@article {pmid41400723,
year = {2025},
author = {Leney, M and Kahale, F and Martin, VM},
title = {Diagnosis and Management of Food Protein-Induced Allergic Proctocolitis.},
journal = {Current gastroenterology reports},
volume = {27},
number = {1},
pages = {76},
pmid = {41400723},
issn = {1534-312X},
mesh = {Humans ; *Proctocolitis/diagnosis/therapy/etiology/immunology ; *Food Hypersensitivity/diagnosis/complications/therapy ; *Dietary Proteins/adverse effects/immunology ; Infant ; Biomarkers/analysis ; Breast Feeding ; },
abstract = {PURPOSE OF REVIEW: Food protein-induced allergic proctocolitis (FPIAP) is a frequent cause of rectal bleeding in otherwise healthy infants. Although benign and self-limited, wide variation in diagnostic and management practices often leads to overdiagnosis, unnecessary dietary restriction, and disruption of breastfeeding. This review summarizes contemporary evidence to guide a pragmatic, challenge-anchored approach to diagnosis and management.

RECENT FINDINGS: Diagnosis of FPIAP remains clinical, based on symptom resolution after elimination and recurrence upon reintroduction of the trigger food; however, confirmatory challenges are seldom performed. Fecal calprotectin and other proposed biomarkers-such as eosinophil-derived neurotoxin, zonulin, and microbiome signatures-show poor reliability in infants and are not ready for clinical use. Management should prioritize the least restrictive diet - maternal dairy elimination for breastfed infants and extensively hydrolyzed formulas for formula-fed infants - only in challenge-proven FPIAP. Growing data support earlier reintroduction once colitis resolves, and early introduction of other allergens may reduce future IgE-mediated allergy risk. A standardized, challenge-confirmed framework minimizes over-restriction and supports continued breastfeeding. Future priorities include validation of non-invasive biomarkers and trials comparing timing and strategies for safe dietary reintroduction in FPIAP.},
}

Humans
*Proctocolitis/diagnosis/therapy/etiology/immunology
*Food Hypersensitivity/diagnosis/complications/therapy
*Dietary Proteins/adverse effects/immunology
Infant
Biomarkers/analysis
Breast Feeding

@article {pmid41400573,
year = {2025},
author = {Wang, L and Chen, Q and Zhang, H and Zhao, X and Dong, J and Wu, D and Lian, Y and Liu, M and Liu, H and Chen, Y and Chen, Q and Lyu, W and Bai, Y},
title = {New Perspectives on Gastric Inflammaging: Integrating Multi-Omics Mechanisms and Gerotherapeutic Strategies in Chronic Gastritis.},
journal = {Aging and disease},
volume = {},
number = {},
pages = {},
doi = {10.14336/AD.2025.1444},
pmid = {41400573},
issn = {2152-5250},
abstract = {Chronic gastritis (CG) is a highly prevalent, age-associated inflammatory disorder of gastric mucosa and a key precursor of gastric cancer in older adults. Beyond Helicobacter pylori infection and environmental insults, accumulating evidence indicates that chronic, low-grade inflammation coupled with aging biology, "gastric inflammaging", plays a central role in driving mucosal degeneration, atrophy, and malignant transformation. Here, we synthesize current mechanistic and multi-omics evidence to conceptualize CG as a tractable model of organ-specific inflammaging. We first summarize how hallmarks of aging-including cellular senescence and the senescence-associated secretory phenotype (SASP), mitochondrial dysfunction, impaired autophagy, immune exhaustion, and microbiome dysbiosis-converge to create a self-perpetuating inflammatory microenvironment in the stomach. We then review emerging single-cell and spatial multi-omics studies that delineate senescence-inflammation niches and reveal how these molecular neighborhoods relate to disease stage and cancer risk. Finally, we discuss therapeutic implications, highlighting geroscience-guided interventions such as senolytics/senomorphics, inflammasome and cGAS-STING pathway modulators, microbiota- and metabolite-targeted strategies, lifestyle interventions, and natural products, and propose a precision framework linking inflammaging biomarkers to patient stratification and clinical endpoints. Reframing CG as a gastric inflammaging model may provide a prototype for organ-specific healthy aging strategies and near-term gerotherapeutic trials aimed at extending healthspan.},
}

@article {pmid41400485,
year = {2025},
author = {Mukherjee, A},
title = {The maternal-infant microbiome axis as an epigenetic and immunometabolic orchestrator: redefining early-life programming and precision interventions for lifelong women's and children's health.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0050225},
doi = {10.1128/iai.00502-25},
pmid = {41400485},
issn = {1098-5522},
abstract = {The maternal-infant microbiome axis represents a dynamic interface that shapes neonatal immune and metabolic development from the earliest stages of life. Microbial communities from the maternal gut, vaginal tract, and breast milk seed the infant microbiome, influencing chromatin remodeling, transcriptional activity, and immunometabolic programming. Rather than functioning solely as a conduit of microbial inheritance, this axis operates as a regulatory network where microbial metabolites such as short-chain fatty acids and indole derivatives modulate histone acetylation, DNA methylation, and noncoding RNA pathways that calibrate immune tolerance and pathogen defense. Perturbations, including cesarean delivery, perinatal antibiotic exposure, or maternal metabolic disorders, disrupt these processes and are associated with altered immune set points, heightened infection susceptibility, and increased risk of inflammatory and metabolic disease. Multi-omics studies now provide mechanistic insights linking microbial signals to epigenetic regulation of neonatal immune responses, while also exposing important controversies, such as the debated presence of a placental microbiome and the variable efficacy of probiotic interventions. Emerging strategies, including maternal dietary modulation of the microbiome, perinatal microbiota restoration, and development of live biotherapeutics, show promise, but their translational potential remains constrained by limited sample sizes, heterogeneous outcomes, and safety concerns. Framing the maternal-infant microbiome axis as an epigenetic and immunometabolic orchestrator highlights both its therapeutic promise and the need for rigorous mechanistic and clinical evaluation to advance preventive strategies for women's and children's health.},
}

@article {pmid41399631,
year = {2025},
author = {Su, J and Hansen, BE and Wang, Z and Sharmenov, A and Xia, X and Broekhuizen, M and Ma, Z and Peppelenbosch, MP},
title = {Yogurt reintroduction and the circulating microbiome in healthy volunteers: protocol for a prospective, longitudinal, species-controlled crossover clinical trial (MAMI).},
journal = {Contemporary clinical trials communications},
volume = {48},
number = {},
pages = {101579},
pmid = {41399631},
issn = {2451-8654},
abstract = {BACKGROUND: Although the gut microbiome plays a crucial role for maintaining overall host homeostasis and metabolism, it is significantly influenced by dietary changes, leading to substantial temporal variations in microbial composition within and between individuals. Despite this, incidental fecal sampling remains the standard method for microbiome assessment. Recently, the blood microbiome, defined by microbial DNA (cmDNA) circulating in the bloodstream, has emerged as a potentially more stable and integrated alternative. Preliminary data suggest that blood microbiome analysis may offer more consistent insights than fecal-based approaches, although the methodological validity of the approach has been questioned.

METHOD/DESIGN: This study aims to establish or rule-out cmDNA as a representative of the gut microbiome. In a prospective, single-arm crossover trial, effects of dairy product withdrawal and reintroduction of a yoghurt with a known consortium of bacteria will be assessed in healthy volunteers aged 18-65. Participants will first abstain from all dairy products, a phase expected to reduce yogurt-associated cmDNA in the bloodstream. Yogurt will then be reintroduced, during which reappearance of cmDNA of specific bacteria (especially LGG, LA-5 and BB-12) is anticipated. Shotgun metagenomic sequencing will be used to track cmDNA dynamics over time. This longitudinal sampling approach will provide experimental evidence supporting the existence and responsiveness of the circulating microbiome, while also revalidating the bioinformatic pipeline used for its analysis.

CONCLUSION: This pilot study will test whether blood-derived microbial DNA can serve as a valid surrogate for gut microbiome composition. If successful, this approach may provide a more stable and integrative alternative to fecal sampling and support future biomarker development and mechanistic research.

CLINICAL TRIAL REGISTRATION: NCT06944002.},
}

@article {pmid41399570,
year = {2025},
author = {Bheemaneni, RS and Sakarkar, P and Nigam, A and Nwachukwu, EC and Sekar Lakshmisai, S and Mohammed, L},
title = {Unraveling the Association Between Fibromyalgia and Irritable Bowel Syndrome: A Systematic Review.},
journal = {Cureus},
volume = {17},
number = {11},
pages = {e96801},
pmid = {41399570},
issn = {2168-8184},
abstract = {Fibromyalgia (FM) and irritable bowel syndrome (IBS) often occur together. Patients with FM and IBS present similar symptoms, such as pain and fatigue; this leads to a delay in diagnosis and management. This systematic review explored the shared pathophysiology of these conditions in adults, focusing on the roles of immune dysfunction, gut dysbiosis, neurotransmitter imbalances, and disturbances in the gut-brain axis. We searched five databases, PubMed, PubMed Central, Google Scholar, Cochrane, and ScienceDirect, for relevant free full-text English articles from 2015 to 2025. Ten studies were selected after screening, identification, and quality assessment, adhering to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) 2020 guidelines. Our review found that immune system dysregulation involves mast cells and pro-inflammatory cytokines that damage the gut barrier. The gut microbiome and neurotransmitter levels seem to have a reciprocal influence on each other, and their alteration contributes to pathogenesis, with an increase of certain species showing an association with symptom severity. Serotonin and tryptophan metabolism appear to have a crucial role in pain perception, particularly visceral hypersensitivity. Therapeutic strategies targeting the gut microbiome, such as probiotics and fecal microbiota transplantation, have potential but require further research. Overall, this review identified overlapping mechanisms of FM-IBS comorbidity, which can pave the way to effective and combined treatment approaches. Future research should explore gender distinctions in the mechanisms, medications that act on neurotransmitter receptors (especially serotonergic pathways), and the utility of fecal microbiota transplantation and probiotics.},
}

@article {pmid41399387,
year = {2026},
author = {Yu, Y and Zhao, W and Yang, M and Wu, B and Yuan, X},
title = {Tumor-Promoting Gut Microbes in Colorectal Cancer: Mechanisms and Translational Perspectives.},
journal = {International journal of medical sciences},
volume = {23},
number = {1},
pages = {63-75},
pmid = {41399387},
issn = {1449-1907},
mesh = {Humans ; *Colorectal Neoplasms/microbiology/therapy/diagnosis/pathology/immunology ; *Gastrointestinal Microbiome/immunology/physiology ; *Dysbiosis/microbiology/complications/therapy/immunology ; Fecal Microbiota Transplantation/methods ; Probiotics/therapeutic use ; Carcinogenesis/immunology ; Translational Research, Biomedical ; },
abstract = {Colorectal cancer (CRC) represents a predominant global malignancy, characterized by increasing incidence and mortality rates. Recent investigations have underscored the gut microbiota as a pivotal element in the pathogenesis and progression of CRC. This review synthesizes current evidence regarding the association between gut microbial dysbiosis and CRC, with a particular emphasis on pathogenic bacteria such as Fusobacterium nucleatum, enterotoxigenic Bacteroides fragilis, pks[+] Escherichia coli, and Enterococcus faecalis, among others. The mechanisms through which these microbes contribute to tumorigenesis include the induction of DNA damage, the promotion of chronic inflammation, and the induction of immunosuppression, and the production of oncogenic metabolites. Additionally, the review examines the clinical implications of gut microbiota, highlighting their potential as non-invasive biomarkers for early CRC detection and their impact on the efficacy and toxicity of chemotherapy, radiotherapy, and immunotherapy. Furthermore, emerging microbiota-targeted interventions, such as fecal microbiota transplantation, dietary modification, and probiotics, are evaluated for their therapeutic potential. Despite substantial progress, challenges remain in standardizing microbial markers and optimizing individualized microbiota modulation strategies. Future studies integrating multi-omics and machine learning approaches may pave the way for microbiome-based precision medicine in CRC.},
}

Humans
*Colorectal Neoplasms/microbiology/therapy/diagnosis/pathology/immunology
*Gastrointestinal Microbiome/immunology/physiology
*Dysbiosis/microbiology/complications/therapy/immunology
Fecal Microbiota Transplantation/methods
Probiotics/therapeutic use
Carcinogenesis/immunology
Translational Research, Biomedical

@article {pmid41399344,
year = {2025},
author = {Hillman, EBM and Carson, D and Walters, JRF and Fritzsche, M and Mate, R and Chappell, KE and Chekmeneva, E and Romero, MG and Lewis, SJ and Rijpkema, S and Wellington, EMH and Arasaradnam, R and Amos, GCA},
title = {Ruminococcus gnavus and Biofilm Markers in Feces From Primary Bile Acid Diarrhea Patients Indicate New Disease Mechanisms and Potential for Diagnostic Testing.},
journal = {Gastro hep advances},
volume = {4},
number = {9},
pages = {100712},
pmid = {41399344},
issn = {2772-5723},
abstract = {BACKGROUND AND AIMS: Bile acid diarrhea (BAD) is a common cause of frequent loose stools, urgency, and incontinence, which is under-recognized due to limited diagnostic test availability and unclear pathogenesis. This study aimed to investigate fecal changes in well-defined subjects.

METHODS: Fecal samples were compared in BAD patients (n = 26), diagnosed by SeHCAT testing, and healthy controls (n = 21). Shotgun metagenomic sequencing was used to identify microbiome species and functional genes. An extended set of 38 bile acids was quantified by liquid chromatography mass spectrometry, including various epimers and intermediates, such as iso- (3-beta-OH), oxo (keto), allo (5-alpha), and 3-sulfated forms.

RESULTS: Alpha diversity, reflecting microbial richness, was reduced in BAD patients with severe forms of the disease, while beta diversity demonstrated distinct microbial profiles between groups. Ruminococcus gnavus (R. gnavus) was prevalent in BAD patients but rare in controls (odds ratio = 73), while Firmicutes bacterium CAG110, Eubacterium siraeum and 2 Oscillibacter species were less common in BAD (odds ratios = 25-30). Overall, 99 taxa differed significantly between groups. Bile acidtransforming genes (baiA, baiB, hdhA) were more abundant in BAD samples (P ≤ .0012). Most fecal bile acids, including iso-bile acids and intermediates, were higher in BAD. Elevated ursodeoxycholic acid-3-sulfate and relatively lower lithocholic acid and allo-bile acids, including isoallolithocholic acid, reflect changes in bacterial metabolism. Biofilm-associated genes (bssS, pgaA, pgaB) were markedly elevated in BAD patients (P ≤ .00008). SeHCAT values negatively correlated with R. gnavus (rho -0.53, P = .008) and positively with E ubacterium siraeum (rho 0.41, P = .041).

CONCLUSION: BAD may result from an overgrowth of R. gnavus, associated with intestinal biofilms and an altered bile acid metabolism.},
}

@article {pmid41399266,
year = {2025},
author = {Lee, SG and Lee, JH and Baek, Y and Chu, J and Kim, KH and Ham, S and Shin, CH and Lee, YI},
title = {Efficacy and Safety of Human Skin Microbiome-Derived Strains as Topical Treatment for Acne: An In Vitro and In Vivo Study.},
journal = {Journal of Korean medical science},
volume = {40},
number = {48},
pages = {e327},
doi = {10.3346/jkms.2025.40.e327},
pmid = {41399266},
issn = {1598-6357},
support = {20024192/MOTIE/Ministry of Trade, Industry and Energy/Korea ; },
mesh = {*Acne Vulgaris/microbiology/pathology/therapy/drug therapy ; Humans ; Animals ; *Skin/microbiology ; *Microbiota ; Mice ; Keratinocytes/metabolism/cytology ; Disease Models, Animal ; Staphylococcus epidermidis/isolation & purification ; Propionibacterium acnes ; Cytokines/metabolism ; Male ; Female ; Cyclooxygenase 2/metabolism ; Skin Microbiome ; },
abstract = {BACKGROUND: The skin microbiome plays a crucial role in defending against pathogens and modulating immunity, and its dysregulation is linked to various skin conditions, including acne.

METHODS: In this study, four previously identified strains-Staphylococcus epidermidis B424F-5, S. epidermidis BS47C-1, Dermacoccus profundi BS35F-3, and Streptococcus salivarius BS320F-4- were selected from a skin microbiome database of healthy individuals. The efficacy and safety of these strains against acne-related inflammation were evaluated using in vitro and in vivo animal model experiments.

RESULTS: Cutibacterium acnes exposure increased the expression of acne-associated inflammatory mediators-such as IL-1β, IL-6, IL-8, COX-2, iNOS, and TNF-α-particularly in keratinocytes, without inducing cytotoxicity. Treatment with heat-killed S. epidermidis BS47C-1 (SE2), D. profundi BS35F-3 (DP), and S. salivarius BS320F-4 (SS) significantly reduced these markers in vitro. In vivo, topical application of the strains alleviated inflammation in a C. acnes-induced mouse model, with histological evidence of reduced erythema and immune cell infiltration. Bulk RNA sequencing of keratinocytes showed that SE2 and DP downregulated cytokine and interferon signaling while enhancing skin barrier and antimicrobial gene expression, suggesting a dual anti-inflammatory and barrier-supporting mechanism.

CONCLUSION: These results provide compelling evidence of the efficacy and safety of human skin microbiome-derived strains as potential topical treatments for acne. By targeting both microbial colonization and inflammatory pathways, these strains offer a promising avenue for the development of novel acne therapeutics.},
}

*Acne Vulgaris/microbiology/pathology/therapy/drug therapy
Humans
Animals
*Skin/microbiology
*Microbiota
Mice
Keratinocytes/metabolism/cytology
Disease Models, Animal
Staphylococcus epidermidis/isolation & purification
Propionibacterium acnes
Cytokines/metabolism
Male
Female
Cyclooxygenase 2/metabolism
Skin Microbiome

@article {pmid41399025,
year = {2025},
author = {Zhao, D and Wang, X and Wang, K and Yang, B and Zhu, H and Xu, Y and Ye, C and Li, L and Lv, X and Zhou, S and Ma, C and Chen, X and Yin, F and Zhu, Y and Cao, Z and Li, N and Zuo, T and Qin, H and Chen, Q},
title = {Recipients' native bacteria determine the outcome of FMT treatment in inflammatory bowel disease.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2600055},
doi = {10.1080/19490976.2025.2600055},
pmid = {41399025},
issn = {1949-0984},
mesh = {Humans ; Male ; Female ; Adult ; *Gastrointestinal Microbiome ; *Fecal Microbiota Transplantation/adverse effects ; Middle Aged ; *Bacteria/classification/isolation & purification/genetics ; Treatment Outcome ; Retrospective Studies ; Feces/microbiology ; *Colitis, Ulcerative/therapy/microbiology ; *Inflammatory Bowel Diseases/therapy/microbiology ; *Crohn Disease/therapy/microbiology ; Young Adult ; Prospective Studies ; Aged ; },
abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) is a promising treatment for inflammatory bowel disease (IBD), achieving clinical response rate of ~50% for ulcerative colitis (UC), and Crohn's disease (CD). While prior research has emphasized donor selection and treatment protocols, the role of the patient's native intestinal microbiota in FMT outcomes remains underexplored.

METHODS: This study analyzed a retrospective cohort of 96 IBD patients (45 CD, 51 UC) undergoing FMT, with 192 paired stool samples collected pre- and post-treatment, alongside 332 healthy donor samples from 18 donors. A prospective cohort of 45 IBD patients provided 45 baseline stool samples, and a validation cohort of 112 non-IBD patients contributed 224 paired samples. Retrospective cohort patients were monitored for 4 weeks to assess FMT responsiveness and 52 weeks for treatment effectiveness. Microbiome analysis identified enterotype-specific bacteria and native bacterial genera influence FMT outcomes. Random forest, permissivity, and mathematical models predicted treatment response, characterized microbiome remodeling, and defined microecological remission thresholds.

RESULTS: The FMT regimen was safe, with no serious adverse events reported. At week 4, the clinical response rates were 58.8% (26/45) for CD patients and 66.7% (34/51) for UC patients; by week 52, the remission rates were 82.4% (37/45) for CD patients and 84.4% (43/51) for UC patients. Microbiome analysis identified 54 bacterial genera linked to enterotype classification, 57 to UC response, and 93 to CD response. Notably, 38 high-frequency retentions of recipient native bacteria after FMT were predictive of FMT responsiveness. The permissivity model revealed a shift toward Bacteroidetes-dominated enterotypes in IBD patients post-FMT, which was validated in 112 non-IBD patients. The abundance ranges of recipients' native bacteria predictive of treatment responsewere determined by mathematical interpretation model.

CONCLUSION: The patient's native microbiota significantly influences FMT efficacy in IBD, influencing microbiome remodeling and clinical outcomes, highlighting the importance of baseline microbial profiles in predicting FMT responsiveness and optimizing therapy.},
}

Humans
Male
Female
Adult
*Gastrointestinal Microbiome
*Fecal Microbiota Transplantation/adverse effects
Middle Aged
*Bacteria/classification/isolation & purification/genetics
Treatment Outcome
Retrospective Studies
Feces/microbiology
*Colitis, Ulcerative/therapy/microbiology
*Inflammatory Bowel Diseases/therapy/microbiology
*Crohn Disease/therapy/microbiology
Young Adult
Prospective Studies
Aged

@article {pmid41399002,
year = {2025},
author = {Ma, C and Ding, W and Li, P and Wang, Q and Li, X and Meng, Z and Ren, H},
title = {ROS-Responsive Hydrogel with M2 Macrophage Nanovesicles for Diabetic Wound Healing: Targeted CO Delivery to Regulate Mitochondrial Metabolism and Reprogram Wound Microbiota.},
journal = {ACS applied materials & interfaces},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsami.5c18140},
pmid = {41399002},
issn = {1944-8252},
abstract = {Macrophage dysregulation and microbial dysbiosis at diabetic chronic wound sites are two of the main drivers that hinder the healing process. To address this, a reactive oxygen species (ROS)-responsive hydrogel wound dressing (NVs@CO-TP) is fabricated through boronic ester bonds between poly(vinyl alcohol) hydroxyl groups and phenylboronic acid moieties, which incorporates M2 macrophage-derived nanovesicles (NVs) loaded with manganese carbonyl (NVs@CO). Upon exposure to a high level of ROS in the wound, the hydrogel responds, scavenges ROS, and subsequently releases NVs@CO, exhibiting the synergistic efficacy of CO gas and NVs. Due to its intrinsic inflammation-tendency ability, NVs@CO specifically targets activated M1 macrophages and releases CO to regulate mitochondrial metabolism, promoting M1 apoptosis and increasing the M2 phenotype. This process decreases the release of inflammatory cytokines and enhances anti-inflammatory processes, promoting chronic diabetic wound healing. More interestingly, the dressing also beneficially modulates the wound microbiota by enhancing the beneficial microbial richness and overall microbiome composition, which further improves the healing microenvironment. Therefore, NVs@CO-TP acts through two primary mechanisms: the targeted delivery of CO to M1 macrophages regulates the mitochondrial metabolism to repolarize macrophages while simultaneously modulating the wound microbiome. This combined anti-inflammatory strategy facilitates chronic wound healing and demonstrates significant potential for clinical translation in treating various difficult-to-heal wounds.},
}

@article {pmid41398941,
year = {2025},
author = {Song, Y and Hou, S and Xiang, Y and Zou, D and Gu, S and Pu, X and Liu, Q and Chu, M},
title = {Dietary energy levels modulate rumen metabolites and function in sheep by regulating the rumen microbiome.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04636-7},
pmid = {41398941},
issn = {1471-2180},
support = {XQSWYZQZ-JBKY-4//Project of State Key Laboratory of Animal Biotech Breeding of China/ ; CAAS-ZDRW202502 and ASTIP-IAS13//Agricultural Science and Technology Innovation Program of China/ ; CARS-38-02//Earmarked Fund for China Agriculture Research System of MOF and MARA/ ; },
abstract = {In intensive ruminant production, high-energy diets are commonly used to enhance animal productivity, as dietary formulation significantly influences rumen fermentation and microbial communities. This study investigated the effects of varying dietary energy levels on the rumen microbial community structure, function, and metabolic profiles in Small-tailed Han (STH) sheep. Thirty 6-month-old sheep were randomly assigned to three groups: high-energy (HE), conventional-energy (CE), and low-energy (LE). All groups were fed iso-nitrogenous diets formulated to provide high-, conventional-, and low-energy levels of 10.8, 9.5, and 8.2 MJ/kg of digestible energy (DE), respectively. Rumen content was collected post-slaughter and analyzed via metagenomic sequencing to assess microbial composition and function, alongside non-targeted metabolomics to characterize the rumen fluid metabolome. Results revealed that Bacteroidota and Bacillota were the dominant phyla. High-energy feeding significantly reduced the relative abundance of Bacteroidota while increasing that of Bacillota, leading to a markedly higher Bacillota-to-Bacteroidota ratio. Functional analysis indicated significant enrichment of carbohydrate metabolism pathways in the HE group, whereas the LE group exhibited enrichment in fundamental cellular processes such as ABC transporters and ribosome, indicating a "survival mode". Metabolomic analysis demonstrated that dietary energy levels substantially reshaped the rumen metabolomic profile. Metabolites in the HE group were enriched in pathways including steroid hormone biosynthesis and the prolactin signaling pathway, while the LE group showed enrichment in histidine metabolism and the TCA cycle. Several aromatic amino acid metabolic pathways were commonly enriched across comparisons. These findings indicate that while the composition of the dominant phyla (Bacteroidota and Bacillota) was conserved across diets with different digestible energy levels, this dietary variation altered community diversity, structure, functional potential, and profoundly reshaped the rumen metabolic environment. This study provides scientific evidence regarding the impact of dietary energy on rumen fermentation and production performance in fattening sheep.},
}

@article {pmid41398793,
year = {2025},
author = {Yang, W},
title = {The causal links between gut microbiota and both acute and chronic renal failure: A two-sample mendelian randomization study.},
journal = {Medicine},
volume = {104},
number = {50},
pages = {e46336},
doi = {10.1097/MD.0000000000046336},
pmid = {41398793},
issn = {1536-5964},
mesh = {Humans ; Mendelian Randomization Analysis ; *Gastrointestinal Microbiome/genetics ; *Acute Kidney Injury/microbiology/genetics ; Genome-Wide Association Study ; *Kidney Failure, Chronic/microbiology/genetics ; Male ; Female ; Middle Aged ; },
abstract = {This study aimed to investigate the potential causal relationships between gut microbiota composition and both acute renal failure (ARF) and chronic renal failure (CRF), using a two-sample Mendelian randomization approach. We characterized the gut microbiota composition at various taxonomic levels (phylum, class, order, family, and genus) and obtained genome-wide association study data for both ARF and CRF from the FinnGen and UK Biobank databases. Subsequently, we employed a two-sample Mendelian randomization approach to explore the causal relationship between the gut microbiota and renal failure. We identified 10 causal relationships between the genetic liability in the gut microbiome and ARF. We found 4 associations between genetic liability in the gut microbiome and CRF. The results indicated that Haemophilus (inverse variance weighted, IVW OR = 0.816, 95% CI = 0.719-0.926, P = .002, q = 0.054) and Ruminococcaceae UCG005 (IVW OR = 0.804, 95% CI = 0.694-0.931, P = .004, q = 0.078) showed negative associations with ARF. Moreover, Ruminococcaceae UCG005 (IVW OR = 1.001, 95% CI = 1.00-1.002, P = .008, q = 0.091) positively correlated with CRF risk. Sensitivity analyses did not provide statistical evidence of bias due to pleiotropy or genetic confounding factors. Our research contributes significantly to the growing body of knowledge linking the gut microbiota to renal health, offering new perspectives for the diagnosis, treatment, and prevention of renal diseases.},
}

Humans
Mendelian Randomization Analysis
*Gastrointestinal Microbiome/genetics
*Acute Kidney Injury/microbiology/genetics
Genome-Wide Association Study
*Kidney Failure, Chronic/microbiology/genetics
Male
Female
Middle Aged

@article {pmid41398791,
year = {2025},
author = {Ye, C and Lian, G and Wang, T and Wang, H and Xie, L},
title = {Causal effects of the gut microbiota, circulating metabolites, and cardiometabolic diseases: A Mendelian randomization study.},
journal = {Medicine},
volume = {104},
number = {50},
pages = {e46523},
doi = {10.1097/MD.0000000000046523},
pmid = {41398791},
issn = {1536-5964},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics/physiology ; Mendelian Randomization Analysis ; Diabetes Mellitus, Type 2/genetics/microbiology ; *Cardiovascular Diseases/microbiology/genetics ; Stroke/genetics/microbiology ; Hypertension/genetics/microbiology ; },
abstract = {The gut microbiota is associated with cardiometabolic disorders (including coronary artery disease, type 2 diabetes, stroke, heart failure, and hypertension) through the gut-heart or gut-brain axis, among which metabolic processes play crucial roles. However, the exact causal mechanisms remain unknown. Our study sought to uncover the causal relationships between the gut microbiota, circulating metabolites and cardiometabolic diseases via Mendelian randomization (MR) analysis. Forward MR was utilized to investigate the causal effects of the gut microbiota and circulating metabolites on the risk of cardiometabolic diseases. Reverse MR was subsequently performed to analyze the significant gut microbiota and circulating metabolites. Two-step MR was employed to examine the impact of circulating metabolites on the relationship between the gut microbiota and cardiometabolic diseases and to determine the mediated fractions. Our results revealed a nominal causal relationship with 23, 23, 22, 20, and 19 gut microbiota constituents for coronary artery disease, type 2 diabetes, stroke, heart failure, and hypertension, respectively. We also identified 2 significant associations and 13 suggestive associations between circulating metabolites and these cardiometabolic diseases. Reverse MR analysis revealed that genetically predicted type 2 diabetes was suggestively associated with 3 circulating metabolites, whereas stroke demonstrated a suggestive association with 3 distinct gut microbiota. Further screening identified 4 circulating metabolites as potential mediators in the pathway from the gut microbiota to cardiometabolic diseases. Our study revealed a causal link between gut microbiome components and cardiometabolic diseases and that circulating metabolites potentially act as intermediaries in this association.},
}

Humans
*Gastrointestinal Microbiome/genetics/physiology
Mendelian Randomization Analysis
Diabetes Mellitus, Type 2/genetics/microbiology
*Cardiovascular Diseases/microbiology/genetics
Stroke/genetics/microbiology
Hypertension/genetics/microbiology

@article {pmid41398743,
year = {2026},
author = {Yang, X and Ji, XH and Li, C and Lai, JL and Luo, XG},
title = {Soil microecosystem collapse and revival: Dual-targeted HMX toxicity versus secretion system-mediated synthetic microbiome restoration.},
journal = {Bioresource technology},
volume = {441},
number = {},
pages = {133557},
doi = {10.1016/j.biortech.2025.133557},
pmid = {41398743},
issn = {1873-2976},
mesh = {*Soil Microbiology ; *Microbiota/drug effects ; Biodegradation, Environmental ; *Soil Pollutants/toxicity/metabolism ; *Soil/chemistry ; Triazines ; },
abstract = {The persistent energetic compound cyclotetramethylene tetranitramine (HMX) poses increasing ecological threats. However, its micro-ecological toxicity mechanisms and effective remediation strategies remain inadequately understood. This study aimed to elucidate HMX's inhibitory mechanisms on soil microecology and develop a synergistic synthetic microbiome for effective remediation. HMX exhibited high persistence (94.4 % residual after 40 days) and acts through a 'dual-target inhibition' mechanism in soil: 1) inhibiting cytochrome c oxidase, disrupting the electron transport chain and reducing ATP synthesis; 2) chelating Zn[2+]/Ni[2+] cofactors, inactivating key enzymes like β-glucosidase (reduced by 63.4 %). These actions culminated in a dual "energy-nutrition" crisis, suppressed functional genes (pccA, nosZ, phoD), and reduced microbial diversity (OTUs decreased by 11.7 %). Metabolomic analysis revealed five HMX transformation pathways in soil. To address this, a synthetic microbiome of six efficient strains (e.g., Bacillus megaterium) was constructed. This consortium achieved HMX degradation via a secretion system-mediated extracellular enzymatic cascade, confirmed by product deposition on cell surfaces (degradation rate: 84.7-96.4 % in 48 h). The ring-opening products were assimilated into the TCA cycle, fueling lipid and nucleotide metabolism. Inoculation with this functional consortium for 40 days successfully restored soil health, achieving 92.4 % HMX removal, a 3.11-fold increase in respiration, and recovered alpha diversity. This study provides a novel "microbiome-enhanced element cycle steady-state" paradigm for remediating military-contaminated sites.},
}

*Soil Microbiology
*Microbiota/drug effects
Biodegradation, Environmental
*Soil Pollutants/toxicity/metabolism
*Soil/chemistry
Triazines

@article {pmid41398701,
year = {2025},
author = {Wang, M and Zhang, C and Zhao, L and Yin, Q and Cui, Z and Chen, X and Ren, J and Wang, Y and Xu, M and Cao, Y and Wu, S and Yao, J},
title = {Unraveling the interaction between the phageome and bacteriome in the rumen and its role in influencing metabolome dynamics in dairy cows at different lactation stages.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02260-1},
pmid = {41398701},
issn = {2049-2618},
support = {2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022GD-TSLD-46-0501//Shaanxi Livestock and Poultry Breeding Double-chain Fusion Key Project/ ; 2022GD-TSLD-46-0501//Shaanxi Livestock and Poultry Breeding Double-chain Fusion Key Project/ ; 2022GD-TSLD-46-0501//Shaanxi Livestock and Poultry Breeding Double-chain Fusion Key Project/ ; 2022GD-TSLD-46-0501//Shaanxi Livestock and Poultry Breeding Double-chain Fusion Key Project/ ; 2022GD-TSLD-46-0501//Shaanxi Livestock and Poultry Breeding Double-chain Fusion Key Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 2022ZDLNY01-09//Key Research and Development Program of Shaanxi Province/ ; 2022ZDLNY01-09//Key Research and Development Program of Shaanxi Province/ ; 2022ZDLNY01-09//Key Research and Development Program of Shaanxi Province/ ; 2022ZDLNY01-09//Key Research and Development Program of Shaanxi Province/ ; 2022ZDLNY01-09//Key Research and Development Program of Shaanxi Province/ ; 32272829//National Natural Science Foundation of China/ ; 32272829//National Natural Science Foundation of China/ ; 32272829//National Natural Science Foundation of China/ ; 32272829//National Natural Science Foundation of China/ ; 32272829//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Although the roles of rumen microbiome in milk yield and milk protein synthesis have been widely recognized, knowledge on how ruminal microbiome dynamic changes affect these two traits during the whole lactation is lacking. Phages have been shown to affect the microbiota, but little is known about the shift patterns of ruminal phages and if they may modulate rumen microbiome during lactation. Herein, a longitudinal study was performed to identify the potential roles of ruminal phageome and bacteriome interactions, and metabolic function shift in affecting milk yield and protein content using metagenomic and metabolomic profiling of rumen microbiome from the peak, early, and later mid-lactation stages.

RESULTS: A total of 780 ruminal bacterial phages were identified, which exhibited two primary shifting patterns: (1) decreasing then increasing; (2) decreasing then stabilizing through the lactation. Bacteriome also showed first increasing then stabilizing or continuously declining besides exhibiting two similar shifting patterns to those of phages. By associating the differentially abundant phages with their host bacteria, we observed that significantly increased Lactococcus phage BM13, Corynebacterium phage P1201, and Campylobacter phage CJIE4-5 in peak lactation, along with Lactobacillus phage Lv-1 in early and later mid-lactation, were positively correlated with the relative abundance of their hosts. However, significantly increased Bacillus phage BCU4 and the Enterococcus phage phiNASRA1 in early mid-lactation were negatively related to their host abundance. In terms of bacteria, Ruminococcus flavefaciens and Faecalibacterium sp. CAG 74 had the highest abundance in peak lactation, whereas most Prevotella species were more abundant in early and later mid-lactation. Notably, ruminal carbohydrate and amino acid metabolism functions were enhanced in early mid-lactation. Further structural equation model and network analysis revealed that abundant Bacillus phage BCU4 and Enterococcus phage phiNASRA1 in early mid-lactation were associated with increased relative abundance of Prevotella species, possibly due to a reduction in Bacillus cereus and Enterococcus faecalis. Additionally, these Prevotella species exhibited positive relationships with rumen metabolites, such as L-phenylalanine, phenylacetylglycine, N-acetyl-D-phenylalanine, and propionate content, which contributed to the improved milk protein yield.

CONCLUSIONS: This study revealed the bacteriome and phageome interactions at different lactation stages, and the key phages and bacteria regulating the rumen function and metabolism thus contributing to the milk traits of cows. The potential regulatory roles of phages in affecting the rumen bacteriome suggest that they can be powerful targets for future interventions to improve rumen functions. Video Abstract.},
}

@article {pmid41398611,
year = {2025},
author = {Chen, X and Zhang, F and Cheng, L and Niu, D and Hu, J and Huang, S and Wang, F and Pang, G and Huang, C and Li, M and Wang, C and Mo, Z},
title = {Dysbiosis of the gut microbiota in calcium oxalate nephrolithiasis is associated with impaired short-chain fatty acid production and systemic metabolomic disruptions.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02224-5},
pmid = {41398611},
issn = {2049-2618},
support = {Guike AB21196022//Guangxi Key Research and Development Project/ ; Guike AA22096032//Guangxi Science and Technology Major Project/ ; AA18118016//Major Project of Guangxi Innovation Driven/ ; 22-35-17//Guangxi key Laboratory for Genomic and Personalized Medicine/ ; 62272065//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: The prevalence of calcium oxalate (CaOx) kidney stones is increasing, yet the underlying mechanisms remain incompletely understood. Emerging evidence suggests that gut microbiota-particularly short-chain fatty acid (SCFA)-producing bacteria-may modulate host metabolism and inflammation, thereby influencing stone formation. However, the mechanistic links between gut dysbiosis, metabolic disturbances, and CaOx stone pathophysiology remain to be fully elucidated. This study investigates gut microbiota composition, SCFA levels, and metabolomic alterations in CaOx stone formers (CSF), aiming to uncover potential pathophysiological mechanisms and therapeutic targets.

RESULTS: Among 59 CSF and 60 healthy controls (HC), CSF exhibited significantly reduced microbial richness, with marked depletion of SCFA-producing bacteria such as Faecalibacterium prausnitzii and Eubacterium rectale. This dysbiosis was associated with decreased fecal and plasma SCFA levels, reduced 24-h urinary citrate, and widespread metabolic disturbances, particularly in tryptophan metabolism and the citrate cycle. Plasma SCFA levels were positively correlated with urinary citrate excretion, suggesting a regulatory link within the gut-kidney axis. Mendelian randomization analysis suggested that Bacteroides thetaiotaomicron may be a potential microbial risk factor for stone formation (OR = 1.26, 95% CI: 1.03-1.54, p = 0.028). In a hyperoxaluria rat model, interventions with F. prausnitzii, E. rectale, or sodium butyrate reduced renal CaOx crystal deposition and kidney injury.

CONCLUSIONS: Our findings highlight the central role of SCFA-producing bacteria and their metabolites in maintaining metabolic balance and protecting against CaOx stone formation. Gut dysbiosis and reduced SCFA levels appear to drive metabolic changes that contribute to stone development. B. thetaiotaomicron may increase stone risk, while F. prausnitzii, E. rectale, and sodium butyrate show therapeutic potential. These insights support further exploration of microbiome-based strategies for the prevention and personalized management of kidney stones. Video Abstract.},
}

@article {pmid41398357,
year = {2025},
author = {Yassine, F and Abbas, H and Kurdi, A and Mansour, R and Mourad, FH and Matar, G and Bilen, M},
title = {Gut microbiota profiling in Lebanese ulcerative colitis patients and healthy controls from a pilot study.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-31435-x},
pmid = {41398357},
issn = {2045-2322},
support = {Seed grant//Faculty of Medicine, American University of Beirut/ ; },
abstract = {Ulcerative colitis (UC) is a chronic inflammatory disease of the colon, associated with gut microbiota dysbiosis. While global studies have explored this link, region-specific microbial profiles remain underreported. This pilot study aimed to characterize and compare, for the first time, the gut microbiota of Lebanese UC patients and healthy controls using 16 S rRNA gene sequencing (V3-V4 region). Fecal samples from 11 UC patients and 11 healthy individuals were analyzed. Alpha and beta diversity metrics were computed, and gut microbial composition was assessed across taxonomic levels. Statistical comparisons used Mann-Whitney and Fisher's exact tests. UC patients showed significantly reduced microbial diversity based on Faith's Phylogenetic Diversity and Shannon index (p < 0.05), though evenness was unaffected. Beta diversity also revealed significant group-level dissimilarities (p < 0.05). At the phylum level, Bacteroidota was elevated in UC, while Bacillota and Actinomycetota were reduced. Genera such as Ruminococcus, Bacteroides, and Coprococcus were depleted in UC. Faecalibacterium, commonly reduced in UC, showed no significant difference. This first analysis of gut microbiota in Lebanese UC patients reveals a distinct microbial signature that partially diverges from global trends, supporting the need for region-specific microbiome studies and personalized microbiota-targeted therapies.},
}

@article {pmid41398112,
year = {2025},
author = {Sayin, S and ElGamel, M and Rosener, B and Brehm, M and Mugler, A and Mitchell, A},
title = {Bacterial population dynamics during colonization of solid tumors.},
journal = {Molecular systems biology},
volume = {},
number = {},
pages = {},
pmid = {41398112},
issn = {1744-4292},
support = {R35GM133775//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R35GM156451//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; DMS-2245816//National Science Foundation (NSF)/ ; OAC-2117681//National Science Foundation (NSF)/ ; Mellon Fellowship//University of Pittsburgh (Pitt)/ ; },
abstract = {Bacterial colonization of tumors is widespread, yet the dynamics during colonization remain underexplored. Here we discover strong variability in the sizes of intratumor bacterial clones and use this variability to infer the mechanisms of colonization. We monitored bacterial population dynamics in murine tumors after introducing millions of genetically barcoded Escherichia coli cells. Results from intravenous injection revealed that roughly a hundred bacteria seeded a tumor and that colonizers underwent rapid, yet highly nonuniform growth. Within a day, bacteria reached a steady-state and then sustained load and clone diversity. Intratumor injections, circumventing colonization bottlenecks, revealed that the nonuniformity persists and that the sizes of bacterial progenies followed a scale-free distribution. Theory suggested that our observations are compatible with a growth model constrained by a local niche load, global resource competition, and noise. Our work provides the first dynamical model of tumor colonization and may allow distinguishing genuine tumor microbiomes from contamination.},
}

@article {pmid41398090,
year = {2025},
author = {Denisov, N and Springer, F and Brauer-Nikonow, A and Maftei, G and Zeller, G and Selegato, DM and Zimmermann, M},
title = {Development of a GC-MS/MS method to quantify 120 gut microbiota-derived metabolites.},
journal = {Analytical and bioanalytical chemistry},
volume = {},
number = {},
pages = {},
pmid = {41398090},
issn = {1618-2650},
support = {GutTransForm-101078353/ERC_/European Research Council/International ; Mi-EOCRC//Bundesministerium für Bildung und Forschung/ ; 01KD2102E//Bundesministerium für Bildung und Forschung/ ; },
abstract = {The gut microbiota produces metabolites that are important for host physiology and have critical roles in the development of diseases, such as metabolic disorders, cardiovascular diseases, and cancer. Here, we developed a gas chromatography-coupled tandem mass spectrometry (GC-MS/MS) method for the quantification of 120 volatile and semi-volatile compounds produced by gut bacteria, including short-chain fatty acids, indols, nucleotides, organic acids, and amino acid derivatives. The method is based on multiple-reaction-monitoring (MRM) of each analyte and their respective isotopically labeled internal standard, enabling absolute metabolite quantification between 0.45 pmol and 1 nmol. Applying the method to different tissue samples from germfree and conventionally colonized mice, we illustrate the ability to quantify microbiota-produced metabolites in different sample matrices-plasma, liver, feces, and intestinal content-and at different concentrations. Lastly, we demonstrate that this protocol is capable of quantifying microbiota-derived metabolites in stool samples stored in DNA stabilization buffers that are typically used in sequencing-based microbiome studies. Altogether, the developed GC-MS/MS method adds a valuable analytical tool to quantify microbiota-host metabolic interactions.},
}

@article {pmid41397898,
year = {2025},
author = {Gao, B and Luo, J and Nong, X and Yao, Z and Wang, H},
title = {Combined Analysis of Salivary Metabolomics and Microbiota in Type 1 Diabetics With Xerostomia: A Pilot Study.},
journal = {Journal of oral pathology & medicine : official publication of the International Association of Oral Pathologists and the American Academy of Oral Pathology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jop.70097},
pmid = {41397898},
issn = {1600-0714},
support = {82160187//National Natural Science Foundation of China/ ; 2019GXNSFDA245016//Key Project of Guangxi Natural Science Foundation/ ; 2023JJA141002//General Program of Guangxi Natural Science Foundation/ ; },
abstract = {OBJECTIVE: Given that the oral ecological environment undergoes alterations during the pathological progression of type 1 diabetes mellitus (T1DM) with xerostomia, this study employed microbiomics in conjunction with metabolomics to identify the distinct oral microbiota and salivary metabolites in patients with type 1 diabetic xerostomia and healthy individuals, aiming to elucidate the microorganisms, metabolites, and metabolic pathways potentially implicated in T1DM-associated xerostomia.

METHODS: Saliva samples were obtained from individuals diagnosed with T1DM and xerostomia (patient group, n = 9) as well as from healthy volunteers (control group, n = 9), and were subsequently subjected to microbiota profiling and untargeted metabolomic analysis. Bioinformatics methodologies were applied to assess the microbiota and metabolomics datasets both independently and integratively.

RESULTS: A total of 88 differential metabolites were identified between the patient and control groups. These metabolites were predominantly enriched in the caffeine and Vitamin B6 metabolic pathways. Additionally, an average of 280 operational taxonomic units (OTUs) were detected, with species diversity found to be lower in the patient group compared to the controls. At the genus level, 20 significantly altered microbial taxa were identified. Differential genera, including Leptotrichia and Corynebacterium, exhibited higher abundance in the patient group, whereas genera such as Haemophilus and Streptococcus were predominantly present in the control group. Correlation analysis indicated that the differential microbiota did not exhibit strong associations with the identified differential metabolites. However, certain oral microorganisms were associated with specific metabolites enriched in the caffeine metabolic pathway.

CONCLUSION: In summary, the findings demonstrated notable differences in both oral microbiota composition and salivary metabolite profiles between T1DM patients with xerostomia and healthy individuals. Furthermore, a moderate degree of association between the oral microbiome and metabolome was observed, which may serve as a potential biomarker for T1DM-related xerostomia and contribute to the development of targeted therapeutic strategies.},
}

@article {pmid41397647,
year = {2025},
author = {Guha, R and Lakshmi, S and Krebs, T and Schroers, VJ and Adamek, M and Elumalai, P},
title = {Efficacy of a novel oral bivalent vaccine with fucoidan as adjuvant against Aeromonas hydrophila and Edwardsiella tarda infections in Nile tilapia aquaculture.},
journal = {Fish & shellfish immunology},
volume = {169},
number = {},
pages = {111074},
doi = {10.1016/j.fsi.2025.111074},
pmid = {41397647},
issn = {1095-9947},
abstract = {The emerging diseases caused by Aeromonas hydrophila and Edwardsiella tarda severely impact aquaculture and lead to economic losses. Vaccines, as a safe prophylaxis method, can only protect against specific infections. Therefore, the development of a multivalent vaccine is necessary to enhance protection and cost-effectiveness for sustainable aquaculture. In this study, a bivalent vaccine against A. hydrophila and E. tarda was developed using fucoidan as an adjuvant. The vaccines were administered via the oral route to assess their protective efficacy against challenges. A survival rate of 63 % and 73 % was observed in the orally vaccinated fish where fucoidan was utilized as an adjuvant. Other immunological parameters, such as serum lysozyme, catalase, superoxide dismutase, bactericidal activity, and total IgM production, were measured. TCRβ, IgM, MHCI, MHCII, IFNγ, and IL8 gene expressions were significantly altered in the vaccinated fish. The gut microbiome alterations were noticeable in the vaccinated fish. Although feed-based oral vaccines necessitate antigen stability to withstand degradation in the fish gut, fucoidan used as an adjuvant has enhanced vaccine efficacy in orally vaccinated groups, indicating the potential of fucoidan as a novel immunomodulator and vaccine adjuvant in aquaculture.},
}

@article {pmid41397585,
year = {2025},
author = {Hsu, CY and Polatova, D and Hamad, RH and Patel, PN and Akram, M and Singh, G and Arora, V and Nayak, PP and Kadhem, M and Hamzah, HF},
title = {Phage Therapy in Cancer Treatment: Mechanisms, Emerging Innovations, and Translational Progress.},
journal = {Critical reviews in oncology/hematology},
volume = {},
number = {},
pages = {105085},
doi = {10.1016/j.critrevonc.2025.105085},
pmid = {41397585},
issn = {1879-0461},
abstract = {Bacteriophage therapy has re-emerged as a rapidly advancing field in oncology, bridging antimicrobial precision with tumor-targeted biotherapy. Beyond infection control, phages are now recognized as programmable biological systems capable of eradicating multidrug-resistant (MDR) pathogens, modulating tumor-associated microbiota, activating immune responses, and delivering therapeutic genes or drugs. Preclinical evidence shows that phages can selectively eliminate Fusobacterium nucleatum in oral squamous cell carcinoma, restore microbial balance in colorectal cancer, and enhance immune infiltration via cytokine or antigen display. Engineered constructs including GM-CSF-expressing and MAGE-A1-displaying phages, λ-phage ASPH vaccines, and PEGylated nanocarriers delivering MEG3 or TRAIL have demonstrated strong anti-tumor efficacy across melanoma, hepatocellular, and colorectal cancer models. Additionally, CRISPR-Cas-armed phages precisely remove resistance genes such as bla-CTX-M and mecA, while AI-driven selection pipelines enable data-guided design of personalized phage cocktails. These advances represent a paradigm shift from empirical antibacterial use toward mechanistically engineered, multifunctional phage platforms that integrate microbiome modulation, immune activation, and nanocarrier-mediated gene delivery. Although challenges such as immune clearance, bacterial resistance, and regulatory complexity remain, the convergence of AI, CRISPR, and synthetic biology is accelerating the evolution of phage therapy into a clinically viable precision-oncology strategy. In this context, bacteriophages emerge not merely as antibacterial agents but as intelligent, patient-specific nanomedicines poised to redefine therapeutic boundaries in cancer treatment.},
}

@article {pmid41396813,
year = {2025},
author = {Chirumbolo, S},
title = {Methodological and statistical concerns in MINERVA microbiome-disease knowledge graph.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {6},
pages = {},
doi = {10.1093/bib/bbaf673},
pmid = {41396813},
issn = {1477-4054},
}

@article {pmid41396812,
year = {2025},
author = {Langarica, S and Kim, YT and Alkhadrawi, A and Kim, JB and Do, S},
title = {Response to 'Methodological and statistical concerns in MINERVA microbiome-disease knowledge graph' by Salvatore Chirumbolo.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {6},
pages = {},
doi = {10.1093/bib/bbaf671},
pmid = {41396812},
issn = {1477-4054},
support = {//HEM Pharma/ ; //AWS Health Equity Initiative/ ; },
}

@article {pmid41396495,
year = {2025},
author = {Sari, DWK and Khamid, NL and Ikhrami, MA and Hardaningsih, I and Satriyo, TB and Suparmin, A},
title = {A Metagenomic Analysis of Gut Microbiome and Growth Performance of Giant Gourami (Osphronemus goramy) Fed with Raw Plant-Based Diet.},
journal = {Marine biotechnology (New York, N.Y.)},
volume = {27},
number = {6},
pages = {168},
pmid = {41396495},
issn = {1436-2236},
support = {2938/UN1/PN/PT.01.10/2022//Universitas Gadjah Mada/ ; },
mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; *Animal Feed/analysis ; Plant Leaves/chemistry ; Aquaculture ; Diet/veterinary ; *Perciformes/growth & development/microbiology ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Bacteria/classification/genetics ; Diet, Plant-Based ; },
abstract = {The increasing demand for global protein and awareness of environmental issues challenge sustainable aquaculture growth. The freshwater fish giant gourami (Osphronemus goramy) has the potential to be farmed sustainably. The gut microbiome approach is key to sustainable aquaculture by supporting fish health and feed utilization. This study evaluated the effect of taro leaves supplementation on giant gourami growth and gut microbiome composition. Four groups of fish (initial weight 378 ± 26.14 g) were fed commercial feed with 0%, 25%, 50%, and 75% taro leaves substitution for 16 weeks. Growth parameters such as absolute weight gain (AWG), specific growth rate (SGR), protein efficiency ratio (PER), survival rate (SR), and condition factor (CF) were measured, and gut microbiota was analyzed using 16 S rRNA gene sequencing via Oxford Nanopore Technology. The 50% taro leaves group showed significantly higher AWG (78.87 ± 11.96 g, p < 0.05) and PER (1.92 ± 0.37, p < 0.05) compared to the 100% commercial feed (53 ± 5.6 g and 0.54 ± 0.18, respectively). The condition factor of fish in all feeding experiments (1.40-1.55) demonstrated optimal growth conditions. The gut microbiome was dominated by Clostridium, with taro leaves substitution increasing Cellulosilyticum, Fusobacterium, and Ilyobacter, which are linked to cellulose breakdown and SCFA production. These findings suggest that giant gourami do not require solely commercial feed and are promising for sustainable aquaculture practice.},
}

*Gastrointestinal Microbiome/genetics
Animals
*Animal Feed/analysis
Plant Leaves/chemistry
Aquaculture
Diet/veterinary
*Perciformes/growth & development/microbiology
RNA, Ribosomal, 16S/genetics
Metagenomics
Bacteria/classification/genetics
Diet, Plant-Based

@article {pmid41396345,
year = {2025},
author = {Fan, Y and Gu, X and Yang, H and Chen, Y and Fang, C and Deng, H and Dai, L},
title = {Intratumoral microbiome: a crucial regulating factor in development and progression of colorectal cancer.},
journal = {Molecular biomedicine},
volume = {6},
number = {1},
pages = {138},
pmid = {41396345},
issn = {2662-8651},
support = {82372647//Innovative Research Group Project of the National Natural Science Foundation of China/ ; 82203108//Innovative Research Group Project of the National Natural Science Foundation of China/ ; 2024YFFK0381//Program of Sichuan Province, China/ ; 2024YFFK0396//Program of Sichuan Province, China/ ; No. 2025ZNSFSC0549//Natural Science Foundation of Sichuan Province/ ; 2023NSFC1895//Natural Science Foundation of Sichuan Province/ ; },
mesh = {Humans ; *Colorectal Neoplasms/microbiology/pathology/therapy/etiology ; Disease Progression ; Tumor Microenvironment ; Animals ; *Gastrointestinal Microbiome ; *Microbiota ; },
abstract = {Colorectal cancer (CRC) is one of the most malignant cancers, and studies have indicated that microbes within tumors play a crucial role in CRC. Advanced methodologies, including single-cell and spatial technologies, high-resolution sequencing, and multi-omic integration, are now unraveling the complex composition and function of the intratumoral microbiome. Mechanistically, these microbial communities contribute to CRC initiation by serving as direct mutagens that induce genomic instability, perpetuating a state of chronic inflammation, and activating specific carcinogenic pathways. Furthermore, they actively promote tumor progression and metastatic dissemination through multiple means, including the modulation of key oncogenic signaling pathways, extensive remodeling of the tumor immune microenvironment, and facilitation of a pro-metastatic niche. Given these profound and multifaceted influences, the intratumoral microbiome shows significant promise as a source of diagnostic and prognostic biomarkers, offering considerable potential for non-invasive monitoring and improved risk stratification in clinical practice. Therapeutically, intervention strategies are rapidly evolving, encompassing approaches such as microbiome modulation to enhance conventional therapies, precise clearance of pathogenic bacteria, utilization of intrinsically antitumor microbes, and the engineering of synthetic bacteria as targeted living therapeutics. This review comprehensively outlines the current research methods, elaborates on the mechanistic insights, and discusses the therapeutic targeting of the intratumoral microbiome, aiming to provide a foundational framework for developing new and effective strategies in CRC precision medicine.},
}

Humans
*Colorectal Neoplasms/microbiology/pathology/therapy/etiology
Disease Progression
Tumor Microenvironment
Animals
*Gastrointestinal Microbiome
*Microbiota

@article {pmid41396065,
year = {2025},
author = {Herrera, G and Zouiouich, S and Diaz-Mayoral, N and Purandare, V and Trabert, B and Wan, Y and Liu, J and Dagnall, CL and Jones, K and Hicks, BD and Hutchinson, A and Li, S and Shi, J and Abnet, CC and Vogtmann, E},
title = {Comparison of oral collection methods for 16S rRNA gene and shotgun metagenomic sequencing.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0180625},
doi = {10.1128/spectrum.01806-25},
pmid = {41396065},
issn = {2165-0497},
abstract = {UNLABELLED: To understand how sample collection affects oral microbiome studies, we evaluated the comparability of unpreserved saliva, saliva in glycerol, and mouthwash samples, their room temperature stability, and intraindividual stability over 6 months. Saliva and mouthwash samples were collected from 20 healthy participants 6 months apart. Saliva was divided, with half preserved in glycerol. Some aliquots were frozen immediately, while others were stored at room temperature for a week. DNA was extracted using the PowerSoil Pro and 16S rRNA gene, and shotgun metagenomic sequencing was conducted. Intraclass correlation coefficients (ICCs) from taxonomic and functional tables were compared to assess variability. We estimated sample size requirements based on the intraindividual stability over 6 months. Saliva in glycerol appeared more similar to unpreserved saliva than mouthwash, with higher median ICCs at genus (0.88 vs 0.60), species (0.92 vs 0.64), and gene levels (0.84 vs 0.36; all P < 0.01). Room temperature storage affected saliva in glycerol more than mouthwash (median genus-level ICC = 0.65). No significant differences were observed at the gene level. Intraindividual stability over 6 months was moderate. To detect an odds ratio of 1.5 with one sample per individual, estimated sample sizes ranged from 665 (common species) to 219,547 (rare species). Oral microbiome stability varies by collection method; mouthwash provides greater room temperature stability and may be preferable when immediate freezing is not feasible. For epidemiological studies, consistent use of a single collection method and inclusion of longitudinal sampling can improve reproducibility and power to detect associations with health outcomes.

IMPORTANCE: The oral microbiome plays a key role in health and disease, yet methodological inconsistencies in sample collection and processing can introduce variability and limit comparability across studies. This study investigates the impact of different oral sample collection methods on microbiome profiling and their stability over time. We demonstrate that sample type significantly influences taxonomic and functional microbiome profiles, with mouthwash showing greater stability during delayed processing and saliva in glycerol more closely resembling fresh saliva. Importantly, intraindividual microbial communities were only moderately stable over 6 months, emphasizing the need for consistent sampling protocols and consideration of temporal variation. These findings have direct implications for microbiome study design, highlighting that methodological choices can affect reproducibility, statistical power, and biological interpretation. Our results support the use of mouthwash as a practical alternative when freezing is delayed and underscore the value of longitudinal sampling for detecting biologically meaningful changes.},
}

@article {pmid41395968,
year = {2025},
author = {Almuhaideb, E and Hasan, NA and Grim, C and Rashed, SM and Parveen, S},
title = {Effects of aquaculture practices on Vibrio population dynamics and oyster microbiome.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0198525},
doi = {10.1128/aem.01985-25},
pmid = {41395968},
issn = {1098-5336},
abstract = {Oyster aquaculture is essential for ensuring a sustainable food source. Despite stringent controls, cases of oyster-related illnesses linked to pathogenic Vibrio parahaemolyticus (Vp) and Vibrio vulnificus (Vv) persist. This study investigated the impact of aquaculture practices on the oyster microbiome and pathogen levels, focusing on two common systems: on-bottom and floating cages. From June to November 2019, monthly samples were collected from the Chesapeake Bay, including oysters and water from each aquaculture system. Oyster samples included both fresh and temperature-abused oysters. The study utilized the most probable number and real-time PCR (MPN-qPCR) method to quantify total and pathogenic Vp and Vv in water and oyster samples. DNA was extracted from oyster homogenates and filtered water samples for shotgun metagenomic sequencing. The results revealed significant impacts of aquaculture practices on the diversity of the oyster microbiome, particularly affecting the distribution of phages, antibiotic resistance, and virulence factor genes. Shotgun metagenomic sequencing consistently showed higher genetic representation of Vibrio in floating cages for both fresh and temperature-abused oyster samples. MPN-qPCR results differed between practices, showing higher Vibrio levels in bottom cages for fresh oysters and higher levels in floating cages under temperature abuse. These discrepancies are likely explained by the stable conditions in bottom cages, the effects of temperature abuse, and the growth bias inherent to the MPN method. These results underscore the need for a holistic, time-sensitive approach, taking into account microbial states and the dynamic aspects of the oyster environment to understand the complex relationship between aquaculture practices and the oyster microbiome.IMPORTANCEThis study holds great importance for food safety, antibiotic resistance surveillance, aquaculture management, and environmental health. Unraveling the population dynamics of microbial communities in oysters and their responses to different aquaculture practices enhances our ability to ensure safer seafood, monitor antibiotic resistance, optimize aquaculture methods, and mitigate potential public health challenges. Moreover, it demonstrates the applicability of advanced metagenomic tools for future research. Furthermore, this research addresses critical aspects of food safety, food security, public health, and sustainable aquaculture practices, making it highly relevant in today's context.},
}

@article {pmid41395966,
year = {2025},
author = {Watrous, KM and Larson, MJ and Nelson, AS and Hammer, TJ},
title = {A culture collection of gut bacteria from wild bumble bees (Bombus impatiens).},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0079125},
doi = {10.1128/mra.00791-25},
pmid = {41395966},
issn = {2576-098X},
abstract = {Gut bacteria are important to the ecology and health of social bees. We present a collection of 55 isolates, representing a diverse range of bacterial taxa, from wild- and captive-reared bumble bees (Bombus impatiens). Culture conditions and full-length 16S rRNA gene sequences are provided.},
}

@article {pmid41395947,
year = {2025},
author = {Bouchali, R and Sentenac, H and Bates, KA and Fisher, MC and Schmeller, DS and Loyau, A},
title = {Unraveling the disease pyramid: the role of environmental micro-eukaryotes in amphibian resistance to the deadly fungal pathogen Batrachochytrium dendrobatidis.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0143625},
doi = {10.1128/msystems.01436-25},
pmid = {41395947},
issn = {2379-5077},
abstract = {The disease pyramid conceptualizes the predictors of host infection risk, linking the host, the pathogen, environmental conditions, and both host and environmental microbiomes. However, the importance of the interaction between environmental and host-associated microbiomes in shaping infectious disease dynamics remains poorly understood. While the majority of studies have focused on bacteria, the role of micro-eukaryotes has been seldom investigated. Here, we explore three axes of the disease pyramid using an 18S rRNA gene metabarcoding approach to analyze the micro-eukaryotic assemblages of biofilm, water, and skin samples from three European amphibian species. Skin bacterial communities of the investigated amphibian populations have already been shown to be impacted by the presence of the lethal fungal pathogen Batrachochytrium dendrobatidis (Bd), with a higher abundance of protective bacteria in infected populations and a greater environmental microbial contribution to the skin microbiota in Bd-positive lakes. Here, we explored the relationships between the micro-eukaryotic skin communities of these tadpole populations with their surrounding environment. Tadpoles were sampled at 22 mountain lakes located in the Pyrenees (France), 8 of which harbored amphibian populations infected by Bd. We found that biofilms from Bd-negative lakes had higher environmental micro-eukaryotic diversity and a greater abundance of putative anti-Bd fungi, both in the environment and on the skin microbiota of Bufo spinosus and Rana temporaria, but not of Alytes obstetricans. Bayesian SourceTracker analysis further showed that the environmental contribution from biofilms to amphibian skin micro-eukaryotic assemblages was higher in Bd-positive lakes for B. spinosus and R. temporaria, but not for A. obstetricans.IMPORTANCEResearch on host-associated microbiomes and infectious diseases has mostly focused on bacteria, overlooking the potential contributions of micro-eukaryotes to infection dynamics. Here, we show that environmental and skin-associated micro-eukaryotes-especially putative anti-Batrachochytrium dendrobatidis (Bd) fungi-differ between Bd-positive and Bd-negative amphibian populations in mountain lakes. Our results suggest that micro-eukaryotes influence disease resistance and microbiome assembly, similarly to bacteria. Importantly, environmental reservoirs of micro-eukaryotes appear to contribute differently across infection contexts. These findings demonstrate the importance of adopting a broader microbiome perspective that includes micro-eukaryotes when investigating the ecological mechanisms underlying infectious disease risk.},
}

@article {pmid41395946,
year = {2025},
author = {Jansen, D and Bens, L and Wagemans, J and Green, SI and Hillary, T and Vanhoutvin, T and Van Laethem, A and Vermeire, S and Sabino, J and Lavigne, R and Matthijnssens, J},
title = {Hidradenitis suppurativa patients exhibit a distinctive and highly individualized skin virome.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0129025},
doi = {10.1128/msystems.01290-25},
pmid = {41395946},
issn = {2379-5077},
abstract = {Hidradenitis suppurativa (HS) is a chronic inflammatory disease characterized by recurring skin lesions. Despite ongoing research, the exact cause underlying initiation and progression of disease remains unknown. While prior research has linked the skin microbiota to HS pathology, the role of viruses has remained unexplored. To investigate the skin virome, metagenomic sequencing of viral particles was performed on 144 skin samples from 57 individuals (39 HS patients and 18 controls). It was found that the virome is not only linked to BMI, but also to the presence and severity of HS, marking a diverging viral profile in the progression of disease. Despite no differences in alpha-diversity, HS patients exhibited a significantly higher beta-diversity compared to healthy controls, indicating a more personalized virome with reduced viral sharing among patients. We identified distinct groups of commonly shared phages, referred to as the core phageome, associated with either healthy controls or patients. Healthy controls displayed a higher abundance of two core Caudoviricetes phages predicted to infect Corynebacterium and Staphylococcus, comprising normal skin commensals. In contrast, HS patients carried previously uncharacterized phages that were more prevalent in advanced stages of the disease, which likely infect Peptoniphilus and Finegoldia, known HS-associated pathogens. Interestingly, genes involved in superinfection exclusion and antibiotic resistance could be found in phage genomes of healthy controls and HS patients, respectively. In conclusion, we report the existence of distinct core phages that may have clinical relevance in HS pathology by influencing skin bacteria through mechanisms such as superinfection exclusion and antibiotic resistance.IMPORTANCEAn increasing body of research showed that the microbiome has an important role in complex human disease. In line with this, here, we analyzed a longitudinal HS cohort and found a relationship between the skin virome and HS pathology. This relationship was defined by distinct groups of phages associated with either healthy controls or HS patients, yet, in both instances, capable of enhancing bacterial fitness. In healthy individuals, these phages were widely shared, fostering symbiosis by ensuring stability of the commensal skin microbiota. Conversely, in HS patients, these phages revealed a more individualistic nature and could contribute to dysbiosis by providing antibiotic resistance genes to bacterial pathogens. Overall, these findings point to a potential clinical significance of the virome in understanding and addressing HS pathology.},
}

@article {pmid41395750,
year = {2025},
author = {Abbas-Egbariya, H and Elwahidi, L and Levy, DJ and Braun, T and Levhar, N and Hadar, R and Efroni, G and Granot, M and Leichtmann-Bardogoo, Y and Maoz, BM and Weiss, B and Gal-Mor, O and Agranovich, B and Abramovich, I and Denson, L and Ben-Horin, S and VanDussen, KL and Amir, A and Haberman, Y},
title = {Supplementation with endogenous healthy gut metabolites reverses the disruptions of in vitro and ex vivo epithelial functions induced by fecal content from IBD patients.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2597568},
doi = {10.1080/19490976.2025.2597568},
pmid = {41395750},
issn = {1949-0984},
mesh = {Humans ; *Feces/microbiology/chemistry ; *Inflammatory Bowel Diseases/microbiology/metabolism ; *Gastrointestinal Microbiome ; Caco-2 Cells ; *Epithelial Cells/metabolism/drug effects ; Female ; Male ; *Intestinal Mucosa/metabolism ; Adult ; Metabolomics ; Middle Aged ; },
abstract = {Despite epithelial involvement in inflammatory bowel disease (IBD) pathogenesis and the gaps in treatment goals with existing immune-directed therapy, epithelial-directed interventions are unavailable. Using patient-based models, we aimed to identify bioactive endogenous metabolites that can improve IBD epithelial dysfunction, are generally regarded as safe, and can enhance epithelial homeostasis. We pooled fecal material from subjects with and without IBD to capture patient heterogeneity and analyzed the fecal contents for microbiome composition and metabolomics. Epithelial cells (Caco-2 cells and patient-derived colonoids) were cultured, and fecal material was applied apically to replicate the gut's physiological orientation. Measurable epithelial outputs included epithelial proinflammatory signals, integrity, and cellular ATP levels. We show that fecal content pools from several independent IBD patients disturb epithelial functions significantly more than does the fecal content from controls. Improved epithelial readouts in the functional patient-based models were linked with several gut metabolite levels, and these findings were further validated in an independent published human biospecimen multi-omics in vivo cohort. This guided the supplementation of five prioritized metabolites (azelate, pyridoxal, fructose-6-phosphate, galactose 1-phosphate, and ribose 5-phosphate) into the IBD fecal content, which reversed the related IBD epithelial dysfunction. We streamline a proof-of-concept pipeline for the prioritization of epithelial-targeted metabolite interventions that can direct safe future novel adjunct interventions.},
}

Humans
*Feces/microbiology/chemistry
*Inflammatory Bowel Diseases/microbiology/metabolism
*Gastrointestinal Microbiome
Caco-2 Cells
*Epithelial Cells/metabolism/drug effects
Female
Male
*Intestinal Mucosa/metabolism
Adult
Metabolomics
Middle Aged

@article {pmid41395693,
year = {2025},
author = {Stone, J and Tripyla, A and Scalise, MC and Balmer, ML and Bally, L and Meinel, DM},
title = {Taxonomic and functional shifts in the microbiome of severely obese, prediabetic patients: Ketogenic diet versus energy-matched standard diet.},
journal = {Diabetes, obesity & metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1111/dom.70364},
pmid = {41395693},
issn = {1463-1326},
support = {PCEFP3_194618/1//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; PCEGP3_186978//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; //Stiftung FHNW/ ; //Nestlé Health Science/ ; //Pierre Mercier Foundation/ ; },
abstract = {AIMS: Obesity and type 2 diabetes mellitus (T2DM) are among the leading global health challenges of the 21st century. While caloric restriction remains the cornerstone of weight loss interventions, ketogenic diets (KD), characterised by low carbohydrate and high fat intake, have been shown to improve metabolic health partly by modulating the gut microbiome. This study investigated the effects of a short-term KD on gut microbiome composition and function in severely obese, prediabetic patients, compared to an energy-matched standard diet (SD).

METHODS: In a randomised trial, patients with BMI >35 kg/m[2] and prediabetes underwent either a 2-week KD or isocaloric SD, both inducing a 30% energy deficit. Faecal samples collected before and after the intervention, alongside samples from healthy controls, were analysed by whole-genome metagenomic sequencing.

RESULTS: At baseline, prediabetic patients exhibited greater interindividual variability and lower alpha diversity than healthy controls. KD resulted in a significant reduction of alpha diversity, largely driven by a selective loss of Lachnospiraceae, with a concomitant increase in Bacteroidaceae. Functional profiling revealed that KD, but not SD, altered genes coding for enzymes involved in energy metabolism, amino acid synthesis, nucleic acid activity, RNA modification, and vitamin biosynthesis. Additionally, serum acetate levels increased significantly following KD.

CONCLUSIONS: These findings underscore that KD, independent of caloric intake, acutely remodels the gut microbiome's taxonomic and functional landscape, highlighting the microbiome as a potential mediator of KD's metabolic effects.},
}

@article {pmid41395680,
year = {2025},
author = {Aldewereld, ZT and Megli, CJ and Olson, AC and Morowitz, MJ},
title = {ALARA in Antimicrobial Stewardship: Adapting Radiation Safety Principles to Address Antibiotic Overuse.},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
volume = {},
number = {},
pages = {},
doi = {10.1093/cid/ciaf688},
pmid = {41395680},
issn = {1537-6591},
abstract = {Despite decades of antimicrobial stewardship programs, antibiotic overuse persists due to imprecise guidelines relying on subjective terms like "optimal" and "appropriate" use. Current stewardship approaches lack a unifying communication framework that effectively bridges technical recommendations with real-world prescribing decisions across medical specialties. We propose adapting ALARA (As Low As Reasonably Achievable) from radiation safety as a transformative framework for antibiotic stewardship. Like radiation, antibiotics provide indisputable benefits while carrying hidden cumulative costs-including microbiome disruption, immune dysfunction, and increased mortality in specific populations. ALARA's three pillars (justification, optimization, dose limitation) map directly to antimicrobial stewardship needs and could standardize prescribing approaches across specialties. This framework addresses the distributed nature of antibiotic prescribing by providing clear principles that transcend subjective judgments. By treating antibiotics as beneficial but inherently risky interventions requiring careful justification, ALARA could reduce unnecessary exposure while maintaining efficacy, ultimately improving both patient outcomes and global antimicrobial resistance patterns.},
}

@article {pmid41395614,
year = {2025},
author = {Zhang, B and Mohd Sahardi, NFN and Chew, KT and Di, W and Shafiee, MN},
title = {Gut microbiome alterations and their clinical and biological implications in ovarian cancer: a systematic review.},
journal = {Frontiers in oncology},
volume = {15},
number = {},
pages = {1690541},
pmid = {41395614},
issn = {2234-943X},
abstract = {BACKGROUND: Increasing evidence shows the that gut microbiome (GM) plays a crucial role in ovarian cancer (OC) progression, offering potential avenues for microbiome-based intervention strategies. However, research in this area remains limited. This systematic review aimed to synthesize current evidence on microbiome composition and diversity in OC, focusing on its association with disease diagnosis, postoperative changes, and responses to chemotherapy or PARP inhibitor (PARPi) therapy.

METHODS: A literature search was performed in PubMed and Web of Science up to October 2025 using keywords: (gut microb* OR gut bacteri* OR intestinal microb* OR intestinal bacteri*) AND (ovarian cancer OR ovarian carcinoma OR carcinoma of ovary). Only original research articles involving human subjects were included. Data on GM alterations in OC patients, postoperative changes, and responses to chemotherapy or PARP inhibitor (PARPi) therapy were extracted and analysed.

RESULTS: Nine eligible studies, comprising longitudinal and case-control studies were reviewed. At diagnosis, OC patients displayed gut dysbiosis characterised by an increase in Proteobacteria and a decrease in Firmicutes. Genus-level analysis revealed lower levels of Akkermansia and elevated levels of Bacteroides and Prevotella, suggesting disrupted microbial homeostasis. Following surgery, both Firmicutes and Proteobacteria declined, indicating significant microbiome shifts. During chemotherapy, especially neoadjuvant treatment, Firmicutes re-emerged as the dominant phylum. Family-level analyses identified increased Coriobacteriaceae and decreased Ruminococcaceae. Platinum-sensitive patients demonstrated more stable GM profiles than those with platinum resistance Genera such as Angelakisella, Arenimonas, and Roseburia emerged as potential candidates for diagnostic or prognostic markers of chemotherapy resistance. Meanwhile, Phascolarbacterium is identified as a PARPi response in BRCA1/2-negative OC, with higher levels linked to longer progression-free survival.

CONCLUSION: This review highlights a dynamic GM composition in OC across disease stages and treatments, underscoring the need for further research on microbiome-targeted therapeutic strategies.},
}

@article {pmid41395472,
year = {2025},
author = {Son, Y and He, P and Baldwin, M and Li, G and Wang, Z and Gu, AZ and Kao-Kniffin, J},
title = {Geno-pheno characterization of crop rhizospheres: an integrated Raman spectroscopy and microbiome approach in conventional and organic agriculture.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1721013},
pmid = {41395472},
issn = {1664-302X},
abstract = {INTRODUCTION: Agricultural management practices strongly influence soil microbiomes, with broad implications for ecosystem function. Yet, the combined phenotypic and compositional dynamics of rhizosphere microbial communities across conventional and organic farming systems remain poorly characterized, underscoring the need for integrated approaches to understand how management decisions drive microbial assembly and function.

METHODS: We investigated microbial communities associated with conventionally and organically cultivated horticultural crops across multiple farms in New York State. To capture both taxonomic and functional dimensions, community composition was characterized using 16S rRNA gene sequencing, and phenotypic traits were assessed with a newly developed single-cell Raman microspectroscopy (SCRS) approach. This dual strategy allowed us to link microbial identity with metabolic potential and adaptive traits.

RESULTS: Farming practice significantly shaped microbiome clustering, independent of site or plant species. SCRS-based phenotyping revealed distinct biochemical profiles: organic systems favored lipid-accumulating phenotypes linked to energy storage and stress resilience, whereas conventional systems promoted carbon-rich phenotypes associated with rapid assimilation and biomass production. Network analysis identified Pseudomonas and nitrogen-fixing taxa as ecological hubs in conventional systems, while organic soils were enriched in Bacilli class plant growth-promoting rhizobacteria (e.g., Tumebacillus, Bacillus, Paenibacillus, Brevibacillus) and contained microorganisms bearing antibiotic resistance genes.

DISCUSSION: Our findings highlighted that management regimes drive distinct microbial functional traits and community structures. By integrating genotypic and phenotypic analyses, particularly microbial phenotyping via SCRS, we uncovered adaptive traits that differentiate conventional and organic systems, offering new insight into how plant production practices shape microbial assembly and ecological function.},
}

@article {pmid41395471,
year = {2025},
author = {Cheng, YN and Chen, GT and Huang, WC and Chiu, YP and Tang, Y and Fu, PK and Lee, TY},
title = {Lung microbiome signatures and explainable predictive modeling of glucocorticoid response in severe community acquired pneumonia.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1706432},
pmid = {41395471},
issn = {1664-302X},
abstract = {INTRODUCTION: Systemic glucocorticoids (SG) are administered to quell hyper-inflammation in severe community acquired pneumonia (SCAP), yet trials report inconsistent efficacy and no mechanistic explanation.

METHODS: We enrolled 200 ventilated SCAP patients, whom received hydrocortisone within 48 h of ICU admission, and generated longitudinal lower-airway microbiome profiles by 16S rRNA amplicon and metagenomic sequencing on ICU Days 1, 3 and 7. Compositional data were integrated with clinical variables through a fully reproducible bioinformatics analysis workflow.

RESULTS: Baseline community structures did not differ between SG and control cohorts, but by Day 7 survivors exhibited enrichment of Actinobacteria and Gammaproteobacteria whereas non-survivors accumulated Alphaproteobacteria and Campylobacteria. A random-forest model restricted to Bacilli and Alphaproteobacteria achieved AUROC = 0.89 (sensitivity 0.83, specificity 0.81) on a patient-held-out test set, significantly outperforming conventional severity indices like APACHE II, SOFA and mNUTRIC scores.

DISCUSSION: Collectively, our results demonstrate that SG therapy imposes reproducible ecological pressures on the lung microbiome and that a two-feature microbial fingerprint can forecast treatment success with single-sample resolution. These findings show that SG therapy actively reshapes the respiratory ecosystem and that lightweight microbiome-aware machine learning can stratify treatment response, offering a tractable path toward precision corticosteroid stewardship.},
}

@article {pmid41395467,
year = {2025},
author = {Hagarová, L and Kupka, D},
title = {Insights into the microbiome of mine drainage from the Mária mine in Rožňava, Slovakia: a metagenomic approach.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1675058},
pmid = {41395467},
issn = {1664-302X},
abstract = {The Mária mine, particularly the Strieborná vein, in Rožňava, is one of the most important mines in Slovakia, containing Ag-bearing tetrahedrite (40-46 wt% Cu, 26 wt% Sb, ~1 wt% Ag), making it an important source of strategic and critical raw materials. This mine discharges a unique neutral-pH (6.9), metal-rich mine water drainage (402 mg L[-1] SO4 [2-], 4.65 mg L[-1] Fe) that has remained microbiologically uncharacterized. This study presents the first comprehensive shotgun metagenomic survey of this mine effluent, generating ~227 million high-quality reads that assembled into 157,676 contigs and 378,023 non-redundant genes. Taxonomic analysis revealed a community dominated by Betaproteobacteria (> 66%), with abundant lithotrophic genera Sulfuritalea (6.93%), Ferrigenium (5.45%), Gallionella (3.79%), and Sideroxydans (3.65%), alongside the heterotrophic genus Pseudomonas (5.2%). Among the most prevalent neutrophilic iron-oxidizing bacterial strains were Sulfuritalea hydrogenivorans (6.93%), Ferrigenium kumadai (5.45%) and Gallionella capsiferriformas (3.79%). Acidophilic genera (e.g., Thiobacillus sp. at 0.43%, Ferrovum myxofaciens, Acidithiobacillus ferrivorans, Leptospirillum ferrooxidans) collectively accounted for <1% of the community. Functional annotation against KEGG, CAZy, COG, eggNOG, Swiss-Prot, CARD and BacMet databases demonstrated pronounced enrichment of iron cycling (e.g., the iron complex outer-membrane receptor protein TC.FEV.OM), sulfur oxidation (e.g., SoxA, SoxX, SoxB), carbon turnover (glycosyltransferase and glycoside hydrolase families) and nitrogen cycling (e.g., NifH, NifD, NirK, glnA). The antibiotic-resistance profile was dominated (> 95%) by tetracycline and fluoroquinolone determinants, while metal-resistance systems for Ni, Ag, As, Cu and Zn (including CzcD, CzcA, CznA, ArsD and AioX/AoxX) were likewise pervasive. This integrated taxonomic-functional portrait highlights a microbiome finely adapted to this unique geochemistry, combining lithotrophic metabolisms with multi-metal resistance. Our findings establish a critical baseline for long-term monitoring and highlight a high abundance of neutrophilic Fe(II)-oxidizers, suggesting they may represent promising candidates for targeted cultivation and subsequent evaluation in biotechnology applications.},
}

@article {pmid41395466,
year = {2025},
author = {Zou, W and Zheng, R and Lin, S and Lu, C and Xie, B},
title = {Lung and gut microbiota profiling in severe community acquired pneumonia patients: a prospective pilot study.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1717822},
pmid = {41395466},
issn = {1664-302X},
abstract = {BACKGROUND: The gut and lung microbiomes play crucial roles in host defense and may serve as predictive markers for severe community-acquired pneumonia (SCAP) patients. However, the simultaneous landscapes of lung and gut microbiomes for SCAP patients remain unclear. The primary objective of this research is to investigate the concomitant landscape of the lung and gut microbiota between the death group and the survival group of SCAP patients and to identify microbial features predictive of clinical parameters.

METHODS: We analyzed 50 respiratory samples and 50 stool samples collected from 50 SCAP patients in this prospective observational study. Patients were categorized into the survival group (n = 41) and the death group (n = 9) according to clinical outcomes. We characterized microbiome compositions, LEfSe analysis, UPGMA analysis and correlation of microbiota features with clinical parameters of respiratory and intestinal flora between two groups using 16S rRNA gene sequencing.

RESULTS: In comparison with the survival group, the death group demonstrated a reduction in alpha diversity, most markedly reflected in the lung microbiota. We found enrichment of specific lung bacterial taxa (Bacteroidales, Streptococcus) in the survival group compared to the death group. Similarly, specific gut bacterial taxa (Anaerotruncus, Peptacetobacter, Rutheniibacterium) were also enriched in the survival group Our study revealed that lung bacteria such as Asteroleplasma, Campylobacter and Acinetobacter and intestinal bacteria such as Bifidobacterium, Ligilactobacillus, Veillonella, and Corynebacterium were positively correlated with inflammatory markers PCT or CRP or neutrophil percentage. Besides, lung bacteria such as Schaalia and intestinal bacteria Alistipes were positively correlated with PaO2/FiO2, while lung bacteria such as Stenotrophomonas was negatively correlated with PaO2/FiO2.

CONCLUSIONS: Our findings reveal distinctive microbial profiles in lung and gut microbiota that correlate with clinical outcomes in SCAP patients. Unraveling these microbial patterns could enable targeted interventions to improve outcomes of SCAP patients.},
}

@article {pmid41395464,
year = {2025},
author = {Gong, J and Lin, M and Chen, L and Xiong, W and Zhang, Y and Liu, C and Chen, S and Lin, W and Zhu, C and Huang, H},
title = {Microbiota-sphingolipid pathway in generalized epilepsy: evidence from Mendelian randomization and clinical metabolomics.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1662050},
pmid = {41395464},
issn = {1664-302X},
abstract = {OBJECTIVE: Epilepsy is a complex disorder with growing evidence linking gut microbiota and metabolism, though causal relationships unclear. This study investigated causal effects of gut microbiota on three epilepsy types via metabolic pathways, using Mediation Mendelian randomization (MR), evaluated directional consistency metabolomics of refractory epilepsy (RE) patients before and after medium-chain triglyceride (MCT) diet intervention.

METHODS: Two-step MR was applied to summary statistics for 207 species (Dutch Microbiome Project) and 196 species (MiBioGen consortium), evaluating 871 serum metabolites as mediators of three epilepsy types. For validation, directional consistency in metabolomics was conducted on serum samples from 9 RE patients before and after MCT diet intervention.

RESULTS: Only sphingomyelin (SM; d18:0/20:0, d16:0/22:0) and Glycocholate glucuronide (1) were the metabolites significantly associated with three epilepsy types. Mediation MR analysis revealed Mollicutes RF9 had a unidirectional effect via sphingomyelin (d18:1/22:1, d18:2/22:0, d16:1/24:1) modulation (P = 0.009). In contrast, Gamma-proteobacteria and Oxalobacter demonstrated bidirectional mediation: via glutamine conjugate of C6H10O2(2) and cerotoylcarnitine (C26) (P = 0.026 and P = 0.033, respectively); while these pathways were protective in mediation, higher abundances were associated with increased risk of generalized epilepsy. Notably, no significant mediators were identified for epilepsy or focal epilepsy. Metabolomics further confirmed MCT diet-induced elevations in 7 specific SM species. Among these, SM (d18:1/36:8) remained statistically significant after Benjamini-Hochberg false discovery rate (BH-FDR) correction. Notably, changes in SM (d18:1/36:8) and SM (d18:1/14:3) were positively correlated with seizure control rates.

CONCLUSION: This study identifies both unidirectional and bidirectional microbiota-metabolite pathways modulating generalized epilepsy risk, with converging evidence pointing to sphingomyelin as a potential lipid biomarker and therapeutic target.},
}

@article {pmid41395460,
year = {2025},
author = {Popowski, W and Koseski, D and Domanowska, D and Zalewska, M and Popowska, M},
title = {Bacterial colonization of bone substitute materials used in oral surgery: mechanisms, clinical implications, and preventive strategies-A narrative review.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1715632},
pmid = {41395460},
issn = {1664-302X},
abstract = {The advancement of tissue engineering and the development of novel biomaterials have opened new possibilities for the effective treatment of patients with edentulism and other dental deficiencies, as well as for the prosthetic reconstruction and functional rehabilitation of the stomatognathic system. Bone substitute materials are now widely used in orthopedics, reconstructive surgery, and dentistry to support the regeneration of bone tissue lost due to trauma, inflammation, or tooth extraction. However, surgical procedures within the oral cavity inherently carry a risk of postoperative infection, which can impair healing and compromise treatment outcomes. Unlike natural bone regeneration, bone healing following grafting functions as a repair process that may involve partial resorption of the graft material. Such bone deficiencies can hinder prosthetic reconstruction, making the use of bone substitute materials essential for guided bone regeneration. Bone substitutes can be classified as autogenous, allogenic, xenogenic, or alloplastic, each exhibiting distinct osteoinductive and osteoconductive properties. This review discusses the biological and clinical characteristics of these material groups, with particular attention to their susceptibility to colonization by bacterial strains commonly found in the human oral cavity. It also highlights the risks associated with bacterial biofilm formation and examines its implications for the oral microbiome under dysbiotic conditions.},
}

@article {pmid41395459,
year = {2025},
author = {Li, Q and Liu, Y},
title = {Analyzing the gut liver axis: a dual role of the microbiome in the genesis, progression, and treatment of liver cell carcinoma.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1701101},
pmid = {41395459},
issn = {1664-302X},
abstract = {Hepatocellular carcinoma (HCC) remains a leading cause of cancer-related mortality worldwide, and the poor prognosis highlights the pressing need for innovative therapeutic strategies. The gut-liver axis, a critical bidirectional pathway linking the gut microbiota to the liver, plays a pivotal role in HCC pathogenesis. This review systematically delineates current evidence on how gut dysbiosis, compromised intestinal barrier function, and resultant microbial metabolites (e.g., bacterially metabolized bile acids) drive hepatocarcinogenesis via specific signaling pathways, while also addressing the loss of protective effects due to the depletion of beneficial microbes. Moving beyond descriptive summaries, this article focuses on elucidating the core molecular mechanisms of microbiome-regulated HCC-a key knowledge gap that remains unaddressed-and reconciles conflicting findings into a unified framework. We further explore the translational potential of microbiome signatures as non-invasive biomarkers and evaluate microbiota-targeting interventions (e.g., probiotics, dietary modulation, fecal microbiota transplantation) for enhancing treatment efficacy. Ultimately, this review aims to provide a clear roadmap for developing microbiome-based precision medicine in HCC, with the goal of improving clinical management and patient outcomes.},
}

@article {pmid41395458,
year = {2025},
author = {Sun, N and Wang, Y and Zhang, M and Ma, P and Wang, Z and Zhao, H and Cao, C},
title = {The effect of chili pepper-Chinese chives intercropping on rhizosphere microorganisms and root-stem endophytes.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1716326},
pmid = {41395458},
issn = {1664-302X},
abstract = {INTRODUCTION: This study adopted the intercropping pattern opepper (Capsicum annuum L.) and Chinese chives (Allium tuberosum), combined with high-throughput sequencing and microbial network analysis, to systematically reveal the mechanisms of intercropping on the structural regulation and functional synergy of the crop rhizosphere microbiome and root-stem endophyte communities.

METHODS: Three treatments were set up: blank control, solo cultivation, and intercropping.Combined with high-throughput sequencing and network analysis, the reorganization patterns of rhizosphere and endophyte communities were systematically analyzed.

RESULTS: Intercropping induced differential responses of microbial communities in the two crops: it significantly increased the bacterial α-diversity in Chinese chives leaves, and the Shannon index of pepper roots also showed an upward trend, while the microbial diversity in pepper rhizosphere soil was inhibited. In contrast, among roots, the "pepper intercropped with Chinese chives" group had the highest total number of OTUs and the largest number of unique OTUs. Microbial communities exhibited cross-host transfer characteristics: the migration rate of microbial communities from pepper roots to Chinese chives rhizosphere reached 46.57%, and 69.54% of the microbial communities in Chinese chives roots originated from pepper roots. Specifically, Aureimonas and Sphingomonadaceae were significantly enriched in pepper leaves, the relative abundance of Pantoea in Chinese chives leaves increased by 11.5 times, and the abundance of Flavobacterium in pepper rhizosphere increased by 94%. Microbial co-occurrence network analysis confirmed the optimization of functional synergy: the proportion of positive interactions in pepper leaves increased to 90.45%, and the negative interactions of Bradyrhizobium decreased by 97%, the proportion of positive interactions of functional bacteria in Chinese chives rhizosphere reached 88.96%, and Bacillus enhanced positive connections while maintaining an abundance of 10.23%-20.87%, the number of positive interactions of Streptomyces in pepper rhizosphere doubled. Network stability showed spatial variation: the robustness of stem microbial networks was significantly improved, while the vulnerability of rhizosphere microbial networks increased.

DISCUSSION: This study provides microbial theoretical support for the intercropping system to optimize nitrogen utilization by driving pepper to enrich the growth-promoting bacteria Sphingomonadaceae, and to enhance disease resistance by promoting Chinese chives to recruit the biocontrol bacteria Bacillus, thereby forming a microecological regulation mechanism with functional complementarity.},
}

@article {pmid41395398,
year = {2025},
author = {Chen, X and Mei, XY and Ren, ZM and Chen, SS and Tong, YL and Zhang, CP and Chen, J and Dai, GH},
title = {Corrigendum to "Comprehensive insights into berberine's hypoglycemic mechanisms: A focus on ileocecal microbiome in db/db mice" [Heliyon Volume 10, Issue 13, July 15, 2024, Article e33704].},
journal = {Heliyon},
volume = {11},
number = {16},
pages = {e44124},
doi = {10.1016/j.heliyon.2025.e44124},
pmid = {41395398},
issn = {2405-8440},
abstract = {[This corrects the article DOI: 10.1016/j.heliyon.2024.e33704.].},
}

@article {pmid41395292,
year = {2025},
author = {Ren, H and Wen, J and Liu, J and Wang, L},
title = {Gut microbiota in immunomodulation and infection prevention among multiple myeloma patients after chemotherapy: current evidence and clinical prospects.},
journal = {American journal of cancer research},
volume = {15},
number = {11},
pages = {4621-4638},
pmid = {41395292},
issn = {2156-6976},
abstract = {Multiple Myeloma (MM) is the second most common hematological malignancy, with its pathogenesis involving complex cytogenetic variations, tumor clonal evolution, and dynamic interactions between tumor cells and bone marrow stromal microenvironment. Recent studies highlight the role of the intestinal microbiota, a key component of the tumor-associated microenvironment, in regulates MM occurrence, progression, and treatment response via the "gut-bone marrow axis". Under physiological conditions, it protects the local microenvironment by regulating host metabolism and maintaining immune homeostasis. However, intestinal dysbiosis causes metabolic disorders and immune surveillance defects, promoting tumor growth, drug resistance, and poor prognosis. Though traditional treatments such as chemotherapy and hematopoietic stem cell transplantation have been optimized, chemotherapy disrupts intestinal mucosal integrity and impairs immunity, significantly increasing post-chemotherapy infections. These infections can interrupt treatment, worsen conditions, and reduce quality of life, leaving MM still intractable. Notably, microbiota-targeted interventions (e.g., probiotics, fecal microbiota transplantation [FMT]) have shown potential to reduce infection risk by restoring microbiota balance and repairing intestinal barriers. These interventions may also exert potential anti-tumor effects through immune microenvironment regulation and alleviate chemo/radiotherapy-related adverse reactions (e.g., nausea, diarrhea), offering a new direction for relapsed/refractory MM. This article summarizes the molecular regulatory network of the intestinal microbiota in the pathogenesis of MM and the research progress of microbiota-based interventions, aiming to provide a foundation for developing novel microbiome-oriented precision treatment regimens and improving chemotherapy tolerance and patient prognosis.},
}

@article {pmid41394993,
year = {2025},
author = {Olanrewaju, OS and Glick, BR and Babalola, OO},
title = {Retraction notice to "Beyond correlation: Understanding the causal link between microbiome and plant health" [Heliyon 10 (2024) e40517].},
journal = {Heliyon},
volume = {11},
number = {15},
pages = {e44065},
doi = {10.1016/j.heliyon.2025.e44065},
pmid = {41394993},
issn = {2405-8440},
abstract = {[This retracts the article DOI: 10.1016/j.heliyon.2024.e40517.].},
}

@article {pmid41394959,
year = {2025},
author = {Guo, XY and Song, DY and Wu, MY and Zhang, JQ and Li, JY and Yuan, L},
title = {Parkinson's Disease: The Epidemiology, Risk Factors, Molecular Pathogenesis, Prevention, and Therapy.},
journal = {MedComm},
volume = {6},
number = {12},
pages = {e70540},
pmid = {41394959},
issn = {2688-2663},
abstract = {Parkinson's disease (PD) is a progressive neurodegenerative disorder with a growing global burden. Current pharmacological therapies remain limited to symptomatic management, owning to an incomplete understanding of the mechanisms driving α‑synuclein aggregation and disease progression. This review provides an integrated overview of PD across epidemiological, etiological, pathophysiological, and clinical dimensions. It emphasizes established and emerging risk factors, including environmental toxins, lifestyle variables, and gut microbiota dysbiosis and delineates how peripheral-central pathways such as the gut-brain, erythrocyte-brain, and kidney-brain axes contribute to PD pathogenesis. At the molecular level, we explore key disruptions including proteostatic failure, aberrant phase separation, oxidative stress, neuroinflammation, synaptic dysfunction, iron dyshomeostasis, and impaired cholesterol metabolism. These encompass microbiome‑targeted interventions and blood-based approaches. We further evaluate a spectrum of management strategies ranging from primary prevention and biomarker‑guided early detection to innovative experimental treatments such as cellular therapies, transfusion‑based modalities, and microbial modulation. By integrating recent advances in systemic pathophysiology with translational perspectives, this review highlights how molecular and cellular dysregulations underlie clinical phenotypes. Finally, we discuss promising biomarkers derived from microbial, inflammatory, and erythrocyte pathways that may facilitate early diagnosis and the development of disease‑modifying therapies.},
}

@article {pmid41394950,
year = {2026},
author = {Krishnan, LRA and Nair, S and Girija, D and Vishnu, BR},
title = {Unravelling the complex bacterial diversity in the rice rhizosphere of Kole lands of Thrissur through the metagenomics approach.},
journal = {3 Biotech},
volume = {16},
number = {1},
pages = {27},
pmid = {41394950},
issn = {2190-572X},
abstract = {UNLABELLED: The Kole wetlands of Kerala are highly productive rice ecosystems that lie below mean sea level and alternate between flooded and dry phases, shaping their ecological structure. This study focused on assessing bacterial diversity in the rice rhizosphere of Thrissur Kole lands. Rhizosphere soil was sampled from three Kole wetland locations, Puzhakkal (Pzk), Mullassery (Mls), and Cherpu (Chr). Bacterial communities were profiled by constructing metagenomic libraries and sequencing the 16S rRNA V3-V4 regions using the Illumina MiSeq platform. The sequences of the samples Pzk, Mls, and Chr were submitted in the SRA portal under the bioaccession numbers SAMN17776076, SAMN17776077, and SAMN17776078, respectively. High-quality, chimera-free sequences were clustered into OTUs using the QIIME pipeline. Taxonomic assignment was performed in MEGAN by matching reads to sequence databases and allocating NCBI-based taxon IDs. Phylum-level bacterial and archaeal diversity was further analyzed using the MG-RAST pipeline. The predominant bacterial phyla identified were Proteobacteria, Chloroflexi, Acidobacteria, Actinobacteria, Bacteroidetes, and Nitrospirae, with bacterial relative abundance being highest in the Pzk sample and comparatively lower in the Chr sample. The major archaeal phyla included Euryarchaeota, Crenarchaeota, and Thaumarchaeota. Many members of these bacterial and archaeal groups are known to thrive in waterlogged, oxygen-limited, or anoxic conditions, characteristic of Kole lands. Plant Growth Promoting Rhizobacteria (PGPR) such as Azospirillum, Paenibacillus, and Cellulosimicrobium were detected and could potentially be exploited as acid-tolerant biofertilizers. Biocontrol agents belonging to the genera Bacillus and Pseudomonas were also present. Further investigation is required for the characterization of the 'Unclassified' genera at taxonomic and functional levels to elucidate their ecological functions.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-025-04630-w.},
}

@article {pmid41394893,
year = {2025},
author = {Ramesh, AV and Joseph, SC and Bohm, MS and Grey, EW and Elasy, JH and Hibl, BM and Asunloye, OT and Kim, KS and Doss, TD and Pierre, JF and Cook, KL and Makowski, L and Sipe, LM},
title = {A Standardized Method for Vertical Sleeve Gastrectomy Bariatric Surgery Investigations in Cancer.},
journal = {Frontiers in microbiomes},
volume = {4},
number = {},
pages = {},
pmid = {41394893},
issn = {2813-4338},
abstract = {UNLABELLED: Obesity is a global epidemic that has affected the lives of over 14% of adults worldwide and over a third of Americans. Obesity is associated with the increased risk of thirteen obesity-associated cancers and poor cancer outcomes. Bariatric surgery is the most effective method of sustained weight loss and has been steadily increasing in clinical use over the past 4 decades. Importantly, bariatric surgery is established to decrease cancer risk. Vertical sleeve gastrectomy (VSG) is currently the most common bariatric surgery procedure. To evaluate underlying mechanisms of bariatric associated cancer protection, we developed a robust pre-clinical model of bariatric surgery-induced weight loss in mice. Using multiple strains, we established detailed procedures, defined best practices, and noted specific controls to include to examine mediators critical to cancer onset. This VSG protocol includes stringent pre- and post-operational measures to reduce stress-associated weight loss in obese mice to achieve rigorous and reproducible bariatric surgery-associated weight loss. In addition, we describe collection of fecal and intestinal samples as well as Peyer's patches as important mediators of bariatric surgery's impact on cancer risk. In conclusion, as obesity and weight loss approaches including bariatric surgery are increasingly examined in cancer risk and outcomes including immunotherapy, the establishment of robust pre-clinical interventions will allow the field to address critical underlying mechanisms mediating the benefits of weight loss and cancer.

NEW AND NOTEWORTHY: Obesity increases cancer risk and leads to poor outcomes and survival. Bariatric surgery is an effective method of sustained weight loss. To best model obesity, weight loss, and impacts on cancer risk or outcomes, we developed a robust pre-clinical model of bariatric surgery in mice. Because bariatric surgery leads to sustained impacts on the gut microbiome, which can inform anti-tumor immunity, this protocol provides rigorous methods for the collection of intestinal microbiota and Peyer's patches.},
}

@article {pmid41394880,
year = {2025},
author = {Matera, M and Biagioli, V and Illiceto, MT and Palazzi, CM and Cavecchia, I and Manzi, A and Lugli, S and Pennazzi, L and Meocci, M and Pedaci, FA and Bertuccioli, A},
title = {Pediatric acute-onset neuropsychiatric syndromes and the gut-oral-brain axis: a narrative review of emerging microbiome-immune interactions and therapeutic perspectives.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1726630},
pmid = {41394880},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Autoimmune Diseases/immunology/microbiology/therapy ; Child ; *Streptococcal Infections/immunology/microbiology/therapy ; *Brain/immunology ; *Mouth/microbiology/immunology ; Probiotics/therapeutic use ; Obsessive-Compulsive Disorder ; },
abstract = {BACKGROUND: Pediatric Acute-onset Neuropsychiatric Syndromes (PANS) and Pediatric Autoimmune Neuropsychiatric Disorders Associated with Streptococcal infections (PANDAS) are characterized by sudden-onset neuropsychiatric symptoms. Growing evidence indicates that gut and oral microbiota may contribute to disease pathogenesis through immune and inflammatory pathways.

METHODS: This narrative review analyzed approximately 250 studies published between 2000 and 2024, retrieved from PubMed, Scopus, and Google Scholar. The selected works included clinical, immunological, and microbiome-related studies investigating the role of gut-oral-brain interactions in neuroinflammation or in pediatric PANS/PANDAS.

FINDINGS: Alterations in gut and oral microbial communities appear to modulate neuroinflammation through increased intestinal and blood-brain barrier permeability, immune dysregulation, and altered production of neuroactive metabolites. Specific bacterial families, such as Bacteroidaceae, Rikenellaceae, and Odoribacteriaceae, have been associated with pro-inflammatory states, while oral pathogens may exacerbate systemic inflammation via the gut-oral-brain axis.

CONCLUSIONS: The reviewed evidence highlights the potential of microbiome-targeted strategies-including dietary modulation, probiotics, and anti-inflammatory approaches-as promising avenues for future personalized diagnosis and therapy in PANS/PANDAS. However, further controlled studies integrating microbial, immunological, and clinical data are required to confirm causal mechanisms and establish personalized therapeutic protocols.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Autoimmune Diseases/immunology/microbiology/therapy
Child
*Streptococcal Infections/immunology/microbiology/therapy
*Brain/immunology
*Mouth/microbiology/immunology
Probiotics/therapeutic use
Obsessive-Compulsive Disorder

@article {pmid41394872,
year = {2025},
author = {Wang, P and Ge, C and Jing, X and Han, Q and Wang, M and Huang, M and Xiang, Z},
title = {Respiratory microbiome-host interaction on lung carcinogenesis, immunity, and immunotherapy.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1676302},
pmid = {41394872},
issn = {1664-3224},
mesh = {Humans ; *Lung Neoplasms/therapy/immunology/microbiology/pathology/etiology ; *Immunotherapy/methods ; *Microbiota/immunology ; Animals ; Dysbiosis/immunology ; *Carcinogenesis/immunology ; *Host Microbial Interactions/immunology ; Tumor Microenvironment/immunology ; Immune Checkpoint Inhibitors/therapeutic use ; },
abstract = {The respiratory microbiome, as an integral component of the lung cancer microenvironment, exerts pivotal influences on tumorigenesis, immune homeostasis, and therapeutic response through intricate crosstalk with host immunity. Despite advancements, current limitations in lung cancer immunotherapy persist, including heterogeneous therapeutic responses, immune-related adverse events, and the lack of predictive biomarkers. These unmet clinical needs underscore the imperative to delineate the complex immune landscape of respiratory microbiome in lung cancer pathogenesis. This review systematically analyzes the hallmarks of respiratory dysbiosis (reduced α-diversity and enrichment of Streptococcus and Veillonella) and their associations with lung cancer staging, histological subtypes, and prognosis. We further elucidate how these microbial alterations influence tumor progression via metabolic-epigenetic-immune pathways. Additionally, we establish clinical correlations between microbiome signatures and both immune checkpoint inhibitor therapeutic efficacy/toxicity profiles, while examining the paradoxical effects of antibiotic exposure during immunotherapy. Emerging intervention strategies targeting the respiratory microbiome, such as aerosolized probiotics, engineered bacteria (e.g., Escherichia coli), and microbiota-derived nanomaterials, showcase potential in remodeling antitumor immunity and improving therapeutic outcomes. Our findings highlight the double-edged sword effect of the respiratory microbiota as biomarkers and therapeutic targets in lung cancer management, providing critical insights for clinical translation.},
}

Humans
*Lung Neoplasms/therapy/immunology/microbiology/pathology/etiology
*Immunotherapy/methods
*Microbiota/immunology
Animals
Dysbiosis/immunology
*Carcinogenesis/immunology
*Host Microbial Interactions/immunology
Tumor Microenvironment/immunology
Immune Checkpoint Inhibitors/therapeutic use

@article {pmid41394835,
year = {2025},
author = {Mikaelyan, A and Receveur, J and Bernstein, K and Babcock, NJ and Pechal, JL and Welsh, MV and Waters, KA and Yoskowitz, KH and Benbow, ME},
title = {Host-specific microbiomes of blow flies: ecological drivers and implications for pathogen carriage.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1673934},
pmid = {41394835},
issn = {1664-3224},
mesh = {Animals ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification ; *Calliphoridae/microbiology ; Male ; Female ; *Diptera/microbiology ; Humans ; },
abstract = {Blow flies (Lucilia sericata and Phormia regina) are necrophagous insects that interact with dense microbial reservoirs and are opportunistic vectors of human and animal pathogens. Despite constant exposure to diverse environmental microbes, it is unclear whether their bacterial communities are primarily acquired stochastically or shaped by host factors that could influence pathogen carriage. We conducted a systematic comparison of wild L. sericata and P. regina collected from seven cities across an urban-rural gradient to determine whether microbiome composition is structured by host species identity or environmental variables. Using 16S rRNA gene sequencing of individual flies, we profiled bacterial communities and applied alpha- and beta-diversity analyses, PERMANOVA, and Random Forest classification to quantify species-level microbiome differentiation. Species identity was the strongest predictor of microbiome composition (PERMANOVA, p = 0.001), while location, land cover type, sampling month, and sex had no significant effects. Random Forest modeling identified multiple bacterial taxa that consistently distinguished the two species, including Ignatzschineria and Dysgonomonas, which were enriched in P. regina, and Vagococcus and Escherichia-Shigella, which were enriched in L. sericata. These taxa are of clinical relevance, with Ignatzschineria in particular increasingly reported from human myiasis and soft-tissue infections, sometimes exhibiting antimicrobial resistance. Our findings demonstrate that wild blow flies maintain species-specific microbiomes despite shared environments, suggesting that host identity strongly filters microbial communities. The presence of opportunistic pathogens within these structured microbiomes underscores the need to understand how blow fly-microbe associations contribute to pathogen persistence and dissemination. By revealing predictable, species-dependent microbiome patterns, this study highlights potential targets for microbiome-based strategies aimed at mitigating blow fly-associated disease risks.},
}

Animals
*Microbiota
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification
*Calliphoridae/microbiology
Male
Female
*Diptera/microbiology
Humans

@article {pmid41394818,
year = {2025},
author = {Lu, Q and Wu, J and Yu, X and Qian, J and Song, Z},
title = {Unveiling the interplay between microbiota and PD1/PD-L1 axis in tumor immunity and immunotherapy.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1690374},
pmid = {41394818},
issn = {1664-3224},
mesh = {Humans ; *B7-H1 Antigen/metabolism/immunology ; *Neoplasms/immunology/therapy/microbiology/metabolism ; *Immunotherapy/methods ; *Programmed Cell Death 1 Receptor/metabolism/immunology ; Tumor Microenvironment/immunology ; Animals ; *Microbiota/immunology ; Immune Checkpoint Inhibitors/therapeutic use ; Signal Transduction ; Gastrointestinal Microbiome ; },
abstract = {Microbial communities across diverse body sites critically shape host immunity and tumor responses. Within this framework, the PD-1/PD-L1 axis emerges as a central pathway governing tumor immune evasion and resistance to therapy. Recent evidence reveals that microbiota-from the gut, lungs, and elsewhere-significantly influence PD-1/PD-L1 signaling, thereby altering immune checkpoint blockade efficacy. This review synthesizes current understanding of the microbiota-PD-1/PD-L1 interplay, examining how microbial composition and metabolites impact immune cell activity, the tumor microenvironment, and immunotherapy outcomes. We detail mechanisms through which microbiota regulate PD-1/PD-L1 expression, fostering immune tolerance and tumor progression while modulating therapeutic responses. The translational potential of microbiota-targeted strategies to enhance PD-1/PD-L1 therapy and overcome resistance is discussed. Integrating microbiota modulation with existing immunotherapies offers promising avenues for precision cancer treatment. Advancing these concepts into clinical practice will require future research to establish microbiome-based interventions as transformative tools in oncology.},
}

Humans
*B7-H1 Antigen/metabolism/immunology
*Neoplasms/immunology/therapy/microbiology/metabolism
*Immunotherapy/methods
*Programmed Cell Death 1 Receptor/metabolism/immunology
Tumor Microenvironment/immunology
Animals
*Microbiota/immunology
Immune Checkpoint Inhibitors/therapeutic use
Signal Transduction
Gastrointestinal Microbiome

@article {pmid41394806,
year = {2025},
author = {Young, MR and Mehta, CC and Staple, T and Herring, GB and Govindaraj, S and Ibegbu, C and Herold, BC and Velu, V and Haddad, LB and Smith, AK},
title = {No change in key HIV target cell markers following initiation of three progestin-based hormonal contraception methods: findings from the CHIME study.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1655678},
pmid = {41394806},
issn = {1664-3224},
mesh = {Humans ; Female ; Adult ; *HIV Infections/immunology ; Young Adult ; Middle Aged ; Adolescent ; Biomarkers ; Medroxyprogesterone Acetate/administration & dosage/adverse effects ; *CD4-Positive T-Lymphocytes/immunology/drug effects ; *Hormonal Contraception/methods/adverse effects ; Receptors, CCR5/metabolism ; Levonorgestrel/administration & dosage ; *Progestins/administration & dosage/adverse effects ; Desogestrel/administration & dosage/adverse effects ; *Contraceptive Agents, Female/administration & dosage ; *Contraceptive Agents, Hormonal/administration & dosage ; },
abstract = {INTRODUCTION: Depot medroxyprogesterone acetate (DMPA) injectable, etonogestrel subdermal implant (ENG-implant), and levonorgestrel intrauterine device (LNG-IUD) are effective, widely used female hormonal contraceptives (HC). Observational studies, but not a randomized trial, suggest increased risk of HIV acquisition with HC use, particularly DMPA. Sexual acquisition of HIV occurs via CD4+ T cells expressing C-C chemokine receptor type 5 (CCR5), though other immunologic cells play a role. This study examined longitudinal changes in CCR5+ T cells and other immunologic cells in the female genital tract following HC initiation.

METHODS: HIV negative participants aged 18-45 years, not using HC, were recruited in Atlanta, Georgia. After two pre-HC visits, participants initiated DMPA, ENG-implant, or LNG-IUD and completed visits every three months for one year. Specimens (peripheral blood, endocervical cells, cervical tissue biopsy, and cervicovaginal lavage [CVL]) were analyzed for immune cellular markers (CD45, CD3, CD4, CCR5, CD69, HLA-DR, CD38, α4β7, CD103, Fox-P3, and Ki-67) using flow cytometry. Effects of CVL on HIV infection of cells in vitro was assessed. Vaginal microbiome was characterized via 16S rRNA gene amplicon sequencing. Multivariable linear mixed effects models estimated association between HC and immune markers (Primary outcome: proportion of CD4+ T cells expressing CCR5; Secondary outcomes: other immune markers, in vitro HIV enhancement). A Bonferroni correction was applied.

RESULTS: Among 118 participants (mean age 25.9; 44.1% self-identified as Black race), 545 visits were completed from 2019-2023. No significant changes were observed in proportion of CCR5+ T cells in any tissue type post-HC. There were statistically significant but moderate absolute decreases in proportion of CD45+ and CD4+ T cells in CVL, and CD4+ T cells in blood, and increased proportion of CD69+ T cells in blood post-HC. Post-HC CVL vs. pre-HC enhanced HIV infection of cells in vitro for all three HC groups (p<0.01) and was modified by the vaginal microbiome. There was also evidence of interaction by time and microbiome parameters for several other immune cells.

DISCUSSION: Our findings suggest that commonly used HC methods do not result in immunologic changes that increase HIV acquisition risk. However, HIV infection enhancement with post-HC CVL in vitro warrants further study.},
}

Humans
Female
Adult
*HIV Infections/immunology
Young Adult
Middle Aged
Adolescent
Biomarkers
Medroxyprogesterone Acetate/administration & dosage/adverse effects
*CD4-Positive T-Lymphocytes/immunology/drug effects
*Hormonal Contraception/methods/adverse effects
Receptors, CCR5/metabolism
Levonorgestrel/administration & dosage
*Progestins/administration & dosage/adverse effects
Desogestrel/administration & dosage/adverse effects
*Contraceptive Agents, Female/administration & dosage
*Contraceptive Agents, Hormonal/administration & dosage

@article {pmid41394752,
year = {2025},
author = {Hillary, LS and Knotts, TA and Adams, SH and Ali, MR and Olm, MR and Emerson, JB},
title = {DNA extraction and virome processing methods strongly influence recovered human gut viral community characteristics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.25.690293},
pmid = {41394752},
issn = {2692-8205},
abstract = {Accurately characterising the human gut virome is critical to understanding virus-microbiome-host interactions. However, widely used methods introduce biases that complicate data interpretation and limit cross-study comparability. For instance, multiple-displacement amplification (MDA) preferentially amplifies single-stranded DNA viruses, while total metagenomes are dominated by non-viral sequences, reducing viral signal. These traditional methods have not been systematically compared to viral size-fraction metagenomes (viromes) prepared without MDA. To address this, we applied four common methods for characterising human gut viral community composition (total metagenomes, viromes with/ without DNase treatment (to remove free DNA), and MDA viromes) to a human stool sample, with technical triplicates for each approach. MDA biased viral community composition to a shocking degree: Microviridae formed ∼90% of MDA viromes compared to just 2% of non-MDA viromes. Removing ssDNA viruses from data analyses substantially reduced, but did not eliminate, MDA bias. Metagenomes were enriched for putative temperate phages and predicted Bacillota-phages , whereas predicted Bacteroidetes -phages dominated all viromes, suggesting that metagenomes and viromes select for different populations within the total viral community. DNase treatment had little-to-no effect on virome richness or community composition. This proof-of-principle experiment demonstrates that preparatory methods for viral community analysis can lead to substantially different conclusions from the same faecal sample, and we provide a comprehensive omic data analysis framework for comparing laboratory methodologies for viral ecology. With sufficient DNA yields now easily achievable from human gut viromes without the use of MDA, our results suggest that this biased amplification method should be avoided in human gut virome studies.},
}

@article {pmid41394746,
year = {2025},
author = {Shoer, S and Godneva, A and Weinberger, A and Pollard, KS and Pilpel, Y and Segal, E},
title = {Bacterial strains in the human gut associate with host physiology.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.30.691432},
pmid = {41394746},
issn = {2692-8205},
abstract = {The human microbiota influences host physiology, yet much of its complexity lies beneath the species level. Here, we analyzed the intra-species genetic diversity of 936 gut bacteria across 24,997 individuals from three countries. Our findings show that highly abundant species exhibit greater strain stability, whereas low-abundance species display increased in-clonal mutations. Clonal strains are often mutually exclusive, while genetically variable strains tend to coexist. Strain turnover is associated with the presence of annotated chemotaxis and sporulation genes in reference genomes, whereas strain coexistence is associated with quorum sensing and secretion systems. Leveraging deep phenotypic data, we constructed an atlas detailing strain-level associations with diverse host physiological domains. For example, Phocaeicola vulgatus sub-types relate to host obesity, Lachnospira eligens to sleep, and Parabacteroides distasonis to iron hemostasis. This resource may guide personalized microbiome-based interventions to improve human health.},
}

@article {pmid41394616,
year = {2025},
author = {Hunt, NK and Liu, C and Liu, J and Tang, Q and Stephen, SJ and Wang, B and Schurman, CA and King, CD and Liu, Q and Vashisth, D and Schilling, B and Hassani, M and Hernandez, CJ},
title = {Modifications to the gut microbiome alter bone matrix proteomics and fracture toughness at the cellular scale.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.21.689836},
pmid = {41394616},
issn = {2692-8205},
abstract = {UNLABELLED: The gut microbiome can regulate the strength of bone matrix but the specific changes in matrix function and composition are not yet understood. Here we introduce micropillar splitting to determine the fracture toughness of matrix at the cellular scale in concert with proteomic analysis of bone matrix when the gut microbiome was altered by oral antibiotics (ampicillin+neomycin). Male mice were divided into four groups (n = 3-4/group): (1) Unaltered (no alteration), (2) Continuous (alteration from 4-24 weeks), (3) Delayed (alteration from 16-24 weeks) and (4) Reconstituted (alteration from 1-16 weeks following by reconstitution). Micropillars (5 µm diameter) were fabricated using focused ion beam milling on femur cross-sections in regions of matrix formed either before or after changes in the microbiome (16 weeks) (n = 4/group). Proteomics was used to identify differences in matrix protein composition. Micropillar fracture toughness differed by group (p < 0.001) and region (p < 0.001). Fracture toughness in the Unaltered group (1.34 ± 0.32 MPa√m, mean ± SD) was substantially greater than the Continuous group (0.95 ± 0.20) and the Delayed group (0.90 ± 0.21) but not different from the Reconstituted group (1.22 ± 0.25). Bone matrix formed from 16-24 weeks of age had lower fracture toughness than matrix formed before 16 weeks of age in all groups. Notably, micropillar splitting was substantially more precise than whole bone testing; whole bone notched 3-point bending tests did not detect differences in fracture toughness. Proteomics identified 46 extracellular matrix proteins that were differentially abundant between groups, including decreased abundance of Periostin (q < 0.001) and Emilin-1 (q < 0.001) in groups with impaired bone matrix. These findings demonstrate that modifications to the gut microbiome lead to changes in bone matrix throughout cortical bone volume and establish micropillar splitting as a high-precision approach for characterizing matrix material properties.

PLAIN LANGUAGE SUMMARY: This study investigated the effect of the gut microbiome on the brittleness of bone as a material. We used a new technique for measuring the brittleness of bone that involves making microscopic pillars on the bone surface and splitting them down the middle to measure a material property called fracture toughness. Mice with altered gut microbiomes had bone with reduced fracture toughness (by 35-40%). Restoration of an altered gut microbiome for two months reversed the effects. The effect of the microbiome on bone occurred throughout the whole bone and was not limited to regions of the bone formed after a change in the gut microbiome.},
}

@article {pmid41394473,
year = {2025},
author = {Chatchatee, P and Breedveld, AC and Eussen, SRBM and Nowak-Wegrzyn, A and Lange, L and Benjaponpitak, S and Chong, KW and Sangsupawanich, P and Wopereis, H and Oude Nijhuis, MM and Langford, JE and Kostadinova, AI and Trendelenburg, V and Pesek, R and Davis, CM and Muraro, A and Erlewyn-Lajeunesse, M and Fox, AT and Michaelis, LJ and Beyer, K},
title = {Effects of a specific synbiotic blend on fecal short-chain fatty acids and gut inflammation in cow's milk-allergic children receiving amino acid-based formula during early life: results of a randomized controlled trial (PRESTO study).},
journal = {Frontiers in allergy},
volume = {6},
number = {},
pages = {1667162},
pmid = {41394473},
issn = {2673-6101},
abstract = {Consumption of an amino acid-based formula (AAF) with added synbiotics [short-chain oligofructose and long-chain inulin (scFOS/lcFOS, 9:1 ratio) and Bifidobacterium breve M-16V] (AAF-S) beneficially impacts the gut microbiome of infants with cow's milk allergy (CMA). We assessed the effect of consuming AAF with or without synbiotics by children with CMA for 12 months on their fecal (branched) short-chain fatty acids (SCFA/BCFA) concentrations, and on gut barrier and inflammation markers (Netherlands Trial Register NTR3725). Feces and saliva were collected from 161 children (≤13 months) with IgE-mediated CMA at baseline, 6 and 12 months after enrollment, and at 24 and 36 months follow-up. Fecal SCFA and BCFA were analyzed by gas chromatography, and gut barrier and inflammation markers were measured in saliva/feces by ELISA or ImmunoCAP. At 6 months, children receiving AAF-S had significantly lower fecal propionate, valerate and BCFA concentrations compared to children consuming AAF. The percentage of propionate from the total 6 SCFA/BCFA (acetate + butyrate + propionate + valerate + isobutyrate + isovalerate) was significantly lower, while the percentage of acetate from the total 6 SCFA/BCFA was significantly higher in the AAF-S group. There were no significant differences between groups in fecal concentrations of butyrate at 6 months, nor in SCFA or BCFA at baseline and after 12, 24 or 36 months. Intestinal inflammation and barrier markers did not differ between groups. Addition of synbiotics to AAF brings concentrations of key fecal microbial metabolites more in line with patterns observed in healthy breastfed infants. The effects on SCFA and BCFA concentrations were transient and only seen at 6 months.},
}

@article {pmid41394296,
year = {2025},
author = {Vasa, SR and Girard, M and Gardiner, GE and Cormican, P and Bee, G and O'Driscoll, K and Lawlor, PG},
title = {Effect of feeding a gestation diet to sows for 5 days post-farrowing and feeding a liquid mixture of milk replacer and starter diet to suckling piglets on growth, selected health parameters and faecal microbiota of suckling pigs on two research farms.},
journal = {Translational animal science},
volume = {9},
number = {},
pages = {txaf138},
pmid = {41394296},
issn = {2573-2102},
abstract = {This study involved 50 sows and was a 2 × 2 factorial arrangement with factors being sow feeding [lactation diet throughout lactation (CON) or gestation diet for the first 5 days of lactation, followed by lactation diet (GEST5)] and creep feeding from day (d) 5 after birth [dry pelleted starter diet (DPS) or liquid mixture of milk replacer and starter diet (LMR+S)]. The study was conducted on two research farms, one in Ireland (IE) and the other in Switzerland (CH). All sows were limit-fed the gestation diet until farrowing. During lactation, both sow treatments followed the same feeding curve with daily digestible energy allocation increasing from 58.1 to 135 MJ between d1 and 28. Sow feed intake, weight and backfat depth and piglet weight and total dry matter disappearance (TDMD) of creep feed during lactation were recorded. On d5 after birth, milk was collected from sows on both farms and sow faeces was collected at CH for short chain fatty acid (SCFA) analysis. Following weaning at d29 ± 0.2 in IE and d25.5 ± 1.3 in CH, pigs were followed until d43 post-weaning (pw) in IE (n = 7 pens/treatment) and d14 pw in CH (n = 11 pens/treatment). In IE, faecal samples were collected from sows before farrowing and on d5, 12 and 26 after birth and from piglets on d2, 5, 12 and 26 after birth and on d7 and d41 pw for microbiota analysis. Feeding GEST5 did not affect overall sow feed intake, backfat depth or weight loss during lactation on both farms (P > 0.05) but reduced the solids, fat and SCFA content of milk and increased faecal SCFA in CH (P < 0.05). In CH, LMR+S-fed pigs had higher TDMD than those fed DPS, while in IE, DPS had higher TDMD than LMR+S (P < 0.05). However, neither GEST5 nor LMR+S influenced pre- or pw pig growth or diarrhoea prevalence on either farm (P > 0.05). In IE, on d5 post-farrowing, GEST5 sows had a higher relative abundance of Prevotella and Succinivibrio in their faeces compared to CON (P < 0.05) and both GEST5 and LMR+S increased bacterial alpha diversity in piglet faeces on d7 pw (P < 0.05). In conclusion, while providing a gestation diet during the first 5 days of lactation increased physical feed intake then, it did not increase overall lactation feed intake in sows. Additionally, creep feeding a liquid mixture of milk replacer and starter diet to suckling piglets did not improve pre- or pw pig growth.},
}

@article {pmid41394287,
year = {2025},
author = {Stögbauer, J and Kämpfer, N and Becker-Dorison, A and Schwiertz, A and Groppa, S and Unger, MM and Fousse, M},
title = {Alterations of fecal short-chain fatty acids solely in the course of multiple sclerosis: rethinking the gut-brain axis in the early stages of MS.},
journal = {Therapeutic advances in neurological disorders},
volume = {18},
number = {},
pages = {17562864251396028},
pmid = {41394287},
issn = {1756-2856},
abstract = {BACKGROUND: The role of gut microbiota in multiple sclerosis (MS) has become increasingly important, intestinal dysbiosis with reduced production of short-chain fatty acids (SCFA) being the prevailing paradigm. However, the direction of causality, that is, whether intestinal changes are cause or consequence of chronic central nervous system inflammation, remains to be elucidated. Previous studies have focused on long-term MS patients. Alteration in fecal SCFA concentrations in early MS, particularly during relapses, remains to be extensively studied.

OBJECTIVES: To compare fecal SCFA concentrations in patients with a first diagnosis of MS with those in patients with long-term MS and in healthy controls (HCs).

DESIGN: Prospective cohort study.

METHODS: The prospective case-control study was conducted on relapsing-remitting MS (RRMS) patients at the time of first, acute relapse without ongoing immunotherapy (Early-RRMS). Clinical and demographic parameters, as well as fecal SCFA concentrations (measured by gas chromatography) were collected. The parameters were compared with those of matched RRMS patients under different, long-term immunotherapy (Late-RRMS) and HCs.

RESULTS: SCFA concentrations of propionate, butyrate, isobutyrate, valerate, and isovalerate were not significantly different between the early-RRMS cohort and HCs, but were lower in the late-RRMS cohort.

CONCLUSION: The findings indicate that reduction in SCFA levels is exclusively observed in patients with RRMS during the further course of the disease and not at the onset. Decrease in SCFA concentration may be rather consequence or related to neurodegeneration than linked to the first demyelinating event. Further investigation related to disease trajectories of immunomodulatory or neuroprotective treatments are required.},
}

@article {pmid41394226,
year = {2025},
author = {Lyu, Z and Zhu, J and Chen, D},
title = {Chronic Periodontitis and Non-Alcoholic Fatty Liver Disease: Recent Advances in Mechanisms of Association.},
journal = {International journal of general medicine},
volume = {18},
number = {},
pages = {7357-7369},
pmid = {41394226},
issn = {1178-7074},
abstract = {BACKGROUND: Chronic periodontitis (CP) and non-alcoholic fatty liver disease (NAFLD) are increasingly prevalent worldwide. Although mechanisms remain incompletely defined, recent studies suggest a close association between these two diseases. This review systematically outlines potential links between periodontitis and NAFLD, emphasizing their pathological mechanisms and interactions within an oral-gut-liver framework.

METHODS: We reviewed observational, interventional, and mechanistic studies evaluating associations between periodontal status/treatment and NAFLD-related outcomes, integrating evidence on dysbiosis, inflammatory mediators, microbial metabolites, oxidative stress, microRNA regulation, and gut barrier function.

RESULTS: Across epidemiological studies, periodontitis is associated with higher risk and greater severity of NAFLD. Mechanistically, oral dysbiosis, especially enrichment of oral pathobionts, is linked to hepatic steatosis and fibrosis. Translocation of microbial products and the resulting cytokine release drive systemic inflammation, impair gut barrier integrity, and induce hepatocellular injury. Microbial metabolites (such as short-chain fatty acids (SCFAs) and trimethylamine N-oxide (TMAO)) and oxidative stress contribute to metabolic dysregulation. Emerging evidence suggests that microRNAs (miRNAs) function as epigenetic regulators linking periodontal inflammation and bone remodeling to immune-metabolic pathways relevant to non-alcoholic fatty liver disease (NAFLD). However, direct evidence on whether treating periodontitis can improve NAFLD outcomes remains limited. Despite heterogeneity in study designs and diagnostic criteria, cumulative evidence supports periodontitis as a modifiable risk factor for the progression of NAFLD.

CONCLUSION: CP and NAFLD appear to be linked through systemic inflammation, dysbiosis, and metabolic disturbances. Future research should prioritize microbiome modulation, advance interdisciplinary care models, and develop personalized prevention and treatment strategies. Integrating oral and liver health within comprehensive management may provide new options for preventing and treating these frequently coexisting diseases.},
}

@article {pmid41394107,
year = {2025},
author = {Yang, Y and Jia, XF and Cui, GH and Huang, QY and Lin, MM and Shi, ZM and Ye, H and Zhang, XZ},
title = {Jinghuaweikang capsule alleviates Helicobacter pylori-infected gastric mucosal inflammation and drug resistance by regulating intestinal microbiota and MAPK pathway.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1628594},
pmid = {41394107},
issn = {2235-2988},
mesh = {Animals ; *Helicobacter Infections/drug therapy/microbiology/pathology ; *Helicobacter pylori/drug effects ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Drugs, Chinese Herbal/administration & dosage/pharmacology ; Disease Models, Animal ; *Gastric Mucosa/pathology/drug effects/microbiology ; *MAP Kinase Signaling System/drug effects ; *Drug Resistance, Bacterial/drug effects ; Anti-Bacterial Agents/pharmacology ; Male ; Inflammation/drug therapy ; *Gastritis/drug therapy/microbiology ; Capsules ; },
abstract = {BACKGROUND: Helicobacter pylori (H. pylori) infection represents a prevalent global health burden. Current eradication strategies are complicated by increasing antibiotic resistance and detrimental alterations to the gut microbiome. Jinghuaweikang capsule (JWC), a traditional Chinese medicine, has demonstrated efficacy against H. pylori, yet its mechanisms involving microbiota-inflammation interactions remain incompletely elucidated.

AIM: This study aimed to investigate the effects of the JWC on gastric mucosal inflammation and the expression of drug-resistance genes in H. pylori-infected mice.

METHODS: Sixty Kunming mice were randomly allocated into six groups, including normal control group (Control), model group (Model), Western medicine triple group (AC), low-dose JWC group (JWCL), medium-dose JWC group (JWCM), and high-dose JWC group (JWCH). A mouse model of H. pylori infection was established by intragastric administration of an H. pylori SS1 solution for two weeks. The efficacy of this model was evaluated using rapid urease test (RUT) and Warthin-Starry (WS) silver stain. Subsequently, the experimental cohort of mice underwent pharmacological intervention. Hematoxylin and eosin (HE) staining, enzyme-linked immunosorbent assay (ELISA), and quantitative real-time polymerase chain reaction (qRT-PCR) were used to assess the impact of JWC on inflammation within the gastric mucosa of mice infected with H. pylori. Metagenomic sequencing technology was used to identify alterations in the intestinal microbiota and antibiotic resistance genes in the murine models. Western blotting was used to assess the expression levels of proteins involved in the mitogen-activated protein kinase (MAPK) signaling pathway.

RESULTS: JWC mitigated gastric mucosal inflammation induced by H. pylori infection and reduced the concentrations of interleukin- (IL-) 6, IL-1β, and tumor necrosis factor-α (TNF-α) while inhibiting gene expression level. Metagenomic sequencing revealed that triple therapy in Western medicine markedly diminished the diversity of the intestinal microbiota while elevating the abundance of antibiotic-resistance genes, including macB, arlR, evgS, tetA(58), and mtrA. The diversity and richness of the intestinal microbiota in the JWC group were comparable to those in the control group, with an increase in the abundance of beneficial bacteria such as Muribaculaceae_bacterium. Furthermore, the expression levels of the antibiotic resistance genes macB, tetA(58), bcrA, oleC, and arlS were downregulated. Moreover, the activation of MAPK signaling pathway components phospho-ERK and phospho-p38 was inhibited.

CONCLUSION: JWC preserves microbial diversity and promotes a beneficial compositional shift, mitigates the risk of antibiotic resistance, modulates the MAPK signaling pathway, and alleviates gastric mucosal inflammation in mice infected with H. pylori.},
}

Animals
*Helicobacter Infections/drug therapy/microbiology/pathology
*Helicobacter pylori/drug effects
*Gastrointestinal Microbiome/drug effects
Mice
*Drugs, Chinese Herbal/administration & dosage/pharmacology
Disease Models, Animal
*Gastric Mucosa/pathology/drug effects/microbiology
*MAP Kinase Signaling System/drug effects
*Drug Resistance, Bacterial/drug effects
Anti-Bacterial Agents/pharmacology
Male
Inflammation/drug therapy
*Gastritis/drug therapy/microbiology
Capsules

@article {pmid41393947,
year = {2025},
author = {Semchyshyn, H},
title = {Balancing the dual nature of glycotoxins: interplay of diet, digestion, and gut microbiome.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1693167},
pmid = {41393947},
issn = {2296-861X},
abstract = {Glycation chemistry, both in vitro and in vivo, is well-studied and known to result in a variety of products-from early glycation products, reactive carbonyl and oxygen species (RCS and ROS, respectively) to advanced glycation end products (AGEs). Exogenous glycation products from the regular diet contribute substantially to the total AGE burden, often exceeding endogenous formation. AGEs and other products of glycation, whether formed endogenously or derived exogenously, may have similar biological effects and are mainly known for their harmful impact, therefore, the term "glycotoxins" is used to emphasize the toxicity of certain of them. Nevertheless, the human body as well as gut microbiome have adapted to the presence of glycation products and can even use them beneficially at low concentrations. Maintaining an appropriate balance of glycotoxins depends largely on digestion in the gastrointestinal tract, mediated by both host and microbiome enzymes. The fate of dietary glycation products in the gut strongly depends on their interaction with the intestinal microbiota. A key open question is how human and microbial enzymes work together to degrade AGEs and maintain their concentrations within a potentially "beneficial" range. This review is focused on the metabolism and digestion of glycation products by both human and microbial enzymes, highlighting their dual nature and overall impact on human health.},
}

@article {pmid41393931,
year = {2025},
author = {Geng, J and Zhang, G and Dong, J and Tian, H and Lou, Z},
title = {Multi-omics techniques revealing the mechanism of Polygonatum sibiricum Huangjiu in alleviating hyperlipidemia in mice.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1705061},
pmid = {41393931},
issn = {2296-861X},
abstract = {INTRODUCTION: Hyperlipidemia poses a serious threat to human health. However, given the significant adverse effect of drug therapy, finding safe and efficient lipid-lowering agents has become a focal point of interest. Polygonatum sibiricum Huangjiu (PSHJ) is hypothesized to exert lipid-lowering effects. This study examined PSHJ's ability to alleviate hyperlipidemia in mice caused by a high-fat diet, and the regulatory mechanism was studied via gut microbiome and fecal lipidomics.

METHODS: A mouse model of hyperlipidemia was established using a high-fat diet. The experimental groups were administered PSHJ, and serum lipid profiles-including triglycerides (TG), total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C), and high-density lipoprotein cholesterol (HDL-C)-were measured. Histopathological examinations of the liver, kidney, and small intestine were performed to assess tissue damage. The gut microbiota composition was analyzed to evaluate diversity and the abundance of short-chain fatty acids (SCFAs)-producing bacteria. Fecal lipidomics was employed to investigate alterations in lipid metabolic pathways.

RESULTS: PSHJ treatment significantly increased HDL-C levels while reducing serum TG, TC, and LDL-C levels in hyperlipidemic mice. Histological analysis revealed that PSHJ alleviated damage in the liver, kidney, and small intestine. Furthermore, PSHJ enhanced gut microbial diversity and promoted the proliferation of SCFA-producing bacteria, leading to elevated SCFA levels. Lipidomic analysis indicated that PSHJ modulated metabolic pathways related to glycerophospholipids, glycerolipids, and fatty acids, thereby facilitating the breakdown of TG and diacylglycerol (DG).

DISCUSSION: The findings suggest that polysaccharides in PSHJ function as prebiotics, enriching beneficial gut microbiota and increasing SCFA production. These SCFAs, along with polysaccharides, appear to regulate key lipid metabolic pathways, enhancing the degradation of TG and DG. This study shows that PSHJ has active components that can alleviate hyperlipidemia, thereby laying a theoretical foundation for extracting bioactive substances from Huangjiu for future medical or dietary use.},
}

@article {pmid41393901,
year = {2025},
author = {Wang, JJ and Hu, Y and Jennings, S and Luo, M and Taylor, CM and Nauseef, WM and Wang, G},
title = {Myeloperoxidase gene knockout causes local inflammation and dysbiosis in the murine gut.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {},
pmid = {41393901},
issn = {2993-3935},
abstract = {Myeloperoxidase (MPO), predominantly expressed in neutrophils, catalyzes the production of hypochlorous acid (HOCl) that plays an integral role in the host defense against invading pathogens. However, little is known about its role in maintaining normal gut microbiome and function. Here, we report the comparisons of inflammation and microbiome in the intestines of WT and MPO[-/-] mice. Immune cell profiling demonstrated that the MPO[-/-] mice had significantly more neutrophils and T cells in their intestinal mucosae and significantly more fecal calprotectin as compared to the WT mice. Fluorescent dextran permeability of the bowel showed no difference between the two strains of mice. Carmine Red transit demonstrated that the MPO[-/-] intestines had slower movements than did the WT controls. Sequencing the intestinal 16S rDNA of co-housed MPO[-/-] and WT mice identified 13 bacterial families, 2 of which were unique to MPO[-/-] and 7 to WT mice. Alpha diversity of the microbiome in WT intestines was significantly higher than that of MPO[-/-] ones, and beta diversity of the two microbial communities of the two genotypes also differed significantly. Functional pathway analyses revealed distinct metabolic signatures. Thus, normal MPO function is important to intestinal health and its deficiency leads to gut inflammation and dysbiosis.},
}

@article {pmid41393784,
year = {2025},
author = {Longhi, G and Tarracchini, C and Angelini, L and Anzalone, R and Viappiani, A and Ventura, M and Milani, C and Turroni, F},
title = {Exploring diversity and functional contribution of the microbiome of traditional Italian dry-cured hams.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100516},
pmid = {41393784},
issn = {2666-5174},
abstract = {Traditional dry-cured hams host diverse microbial communities; however, their taxonomic composition, functional capacity, and potential interactions with the human gut remain poorly understood. This study aimed to provide a comprehensive characterization of the microbiota associated with Italian Protected Designation of Origin (PDO) dry-cured hams and to investigate their functional relevance in the food matrix and under simulated intestinal conditions. A total of 96 samples, representing different geographical origins and maturation stages, were analyzed using metagenomics approaches. A conserved microbial core dominated by Staphylococcus equorum (prevalence 80 %) was identified, accompanied by accessory taxa such as Tetragenococcus halophilus (62 %) and Leuconostoc carnosum (10 %). Cluster analyses revealed substantial variability across samples, with community structures influenced more by producer-specific factors than by product type or ripening stage. Functional metagenomics investigation highlighted the presence of metabolic pathways associated with amino acid degradation, carbohydrate metabolism, and lipid transformation, supporting a role for ham-associated microbes in flavor and texture development. Furthermore, cultivation in a simulated gut environment showed a marked reshaping of the microbial community, with low-abundance taxa, including Bacillus spp. and Lactococcus lactis, proliferating under intestinal-like conditions, while the dominance of S. equorum was reduced. Our findings showed that the microbiota of dry-cured ham not only drives key sensory qualities of the product but also comprises a reservoir of live microorganisms capable of tolerating the gut-like conditions. These results highlight the dual role of foodborne microbiota in shaping both food properties and potential interactions with the human host, underscoring the need for further in vivo investigations.},
}

@article {pmid41393412,
year = {2025},
author = {V Manek, P and M, A and Sinha, R and Pradeep, O and Dixit, H and Sharma, D and Tiwari, R},
title = {Daily probiotic supplementation on plaque pH and gingival health in adults: A clinical study.},
journal = {Bioinformation},
volume = {21},
number = {8},
pages = {2365-2368},
pmid = {41393412},
issn = {0973-2063},
abstract = {Oral health is strongly influenced by the balance of the oral microbiome, with plaque pH and gingival status serving as critical indicators of dental and periodontal well-being. A randomized, controlled clinical trial was conducted involving 60 healthy adults aged 20-45 years. The probiotic group exhibited a significant increase in plaque pH (from 5.89 ± 0.12 to 6.52 ± 0.10, p < 0.001) and a marked reduction in gingival index scores (from 1.83 ± 0.18 to 0.97 ± 0.15, p < 0.001). The control group showed no significant changes. Daily probiotic intake effectively enhanced plaque pH and gingival health, supporting its role as a preventive adjunct in routine dental care.},
}

@article {pmid41393294,
year = {2025},
author = {Kellenberger, A and Dewal, RS and de Wouters d'Oplinter, A and Sichert, A and Heine, M and Fuh, MM and Slack, E and Delessa Challa, T and Wolfrum, C},
title = {Antibiotic-induced gut microbiota depletion enhances glucose tolerance linked to GLP-1 signaling.},
journal = {Frontiers in endocrinology},
volume = {16},
number = {},
pages = {1684155},
pmid = {41393294},
issn = {1664-2392},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Glucagon-Like Peptide 1/metabolism ; Mice ; *Anti-Bacterial Agents/pharmacology ; Signal Transduction/drug effects ; Mice, Knockout ; Male ; *Glucose Intolerance/metabolism ; Mice, Inbred C57BL ; *Glucose/metabolism ; Glucose Tolerance Test ; Bile Acids and Salts/metabolism ; Glucagon-Like Peptide-1 Receptor/genetics ; Uncoupling Protein 1/metabolism/genetics ; },
abstract = {INTRODUCTION: Depletion of the gut microbiota is known to improve glucose metabolism and modify thermogenic capacity in mice. However, the underlying mechanisms remain unclear. In this study, we aimed to determine whether the browning effect observed after antibiotic treatment contributes to metabolic modifications and to investigate the potential central role of GLP-1 in enhancing glucose metabolism.

METHODS: Using an inducible Ucp1DTR mouse model to transiently ablate UCP1[+] cells, we assessed glucose tolerance, cold sensitivity, and circulating GLP-1 levels following gut microbiota depletion. We additionally examined GLP-1 levels in germ-free mice. Glucose tolerance was compared to GLP1R KO mice following gut microbiota depletion. Bile acid profiling in wild-type mice treated with antibiotics identified regulated bile acids, which were subsequently tested in an in vitro STC-1 cell assay and in vivo in Cyp2c70 mice to identify potential basal GLP-1 secretion inhibitors.

RESULTS: We demonstrate that gut microbiota depletion improved glucose tolerance independent of UCP1[+] cell presence and increased cold sensitivity. Antibiotic treatment increased circulating active GLP-1 levels within one day, and this increase was also observed in germ-free mice, supporting the suggestion that GLP-1 elevation is driven by gut microbiota depletion. The improvement in glucose tolerance was lost in GLP1R KO mice upon oral glucose ingestion. Bile acid profiling and subsequent validation led to the identification of two potential basal GLP-1 secretion inhibitors.

DISCUSSION: Our findings suggest that the metabolic improvements following gut microbiota depletion are primarily driven by GLP-1 signaling, rather than UCP1⁺ cell activation. These results highlight the complex interplay between the gut microbiome and metabolic health, offering insights into potential therapeutic targets for improving glucose metabolism through modulation of basal GLP-1 signaling.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Glucagon-Like Peptide 1/metabolism
Mice
*Anti-Bacterial Agents/pharmacology
Signal Transduction/drug effects
Mice, Knockout
Male
*Glucose Intolerance/metabolism
Mice, Inbred C57BL
*Glucose/metabolism
Glucose Tolerance Test
Bile Acids and Salts/metabolism
Glucagon-Like Peptide-1 Receptor/genetics
Uncoupling Protein 1/metabolism/genetics

@article {pmid41393148,
year = {2025},
author = {Wang, D and Li, J and Wang, L and Tian, H and Zhou, X and Wang, X and Tian, H},
title = {Intestinal dysbiosis in critically ill patients: a case-control study of Enterobacteriaceae enrichment and reduced microbial diversity.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1680262},
pmid = {41393148},
issn = {2296-858X},
abstract = {INTRODUCTION: Critical illness disrupts gut microbiota homeostasis, potentially exacerbating systemic inflammation and adverse outcomes. This study investigates gut dysbiosis patterns in ICU patients, with a focus on Enterobacteriaceae enrichment and microbial diversity loss, to identify biomarkers and therapeutic targets.

METHODS: In this case-control study, 37 ICU patients (sepsis: n = 17; non-sepsis: n = 20) and 20 healthy controls were enrolled. Fecal samples underwent 16S rRNA sequencing (V3-V4 regions). Microbial diversity (Shannon/Simpson indices), beta diversity (Bray-Curtis PCoA), and taxonomic differences (LEfSe, LDA > 2.5) were analyzed using QIIME2 and R.

RESULTS: Critically ill patients showed reduced alpha diversity vs. controls (Shannon p = 0.04; Simpson p = 0.04). Enterobacteriaceae (phylum Proteobacteria) were significantly enriched in ICU patients (LDA = 4.2, p < 0.01), while Ruminococcus dominated controls. Beta diversity differed markedly (PERMANOVA R [2] = 0.199, p = 0.001). No diversity differences were observed between sepsis/non-sepsis subgroups (p > 0.05).

CONCLUSION: ICU patients exhibit gut dysbiosis characterized by Enterobacteriaceae expansion and diversity loss, independent of sepsis status. These findings underscore the gut microbiome's role in critical illness and support exploring microbiota-targeted interventions (e.g., selective probiotics) to improve outcomes.},
}

@article {pmid41393116,
year = {2025},
author = {Ahmed, N and Gaur, V and Kamle, M and Chauhan, A and Chauhan, R and Kumar, P and Singh, NA},
title = {Correction: Microbiome-based therapeutics for metabolic disorders: harnessing microbial intrusions for treatment.},
journal = {Frontiers in medical technology},
volume = {7},
number = {},
pages = {1736962},
doi = {10.3389/fmedt.2025.1736962},
pmid = {41393116},
issn = {2673-3129},
abstract = {[This corrects the article DOI: 10.3389/fmedt.2025.1695329.].},
}

@article {pmid41393108,
year = {2025},
author = {Sun, Y and Yang, H and Zhang, J and Cong, S and Wang, L and Yu, T},
title = {Development and emerging trends in gastrointestinal dysfunction of Parkinson's disease: a decade-long bibliometric analysis.},
journal = {Frontiers in aging neuroscience},
volume = {17},
number = {},
pages = {1712302},
pmid = {41393108},
issn = {1663-4365},
abstract = {Gastrointestinal (GI) dysfunction represents a prevalent non-motor symptom of Parkinson's disease (PD) that not only contributes significantly to disease progression but also substantially compromises patients' quality of life. Over the past decade, research in this domain has expanded considerably. To systematically delineate the knowledge framework and evolving trends, we performed a bibliometric analysis of publications on GI and PD from 2015 to 2025. A total of 924 articles were retrieved from the Web of Science Core Collection (WoSCC). Co-occurrence, clustering, and collaboration network analyses were performed using VOSviewer, CiteSpace, and the R package Bibliometrix. For findings validation, the PubMed database was incorporated as an independent external validation dataset, providing complementary verification of keyword analyses derived from WoSCC. Our analysis revealed a steady annual increase in publication output. China and the United States emerged as the most prolific contributors globally, with the latter attaining the highest total citation count. At the institutional level, Capital Medical University led in publication output, whereas the University of Helsinki ranked highest in both total and average citations. Among journals, Parkinsonism & Related Disorders published the most papers on this topic, while Movement Disorders received the most citations. Keyword cluster analyses identified three primary research frontiers: (1) pathogenesis, focusing on α-synuclein (α-syn), the brain-gut-microbiome axis, and the enteric nervous system; (2) clinical manifestations, especially dysphagia and constipation; and (3) therapeutic interventions, particularly fecal microbiota transplantation and probiotics. By integrating established knowledge and highlighting emerging trends, this review aims to inform and guide future research and clinical practice in the field of gastrointestinal dysfunction in PD.},
}

@article {pmid41392764,
year = {2025},
author = {Wu, Q and Gao, G and Kwok, LY and Qiao, J and Wei, Z and He, Q and Sun, Z},
title = {Bifidobacterium animalis subsp. lactis Bbm-19 ameliorates insomnia by remodeling the gut microbiota and restoring γ-aminobutyric acid and serotonin signaling.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo04374c},
pmid = {41392764},
issn = {2042-650X},
abstract = {Insomnia is associated with dysregulation of the gut-brain axis, yet microbiome-targeted interventions remain underexplored. In this study, we investigated the effects of Bifidobacterium animalis subsp. lactis Bbm-19 (Bbm-19), a strain isolated from human breast milk, in a 4-chloro-DL-phenylalanine-induced mouse model of insomnia. Using integrated behavioral, neurochemical, immunological, and multi-omics approaches, this study demonstrates that insomnia is characterized by shortened sleep duration, prolonged sleep latency, anxiety-like behaviors, and reduced levels of serotonin and gamma-aminobutyric acid in the gut, serum, and brain. Administration of Bbm-19 significantly improved sleep parameters, reduced anxiety-like behaviors, and increased survival. Metagenomic and metabolomic analyses revealed that Bbm-19 restored gut microbiota balance, enriched beneficial taxa, including Muribaculaceae bacterium and Stercoribacter sp., and reprogrammed microbial metabolic modules, particularly those involved in amino acid metabolism (including alanine, aspartate, glutamate, arginine, proline, and tryptophan pathways). Targeted metabolomics confirmed increased levels of gamma-aminobutyric acid and serotonin in fecal and brain tissues, along with normalization of inflammatory cytokine profiles. Spearman correlation analysis linked Bbm-19-enriched taxa to improved neurotransmitter levels and sleep outcomes. Notably, Bbm-19 outperformed lorazepam in modulating gut-specific metabolic functions and synergistically enhanced its effects when co-administered. These findings demonstrate that Bbm-19 ameliorates insomnia through coordinated regulation of the gut microbiota, host metabolism, and neuroimmune signaling, highlighting its potential as a targeted psychobiotic intervention for sleep disorders.},
}

@article {pmid41392395,
year = {2025},
author = {Giangiulio, O and Maccarone, R},
title = {The Blood-Brain Barrier as an Integration Hub in Alzheimer's Disease: How Microbiota Metabolites Modulate Central Signal Processing.},
journal = {CNS neuroscience & therapeutics},
volume = {31},
number = {12},
pages = {e70703},
doi = {10.1002/cns.70703},
pmid = {41392395},
issn = {1755-5949},
mesh = {Humans ; *Alzheimer Disease/metabolism/microbiology/physiopathology ; *Blood-Brain Barrier/metabolism ; *Gastrointestinal Microbiome/physiology ; Animals ; Signal Transduction/physiology ; },
abstract = {BACKGROUND: While both gut-brain axis dysfunction and blood-brain barrier (BBB) breakdown are documented in Alzheimer's disease (AD), current research treats these as separate phenomena. However, emerging evidence suggests that the BBB may function as an active integration interface that processes microbiota-derived metabolites and thereby potentially modulates how peripheral signals influence cognitive health.

OBJECTIVE: This review synthesizes current evidence on microbiota metabolites as modulators of BBB integration capacity, discussing how such mechanisms may contribute to variability in cognitive outcomes despite similar gut microbiome profiles by demonstrating how BBB signal-integration mechanisms determine gut-brain communication effectiveness in AD.

METHODS: We analyzed peer-reviewed literature from 2010 to 2025, focusing on BBB dynamic properties, microbiota metabolite effects on BBB function, and their integration patterns, emphasizing functional evidence supporting the BBB's active signal processing capabilities.

RESULTS: Current evidence suggests that the BBB exhibits integration properties, including dynamic permeability regulation, context-dependent metabolite processing, and coordinated responses to complex signal streams. Short-chain fatty acids enhance integration capacity through HDAC inhibition and coordinated receptor activation, while lipopolysaccharides and trimethylamine N-oxide may overwhelm integration processes through TLR4-mediated disruption. BBB dysfunction precedes classical AD pathology and correlates with altered metabolite processing capacity. Individual variations in BBB integration capacity may help account for why individuals with similar gut microbiome profiles show different cognitive outcomes.

CONCLUSION: Viewing the BBB as an active integration interface offers a useful perspective for organizing current evidence on gut-brain interactions in AD. This conceptual perspective suggests that therapeutic strategies might benefit from supporting BBB integration capacity and optimizing metabolite-processing mechanisms alongside improving gut health.},
}

Humans
*Alzheimer Disease/metabolism/microbiology/physiopathology
*Blood-Brain Barrier/metabolism
*Gastrointestinal Microbiome/physiology
Animals
Signal Transduction/physiology

@article {pmid41392314,
year = {2025},
author = {Abahussin, HM and Alotaibi, MS and Alhazzaa, OA and Alotaibi, AG and Alsaab, SM and Aljawini, NA and Alawad, AO},
title = {Exploring the intricate link between gut microbiota dysbiosis and the aging process: implications for age-related diseases.},
journal = {Gut pathogens},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13099-025-00788-z},
pmid = {41392314},
issn = {1757-4749},
abstract = {Aging is a complex process marked by the gradual accumulation of impairments in molecules and tissues, leading to frailty and dysfunction. This decline is a significant risk factor for many debilitating conditions. Recently, gut microbiota dysbiosis has been identified as one of the hallmarks of aging. This review sheds light on the role of gut microbiota dysbiosis in accelerating aging and its relation to age-associated diseases, including neurodegenerative disorders, cardiovascular diseases, cancer and diabetes. Emerging research demonstrates a strong link between the gut microbiome and the aging process, although the underlying mechanisms remain under investigation. Animal studies suggest that targeting the gut microbiome may offer a promising approach to mitigate aging and related diseases. However, further human studies are needed to confirm these findings.},
}

@article {pmid41392229,
year = {2025},
author = {Bernal, SPF and Soares, C and Ottoni, JR and da Costa Silva Gonçalves, C and Lima, N and Passarini, MRZ},
title = {Caracterização taxonômica integrativa de comunidades bacterianas e fúngicas de tripas de cupins e areia de folhas.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {57},
number = {1},
pages = {10},
pmid = {41392229},
issn = {1678-4405},
support = {205/2021/PRPPG//Triple Agenda institutional program/ ; },
mesh = {*Isoptera/microbiology ; Animals ; *Fungi/classification/genetics/isolation & purification ; *Bacteria/classification/genetics/isolation & purification ; Phylogeny ; Plant Leaves/microbiology ; *Sand/microbiology ; Soil Microbiology ; *Mycobiome ; },
abstract = {The search for microbial cells from different sources is a crucial strategy for discovering new strains with biotechnological potential. Leaf litter fungi, which decompose organic matter, and symbiotic termite bacteria, which digest cellulose, can be harnessed for the development of biotechnologies focused on nutrient recycling, biofuel production, and organic waste treatment. The precise identification of these strains allows the use of their biological capabilities, promoting innovative and sustainable solutions to environmental challenges. In this study, filamentous fungi and bacteria recovered from soil with leaf litter and termite guts were characterized using an integrative taxonomy approach, including classical morphology, ribosomal RNA gene sequencing, MALDI-TOF MS, and FTIR. A total of nine filamentous fungi and nine bacteria were identified. After taxonomic analysis, the bacterial strains were identified as belonging to Rossellomorea marisflavi (n = 2), Bacillus subtilis (n = 2), B. amyloliquefaciens (n = 2), B. cereus (n = 1), Priestia megaterium (n = 1), and Pseudomonas azotoformans (n = 1). The fungal species were identified as Talaromyces mycothecaei (n = 3), Aspergillus fumigatus (n = 1), A. tubingensis (n = 1), A. hiratsukae (n = 1), Trichoderma sp. (n = 1), T. harzianum (n = 1), and Coniochaeta velutina (n = 1). This may be the first report of the isolation of Rossellomorea from the gut microbiome of termites. The results showed that the use of an integrative approach for the taxonomic characterization of microbial strains recovered from environmental samples can improve the accurate identification and understanding of microbial species associated with different environments, such as the termite gut and litter.},
}

*Isoptera/microbiology
Animals
*Fungi/classification/genetics/isolation & purification
*Bacteria/classification/genetics/isolation & purification
Phylogeny
Plant Leaves/microbiology
*Sand/microbiology
Soil Microbiology
*Mycobiome

@article {pmid41392171,
year = {2025},
author = {Chowdhury, J and Milne, N and Wade, M and Sharwood, R and Thuaux, B and Green, P and Last, I and Senior, J and Carnegie, AJ and Anderson, IC and Elms, S and Plett, KL and Plett, JM},
title = {Amino acid biostimulant increases radiata pine photosynthetic efficiency and growth with shifts in mycobiome and nitrogen assimilation.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-025-00835-x},
pmid = {41392171},
issn = {2524-6372},
abstract = {BACKGROUND: Amino-acid biostimulants have emerged as powerful alternatives to conventional inorganic nitrogen fertilisers, yet their potential in forestry species like radiata pine (Pinus radiata) remains largely unexplored. In this study, we reveal physiological mechanisms of enhanced growth of radiata pine seedlings that are achieved by substituting standard inorganic fertigation, either partially or entirely, with amino-acid-based biostimulants.

RESULTS: Amino-acid fertigation notably increased shoot biomass, plant height, and root collar diameter. Critically, this approach reshaped the root fungal community, selectively enriching fungi with diverse ecological roles, including several taxa known for auxin production. These microbial shifts coincided with higher needle auxin, a plausible link that merits testing. Machine learning models further identified key fungal genera that strongly associated with plant biomass, reinforcing microbiome shifts as a contributing mechanism to enhanced growth. Additionally, amino-acid fertigation improved nitrogen assimilation, correlating positively with increased chlorophyll content and photosynthetic efficiency.

CONCLUSIONS: Our findings highlight that the transition from inorganic source to amino-acid biostimulants not only enhances plant growth and nitrogen use but also associated with a shift in the root mycobiome, including taxa often considered beneficial, thereby offering a sustainable pathway to nursery production of radiata pine.},
}

@article {pmid41392089,
year = {2025},
author = {Wilson, BC and Tweedie-Cullen, RY and Albert, BB and Derraik, JGB and Ho, D and Depczynski, M and Creagh, C and Edwards, T and Gali, S and Thabrew, H and Cutfield, WS and O'Sullivan, JM},
title = {Encapsulated faecal microbiota transfer in young women with anorexia nervosa: an open-label feasibility pilot trial.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-67267-6},
pmid = {41392089},
issn = {2041-1723},
abstract = {Perturbations of the gut microbiome have been associated with anorexia nervosa (AN) suggesting microbiome-modulation treatments, like faecal microbiota transfer (FMT), may offer therapeutic benefits. This open-label feasibility pilot trial evaluated the tolerability and microbiological impact of encapsulated, multi-donor FMT in 18 young women with AN (Registration: ACTRN12621001504808). Participants completed clinical and microbiome assessments at enrolment (3 weeks pre-treatment), baseline, and 3, 6, and 12 weeks post-treatment. Fifteen participants completed FMT, and 11 completed the final follow-up. The primary outcome was the change in gut microbiome composition from baseline to 3 weeks compared with natural variation between enrolment and baseline. FMT produced a significantly greater shift post-treatment (mean ± SD Bray-Curtis dissimilarity 0.36 ± 0.11; p = 0.0007), with participants gaining 38 ± 16 new species. Donor-derived strains comprised 41 ± 12% of the microbiome at 3 weeks, with engraftment persisting at 6 and 12 weeks. FMT was generally well tolerated; adverse events were mostly mild to moderate and overlapped with typical AN symptomatology. Monitoring of clinical outcomes supported the safety profile and suggested potential improvements in anxiety and metabolic parameters; however, the small sample and absence of a control arm preclude safety and efficacy inference. Overall, these findings warrant further investigation through randomised controlled trials in AN.},
}

@article {pmid41391848,
year = {2025},
author = {Manea, E and Galand, PE and Comeau, S and Ferrier-Pagès, C and Giordano, B and Pezzolesi, L and Raina, JB and Elahee Doomun, SN and Tignat-Perrier, R and Bramanti, L},
title = {Positive Interactions Under Ocean Warming and Acidification: Crustose Coralline Algae Holobionts Enhance Gorgonian Larval Settlement Under Climate Change.},
journal = {Environmental microbiology},
volume = {27},
number = {12},
pages = {e70217},
doi = {10.1111/1462-2920.70217},
pmid = {41391848},
issn = {1462-2920},
support = {101062275//HORIZON European Union programme Marie-Sklodowska Curie Actions/ ; //Prince Albert II of Monaco Foundation/ ; //Scholarship from the University of Cagliari/ ; CA20102//COST Action MAFWORLD/ ; },
mesh = {Animals ; Larva/growth & development/physiology/microbiology ; *Climate Change ; *Anthozoa/microbiology/physiology/growth & development ; Hydrogen-Ion Concentration ; *Rhodophyta/physiology/microbiology ; Bacteria/classification/genetics/isolation & purification/metabolism ; *Seawater/chemistry/microbiology ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; Microbiota ; Global Warming ; Oceans and Seas ; },
abstract = {Crustose coralline algae (CCA) and their bacterial communities can emit chemical cues favoring coral larval settlement. Indeed, larvae of Eunicella singularis (white gorgonian) preferentially settle on CCA. Here, we investigated the effect of two Mediterranean CCA holobionts, Macroblastum dendrospermum and Lithophyllum stictiforme, on E. singularis larvae settlement and their bacterial communities, after warming and acidification treatments. We exposed CCA to temperature and pH expected for 2100 (SSP5-8.5) and to a marine heatwave event. Larval settlement increased 1.8-2.7 times in the presence of CCA exposed to warming and acidification compared to non-exposed CCA. High abundance of bacteria belonging to the Pirellulaceae family was observed in all CCA, while a higher abundance of monosaccharides was found in exudates of exposed CCA. Based on CCA-related 16S rDNA metabarcoding and metabolomics results, we hypothesize that the enhanced larval settlement was driven by the Pirellulaceae breakdown and utilization of CCA polysaccharides, in combination with polysaccharide release through the CCA cell walls likely augmented by decalcification. Furthermore, CCA acted as sources of bacterial taxa that may establish and persist in the adult E. singularis holobiont, independently of climate change effects. We conclude that CCA are key for E. singularis recruitment success, especially under future climate conditions, and contribute to their microbiome development.},
}

Animals
Larva/growth & development/physiology/microbiology
*Climate Change
*Anthozoa/microbiology/physiology/growth & development
Hydrogen-Ion Concentration
*Rhodophyta/physiology/microbiology
Bacteria/classification/genetics/isolation & purification/metabolism
*Seawater/chemistry/microbiology
RNA, Ribosomal, 16S/genetics
Symbiosis
Microbiota
Global Warming
Oceans and Seas

@article {pmid41391818,
year = {2025},
author = {Zhou, H and Gao, and Wu, B and Xu, G and Tian, L and Sun, Y and Yang, F and Ni, K},
title = {Phyllosphere microbiomes in grassland plants harbor a vast reservoir of novel antimicrobial peptides and biosynthetic diversity.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.12.017},
pmid = {41391818},
issn = {2090-1224},
abstract = {INTRODUCTION: The phyllosphere microorganisms colonizing plant surface harbor capacities to synthesize diverse specialized metabolites that mediate communication and interactions with environment and host. However, most known metabolites are derived from a few culturable microorganisms, and the genomic diversity and biosynthetic potential of the vast majority of bacteria associated with plants remain largely unexplored.

OBJECTIVES: Here, we aim to explore the genome architecture, biosynthetic ability, and host specific adaptability of grassland ecosystems, uncovering new perspectives on grassland phyllosphere microbial resources.

METHODS: We employed ultra-deep metagenomic sequencing, functional analysis, host-associated characterization, and bioactivity assays to explore the phyllosphere microbiome across 221 grassland plant samples representing 45 families. This approach revealed host preference in biosynthetic gene clusters (BGCs) and validated the antimicrobial efficacy of phyllosphere-derived antimicrobial peptides (AMPs).

RESULTS: Grassland plant phyllosphere microbiomes encode diverse BGCs. We identified 885,396 potential AMPs from over 68 million non-redundant gene sequences. Then, we reconstructed hundreds of near-complete genomes from phyllosphere metagenomes, and 32.61 % of reconstructed genomes were identified as unclassified genomes, primarily within Pseudomonadota, Actinomycetota, Bacillota and Bacteroidota phyla. Of the near-complete genomes, 91.97 % of the BGCs and 99.76 % of the identified AMPs were previously uncharacterized. Host phylogenetic analysis revealed functional divergence. Poaceae-associated Pseudomonas genomes contain an average of 28 BGCs, significantly higher than those in Asteraceae-associated genomes (mean = 14.76, P = 0.033). Similarly, Poaceae-associated Pantoea genomes carried an average of 9 BGCs, exhibiting significant enrichment compared to genomes from Asteraceae (mean = 7.13, P = 6.1e-05), Lamiaceae (mean = 7, P = 0.015), Ranunculaceae (mean = 8.22, P = 0.0053), and Rosaceae (mean = 7.75, P = 0.00069). ParaFit analyses further confirmed that host phylogeny significantly structures microbial functional repertoires, with intra-family hosts sharing more KEGG pathways than inter-family hosts. These results suggest that host evolutionary relationships are associated with metabolic specialization in phyllosphere microbiomes. All 13 AMPs synthesized via solid-phase peptide synthesis demonstrated antimicrobial activity, inhibiting the growth of at least one tested bacterial strain.

CONCLUSION: This study demonstrates the promise of grassland plant phyllosphere microbiome as a rich source for novel antimicrobial agents.},
}

@article {pmid41391800,
year = {2025},
author = {Li, Y and Li, J and Zhang, F and Liang, Z and Lan, M and Kang, W and Zhang, Y},
title = {The gut-liver axis mediates the protective effect of Cinnamomum chago polysaccharide against acute liver injury: Insights from integrated microbiome and metabolomics analysis.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {149679},
doi = {10.1016/j.ijbiomac.2025.149679},
pmid = {41391800},
issn = {1879-0003},
abstract = {Cinnamomum chago B. S. Sun et H. L. Zhao polysaccharide (CCP) was evaluated for its hepatoprotective effects against carbon tetrachloride (CCl4)-induced acute liver injury (ALI). The results demonstrated that CCP improved liver histopathology in ALI mice, significantly decreased serum biochemical indicators of liver injury, and enhanced hepatic antioxidant capacity. Western blot analysis further revealed that CCP activated the Nrf2/NQO1 signaling pathway, thereby strengthening the antioxidant defense system and alleviating liver damage. Untargeted metabolomics and gut microbiota profiling indicated that CCP increased linoleic acid levels through the biosynthesis of unsaturated fatty acids pathway. The elevated linoleic acid promoted the abundance of Lactobacillus in the gut microbiota, and metabolites produced from their interaction further enhanced systemic antioxidant capacity. Moreover, the CCP-induced increase in linoleic acid activated the hepatic Nrf2 signaling pathway, contributing to the improvement of liver injury. In conclusion, the gut-liver axis plays a crucial protective role in liver health, and the hepatoprotective effects of CCP are mediated by Lactobacillus and linoleic acid through activation of the hepatic Nrf2/NQO1 signaling pathway.},
}

@article {pmid41391761,
year = {2025},
author = {Liu, X and Hu, Y and An, J and Zhang, C and Tan, J and Wei, Y and Zhang, Y},
title = {A pathway for D-cysteinolate degradation in sulfate- and sulfite-reducing bacteria.},
journal = {The Journal of biological chemistry},
volume = {},
number = {},
pages = {111055},
doi = {10.1016/j.jbc.2025.111055},
pmid = {41391761},
issn = {1083-351X},
abstract = {Sulfonates, characterized by a C-SO3[-] moiety, are widespread in the environment. Sulfate- and sulfite-reducing bacteria (SRB) degrade many naturally occurring sulfonates to produce H2S, playing a vital role in sulfur metabolism in anaerobic environments, including the human gut. One of the most abundant sulfonates in marine environments is D-cysteinolate, which functions as an osmolyte in many marine organisms, though mechanisms for its anaerobic degradation remain unknown. Here, we identify and characterize a gene cluster encoding a D-cysteinolate degradation pathway, found in SRB from both environmental sources and the human gut. In this pathway, D-cysteinolate is first epimerized by a PLP-dependent cysteinolate racemase and oxidized by L-cysteinolate dehydrogenase to produce L-cysteate. Subsequent degradation by the recently characterized PLP-dependent enzymes cysteate racemase and D-cysteate sulfo-lyase yields ammonia, pyruvate, and sulfite, for further reduction to H2S. Given the abundance of cysteinolate in marine-derived foods, our study lays the foundation for further exploring its role in H2S production within the human gut microbiome.},
}

@article {pmid41391742,
year = {2025},
author = {Cui, G and Wu, X and Lei, X and Huang, K and Lü, F and He, P and Xu, Q},
title = {Bioaugmentation influences PBAT biodegradation patterns during composting through associated shifts in plastisphere communities and surface properties.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133792},
doi = {10.1016/j.biortech.2025.133792},
pmid = {41391742},
issn = {1873-2976},
abstract = {The plastisphere microbiome plays a critical yet incompletely resolved role in the biodegradation of bioplastics during aerobic composting. Here, we investigated the degradation of poly(butylene adipate-co-terephthalate) (PBAT) by integrating surface physicochemical characterization with high-throughput microbial profiling under simulated industrial composting conditions. Inoculant amendment significantly enhanced PBAT degradation, yielding a 12.7 % carbon loss compared with 3.2 % in the control. Gel permeation chromatography further confirmed polymer depolymerization, showing pronounced declines in molecular weight (particularly Mz). These structural changes were accompanied by accelerated ester bond hydrolysis, reflected by reduced water contact angle and attenuation of the CO stretching peak. Plastisphere succession revealed that inoculants reshaped surface-associated communities, increasing α-diversity and selectively enriching thermophilic taxa. Temporal community shifts suggested stage-dependent contributions, with hydrolytic genera (Bacillus, Lactobacillus) dominating the thermophilic phase, whereas oxidative taxa (Pseudomonas) became more prominent during maturation. Neutral community model analysis indicated that plastisphere assembly followed a largely deterministic pattern linked to compost stabilization parameters. Although direct functional validation was not performed, the study reveals correlated changes among PBAT depolymerization, surface hydrolysis/oxidation, and plastisphere restructuring. On this basis, we propose a conceptual degradation framework while emphasizing that specific enzymatic pathways and microbial functions require future confirmation. These findings advance understanding of biopolymer-microbe interactions and provide guidance for optimizing inoculant-assisted composting of biodegradable plastics.},
}

@article {pmid41391696,
year = {2025},
author = {Jiang, Q},
title = {The effects of different forms of vitamin E on gut microbiota, mechanisms and implications in disease prevention.},
journal = {The Journal of nutritional biochemistry},
volume = {},
number = {},
pages = {110235},
doi = {10.1016/j.jnutbio.2025.110235},
pmid = {41391696},
issn = {1873-4847},
abstract = {The gut microbiota plays an important role in host health and dysbiosis contributes to disease development. Natural forms of vitamin E consist of eight lipophilic antioxidants, i.e., alpha-, beta-. gamma- and delta-tocopherol (αT, βT, γT and δT) and alpha-, beta-. gamma- and delta-tocotrienol (αTE, βTE, γTE and δTE). Vitamin E forms and their metabolites including 13'-carboxychromanols (13'-COOHs) have been shown to possess anti-inflammatory activities. Interestingly, recent human and animal studies reveal that vitamin E forms and δTE-13'-COOH (metabolite of δTE) can modulate gut microbiota. Specifically, supplementation of αT, γT, tocotrienols or δTE-13'-COOH elevated some beneficial bacteria or attenuated disease-associated decrease of probiotics including butyrate producers. This review focuses on the current knowledge of the effects of different forms of vitamin E and δTE-13'-COOH on gut microbiome. Although the mechanisms underlying modulation of gut microbiota remain to be determined, this author proposes that promotion of beneficial gut microbes by vitamin E forms may in part be rooted in their antioxidant and anti-inflammatory activities as well as protection of intestinal barrier integrity, and that the modulatory effects on gut microbes likely contributes to vitamin E-facilitated disease prevention. Finally, this review discusses knowledge gaps and future research efforts needed to uncover how vitamin E forms interact with gut microbiota and utilize such knowledge for improving human health.},
}

@article {pmid41391685,
year = {2025},
author = {Wang, H and Qiao, Y and Lu, H and Bo, X and Chen, F and Pu, N and Zhou, Y and Cheng, Q},
title = {Central integration mechanisms of neurovascular unit dysfunction and novel synergistic therapeutic strategies.},
journal = {Neurobiology of disease},
volume = {},
number = {},
pages = {107224},
doi = {10.1016/j.nbd.2025.107224},
pmid = {41391685},
issn = {1095-953X},
abstract = {The neurovascular unit (NVU) is a highly integrated multicellular complex composed of neurons, astrocytes, microglia, brain microvascular endothelial cells (BMECs), pericytes, and the extracellular matrix (ECM). It forms the structural and functional basis of the blood-brain barrier (BBB) and is pivotal for maintaining the homeostasis of the brain. Traditional neuroprotective strategies targeting individual cell types have shown limited efficacy in central nervous system (CNS) diseases, mainly due to the neglect of intricate intercellular crosstalk within the NVU. In this review, we first systematically summarize the core mechanisms by which the NVU functional unit causes NVU dysfunction in representative acute CNS injuries (ischemic/hemorrhagic stroke, traumatic brain injury), neurodegenerative diseases (Alzheimer's disease, Parkinson's disease, multiple sclerosis), and systemic diseases (diabetic encephalopathy, depression). Based on this, we innovatively summarize and clarify six major cross-disease pathological mechanisms of NVU dysfunction, including intercellular communication disorders, abnormal epigenetic modifications, microbiome-NVU interaction dysregulation, metabolic reprogramming dysfunction, neuroimmune-vascular coupling imbalance, and mechanical microenvironment imbalance. Additionally, we integrate emerging NVU models (co-culture systems, organoids, microfluidic chips, 3D bioprinting) with multi-omics technologies to establish a cross-scale dynamic research paradigm, and propose multicomponent coordinated regulatory strategies for NVU-targeted therapies. This framework aims to expand the understanding of NVU-centered pathological processes across diverse CNS diseases and provides a novel theoretical basis for precise therapeutic interventions, thereby bridging the gap between basic research and clinical translation.},
}

@article {pmid41391096,
year = {2025},
author = {Ingawale, S},
title = {The Epigenome-Microbiome Axis: Host Regulation of Gut Ecology.},
journal = {The Journal of the Association of Physicians of India},
volume = {73},
number = {12},
pages = {95-96},
doi = {10.59556/japi.73.1257},
pmid = {41391096},
issn = {0004-5772},
}

@article {pmid41391055,
year = {2025},
author = {An, X and Niu, S and Al, MA and Su, E and Chen, L and He, H and Wang, Y and Zhang, S and Yang, Y and Wang, S and Wen, Z and Xu, B and Ming, Y and Zhu, W and Zhao, Z and Wu, K and Yang, Y and Xie, W and He, Z and Yan, Q},
title = {Dietary macroalgae enhances amino acid metabolism via intestinal Shewanella in grass carp (Ctenopharyngodon idella).},
journal = {Advanced biotechnology},
volume = {3},
number = {4},
pages = {36},
pmid = {41391055},
issn = {2948-2801},
support = {2320004002504//Zhuhai Industry-University-Research Cooperation Project/ ; SML2021SP203//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; SML2024SP002//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; SML2024SP022//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; },
abstract = {The gut microbiome plays pivotal roles in the host's metabolic response to dietary interventions. Dietary macroalgae supplementation represents a promising strategy for enhancing animal growth and health via microbiome modulation. However, the underlying mechanism of how macroalgae supplementation regulates microbiome-host interactions in aquatic species remains unclear. This study investigated the effects of three dietary macroalgae-Sargassum hemiphyllum (S), Asparagopsis taxiformis (A), and Gracilaria lemaneiformis (G)-each supplemented at 5% in feed, on the gut microbiome and metabolism of grass carp (Ctenopharyngodon idella), using integrated approaches of 16S rRNA sequencing, metagenomics, and metabolomics. While all three macroalgae influenced host growth, supplementation of S provided the most comprehensive benefits, with significant enhancement of body weight and hepatic superoxide dismutase activity. Integrated multi-omics analysis revealed that dietary macroalgae supplementation increased the relative abundance of the key gut bacterial genus Shewanella, with the most notable effect observed in the supplementation of S. Subsequent analysis of a metagenome-assembled genome (MAG) of Shewanella (MAG C3_bin52) demonstrated its considerable potential for amino acid biosynthesis and metabolism. This genomic potential was further supported by metabolomic profiling, which indicated significant upregulation of amino acid-related metabolites, particularly in the supplementation S. Pathway analysis confirmed enrichment in processes associated with protein digestion and absorption, amino acid biosynthesis, and related metabolic pathways. These findings highlight the modulation of a macroalgae-microbiome-metabolite axis in grass carp, primarily mediated by the enrichment of Shewanella in gut ecosystem for enhancing host amino acid metabolism. This study advances understanding of dietary modulation of the gut microbiome and provides insights for the sustainable development of aquaculture.},
}

@article {pmid41248092,
year = {2025},
author = {Richie, T and Lee, STM},
title = {Decoding the Gut Microbiota: Mechanisms of Host-Microbe Interactions and Inflammatory Pathologies.},
journal = {Digestion},
volume = {},
number = {},
pages = {1-18},
doi = {10.1159/000549457},
pmid = {41248092},
issn = {1421-9867},
abstract = {BACKGROUND: Microbes residing in the gastrointestinal tract are intertwined with the immune development and overall health of the host throughout stages of life. It is well established that these microbes can have both positive and negative impacts on host health. Having foundational knowledge of these interactions with the host is critical in understanding gastrointestinal health.

SUMMARY: This review discusses the importance of high-resolution study of the gut microbiota, which includes potential modern approaches for analyzing the gut microbiota and considers the challenges and aspects necessary for robust investigation of the gut microbiota. Here, we highlight the complex and highly individualized relationship of microbes interacting within the host results in an ever-changing landscape in the gastrointestinal tract, whether due to host conditions or microbial conditions including microbe-microbe and microbe-host interactions. The vastness and complexity of the gut microbiota contribute to the challenge of quantifying not only a community of microbes in the gut environment, but also maintaining resolution to investigate individual microbes, capturing the network of interactions coinciding in the gastrointestinal tract. Furthermore, the review emphasizes the importance of microbial functions and products to host health outcomes in the context of inflammatory diseases.

KEY MESSAGES: Consideration for microbial functions and interactions with the gut immune system is critical for developing effective treatment strategies of inflammatory disorders. Employing high-resolution microbial techniques to investigate microbes with environmental relevance and community functions are a major challenge in the microbiome field. With new techniques and improvements on existing methodologies, investigating microbes at various community levels is feasible and becoming critical in understanding the community interactions with the host influencing the immune status and overall health outcomes.},
}

@article {pmid41390863,
year = {2025},
author = {Tran, L and Deckers, TB and Ho, J and Lansing, L and Cunningham, M and Morfin, N and Pepinelli, M and De la Mora, A and Conflitti, IM and Gregoris, A and Wu, L and Trepanier-Leroux, D and Muntz, L and Newman, T and Vishwakarma, S and Bixby, M and Jabbari, H and Guzman-Novoa, E and Hoover, SE and Currie, RW and Pernal, SF and Giovenazzo, P and Foster, LJ and Zayed, A and Ortega Polo, R and Guarna, MM},
title = {Neonicotinoid-induced signature dysbiosis identified via metagenomic sequencing of the honey bee gut microbiome.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-30907-4},
pmid = {41390863},
issn = {2045-2322},
support = {Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; },
}

@article {pmid41390845,
year = {2025},
author = {Romero, F and Labouyrie, M and Orgiazzi, A and Ballabio, C and Panagos, P and Jones, A and Tedersoo, L and Bahram, M and Eisenhauer, N and Sünnemann, M and Guerra, CA and Tao, D and Rog, I and Jiao, S and Mocali, S and Rillig, MC and Lehmann, A and Delgado-Baquerizo, M and van der Heijden, MGA},
title = {The soil microbiome as an indicator of ecosystem multifunctionality in European soils.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-67353-9},
pmid = {41390845},
issn = {2041-1723},
abstract = {The role of soil microorganisms in supporting multiple ecosystem functions (multifunctionality) remains poorly understood across diverse environmental conditions. Here, we investigate 484 soils from 27 European countries spanning a range of climatic and edaphic contexts. We assess the contribution of climate, soil properties, and soil microbiome traits (i.e., the relative abundance of co-occurring taxa) to explain six key functional proxies related to soil structure, biochemical activity, and productivity. We find the highest multifunctionality values in grasslands, woodlands, loamy and acidic soils, and temperate humid regions, and the lowest in croplands, alkaline soils, and drier regions. Soil properties explain 12-31% of variation in multifunctionality, with microbial biomass and nitrogen content emerging as the strongest predictors. The soil microbiome accounts for 2-14% of unique variance in multifunctionality but explains more than 25% of variation in enzymatic activities and primary productivity in clay-rich soils and soils originating from temperate dry regions. Specific taxa, particularly within Actinobacteria, Acidobacteria, and the fungal genus Mortierella consistently emerge as strong predictors of ecosystem multifunctionality. Our findings highlight that ecosystem multifunctionality is jointly shaped by soil properties and microbial communities. We argue that specific taxa hold potential as context-dependent indicators for multifunctionality monitoring across environmental gradients.},
}

@article {pmid41390780,
year = {2025},
author = {Bommana, S and Olagoke, O and Hu, YJ and Wang, R and Kama, M and Dehdashti, M and Kodimerla, R and Read, TD and Dean, D},
title = {Azithromycin alters the microbiome composition, function and resistome in women with Chlamydia trachomatis infections.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-025-00858-9},
pmid = {41390780},
issn = {2055-5008},
support = {R01 AI151075/AI/NIAID NIH HHS/United States ; R01 AI151075/AI/NIAID NIH HHS/United States ; },
abstract = {Antibiotics disrupt mucosal microbial communities, yet the effects on microbiomes infected with Chlamydia trachomatis (Ct) remain poorly understood. Some data exist on vaginal microbiomes, but none exist for the endocervix or rectum that are primary sites of infection. We applied metagenomic shotgun sequencing to vaginal, endocervical and rectal samples collected longitudinally from women who cleared their infection post-treatment (n = 10), had persistent infection (n = 11), or remained uninfected (n = 18) to evaluate azithromycin-induced changes in microbial composition, function, and the resistome over time. Our results show shifts in composition and function post-treatment that support persistent Ct, nonsynonymous Ct L22 amino acid substitutions that may be linked to azithromycin resistance, and significant endocervical increases in azithromycin resistance genes in Lactobacillus iners and Gardnerella vaginalis strains with moderate/high biofilm formation potential. These findings highlight the unintended ecological consequences of azithromycin treatment, including likely resistance gene propagation, emphasizing the need for novel treatment and microbiome-preserving strategies.},
}

@article {pmid41390744,
year = {2025},
author = {Malik, K and Jousselin, E and Clamens, AL and Sugimoto, S and Wieczorek, K},
title = {Molecular phylogeny of the Acer-feeding aphid subfamily Drepanosiphinae (Insecta: Hemiptera: Aphididae) and the evolution of its endosymbiotic consortia.},
journal = {Zoological letters},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40851-025-00255-2},
pmid = {41390744},
issn = {2056-306X},
}

@article {pmid41390665,
year = {2025},
author = {Cotto, I and Albán, V and Durán-Viseras, A and Jesser, KJ and Zhou, NA and Hemlock, C and Ballard, AM and Fagnant-Sperati, CS and Lee, GO and Hatt, JK and Royer, CJ and Eisenberg, JNS and Trueba, G and Konstantinidis, KT and Levy, K and Fuhrmeister, ER and , },
title = {Environmental exposures associated with the gut microbiome and resistome of pregnant women and children in Northwest Ecuador.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66567-1},
pmid = {41390665},
issn = {2041-1723},
support = {P30 ES007033/ES/NIEHS NIH HHS/United States ; R01AI162867//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 2127509//American Society for Engineering Education (ASEE)/ ; },
abstract = {Inadequate water, sanitation, and hygiene (WASH) infrastructure may increase exposure to antimicrobial resistance (AMR). In addition, close human-animal interactions and unregulated antibiotic use in livestock facilitate the spread of resistant bacteria. We use metagenomic sequence data and multivariate models to assess how animal exposure and WASH conditions affect the gut resistome and microbiome in 53 pregnant women and 84 children in Ecuador. Here we show improving WASH infrastructure and managing animal exposure may be important in reducing AMR but could also reduce taxonomic diversity in the gut. Escherichia coli, Klebsiella pneumoniae, and clinically relevant antimicrobial resistance genes (ARGs) are detected across all age groups, but the highest abundance is found in children compared to mothers. In mothers, higher animal exposure trends towards a higher number of unique ARGs compared to low animal exposure and is significantly associated with greater taxonomic diversity. In addition, mothers with sewer systems or septic tanks and piped drinking water have fewer unique ARGs compared to those without, and mothers with longer duration of drinking water access have lower total ARG abundance. In contrast, few associations are observed in children, likely due to the dynamic nature of the gut microbiome during early childhood.},
}

@article {pmid41390664,
year = {2025},
author = {Cao, Q and Deng, Z and Li, M and Zhu, S and Huo, Y and Dong, H and Aernouts, B and Psifidi, A and Xu, C},
title = {Integrated metagenomic and metabolomic analyses reveal tenacissoside G as a potential non-antimicrobial treatment for bovine endometritis.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02264-x},
pmid = {41390664},
issn = {2049-2618},
support = {No. 2024B02016//the Key Research and Development Program of the Xinjiang Uygur Autonomous Region/ ; 32125038//the National Natural Science Foundation of China/ ; 2023YFD1801100//National Key Research and Development Program of China/ ; CARS-36//China Agriculture Research System/ ; },
abstract = {BACKGROUND: Bovine endometritis is a prevalent uterine disease that directly curtails reproductive performance and indirectly reduces milk production by increasing calving intervals. Postpartum uterine bacterial infection is the primary cause of bovine endometritis, which is typically treated with prostaglandin F2α and antimicrobials. However, abuse of antimicrobials has led to the emergence of multidrug-resistant bacteria, threatening both human and animal health. To explore alternatives to antimicrobial therapy for bovine endometritis, we integrated uterine metagenomic and metabolomic analyses and identified a novel bioactive metabolite with therapeutic potential. The potential antibacterial and anti-inflammatory effects of this metabolite against bovine endometritis were evaluated by assessing its inhibitory effect on the growth of F. necrophorum in vitro, and by quantifying histopathological scores and inflammatory cytokine expression levels in an in vivo mouse model of endometritis, respectively.

RESULTS: A total of 40 Holstein dairy cows at 21 days to 30 days postpartum were assigned into heathy cows (n = 15), subclinical endometritis cows (n = 12) and clinical endometritis cows (n = 13) according to clinical signs and laboratory tests for bovine endometritis. The uterine fluid was collected aseptically for metagenomics and metabolomics sequencing to identify bacterial species associated with bovine endometritis and metabolites that could potentially be used for treatment of bovine endometritis. A total of 17 bacterial species were significantly associated with bovine endometritis, with Fusobacterium necrophorum as the most significantly enriched in cows with clinical endometritis compared to healthy counterparts. In total, 391 metabolites were significantly differentially abundant between healthy and clinical endometritis cows. Among these, a plant-derived compound, tenacissoside G was significantly enriched in healthy cows. Notably, the abundance of F. necrophorum was significantly negatively associated with the concentration of tenacissoside G in clinical endometritis cows. Moreover, tenacissoside G significantly inhibited the growth of F. necrophorum in vitro and ameliorated inflammation in endometritis caused by F. necrophorum in a mice model.

CONCLUSION: This study provides new insights into the relationship between uterine microbiome and metabolites in bovine endometritis, potentially leading to novel strategies for treating bovine endometritis. Furthermore, tenacissoside G exhibits therapeutic effects against endometritis induced by F. necrophorum, and could serve as a potential alternative to antimicrobials for treating endometritis. Video Abstract.},
}

@article {pmid41390654,
year = {2025},
author = {Manzoor, H and Jabeen, I and Saeed, MT and Kayani, MUR and Huang, L},
title = {Metagenomic analyses reveal E. coli-derived siderophores as potential signatures for breast cancer.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-025-07513-z},
pmid = {41390654},
issn = {1479-5876},
}

@article {pmid41390642,
year = {2025},
author = {Vargas Ribera, PR and Parladé, J and Luque, J and Biel, C and Calvet, C and Miarnau, X and Nogales, A},
title = {Rootstock genetic background in almond cultivation influences the composition of root-associated microbial communities and enrichment of taxa associated with plant defense and nutrient availability.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-025-07895-8},
pmid = {41390642},
issn = {1471-2229},
support = {TED2021-130185B-I00//European Union NextGenerationEU/PRTR/ ; TED2021-130185B-I00//European Union NextGenerationEU/PRTR/ ; TED2021-130185B-I00//European Union NextGenerationEU/PRTR/ ; TED2021-130185B-I00//European Union NextGenerationEU/PRTR/ ; TED2021-130185B-I00//European Union NextGenerationEU/PRTR/ ; TED2021-130185B-I00//European Union NextGenerationEU/PRTR/ ; TED2021-130185B-I00//European Union NextGenerationEU/PRTR/ ; },
abstract = {BACKGROUND: Beneficial root microorganisms play a crucial role in influencing key agronomic traits in rootstocks. However, little is known about the microbial communities naturally associated with almond rootstocks in Spain. To address this gap, we sampled roots of six commercial Prunus rootstocks in a 15-year-old almond orchard representing two different genetic backgrounds: P. cerasifera background (PCB) with Rootpac[®] 20, and Rootpac[®] R; and P. persica background (PPB), with Cadaman, Garnem, GF677, and Rootpac[®] 40. Root-associated bacterial, fungal, and arbuscular mycorrhizal fungi communities were evaluated applying a metabarcoding approach.

RESULTS: Bacterial and fungal communities differed according to the genetic background of the rootstocks. Roots of PCB rootstocks were significantly enriched with amplicon sequence variants (ASVs) identified as Streptomyces, which contain bacterial species known as biocontrol agents. In contrast, PPB rootstocks were significantly enriched with ASVs identified as Hyalorbilia, Rhizoglomus, and Entrophospora, the first one being an ascomycete known for its nematophagous activity, and the two latter for their role as mycorrhizal fungi. Interestingly, taxa including known fungal plant pathogens were significantly enriched in PCB rootstocks, namely ASVs included in Venturiales and Nectriaceae (Hypocreales). Moreover, in PCB rootstocks we identified bacterial and fungal ASVs that were positively correlated with N and P soil concentrations, respectively, thus suggesting their potential role in enhancing nutrient availability for plants. Similarly, a number of bacterial and fungal ASVs were positively and highly correlated with soil Na concentration among PPB rootstocks.

CONCLUSION: These results suggest that the genetic background of the rootstock may influence bacterial and fungal taxa recruitment in field conditions, thus potentially influencing nutrient cycling and plant defense.},
}

@article {pmid41390545,
year = {2025},
author = {Guo, N and Gou, N and Shi, F and Wang, W and Li, S and Bi, S and Jiao, J and Luo, B and Huang, M and Degen, AA and Shang, Z},
title = {Short-chain fatty acids mediate interactions between immune responses and commensal bacteria in high altitude yaks.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-025-09351-7},
pmid = {41390545},
issn = {2399-3642},
support = {U21A20183//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32471581//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {The complex interplay between host and commensal gut microbiota affects the major biological functions such as metabolism and stress adaptation, and displays pronounced seasonality in mammals. However, the seasonal dynamic patterns of immune responses and microbiota, and their interactions remain uncertain in animals inhabiting extreme environments. We analyzed monthly hormones, immunoglobulins and fecal microbiota from yaks grazing on the Tibetan plateau. Clear seasonal patterns were observed: glucocorticoid levels peaked in the cold season, while concentrations of IgA, IgG, IgM, and short-chain fatty acids (SCFAs) increased during the warm season. Yak fecal microbiota also fluctuated seasonally, with lowest diversity in the warm season but accompanied by an enrichment of Firmicutes and Actinobacteria. Taxa such as Alistipes, Bacteroides, Romboutsia and Arthrobacter contributed to seasonal shifts in the levels of SCFAs and immunoglobulins. These results indicate that yaks synchronize peak immune activation and energy production with the nutrient-rich warm season, suggesting a role for microbiome plasticity in driving immune flexibility for high-altitude animals.},
}

@article {pmid41390520,
year = {2025},
author = {Alfaro-Núñez, A and Christensen, S and Ellehauge, J and Eriksen, JO and Andersen, G and Jensen, EA},
title = {Beyond colonoscopy, faecal DNA mutation screening provides a potential and viable path to early colorectal cancer detection.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-30802-y},
pmid = {41390520},
issn = {2045-2322},
support = {DNRF148//Danish National Research Foundation/ ; R45-A2128, A1696, and A1009//Research Fund of Naestved, Slagelse and Ringsted Hospitals/ ; R41-A1910 and Kræftplan III//Region Zealand Health Science Research Foundation/ ; },
abstract = {Colorectal cancer (CRC) remains a leading cause of cancer-related morbidity and mortality worldwide, with early detection critical for improving clinical outcomes. In Denmark's CRC screening program, nearly 60% of patients undergoing colonoscopy do not have polyps requiring treatment, highlighting the need for more sensitive and less invasive screening methods to improve early detection and reduce unnecessary procedures. In this study, we assessed the potential of two faecal DNA-based methods for detecting CRC-related mutations. Extracted DNA was analysed using next-generation sequencing (NGS) and digital PCR (dPCR). NGS targeted a gene panel covering the most frequently mutated sites in CRC, while dPCR focused on six specific CRC-associated mutations. A common limitation across both methods was the low abundance of human DNA in faecal samples, which reduced the reliability of variant detection. Nevertheless, both NGS and dPCR showed promise, particularly when DNA input was sufficient. Significant associations were observed between mutation counts and clinical diagnosis, with key CRC mutations reliably detected. The findings suggest that, with further implementation, these methods could serve as a less invasive and more cost-effective alternative to colonoscopy, especially for high-risk individuals. However, the sensitivity of both methods was limited in samples with low DNA yield, likely due to inhibitory effects during sample preservation or extraction. While faecal samples may be better suited for gut microbiome profiling, our findings underscore the potential of human DNA-based faecal screening in CRC and highlight the need for optimized extraction protocols to improve diagnostic accuracy, minimize unnecessary procedures, and provide personalized care for high-risk populations.},
}

@article {pmid41390484,
year = {2025},
author = {Song, D and Feng, G and Ma, Y and Shi, Y and Qian, C and Wang, C and Xu, J and Li, Y and Wang, X and Fan, N and Dong, W and Li, X and Fan, J and Chu, L and Gao, F and He, S and Wang, J and Wang, S and Zhou, H and Gu, Q and Wang, H and Feng, B and Zhang, H and Zhang, X and Li, L and Fan, E and Wang, Y and Wu, M and Zhang, Y and Huang, A and Teng, J and Zhu, Y and Zhai, R and Ding, X and Zhang, C and Peng, Y},
title = {Gut microbiome predicts personalized responses to dietary fiber in prediabetes: a randomized, open-label trial.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66498-x},
pmid = {41390484},
issn = {2041-1723},
abstract = {Gut microbiota contributes to prediabetes progression, however, whether microbiota features can guide targeted prevention and treatment for diabetes requires validation through large-scale clinical trials. Here, in a randomized, open-label trial, we randomly assigned 802 prediabetic subjects to a usual care control group (patient education and dietary recommendations, n = 393) or a dietary fiber intervention group (n = 409) for 6 months. The primary outcome was the percentage change in whole-blood HbA1c, and secondary outcomes were the changes in other glucose, insulin, lipid, liver and kidney function, and anthropometric parameters. There were no statistically significant differences in the primary and secondary outcomes between groups. In post-hoc analysis, we reclassified subjects into four clusters using a multivariate clustering model based on age, BMI, HbA1c, HOMA2-IR and HOMA2-B. These clusters differed in metabolic status, risks of diabetes and its complications, gut microbiome and serum metabolites. Notably, dietary fiber improved glycemic control in Clusters 3 and 4, but not in Clusters 1 and 2, consistent with observed gut microbiota alleviations. By using a LightGBM machine learning model, we calculated a microbiome-based clinical decision score to predict personalized fiber intervention responses and identified individuals who can get glycemic benefits. In conclusion, our study suggests that the gut microbiota response influences the effectiveness of dietary fiber intervention and provides a clinically applicable model to guide microbiome-targeted personalized medicine for prediabetes. Clinical Trial Registry: ChiCTR1900027663.},
}

@article {pmid41390460,
year = {2025},
author = {Sameeha, FNU and Riaz, S and Aslam, MN and Perveen, A},
title = {Association between early-life antibiotic exposure and gut microbiome alterations linked to allergic diseases in children: a systematic review.},
journal = {European journal of medical research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40001-025-03685-y},
pmid = {41390460},
issn = {2047-783X},
abstract = {BACKGROUND: Early-life exposure to antibiotics has been implicated in the disruption of gut microbiota development, potentially contributing to the onset of allergic diseases in childhood. This systematic review aimed to evaluate the association between early antibiotic exposure, gut microbiome alterations, and the risk of developing allergic conditions such as asthma, atopic dermatitis, and allergic rhinitis.

METHODS: This review followed PRISMA 2020 guidelines. A comprehensive search of PubMed, Embase, Web of Science, and the Cochrane Library was conducted up to [insert date]. Eligible studies included observational and interventional designs involving participants from the prenatal stage to 10 years of age. Data were extracted on antibiotic type, exposure timing, microbiome changes, and allergic outcomes. Study quality was assessed using the Newcastle-Ottawa Scale for observational studies and the Cochrane Risk of Bias tool for randomized trials.

RESULTS: Fifteen studies involving over 1.5 million children met the inclusion criteria. The majority reported that antibiotic exposure during the prenatal period or the first two years of life was significantly associated with an increased risk of allergic diseases, particularly asthma and atopic dermatitis. Several studies also documented alterations in gut microbiota composition, including reduced Bifidobacterium and increased Clostridium and Klebsiella spps. Antibiotic type, duration, and timing of exposure were key factors influencing microbiota disruption and allergy development.

CONCLUSION: There is growing evidence that early-life antibiotic exposure may predispose children to allergic diseases through gut microbiota disturbances. These findings support the cautious use of antibiotics during pregnancy and early childhood and underscore the need for further research into microbiota-preserving interventions and long-term outcomes.},
}

@article {pmid41390429,
year = {2025},
author = {Li, G and Jia, L and Li, J and Gao, A and Chen, X and Li, JH and Xia, LJ and Zhou, SY and Lin, YH and Yang, JT and Wan, L and He, YZ and Sun, RY and Ren, H and Lian, XL and Zhao, DH and Liao, XP and Liu, YH and Chen, L and Sun, J},
title = {Carbohydrate competition by Enterobacteriaceae enhances colonization resistance to carbapenem-resistant hypervirulent K. pneumoniae.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02245-0},
pmid = {41390429},
issn = {2049-2618},
support = {32402943//National Natural Science Foundation of China/ ; 32202859//National Natural Science Foundation of China/ ; 2025A1515012412//Guangdong Provincial Natural Science Foundation/ ; 32121004//Foundation for Innovative Research Groups of the National Natural Science Foundation of China/ ; NSF2025CB07//the school level scientific research project of JiangsuAgri-Animal Husbandry Vocational College/ ; 2019BT02N054//Local Innovative and Research Teams Project of Guangdong Pearl River Talents Program/ ; 2020B0301030007//Guangdong Major Project of Basic and Applied Basic Research/ ; D20008//the 111 Center/ ; 2023B10564003//Double First-Class Discipline Promotion Project/ ; },
abstract = {BACKGROUND: Carbapenem-resistant hypervirulent K. pneumoniae (CR-HvKP) is a growing public health threat due to its virulence and limited treatment options. While prevalent in hospitals, its presence in livestock, particularly pigs, is poorly understood. The gut microbiome provides colonization resistance, but how it restricts CR-HvKP remains unclear.

RESULTS: To further elucidate the colonization resistance mechanisms of the gut microbiota against CR-HvKP, we analyzed stool samples from piglets (L), nursery (N), fattening (F), and sows (PS) using microbiome modeling (Micolo) and competition assays. ST290 K. pneumoniae isolated from PS inhibited CR-HvKP via carbohydrate competition, with a pronounced effect observed for sucrose. Niche-specific supplementation with methyl pyruvate was found to partially alleviate this ecological inhibitory effect.

CONCLUSIONS: Carbohydrate-based interventions could be explored as potential therapeutic or prophylactic strategies to combat CR-HvKP colonization, thereby potentially improving animal and public health outcomes. Video Abstract.},
}