Dietary manipulation of the gut microbiome in inflammatory bowel disease patients: Pilot study

Dietary therapies for adult and pediatric inflammatory bowel disease

Diet is an environmental exposure implicated in the development of inflammatory bowel disease (IBD), including Crohn's disease (CD) and ulcerative colitis (UC). Dietary therapy is also a tool for management of these conditions. Nutrition therapy for IBD has been shown to reduce intestinal inflammation, promote healing, and alleviate symptoms, as well as improve patients' nutrition status. Although the mechanisms of action of most nutrition therapies for IBD are not well understood, the diets are theorized to eliminate triggers for gut dysbiosis and mucosal immune dysfunction associated with the typical Western diet. Exclusive enteral nutrition and the Crohn's disease exclusion diet are increasingly being used as the primary treatment modality for the induction of remission and/or maintenance therapy in children, and in some adults, with CD. Several other diets, such as the Mediterranean diet, anti-inflammatory diet for IBD, and diets excluding gluten, FODMAPs (fermentable oligosaccharides, disaccharides, monosaccharides, and polyols), lactose, or other compounds, may be helpful in symptom management in both CD and UC, though evidence for biochemical efficacy is limited. In this review, we discuss the role of diet components in IBD pathogenesis and examine diets currently used in the management of children and adults with IBD. We also address practical, psychosocial, and cultural considerations for dietary therapy across diverse populations.

Meeting the Challenge of Controlling Viral Immunopathology

The mission of this review is to identify immune-damaging participants involved in antiviral immunoinflammatory lesions. We argue these could be targeted and their activity changed selectively by maneuvers that, at the same time, may not diminish the impact of components that help resolve lesions. Ideally, we need to identify therapeutic approaches that can reverse ongoing lesions that lack unwanted side effects and are affordable to use. By understanding the delicate balance between immune responses that cause tissue damage and those that aid in resolution, novel strategies can be developed to target detrimental immune components while preserving the beneficial ones. Some strategies involve rebalancing the participation of immune components using various approaches, such as removing or blocking proinflammatory T cell products, expanding regulatory cells, restoring lost protective cell function, using monoclonal antibodies (moAb) to counteract inhibitory molecules, and exploiting metabolic differences between inflammatory and immuno-protective responses. These strategies can help reverse ongoing viral infections. We explain various approaches, from model studies and some clinical evidence, that achieve innate and adaptive immune rebalancing, offering insights into potential applications for controlling chronic viral-induced lesions.

Oral Cardiac Drug-Gut Microbiota Interaction in Chronic Heart Failure Patients: An Emerging Association

Regardless of the currently proposed best medical treatment for heart failure patients, the morbidity and mortality rates remain high. This is due to several reasons, including the interaction between oral cardiac drug administration and gut microbiota. The relation between drugs (especially antibiotics) and gut microbiota is well established, but it is also known that more than 24% of non-antibiotic drugs affect gut microbiota, altering the microbe's environment and its metabolic products. Heart failure treatment lies mainly in the blockage of neuro-humoral hyper-activation. There is debate as to whether the administration of heart-failure-specific drugs can totally block this hyper-activation, or whether the so-called intestinal dysbiosis that is commonly observed in this group of patients can affect their action. Although there are several reports indicating a strong relation between drug-gut microbiota interplay, little is known about this relation to oral cardiac drugs in chronic heart failure. In this review, we review the contemporary data on a topic that is in its infancy. We aim to produce scientific thoughts and questions and provide reasoning for further clinical investigation.

Commensal antimicrobial resistance mediates microbiome resilience to antibiotic disruption

Despite their therapeutic benefits, antibiotics exert collateral damage on the microbiome and promote antimicrobial resistance. However, the mechanisms governing microbiome recovery from antibiotics are poorly understood. Treatment of Mycobacterium tuberculosis, the world's most common infection, represents the longest antimicrobial exposure in humans. Here, we investigate gut microbiome dynamics over 20 months of multidrug-resistant tuberculosis (TB) and 6 months of drug-sensitive TB treatment in humans. We find that gut microbiome dynamics and TB clearance are shared predictive cofactors of the resolution of TB-driven inflammation. The initial severe taxonomic and functional microbiome disruption, pathobiont domination, and enhancement of antibiotic resistance that initially accompanied long-term antibiotics were countered by later recovery of commensals. This resilience was driven by the competing evolution of antimicrobial resistance mutations in pathobionts and commensals, with commensal strains with resistance mutations reestablishing dominance. Fecal-microbiota transplantation of the antibiotic-resistant commensal microbiome in mice recapitulated resistance to further antibiotic disruption. These findings demonstrate that antimicrobial resistance mutations in commensals can have paradoxically beneficial effects by promoting microbiome resilience to antimicrobials and identify microbiome dynamics as a predictor of disease resolution in antibiotic therapy of a chronic infection.

Association between microbiome and the development of adverse posttraumatic neuropsychiatric sequelae after traumatic stress exposure

Patients exposed to trauma often experience high rates of adverse post-traumatic neuropsychiatric sequelae (APNS). The biological mechanisms promoting APNS are currently unknown, but the microbiota-gut-brain axis offers an avenue to understanding mechanisms as well as possibilities for intervention. Microbiome composition after trauma exposure has been poorly examined regarding neuropsychiatric outcomes. We aimed to determine whether the gut microbiomes of trauma-exposed emergency department patients who develop APNS have dysfunctional gut microbiome profiles and discover potential associated mechanisms. We performed metagenomic analysis on stool samples (n = 51) from a subset of adults enrolled in the Advancing Understanding of RecOvery afteR traumA (AURORA) study. Two-, eight- and twelve-week post-trauma outcomes for post-traumatic stress disorder (PTSD) (PTSD checklist for DSM-5), normalized depression scores (PROMIS Depression Short Form 8b) and somatic symptom counts were collected. Generalized linear models were created for each outcome using microbial abundances and relevant demographics. Mixed-effect random forest machine learning models were used to identify associations between APNS outcomes and microbial features and encoded metabolic pathways from stool metagenomics. Microbial species, including Flavonifractor plautii, Ruminococcus gnavus and, Bifidobacterium species, which are prevalent commensal gut microbes, were found to be important in predicting worse APNS outcomes from microbial abundance data. Notably, through APNS outcome modeling using microbial metabolic pathways, worse APNS outcomes were highly predicted by decreased L-arginine related pathway genes and increased citrulline and ornithine pathways. Common commensal microbial species are enriched in individuals who develop APNS. More notably, we identified a biological mechanism through which the gut microbiome reduces global arginine bioavailability, a metabolic change that has also been demonstrated in the plasma of patients with PTSD.

Refined fiber inulin promotes inflammation-associated colon tumorigenesis by modulating microbial succinate production

BACKGROUND AND AIM

There is an increased risk of colon cancer associated with inflammatory bowel disease (IBD). Dietary fibers (DFs) naturally present in vegetables and whole grains offer numerous beneficial effects on intestinal health. However, the effects of refined DFs on intestinal health remain unclear. Therefore, we elucidated the impact of the refined DF inulin on colonic inflammation and tumorigenesis.

METHODS

Four-week-old wild-type (WT) mice were fed diets containing insoluble DF cellulose (control) or refined DF inulin for 4 weeks. A subgroup of mice was then switched to drinking water containing dextran sulfate sodium (DSS, 1.4% wt/vol) for colitis induction. In another subgroup of mice, colitis-associated colorectal cancer (CRC) was initiated with three 7-day alternate cycles of DSS following an initial dose of mutagenic substance azoxymethane (AOM; 7.5 mg/kg body weight; i.p.). Post 7 weeks of AOM treatment, mice were euthanized and examined for CRC development.

RESULTS

Mice consuming inulin-containing diet exhibited severe colitis upon DSS administration, as evidenced by more body weight loss, rectal bleeding, and increased colonic inflammation than the DSS-treated control group. Correspondingly, histological analysis revealed extensive disruption of colon architecture and massive infiltration of immune cells in the inulin-fed group. We next examined the effect of inulin on CRC development. Surprisingly, significant mortality (~50%) was observed in the inulin-fed but not in the control group during the DSS cycle. Consequently, the remaining inulin-fed mice, which completed the study exhibited extensive colon tumorigenesis. Immunohistochemical characterization showed comparatively high expression of the cell proliferation marker Ki67 and activation of the Wnt signaling in tumor sections obtained from the inulin-fed group. Gut microbiota and metabolite analysis revealed expansion of succinate producers and elevated cecal succinate in inulin-fed mice. Human colorectal carcinoma cells (HCT116) proliferated more rapidly when supplemented with succinate in an inflamed environment, suggesting that elevated luminal succinate may contribute to tumorigenesis.

CONCLUSIONS

Our study uncovers that supplementation of diet with refined inulin induces abnormal succinate accumulation in the intestinal lumen, which in part contributes to promoting colon inflammation and tumorigenesis.

Strategies for applying probiotics in the antibiotic management of Clostridioides difficile infection

The vital role of probiotics in the food field has been widely recognized, and at the same time, probiotics are gradually exhibiting surprising effects in the field of nutraceuticals, especially in regulating gut inflammation and the nutritional environment. As a dietary supplement in clinical nutrition, the coadministration of probiotics with antibiotics model has been applied to prevent intestinal infections caused by Clostridioides difficile. However, the mechanism behind this "bacteria-drug combination" model remains unclear. In particular, the selection of specific probiotic strains, the order of probiotics or antibiotics, and the time interval of coadministration are key issues that need to be further explored and clarified. Here, we focus on the issues mentioned above and give reasonable opinions, mainly including: (1) probiotics are safer and more effective when they intervene after antibiotics have been used; (2) the choice of the time interval between coadministration should be based on the metabolism of antibiotics in the host, differences in probiotic strains, the baseline ecological environment of the host's intestine, and the host immune level; in addition, the selection of the coadministration regime should also take into account factors such as the antibiotic sensitivity of probiotics and dosage of probiotics; and (3) by encapsulating probiotics, combining probiotics with prebiotics, and developing next-generation probiotics (NGPs) and postbiotic formulations, we can provide a more reasonable reference for this type of "bacteria-drug combination" model, and also provide targeted guidance for the application of probiotic dietary supplements in the antibiotic management of C. difficile infection.

Identification of robust and generalizable biomarkers for microbiome-based stratification in lifestyle interventions

BACKGROUND

A growing body of evidence suggests that the gut microbiota is strongly linked to general human health. Microbiome-directed interventions, such as diet and exercise, are acknowledged as a viable and achievable strategy for preventing disorders and improving human health. However, due to the significant inter-individual diversity of the gut microbiota between subjects, lifestyle recommendations are expected to have distinct and highly variable impacts to the microbiome structure.

RESULTS

Here, through a large-scale meta-analysis including 1448 shotgun metagenomics samples obtained longitudinally from 396 individuals during lifestyle studies, we revealed Bacteroides stercoris, Prevotella copri, and Bacteroides vulgatus as biomarkers of microbiota's resistance to structural changes, and aromatic and non-aromatic amino acid biosynthesis as important regulator of microbiome dynamics. We established criteria for distinguishing between significant compositional changes from normal microbiota fluctuation and classified individuals based on their level of response. We further developed a machine learning model for predicting "responders" and "non-responders" independently of the type of intervention with an area under the curve of up to 0.86 in external validation cohorts of different ethnicities.

CONCLUSIONS

We propose here that microbiome-based stratification is possible for identifying individuals with highly plastic or highly resistant microbial structures. Identifying subjects that will not respond to generalized lifestyle therapeutic interventions targeting the restructuring of gut microbiota is important to ensure that primary end-points of clinical studies are reached. Video Abstract.

ietanti-flamatoria or DAIN: A Crohn's disease management strategy tailored for Puerto Ricans

Diet has been increasingly shown to be of therapeutic benefit for patients with inflammatory bowel diseases (IBD), especially Crohn's disease (CD). Yet dietary guidelines are nonexistent. Moreover, diets tailored to Puerto Ricans with IBD living on the island, have not been developed and tested. The rising prevalence of IBD in Puerto Rico warrants exploring the use of diet as part of the treatment strategies for these patients [1]. Here, we describe the study design of "Dieta Anti-Inflamatoria" or DAIN, a parallel two-arm randomized pilot trial aiming at testing the efficacy of IBD-Anti-inflammatory diet (IBD-AID) adapted for adults with CD living in Puerto Rico (clinical trial registration number: NCT05627128). We tailored the IBD-AID to the local cuisine preferences and food availability by creating and adapting recipes consistent with the IBD-AID principles [2,3]. In focus groups with a Community Research Advisory Panel and one-on-one consultations with implementation experts, we identified several aspects of the intervention to adapt before the implementation. The objectives of the stakeholder/expert-informed adaptation were to improve feasibility and compliance while developing the culturally tailored dietary intervention. DAIN was designed for adults living in Puerto Rico with CD and geared to be affordable, appropriate, and acceptable for patients with mild-to-moderate CD. The significance of this work is the validation of culturally appropriate nutritional guidelines to help manage CD symptoms. DAIN provides a blueprint for a comprehensive nutritional program that can be adapted to regional preferences and local food availability allowing wider implementation of diet as an adjunct treatment in diverse clinical settings.

Dietary Intake of Pregnant Women with and without Inflammatory Bowel Disease in the United States

BACKGROUND

Pregnancy is a vulnerable time where the lives of mother and baby are affected by diet, especially high-risk pregnancies in women with inflammatory bowel disease (IBD). Limited research has examined diet during pregnancy with IBD.

AIMS

Describe and compare the diet quality of pregnant women with and without IBD, and examine associations between dietary intake and guidelines during pregnancy.

METHODS

Three 24 h recalls were utilized to assess the diets of pregnant women with IBD (n = 88) and without IBD (n = 82) during 27-29 weeks of gestation. A customized frequency questionnaire was also administered to measure pre- and probiotic foods.

RESULTS

Zinc intake (p = 0.02), animal protein (g) (p = 0.03), and ounce equivalents of whole grains (p = 0.03) were significantly higher in the healthy control (HC) group than the IBD group. Nutrients of concern with no significant differences between groups included iron (3% IBD and 2% HC met the goals), saturated fat (only 1% of both groups met the goals), choline (23% IBD and 21% HC met the goals), magnesium (38% IBD and 35% HC met the goals), calcium (48% IBD and 60% HC met the goals), and water intake (49% IBD and 48% HC met the goals).

CONCLUSIONS

Most pregnant women in this cohort fell short of the dietary nutrients recommended in pregnancy, especially concerning for women with IBD.

The Interplay between Gut Microbiota and Oral Medications and Its Impact on Advancing Precision Medicine

Trillions of diverse microbes reside in the gut and are deeply interwoven with the human physiological process, from food digestion, immune system maturation, and fighting invading pathogens, to drug metabolism. Microbial drug metabolism has a profound impact on drug absorption, bioavailability, stability, efficacy, and toxicity. However, our knowledge of specific gut microbial strains, and their genes that encode enzymes involved in the metabolism, is limited. The microbiome encodes over 3 million unique genes contributing to a huge enzymatic capacity, vastly expanding the traditional drug metabolic reactions that occur in the liver, manipulating their pharmacological effect, and, ultimately, leading to variation in drug response. For example, the microbial deactivation of anticancer drugs such as gemcitabine can lead to resistance to chemotherapeutics or the crucial role of microbes in modulating the efficacy of the anticancer drug, cyclophosphamide. On the other hand, recent findings show that many drugs can shape the composition, function, and gene expression of the gut microbial community, making it harder to predict the outcome of drug-microbiota interactions. In this review, we discuss the recent understanding of the multidirectional interaction between the host, oral medications, and gut microbiota, using traditional and machine-learning approaches. We analyze gaps, challenges, and future promises of personalized medicine that consider gut microbes as a crucial player in drug metabolism. This consideration will enable the development of personalized therapeutic regimes with an improved outcome, ultimately leading to precision medicine.

Leveraging Scheme for Cross-Study Microbiome Machine Learning Prediction and Feature Evaluations

The microbiota has proved to be one of the critical factors for many diseases, and researchers have been using microbiome data for disease prediction. However, models trained on one independent microbiome study may not be easily applicable to other independent studies due to the high level of variability in microbiome data. In this study, we developed a method for improving the generalizability and interpretability of machine learning models for predicting three different diseases (colorectal cancer, Crohn's disease, and immunotherapy response) using nine independent microbiome datasets. Our method involves combining a smaller dataset with a larger dataset, and we found that using at least 25% of the target samples in the source data resulted in improved model performance. We determined random forest as our top model and employed feature selection to identify common and important taxa for disease prediction across the different studies. Our results suggest that this leveraging scheme is a promising approach for improving the accuracy and interpretability of machine learning models for predicting diseases based on microbiome data.

Assessing the Relationship between the Gut Microbiota and Inflammatory Bowel Disease Therapeutics: A Systematic Review

Current inflammatory bowel disease (IBD) treatments including non-biological, biological, and nutritional therapies aim to achieve remission and mucosal healing. Treatment efficacy, however, is highly variable, and there is growing evidence that the gut microbiota influences therapeutic efficacy. The aim of this study was to conduct a systematic review and meta-analysis to define changes in the gut microbiota following IBD treatment and to identify microbial predictors of treatment response. A systematic search using MEDLINE/Embase and PubMed was performed in July 2022. The review was conducted based on the Preferred Reporting Items for Systematic reviews and Meta-Analyses guidelines. Studies were included if they reported longitudinal microbiota analysis (>2 weeks) using next-generation sequencing or high-throughput sequencing of faecal/mucosal samples from IBD patients commencing treatment. Meta-analysis on alpha-diversity changes following infliximab treatment was conducted. Thirty-nine studies met the inclusion criteria, and four studies were included in the meta-analysis. An increase in alpha diversity was observed following treatment with 5-aminosalicylates, corticosteroids, and biological therapies in most studies. Characteristic signatures involving the enrichment of short-chain-fatty-acid-producing bacteria including Faecalibacterium prausnitzii and a reduction of pathogenic bacteria including various Proteobacteria were demonstrated following treatment with specific signatures identified based on treatment outcome. The meta-analysis demonstrated a statistically significant increase in bacterial richness following infliximab treatment (standardised mean difference -1.16 (-1.50, -0.83), p < 0.00001). Conclusion: Distinct microbial signatures are seen following treatment and are associated with treatment response. The interrogation of large longitudinal studies is needed to establish the link between the gut microbiota and IBD therapeutic outcomes.

Metagenomic characterization of the maternal prenatal gastrointestinal microbiome by pregravid BMI

OBJECTIVE

The incidence of women entering into pregnancy with BMI indicating overweight or obesity is rising with concurrent increases in adverse complications such as gestational diabetes. Although several studies have examined the compositional changes to the microbiome across BMI classifications, there has been no investigation regarding changes in microbial function during pregnancy.

METHODS

A total of 105 gastrointestinal microbiome biospecimens were used in this analysis. Biospecimens were sequenced by using the Illumina NovaSeq 6000 shotgun metagenomics platform.

RESULTS

Findings indicate an enrichment in microbiota from the phylum Firmicutes across all pregravid BMI groups with a decrease in α diversity in groups with BMI indicating obesity or overweight compared with a group with BMI indicating normal weight (p = 0.02). More specifically, women with BMI indicating obesity or overweight had enrichment in Bifidobacterium bifidum and B. adolescentis. Women with BMI > 25 kg/m² had a higher abundance of microbiota that support biotin synthesis and regulate epithelial cells in the lower gastrointestinal tract. These epithelial cells are responsible for host adaptability to dietary lipid variation and caloric absorption.

CONCLUSIONS

Our analysis suggests that there are differences in microbial composition and function between BMI groups. Future research should consider how these changes contribute to specific clinical outcomes during pregnancy.

Citrate and hydroxycinnamate derivatives from Mume Fructus protect LPS-injured intestinal epithelial cells by regulating the FAK/PI3K/AKT signaling pathway

ETHNOPHARMACOLOGICAL RELEVANCE

Mume Fructus (MF) is processed from the near-ripe fruit of Prunus mume (Siebold) Siebold & Zucc by drying at low temperature until the color turns black. MF is often used in Chinese medicine for the treatment of chronic diarrhea and dysentery. Previous studies have shown that the active components of MF against Crohn's disease (CD) are mainly citrate and hydroxycinnamate derivatives, which can alleviate the CD-induced inflammatory response and intestinal barrier damage. However, their molecular mechanisms on CD still need further elucidation.

AIM OF THE STUDY

To investigate the protective effects and underlying mechanisms of citrate and hydroxycinnamate derivatives in MF on intestinal epithelial injury.

MATERIALS AND METHODS

Network pharmacology technology was used to predict the anti-CD targets and molecular mechanisms of 4 citrate and 11 hydroxycinnamate derivative prototypes and 5 hydroxycinnamate derivative metabolites in the 40% ethanol fraction of MF (MFE40), the active anti-CD ingredient group of MF. Lipopolysaccharide (LPS)-treated IEC-6 cells were used to investigate the effects of the above components on the proliferation of damaged IEC-6 cells and to verify the molecular mechanism of their regulation on the FAK/PI3K/AKT signaling pathways for the promotion of the proliferation of IEC-6 cells.

RESULTS

A "compound-target-pathway" network was constructed based on network pharmacology analysis, including 20 citrate and hydroxycinnamate derivatives that target 316 core proteins and 36 CD-related pathways, of which PI3K-AKT pathway and focal adhesion were the most enriched pathways. Further cell validation experiments showed that 1 citric acid (CA) compound and 10 hydroxycinnamate derivatives, including 3-O-caffeoylquinic acid (3CQA), 4-O-caffeoylquinic acid (4CQA), 5-O-caffeoylquinic acid (5CQA), caffeic acid (CFA), p-coumaric acid (PCMA), m-coumaric acid (MCMA), ferulic acid (FUA), isoferulic acid (IFUA), 3-hydroxyphenylpropionic acid (3HPPA) and hippuric acid (HPP), could promote the proliferation of IEC-6 cells and inhibit the damage of LPS to IEC-6 cells. Ethyl caffeate (ECFA), a hydroxycinnamic acid derivative, had no effect on promoting the proliferation of IEC-6 cells and was weak in inhibiting the damage of IEC-6 cells caused by LPS. Further mechanistic verification experiments showed that 7 citrate and hydroxycinnamate derivatives (CA, CFA, 3CQA, MCMA, FUA, 3HPPA, and HPP) could upregulate the expression of p-FAK, p-PI3K, and p-AKT proteins. Among them, CA had the better effect on activating the FAK-PI3K-AKT signaling pathway.

CONCLUSIONS

Citrate and hydroxycinnamate derivatives in MF can ameliorate LPS-induced intestinal epithelial cell injury to demonstrate potential for Crohn's disease alleviation. This protective effect can be achieved by upregulating FAK/PI3K/AKT pathway.

Dietary Exposures and Interventions in Inflammatory Bowel Disease: Current Evidence and Emerging Concepts

Diet is intimately linked to the gastrointestinal (GI) tract and has potent effects on intestinal immune homeostasis. Inflammatory bowel disease (IBD) is characterized by chronic inflammation of the GI tract. The therapeutic implications of diet in patients with IBD have received significant attention in recent years. In this review, we provide a contemporary and comprehensive overview of dietary exposures and interventions in IBD. Epidemiological studies suggest that ultra-processed foods, food additives, and emulsifiers are associated with a higher incidence of IBD. Exclusion and elimination diets are associated with improved symptoms in patients with IBD, but no effects on objective markers of inflammation. Specific dietary interventions (e.g., Mediterranean, specific carbohydrate, high fiber, ketogenic, anti-inflammatory diets) have been shown to reduce symptoms, improve inflammatory biomarkers, and quality of life metrics to varying degrees, but these studies are limited by study design, underpowering, heterogeneity, and confounding. To date, there is no robust evidence that any dietary intervention alone may replace standard therapies in patients with IBD. However, diet may play an adjunct role to induce or maintain clinical remission with standard IBD therapies. The results of novel dietary trials in IBD such as personalized fiber, intermittent fasting, and time-restricted diets are eagerly awaited.

The Therapeutic Role of Short-Chain Fatty Acids Mediated Very Low-Calorie Ketogenic Diet-Gut Microbiota Relationships in Paediatric Inflammatory Bowel Diseases

The very low-calorie ketogenic diet (VLCKD) has been recognized as a promising dietary regimen for the treatment of several diseases. Short-chain fatty acids (SCFAs) produced by anaerobic bacterial fermentation of indigestible dietary fibre in the gut have potential value for their underlying epigenetic role in the treatment of obesity and asthma-related inflammation through mediating the relationships between VLCKD and the infant gut microbiota. However, it is still unclear how VLCKD might influence gut microbiota composition in children, and how SCFAs could play a role in the treatment of inflammatory bowel disease (IBD). To overcome this knowledge gap, this review aims to investigate the role of SCFAs as key epigenetic metabolites that mediate VLCKD-gut microbiota relationships in children, and their therapeutic potential in IBD.

Microbial Metabolites Orchestrate a Distinct Multi-Tiered Regulatory Network in the Intestinal Epithelium That Directs P-Glycoprotein Expression

P-glycoprotein (P-gp) is a key component of the intestinal epithelium playing a pivotal role in removal of toxins and efflux of endocannabinoids to prevent excessive inflammation and sustain homeostasis. Recent studies revealed butyrate and secondary bile acids, produced by the intestinal microbiome, potentiate the induction of functional P-gp expression. We now aim to determine the molecular mechanism by which this functional microbiome output regulates P-gp. RNA sequencing of intestinal epithelial cells responding to butyrate and secondary bile acids in combination discovered a unique transcriptional program involving multiple pathways that converge on P-gp induction. Using shRNA knockdown and CRISPR/Cas9 knockout cell lines, as well as mouse models, we confirmed the RNA sequencing findings and discovered a role for intestinal HNF4α in P-gp regulation. These findings shed light on a sophisticated signaling network directed by intestinal microbial metabolites that orchestrate P-gp expression and highlight unappreciated connections between multiple pathways linked to colonic health. IMPORTANCE Preventing aberrant inflammation is essential to maintaining homeostasis in the mammalian intestine. Although P-glycoprotein (P-gp) expression in the intestine is critical for protecting the intestinal epithelium from toxins and damage due to neutrophil infiltration, its regulation in the intestine is poorly understood. Findings presented in our current study have now uncovered a sophisticated and heretofore unappreciated intracellular signaling network or "reactome" directed by intestinal microbial metabolites that orchestrate regulation of P-gp. Not only do we confirm the role of histone deacetylases (HDAC) inhibition and nuclear receptor activation in P-gp induction by butyrate and bile acids, but we also discovered new signaling pathways and transcription factors that are uniquely activated in response to the combination of microbial metabolites. Such findings shed new light into a multi-tiered network that maintains P-gp expression in the intestine in the context of the fluctuating commensal microbiome, to sustain a homeostatic tone in the absence of infection or insult.

Bifidobacterium infantis regulates the programmed cell death 1 pathway and immune response in mice with inflammatory bowel disease

BACKGROUND

Inflammatory bowel disease (IBD) is caused by an abnormal immune response. Programmed cell death 1 (PD-1) is an immunostimulatory molecule, which interacts with PD ligand (PD-L1) playing a prime important role among autoimmune diseases. Bifidobacterium infantis (B. infantis) can promote the differentiation of CD (cluster of differentiation) 4⁺ T cells into regulatory T cells (Tregs). Tregs participate in the development of IBD and may be related to disease activity. B. infantis amplify the expression level of PD-1, PD-L1 and Tregs’ nuclear transcription factor forkhead box protein 3 (Foxp3). But the mechanism of B. infantis on PD-1/PD-L1 signaling remains unclear.

AIM

To explore the mechanism of B. infantis regulating the immune response in IBD.

METHODS

Forty-eight-week-old BALB/c mice were randomly divided into five groups: The control group, dextran sulphate sodium (DSS) model group, DSS + B. infantis group, DSS + B. infantis + anti-PD-L1 group, and DSS + anti-PD-L1 group. The control group mice were given drinking water freely, the other four groups were given drinking water containing 5% DSS freely. The control group, DSS model group, and DSS + anti-PD-L1 group were given normal saline (NS) 400 μL daily by gastric lavage, and the DSS + B. infantis group and DSS + B. infantis + anti-PD-L1 group were given NS and 1 × 10⁹ colony-forming unit of B. infantis daily by gastric lavage. The DSS + B. infantis + anti-PD-L1 group and DSS + anti-PD-L1 group were given 200 μg of PD-L1 blocker intraperitoneally at days 0, 3, 5, and 7; the control group, DSS + anti-PD-L1 group, and DSS + B. infantis group were given an intraperitoneal injection of an equal volume of phosphate buffered saline (PBS). Changes in PD-L1, PD-1, Foxp3, interleukin (IL)-10, and transforming growth factor β (TGF-β) 1 protein and gene expression were observed. Flow cytometry was used to observe changes in CD4⁺, CD25⁺, Foxp3⁺ cell numbers in the blood and spleen.

RESULTS

Compared to the control group, the expression of PD-1, Foxp3, IL-10, and TGF-β1 was significantly decreased in the intestinal tract of the DSS mice (P < 0.05). Compared to the control group, the proportion of CD4⁺, CD25⁺, Foxp3⁺ cells in spleen and blood of DSS group was visibly katabatic (P < 0.05). B. infantis upgraded the express of PD-L1, PD-1, Foxp3, IL-10, and TGF-β1 (P < 0.05) and increased the proportion of CD4⁺, CD25⁺, Foxp3⁺ cells both in spleen and blood (P < 0.05). After blocking PD-L1, the increase in Foxp3, IL-10, and TGF-β1 protein and gene by B. infantis was inhibited (P < 0.05), and the proliferation of CD4⁺, CD25⁺, Foxp3⁺ cells in the spleen and blood was also inhibited (P < 0.05). After blocking PD-L1, the messenger ribonucleic acid and protein expression of PD-1 were invariant.

CONCLUSION

It is potential that B. infantis boost the proliferation of CD4⁺, CD25⁺, Foxp3⁺ T cells in both spleen and blood, as well as the expression of Foxp3 in the intestinal tract by activating the PD-1/PD-L1 pathway.

Gut Microbiome in Inflammatory Bowel Disease: Role in Pathogenesis, Dietary Modulation, and Colitis-Associated Colon Cancer

The gut microbiome has increasingly been recognized as a critical and central factor in inflammatory bowel disease (IBD). Here, we review specific microorganisms that have been suggested to play a role in the pathogenesis of IBD and the current state of fecal microbial transplants as a therapeutic strategy in IBD. We discuss specific nutritional and dietary interventions in IBD and their effects on gut microbiota composition. Finally, we examine the role and mechanisms of the gut microbiome in mediating colitis-associated colon cancer.