Role and mechanisms of action of Escherichia coli Nissle 1917 in the maintenance of remission in ulcerative colitis patients: An update

Insights into Probiotic Prescription among Gastroenterologists and Other Healthcare Professionals: Evidence from an Italian Survey

Background: Probiotics, which are live microorganisms that provide health benefits, have been extensively studied for their various clinical applications. However, despite their potential, high-quality data supporting their use in several gastrointestinal diseases are often lacking, and prescription behaviors can widely differ. This study aimed to assess different behaviors in probiotics knowledge and prescriptions among Italian gastroenterologists and healthcare professionals (HPs). Methods: A web-based electronic survey was distributed to all participants at the National Meeting of the Italian Young Gastroenterologist and Endoscopist Association (AGGEI) held in 2023. The survey investigated probiotic prescription practices for several gastrointestinal conditions, such as acute diarrhea, irritable bowel syndrome, inflammatory bowel disease, and diverticular disease. Results: Among 200 participants, 142 completed the survey, of whom 59 were gastroenterologists and 83 were HPs (surgeons, nutrition biologists, and other physicians). Significant differences were observed in the prescription of probiotics for the treatment of acute diarrhea and H. pylori. Both groups prescribed probiotics in monthly cycles for patients with IBS, although the majority prescribed multistrain formulations. Gastroenterologists were more likely to prescribe cyclic courses for IBS, while HPs tended to continue therapy by changing the probiotic strain in case of inefficacy. For ulcerative colitis, gastroenterologists prescribed probiotics more but for shorter durations. In Crohn's disease, gastroenterologists prescribed probiotics less and were less likely to prescribe multistrain formulations. Regarding SUDD, gastroenterologists tended to prescribe probiotics less frequently, although without a significant difference, with similar rates of preference for multistrain formulations. Conclusions: This survey highlights heterogeneous behaviors in probiotic prescription between gastroenterologists and HPs, with gastroenterologists more aligned with guidelines and available scientific evidence. Hence, enhancing probiotic education among healthcare professionals and gastroenterologists is crucial. Further studies are needed to better understand probiotics' role in gastrointestinal disorders through large-scale randomized controlled trials.

Genetic heterogeneity of engineered Escherichia coli Nissle 1917 strains during scale-up simulation

Advanced microbiome therapeutics have emerged as a powerful approach for the treatment of numerous diseases. While the genetic instability of genetically engineered microorganisms is a well-known challenge in the scale-up of biomanufacturing processes, it has not yet been investigated for advanced microbiome therapeutics. Here, the evolution of engineered Escherichia coli Nissle 1917 strains producing Interleukin 2 and Aldafermin were investigated in two strain backgrounds with and without the three error-prone DNA polymerases polB, dinB, and umuDC, which contribute to the mutation rate of the host strain. Whole genome short-read sequencing revealed the genetic instability of the pMUT-based production plasmid after serial passaging for approximately 150 generations using an automated platform for high-throughput microbial evolution in five independent lineages for six distinct strains. While a reduction of the number of mutations of 12%-43% could be observed after the deletion of the error-prone DNA polymerases, the interruption of production-relevant genes could not be prevented, highlighting the need for additional strategies to improve the stability of advanced microbiome therapeutics.

Potential of using an engineered indole lactic acid producing Escherichia coli Nissle 1917 in a murine model of colitis

The gut microbiome is a significant factor in the pathophysiology of ulcerative colitis (UC), prompting investigations into the use of probiotic therapies to counter gastrointestinal inflammation. However, while much attention has been given to the therapeutic potential of microbes at the species and strain level, the discovery and application of their metabolic products may offer more precise and controlled solutions in battling disease. In this work, we examined the therapeutic potential of indole lactic acid (ILA) to alleviate inflammation in a murine model of colitis. A previously constructed ILA-producing Escherichia coli Nissle 1917 strain (EcN aldh) and its isogenic non-ILA producing counterpart (EcN) were studied in a murine model of Dextran Sodium Sulfate (DSS) induced colitis. The colitic animals suffered from severe colitic symptoms, with no differentiation between the groups in body weight loss and disease activity index. However, three days after cessation of DSS treatment the EcN aldh-treated mice showed signs of reduced intestinal inflammation, as manifested by lower concentrations of fecal lipocalin-2. Additionally, expression analysis of the inflamed tissue revealed distinct effects of the EcN aldh strain on proteins associated with intestinal health, such as TFF3, occludin and IL-1β expression. These results show no impact of EcN or EcN aldh on acute DSS-induced colitis, but suggest that in particular EcN aldh may assist recovery from intestinal inflammation.

The role of the fecal microbiota in inflammatory bowel disease

The understanding of the potential role of the microbiota in the pathogenesis of inflammatory bowel disease (IBD) is ever-evolving. Traditionally, the management of IBD has involved medical therapy and/or surgical intervention. IBD can be characterized by gut microbiome alterations through various pathological processes. Various studies delve into nontraditional methods such as probiotics and fecal microbiota transplant and their potential therapeutic effects. Fecal microbiota transplant involves the delivery of a balanced composition of gut microorganisms into an affected patient via multiple possible routes and methods, while probiotics consist of live microorganisms given via the oral route. At present, neither method is considered first-line treatment, however, fecal microbiota transplant has shown potential success in inducing and maintaining remission in ulcerative colitis. In a study by Kruis and colleagues, Escherichia coli Nissle 1917 was considered to be equivalent to mesalamine in mild ulcerative colitis. Alteration of the microbiome in the management of Crohn's disease is less well defined. Furthermore, variation in the clinical usefulness of 5-aminosalicylic acid medication has been attributed, in part, to its acetylation and inactivation by gut microbes. In summary, our understanding of the microbiome's role is continually advancing, with the possibility of paving the way for personalized medicine based on the microbiome.

Proteomic Analysis of Caco-2 Cells Disrupted by EcN 1917-Derived OMVs Reveals Molecular Information on Bacteria-Mediated Cancer Cell Migration

Escherichia coli Nissle 1917 (EcN 1917) exhibits distinct tumor-targeting activity, and early studies demonstrated that outer membrane vesicles (OMVs) mediate bacteria-host interactions. To decipher the molecular mechanism underlying the interaction between EcN 1917 and host cells via OMV-mediated communication, we investigated the phenotypic changes in Caco-2 cells perturbed by EcN 1917-derived OMVs and constructed proteomic maps of the EcN 1917-derived OMV components and OMV-perturbed host cells. Our findings revealed that the size of the EcN 1917-derived OMV proteome increased 4-fold. Treatment with EcN 1917-derived OMVs altered the proteomic and phosphoproteomic profiles of host cells. Importantly, for the first time, we found that treatment with EcN 1917-derived OMVs inhibited cancer cell migration by suppressing the expression of ANXA9. In addition, phosphoproteomic data suggested that the ErbB pathway may be involved in OMV-mediated cell migration. Taken together, our study provides valuable data for further investigations of OMV-mediated bacteria-host interactions and offers great insights into the underlying mechanism of probiotic-assisted colorectal cancer therapy.

Importance of Gut Microbiota in Patients with Inflammatory Bowel Disease

Inflammatory bowel diseases (IBDs), such as Crohn's disease (CD) and ulcerative colitis (UC), are chronic diseases of the digestive system with a multifactorial and not fully understood etiology. There is research suggesting that they may be initiated by genetic, immunological, and lifestyle factors. In turn, all of these factors play an important role in the modulation of intestinal microflora, and a significant proportion of IBD patients struggle with intestinal dysbiosis, which leads to the conclusion that intestinal microflora disorders may significantly increase the risk of developing IBD. Additionally, in IBD patients, Toll-like receptors (TLRs) produced by intestinal epithelial cells and dendritic cells treat intestinal bacterial antigens as pathogens, which causes a disruption of the immune response, resulting in the development of an inflammatory process. This may result in the occurrence of intestinal dysbiosis, which IBD patients are significantly vulnerable to. In this study, we reviewed scientific studies (in particular, systematic reviews with meta-analyses, being studies with the highest level of evidence) regarding the microflora of patients with IBD vs. the microflora in healthy people, and the use of various strains in IBD therapy.

Immunological nanomaterials to combat cancer metastasis

Metastasis causes greater than 90% of cancer-associated deaths, presenting huge challenges for detection and efficient treatment of cancer due to its high heterogeneity and widespread dissemination to various organs. Therefore, it is imperative to combat cancer metastasis, which is the key to achieving complete cancer eradication. Immunotherapy as a systemic approach has shown promising potential to combat metastasis. However, current clinical immunotherapies are not effective for all patients or all types of cancer metastases owing to insufficient immune responses. In recent years, immunological nanomaterials with intrinsic immunogenicity or immunomodulatory agents with efficient loading have been shown to enhance immune responses to eliminate metastasis. In this review, we would like to summarize various types of immunological nanomaterials against metastasis. Moreover, this review will summarize a series of immunological nanomaterial-mediated immunotherapy strategies to combat metastasis, including immunogenic cell death, regulation of chemokines and cytokines, improving the immunosuppressive tumour microenvironment, activation of the STING pathway, enhancing cytotoxic natural killer cell activity, enhancing antigen presentation of dendritic cells, and enhancing chimeric antigen receptor T cell therapy. Furthermore, the synergistic anti-metastasis strategies based on the combinational use of immunotherapy and other therapeutic modalities will also be introduced. In addition, the nanomaterial-mediated imaging techniques (e.g., optical imaging, magnetic resonance imaging, computed tomography, photoacoustic imaging, surface-enhanced Raman scattering, radionuclide imaging, etc.) for detecting metastasis and monitoring anti-metastasis efficacy are also summarized. Finally, the current challenges and future prospects of immunological nanomaterial-based anti-metastasis are also elucidated with the intention to accelerate its clinical translation.

A critical assessment of microbial-based antimicrobial sanitizing of inanimate surfaces in healthcare settings

The global rise in antimicrobial resistance (AMR) poses a significant public health threat, especially in healthcare settings, where controlling the spread of antimicrobial genes is crucial. While person-to-person transmission remains the primary route for healthcare-associated infections (HAIs), hospital surfaces serve as key reservoirs for antimicrobial-resistant microorganisms. Regular cleaning and disinfection of these surfaces are essential. Microbial-based products for sanitizing hospital surfaces have emerged as promising tools to combat HAIs and AMR. However, a review of 32 publications found inconsistencies and potential risks. A total of 15 publications included hospital-based trials, while the rest were either in vitro or in situ assays, reviews, book chapters, or commentaries. In most of the hospital-based studies, specific strains of applied microorganisms were not identified, and the term "probiotic" was inaccurately used. These products mainly featured spores from Bacillus and Priestia genera, which was mainly hypothesized to work through competitive exclusion. Most hospital-based studies have shown that the application of microbial-based products resulted in a significant reduction in pathogens on surfaces, thereby contributing to a decrease in the incidence of healthcare-associated infections (HAIs). Further research is however needed to understand the effectiveness, mechanisms of action, and safety of microbial-based sanitizing agents. Strain-level identification is crucial for safety assessments, yet many reviewed products lacked this information. Consequently, there is a need for rigorous safety evaluations within existing regulatory frameworks to ensure the efficacy and safety of microbial-based cleaning products in healthcare settings.

Efficient Isolation of Outer Membrane Vesicles (OMVs) Secreted by Gram-Negative Bacteria via a Novel Gradient Filtration Method

Bacterial extracellular vesicles (bEVs) secreted by Gram-negative bacteria are referred to as outer membrane vesicles (OMVs) because they originate in the outer membrane. OMVs are membrane-coated vesicles 20-250 nm in size. They contain lipopolysaccharide (LPS), peptidoglycan, proteins, lipids, nucleic acids, and other substances derived from their parent bacteria and participate in the transmission of information to host cells. OMVs have broad prospects in terms of potential application in the fields of adjuvants, vaccines, and drug delivery vehicles. Currently, there remains a lack of efficient and convenient methods to isolate OMVs, which greatly limits OMV-related research. In this study, we developed a fast, convenient, and low-cost gradient filtration method to separate OMVs that can achieve industrial-scale production while maintaining the biological activity of the isolated OMVs. We compared the gradient filtration method with traditional ultracentrifugation to isolate OMVs from probiotic Escherichia coli Nissle 1917 (EcN) bacteria. Then, we used RAW264.7 macrophages as an in vitro model to study the influence on the immune function of EcN-derived OMVs obtained through the gradient filtration method. Our results indicated that EcN-derived OMVs were efficiently isolated using our gradient filtration method. The level of OMV enrichment obtained via our gradient filtration method was about twice as efficient as that achieved through traditional ultracentrifugation. The EcN-derived OMVs enriched through the gradient filtration method were successfully taken up by RAW264.7 macrophages and induced them to secrete pro-inflammatory cytokines such as tumor necrosis factor α (TNF-α) and interleukins (ILs) 6 and 1β, as well as anti-inflammatory cytokine IL-10. Furthermore, EcN-derived OMVs induced more anti-inflammatory response (i.e., IL-10) than pro-inflammatory response (i.e., TNF-α, IL-6, and IL-1β). These results were consistent with those reported in the literature. The related literature reported that EcN-derived OMVs obtained through ultracentrifugation could induce stronger anti-inflammatory responses than pro-inflammatory responses in RAW264.7 macrophages. Our simple and novel separation method may therefore have promising prospects in terms of applications involving the study of OMVs.

Microbiota and IBD: Current knowledge and future perspectives

Inflammatory Bowel Disease (IBD) is a chronic relapsing-remitting disease with a remarkable increase in incidence worldwide and a substantial disease burden. Although the pathophysiology is not fully elucidated yet an aberrant immune reaction against the intestinal microbiota and the gut microbial dysbiosis have been identified to play a major role. The composition of gut microbiota in IBD patients is distinct from that of healthy individuals, with certain organisms predominating over others. Differences in the microbial dysbiosis have been also observed between Crohn Disease (CD) and Ulcerative Colitis (UC). A disruption of the microbiota's balance can lead to inflammation and intestinal damage. Microbiota composition in IBD can be affected both by endogenous (i.e., interaction with the immune system and intestinal epithelial cells) and exogenous (i.e., medications, surgery, diet) factors. The complex interplay between the gut microbiota and IBD is an area of great interest for understanding disease pathogenesis and developing new treatments. The purpose of this review is to summarize the latest evidence on the role of microbiota in IBD pathogenesis and to explore possible future areas of research.

Modulation of Serotonin-Related Genes by Extracellular Vesicles of the Probiotic Escherichia coli Nissle 1917 in the Interleukin-1β-Induced Inflammation Model of Intestinal Epithelial Cells

Inflammatory bowel disease (IBD) is a chronic inflammatory condition involving dysregulated immune responses and imbalances in the gut microbiota in genetically susceptible individuals. Current therapies for IBD often have significant side-effects and limited success, prompting the search for novel therapeutic strategies. Microbiome-based approaches aim to restore the gut microbiota balance towards anti-inflammatory and mucosa-healing profiles. Extracellular vesicles (EVs) from beneficial gut microbes are emerging as potential postbiotics. Serotonin plays a crucial role in intestinal homeostasis, and its dysregulation is associated with IBD severity. Our study investigated the impact of EVs from the probiotic Nissle 1917 (EcN) and commensal E. coli on intestinal serotonin metabolism under inflammatory conditions using an IL-1β-induced inflammation model in Caco-2 cells. We found strain-specific effects. Specifically, EcN EVs reduced free serotonin levels by upregulating SERT expression through the downregulation of miR-24, miR-200a, TLR4, and NOD1. Additionally, EcN EVs mitigated IL-1β-induced changes in tight junction proteins and oxidative stress markers. These findings underscore the potential of postbiotic interventions as a therapeutic approach for IBD and related pathologies, with EcN EVs exhibiting promise in modulating serotonin metabolism and preserving intestinal barrier integrity. This study is the first to demonstrate the regulation of miR-24 and miR-200a by probiotic-derived EVs.

Sensitive delivery systems and novel encapsulation technologies for live biotherapeutic products and probiotics

Live biotherapeutic product (LBP), a type of biological product, holds promise for the prevention or treatment of metabolic disease and pathogenic infection. Probiotics are live microorganisms that improve the intestinal microbial balance and beneficially affect the health of the host when ingested in sufficient numbers. These biological products possess the advantages of inhibition of pathogens, degradation of toxins, and modulation of immunity. The application of LBP and probiotic delivery systems has attracted great interest to researchers. The initial used technologies for LBP and probiotic encapsulation are traditional capsules and microcapsules. However, the stability and targeted delivery capability require further improved. The specific sensitive materials can greatly improve the delivery efficiency of LBPs and probiotics. The specific sensitive delivery systems show advantages over traditional ones due to their better properties of biocompatibility, biodegradability, innocuousness, and stability. Moreover, some new technologies, including layer-by-layer encapsulation, polyelectrolyte complexation, and electrohydrodynamic technology, show great potential in LBP and probiotic delivery. In this review, novel delivery systems and new technologies of LBPs and probiotics were presented, and the challenges and prospects were explored in specific sensitive materials for LBP and probiotic delivery.

Next generation probiotics: Engineering live biotherapeutics

The population dynamics of the human microbiome have been associated with inflammatory bowel disease, cancer, obesity, autoimmune diseases, and many other human disease states. An emerging paradigm in treatment is the administration of live engineered organisms, also called next-generation probiotics. However, the efficacy of these microbial therapies can be limited by the organism's overall performance in the harsh and nutrient-limited environment of the gut. In this review, we summarize the current state of the art use of bacterial and yeast strains as probiotics, highlight the recent development of genetic tools for engineering new therapeutic functions in these organisms, and report on the latest therapeutic applications of engineered probiotics, including recent clinical trials. We also discuss the supplementation of prebiotics as a method of manipulating the microbiome and improving the overall performance of engineered live biotherapeutics.

Microbiota-Derived Extracellular Vesicles as a Postbiotic Strategy to Alleviate Diarrhea and Enhance Immunity in Rotavirus-Infected Neonatal Rats

Rotavirus (RV) infection is a major cause of acute gastroenteritis in children under 5 years old, resulting in elevated mortality rates in low-income countries. The efficacy of anti-RV vaccines is limited in underdeveloped countries, emphasizing the need for novel strategies to boost immunity and alleviate RV-induced diarrhea. This study explores the effectiveness of interventions involving extracellular vesicles (EVs) from probiotic and commensal E. coli in mitigating diarrhea and enhancing immunity in a preclinical model of RV infection in suckling rats. On days 8 and 16 of life, variables related to humoral and cellular immunity and intestinal function/architecture were assessed. Both interventions enhanced humoral (serum immunoglobulins) and cellular (splenic natural killer (NK), cytotoxic T (Tc) and positive T-cell receptor γδ (TCRγδ) cells) immunity against viral infections and downregulated the intestinal serotonin receptor-3 (HTR3). However, certain effects were strain-specific. EcoR12 EVs activated intestinal CD68, TLR2 and IL-12 expression, whereas EcN EVs improved intestinal maturation, barrier properties (goblet cell numbers/mucin 2 expression) and absorptive function (villus length). In conclusion, interventions involving probiotic/microbiota EVs may serve as a safe postbiotic strategy to improve clinical symptoms and immune responses during RV infection in the neonatal period. Furthermore, they could be used as adjuvants to enhance the immunogenicity and efficacy of anti-RV vaccines.

Benefits and concerns of probiotics: an overview of the potential genotoxicity of the colibactin-producing Escherichia coli Nissle 1917 strain

Recently, the mounting integration of probiotics into human health strategies has gathered considerable attention. Although the benefits of probiotics have been widely recognized in patients with gastrointestinal disorders, immune system modulation, and chronic-degenerative diseases, there is a growing need to evaluate their potential risks. In this context, new concerns have arisen regarding the safety of probiotics as some strains may have adverse effects in humans. Among these strains, Escherichia coli Nissle 1917 (EcN) exhibited traits of concern due to a pathogenic locus in its genome that produces potentially genotoxic metabolites. As the use of probiotics for therapeutic purposes is increasing, the effects of potentially harmful probiotics must be carefully evaluated. To this end, in this narrative review article, we reported the findings of the most relevant in vitro and in vivo studies investigating the expanding applications of probiotics and their impact on human well-being addressing concerns arising from the presence of antibiotic resistance and pathogenic elements, with a focus on the polyketide synthase (pks) pathogenic island of EcN. In this context, the literature data here discussed encourages a thorough profiling of probiotics to identify potential harmful elements as done for EcN where potential genotoxic effects of colibactin, a secondary metabolite, were observed. Specifically, while some studies suggest EcN is safe for gastrointestinal health, conflicting findings highlight the need for further research to clarify its safety and optimize its use in therapy. Overall, the data here presented suggest that a comprehensive assessment of the evolving landscape of probiotics is essential to make evidence-based decisions and ensure their correct use in humans.

The Microbiome and Uveitis: A Narrative Review

The human intestinal microbiome is composed of hundreds of species and has recently been recognized as an important source of immune homeostasis. While dysbiosis, an altered microbiome from the normal core microbiome, has been associated with both intestinal and extraintestinal autoimmune disorders, including uveitis, causality has been difficult to establish. There are four proposed mechanisms of how the gut microbiome may influence the development of uveitis: molecular mimicry, imbalance of regulatory and effector T cells, increased intestinal permeability, and loss of intestinal metabolites. This review summarizes current literature on both animal and human studies that establish the link between dysbiosis and the development of uveitis, as well as provides evidence for the above mechanisms. Current studies provide valuable mechanistic insights as well as identify potential therapeutic targets. However, study limitations and the wide variability in the intestinal microbiome among populations and diseases make a specific targeted therapy difficult to establish. Further longitudinal clinical studies are required to identify any potential therapeutic that targets the intestinal microbiome.

Nanoprobiotics for Remolding the Pro-inflammatory Microenvironment and Microbiome in the Treatment of Colitis

Despite the great progress of current bacterially based biotherapeutics, their unsatisfying efficacy and underlying safety problems have limited their clinical application. Herein, inspired by probiotic Escherichia coli strain Nissle 1917, probiotic-derived outer membrane vesicles (OMVs) are found to serve as an effective therapeutic platform for the treatment of inflammatory bowel disease (IBD). To further enhance the therapeutic effect, the probiotic-derived OMV-encapsulating manganese dioxide nanozymes are constructed, named nanoprobiotics, which can adhere to inflamed colonic epithelium and eliminate intestinal excess reactive oxygen species in the murine IBD model. Moreover, combined with the anti-inflammatory medicine metformin, nanoprobiotics could further remold the pro-inflammatory microenvironment, improve the overall richness and diversity of the gut microbiota, and exhibit better therapeutic efficacy than commercial IBD chemotherapeutics. Importantly, insignificant overt systemic toxicity in this treatment was observed. By integrating cytokine storm calm with biotherapy, we develop a safe and effective bionanoplatform for the effective treatment of inflammation-mediated intestinal diseases.

Managing the clinical effects of drug-induced intestinal dysbiosis with a focus to antibiotics: Challenges and opportunities

The term "intestinal dysbiosis" is used for indicating change(s) of the intestinal microbiota which have been associated with the development of diseases and the deterioration of disease treatments in humans. In this review, documented clinical effects of drug-induced intestinal dysbiosis are briefly presented, and methodologies which could be considered for the management of drug-induced intestinal dysbiosis based on clinical data are critically reviewed. Until relevant methodologies are optimized and/or their effectiveness to the general population is confirmed, and, since drug-induced intestinal dysbiosis refers predominantly to antibiotic-specific intestinal dysbiosis, a pharmacokinetically-based approach for mitigating the impact of antimicrobial therapy on intestinal dysbiosis is proposed.

From the updated landscape of the emerging biologics for IBDs treatment to the new delivery systems

Inflammatory bowel diseases (IBDs) treatments have shifted from small-molecular therapeutics to the oncoming biologics. The first-line biologics against the moderate-to-severe IBDs are mainly involved in antibodies against integrins, cytokines and cell adhesion molecules. Besides, other biologics including growth factors, antioxidative enzyme, anti-inflammatory peptides, nucleic acids, stem cells and probiotics have also been explored at preclinical or clinical studies. Biologics with variety of origins have their unique potentials in attenuating immune inflammation or gut mucosa healing. Great advances in use of biologics for IBDs treatments have been archived in recent years. But delivering issues for biologic have also been confronted due to their liable nature. In this review, we will focus on biologics for IBDs treatments in the recent publications; summarize the current landscapes of biologics and their promise to control disease progress. Alternatively, the confronted challenges for delivering biologics will also be analyzed. To combat these drawbacks, some new delivering strategies are provided: firstly, designing the functional materials with high affinity toward biologics; secondly, the delivering vehicle systems to encapsulate the liable biologics; thirdly, the topical adhering delivery systems as enema. To our knowledge, this review is the first study to summarize the updated usage of the oncoming biologics for IBDs, their confronted challenges in term of delivery and the potential combating strategies.

Biofilm's Impact on Inflammatory Bowel Diseases

The colon has a large surface area covered with a thick mucus coating. Colon's biomass consists of about 1,012 colony-forming units per gram of feces and 500-1,000 distinct bacterial species. The term inflammatory bowel disease (IBD) indicates the collection of intestinal illnesses in which the digestive system (esophagus, large intestine, mouth, stomach, and small intestine) experiences persistent inflammation. IBD development is influenced by environmental (infections, stress, and nutrition) and genetic factors. The microbes present in gut microbiota help maintain intestinal homeostasis and support immune and epithelial cell growth, differentiation, as well as proliferation. It has been discovered that a variety of variables and microorganisms are crucial for the development of biofilms and mucosal colonization during IBD. An extracellular matrix formed by bacteria supports biofilm production in our digestive system and harms the host's immunological response. Irritable bowel syndrome (IBS) and IBD considerably affect human socioeconomic well-being and the standard of living. IBD is a serious public health issue, affecting millions of people across the globe. The gut microbiome may significantly influence IBS pathogenesis, even though few diagnostic and treatment options are available. As a result, current research focuses more on disrupting biofilm in IBD patients and stresses primarily on drugs that help improve the quality of life for human well-being. We evaluate studies on IBD and bacterial biofilm to add fresh insights into the existing state of knowledge of biofilm formation in IBD, incidence of IBD patients, molecular level of investigations, bacteria that are involved in the formation of biofilm, and present and down the line regimens and probiotics. Planning advanced ways to control and eradicate bacteria in biofilms should be the primary goal to add fresh insights into generating innovative diagnostic and alternative therapy options for IBD.

The gut microbes in inflammatory bowel disease: Future novel target option for pharmacotherapy

Gut microbes constitute the main microbiota in the human body, which can regulate biological processes such as immunity, cell proliferation, and differentiation, hence playing a specific function in intestinal diseases. In recent years, gut microbes have become a research hotspot in the pharmaceutical field. Because of their enormous number, diversity, and functional complexity, gut microbes have essential functions in the development of many digestive diseases. Inflammatory bowel disease (IBD) is a chronic non-specific inflammatory disease with a complex etiology, the exact cause and pathogenesis are unclear. There are no medicines that can cure IBD, and more research on therapeutic drugs is urgently needed. It has been reported that gut microbes play a critical role in pathogenesis, and there is a tight and complex association between gut microbes and IBD. The dysregulation of gut microbes may be a predisposing factor for IBD, and at the same time, IBD may exacerbate gut microbes' disorders, but the mechanism of interaction between the two is still not well defined. The study of the relationship between gut microbes and IBD is not only important to elucidate the pathogenesis but also has a positive effect on the treatment based on the regimen of regulating gut microbes. This review describes the latest research progress on the functions of gut microbes and their relationship with IBD, which can provide reference and assistance for further research. It may provide a theoretical basis for the application of probiotics, fecal microbiota transplantation, and other therapeutic methods to regulate gut microbes in IBD.

Probiotic Escherichia coli Nissle 1917-derived outer membrane vesicles modulate the intestinal microbiome and host gut-liver metabolome in obese and diabetic mice

Introduction

Obesity and diabetes are common chronic metabolic disorders which can cause an imbalance of the intestinal flora and gut-liver metabolism. Several studies have shown that probiotics, including Escherichia coli Nissle 1917 (EcN), promote microbial balance and metabolic health. However, there are no studies on how EcN outer membrane vesicles (EcN-OMVs) influence the intestinal microflora and affect the metabolic disorders of obesity and diabetes.

Methods

In this study, we evaluated the effects of EcN-OMVs on high-fat diet (HFD)-induced obesity and HFD + streptozotocin (STZ)-induced diabetes.

Results

EcN-OMVs could reduce body weight, decrease blood glucose, and increase plasma insulin in obese mice. Similarly, EcN-OMVs treatment could modify the ratio of Firmicutes/Bacteroidetes in the gut, elevate intestinal short-chain fatty acid (SCFA)-producing flora, and influence the SCFA content of the intestine. Furthermore, the intestinal metabolites ornithine and fumaric acid, hepatic ω-6 unsaturated fatty acids, and SCFAs were significantly increased after administering EcN-OMVs.

Discussion

Overall, this study showed that EcN-OMVs might act as post-biotic agents that could modulate gut-liver metabolism and ameliorate the pathophysiology of obesity and diabetes.

Harnessing the potential of probiotics in the treatment of alcoholic liver disorders

In the current scenario, prolonged consumption of alcohol across the globe is upsurging an appreciable number of patients with the risk of alcohol-associated liver diseases. According to the recent report, the gut-liver axis is crucial in the progression of alcohol-induced liver diseases, including steatosis, steatohepatitis, fibrosis, cirrhosis, and hepatocellular carcinoma. Despite several factors associated with alcoholic liver diseases, the complexity of the gut microflora and its great interaction with the liver have become a fascinating area for researchers due to the high exposure of the liver to free radicals, bacterial endotoxins, lipopolysaccharides, inflammatory markers, etc. Undoubtedly, alcohol-induced gut microbiota imbalance stimulates dysbiosis, disrupts the intestinal barrier function, and trigger immune as well as inflammatory responses which further aggravate hepatic injury. Since currently available drugs to mitigate liver disorders have significant side effects, hence, probiotics have been widely researched to alleviate alcohol-associated liver diseases and to improve liver health. A broad range of probiotic bacteria like Lactobacillus, Bifidobacteria, Escherichia coli, Sacchromyces, and Lactococcus are used to reduce or halt the progression of alcohol-associated liver diseases. Several underlying mechanisms, including alteration of the gut microbiome, modulation of intestinal barrier function and immune response, reduction in the level of endotoxins, and bacterial translocation, have been implicated through which probiotics can effectively suppress the occurrence of alcohol-induced liver disorders. This review addresses the therapeutic applications of probiotics in the treatment of alcohol-associated liver diseases. Novel insights into the mechanisms by which probiotics prevent alcohol-associated liver diseases have also been elaborated.

The Effect of Probiotic Supplementation on the Gut-Brain Axis in Psychiatric Patients

The pathophysiology of several psychiatric diseases may entail disturbances in the hypothalamic-pituitary-adrenal (HPA) axis and metabolic pathways. Variations in how these effects present themselves may be connected to individual variances in clinical symptoms and treatment responses, such as the observation that a significant fraction of participants do not respond to current antipsychotic drugs. A bidirectional signaling pathway between the central nervous system and the gastrointestinal tract is known as the microbiota-gut-brain axis. The large and small intestines contain more than 100 trillion microbial cells, contributing to the intestinal ecosystem's incredible complexity. Interactions between the microbiota and intestinal epithelium can alter brain physiology and affect mood and behavior. There has recently been a focus on how these relationships impact mental health. According to evidence, intestinal microbiota may play a role in neurological and mental illnesses. Intestinal metabolites of microbial origin, such as short-chain fatty acids, tryptophan metabolites, and bacterial components that might stimulate the host's immune system, are mentioned in this review. We aim to shed some on the growing role of gut microbiota in inducing/manipulating several psychiatric disorders, which may pave the way for novel microbiota-based therapies.

Biotherapy Using Probiotics as Therapeutic Agents to Restore the Gut Microbiota to Relieve Gastrointestinal Tract Inflammation, IBD, IBS and Prevent Induction of Cancer

The gut microbiota is composed of several microbial strains with diverse and variable compositions in both healthy and sick people. An undisturbed gut microbiota needs to be sustained in order to perform all physiological, metabolic, and immune functions in a normal way to prevent the development of diseases. This article has reviewed the published information on the issue of disruption of the balance of the gut microbiota. This disruption could be for many reasons, such as microbial infection in the gastrointestinal tract, food poisoning, diarrhoea, chemotherapy, malnutrition, lifestyle, and ageing. If this disruption is not restored to normal, it might cause dysbiosis. Eventually, a gut microbiota interrupted by dysbiosis might initiate several health issues, such as inflammation of the gastrointestinal tract, the induction of cancer, and the progression of a variety of diseases such as irritable bowel syndrome and inflammatory bowel disease. This review concluded that biotherapy is a natural way of using probiotic products, whether in form of food, beverages, or supplements, to restore the gut microbiota disrupted by dysbiosis. Metabolites secreted by the ingested probiotics help to relieve gastrointestinal tract inflammation and can avoid the induction of cancer.

Inulin impacts tumorigenesis promotion by colibactin-producing Escherichia coli in ApcMin/+ mice

Introduction

The prebiotic inulin has previously shown both protective and tumor-promoting effects in colorectal cancer (CRC). These inconsistencies may be due to the gut microbial composition as several bacteria have been associated with CRC. Specifically, polyketide synthase-positive (pks+) Escherichia coli promotes carcinogenesis and facilitates CRC progression through the production of colibactin, a genotoxin that induces double-strand DNA breaks (DSBs). We investigated whether colibactin-producing Escherichia coli changed the protection conferred by inulin against tumor growth and progression using the Apc^Min/+ mouse model of CRC.

Methods

Mice received a 2% dextran sodium sulfate (DSS) solution followed by oral gavage with the murine pks + E. coli strain NC101 (EcNC101) and were fed a diet supplemented with 10% cellulose as control or 10% inulin for 4 weeks.

Results

Inulin supplementation led to increase EcNC101 colonization compared to mice receiving the control diet. The increased colonization of EcNC101 resulted in more DSBs, tumor burden, and tumor progression in Apc^Min/+ mice. The tumorigenic effect of EcN101 in Apc^Min/+ mice mediated by inulin was dependent on colibactin production. Pasteurized E. coli Nissle 1917 (EcN), a probiotic, suppressed the inulin-driven EcNC101 expansion and impacted tumor progression.

Discussion

Our results suggest that the presence of pks + E. coli influences the outcome of inulin supplementation in CRC and that microbiota-targeted interventions may mitigate this effect. Given the prevalence of pks + E. coli in both healthy and CRC populations and the importance of a fiber-rich diet, inulin supplementation in individuals colonized with pks + bacteria should be considered with caution.

Advances in Escherichia coli Nissle 1917 as a customizable drug delivery system for disease treatment and diagnosis strategies

With the in-depth and comprehensive study of bacteria and their related ecosystems in the human body, bacterial-based drug delivery system has become an emerging biomimetic platform that can retain the innate biological functions. Benefiting from its good biocompatibility and ideal targeting ability as a biological carrier, Escherichia coli Nissle 1917 (ECN) has been focused on the treatment strategies of inflammatory bowel disease and tumor. The advantage of a bacterial carrier is that it can express exogenous protein while also acting as a natural capsule by releasing drug slowly as a result of its own colonization impact. In order to survive in harsh environments such as the digestive tract and tumor microenvironment, ECN can be modified or genetically engineered to enhance its function and host adaptability. The adoption of ECN carries or expresses drugs which are essential for accurate diagnosis and treatment. This review briefly describes the properties of ECN, the relationship between ECN and inflammation and tumor, and the strategy of using surface modification and genetic engineering to modify ECN as a delivery carrier for disease treatment.

Transcriptome profiling Revealed the potential mechanisms of Shen Lin Bai Zhu San n-butanol extract on DSS induced Colitis in Mice and LC-MS analysis

BACKGROUND

Inflammatory bowel disease (IBD) is a chronic and recurrent inflammatory disorder in gastrointestinal tract. Shen Ling Bai Zhu San (SLBZS), which has a long history of use in Traditional Chinese Medicine (TCM), has been widely used to treat gastrointestinal diseases. The isolated fractions of TCM have also been proved to possess an important potential for treating diseases, which are due to their effective components.

PURPOSE

In this study, we examined the possibility that SLBZS and its isolated active fractions may prevent DSS-induced colitis, and investigated the potential mechanisms by regulating genetic profile of colon.

METHODS

Colitis mice were induced by 2.5% DSS for 7 days, and then SLBZS and different SLBZS extracts were administrated to protect the mice for 7 days. Body weight, diarrhea, bleeding in stool, colon length, spleen weight, cytokines of serum and colon and pathology of colon were assessed. The level of Ginsenoside Rg1, Re and Rb1 in different SLBZS extracts and qualitative analysis of n-butanol extract of SLBZS (S-Nb) was performed by HPLC and LC-MS, respectively. And the effects of S-Nb on the transcriptome in colitis were investigated.

RESULTS

Our results showed that SLBZS and S-Nb significantly regained body weight, reduced DAI, splenomegaly and the length of colon and attenuated histological damage of the colon. Meanwhile, SLBZS and S-Nb markedly reduced the levels of TNF-α, IL-1β and IL-6 and increased the level of IL-10 in serum and colon. These effects may be associated with the high levels of Ginsenoside Rg1, Re and Rb1 and rich variety of compounds in S-Nb including 6 ginsenosides, glycyrrhizin, L-tryptophan, and so on. Transcriptome analysis revealed that S-Nb selectively regulated 103 differentially expressed genes (DEGs), 36 of which were changed in DSS-induced mice. And the genes of Per2, Per3, Npy and Serpina3m were closely related to colitis and also restored by S-Nb with different extent. Remarkably, these DEGs modulated the biological functions of colitis mice, including extracellular region, response to external stimulus, MAPK signaling pathway and arginine and proline metabolism.

CONCLUSIONS

These data indicated that SLBZS and S-Nb blunted DSS-induced colitis by modulating differentially expression gene profile and biological functions based on their ginsenosides and rich compounds.

Delivery of E. coli Nissle to the mouse gut by mucoadhesive microcontainers does not improve its competitive ability against strains linked to ulcerative colitis

For patients with ulcerative colitis (UC), administration of the probiotic E. coli Nissle (EcN) holds promise for alleviation of disease symptoms. The mechanisms are unclear, but it has been hypothesised that a capacity of the probiotic to outcompete potentially detrimental UC-associated E. coli strains plays an important role. However, this could previously not be confirmed in a mouse model of competition between EcN and two UC-associated strains, as reported by Petersen et al. 2011. In the present study, we re-evaluated the idea, hypothesising that delivery of EcN by a micro device dosing system (microcontainers), designed for delivery into the intestinal mucus, could support colonisation and confer a competition advantage compared to classical oral dosing. Six groups of mice were pre-colonised with one of two UC-associated E. coli strains followed by oral delivery of EcN, either in capsules containing microcontainers with freeze-dried EcN powder, capsules containing freeze-dried EcN powder, or as a fresh sucrose suspension. Co-colonisation between the probiotic and the disease-associated strains was observed regardless of dosing method, and no competition advantages linked to microcontainer delivery were identified within this setup. Other approaches are thus needed if the competitive capacity of EcN in the gut should be improved.

High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917

BACKGROUND

Escherichia coli Nissle 1917 (EcN) is a probiotic bacterium used to treat various gastrointestinal diseases. EcN is increasingly being used as a chassis for the engineering of advanced microbiome therapeutics. To aid in future engineering efforts, our aim was to construct an updated metabolic model of EcN with extended secondary metabolite representation.

RESULTS

An updated high-quality genome-scale metabolic model of EcN, iHM1533, was developed based on comparison with 55 E. coli/Shigella reference GEMs and manual curation, including expanded secondary metabolite pathways (enterobactin, salmochelins, aerobactin, yersiniabactin, and colibactin). The model was validated and improved using phenotype microarray data, resulting in an 82.3% accuracy in predicting growth phenotypes on various nutrition sources. Flux variability analysis with previously published ¹³C fluxomics data validated prediction of the internal central carbon fluxes. A standardised test suite called Memote assessed the quality of iHM1533 to have an overall score of 89%. The model was applied by using constraint-based flux analysis to predict targets for optimisation of secondary metabolite production. Modelling predicted design targets from across amino acid metabolism, carbon metabolism, and other subsystems that are common or unique for influencing the production of various secondary metabolites.

CONCLUSION

iHM1533 represents a well-annotated metabolic model of EcN with extended secondary metabolite representation. Phenotype characterisation and the iHM1533 model provide a better understanding of the metabolic capabilities of EcN and will help future metabolic engineering efforts.

Probiotics and gastrointestinal diseases

During the past decades, scientists have discovered the intimate role of the gut microbiome in human health, and since then, several papers have been published to investigate if the use of biotics (probiotics, prebiotics, synbiotics, and postbiotics) may have a beneficial impact on human health both in treatment and prevention. We now ask ourselves whether we have reached the finish line or just a new starting point, as the evidence supporting the use of biotics in several conditions still needs a lot of work. Many questions remain unanswered today because the evidence differs depending on the indication, used strain, and amount and duration of administration. Herein we will summarize the evidence on probiotics in some gastrointestinal diseases such as infantile colic, functional abdominal pain disorders, celiac disease, acute gastroenteritis, inflammatory bowel disease, and Helicobacter pylori infection.

Nattokinase enhances the preventive effects of Escherichia coli Nissle 1917 on dextran sulfate sodium-induced colitis in mice

Nattokinase with excellent anti-thrombotic, anti-inflammatory, anti-tumor, and anti-hypertension properties has been used in the development of several healthcare products in many countries. The probiotic Escherichia coli Nissle 1917 (EcN) with anti-inflammatory effect is commonly used to treat inflammatory bowel disease. To determine whether nattokinase could enhance the therapeutic efficacy of EcN in colitis, a recombinant E. coli Nissle 1917 strain (EcNnatto) with nattokinase-expressing ability was successfully constructed, and the protective effect of the engineered strain on mice with experimental chronic colitis was investigated. Although both EcN and EcNnatto strains substantially alleviated the clinical symptoms and pathological abnormalities in colitis mice by regulating gut flora and maintaining intestinal barrier function, the EcNnatto strain was found to perform better than the control strain, based on a further increase in colon length and a downregulation in pro-inflammatory cytokines (IL-6 and TNF-α). Nattokinase expressed in EcN attenuated DSS-induced epithelial damage and restored the mucosal integrity by upregulating the levels of tight junction proteins, including ZO-1 and occludin. The expression level of Lgr5, a marker of intestinal stem cells, was also increased. Moreover, constitutively expressed nattokinase in EcN reversed the gut microbial richness and diversity in colitis mice. Based on our findings, nattokinase could strengthen the capacity of EcN to treat intestinal inflammation.

Prospects of Probiotic Adjuvant Drugs in Clinical Treatment

In modern society, where new diseases and viruses are constantly emerging, drugs are still the most important means of resistance. However, adverse effects and diminished efficacy remain the leading cause of treatment failure and a major determinant of impaired health-related quality of life for patients. Clinical studies have shown that the disturbance of the gut microbial structure plays a crucial role in the toxic and side effects of drugs. It is well known that probiotics have the ability to maintain the balance of intestinal microecology, which implies their potential as an adjunct to prevent and alleviate the adverse reactions of drugs and to make medicines play a better role. In addition, in the past decade, probiotics have been found to have excellent prevention and alleviation effects in drug toxicity side effects, such as liver injury. In this review, we summarize the development history of probiotics, discuss the impact on drug side effects of probiotics, and propose the underlying mechanisms. Probiotics will be a new star in the world of complementary medicine.

Role of microbes in colorectal cancer therapy: Cross-talk between the microbiome and tumor microenvironment

The human gut microbiota is associated with the development and progression of colorectal cancer, and manipulation of the gut microbiota is a novel strategy for the prevention and treatment of colorectal cancer. Some bacteria have antitumor activity against colorectal cancer, where specific bacteria can improve the tumor microenvironment, activate immune cells including dendritic cells, helper T cells, natural killer cells, and cytotoxic T cells, and upregulate the secretion of pro-tumor immune cytokines such as interleukin-2 and interferon. In this paper, we summarize some bacteria with potential benefits in colorectal cancer and describe their roles in the tumor microenvironment, demonstrate the application of gut microbes in combination with immunosuppressive agents, and provide suggestions for further experimental studies and clinical practice applications.

Escherichia coli BarA-UvrY regulates the pks island and kills Staphylococci via the genotoxin colibactin during interspecies competition

Wound infections are often polymicrobial in nature, biofilm associated and therefore tolerant to antibiotic therapy, and associated with delayed healing. Escherichia coli and Staphylococcus aureus are among the most frequently cultured pathogens from wound infections. However, little is known about the frequency or consequence of E. coli and S. aureus polymicrobial interactions during wound infections. Here we show that E. coli kills Staphylococci, including S. aureus, both in vitro and in a mouse excisional wound model via the genotoxin, colibactin. Colibactin biosynthesis is encoded by the pks locus, which we identified in nearly 30% of human E. coli wound infection isolates. While it is not clear how colibactin is released from E. coli or how it penetrates target cells, we found that the colibactin intermediate N-myristoyl-D-Asn (NMDA) disrupts the S. aureus membrane. We also show that the BarA-UvrY two component system (TCS) senses the environment created during E. coli and S. aureus mixed species interaction, leading to upregulation of pks island genes. Further, we show that BarA-UvrY acts via the carbon storage global regulatory (Csr) system to control pks expression. Together, our data demonstrate the role of colibactin in interspecies competition and show that it is regulated by BarA-UvrY TCS during interspecies competition.

Wound infections are often polymicrobial in nature and are associated with poor disease prognoses. Escherichia coli and Staphylococcus aureus are among the top five most cultured pathogens from wound infections. However, little is known about the polymicrobial interactions between E. coli and S. aureus during wound infections. In this study, we show that E. coli kills S. aureus both in vitro and in a mouse excisional wound model via the genotoxin, colibactin. We also show that the BarA-UvrY two component system (TCS) regulates the pks island during this mixed species interaction, acting through the carbon storage global regulatory (Csr) system to control colibactin production. Together, our data demonstrate the role of colibactin in interspecies competition and show that it is regulated by BarA-UvrY TCS during interspecies competition.

Modulation of hepatic stellate cells by Mutaflor® probiotic in non-alcoholic fatty liver disease management

BACKGROUND

NAFLD and NASH are emerging as primary causes of chronic liver disease, indicating a need for an effective treatment. Mutaflor® probiotic, a microbial treatment of interest, was effective in sustaining remission in ulcerative colitis patients.

OBJECTIVE

To construct a genetic-epigenetic network linked to HSC signaling as a modulator of NAFLD/NASH pathogenesis, then assess the effects of Mutaflor^® on this network.

METHODS

First, in silico analysis was used to construct a genetic-epigenetic network linked to HSC signaling. Second, an investigation using rats, including HFHSD induced NASH and Mutaflor^® treated animals, was designed. Experimental procedures included biochemical and histopathologic analysis of rat blood and liver samples. At the molecular level, the expression of genetic (FOXA2, TEAD2, and LATS2 mRNAs) and epigenetic (miR-650, RPARP AS-1 LncRNA) network was measured by real-time PCR. PCR results were validated with immunohistochemistry (α-SMA and LATS2). Target effector proteins, IL-6 and TGF-β, were estimated by ELISA.

RESULTS

Mutaflor^® administration minimized biochemical and histopathologic alterations caused by NAFLD/NASH. HSC activation and expression of profibrogenic IL-6 and TGF-β effector proteins were reduced via inhibition of hedgehog and hippo pathways. Pathways may have been inhibited through upregulation of RPARP AS-1 LncRNA which in turn downregulated the expression of miR-650, FOXA2 mRNA and TEAD2 mRNA and upregulated LATS2 mRNA expression.

CONCLUSION

Mutaflor^® may slow the progression of NAFLD/NASH by modulating a genetic-epigenetic network linked to HSC signaling. The probiotic may be a useful modality for the prevention and treatment of NAFLD/NASH.

Anti-Campylobacter Probiotics: Latest Mechanistic Insights

The Campylobacter genus is the leading cause of human gastroenteritis, with the consumption of contaminated poultry meat as the main route of infection. Probiotic bacteria, such as Lactobacillus, Bacillus, Escherichia coli Nissle, and Bifidobacterium species, have a great immunomodulatory capacity and exhibit antipathogenic effects through various molecular mechanisms. Reducing Campylobacter levels in livestock animals, such as poultry, will have a substantial benefit to humans as it will reduce disease transmissibility through the food chain. Moreover, probiotic-based strategies might attenuate intestinal inflammatory processes, which consequently reduce the severity of Campylobacter disease progression. At a molecular level, probiotics can also negatively impact on the functionality of various Campylobacter virulence and survival factors (e.g., adhesion, invasion), and on the associated colonization proteins involved in epithelial translocation. The current review describes recent in vitro, in vivo, and preclinical findings on probiotic therapies, aiming to reduce Campylobacter counts in poultry and reduce the pathogen's virulence in the avian and human host. Moreover, we focused in particular on probiotics with known anti-Campylobacter activity seeking to understand the biological mechanisms involved in their mode of action.

Fucosyltransferase 2: A Genetic Risk Factor for Intestinal Diseases

The fucosyltransferase 2 gene (FUT2) mediates the synthesis of histoblood group antigens (HBGA) that occur in vivo from multiple organs, particularly on the surface of intestinal epithelial cells and body fluids. To date, many studies have demonstrated that the interaction of HBGA with the host microbiota is the cause of pathogenesis of intestinal diseases, making FUT2 non-secretor a risk factor for inflammatory bowel disease (IBD) due to the lack of HBGA. As HBGA also acts as an attachment site for norovirus (NoV) and rotavirus (RV), the non-secretor becomes a protective factor for both viral infections. In addition, the interaction of norovirus and rotavirus with symbiotic bacteria has been found to play an important role in regulating enteroviral infection in IBD. Given the current incomplete understanding of the complex phenomenon and the underlying pathogenesis of intestinal diseases such as IBD, it has recently been hypothesized that the FUT2 gene regulates intestinal bacteria through attachment sites, may help to unravel the role of FUT2 and intestinal flora in the mechanism of intestinal diseases in the future, and provide new ideas for the prevention and treatment of intestinal diseases through more in-depth studies.

Isolation and biological activities of compounds from Rumex vesicarius L. and their use as a component of a synbiotic preparation

The study evaluated prebiotic potential and the enzyme inhibition of extracts and isolated compounds of Rumex vesicarius (ruby dock), family Polygonaceae. Eight known compounds were identified in the roots of R. vesicarius. Extracts and compounds (1-8) increased the growth rate of Escherichia coli Nissle 1917 differentially compared to controls. The highest prebiotic index (PI) and activity score was recorded for EcN in the presence of compound 4, followed by, in descending order, petroleum ether, ethyl acetate, and total methanol extracts. The compounds and extracts reduced protease, α-amylase, and angiotensin-converting enzyme activities. This inhibitory activity was positively correlated with PI, P_score, µ_u, and Y_max. These findings suggest that R. vesicarius is a good source of potential prebiotic and can boost beneficial bacteria. It may also be considered promising for treatment of diabetes mellitus, controlling weight, and regulating blood pressure.

Microbial Imbalance Induces Inflammation by Promoting Salmonella Penetration through the Mucosal Barrier

The balance of microbial species in the intestine must be maintained to prevent inflammation and disease. Healthy bacteria suppress infection by pathogens and prevent disorders such as inflammatory bowel diseases (IBDs). The role of mucus in the relation between pathogens and the intestinal microbiota is poorly understood. Here, we hypothesized that healthy bacteria inhibit infection by preventing pathogens from penetrating the mucus layer and that microbial imbalance leads to inflammation by promoting the penetration of the mucosal barrier. We tested this hypothesis with an in vitro model that contains mucus, an epithelial cell layer, and resident immune cells. We found that, unlike probiotic VSL#3 bacteria, Salmonella penetrated the mucosal layers and induced the production of interleukin-8 (IL-8) and tumor necrosis factor (TNF)-α. At ratios greater than 10⁴:1, probiotic bacteria suppressed the growth and penetration of Salmonella and reduced the production of inflammatory cytokines. Counterintuitively, low densities of healthy bacteria increased both pathogen penetration and cytokine production. In all cases, mucus increased Salmonella penetration and the production of cytokines. These results suggest that mucus lessens the protective effect of probiotic bacteria by promoting barrier penetration. In this model, a more imbalanced microbial population caused infection and inflammation by selecting pathogens that are more invasive and immunogenic. Combined, the results suggest that the depletion of commensal bacteria or an insufficient dosage of probiotics could worsen an infection and cause increased inflammation. A better understanding of the interactions between pathogens, healthy microbes, and the mucosal barrier will improve the treatment of infections and inflammatory diseases.

Probiotic Escherichia coli Nissle 1917 Expressing Elafin Protects Against Inflammation and Restores the Gut Microbiota

Intestinal mucosal inflammation and epithelial barrier dysfunction have been implicated as pathological factors in inflammatory bowel disease (IBD). An emerging area of IBD research focuses on probiotics. The probiotic Escherichia coli Nissle 1917 (EcN) is an excellent choice for engineering therapeutic microbes. Elafin is an endogenous specific inhibitor of neutrophil elastase (NE) and proteinase 3, and we previously found Elafin can effectively suppress the development of colitis. Here, we genetically engineered EcN to deliver Elafin (EcN-Elafin) directly to the colonic mucosa and explored the protective effects of EcN-Elafin against colitis in mice. EcN-Elafin significantly alleviated dextran sodium sulfate (DSS) induced colitis. Compared with wild-type EcN, oral administration of EcN-Elafin displayed better effects on loss of weight, colon length shortening, elevated expression of myeloperoxidase (MPO), and proinflammatory cytokines and chemokine in colonic tissues. In addition, EcN-Elafin restored the expression and distribution of tight junction protein ZO-1 in colonic tissues back to normal. In a damaged colonic epithelial model utilizing Caco-2 cells stimulated with TNF-α, EcN-Elafin efficiently downregulated the activation level of NF-κB signaling. EcN-Elafin was also found to have restored the dysbiosis in gut caused by DSS administration. Moreover, EcN-Elafin significantly enhanced the concentrations of butyrate and valerate in the gut lumen. Thus, our findings demonstrated that EcN-Elafin enhanced the colonic epithelial barrier, promoted the resolution of inflammation, modulated the gut microbiota, and elevated concentrations of short-chain fatty acids (SCFAs) in the gut. EcN-Elafin may be a potential therapeutic method for IBD.

The Gut Microbiota Influenced by the Intake of Probiotics and Functional Foods with Prebiotics Can Sustain Wellness and Alleviate Certain Ailments like Gut-Inflammation and Colon-Cancer

The gut microbiota is composed of several microbial strains, with diverse and variable combinations in healthy and sick persons, changing at different stages of life. A healthy balance between host and gut microorganisms must be maintained in order to perform the normal physiological, metabolic, and immune functions and prevent disease development. Disturbances in the balance of the gut microbiota by diverse reasons initiate several health issues and promote the progression of certain diseases. This review is based on published research and reports that describe the role of probiotic microorganisms in the sustainability of health and the alleviation of certain diseases. Information is presented on the GRAS strains that are used as probiotics in the food industry for the production of fermented milk, yogurt, fermented food, functional foods, and probiotic drinks. To maintain a healthy microbiota, probiotic supplements in the form of freeze-dried live cells of probiotic strains are also available in different forms to consumers. The health benefits of lactic acid bacteria and other microorganisms and their role in the control of certain diseases such as gut inflammation, diabetes, and bowel cancer and in the safeguarding of the gut epithelial permeability from the invasion of pathogens are discussed.

Physiological activity of E. coli engineered to produce butyric acid

Faecalibacterium prausnitzii (F. prausnitzii) is one of the most abundant bacteria in the human intestine, with its anti-inflammatory effects establishing it as a major effector in human intestinal health. However, its extreme sensitivity to oxygen makes its cultivation and physiological study difficult. F. prausnitzii produces butyric acid, which is beneficial to human gut health. Butyric acid is a short-chain fatty acid (SCFA) produced by the fermentation of carbohydrates, such as dietary fibre in the large bowel. The genes encoding butyryl-CoA dehydrogenase (BCD) and butyryl-CoA:acetate CoA transferase (BUT) in F. prausnitzii were cloned and expressed in E. coli to determine the effect of butyric acid production on intestinal health using DSS-induced colitis model mice. The results from the E. coli Nissle 1917 strain, expressing BCD, BUT, or both, showed that BCD was essential, while BUT was dispensable for producing butyric acid. The effects of different carbon sources, such as glucose, N-acetylglucosamine (NAG), N-acetylgalactosamine (NAGA), and inulin, were compared with results showing that the optimal carbon sources for butyric acid production were NAG, a major component of mucin in the human intestine, and glucose. Furthermore, the anti-inflammatory effects of butyric acid production were tested by administering these strains to DSS-induced colitis model mice. The oral administration of the E. coli Nissle 1917 strain, carrying the expression vector for BCD and BUT (EcN-BCD-BUT), was found to prevent DSS-induced damage. Introduction of the BCD expression vector into E. coli Nissle 1917 led to increased butyric acid production, which improved the strain's health-beneficial effects.

Natural compounds as safe therapeutic options for ulcerative colitis

Ulcerative colitis (UC) is a chronic inflammatory bowel disease of unknown etiology. Several conventional treatments for UC such as corticosteroids, immunosuppressive agents, tumor necrosis factor antagonist, integrin blockers, and interleukin antagonist, and salicylates are available but are associated with the various limitations and side-effects. None of the above treatments helps to achieve the ultimate goal of the therapy, i.e., maintenance of remission in the long-term. Natural remedies for the treatment of UC show comparatively less side effects as compared to conventional approaches, and affordable. The current review presents details on the role of herbal drugs in the treatment and cure of UC. Google, PubMed, Web of Science, and Scopus portals have been searched for potentially relevant literature to get the latest developments and updated information related to use of natural drugs in the treatment of UC. Natural products have been used over centuries to treat UC. Some of the essential herbal constituents exhibiting antiulcerogenic activity include gymnemic acid (Gymnema sylvestre), shagoal (Zingiber officinale), catechin (Camellia sinensis), curcumin (Curcuma longa), arctigenin (Arctium lappa), and boswellic acid (Boswellia serrata). Although many plant-derived products have been recommended for UC, further research to understand the exact molecular mechanism is still warranted to establish their usefulness clinically.

The Gut Microbiota in Inflammatory Bowel Disease

Epidemiological surveys indicate that the incidence of inflammatory bowel disease (IBD) is increasing rapidly with the continuous growth of the economy. A large number of studies have investigated the relationship between the genetic factors related to the susceptibility to IBD and the gut microbiota of patients by using high-throughput sequencing. IBD is considered the outcome of the interaction between host and microorganisms, including intestinal microbial factors, abnormal immune response, and a damaged intestinal mucosal barrier. The imbalance of microbial homeostasis leads to the colonization and invasion of opportunistic pathogens in the gut, which increases the risk of the host immune response and promotes the development of IBD. It is critical to identify the specific pathogens related to the pathogenesis of IBD. An in-depth understanding of various pathogenic factors is of great significance for the early detection of IBD. This review highlights the role of gut microbiota in the pathogenesis of IBD and provides a theoretical basis for the personalized approaches that modulate the gut microbiota to treat IBD.

Reply to von Bünau et al. Comment on "Depoorter, L.; Vandenplas, Y. Probiotics in Pediatrics. A Review and Practical Guide. Nutrients 2021, 13, 2176"

We agree with Prof. Stange and Erhardt for their comment on our paper on Probiotics in Pediatrics [...].