Short chain fatty acids and its producing organisms: An overlooked therapy for IBD?

Immunopathological and microbial signatures of inflammatory bowel disease in partial RAG deficiency

Partial RAG deficiency (pRD) can manifest with systemic and tissue-specific immune dysregulation, with inflammatory bowel disease (IBD) in 15% of the patients. We aimed at identifying the immunopathological and microbial signatures associated with IBD in patients with pRD and in a mouse model of pRD (Rag1w/w) with spontaneous development of colitis. pRD patients with IBD and Rag1w/w mice showed a systemic and colonic Th1/Th17 inflammatory signature. Restriction of fecal microbial diversity, abundance of pathogenic bacteria, and depletion of microbial species producing short-chain fatty acid were observed, which were associated with impaired induction of lamina propria peripheral Treg cells in Rag1w/w mice. The use of vedolizumab in Rag1w/w mice and of ustekinumab in a pRD patient were ineffective. Antibiotics ameliorated gut inflammation in Rag1w/w mice, but only bone marrow transplantation (BMT) rescued the immunopathological and microbial signatures. Our findings shed new light in the pathophysiology of gut inflammation in pRD and establish a curative role for BMT to resolve the disease phenotype.

Personalized Dietary Approaches to Optimizing Intestinal Microbial Health and Homeostasis

Diet has a profound impact in human health, which is partly driven by changes in the intestinal microbiota. Several associations between dietary intake and the intestinal microbiota composition and function have been described. Namely, the Mediterranean diet is associated with beneficial bacteria, while the intake of ultraprocessed foods is linked to dysbiosis. It is, therefore, very tempting to tailor dietary approaches to the individual needs of the microbiota; however, high-quality prospective data are lacking. Provisionally, a diet rich in fruits and vegetables and low in ultraprocessed foods is recommended to improve the intestinal microbiota composition and function.

Prebiotic potential of oligosaccharides extracted from improved Ugandan varieties of millet, sesame, soybean, and sorghum: enhancing probiotic growth and enteric pathogen inhibition

Functional gastrointestinal disorders like diarrhea continue to affect children under five years in low-income countries. Incorporating health-enhancing bioactive compounds such as prebiotics in diet offers a promising solution. This study investigated prebiotic potential of oligosaccharides extracted from improved varieties of millet (Seremi 2, Naromil 2), sesame (Sesim 2, Sesim 3), soybean (Maksoy 3N, Maksoy 6N), and sorghum (Narosorg 2, Narosorg 4), commonly consumed in Uganda. These were compared to their respective indigenous variety. This study employed standardized methods for optical density measurement, culture preparation, and oligosaccharide extraction to evaluate prebiotic properties. We investigated whether plant-based oligosaccharides could enhance the effectiveness of probiotics, specifically Lactiplantibacillus plantarum (ATCC 14917) and Lacticaseibacillus rhamnosus (ATCC 7469), in antagonizing common enteric pathogens (Salmonella enterica subsp. enterica (ATCC 13076) and Shigella flexneri (ATCC 12022)). Approximately 4-8 log CFU/ml of each probiotic was incubated in 2% w/v oligosaccharide extracts at 37 °C to evaluate the influence of the extracts on their growth, short-chain fatty acid (SCFA) production and antagonistic activity. Maximum cell density, which exceeded the minimum recommended probiotic cell density (6 log CFU/ml), was achieved during 24-h incubation period. The probiotics exhibited optimal growth in extracts of Sesim 2, Maksoy 3N, Narosorg 2 and indigenous millet variety resulting in a 68-84% increase in cell densities. The concentration of SCFA concentration was significantly higher (p < 0.05) in soybean-based oligosaccharides. Both probiotics antagonized growth of Salmonella and Shigella by more than 40% when cultured on Sesim 2, Maksoy 3N, Narosorg 2 and indigenous millet variety, while maintaining the probiotic cell densities above the minimum recommended level. These varieties show great potential as functional ingredients for developing synbiotic-rich foods to promote gut and public health. However, to evaluate the oligosaccharides prebiotic efficacy, in vitro fermentation using fecal microbiota and in vivo studies are necessary to determine gut microbiota changes and interactions.

Exploring the dual role of Mangifera indica L. in regulating immune response and pain persistence in inflammatory bowel disease

Inflammatory bowel disease (IBD), encompassing ulcerative colitis and Crohn's disease, is characterized by chronic intestinal inflammation and immune dysregulation, driven mainly by Th1 and Th17 cells and sustained by pro-inflammatory cyto-chemokines. This inflammatory milieu is associated with visceral pain, a key symptom affecting patient quality of life. Addressing both gut inflammation/immunity and visceral pain is crucial for improving IBD therapy. This study assessed the therapeutic potential of Mangifera indica L. extract (MIE), a mangiferin-rich formulation, in a DNBS-induced colitis model in rats. MIE treatment administered either simultaneously or post-DNBS induction, significantly reduced pathogenic Th1 and Th17 cell infiltration, along with pro-inflammatory cytokines (IL-1β, TNF-α) and chemokines (CXCL1, CXCL2), though histopathology showed no significant improvements in tissue healing. Additionally, MIE restored microbiota-derived short-chain fatty acids (acetate and butyrate) in colon and faecal samples. Importantly, MIE alleviated post-inflammatory visceral hypersensitivity, reducing the abdominal withdrawal reflex (AWR) to colorectal distension (CRD), after either acute or repeated treatment. These findings suggest that MIE, in the context of nutraceuticals and functional foods, shows promise as a dual-action therapeutic strategy for complementary and/or adjuvant therapy in IBD.

Complex system modeling reveals oxalate homeostasis is driven by diverse oxalate-degrading bacteria

Decades of research have made clear that host-associated microbiomes touch all facets of health. However, effective therapies that target the microbiome have been elusive given its inherent complexity. Here, we experimentally examined diet-microbe-host interactions through a complex systems framework, centered on dietary oxalate. Using multiple, independent molecular, rodent, and in vitro experimental models, we found that microbiome composition influenced multiple oxalate-microbe-host interfaces. Importantly, the administration of the oxalate-degrading specialist, Oxalobacter formigenes, was only effective against a poor oxalate-degrading microbiota background and gives critical new insights into why clinical intervention trials with this species exhibit variable outcomes. Data suggest that, while heterogeneity in the microbiome impacts multiple diet-host-microbe interfaces, metabolic redundancy among diverse microorganisms in specific diet-microbe axes is a critical variable that may impact the efficacy of bacteriotherapies, which can help guide patient and probiotic selection criteria in probiotic clinical trials.

Bariatric surgery promotes recruitment of brown fat linked to alterations in the gut microbiota

OBJECTIVE

The mechanisms of bariatric surgery-induced weight loss and metabolic improvements are still incompletely understood and reach beyond malabsorption or calorie restriction. We sought to investigate the effect of bariatric surgery on brown adipose tissue (BAT) activity and a potential connection with changes in energy metabolism, the gut microbiota, and short-chain fatty acid (SCFA) composition.

METHODS

We included 32 subjects (25 females) with morbid obesity and analyzed their metabolic profile, gut microbiota composition, circulating SCFAs, energy expenditure, and cold-induced BAT activity using [18F]Fluorodeoxyglucose-positron emission tomography-computed tomography before and up to 1 year after bariatric surgery.

RESULTS

Twelve months after surgery, the percentage of individuals with active BAT had increased from 28% to 53%. The BAT-negative (BATneg) individuals who had an adverse metabolic profile at baseline compared with subjects with active BAT (BATpos) showed a greater metabolic benefit after surgery. While no changes in overall gut bacterial diversity were observed between BATpos and BATneg, the abundance of 3 specific bacterial families, including Akkermansiaceae, Pasteurellaceae, and Carnobacteriaceae, was distinctly regulated between BAT groups. The bacterial genera most strongly increased in BATpos vs BATneg subjects were all positively correlated with BAT volume and BAT activity. Finally, circulating concentrations of the SCFAs acetate, butyrate, and propionate rose after bariatric surgery and were related to bacterial genera such as Akkermansia, Dialister, and Lachnospiraceae FCS020 group, all known SCFA producers.

CONCLUSIONS

Bariatric surgery helps recruit active BAT in individuals with obesity and is linked to distinct alterations in the gut microbiome and SCFA composition.

TRIAL REGISTRATION NUMBER

ClinicalTrials.gov (NCT03168009).

Maltotriosyl-erythritol, a transglycosylation product of erythritol by Thermus sp. amylomaltase and its application to prebiotic

In this study, maltotriosyl-erythritol (EG3) was synthesized as a novel prebiotic candidate via transglycosylation using recombinant amylomaltase (AMase) from Thermus sp. Tapioca starch served as the glucosyl donor, and erythritol as the acceptor. High-performance liquid chromatography (HPLC) revealed an EG3 yield of 14.0 % with a concentration of 2.8 mg/mL. Mass spectrometry confirmed the molecular weight of EG3 as 608 Da, and its strucopture was verified by 1H and 13C NMR analysis. EG3 exhibited greater resistance to acid, heat, and digestive enzymes compared to erythritol glucosides (EG1-2) and significantly promoted the growth of Lactobacillus casei BCC36987. Fermentation of EG3 resulted in the highest levels of lactic acid and total short-chain fatty acids, which may contribute to reduced pH levels. These findings suggest that erythritol-receptor products formed via AMase-catalyzed reactions, particularly EG3, are promising prebiotic ingredients, with the prebiotic activity of erythritol derivatives being influenced by the length of the carbohydrate chain.

Research trends and hotspots of metabolites and inflammatory bowel disease: a bibliometric analysis

Purpose

The purpose of this study is to analyze the current research status and explore the relationship between metabolites and inflammatory bowel disease (IBD), providing insights for future research.

Methods

In this study, we retrieved publications on metabolites and IBD from the Web of Science Core Collection (WOSCC), covering the period from 1994 to 2024. We conducted descriptive and visual analyses of the topics, journals, countries/regions, institutions, authors, and citation counts of these publications.

Results

From January 1994 to June 2024, a total of 509 relevant publications were retrieved from the WOSCC, with the number of publications steadily increasing each year. These articles were published in 222 journals, with the top three most productive journals being inflammatory bowel diseases (36 publications), Alimentary Pharmacology & Therapeutics (16 publications), and Digestive Diseases and Sciences (13 publications). The leading countries in publication output were China (154 publications, 30.3%), the USA (101 publications, 19.8%), and the UK (32 publications, 6.3%), with total citation counts of 3,175, 7,439, and 1,444, respectively. The most recent trending keywords in this field include "gut microbiota," "inflammation," and "pathogenesis."

Conclusion

Recent research on the relationship between metabolites and inflammatory bowel disease (IBD) has grown significantly, deepening our understanding of their connection. Further exploration of this relationship could not only enhance the quality of life for IBD patients but also offer new insights into potential cures for the disease.

Magnetite Micro/Nanorobots for Efficient Targeted Alleviation of Inflammatory Bowel Disease

Millions of people worldwide have inflammatory bowel disease (IBD). Self-driven micro/nanorobots (MNRs) are efficient in the treatment of IBD. However, their lack of controllability regarding direction of motion in the organism and their inability to achieve continuous navigation limits their further application. In this study, polydopamine is wrapped around the magnetite surface, loaded with an anti-inflammatory drug resveratrol, and wrapped with pH-responsive sodium alginate to obtain magnetic MNRs. MNRs can be driven by magnetic fields to achieve directional movement and targeted transportation. In addition, MNRs can effectively remove reactive oxygen species from the inflammation site, repair intestinal damage, inhibit the cellular pathway of pro-inflammatory factors, such as MAPK and NF-κB pathways, and restore intestinal flora, thereby relieving IBDs. MNRs are safe and effective for in vivo treatment of IBD and have proven to be a promising therapeutic platform. This MNRs therapeutic strategy provides new insights into comprehensive IBD therapy.

Effects of Probiotics Supplementation on Short-Chain Fatty Acids: A Systematic Review of Randomized Controlled Trials

CONTEXT

With the increased use of fermented products and probiotic foods, interest in knowing their benefits and safety of their intake is increasing.

OBJECTIVE

The current systematic review investigated the effects of probiotics supplementation on short-chain fatty acid (SCFA) levels.

METHODS

A systematic review was conducted according to the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines. Medline/PubMed, Scopus, Web of Science, and Embase databases were searched from inception to February 2024, including only randomized controlled trials.

RESULTS

A total of 30 studies were included, involving 1499 participants. The vast majority of trials investigated Bifidobacterium and Lactobacillus strains. These were categorized into healthy adults (n = 6), gastrointestinal/inflammatory diseases (n = 7), metabolic diseases (n = 6), elderly individuals (n = 3), children (n = 4), and infant formula (n = 4). Most studies evaluated isolated strain supplementation (n = 12), followed by fermented beverages (n = 11) and probiotic mixes (n = 3). Globally, 16 studies (53.3%) revealed an increase in at least 1 SCFA in participants supplemented with probiotics. In comparison, 5 studies (16.7%) reported a reduction and 9 studies showed no statistically significant impact in their findings (30%). The subgroup evaluation showed heterogeneity in the results, with low to moderate evidence grading levels.

CONCLUSION

Probiotics supplementation during childhood was the intervention period more effective in increasing fecal SCFAs and immunoglobulin A (IgA) levels (GRADE: moderate/high-certainty evidence).

SYSTEMATIC REVIEW REGISTRATION

PROSPERO registration no. CRD42024513221.

Interplay of Neuroinflammation and Gut Microbiota Dysbiosis in Alzheimer's Disease Using Diffusion Kurtosis Imaging Biomarker in 3 × Tg-AD Mouse Models

The relationship between alterations in brain microstructure and dysbiosis of gut microbiota in Alzheimer's disease (AD) has garnered increasing attention, although the functional implications of these changes are not yet fully elucidated. This research examines how neuroinflammation, systemic inflammation, and gut microbiota interact in male 3 × Tg-AD and B6129SF1/J wild-type (WT) mice at 6 months-old (6-MO) and 12 months-old (12-MO). Employing a combination of behavioral assessments, diffusion kurtosis imaging (DKI), microbiota profiling, cytokine analysis, short-chain fatty acids (SCFAs), and immunohistochemistry, we explored the progression of AD-related pathology. Significant memory impairments in AD mice at both assessed ages were correlated with altered DKI parameters that suggest neuroinflammation and microstructural damage. We observed elevated levels of pro-inflammatory cytokines, such as IL-1β, IL-6, TNFα, and IFN-γ, in the serum, which were associated with increased activity of microglia and astrocytes in brain regions critical for memory. Although gut microbiota analysis did not reveal significant changes in alpha diversity, it did show notable differences in beta diversity and a diminished Firmicutes/Bacteroidetes (F/B) ratio in AD mice at 12-MO. Furthermore, a reduction in six kinds of SCFAs were identified at two time points of 6-MO and 12-MO, indicating widespread disruption in gut microbial metabolism. These findings underscore a complex bidirectional relationship between systemic inflammation and gut dysbiosis in AD, highlighting the gut-brain axis as a crucial factor in disease progression. This study emphasizes the potential of integrating DKI metrics, microbiota profiling, and SCFA analysis to enhance our understanding of AD pathology and to identify new therapeutic targets.

Gut microbiota and metabolites are linked to disease progression in multiple sclerosis

Progressive multiple sclerosis (MS) is a neurological disease with limited understanding of the biology associated with transition from relapsing to progressive disease. Intestinal microbes and metabolites are altered in MS, but relation to disease progression is largely unknown. We investigate microbiota and metabolites in subjects with stable MS, those who worsened, and in those with relapsing MS who became progressive over 2 years. We find that Eubacterium hallii, Butyricoccaceae, Blautia, and other short-chain fatty-acid-producing microbes have beneficial associations with worsening of disability, 3T magnetic resonance imaging (MRI) measures, cognition, and quality of life, while Alistipes is detrimentally associated. Global metabolomics identified serum and stool metabolites that are altered in progressive MS and in relapsing subjects who transitioned to progressive disease. Most fecal metabolites associated with disease progression are decreased, suggesting a deficiency of protective factors in the gut. Using a unique MS cohort, our findings identify gut microbiome and metabolite pathways influencing progressive MS.

Escherichia coli Nissle Improves Short-Chain Fatty Acid Absorption and Barrier Function in a Mouse Model for Chronic Inflammatory Diarrhea

BACKGROUND

Defects in SLC26A3, the major colonic Cl-/HCO3- exchanger, result in chloride-rich diarrhea, a reduction in short-chain fatty acid (SCFA)-producing bacteria, and a high incidence of inflammatory bowel disease in humans and in mice. Slc26a3-/- mice are, therefore, an interesting animal model for spontaneous but mild colonic inflammation and for testing strategies to reverse or prevent the inflammation. This study investigates the effect of Escherichia coli Nissle (EcN) application on the microbiome, SCFA production, barrier integrity, and mucosal inflammation in slc26a3-/- mice.

METHODS

In vivo fluid absorption and bicarbonate secretion were assessed in the gut of slc26a3+/+ and slc26a3-/- mice before and during luminal perfusion with 100 mM sodium acetate. Age-matched slc26a3+/+ and slc26a3-/- mice were intragastrically gavaged twice daily with 2 × 108 CFU/100 µL of EcN for 21 days. Body weight and stool water content were assessed daily, and stool and tissues were collected for further analysis.

RESULTS

Addition of sodium acetate to the lumen of the proximal colon significantly increased fluid absorption and luminal alkalinization in the slc26a3-/- mice. Gavage with EcN resulted in a significant increase in SCFA levels and the expression of SCFA transporters in the slc26a3-/- cecum, the predominant habitat of EcN in mice. This was accompanied by an increase in mucus-producing goblet cells and a decrease in the expression of inflammatory markers as well as host defense antimicrobial peptides. EcN did not improve the overall diversity of the luminal microbiome but resulted in a significant increase in SCFA producers Lachnospiraceae and Ruminococcaceae in the slc26a3-/- feces.

CONCLUSIONS

These findings suggest that EcN is able to proliferate in the inflamed cecum, resulting in increased microbial SCFA production, decreased inflammation, and improved gut barrier properties. In sufficient dosage, probiotics may thus be an effective anti-inflammatory strategy in the diseased gut.

Rhubarb with Different Cooking Methods Restored the Gut Microbiota Dysbiosis and SCFAs in Ischemic Stroke Mice

Ischemic stroke is a significant public health problem worldwide. Growing evidence has shown gut microbiota served a vital function in ischemic stroke. Rhubarb, always used after processing, is a promising therapy for ischemic stroke. However, the possible mechanism of rhubarb with different cooking methods has remained unclear. Herein, the constitutes of steaming rhubarb (SP), raw rhubarb (RP), and nine steaming nine sun-drying rhubarb (NSP) were identified via LC-QTOF-MS. The middle cerebral artery occlusion (MCAO) mice model was constructed. Infarction area, neurological score, Nissl staining, IBA-1 immunofluorescence, and ELISA were performed to confirm the neuroprotective effect of SP, RP, and NSP. The gut microbiota in fetal was studied via 16sRNA sequencing, and the level of short-chain fatty acids (SCFAs) in brain and gut were measured via GC-MS. The function of microbiota signature was identified through PICRUSt2; the possible mechanism was studied. SP, RP, and NSP alleviated the neurological dysfunction, decreased the inflammation, suppressed dysbiosis of gut microbiota, restored SCFA-producing bacteria, and enhanced the SCFA level in MCAO mice. Moreover, the NSP and SP enriched the proportion of anti-inflammation and beneficial bacteria, deleted the proportion of pro-inflammation. It observed energy metabolism was involved in the possible mechanism of rhubarb; activities of COXI and Na+-K+-ATPase were increased in the brain of NSP and SP treatment mice. Furthermore, the expression of GLUT4 and PFK1 (the energy metabolism-related genes) was elevated in the brain after RP, NSP and SP administration. In this study, it provided proof for the treatment of ischemic stroke with rhubarb. Rhubarb restored the gut microbiota and regulated the expression of GLUT4 and PFK1 to alleviate ischemic stroke.

The double-edged sword: impact of antibiotic use on immunotherapy efficacy in advanced hepatocellular carcinoma

OBJECTIVE

This retrospective study aims to evaluate the impact of antibiotics (ATBs) use on the efficacy of immunotherapy in patients with advanced hepatocellular carcinoma (HCC), providing insights into the prudent use of ATBs in patients undergoing immunotherapy.

METHODS

We retrospectively collected data from patients with advanced HCC treated with immune checkpoint inhibitors (ICIs) at our institution between January 1, 2021, and December 30, 2023. Patients were divided into two groups based on ATBs use: an ATB group and a non-ATB group. Clinical baseline characteristics were analyzed, and survival curves were plotted using the Kaplan-Meier model. A Cox proportional hazards model was employed to analyze influencing factors.

RESULTS

Among the 102 advanced HCC patients receiving ICIs treatment, 29 were in the ATB group, and 73 were in the non-ATB group. The progression-free survival (PFS) (P = 0.034) and overall survival (OS) (P = 0.021) were significantly shorter in the ATB group compared to the non-ATB group. The difference in PFS between the two groups was associated with ATBs use and patients' AFP levels, while ATBs use was identified as an independent risk factor for the difference in OS between the groups.

CONCLUSION

ATB use in the context of immunotherapy for advanced HCC is associated with reduced PFS and OS. Caution is warranted in the administration of ATBs to patients undergoing immunotherapy.

Recent developments in managing luminal microbial ecology in patients with inflammatory bowel disease: from evidence to microbiome-based diagnostic and personalized therapy

INTRODUCTION

Inflammatory bowel disease (IBD), including Crohn's disease and ulcerative colitis, is a chronic condition characterized by abnormal immune responses and intestinal inflammation. Emerging evidence highlights the vital role of gut microbiota in IBD's onset and progression. Recent advances have shaped diagnostic and therapeutic strategies, increasingly focusing on microbiome-based personalized care. Methodology: this review covers studies from 2004 to 2024, reflecting the surge in research on luminal microbial ecology in IBD. Human studies were prioritized, with select animal studies included for mechanistic insights. Only English-language, peer-reviewed articles - clinical trials, systematic reviews, and meta-analyses - were considered. Studies without clinical validation were excluded unless offering essential insights. Searches were conducted using PubMed, Scopus, and Web of Science.

AREAS COVERED

we explore mechanisms for managing IBD-related microbiota, including microbial markers for diagnosis and novel therapies such as fecal microbiota transplantation, metabolite-based treatments, and precision microbiome modulation. Additionally, we review technologies and diagnostic tools used to analyze gut microbiota composition and function in clinical settings. Emerging data supporting personalized therapeutic strategies based on individual microbial profiles are discussed.

EXPERT OPINION

Standardized microbiome research integration into clinical practice will enhance precision in IBD care, signaling a shift toward microbiota-based personalized medicine.

Sakuranetin ameliorates experimental colitis in a gut microbiota-dependent manner

BACKGROUND

The progression of inflammatory bowel disease (IBD) is closely connected with intestinal flora dysbiosis. Sakuranetin (SAK) is a natural compound with anti-inflammatory and antibiosis activities. We investigated the properties and mechanisms of SAK on IBD-like colitis.

METHODS

Mice with dextran sulfate sodium (DSS)-induced colitis were accomplished to assess the effects of SAK on colitis, as well as intestinal mucosal immune imbalance and intestinal barrier dysfunction. 16S rDNA was used to characterize the intestinal flora, and the short-chain fatty acid (SCFA) content in faeces was calculated using GS‒MS. Faecal microbiota transplantation (FMT) and a pseudosterile model (antibiotic cocktail, ABX) were used to evaluate whether the effects of SAK on colitis were dependent on the gut flora. Pathohistological and biochemical tests were used to estimate the safety of SAK.

RESULTS

SAK significantly ameliorated DSS-induced colitis in mice, verified by decreased weight loss, less colon shortening, and lower disease activity, histology and colonoscopy scores. Moreover, SAK alleviated gut dysbiosis and elevated the abundance of SCFA-producing bacteria in DSS-treated mice. Meanwhile, SAK increased faecal SCFA levels and activated GPR41/43 signalling. SAK also improved Treg/Th17 homeostasis and intestinal barrier function. In addition, ABX and FMT experiments confirmed that the ability of SAK to alleviate colitis was mediated through the gut flora. Finally, a safety experiment revealed that SAK had no significant adverse effects on major organ or liver/kidney function.

CONCLUSIONS

SAK may improve the intestinal immune balance and barrier function by regulating intestinal flora dysbiosis and increasing SCFA production, thereby protecting against colitis.

The role of colonic microbiota amino acid metabolism in gut health regulation

The human gut microbiota plays a critical role in maintaining host homeostasis through metabolic activities. Among these, amino acid (AA) metabolism by the microbiota in the large intestine is highly heterogeneous and relevant to host health. Despite increasing interest, microbial AA metabolism remains relatively unexplored. This review highlights recent advances in colonic microbial AA metabolism, including auxotrophies, AA synthesis, and dissimilatory AA metabolites, and their implications in gut health, focusing on major gastrointestinal diseases including colorectal cancer, inflammatory bowel disease, and irritable bowel syndrome.

The Role of Short-Chain Fatty Acids in Metabolic Dysfunction-Associated Steatotic Liver Disease and Other Metabolic Diseases

With its increasing prevalence, metabolic dysfunction-associated steatotic liver disease (MASLD) has emerged as a major global public health concern over the past few decades. Growing evidence has proposed the microbiota-derived metabolites short-chain fatty acids (SCFAs) as a potential factor in the pathophysiology of MASLD and related metabolic conditions, such as obesity and type 2 diabetes mellitus (T2DM). By influencing key pathways involved in energy homeostasis, insulin sensitivity, and inflammation, SCFAs play an important role in gut microbiota composition, intestinal barrier function, immune modulation, and direct metabolic signaling. Furthermore, recent animal and human studies on therapeutic strategies targeting SCFAs demonstrate their potential for treating these metabolic disorders.

Effects of psychological stress on inflammatory bowel disease via affecting the microbiota-gut-brain axis

ABSTRACT

Inflammatory bowel disease (IBD) is an idiopathic intestinal inflammatory condition with chronic and relapsing manifestations and is characterized by a disturbance in the interplay between the intestinal microbiota, the gut, and the brain. The microbiota-gut-brain axis involves interactions among the nervous system, the neuroendocrine system, the gut microbiota, and the host immune system. Increasing published data indicate that psychological stress exacerbates the severity of IBD due to its negative effects on the microbiota-gut-brain axis, including alterations in the stress response of the hypothalamic-pituitary-adrenal (HPA) axis, the balance between the sympathetic nervous system and vagus nerves, the homeostasis of the intestinal flora and metabolites, and normal intestinal immunity and permeability. Although the current evidence is insufficient, psychotropic agents, psychotherapies, and interventions targeting the microbiota-gut-brain axis show the potential to improve symptoms and quality of life in IBD patients. Therefore, further studies that translate recent findings into therapeutic approaches that improve both physical and psychological well-being are needed.

Kismet/CHD7/CHD8 affects gut microbiota, mechanics, and the gut-brain axis in Drosophila melanogaster

The gut microbiome affects brain and neuronal development and may contribute to the pathophysiology of neurodevelopmental disorders. However, it is unclear how risk genes associated with such disorders affect gut physiology in a manner that could impact microbial colonization and how the mechanical properties of the gut tissue might play a role in gut-brain bidirectional communication. To address this, we used Drosophila melanogaster with a null mutation in the gene kismet, an ortholog of chromodomain helicase DNA-binding protein (CHD) family members CHD7 and CHD8. In humans, these are risk genes for neurodevelopmental disorders with co-occurring gastrointestinal symptoms. We found that kismet mutant flies have a significant increase in gastrointestinal transit time, indicating the functional homology of kismet with CHD7/CHD8 in vertebrates. Rheological characterization of dissected gut tissue revealed significant changes in the mechanics of kismet mutant gut elasticity, strain stiffening behavior, and tensile strength. Using 16S rRNA metagenomic sequencing, we also found that kismet mutants have reduced diversity and abundance of gut microbiota at every taxonomic level. To investigate the connection between the gut microbiome and behavior, we depleted gut microbiota in kismet mutant and control flies and quantified the flies' courtship behavior. Depletion of gut microbiota rescued courtship defects of kismet mutant flies, indicating a connection between gut microbiota and behavior. In striking contrast, depletion of the gut microbiome in the control strain reduced courtship activity, demonstrating that antibiotic treatment can have differential impacts on behavior and may depend on the status of microbial dysbiosis in the gut prior to depletion. We propose that Kismet influences multiple gastrointestinal phenotypes that contribute to the gut-microbiome-brain axis to influence behavior. We also suggest that gut tissue mechanics should be considered as an element in the gut-brain communication loop, both influenced by and potentially influencing the gut microbiome and neurodevelopment.

Operationalizing Team Science at the Academic Cancer Center Network to Unveil the Structure and Function of the Gut Microbiome

Oncologists increasingly recognize the microbiome as an important facilitator of health as well as a contributor to disease, including, specifically, cancer. Our knowledge of the etiologies, mechanisms, and modulation of microbiome states that ameliorate or promote cancer continues to evolve. The progressive refinement and adoption of "omic" technologies (genomics, transcriptomics, proteomics, and metabolomics) and utilization of advanced computational methods accelerate this evolution. The academic cancer center network, with its immediate access to extensive, multidisciplinary expertise and scientific resources, has the potential to catalyze microbiome research. Here, we review our current understanding of the role of the gut microbiome in cancer prevention, predisposition, and response to therapy. We underscore the promise of operationalizing the academic cancer center network to uncover the structure and function of the gut microbiome; we highlight the unique microbiome-related expert resources available at the City of Hope of Comprehensive Cancer Center as an example of the potential of team science to achieve novel scientific and clinical discovery.

Gut commensals-derived succinate impels colonic inflammation in ulcerative colitis

Gut microbiota-derived metabolites play a crucial role in modulating the inflammatory response in inflammatory bowel disease (IBD). In this study, we identify gut microbiota-derived succinate as a driver of inflammation in ulcerative colitis (UC) by activating succinate-responsive, colitogenic helper T (Th) cells that secrete interleukin (IL)-9. We demonstrate that colitis is associated with an increase in succinate-producing gut bacteria and decrease in succinate-metabolizing gut bacteria. Similarly, UC patients exhibit elevated levels of succinate-producing gut bacteria and luminal succinate. Intestinal colonization by succinate-producing gut bacteria or increased succinate availability, exacerbates colonic inflammation by activating colitogenic Th9 cells. In contrast, intestinal colonization by succinate-metabolizing gut bacteria, blocking succinate receptor signaling with an antagonist, or neutralizing IL-9 with an anti-IL-9 antibody alleviates inflammation by reducing colitogenic Th9 cells. Our findings underscore the role of gut microbiota-derived succinate in driving colitogenic Th9 cells and suggesting its potential as a therapeutic target for treating IBD.

Gut Microbiota Serves as a Crucial Independent Biomarker in Inflammatory Bowel Disease (IBD)

Inflammatory bowel disease (IBD), encompassing Crohn's disease (CD), ulcerative colitis (UC), and IBD unclassified (IBD-U), is a complex intestinal disorder influenced by genetic, environmental, and microbial factors. Recent evidence highlights the gut microbiota as a pivotal biomarker and modulator in IBD pathogenesis. Dysbiosis, characterized by reduced microbial diversity and altered composition, is a hallmark of IBD. A consistent decrease in anti-inflammatory bacteria, such as Faecalibacterium prausnitzii, and an increase in pro-inflammatory species, including Escherichia coli, have been observed. Metabolomic studies reveal decreased short-chain fatty acids (SCFAs) and secondary bile acids, critical for gut homeostasis, alongside elevated pro-inflammatory metabolites. The gut microbiota interacts with host immune pathways, influencing morphogens, glycosylation, and podoplanin (PDPN) expression. The disruption of glycosylation impairs mucosal barriers, while aberrant PDPN activity exacerbates inflammation. Additionally, microbial alterations contribute to oxidative stress, further destabilizing intestinal barriers. These molecular and cellular disruptions underscore the role of the microbiome in IBD pathophysiology. Emerging therapeutic strategies, including probiotics, prebiotics, and dietary interventions, aim to restore microbial balance and mitigate inflammation. Advanced studies on microbiota-targeted therapies reveal their potential to reduce disease severity and improve patient outcomes. Nevertheless, further research is needed to elucidate the bidirectional interactions between the gut microbiome and host immune responses and to translate these insights into clinical applications. This review consolidates current findings on the gut microbiota's role in IBD, emphasizing its diagnostic and therapeutic implications, and advocates for the continued exploration of microbiome-based interventions to combat this debilitating disease.

Deconstruct the link between gut microbiota and neurological diseases: application of Mendelian randomization analysis

Background

Recent research on the gut-brain axis has deepened our understanding of the correlation between gut bacteria and the neurological system. The inflammatory response triggered by gut microbiota may be associated with neurodegenerative diseases. Additionally, the impact of gut microbiota on emotional state, known as the "Gut-mood" relationship, could play a role in depression and anxiety disorders.

Results

This review summarizes recent data on the role of gut-brain axis in the pathophysiology of neuropsychiatric and neurological disorders including epilepsy, schizophrenia, Alzheimer's disease, brain cancer, Parkinson's disease, bipolar disorder and stroke. Also, we conducted a Mendelian randomization study on seven neurological disorders (Epilepsy, schizophrenia, Alzheimer's disease, brain cancer, Parkinson's disease, bipolar disorder and stroke). MR-Egger and MR-PRESSO tests confirmed the robustness of analysis against horizontal pleiotropy.

Conclusions

By comparing the protective and risk factors for neurological disorders found in our research and other researches, we can furtherly determine valuable indicators for disease evolution tracking and potential treatment targets. Future research should explore extensive microbiome genome-wide association study datasets using metagenomics sequencing techniques to deepen our understanding of connections and causality between neurological disorders.

Sedanolide alleviates DSS-induced colitis by modulating the intestinal FXR-SMPD3 pathway in mice

INTRODUCTION

Inflammatory bowel disease (IBD) is a global disease with limited therapy. It is reported that sedanolide exerts anti-oxidative and anti-inflammatory effects as a natural phthalide, but its effects on IBD remain unclear.

OBJECTIVES

In this study, we investigated the impacts of sedanolide on dextran sodium sulfate (DSS)-induced colitis in mice.

METHODS

The mice were administered sedanolide or vehicle followed by DSS administration, after which colitis symptoms, inflammation levels, and intestinal barrier function were evaluated. Transcriptome analysis, 16S rRNA sequencing, and targeted metabolomics analysis of bile acids and lipids were performed.

RESULTS

Sedanolide protected mice from DSS-induced colitis, suppressed the inflammation, restored the weakened epithelial barrier, and modified the gut microbiota by decreasing bile salt hydrolase (BSH)-expressing bacteria. The downregulation of BSH activity by sedanolide increased the ratio of conjugated/unconjugated bile acids (BAs), thereby inhibiting the intestinal farnesoid X receptor (FXR) pathway. The roles of the FXR pathway and gut microbiota were verified using an intestinal FXR-specific agonist (fexaramine) and germ-free mice, respectively. Furthermore, we identified the key effector ceramide, which is regulated by sphingomyelin phosphodiesterase 3 (SMPD3). The protective effects of ceramide (d18:1/16:0) against inflammation and the gut barrier were demonstrated in vitro using the human cell line Caco-2.

CONCLUSION

Sedanolide could reshape the intestinal flora and influence BA composition, thus inhibiting the FXR-SMPD3 pathway to stimulate the synthesis of ceramide, which ultimately alleviated DSS-induced colitis in mice. Overall, our research revealed the protective effects of sedanolide against DSS-induced colitis in mice, which indicated that sedanolide may be a clinical treatment for colitis. Additionally, the key lipid ceramide (d18:1/16:0) was shown to mediate the protective effects of sedanolide, providing new insight into the associations between colitis and lipid metabolites.

Impact of Vegan and Vegetarian Diets on Neurological Health: A Critical Review

BACKGROUND/OBJECTIVES

The global shift towards vegan and vegetarian diets has garnered attention for their ethical, environmental, and potential health benefits. These diets are often rich in phytonutrients and antioxidants, which have been associated with lower levels of inflammatory markers, such as C-reactive protein (CRP) and interleukin-6 (IL-6), suggesting a potential protective effect against systemic inflammation and oxidative stress. However, despite these benefits, concerns remain regarding their impact on neurological health due to the possible deficiencies of critical nutrients such as vitamin B12, DHA, EPA, and iron. This review critically evaluates the influence of these dietary patterns on neurological outcomes, emphasizing their nutritional composition, potential deficiencies, and their interplay with inflammation and oxidative stress.

METHODS

A systematic review of the literature published between 2010 and 2023 was conducted, focusing on studies that explore the relationship between vegan and vegetarian diets and neurological health. Key nutrients such as vitamin B12, omega-3 fatty acids, iron, and zinc were analyzed alongside antinutritional factors and their effects on the nervous system.

RESULTS

Evidence suggests that vegan and vegetarian diets, when well planned, can be rich in phytonutrients and antioxidants, which have been associated with lower levels of inflammatory markers, such as C-reactive protein (CRP) and interleukin-6 (IL-6). These findings indicate a potential role in reducing systemic inflammation and oxidative stress, both of which are linked to neurodegenerative diseases. However, deficiencies in critical nutrients such as vitamin B12, DHA, EPA, and iron have been consistently associated with an increased risk of cognitive decline, mood disturbances, and neurodegenerative disorders. Additionally, the presence of antinutritional factors like phytates and oxalates may further impair nutrient absorption, necessitating careful dietary planning and supplementation.

CONCLUSIONS

While plant-based diets provide anti-inflammatory and antioxidant benefits, their neurological implications depend on nutrient adequacy. Proper planning, supplementation, and food preparation techniques are essential to mitigate risks and enhance cognitive health. Further research is needed to explore long-term neurological outcomes and optimize dietary strategies.

Impact of Ligilactobacillus salivarius Li01 on benzo[a]pyrene-induced colitis, based on host-microbiome interactions in Mongolian gerbils

Background

Probiotics supplementations have been regarded as an effective strategy for colitis treatment. However, the effect of Ligilactobacillus salivarius Li01 on benzo[a]pyrene (BaP)-induced colitis in Mongolian gerbils remains unclear. In this study, we leverage a BaP-induced model of colitis that exhibits significant remission following Ligilactobacillus salivarius Li01 intervention, to conduct an animal experiment that integrates histopathological assessment, inflammatory cytokines, 16S rRNA sequencing, targeted metabolomic profiling to investigate the relationship between Ligilactobacillus salivarius Li01, gut microbiota, and colitis.

Results

We demonstrated that the improvements in colon histopathological assessment and inflammatory cytokines by Ligilactobacillus salivarius Li01 supplementation are accompanied by alterations in gut microbiota structure marked by increased abundance of strains with probiotic potential belonging to Bifidobacterium and Eubacterium_coprostanoligenes. Targeted metabolomic profiling analysis showed that Ligilactobacillus salivarius Li01 supplementation increases the concentration of acetic, propionic, butyric, and valeric acid. Correlation analysis showed that the alteration in the indicators associated with colitis is closely correlated to the changed microbial taxa and short-chain fatty acids (SCFAs).

Conclusion

These data highlighted that Ligilactobacillus salivarius Li01 supplementation ameliorated the BaP-induced colitis, probably via modulating the structure of gut microbiota and promoting the production of SCFAs. Our findings provide preliminary evidence for a possible therapeutic strategy for the treatment of colitis based on host-microbiome interactions.

Complex system modelling reveals oxalate homeostasis is driven by diverse oxalate-degrading bacteria

Decades of research have made clear that host-associated microbiomes touch all facets of health. However, effective therapies that target the microbiome have been elusive given its inherent complexity. Here, we experimentally examined diet-microbe-host interactions through a complex systems framework, centered on dietary oxalate. Using multiple, independent molecular, animal, and in vitro experimental models, we found that microbiome composition influenced multiple oxalate-microbe-host interfaces. Importantly, administration of the oxalate-degrading specialist, Oxalobacter formigenes, was only effective against a poor oxalate-degrading microbiota background and gives critical new insights into why clinical intervention trials with this species exhibit variable outcomes. Data suggest that, while heterogeneity in the microbiome impacts multiple diet-host-microbe interfaces, metabolic redundancy among diverse microorganisms in specific diet-microbe axes is a critical variable that may impact the efficacy of bacteriotherapies, which can help guide patient and probiotic selection criteria in probiotic clinical trials.

Targeting gut microbiota dysbiosis in inflammatory bowel disease: a systematic review of current evidence

Introduction

The dysbiosis of the gut microbiota has been identified as a central factor in the pathogenesis of inflammatory bowel disease (IBD), a chronic condition characterized by frequent recurrence and various adverse effects of traditional therapies. While treatments targeting the gut microbiota show promise, their efficacy in IBD management still requires extensive evaluation. Our systematic review analyzes recent studies to elucidate the advancements and challenges in treating IBD using microbial-based therapies.

Methods

Through a comprehensive systematic review spanning key scientific databases-PubMed, Embase, Cochrane, Web of Science, Scopus, and Google Scholar-we scrutinized the impact of probiotics, prebiotics, synbiotics, and fecal microbiota transplantation (FMT) on individuals with IBD. Our detailed analysis covered study and participant demographics, along with seven key outcome measures: disease activity index, inflammatory markers, serum cytokines, microbiome composition, adverse effects, and the rates of remission and relapse.

Results

From 6,080 initial search hits, we included 71 studies that assessed various interventions compared to placebo or standard medical therapy. Although there was notable variation in clinical results while assessing different outcomes, overall, probiotics, prebiotics, and synbiotics enhanced the success rates in inducing remission among IBD patients. Furthermore, we noted significant reductions in levels of pro-inflammatory markers and cytokines. Additionally, the requirement for steroids, hospitalization, and poor outcomes in endoscopic and histological scores were significantly reduced in individuals undergoing FMT.

Conclusion

Our investigation highlights the potential of targeting gut microbiota dysbiosis with microbial-based therapies in patients with IBD. We recommend conducting larger, placebo-controlled randomized trials with extended follow-up periods to thoroughly assess these treatments' clinical efficacy and safety before widespread recommendations for clinical application.

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.

Gut microbiota-derived short chain fatty acids act as mediators of the gut-liver-brain axis

The gut microbiota plays a crucial role in the communication between the gut, liver, and brain through the production of short chain fatty acids (SCFAs). SCFAs serve as key mediators in the Gut-Liver-Brain Axis, influencing various physiological processes and contributing to overall health. SCFAs are produced by bacterial fermentation of dietary fiber in the gut, and they exert systemic effects by signaling through various pathways. In the Gut-Liver axis, SCFAs regulate liver metabolism through peroxisome proliferator-activated receptor-γ (PPAR-γ), AMP-activated protein kinase (AMPK) and other pathways, promotes fat oxidation, modulate inflammation through mTOR pathway, and impact metabolic health. In the Gut-Brain axis, SCFAs influence brain function, behavior, and may have implications for neurological disorders, in which G-protein coupled receptors (GPCRs) play an essential role, along with other pathways such as hypothalamic-pituitary-adrenal (HPA) pathway. Understanding the mechanisms by which SCFAs mediate communication between the gut, liver, and brain is crucial for elucidating the complex interplay of the Gut-Liver-Brain Axis. This review aims to provide insight into the role of gut microbiota-derived SCFAs as mediators of the Gut-Liver-Brain Axis and their potential therapeutic implications. Further research in this area will be instrumental in developing novel strategies to target the Gut-Liver-Brain Axis for the prevention and treatment of various health conditions.

Novel anti-inflammatory properties of mannose oligosaccharides in the treatment of inflammatory bowel disease via LGALS3 modulation

This study investigates the role of Gum Arabic Mannose Oligosaccharides (GA-MOS) in modulating gut microbiota and alleviating symptoms of Inflammatory Bowel Disease (IBD). Employing both in vitro and in vivo models, we explored how GA-MOS influences microbial communities, particularly focusing on their capacity to enhance health-associated bacteria and reduce pathogenic species within the gut environment. Our findings reveal that GA-MOS treatment significantly altered the gut microbiota composition, increasing the abundance of anti-inflammatory bacteria while decreasing pro-inflammatory species, thus contributing to a reduction in gut inflammation and an improvement in intestinal barrier function. Detailed molecular analyses further demonstrated that these changes in microbiota were associated with modifications in the host's immune response, particularly through the suppression of key inflammatory pathways and cytokines involved in IBD progression. These results underscore the potential of dietary polysaccharides like GA-MOS as therapeutic agents in managing dysbiosis and inflammatory conditions in the gut, offering a promising approach for enhancing microbial health and overall disease management in IBD. This study provides novel insights into the bioactive properties of MOS and their interactions with gut microbiota, suggesting broader implications for their use in microbiome-centered therapies.

A Promising Approach for the Food Industry: Enhancing Probiotic Viability Through Microencapsulated Synbiotics

The role of prebiotics and probiotics in promoting gut health is increasingly recognized in food development and nutrition research. This study explored the enhancement of probiotic viability in the food industry through microencapsulated synbiotics, focusing on Lactiplantibacillus plantarum NCIMB 11974 with fructooligosaccharides (FOSs) and inulin as prebiotics. The effect of encapsulation in a chitosan-coated alginate matrix on probiotic survival under simulated gastrointestinal conditions showed a significant effect of 2% FOS concentration on the growth of Lactiplantibacillus plantarum NCIMB 11974. The optimization of microencapsulation parameters by the Taguchi method revealed a 2% sodium alginate concentration, a nozzle size of 200 µm, and a concentration of 0.4% chitosan solution as ideal, producing microcapsules with an estimated average diameter of 212 µm. Viability assessments in simulated gastric juice and simulated intestinal juice showed that chitosan-coated alginate microcapsules notably enhanced probiotic survival, achieving log 8 CFU mL-1 viability in both environments, a marked improvement over the uncoated variant. The study emphasizes the importance of microencapsulation, particularly by sodium alginate and chitosan, as a viable strategy to improve the survival and delivery of probiotics through the digestive system. By improving the stability and survivability of probiotics, microencapsulation promises to expand the use of synbiotics in various foods, contributing to the development of functional foods with health-promoting properties.

Open Label Vancomycin in Primary Sclerosing Cholangitis-Inflammatory Bowel Disease: Improved Colonic Disease Activity and Associations With Changes in Host-Microbiome-Metabolomic Signatures

BACKGROUND

We conducted a single-arm interventional study, to explore mucosal changes associated with clinical remission under oral vancomycin (OV) treatment, in primary sclerosing cholangitis-associated inflammatory bowel disease (PSC-IBD); NCT05376228.

METHODS

Fifteen patients with PSC and active colitis (median fecal calprotectin 459 µg/g; median total Mayo score 5) were treated with OV (125 mg QID) for 4 weeks and followed-up for a further 4 weeks of treatment withdrawal (8 weeks, end-of-study). Colonic biopsies were obtained at baseline and Week 4. Clinical assessments, and serum and stool samples (metagenomics, metatranscriptomics, and metabolomics) were collected at Weeks 0, 2, 4, and 8. The primary efficacy outcome measure was the induction of clinical remission.

RESULTS

Oral vancomycin resulted in clinical remission in 12/15 patients and significant reductions in fecal calprotectin. Oral vancomycin was associated with reduced abundances of Lachnospiraceae, genera Blautia and Bacteroides; and enrichment of Enterobacteriaceae, and genera Veillonella, Akkermansia, and Escherichia. Oral vancomycin treatment was associated with the downregulation of multiple metatranscriptomic pathways (including short-chain fatty acid [SCFA] metabolism and bile acid [BA] biotransformation), along with host genes and multiple pathways involved in inflammatory responses and antimicrobial defence; and an upregulation of genes associated with extracellular matrix repair. Oral vancomycin use resulted in the loss of specific fecal SCFAs and secondary BAs, including lithocholic acid derivatives. Colitis activity relapsed following OV withdrawal, with host mucosal and microbial changes trending toward baseline.

CONCLUSIONS

Four weeks of OV induces remission in PSC-IBD activity, associated with a reduction in gut bacterial diversity and compositional changes relating to BA and SCFA homeostasis.

Protective Role of Nano-encapsulated Bifidobacterium breve, Bacilllus coagulans, and Lactobacillus plantarum in Colitis Model: Insights Toward Propagation of Short-Chain Fatty Acids and Reduction of Exaggerated Inflammatory and Oxidative Response

Irritable bowel disease (IBD), also known as ulcerative colitis and Crohn's disease, is a chronic inflammatory disorder affecting millions of people worldwide. Herein, nano-encapsulated multi-strain probiotics formulation, comprising Bifidobacterium breve DSM24732 and B. coagulans SANK 70258 and L. plantarum DSM24730 (BBLNPs) is used as an effective intervention technique for attenuating IBD through gut microenvironment regulation. The efficacy of the prophylactic role of BBLNPs in alleviating injury induced by dextran sulfate sodium (DSS) was evaluated by assessing oxidative and inflammatory responses, levels of short-chain fatty acids (SCFAs) and their regulation on GPR41/43 pathway, expression of genes related to tight-junctions and autophagy, immunohistochemistry of IL1β and GPR43, and histological examination of inflamed colonic tissue. The severity of clinical signs and paracellular permeability to FITC (fluorescein isothiocyanate)-labeled dextran was significantly decreased after BBLNP treatment. Reduction of oxidative stress-associated biomarkers (MDA, ROS, and H2O2) and acceleration of antioxidant enzyme activities (SOD, CAT, and GSH-Px) were noted in the BBLNP-treated group. Subsiding of inflammatory markers (TNF-α, IL-18, IL-6, TRL-4, CD-8, NLRP3, and caspase 1) and upregulation of tight-junction-related genes (occludin and JAM) was detected in BBLNPs. Administration of BBLNPs remarkably resulted in a higher level of SCFAs which parrel with colonic upregulation of GPR41 and GPR43 expression compared to DSS-treated rats. Notable modulation of autophagy-related genes (p62, mTOR, LC3, and Beclin-1) was identified post BBLNP treatment. The mRNA expressions of p62 and mTOR were significantly downregulated, while LC3 and Beclin-1 were upregulated after prophylactic treatment with BBLNPs. Immune-stained labeled cells showed lower expression of IL-1β and higher expression levels of GPR43 in BBLNPs compared to the DSS-induced group. The intestinal damage caused by DSSwas effectively mitigated by oral BBLNP treatment, as supported by the restoration of healthy colonic tissue architecture. The findings suggest that BBLNPs have a promising avenue in the remission of IBD by modulating inflammation, oxidative stress, microbial metabolites such as SCFAs, and autophagy.

Precision Dietary Intervention: Gut Microbiome and Meta-metabolome as Functional Readouts

Gut microbiome, the group of commensals residing within the intestinal tract, is closely associated with dietary patterns by interacting with food components. The gut microbiome is modifiable by the diet, and in turn, it utilizes the undigested food components as substrates and generates a group of small molecule-metabolites that addressed as "meta-metabolome" in this review. Profiling and mapping of meta-metabolome could yield insightful information at higher resolution and serve as functional readouts for precision nutrition and formation of personalized dietary strategies. For assessing the meta-metabolome, sample preparation is important, and it should aim for retrieval of gut microbial metabolites as intact as possible. The meta-metabolome can be investigated via untargeted and targeted meta-metabolomics with analytical platforms such as nuclear magnetic resonance spectroscopy and mass spectrometry. Employing flux analysis with meta-metabolomics using available database could further elucidate metabolic pathways that lead to biomarker discovery. In conclusion, integration of gut microbiome and meta-metabolomics is a promising supplementary approach to tailor precision dietary intervention. In this review, relationships among diet, gut microbiome, and meta-metabolome are elucidated, with an emphasis on recent advances in alternative analysis techniques proposed for nutritional research. We hope that this review will provide information for establishing pipelines complementary to traditional approaches for achieving precision dietary intervention.

Energy metabolism and the intestinal barrier: implications for understanding and managing intestinal diseases

The interplay between energy metabolism and the gut barrier is crucial for maintaining intestinal physiological homeostasis. Energy metabolism and the intestinal barrier perform distinct yet complementary roles that uphold intestinal ecological equilibrium. Disruptions in energy metabolism can compromise the integrity of the intestinal barrier; for example, inactivation of the AMPK pathway may lead to reduced expression of proteins associated with tight junctions. Conversely, impairment of the intestinal barrier can result in metabolic dysregulation, such as alterations in the gut microbiota that impede the production of short-chain fatty acids (SCFAs), which are essential substrates for energy metabolism. This disruption can affect energy production and modify the gut's hypoxic environment. Imbalances in these systems have been associated with the onset of various intestinal diseases. Research indicates that dietary interventions, such as a low FODMAP diet, can enhance the colonization of probiotics and improve the fermentation metabolism of SCFAs. Pharmacological strategies to elevate SCFA levels can activate the AMPK pathway and rectify abnormalities in energy metabolism. This review provides a comprehensive summary of recent advancements in elucidating the interactions between energy metabolism and the intestinal barrier.

Transcriptome analysis reveals the molecular mechanism of γ-linolenic acid eradicating the biofilm of vancomycin-resistant Enterococcus faecium

Introduction

Vancomycin-resistant Enterococcus faecium (VRE-fm) biofilms pose a significant clinical challenge due to the limited effectiveness of traditional antibiotics. This study investigates the potential of γ-linolenic acid (GLA) as a novel antibiofilm agent.

Methods

Transcriptome analysis was performed on the V27 isolate, comparing cells in mature biofilms treated with and without GLA. The findings were further validated using qRT-PCR on six VRE-fm isolates and two E. faecalis isolates.

Results

Transcriptome analysis revealed a significant downregulation in the expression levels of genes associated with biofilm formation, including fruA, fruB, sgrA, lpxtg-cwa, tfpp, lafA, lafB, malP, fsrA, and fsrC', while a significant upregulation was observed in the expression of fsrBD. Validation by qRT-PCR in six VRE-fm isolates confirmed the significant changes in the expression levels of all genes except for lpxtg-cwa, with statistical significance. The expression of bgsB and bgsA genes, which are the homologs of lafA and lafB genes, along with the Fsr-regulated genes gelE and sprE in E. faecalis, were also found to be downregulated by GLA. In addition, KEGG analysis identified specific metabolic pathways that were significantly downregulated by GLA.

Conclusion

GLA effectively targets multiple aspects of biofilm formation in VRE-fm, including the downregulation of key biofilm-related genes, the inhibition of quorum sensing systems, and the modulation of metabolic pathways. GLA emerges as a promising candidate for eradicating Enterococcus biofilms.

Codonopsis pilosula polysaccharide alleviates ulcerative colitis by modulating gut microbiota and SCFA/GPR/NLRP3 pathway

ETHNOPHARMACOLOGICAL RELEVANCE

Codonopsis pilosula (Franch.) Nannf. (CP) is a Chinese herb commonly used in traditional Chinese medicine to treat ulcerative colitis (UC). C. pilosula polysaccharide (CPPS) is an important bioactive compound in CP. Polysaccharides are degraded by and interact with the gut microbiota, exerting therapeutic effects. However, the mechanism of action of CPPS in treating UC by regulating gut microbiota is unclear.

AIM OF THE STUDY

This study aimed to elucidate the therapeutic efficacy of CPPS on UC mice and its mechanism of action.

MATERIALS AND METHODS

Size-exclusion chromatography with multi-angle laser-light scattering and refractive index analysis was employed to ascertain the molecular weight of CPPS, while its monosaccharide composition was determined using ion chromatography. An experimental colitis mouse model was induced by administering 3% (dextran sulfate sodium) DSS in drinking water for five consecutive days. Three doses of CPPS were administered to evaluate their therapeutic effects on UC. CPPS was administered for seven days, and salicylazosulfapyridine was used as a positive control. Inflammatory cytokine secretion in the colon tissue was measured, and histopathological evaluation was performed on colon sections. Alterations in the abundance of the intestinal microbiota species were also analyzed. We then quantified short-chain fatty acids (SCFAs) in the cecal content and verified the G protein-coupled receptor (GPR)/nucleotide-binding oligomerization domain-like receptor protein 3 (NLRP3) pathways using Western blot. Furthermore, the ameliorative effect of gut microbiota on DSS-induced UC symptoms was verified using the fecal microbiota transplantation (FMT) experiment.

RESULTS

CPPS comprised of rhamnose, arabinose, galactose, glucose, and galacturonic acid. CPPS significantly alleviated DSS-induced UC. Compared to the DSS group, CPPS treatment significantly increased the ratio of the Firmicutes to the Bacteroidetes and upregulated the abundance of beneficial bacteria such as g__Ligilactobacillus, g_Akkermansia, g_Faecalibaculum, g_Odoribacter. The release of acetic acid and butyric acid were further promoted. CPPS can inhibit NLRP3 activation by binding SCFAs to GPR proteins, thereby reducing intestinal inflammation. FMT confirmed that the gut microbiota in the CPPS-trans group sufficiently mitigated DSS-induced UC symptoms.

CONCLUSIONS

CPPS ameliorates the symptoms of DSS-induced UC primarily through the gut microbiota modulation and SCFA/GPR/NLRP3 pathways, making it a promising candidate for UC treatment.

Dietary content and eating behavior in ulcerative colitis: a narrative review and future perspective

Ulcerative colitis (UC) has experienced a steady increase in global incidence and prevalence recently. Current research into UC pathogenesis focuses on the complex interplay of genetic and environmental factors with the immune system and gut microbiome, leading to disruption of the intestinal barrier. Normally, the microbiome, intestinal epithelium, and immune system interact to maintain intestinal homeostasis. However, when this equilibrium is disturbed, a harmful cycle of dysbiosis, immune dysregulation, and inflammation emerges, resulting in intestinal barrier dysfunction and UC progression. Among various risk factors, diet significantly influences epithelial barrier integrity and architectural stability through both direct and indirect mechanisms, shaping the entire UC continuum from pre-clinical prevention to active phase treatment and remission maintenance. This review provides insights into the impact of dietary content and eating behaviors on UC, focusing on specific food, food groups, nutrients, and intermittent fasting, while providing a detailed explanation of why the gut microbiota may mediate the sustained effects of diet across all stages of UC. Additionally, it addresses the limitations of current studies, explores underexamined areas in UC dietary research and proposes potential directions for future research and expansion.

Type 5 Resistant Starch Can Effectively Alleviate Experimentally Induced Colitis in Mice by Modulating Gut Microbiota

Resistant starch (RS) has been shown to modulate intestinal microbiota in animal models in ways that could reduce the effects of dysbiosis-related diseases. However, the mechanism of how this is achieved is not understood. The present study aimed to reveal the mechanism of how RS mitigates dextran sulfate sodium (DSS)-induced colitis in mice by using a starch-lipid complex (RS type 5), with an RS type 2 from high-amylose maize starch as a comparison. Both RS5 and RS2 induced changes in the diversity and composition of the gut bacteria, leading to the alleviation of the induced colitis symptoms including decreasing the loss in body weight, disease activity index score, and colonic shortening. The levels of inflammatory cytokines were modulated and accompanied by an increase in goblet cell numbers and thickening of the intestinal mucus layer. RS5 was more effective, compared to RS2, in alleviating all of the colitis symptoms, mainly through improving the gut microflora dysbiosis and stimulating the generation of short-chain fatty acids (SCFAs). Our study shows that RS5 could effectively alleviate the symptoms of colitis, highlighting a potential use for RS5, particularly in relieving inflammatory bowel disease.

Sesamin Alleviates Allergen-Induced Diarrhea by Restoring Gut Microbiota Composition and Intestinal Barrier Function

Food allergens are the key triggers of allergic diarrhea, causing damage to the immune-rich ileum. This weakens the mucosal barrier and tight junctions, increases intestinal permeability, and exacerbates allergen exposure, thereby worsening the condition. Sesamin, a natural lignan isolated from sesame seed, has shown potential in regulating immune responses, but its effects on intestinal health remain unclear. In this study, we constructed an ovalbumin (OVA)-induced allergic diarrhea mouse model, which demonstrated increased mast cell degranulation, reduced tight junction integrity, and impaired intestinal barrier function. Pro-inflammatory cytokines were significantly increased in the ileum, along with unbalanced cluster of differentiation 4 (CD4+) T-cell immunity, altered gut microbiota composition, and disrupted bacterial metabolism. Sesamin treatment significantly alleviated intestinal damage by modulating gut microbiota abundance, enhancing short-chain fatty acid (SCFA) production, and increasing SCFA receptor expression. This study suggests that sesamin may be a promising therapeutic candidate for allergic diarrhea and intestinal injury.

Appendectomy and the risk of microscopic colitis - A systematic review and meta-analysis

BACKGROUND

Microscopic colitis (MC), a chronic intestinal inflammatory disorder characterised by persistent watery diarrhoea, is categorised into collagenous and lymphocytic subtypes. Recent studies suggest that appendectomy influences the risk of MC, although the evidence remains inconclusive. This meta-analysis of available research was conducted to clarify the relationship between appendectomy and MC risk.

METHODS

In accordance with the PRISMA guidelines, a comprehensive search was conducted in the Web of Science, EMBASE, and PubMed up to January 2024, focusing on studies that explored the association between appendectomy and MC. Quality was assessed using the Newcastle-Ottawa Scale, with data synthesis using the DerSimonian and Laird random-effects model. Heterogeneity and potential biases were evaluated; subgroup analyses were performed to investigate specific associations.

RESULTS

Six studies were analysed, including one cohort and five case-control studies involving 85,845 participants. The combined analysis showed no significant link between appendectomy and MC risk (OR: 1.20, 95% CI: 0.91-1.58), despite moderate heterogeneity (I² = 59%). Subgroup analyses indicated potential associations in specific contexts. Notably, significant associations were found in subgroups based on MC subtypes (CC: OR 1.59, 95% CI: 1.20-2.10; LC: OR 1.45, 95% CI: 1.34-1.58), unadjusted ORs (OR 1.42, 95% CI: 1.17-1.73), healthy control groups (OR 1.51, 95% CI: 1.38-1.67) and studies using medical records for appendectomy history (OR 1.50, 95% CI: 1.28-1.75). Other subgroup analyses did not yield significant results.

CONCLUSION

This meta-analysis did not support a significant association between appendectomy and increased risk of MC. These findings highlight the need for further large-scale, prospective studies to explore this relationship in greater detail, considering the potential for nuanced interactions and the impacts of various confounding factors.

A systematic review on gut microbiota in type 2 diabetes mellitus

Aims/hypothesis

The gut microbiota play crucial roles in the digestion and degradation of nutrients, synthesis of biological agents, development of the immune system, and maintenance of gastrointestinal integrity. Gut dysbiosis is thought to be associated with type 2 diabetes mellitus (T2DM), one of the world's fastest growing diseases. The aim of this systematic review is to identify differences in the composition and diversity of the gut microbiota in individuals with T2DM.

Methods

A systematic search was conducted to identify studies reporting on the difference in gut microbiota composition between individuals with T2DM and healthy controls. Relevant studies were evaluated, and their characteristics and results were extracted using a standardized data extraction form. The studies were assessed for risk of bias and their findings were reported narratively.

Results

58 observational studies published between 2010 and 2024 were included. Beta diversity was commonly reported to be different between individuals with T2DM and healthy individuals. Genera Lactobacillus, Escherichia-Shigella, Enterococcus, Subdoligranulum and Fusobacteria were found to be positively associated; while Akkermansia, Bifidobacterium, Bacteroides, Roseburia, Faecalibacteirum and Prevotella were found to be negatively associated with T2DM.

Conclusions

This systematic review demonstrates a strong association between T2DM and gut dysbiosis, as evidenced by differential microbial abundances and altered diversity indices. Among these taxa, Escherichia-Shigella is consistently associated with T2DM, whereas Faecalibacterium prausnitzii appears to offer a protective effect against T2DM. However, the heterogeneity and observational nature of these studies preclude the establishment of causative relationships. Future research should incorporate age, diet and medication-matched controls, and include functional analysis of these gut microbes.

Systematic review registration

https://www.crd.york.ac.uk/prospero/, identifier CRD42023459937.

Deer oil improves ulcerative colitis induced by DSS in mice by regulating the intestinal microbiota and SCFAs metabolism and modulating NF-κB and Nrf2 signaling pathways

BACKGROUND

Deer oil (DO), a byproduct of deer meat processing, possesses high nutritional value. This study aims to evaluate the protective effects of DO on dextran sulfate sodium (DSS)-induced ulcerative colitis (UC) in mice and to explore its potential mechanisms of action.

RESULTS

DO was found to inhibit weight loss and colon shortening in colitis mice, significantly reduce disease activity index scores, and notably enhance the levels of tight junction proteins in colon tissues, thus improving intestinal barrier function. ELISA results indicated that DO markedly alleviated the mice's oxidative stress and inflammatory responses. Western blot analysis further demonstrated that DO significantly inhibited the phosphorylation of NF-κB while up-regulating the expression levels of Nrf2 and HO-1 proteins. Additionally, DO increased the abundance of beneficial bacteria such as Odoribacter, Blautia, and Muribaculum, reduced the abundance of harmful bacteria such as Bacteroides, Helicobacter, and Escherichia-Shigella, and promoted the production of short-chain fatty acids.

CONCLUSION

Our study provides the first evidence that DO can effectively improve DSS-induced UC in mice. The underlying mechanisms may involve maintaining intestinal barrier function, inhibiting inflammation, alleviating oxidative stress, and modulation of gut microbiota. These findings offer valuable insights for developing DO as an adjunct treatment for UC and as a functional food. © 2024 Society of Chemical Industry.

Prolonged storage reduces viability of Peptacetobacter (Clostridium) hiranonis and core intestinal bacteria in fecal microbiota transplantation preparations for dogs

Introduction

Fecal microbiota transplantation (FMT) has been described useful as an adjunct treatment for chronic enteropathy in dogs. Different protocols can be used to prepare and store FMT preparations, however, the effect of these methods on microbial viability is unknown. We aimed (1) to assess the viability of several core intestinal bacterial species by qPCR and (2) to assess Peptacetobacter (Clostridium) hiranonis viability through culture to further characterize bacterial viability in different protocols for FMT preparations.

Methods

Bacterial abundances were assessed in feces from six healthy dogs by qPCR after propidium monoazide (PMA-qPCR) treatment for selective quantitation of viable bacteria. Conservation methods tested included lyophilization (stored at 4°C and at -20°C) and freezing with glycerol-saline solution (12.5%) and without any cryoprotectant (stored at -20°C). Additionally, the abundance of P. hiranonis was quantified using bacterial culture.

Results

Using PMA-qPCR, the viability of Faecalibacterium, Escherichia coli, Streptococcus, Blautia, Fusobacterium, and P. hiranonis was reduced in lyophilized fecal samples kept at 4°C and -20°C up to 6 months (p < 0.05). In frozen feces without cryoprotectant, only Streptococcus and E. coli were not significantly reduced for up to 3 months (p > 0.05). Lastly, no differences were observed in the viability of those species in glycerol-preserved samples up to 6 months (p > 0.05). When using culture to evaluate the viability of P. hiranonis, we observed that P. hiranonis abundance was lower in lyophilized samples kept at 4°C than -20°C; and P. hiranonis abundance was higher in glycerol-preserved samples for up to 6 months than in samples preserved without glycerol for up to 3 months. Moreover, the highest abundance of P. hiranonis was observed in glycerol-preserved feces. After 3 months, P. hiranonis was undetectable by culture in 83% (5/6) of the frozen samples without glycerol.

Discussion

While the lyophilization procedure initially reduced P. hiranonis abundance, P. hiranonis viability was stable thereafter for up to 6 months at -20°C. The higher bacterial viability detected in fecal samples preserved with glycerol confirms the use of this cryoprotectant as a reliable method to keep bacteria alive in the presence of fecal matrix for FMT purposes.

Understanding the role of the gut microbiome in solid tumor responses to immune checkpoint inhibitors for personalized therapeutic strategies: a review

Immunotherapy, especially immune checkpoint inhibitor (ICI) therapy, has yielded remarkable outcomes for some patients with solid cancers, but others do not respond to these treatments. Recent research has identified the gut microbiota as a key modulator of immune responses, suggesting that its composition is closely linked to responses to ICI therapy in cancer treatment. As a result, the gut microbiome is gaining attention as a potential biomarker for predicting individual responses to ICI therapy and as a target for enhancing treatment efficacy. In this review, we discuss key findings from human observational studies assessing the effect of antibiotic use prior to ICI therapy on outcomes and identifying specific gut bacteria associated with favorable and unfavorable responses. Moreover, we review studies investigating the possibility of patient outcome prediction using machine learning models based on gut microbiome data before starting ICI therapy and clinical trials exploring whether gut microbiota modulation, for example via fecal microbiota transplantation or live biotherapeutic products, can improve results of ICI therapy in patients with cancer. We also briefly discuss the mechanisms through which the gut microbial-derived products influence immunotherapy effectiveness. Further research is necessary to fully understand the complex interactions between the host, gut microbiota, and immunotherapy and to develop personalized strategies that optimize responses to ICI therapy.

A specific blend of prebiotics and postbiotics improved the gut microbiome of dogs with soft stools in the in vitro Simulator of the Canine Intestinal Microbial Ecosystem

The Simulator of the Canine Intestinal Microbial Ecosystem (SCIME) allows for the study of the long-term effects of food, supplements, or ingredients on the canine gut microbiome in a simulated proximal and distal colon. This model has been used to evaluate the impact of repeated administration of a test product blend composed of a mixture of baobab fruit pulp, acacia gum, heat-killed Lactobacillus helveticus HA-122, and specific fractions of selected inactivated yeast strains (including Saccharomyces cerevisiae AQP 12260 and AQP 12988 and Cyberlindnera jadinii AQP 12549), on the activity and composition of the gut microbiome of canine donors with soft stools. The SCIME colonic reactors were inoculated with fecal material from 3 different canine donors. After 2 d of stabilization, the 8-d parallel control/treatment period was initiated; reactors were fed with SCIME nutritional medium with or without test product. Changes in microbial metabolic activity were assessed by measuring levels of acetate, propionate, butyrate, lactate, branched short-chain fatty acids, and ammonium. Changes in microbial community composition were assessed using 16S-targeted Illumina sequencing. Overall, test product supplementation resulted in increased saccharolytic fermentation, as evidenced by increases in the health-promoting bacterial metabolites such as propionate (donor-dependent), acetate, and butyrate (donor-dependent) as well as increased abundances of several saccharolytic fermenting microbes, including Bifidobacterium. Conversely, proteolytic bacteria like Proteobacteria were reduced with the test product compared to control. Repeated supplementation with the test product was therefore able to induce-in vitro-a positive modulation of the microbiome originated from dogs with soft stools.

In vitro fermentation characteristics of dietary fibers using fecal inoculum from dogs consuming commercial or grain kefir

Traditional grain kefir is produced from the fermentation of milk with yeast- and bacteria-containing cultures. To maintain consistency and adhere to food safety guidelines, commercial kefir products are based on starter bacterial cultures. Bacterial profiles of starter vs. grain kefirs differ, and their influence on health effects is unknown. Our objectives were to determine the in vitro fermentation characteristics of common dietary fibers using fecal inoculum from dogs supplemented with kefir or kefir bacterial culture as inoculum. Healthy adult dogs were allotted to one of 3 treatments and supplemented for 14 d (n = 4/treatment): 1) 2% reduced-fat milk treated with lactase (CNTL), 2) starter kefir (S-Kefir), or 3) grain kefir (G-Kefir). After 14 d, fresh fecal samples were collected and frozen in a 20% glycerol solution. For the in vitro experiment, fecal samples were thawed, diluted in an anaerobic diluting solution, and used to inoculate tubes containing semi-defined medium and either cellulose (CEL), pectin (PC), beet pulp (BP), or chicory pulp (CP). Tubes were incubated for 0, 6, 12, or 18 h, with short-chain fatty acids (SCFA), pH, and microbiota measured at each time point. A second in vitro experiment was conducted using similar methods and measurements but with S-Kefir and G-Kefir as inoculum sources. Effects of treatment (inoculum), time, and treatment*time interactions within the fiber source were analyzed statistically using Mixed Models and repeated measures, with P < 0.05 being significant. Using fecal inoculum, BP and PC were rapidly fermented, leading to large pH reductions, SCFA increases, and microbiota shifts. pH change was of greater (P < 0.05) magnitude (PC) and higher (P < 0.05) kinetic rate (CP) when using feces from dogs fed S-Kefir or G-Kefir than controls. Butyrate increases were greater (P < 0.05) in tubes inoculated with G-Kefir feces than in S-Kefir or control feces. When PC and BP were fermented, tubes with S-Kefir feces had greater (P < 0.05) acetate, propionate, and total SCFA increases than G-Kefir or control feces. Fermentations were slower when using kefir cultures as inoculum, but some differences were noted. Bacterial beta diversity and relative abundances shifted over time within each substrate and were unique to the inoculum source. Our data suggest that the activity of kefir bacterial populations differs and that kefir consumption changes the abundance and activity of the fecal microbiota of dogs, justifying in vivo investigation.