@article {pmid40926100,
year = {2025},
author = {Gibson, TE and Kim, Y and Acharya, S and Kaplan, DE and DiBenedetto, N and Lavin, R and Berger, B and Allegretti, JR and Bry, L and Gerber, GK},
title = {Learning ecosystem-scale dynamics from microbiome data with MDSINE2.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40926100},
issn = {2058-5276},
support = {BRICS HR0011-15-C-0094//United States Department of Defense | Defense Advanced Research Projects Agency (DARPA)/ ; R01GM130777//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R35GM149270//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R35GM143056//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R21AI154075//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R35GM141861//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; P30DK056338//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; MTM2 2025512//National Science Foundation (NSF)/ ; },
abstract = {Although dynamical systems models are a powerful tool for analysing microbial ecosystems, challenges in learning these models from complex microbiome datasets and interpreting their outputs limit use. We introduce the Microbial Dynamical Systems Inference Engine 2 (MDSINE2), a Bayesian method that learns compact and interpretable ecosystems-scale dynamical systems models from microbiome timeseries data. Microbial dynamics are modelled as stochastic processes driven by interaction modules, or groups of microbes with similar interaction structure and responses to perturbations, and additionally, noise characteristics of data are modelled. Our open-source software package provides multiple tools for interpreting learned models, including phylogeny/taxonomy of modules, and stability, interaction topology and keystoneness. To benchmark MDSINE2, we generated microbiome timeseries data from two murine cohorts that received faecal transplants from human donors and were then subjected to dietary and antibiotic perturbations. MDSINE2 outperforms state-of-the-art methods and identifies interaction modules that provide insights into ecosystems-scale interactions in the gut microbiome.},
}

@article {pmid40925203,
year = {2025},
author = {Kapoor, B and Gulati, M},
title = {Gut microbiome and rheumatoid arthritis: Revisiting the gut-joint axis.},
journal = {International immunopharmacology},
volume = {165},
number = {},
pages = {115503},
doi = {10.1016/j.intimp.2025.115503},
pmid = {40925203},
issn = {1878-1705},
abstract = {Over the past few decades, the scientific perspective on gut microbiota has undergone a profound transformation, particularly with the emergence and advancement of microbiome research. Next-generation sequencing technologies have emerged as a foundational tool in microbiome research, facilitating comprehensive characterization of microbial communities across diverse sample types and ecological niches. Significant alterations in gut microbiota composition have been observed in disease states compared to healthy individuals, suggesting a direct association between gut dysbiosis and host health status. Initially, alterations in gut microbiota were primarily thought to be associated with gastrointestinal disorders. With advancing research, however, it has become evident that gut dysbiosis is also implicated in a broad spectrum of extra-intestinal conditions, including neurological, dermatological, metabolic, and musculoskeletal diseases. The present review provides a comprehensive analysis of preclinical and clinical studies elucidating the role of gut dysbiosis in the pathogenesis and progression of rheumatoid arthritis. Advancements in the understanding of the gut-joint axis have facilitated the development of novel therapeutic modalities, including probiotics, prebiotics, synbiotics, and fecal microbiota transplantation, that have been comprehensively discussed in present review.},
}

@article {pmid40925130,
year = {2025},
author = {Sahu, KK and Yadav, K and Pradhan, M and Sharma, M and Dubey, A and Sucheta, and Kirubakaran, JJ},
title = {Pharmacological insights into gut microbiota modulation in systemic lupus erythematosus: Mechanisms, treatment strategies, and clinical implications.},
journal = {The Journal of pharmacology and experimental therapeutics},
volume = {392},
number = {9},
pages = {103659},
doi = {10.1016/j.jpet.2025.103659},
pmid = {40925130},
issn = {1521-0103},
abstract = {Systemic lupus erythematosus (SLE) is a complex autoimmune disease characterized by widespread inflammation and immune system dysregulation. Recent research suggests that the gut microbiota may play a role in the development of SLE by modulating immune system responses, affecting cytokine production, and altering the activity of T and B cells lymphocytes. As a result, there is a growing interest in microbiota-targeted therapies, including probiotics, dietary changes, and fecal microbiota transplantation. These methods may help restore the balance of microbes and reduce disease activity, but there are still a number of problems to solve. For example, microbiota composition varies greatly from person to person, and it is not clear how dysbiosis causes disease onset. There are also safety concerns about fecal microbiota transplantation. Experimental and clinical studies have started to shed light on the complicated ways in which microbial communities and immune function affect each other in SLE. These studies provide useful information, but their results are often inconsistent. As research continues, integrative methods like metagenomics and metabolomics may help find microbial signatures linked to disease, helping create more accurate and personalized treatments. The gut microbiome is a promising yet still developing area of research that could help us learn more about autoimmune diseases and their treatment, such as SLE. SIGNIFICANCE STATEMENT: Grasping the complex interplay between gut microbiota and systemic lupus erythematosus (SLE) has provided an avenue for therapeutic intervention. This study emphasizes the importance of gut dysbiosis in immune dysregulation, with connections between microbial translocation, molecular mimicry, and inflammatory pathways as contributing factors to the progression of SLE. This work sets the stage for novel and targeted approaches to treating SLE and improving patient outcomes by investigating microbiota-centric treatment options, such as probiotics, dietary interventions, and fecal microbiota transplantation.},
}

@article {pmid40923448,
year = {2025},
author = {He, MC and Ferrini, A and Parvizi, J},
title = {Periprosthetic joint infection: Time to think outside the box.},
journal = {Knee surgery, sports traumatology, arthroscopy : official journal of the ESSKA},
volume = {},
number = {},
pages = {},
doi = {10.1002/ksa.70056},
pmid = {40923448},
issn = {1433-7347},
abstract = {Despite undisputed success of orthopaedic procedures, surgical site infections (SSI) such as periprosthetic joint infection (PJI) continues to compromise the outcome and result in major clinical and economic burden. The overall rate of infection is expected to rise in the future resulting in significant associated mortality and morbidity. Traditional concepts have largely attributed the source of PJI to exogenous pathogens. However, recent studies indicate that pathogens from the patient's own microbiome, colonizing the skin, nasal passages, gut microbiota, and even the surgical site play a major role in causing SSIs. Immune cell-mediated 'Trojan Horse' pathways have been posited as the mechanism of how bacteria reach and persist at the surgical site. In light of these developing insights, novel therapeutic strategies are under investigation. Some exciting developments include the use of membrane-permeable antibiotics, bacteriophage therapy targeting intracellular pathogens as well as probiotics, prebiotics, or faecal microbiota transplantation. Overall, targeting the endogenous microbiome represents a promising frontier for improving the prevention and management of PJI in the era of rapidly increasing total joint arthroplasty procedures.},
}

@article {pmid40920777,
year = {2025},
author = {Nendl, A and Raju, SC and Braadland, PR and Nordborg, A and Bratseth, V and Broch, K and Jørgensen, SF and Aukrust, P and Kristiansen, K and Hov, JR and Trøseid, M and Awoyemi, A},
title = {Circulating metabolites in patients with chronic heart failure are not related to gut leakage or gut dysbiosis.},
journal = {PloS one},
volume = {20},
number = {9},
pages = {e0331692},
doi = {10.1371/journal.pone.0331692},
pmid = {40920777},
issn = {1932-6203},
mesh = {Humans ; *Dysbiosis/blood/microbiology/metabolism ; *Heart Failure/blood/microbiology/metabolism/physiopathology ; Male ; Female ; *Gastrointestinal Microbiome ; Middle Aged ; Aged ; Feces/microbiology ; Chronic Disease ; Case-Control Studies ; Metabolomics ; Metabolome ; },
abstract = {BACKGROUND: The gut microbiota produces numerous metabolites that can enter the circulation and exert effects outside the gut. Several studies have reported altered gut microbiota composition and circulating metabolites in patients with chronic heart failure (HF) compared to healthy controls. Limited data is available on the interplay between dysbiotic features of the gut microbiota and altered circulating metabolites in HF patients. We aimed to examine differences in circulating metabolites between people with and without chronic HF, and their association with gut microbiota dysbiosis and cardiac function.

METHODS: We collected plasma, serum, and stool samples from 123 adult patients with stable chronic HF and left ventricular ejection fraction (LVEF) ≤40%, and healthy controls (plasma: n = 51, stool samples: n = 69). Metabolomic and lipidomic profiling of plasma was performed using liquid chromatography with tandem mass spectrometry. Principal component analysis was used to explore differences in circulating profiles. Over-representation analysis was performed to identify pathways in which relevant metabolites were involved. Stool samples were sequenced using shotgun metagenomics. We calculated a dysbiosis index based on differential abundances of microbial taxa in patients vs. controls.

RESULTS: After adjusting for age, sex, and sampling location, we identified 67 enriched metabolites and 24 enriched lipids, and 115 depleted metabolites and 6 depleted lipids in HF patients compared to healthy controls. LVEF, N-terminal pro B-type natriuretic peptide, gut leakage markers, dysbiosis index, and fiber intake were not significantly related to any of the differentially abundant metabolites or lipids. Pathways related to energy metabolism differed most between HF patients and controls, however medication adjustment abolished all differences in circulating profiles.

CONCLUSIONS: Patients with chronic HF had distinct metabolomic and lipidomic profiles and energy metabolism differed significantly compared to healthy controls before adjusting for medication use. However, the alterations were not related to gut dysbiosis, gut leakage markers, cardiac function, or fiber intake.},
}

Humans
*Dysbiosis/blood/microbiology/metabolism
*Heart Failure/blood/microbiology/metabolism/physiopathology
Male
Female
*Gastrointestinal Microbiome
Middle Aged
Aged
Feces/microbiology
Chronic Disease
Case-Control Studies
Metabolomics
Metabolome

@article {pmid40919202,
year = {2025},
author = {Liu, W and Cheng, Y and Han, X and Xia, J and Wei, Q and Chang, B and Li, Q},
title = {Rivaroxaban alleviates hepatic sinusoidal obstruction syndrome in mice by modulating the gut microbiota and inhibiting the PI3K/Akt signaling pathway.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1607131},
pmid = {40919202},
issn = {1664-302X},
abstract = {INTRODUCTION: Hepatic sinusoidal obstruction syndrome (HSOS) is a vascular liver disease with a high mortality rate, and treatment methods are limited. Rivaroxaban is an oral anticoagulant. This study aimed to investigate the pharmacological effect and potential mechanism of rivaroxaban on HSOS.

METHODS: In this study, we induced an HSOS mouse model in male C57BL/6J mice by administering monocrotaline orally. The mice were randomly divided into four groups: the control group, the rivaroxaban (RIV) group, the monocrotaline (MCT) group, and the monocrotaline + rivaroxaban (MCT + RIV) group. Liver function and histopathology were evaluated. 16S rDNA sequencing of the small intestinal contents, transcriptomic sequencing of small intestine tissues, real-time qPCR, Western blot analysis of liver tissues, and correlation analysis were conducted. Antibiotic (ABX) treatment and fecal microbiota transplantation (FMT) experiments were also performed to explore the role of the gut microbiota.

RESULTS: Compared with the MCT group, rivaroxaban alleviated serum biochemical liver function analysis and liver histopathology in the MCT + RIV group. Additionally, 16S rDNA sequencing of the small intestinal contents revealed that, compared with the MCT group, the MCT + RIV group presented increased relative abundances of Allobaculum and Pediococcus but decreased relative abundances of Streptococcus, Staphylococcus, and Candidatus Arthromitus. Mechanistically, integrated analyses, including transcriptomic sequencing of small intestin e tissues, real-time qPCR, Western blot analysis of liver tissues, and correlation analysis, demonstrated that rivaroxaban protected against MCT-HSOS by inhibiting the PI3K/Akt signaling pathway. In addition, antimicrobial cocktail (ABX) treatment eliminated the beneficial effects of rivaroxaban on liver function and histopathological injury, whereas fecal microbiota transplantation (FMT) from rivaroxaban-treated donors significantly ameliorated liver dysfunction and histological damage in MCT-HSOS mice.

DISCUSSION: These findings suggest that rivaroxaban alleviates hepatic sinusoidal obstruction syndrome in mice by modulating the gut microbiota and inhibiting the PI3K/Akt signaling pathway. Rivaroxaban may be a promising therapeutic option for treating HSOS.},
}

@article {pmid40917756,
year = {2025},
author = {Vescovo, T and Bontempi, G and Bayat, M and Piredda, L and Fidaleo, M and Strippoli, R and Antonioli, M},
title = {Gut microbiota interplay with autophagy-EMT dynamics in colorectal cancer.},
journal = {Frontiers in cell and developmental biology},
volume = {13},
number = {},
pages = {1608248},
pmid = {40917756},
issn = {2296-634X},
abstract = {The human microbiota is composed of a complex community of microorganisms essential for maintaining host homeostasis, especially in the gastrointestinal tract. Emerging evidence suggests that dysbiosis is linked to various cancers, including colorectal cancer (CRC). The microbiota contributes to CRC development and progression by influencing inflammation, genotoxic stress, and key cell growth, proliferation, and differentiation pathways. Certain bacterial species, including Fusobacterium nucleatum and Escherichia coli, play a role in tumorigenesis by facilitating epithelial-mesenchymal transition (EMT), perturbing autophagy, and supporting immune evasion. In contrast, beneficial microorganisms such as Bifidobacterium and Lactobacillus provide protective effects by boosting immune surveillance and supporting the integrity of the intestinal barrier. This review examines the complex connection between gut microbiota and CRC, emphasizing how changes in microbial composition facilitate tumor development and influence treatment outcomes. We cover recent progress in microbiota-based biomarkers for CRC diagnosis and prognosis, showcasing their promise for early detection and improved patient stratification. Furthermore, we explore microbiota-focused therapeutic methods such as probiotics, prebiotics, faecal microbiota transplantation (FMT), and precision antibiotics, which show potential to complement standard CRC treatments. By highlighting the latest advancements in this area, we emphasise how microbiome research is transforming our comprehension of CRC and leading to new diagnostic and treatment approaches.},
}

@article {pmid40916806,
year = {2025},
author = {Javan, N and Ghotaslou, R and Samadi Kafil, H and Memar, MY and Sadeghi, J and Ghotaslou, P},
title = {Overcoming Multi-Drug-Resistant Klebsiella pneumoniae Infections.},
journal = {Microbial drug resistance (Larchmont, N.Y.)},
volume = {},
number = {},
pages = {},
doi = {10.1177/10766294251375937},
pmid = {40916806},
issn = {1931-8448},
abstract = {Antimicrobial resistance (AMR) is one of the most important concerns in the world, occurring for both Gram-positive and Gram-negative bacteria. Klebsiella pneumoniae (K. pneumoniae) is a Gram-negative bacterium belonging to the family of Enterobacteriaceae and also plays an important role in development of nosocomial infections. Three forms have emerged as a result of AMR including multi-drug resistant (MDR), extensively drug-resistant, and pan-drug-resistant. Nowadays, physicians cannot save most of the patients that suffer from MDR K. pneumoniae infections by typical antibiotics, so they should try other useful alternative treatments. Our aim in this review study was to search about the latest useful alternative methods against MDR K. pneumoniae infections. We collected some articles from PubMed, MEDLINE, and Google Scholar by the keywords of multi-drug-resistant K. pneumoniae, AMR, and alternative treatments, where finally 183 articles were selected. Also, inclusion criteria and exclusion criteria were identified separately. It was understood that there are novel therapeutic options against MDR K. pneumoniae infections, which include odilorhabdins, drug delivery systems, antibody drug conjugation treatments, nano-antibiotics, bacteriocins, probiotics, fecal transplant therapy, predatory bacteria, combined antibiotics, double-carbapenem therapy, synthetic lipopeptides, and phage therapy.},
}

@article {pmid40916606,
year = {2025},
author = {Piwchan, S and Aumpan, N and Chonprasertsuk, S and Pornthisarn, B and Siramolpiwat, S and Bhanthumkomol, P and Nunanan, P and Issariyakulkarn, N and Wongcha-Um, A and Miftahussurur, M and Mahachai, V and Yamaoka, Y and Vilaichone, RK},
title = {Fecal Microbiota Transplantation by Rectal Enema Improves Short-Term Insulin Resistance in Metabolic Syndrome: A Pilot Randomized Controlled Trial.},
journal = {Journal of obesity & metabolic syndrome},
volume = {},
number = {},
pages = {},
doi = {10.7570/jomes25014},
pmid = {40916606},
issn = {2508-7576},
abstract = {BACKGROUND: The gut microbiota plays a vital role in various physiological processes, including metabolism. Fecal microbiota transplantation (FMT) involves transferring fecal matter from a healthy donor to rebalance a patient's intestinal dysbiosis. The impact of FMT on metabolic syndrome (MetS) is subject to debate. This study assesses the effects of FMT on MetS when administered by rectal enema.

METHODS: In a double-blind, randomized controlled trial, subjects with MetS were assigned to receive either FMT (n=8) or a sham intervention (n=10) via rectal enema. Participants were followed at 6 and 12 weeks. The primary outcome was changes in the homeostatic model assessment of insulin resistance (HOMA-IR). Secondary outcomes included fasting blood glucose (FBG), body mass index (BMI), inflammatory markers, and hepatic steatosis. The mean adjusted difference (MAD) and 95% confidence interval (CI) between groups were reported as treatment effects using a linear marginal model for repeated measures.

RESULTS: The study included patients with a mean age of 50.4±10.7 years. Baseline BMI and HOMA-IR were similar between groups. Over 6 weeks, FMT significantly improved HOMA-IR (MAD, -1.63; 95% CI, -2.63 to -0.64; P=0.001). The FMT group also showed improvements in serum FBG and high-sensitivity C-reactive protein compared with levels in the sham group (P=0.044 and P=0.025, respectively). However, no significant changes in MetS-associated variables or liver steatosis were evident at 12 weeks. Stool microbiota analysis revealed a reduced relative abundance of Desulfovibrio, Bacteroides, and Parabacteroides after FMT.

CONCLUSION: FMT by rectal enema produced favorable changes in IR in patients with MetS. FMT may be an effective treatment for patients with metabolism-related diseases. Further research into the long-term benefits of the procedure is warranted.},
}

@article {pmid40914633,
year = {2025},
author = {Coman, T and Andreozzi, F and Bay, JO and Cornillon, J and Guillaume, T and Hamzy, F and Souchet, L and Turlure, P and Marçais, A and Dachy, F and Beguin, Y and Bulabois, CE and Daghri, S and Huynh, A and Magro, L and Chalandon, Y},
title = {[Acute graft-versus-host disease therapy: Which third line treatment after steroids and ruxolitinib? (SFGM-TC)].},
journal = {Bulletin du cancer},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bulcan.2025.05.014},
pmid = {40914633},
issn = {1769-6917},
abstract = {Acute graft-versus-host disease (GVHDa) is one of the leading causes of morbidity and mortality after allogeneic hematopoietic stem cell transplant (HSCT) patients. While the first-line consensus treatment has been based on systemic corticosteroid therapy for many years, ruxolitinib has recently been approved and has become the standard second-line treatment. Nevertheless, the effectiveness of ruxolitinib remains limited to 40 % of cortico-resistant patients, raising the crucial question of selecting a third-line treatment. Among the therapeutic modalities described, this workshop selected fecal microbiota transplantation (FMT), mesenchymal stromal cells (MSC) injection, and extracorporeal photopheresis (ECP) as the most promising or with a benefit/risk balance that favors their prescription at this stage. The workshop also highlighted the importance of research aimed at identifying markers or score calculations that guide toward a risk-adapted approach as early as possible. To date, aside from calprotectin, no marker or score is routinely used, but all are the subject of intense research. Finally, measures associated with specific treatment remain crucial, and new developments in dietary contributions, infection prophylaxis, and tissue regeneration are also addressed.},
}

@article {pmid40913864,
year = {2025},
author = {Xiang, X and Zhu, Y and Wang, T and Zhu, J and Ding, P and Cheng, K and Ming, Y},
title = {Gut microbiota and metabolites related intra-patient variability of tacrolimus pharmacokinetics predicted adverse one-year outcomes following kidney transplantation.},
journal = {International immunopharmacology},
volume = {165},
number = {},
pages = {115506},
doi = {10.1016/j.intimp.2025.115506},
pmid = {40913864},
issn = {1878-1705},
abstract = {Kidney transplantation (KT) is an effective treatment for end-stage renal disease, with over 90 % of recipients requiring lifelong tacrolimus (Tac). However, The Tac pharmacokinetics exhibit high intra-patient variability (IPV), posing significant challenges. This study included 102 KT recipients at our center from October 2022 to December 2023. Patients were stratified into high- and low-IPV groups based on the median coefficient of variation of the the Tac trough concentration-to-dose ratio during the first post-transplant month. Fecal samples were collected for 16S rRNA sequencing and untargeted metabolomics analysis, while clinical outcomes within the first year were assessed for associations with the Tac IPV. Microbiome analysis revealed significant beta diversity differences (p = 0.0451) and 19 differential taxa, including g__Clostridia_vadinBB60_group enriched in high-IPV patients and g__Clostridia_UCG_014 in the low-IPV group. Metabolomics identified 1298 differential metabolites, with 729 enriched in high-IPV patients. Network analysis highlighted cholesterol and unsaturated fatty acid biosynthesis as central pathways, while both microbial functional predictions and metabolic enrichment analyses emphasized bile secretion. A random forest model validated the classification potential of these biomarkers, and associations between differential taxa and metabolites were observed. Clinical correlation analysis indicated the high Tac IPV as an independent protective factor against post-transplant hyperuricemia but a positive predictor of new-onset diabetes. This study is the first to link the Tac IPV, gut microbiota, metabolism, and one-year outcomes, offering novel insights into personalized care and the mechanisms underlying the Tac IPV.},
}

@article {pmid40913709,
year = {2025},
author = {Jamal, A and Kamal, MA and Alqurashi, YE and Al-Malki, ES and Naiyer, MM and Hussain, SA and Hattiwale, HM},
title = {The microbiome-cancer axis as a hidden contributor to early-onset tumorigenesis.},
journal = {Medical oncology (Northwood, London, England)},
volume = {42},
number = {10},
pages = {464},
pmid = {40913709},
issn = {1559-131X},
mesh = {Humans ; *Neoplasms/microbiology ; *Carcinogenesis/pathology ; *Gastrointestinal Microbiome ; *Microbiota ; Dysbiosis/microbiology ; Age of Onset ; },
abstract = {The global incidence of early-onset cancer has surged by nearly 80% over the past three decades, yet the underlying causes remain poorly understood. While genetics and lifestyle are among the traditional risk factors, emerging evidence implicates the human microbiome as a potent and overlooked contributor to early tumorigenesis. Increases in the studies that are exploring the tissue-specific microbiome signatures such as the enrichment of Actinomyces and Bacteroidia in early-onset colorectal cancer, or Enterobacter and Neisseria in pancreatic tumors offer compelling evidence for age-stratified microbial contributions. Additionally, the recent works on the establishment of gut-testis, oral-gut, and gut-liver microbial axes are being explored to understand the modulation of systemic immune and endocrine landscapes in younger individuals that might unravel their unique predisposition to malignancy. Further, the microbiome-cancer axis has been regarded as a hidden driver in the initiation and progression of early-onset malignancies across diverse tissue types. Understanding this link will provide the missing mechanistic insights showcasing how microbial dysbiosis, biofilm formation, and microbially derived metabolites promote oncogenic inflammation, DNA damage, and immune evasion contributing to early-onset cancers. Considering the potential of these studies, microbial biomarkers with diagnostic promises that include probiotics, fecal microbiota transplantation, and diet have also been explored as emerging tools for prevention and therapy. Through this study, we aim to understand early-onset cancer through a patient microbiota and underscore an urgent need to integrate microbial dynamics into cancer surveillance and intervention strategies, especially for young and largely asymptomatic populations.},
}

Humans
*Neoplasms/microbiology
*Carcinogenesis/pathology
*Gastrointestinal Microbiome
*Microbiota
Dysbiosis/microbiology
Age of Onset

@article {pmid40913635,
year = {2025},
author = {Ali, AQ and Mersal, EA and Samer, R and Alhjmohammad, SA and Alabdrabalridha, ZH and Alseeni, FY and Dawood, AF and Abdel All, MO and Abdelmoneim, AM and Shawky, TM},
title = {Berberine contributes to protecting against the cadmium-induced pancreatic damage: role of intestinal microbiome modulation and barrier function.},
journal = {Journal of molecular histology},
volume = {56},
number = {5},
pages = {296},
pmid = {40913635},
issn = {1567-2387},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Berberine/pharmacology ; *Cadmium/toxicity ; Rats ; Rats, Wistar ; Male ; *Pancreas/drug effects/pathology ; Intestinal Mucosa/drug effects/metabolism/microbiology ; *Protective Agents/pharmacology ; Disease Models, Animal ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Cadmium (Cad) is a worldwide heavy metal pollutant associated with global health challenges. Alteration of the intestinal microbiome, due to chemicals' exposure, plays a vital role in the pathogenesis of gastrointestinal diseases such as pancreatic disorders. Hence, modulation of the gut microbiota might be a targeted approach to manage pancreatic diseases. Using murine modeling, this study consisted of two dependent experiments to investigate the curative potential of berberine (BBR) in a Wistar rat model of Cad-provoked pancreatic toxicity and the possible contribution of gut microbiota to BBR protection. In experiment 1, Cad-induced pancreatic injury was established in rats via 8-week oral gavage of Cad at 4 mg/kg. The treatment group was exposed to BBR at 200 mg/kg body weight, oral gavage for 8 weeks. In experiment 2, transplantation of the fecal microbiome was done, in which the fecal microbiota in each group of experiment 1 was orally gavaged to the healthy rats of each corresponding group in experiment 2, once weekly for 8 weeks. The serum amylase and lipase levels, pancreatic inflammatory and oxidative markers, histological, and immunohistochemical analyses were evaluated. The markers of gut mucosal barrier, and mRNA expression of cell junction proteins were investigated for possible intestinal injury. 16S rRNA sequencing was applied to identify the gut bacterial changes and possible pancreatic bacterial translocation. Cad induced intestinal barrier disruption and elicited a state of pancreatic inflammation and apoptosis as indicated by TGF-β and BAX immunohistochemistry, which were relieved by BBR. A decreased firmicutes/bacteroidetes ratio and microbial migration due to interrupted intestinal mucosal barrier were reported. Furthermore, BBR restored the bacterial richness and proportions in the gut, thereby maintaining the intestinal microbial community, fixing the intestinal mucosal barrier structure, and inhibiting the pathway of bacterial migration. BBR protected against Cad-induced pancreatic damage, mostly through safeguarding the intestinal barrier function. Modulation of the intestinal bacterial community, repairing the gut barrier structure, and interference with the pancreatic bacterial migration and colonization were suggested BBR effects, potentially alleviating Cad-related pancreatic injury.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Berberine/pharmacology
*Cadmium/toxicity
Rats
Rats, Wistar
Male
*Pancreas/drug effects/pathology
Intestinal Mucosa/drug effects/metabolism/microbiology
*Protective Agents/pharmacology
Disease Models, Animal
RNA, Ribosomal, 16S/genetics

@article {pmid40912813,
year = {2025},
author = {Yang, X and Li, S and Feng, Y and Guo, Y and Guo, Z and Hu, Y},
title = {A novel extracellular mannan from Bacillus velezensis ameliorates metabolic-associated fatty liver disease by modulating gut microbiota in mice model.},
journal = {Carbohydrate polymers},
volume = {368},
number = {Pt 1},
pages = {124150},
doi = {10.1016/j.carbpol.2025.124150},
pmid = {40912813},
issn = {1879-1344},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Bacillus/chemistry ; *Mannans/pharmacology/chemistry/isolation & purification/therapeutic use ; Mice ; Male ; Mice, Inbred C57BL ; Disease Models, Animal ; *Fatty Liver/drug therapy/metabolism ; Lipid Metabolism/drug effects ; Liver/drug effects/metabolism/pathology ; },
abstract = {Metabolic associated fatty liver disease (MAFLD) is a globally recognized chronic metabolic disorder characterized by lipid metabolism abnormalities. Accumulating evidence indicates that exopolysaccharides (EPS) could modulate the gut microbiota structure and function to prevent and treat MAFLD. Herein, a novel EPS designated BVP1 was isolated from Bacillus velezensis CGMCC 24752. Structural analysis revealed that BVP1 is a neutral α-mannan consisting of a backbone of 1,2,6-linked α-D-Manp, with branches composed of T-linked α-D-Manp, 1,2-linked α-D-Manp, and 1,3-linked α-D-Manp. Animal experiments showed that BVP1 significantly alleviated hepatic steatosis, liver injury and inflammation, and enhanced antioxidant activity in MAFLD mice. Single-nucleus RNA sequencing analysis revealed that BVP1 could restore HFD-induced imbalances in liver sinusoidal endothelial cells, hepatic stellate cells, macrophages and Kupffer cells by upregulating the expression of the lipid degradation gene Cps1 and downregulating the expression of the lipid synthesis gene Acsl1 in these cell subpopulations. Interestingly, BVP1 reshaped the gut microbiota and fecal metabolite profile by enriching beneficial bacteria and associated metabolites including salicylic acid, spermidine, and 4-hydroxyphenyl acetate. Fecal microbiota transplantation experiments verified that the anti-MAFLD effects are mediated by the BVP1-modified gut microbiota. Our findings highlight the potential of BVP1 as a promising therapeutic agent for MAFLD treatment.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Bacillus/chemistry
*Mannans/pharmacology/chemistry/isolation & purification/therapeutic use
Mice
Male
Mice, Inbred C57BL
Disease Models, Animal
*Fatty Liver/drug therapy/metabolism
Lipid Metabolism/drug effects
Liver/drug effects/metabolism/pathology

@article {pmid40912415,
year = {2025},
author = {Liu, X and He, J and Cui, L and Ye, Y and Luo, M and Xu, H and Zhai, Y and Zhao, Z and Huang, T and Li, Y and Wu, JL and Wen, J and Wang, Y and Zhou, T},
title = {Limosilactobacillus reuteri-Butyrate Axis in Depression Therapy: A Key Pathway Discovered Through a Novel Preclinical Human Flora-Associated Animal Model.},
journal = {Pharmacological research},
volume = {},
number = {},
pages = {107941},
doi = {10.1016/j.phrs.2025.107941},
pmid = {40912415},
issn = {1096-1186},
abstract = {The transition from preclinical to clinical drug development is critically impeded by interspecies disparities, which limit the predictive validity of preclinical efficacy for human outcomes. To address this limitation, we established a human flora-associated depression rat (HFADR) model through fecal microbiota transplantation (FMT). The HFADR model bridges the preclinical-clinical translation by recapitulating conserved microbial-host interactions identified through multi-omics analysis in a chronic unpredictable mild stress (CUMS) rat model and in patients with major depressive disorder. The HFADR model simulated the pathophysiological characteristics of clinical depression validated by gut-brain axis indices, including microbial composition, inflammatory biomarkers, brain-derived neurotrophic factor (BDNF), and monoamine neurotransmitters. Employing geniposide, a bioactive iridoid compound derived from medicinal plants, as a therapeutic prototype, the HFADR model revealed the novel Limosilactobacillus reuteri-butyrate axis as a conserved regulatory hub for the treatment of depression. Geniposide administration restored L. reuteri abundance in the HFADR model, which significantly correlated with improved gut-brain axis homeostasis. Metabolomics confirmed that L. reuteri exerts antidepressant effects via butyrate restoration in CUMS mice, with parallel butyrate level alterations observed in geniposide-treated HFADR model. Both L. reuteri supplementation and exogenous butyrate administration reversed depression-like behavior, mechanistically confirming the axis by reduced hippocampal astrocyte activation and elevated Nrf2 expression. This study established the HFADR model as a translational tool for evaluating microbiota-targeted therapies and identified the L. reuteri-butyrate axis as a novel therapeutic target. Our findings provide a theoretical and practical framework for refining preclinical models and advancing antidepressant development using microbiome-based strategies.},
}

@article {pmid40912148,
year = {2025},
author = {Gibril, BAA and Tu, X and Chai, X and Xu, J},
title = {Gut microbiota composition and dietary interventions modulate abdominal fat deposition in poultry: Mechanisms and applications.},
journal = {Poultry science},
volume = {104},
number = {11},
pages = {105754},
doi = {10.1016/j.psj.2025.105754},
pmid = {40912148},
issn = {1525-3171},
abstract = {Excessive abdominal fat deposition (AFD) in poultry reduces meat yield and efficiency. The gut microbiota regulates AFD through shifts in microbial composition and the production of metabolites. Reduced microbial diversity and fat-promoting taxa (e.g., Methanobrevibacter, Escherichia-Shigella) elevate AFD, while lean-linked bacteria (e.g., Bacteroides, Oscillospira) promote leanness. Dietary interventions, including botanical ingredients (e.g., honeycomb flavonoids elevating short-chain fatty acid producers), fermented feeds (e.g., cottonseed meal enriching butyrogenic taxa), probiotics (e.g., Lactobacillus johnsonii downregulating PPARγ/FAS), and additives (bile acids activating FXR/PPARα), modulate gut microbiota to reduce AFD by enhancing barrier function, suppressing pathogens, and regulating lipid metabolism. Fecal microbiota transplantation confirms microbiota-driven AFD reduction but faces donor-matching challenges. Breed-specific microbial signatures and context-dependent outcomes inform precision strategies to improve feed efficiency and lean yield.},
}

@article {pmid40911227,
year = {2025},
author = {Omar, TM and Alfarttoosi, KH and Sanghvi, G and Roopashree, R and Kashyap, A and Krithiga, T and Taher, WM and Alwan, M and Jawad, MJ and Al-Nuaimi, AMA},
title = {Engineering the Microbiome: a Novel Approach to Managing Autoimmune Diseases.},
journal = {Neuromolecular medicine},
volume = {27},
number = {1},
pages = {63},
pmid = {40911227},
issn = {1559-1174},
mesh = {Humans ; *Autoimmune Diseases/therapy/microbiology/immunology ; *Gastrointestinal Microbiome/immunology/genetics ; Animals ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; Inflammatory Bowel Diseases/therapy/microbiology ; Immune Tolerance ; Multiple Sclerosis/therapy/microbiology ; },
abstract = {Autoimmune diseases occur when the immune system mistakenly attacks the body's own tissues, affecting millions of people and often requiring long-term treatment. Current therapies, such as immunosuppressants and biologics, help manage symptoms but can cause serious side effects. A promising new approach involves engineered microbiota-a method that modifies gut bacteria to influence immune function and potentially ease autoimmune conditions. The gut microbiome is crucial in regulating immunity, and imbalances in its composition have been linked to diseases, such as rheumatoid arthritis (RA), multiple sclerosis (MS), and inflammatory bowel disease (IBD). Engineered microbiota works by altering microbial communities, either by adding new strains, genetically modifying existing bacteria, or using carefully selected groups of microbes to control inflammation and immune responses. Recent studies in both animal models and human trials suggest this approach could help restore immune tolerance, reduce inflammation, and repair the gut barrier. However, challenges remain, including ensuring safety, long-term effectiveness, and meeting regulatory standards. Despite being in its early stages, engineered microbiota holds great promise as a future treatment for autoimmune diseases, paving the way for more precise and personalized therapies that leverage the power of the microbiome to improve health.},
}

Humans
*Autoimmune Diseases/therapy/microbiology/immunology
*Gastrointestinal Microbiome/immunology/genetics
Animals
Probiotics/therapeutic use
Fecal Microbiota Transplantation
Inflammatory Bowel Diseases/therapy/microbiology
Immune Tolerance
Multiple Sclerosis/therapy/microbiology

@article {pmid40911047,
year = {2025},
author = {Che, Z and Xue, W and Zhao, X and Hu, C and Tian, Y},
title = {Regulatory Role and Biomarker Potential of Gut Microbiota Metabolites in the Progression of Metabolic dysfunction-associated steatotic liver disease (MASLD) to Hepatocellular Carcinoma (HCC).},
journal = {Clinical and translational gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.14309/ctg.0000000000000914},
pmid = {40911047},
issn = {2155-384X},
abstract = {Nonalcoholic fatty liver disease (NAFLD) is the most prevalent chronic liver disease worldwide. It is now updated as metabolic dysfunction-associated steatotic liver disease (MASLD). The progression of MASLD to hepatocellular carcinoma (HCC) involves complex mechanisms, with the gut microbiota and its metabolites playing a pivotal role in this transformation through the "gut-liver axis." This review systematically summarizes the characteristics of gut microbiota dysbiosis in NAFLD patients and the regulatory mechanisms of its metabolites (e.g., short-chain fatty acids [SCFAs], secondary bile acids, trimethylamine N-oxide [TMAO], and lipopolysaccharides [LPS]) in the progression from MASLD to HCC. SCFAs exert protective effects in the early stages by enhancing the intestinal barrier and modulating immune and metabolic responses. However, metabolic disturbances, such as the "paradoxical effect" of butyrate and the lipogenic effect of acetate, may promote the formation of a tumor microenvironment in the later stages. Secondary bile acids (e.g., deoxycholic acid) exacerbate liver fibrosis and carcinogenesis by activating inflammatory pathways (NF-κB, MAPK), inducing oxidative stress, and inhibiting foresaid X receptor (FXR) signaling. TMAO directly drives HCC progression by activating the MAPK/NF-κB pathway, promoting epithelial-mesenchymal transition (EMT), and creating an immunosuppressive microenvironment. LPS accelerates fibrosis and metabolic reprogramming through TLR4-mediated chronic inflammation and hepatic stellate cell activation. This review highlights that the dynamic changes in gut microbiota metabolites are closely associated with MASLD -HCC progression. Specific monitoring of these metabolites may serve as potential biomarkers for early detection. Furthermore, gut-targeted therapies (e.g., fecal microbiota transplantation) have shown translational potential. Future studies are needed to further validate their clinical value and develop precise prevention and treatment strategies.},
}

@article {pmid40910235,
year = {2025},
author = {Kaabi, YA},
title = {The Role of Gut Microbiota in Modulating Inflammation and Insulin Resistance in Type 2 Diabetes Mellitus: Implications for Complication Management.},
journal = {Current molecular medicine},
volume = {},
number = {},
pages = {},
doi = {10.2174/0115665240393897250826074023},
pmid = {40910235},
issn = {1875-5666},
abstract = {Type 2 diabetes mellitus (T2DM) is a chronic metabolic disorder characterized by insulin resistance and severe complications, including cardiovascular diseases, neuropathy, retinopathy, and nephropathy. This article examines the role of gut microbiota in modulating inflammation and insulin resistance in type 2 diabetes mellitus (T2DM), as well as its implications for managing complications associated with the disease. We analyzed published literature to elucidate mechanisms linking microbial dysbiosis, impaired gut barrier function, and chronic inflammation to glycemic control and T2DM complications. Key findings suggest that gut microbiota dysbiosis contributes to systemic inflammation and insulin resistance, thereby exacerbating the complications of type 2 diabetes mellitus (T2DM). Therapeutic strategies, such as probiotics, prebiotics, and fecal microbiota transplantation, promise to improve glycemic control and mitigate complications by restoring microbial balance. This review provides a comprehensive framework for understanding the role of the gut microbiota in type 2 diabetes mellitus (T2DM) and highlights potential therapeutic interventions to enhance the management of complications.},
}

@article {pmid40909921,
year = {2025},
author = {Shi, M and Wang, LF and Hu, WT and Liang, ZG},
title = {The gut microbiome in lung cancer: from pathogenesis to precision therapy.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1606684},
pmid = {40909921},
issn = {1664-302X},
abstract = {The gut microbiome has emerged as a key modulator of immune responses and treatment efficacy in oncology. Growing evidence links gut dysbiosis to resistance against immune checkpoint inhibitors (ICIs) in advanced cancers, prompting exploration of the gut-lung axis-a bidirectional network connecting intestinal microbiota with pulmonary health. Given lung cancer's status as the leading cause of cancer mortality worldwide, understanding this axis holds significant therapeutic potential. This review synthesizes current knowledge on gut microbiota's role in lung cancer development, diagnosis, and treatment. We highlight microbial signatures predictive of disease and therapy response, discuss microbiota-targeted interventions (e.g., probiotics, Fecal Microbiota Transplantation), and elucidate mechanistic insights into microbial-immune crosstalk. Finally, we outline future directions for leveraging the gut microbiome in personalized lung cancer management.},
}

@article {pmid40909294,
year = {2025},
author = {Zhou, L and Wu, Q and Jiang, L and Rao, J and Gao, J and Zhao, F and Wang, X},
title = {Role of the microbiota in inflammation-related related psychiatric disorders.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1613027},
pmid = {40909294},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Mental Disorders/microbiology/etiology/immunology/metabolism/therapy ; Animals ; *Inflammation/microbiology/immunology/metabolism ; Neuroimmunomodulation ; },
abstract = {The immune interactions within the gut-brain axis represent a critical etiological factor in psychiatric disorders. The gut microbiota and their metabolites serve as biological mediators that regulate neuroimmune activation and suppression in the central nervous system (CNS). During intestinal immune activation, pro-inflammatory cytokines (e.g., IL-6, TNF-α) propagate to the CNS via compromised blood-brain barrier (BBB) integrity or vagal afferent fibers, disrupting neurotransmitter metabolism and inducing microglial hyperactivation, thereby exacerbating neuroinflammation. Microglia, the principal immune sentinels of the CNS, adopt a pro-inflammatory phenotype upon peripheral inflammatory signaling characterized by morphological transformations, excessive chemokine/cytokine production (e.g., IL-1β, IL-6), and dysregulated neurotransmitter dynamics. These mechanisms are strongly implicated in neuropsychiatric conditions such as major depressive disorder, anxiety disorders, autism spectrum disorder, and schizophrenia. Emerging microbiota-targeted therapies, including probiotic interventions and fecal microbiota transplantation, demonstrate therapeutic potential by restoring tryptophan homeostasis and modulating systemic inflammation. This review synthesizes current evidence on the regulatory role of the gut microbiota in inflammation-related psychiatric disorders, specifically emphasizing the microbial modulation of neuroimmune crosstalk and neurotransmitter synthesis (e.g., serotonin, dopamine). Mechanistic insights into microbial metabolites, such as short-chain fatty acids and tryptophan derivatives, are critically evaluated for their dual roles in psychiatric disorders. These findings advance a unified framework for managing psychiatric comorbidities through precision modulation of the gut-brain axis.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Mental Disorders/microbiology/etiology/immunology/metabolism/therapy
Animals
*Inflammation/microbiology/immunology/metabolism
Neuroimmunomodulation

@article {pmid40909137,
year = {2025},
author = {Chen, K and Sun, L and Liu, Y and Chen, R},
title = {Safety and efficacy of fecal microbiota transplantation in the treatment of Parkinson's disease: a systematic review of clinical trials.},
journal = {Frontiers in neuroscience},
volume = {19},
number = {},
pages = {1639911},
pmid = {40909137},
issn = {1662-4548},
abstract = {INTRODUCTION: Parkinson's disease (PD) is the second most common neurodegenerative disease with limited treatment options and increasing incidence. The Microbiota-Gut-Brain Axis (MGBA) offers new insights for PD treatment, as gut microbiota imbalances are linked to PD. Fecal microbiota transplantation (FMT) shows potential to improve gut dysbiosis and has gained attention for PD treatment.

METHODS: We conducted a review following PRISMA 2009 guidelines, searching PubMed, EMBASE, Web of Science, and Scopus up to December 1, 2024. We included clinical trials of FMT for PD patients, regardless of stage or type, with outcomes related to efficacy or safety. Non-clinical trials were excluded. Two investigators independently assessed studies, extracted data, and evaluated risk of bias and quality.

RESULTS: A total of 1,147 articles were retrieved, and six studies involving 104 patients were included. Four were randomized controlled trials, one was a cohort study, and one was a case series. Patients had a mean age of 63.2 years and disease duration of 5.6 years. After FMT, some patients showed improvements in UPDRS scores, H-Y grades, NMSS scores, and constipation symptoms, but results varied across studies. No serious FMT-related adverse events occurred. Most were mild gastrointestinal issues. Gut microbiota diversity and beneficial bacterial abundance changed after FMT, correlating with clinical outcomes. FMT materials were mostly from unrelated donors with diverse preparation and delivery methods.

DISCUSSION: FMT shows efficacy and safety in PD treatment but is insufficient as a standard due to study heterogeneity and small sample sizes. Future research needs larger samples, unified tools, and standardized FMT procedures. Combining FMT with other therapies may improve efficacy.},
}

@article {pmid40909091,
year = {2025},
author = {Vineesh, A and Shah, S and Shah, K and Zaigham Hassan, M and Sapkota, A and Khadka, SR and Rizwanullah, F and Dare Ibrahim, A and Kanduri Hanumantharayudu, S and Kumar Makam Surendraiah, P and Ahmed, B and Gyullu, N},
title = {Exploring the Relationship Between Gut Health and Autoimmune Diseases: A Systematic Review and Meta-Analysis.},
journal = {Cureus},
volume = {17},
number = {8},
pages = {e89300},
pmid = {40909091},
issn = {2168-8184},
abstract = {Autoimmune diseases (AIDs) are multifaceted, chronic illnesses characterized by immune dysregulation and systemic inflammation. Newer evidence has pointed a finger at the human gut microbiota, a trillion-fold population of microorganisms that inhabits the human GI tract, as a major influential modulator of immune reactivity and a significant contributor to autoimmune pathogenesis. This systematic review will seek to address how the literature correlates with systematic changes in the gut microbiota in AIDs as well as explore mechanistic associations with biological processes like intestinal permeability and modulation of the immune system, coupled with determining the effectiveness of microbiota-directed interventions. An extensive literature search was conducted in PubMed, Embase, Cochrane Central, and Web of Science, involving the availability of studies until May 2025. The eligible studies included observational studies, randomized controlled trials, and relevant mechanistic research regarding autoimmune diseases and alterations of the gut microbiome or administered interventions. Data extraction and risk of bias (ROB) assessments were performed by two independent reviewers, and a narrative synthesis with an illustrative meta-analysis was applied. Inclusion criteria were met by 10 studies, encompassing various autoimmune diseases, including systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), multiple sclerosis (MS), type 1 diabetes mellitus (T1DM), autoimmune thyroid diseases (AITDs), and psoriasis. Familiar patterns of microbiome dysbiosis were identified, such as a reduction in microbial diversity, increased intestinal permeability, and the expansion of pro-inflammatory species like Ruminococcus gnavus. Dietary interventions, fecal microbiota transplantation, and probiotics demonstrated positive effects on clinical outcomes and immune measures across multiple studies. The meta-analysis revealed that microbiota-directed interventions significantly improved disease activity and immune response markers in AIDs, indicating a robust link between gut microbiota composition and autoimmune pathology. In autoimmune disorders, gut microbiota is a key factor in immunopathology. Gut biology as an adjunct interventional strategy provides potential in managing these diseases. Additional studies are required to help standardize methods and identify microbial targets specific to diseases that can then be addressed through therapeutic interventions.},
}

@article {pmid40908772,
year = {2025},
author = {Faysal, M and Zehravi, M and Sutradhar, B and Al Amin, M and Shanmugarajan, TS and Arjun, UVNV and Ethiraj, S and Durairaj, A and Dayalan, G and Ahamad, SK and Rab, SO and Raman, K and Emran, TB},
title = {The Microbiota-Gut-Brain Connection: A New Horizon in Neurological and Neuropsychiatric Disorders.},
journal = {CNS neuroscience & therapeutics},
volume = {31},
number = {9},
pages = {e70593},
doi = {10.1111/cns.70593},
pmid = {40908772},
issn = {1755-5949},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Mental Disorders/microbiology/metabolism/therapy ; *Nervous System Diseases/microbiology/metabolism/therapy ; *Brain/metabolism ; Animals ; Dysbiosis ; *Brain-Gut Axis/physiology ; Probiotics ; },
abstract = {INTRODUCTION: The microbiota-gut-brain axis (MGBA), a complex two-way connection between the gut microbiota and the brain, has become a key regulator of neurological and neuropsychiatric disorders. Neurological disorders and gut microbiota dysbiosis are linked to these diseases. Changes in gut microbiota can lead to neurotransmitter imbalances, oxidative stress, and neuroinflammation. Gut dysbiosis may contribute to the development of diseases such as depression, autism, schizophrenia, bipolar disorder, Parkinson's disease, Alzheimer's disease, dementia, multiple sclerosis, epilepsy, anxiety, and autism spectrum disorders through immunological regulation, neuroinflammation, and neurotransmitter metabolism changes.

METHOD: This review systematically sourced articles related to microbiota gut brain axis, neurological disorders, neuropsychiatric disorders and clinical studies from major medical databases, including Scopus, PubMed, and Web of Science.

RESULTS: This review explores the molecular processes underlying MGBA interactions, including vagus nerve signaling, systemic immunological responses, and metabolites produced by microorganisms. The discussion explores the potential of microbiome-targeted treatments like fecal microbiota transplantation, probiotics, and prebiotics as effective treatment methods. The comprehension of the MGBA can revolutionize neurology and psychiatry, introducing innovative diagnostic and therapeutic approaches. Multiple elements, including diet, metabolism, age, stress, and medications, shape the human gut microbiota, and intestinal imbalances can lead to CNS diseases. The MGBA interacts with gut bacteria, and gut dysbiosis is associated with neurological disorders.

CONCLUSIONS: The review demonstrates the correlation between gut microbiota and neurologically associated diseases, highlighting its importance in neurogenesis, mental development, emotions, and behaviors. MGBA, mediated by microbial metabolites, affects brain function and neuroinflammation. Interventions like fetal microbiota transplantation, probiotics, and prebiotics can improve microbial balance, but more clinical research is needed.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Mental Disorders/microbiology/metabolism/therapy
*Nervous System Diseases/microbiology/metabolism/therapy
*Brain/metabolism
Animals
Dysbiosis
*Brain-Gut Axis/physiology
Probiotics

@article {pmid40907403,
year = {2025},
author = {Zhang, D and Wu, J and Feng, H and Tang, P and Zhou, Y and Zhao, C and Liu, J and Feng, W and Peng, C},
title = {Gastrodin ameliorates ulcerative colitis via modulating gut microbial tryptophan metabolism and AhR/NLRP3 pathway.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {147},
number = {},
pages = {157217},
doi = {10.1016/j.phymed.2025.157217},
pmid = {40907403},
issn = {1618-095X},
abstract = {BACKGROUND: Ulcerative colitis (UC), a chronic idiopathic inflammatory bowel disorder, presents persistent therapeutic challenges in clinical management. Gastrodin (GAS) is an active compound isolated from traditional Chinese medicine Gastrodia elata (Tianma), exhibits robust anti-inflammatory bioactivity. However, the role of GAS in UC has not been thoroughly studied.

PURPOSE: The study aimed to investigate the protective effect of GAS against UC induced by DSS and its underlying mechanisms, with a particular emphasis on gut microbiota-metabolite interactions.

METHODS: The ameliorative effect of GAS on UC was examined, followed by 16S rRNA sequencing, targeted metabolomics, MALDI-MSI analysis, and western blotting analysis, fecal microbiota transplantation (FMT) to investigate the underlying mechanism of GAS on UC.

RESULTS: Evaluation of symptoms showed that GAS exhibited dose-dependent beneficial effects on UC. Targeted metabolites showed that GAS increased the production of tryptophan-derived metabolites, including kynurenic acid (Kyna), indole-3-acetic acid (IAA), indole-3-carboxaldehyde (IAld), and indole-3-lactic acid (ILA), etc. MALDI-MSI confirmed that GAS increased the levels of aryl hydrocarbon receptor (AhR) ligands IAld and IAA in the colon tissue. Western blotting showed that GAS mitigated colon inflammation through the activation of the AhR/NOD-like receptor protein 3 (NLRP3) pathway. Finally, FMT confirmed that GAS ameliorates UC in a microbiota-dependent manner and the involvement of gut microbiota derived AhR ligands and AhR/NLRP3 pathway.

CONCLUSION: GAS alleviates UC via modulating gut microbiota-derived tryptophan metabolites (Kyna, IAA, IAld, ILA) in a microbiota-dependent manner and suppressing AhR/NLRP3 pathway. Our study has important practical implications for the application of traditional Chinese medicine-derived active ingredients in the treatment of UC.},
}

@article {pmid40906320,
year = {2025},
author = {Ilozumba, MN and Gomez, MF and Lin, T and Himbert, C and Round, JL and Zac Stephens, W and Warby, CA and Hardikar, S and Li, CI and Figueiredo, JC and Damerell, V and Fillmore, GC and Pickron, B and Toriola, AT and Shibata, D and Holowatyj, AN and Kahlert, C and Sankar, K and Siegel, EM and Jedrzkiewicz, J and Gigic, B and Byrd, DA and Ose, J and Ulrich, CM},
title = {Pre-surgery gut microbial diversity and abundance are associated with post-surgery onset of cachexia in colorectal cancer patients: the ColoCare Study.},
journal = {Cancer causes & control : CCC},
volume = {},
number = {},
pages = {},
pmid = {40906320},
issn = {1573-7225},
support = {U01 CA206110, R01 CA189184, R01 CA207371, R01 CA211705, R01 CA254108//National Institutes of Health/ National Cancer Institute/ ; U01 CA206110, R01 CA189184, R01 CA207371, R01 CA211705, R01 CA254108//National Institutes of Health/ National Cancer Institute/ ; U01 CA206110, R01 CA189184, R01 CA207371, R01 CA211705, R01 CA254108//National Institutes of Health/ National Cancer Institute/ ; U01 CA206110, R01 CA189184, R01 CA207371, R01 CA211705, R01 CA254108//National Institutes of Health/ National Cancer Institute/ ; U01 CA206110, R01 CA189184, R01 CA207371, R01 CA211705, R01 CA254108//National Institutes of Health/ National Cancer Institute/ ; U01 CA206110, R01 CA189184, R01 CA207371, R01 CA211705, R01 CA254108//National Institutes of Health/ National Cancer Institute/ ; U01 CA206110, R01 CA189184, R01 CA207371, R01 CA211705, R01 CA254108//National Institutes of Health/ National Cancer Institute/ ; U01 CA206110, R01 CA189184, R01 CA207371, R01 CA211705, R01 CA254108//National Institutes of Health/ National Cancer Institute/ ; 01KD2101D//the German Ministry of Education and Research project PerMiCCion/ ; 01KD2101D//the German Ministry of Education and Research project PerMiCCion/ ; },
abstract = {BACKGROUND: Cachexia accounts for about 20% of all cancer-related deaths and it is indicative of poor prognosis and progressive functional impairment. The role of the gut microbiome in the development of cachexia in colorectal cancer (CRC) patients has not been established.

METHODS: Pre-surgical stool samples from n = 103 stage I-III CRC patients in the ColoCare Study were analyzed using 16S rRNA gene sequencing (Illumina) to characterize fecal bacteria. We calculated estimates of alpha- and beta-diversity and a priori- and exploratory-selected bacterial relative abundance. Using Fearon criteria, cachexia onset at 6 months post-surgery was defined as > 5% weight loss over the past 6 months and/or body mass index (BMI) of < 20 kg/m[2] and weight loss of > 2%. Associations of microbial metrics with cachexia onset were estimated using multivariable logistic regression models.

RESULTS: Higher alpha-diversity was positively associated with cachexia onset, with stronger associations in females, patients < 65 years, those receiving adjuvant treatment, consuming high fiber, or with energy intake outside USDA recommendations (p < 0.05). Porphyromonas (OR = 0.51, 95% CI 0.26-0.89, p = 0.03) and Actinomyces (OR = 0.72, 95% CI 0.48-1.03, p = 0.08) were inversely associated with cachexia, although the association for Actinomyces did not reach statistical significance. Stratified analyses revealed a stronger inverse association between Porphyromonas and cachexia onset in males, patients with rectal or stage III tumors, those receiving neoadjuvant treatment, physically inactive individuals, and those consuming low fiber. However, these associations did not reach statistical significance (0.05 ≤ p < 0.10).

CONCLUSION: Higher gut microbial alpha-diversity and lower relative abundances of the genera Porphyromonas and Actinomyces in pre-surgery stool samples were associated with onset of cachexia in CRC patients six months post-surgery. This is the first study to explore a link between the gut microbiome and cachexia in CRC patients, providing novel insights into the biology of cachexia and potential clinical interventions.},
}

@article {pmid40906312,
year = {2025},
author = {Arjmand, B and Badamchizadeh, S and Mehran, P and Sarvari, M and Alavi-Moghadam, S and Arjmand, R and Rezaei-Tavirani, M and Janbabaei, G and Vaezi, M and Larijani, B},
title = {Gut Microbiome and its Impact on Outcomes following Hematopoietic Stem Cell Transplantation: a Comprehensive Review.},
journal = {Stem cell reviews and reports},
volume = {},
number = {},
pages = {},
pmid = {40906312},
issn = {2629-3277},
abstract = {Hematopoietic stem cell transplantation is an important treatment for hematological malignancy and disorders, but is fraught with high risks, including graft-versus-host disease, infection, and relapse. Recent evidence now identifies that the microbiome plays a significant role in influencing transplant outcomes, in which microbial dysbiosis-defined by reduced diversity and pathogen overgrowth-is linked to greater complications and death. Microbiome manipulation with approaches including beneficial microbial species, fiber, fecal transplants, and diet has the potential to mitigate these risks. Experiments show that the restoration of beneficial microbes can restore immunity, reduce graft-versus-host disease severity, and reduce infection. Some challenges remain, including standardization of protocols, long-term efficacy, and safety in immunocompromised recipients. Future research will be focused on mechanisms, trials, and new technology for microbiome-based therapy, with the ultimate goal of improving survival and quality of life for transplant recipients. Hereupon, this review addresses how microbiome engineering can revolutionize cancer treatment by optimizing gut microbial communities for better outcomes in hematopoietic stem cell transplantation (HSCT).},
}

@article {pmid40905977,
year = {2025},
author = {Liu, Y and Gao, J and Chen, L and Chen, Y and Jiang, J and Chen, H and Ma, L},
title = {Lithocholic acid ameliorates ulcerative colitis via the PXR/TLR4/NF-κB/NLRP3 signaling pathway and gut microbiota modulation.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {82},
number = {1},
pages = {336},
pmid = {40905977},
issn = {1420-9071},
mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Colitis, Ulcerative/drug therapy/pathology/metabolism/microbiology/chemically induced ; *NLR Family, Pyrin Domain-Containing 3 Protein/metabolism ; *Toll-Like Receptor 4/metabolism ; *Pregnane X Receptor/metabolism ; *Signal Transduction/drug effects ; *Lithocholic Acid/pharmacology/therapeutic use ; *NF-kappa B/metabolism ; Male ; Mice, Inbred C57BL ; Mice ; Dextran Sulfate ; Disease Models, Animal ; Humans ; },
abstract = {Ulcerative colitis (UC) is a chronic inflammatory condition of the colon, closely linked to dysbiosis of gut microbiota and imbalances in bile acids. Lithocholic acid (LCA), a secondary bile acid, plays a crucial role in maintaining gut health; however, its specific therapeutic potential in UC remains to be fully elucidated. This study investigates the efficacy of LCA in alleviating UC and explores the underlying mechanisms, particularly focusing on the PXR/TLR4/NF-κB/NLRP3 signaling pathway and gut microbiota modulation. Using a dextran sulfate sodium (DSS)-induced colitis model, our findings demonstrate that LCA administration significantly alleviates colitis symptoms, evidenced by reduced disease activity index (DAI), increased colon length, improved intestinal barrier function, and decreased colonic inflammation. Mechanistically, LCA activates the pregnane X receptor (PXR), which inhibits TLR4-mediated NF-κB/NLRP3 inflammasome activation, leading to reduced colonic inflammation and lower levels of pro-inflammatory cytokines. Furthermore, LCA remodels gut microbiota by promoting beneficial bacterial growth, such as Akkermansiaceae, Lactobacillaceae and Muribaculaceae, while suppressing pathogenic and opportunistic pathogens, including Enterobacteriaceae and Bacteroidaceae. The gut microbiota-dependent effects of LCA were corroborated through antibiotic treatment and fecal microbiota transplantation (FMT) experiments. Notably, the absence of intestinal flora affected PXR expression and activity, modifying the aforementioned effects. Overall, our findings reveal that LCA ameliorates experimental colitis by regulating the PXR/TLR4/NF-κB/NLRP3 signaling cascade and modulating gut microbiota composition. This study underscores LCA's potential as a targeted therapeutic strategy and a promising microbiota-focused approach for managing UC, offering new insights into the role of bile acids in intestinal health and disease management.},
}

*Gastrointestinal Microbiome/drug effects
Animals
*Colitis, Ulcerative/drug therapy/pathology/metabolism/microbiology/chemically induced
*NLR Family, Pyrin Domain-Containing 3 Protein/metabolism
*Toll-Like Receptor 4/metabolism
*Pregnane X Receptor/metabolism
*Signal Transduction/drug effects
*Lithocholic Acid/pharmacology/therapeutic use
*NF-kappa B/metabolism
Male
Mice, Inbred C57BL
Mice
Dextran Sulfate
Disease Models, Animal
Humans

@article {pmid40904889,
year = {2025},
author = {Lv, J and Zhao, HP and Yu, Y and Wang, JH and Zhang, XJ and Guo, ZQ and Jiang, WY and Wang, K and Guo, L},
title = {From gut microbial ecology to lipid homeostasis: Decoding the role of gut microbiota in dyslipidemia pathogenesis and intervention.},
journal = {World journal of gastroenterology},
volume = {31},
number = {30},
pages = {108680},
pmid = {40904889},
issn = {2219-2840},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Dyslipidemias/microbiology/therapy/metabolism/etiology ; Homeostasis ; *Lipid Metabolism ; Animals ; Fecal Microbiota Transplantation ; Probiotics/therapeutic use ; Prebiotics/administration & dosage ; Dysbiosis/microbiology/therapy ; },
abstract = {Dyslipidemia, a complex disorder characterized by systemic lipid profile abnormalities, affects more than half of adults globally and constitutes a major modifiable risk factor for atherosclerotic cardiovascular disease. Mounting evidence has established the gut microbiota (GM) as a pivotal metabolic modulator that is correlated with atherogenic lipid profiles through dietary biotransformation, immunometabolic regulation, and bioactive metabolite signaling. However, the host-microbe interactions that drive dyslipidemia pathogenesis involve complex gene-environment crosstalk spanning epigenetic modifications to circadian entrainment. Mechanistically, GM perturbations disrupt lipid homeostasis via lipopolysaccharide-triggered hepatic very low-density lipoprotein overproduction, short-chain fatty acid-G protein-coupled receptor 43/41-mediated adipocyte lipolysis, bile acid-farnesoid X receptor/Takeda G protein-coupled receptor 5 axis dysfunction altering cholesterol flux, microbial β-oxidation intermediates impairing mitochondrial energetics, and host-microbiota non-coding RNA crosstalk regulating lipogenic genes. This comprehensive review systematically examines three critical dimensions, including bidirectional GM-lipid axis interactions, molecular cascades bridging microbial ecology to metabolic dysfunction, and translational applications of GM modulation through precision probiotics, structure-specific prebiotics, and a metabolically optimized fecal microbiota transplantation protocol. Notwithstanding these advances, critical gaps persist in establishing causal microbial taxa-pathway relationships and optimal intervention timing. Future directions require longitudinal multi-omic studies, gnotobiotic models for mechanistic validation, and machine learning-driven personalized microbiota profiling. This synthesis provides a framework for developing microbiota-centric strategies targeting dyslipidemia pathophysiology, with implications for precision dyslipidemia management and next-generation cardiovascular disease prevention.},
}

*Gastrointestinal Microbiome/physiology
Humans
*Dyslipidemias/microbiology/therapy/metabolism/etiology
Homeostasis
*Lipid Metabolism
Animals
Fecal Microbiota Transplantation
Probiotics/therapeutic use
Prebiotics/administration & dosage
Dysbiosis/microbiology/therapy

@article {pmid40904642,
year = {2025},
author = {Sun, Q and Jiang, Z and Yang, L and Liu, H and Song, P and Yuan, L},
title = {Towards an Asian paradigm of inflammatory bowel disease management: A comparative review of China and Japan.},
journal = {Intractable & rare diseases research},
volume = {14},
number = {3},
pages = {192-202},
pmid = {40904642},
issn = {2186-3644},
abstract = {This systematic review compares inflammatory bowel disease (IBD) management between China and Japan across epidemiology, clinical strategies, health insurance, and social security policies. Epidemiologically, the incidence of IBD is rapidly increasing in China, contributing to a growing disease burden. In contrast, Japan has a stabilized incidence but a rising prevalence, driven by an aging patient population. Clinically, step-up therapy remains the mainstream approach in China, limited by regional and financial disparities in biologic access. In contrast, Japan, benefiting from the "Designated Intractable Diseases" program, favors early intensive therapy with a focus on mucosal healing. In the area of precision medicine, China is advancing rapidly in therapeutic drug monitoring (TDM) for anti-TNF agents. In contrast, Japan leads in AI-assisted endoscopic assessment, despite slower adoption of TDM. Japan's comprehensive insurance covers most costs of IBD; China has significantly reduced drug prices via national negotiations, and yet reimbursement rates vary regionally. China has made progress in telemedicine and standardized fecal microbiota transplantation (FMT); Japan excels in AI endoscopy and use of an elemental diet. To optimize IBD care in the Asia-Pacific, China should enhance access to advanced therapies, implement hierarchical diagnosis/ treatment, and develop multi-tiered insurance. Japan must address aging-related challenges and insurance sustainability while expanding use of TDM. Sino-Japanese collaboration in genetics, microbiome research, and AI-driven diagnostics, supported by sustained policy dialogue, is key to advancing precision IBD care and shaping a scalable "Asian model" for chronic disease management.},
}

@article {pmid40904056,
year = {2025},
author = {Dassanayake, P and Diksha, D and Varela-Mattatall, G and Sun, Q and Donnelly, SC and Suchy, M and Bartolome, D and Furlong, S and Deans, L and Biernaski, H and Huston, Y and Thompson, RT and Burton, JP and Moran, G and Gelman, N and Prato, FS and Kovacs, MS and Thiessen, JD and Goldhawk, DE and Schellenberg, J and Fox, MS},
title = {Biodistribution and dosimetry of [89]Zirconium-labeled microbiota transplants in the pig gut.},
journal = {Medical physics},
volume = {52},
number = {9},
pages = {e18087},
doi = {10.1002/mp.18087},
pmid = {40904056},
issn = {2473-4209},
mesh = {Animals ; *Zirconium/chemistry ; *Radioisotopes/chemistry ; Swine ; Tissue Distribution ; Radiometry ; Female ; Escherichia coli ; *Gastrointestinal Microbiome ; Positron-Emission Tomography ; Magnetic Resonance Imaging ; Isotope Labeling ; },
abstract = {BACKGROUND: The gastrointestinal (GI) microbiota, composed of diverse microbial communities, is essential for physiological processes, including immune modulation. Strains such as Escherichia coli Nissle 1917 support gut health by reducing inflammation and resisting pathogens. Microbial therapies using such strains may restore GI balance and offer alternatives to antibiotics, whose overuse contributes to antibiotic resistance. However, effective treatment will require optimizing delivery and understanding microbial dissemination and engraftment.

PURPOSE: We developed a method to monitor microbial migration and GI permeability post-ingestion using hybrid PET/MRI. To simulate probiotic therapy, bacteria were radiolabeled with [89]Zr, encapsulated, and administered to pigs. Organ level and whole-body dosimetry was determined from the time activity curves recorded over 7 days post ingestion.

METHODS: We administered [89]Zr-labeled Lactobacillus crispatus ATCC33820 (Gram-positive) to six female Duroc pigs (weight = 33.3 ± 4.6 kg) and E. coli Nissle 1917 (Gram-negative). Scans were performed between 6 h and 7 days post-ingestion using a hybrid PET/MRI system. The mean administered dose was 74.7 ± 12.9 MBq. Whole-body PET scans were acquired simultaneously with MRI using a T2-weighted HASTE sequence. Images were processed using 3D-Slicer co-registering PET with MRI and semi-automated organ segmentation was performed. Gender-averaged human equivalent organ-level effective doses (ED) and whole body ED were calculated using OLINDA.

RESULTS: PET imaging showed [89]Zr-labeled L. crispatus and E. coli post-ingestion localized primarily within the GI tract before excretion within feces. The highest mean ED for [89]Zr-labeled L. crispatus and E. coli were in the distal colon (26.8 ± 4.9 µSv/MBq and 28.4 ± 7.9 µSv/MBq, respectively) and proximal colon (17.9 ± 3.7 µSv/MBq and 18.4 ± 5.1 µSv/MBq, respectively). EDs in other organs were low. Whole body ED were 60.5 ± 9.5 µSv/MBq (L. crispatus) and 66.7 ± 14.9 µSv/MBq (E. coli).

CONCLUSIONS: The whole-body ED for L. crispatus and E. coli is lower than reported values for ingested tracers, such as that from [89]Zr labelled antibodies and [111]In labelled "meals" used to determine gut transit times. Hence ingestion of [89]Zr labelled bacteria shows promise for becoming a human nuclear-medicine procedure to determine the effectiveness of probiotic therapies.},
}

Animals
*Zirconium/chemistry
*Radioisotopes/chemistry
Swine
Tissue Distribution
Radiometry
Female
Escherichia coli
*Gastrointestinal Microbiome
Positron-Emission Tomography
Magnetic Resonance Imaging
Isotope Labeling

@article {pmid40903950,
year = {2025},
author = {Liu, Y and Tang, T and Cai, H and Liu, Z},
title = {Bidirectional communication between the gut microbiota and the central nervous system.},
journal = {Neural regeneration research},
volume = {},
number = {},
pages = {},
doi = {10.4103/NRR.NRR-D-25-00434},
pmid = {40903950},
issn = {1673-5374},
abstract = {In recent years, an increasing number of researchers have become interested in the bidirectional communication between the gut microbiota and the central nervous system. This communication occurs through the microbiota-gut-brain axis. As people age, the composition of the gut microbiota undergoes considerable changes, which are now known to play an important role in the development of many neurodegenerative diseases. This review aims to investigate the complex bidirectional signaling pathways between the gut and the brain. It summarizes the latest research findings on how the gut microbiota and its metabolites play critical roles in regulating inflammation, maintaining gut health, and influencing the development of neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. The review also analyzes the current clinical applications of gut microbiota-based treatments for neurological disorders, including fecal microbiota transplantation, probiotics, and prebiotics. Many studies show that the gut microbiota affects the brain in several ways. For example, it can produce substances such as short-chain fatty acids and activate inflammatory pathways. Studies involving animals and laboratory models have demonstrated that adjusting the gut microbiota can help improve behavior and reduce neurological problems. Recent metagenomic and metabolomics studies have shown that the microbiota plays a crucial role in maintaining the organism's health. Microorganisms primarily colonize the gut and are involved in host nutrient metabolism, maintaining the structural integrity of the intestine, preserving the intestinal mucosal barrier, and modulating the immune system. The gut microbiota communicates with the brain through a bidirectional microbiota-gut-brain axis. The composition of the gut flora changes considerably with age, and ecological dysregulation has been recognized as one of the twelve most recent hallmarks of aging. Recent studies have linked these changes to a variety of age-related neurological disorders, including Alzheimer's disease, amyotrophic lateral sclerosis, Parkinson's disease, multiple sclerosis, and Huntington's disease. Specifically, the gut microbiota influences the brain through the production of key metabolites such as short-chain fatty acids and the activation of inflammatory and other relevant signaling pathways. In preclinical studies, targeted modulation of the gut microbiota, through methods such as fecal microbiota transplantation, probiotics, and prebiotics, has demonstrated potential in improving host behavioral outcomes. Therefore, gut microbiotabased treatments offer new hope for the treatment of nervous system diseases. However, due to the complexity of the gut microbiota and the potential adverse reactions associated with these therapies, researchers need to carefully assess their safety and efficacy before widespread clinical application.},
}

@article {pmid40903035,
year = {2025},
author = {Hou, Y and Wu, H and Zhang, Z and Wang, J and Chen, Q and Lian, C and He, D and Li, Z and Wei, W and Lin, X and Sun, D and Cao, B and Xu, T and Cai, M and Wang, G and Zhang, X and Duan, L and Hao, H and Zheng, X},
title = {Bacteroides intestinalis mediates the sensitivity to irinotecan toxicity via tryptophan catabolites.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2024-334699},
pmid = {40903035},
issn = {1468-3288},
abstract = {BACKGROUND: Late-onset diarrhoea remains a poorly managed concern for clinical irinotecan therapy. Although bacterial β-glucuronidases (β-GUS) mediated SN-38 production is prevailingly thought to mediate intestinal toxicity, β-GUS inhibitors confer limited benefits in the clinic.

OBJECTIVE: This study aimed to explore the role and mechanism of endogenous bacterial metabolites in susceptibility to irinotecan toxicity.

DESIGN: Gut microbiota profiles and metabolites in patients with colorectal cancer (CRC) with or without diarrhoea were investigated via 16S rRNA sequencing, shotgun metagenomics and metabolomics. The role of microbial metabolites was investigated in mice by metabolic bioengineering and intestinal organoid culture. The mechanism of microbial metabolites on intestinal stem cells was investigated by transcriptional profiling and chemical intervention.

RESULTS: Gut microbial configuration was differentially remodelled in diarrhoea and non-diarrhoea patients with irinotecan therapy, and the susceptibility was transmissible to recipient mice via transplantation of baseline faecal microbiome. Bacteroides intestinalis (B. intestinalis) was notably expanded in the diarrhoea-prone cohorts as well as in irinotecan-treated mice. B. intestinalis colonisation sensitised intestinal epithelia to irinotecan-induced chemical injury, partially via tryptophan metabolite indole-3-acetate (IAA). Both B. intestinalis and bioengineered bacteria that produce IAA exacerbated irinotecan-induced intestinal epithelial injury in mice. Mechanistically, IAA suppressed PI3K-Akt signalling, thereby impairing the renewal of intestinal epithelia under the insult of irinotecan. In clinical patients receiving irinotecan therapy, faecal IAA level was closely associated with the diarrhoea severity.

CONCLUSION: Our study uncovers the mechanism of endogenous bacterial metabolite in shaping the individual susceptibility to irinotecan toxicity and suggests IAA as a potential predictive biomarker.},
}

@article {pmid40902967,
year = {2025},
author = {Lu, Y and Liu, Y and Bai, X and Jiang, T and Chen, X and Wang, Y and Du, P and Sun, Y and Liu, C and Duan, J},
title = {Mechanisms of Podophyllotoxin-induced Enterotoxicity: A Multi-omics Integration of Gut Microbiota, Short-chain Fatty Acids, and Inflammatory Mediators.},
journal = {Toxicology},
volume = {},
number = {},
pages = {154274},
doi = {10.1016/j.tox.2025.154274},
pmid = {40902967},
issn = {1879-3185},
abstract = {Podophyllotoxin (PPT), a lignan extracted from the roots and stems of Podophyllum species, exhibits significant enterotoxicity that limits its clinical application. However, its underlying mechanisms remain unclear. This study aimed to elucidate the mechanisms underlying PPT-induced enterotoxicity. Changes in body weight, fecal morphology, toxic phenotypes, and histopathological features were evaluated. 3D reconstruction, 16S rRNA sequencing, targeted short-chain fatty acids (SCFAs) analysis, and inflammatory cytokine assays were performed. The findings demonstrated that PPT induced pathological changes in rats, including weight loss, diarrhea, and colonic damage. PPT administration significantly reduced beneficial bacteria such as Lactobacillus, while increasing harmful bacteria such as Escherichia-Shigella. The predicted pathways of bacterial invasion of epithelial cells and lipopolysaccharide biosynthesis were significantly upregulated. Levels of pro-inflammatory cytokines, including tumor necrosis factor-alpha (TNF-α) and interleukin-6 (IL-6), were also increased. Additionally, the expression of undecaprenyl-diphosphate synthase (UPPS) and SCFAs production was reduced. These findings indicate that PPT may alter gut microbial composition, increase Escherichia-Shigella invasion in the intestinal epithelial cells, promote lipopolysaccharide production, enhance the release of pro-inflammatory cytokines, including TNF-α and IL-6, and inhibit UPPS expression and SCFAs generation, collectively contributing to enterotoxicity. This study provides novel insights into the mechanisms behind PPT-induced enterotoxicity, which is essential for preventing and treating PPT toxicity.},
}

@article {pmid40902672,
year = {2025},
author = {Sharma, S and Bashir, B and Kolekar, KA and Acharya, A and Gupta, M and Jena, R and Vishwas, S and Kaur, J and Gupta, G and Kumbhar, PS and Patle, D and Chaitanya, M and Gulati, M and Singh, SK},
title = {Tailoring the biomarkers of Alzheimer's disease using a gut microbiome-centric approach: Preclinical, clinical, and regulatory perspectives.},
journal = {Ageing research reviews},
volume = {},
number = {},
pages = {102888},
doi = {10.1016/j.arr.2025.102888},
pmid = {40902672},
issn = {1872-9649},
abstract = {Alzheimer's disease (AD), a progressive neurodegenerative disorder, poses significant therapeutic challenges due to its complex etiology and limited treatment options. Traditional pharmacotherapies targeting amyloid-β (Aβ) and cholinergic pathways offer modest benefits and are often associated with adverse effects. Emerging evidence implicates gut dysbiosis and the gut-brain axis in the pathogenesis and progression of AD. This review explores the multifactorial pathophysiology of AD and evaluates the therapeutic potential of gut-based interventions such as probiotics, prebiotics, synbiotics, metabiotics, postbiotics, and fecal microbiota transplantation (FMT) in mitigating disease pathology. Emphasis has also been given on role of miRNA released from FMT in management of AD. Preclinical and clinical studies demonstrate that these strategies can restore microbial homeostasis, reduce neuroinflammation, enhance gut barrier integrity, and improve cognitive outcomes. The regulatory aspects with use of probiotics based products and FMT is also highlighted. The modulation of neuroimmune, neuroendocrine, and neural pathways through microbiota-derived metabolites offers a promising avenue for AD management. Despite encouraging findings, further research is needed to address interindividual microbiome variability, delivery challenges, and the requirement for large-scale, randomized trials. Personalized gut-targeted approaches may open new horizons for the prevention and treatment of AD.},
}

@article {pmid40901606,
year = {2025},
author = {Al-Busafi, SA and Alwassief, A and Madian, A and Atalla, H and Alboraie, M and Elbahrawy, A and Eslam, M},
title = {Exploring the interplay between metabolic dysfunction-associated fatty liver disease and gut dysbiosis: Pathophysiology, clinical implications, and emerging therapies.},
journal = {World journal of hepatology},
volume = {17},
number = {8},
pages = {108730},
doi = {10.4254/wjh.v17.i8.108730},
pmid = {40901606},
issn = {1948-5182},
abstract = {Metabolic dysfunction-associated fatty liver disease (MAFLD) now affects roughly one-quarter of the world's population, reflecting the global spread of obesity and insulin resistance. Reframing non-alcoholic fatty liver disease as MAFLD emphasizes its metabolic roots and spotlights the gut-liver axis, where intestinal dysbiosis acts as a key driver of hepatic injury. Altered microbial communities disrupt epithelial integrity, promote bacterial translocation, and trigger endotoxin-mediated inflammation that accelerates steatosis, lipotoxicity, and fibrogenesis. Concurrent shifts in bile acid signaling and short-chain fatty acid profiles further impair glucose and lipid homeostasis, amplifying cardiometabolic risk. Epidemiological studies reveal pervasive dysbiosis in MAFLD cohorts, linked to diet quality, sedentary behavior, adiposity, and host genetics. Newly developed microbiome-derived biomarkers, advanced elastography, and integrated multi-omics panels hold promise for non-invasive diagnosis and stratification, although external validation remains limited. In early trials, interventions that re-engineer the microbiota including tailored pre-/pro-/synbiotics, rational diet patterns, next-generation fecal microbiota transplantation, and bile-acid-modulating drugs show encouraging histological and metabolic gains. Optimal care will likely couple these tools with weight-centered lifestyle programmes in a precision-medicine framework. Key challenges include inter-ethnic variability in microbiome signatures, the absence of consensus treatment algorithms, and regulatory barriers to live biotherapeutics. Rigorous longitudinal studies are required to translate mechanistic insight into durable clinical benefit and improve patient-centered outcome measures.},
}

@article {pmid40901203,
year = {2025},
author = {Elendu, C and Omeludike, EK and Aregbesola, ET and Mordi, P and Blewusi, GS and Ogidan, AO and Okeke, NG and Obidigbo, BT and Asini, AO and Ubi, ES and Etakewen, PO and Amahalu, CA and Foncham, RF and Gana, LT and Onwe, CJ and Ojeabuo, OF and Ojo, AO and Ikeaba, CS and Opara, NC},
title = {Fecal microbiota transplantation as a therapeutic modality for recurrent Clostridioides difficile infection: reviewing efficacy, safety, mechanisms of action, and outcomes.},
journal = {Annals of medicine and surgery (2012)},
volume = {87},
number = {9},
pages = {5829-5850},
doi = {10.1097/MS9.0000000000003649},
pmid = {40901203},
issn = {2049-0801},
abstract = {Recurrent Clostridioides difficile infection (rCDI) remains a significant global health challenge, characterized by high morbidity, substantial healthcare costs, and an increased risk of severe complications. C. difficile, a gram-positive, spore-forming bacterium, is the primary cause of healthcare-associated diarrhea. The pathogenesis of rCDI is closely tied to gut microbiota disruptions, often triggered by antibiotic use, immunosuppression, and prolonged hospital stays. While effective for initial episodes, standard antibiotic therapies paradoxically exacerbate microbiota dysbiosis, increasing the risk of recurrence. Approximately 20%-30% of patients experience a recurrence after the initial episode, with rates rising to 45%-65% in those with multiple episodes. Fecal microbiota transplantation (FMT) has arrived as a transformative therapy for rCDI, leveraging donor microbiota to restore gut homeostasis and suppress C. difficile colonization. Clinical trials consistently report success rates exceeding 80%, markedly surpassing outcomes with antibiotics. Innovations in delivery methods, including oral capsules, have enhanced FMT's accessibility and patient acceptability. However, concerns surrounding safety and standardization persist. Adverse events, such as gastrointestinal discomfort and rare cases of multidrug-resistant organism transmission, underscore the need for stringent donor screening protocols. Emerging evidence reveals complex mechanisms underpinning FMT's efficacy, including restoring microbial diversity, bile acid metabolism, and short-chain fatty acid production. Long-term benefits, such as sustained microbiota stability, and potential applications in other conditions, including inflammatory bowel disease and metabolic disorders, are promising but require further validation. Addressing challenges in donor selection, regulatory oversight, and personalized approaches will be critical to optimizing FMT as a safe and effective therapeutic strategy for rCDI.},
}

@article {pmid40901024,
year = {2025},
author = {Chen, N and Li, L and Han, Y and Chen, Z},
title = {The Role of Gut Microbiota in the Modulation of Pulmonary Immune Response to Viral Infection Through the Gut-Lung Axis.},
journal = {Journal of inflammation research},
volume = {18},
number = {},
pages = {11755-11781},
doi = {10.2147/JIR.S525880},
pmid = {40901024},
issn = {1178-7031},
abstract = {Viral respiratory infections, including influenza, respiratory syncytial virus (RSV), and SARS-CoV-2, remain major global health challenges due to their high morbidity and mortality. Emerging evidence highlights the pivotal role of the gut-lung axis in regulating pulmonary immunity. The gut microbiota communicates with the lungs via endocrine, immune, and neuroimmune pathways-particularly through metabolites such as short-chain fatty acids (SCFAs) and vagus nerve-mediated signaling-which modulate immune cells including alveolar macrophages and dendritic cells. Disruption of gut microbial balance has been linked to impaired pulmonary immune responses and increased susceptibility to infection. This review synthesizes findings from animal models and clinical studies, demonstrating that interventions such as probiotics (eg, Lactobacillus gasseri), prebiotics (eg, galacto-oligosaccharides), fecal microbiota transplantation (FMT), and Traditional Chinese Medicine (eg, Astragalus, curcumin) can enhance antiviral cytokine production, restore gut-lung homeostasis, and reduce lung inflammation. For example, FMT from H7N9-survivor mice improved influenza resistance in recipients, and oral probiotics reduced respiratory failure risk in COVID-19 patients. These findings suggest that gut-lung axis modulation is a promising adjunctive approach for treating viral respiratory infections. Future research should prioritize personalized microbiome-based therapies and large-scale clinical trials to validate efficacy and safety.},
}

@article {pmid40900873,
year = {2025},
author = {Hafez, MM and Bahcecioglu, IH and Yalniz, M and Kouta, KA and Tawheed, A},
title = {Future of inflammatory bowel disease treatment: A review of novel treatments beyond guidelines.},
journal = {World journal of methodology},
volume = {15},
number = {4},
pages = {107643},
doi = {10.5662/wjm.v15.i4.107643},
pmid = {40900873},
issn = {2222-0682},
abstract = {Inflammatory bowel disease (IBD) is a chronic condition consisting of two main types: Crohn's disease and ulcerative colitis. Conventional treatments for these diseases include aminosalicylates, corticosteroids, immunomodulators, and biologics. However, these treatments have several drawbacks, including high costs for patients and numerous side effects. Recently, advanced treatments have been developed, such as small-molecule therapies, targeted biologics, innovative drug delivery systems, and microbiome-based interventions. Emerging therapies like anti-interleukin-23 monoclonal antibody inhibitors, sphingosine-1-phosphate receptor modulators, and Janus kinase inhibitors are more specialized in reducing immune activity. They enhance bioavailability, reduce side effects, and specifically target the gastrointestinal tract without affecting other systems. Innovative drug delivery systems for IBD, such as nanoparticles, hydrogels, and microgrippers, improve bioavailability and prolong drug release. The combination of conventional and advanced therapies may benefit from the synergistic effects of both. Furthermore, fecal microbiota transplantation and probiotics can help restore the balance of gastrointestinal microbiota, reducing disease flare-ups. Advances in artificial intelligence, endoscopic techniques, and stem cell therapies have shown great potential in treating IBD, although several significant challenges remain. Treating this disease requires multidisciplinary integration and the application of technology and telemedicine.},
}

@article {pmid40900872,
year = {2025},
author = {Singh, JP and Aleissa, M and Chitragari, G and Drelichman, ER and Mittal, VK and Bhullar, JS},
title = {Uncovering the role of microbiota and fecal microbiota transplantation in Crohn's disease: Current advances and future hurdles.},
journal = {World journal of methodology},
volume = {15},
number = {4},
pages = {106148},
doi = {10.5662/wjm.v15.i4.106148},
pmid = {40900872},
issn = {2222-0682},
abstract = {Crohn's disease (CD) is an idiopathic, chronic, and recurrent inflammatory condition of the gastrointestinal tract. Recent studies suggest a potential role of gut microbiota in CD, particularly dysbiosis-an imbalance in gut bacteria. While dysbiosis is consistently observed in CD, it remains uncertain whether it is a cause or a consequence of the disease. Given its association with CD, the therapeutic potential of fecal microbiota transplantation (FMT) has been explored. This review examines the role of gut microbiota in CD, evaluates the therapeutic potential of probiotics and FMT, and highlights current research findings and limitations. Key studies on the relationship between gut dysbiosis, probiotics, and FMT in CD were analyzed, with a focus on randomized trials, meta-analyses, and clinical observations. Dysbiosis is a consistent feature of CD, but its causative role remains unclear. Probiotics, prebiotics, and synbiotics have shown no efficacy in inducing or maintaining remission in CD. FMT shows potential as a therapeutic option for CD, but its efficacy remains inconsistent and inconclusive. The variability in outcomes, including diminished effects over time despite repeated FMT, underscores the need for larger, well-controlled trials. Only one randomized controlled trial (RCT) has compared FMT with sham transplantation, but the sample size was very small. Other studies are limited by factors such as small sample sizes, lack of control groups, short follow-up periods, and inconsistent methodologies, making it challenging to draw definitive conclusions. While gut dysbiosis likely plays a role in CD pathogenesis, its causative role remains uncertain. Current evidence does not support FMT as a reliable treatment for inducing or maintaining remission in CD, though it appears generally safe. Larger, standardized, RCTs are necessary to clarify the therapeutic role of FMT in CD management.},
}

@article {pmid40900041,
year = {2025},
author = {Xue, M and Zhang, X and Zhou, Y and Yan, J and Gao, H and Bai, Y and Shi, J and Liu, Y and Xu, Y and Zhang, N and Li, L and Shi, S and Liang, H},
title = {Sulfated Fucooligosaccharides Ameliorated Neuroinflammation in D-Galactose-Induced Aging Model Mice via the Gut-Brain Axis.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c08350},
pmid = {40900041},
issn = {1520-5118},
abstract = {This study was aimed to reveal the neuroprotective effect of sulfated fucooligosaccharides (FOS) in an aging mouse model induced by d-galactose. The results showed that FOS treatment ameliorated inflammation, improved behavioral decline in memory and cognition, and exerted neuroprotective effects. FOS reduced microglia activation by decreasing the expression of P38 mitogen-activated protein kinase (P38 MAPK), cyclic-AMP response binding protein (CREB), cyclooxygenase-2 (COX-2), and prostaglandin E2 (PGE2). In addition, FOS improved intestinal mucosal barrier damage and reduced the release of lipopolysaccharide. FOS increased the diversity of the gut flora and promoted a significant enrichment of the Akkermansia genus. FOS also increased the butyric acid level and reduced the expression of histone deacetylase 3 (HDAC3), Toll-like receptor 4 (TLR4), and nuclear factor kappa-B (NF-κB). Fecal microbiota transplantation from the FOS-treated mice showed a similar effect to FOS treatment in inhibiting neuroinflammation and reduced d-galactose-induced cognitive dysfunction. The results suggested that FOS supplementation ameliorated d-galactose-induced neuron damage and exerted neuroprotective effects through the gut-brain axis.},
}

@article {pmid40899744,
year = {2025},
author = {Jin, JY and Yang, XY and Feng, R and Ye, ML and Xu, H and Wang, JY and Hu, JC and Zuo, HT and Lu, JY and Song, JY and Zhao, Y and Wang, Y and Tong, Q},
title = {Gut Microbiota-Derived Metabolites Orchestrate Metabolic Reprogramming in Diabetic Cardiomyopathy: Mechanisms and Therapeutic Frontiers.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {39},
number = {17},
pages = {e71004},
pmid = {40899744},
issn = {1530-6860},
support = {2022YFA0806400//the National Key R&D Program of China/ ; 2022YFC3601305//the National Key R&D Program of China/ ; 2021-I2M-1-028//the CAMS Innovation Fund for Medical Sciences/ ; 2021-I2M-1-027//the CAMS Innovation Fund for Medical Sciences/ ; 2023-I2M-2-006//the CAMS Innovation Fund for Medical Sciences/ ; 82173888//the National Natural Science Foundation of China/ ; 81973290//the National Natural Science Foundation of China/ ; Z141102004414062//the Beijing Key Laboratory of Non-Clinical Drug Metabolism and PK/PD study/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Animals ; *Diabetic Cardiomyopathies/metabolism/microbiology/therapy ; Energy Metabolism ; Oxidative Stress ; Metabolic Reprogramming ; },
abstract = {Diabetic cardiomyopathy (DCM) is a major cardiovascular complication of diabetes mellitus, characterized by myocardial structural and functional abnormalities in the absence of overt coronary artery disease or hypertension. A growing body of evidence implicates the gut microbiota and its metabolites as key modulators of systemic metabolic homeostasis, influencing energy metabolism, inflammation, and oxidative stress. The gut microbiota emerges as a novel regulator of cardiac remodeling and metabolic reprogramming in DCM through the gut-heart axis. This review aims to synthesize current mechanistic insights into how gut microbiota and its bioactive metabolites contribute to metabolic reprogramming in DCM. It further evaluates the potential of microbiota-targeted interventions as emerging therapeutic strategies to mitigate disease progression and restore cardiac homeostasis. A narrative, mechanistically focused literature review was conducted using PubMed and Web of Science databases. It covered experimental, preclinical, and translational studies up to April 2025. Articles were selected based on relevance to gut microbial metabolism, host cardiac metabolic pathways, and therapeutic interventions linked to DCM. Gut microbiota-derived metabolites-including short-chain fatty acids (SCFAs), trimethylamine N-oxide (TMAO), bile acids, lipopolysaccharides (LPS), tryptophan catabolites, and hydrogen sulfide-modulate cardiometabolic pathways via epigenetic regulation, altered energy substrate utilization, inflammatory signaling, and mitochondrial oxidative stress. These metabolites influence insulin resistance, lipid accumulation, mitochondrial dynamics, and cardiac fibrosis. Therapeutic strategies such as dietary modulation, probiotics, prebiotics, fecal microbiota transplantation, and drugs like SGLT2 inhibitors and GLP-1 receptor agonists have shown promising effects in modulating gut microbiota composition and alleviating DCM phenotypes in animal models. However, clinical evidence remains limited. The gut microbiota plays a pivotal role in the pathogenesis and potential treatment of DCM through its ability to reprogram host metabolism and inflammation. While preclinical data are compelling, further translational research-including humanized models and multi-omics integration-is required to validate microbiota-targeted therapies for cardiovascular applications. Targeting the microbiota-metabolite axis offers an innovative therapeutic avenue for personalized intervention in diabetic heart disease.},
}

Humans
*Gastrointestinal Microbiome/physiology
Animals
*Diabetic Cardiomyopathies/metabolism/microbiology/therapy
Energy Metabolism
Oxidative Stress
Metabolic Reprogramming

@article {pmid40899722,
year = {2025},
author = {Shi, X and Wan, L and Ni, S and Wu, X and Mu, J and Pei, W and Chen, Z and Xia, Y and Li, L and Zhang, Z},
title = {Chronic Exposure to Sunset Yellow Promotes Susceptibility to Experimental Colitis in Mice through Gut Microbiota.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c06410},
pmid = {40899722},
issn = {1520-5118},
abstract = {Sunset yellow (SY) is a widely used food additive. However, its impacts on ulcerative colitis (UC) development remain unclear. Here, SY exposure exacerbated dextran sulfate sodium (DSS)-induced UC symptoms in mice, including body weight loss, elevated disease activity index, histological damage, inflammation, gut barrier impairment, disruption of gut microbiota composition, and sulfur metabolism. Moreover, fecal microbiota transplantation from SY-exposed mice also exacerbated colitis in the recipient mice. Notably, SY exposure both in vivo and in vitro inhibited the growth of Akkermansia muciniphila (AKK). Nontargeted metabolomics revealed that SY exposure impaired glutathione (GSH) metabolism, as evidenced by reduced GSH and glutathione disulfide levels in both normal and colitis mice. In AKK, SY exposure significantly decreased GSH content, suppressed glutathione S-transferase activity, and disrupted sulfur metabolism. Importantly, GSH supplementation markedly reversed the SY-induced AKK growth inhibition. Collectively, these findings suggest that long-term SY exposure promotes experimental colitis in mice through gut microbiota-dependent GSH metabolic dysregulation.},
}

@article {pmid40899693,
year = {2025},
author = {Bo, T and Xu, X and Liu, H and Tang, L and Xu, H and Zhao, S and Lv, J and Wang, D},
title = {Convergent gut microbial functional strategies drive energy metabolism adaptation across Ursidae species and challenge the uniqueness of giant panda.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf201},
pmid = {40899693},
issn = {1751-7370},
abstract = {The gut microbiota is a key regulator of host energy metabolism, but its role in seasonal adaptation and evolution of bears is still unclear. Although giant pandas are considered an extraordinary member of the Ursidae family due to their specialized herbivory and low metabolic rate, there is still controversy over whether the metabolic regulation mechanism of their gut microbiota is unique. This study analyzed the seasonal dynamics of gut microbiota in giant pandas (Ailuropoda melanoleuca), Asian black bears (Ursus thibetanus), brown bears (Ursus arctos), and polar bears (Ursus maritimus), and combined with fecal microbiota transplantation (FMT) experiments, revealed the following findings. The microbial composition of the four bear species is similar, with both Firmicutes and Proteobacteria dominating. The enrichment of Firmicutes in winter enhances lipid metabolism, and adapts to dietary differences, indicating the existence of convergent microbial functional strategies in the Ursidae family. Our results demonstrate that bear gut microbiota promoted seasonal adaptation. In FMT experiments, bear gut microbiota in winter may had stronger functional capabilities on regulating host energy metabolism in mice, and regulate host appetite to increase energy intake. Finally, despite feeding on bamboo, giant pandas microbiota driven energy metabolism pathways (such as SCFAs) are highly conserved compared to other bears, suggesting a deep commonality in the adaptability of bear microbiota in evolution. Therefore, this study challenges the traditional view of microbial uniqueness of giant pandas, and emphasizes the co-evolutionary mechanism of energy metabolism adaptation in bear animals through microbial plasticity. In the future, it is necessary to integrate wild samples to eliminate the interference of captive diet and further analyze the genetic basis of host gut microbiota interactions.},
}

@article {pmid40541100,
year = {2025},
author = {Tang, X and Mao, M and Zhang, X and Gao, H and Wang, Z and Fang, R and Cheng, HW and Jiang, S},
title = {Cecal microbiota transplantation enhances calcium retention through modulation of gut microbiota and intestinal calcium transporter gene expression in chicks.},
journal = {Poultry science},
volume = {104},
number = {9},
pages = {105437},
pmid = {40541100},
issn = {1525-3171},
mesh = {Animals ; *Chickens/microbiology/genetics/metabolism/growth & development/physiology ; *Gastrointestinal Microbiome/physiology ; Cecum/microbiology ; Female ; *Fecal Microbiota Transplantation/veterinary ; *Avian Proteins/metabolism/genetics ; Random Allocation ; *Gene Expression ; *Calcium/metabolism ; },
abstract = {Bone development during early life is crucial for maintaining skeletal health and productivity in laying hens. The aim of this study was to investigate the effects of transferring cecal bacterial material of healthy adult hens on growth performance, gut integrity, microbial development, and bone metabolism of recipient chicks. Cecal contents were collected from 12 healthy Lohmann Pink-shell laying hens aged 47 weeks (donors). A total of 120 1-day-old Lohmann Pink chicks (recipients) were randomly assigned to 2 treatments for a 34-day trial: CONT (0.1 mL saline, Control) and CMT (0.1 mL cecal microbial solution). Each group had 10 replicates and 6 chicks per replicate. The pooled cecal sample as well as saline was administered via oral gavage once daily from day 1 to day 10, and then boosted on days 16, 23, and 30. One bird from each replicate was randomly taken for sample collection at day 34 (n=10). The results showed that CMT chicks had significantly higher Ca and P retention rates than CONT chicks. The mRNA expressions of intestinal Ca transporters, CaBP-D28K and VDR in the ileum and NCX1 in the jejunum, were also upregulated in CMT chicks. Additionally, the mRNA expression of a tight junction protein, ZO-1, was upregulated in the duodenum of CMT chicks. CMT chicks also had higher mRNA expressions of pro-inflammatory cytokines, IL-6, IL-1β, and TNF-α, in the intestinal tract. Furthermore, CMT chicks had a more diverse and mature gut microbial community compared to CONT chicks. The relative abundances of SCFA-produced bacteria (e.g., Bacteroides, Rikenellaceae_RC9_gut_group, and Prevotellaceae_UCG-001) were increased, while the relative abundances of Alistipes, Lactobacillus, and Barnesiella were reduced in CMT chicks. However, there were no CMT effects on body weight, organ indexes, bone morphology, and gene expression-associated with bone metabolism. This study demonstrates that transferring cecal bacteria from adult laying hens enhances calcium absorption and retention in newly hatched chicks by upregulating key calcium transporters and enhancing intestinal barrier integrity via modulating the gut microbiome.},
}

Animals
*Chickens/microbiology/genetics/metabolism/growth & development/physiology
*Gastrointestinal Microbiome/physiology
Cecum/microbiology
Female
*Fecal Microbiota Transplantation/veterinary
*Avian Proteins/metabolism/genetics
Random Allocation
*Gene Expression
*Calcium/metabolism

@article {pmid40898211,
year = {2025},
author = {Ma, X and Shi, W and Wang, Z and Li, S and Ma, R and Zhu, W and Wu, L and Feng, X and Cong, B and Li, Y},
title = {Butyric acid and valeric acid attenuate stress-induced ferroptosis and depressive-like behaviors by suppressing hippocampal neuroinflammation.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {974},
pmid = {40898211},
issn = {1479-5876},
support = {82130055//Key Projects of the National Natural Science Foundation of China/ ; 82293651//Major Projects of the National Natural Science Foundation of China/ ; 82072109//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Depression is closely associated with stress-induced hippocampal damage and dysfunction. Emerging evidence demonstrates that the gut microbiota and its metabolites, acting as probiotics or prebiotics, can modulate brain structure and function via the gut-brain axis, thereby offering therapeutic potential for ameliorating related neurological and psychiatric disorders. This study delves into the contribution of the gut microbiota and its metabolites to stress-induced ferroptosis of hippocampal neurons and the associated molecular pathways.

METHODS: This study used time-course stress paradigms combined with ferroptosis inhibitors to identify hippocampal neuronal ferroptosis. Fecal microbiota transplantation were conducted to analyze the role of gut microbiota in this process. Subsequently, 16 S rDNA sequencing and metabolomics techniques were applied to identify key gut microbiota and metabolites. Metabolites intervention were performed to examine their causal relationship with neuronal ferroptosis. Finally, we used histochemical and molecular assays to assess both intestinal and blood-brain barrier integrity as well as inflammation in peripheral blood and hippocampal tissue, along with GPR41/RhoA/Rock1 pathway changes, to preliminarily investigate the molecular mechanisms underlying stress-induced hippocampal neuronal ferroptosis.

RESULTS: We demonstrated that stress triggered hippocampal neuronal ferroptosis and subsequent depressive-like behaviors in mice. Fecal microbiota transplantation successfully replicated the ferroptosis phenotype. Butyric acid and valeric acid were identified as key metabolites significantly reduced in the serum of acutely and chronically stressed mice, respectively. Intervention with these metabolites markedly alleviated ferroptosis. Furthermore, valerate intervention increased hippocampal GPR41 expression and significantly suppressed the pro-inflammatory RhoA/Rock1 pathway in chronically stressed mice, thereby reducing neuroinflammation and ameliorating neuronal ferroptosis. However, butyrate intervention showed no significant effect on the GPR41/RhoA/Rock1 pathway.

CONCLUSION: Stress induces ferroptosis in hippocampal neurons, where reduced abundance of short-chain fatty acid-producing bacteria plays a key role. Key metabolites butyric acid and valeric acid alleviate neuroinflammation to improve ferroptosis via the gut-brain axis in acute and chronic stress, respectively. Specifically, valeric acid exerts neuroprotective effect through the GPR41/RhoA/Rock1 pathway, whereas butyric acid-mediated protection likely operates through alternative mechanisms.},
}

@article {pmid40895486,
year = {2025},
author = {Ge, S and Zhang, S and She, L and Gu, T and Wang, S and Huang, X and Wang, L and Miao, M},
title = {Synergistic therapy of Chinese herbal medicine and gut microbiota modulation for post-stroke cognitive recovery: focus on microbial metabolite and immunoinflammation.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1623843},
doi = {10.3389/fmicb.2025.1623843},
pmid = {40895486},
issn = {1664-302X},
abstract = {Post-stroke cognitive impairment (PSCI), a common complication following stroke, significantly impacts patients' quality of life and rehabilitation. Recent studies have highlighted the role of gut microbiota and their metabolites in modulating immunoinflammation and cognitive function via the gut-brain axis. Traditional Chinese medicine (TCM) and microbiota interventions including probiotics and fecal microbiota transplantation, have shown potential in reshaping gut microbial communities and metabolite profiles. Some studies suggest that combining these approaches via identical or related therapeutic mechanisms may yield enhanced efficacy in treating Post-Stroke Cognitive Impairment (PSCI). These findings establish a theoretical foundation for future research and clinical practice. This review systematically examines the mechanistic role of gut microbial metabolites in neuroimmune modulation and comprehensively evaluates the therapeutic potential of combined TCM and microbiota-targeted therapies for PSCI, adopting a multifactorial approach that addresses neuroinflammation, microbial dysbiosis, and metabolic dysregulation.},
}

@article {pmid40895468,
year = {2025},
author = {Yang, J and Chen, J and Li, D and Wu, Q and Zhang, Y and Li, Y and Deng, Y},
title = {Hyperuricemia and the gut microbiota: current research hotspots and future trends.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1620561},
doi = {10.3389/fmicb.2025.1620561},
pmid = {40895468},
issn = {1664-302X},
abstract = {BACKGROUND: Hyperuricemia (HUA), found widely in humans and birds, is a key physiological factor responsible for the development of gout. In recent years, the relationship between the gut microbiota and HUA has garnered significant attention from researchers. This study aims to explore the current research hotspots, knowledge gaps, and future research trends regarding the gut microbiota and HUA.

METHODS: We performed a thorough search of the literature on gut flora and HUA published between 2005 and 2024 using the Web of Science and PubMed databases. The resulting data were analyzed using VOSviewer, CiteSpace, and Bibliometrix.

RESULTS: Including 735 papers in total, the study found that the number of publications in the subject increased significantly between 2020 and 2024, with 2024 being the year with the highest number of publications. The primary research countries are highlighted as China and the United States, with institutions such as the University of California, San Diego, and Qingdao University making significant contributions. Sanjay K. Nigam and Chenyang Lu have made the most important contributions as authors. Keywords analysis highlighted high-frequency terms including "gastrointestinal microbiome," "uric acid," "hyperuricemia," "inflammation," "gout," and "probiotics." In the visualization map of the keyword timeline, emerging research hotspots include "diets," "dietary fiber," "fecal microbiota transplantation," and "gut-kidney axis."

CONCLUSION: This study is the first to conduct a quantitative literature analysis in the field of gut microbiota in HUA, revealing that the core research hotspots include disease-related microbiota characteristics, probiotic therapy, microecological intervention, and the gut-distal target organ axis. The emerging hotspots focus on dietary supplementation, fecal microbiota transplantation (FMT) treatment strategies, and in-depth research on the above organ axes. Provide valuable guidance for future research directions.},
}

@article {pmid40895097,
year = {2025},
author = {Jin, Y and Wang, H and Song, J},
title = {Gut-brain axis modulation in remote rehabilitation of Parkinson's disease: reconstructing the fecal metabolome and nigral network connectivity.},
journal = {Frontiers in neurology},
volume = {16},
number = {},
pages = {1644490},
doi = {10.3389/fneur.2025.1644490},
pmid = {40895097},
issn = {1664-2295},
abstract = {The pathogenesis of Parkinson's disease (PD) is gradually evolving from a central neurodegeneration-centered concept to a multi-pathway pathological model at the gut-brain system level. Studies have shown that PD patients commonly exhibit dysbiosis, reduced short-chain fatty acids (SCFAs; microbial fermentation products of dietary fiber that play key roles in host metabolism and immune regulation), abnormal tryptophan metabolism, and impaired gut barrier function. These alterations may contribute to dopaminergic neuronal damage through mechanisms including neuroinflammation, oxidative stress, and α-synuclein (α-syn) aggregation. The vagus nerve plays a critical role in bidirectional gut-brain signaling, and its dysfunction may represent a key route for pathological protein transmission from the periphery to the brain. In response, remote rehabilitation and gut-targeted interventions-including probiotics, prebiotics, dietary modulation, fecal microbiota transplantation (FMT), and transcutaneous vagus nerve stimulation (tVNS)-have shown potential in improving neurological function and inflammation in both animal and clinical studies. Multimodal data analyses have revealed significant associations between SCFA levels in fecal metabolomics and brain imaging features. Despite ongoing challenges in mechanistic extrapolation, biomarker sensitivity, and translational implementation, the integration of metagenomics, metabolomics, neuroimaging, and digital therapeutics-collectively referred to as multi-omics and digital profiling techniques-represents an emerging research direction with the potential to inform future clinical paradigms for precision remote management of PD.},
}

@article {pmid40894980,
year = {2025},
author = {Wang, YM},
title = {How to Approach Immune Checkpoint Inhibitor Enterocolitis.},
journal = {Gastroenterology & hepatology},
volume = {21},
number = {8},
pages = {501-503},
pmid = {40894980},
issn = {1554-7914},
}

@article {pmid40894608,
year = {2025},
author = {Lopez, ML and Kang, T and Espeleta, A and Rubtsova, VI and Baek, J and Songcuan, J and Moyer, EM and Kim, J and Song, WS and Jung, S and D'Sa, N and Anica, A and Tran, E and Chun, Y and Choi, W and Jang, KH and Kelly, ME and Tamburini, IJ and Alam, YH and Le, J and Ramirez, CB and Kataru, RP and Hong, SP and Nicholas, DA and Xue, KS and Lee, G and Bae, H and Jang, C},
title = {Intestinal catabolism of dietary fructose promotes obesity and insulin resistance via ileal lacteal remodeling.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.08.18.670963},
pmid = {40894608},
issn = {2692-8205},
abstract = {UNLABELLED: High-fructose corn syrup (HFCS) consumption is a risk factor for obesity and metabolic syndrome, yet the underlying mechanisms are incompletely understood. Catabolism of dietary fructose primarily occurs in the small intestine and liver, with fructose breakdown in the liver being pathological, while small intestinal fructose clearance protects the liver. Here, we unexpectedly found that inhibition of fructose catabolism specifically in the small intestine mitigates fructose-induced obesity and insulin resistance. Mechanistically, blocking intestinal fructose catabolism reduces dietary fat absorption, which is associated with a decrease in the surface area of the ileal lacteals and alterations in gut microbiome. Fecal transplantation experiments revealed that such a microbiome stimulates the intestine-resident macrophages, promoting lacteal growth and boosting dietary fat absorption. Given the preclinical and clinical studies reporting the effect of fructose catabolism suppression on mitigating diet-induced obesity, our data suggest that such effects are partly mediated by intestinal lacteal remodeling.

SIGNIFICANCE STATEMENT: Here, we uncover a previously unappreciated link between intestinal fructose catabolism and ileal lacteal remodeling, suggesting the mechanisms by which fructose intake promotes obesity. Using mice lacking the fructose-processing enzyme specifically in the intestine, we show that blocking intestinal fructose metabolism protects against diet-induced obesity by reducing fat absorption. Changes in gut microbiome and immune cell interactions drive this effect.},
}

@article {pmid40894444,
year = {2025},
author = {Xu, P},
title = {Gut Microbiota Metabolites Targeting the Immune Response in Sepsis: Mechanisms and Therapies.},
journal = {International journal of general medicine},
volume = {18},
number = {},
pages = {4709-4734},
doi = {10.2147/IJGM.S539237},
pmid = {40894444},
issn = {1178-7074},
abstract = {Sepsis is a global health challenge, affecting millions annually and remaining a leading cause of mortality in intensive care units. Gut microbiota plays a complex role in the onset and progression of sepsis, with its alterations reflecting disease severity. Recently, modulating gut microbiota and its metabolites has emerged as a promising therapeutic strategy for sepsis. This review highlights the role of gut microbiota in sepsis and systematically identifies key immune response targets directly influenced by gut microbiota metabolites, such as short-chain fatty acids (SCFAs), bile acids, and indoleacetic acid, among other important metabolites. Additionally, it offers a full overview of current research on gut microbiota-regulated therapeutic approaches, including fecal microbiota transplantation (FMT) and artificial intelligence (AI) applications. These insights offer a novel perspective for advancing the understanding of sepsis pathogenesis and its treatment.},
}

@article {pmid40893829,
year = {2025},
author = {Allegretti, JR},
title = {Current Status of Fecal Microbiota Transplantation for Inflammatory Bowel Disease Management.},
journal = {Gastroenterology & hepatology},
volume = {21},
number = {7},
pages = {451-453},
pmid = {40893829},
issn = {1554-7914},
}

@article {pmid40891897,
year = {2025},
author = {Bertin, L and Bonazzi, E and Facchin, S and Lorenzon, G and Maniero, D and DE Barba, C and Tomasulo, A and Fortuna, A and Zingone, F and Barberio, B and Savarino, EV},
title = {The microbiota-brain connection in neurological diseases: the ubiquitous short-chain fatty acids.},
journal = {Minerva gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.23736/S2724-5985.25.03866-5},
pmid = {40891897},
issn = {2724-5365},
abstract = {The connection between the gut and brain forms a sophisticated two-way communication system where compounds produced by intestinal bacteria, especially short-chain fatty acids, play essential roles in brain-related disease processes. Evidence across multiple neurological disorders reveals convergent pathophysiological pathways involving SCFAs, which modulate neurological function via histone deacetylase inhibition, G-protein coupled receptor activation, and blood-brain barrier regulation. Clinical investigations demonstrate disorder-specific signatures: reduced butyrate-producing bacteria correlate with Parkinson's disease progression; Alzheimer's disease exhibits significant reductions in key SCFAs; and diminished butyrate production disrupts immunoregulatory homeostasis in multiple sclerosis. Additionally, neurodevelopmental disorders like autism show distinctive microbiome alterations affecting both gut and brain function. Beyond SCFAs, microbiota influence neural communication through immune modulation, neurotransmitter production, and vagus nerve signaling. Interventional studies targeting the microbiome through precision probiotics, prebiotics, and fecal microbiota transplantation demonstrate preliminary efficacy, particularly in Parkinson's disease and autism. Methodological heterogeneity and challenges establishing causality remain significant limitations. Future priorities include longitudinal characterization of microbiome dynamics preceding symptom onset, development of personalized therapeutics, and implementation of predictive computational models. Progress in these domains could transform microbiome-based approaches from experimental interventions to precision medicine applications in neurological disease management.},
}

@article {pmid40890737,
year = {2025},
author = {Lu, G and Zhang, S and Wang, R and Wu, X and Chen, Y and Wen, Q and Cui, B and Zhang, F and Li, P},
title = {Fecal microbiota transplantation improves bile acid malabsorption in patients with inflammatory bowel disease: results of microbiota and metabolites from two cohort studies.},
journal = {BMC medicine},
volume = {23},
number = {1},
pages = {511},
pmid = {40890737},
issn = {1741-7015},
support = {81873548//National Natural Science Foundation of China/ ; 82100583//National Natural Science Foundation of China/ ; 2020-3//Nanjing Medical University Fan Daiming Research Funds for Holistic Integrative Medicine/ ; },
abstract = {BACKGROUND: Bile acid malabsorption (BAM) or bile acid diarrhea (BAD) complicates more than 30% of Crohn's disease (CD), yet no non-invasive biomarker reliably identifies patients who will benefit from fecal microbiota transplantation (FMT). We investigated whether serum 7α-hydroxy-4-cholesten-3-one (C4), a hepatic bile-acid synthesis precursor, can predict BAM and FMT response in inflammatory bowel disease (IBD).

METHODS: We included 106 pairs of IBD patients treated with FMT from two longitudinal cohorts of prospective trials and 24 matched healthy individuals to identify a multi-omics analysis of microbiota-metabolism and evaluate real-world effectiveness of FMT. Fecal and serum samples before and after FMT along with medical information were collected and detected through 16S rRNA amplicon sequencing and untargeted liquid chromatography mass spectrometry. Mice models were used to preliminarily verify the exacerbation of colitis through administration of primary BAs and treated by FMT.

RESULTS: Patients in BAM group tended to achieve sustained higher and stable clinical response (66.67% vs. 49.41%) and remission (52.38% vs. 40.00%) than non-BAM group at 3 months after FMT, along with a significantly decrease of C4 (P < 0.001), improvement of obvious abdominal pain and diarrhea, which was especially obvious in CD patients with ileal resection and ileal /ileocolonic type. Random forest classifiers predicted BAM in IBD patients with 18 or top 4 differential OTUs, showing an area under the curve of 0.92 and 0.83, respectively. Furthermore, results from primary bile acid-induced colitis mice models reinforced these findings.

CONCLUSIONS: Serum C4 and a minimal gut microbiota may identify IBD patients with BAM who are most likely to achieve durable remission after FMT. These translatable biomarkers can guide precision use of microbiota-directed therapy.

TRIAL REGISTRATION: ClinicalTrials.gov: NCT01790061 and NCT01793831.},
}

@article {pmid40889045,
year = {2025},
author = {Wang, H and Wang, Y and Wu, H and Shen, C and Li, Y and Bai, B and Sun, X and Liu, Y and Zhang, Q and Shi, L},
title = {High-fat diet-induced obesity-related hypertension via altered gut microbiota-mediated histone butyrylation.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {40889045},
issn = {1869-1889},
abstract = {Hypertension is a chronic cardiovascular disease that significantly impacts human quality of life. Gut microbiota and its metabolites have been reported to be involved in lipid metabolism and blood pressure regulation, but the specific alterations and pathogenic mechanisms of gut microbiota in obesity-related hypertension (OrHTN) remain unclear. In this study, we observed a significant proliferation of Desulfobacterota and Proteobacteria, while a decrease in the abundance of several butyrate-producing bacterial genera, accompanied by decreased fecal and plasma butyrate levels in high-fat diet (HFD)-induced OrHTN rats. Histone 3 lysine 9 butyrylation (H3K9bu) modification in the kidney of OrHTN rats was reduced and downregulated the expression of the hypertension-related gene MAS1. Subsequent transplantation of cecal contents from OrHTN rats on HFD into recipient rats on a normal chow diet resulted in hypertension but without obesity. Furthermore, in vitro experiments suggested that sodium butyrate increased H3K9bu modification and the expression of MAS1 in a concentration-dependent manner. In conclusion, our findings suggest that gut microbiota may contribute to the development of OrHTN by altering the expression of hypertension-related genes through butyrate-mediated histone butyrylation. This work may provide new insights into the prevention and treatment of hypertension by targeting the regulation of gut microbiota and metabolites.},
}

@article {pmid40886868,
year = {2025},
author = {Wang, Z and Ren, X and Peng, Z and Zeng, M and Wang, Z and Chen, Q and Chen, J and Dai, X and Christian, M and Qie, X and He, Z},
title = {Flavonoid-rich extracts of Nelumbo nucifera leaves alleviate obesity in HFD-fed mice via microbiota-dependent modulation of brown fat thermogenesis.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {120513},
doi = {10.1016/j.jep.2025.120513},
pmid = {40886868},
issn = {1872-7573},
abstract = {Nelumbo nucifera Gaertn (lotus) leaf is a commonly used traditional Chinese herbal medicine with a wide range of pharmacological properties, especially lipid-lowering and weight-loss effects. Accumulating evidence highlights activation of the thermogenic program of brown adipose tissue (BAT) as a promising anti-obesity strategy. However, it remains unclear whether such beneficial metabolic effects induced by the lotus leaf are related to its regulatory role in BAT function.

AIM OF THE STUDY: This work aims to investigate whether the lotus leaf reduces obesity by activating BAT and to elucidate whether the mechanism behind it is related to the regulation of gut microbiota.

MATERIAL AND METHODS: A mouse model of obesity was established using a high-fat diet (HFD), and the anti-obesity effect of flavonoid-rich lotus leaf extract (LLE) was determined in vivo. An animal energy metabolism monitoring system confirmed that LLE promoted energy expenditure. Then, RT-qPCR, immunohistochemistry, and Western blotting were conducted to detect the expression of genes and proteins involved in BAT thermogenesis. Subsequently, the underlying mechanisms were demonstrated by 16S rRNA gene sequencing and non-targeted metabolism analysis. Finally, fecal microbiota transplantation (FMT) was performed to investigate the LLE-dependent alleviation of obesity via the gut microbiota-BAT axis.

RESULTS: Our study demonstrated that LLE effectively reduced weight gain, ameliorated glucolipid disorders, and enhanced energy expenditure in HFD-fed mice. Notably, LLE augmented BAT activity by increasing thermogenic markers (e.g., SIRT1, PGC-1α, UCP1) and repressing inflammatory responses, potentially through activation of β3-AR/AMPK/p38 signaling pathways. Importantly, LLE could mitigate HFD-induced microbial dysbiosis (decrease in Proteobacteria, Verrucomicbiota, Acidobacteriota, Bacteroides, Dubosiella, and increase in Bilophila, Tyzzerella, Oscillibacter, Akkermansia, and Alistipes) and significantly altered 5 metabolite pathways, especially primary bile acid biosynthesis and linoleic acid metabolism. The FMT experiment confirmed that the microbial changes induced by LLE were associated with reduced body weight, enhanced energy expenditure, increased BAT activity, and thermogenesis.

CONCLUSIONS: Collectively, our findings reveal that lotus leaf promotes brown fat thermogenesis by modulating gut microbiota, identifying it as a promising new treatment target for obesity.},
}

@article {pmid40886596,
year = {2025},
author = {Li, W and Wang, N and Lyu, D and Yu, X and He, X and Yu, K and Qiu, Y and Jiao, X},
title = {Gut dysbiosis mediates neurotoxic effects of environmentally relevant tylosin exposure in adult zebrafish.},
journal = {Ecotoxicology and environmental safety},
volume = {303},
number = {},
pages = {118960},
doi = {10.1016/j.ecoenv.2025.118960},
pmid = {40886596},
issn = {1090-2414},
abstract = {Tylosin, a widely used veterinary macrolide antibiotic, raises environmental concerns due to its persistence and potential health risks. However, the neurotoxic effects of chronic low-dose tylosin exposure remain unclear. This study assessed the neurotoxicity of chronic exposure to environmentally relevant tylosin concentrations (5000 ng/L) in adult zebrafish. Behavioral tests indicated anxiety- and depression-like behaviors, including reduced exploration and increased freezing. Histopathology revealed neuronal degeneration, evidenced by decreased Nissl staining in key brain areas. Transcriptomic analysis identified significant changes in genes related to neuroinflammation, synaptic dysfunction, immune response, and steroid metabolism. Multi-omics approaches further showed substantial alterations in gut microbiota composition and metabolic profiles, particularly involving tryptophan metabolism and steroid hormone synthesis. These gut changes correlated with impaired intestinal barrier function, including fewer goblet cells and reduced tight junction and mucin-2 protein expression. Fecal microbiota transplantation confirmed the role of altered gut microbiota in inducing anxiety- and depression-like behaviors, highlighting microbiota-gut-brain axis involvement. Molecular docking identified microbial metabolites (MG 20:4, 2E-dodecenedioic acid, Ononin) interacting with critical neurodevelopmental and stress-response proteins (LRAT, BHLHE40, HSPA5), potentially linking microbiota shifts to brain dysfunction. Our results demonstrate that chronic environmental tylosin exposure induces neurotoxicity through gut dysbiosis and compromised intestinal barriers, disrupting essential neuroactive pathways. These findings emphasize the importance of considering microbiota-gut-brain axis disruption in environmental antibiotic risk assessments.},
}

@article {pmid40885910,
year = {2025},
author = {Huang, W and Chai, Y and Li, X and Zhang, Q and Yan, Z and Wang, Y and Tao, X and Zhang, J and Qiu, F},
title = {Metagenomics and metabolomics to evaluate the potential role of gut microbiota and blood metabolites in patients with cerebral infarction.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {567},
pmid = {40885910},
issn = {1471-2180},
support = {2018YFA0108601//Clinical research on intracerebral precision transplantation of neural stem cells for stroke treatment/ ; L255012//The Huairou Innovation Joint Fund Project of Beijing Natural Science Foundation/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Cerebral Infarction/microbiology/blood/metabolism ; *Metabolomics/methods ; *Metagenomics/methods ; Male ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Middle Aged ; Female ; Aged ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Tandem Mass Spectrometry ; Adult ; Chromatography, High Pressure Liquid ; },
abstract = {Cerebral infarction, a cerebrovascular disorder, is characterized by the sudden onset of neurological deficits and clinical symptoms. It ranks among the leading causes of death and severe disability worldwide. The etiology of cerebral infarction is multifaceted, with common risk factors including dietary patterns, smoking, hypertension, and diabetes mellitus. In recent years, the role of the gut microbiota in systemic immunity and tumorigenesis has been intensively explored, thrusting the research on the gut-brain axis into the spotlight. However, there is a lack of literature investigating the relationship between the gut microbiota and blood metabolites in cerebral infarction. In this study, we employed 16S rRNA analysis and ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) for a comprehensive metagenomic and metabolomic analysis of fecal samples from cerebral infarction patients and the general population. Our results revealed a significant correlation between the gut microbiome and serum metabolites, highlighting the impact of the microbiome on metabolic pathways. Specifically, we found that 35 gut microbiome taxa, such as Actinobacteriota and Peptostreptococcales-Tissierellales, were significantly enriched in the control group (N group). Through Linear Discriminant Analysis Effect Size (LEfSe) analysis, 72 taxa showed significant differences between cerebral infarction patients and healthy individuals. Among them, 22 key taxa were identified as microbial biomarkers for differentiating patients from healthy controls. These findings suggest that variations in the microbiome and metabolites could potentially serve as biomarkers for future diagnostic and therapeutic strategies in cerebral infarction.},
}

Humans
*Gastrointestinal Microbiome
*Cerebral Infarction/microbiology/blood/metabolism
*Metabolomics/methods
*Metagenomics/methods
Male
RNA, Ribosomal, 16S/genetics
Feces/microbiology
Middle Aged
Female
Aged
*Bacteria/classification/genetics/isolation & purification/metabolism
Tandem Mass Spectrometry
Adult
Chromatography, High Pressure Liquid

@article {pmid40884832,
year = {2025},
author = {Chen, S and Liu, F and Han, X and Jia, D and Chen, J and Wei, Y and Yu, Z and He, L and Liao, C and Ding, K},
title = {Exposure to Bovine Viral Diarrhea Virus Disrupts Intestinal Barrier Function via NLRP3/Caspase-1-Mediated Pyroptosis and Gut Microbiota Dysbiosis.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c04854},
pmid = {40884832},
issn = {1520-5118},
abstract = {Bovine viral diarrhea virus (BVDV) is a major global pathogen that causes severe economic losses in dairy herds due to diarrhea, reproductive disorders, and reduced milk yield. Despite its well-documented systemic effects, the mechanism of BVDV-induced intestinal damage remains unclear. In our study, BVDV triggered cytopathic effects in intestinal epithelial cells, including cell death, goblet cell depletion, and disruption of barrier proteins. Although BVDV alters gut microbiota by activating the NLRP3/caspase-1 inflammasome pathway and thereby causing pyroptosis and intestinal injury, fecal microbiota transplantation mitigated those effects by suppressing NLRP3/caspase-1's activation. Those findings reveal key pathways in BVDV's pathogenesis and suggest novel therapeutic strategies to combat livestock infections.},
}

@article {pmid40882395,
year = {2025},
author = {Chen, X and Zou, J and Hong, T and Zhang, H and Yang, J and Mai, H and Shi, H and Li, X and Feng, D},
title = {Bisphenol A increases fat mass in adipose tissue by disturbing gut microbiota-dependent bile acid metabolism and TGR5/UCP1 signaling pathways in CD-1 mice.},
journal = {Ecotoxicology and environmental safety},
volume = {303},
number = {},
pages = {118922},
doi = {10.1016/j.ecoenv.2025.118922},
pmid = {40882395},
issn = {1090-2414},
abstract = {Disorder of gut microbiota-mediated bile acid (BA) metabolism plays a pivotal role in the pathogenesis of obesity. Our previous research showed that bisphenol A (BPA) exposure induced hepatic fat accumulation and gut microbiota dysbiosis. However, whether the gut microbiota-dependent BA metabolism alteration is involved in BPA-induced fat accumulation and obesity remains elusive. This study aimed to investigate the gut microbiota-dependent metabolic mechanism of obesity induced by BPA. Male CD-1 mice were exposed to a low dose of BPA (50 μg/kg/day) for six months. Our findings demonstrated that BPA exposure significantly augmented the fat mass of both brown and white adipose tissue, along with the proportion of adipose tissue weight relative to body weight. Furthermore, BPA reduced the relative abundance of Bacteroides, Parabacteroides, and Akkermansia, which are associated with BA metabolism. Additionally, serum levels of lithocholic acid, the most potent activator of Takeda G protein-coupled receptor 5 (TGR5), and TGR5 expression in adipose tissue were substantially diminished following BPA exposure. Inhibition of TGR5 reduced cyclic adenosine monophosphate levels, subsequently decreasing the expression of iodothyronine deiodinase 2 and fibroblast growth factor 21. These changes down-regulated the expression of uncoupling protein 1 (UCP1), ultimately leading to reduced energy expenditure and increased fat mass. Moreover, further fecal microbiota transplantation and microbiota elimination confirmed the role of gut microbiota in BPA-induced adverse effects. Collectively, our study demonstrated that the suppression of gut microbiota-BA-TGR5/UCP1 signaling pathways may constitute a potential mechanism underlying BPA-induced fat mass gain, providing a novel target for the prevention of BPA-induced obesity.},
}

@article {pmid40881288,
year = {2025},
author = {Pourrat, A and Baillieu, V and Ansel, S and Leonardi, M and Poiron, P and Bellais, S and Paul, M and Nebbad, B},
title = {Standardized freeze-dried FMT: is the ideal protectant out there?.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1618067},
doi = {10.3389/fmicb.2025.1618067},
pmid = {40881288},
issn = {1664-302X},
abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) is an effective treatment for recurrent Clostridioides difficile infections. Freeze-drying offers a next-generation, more practical, and aesthetically acceptable FMT formulation that could facilitate standardized preparation methods. Viable preservation is a critical step in freeze-drying, yet no universal medium effectively protects both anaerobes and aerobes.

OBJECTIVE: This study aimed to evaluate different protectants compared to trehalose 5% (T5) after confirming its efficacy.

METHODS: A mix of inulin and glucosamine (IG5) and a High-antioxidant Matrix with trehalose (HM) were tested. Viability was assessed using colony-forming unit (CFU) enumeration and flow cytometry with a LIVE/DEAD™ staining method.

RESULTS: T5 demonstrated satisfactory bacterial recovery after freeze-drying, with viability of 84 ± 28% for anaerobes and 59 ± 39% for Bifidobacterium (BIF), confirming its efficiency in our preparation facilities. While HM showed highest results (91 ± 7% for anaerobes, 121 ± 33% for BIF), it did not significantly outperform T5. IG5, however, resulted in a significant loss of bacteria, with only 16 ± 12% viability for anaerobes (p = 0.016) and 19 ± 9% for BIF (p = 0.031).

CONCLUSION: HM and T5 both proved effective for freeze-dried FMT, with HM yielding the highest recovery but not significantly outperforming T5. Given its simplicity and consistent results, T5 may serve as a reliable standalone protectant or as a base for improved formulations. IG5 showed significant bacterial loss and is unsuitable. Further biological validation and stability data will guide the development of optimized freeze-dried oral FMT capsules.},
}

@article {pmid40880458,
year = {2025},
author = {Dinis, L and Pinheiro, H and Póvoa, P and Calhau, C and Pestana, D and Marques, C},
title = {Advancing Access to Intestinal Microbiota Transplant: Bridging the Gap Between National Practices and the European Strategy.},
journal = {Acta medica portuguesa},
volume = {},
number = {},
pages = {},
doi = {10.20344/amp.22750},
pmid = {40880458},
issn = {1646-0758},
abstract = {Clostridioides difficile is an opportunistic pathogen that can cause a range of conditions, from asymptomatic carriage to severe illness, posing a significant public health threat due to its high mortality rates and substantial healthcare costs. Traditional treatment options, including antibiotics, often fail to eradicate the infection, leading to recurrent cases that severely impact patients' lives. Intestinal microbiota transplant (IMT) has emerged as an effective strategy for decolonizing pathogenic agents, demonstrating safety and efficacy, particularly in treating recurrent Clostridioides difficile infection (rCDI). Despite its potential, access to IMT is limited due to safety concerns, logistical challenges, and a lack of proper guidance, underscoring the urgent need for structured intestinal microbiota banks (IMBs). These organized facilities are crucial for the collection, screening, processing, and distribution of intestinal microbiota preparations, thereby facilitating the clinical application of IMT. In this narrative review, we discuss the relevance of applying IMT for the treatment of rCDI in Europe, with a focus on Portugal. We highlight the existence and distribution of IMBs across Europe and their importance in improving access to IMT. This review also addresses the challenges in creating an IMB and the development of such a structure in Portugal as a centralized repository for high-quality, standardized microbiota preparations, making IMT accessible for national hospitals. Additionally, it emphasizes the need to raise awareness among healthcare providers and the public to support the broader adoption of IMT.},
}

@article {pmid40878918,
year = {2025},
author = {Liu, X and Xie, Y and Yang, S and Jiang, C and Shang, K and Luo, J and Zhang, L and Hu, G and Liu, Q and Yue, B and Fan, Z and He, Z and Li, J},
title = {Multi-omics investigation of spontaneous T2DM macaque emphasizes gut microbiota could up-regulate the absorption of excess palmitic acid in the T2DM progression.},
journal = {eLife},
volume = {14},
number = {},
pages = {},
pmid = {40878918},
issn = {2050-084X},
support = {2021YJ0136//Science and Technology Foundation of Sichuan Province/ ; 32171607//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Diabetes Mellitus, Type 2/microbiology/pathology/metabolism ; *Palmitic Acid/metabolism ; Macaca mulatta ; Mice ; Disease Models, Animal ; Male ; Gene Expression Profiling ; Metabolome ; RNA, Ribosomal, 16S/genetics ; Disease Progression ; Multiomics ; },
abstract = {Although gut microbiota and lipid metabolites have been suggested to be closely associated with type 2 diabetes mellitus (T2DM), the interactions between gut microbiota, lipid metabolites, and the host in T2DM development remains unclear. Rhesus macaques may be the best animal model to investigate these relationships given their spontaneous development of T2DM. We identified eight spontaneous T2DM macaques and conducted a comprehensive study investigating the relationships using multi-omics sequencing technology. Our results from 16 S rRNA, metagenome, metabolome, and transcriptome analyses identified that gut microbiota imbalance, tryptophan metabolism and fatty acid β oxidation disorders, long-chain fatty acid (LCFA) accumulation, and inflammation occurred in T2DM macaques. We verified the accumulation of palmitic acid (PA) and activation of inflammation in T2DM macaques. Importantly, mice transplanted with spontaneous T2DM macaque fecal microbiota and fed a high PA diet developed prediabetes within 120 days. We determined that gut microbiota mediated the absorption of excess PA in the ileum, resulting in the accumulation of PA in the serum, consequently leading to T2DM in mice. In particular, we demonstrated that the specific microbiota composition was probably involved in the process. This study provides new insight into interactions between microbiota and metabolites and confirms causative effect of gut microbiota on T2DM development.},
}

Animals
*Gastrointestinal Microbiome
*Diabetes Mellitus, Type 2/microbiology/pathology/metabolism
*Palmitic Acid/metabolism
Macaca mulatta
Mice
Disease Models, Animal
Male
Gene Expression Profiling
Metabolome
RNA, Ribosomal, 16S/genetics
Disease Progression
Multiomics

@article {pmid40877311,
year = {2025},
author = {Wilson, BC and Zuppi, M and Derraik, JGB and Albert, BB and Tweedie-Cullen, RY and Leong, KSW and Beck, KL and Vatanen, T and O'Sullivan, JM and Cutfield, WS and , },
title = {Long-term health outcomes in adolescents with obesity treated with faecal microbiota transplantation: 4-year follow-up.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {7786},
pmid = {40877311},
issn = {2041-1723},
mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; Adolescent ; Male ; Female ; Follow-Up Studies ; Double-Blind Method ; *Pediatric Obesity/therapy ; Treatment Outcome ; Body Composition ; Body Mass Index ; Gastrointestinal Microbiome ; *Obesity/therapy ; Metabolic Syndrome/therapy ; Feces/microbiology ; },
abstract = {Faecal microbiota transplantation (FMT) has been explored as a potential treatment for obesity, but its long-term effects on metabolic health remain unclear. Here, we report 4-year follow-up findings from a double-blind, randomised, placebo-controlled trial assessing FMT in adolescents with obesity (ACTRN12615001351505, Australian New Zealand Clinical Trials Registry). This unblinded follow-up study evaluated 63% (55/87) of the original participants (27 FMT, 28 placebo). There was no difference in BMI between the two groups, after adjusting for sex, age, diet, and physical activity (-3.6 kg/m[2], p = 0.095). However, FMT recipients showed clinical improvements in body composition and metabolic health compared to the placebo group. Specifically, FMT recipients had smaller waist circumference (-10.0 cm, p = 0.026), total body fat (-4.8%, p = 0.024), metabolic syndrome severity score (-0.58, p = 0.003), and systemic inflammation (-68% hs-CRP, p = 0.002) and higher levels of HDL cholesterol (0.16 mmol/L, p = 0.037). No group differences were observed in glucose markers, or other lipid parameters. Shotgun metagenomic sequencing revealed sustained long-term alterations in gut microbiome richness, composition and functional capacity, with persistence of donor-derived bacterial and bacteriophage strains. These findings highlight the potential relevance of FMT as a microbiome-augmenting intervention for obesity management and metabolic health, warranting further investigation.},
}

Humans
*Fecal Microbiota Transplantation/methods
Adolescent
Male
Female
Follow-Up Studies
Double-Blind Method
*Pediatric Obesity/therapy
Treatment Outcome
Body Composition
Body Mass Index
Gastrointestinal Microbiome
*Obesity/therapy
Metabolic Syndrome/therapy
Feces/microbiology

@article {pmid40876612,
year = {2025},
author = {Xie, X and Ge, W and Luo, Y and Xing, X and Sun, X},
title = {Ginsenoside Rb3 Modulates Gut Microbiota to Alleviate Cerebral Inflammation and Ferroptosis via the NLRP3/NF-κB/GPX4 Pathway in Rats with Cerebral Ischemia/Reperfusion Injury.},
journal = {European journal of pharmacology},
volume = {},
number = {},
pages = {178091},
doi = {10.1016/j.ejphar.2025.178091},
pmid = {40876612},
issn = {1879-0712},
abstract = {Cerebral ischemia/reperfusion injury (CIRI) poses a significant threat to human life and health. Ginsenoside Rb3 (Rb3) is known to exhibit protective effects against myocardial ischemia, its impact on CIRI remains unclear. Therefore, we investigated the protective effects of Rb3 on CIRI and its underlying mechanisms. Our results showed that Rb3 reduced cerebral infarct volume, decreased blood-brain barrier (BBB) permeability, and improved neurological deficits in CIRI rats. Rb3 also mitigated cerebral ferroptosis and alleviated neuroinflammation, as evidenced by decreased iron levels, reduced MDA content, an improved GSH/GSSG ratio, and lower levels of TNF-α, IL-1β, and IL-6, through modulation of the NLRP3/NF-κB/GPX4 pathway. Additionally, Rb3 alleviated intestinal inflammation, improved the intestinal barrier, and corrected gut microbiota dysbiosis and reduced the microbial metabolites TMAO and LPS in CIRI rats. It is noteworthy that in pseudo germ-free rats with CIRI, fecal microbiota transplants (FMT) from Rb3-treated rats conferred similar protective effects as Rb3. Summarily, this study reveals that Rb3 reduces neuroinflammation and ferroptosis in the brains of middle cerebral artery occlusion/reperfusion (MCAO/R) rats via the NLRP3/NF-κB/GPX4 pathway in a gut microbiota-dependent manner.},
}

@article {pmid40876561,
year = {2025},
author = {de Oliveira, DG and Machado, A and Lacerda, PC and Karakikla-Mitsakou, Z and Vasconcelos, C},
title = {Systemic lupus erythematosus and the gut microbiome: To look forward is to look within - A systematic review and narrative synthesis.},
journal = {Autoimmunity reviews},
volume = {},
number = {},
pages = {103921},
doi = {10.1016/j.autrev.2025.103921},
pmid = {40876561},
issn = {1873-0183},
abstract = {BACKGROUND: Systemic lupus erythematosus (SLE) is a heterogeneous autoimmune disease shaped by complex interactions involving genetic and environmental factors. Among these, the gut microbiome is emerging as potentially modulating immune responses and influencing disease susceptibility, progression, and activity.

OBJECTIVES: To synthesize current evidence on gut microbiome changes in adult SLE patients, framed along the clinical pathway - from diagnosis to treatment - to help bridge bench and bedside for microbiome-informed SLE care and research.

METHODS: A systematic search identified primary research studies examining gut microbiota in adult SLE patients. Studies were reviewed in a stepwise manner by independent investigators. Findings were synthesized narratively, emphasizing human data.

RESULTS: SLE patients exhibit gut microbiome dysbiosis, with reduced microbial richness and altered bacterial taxa. A lower Firmicutes/Bacteroidetes ratio is frequently observed. Enrichment of specific taxa, such as Enterococcus, Lactobacillus, and Ruminococcus gnavus, is reported. Dysbiosis correlates with increased gut permeability, immune activation, and autoreactivity. Clinical associations include disease activity, flares, nephritis, and other manifestations. SLE treatments, such as hydroxychloroquine and corticosteroids, influence the microbiome. Emerging interventions such as dietary modulation and fecal microbiota transplantation show promise in early studies. However, considerable heterogeneity exists across studies in terms of patient characteristics, methodology, and taxa-level findings.

CONCLUSIONS: The gut microbiome has multifaceted associations with SLE pathogenesis, disease activity, and therapeutic response. Translation will require standardized methods, functional validation, longitudinal follow-up, and clinical integration. While uncertainties remain, the gut microbiome is increasingly relevant, and clinicians caring for patients with SLE should be aware of its emerging implications.},
}

@article {pmid40876127,
year = {2025},
author = {Cao, S and Guo, X and Xin, M and Wang, X and Huo, J and Yue, Y and Li, X and Xu, D and Liu, L},
title = {Sesamin ameliorates ulcerative colitis by modulating the DUSP1/ERK feedback loop and restoring gut microbiota homeostasis.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {147},
number = {},
pages = {157188},
doi = {10.1016/j.phymed.2025.157188},
pmid = {40876127},
issn = {1618-095X},
abstract = {BACKGROUND: Sesamin (SSM), a plant-derived lignan, possesses anti-inflammatory and immunomodulatory effects. The pathogenesis of ulcerative colitis (UC) is complex and involves intestinal mucosal damage, inflammation, and dysbiosis of the gut microbiota. However, to date, the protective effects and therapeutic mechanisms of SSM in UC have hardly been investigated.

PURPOSE: The purpose of the study was to investigate the protective effects and therapeutic mechanisms of SSM in UC.

METHODS: This study utilized a dextran sulfate sodium-induced mouse model of UC to investigate the therapeutic effects of SSM and its impact on gut microbiota using molecular biology techniques, including histological staining, western blotting, proteomics, molecular docking, 16S rRNA sequencing, and fecal microbiota transplantation.

RESULTS: SM significantly alleviated inflammation, repaired intestinal mucosal barrier, and improved gut microbiota structure in mice with UC (p < 0.05). Further studies revealed that SSM upregulated dual-specificity phosphatase 1 (DUSP1) by suppressing extracellular signal-regulated protein kinase (ERK) phosphorylation, whereas DUSP1 knockdown increased p-ERK levels (p < 0.05). Additionally, SSM regulated the distribution of gut microbiota by increasing the abundance of beneficial bacteria (such as Lactobacillus), reducing the abundance of opportunistic pathogens (such as Staphylococcus), and restoring gut microbiota homeostasis (p < 0.05).

CONCLUSION: In summary, this is the first study to demonstrate that SSM exerts anti-inflammatory and intestinal barrier-restoring effects through modulating the DUSP1/ERK feedback loop and restoring gut microbiota homeostasis, thereby offering a novel therapeutic strategy for UC.},
}

@article {pmid40875477,
year = {2025},
author = {Guo, YF and Wang, Y and Wu, H and Wang, L and Miao, X},
title = {Rauvolfia Verticillata Pectic Polysaccharides Alleviate Inflammation-Associated Colorectal Cancer and Correlate with Modulation of Gut Microbiota, Short-Chain Fatty Acid Metabolism, and NF-κB/IL-6/STAT3 Signaling Pathways.},
journal = {Nutrition and cancer},
volume = {},
number = {},
pages = {1-17},
doi = {10.1080/01635581.2025.2551294},
pmid = {40875477},
issn = {1532-7914},
abstract = {Background: Colorectal cancer (CRC) is increasingly common in younger individuals and strongly linked to chronic inflammation. Gut microbiota and pathways like NF-κB/STAT3 play key roles, which highlights the therapeutic potential of natural compounds that target intestinal immunity and microbial balance. Objective: To investigate the therapeutic effects of pectic polysaccharides (PPs) from Rauvolfia verticillata in inflammation-associated CRC via the modulation of of gut microbiota and NF-κB/IL-6/STAT3 signaling pathways. Methods: C57BL/6 mice were subjected to azoxymethane (AOM)/dextran sulfate sodium (DSS)-induced CRC and treated with PP (100 mg/kg/day), the STAT3 inhibitor W2014-S (10 mg/kg), or fecal microbiota transplantation (FMT) from PP-treated donors. Histopathology, immunohistochemistry (IHC), Western blot, immunofluorescence (IF), 16S rRNA sequencing, and SCFA analysis were performed to assess inflammation, signaling pathways, gut microbiota composition, and metabolic changes. Results: PP intervention significantly mitigated AOM/DSS-induced weight loss, intestinal lesions, and disease activity index (DAI) scores while suppressing NF-κB and STAT3 activation. PP restored gut microbiota diversity, reduced pro-inflammatory genera, and regulated SCFA levels, particularly hexanoic those of and isohexanoic acids. FMT from PP-treated donors similarly attenuated colitis and inhibited NF-κB/STAT3 pathways. Conclusions: PP alleviates CRC and is associated with modulation of gut microbiota, SCFA metabolism, and NF-κB/IL-6/STAT3 signaling, offering a potential therapeutic strategy for inflammation-driven CRC.},
}

@article {pmid40873786,
year = {2025},
author = {Pinto, S and Benincà, E and Nooij, S and Terveer, EM and Keller, JJ and van der Meulen-de Jong, AE and Steyerberg, EW and Bogaards, JA},
title = {Ecological resilience in ulcerative colitis: microbial dynamics of donor and resident species in a longitudinal fecal microbiota transplantation study.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf119},
pmid = {40873786},
issn = {2730-6151},
abstract = {Fecal microbiota transplantation (FMT) is a promising treatment for the chronic immune-mediated disease ulcerative colitis (UC). However, the microbial dynamics underlying clinical remission remain poorly understood. To investigate these dynamics, we analysed data from 22 UC patients treated with four rounds of FMT donated by two healthy donors. Microbiota samples from patients were collected at nine timepoints before, during, and after treatment, covering a period of 14 weeks. Additionally, 27 donor samples were analysed. Species in the recipients' gut microbiota were categorised into ecological categories based on their origin and temporal dynamics: species already present in the recipient pre-FMT, species derived from the donor, or novel species, i.e. absent before FMT in both recipient and donor but detected during or after treatment. Overdispersed Poisson regression models were employed to model the number of species within each category over time. Furthermore, we investigated the change in relative abundance for recipient, colonising, and novel species. The results revealed that recipient species with higher relative abundances prior to FMT were more likely to persist following FMT. Notably, patients who achieved combined clinical and endoscopic remission at week 14 retained a higher number of recipient species compared to non-responders. In contrast, non-responders initially exhibited colonisation of more donor species than responders, but colonisation rate decreased over time in non-responders whereas colonisation rate remained stable in responders. These findings suggest that clinical remission following FMT is associated with controlled incorporation of donor species without replacement of resident species, which may reflect a resilient recipient gut community.},
}

@article {pmid40873717,
year = {2025},
author = {Li, D and Tao, H and Tan, X and Ling, H and Lu, Y and Zhang, H and Theany, S and Xu, H},
title = {Gut microbiota and their metabolites ameliorate acute and chronic colitis in mice via modulating Th17/Treg balance.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1643209},
pmid = {40873717},
issn = {1664-302X},
abstract = {INTRODUCTION: Ulcerative colitis (UC) is a recurrent inflammatory bowel disease affecting the colorectum, which remains a prominent research focus due to significant individual variations in clinical therapeutic outcomes. Fecal microbiota transplantation (FMT), as a therapeutic approach to restore intestinal homeostasis, has demonstrated favorable efficacy in UC management. However, given the characteristic alternating cycles of active and remission phases in UC, there remains a paucity of in-depth research regarding the optimal timing for FMT intervention. Concurrently, butyrate - a crucial microbial metabolite - ameliorates murine colitis through both direct and indirect mechanisms, while the therapeutic effectiveness of FMT in UC correlates closely with intestinal butyrate concentration.

METHODS: This study established acute and chronic UC murine models and employed FMT and butyrate interventions to monitor dynamic alterations in gut microbiota and lymphocyte subsets. Through comprehensive analyses, we aimed to elucidate the interplay between gut microbiota and host immune mechanisms, identify the optimal therapeutic timing for UC interventions, and evaluate the mechanistic role of butyrate. These findings provide theoretical foundations for personalized microbiota-targeted therapies in UC.

RESULTS: Our findings demonstrate that gut microbiota and their metabolites exert therapeutic effects on murine acute/chronic colitis through modulation of the T helper cell 17 (Th17)/T regulatory cell (Treg) ratio. Specifically, the remission phase represents a more favorable window for intestinal homeostasis modulation, with combination therapy involving microbial metabolites exhibiting superior anti-inflammatory efficacy.

DISCUSSION: The maintenance of an appropriate Th17/Treg equilibrium during microbiota restoration demonstrates therapeutic advantages. Notably, butyrate synergistically enhances microbial therapeutic effects, providing experimental evidence for personalized modulation of gut ecosystems in inflammatory bowel disease management.},
}

@article {pmid40873657,
year = {2025},
author = {Chapon, J and Scanzi, J and Sokol, H and Pereira, B and Buisson, A},
title = {Efficacy of different modalities of faecal microbiota transplantation in ulcerative colitis: systematic review and network meta-analysis.},
journal = {Therapeutic advances in gastroenterology},
volume = {18},
number = {},
pages = {17562848251369624},
pmid = {40873657},
issn = {1756-283X},
abstract = {BACKGROUND: While several small sample size randomized controlled trials suggested the superiority of faecal microbiota transplantation (FMT) over placebo in ulcerative colitis (UC), the most effective modality to perform FMT remains unknown.

OBJECTIVES: To compare the efficacy of different modalities of FMT to induce clinical remission in patients with UC.

DATA SOURCES AND METHODS: We performed a systematic review and network analysis (sources: MEDLINE, Embase, Cochrane CENTRAL; random effects model) of randomized controlled trials including at least one arm of FMT in adult patients with active UC. The primary endpoint, that is, clinical remission (total Mayo score ⩽2 with Mayo endoscopic score ⩽1), was assessed between weeks 6 and 12. Results are expressed as relative risks with 95% confidence intervals, adjusted for bowel cleansing and pre-FMT antibiotics. Ranking of FMT modalities was calculated as their surface under the cumulative ranking (SUCRA).

RESULTS: Among the 12 selected studies, patients were exclusively bio-naïve in 4 studies (4/12), while between 9% and 32% had prior biologics exposure in the other trials. The risk of bias was low across all domains in seven studies. Contrary to upper gastrointestinal tract (GI) FMT (Relative risk (RR) = 1.1 (0.2-7.7)), oral capsule (RR = 7.1 (1.8-33.3)), lower GI FMT (RR = 4.5 (1.7-12.5) and combination of both (RR = 12.5 (2.1-100)) are more effective than placebo to induce clinical remission. The combination of lower GI FMT and oral capsule was significantly more effective than upper GI FMT to induce clinical remission (RR = 10.7 (1.1-104.2)). Combination of lower GI FMT and oral capsule ranked the highest for the induction of clinical remission (SUCRA = 0.93). Multidonor FMT did not perform better than single donor FMT. Autologous FMT ranked lower than placebo (SUCRA = 0.12 vs 0.22).

CONCLUSION: The combination of lower GI and oral capsule FMT seems to be the best modality of FMT for patients with UC. In clinical trials, autologous FMT should be avoided due to a potential detrimental effect.

TRIAL REGISTRATION: PROSPERO registration number: CRD42023385511.},
}

@article {pmid40873417,
year = {2025},
author = {You, Y and Xiang, T and Yang, C and Xiao, S and Tang, Y and Luo, G and Ling, Z and Luo, F and Chen, Y},
title = {Interactions between the gut microbiota and immune cell dynamics: novel insights into the gut-bone axis.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2545417},
doi = {10.1080/19490976.2025.2545417},
pmid = {40873417},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Bone and Bones/immunology ; Dysbiosis/immunology/microbiology ; Animals ; Osteoarthritis/immunology/microbiology ; Arthritis, Rheumatoid/immunology/microbiology ; Probiotics ; Osteoporosis/immunology/microbiology ; *Bone Diseases/immunology/microbiology ; Immune System ; Gastrointestinal Tract/immunology/microbiology ; Prebiotics ; },
abstract = {Over the past few decades, accumulating evidence has demonstrated that gut microbiota engages in a sustained dialog with the immune system, leading to microbiota-driven immune responses that mediate the regulation of bone-related diseases. Despite the complexity of the dynamic interactions within the gut-immune-bone axis, advancements in high-throughput multi-omics sequencing have significantly facilitated the detailed exploration of this intricate network, thereby providing the potential to develop novel therapeutic strategies for bone-related diseases. In this review, we first summarize the variations in gut microbiota composition observed in patients with bone-related diseases, such as rheumatoid arthritis (RA), osteoarthritis (OA), and osteoporosis (OP), in comparison to healthy controls, along with the factors influencing these changes. The review that follows synthesize evidences highlighting the profound effects of gut microbial dysbiosis on immune homeostasis and bone microenvironment, respectively. We further elaborate that the gut-immune axis and gut-bone axis are not independent but three-dimensional networks, emphasizing gut microbial dysbiosis as a pivotal driver of immune dysregulation and subsequent bone homeostasis imbalance. Therapeutic strategies to manipulate the gut-immune-bone axis based on the use of probiotics as well as prebiotics, fecal microbiota transplantation, dietary modifications, and pharmacological interventions are also discussed. Finally, we discuss the challenges of current research on the gut-immune-bone axis and propose future directions for identifying novel therapeutic targets based on this axis to treat these diseases.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Bone and Bones/immunology
Dysbiosis/immunology/microbiology
Animals
Osteoarthritis/immunology/microbiology
Arthritis, Rheumatoid/immunology/microbiology
Probiotics
Osteoporosis/immunology/microbiology
*Bone Diseases/immunology/microbiology
Immune System
Gastrointestinal Tract/immunology/microbiology
Prebiotics

@article {pmid40873073,
year = {2025},
author = {, },
title = {[Expert consensus on the clinical application of gut microbiota transplant therapy in chronic liver disease (version 2025)].},
journal = {Zhonghua gan zang bing za zhi = Zhonghua ganzangbing zazhi = Chinese journal of hepatology},
volume = {33},
number = {8},
pages = {738-746},
doi = {10.3760/cma.j.cn501113-20250429-00163},
pmid = {40873073},
issn = {1007-3418},
support = {82470598//National Natural Science Foundation of China/ ; 2023A0505010007//Science and Technology Planning Project of Guangdong Province/ ; K-202401210//Guangdong Weiji Medical Development Foundation Specialized Research Fund for Gastroenterology/ ; },
mesh = {Humans ; *Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome ; *Liver Diseases/therapy ; Chronic Disease ; Consensus ; Liver Cirrhosis/therapy ; Liver Neoplasms/therapy ; },
abstract = {The gut microbiota plays an important role in maintaining host health and liver function, and gut microbiota transplant (also known as fecal microbiota transplantation) has shown potential clinical benefits in the treatment of chronic liver disease. To help clinical professionals to quickly master and standardize the clinical application of gut microbiota transplant in chronic liver disease, the Group of the Liver Disease-related Gastroenterology Branch of the Chinese Medical Association organized experts in related fields to formulate the "Expert Consensus on the Clinical Application of Gut Microbiota Transplant in the Treatment of Chronic Liver Disease" such as chronic hepatitis, cirrhosis and liver cancer, including indications, contraindications, effectiveness, safety, donor selection, transplant routes, transplant precautions, prevention and treatment of adverse reactions, and other aspects to provide reference and guidance for clinicians to implement gut microbiota transplant.},
}

Humans
*Fecal Microbiota Transplantation
*Gastrointestinal Microbiome
*Liver Diseases/therapy
Chronic Disease
Consensus
Liver Cirrhosis/therapy
Liver Neoplasms/therapy

@article {pmid40872257,
year = {2025},
author = {Cianci, G and Maini, G and Ferraresi, M and Pezzi, G and Bortolotti, D and Rizzo, S and Beltrami, S and Schiuma, G},
title = {Immune Modulation by Microbiota and Its Possible Impact on Polyomavirus Infection.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/pathogens14080747},
pmid = {40872257},
issn = {2076-0817},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Polyomavirus Infections/immunology/microbiology/virology/therapy ; *Polyomavirus/immunology ; Dysbiosis/immunology ; Fecal Microbiota Transplantation ; Animals ; Immunocompromised Host ; },
abstract = {Polyomaviruses are a family of small DNA viruses capable of establishing persistent infections, and they can pose significant pathogenic risks in immunocompromised hosts. While traditionally studied in the context of viral reactivation and immune suppression, recent evidence has highlighted the gut microbiota as a critical regulator of host immunity and viral pathogenesis. This review examines the complex interactions between polyomaviruses, the immune system, and intestinal microbiota, emphasizing the role of short-chain fatty acids (SCFAs) in modulating antiviral responses. We explore how dysbiosis may facilitate viral replication, reactivation, and immune escape and also consider how polyomavirus infection can, in turn, alter microbial composition. Particular attention is given to the Firmicutes/Bacteroidetes ratio as a potential biomarker of infection risk and immune status. Therapeutic strategies targeting the microbiota, including prebiotics, probiotics, and fecal microbiota transplantation (FMT), are discussed as innovative adjuncts to immune-based therapies. Understanding these tri-directional interactions may offer new avenues for mitigating disease severity and improving patient outcomes during viral reactivation.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Polyomavirus Infections/immunology/microbiology/virology/therapy
*Polyomavirus/immunology
Dysbiosis/immunology
Fecal Microbiota Transplantation
Animals
Immunocompromised Host

@article {pmid40871460,
year = {2025},
author = {Ren, J and Wang, Q and Hong, H and Tang, C},
title = {Fecal Microbiota Transplantation in Alzheimer's Disease: Mechanistic Insights Through the Microbiota-Gut-Brain Axis and Therapeutic Prospects.},
journal = {Microorganisms},
volume = {13},
number = {8},
pages = {},
doi = {10.3390/microorganisms13081956},
pmid = {40871460},
issn = {2076-2607},
support = {HY202411//One health Interdisciplinary Research Project, Ningbo University/ ; D16013//National 111 Project of China/ ; the Health Fund of Translational Biomedicine//the Health Fund of Translational Biomedicine/ ; },
abstract = {Alzheimer's disease (AD), a prevalent neurodegenerative disorder in the aging population, remains without definitive therapeutic solutions. Emerging insights into the gut microbiota (GM) and its bidirectional communication with the central nervous system(CNS) through the microbiota-gut-brain axis (MGBA) have unveiled potential correlative mechanisms that may contribute to AD pathogenesis, though causal evidence remains limited. Dysregulation of GM composition (dysbiosis) exacerbates AD progression via neuroinflammation, amyloid-β (Aβ) deposition, and tau hyperphosphorylation (p-tau), while restoring microbial homeostasis presents a promising therapeutic strategy. Fecal microbiota transplantation (FMT), a technique to reconstitute gut ecology by transferring processed fecal matter from healthy donors, has demonstrated efficacy in ameliorating cognitive deficits and neuropathology in AD animal models. Preclinical studies reveal that FMT reduces Aβ plaques, normalizes tau phosphorylation, suppresses inflammasome activation, and restores microglial homeostasis through modulation of microbial metabolites and immune pathways. Although clinical evidence remains limited to case reports and small-scale trials showing potential therapeutic effect, safety concerns regarding long-term effects and protocol standardization necessitate further investigation. This review synthesizes current knowledge on GM-AD interactions, evaluates FMT's mechanistic potential, and discusses challenges in translating this ancient practice into a cutting-edge AD therapy. Rigorous randomized controlled trials and personalized microbiota-based interventions are imperative to advance FMT from bench to bedside.},
}

@article {pmid40871301,
year = {2025},
author = {Chen, S and Liu, T and Chen, J and Shen, H and Wang, J},
title = {Fecal Virome Transplantation Confirms Non-Bacterial Components (Virome and Metabolites) Participate in Fecal Microbiota Transplantation-Mediated Growth Performance Enhancement and Intestinal Development in Broilers with Spatial Heterogeneity.},
journal = {Microorganisms},
volume = {13},
number = {8},
pages = {},
doi = {10.3390/microorganisms13081795},
pmid = {40871301},
issn = {2076-2607},
support = {Project No. CZ004306//"Tianshan Talent" Program/ ; Project No. XJLG-CYJSTX-10//Xinjiang Modern Agriculture Industry Technology System/ ; },
abstract = {Fecal microbiota transplantation (FMT) promotes growth performance and intestinal development in yellow-feathered broilers, but whether the virome and metabolites contribute to its growth-promoting effect remains unclear. This study removed the microbiota from FMT filtrate using a 0.45 μm filter membrane, retaining the virome and metabolites to perform fecal virome transplantation (FVT), aiming to investigate its regulatory role in broiler growth. Healthy yellow-feathered broilers with high body weights (top 10% of the population) were used as FVT donors. Ninety-six 8-day-old healthy male yellow-feathered broilers (95.67 ± 3.31 g) served as FVT recipients. Recipient chickens were randomly assigned to a control group and an FVT group. The control group was gavaged with 0.5 mL of normal saline daily, while the FVT group was gavaged with 0.5 mL of FVT solution daily. Growth performance, immune and antioxidant capacity, intestinal development and related gene expression, and microbial diversity were measured. The results showed that FVT improved the feed utilization rate of broilers (the feed conversion ratio decreased by 3%; p < 0.05), significantly increased jejunal length (21%), villus height (69%), and crypt depth (84%) (p < 0.05), and regulated the jejunal barrier: insulin-like growth factor-1 (IGF-1) (2.5 times) and Mucin 2 (MUC2) (63 times) were significantly upregulated (p < 0.05). FVT increased the abundance of beneficial bacteria Lactobacillales. However, negative effects were also observed: Immunoglobulin A (IgA), Immunoglobulin G (IgG), Immunoglobulin M (IgM), Interleukin-1 beta (IL-1β), Interleukin-6 (IL-6), Tumor Necrosis Factor-alpha (TNF-α), and Interferon-gamma (IFN-γ) in broilers were significantly upregulated (p < 0.05), indicating immune system overactivation. Duodenal barrier-related genes Mucin 2 (MUC2), Occludin (OCLN), Claudin (CLDN1), and metabolism-related genes solute carrier family 5 member 1 (SLC5A1) and solute carrier family 7 member 9 (SLC7A9) were significantly downregulated (p < 0.05). The results of this trial demonstrate that, besides the microbiota, the gut virome and metabolites are also functional components contributing to the growth-promoting effect of FMT. The differential responses in the duodenum and jejunum reveal spatial heterogeneity and dual effects of FVT on the intestine. The negative effects limit the application of FMT/FVT. Identifying the primary functional components of FMT/FVT to develop safe and targeted microbial preparations is one potential solution.},
}

@article {pmid40870405,
year = {2025},
author = {Bibolar, AC and Nechita, VI and Lung, FC and Crecan-Suciu, BD and Păunescu, RL},
title = {Gut Feelings: Linking Dysbiosis to Depression-A Narrative Literature Review.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {61},
number = {8},
pages = {},
doi = {10.3390/medicina61081360},
pmid = {40870405},
issn = {1648-9144},
mesh = {Humans ; *Dysbiosis/complications/psychology/physiopathology/microbiology ; *Depression/microbiology/etiology/psychology/physiopathology ; *Gastrointestinal Microbiome/physiology ; Animals ; Probiotics/therapeutic use ; },
abstract = {The balance between physiological, psychological, and environmental factors often shapes human experience. In recent years, research has drawn attention to the gut microbiota as a significant contributor to brain function and emotional regulation. This narrative review examines how changes in gut microbiota may relate to depression. We selected studies that explore the link between intestinal dysbiosis and mood, focusing on mechanisms such as inflammation, vagus nerve signaling, HPA axis activation, gut permeability, and neurotransmitter balance. Most of the available data come from animal models, but findings from human studies suggest similar patterns. Findings are somewhat difficult to compare due to differences in measurement procedures and patient groups. However, several microbial shifts have been observed in people with depressive symptoms, and trials with probiotics or fecal microbiota transplant show potential. These results remain limited. We argue that these interventions deserve more attention, especially in cases of treatment-resistant or inflammation-driven depression. Understanding how the gut and brain interact could help define clearer subtypes of depression and guide new treatment approaches.},
}

Humans
*Dysbiosis/complications/psychology/physiopathology/microbiology
*Depression/microbiology/etiology/psychology/physiopathology
*Gastrointestinal Microbiome/physiology
Animals
Probiotics/therapeutic use

@article {pmid40869967,
year = {2025},
author = {Fu, Y and Bonifacio-Mundaca, J and Desterke, C and Casafont, Í and Mata-Garrido, J},
title = {Genomic Alterations and Microbiota Crosstalk in Hepatic Cancers: The Gut-Liver Axis in Tumorigenesis and Therapy.},
journal = {Genes},
volume = {16},
number = {8},
pages = {},
doi = {10.3390/genes16080920},
pmid = {40869967},
issn = {2073-4425},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Liver Neoplasms/genetics/microbiology/therapy/pathology ; *Carcinoma, Hepatocellular/genetics/microbiology/therapy/pathology ; *Carcinogenesis/genetics ; Liver/pathology/metabolism/microbiology ; *Cholangiocarcinoma/genetics/microbiology/therapy ; Mutation ; Epigenesis, Genetic ; Animals ; },
abstract = {Background/Objectives: Hepatic cancers, including hepatocellular carcinoma (HCC) and cholangiocarcinoma (CCA), are major global health concerns due to rising incidence and limited therapeutic success. While traditional risk factors include chronic liver disease and environmental exposures, recent evidence underscores the significance of genetic alterations and gut microbiota in liver cancer development and progression. This review aims to integrate emerging knowledge on the interplay between host genomic changes and gut microbial dynamics in the pathogenesis and treatment of hepatic cancers. Methods: We conducted a comprehensive review of current literature on genetic and epigenetic drivers of HCC and CCA, focusing on commonly mutated genes such as TP53, CTNNB1, TERT, IDH1/2, and FGFR2. In parallel, we evaluated studies addressing the gut-liver axis, including the roles of dysbiosis, microbial metabolites, and immune modulation. Key clinical and preclinical findings were synthesized to explore how host-microbe interactions influence tumorigenesis and therapeutic response. Results: HCC and CCA exhibit distinct but overlapping genomic landscapes marked by recurrent mutations and epigenetic reprogramming. Alterations in the gut microbiota contribute to hepatic inflammation, genomic instability, and immune evasion, potentially enhancing oncogenic signaling pathways. Furthermore, microbiota composition appears to affect responses to immune checkpoint inhibitors. Emerging therapeutic strategies such as probiotics, fecal microbiota transplantation, and precision oncology based on mutational profiling demonstrate potential for personalized interventions. Conclusions: The integration of host genomics with microbial ecology provides a promising paradigm for advancing diagnostics and therapies in liver cancer. Targeting the gut-liver axis may complement genome-informed strategies to improve outcomes for patients with HCC and CCA.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Liver Neoplasms/genetics/microbiology/therapy/pathology
*Carcinoma, Hepatocellular/genetics/microbiology/therapy/pathology
*Carcinogenesis/genetics
Liver/pathology/metabolism/microbiology
*Cholangiocarcinoma/genetics/microbiology/therapy
Mutation
Epigenesis, Genetic
Animals

@article {pmid40868265,
year = {2025},
author = {Haidar, L and Bănărescu, CF and Uța, C and Zimbru, EL and Zimbru, RI and Tîrziu, A and Pătrașcu, R and Șerb, AF and Georgescu, M and Nistor, D and Panaitescu, C},
title = {Beyond the Skin: Exploring the Gut-Skin Axis in Chronic Spontaneous Urticaria and Other Inflammatory Skin Diseases.},
journal = {Biomedicines},
volume = {13},
number = {8},
pages = {},
doi = {10.3390/biomedicines13082014},
pmid = {40868265},
issn = {2227-9059},
abstract = {Emerging evidence suggests a critical role of the gut microbiome in modulating systemic immune responses, with increasing relevance in dermatological diseases. Chronic spontaneous urticaria (CSU), traditionally viewed as an isolated cutaneous disorder, is now recognized as a systemic immune condition involving complex interactions between innate and adaptive immunity, mast cell dysregulation, and non-IgE-mediated pathways. This review explores the gut-skin axis as a unifying concept linking intestinal dysbiosis to inflammatory skin diseases, including atopic dermatitis, psoriasis, rosacea, and acne. Special emphasis is placed on CSU, where altered gut microbial composition, characterized by reduced diversity, depletion of short-chain fatty acid-producing bacteria, and expansion of Proteobacteria, may contribute to increased intestinal permeability, systemic immune activation via toll-like receptors, and heightened mast cell sensitivity. We discuss findings from animal models demonstrating that gut microbiota modulation can attenuate mast cell hyperreactivity and reduce urticarial symptoms. In parallel, we examine clinical evidence supporting the potential role of probiotics, prebiotics, dietary interventions, and fecal microbiota transplantation as adjunctive strategies in CSU management. Despite promising findings, challenges remain in translating microbiome research into effective therapies due to interindividual variability, the complexity of host-microbiome interactions, and a lack of standardized protocols. Future research should focus on identifying predictive microbial patterns and developing personalized microbiome-targeted interventions. Understanding the bidirectional gut-skin relationship may open new therapeutic avenues beyond symptomatic treatment, positioning the microbiome as a novel target in CSU and related inflammatory dermatoses.},
}

@article {pmid40868053,
year = {2025},
author = {Maruyama, T and Ishikawa, D and Kurokawa, R and Masuoka, H and Nomura, K and Haraikawa, M and Orikasa, M and Odakura, R and Koma, M and Omori, M and Ishino, H and Ito, K and Shibuya, T and Suda, W and Nagahara, A},
title = {Hydrogen Gas Inhalation Improved Intestinal Microbiota in Ulcerative Colitis: A Randomised Double-Blind Placebo-Controlled Trial.},
journal = {Biomedicines},
volume = {13},
number = {8},
pages = {},
doi = {10.3390/biomedicines13081799},
pmid = {40868053},
issn = {2227-9059},
support = {None//MiZ Co., Ltd/ ; },
abstract = {Background/Objective: Dysbiosis is implicated in the pathogenesis of ulcerative colitis. Hydrogen has been reported to promote intestinal microbiota diversity and suppress ulcerative colitis progression in mice models. In this study, we investigated changes in the intestinal microbiota, therapeutic effects, and safety of hydrogen inhalation in patients with ulcerative colitis. Methods: In this randomised, double-blind, placebo-controlled trial, 10 active patients with ulcerative colitis (aged ≥20 years; Lichtiger's clinical activity index, 3-10; and Mayo endoscopic subscores ≥1) participated, and they were assigned to either a hydrogen or air inhalation group (hydrogen and placebo groups, respectively). All patients inhaled gas for 4 h every day for 8 weeks. Subsequently, we performed clinical indices and microbiota analyses using the metagenomic sequencing of stool samples before and after inhalation. Results: There was significant difference in the sum of the Mayo endoscopic subscores before and after inhalation in the clinical assessment indices. The hydrogen group showed higher α-diversity (p = 0.19), and the variation in β-diversity was markedly different, compared to the placebo group, in intestinal microbiota analysis (p = 0.02). Functional gene analysis revealed 115 significant genetic changes in the hydrogen group following treatment. No inhalation-related adverse events were observed. Conclusions: Hydrogen inhalation appeared to improve intestinal microbiota diversity; however, no clear therapeutic effect on ulcerative colitis was observed. Further studies are needed, and hydrogen inhalation may possibly lead to a logical solution combined with microbiome therapy, such as faecal microbiota transplantation, with fewer adverse events.},
}

@article {pmid40868023,
year = {2025},
author = {Kullar, R and Johnson, S and Goldstein, EJC},
title = {Clostridioides difficile in Peripartum Women: Review of Outcomes and Treatment.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/antibiotics14080829},
pmid = {40868023},
issn = {2079-6382},
abstract = {Background:Clostridioides difficile infection (CDI) is one of the most common healthcare-associated infections in the United States with increasing rates in younger patients and those in the community. CDI incidence may also be on the rise in peripartum women. Methods: We conducted a literature review to assess the incidence and outcomes of CDI in the peripartum population and review treatment options. Results: Peripartum patients have a high risk of complications and adverse events associated with CDI. Most patients have been treated with vancomycin or metronidazole; however, cases of patients recurring on standard treatment have been described, with patients having successful outcomes with fidaxomicin or fecal microbiota transplantation (FMT). Probiotics have been shown to be safe in peripartum women; however, the role in preventing primary and secondary CDI has not been studied. Conclusions: Peripartum women that develop CDI are at increased risk for complications. Treatment includes vancomycin, metronidazole, or fidaxomicin or FMT for recurrent cases.},
}

@article {pmid40867077,
year = {2025},
author = {Ebadi, M and Reddi, S and Senyshyn, L and Minot, SS and Gooley, T and Kabage, AJ and Lee, SJ and Hill, GR and Khoruts, A and Rashidi, A},
title = {Effect of fecal microbiota transplantation on gut microbiota functional profile in recipients of allogeneic hematopoietic cell transplantation.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2551882},
doi = {10.1080/19490976.2025.2551882},
pmid = {40867077},
issn = {1949-0984},
mesh = {Humans ; *Fecal Microbiota Transplantation ; *Hematopoietic Stem Cell Transplantation/adverse effects ; *Gastrointestinal Microbiome ; Male ; Middle Aged ; Female ; Adult ; Bacteria/classification/genetics/isolation & purification/metabolism ; *Dysbiosis/therapy/microbiology ; Transplantation, Homologous ; Feces/microbiology ; Aged ; },
abstract = {Intestinal dysbiosis has been associated with both the effectiveness and toxicity of immunotherapy in cancer patients, inspiring multiple trials investigating fecal microbiota transplantation (FMT) in these patients. FMT restores microbial community structures damaged by antibiotics and enriches the microbiota with beneficial bacteria. However, the precise mechanism through which FMT exerts its effects and provides clinical benefits remains incompletely understood. Efforts to date have primarily focused on characterizing taxonomic changes following FMT. We hypothesized that FMT may also modify the functional pathways and metabolic capabilities of the gut microbiota, with possible clinical impact. To investigate this, we conducted a study involving 17 patients with blood disorders who received prophylactic FMT from one of the three healthy donors shortly after hematopoietic cell transplantation (HCT). By analyzing shotgun metagenomic profiles of the baseline, pre-FMT, and post-FMT gut microbiota, we demonstrate that FMT effectively restored pathways that had been depleted following HCT. However, it did not significantly reduce pathways that had expanded, indicating that FMT operates primarily through a restorative mechanism, reestablishing lost functional capabilities in the microbiota rather than suppressing overactive pathways. These findings highlight the potential for optimizing FMT protocols and identifying patient populations where FMT may be particularly beneficial.},
}

Humans
*Fecal Microbiota Transplantation
*Hematopoietic Stem Cell Transplantation/adverse effects
*Gastrointestinal Microbiome
Male
Middle Aged
Female
Adult
Bacteria/classification/genetics/isolation & purification/metabolism
*Dysbiosis/therapy/microbiology
Transplantation, Homologous
Feces/microbiology
Aged

@article {pmid40866789,
year = {2025},
author = {Kusakabe, S and Kurashige, R and Fukushima, K and Shimizu, K and Yoshihara, T and Motooka, D and Nakamura, S and Kurashige, M and Nakata, K and Hino, A and Kasahara, H and Ueda, T and Fujita, J and Hosen, N and Takehara, T and Oda, J},
title = {Fecal microbiota transplantation for Crohn's disease-like intestinal lesions arising after allogeneic stem cell transplantation.},
journal = {International journal of hematology},
volume = {},
number = {},
pages = {},
pmid = {40866789},
issn = {1865-3774},
abstract = {Several cases of inflammatory bowel disease (or similar gastrointestinal lesions) arising after allogeneic hematopoietic stem cell transplantation have been reported, but the effect of intestinal dysbiosis on development of these lesions remains unclear. We performed fecal microbiota transplantation (FMT) and 16S rRNA microbiome analysis in a patient who developed Crohn's disease-like lesions after allogeneic transplantation. A 62-year-old woman underwent haploidentical stem cell transplantation from her daughter to treat double-hit lymphoma relapsed after chimeric antigen receptor T-cell therapy, and achieved remission without developing acute graft-versus-host disease. Eight months later, she developed Crohn's disease-like intestinal lesions after cytomegalovirus enteritis. Her condition did not improve with the conventional treatment, so she underwent FMT from her daughter as part of a clinical trial. Diarrhea gradually improved, and follow-up endoscopy 4 months after the FMT showed ulcer healing and scarring. The 16S rRNA analysis revealed a reduction in the relative abundance of the Enterococcus genus after FMT, suggesting that dysbiosis may have contributed to lesion development. The patient is currently on a regular diet, with no symptom recurrence, and the primary disease remains in remission. Although this outcome suggests that FMT is effective, careful patient selection is required to reduce the risk of FMT-associated sepsis.},
}

@article {pmid40865967,
year = {2025},
author = {Jee, JJ and Park, S and Kim, J and Lee, H and Koh, H and Koo, BN},
title = {Bacterial extracellular vesicle as a predictive biomarker for postoperative delirium status after spinal surgery: a prospective cohort study.},
journal = {International journal of surgery (London, England)},
volume = {},
number = {},
pages = {},
doi = {10.1097/JS9.0000000000003024},
pmid = {40865967},
issn = {1743-9159},
abstract = {BACKGROUND: Prognostic factors significantly associated with postoperative delirium (POD) have been reported discordantly, possibly due to heterogeneous cohorts. Here, bacteria extracellular vesicles (BEVs) were introduced to predict the POD status of a unique patient cohort.

METHODS: One hundred twenty-eight patients who underwent spinal surgery participated in this prospective cohort study. Significant preoperative factors (i.e., baseline characteristics, and sequences of 16s rRNA genes from bloods and stools) between patients with and without delirium were subjected to random forest classifiers for prediction model, and potential metabolites that regulate the POD were inferred in silico.

RESULTS: No significant differences were found between patients with and without delirium in terms of demographics, anthropometrics, intervention history or preoperative cognitive function scores, except for circulating BEVs; delirium group had less diverse BEVs dominated with EVs from Gammaproteobacteria, whereas more diverse BEVs enriched with EVs from Bacilli and Alphaproteobacteria were significantly associated with non-delirium. Compared to that with baseline characteristics or gut microbiome, prediction model using random forest classifier with the significant BEVs yielded the lowest error rate of 21.59%, and was validated with an independent data set, resulting in 80% accuracy. Moreover, EVs from Moraxellaceae and Acinetobacter showed the highest probabilities of prediction of the POD despite their low relative abundance, indicating the most significant prognostic markers for the POD. As the inference of a potential metabolites that regulate the POD, succinate and enterobacterial common antigens delivered from BEV cargo were expected to participate in pathogenic events, whereas S-methyl-5'-thioadenosine, 2-oxoglutarate, pyruvate, acetate and butyrate may play a neuroprotective role in the POD.

CONCLUSIONS: The profile of circulating preoperative BEVs is the key prognostic factor for distinguishing POD in elderly surgical patients with controlled baseline conditions. Metabolites of defensive and offensive mechanisms inferred from BEVs will be essential for developing next-generation POD prevention strategies.},
}

@article {pmid40865561,
year = {2025},
author = {Wei, S and Lu, J},
title = {Microbial Modulation of the Gut-Liver Axis in Autoimmune Liver Diseases.},
journal = {Seminars in liver disease},
volume = {},
number = {},
pages = {},
doi = {10.1055/a-2679-3641},
pmid = {40865561},
issn = {1098-8971},
abstract = {Autoimmune liver diseases (AILDs), including autoimmune hepatitis, primary biliary cholangitis, and primary sclerosing cholangitis, are chronic inflammatory conditions influenced by complex interactions among genetic, environmental, and immunological factors. Recent studies have highlighted the critical role of the gut microbiota in regulating immune responses beyond the gastrointestinal tract via the gut-liver axis. This review examines the interactions between intestinal microecology and AILDs, with a focus on mechanisms such as bacterial translocation, disruption of the intestinal barrier, and modulation of microbial metabolites. Dysbiosis, involving alterations in both bacterial and fungal communities, has been associated with immune dysregulation and hepatic inflammation. Evidence indicates that short-chain fatty acids, bile acids, and microbial products such as lipopolysaccharides influence hepatic immune tolerance and inflammatory signaling pathways. Several diagnostic and therapeutic approaches, including probiotics, fecal microbiota transplantation, and bile acid regulation, have shown potential to slow or alter disease progression. However, the clinical translation of these findings remains limited due to interindividual variability and the complex nature of the gut-liver axis. Continued research is needed to develop precision medicine strategies that can harness intestinal microecology for improved management of AILDs.},
}

@article {pmid40865528,
year = {2025},
author = {Shi, Y and Li, Y and Li, H and Haerheng, A and Marcelino, VR and Lu, M and Lemey, P and Tang, J and Bi, Y and Pettersson, JH and Bohlin, J and Klaps, J and Wu, Z and Wan, W and Sun, B and Kang, M and Holmes, EC and He, N and Su, S},
title = {Extensive cross-species transmission of pathogens and antibiotic resistance genes in mammals neglected by public health surveillance.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.08.016},
pmid = {40865528},
issn = {1097-4172},
abstract = {Non-traditional farmed and wild mammals are often neglected in pathogen surveillance. Through metagenomic and metatranscriptomic sequencing of fecal and tissue samples from 973 asymptomatic mammals, we identified 128 viruses (30 novel), including a new coronavirus genus, 10,255 bacterial species (over 7,000 undescribed), 201 fungi, and 7 parasites. Farmed and wild mammals shared 13.3% of virus species, including canine coronavirus in Asiatic black bears and Getah virus in rabbits, while the 2.3.4.4b clade of H5N1 avian influenza virus was found in a wild leopard cat. We identified potential bacterial pathogen transmission between farmed and wild mammals and bacterial strains with high genetic similarity to those found in humans. We observed 157 clinically prioritized antibiotic resistance genes (ARGs) in mammalian microbiomes with greater than 99% identity to ARGs from human microbiomes, often co-occurring with mobile genetic elements. Overall, this work highlights cross-species risks at the human-animal interface.},
}

@article {pmid40865242,
year = {2025},
author = {Zhang, Y and Chen, Q and Xu, Y and Lv, Y and Wang, Y and Shi, XY and Liu, J and Wen, J and Li, X and Li, B},
title = {Soy isoflavones mitigate atrazine-induced dopaminergic neuron damage via reshaping short-chain fatty acid-producing bacteria in gut microbiota and modulating the GPR43/GLP-1/GLP-1R axis.},
journal = {Ecotoxicology and environmental safety},
volume = {303},
number = {},
pages = {118938},
doi = {10.1016/j.ecoenv.2025.118938},
pmid = {40865242},
issn = {1090-2414},
abstract = {Atrazine (ATR), a widely used herbicide, is linked to dopaminergic neurotoxicity and persistent gut microbiota dysbiosis after early life exposure. However, whether the gut microbiota mediates ATR-induced loss of dopaminergic neurons remains unclear. Mice were exposed to ATR from juvenility (4th week) until adulthood (12th week), after which exposure ceased until the 20th week. The role of gut microbiota was confirmed through fecal microbiota transplantation (FMT), which was classified into different groups based on the donor's ATR treatment status. 16S rRNA sequencing revealed that Akkermansia, which exhibited significant differences across FMT groups, is a classic short-chain fatty acid (SCFA)-producing bacteria. FMT recipients receiving ATR-donor microbiota exhibited reduced colonic G Protein-Coupled Receptor 43 (GPR43), serum Glucagon-like Peptide-1 (GLP-1), and substantia nigra Glucagon-like Peptide-1 receptor (GLP-1R)/Tyrosine hydroxylase (TH) levels. Soy isoflavones (SIF), selected for their dual prebiotic and neuroprotective effects, attenuated ATR-induced dopaminergic neurotoxicity by enriching SCFA-producing gut microbiota and the level of SCFAs, thereby activating the GPR43/GLP-1/GLP-1R axis and reducing neuronal loss. These findings demonstrate the critical role of gut microbiota in ATR-induced dopaminergic neurodegeneration, positioning SIF-mediated microbiota modulation as a promising therapeutic approach within the "food-medicine homology" framework.},
}

@article {pmid40863733,
year = {2025},
author = {Alaeddin, S and Ko, Y and Steiner-Lim, GZ and Jensen, SO and Roberts, TL and Ho, V},
title = {The Effect of Faecal Microbiota Transplantation on Cognitive Function in Cognitively Healthy Adults with Irritable Bowel Syndrome: Protocol for a Randomised, Placebo-Controlled, Double-Blinded Pilot Study.},
journal = {Methods and protocols},
volume = {8},
number = {4},
pages = {},
pmid = {40863733},
issn = {2409-9279},
abstract = {Faecal microbiota transplantation (FMT) is an emerging therapy for gastrointestinal and neurological disorders, acting via the microbiota-gut-brain axis. Altering gut microbial composition may influence cognitive function, but this has not been tested in cognitively healthy adults. This randomised, double-blinded, placebo-controlled pilot trial investigates whether FMT is feasible and improves cognition in adults with irritable bowel syndrome (IBS). Participants receive a single dose of FMT or placebo via rectal retention enema. Cognitive performance is the primary outcome, assessed using the Cambridge Neuropsychological Test Automated Battery (CANTAB). Secondary outcomes include IBS symptom severity and mood. Tertiary outcomes include microbiome composition and plasma biomarkers related to inflammation, short-chain fatty acids, and tryptophan metabolism. Outcomes are assessed at baseline and at one, three, six, and twelve months following treatment. We hypothesise that FMT will lead to greater improvements in cognitive performance than placebo, with benefits extending beyond practice effects, emerging at one month and persisting in the long term. The findings will contribute to evaluating the safety and efficacy of FMT and enhance our understanding of gut-brain interactions.},
}

@article {pmid40861872,
year = {2025},
author = {Baydoun, H and Hussain, N and Wu, KO and Kelly, CR and Fischer, M},
title = {What's New and What's Next in Fecal Microbiota Transplantation?.},
journal = {Biologics : targets & therapy},
volume = {19},
number = {},
pages = {481-496},
pmid = {40861872},
issn = {1177-5475},
abstract = {Fecal microbiota transplantation (FMT) has evolved from a niche therapy to a cornerstone in the treatment of recurrent Clostridioides difficile infection (rCDI). Initially introduced in the 1950s, its relevance has surged with the emergence of virulent and antibiotic-resistant C. difficile strains. In recent years, the FDA approved two standardized microbiota-based therapeutics-Rebyota™ (fecal microbiota, live-jslm) and Vowst™ (fecal microbiota spores, live-brpk)-for rCDI prevention. Multiple pivotal trials support the efficacy and safety of both traditional FMT and the FDA-approved prescription FMTs, with sustained response rates surpassing 80% in select populations. In parallel, live biotherapeutic products (LBPs)-donor independent, well-defined microbial consortia produced in laboratory setting are under development. Examples include VE303 and NTCD-M3, a single non-toxigenic C. difficile strain (M3). Beyond the FDA approved therapeutics, conventional FMT is gaining traction as a potential treatment for severe or fulminant CDI, especially in patients not responding to antibiotics and ineligible for surgery. Investigational indications include decolonizing multidrug-resistant organisms and treatment of noninfectious conditions such as inflammatory bowel disease, irritable bowel syndrome, liver disease, and metabolic syndrome. Given the differing pathophysiology of these conditions, a tailored approach supported by rigorous clinical trials is essential. Although there is a growing shift, particularly in the United States, toward the use of FDA-approved FMTs, global practices remain heterogeneous, with conventional FMT still widely employed. Meanwhile, regulatory pathways and clinical guidelines for microbiota-derived biologics and live biotherapeutic products continue to evolve. In this manuscript, we provide an update on the emerging use of FDA-approved prescription microbiota-derived therapeutics for the prevention of rCDI, review data on investigational agents including both donor dependent and donor independent microbial products, and summarize current evidence on the use of conventional FMT for indications beyond prevention of rCDI.},
}

@article {pmid40861794,
year = {2025},
author = {Wang, B and Stephen, SJ and Cyphert, EL and Liu, C and Hernandez, CJ and Vashishth, D},
title = {Fecal microbiota transplantation in mice improves bone material properties through altered mineral quality.},
journal = {JBMR plus},
volume = {9},
number = {9},
pages = {ziaf115},
pmid = {40861794},
issn = {2473-4039},
abstract = {Disruptions of the composition of the gut microbiome are linked to impaired bone tissue strength. Fecal microbiota transplantation (FMT) is an established clinical therapy that can restore a healthy gut microbiome and reduce systemic inflammation. However, whether FMT from a healthy donor could rescue bone fragility is unknown. As induced inflammation causes mineralization defects, we hypothesize that manipulations of the gut microbiota alter bone fracture resilience through changes in mineral quality. Here, we altered the compositions of the gut microbiome in mice via antibiotics (ampicillin and neomycin) and FMT. Mice were allocated to 5 groups (M/F, N = 13-18/group): Unaltered, Continuous (dosed 4-24 wk), Initial (dosed 4-16 wk), Reconstituted (dosed 4-16 wk with subsequent FMT from age- and sex-matched mice with unaltered gut microbiota), and Delayed (dosed 16-24 wk). Fracture toughness testing and Raman spectroscopy were conducted on the femora. The maximum toughness was greater in the Reconstituted group (for females, p < .05 compared to Continuous, Unaltered, and Delayed groups; for males, p < .05 compared to groups with antibiotic dosing). The Reconstituted group showed lower type-B carbonate substitution in the bone mineral (all p < .01 for both sexes), and lower mineral-to-matrix ratio (all p < .01 for males, for females, p < .01 compared to Unaltered, Initial, and Delayed groups). In females, mineral crystallinity was higher in the Reconstituted group than those dosed with antibiotics (all p < .05). Serum inflammation marker TNF-α was positively correlated with type-B carbonate substitutions (ρ = 0.66), mineral-to-matrix ratio (ρ = 0.71), and carboxymethyl-lysine (CML) in bone matrix (ρ = 0.43). Enhanced bone maximum fracture toughness was associated with reduced type-B carbonate substitution (r = -0.45), decreased mineral-to-matrix ratio (r = -0.40), increased mineral crystallinity (r = 0.33), and lower levels of bone CML (r = -0.49, all p < .01). These results suggest that the introduction of more beneficial gut microbiota can increase fracture resistance by modifying mineral composition and quality, likely through the reduction of systemic inflammation.},
}

@article {pmid40861764,
year = {2025},
author = {Mishra, AP and Marrelli, LM and Bonner-Reid, FT and Shekhawat, P and Toney, R and Benipal, IK and Dias, HA and Kandi, A and Siddiqui, HF},
title = {Gut-Brain Axis: Understanding the Interlink Between Alterations in the Gut Microbiota and Autism Spectrum Disorder.},
journal = {Cureus},
volume = {17},
number = {7},
pages = {e88579},
pmid = {40861764},
issn = {2168-8184},
abstract = {Autism spectrum disorder (ASD) is an umbrella term used for a complex neurobehavioral disorder. ASD is a multifactorial condition, with significant roles played by environmental, immunological, and genetic factors. The microbiota-gut-brain axis has been implicated in the pathophysiology of ASD in recent years. This review article aims to explore the correlation between gut dysbiosis and autism, and its potential impact on management strategies. Gastrointestinal (GI) symptoms, including diarrhea, constipation, and bloating, are prevalent among children with ASD. These disorders are commonly linked to increased behavioral symptoms, such as social disengagement, anxiety, and irritability. Increased gut permeability, attributable to gut dysbiosis, plays a significant role in disrupting the gut-brain axis, which is coordinated by neurological, immunological, and endocrinological routes. Elevated levels of inflammatory cytokines, changes in the generation of neurotransmitters, and disturbances in gut-derived metabolites are all considered direct consequences of dysbiosis. Treatment options, including probiotics, prebiotics, fecal microbiota transplantation (FMT), and dietary changes, have shown promising results. However, the effectiveness and long-term safety of these therapies are still being studied. It is imperative to explore this perplexing interaction through further research to encourage clinicians to adopt therapeutic approaches targeting the gut microbiota in patients with ASD.},
}

@article {pmid40861492,
year = {2025},
author = {Yu, X and Yu, X and Wang, Y and Guo, X and Wang, C and Wang, F},
title = {Respiratory diseases and the gut microbiota: an updated review.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1629005},
pmid = {40861492},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Dysbiosis/microbiology ; COVID-19/microbiology ; Lung/microbiology/immunology ; *Respiratory Tract Diseases/microbiology ; SARS-CoV-2 ; Probiotics ; Animals ; Pulmonary Disease, Chronic Obstructive/microbiology ; },
abstract = {The gut microbiota constitutes a vital ecosystem within the human body playing a pivotal role in immune regulation and metabolic homeostasis. Emerging research underscores a sophisticated interplay between the gut and lungs, termed the "gut-lung axis." Gut microbes exert influence over pulmonary immunity and metabolism via immune mediators (e.g., cytokines and interleukins), metabolites (e.g., short-chain fatty acids) and direct microbial translocation. Dysbiosis of the gut microbiota has been implicated in a spectrum of respiratory diseases, including asthma, chronic obstructive pulmonary disease (COPD), acute lung injury (ALI), Coronavirus Disease 2019 (COVID-19), lung cancer, idiopathic pulmonary fibrosis (IPF), pulmonary arterial hypertension (PAH), acute lower respiratory infection (ALRI) and tuberculosis (TB). Although multi-omics technologies have elucidated certain mechanisms underlying the gut-lung axis, numerous pathways remain to be fully delineated. This review synthesizes current knowledge on the role of gut microbiota and their metabolites in respiratory diseases and assesses their therapeutic potential. Future investigations should prioritize strategies to restore and maintain microbial homeostasis, such as dietary modifications, probiotic supplementation and fecal microbiota transplantation to pioneer novel preventive and therapeutic approaches. These summaries of advances in gut microbiology research promise better management and exploration of therapeutic strategies for respiratory diseases.},
}

Humans
*Gastrointestinal Microbiome/physiology
Dysbiosis/microbiology
COVID-19/microbiology
Lung/microbiology/immunology
*Respiratory Tract Diseases/microbiology
SARS-CoV-2
Probiotics
Animals
Pulmonary Disease, Chronic Obstructive/microbiology

@article {pmid40861487,
year = {2025},
author = {Tao, W and Yu, Y and Tan, D and Huang, X and Huang, J and Lin, C and Yu, R},
title = {Microbiota and enteric nervous system crosstalk in diabetic gastroenteropathy: bridging mechanistic insights to microbiome-based therapies.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1603442},
pmid = {40861487},
issn = {2235-2988},
mesh = {Humans ; *Enteric Nervous System/physiopathology ; *Gastrointestinal Microbiome/physiology ; Dysbiosis/microbiology ; Animals ; *Gastrointestinal Diseases/microbiology/therapy ; *Diabetes Complications/microbiology/therapy ; },
abstract = {Diabetes mellitus has emerged as a global public health crisis, with over half of patients experiencing gastrointestinal (GI) symptoms that exacerbate glucose fluctuations and impair quality of life. While prior research on the pathophysiology of diabetic gastroenteropathy (DGE) focused primarily on autonomic neuropathy, particularly involving the vagus nerve, recent studies have shifted toward the impairment of the enteric nervous system (ENS). As the largest autonomous neural network governing GI motility independent of central control, structural and functional abnormalities of the ENS constitute the fundamental pathological basis for DGE. This review first delineates gut microbial alterations in diabetes and mechanisms by which dysbiosis compromises the integrity of the ENS. Second, we analyze how microbiota-derived metabolites (short-chain fatty acids, bile acids, tryptophan), gut hormones (glucagon-like peptide-1, ghrelin), and neurotransmitters (acetylcholine, vasoactive intestinal peptide, nitric oxide) multitarget the ENS-collectively establishing the "microbiota-ENS axis" as the central hub for GI sensorimotor control. Finally, we provide an overview of preclinical and clinical evidence for microbiome-targeted therapies (probiotics, prebiotics, fecal microbiota transplantation) in alleviating DGE symptoms and repairing ENS while outlining translational challenges and future research priorities.},
}

Humans
*Enteric Nervous System/physiopathology
*Gastrointestinal Microbiome/physiology
Dysbiosis/microbiology
Animals
*Gastrointestinal Diseases/microbiology/therapy
*Diabetes Complications/microbiology/therapy

@article {pmid40860437,
year = {2025},
author = {Ma, C and He, H and Wang, K and Guo, J and Liu, L and Chen, Y and Li, B and Xiao, H and Li, X and Lu, X and Wang, T and Wen, Y and Wang, H and Chen, L},
title = {Maternal gut microbiota-derived daidzein prevents osteoporosis in female offspring following prenatal prednisone exposure.},
journal = {iMeta},
volume = {4},
number = {4},
pages = {e70037},
pmid = {40860437},
issn = {2770-596X},
abstract = {Prenatal exposure to glucocorticoids is linked to long-term health risks in offspring, but the role of maternal gut microbiota in mediating these effects remains unclear. Here, we demonstrate that prenatal prednisone therapy (PPT) in humans and prenatal prednisone exposure (PPE) in rats result in sex-specific long bone dysplasia in offspring, including reduced peak bone mass (PBM) and heightened osteoporosis risk in female offspring. Multi-omics profiling and fecal microbiota transplantation show that PPE alters maternal gut microbiota composition and depletes the microbial metabolite daidzein (DAI). DAI deficiency suppresses Hoxd12 expression, impairs osteogenesis, and leads to PBM decline in female offspring. In bone marrow-derived mesenchymal stem cells from PPE female offspring, DAI promoted Hoxd12 expression and osteogenic differentiation. Notably, DAI supplementation restored H3K9ac levels, enhanced Hoxd12 expression, and promoted osteogenic differentiation through the ERβ/KAT6A pathway. Furthermore, maternal DAI supplementation during pregnancy prevented osteoporosis susceptibility in PPE female offspring and alleviated functional abnormalities in multiple organs, including the liver, hippocampus, ovary, and adrenal gland. In conclusion, PPE induces multiorgan dysplasia and increases disease predisposition (e.g., osteoporosis) in female offspring by disrupting maternal gut microbiota and depleting DAI. Maternal DAI supplementation provides a promising preventive strategy to counteract these adverse outcomes.},
}

@article {pmid40860435,
year = {2025},
author = {Wang, C and Liu, Z and Zhou, T and Wu, J and Feng, F and Wang, S and Chi, Q and Sha, Y and Zha, S and Shu, S and Qu, L and Du, Q and Yu, H and Yang, L and Malashicheva, A and Dong, N and Xie, F and Wang, G and Xu, K},
title = {Gut microbiota-derived butyric acid regulates calcific aortic valve disease pathogenesis by modulating GAPDH lactylation and butyrylation.},
journal = {iMeta},
volume = {4},
number = {4},
pages = {e70048},
pmid = {40860435},
issn = {2770-596X},
abstract = {The involvement of gut microbiota in calcific aortic valve disease (CAVD) pathogenesis remains underexplored. Here, we provide evidence for a strong association between the gut microbiota and CAVD development. ApoE[-/-] mice were stratified into easy- and difficult- to calcify groups using neural network and cluster analyses, and subsequent faecal transplantation and dirty cage sharing experiments demonstrated that the microbiota from difficult-to-calcify mice significantly ameliorated CAVD. 16S rRNA sequencing revealed that reduced abundance of Faecalibacterium prausnitzii (F. prausnitzii) was significantly associated with increased calcification severity. Association analysis identified F. prausnitzii-derived butyric acid as a key anti-calcific metabolite. These findings were validated in a clinical cohort (25 CAVD patients vs. 25 controls), where serum butyric acid levels inversely correlated with disease severity. Functional experiments showed that butyric acid effectively hindered osteogenic differentiation in human aortic valve interstitial cells (hVICs) and attenuated CAVD progression in mice. Isotope labeling and [13]C flux analyses confirmed that butyric acid produced in the intestine can reach heart tissue, where it reshapes glycolysis by specifically modifying GAPDH. Mechanistically, butyric acid-induced butyrylation (Kbu) at lysine 263 of GAPDH competitively inhibited lactylation (Kla) at the same site, thereby counteracting glycolysis-driven calcification. These findings uncover a novel mechanism through which F. prausnitzii and its metabolite butyric acid contribute to the preservation of valve function in CAVD, highlighting the gut microbiota-metabolite-glycolysis axis as a promising therapeutic target.},
}

@article {pmid40860180,
year = {2025},
author = {Pan, Z and Jin, X and Li, Q and Zhou, Y and Zeng, Y and Wang, X and Jin, Y and Chen, Y and Li, D and Ling, W},
title = {Citrus Pectin Supplementation Alleviated Hepatic Lipid Accumulation through Gut Microbiota Indole Lactic Acid Promoting Hepatic Bile Acid Synthesis and Excretion.},
journal = {International journal of biological sciences},
volume = {21},
number = {11},
pages = {5015-5033},
pmid = {40860180},
issn = {1449-2288},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Pectins/pharmacology ; Mice ; *Bile Acids and Salts/metabolism/biosynthesis ; Male ; *Liver/metabolism/drug effects ; Mice, Inbred C57BL ; *Lipid Metabolism/drug effects ; *Indoles/metabolism ; Diet, High-Fat ; Dietary Supplements ; },
abstract = {Metabolic-associated fatty liver disease (MAFLD) represents a critical global health challenge. A few studies have suggested that citrus pectin may confer protective effects against MAFLD; however, the underlying mechanism remains unclear. The gut microbiota and its metabolites strongly contribute to MAFLD regulation by the gut‒liver axis. The present study explored the influence of pectin intervention on liver lipid accumulation in high-fat and high-sugar diet-fed mouse models. Pectin supplementation alleviated hepatic lipid accumulation and substantially restructured the gut microbial communities, particularly enhancing the proliferation of Akkermansia muciniphila (A. muciniphila) and Escherichia coli (E. coli), which subsequently increased indole-3-lactic acid (ILA) production. Mechanistic investigations revealed that ILA upregulated hepatic CYP7A1 and FXR-BSEP expression, stimulating hepatic bile acid biosynthesis and biliary excretion to alleviate liver steatosis. Results of previous fecal microbiota transplantation (FMT) and antibiotic-mediated microbial dysbiosis studies have confirmed the microbiota-dependent nature of the therapeutic effects of pectin. Furthermore, the administration of exogenous ILA has been demonstrated to be an effective intervention for the rescue of metabolic dysregulation in dysbacteriosis mouse models. This work delineated an unrecognized dietary pectin-microbiota-ILA-hepatic bile acid synthesis and excretion regulatory axis for the improvement of MAFLD.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Pectins/pharmacology
Mice
*Bile Acids and Salts/metabolism/biosynthesis
Male
*Liver/metabolism/drug effects
Mice, Inbred C57BL
*Lipid Metabolism/drug effects
*Indoles/metabolism
Diet, High-Fat
Dietary Supplements

@article {pmid40859356,
year = {2025},
author = {Yang, K and Du, J and Huang, F and Si, Y and Gu, Y and Xu, N and Fan, Z and Xue, R and Wang, P and Yao, X and Liu, H and Li, X and Xu, J and Wang, Z and Sun, J and Chen, Y and Xuan, L and Liu, Q},
title = {Fecal microbiota transplantation for refractory chronic graft-versus-host disease after allogeneic hematopoietic cell transplantation: a pilot open-label, non-placebo-controlled study.},
journal = {BMC medicine},
volume = {23},
number = {1},
pages = {498},
pmid = {40859356},
issn = {1741-7015},
support = {2023M741581, 2024T170387, GZC20231061//China Postdoctoral Science Foundation/ ; 2023KF04//Open Research Funds of the State Key Laboratory of Ophthalmology/ ; 2025A1515010737//GuangDong Basic and Applied Basic Research Foundation/ ; 82293634, 82170213, 82370216//Major Program of National Natural Science Foundation of China/ ; 2022YFA1105003, 2022YFC2502600-5//National Key Research and the Development Program of China/ ; },
mesh = {Humans ; *Graft vs Host Disease/therapy/etiology/microbiology ; *Fecal Microbiota Transplantation/methods ; Male ; Female ; Middle Aged ; *Hematopoietic Stem Cell Transplantation/adverse effects ; Pilot Projects ; Adult ; Gastrointestinal Microbiome ; Chronic Disease ; Transplantation, Homologous ; Young Adult ; Treatment Outcome ; Feces/microbiology ; },
abstract = {BACKGROUND: Dysbiosis of the intestinal microbiota plays a crucial role in the initiation and development of graft-versus-host disease (GVHD). Fecal microbiota transplantation (FMT) has been reported to be effective for refractory acute GVHD; however, whether FMT is effective for refractory chronic GVHD (cGVHD) remains unknown.

METHODS: To investigate the efficacy and safety of FMT for refractory cGVHD and the underlying mechanism, 12 patients with refractory cGVHD received FMT via colonoscopy, and the response was evaluated at 12 weeks after FMT.

RESULTS: Among the 12 patients who underwent FMT, 1 patient achieved a complete response, and 5 patients achieved a partial response. Patients with refractory cGVHD presented lower α diversity and higher abundance of Escherichia-Shigella and Enterobacteriaceae. FMT increased gut microbial diversity, increased the abundance of short-chain fatty acid (SCFA)-producing bacteria, and decreased the abundance of Escherichia-Shigella and Enterobacteriaceae in responder patients. Moreover, it increased SCFA levels in fecal samples from the responder group and promoted the expansion of peripheral CD4[+]CD127[-] regulatory T (Treg) cells. Colon pathological examination revealed that CD4[+] T and CD19[+] B cell infiltration decreased and that CD4[+] Treg infiltration increased after FMT.

CONCLUSIONS: The results of the present study suggest that FMT is feasible and deserves further investigation for use in patients with refractory cGVHD.

TRIAL REGISTRATION: ClinicalTrials.gov (NCT06938165).},
}

Humans
*Graft vs Host Disease/therapy/etiology/microbiology
*Fecal Microbiota Transplantation/methods
Male
Female
Middle Aged
*Hematopoietic Stem Cell Transplantation/adverse effects
Pilot Projects
Adult
Gastrointestinal Microbiome
Chronic Disease
Transplantation, Homologous
Young Adult
Treatment Outcome
Feces/microbiology

@article {pmid40858171,
year = {2025},
author = {Lin, W and Wang, X and Zhuang, T and Wang, Z and Yang, L and Wang, X and Ding, L and Tao, F},
title = {Lithospermum erythrorhizon polysaccharide alleviates obesity via gut microbiota-mediated reprogramming of bile acid and short-chain fatty acid metabolism.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {147082},
doi = {10.1016/j.ijbiomac.2025.147082},
pmid = {40858171},
issn = {1879-0003},
abstract = {Lithospermum erythrorhizon, a traditional Chinese medicinal herb and functional food ingredient, contains bioactive soluble polysaccharide with documented anti-obesity and metabolic regulatory properties. However, the precise mechanisms underlying the anti-obesity effects of Lithospermum erythrorhizon polysaccharide (LEP) fraction remain poorly characterized. In this study, diet-induced obese (DIO) mice treated with LEP exhibited significant suppression of body weight gain and hepatic lipid deposition, accompanied by improved liver function and elevated systemic energy expenditure. Mechanistic investigations revealed that LEP administration selectively suppressed the intestinal colonization of bile salt hydrolase (BSH)-producing bacterial taxa, leading to increased circulating levels of taurine-conjugated bile acids and enhanced cecal short-chain fatty acids (SCFAs) production. Concurrently, LEP activated adipose tissue thermogenesis, as evidenced by upregulated expression of thermogenic markers. Antibiotic-induced gut microbiota ablation abolished these metabolic benefits, whereas fecal microbiota transplantation from LEP-treated mice recapitulated the anti-obesity phenotype in recipient animals. These results establish that LEP ameliorates obesity through a gut microbiota-dependent mechanism involving BSH inhibition, taurine-conjugated bile acid accumulation, SCFAs elevation, and subsequent activation of adipose thermogenic pathways. These findings highlight the potential of LEP as a dietary supplement or microbiota-targeted intervention for obesity management.},
}

@article {pmid40856929,
year = {2025},
author = {Yan, C and Chen, Y and Tian, Y and Hu, S and Wang, H and Zhang, X and Chu, Q and Huang, S and Sun, W},
title = {The emerging role of microbiota in lung cancer: a new perspective on lung cancer development and treatment.},
journal = {Cellular oncology (Dordrecht, Netherlands)},
volume = {},
number = {},
pages = {},
pmid = {40856929},
issn = {2211-3436},
support = {Y-2023AZMETQN-0066//Beijing Xisike Clinical Oncology Research Foundation/ ; 62131009//National Natural Science Foundation of China/ ; },
abstract = {Lung cancer remains the leading cause of cancer-related mortality worldwide, with limited treatment efficacy and frequent resistance to conventional therapies. Recent advances have uncovered the critical influence of the human microbiota-complex communities of bacteria, viruses, fungi, and other microorganisms-on lung cancer pathogenesis and therapeutic responses. This review synthesizes current knowledge on the compositional and functional roles of microbiota across multiple body sites, including the gut, lung, tumor microenvironment, circulation, and oral cavity, highlighting their contributions to tumor initiation, progression, metastasis, and immune regulation. We emphasize the bidirectional communication between microbial metabolites and host immune pathways, particularly the gut-lung axis, which modulates systemic and local antitumor immunity. Importantly, microbiota composition has been linked to differential responses and toxicities in chemotherapy, radiotherapy, targeted therapy, and immune checkpoint blockade. Microbiota-targeted interventions, such as probiotics, fecal microbiota transplantation, and selective antibiotics, show promising potential to enhance treatment efficacy and mitigate adverse effects. However, challenges remain in clinical translation due to interindividual microbiome variability, mechanistic complexities, and limited longitudinal data. Future research integrating multi-omics, microbial functional profiling, and controlled clinical trials is essential to harness the microbiome as a precision medicine tool in lung cancer management. This review provides a comprehensive overview of the emerging role of microbiota in lung cancer development and therapy, offering new perspectives for innovative therapeutic strategies.},
}