Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach

Lactobacillus plantarum-derived extracellular vesicles from dietary barley leaf supplementation attenuate Citrobacter rodentium infection and intestinal inflammation

BACKGROUND

Inflammatory bowel disease (IBD) is a gastrointestinal inflammatory disorder characterized by disturbed interactions between gut microbiota and host immune response. Barley leaf (BL) is a traditional Chinese herb recorded to have health-promoting effects. However, little is known about the beneficial role of BL against enteric infection-induced intestinal inflammation. Here, we uncover that BL protects against Citrobacter rodentium (C. rodentium)-induced infectious colitis by improving host-microbiota interactions.

METHODS

C3H/HeN mice were fed a diet with/without BL and infected with C. rodentium. Transcriptome sequencing, anti-CD4 antibody treatment, and flow cytometry were conducted to investigate the mechanisms of T cell immune modulation. The intervention involved administering anti-CD4 antibody at 500 µg each time for three times before and during C. rodentium infection. Analysis of gut microbiota composition was performed by 16S rRNA gene sequencing on fecal samples. Fecal microbiota transplantation was conducted by administering microbiota from donor group to recipient group via oral gavage to investigate the role of intestinal microbiota in immune modulation.

RESULTS

BL ameliorated the severity of C. rodentium-induced colitis, and this effect was linked to improved gut homeostasis and enhanced mucosal barrier function. BL enriched the pathways of T helper 1 (Th1)/Th2 and Th17 cell differentiation in the colon, suggesting the involvement of CD4+ T cells. Consistent with this, anti-CD4 antibody treatment abrogated the effect of BL and flow cytometry analysis revealed that BL mitigated C. rodentium-induced pro-inflammatory Th1 immune response. Moreover, the protective effect of BL was associated with alleviation of gut microbiota dysbiosis and increased abundance of Lactobacillus. Our in vivo studies further revealed that live Lactobacillus plantarum (L. plantarum) administration attenuated the pathogenic effects induced by C. rodentium infection, whereas heat-inactivated L. plantarum did not show the same results. Mechanistically, BL supplementation enriched L. plantarum, which subsequently released nanosized extracellular vesicles (EVs) that serve as a key mediator in alleviating C. rodentium-associated pathology and Th1 cell dysregulation.

CONCLUSIONS

Our work thus provides evidence for utilizing BL and L. plantarum-derived EVs to manage enteric infection-associated IBD.

Beneficial effects of Akkermansia muciniphila on benign prostatic hyperplasia and metabolic syndrome

Benign prostatic hyperplasia (BPH) is a prevalent condition associated with male lower urinary tract symptoms (LUTS) and is influenced by metabolic syndrome (MetS) and gut microbiota. Akkermansia muciniphila (AKK) is a gut commensal that has emerged as a potential modulator of metabolic health and inflammatory conditions. This study investigated the correlation between Akkermansia abundance and BPH severity and metabolic indices in fecal and serum samples from BPH patients and healthy donors using 16S rRNA sequencing and metabolic profiling. A testosterone-induced BPH mouse model was used to evaluate the effects of AKK administration on BPH severity and metabolic indices. Altered gut microbiota diversity was observed in BPH patients, with a significant reduction in Akkermansia abundance. Akkermansia abundance was negatively correlated with BPH symptom score, serum lipopolysaccharides (LPS), body mass index (BMI), blood glucose, total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C), and high-density lipoprotein cholesterol (HDL-C). AKK administration in BPH mice resulted in histopathological improvements, reduced prostate index, and amelioration of glandular hyperplasia. Although changes in blood glucose, TC, and LDL-C levels post-AKK supplementation were not statistically significant, a trend toward improvement was noted. Additionally, AKK administration led to a reduction in systemic inflammation markers and restoration of intestinal barrier integrity. In conclusion, AKK might modulate the gut microbiota-prostate axis and MetS. AKK's influence on systemic inflammation and gut barrier function suggests its therapeutic promise in managing BPH and associated metabolic disorders. These findings pave the way for novel microbiota-targeted therapies in the treatment of BPH and MetS.

Small molecule drug absorption in inflammatory bowel disease and current implementation in physiologically- based pharmacokinetic models

Inflammatory bowel disease (IBD) is characterized by a chronic inflammation of the intestinal mucosa, with predominant localization in the colon in ulcerative colitis (UC) or affecting the entire length of the gastrointestinal tract in Crohn's disease (CD). Recent advances in the drug development space have been marked by a return to orally administered small molecules with novel mechanisms of action such as Janus kinase inhibitors. Additionally, the prevalence of certain chronic conditions is higher in IBD patients, many of which are treated with orally administered drugs. Given the pathophysiology and localization of IBD, altered drug absorption from the gastrointestinal tract can be expected. This review discusses several physiological differences between the small and large intestine with the potential to influence drug absorption including pathophysiology related alterations associated with IBD. The main physiological parameters which are identified include luminal fluid volume, luminal pH, transit time, bile salt concentration, microbiome, absorptive surface area, permeability and metabolizing enzymes and transporters. Literature regarding these factors in IBD patients is marked with high heterogeneity in reporting of disease severity and location leading to difficulties in interpreting data across different studies. While the influence of most of these factors has been directly assessed in healthy volunteers, this is rarely the case for IBD patients. Furthermore, studies which used PBPK modelling to describe the PK of an orally administered drug in an IBD population and were able to verify their findings using clinical data are critically examined. These models were able to incorporate the pathophysiological changes associated with IBD and partly succeeded in adequately predicting drug absorption in this population. Given the limited amount of PBPK studies performed on a limited number of drugs, the developed models are most likely not suitable to be used as a general PBPK model for the IBD population.

The role of plant-based dietary compounds in gut microbiota modulation in inflammatory bowel disease

IBD, which includes Crohn's and ulcerative colitis, is associated with gut microbiota dysbiosis. The dysbiotic environment results in an elevation of harmful microbiota and a diminution of advantageous microbiota, leading to IBD. Interestingly, plant-based dietary compounds consisting of dietary fibers and polyphenols have demonstrated promise to be safe and successful in IBD treatment, with studies revealing that they can improve dysbiosis, increase anti-inflammatory cytokines, decrease pro-inflammatory cytokines, lower oxidative stress, and improve barrier function. Plant-based dietary compounds have shown potential to reduce IBD by regulating signaling pathways such as TGF-β/Smad, TRL-4/NF-κB/MAPK, TLR2-NF-κB, autophagy, pyroptosis, glycolysis/gluconeogenesis and amino acid metabolism, Nrf-2/HO-1, microbiota-macrophage-arginine metabolism, and bile acid metabolism. Additionally, they assist in forming short-chain fatty acids and other metabolites, which help regulate immune cells to alleviate IBD. Recent research indicates that dietary compounds, either as nanoparticles or encapsulated in nanoparticles, have shown potential in effectively treating IBD. Despite the beneficial role of plant-based dietary compounds, other studies have shown detrimental effects such as cancer promotion and exacerbation of immune responses. Therefore, this will help clinicians/individuals to plan their nutrition to prevent IBD exacerbation. This review highlights the microbiota signatures linked to IBD and examines the impact of gut dysbiosis on IBD. It also provides a comprehensive discussion of how plant-based dietary compounds can influence the modulation of dysbiotic gut microbiota in IBD. Plant-based dietary compounds hold potential for treating IBD.

Development of the Gut Microbial Immune and Epithelial Cellular System (GutMICS) to Investigate the Immunological Role of Gut Anaerobes

The gut microbiota plays an essential role in host health by regulating gut barrier function and immune system homeostasis. However, research into the physiological and immunological functions of the gut microbiota using In Vitro models that mimic the immune environment of the gut remains limited. Herein, we developed the Gut Microbial Immune & Epithelial Cellular System (GutMICS), a device for coculturing anaerobic gut microbes with host cells, including intestinal epithelial and immune cells. Coculturing Akkermansia muciniphila with GutMICS sustained host cell viability and microbial activity for 72 h. In a lipopolysaccharide- and tumor necrosis factor-α (TNF-α)-induced inflammation model, A. muciniphila enhanced the intestinal barrier function, prevented barrier disruption, reduced pro-inflammatory cytokines (interleukin (IL)-6, TNF-α), and increased anti-inflammatory cytokines (IL-10). Additionally, A. muciniphila protected against Salmonella Typhimurium infection by reducing adhesion and invasion, thereby preventing pathogen-induced cell death. This study used GutMICS to characterize the anti-inflammatory properties of A. muciniphila and its ability to inhibit pathogen infection, demonstrating that GutMICS is a valuable tool for assessing the effects of anaerobic gut microbes on host cells. The ability of the system to simulate various inflammatory environments is expected to have broad applications in the study of host-microbe interactions.

Gut microbiota variations over the lifespan and longevity in rabbit's maternal lines

In rabbit breeding, selection for production efficiency traits has been successful but has reduced rabbit functional longevity. The gut microbiota, which influences host health, is linked to longevity and undergoes significant changes with age. While previous studies have focused on young rabbits, research on gut microbiota changes in adult rabbits is limited. Understanding how gut microbiota evolves with age and its impact on longevity of does during reproductive life could offer insights into improving productivity, health and welfare. This study aims to investigate the evolution of gut microbiota through age and to compare different functional longevity groups between and within two maternal rabbit lines with different longevities; a standard commercial line (A) and another founded using longevity criteria (LP). Our analysis demonstrated a significant impact of age on the gut microbiome of does during their reproductive lifespan, with a decline in alpha diversity and change in beta diversity composition as age progressed. Differential abundance analysis revealed that 20% and 16% of taxa in lines A and LP, respectively, were influenced by age, predominantly showing a negative correlation. In terms of functional longevity, differences in abundance between groups were more pronounced within line A, with up to 16% of taxa differing between high-longevity HL (females with more than 10 parities) and low-longevity LL (females died/culled before 5th parity) groups, compared to only 4% within line LP, highlighting the role of genetic background in shaping microbiota composition and its potential influence on longevity. Finally, differences in microbiome between the two lines A and LP were consistent and maintained through their lifespan independently from their longevity. This study reveals that age significantly influences gut microbiome diversity and composition in adult female rabbits, leading to decreased alpha diversity and notable shifts in composition. Microbiome also differs according to functional longevity, with differences varying by genetic line. This suggests that using microbiome through selection or using specific taxa within it as biomarkers could be a promising avenue for improving longevity. Moreover, microbiome differences between genetic lines persist throughout life, even among animals with the same longevity.

Unraveling the role of Ctla-4 in intestinal immune homeostasis through a novel Zebrafish model of inflammatory bowel disease

Inflammatory bowel disease (IBD) is a chronic and relapsing immune-mediated disorder characterized by intestinal inflammation and epithelial injury. The underlying causes of IBD are not fully understood, but genetic factors have been implicated in genome-wide association studies, including CTLA-4, an essential negative regulator of T cell activation. However, establishing a direct link between CTLA-4 and IBD has been challenging due to the early lethality of CTLA-4 knockout mice. In this study, we identified zebrafish Ctla-4 homolog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla-4-deficient (ctla-4-/-) zebrafish line. These mutant zebrafish exhibited reduced weight, along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation-related genes, disturbing immune system homeostasis. Moreover, single-cell RNA-sequencing analysis indicated increased Th2 cells and interleukin 13 expression, along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally, Ctla-4-deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly, supplementation with Ctla-4-Ig successfully alleviated intestinal inflammation in these mutants. Altogether, our findings demonstrate the pivotal role of Ctla-4 in maintaining intestinal homeostasis. Additionally, they offer substantial evidence linking CTLA-4 to IBD and establish a novel zebrafish model for investigating both the pathogenesis and potential treatments.

Effects of cecropin antimicrobial peptides on growth and intestinal health in growing male minks

This study investigated the effects of dietary supplementation with cecropin antimicrobial peptides (CAD) on growth performance and intestinal health in growing male minks (Neovison vison). A cohort of 60 male minks (65 days old) were evenly divided into six groups and fed a basal diet supplemented with CAD at 0 (control), 100, 200, 300, 400, or 500 mg/kg for 8 weeks. The findings revealed that the minks in 200 mg/kg CAD group had greater growth performance, with significantly higher final body weight (FBW) and average daily gain (ADG). Compared to the minks in the control (p < 0.05). Digestibility analyses at week 3 demonstrated that CAD supplementation enhanced ether extract (EE) digestibility (p < 0.05), while 200, 400, and 500 mg/kg CAD improved crude protein (CP) digestibility (p < 0.05). Intestinal morphology assessments indicated that 200 mg/kg CAD significantly increased duodenal and jejunal villus height (both p < 0.05) and jejunal villus height-to-crypt depth ratio (p < 0.05) compared to the control. Serum immunological analyses revealed elevated levels of complement C4 and IgG in CAD-supplemented groups (p < 0.05). Notably, the 100 mg/kg CAD group exhibited the higher serum IgA, IgM, and complement C3, and less jejunal TNF-α levels (all p < 0.05). Microbiota profiling showed that CAD supplementation reduced the relative abundance of Escherichia-Shigella and Mycoplasma, while 100, 200 and 400 mg/kg CAD decreased Peptostreptococcaceae populations (p < 0.05). The 100 mg/kg CAD group displayed optimal immune enhancement and microbiota modulation, whereas the 200 mg/kg group achieved the best growth performance and intestinal function. These results suggest that dietary CAD supplementation at 100-200 mg/kg effectively improves growth, nutrient utilization, and intestinal health in growing male minks.

Community-Acquired Clostridioides difficile Infection: The Fox Among the Chickens

Clostridioides difficile infection (CDI) appears mainly as nosocomial antibiotic-associated diarrhea, and community-acquired infection is increasingly being recognized. The threshold of asymptomatic colonization and the clinical manifestation of CDI need further elucidation. Community-acquired CDI (CA-CDI) should be considered when the disease commences within 48 h of admission to hospital or more than 12 weeks after discharge. Although CDI is not established as a food-borne or zoonotic disease, some data support that direction. The spores' ability to survive standard cooking procedures and on abiotic surfaces, the formation of biofilms, and their survival within biofilms of other bacteria render even a low number of spores capable of food contamination and spread. Adequate enumeration methods for detecting a low number of spores in food have not been developed. Primary care physicians should take CA-CDI into consideration in the differential diagnosis of diarrhea, as there is a thin line between colonization and infection. In patients diagnosed with inflammatory bowel disease and other comorbidities, C. difficile can be the cause of recurrent disease and should be included in the estimation of diarrhea and worsening colitis symptoms. In the community setting, it is difficult to distinguish asymptomatic carriage from true infection. For asymptomatic carriage, antibiotic therapy is not suggested but contact isolation and hand-washing practices are required. Primary healthcare providers should be vigilant and implement infection control policies for the prevention of C. difficile spread.

Exploring the mechanism of Sinisan in the treatment of ulcerative colitis with depression based on UPLC-Q-Orbitrap-MS combined with network pharmacology, molecular docking, and experimental validation

ETHNOPHARMACOLOGICAL RELEVANCE

SiniSan (SNS), a traditional formula from the Treatise on Typhoid Fever, has been shown in modern clinical practice to effectively treat both ulcerative colitis (UC) and depression, although the underlying mechanisms remain incompletely understood.

AIM OF THE STUDY

This study employed UPLC-Q-Orbitrap-MS, network pharmacology, molecular docking, and experimental validation to investigate SNS's mechanism in treating UC with comorbid depression.

MATERIALS AND METHODS

UPLC-Q-Orbitrap-MS, in conjunction with network pharmacology and molecular docking, identified active constituents and potential targets of SNS. A UC model induced by a 3 % dextran sulfate sodium (DSS) solution was used for experimental validation. Therapeutic efficacy was assessed through behavioral tests, ELISA, routine blood tests, histopathology, immunofluorescence, Western blot, and qRT-PCR.

RESULTS

SNS alleviated weight loss and inflammation in DSS-induced colitis in mice while exhibiting antidepressant effects in the open field test, forced swim test, and tail suspension test. Furthermore, SNS improved intestinal mucosal barrier function and restored hippocampal blood-brain barrier integrity. It inhibited microglial proliferation and neuroinflammation in the Hippocampus Cornu Ammonis 1 and dentate gyrus regions. Mechanistic analysis revealed that SNS mediates its effects on UC by modulating targets in the PI3K/AKT signaling pathway.

CONCLUSIONS

SNS ameliorates UC with comorbid depression by restoring the integrity of both the intestinal mucosal barrier and the blood-brain barrier, alleviating DSS-induced colitis and neuroinflammation.

Mitigation of oxidative stress-induced aging by extracellular polysaccharides from Lactiplantibacillus plantarum R6-1 from Sayram ketteki

Oxidative stress within the body is associated with aging, playing a crucial role in its progression. Polysaccharides from lactic acid bacteria are well recognized for their antioxidant effects, potentially improving the aging process. This study investigated the characterization and antioxidant activities of extracellular polysaccharides (EPS-1: 59,978 Da, 40.9 % mannose, 4.5 % ribose, 5.8 % glucuronic acid, 44.1 % glucose, 2.9 % galactose; EPS-2: 25,686 Da, 22.9 % mannose, 5.4 % ribose, 5.5 % glucuronic acid, 59.6 % glucose, 5.4 % galactose) produced by Lactiplantibacillus plantarum R6-1. The results showed that EPS could increase the survival rates of Caco-2 cells exposed to hydrogen peroxide and mitigate the D-galactose (D-Gal)-induced oxidative stress in mice. Administration of EPS activated the hepatic nuclear factor erythroid 2-related factor 2 (Nrf2) pathway in mice. Subsequently, this pathway activated various oxidation-related enzymes such as superoxide dismutase, catalase, and glutathione peroxidase. Meanwhile, EPS regulated mouse intestinal microbiota by increasing the relative abundance of beneficial bacteria secreting anti-inflammatory factors, such as Norank_f_Muribaculaceae and Dubosiella, and restoring the imbalance of Firmicutes to Bacteroidetes caused by oxidative stress. This study shows that L. plantarum R6-1's EPS exhibited the ability to concurrently influence both the liver and intestinal microbiota of mice, thereby achieving an anti-oxidative effect through their interconnected interactions.

Neuroimmune interactions: The bridge between inflammatory bowel disease and the gut microbiota

BACKGROUND

The multidimensional regulatory mechanism of the gut-brain-immune axis in the context of inflammatory bowel disease (IBD) has garnered significant attention, particularly regarding how intestinal microbiota finely regulates immune responses through immune cells and sensory neurons.

MAIN BODY

Metabolites produced by intestinal microbiota influence the phenotype switching of immune cells via complex signalling pathways, thereby modulating their anti-inflammatory and pro-inflammatory functions during intestinal inflammation. Furthermore, sensory neurons exhibit heightened sensitivity to microbial-derived signals, which is essential for preserving intestinal balance and controlling pathological inflammation by integrating peripheral environmental signals with local immune responses. The dynamic equilibrium between immune cells and the neuroimmunoregulation mediated by sensory neurons collectively sustains immune homeostasis within the intestine. However, this coordination mechanism is markedly disrupted under the pathological conditions associated with IBD.

CONCLUSION

An in-depth exploration of the interactions among immune cells, gut microbiota and sensory neurons may yield significant insights into the pathological mechanisms underlying IBD and guide the creation of new treatment approaches.

KEY POINTS

The gut microbiota regulates the gut-brain-immune axis, modulating neuroimmune interactions in IBD. Microbiota-derived metabolites influence immune cells, thereby affecting neurons. Neurons secrete mediators, enabling bidirectional neuroimmune communication essential for intestinal homeostasis. Disruptions contribute to IBD, offering therapeutic targets.

Unraveling the interplay between mesenchymal stem cells, gut microbiota, and systemic sclerosis: therapeutic implications

Systemic sclerosis (SSc) is an autoimmune disease with progressive fibrotic disorders in multiple organs. Mesenchymal stem cells (MSCs) have shown great potential in treating SSc, but the exact regulatory mechanism is not fully understood. In this study, we used human umbilical cord-derived MSCs (hUC-MSCs) to treat SSc mice induced by bleomycin. The gut microbiota composition and predicted functions were analyzed using 2bRAD sequencing of fecal samples from control, SSc, and MSCs-treated mice. Treatment with MSCs improved the bleomycin-induced SSc mice, characterized by significantly reduced collagen deposition and dermal thickness. The gut microbiota of SSc mice exhibited lower species evenness and was clearly separated from the control mice based on beta diversity. MSC treatment led to a significant reduction of conditionally pathogenic bacteria enriched in SSc, including Akkermansia muciniphila and Parasutterella excrementihominis. Conversely, the relative abundance of butyrate-producing bacteria, such as Roseburia, Butyricicoccus porcorum, and Gemmiger formicilis, was notably increased in MSCs-treated SSc mice. Additionally, the functional analysis revealed that MSCs intervention effectively enhanced sulfur metabolism, tryptophan metabolism, citrate cycle, RNA polymerase, and beta-lactam resistance. In summary, the findings in the present study have suggested the close association between gut microbiota and metabolic dysbiosis in mice with SSc. The administration of MSCs has been shown to regulate the disrupted metabolic pathways in SSc mice, thus restoring the normal function of the gut microbiota. This study provides valuable insights into the specific gut microbiota and metabolic pathways involved in the efficacy of MSC treatment, thereby proposing a novel therapeutic strategy for SSc.

IMPORTANCE

Human umbilical cord-derived mesenchymal stem cells (HUC‑MSCs) demonstrate efficacy in alleviating skin thickening and collagen deposition in systemic sclerosis (SSc) mice, which also regulate the gut microbiota composition and function. Specifically, MSC intervention leads to a notable increase in butyrate-producing bacteria, a decrease in Akkermansia muciniphila and Parasutterella excrementihominis, and a reversal of the dysregulated microbial function in SSc mice. These findings underscore the potential significance of gut microbiota in the therapeutic effects of MSCs in SSc.

Faecal microbiota transplantation in Crohn's disease: an Australian randomised placebo-controlled trial protocol

INTRODUCTION

The enteric microbiota drives inflammation in Crohn's disease. Yet, there are no placebo controlled trials evaluating the efficacy and safety of faecal microbiota transplantation (FMT) in inducing and maintaining remission in patients with active Crohn's disease. The Microbial Restoration (MIRO) study aims to establish this evidence.

METHODS AND ANALYSIS

At two specialist inflammatory bowel disease centres, 120 enrolled patients will have a 3-week period of diet optimisation (removal of ultra-processed foods) together with a 7-day course of antibiotics (to facilitate subsequent FMT engraftment). Patients will then be stratified to upper gut (for disease proximal to the splenic flexure) or lower gut (distal to the splenic flexure) disease. Patients will then be randomised in a 2:1 ratio to receive anaerobically prepared stool or placebo for 8 weeks either by gastroscopy, or colonoscopy and enemas. Clinical response at 8 weeks (Crohn's Disease Activity Index (CDAI) reduction ≥100 points or to <150 points) is the primary outcome measure. Non-responders to placebo and partial responders to FMT (CDAI decrease <100 but >70) receive FMT for weeks 8-16.Patients achieving clinical response from FMT after 8 or 16 weeks will be randomised in a 1:1 ratio to either a 44-week maintenance phase of FMT or placebo. Patients will receive FMT from one donor throughout the study.The MIRO study will establish whether FMT is an effective and safe therapy to induce and maintain remission in patients with active Crohn's disease.

ETHICS AND DISSEMINATION

Ethical approval has been received by the St Vincent's Hospital Melbourne Human Research Ethics Committee (HREC-A 084/21). The results will be disseminated in peer-reviewed journals and presented at international conferences.

TRIAL REGISTRATION NUMBER

ClinicalTrials.gov: NCT04970446; Registered on 20 July 2021.

Nucleic Acid-Functionalized Gold Nanorods Modulate Inflammation and Dysregulated Intestinal Barriers for Treatment of Ulcerative Colitis

Traditional oral treatments for ulcerative colitis (UC) face marked limitations including their single therapeutic effect, potential off-target interactions, and toxic side effects. In this study, we present nucleic acid-functionalized gold nanorods (NAF AuNRs), a biocompatible nanomaterial designed for the oral treatment of dextran sulfate sodium (DSS)-induced colitis. The NAF AuNRs alleviate immune responses by inhibiting pro-inflammatory macrophages and enhancing the expression of barrier proteins in intestinal epithelial cells. Due to the negatively charged nucleic acid shell, NAF AuNRs preferentially target anionic, inflamed colon tissues upon oral administration, reducing pro-inflammatory cytokine levels and promoting the recovery of intestinal barrier in DSS-induced colitis mice. Collectively, these findings suggest that NAF AuNRs represent an innovative and promising therapeutic approach for UC management, offering novel insights into the application of nucleic acid-functionalized nanomaterials.

A Similar Mutation in the AAUU-Rich Elements of the Mouse TNF Gene Results in a Distinct Ileocolitic Phenotype: A New Strain of TNF-Overexpressing Mice

BACKGROUND

Tumor necrosis factor (TNF) is a pleiotropic cytokine that plays a critical role in the pathogenesis of immune-mediated diseases including inflammatory bowel disease (IBD). The stability of its mRNA transcript, determined in part by destabilizing sequences in its AAUU repeats (ARE) gene region, is an important regulator of its tissue and systemic levels. A deletion in the ARE region of the gene resulted in IBD and arthritis in mice and pigs, supporting a critical role for the cytokine in human IBD and several human arthritides. A mutation in the same area of the mouse genome by Genentech scientists (T.Y., M.K.) resulted in a similar but not identical phenotype.

METHODS

Here, we compare histopathological, cellular, and molecular features of the strains and propose reasons for their distinct phenotypes. First, while homozygous TNFΔARE mice develop severe arthritis and die after weaning, homozygous Genentech TNFΔARE (ΔG/ΔG) mice have normal lifespans, and males are often fertile.

RESULTS

We found that while the ileitic phenotype had peaked at 12 weeks of age in all mice, colitis progressed mostly after 20 weeks of age in heterozygous mice. Their variably penetrant arthritic phenotype progressed mostly after 20 weeks, also in heterozygous mice from both strains. There was expansion of central memory T and B cells in lymphoid organs of TNF-overproducing strains and their transcriptional profile shared well-known pathogenetic pathways with human IBD. Finally, we found differences in the mutated sequences within the ARE regions of the TNF gene and in their microbiota composition and genetic background. These differences likely explain their phenotypic differences.

CONCLUSIONS

In summary, we describe a different strain of TNF-overproducing mice with an overlapping, yet not identical phenotype, which may have differential applications than the original strain.

Disentangling the nutrition-microbiota liaison in inflammatory bowel disease

Inflammatory Bowel Disease (IBD) is a set of chronic intestinal inflammatory disorders affecting the gastrointestinal (GI) tract. Beside compromised intestinal barrier function and immune hyperactivation, a common IBD feature is dysbiosis, characterized by a reduction of some strains of Firmicutes, Bacteroidetes, Actinobacteria and an increase in Proteobacteria and pathobionts. Emerging evidence points to diet and nutrition-dependent gut microbiota (GM) modulation, as etiopathogenetic factors and adjuvant therapies in IBD. Currently, no nutritional regimen shows universal efficacy, and advice are controversial, especially those involving restrictive diets potentially resulting in malnutrition. This review provides an overview of the role of macronutrients, dietary protocols and GM modulation in IBD patients. A Western-like diet contributes to an aberrant mucosal immune response to commensal bacteria and impairment of the intestinal barrier integrity, thereby triggering intestinal inflammation. Conversely, a Mediterranean nutritional pattern appears to be one of the most beneficial dietetic regimens able to restore the host intestinal physiology, by promoting eubiosis and preserving the intestinal barrier and immune function, which in turn create a virtuous cycle improving patient adherence to the pattern. Further clinical studies are warranted, to corroborate current IBD nutritional guidelines, and develop more accurate models to move forward precision nutrition and ameliorate patients' quality of life.

Comparative analysis of dominant gut microbiota in Inflammatory Bowel Disease patients and healthy individuals: A case-control study

Background

Chronic inflammation in the gut might be linked to microbiota dysbiosis.

Objective

This study aimed to investigate alterations in the gut microbiota composition of adult IBD patients compared to healthy controls.

Methods

This case-control study investigated the relationship between faecal microbiota composition and IBD in adults. Real-time qPCR analysis using bacterial 16S rRNA gene quantified the abundance of six key bacterial groups (Firmicutes, Lactobacillus spp., Bifidobacterium spp., Fusobacterium spp., Bacteroides fragilis, and Faecalibacterium prausnitzii) in faecal samples from 30 IBD patients (13 Crohn's disease, 17 ulcerative colitis) and 30 healthy controls. A correlation matrix was employed to assess relationships between these bacteria.

Results

Real-time qPCR revealed significant differences (p-value <0.05) in the abundance of several bacterial groups between IBD patients and healthy controls. Firmicutes, Fusobacterium spp., and B. fragilis were significantly more abundant (p-value <0.05) in IBD patients compared to controls. Conversely, Lactobacillus spp. and F. prausnitzii were both significantly less abundant (p-value <0.05) in IBD patients. While some bacterial groups exhibited trends toward higher abundance in either CD or UC patients, these differences were not statistically significant (p-value >0.111). The correlation matrix analysis revealed specific co-occurrence patterns: Bacteroides showed a strong negative correlation with Prevotella, more abundant in healthy controls, suggesting a shift in dominance in IBD patients. Lactobacillus spp. and F. prausnitzii exhibited a positive correlation in healthy individuals, indicating their potential cooperative role in maintaining gut homeostasis.

Conclusion

This study identified significant alterations in gut microbiota composition in adult IBD patients compared to healthy controls, with notable differences in the abundance of specific bacterial groups. These findings suggest that gut microbiota dysbiosis may play a critical role in IBD pathogenesis. The identification of specific bacterial imbalances provides a foundation for developing microbiota-based therapies, such as probiotics, prebiotics, and fecal microbiota transplantation, as potential interventions for restoring microbial balance and mitigating disease progression. Further research is needed to translate these insights into targeted therapeutic strategies and to explore their effectiveness in clinical settings.

Regulation of Intestinal Barrier Function and Gut Microbiota by Hot Melt Extrusion-Drug Delivery System-Prepared Mulberry Anthocyanin in an Inflammatory Bowel Disease Model

Background/Objectives: Anthocyanins (ACNs) derived from mulberry (Morus alba L.) exhibit potent antioxidant and anti-inflammatory activities. However, their low stability and bioavailability in physiological environments limit their therapeutic potential. This study aimed to enhance the stability and controlled release ACNs using a hot-melt extrusion drug delivery system (HME-DDS) formulation, HME-MUL-F2, and evaluate its effects on gut barrier function and microbiota composition in a DSS-induced colitis model. Methods: The anthocyanin content of HME-MUL-F2 was quantified and compared with that of raw mulberry extract. The formulation's protective effects were assessed in Caco-2 and RAW 264.7 cells, confirming its biocompatibility and anti-inflammatory properties. The therapeutic efficacy was further evaluated in a dextran sulfate sodium (DSS)-induced inflammatory bowel disease (IBD) model, focusing on gut barrier integrity, inflammatory cytokine modulation, and gut microbiota composition. Results: HME-MUL-F2 significantly improved gut barrier function by upregulating tight junction proteins and reducing inflammatory cytokine levels in the colitis model. Moreover, the formulation modulated gut microbiota composition, promoting beneficial bacteria while suppressing pathogenic strains. HME-MUL-F2 administration led to a significant increase in the Bacteroidetes-to-Firmicutes ratio, which is associated with improved gut health. These results indicate that HME-MUL-F2 significantly enhances anthocyanin bioavailability, leading to improved gut health and potential therapeutic applications for inflammatory conditions. Conclusions: This study highlights the potential of HME technology for improving the stability, bioavailability, and therapeutic efficacy of anthocyanins. HME-MUL-F2 is a sustained-release formulation that enhances gut barrier function and modulates intestinal microbial balance in a DSS-induced inflammatory bowel disease model. These findings strongly suggest that the observed therapeutic effects of HME-MUL-F2 are primarily due to enhanced anthocyanin bioavailability and targeted delivery to the colon, although further clinical studies will provide more definitive confirmation.

Gut Microbiota in Different Treatment Response Types of Crohn's Disease Patients Treated with Biologics over a Long Disease Course

Background and Aims: Crohn's disease (CD) is a chronic inflammatory bowel disease (IBD) with a globally increasing prevalence, partially driven by alterations in gut microbiota. Although biological therapy is the first-line treatment for CD, a significant proportion of patients experience a primary non-response or secondary loss of response over time. This study aimed to explore the differences in gut microbiota among CD patients with divergent long-term responses to biological therapy, focusing on a long disease course. Methods: Sixteen CD patients who applied the biological agents for a while were enrolled in this study and were followed for one year, during which fecal specimens were collected monthly. Metagenomic analysis was used to determine the microbiota profiles in fecal samples. The response to biological therapy was evaluated both endoscopically and clinically. Patients were categorized into three groups based on their response: R (long-term remission), mA (mild active), and R2A group (remission to active). The differences in the gut microbiota among the groups were analyzed. Results: Significant differences in fecal bacterial composition were observed between the groups. The R2A group exhibited a notable decline in gut microbial diversity compared to the other two groups (p < 0.05). Patients in the R group had higher abundances of Akkermansia muciniphila, Bifidobacterium adolescentis, and Megasphaera elsdenii. In contrast, Veillonella parvula, Veillonella atypica, and Klebsiella pneumoniae were higher in the R2A group. Conclusions: Gut microbial diversity and specific bacterial significantly differed among groups, reflecting distinct characteristics between responders and non-responders.

Gut microbiome reveals the trophic variation and significant adaption of three sympatric forest-dwelling ungulates on the eastern Qinghai-Xizang Plateau

BACKGROUND

The gut microbiome of herbivorous mammals regulates numerous physiological processes, including digestion and energy metabolism. The complex stomach architecture of ruminants, in conjunction with the metabolic capabilities of their microbiota, confers a considerable adaptive advantage to these animals. Nevertheless, a significant gap persists in comparative studies on the variations in the gut microbiome among sympatric ruminants and their potential adaptive implications. Accordingly, in this study, 16S rRNA gene sequencing and metagenomic approaches were used to analyse the composition and functional attributes of the gut microbiome of sympatric Moschus chrysogaster, Capricornis sumatraensis, and Cervus albirostris inhabiting the eastern periphery of the Qinghai-Xizang Plateau.

RESULTS

The gut microbiome of C. albirostris exhibited a higher diversity than that of M. chrysogaster and C. sumatraensis, whereas those of M. chrysogaster and C. sumatraensis were similar. Although species-specific variations existed among the three mammalian microbiomes, the microbiomes of C. albirostris and C. sumatraensis were more similar, whereas that of M. chrysogaster was markedly distinct. Metagenomic analysis revealed a pattern of functional convergence in the gut microbiome of the three species, with the gut microbiome of C. albirostris exhibiting a pronounced emphasis on carbohydrate metabolism, significantly surpassing that of M. chrysogaster and C. sumatraensis. Compared to the other two species, the gut microbiome of C. sumatraensis presented significantly elevated levels of amino acids and energy metabolism, whereas that of M. chrysogaster presented an increased capacity for 3-hydroxyacyl- [acyl carrier protein]-dehydratase production.

CONCLUSION

These findings suggest that the gut microbiome of sympatric M. chrysogaster, C. sumatraensis, and C. albirostris tend to converge. Metabolic variations within their gut microbiome may result in differential food resource utilisation, potentially indicating significant nutritional and ecological trait characteristics for stable coexistence.

Microbiota in inflammatory bowel disease: mechanisms of disease and therapeutic opportunities

Perturbations in the intestinal microbiome are strongly linked to the pathogenesis of inflammatory bowel disease (IBD). Bacteria, fungi and viruses all make up part of a complex multi-kingdom community colonizing the gastrointestinal tract, often referred to as the gut microbiome. They can exert various effects on the host that can contribute to an inflammatory state. Advances in screening, multiomics and experimental approaches have revealed insights into host-microbiota interactions in IBD and have identified numerous mechanisms through which the microbiota and its metabolites can exert a major influence on the gastrointestinal tract. Looking into the future, the microbiome and microbiota-associated processes will be likely to provide unparalleled opportunities for novel diagnostic, therapeutic and diet-inspired solutions for the management of IBD through harnessing rationally designed microbial communities, powerful bacterial and fungal metabolites, individually or in combination, to foster intestinal health. In this Review, we examine the current understanding of the cross-kingdom gut microbiome in IBD, focusing on bacterial and fungal components and metabolites. We examine therapeutic and diagnostic opportunities, the microbial metabolism, immunity, neuroimmunology and microbiome-inspired interventions to link mechanisms of disease and identify novel research and therapeutic opportunities for IBD.

Microbiome functional gene pathways predict cognitive performance in older adults with Alzheimer's disease

Disturbances in the gut microbiome is increasing correlated with neurodegenerative disorders, including Alzheimer's Disease. The microbiome may in fact influence disease pathology in AD by triggering or potentiating systemic and neuroinflammation, thereby driving disease pathology along the "microbiota-gut-brain-axis". Currently, drivers of cognitive decline and symptomatic progression in AD remain unknown and understudied. Changes in gut microbiome composition may offer clues to potential systemic physiologic and neuropathologic changes that contribute to cognitive decline. Here, we recruited a cohort of 260 older adults (age 60+) living in the community and followed them over time, tracking objective measures of cognition, clinical information, and gut microbiomes. Subjects were classified as healthy controls or as having mild cognitive impairment based on cognitive performance. Those with a diagnosis of Alzheimer's Diseases with confirmed using serum biomarkers. Using metagenomic sequencing, we found that relative species abundances correlated well with cognition status (MCI or AD). Furthermore, gene pathways analyses suggest certain microbial metabolic pathways to either be correlated with cognitive decline or maintaining cognitive function. Specifically, genes involved in the urea cycle or production of methionine and cysteine predicted worse cognitive performance. Our study suggests that gut microbiome composition may predict AD cognitive performance.

Sulfoglycolysis sustains Eubacterium rectale in low-fiber diets

The production of short-chain fatty acids (SCFAs) by Firmicutes (Bacillota) within the human gastrointestinal tract is recognized as critical for gut health and the progression of a range of disease states. Firmicutes are the most diverse phylum of human gut bacteria, are highly studied, and are often specialized to degrade just a few polysaccharide substrates. Members of the Firmicutes include key bacteria that produce butyrate, an SCFA that is generally not produced by members of the other major phyla. Recently, it was shown that Eubacterium rectale, a widespread member of the Firmicutes belonging to the Clostridiales cluster XIVa, can grow on the unusual but ubiquitous plant-derived sugar SQ using a sulfoglycolytic sulfofructose transaldolase pathway. Here, we show that in addition to SQ, E. rectale can also grow on the SQ glycoside sulfoquinovosyl glycerol (SQGro). The 3D structure of the E. rectale sulfoquinovosidase (SftG) shares strong structural conservation with other carbohydrate-active enzyme family GH31 SQases. Using sequence-similarity networks, we provide new biological context to a conserved domain of unknown function protein SftX belonging to DUF4867, which is conserved in the sulfoglycolytic sulfofructose transaldolase pathway, and determine its 3D structure. Finally, with the aid of a synthetic mini-human microbiome reconstituted in germ-free mice, we show that an SQ dietary supplement can rescue E. rectale from population crashes that occur upon switching from a high-fiber to a low-fiber, high-fat diet. This suggests that SQ or SQGro has the potential as a prebiotic for promoting the maintenance of this important butyrate-producing bacterium within the colonic microbiota.

Comparative Whole Metagenome Analysis in Lesional and Nonlesional Scalp Areas of Patients with Psoriasis Capitis and Healthy Individuals

Psoriasis is an immune-mediated inflammatory disorder, where the majority of the patients suffer from psoriasis capitis or scalp psoriasis. Current therapeutics remain ineffective to treat scalp lesions. In this study, we present a whole-metagenome characterization of the scalp microbiome in psoriasis capitis. We investigated how changes in the homeostatic cutaneous microbiome correlate with the condition and identified metagenomic biomarkers (taxonomic, functional, virulence factors, antimicrobial resistance genes) that could partly explain its emergence. Within this study, 83 top and back scalp samples from healthy individuals and 64 lesional and nonlesional scalp samples from subjects with untreated psoriasis capitis were analyzed. Using qPCR targeting the 16S and 18S ribosomal RNA genes, we found a significant decrease in microbial load within scalp regions affected by psoriasis compared with that in their nonlesional counterparts. Metagenomic analysis revealed that psoriatic lesions displayed significant lower Cutibacterium species (including C. modestum, C. namnetense, C. granulosum, C. porci), along with an elevation in Staphylococcus aureus. A heightened relative presence of efflux pump protein-encoding genes was detected, suggesting potential antimicrobial resistance mechanisms. These mechanisms are known to specifically target human antimicrobial peptides (including cathelicidin LL-37), which are frequently encountered within psoriasis lesions. These shifts in microbial community dynamics may contribute to psoriasis disease pathogenesis.

HDAC inhibitors and IBD: Charting new approaches in disease management

Inflammatory bowel disease (IBD) represents a group of chronic inflammatory disorders of the gastrointestinal tract. Despite substantial advances in our understanding of IBD pathogenesis, the currently available therapeutic options remain limited in their efficacy and often come with significant side effects. Therefore, there is an urgent need to explore novel approaches for the management of IBD. One promising avenue of investigation revolves around the use of histone deacetylase (HDAC) inhibitors, which have garnered considerable attention for their potential in modulating gene expression and curbing inflammatory responses. This review emphasizes the pressing need for innovative drugs in the treatment of IBD, and drawing from a wealth of preclinical studies and clinical trials, we underscore the multifaceted roles and the therapeutic effects of HDAC inhibitors in IBD models and patients. This review aims to contribute significantly to the understanding of HDAC inhibitors' importance and prospects in the management of IBD, ultimately paving the way for improved therapeutic strategies in this challenging clinical landscape.

Probiotic Bacillus cereus regulates metabolic disorders and activates the cholic acid-FXR axis to alleviate DSS-induced colitis

Inflammatory bowel disease is characterized by severe imbalance of intestinal flora and metabolic disorders. Recent studies have demonstrated that probiotics can effectively alleviate inflammatory bowel disease by restoring the intestinal flora structure and modulating the immune response. However, the role of probiotics in regulating intestinal metabolism disorders is still unclear. This study explores the role of probiotic B. cereus in alleviating DSS-induced colitis. The findings indicated probiotic B. cereus treatment mitigated tissue damage and apoptosis during inflammation. Metabolome and transcriptome analysis revealed B. cereus activated the cholic acid-FXR axis by increasing cholic acid levels, which promoted the gene expression level of NF-κB inhibitor α, reduced the IL-1β, IL-6, IL-18 and TNF-α concentrations. Furthermore, it effectively mitigated the DSS-induced disruption of bile acid metabolism, arginine metabolism, and linoleic acid metabolism. This study explores the effect and mechanisms of probiotic B. cereus on alleviating DSS-induced colitis. It aims to provide a theoretical basis for microbial therapy in inflammatory bowel disease. SIGNIFICANCE: This study used metabolome and transcriptome to reveal the roles and mechanisms, which probiotic Bacillus cereus modulates metabolic disorders and alleviate DSS-induced colitis. We identified the cholic acid-FXR axis as an important target for alleviating DSS-induced colitis. These findings provide new insights into microbial treatment strategies for IBD.

A meta-analysis of the gut microbiome in inflammatory bowel disease patients identifies disease-associated small molecules

Gut microbiome changes have been associated with several human diseases, but the molecular and functional details underlying these associations remain largely unknown. Here, we performed a meta-analysis of small molecule biosynthetic gene clusters (BGCs) in metagenomic samples of the gut microbiome from inflammatory bowel disease (IBD) patients and matched healthy subjects and identified two Clostridia-derived BGCs that are significantly associated with Crohn's disease (CD), a main IBD type. Using synthetic biology, we discovered and solved the structures of six fatty acid amides as the products of the CD-enriched BGCs, which we subsequently detected in fecal samples from IBD patients. Finally, we show that the discovered molecules disrupt gut permeability and exacerbate disease in chemically or genetically susceptible mouse models of colitis. These findings suggest that microbiome-derived small molecules may play a role in the etiology of IBD and represent a generalizable approach for discovering molecular mediators of disease-relevant microbiome-host interactions.

Microbial dynamics of acute pancreatitis: integrating culture, sequencing, and bile impact on bacterial populations and gaseous metabolites

Background

Our study examined the composition of the intestinal microflora in a hospitalized patient with AP symptoms treated several months earlier for diverticulitis. The therapeutic intervention necessitated Hartmann's procedure, culminating in colostomy creation.

Aims

Employing a thorough microbiological analysis we attempted to demonstrate whether the microflora isolated from the peripancreatic fluid exhibited a stronger correlation with the contents of the stoma or with the rectal swab. Additionally, we sought to determine the association between later onset of AP and diverticulitis.

Methods

Following clinical materials from the patient in the initial phase of AP were collected: rectal swab, colostomy bag contents (in the publication referred to as stoma content/stool) and peripancreatic fluid. Microbiological analysis was performed, including classic culture methodology, NGS techniques, and genotyping methodologies. Furthermore, the effect of bile on the shift in the population of selected bacterial species was examined.

Results

The NGS technique confirmed greater consistency in bacteria percentage (phyla/family) between stoma content and peripancreatic fluid. In both samples, a clear dominance of the Proteobacteria phyla (over 75%) and the Enterobacteriaceae family was demonstrated. Moreover, NGS verified the presence of the Fusobacteriota phylum and Fusobacteriaceae family only in rectal swabs, which may indicate a link between this type of bacteria and the etiology of diverticulitis. We observed that Escherichia coli 33 isolated from stool exhibited active gaseous metabolite production (mainly hydrogen).

Conclusions

The abundant production of hydrogen may substantially impact enzymatic processes, inducing specific alterations in disulfide bonds and trypsin inactivation. Our investigation alludes to the conceivable active involvement of bile in effecting qualitative and quantitative modifications in the peripancreatic microbiota composition, establishing a correlation between released bile and bacterial generation of gaseous metabolites.

Gut microbiota dysfunction in Crohn's disease

Introduction

Crohn's disease (CD) results from alterations in the gut microbiota and the immune system. However, the exact metabolic dysfunctions of the gut microbiota during CD are still unclear. Here, we investigated metagenomic functions using PICRUSt2 during the course of CD to better understand microbiota-related disease mechanisms and provide new insights for novel therapeutic strategies.

Methods

We performed 16S rRNA-based microbial profiling of 567 faecal samples collected from a cohort of 383 CD patients, including 291 remissions (CR), 177 mild-moderate (CM) and 99 severe (CS) disease states. Gene and pathway composition was assessed using PICRUSt2 analyses of 16S data.

Results

As expected, changes in alpha and beta diversity, in interaction networks and increases in Proteobacteria abundance were associated with disease severity. However, microbial function was more consistently disrupted than composition from CR, to CM and then to CS. Major shifts in oxidative stress pathways and reduced carbohydrate and amino acid metabolism in favour of nutrient transport were identified in CS compared to CR. Virulence factors involved in host invasion, host evasion and inflammation were also increased in CS.

Conclusions

This functional metagenomic information provides new insights into community-wide microbial processes and pathways associated with CD pathogenesis. This study paves the way for new advanced strategies to rebalance gut microbiota and/or eliminate oxidative stress, and biofilm to downregulate gut inflammation.

A decade of advances in human gut microbiome-derived biotherapeutics

Microbiome science has evolved rapidly in the past decade, with high-profile publications suggesting that the gut microbiome is a causal determinant of human health. This has led to the emergence of microbiome-focused biotechnology companies and pharmaceutical company investment in the research and development of gut-derived therapeutics. Despite the early promise of this field, the first generation of microbiome-derived therapeutics (faecal microbiota products) have only recently been approved for clinical use. Next-generation therapies based on readily culturable and as-yet-unculturable colonic bacterial species (with the latter estimated to comprise 63% of all detected species) have not yet progressed to pivotal phase 3 trials. This reflects the many challenges involved in developing a new class of drugs in an evolving field. Here we discuss the evolution of the live biotherapeutics field over the past decade, from the development of first-generation products to the emergence of rationally designed second- and third-generation live biotherapeutics. Finally, we present our outlook for the future of this field.

Experimental Murine Periodontitis Increases Salivary Gland IgA-Producing B Cells Following Oral Dysbiosis

The oral microbiome is closely involved in the maintenance of host health and the development of systemic diseases. The salivary glands play an essential role in homeostasis in the oral cavity. Here, we investigated the effects of periodontal inflammation on salivary gland function and the oral microbiome. In experimental periodontitis model mice, an increase in IgA⁺ cells in the salivary glands were observed 1 week after treatment. Alteration of the oral microbiome was also induced in this model. Gene expression analysis of the salivary glands showed changes in the expression of genes related to B-cell maturation and plasma cell differentiation and an increase in the expression of genes related to macrophage activation upon experimental periodontitis induction. Furthermore, the relationship between disruption of oral microflora and salivary gland function was examined using a cohousing model in which experimental periodontitis model mice and untreated mice were reared in the same cage. We found that cohoused normal mice underwent alteration of the oral microbiome, with increases in IgA⁺ cells and macrophages in the salivary glands. In summary, our results suggest that, in the oral cavity, there is a close link between oral bacterial flora and immune cells in the salivary glands. Our results also show that localized inflammation disrupts the homeostasis in the oral cavity, inducing pathological conditions such as dysbiosis. Our study suggests the importance of the interaction among local oral inflammation, salivary gland function, and oral microflora, and provides new insights into the mechanisms by which oral health is maintained.

Aerobic exercise regulates gut microbiota profiles and metabolite in the early stage of Alzheimer's disease

Aerobic exercise (AE) has been shown to offer significant benefits for Alzheimer's disease (AD), potentially influencing the gut microbiota. However, the impact of changes in intestinal flora in early Alzheimer's disease induced by aerobic exercise on metabolic pathways and metabolites is not well understood. In this study, 3-month-old APP/PS1 and C57BL/6 mice were divided into two groups each: a control group (ADC for APP/PS1 and WTC for C57BL/6) and an aerobic exercise group (ADE for APP/PS1 and WTE for C57BL/6). The exercise groups underwent a 20-week aerobic training program on a motorized treadmill before the behavioral test (both the Morris water maze experiment (MWM) and the eight-arm maze test). Fecal samples were collected to analyze gut microbiota profiles via 16S rRNA gene sequencing. At the same time, the metabolic pathway analysis and the detection of metabolites were carried out. At the phylum level, the ADE group exhibited a significant reduced in the relative abundance of Bacteroidetes compared to the ADC group. At the genus level, both Ileibacterium and Faecalibaculum were found to be more abundant in the ADE group than in the ADC group. Additionally, PICRUSt analysis revealed that lipid metabolism and bile acid metabolism pathways were significantly enriched in the cecal microbiota of mice in the ADE group. The metabolites detected further confirmed the changes in the metabolic pathways mentioned above. Aerobic exercise may modify gut microbiota profiles and metabolites in APP/PS1 mice, thereby potentially playing a beneficial role in delaying cognitive impairment associated with early-stage Alzheimer's disease.

Progress in the investigation of the Firmicutes/Bacteroidetes ratio as a potential pathogenic factor in ulcerative colitis

Ulcerative colitis (UC) is a chronic inflammatory bowel disease (IBD) that presents significant challenges in terms of treatment owing to a pronounced likelihood of recurrence and an elevated risk of cancer development, thereby imposing substantial risks on affected individuals. The gut microbiota of Firmicutes and Bacteroidetes (F/B) can affect diseases associated with IBD, which is also a risk factor for breast cancer. This review discusses the hazards associated with UC, highlights the existing disparities in UC-associated gut microbiome research, explores the concept of the F/B ratio and scrutinizes its correlation with UC. Moreover, the differences in the F/B ratios between healthy individuals and those with UC were thoroughly examined. These findings suggest that an elevated F/B ratio may promote the occurrence and progression of UC. Consequently, the F/B ratio may play a significant role in UC by influencing gut microbiota composition and inflammatory responses, suggesting that future research should focus on this ratio as a potential biomarker for disease progression and therapeutic targets in managing UC.

The Multiple Roles of Heat Shock Proteins in the Development of Inflammatory Bowel Disease

Inflammatory bowel disease (IBD), a chronic inflammatory condition of the human intestine, comprises Crohn's disease (CD) and ulcerative colitis (UC). IBD causes severe gastrointestinal symptoms and increases the risk of developing colorectal carcinoma. Although the etiology of IBD remains ambiguous, complex interactions between genetic predisposition, microbiota, epithelial barrier, and immune factors have been implicated. The disruption of intestinal homeostasis is a cardinal characteristic of IBD. Patients with IBD exhibit intestinal microbiota dysbiosis, impaired epithelial tight junctions, and immune dysregulation; however, the relationship between them is not completely understood. As the largest body surface is exposed to the external environment, the gastrointestinal tract epithelium is continuously subjected to environmental and endogenous stressors that can disrupt cellular homeostasis and survival. Heat shock proteins (HSPs) are endogenous factors that play crucial roles in various physiological processes, such as maintaining intestinal homeostasis and influencing IBD progression. Specifically, HSPs share an intricate association with microbes, intestinal epithelium, and the immune system. In this review, we aim to elucidate the impact of HSPs on IBD development by examining their involvement in the interactions between the intestinal microbiota, epithelial barrier, and immune system. The recent clinical and animal models and cellular research delineating the relationship between HSPs and IBD are summarized. Additionally, new perspectives on IBD treatment approaches have been proposed.

Houttuynia cordata-Derived Exosome-Like Nanoparticles Mitigate Colitis in Mice via Inhibition of the NLRP3 Signaling Pathway and Modulation of the Gut Microbiota

BACKGROUND

Plant-derived exosome-like nanoparticles (PELNs) have received widespread attention in treating ulcerative colitis (UC). However, the role of Houttuynia cordata-derived exosome-like nanoparticles (HELNs) in UC remains unclear. This study aims to evaluate the efficacy of HELNs in treating colitis in mice and investigate its potential mechanisms.

METHODS

HELNs were isolated from H. cordata for characterization, and their safety and stability were evaluated. A dextran sulfate sodium (DSS)-induced colitis mouse model was utilized to assess the therapeutic potential of HELNs in UC. In vivo, imaging and flow cytometry were utilized to investigate the targeting effect of HELNs on inflamed colonic sites and their modulation of the immune environment. RNA-seq analysis and molecular docking were performed to identify potential pathways recruited by HELNs. Guided by transcriptomic findings, NLRP3-/- mice were used in conjunction with Western blotting, qPCR, immunofluorescence, and other techniques to verify that HELNs alleviated DSS-induced colitis by inhibiting NLRP3/NOD-like receptor signaling pathways. Lastly, the impact of HELNs on the gut microbiota was investigated through 16S rRNA sequencing.

RESULTS

HELNs significantly reduced the severity of DSS-induced colitis in mice, alleviating colitis symptoms and histopathological damage. Furthermore, HELNs can specifically target inflamed colon tissue, regulate the immune environment, and decrease inflammation. RNA-seq analysis, coupled with the use of NLRP3-/- mice, demonstrated that HELNs inhibited the NLRP3/NOD-like receptor signaling pathways. Lastly, HELNs balanced the gut microbiota composition in mice with colitis, decreasing the abundance of harmful bacteria and increasing the abundance of beneficial bacteria in the intestinal tract of these mice.

CONCLUSION

In summary, HELNs exhibit the potential to protect the colon from DSS-induced damage by inhibiting the NLRP3/NOD-like receptor signaling pathway and modulating the gut microbiota, presenting a promising therapeutic option for the management of UC.

Investigating the Immunomodulatory Impact of Fecal Bacterial Membrane Vesicles and Their IgA Coating Patterns in Crohn's Disease Patients

The human intestinal tract contains trillions of bacteria that coexist in a symbiotic relationship with human cells. Imbalances in this interaction can lead to disorders such as Crohn's disease (CD). Bacteria membrane vesicles (MVs), which are released by almost all bacteria, have been demonstrated to play a crucial role in bacteria-host interactions. In this study, we assessed the physical characterizations, immunomodulatory effects, and IgA interactions of MVs derived from fecal samples of CD patients and healthy controls (HCs). MVs were isolated from the frozen fecal samples using a combination of ultrafiltration and size-exclusion chromatography. Using nanoparticle tracking analysis, we found that the MVs of the CD patients showed a significantly lower concentration compared to those of the HCs. Cryo-transmission electron microscopy revealed the larger size of the MVs in active CD (Ac-CD) compared to the MVs of remission CD (Re-CD) and HCs. Differentiated monocyte THP-1 cells released more TNF-a when exposed to MVs from the HCs compared to the CD patients. On the other hand, the MVs from the HCs and Re-CD patients but not the Ac-CD patients induced more anti-inflammatory IL-10. Intriguingly, bead-based flow cytometry analysis showed that the MVs of the HCs and Re-CD patients were more coated with IgA compared to those of the Ac-CD patients. These results suggest the potential role of MVs in the immunomodulatory impact on the pathophysiology of CD. Moreover, IgA seems to regulate these effects by direct binding, which was not the case for the Ac-CD patients. Finally, the IgA coating patterns of the MVs could be used as an additional disease biomarker, as they can clearly identify the exacerbation status of CD.

Exploring the relationship between Faecalibacterium duncaniae and Escherichia coli in inflammatory bowel disease (IBD): Insights and implications

Inflammatory bowel disease (IBD) is a group of disorders characterized by an inflammation of the gastrointestinal tract (GIT) and represents a major social and economic burden. Despite ongoing research into the etiology and pathophysiology of this multifactorial disease, treatment options remain limited. From this perspective, the gut microbiota has emerged as a potential player in the pathogenesis of IBD, and animal and human studies support this hypothesis. Indeed, the human gut is one of the most complex ecological communities (composed of 1013-1014 microorganisms) that plays a critical role in human health by influencing normal physiology and disease susceptibility through its collective metabolic activities and host interactions. In addition, live probiotic bacteria present in some food products (which transit through the GIT) have been shown to interact with the host immune system and confer several health benefits. The aim of this review is to provide an overview of the link between Faecalibacterium duncaniae and Escherichia coli and IBD, highlighting the main areas of research in this field. An ecological perspective on the gut microbiota may offer new insights for the development of clinical therapies targeting this bacterial community to improve human health.

Recognizing the biological barriers and pathophysiological characteristics of the gastrointestinal tract for the design and application of nanotherapeutics

The gastrointestinal tract (GIT) is an important and complex system by which humans to digest food and absorb nutrients. The GIT is vulnerable to diseases, which may led to discomfort or even death in humans. Therapeutics for GIT disease treatment face multiple biological barriers, which significantly decrease the efficacy of therapeutics. Recognizing the biological barriers and pathophysiological characteristics of GIT may be helpful to design innovative therapeutics. Nanotherapeutics, which have special targeting and controlled therapeutic release profiles, have been widely used for the treatment of GIT diseases. Herein, we provide a comprehensive review of the biological barrier and pathophysiological characteristics of GIT, which may aid in the design of promising nanotherapeutics for GIT disease treatment. Furthermore, several typical diseases of the upper and lower digestive tracts, such as Helicobacter pylori infection and inflammatory bowel disease, were selected to investigate the application of nanotherapeutics for GIT disease treatment.

Moderate-intensity continuous training and high-intensity interval training alleviate glycolipid metabolism through modulation of gut microbiota and their metabolite SCFAs in diabetic rats

Glucose and lipid metabolism disorders are typical of diabetic patients and are important factors leading to macrovascular and microvascular complications. The aim of this study was to understand the effects of different exercises on glycolipid metabolism in diabetic rats and the role of gut flora in metabolic maintenance. We measured glycolipid metabolic indices and short-chain fatty acids (SCFAs) content and sequenced and analyzed gut microbes after 8 weeks of moderate-intensity continuous training (MICT) and high-intensity interval training (HIIT) programs in type 2 diabetic rats(T2DM). We found that Enterococcaceae, Enterococcus, Subdoligranulum, Kurthia, Bacillales, and Planococcaceae may be key bacterial taxa related to T2DM and that both programs of exercise regulated the intestinal flora of rats with T2DM, improved their glycolipid metabolism, increased the abundance of SCFA-producing intestinal bacteria, and it was found that the PWY-5676 and P163-PWY pathways which are closely related to production of SCFAs were significantly upregulated in the exercise groups. Notably, MICT appeared to be more effective than HIIT in increasing the homogeneity of rat intestinal flora, enriching species, and increasing acetic acid and butyric acid content. These results suggest that exercise improves glycolipid metabolism in diabetic rats, which may be attributed to alterations in the structure of their intestinal flora.

Extreme drought shapes the gut microbiota composition and function of common cranes (Grus grus) wintering in Poyang Lake

Introduction

Extreme weather events driven by climate change profoundly affect migratory birds by altering their habitats, food sources, and migration routes. While gut microbiota is believed to play a role in helping birds adapt to environmental changes, research on how extreme weather impacts their gut microbiota and how these microbial communities respond to such conditions has been limited.

Methods

16S rRNA gene sequencing was utilized to investigate the gut microbiota of common cranes (Grus grus) wintering at Poyang Lake from 2020 to 2023, with a particular focus on their response to extreme drought conditions on both inter-annual and monthly timescales.

Results

The results revealed that extreme drought conditions substantially impact gut microbiota, with inter-annual water-level fluctuations exerting a more pronounced impact on microbial community structure than that of inter-monthly fluctuations. Notably, a significant decline in bacterial diversity within the gut microbiota of common cranes was observed in the extreme drought year of 2022 compared with other years. Monthly observations indicated a gradual increase in gut microbial diversity, coinciding with relatively minor water-level changes. Key taxa that responded to drought included the Enterobacteriaceae family and Bifidobacterium and Lactobacillus species. Additionally, functional genes related to carbohydrate metabolism, the phosphotransferase system, and the two-component systems were significantly enriched during the extreme drought year. These functions may represent adaptive mechanisms by which the gut microbiota of common cranes respond to drought stress.

Discussion

This research provides novel insights into the temporal variability of gut microbiota in wintering waterbirds, underscoring the significant impact of climatic fluctuations on microbial communities. The findings highlight the importance of understanding the ecological and functional responses of gut microbiota to extreme weather events, which is crucial for the conservation and management of migratory bird populations in the face of climate change.

Unraveling the Role of the Human Gut Microbiome in Health and Diseases

The human gut is a complex ecosystem that supports billions of living species, including bacteria, viruses, archaea, phages, fungi, and unicellular eukaryotes. Bacteria give genes and enzymes for microbial and host-produced compounds, establishing a symbiotic link between the external environment and the host at both the gut and systemic levels. The gut microbiome, which is primarily made up of commensal bacteria, is critical for maintaining the healthy host's immune system, aiding digestion, synthesizing essential nutrients, and protecting against pathogenic bacteria, as well as influencing endocrine, neural, humoral, and immunological functions and metabolic pathways. Qualitative, quantitative, and/or topographic shifts can alter the gut microbiome, resulting in dysbiosis and microbial dysfunction, which can contribute to a variety of noncommunicable illnesses, including hypertension, cardiovascular disease, obesity, diabetes, inflammatory bowel disease, cancer, and irritable bowel syndrome. While most evidence to date is observational and does not establish direct causation, ongoing clinical trials and advanced genomic techniques are steadily enhancing our understanding of these intricate interactions. This review will explore key aspects of the relationship between gut microbiota, eubiosis, and dysbiosis in human health and disease, highlighting emerging strategies for microbiome engineering as potential therapeutic approaches for various conditions.

Microscopic messengers: microbiota-derived bacterial extracellular vesicles in inflammatory bowel disease

Inflammatory bowel disease (IBD) is a persistent and complex condition accomplished by inflammation of the gastrointestinal system, encompassing Crohn's disease (CD) and ulcerative colitis (UC). This condition is caused by the combination of genetic predispositions, environmental triggers, and dysregulated immunological responses, which complicates diagnosis and treatment. The latest developments in gastroenterology have revealed the critical significance of the gut microbiota in the pathogenesis of IBD. Extracellular vesicles (EVs) are a type of microbial component that potentially regulate intestinal inflammation. The impact of microbiota-derived bacterial EVs (bEVs) on intestinal inflammation is mediated through several methods. They can intensify inflammation or stimulate defensive responses by delivering immunomodulatory cargo. Improved comprehension could enhance inventive diagnostic and treatment strategies for IBD. This study aimed to explore the relationship between microbiota-derived bEVs and the complex nature of IBD. We performed a thorough analysis of the formation, composition, mechanisms of action, diagnostic possibilities, therapeutic implications, and future prospects of these microbiota-derived bEVs.

Unraveling the Gut Microbiota: Implications for Precision Nutrition and Personalized Medicine

Recent studies have shown a growing interest in the complex relationship between the human gut microbiota, metabolism, and overall health. This review aims to explore the gut microbiota-host association, focusing on its implications for precision nutrition and personalized medicine. The objective is to highlight how gut microbiota modulate metabolic and immune functions, contributing to disease susceptibility and wellbeing. The review synthesizes recent research findings, analyzing key studies on the influence of gut microbiota on lipid and carbohydrate metabolism, intestinal health, neurobehavioral regulation, and endocrine signaling. Data were drawn from both experimental and clinical trials examining microbiota-host interactions relevant to precision nutrition. Our findings highlight the essential role of gut microbiota-derived metabolites in regulating host metabolism, including lipid and glucose pathways. These metabolites have been found to influence immune responses and gut barrier integrity. Additionally, the microbiota impacts broader physiological processes, including neuroendocrine regulation, which could be crucial for dietary interventions. Therefore, understanding the molecular mechanisms of dietary-microbiota-host interactions is pivotal for advancing personalized nutrition strategies. Tailored dietary recommendations based on individual gut microbiota compositions hold promise for improving health outcomes, potentially revolutionizing future healthcare approaches across diverse populations.

Curcumin-loaded polysaccharide microparticles alleviated DSS-induced ulcerative colitis by improving intestinal microecology and regulating MAPK/NF-κB/Nrf2/NLRP3 pathways

Curcumin (Cur) exerts many benefits on the host, but its application is limited by its poor bioavailability. In this study, composite polysaccharide microparticles loading Cur (Cur-CPM) was prepared by food-grade materials and gel technology. Its properties were analyzed via the in vitro and in vivo models, and then its benefit on gut health was assessed in DSS-treated mice. Compared to free Cur, CPM extended the residence time and absorption efficiency of Cur in the intestine, effectively ameliorating the symptoms of colitis. Cur-CPM alleviated colonic inflammation by inhibiting the activation of the MAPK and NF-κB pathways and suppressing NLRP3 inflammasome activity, affecting the expression of inflammation-related cytokines and mediators. In addition, Cur-CPM regulated the levels of antioxidants and oxidants in the colon tissues via Nrf2 activation, alleviating oxidative stress. Cur-CPM protected gut barrier function by maintaining the integrity of colonic mucosal layer and tight junction. The underlying mechanism can be attributed not only to the anti-inflammatory and antioxidant activities of Cur but also to modulation of Cur and CPM on the gut microbiota and metabolites. It suggests that Cur-CPM holds the potential to be developed as a functional component to enhance gut health.

Modulating the gut microbiota in Crohn's disease: a pilot study on the impact of a plant-based diet with DNA-based monitoring

Introduction

Crohn's Disease (CD) is characterized by chronic intestinal inflammation and dysbiosis. This study aimed to investigate the effects of a plant-based diet (PBD) on gut microbiota composition and inflammation in CD patients and assess the utility of trnL gene sequencing for monitoring dietary adherence.

Methods

Fourteen CD patients participated in a 12-week PBD intervention. Dietary adherence was monitored through self-reported food diaries and trnL sequencing, which detects plant residues in fecal samples. Gut microbiota was analyzed using 16S rRNA sequencing, and fecal calprotectin levels were measured as an indicator of intestinal inflammation.

Results

TrnL sequencing identified 55 plant genera in fecal samples, compared to 41 reported in food diaries, highlighting its accuracy in assessing plant residue diversity. By week 4, participants demonstrated a 1.4-fold increase in plant intake, correlating with a significant increase in microbial diversity. Key genera associated with gut health, such as Faecalibacterium and Bacteroides, increased in abundance. Additionally, fecal calprotectin levels decreased from 472 mg/kg at baseline to 207 mg/kg at week 12, indicating reduced intestinal inflammation.

Discussion

A PBD positively influenced gut microbiota composition and decreased intestinal inflammation in CD patients. The study also demonstrated that trnL sequencing is an effective tool for assessing dietary adherence in clinical settings, offering a more objective measure than self-reported food diaries.

Identification of gut microbiome features associated with host metabolic health in a large population-based cohort

The complex relationship between the gut microbiome and host metabolic health has been an emerging research area. Several recent studies have highlighted the potential effects of the microbiome's diversity, composition and metabolic production capabilities on Body Mass Index (BMI), liver health, glucose homeostasis and Type-2 Diabetes (T2D). The majority of these studies were constrained by relatively small cohorts, mostly focusing on individuals with metabolic disorders, limiting a comprehensive understanding of the microbiome's role in metabolic health. Leveraging a large-scale, comprehensive cohort of nearly 9000 individuals, measured using Continuous Glucose Monitoring (CGM), Dual-energy X-ray absorptiometry (DXA) scan and liver Ultrasound (US) we examined the functional profile of the gut microbiome, and its relation to 38 metabolic health measures. We identified 145 unique bacterial pathways significantly correlated with metabolic health measures, with 86.9% of these showing significant associations with more than one metabolic health measure. Furthermore, 87,678 unique bacterial gene families were found to be significantly associated with at least one metabolic health measure. Notably, "key" bacterial pathways such as purine ribonucleosides degradation and anaerobic energy metabolism demonstrated multiple robust associations across various metabolic health measures, highlighting their potential roles in regulating metabolic processes. Our results remained largely unchanged after adjustments for nutritional habits and for BMI they were replicated in a geographically independent cohort. These insights pave the way for future research and potentially the development of microbiome-targeted interventions to enhance metabolic health.

Recombinant Lactiplantibacilllus plantarum modulate gut microbial diversity and function

BACKGROUND

Gut microbes are important regulators of host health and can also function as disease indicators. Lactiplantibacilllus plantarum(L. plantarum)used as express and delivery vaccines for mucosal immunity have been shown to activate specific immune responses in numerous studies.

RESULTS

The interaction between recombinant L. plantarum and the gut microbiota was investigated in this study. The results indicated a change in the amount of gut OTU by recombinant L. plantarum. Recombinant L. plantarum dramatically boosted the species diversity of gut bacteria based on the Shannon-Wiener index. Beta diversity analysis showed that microbial structure was changed by recombinant L. plantarum. Furthermore, recombinant NC8 L. plantarum expressing a fusion between the P14.5 protein of the African swine fever virus and IL-33 enhanced the functions of gut bacteria in metabolism and immune regulation. Increased levels of IgG and IgG1 in serum and sIgA in feces, as well as enrichment of CD4+ T cells and IgA+ B cells, indicated that the gut microbiota exerted an immunomodulatory role when mediated by recombinant L. plantarum.

CONCLUSIONS

These results revealed that recombinant L. plantarum exerted its potential role in the gut microbiota and gut immunity.These fndings contribute to a broader understanding and utilization of L. plantarum bacteria in various therapeutic applications.

Gut microbiota in gastrointestinal diseases: Insights and therapeutic strategies

Considering the bidirectional crosstalk along the gut-liver axis, gut-derived microorganisms and metabolites can be released into the liver, potentially leading to liver injury. In this editorial, we comment on several studies published in the recent issue of the World Journal of Gastroenterology. We focus specifically on the roles of gut microbiota in selected gastrointestinal (GI) diseases that are prevalent, such as inflammatory bowel disease, metabolic dysfunction-associated steatotic liver disease, and hepatitis B virus-related portal hypertension. Over the past few decades, findings from both preclinical and clinical studies have indicated an association between compositional and metabolic changes in the gut microbiota and the pathogenesis of the aforementioned GI disorders. However, studies elucidating the mechanisms underlying the host-microbiota interactions remain limited. The purpose of this editorial is to summarize current findings and provide insights regarding the context-specific roles of gut microbiota. Ultimately, the discovery of microbiome-based biomarkers may facilitate disease diagnosis and the development of personalized medicine.

Fecal glycoprotein 2 is a marker of gut microbiota dysbiosis and systemic inflammation

BACKGROUND

Antimicrobial autoantigenic glycoprotein 2 (GP2) is an important component of the innate immune system which originates from the exocrine pancreas as well as from the small intestines. The relationship of GP2 with the intestinal microbiome as well as the systemic implications of increased fecal GP2 levels are, however, still unclear. Therefore, fecal samples from 2,812 individuals of the Study of Health in Pomerania (SHIP) were collected to determine GP2 levels (enzyme-linked immunosorbent assay) and gut microbiota profiles (16 S rRNA gene sequencing). These data were correlated and associated with highly standardised and comprehensive phenotypic data of the study participants.

RESULTS

Fecal GP2 levels were increased in individuals with higher body mass index and smokers, whereas lower levels were found in case of preserved exocrine pancreatic function, female sex or a healthier diet. Moreover, higher GP2 levels were associated with increased serum levels of high-sensitivity C-reactive protein, loss of gut microbial diversity and an increase of potentially detrimental bacteria (Streptococcus, Haemophilus, Clostridium XIVa, or Collinsella). At the same time, predicted microbial pathways for the biosynthesis of beneficial short-chain fatty acids or lactic acid were depleted in individuals with high fecal GP2. Of note, GP2 exhibited a stronger association to overall microbiome variation than calprotectin.

CONCLUSION

Fecal GP2 is a biomarker of gut microbiota dysbiosis and associated with increased systemic inflammation. The intestines may be more important as origin for GP2 than pancreatic acinar cells. Future studies need to investigate the potential clinical value in disease specific patient cohorts.