The roles of different Bacteroides fragilis strains in protecting against DSS-induced ulcerative colitis and related functional genes

Bacteroides and NAFLD: pathophysiology and therapy

Non-alcoholic fatty liver disease (NAFLD) is a prevalent chronic liver condition observed globally, with the potential to progress to non-alcoholic steatohepatitis (NASH), cirrhosis, and even hepatocellular carcinoma. Currently, the US Food and Drug Administration (FDA) has not approved any drugs for the treatment of NAFLD. NAFLD is characterized by histopathological abnormalities in the liver, such as lipid accumulation, steatosis, hepatic balloon degeneration, and inflammation. Dysbiosis of the gut microbiota and its metabolites significantly contribute to the initiation and advancement of NAFLD. Bacteroides, a potential probiotic, has shown strong potential in preventing the onset and progression of NAFLD. However, the precise mechanism by which Bacteroides treats NAFLD remains uncertain. In this review, we explore the current understanding of the role of Bacteroides and its metabolites in the treatment of NAFLD, focusing on their ability to reduce liver inflammation, mitigate hepatic steatosis, and enhance intestinal barrier function. Additionally, we summarize how Bacteroides alleviates pathological changes by restoring the metabolism, improving insulin resistance, regulating cytokines, and promoting tight-junctions. A deeper comprehension of the mechanisms through which Bacteroides is involved in the pathogenesis of NAFLD should aid the development of innovative drugs targeting NAFLD.

Microbial dysbiosis index for assessing colitis status in mouse models: A systematic review and meta-analysis

Although countless gut microbiome studies on colitis using mouse models have been carried out, experiments with small sample sizes have encountered reproducibility limitations because of batch effects and statistical errors. In this study, dextran-sodium-sulfate-induced microbial dysbiosis index (DiMDI) was introduced as a reliable dysbiosis index that can be used to assess the state of microbial dysbiosis in DSS-induced mouse models. Meta-analysis of 189 datasets from 11 independent studies was performed to construct the DiMDI. Microbial dysbiosis biomarkers, Muribaculaceae, Alistipes, Turicibacter, and Bacteroides, were selected through four different feature selection methods and used to construct the DiMDI. This index demonstrated a high accuracy of 82.3% and showed strong robustness (88.9%) in the independent cohort. Therefore, DiMDI may be used as a standard for assessing microbial imbalance in DSS-induced mouse models and may contribute to the development of reliable colitis microbiome studies in mouse experiments.

Integrative analysis with microbial modelling and machine learning uncovers potential alleviators for ulcerative colitis

Ulcerative colitis (UC) is a challenging form of inflammatory bowel disease, and its etiology is intricately linked to disturbances in the gut microbiome. To identify the potential alleviators of UC, we employed an integrative analysis combining microbial community modeling with advanced machine learning techniques. Using metagenomics data sourced from the Integrated Human Microbiome Project, we constructed individualized microbiome community models for each participant. Our analysis highlighted a significant decline in both α and β-diversity of strain-level microbial populations in UC subjects compared to controls. Distinct differences were also observed in the predicted fecal metabolite profiles and strain-to-metabolite contributions between the two groups. Using tree-based machine learning models, we successfully identified specific microbial strains and their associated metabolites as potential alleviators of UC. Notably, our experimental validation using a dextran sulfate sodium-induced UC mouse model demonstrated that the administration of Parabacteroides merdae ATCC 43,184 and N-acetyl-D-mannosamine provided notable relief from colitis symptoms. In summary, our study underscores the potential of an integrative approach to identify novel therapeutic avenues for UC, paving the way for future targeted interventions.

A key genetic factor governing arabinan utilization in the gut microbiome alleviates constipation

Impaired gastrointestinal motility is associated with gut dysbiosis. Probiotics, such as Bifidobacteria, can improve this bowel disorder; however, efficacy is strain-dependent. We determine that a genetic factor, the abfA cluster governing arabinan utilization, in Bifidobacterium longum impacts treatment efficacy against functional constipation (FC). In mice with FC, B. longum, but not an abfA mutant, improved gastrointestinal transit time, an affect that was dependent upon dietary arabinan. abfA genes were identified in other commensal bacteria, whose effects in ameliorating murine FC were similarly abfA-dependent. In a double-blind, randomized, placebo-controlled clinical trial, supplementation with abfA-cluster-carrying B. longum, but not an abfA-deficient strain, enriched arabinan-utilization residents, increased beneficial metabolites, and improved FC symptoms. Across human cohorts, abfA-cluster abundance can predict FC, and transplantation of abfA cluster-enriched human microbiota to FC-induced germ-free mice improved gut motility. Collectively, these findings demonstrate a role for microbial abfA cluster in ameliorating FC, establishing principles for genomics-directed probiotic therapies.

Effects of dietary Astragalus membranaceus and Codonopsis pilosula extracts on growth performance, antioxidant capacity, immune status, and intestinal health in broilers

The objective of this study was to examine the effects of dietary Chinese herbal medicine (CHM) consisting of Astragalus membranaceus (Fisch.) Bunge (AMT) and Codonopsis pilosula (Franch.) Nannf (CPO) extracts on growth performance, antioxidant capacity, immune status, and intestinal health of broiler chickens. Two groups were formed, each consisting of six replicates of 12 one-day-old healthy male 817 white feather broilers. Broilers were fed either a basal diet (CON group) or a basal diet supplemented with 500 mg/kg CHM. The trial lasted 50 days. The results showed that CHM supplementation resulted in enhanced feed efficiency and antioxidant capacity in both the serum and liver, while it reduced uric acid and endotoxin levels, as well as diamine oxidase activity (p < 0.05). Additionally, CHM treatment increased the height of jejunum villi and upregulated Claudin-1 expression in the jejunal mucosa accompanied by an increase in the mRNA levels of interleukin-6 (IL-6), interferon-γ (IFN-γ), interferon-β (IFN-β), tumor necrosis factor-α (TNF-α), and anti-inflammatory cytokine interleukin-10 (IL-10) (p < 0.05). The presence of dietary CHM caused an increase in the proportions of Bacteroidetes and unclassified Bacteroidales but led to a decrease in those of Firmicutes and Alistipes (p < 0.05). The composition of the jejunal mucosa microbiota was correlated with the feed conversion ratio, serum metabolites, and gene expression based on Spearman correlation analysis. The findings indicated that the consumption of dietary CHM improved the utilization of feed, increased the mRNA expression of pro-inflammatory cytokines in the jejunal mucosa, and decreased the endotoxin level and activities of diamine oxidase and lactate dehydrogenase in the serum, which could potentially be linked to changes in the gut microbiota of broiler chickens.

Dose-related effects of early-life intake of sn-2 palmitate, a specific positionally distributed human milk fatty acid, on the composition and metabolism of the intestinal microbiota

sn2 Palmitate in human milk plays an important role in the physiological health of infants by reducing mineral loss, improving stool hardness, and relieving constipation. Also, sn-2 palmitate modulates intestinal microbiota. However, it remains unclear whether the effects of sn-2 palmitate on infant gut microbiota are dose-dependent. In this study, we investigated the effects of low, medium, and high doses (600, 1,800, and 5,400 mg/kg body weight, respectively) of sn-2 palmitate on the structure, composition, and metabolic function of intestinal microbes in mice. Our results showed that high doses of sn-2 palmitate significantly modulated α- and β-diversity of the intestinal microbiota. The relative abundance of Lachnospiraceae_NK4A136_group decreased with increasing doses of sn-2 palmitate. In contrast, the abundances of Bacteroidetes phylum, Bacteroides, uncultured_Lachnospiraceae, and uncultured_Muribaculaceae were positively correlated with sn-2 palmitate doses. The number of genes predicted encoding autophagy-yeast, phospholipase D signaling pathway, and pentose and glucuronate interconversion metabolic functions of intestinal microbiota increased with increasing doses of sn-2 palmitate. In addition, low and medium doses of sn-2 palmitate significantly upregulated the arginine and proline metabolic pathways, and high doses of sn-2 palmitate significantly increased purine metabolism. Our results revealed that the effects of sn-2 palmitate intake early in life on the composition and metabolism of the intestinal microbiota of mice showed dose-related differences. The study is expected to provide a scientific basis for the development of infant formulas.

The effect of Bacteroides fragilis and its postbiotics on the expression of genes involved in the endocannabinoid system and intestinal epithelial integrity in Caco-2 cells

Purpose

Gut microbiota and its derivatives by constantly interacting with the host, regulate the host function. Intestinal epithelium integrity is under the control of various factors including the endocannabinoid system (ECS). Accordingly, we aimed at investigating the effect of Bacteroides fragilis and its postbiotics (i.e., heat-inactivated, cell-free supernatants (CFS) and outer membrane vesicles (OMVs)) on the expression of genes involved in ECS (cnr1, faah, pparg) and the epithelial barrier permeability (ocln, tjp1) in a Caco-2 cell line.

Methods

Caco-2 cell line was treated with live or heat-inactivated B. fragilis at MOIs of 50 and 100, or stimulated with 7% V/V CFS and B. fragilis OMVs at a dose of 50 and 100 µg/ml overnight. RT-qPCR was applied for expression analysis.

Results

Heat-inactivated B. fragilis induced cnr1, pparg, tjp1, and suppressed faah expression, while live B. fragilis had the opposite effect. OMVs increased pparg, and tjp1 expression by reducing the activity of ECS through an increase in faah and a reduction in cnr1 expression. Finally, an increase in the expression of pparg and ocln, and a reduction in the expression of cnr1 was detected in Caco-2 cells treated with CFS.

Conclusion

The live and heat-inactivated B. fragilis inversely affected cnr1, faah, pparg, and tjp1 expression in Caco-2 cells. Increased tjp1 mRNA levels by affecting the expression of ECS related genes is taken as an indication of the potential beneficial effects of B. fragilis postbiotics and making them potential candidates for improving permeability in the leaky gut syndrome.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40200-023-01264-8.

Ligilactobacillus salivarius CCFM 1266 modulates gut microbiota and GPR109a-mediated immune suppression to attenuate immune checkpoint blockade-induced colitis

The wide application of immune checkpoint blockade (ICB) therapy is impeded by the development of ICB-induced colitis, a condition intricately linked to alterations in the gut microbiota. In our previous study, Ligilactobacillus salivarius CCFM 1266 and Bacteroides fragilis HCK-B3 exhibited anti-inflammatory properties. In this research, treatment with both L. salivarius CCFM 1266 and B. fragilis HCK-B3 significantly ameliorated body weight loss and colonic inflammation in murine colitis models induced by intravenous ipilimumab injection, with L. salivarius CCFM 1266 demonstrating superior effectiveness. This amelioration was characterized by an augmented ratio of Treg cells and M2 macrophages, a diminishment in pro-inflammatory cytokines (IL-1β, TNF-α, IFN-γ, IL-23), and an elevation in the anti-inflammatory cytokine IL-10. The ingestion of L. salivarius CCFM 1266 exerted a discernible influence on the composition of the gut microbiota. Untargeted metabolomics revealed an increase in colonic nicotinic acid levels following the administration of L. salivarius CCFM 1266, potentially initiating the activation of the colonic GPR109a pathway. This mechanism likely serves as the fundamental basis for the protective capacity of L. salivarius CCFM 1266 against ICB-induced colitis. Importantly, L. salivarius CCFM 1266 did not interfere with the anti-tumor immune response elicited by ipilimumab. Probiotic intervention thus emerges as a promising approach for alleviating ICB-induced colitis.

Regulatory effect of lactulose on intestinal flora and serum metabolites in colitis mice: In vitro and in vivo evaluation

Lactulose is a common component in foods. However, the effect of lactulose on intestinal flora and overall metabolic levels remains unclear. Therefore, this study aims to explore the regulative role of lactulose on intestinal flora and serum metabolites via in vitro simulated colonic fermentation model and in vivo colitis mouse model. The results showed that lactulose significantly enriched beneficial bacteria including Dubosiella and Bifidobacterium, and reduced pathogenic bacteria such as Fusobacterium. Moreover, lactulose significantly inhibited dextran sodium sulfate-induced body weight loss, colon shortening, colonic inflammatory infiltration, and pro-inflammatory cytokines IL-6, TNF-α, IL-17, and IL-1β. Lactulose significantly affected serum metabolome in colitis mice and total 24 metabolites representing a high inter-group difference were obtained. Correlation analysis revealed that the changes in serum metabolites were closely associated with the role of intestinal flora, and thus affected phenotypic indicators. Our study provides a reference for nutritional characteristics and application scenarios of dietary lactulose.

Biointerface mineralization generates ultraresistant gut microbes as oral biotherapeutics

Despite the fact that oral microecologics are effective in modulating the gut microbiome, they always suffer from multiple insults during the journey from manufacture to arrival at the intestine. Inspired by the protective mechanism of mineralization, we describe a cytocompatible approach of biointerface mineralization that can generate an ultraresistant and self-removable coating on bacterial surface to solve these challenges. Mineral coating endows bacteria with robust resistances against manufacture-associated oxygen exposure, ultraviolet irradiation, and 75% ethanol. Following oral ingestion, the coating is able to actively neutralize gastric acid and release encapsulated bacteria through spontaneous yet rapid double-decomposition reaction. In addition to acid neutralization, the generated calcium ions can trigger micellar aggregation of bile acid, enabling dual exemptions from the insults of gastric acid and bile acid to achieve uncompromised bacterial viability. Further supported by the therapeutic efficacy of coated bacteria toward colitis mice, biointerface mineralization provides a versatile platform for developing next-generation living oral biotherapeutics.

Enhancement of oral bioavailability and anti-colitis effect of luteolin-loaded polymer micelles with RA (rosmarinic acid)-SS-mPEG as carrier

OBJECTIVE

Polymer micelles were prepared (L-RSPMs) with luteolin and synthetic RA-SS-mPEG polymeric material before evaluation of their anti-inflammatory effect on 2, 4, 6-trinitro-benzene-sulfonic acid (TNBS)-induced ulcerative colitis (UC) model in rats.

METHODS

The synthetic RA-SS-mPEG was characterized with NMR spectroscopy, before preparation of luteolin-coated RA-SS-mPEG polymer micelles. The in vitro characterization and evaluation of the formulation were accomplished, couple with its pharmacokinetic parameters. The levels of PEG2, MDA, CRP and GSH, as well as concentrations of TNF-α, IL1-β, IL-6 and IL-10 in serum and colon tissue were detected via ELISA kit. The degree of colon injury and inflammation was evaluated via histopathologic examination.

RESULTS

L-RSPMs displayed small average droplet size (133.40 ± 4.52 nm), uniformly dispersed (PDI: 0.163 ± 0.011), good stability, slow release and enhanced solubility. We observed 353.28% increase in the relative bioavailability of L-RSPMs compared to free luteolin, while the half-life of the micelle was extended by 6.16h. Compared to model (M) group, luteolin (low and high doses) and L-RSPMs (low and high doses) significantly reduced levels of MDA, PEG2, CRP, TNF-α, IL-6 and IL-1β in colon tissue and serum of colitic rats but dose dependently increased IL-10 and SOD levels (p < 0.01). Histopathologic examination of colon showed that luteolin (low and high doses) and L-RSPMs (low and high doses) improved colonic inflammation in colitic rats to varying degrees compared to M group.

CONCLUSION

L-RSPMs could improve TNBS-induced colon inflammation by enhancing bioavailability, promoting antioxidant effects and regulating cytokine release, which may become a potential agent for UC treatment in clinical settings.

Disturbances of the Gut Microbiota and Microbiota-Derived Metabolites in Inflammatory Bowel Disease

Inflammatory bowel disease (IBD), comprising Crohn's disease (CD) and ulcerative colitis (UC), is characterized as a chronic and recurrent inflammatory disease whose pathogenesis is still elusive. The gut microbiota exerts important and diverse effects on host physiology through maintaining immune balance and generating health-benefiting metabolites. Many studies have demonstrated that IBD is associated with disturbances in the composition and function of the gut microbiota. Both the abundance and diversity of gut microbiota are dramatically decreased in IBD patients. Furthermore, some particular classes of microbiota-derived metabolites, principally short-chain fatty acids, tryptophan, and its metabolites, and bile acids have also been implicated in the pathogenesis of IBD. In this review, we aim to define the disturbance of gut microbiota and the key classes of microbiota-derived metabolites in IBD pathogenesis. In addition, we also focus on scientific evidence on probiotics, not only on the molecular mechanisms underlying the beneficial effects of probiotics on IBD but also the challenges it faces in safe and appropriate application.

Bacteroides fragilis derived metabolites, identified by molecular networking, decrease Salmonella virulence in mice model

In the gut microbiota, resident bacteria prevent pathogens infection by producing specific metabolites. Among bacteria belonging to phylum Bacteroidota, we have previously shown that Bacteroides fragilis or its cell-free supernatant inhibited in vitro Salmonella Heidelberg translocation. In the present study, we have analyzed this supernatant to identify bioactive molecules after extraction and subsequent fractionation using a semi-preparative reversed-phase Liquid Chromatography High-Resolution Tandem Mass Spectrometry (LC-HRMS/MS). The results indicated that only two fractions (F3 and F4) strongly inhibited S. Heidelberg translocation in a model mimicking the intestinal epithelium. The efficiency of the bioactive fractions was evaluated in BALB/c mice, and the results showed a decrease of S. Heidelberg in Peyer’s patches and spleen, associated with a decrease in inflammatory cytokines and neutrophils infiltration. The reduction of the genus Alistipes in mice receiving the fractions could be related to the anti-inflammatory effects of bioactive fractions. Furthermore, these bioactive fractions did not alter the gut microbiota diversity in mice. To further characterize the compounds present in these bioactive fractions, Liquid Chromatography High-Resolution Tandem Mass Spectrometry (LC-HRMS/MS) data were analyzed through molecular networking, highlighting cholic acid (CA) and deoxycholic acid. In vitro, CA had inhibitory activity against the translocation of S. Heidelberg by significantly decreasing the expression of Salmonella virulence genes such as sipA. The bioactive fractions also significantly downregulated the flagellar gene fliC, suggesting the involvement of other active molecules. This study showed the interest to characterize better the metabolites produced by B. fragilis to make them means of fighting pathogenic bacteria by targeting their virulence factor without modifying the gut microbiota.

The Effect of Probiotics on Intestinal Tight Junction Protein Expression in Animal Models: A Meta-Analysis

This study investigates the effect of probiotics supplementation on tight junction protein (TJP) expression in animal models by meta-analysis. We estimated the effect of probiotics administration in an animal inflammatory bowel disease model based on 47 collected articles from the databases, including Sciencedirect, Pubmed, Scopus, and Google Scholar. The effect size was analyzed with the standardized mean difference, and the heterogeneity of the effect sizes was assessed using Cochran’s Q test. To explain the heterogeneity, moderate analyses, such as meta-ANOVA and meta-regression, were performed using the mixed effects model. Finally, publication bias was assessed using Egger’s linear regression test. Among the evaluated items, zonula occluden (ZO)-1 showed the highest Q statistics value, and the effect sizes of all items were positive with high significance (p < 0.0001). The I2 value of all items reflected high heterogeneity (in excess of 80%). From the results of the meta-ANOVA, the factors of the heterogeneity found in the probiotics strains were investigated. Lactobacillus reuteri was identified as having the greatest effect on claudin and ZO-1 expression. The publication bias was detected by the Egger’s linear regression test, though it revealed that the occludin and ZO-1 had larger sample sizes than the claudin. In sum, this meta-analysis reveals that probiotics are effective at improving TJP expression in a gut environment of inflammatory bowel disease (IBD)-induced animal model. Our findings will interest IBD patients, as they suggest an area warranting future study.

Dietary Saccharomyces cerevisiae improves intestinal flora structure and barrier function of Pekin ducks

This study aimed at investigating the effects of dietary Saccharomyces cerevisiae (SC) on the intestinal flora structure and barrier function of Pekin duck. A total of 180 1-day-old Pekin ducks were randomly divided into 3 groups with 6 replicates in each group and 10 birds per replicate. The birds in the control group (CON) were fed the basal diet, and those in the experimental group were fed the basal diets supplemented with 600 mg/kg SC (LSC) and 1,200 mg/kg (HSC), respectively. The trial lasted for 42 d. Results showed that LSC and HSC treatments tended to improve the feed conversion efficiency during the trial. The ileum length of birds in the LSC and HSC groups was elevated. Additionally, with 600mg/kg SC supplemented, the mRNA levels of villin, claudin3, and MUC 2 in d21 were up-regulated, as well as the mRNA levels of villin, claudin3, occludin, i-FABP, ZO-1, and MUC 2 in d42. In addition, dietary SC supplementation improved the α-diversity of the bacteria in cecal chyme and tended to increase the abundance (RA) of Bacteroidetes (P = 0.071). Besides, the RA of Ruminococcaceae_UCG-014 was raised in the LSC group. Beyond that, the RA of Proteobacteria was descended with two levels of SC added. In conclusion, dietary Saccharomyces cerevisiae, particularly at 600 mg/kg level, improved the intestinal flora structure and barrier function of Pekin duck.

Effect of an infant formula containing sn-2 palmitate on fecal microbiota and metabolome profiles of healthy term infants: a randomized, double-blind, parallel, controlled study

Different infant diets have strong effects on child development and may engender variations in fecal microbiota and metabolites. The objective of this study was to evaluate the effect of an infant formula containing sn-2 palmitate on fecal microbiota and metabolites in healthy term infants. The study involved three groups as indicated below. Investigational: the group fed a formula containing high sn-2 palmitate for 16 weeks. Control: the group fed a formula using a regular vegetable oil for 16 weeks. Breastfed: the group fed breast milk for 16 weeks. Fecal samples were collected at 8 weeks (n = 35, 37, and 35, respectively) and 16 weeks (n = 30, 32, and 30, respectively) for the control, investigational, and breastfed infants. Microbiota data were obtained using 16S rRNA sequencing. Short-chain fatty acid (SCFA) analysis was performed using GC-MS, and untargeted metabolomics was conducted using LC-MS. The effect of the formula containing sn-2 palmitate was different from that of the control formula on microbiota and metabolites. Sn-2 palmitate promoted the proliferation of Bifidobacterium and reduced the abundance of Escherichia-Shigella at 8 weeks. Furthermore, it increased α-diversity and enhanced acetate content in feces at both 8 and 16 weeks. In the investigational group infants, the abundance of DL-tryptophan, indole-3-acrylic acid, acetyl-β-methylcholine, L-methionine, and 2-hydroxyvaleric acid significantly increased at 8 weeks, while a notable increase in the abundance of 3-phenyllactic acid, palmitic acid, L-phenylalanine, and leucylproline was observed at 16 weeks. In addition, compared with that of the control infants, the intestinal microbiota and metabolites of sn-2 palmitate-supplemented infants were more similar to those of the breastfed infants. The study hopes to provide a scientific basis for the development of functional infant formulas in the future.