinal immune function. PBA may be used as a functional additive to regulate intestinal mucosal function, thereby enhancing the health of the intestinal and host.

Astaxanthin could regulate the gut-kidney axis to mitigate kidney injury in high-fat diet/streptozotocin-induced diabetic mice

Accumulating evidences have shown the beneficial effects of astaxanthin (AST) supplementation on metabolic diseases prevention and treatment. The goal of present study was to reveal the favorable interactions among AST supplementation, gut microbiota, and kidneys in vivo, so as to attenuate kidney impairment in diabetic mice. Twenty C57BL/6J mice were assigned to a normal control group and a diabetic model group induced by a high-fat diet plus low-dose streptozotocin, and then the diabetic mice were fed with a high-fat diet without or with AST [0.01% (AST_a) or 0.02% (AST_b)] for 12 weeks. When compared to the diabetes kidney disease (DKD) group, AST supplementation delayed the renal pathological progression, reduced fasting blood glucose (AST_b: 1.53-fold, p<0.05), repressed levels of lipopolysaccharide (LPS; AST_a: 1.24-fold, p=0.008; AST_b: 1.43-fold, p<0.001) and TMAO (AST_a: 1.51-fold, p=0.001; AST_b: 1.40-fold, p=0.003), inhibited IL-6 (AST_a: 1.40-fold, p=0.004; AST_b: 1.57-fold, p=0.001) and reactive oxygen species (ROS; AST_a: 1.30-fold, p=0.004; AST_b: 1.53-fold, p<0.001), as well as regulated the Sirt1/PGC-1α/NFκB p65 signaling pathway. Moreover, the results of 16S rRNA gene-based Illumina deep sequencing in each group revealed that dietary AST supplementation also favorably modulated the gut microbiota compared with the DKD group, as evidenced by the inhibition of the harmful bacteria Clostridium_sensu_stricto_1, Romboutsia, and Coriobacteriaceae_UCG-002, and the enhancement of the probiotics such as Lachnospiraceae_NK4A136_group, Roseburia, and Ruminococcaceae. Taken together, dietary AST supplementation could protect kidneys against inflammation and oxidative stress by adjusting the gut-kidney axis in diabetic mice.

A Multifunctional Therapeutic Strategy Using P7C3 as A Countermeasure Against Bone Loss and Fragility in An Ovariectomized Rat Model of Postmenopausal Osteoporosis

By 2060, an estimated one in four Americans will be elderly. Consequently, the prevalence of osteoporosis and fragility fractures will also increase. Presently, no available intervention definitively prevents or manages osteoporosis. This study explores whether Pool 7 Compound 3 (P7C3) reduces progressive bone loss and fragility following the onset of ovariectomy (OVX)-induced osteoporosis. Results confirm OVX-induced weakened, osteoporotic bone together with a significant gain in adipogenic body weight. Treatment with P7C3 significantly reduced osteoclastic activity, bone marrow adiposity, whole-body weight gain, and preserved bone area, architecture, and mechanical strength. Analyses reveal significantly upregulated platelet derived growth factor-BB and leukemia inhibitory factor, with downregulation of interleukin-1 R6, and receptor activator of nuclear factor kappa-B (RANK). Together, proteomic data suggest the targeting of several key regulators of inflammation, bone, and adipose turnover, via transforming growth factor-beta/SMAD, and Wingless-related integration site/be-catenin signaling pathways. To the best of the knowledge, this is first evidence of an intervention that drives against bone loss via RANK. Metatranscriptomic analyses of the gut microbiota show P7C3 increased Porphyromonadaceae bacterium, Candidatus Melainabacteria, and Ruminococcaceae bacterium abundance, potentially contributing to the favorable inflammatory, and adipo-osteogenic metabolic regulation observed. The results reveal an undiscovered, and multifunctional therapeutic strategy to prevent the pathological progression of OVX-induced bone loss.

Engineered microorganisms: A new direction in kidney stone prevention and treatment

Numerous studies have shown that intestinal and urinary tract flora are closely related to the formation of kidney stones. The removal of probiotics represented by lactic acid bacteria and the colonization of pathogenic bacteria can directly or indirectly promote the occurrence of kidney stones. However, currently existing natural probiotics have limitations. Synthetic biology is an emerging discipline in which cells or living organisms are genetically designed and modified to have biological functions that meet human needs, or even create new biological systems, and has now become a research hotspot in various fields. Using synthetic biology approaches of microbial engineering and biological redesign to enable probiotic bacteria to acquire new phenotypes or heterologous protein expression capabilities is an important part of synthetic biology research. Synthetic biology modification of microorganisms in the gut and urinary tract can effectively inhibit the development of kidney stones by a range of means, including direct degradation of metabolites that promote stone production or indirect regulation of flora homeostasis. This article reviews the research status of engineered microorganisms in the prevention and treatment of kidney stones, to provide a new and effective idea for the prevention and treatment of kidney stones.

Effects of immune cells in mediating the relationship between gut microbiota and myelodysplastic syndrome: a bidirectional two-sample, two-step Mendelian randomization study

BACKGROUND

The definitive establishment of a causal relationship between gut microbiota and myelodysplastic syndrome (MDS) has not been achieved. Furthermore, the involvement of immune cells in mediating the connection between gut microbiota and MDS is presently unclear.

METHODS

To elucidate the bidirectional correlation between gut microbiota and MDS, as well as to investigate the mediating role of immune cells, a bidirectional two-sample, two-step Mendelian randomization (MR) study was conducted. Summary statistics were obtained from genome-wide association studies (GWAS), including MDS (456,348 individuals), gut microbiota (18,340 individuals), and 731 immune cells signatures (3757 individuals).

RESULTS

Genetically predicted eight gut microbiota traits were significantly associated with MDS risk, but not vice versa. Through biological annotation of host-microbiome shared genes, we found that immune regulation may mediate the impact of gut microbiota on MDS. Subsequently, twenty-three immunophenotypes that exhibited significant associations with MDS risk and five of these immunophenotypes were under the causal influence of gut microbiota. Importantly, the causal effects of gut microbiota on MDS were significantly mediated by five immunophenotypes, including CD4 +T cell %leukocyte, CD127 on CD45RA - CD4 not regulatory T cell, CD45 on CD33 + HLA DR + WHR, CD33 on basophil, and Monocyte AC.

CONCLUSIONS

Gut microbiota was causally associated with MDS risk, and five specific immunophenotypes served as potential causal mediators of the effect of gut microbiota on MDS. Understanding the causality among gut microbiota, immune cells and MDS is critical in identifying potential targets for diagnosis and treatment.

Gut Microbiome and Transcriptomic Changes in Cigarette Smoke-Exposed Mice Compared to COPD and CD Patient Datasets

Chronic obstructive pulmonary disease (COPD) patients and smokers have a higher incidence of intestinal disorders. The aim of this study was to gain insight into the transcriptomic changes in the lungs and intestines, and the fecal microbial composition after cigarette smoke exposure. Mice were exposed to cigarette smoke and their lung and ileum tissues were analyzed by RNA sequencing. The top 15 differentially expressed genes were investigated in publicly available gene expression datasets of COPD and Crohn's disease (CD) patients. The murine microbiota composition was determined by 16S rRNA sequencing. Increased expression of MMP12, GPNMB, CTSK, CD68, SPP1, CCL22, and ITGAX was found in the lungs of cigarette smoke-exposed mice and COPD patients. Changes in the intestinal expression of CD79B, PAX5, and FCRLA were observed in the ileum of cigarette smoke-exposed mice and CD patients. Furthermore, inflammatory cytokine profiles and adhesion molecules in both the lungs and intestines of cigarette smoke-exposed mice were profoundly changed. An altered intestinal microbiota composition and a reduction in bacterial diversity was observed in cigarette smoke-exposed mice. Altered gene expression in the murine lung was detected after cigarette smoke exposure, which might simulate COPD-like alterations. The transcriptomic changes in the intestine of cigarette smoke-exposed mice had some similarities with those of CD patients and were associated with changes in the intestinal microbiome. Future research could benefit from investigating the specific mechanisms underlying the observed gene expression changes due to cigarette smoke exposure, focusing on identifying potential therapeutic targets for COPD and CD.

Overview on biotics development

Although probiotics have been used in food products and supplements for decades, there has been a considerable increase in their use more recently. Recent technological advances have thus led to major advances in knowledge of the gut microbiota, enabling a significant development of biotics. In this review, we discuss the uses of traditional probiotics but also the discovery of next-generation probiotics that could be used as live biotherapeutics. These novel preventive and therapeutic strategies hold promise for the treatment of numerous diseases such as inflammatory bowel diseases such as Crohn's disease and ulcerative colitis. Probiotic bacteria can be consumed alone, or in combination with prebiotics as synbiotics, or mixed with other probiotic strains to form a consortium for enhanced effects. We also discuss the benefits of using postbiotics.

Crosstalk between hypoxia-inducible factor-1α and short-chain fatty acids in inflammatory bowel disease: key clues toward unraveling the mystery

The human intestinal tract constitutes a complex ecosystem, made up of countless gut microbiota, metabolites, and immune cells, with hypoxia being a fundamental environmental characteristic of this ecology. Under normal physiological conditions, a delicate balance exists among these complex "residents", with disruptions potentially leading to inflammatory bowel disease (IBD). The core pathology of IBD features a disrupted intestinal epithelial barrier, alongside evident immune and microecological disturbances. Central to these interconnected networks is hypoxia-inducible factor-1α (HIF-1α), which is a key regulator in gut cells for adapting to hypoxic conditions and maintaining gut homeostasis. Short-chain fatty acids (SCFAs), as pivotal gut metabolites, serve as vital mediators between the host and microbiota, and significantly influence intestinal ecosystem. Recent years have seen a surge in research on the roles and therapeutic potential of HIF-1α and SCFAs in IBD independently, yet reviews on HIF-1α-mediated SCFAs regulation of IBD under hypoxic conditions are scarce. This article summarizes evidence of the interplay and regulatory relationship between SCFAs and HIF-1α in IBD, pivotal for elucidating the disease's pathogenesis and offering promising therapeutic strategies.

Intestinal melatonin levels and gut microbiota homeostasis are independent of the pineal gland in pigs

Introduction

Melatonin (MEL) is a crucial neuroendocrine hormone primarily produced by the pineal gland. Pinealectomy (PINX) has been performed on an endogenous MEL deficiency model to investigate the functions of pineal MEL and its relationship with various diseases. However, the effect of PINX on the gastrointestinal tract (GIT) MEL levels and gut microbiome in pigs has not been previously reported.

Methods

By using a newly established pig PINX model, we detected the levels of MEL in the GIT by liquid chromatography-tandem mass spectrometry. In addition, we examined the effects of PINX on the expression of MEL synthesis enzymes, intestinal histomorphology, and the intestinal barrier. Furthermore, 16S rRNA sequencing was performed to analyze the colonic microbiome.

Results

PINX reduced serum MEL levels but did not affect GIT MEL levels. Conversely, MEL supplementation increased MEL levels in the GIT and intestinal contents. Neither PINX nor MEL supplementation had any effect on weight gain, organ coefficient, serum biochemical indexes, or MEL synthetase arylalkylamine N-acetyltransferase (AANAT) expression in the duodenum, ileum, and colon. Furthermore, no significant differences were observed in the intestinal morphology or intestinal mucosal barrier function due to the treatments. Additionally, 16S rRNA sequencing revealed that PINX had no significant impact on the composition of the intestinal microbiota. Nevertheless, MEL supplementation decreased the abundance of Fibrobacterota and increased the abundance of Actinobacteriota, Desulfobacterota, and Chloroflexi.

Conclusion

We demonstrated that synthesis of MEL in the GIT is independent of the pineal gland. PINX had no influence on intestinal MEL level and microbiota composition in pigs, while exogenous MEL alters the structure of the gut microbiota.

Butyrate's (a short-chain fatty acid) microbial synthesis, absorption, and preventive roles against colorectal and lung cancer

Butyrate, a short-chain fatty acid (SCFA) produced by bacterial fermentation of fiber in the colon, is a source of energy for colonocytes. Butyrate is essential for improving gastrointestinal (GI) health since it helps colonocyte function, reduces inflammation, preserves the gut barrier, and fosters a balanced microbiome. Human colonic butyrate producers are Gram-positive firmicutes, which are phylogenetically varied. The two most prevalent subgroups are associated with Eubacterium rectale/Roseburia spp. and Faecalibacterium prausnitzii. Now, the mechanism for the production of butyrate from microbes is a very vital topic to know. In the present study, we discuss the genes encoding the core of the butyrate synthesis pathway and also discuss the butyryl-CoA:acetate CoA-transferase, instead of butyrate kinase, which usually appears to be the enzyme that completes the process. Recently, butyrate-producing microbes have been genetically modified by researchers to increase butyrate synthesis from microbes. The activity of butyrate as a histone deacetylase inhibitor (HDACi) has led to several clinical trials to assess its effectiveness as a potential cancer treatment. Among various significant roles, butyrate is the main energy source for intestinal epithelial cells, which helps maintain colonic homeostasis. Moreover, people with non-small-cell lung cancer (NSCLC) have distinct gut microbiota from healthy adults and frequently have dysbiosis of the butyrate-producing bacteria in their guts. So, with an emphasis on colon and lung cancer, this review also discusses how the microbiome is crucial in preventing the progression of certain cancers through butyrate production. Further studies should be performed to investigate the underlying mechanisms of how these specific butyrate-producing bacteria can control both colon and lung cancer progression and prognosis.

Advanced probiotics: bioengineering and their therapeutic application

The role of gut bacteria in human health has long been acknowledged and dysbiosis of the gut microbiota has been correlated with a variety of disorders. Synthetic biology has rapidly grown over the past few years offering a variety of biological applications such as harnessing the relationship between bacteria and human health. Lactic acid bacteria (LAB) are thought to be appropriate chassis organisms for genetic modification with potential biomedical applications. A thorough understanding of the molecular mechanisms behind their beneficial qualities is essential to assist the multifunctional medicinal sectors. Effective genome editing will aid in the creation of next-generation designer probiotics with enhanced resilience and specialized capabilities, furthering our knowledge of the molecular mechanisms behind the physiological impacts of probiotics and their interactions with the host and microbiota. The goal of this review is to provide a brief overview of the methods used to create modified probiotics with the scientific rationale behind gene editing technology, the mechanism of action of engineered probiotics along with their application to treat conditions like inflammatory bowel disease, cancer, bacterial infections, and various metabolic diseases. In addition, application concerns and future directions are also presented.

Stachyose in combination with L. rhamnosus GG ameliorates acute hypobaric hypoxia-induced intestinal barrier dysfunction through alleviating inflammatory response and oxidative stress

High altitude is closely related to intestinal mucosal damage and intestinal microbiota imbalance, and there is currently no effective prevention and treatment measures. In this study, the effects of stachyose (STA), L. rhamnosus GG (LGG) and their combination on inflammatory response, oxidatve stress and intestinal barrier function in mice exposed to acute hypobaric hypoxia were investigated. Our results indicated the combination of STA and LGG could more effectively regulate intestinal microbiota disorders caused by hypobaric hypoxia than STA or LGG alone. When mice were administered with STA + LGG, the content of short chain fatty acids (SCFAs) especially butyric acid significantly increased, which helped intestinal cells to form tight connections, improve the level of anti-inflammatory cytokine (TGF-β) and antioxidant enzymes (SOD, CAT, GSH-Px), and decrease the expression of pro-inlammatory cytokines and hypoxia-inducing factors (IFN-γ, IL-1β, IL-6, TNF-α and HIF-1α), thereby enhance the strong intestinal barrier function. Furthermore, the synbiotics significantly reduced the ratio of Firmicutes to Bacteroidetes, while significantly increased the relative abundance of Rikenella, Bacteroides, Odoribacter, Ruminiclostridium_5 and Gordonibacter, which were correlated with production of SCFAs and anti-inflammatory role. Correlation analysis showed that the protective effect of synbiotics on intestinal barrier function was associated with its anti-inflammatory activity and antioxidant capacity. It provided a strong foundation for further research on the role of STA and LGG in maintaining normal intestinal function at high altitude. Our study has identified and demonstrated a new synbiotic that may be one of the ideal intervention measures for preventing and treating intestinal dysfunction at high altitude.

The gut microbiota contributes to the infection of bovine viral diarrhea virus in mice

Bovine viral diarrhea virus (BVDV) is prevalent worldwide and causes significant economic losses. Gut microbiota is a large microbial community and has a variety of biological functions. However, whether there is a correlation between gut microbiota and BVDV infection and what kind of relation between them have not been reported. Here, we found that gut microbiota composition changed in normal mice after infecting with BVDV, but mainly the low abundance microbe was affected. Interestingly, BVDV infection significantly reduced the diversity of gut microbiota and changed its composition in gut microbiota-dysbiosis mice. Furthermore, compared with normal mice of BVDV infection, there were more viral loads in the duodenum, jejunum, spleen, and liver of the gut microbiota-dysbiosis mice. However, feces microbiota transplantation (FMT) reversed these effects. The data above indicated that the dysbiosis of gut microbiota was a key factor in the high infection rate of BVDV. It is found that the IFN-I signal was involved by investigating the underlying mechanisms. The inhibition of the proliferation and increase in the apoptosis of peripheral blood lymphocytes (PBL) were also observed. However, FMT treatment reversed these changes by regulating PI3K/Akt, ERK, and Caspase-9/Caspase-3 pathways. Furthermore, the involvement of butyrate in the pathogenesis of BVDV was also further confirmed. Our results showed for the first time that gut microbiota acts as a key endogenous defense mechanism against BVDV infection; moreover, targeting regulation of gut microbiota structure and abundance may serve as a new strategy to prevent and control the disease.IMPORTANCEWhether the high infection rate of BVDV is related to gut microbiota has not been reported. In addition, most studies on BVDV focus on in vitro experiments, which limits the study of its prevention and control strategy and its pathogenic mechanism. In this study, we successfully confirmed the causal relationship between gut microbiota and BVDV infection as well as the potential molecular mechanism based on a mouse model of BVDV infection and a mouse model of gut microbiota dysbiosis. Meanwhile, a mouse model which is more susceptible to BVDV provided in this study lays an important foundation for further research on prevention and control strategy of BVDV and its pathogenesis. In addition, the antiviral effect of butyrate, the metabolites of butyrate-producing bacteria, has been further revealed. Overall, our findings provide a promising prevention and control strategy to treat this infectious disease which is distributed worldwide.

Disrupting the gut microbiota/metabolites axis by Di-(2-ethylhexyl) phthalate drives intestinal inflammation via AhR/NF-κB pathway in mice

Di-(2-ethylhexyl) phthalate (DEHP) is a widely used plasticizer known for its environmental endocrine-disrupting properties, posing potential risks to various organs. However, the precise impact of DEHP on intestinal health and its contribution to the initiation of intestinal inflammation remains elucidated. This study aims to investigate the underlying mechanisms of DEHP-induced intestinal inflammation in mice, specifically focusing on the complex interplay between the gut microbiota-metabolite axis and associated pathophysiological alterations. Our findings showed that DEHP-induced damage of multiple organs systemically, as indicated by abnormal liver and kidney biochemical markers, along with a disrupted ileum morphology. Additionally, DEHP exposure disrupted gut barrier function, causing intestinal inflammation characterized by bacterial translocation and alterations in defense and inflammation-related gene expressions. Moreover, 16S rRNA analysis suggested that DEHP-induced gut microbial remodeling is characterized by an upregulation of detrimental bacteria (Erysipelotrichaceae) and a downregulation of beneficial bacteria (Muribaculaceae, Ruminococcaceae, and Lachnospiraceae). Metabolomics analysis revealed DEHP perturbed gut metabolic homeostasis, particularly affecting the degradation of aromatic compounds, which generated an aberrant activation of the AhR and NF-κB, subsequently causing intestinal inflammation. Consequently, our results elucidate the mechanistic link between disrupted gut microbiota and metabolome and the initiation of DEHP-induced intestinal inflammation, mediated through the AhR/NF-κB signaling pathway.

Gut microbiome-associated predictors as biomarkers of response to advanced therapies in inflammatory bowel disease: a systematic review

Loss of response to therapy in inflammatory bowel disease (IBD) has led to a surge in research focusing on precision medicine. Three systematic reviews have been published investigating the associations between gut microbiota and disease activity or IBD therapy. We performed a systematic review to investigate the microbiome predictors of response to advanced therapy in IBD. Unlike previous studies, our review focused on predictors of response to therapy; so the included studies assessed microbiome predictors before the proposed time of response or remission. We also provide an update of the available data on mycobiomes and viromes. We highlight key themes in the literature that may serve as future biomarkers of treatment response: the abundance of fecal SCFA-producing bacteria and opportunistic bacteria, metabolic pathways related to butyrate synthesis, and non-butyrate metabolomic predictors, including bile acids (BAs), amino acids, and lipids, as well as mycobiome predictors of response.

Engineered probiotics introduced to improve intestinal microecology for the treatment of chronic diseases: present state and perspectives

Purpose

Correcting intestinal microecological imbalance has become one of the core strategies to treat chronic diseases. Some traditional microecology-based therapies targeting intestine, such as prebiotic therapy, probiotic therapy and fecal microbiota transplantation therapy, have been used in the prevention and treatment of clinical chronic diseases, which still facing low safety and poor controllability problems. The development of synthetic biology technology has promoted the development of intestinal microecology-based therapeutics for chronic diseases, which exhibiting higher robustness and controllability, and become an important part of the next generation of microecological therapy. The purpose of this review is to summarize the application of synthetic biology in intestinal microecology-based therapeutics for chronic diseases.

Methods

The available literatures were searched to find out experimental studies and relevant review articles on the application of synthetic biology in intestinal microecology-based therapeutics for chronic diseases from year 1990 to 2023.

Results

Evidence proposed that synthetic biology has been applied in the intestinal microecology-based therapeutics for chronic diseases, covering metabolic diseases (e.g. diabetes, obesity, nonalcoholic fatty liver disease and phenylketonuria), digestive diseases (e.g. inflammatory bowel disease and colorectal cancer), and neurodegenerative diseases (e.g. Alzheimer's disease and Parkinson's disease).

Conclusion

This review summarizes the application of synthetic biology in intestinal microecology-based therapeutics for major chronic diseases and discusses the opportunities and challenges in the above process, providing clinical possibilities of synthetic biology technology applied in microecological therapies.

Exploring the relationship between urinary phthalate metabolites and Crohn's disease via oxidative stress, and the potential moderating role of gut microbiota: A conditional mediation model

OBJECTIVE

Interactions between phthalic acid esters (PAEs) exposure and Crohn's disease (CD) were unknown. This study aims to examine the association between exposure to PAEs and CD activity and to explore the roles of oxidative stress and microbiota.

METHODS

A cross-sectional study with 127 CD patients was conducted. The disease activity was evaluated based on symptoms (Harvey-Bradshaw index, HBI), endoscopy findings (Simple Endoscopic Score for CD, SES-CD), and computed tomography enterography (CTE-scores). Ten urinary PAEs metabolites (mPAEs), two urinary oxidative stress biomarkers, including 8-hydroxydeoxyguanosine (8-OHdG) and 8-iso-prostaglandin-F2α (8-iso-PGF2α), as well as 16S rRNA sequencing of stool samples were determined. Multiple linear regression models and Hayes's PROCESS macro for SPSS were used to evaluate the interplays between urinary PAEs metabolites, CD activities, oxidative stress, and microbiota diversity.

RESULTS

There were positive associations between most mPAEs and HBI. Oxidative stress mediated 20.69-89.29% of the indirect associations between low molecular weight (LMW) mPAEs and HBI, while the majority of the high molecular weight (HMW) mPAEs were directly associated with HBI. In addition, microbiota diversity moderated the indirect associations of LMW mPAEs on HBI.

CONCLUSIONS

PAEs exposure was related to CD activity, and the association could be mediated by oxidative stress and reversed or alleviated by rich gut microbiota.

Genetically engineered bacteria: a new frontier in targeted drug delivery

Genetically engineered bacteria (GEB) have shown significant promise to revolutionize modern medicine. These engineered bacteria with unique properties such as enhanced targeting, versatility, biofilm disruption, reduced drug resistance, self-amplification capabilities, and biodegradability represent a highly promising approach for targeted drug delivery and cancer theranostics. This innovative approach involves modifying bacterial strains to function as drug carriers, capable of delivering therapeutic agents directly to specific cells or tissues. Unlike synthetic drug delivery systems, GEB are inherently biodegradable and can be naturally eliminated from the body, reducing potential long-term side effects or complications associated with residual foreign constituents. However, several pivotal challenges such as safety and controllability need to be addressed. Researchers have explored novel tactics to improve their capabilities and overcome existing challenges, including synthetic biology tools (e.g., clustered regularly interspaced short palindromic repeats (CRISPR) and bioinformatics-driven design), microbiome engineering, combination therapies, immune system interaction, and biocontainment strategies. Because of the remarkable advantages and tangible progress in this field, GEB may emerge as vital tools in personalized medicine, providing precise and controlled drug delivery for various diseases (especially cancer). In this context, future directions include the integration of nanotechnology with GEB, the focus on microbiota-targeted therapies, the incorporation of programmable behaviors, the enhancement in immunotherapy treatments, and the discovery of non-medical applications. In this way, careful ethical considerations and regulatory frameworks are necessary for developing GEB-based systems for targeted drug delivery. By addressing safety concerns, ensuring informed consent, promoting equitable access, understanding long-term effects, mitigating dual-use risks, and fostering public engagement, these engineered bacteria can be employed as promising delivery vehicles in bio- and nanomedicine. In this review, recent advances related to the application of GEB in targeted drug delivery and cancer therapy are discussed, covering crucial challenging issues and future perspectives.

Engineering Escherichia coli Nissle 1917 as a microbial chassis for therapeutic and industrial applications

Genetically engineered microbes, especially Escherichia coli, have been widely used in the biosynthesis of proteins and metabolites for medical and industrial applications. As a traditional probiotic with a well-established safety record, E. coli Nissle 1917 (EcN) has recently emerged as a microbial chassis for generating living therapeutics, drug delivery vehicles, and microbial platforms for industrial production. Despite the availability of genetic tools for engineering laboratory E. coli K-12 and B strains, new genetic engineering systems are still greatly needed to expand the application range of EcN. In this review, we have summarized the latest progress in the development of genetic engineering systems in EcN, as well as their applications in the biosynthesis and delivery of valuable small molecules and biomacromolecules of medical and/or industrial interest, followed by a glimpse of how this rapidly growing field will evolve in the future.

Xianglian Zhixie Tablet Antagonizes Dextran Sulfate Sodium-Induced Ulcerative Colitis by Attenuating Systemic Inflammation and Modulating Gut Microbiota

Purpose

Xianglian Zhixie Tablet (XLZXT), a classical traditional Chinese medicine formulation, is commonly used to treat Ulcerative Colitis (UC) in China. However, the therapeutic mechanisms of XLZXT for UC have yet to be fully understood. This study aimed to investigate the curative benefits of XLZXT and its associated mechanisms for healing UC in mice.

Methods

In the present study, the 1% dextran sulfate sodium (DSS) solution was used to establish the UC model in C57BL/6N mice. To investigate the therapeutic effects of XLZXT on DSS-induced UC mice, several parameters were measured, including DAI score, colon length, spleen index, pathological changes in colon tissue, and levels of inflammatory factors in plasma and colon tissue. By investigating the gut microbiota, assessing the levels of intestinal mucosal protein expression, and looking at the proteins involved in the TLR4/MyD88/NF-B p65 signaling pathway, the mechanisms of XLZXT impact on UC were investigated. Mouse feces were examined for patterns of gut microbiota expression using high-throughput sequencing of 16S rRNA.

Results

XLZXT effectively alleviated UC symptoms and colon pathological damage in DSS-induced UC mice. It improved body weight loss, stool consistency, and hematochezia, while also repairing colon damage. Moreover, it down-regulated pro-inflammatory cytokines (such as TNF-α, IL-1β, and IL-6), and up-regulated anti-inflammatory cytokines (such as IL-10). XLZXT also increased the expression of MUC-2, Occludin and ZO-1, while decreasing the expression of NF-κB, MyD88 and TLR4. Additionally, it regulated gut microbiota disorder by increasing the abundance of beneficial bacteria and reducing the adhesion of intestinal harmful bacteria.

Conclusion

XLZXT demonstrated therapeutic effects on DSS-induced UC mice. The mechanisms may be associated with repairing the intestinal mucosal barrier, regulating the TLR4/MyD88/NF-κB p65 signaling pathway, and restoring the balance of gut microbiota.

Effect of carotenoids on gut health and inflammatory status: A systematic review of in vivo animal studies

Carotenoids have anti-inflammatory and antioxidant properties, being a potential bioactive compound for gut health. The objective of this systematic review was to investigate the effects of carotenoids on gut microbiota, gut barrier, and inflammation in healthy animals. The systematic search from PubMed, Scopus, and Lilacs databases were performed up to March 2023. The final screening included thirty studies, with different animal models (mice, rats, pigs, chicks, drosophila, fish, and shrimp), and different carotenoid sources (β-carotene, lycopene, astaxanthin, zeaxanthin, lutein, and fucoxanthin). The results suggested that carotenoids seem to act on gut microbiota by promoting beneficial effects on intestinal bacteria related to both inflammation and SCFA production; increase tight junction proteins expression, important for reducing intestinal permeability; increase the mucins expression, important in protecting against pathogens and toxins; improve morphological parameters important for digestion and absorption of nutrients; and reduce pro-inflammatory and increase anti-inflammatory cytokines. However, different carotenoids had distinct effects on gut health. In addition, there was heterogeneity between studies regarding animal model, duration of intervention, and doses used. This is the first systematic review to address the effects of carotenoids on gut health. Further studies are needed to better understand the effects of carotenoids on gut health.

Dealcoholized muscadine wine was partially effective in preventing and treating dextran sulfate sodium-induced colitis and restoring gut dysbiosis in mice

Muscadine wine has a unique polyphenol profile consisting of anthocyanins, ellagic acids, and flavonols. This study aims to compare the prevention, treatment, and combined activity (P + T) of dealcoholized muscadine wine (DMW) on DSS-induced colitis in mice and its impact on the gut microbiome. Male C57BL/6 mice in the healthy and colitis group received an AIN-93M diet for 28 days. In the prevention, treatment, and P + T (prevention + treatment) groups, mice received an AIN-93M diet containing 2.79% (v/w) DMW on days 1-14, 15-28, and 1-28, respectively. Except for mice in the healthy group, all mice were given water with 2.5% (w/v) DSS on days 8-14 to induce colitis. DMW in all three receiving groups reduced myeloperoxidase activity, histology scores, and phosphorylation of Iκb-α in the colon. Colon shortening, serum IL-6, and colonic mRNA of TNF-α were blunted only in the P + T group. Gut permeability was reduced in the treatment and P + T groups. DMW in P + T group showed higher activity to increase microbiome evenness, modulate β-diversity, elevate the cecal content of SCFAs, and enrich SCFA-producing bacteria, including Lactobacillaceae, Lachnospiraceae, Ruminococcaceae, and Peptococcaceae. This was accompanied by a decrease in pathogenic Burkholderiaceae in mice. This study suggests that muscadine wine has partial preventive and therapeutic effects against inflammatory bowel disease. The combination of prevention and treatment using DMW showed better activities than either prevention or treatment.

Melatonin improves the homeostasis of mice gut microbiota rhythm caused by sleep restriction

Insufficient sleep is regarded as a disruptor of circadian rhythm, and it also contributes to the occurrence of intestinal diseases. The physiological functions of the gut depend on the normal circadian rhythm of the intestinal microbiota. However, how lack of sleep affects intestinal circadian homeostasis is unclear. Therefore, we subjected mice to sleep restriction and found that chronic sleep loss disrupts the pattern of colonic microbial communities and reduces the proportion of gut microbiota with a circadian rhythm, with concomitant changes in the peak phase of the KEGG pathway. We then found that exogenous melatonin supplementation restored the proportion of gut microbiota with a circadian rhythm and increased the KEGG pathway with a circadian rhythm. And we screened for possible circadian oscillation families, Muribaculaceae and Lachnospiraceae, that are sensitive to sleep restriction and can be rescued by melatonin. Our results suggest that sleep restriction disrupts the circadian rhythm of the colonic microbiota. In contrast, melatonin ameliorates disturbances in the circadian rhythm homeostasis of the gut microbiota due to sleep restriction.

STING Promotes Intestinal IgA Production by Regulating Acetate-producing Bacteria to Maintain Host-microbiota Mutualism

BACKGROUND

Intestinal Immunoglobulin A (IgA) is crucial in maintaining host-microbiota mutualism and gut homeostasis. It has been shown that many species of gut bacteria produce cyclic dinucleotides, along with an abundance of microbiota-derived DNA present within the intestinal lumen, which triggers the tonic activation of the cytosolic cGAS-STING pathway. However, the role of STING in intestinal IgA remains poorly understood. We further investigated whether and how STING affects intestinal IgA response.

METHODS

Intestinal IgA was determined between wild-type (WT) mice and Sting-/- mice in steady conditions and upon enteric Citrobacter rodentium infection. STING agonists were used to stimulating B cells or dendritic cells in vitro. Gut microbiota composition was examined by 16S ribosomal RNA gene sequencing. Bacteria metabolomics functional analyses was performed by PICRUSt2. Fecal short-chain fatty acid (SCFA) was determined by Mass spectrometry and Cedex Bio Analyzer. Gut bacteria from WT mice and Sting-/- mice were transferred into germ-free mice and antibiotic-pretreated mice.

RESULTS

Intestinal IgA response was impaired in Sting-/- mice. However, STING agonists did not directly stimulate B cells or dendritic cells to induce IgA. Interestingly, Sting-/- mice displayed altered gut microbiota composition with decreased SCFA-producing bacteria and downregulated SCFA fermentation pathways. Transfer of fecal bacteria from Sting-/- mice induced less IgA than that from WT mice in germ-free mice and antibiotic-pretreated mice, which is mediated by GPR43. Acetate, the dominant SCFA, was decreased in Sting-/- mice, and supplementation of acetate restored intestinal IgA production in Sting-/- mice.

CONCLUSIONS

STING promotes intestinal IgA by regulating acetate-producing gut bacteria.

Prophylactic effect of Tongxieyaofang polysaccharide on depressive behavior in adolescent male mice with chronic unpredictable stress through the microbiome-gut-brain axis

Major depression disorder is more common among adolescents and is a primary reason for suicide in adolescents. Some antidepressants are ineffective and may possess side effects. Therefore, developing an adolescent antidepressant is the need of the hour. We designed the stress model of adolescent male mice induced by chronic unpredictable stress (CUS). The mice were treated using Tongxieyaofang neutral polysaccharide (TXYF-NP), Tongxieyaofang acidic polysaccharide (TXYF-AP), TXYF-AP + TXYF-NP and fructooligosaccharide + galactooligosaccharides to determine their body weight, behavior, and serum hormone levels. RT-qPCR was used to detect the gene expression of Crhr1, Nr3c1, and Nr3c2 in the hypothalamus and hippocampus and the gene expression of glutamic acid and γ-aminobutyric acid-related receptors in the hippocampus. RT-qPCR, Western blot, and ELISA detected tryptophan metabolism in the colon, serum, and hippocampus. 16s rDNA helped sequence colon microflora, and non-targeted metabolomics enabled the collection of metabolic profiles of colon microflora. In adolescent male mice, CUS induced depression-like behavior, hypothalamic-pituitary-adrenal axis hyperactivity, hippocampal tissue damage, abnormal expression of its related receptors, and dysregulation of tryptophan metabolism. The 16s rDNA and non-targeted metabolomics revealed that CUS led to colon microflora disorder and bile acid metabolism abnormality. Tongxieyaofang polysaccharide could improve the bacterial community and bile acid metabolism disorder by upregulating the relative abundance of Lactobacillus gasseri, Lachnospiraceae bacterium 28-4, Bacteroides and Ruminococcaceae UCG-014 while preventing CUS-induced changes. TXYF-P can inhibit depression-like behavior due to CUS by regulating colonic microflora and restoring bile acid metabolism disorder. Thus, based on the different comparisons, TXYF-NP possessed the best effect.

Short chain fatty acids, a possible treatment option for autoimmune diseases

Gut microbiota can interact with the immune system through its metabolites. Short-chain fatty acids (SCFAs), as one of the most abundant metabolites of the resident gut microbiota play an important role in this crosstalk. SCFAs (acetate, propionate, and butyrate) regulate nearly every type of immune cell in the gut's immune cell repertoire regarding their development and function. SCFAs work through several pathways to impose protection towards colonic health and against local or systemic inflammation. Additionally, SCFAs play a role in the regulation of immune or non-immune pathways that can slow the development of autoimmunity either systematically or in situ. The present study aims to summarize the current knowledge on the immunomodulatory roles of SCFAs and the association between the SCFAs and autoimmune disorders such as celiac disease (CD), inflammatory bowel disease (IBD), rheumatoid arthritis (RA), multiple sclerosis (MS), systemic lupus erythematosus (SLE), type 1 diabetes (T1D) and other immune-mediated diseases, uncovering a brand-new therapeutic possibility to prevent or treat autoimmunity.

Role of prebiotics, probiotics, and synbiotics in management of inflammatory bowel disease: Current perspectives

Experimental evidence supports the fact that changes in the bowel microflora due to environmental or dietary factors have been investigated as implicating factors in the etiopathogenesis of inflammatory bowel disease (IBD). The amassing knowledge that the inhabited microbiome regulates the gut physiology and immune functions in IBD, has led researchers to explore the effectiveness of prebiotics, probiotics, and synbiotics in treating IBD. This therapeutic approach focuses on restoring the dynamic balance between the microflora and host defense mechanisms in the intestinal mucosa to prevent the onset and persistence of intestinal inflammation. Numerous microbial strains and carbohydrate blends, along with their combinations have been examined in experimental colitis models and clinical trials, and the results indicated that it can be an attractive therapeutic strategy for the suppression of inflammation, remission induction, and relapse prevention in IBD with minimal side effects. Several mechanisms of action of probiotics (for e.g., Lactobacillus species, and Bifidobacterium species) have been reported such as suppression of pathogen growth by releasing certain antimicrobial mediators (lactic and hydrogen peroxide, acetic acid, and bacteriocins), immunomodulation and initiation of an immune response, enhancement of barrier activity, and suppression of human T-cell proliferation. Prebiotics such as lactulose, lactosucrose, oligofructose, and inulin have been found to induce the growth of certain types of host microflora, resulting in an enriched enteric function. These non-digestible food dietary components have been reported to exert anti-inflammatory effects by inhibiting the expression of tumor necrosis factor-α-related cytokines while augmenting interleukin-10 levels. Although pro-and prebiotics has established their efficacy in healthy subjects, a better understanding of the luminal ecosystem is required to determine which specific bacterial strain or combination of probiotics and prebiotics would prove to be the ideal treatment for IBD. Clinical trials, however, have given some conflicting results, requiring the necessity to cite the more profound clinical effect of these treatments on IBD remission and prevention. The purpose of this review article is to provide the most comprehensive and updated review on the utility of prebiotics, probiotics, and synbiotics in the management of active Crohn's disease and ulcerative colitis/pouchitis.

The Role of Genetically Engineered Probiotics for Treatment of Inflammatory Bowel Disease: A Systematic Review

BACKGROUND

Many preclinical studies have demonstrated the effectiveness of genetically modified probiotics (gm probiotics) in animal models of inflammatory bowel disease (IBD).

OBJECTIVE

This systematic review was performed to investigate the role of gm probiotics in treating IBD and to clarify the involved mechanisms.

METHODS

PubMed, Web of Science, Cochrane Library, and Medline were searched from their inception to 18 September 2022 to identify preclinical and clinical studies exploring the efficacy of gm probiotics in IBD animal models or IBD patients. Two independent researchers extracted data from the included studies, and the data were pooled by the type of study; that is, preclinical or clinical.

RESULTS

Forty-five preclinical studies were included. In these studies, sodium dextran sulfate and trinitrobenzene sulfonic acid were used to induce colitis. Eleven probiotic species have been genetically modified to produce therapeutic substances, including IL-10, antimicrobial peptides, antioxidant enzymes, and short-chain fatty acids, with potential therapeutic properties against colitis. The results showed generally positive effects of gm probiotics in reducing disease activity and ameliorating intestinal damage in IBD models; however, the efficacy of gm probiotics compared to that of wild-type probiotics in many studies was unclear. The main mechanisms identified include modulation of the diversity and composition of the gut microbiota, production of regulatory metabolites by beneficial bacteria, reduction of the pro- to anti-inflammatory cytokine ratio in colonic tissue and plasma, modulation of oxidative stress activity in the colon, and improvement of intestinal barrier integrity. Moreover, only one clinical trial with 10 patients with Crohn's disease was included, which showed that L. lactis producing IL-10 was safe, and a decrease in disease activity was observed in these patients.

CONCLUSIONS

Gm probiotics have a certain efficacy in colitis models through several mechanisms. However, given the scarcity of clinical trials, it is important for researchers to pay more attention to gm probiotics that are more effective and safer than wild-type probiotics to facilitate further clinical translation.