@article {pmid41270896,
year = {2025},
author = {Diakité, MT and Sun, S and Somboro, AM and Diakité, B and Koné, A and Kassogué, Y and Fofana, D and Balam, S and Traoré, CB and Maiga, A and Kamaté, B and Ba, D and Diarra, M and Boré, S and Maiga, AI and Dai, Q and Nannini, DR and Holl, J and Murphy, R and Hou, L and Fodor, A and Maiga, M},
title = {Characterization of the gut microbiota in patients with stage III colorectal cancer: A case-control study.},
journal = {Gene},
volume = {},
number = {},
pages = {149913},
doi = {10.1016/j.gene.2025.149913},
pmid = {41270896},
issn = {1879-0038},
abstract = {AIM: To conduct a case-control study (pilot study) in Africa (Mali) in comparing the gut microbiota of patients with stage III colorectal cancer (CRC) using next-generation sequencing.

METHODS: Shotgun sequencing was performed to characterize participants' fecal microbiota using Illumina's HiSeq platform. This case-control study involved newly diagnosed CRC patients (n = 23) prior to any treatment initiation, and unrelated healthy controls (n = 24) to elucidate their microbial diversity and relative abundance.

RESULTS: The findings revealed that the gut microbiota in CRC and in healthy were significantly distinctive according to the PERMANOVA test (R[2] = 0.132, P = 0.001), and the alpha-diversity was significantly lower in CRC. Beta-diversity, based on principal coordinate analysis, showed a distinct taxonomy between the CRC and the healthy. Levels of Pseudomonadota, Escherichia, Citrobacter freundii, Klebsiella sp. LTGPAF-6F, Escherichia albertii, Escherichia coli, Caudovirales, Apicomplexa, and Verrucomicrobiota populations were significantly elevated in CRC. The major metabolic pathways with higher relative abundance levels found in CRC compared to healthy were related to HEMESYN2-PWY: heme biosynthesis II (anaerobic), PWY-5154:L-arginine biosynthesis III (via N-acetyl-L-citrulline), FUC-RHAMCAT-PWY: superpathway of fucose and rhamnose degradation, ECASYN-PWY: enterobacterial common antigen biosynthesis, ENTBACSYN-PWY: enterobactin biosynthesis, and AEROBACTINSYN-PWY:aerobactin biosynthesis.

CONCLUSION: Distinct gut microbiome profiles between healthy and CRC were observed. In particular, the findings showed a significant reduction in microbial diversity in stage III CRC. This study provides initial metagenomic data on Malian patients with CRC. It will be used to create a larger cohort to better understand the relationship between CRC and the gut microbiota in the Malian CRC population.},
}

@article {pmid41270740,
year = {2025},
author = {Yi, X and Cai, H and Liu, H and Xu, S and Meng, R and Rao, J and Wu, M and Yang, L and Shi, Y and Zhang, J and Zhu, T and Yang, Y and Wen, P and Qin, Y and Song, W and Li, JT and Shu, W and Dai, J and Sun, J and Lin, L and Guan, WJ and Brightling, CE and Zheng, XY and Wang, Z},
title = {Environmental exposure augments the abundance and transferability of antibiotic resistance genes in the respiratory tract.},
journal = {Cell reports},
volume = {},
number = {},
pages = {116517},
doi = {10.1016/j.celrep.2025.116517},
pmid = {41270740},
issn = {2211-1247},
abstract = {Exposure to environmental pollutants has been linked to increased antibiotic resistance, a critical global health challenge. The respiratory microbiome constitutes a key reservoir of antibiotic resistance genes (ARGs). Here, we constructed a respiratory ARG catalog from sputum metagenomes of 1,128 individuals. We demonstrate that exposures, particularly to cigarette smoke and biofuels, are associated with increased abundance and enhanced mobility of respiratory ARGs. These resistome alterations correlate inversely with lung function, with elevated mobile ARG abundance detectable even in individuals with mild airflow limitation within normal spirometry. Specific ARGs, including opmD and tet(K), interact with smoking in relation to lung function impairment. Murine experiments recapitulate these findings, showing exposure-induced increases in homologous ARGs that confer heightened phenotypic resistance in cultured respiratory bacteria. Our results elucidate a pathway through which environmental pollutants augment the respiratory resistome, suggesting the need for actions to mitigate the antimicrobial resistance burden by addressing environmental pollution.},
}

@article {pmid41270737,
year = {2025},
author = {Long, X and Wang, H and Lu, Y and Gao, X and Xiao, Y and Zhang, M and Guo, J and Yang, J and Zhang, R and Li, Q and Zhou, G and Yang, R and Chen, F and Wu, Q and Sun, L and Chu, C and Zhu, X and Wu, Z and Ren, Q and You, C and Liu, Z and Li, Q and Liu, D and Cheng, D and Kang, P and Chen, A and Wu, Q and Fang, Q and Wei, L and Zhang, L and Li, J and Panagiotou, G and Jia, W and Zeng, R and Ni, Y and Chen, L and Li, H},
title = {Interindividual variability in gut microbiome mediates the efficacy of resistant starch on MASLD.},
journal = {Cell metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmet.2025.10.017},
pmid = {41270737},
issn = {1932-7420},
abstract = {Our randomized, placebo-controlled trial showed resistant starch (RS), a type of prebiotic, has therapeutic effects in metabolic dysfunction-associated steatotic liver disease (MASLD). Here, we observed its heterogeneous efficacy, where 30% of participants exhibited limited benefits, which was replicated in a multi-center trial (ChiCTR2300074588). Multi-omics analysis and fecal microbiota transplantation identified baseline microbiota as a dominant contributor of response. Further population stratification and network analysis combined with in vitro and in vivo experiments revealed Prevotella as the key cause of low response by inhibiting RS-degrading bacteria, thereby impairing RS utilization. Conversely, Bifidobacterium pseudocatenulatum RRP01, a strain isolated from our cohort, restored RS degradation and improved Prevotella-attenuated RS response. Furthermore, we developed a predictive model integrating baseline microbial and clinical features (area under the curve [AUC] = 0.74-0.87), enabling stratification for personalized interventions. Our study indicates that gut microbiota determines the heterogeneity in RS efficacy and offers possibilities for novel microbiota-oriented precision therapeutics for MASLD.},
}

@article {pmid41270734,
year = {2025},
author = {Tibocha-Bonilla, JD and Santibáñez-Palominos, R and Weng, Y and Kumar, M and Zengler, K},
title = {Metabolism and gene expression models for the microbiome reveal how diet and metabolic dysbiosis impact disease.},
journal = {Cell systems},
volume = {},
number = {},
pages = {101451},
doi = {10.1016/j.cels.2025.101451},
pmid = {41270734},
issn = {2405-4720},
abstract = {The gut microbiome plays a critical role in human health, spurring extensive research using multi-omic technologies. Although these tools offer valuable insights, they often fall short in capturing the complexity of microbial interactions that associate with disease onset, progression, and treatment. Thus, integration of multi-omics datasets with metabolic models is needed to predict associations between microbial activity and disease. Here, we automated the reconstruction of 495 metabolic and gene expression models (ME-models), overcoming the main limitation preventing the wide use of this approach. We integrated them with multi-omics data from patients with inflammatory bowel disease (IBD), identifying taxa associated with variations in amino acids, short-chain fatty acids, and pH in the gut of IBD patients. In general, this approach provides testable hypotheses of the metabolic activity of the gut microbiota, and the automated pipeline opens the opportunity to study microbial interactions in other biologically relevant settings using ME-models.},
}

@article {pmid41270627,
year = {2025},
author = {Li, L and Huang, S and Bai, Z and Xu, H and Ji, Q and Song, W},
title = {Combined transcriptome and microbiome characterization highlights digestive system development involved in the metabolism and immunity of the large yellow croaker (Larimichthys crocea).},
journal = {Microbiological research},
volume = {303},
number = {},
pages = {128394},
doi = {10.1016/j.micres.2025.128394},
pmid = {41270627},
issn = {1618-0623},
abstract = {The development of the digestive system and its interaction with microbiota are critical for fish growth and health. Transcriptomic and 16S rRNA sequencing analyses were conducted to investigate the gene expression profiles of the digestive system and microbial community dynamics in Larimichthys crocea from the embryonic stage to day 28 to elucidate their potential roles in larval and juvenile development and their associations with immune and metabolic functions. The results revealed stage-specific changes in gene expression and microbial composition during development, and two critical transitional phases were identified: day 1 vs embryonic stage (C1 vs CE) and day 15 vs day 9 (C15 vs C9). Microbial succession demonstrated clear temporal characteristics: Pseudoalteromonas were dominant during the embryonic stage (CE), which was succeeded by Stenotrophomonas after hatching (C1, C3, C4, and C9), by Cohaesibacter on day 15 (C15), and by Psychrobacter as the core genus after formulated feed introduction on day 19. Functional enrichment analyses revealed predominant enrichment of differentially expressed genes in immune- and metabolic-related pathways, such as calcium signaling, steroid biosynthesis, and amino acid metabolism. Weighted gene co-expression network and correlation analyses revealed significant associations between specific genera (e.g., Rhodococcus and Psychrobacter) and immune- and metabolism-related genes. This study analyzed the developmental patterns of the digestive system of L. crocea and revealed significant correlations between shifts in the microbiota and host metabolism and immunity, highlighting the close association between the microbiota and metabolic and immune responses.},
}

@article {pmid41270591,
year = {2025},
author = {Zahn, G and Hjelmen, CE and Wainwright, BJ},
title = {Distinct temporal trajectories of bacterial and fungal networks during agricultural rewilding.},
journal = {The Science of the total environment},
volume = {1008},
number = {},
pages = {180999},
doi = {10.1016/j.scitotenv.2025.180999},
pmid = {41270591},
issn = {1879-1026},
abstract = {Tropical land-use change from native forests to oil palm plantations has created widespread biodiversity loss, soil degradation, and disruption of microbial communities. As rewilding initiatives emerge to restore ecosystem function in post-agricultural landscapes, understanding microbial community assembly, diversity dynamics, and interaction networks is essential for informing effective restoration strategies. However, the pace and predictability of microbial reorganization following intensive monoculture remain poorly understood, particularly in tropical systems. We examined microbial reassembly across a five-year tropical rewilding chronosequence in a former oil palm plantation, using full-length 16S and ITS amplicon sequencing, ecological network modeling, and soil chemistry analyses. Bacterial and fungal alpha diversity increased over time, though with domain-specific trajectories. Generalized dissimilarity models revealed that soil phosphorus and carbon were dominant environmental filters shaping community turnover. Co-occurrence networks showed increasing complexity over time, with bacterial networks becoming progressively more interconnected, while fungal networks exhibited earlier but less sustained restructuring. These patterns suggest that microbial community coalescence during rewilding is asynchronous, structured, and shaped by deterministic environmental filtering and legacy effects of past land use. Our results provide evidence that tropical rewilding can rapidly reorganize soil microbial communities, enhancing diversity, connectivity, and compositional structure within just a few years. Full recovery is likely to require longer time frames, these early trajectories highlight the potential for rewilding to promote functional microbial reassembly in degraded tropical systems. By identifying taxonomic and network-based indicators of microbial reorganization, this study advances our understanding of community assembly theory and offers guidance for restoration practices in post-agricultural landscapes.},
}

@article {pmid41270390,
year = {2025},
author = {Chen, L and He, W and Gao, L and Lu, Y and Zhu, L},
title = {Shouhui Tongbian Capsules ameliorate heart failure and atrial fibrillation via gut microbiota regulation.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {149},
number = {},
pages = {157549},
doi = {10.1016/j.phymed.2025.157549},
pmid = {41270390},
issn = {1618-095X},
abstract = {BACKGROUND: Heart failure (HF) with atrial fibrillation (AF) poses a significant therapeutic challenge due to its complex pathophysiology. Shouhui Tongbian Capsules (SHTB) contain multiple active components that have been proven to affect HF or AF through the intestinal flora. However, the specific therapeutic effects of this drug on HF combined with AF, as well as whether these effects are achieved by regulating the intestinal flora, still require systematic research.

PURPOSE: This study aimed to elucidate the cardioprotective effects of SHTB in a doxorubicin (DOX)-induced HF/AF rat model, focusing on gut microbiota modulation and myocardial transcriptome regulation.

METHODS: Rats were randomized into control, model (DOX-induced HF/AF), SHTB treatment (low/medium/high doses), and metoprolol groups. Pharmacodynamically, cardiac function was assessed via echocardiography and electrocardiography. And myocardial fibrosis was quantitatively evaluated using pathomorphology analysis. Mechanistically, microvascular integrity was examined via immunofluorescence, while the neural activity ligand-receptor interaction pathway-related protein expression was analyzed by immunohistochemistry. Additionally, gut microbiota composition was determined via 16S rRNA sequencing, and myocardial transcriptome profiling was performed using RNA sequencing. Furthermore, fecal microbiota transplantation (FMT) experiments were performed to validate the role of gut microbiota in the observed effects.

RESULTS: The SHTB intervention significantly improved the cardiac function and electrophysiological stability of HF/AF rats, along with enhancing microvascular maturation and reducing myocardial fibrosis. The analysis of the intestinal microbiota showed that SHTB effectively restored the microbial ecological balance, especially regulating the abundance of key genera (such as Turicibacter) closely related to disease progression and treatment efficacy. Transcriptional analysis identified the neural activity ligand-receptor pathway as the key mechanism, and FMT experiments demonstrated that SHTB modulates the Edn1-Agtr1a-Bdkrb2 axis through gut microbiota, ultimately leading to improved cardiac function. The synergistic effect of the composition of the intestinal microbiota and myocardial molecular targets jointly contributed to the improvement of cardiac remodeling in HF/AF.

CONCLUSION: SHTB ameliorates HF with AF by synergistically modulating the gut-heart axis, involving gut microbiota restoration, myocardial fibrosis suppression, and vascular tension regulation via the Edn1-Agtr1a-Bdkrb2 axis. This multi-target mechanism substantiates SHTB's potential as a promising adjunct therapy for HF/AF.},
}

@article {pmid41270103,
year = {2025},
author = {Shannon, KC and Colwell, FS and Crump, BC and Brennan, E and St John, G and Gould, R and Hartzell, C and Wasley, M and Nichols, C and Kraft, CE and Suffridge, CP},
title = {Bacimethrin, an allelopathic vitamin B1 antagonist, is linked with microbial gene expression patterns in a hypereutrophic watershed.},
journal = {PloS one},
volume = {20},
number = {11},
pages = {e0335861},
doi = {10.1371/journal.pone.0335861},
pmid = {41270103},
issn = {1932-6203},
mesh = {*Thiamine/antagonists & inhibitors/metabolism ; *Cyanobacteria/genetics/drug effects/metabolism ; Harmful Algal Bloom/drug effects ; *Gene Expression Regulation, Bacterial/drug effects ; Microbiota/drug effects/genetics ; },
abstract = {Freshwater cyanobacterial harmful algal blooms (cyanoHABs), often dominated by Aphanizomenon, Dolichospermum, and Microcystis, are intensifying in eutrophic watersheds globally. A potential control on bacterioplankton dynamics in these systems is the availability of the essential metabolic cofactor thiamin (vitamin B1) and presence of the allelopathic thiamin antagonist bacimethrin, which causes competitive inhibition of thiamin-requiring enzymes. We examined dissolved concentrations of thiamin chemical congeners and bacimethrin, 16S amplicon-based microbiome compositions, prokaryotic mRNA-based metatranscriptomes, and reference genomes in hypereutrophic Upper Klamath Basin before and during seasonal cyanoHABs. Our objective was to connect bacterioplankton community compositions and gene expression patterns with thiamin congener and bacimethrin availability under different cyanoHAB conditions. Bacimethrin was present in all samples at similar concentrations to the thiamin precursor, HMP, suggesting that similar mechanisms influence the availability of both compounds. Additionally, bacimethrin concentrations were positively correlated with cyanoHAB species abundance (cells mL-1) and the expression of microbial thiamin biosynthesis genes. Samples with high cyanoHAB abundance also displayed elevated transcription of genes in key biochemical pathways such as the pentose phosphate pathway, photosynthesis, and glycogen biosynthesis. Bacterioplankton such as Limnohabitans spp. that are unable to synthesize thiamin, and are thus vulnerable to bacimethrin allelopathy, showed reduced gene expression when cyanoHAB abundance was high. Reference genomes of cyanoHAB and many picocyanobacteria strains contained complete thiamin biosynthesis gene pathways, implicating these taxa as major thiamin sources. These results suggest that bacimethrin provides a competitive advantage to bacterioplankton that do not require exogenous thiamin by eliminating the risk of bacimethrin uptake with thiamin transporters, potentially facilitating cyanoHAB dominance in Upper Klamath Basin and broader eutrophic watersheds.},
}

*Thiamine/antagonists & inhibitors/metabolism
*Cyanobacteria/genetics/drug effects/metabolism
Harmful Algal Bloom/drug effects
*Gene Expression Regulation, Bacterial/drug effects
Microbiota/drug effects/genetics

@article {pmid41269658,
year = {2025},
author = {Daniel, RC and Okeugo, B and Armbrister, SA and Saleh, ZM and Wang, J and Luo, M and Taylor, CM and Lundberg, LE and Giorgberidze, S and Yin, Z and Roos, S and Rhoads, JM and Liu, Y},
title = {Limosilactobacillus reuteri Strains Differentially Stimulate Immunity in Response to Human Milk Oligosaccharides in Newborn Mice.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41269658},
issn = {1867-1314},
abstract = {Probiotic Limosilactobacillus reuteri DSM 17938 reduces autoimmunity in mouse models. Recently, a novel strain, L. reuteri DSM 32846 (BG-R46®), derived from DSM 17938 was found to have unique properties including bile acid tolerance and enhanced adenosine production. Human milk oligosaccharides (HMOs) help establish the intestinal microbiome and assist immune and neurodevelopment. The objective of the study was to explore the differential effects of each strain (with or without HMOs) with respect to innate and adaptive immunity in the intestine of mice during early development at postnatal d8 (early stage), d14 (rapid growth stage), and d21 (at weaning). C57BL/6J mice received intragastric DSM 17938 or DSM 32846 individually or in combination with HMOs, a mixture of 2`-FL and 6`-SL, daily from d7 to d20. We subsequently assessed circulating and intestinal immune cell markers at d8, d14 and d21. Both strains promoted development of intestinal macrophages, natural killer cells, and activated T and B cells. The cellular responses in the intestine of d8 mice were boosted within one day of treatment with DSM 17938, as opposed to 1-2 weeks after treatment with DSM 32846. This delay could be reversed by supplementing HMOs along with DSM 32846. Both DSM 32846 and DSM 17938 facilitated dendritic cell maturation and enhanced regulatory T cell numbers in the intestines of these newborns. However, HMOs enhanced the effects of DSM 32846, but not DSM 17938. Therefore, an early-life boost of intestinal immune cells by probiotics was observed which could be essential to protection against neonatal inflammatory conditions. This novel difference between two strains of the same species in immune modulation could provide a rationale for co-administration in an HMO-rich environment.},
}

@article {pmid41269457,
year = {2025},
author = {Younis, NK and Alfarttoosi, KH and Sanghvi, G and Roopashree, R and Kashyap, A and Krithiga, T and Taher, WM and Alwan, M and Jawad, MJ and Ali Al-Nuaimi, AM},
title = {Attenuating Neurotoxicity Through Fecal Microbiota Transplant: Mechanisms and Therapeutic Potential.},
journal = {Molecular neurobiology},
volume = {63},
number = {1},
pages = {128},
pmid = {41269457},
issn = {1559-1182},
mesh = {*Fecal Microbiota Transplantation/methods ; Humans ; Animals ; *Gastrointestinal Microbiome/physiology ; *Neurotoxicity Syndromes/therapy/microbiology ; },
abstract = {Neurotoxicity, triggered by drugs, environmental pollutants, metabolic disorders, or infections, can cause lasting neurological dysfunction and cognitive impairment. Recent research highlights the gut microbiota's crucial role in regulating brain health and vulnerability to neurotoxic damage, sparking interest in fecal microbiota transplantation (FMT) as a potential treatment. This review examines how FMT may counteract neurotoxicity and assesses its therapeutic potential for neurodegenerative diseases, neuroinflammation, and cognitive decline. The gut-brain axis-a bidirectional communication system between the gut and the central nervous system (CNS)-acts as the primary route through which gut microbes influence brain function. Growing evidence suggests that microbiota imbalances can exacerbate neuroinflammation, oxidative stress, blood-brain barrier disruption, and altered neurotransmitter production, all of which contribute to neurotoxicity. FMT, the transfer of donor fecal microbes to a recipient's gut, has demonstrated promise in restoring microbial equilibrium and reducing neurotoxic effects in both animal studies and human trials. The review also explores microbial profiles tied to neuroprotection versus those linked to neurotoxic conditions, along with the prospects of tailored microbiome therapies. Despite its potential, FMT faces challenges, including protocol standardization, donor selection criteria, and long-term efficacy. More research is needed to unravel the intricacies of gut-brain interactions and optimize FMT for clinical use. If these hurdles are addressed, FMT could become a transformative therapy for neurotoxicity-related disorders.},
}

*Fecal Microbiota Transplantation/methods
Humans
Animals
*Gastrointestinal Microbiome/physiology
*Neurotoxicity Syndromes/therapy/microbiology

@article {pmid41269281,
year = {2025},
author = {Yazhini, A and Morice, É and Jochheim, A and Lieser, B and Söding, J},
title = {Evaluation of metagenome binning: advances and challenges.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {6},
pages = {},
doi = {10.1093/bib/bbaf617},
pmid = {41269281},
issn = {1477-4054},
support = {101111457//Marie Skłodowska-Curie Actions/ ; //Horizon Europe programme of the European Union and from the Max Planck Society/ ; },
mesh = {*Metagenome ; *Metagenomics/methods ; *Deep Learning ; Computational Biology/methods ; Humans ; Algorithms ; },
abstract = {Several recent deep learning methods for metagenome binning claim improvements in the recovery of high-quality metagenome-assembled genomes. These methods differ in their approaches to learn the contig embeddings and to cluster them. Rapid advances in binning require rigorous benchmarking to evaluate the effectiveness of new methods. We have benchmarked newly developed state-of-the-art deep learning binners on CAMI2 and real metagenomic datasets. The results show that SemiBin2 and COMEBin give the best binning performance, although not always the best embedding accuracy. Interestingly, post-binning reassembly consistently improves the quality of low-coverage bins. We find that binning coassembled contigs with multi-sample coverage is effective for low-coverage dataset, while binning sample-wise assembled contigs with multi-sample coverage (multi-sample) is effective for high-coverage samples. In multi-sample binning, splitting the embedding space by sample before clustering showed enhanced performance compared with the standard approach of splitting final clusters by sample. Deep-learning binners using contrastive models emerged as the top-performing tools overall, with MetaBAT2 and GenomeFace demonstrating superior speed. To facilitate future development, we provide workflows for standardized benchmarking of metagenome binners.},
}

*Metagenome
*Metagenomics/methods
*Deep Learning
Computational Biology/methods
Humans
Algorithms

@article {pmid41268538,
year = {2025},
author = {Jiao, JM and Liu, CG and Zang, D and Chen, J},
title = {Gut microbiota and metabolites: emerging prospects in the treatment of non-small cell lung cancer.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1638942},
pmid = {41268538},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Carcinoma, Non-Small-Cell Lung/therapy/metabolism/microbiology ; *Lung Neoplasms/therapy/metabolism/microbiology ; Fecal Microbiota Transplantation ; Probiotics/therapeutic use ; Animals ; },
abstract = {Non-small cell lung cancer (NSCLC) is the most prevalent form of lung cancer, accounting for approximately 85% of all cases, and is associated with a poor prognosis. Despite significant advancements in treatment modalities, therapeutic efficacy remains suboptimal, underscoring the urgent need for novel strategies. In recent years, increasing attention has been directed toward the pivotal role of gut microbiota-host interactions in the treatment of NSCLC. This review systematically examines the influence of current NSCLC therapies on gut microbiota and metabolism, explores the relationship between the microbiome and therapeutic response, and highlights the critical functions of probiotics, microbial metabolites, fecal microbiota transplantation (FMT), and dietary interventions in NSCLC management. By elucidating the mechanisms through which gut microbiota and their metabolites modulate treatment efficacy, we investigate the potential of exogenous interventions targeting the gut ecosystem to enhance therapeutic outcomes and mitigate adverse effects. Modulating the intestinal microbiota represents a promising clinical avenue and offers a new frontier for the development of future NSCLC treatment strategies.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Carcinoma, Non-Small-Cell Lung/therapy/metabolism/microbiology
*Lung Neoplasms/therapy/metabolism/microbiology
Fecal Microbiota Transplantation
Probiotics/therapeutic use
Animals

@article {pmid41268503,
year = {2025},
author = {Wang, L and Garland, GM and Ge, T and Guo, S and Kebede, EA and He, C and Hijri, M and Plaza-Bonilla, D and Stringer, LC and Davis, KF and Lee, SJ and Feng, S and Wang, L and Wei, Z and Cao, H and Wang, Z and Xu, J and Siddique, KHM and Gan, GY and Zhao, M},
title = {Integrated strategies for enhancing agrifood productivity, lowering greenhouse gas emissions, and improving soil health.},
journal = {Innovation (Cambridge (Mass.))},
volume = {6},
number = {11},
pages = {101006},
pmid = {41268503},
issn = {2666-6758},
abstract = {Global agrifood systems face three interconnected challenges: ensuring food security, promoting environmental sustainability, and restoring soil health in the face of climate change. Conventional practices have prioritized productivity over ecological resilience, leading to soil degradation, increased greenhouse gas (GHG) emissions, and inefficient resource utilization. Here, we introduce a "triple-goal" agrifood framework that enhances food production, soil health, and GHG mitigation simultaneously through integrated innovations. Using a second-order meta-analysis of 104 meta-analyses that cover 39,162 studies and 300,139 global field comparisons, we identified key interventions, including optimized fertigation, diversified cropping systems, organic amendments, and precision N management, that increased productivity by 14%-28% while reducing environmental impacts. Diversified systems boosted yields by 19.6% and reduced land use by 19%. Integrating legumes and cover crops lowered N2O emissions by 18%-65%, while organic amendments increased soil organic carbon stocks by 7%-13%. Structural equation modeling identified nitrogen use efficiency and microbial activity as central to the food-soil-emissions nexus. However, tradeoffs remain; yield-focused strategies can elevate emissions if not tailored to local conditions. By integrating agronomic, biological, and technological interventions such as conservation tillage, biofertilization, and digital agriculture, this triple-goal framework supports a 15%-30% reduction in anthropogenic CO2-equivalent emissions. These findings underscore the need for policy reform and multi-stakeholder collaboration to scale up the adaptation of integrated strategies in alignment with the UN's Sustainable Development Goals and the "One Health" initiative. The triple-goal framework provides a transformative pathway to climate-smart, equitable, and resilient agrifood systems that strike a balance between productivity and planetary health.},
}

@article {pmid41268305,
year = {2025},
author = {Choi, S and Pham, TTD and Jeong, TK and Kang, JG and Lee, SW and Heo, BY and Park, JH and Koh, JS and Lee, MW and Lim, DS and Song, IC and Kwon, J},
title = {Korean red ginseng extract suppresses food allergy by remodeling the gut microbiota and restoring immune homeostasis in IL4ra[F709] mice.},
journal = {Journal of ginseng research},
volume = {49},
number = {6},
pages = {746-757},
pmid = {41268305},
issn = {1226-8453},
abstract = {BACKGROUND: Food allergy (FA) is a growing health concern with limited therapeutic options. While Korean Red Ginseng Extract (KRGE) exhibits immunomodulatory and microbiota-modulating properties, its specific effects and mechanisms in FA are not fully understood.

METHODS: We evaluated the anti-allergic efficacy of KRGE in IL4ra[F709] mice, a model genetically predisposed to IgE-mediated anaphylaxis. Mice were sensitized with ovalbumin(OVA) and staphylococcal enterotoxin B (SEB) and challenged with OVA. KRGE was administered orally prior to and during sensitization. Clinical symptoms, serum IgE levels, IL-33 levels, and intestinal histology were assessed. Mesenteric lymph nodes and Peyer's patches immune cell populations were analyzed by flow cytometry. Fecal microbiota composition was profiled using 16S rRNA sequencing and quantitative PCR; correlations between phenotype and microbiota were investigated.

RESULTS: Results showed KRGE significantly suppressed anaphylactic symptoms, including hypothermia and mortality, and reduced OVA-specific IgE and IL-33 levels. KRGE restored intestinal epithelial integrity and normalized Peyer's patch hypertrophy. Immunologically, it decreased IL-13-producing T follicular helper cells and rebalanced dendritic cell subsets, increasing tolerogenic CD103[+] cDC1 and reducing pro-allergic CD11b[+] cDC2. Microbiome analysis revealed that OVA/SEB increased pro-inflammatory Lachnospiraceae and Ruminococcaceae while depleting beneficial Lactobacillaceae and Bifidobacteriaceae. KRGE reversed these changes, notably enriching Akkermansia muciniphila and Lactobacillus gasseri. Correlation analysis revealed that Akkermansia, Lactobacillus, and Christensenellaceae were negatively correlated with allergic markers and positively correlated with epithelial integrity. In contrast, Oscillospiraceae (Eubacterium_g8, Acetobacter, and Pseudoflavonifractor) was associated with allergy exacerbation.

CONCLUSION: KRGE mitigates FA in IL4ra[F709] mice by restoring gut microbiota balance and immune homeostasis, suggesting its potential as a microbiota-targeted intervention for FA.},
}

@article {pmid41268133,
year = {2025},
author = {Li, J and Popovich, PG and Kigerl, KA and McTigue, DM and Schwab, J and Barnes, S and Yarar-Fisher, C},
title = {Multiomic Analysis of the Gut Microbiome and Serum Metabolome in Response to a Low-Carbohydrate, High-Protein Diet in Individuals With Spinal Cord Injury.},
journal = {Topics in spinal cord injury rehabilitation},
volume = {31},
number = {4},
pages = {111-129},
pmid = {41268133},
issn = {1945-5763},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Spinal Cord Injuries/diet therapy/microbiology/blood/metabolism ; Male ; Female ; *Metabolome ; Adult ; Middle Aged ; *Diet, High-Protein Low-Carbohydrate ; *Diet, High-Protein ; },
abstract = {BACKGROUND: Dietary interventions play a significant role in preventing and managing cardiometabolic diseases partly through their impact on the gut microbiome and circulating metabolites.

OBJECTIVES: To assess the impact of an 8-week low-carbohydrate, high-protein (LC/HP) diet on gut microbiome composition, function, and serum metabolome in individuals with spinal cord injury (SCI).

METHODS: Twenty-four adults with chronic SCI were randomized into an LC/HP diet or a control group for 8 weeks. Stool and fasting serum samples were collected at baseline and week 8. The gut microbiome composition and metabolic potential were determined using metagenomic sequencing, while serum metabolome was assessed through untargeted liquid chromatography-tandem mass spectrometry. Statistical analyses focused on diet and time interaction effects, using R (version 4.1.0).

RESULTS: A trend for increased alpha diversity (Gini-Simpson, P = .09) in the diet group indicated a more evenly distributed microbial community. Compared to the control group, several microbiome species (e.g., Fusicatenibacter saccharivorans, Eubacterium siraeum) that are implicated with better intestinal health and reduced inflammation increased, while other species (e.g., Hungatella hathewayi, Clostridium symbiosum) that are associated with colorectal cancer risk decreased in the diet group. Microbial metabolic pathways related to amino acid and purine nucleotides were altered. Increased tryptophan betaine and decreased 8-hydroxy-deoxyguanosine were observed in the serum in the diet group (P interaction < .05), indicating compliance and reduced oxidative stress, respectively.

CONCLUSION: Adopting an LC/HP diet resulted in favorable gut microbiome and metabolome adaptations that may reduce the risk for cardiometabolic disease and colorectal cancer in individuals with SCI.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Spinal Cord Injuries/diet therapy/microbiology/blood/metabolism
Male
Female
*Metabolome
Adult
Middle Aged
*Diet, High-Protein Low-Carbohydrate
*Diet, High-Protein

@article {pmid41268108,
year = {2025},
author = {Peregrina, S and Aubalat, AP and Manohar, A and Benavente, A and Torres-Carvajal, M and Gabaldón, T},
title = {Effects of removable clear dental aligners on the composition of the oral microbiome.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2579836},
pmid = {41268108},
issn = {2000-2297},
abstract = {Proper tooth alignment is important for oral and periodontal health, allowing better hygiene and reducing plaque build-up. While traditional braces are effective, clear aligners offer an aesthetic advantage and are also thought to promote better oral hygiene. However, their specific impact on the oral microbiome is not yet fully understood. This longitudinal study used 16S amplicon sequencing to study the oral microbiome (from saliva, subgingival, and supragingival samples) of 11 patients undergoing clear aligner treatment. Samples were collected at three time points: before treatment and at 3 and 6 months during therapy. Our results revealed large differences between the microbiomes of different oral sites but no significant overall changes in the oral microbiome composition due to orthodontic treatment. While some species-specific changes were observed, their effect sizes were very small. Although these results should be confirmed in a larger and more diverse cohort, they suggest that the treatment had a small or negligible impact. Given the observed stability of the oral microbiome in all three studied niches throughout the treatment and the known benefits to oral hygiene, clear aligners may present a favorable therapeutic alternative compared to fixed appliances.},
}

@article {pmid41267933,
year = {2025},
author = {Tincati, C and Bono, V and Nozza, S and Bandera, A and Tosi, D and Sala, V and Ancona, G and Calcagno, A and Muscatello, A and Rusconi, S and Augello, M and Rovito, R and Gianelli, U and Pescia, C and Santoro, A and Falleni, M and Gori, A and Marchetti, G},
title = {Three-Month cART Initiated During Primary HIV Does Not Correct the Structural, Immune, and Microbial Abnormalities within the Gastrointestinal Tract.},
journal = {Pathogens & immunity},
volume = {10},
number = {2},
pages = {263-285},
pmid = {41267933},
issn = {2469-2964},
abstract = {BACKGROUND: HIV infection leads to profound alterations of gut structure, immunity, and microbiome, resulting in immune activation and inflammation, which drive the development of non-infectious comorbidities. The introduction of combination antiretroviral therapy (cART) in the chronic stages of disease does not correct such abnormalities; however, the effect of viro-suppressive treatment in the gastrointestinal tract during primary HIV infection (PHI) is largely unknown. We studied the effects of 12-week cART on gastrointestinal (GI) structure, immunity, and mucosal microbiome in people living with HIV (PLWH) with PHI.

METHODS: Eleven participants with PHI enrolled in the INACTION trial underwent colonoscopy with ileum and colon biopsies, as well as peripheral blood mononuclear cell (PBMC) and plasma collection, prior to and at 12 weeks of cART. Gut biopsies were stained with CD14, CD68, CD163, and E-cadherin antibodies and Masson trichrome. Flow cytometry was performed on lamina propria and PBMCs to characterize CD4, γδ T, Treg, and Th17 cells. Gut tissue-associated microbiome analysis was conducted on colon and ileum biopsies. Ten untreated individuals with chronic HIV infection (CHI) were also studied for comparative analysis.

RESULTS: Despite treatment of PHI, gut barrier damage (E-cadherin loss, collagen deposition) progressed, with a partially preserved distribution of intestinal macrophages. Treated PHI showed stable CD4+ and γδ T-cell frequencies and decreased activation of these subsets in the colon, with no effect on intestinal Th17 and Treg cells. No major changes in peripheral inflammation and intestinal barrier integrity markers were observed. Gut tissue-associated microbiome composition evolved during cART treatment in PHI.

CONCLUSION: Despite early initiation, 12-week cART is unable to correct the HIV-mediated gut damage. Since gut injury drives systemic inflammation, which in turn fosters the pathogenesis of non-communicable comorbidities, our findings provide pathogenetic evidence of limited efficacy of early cART in reverting the HIV-associated pro-inflammatory signature and clinical risk.},
}

@article {pmid41267780,
year = {2025},
author = {Sharma, I and Sudarsanan, D and Moonah, S},
title = {The gut microbiome as a major source of drug-resistant infections: emerging strategies to decolonize and target the gut reservoir.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1692582},
pmid = {41267780},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Fecal Microbiota Transplantation ; Probiotics/therapeutic use ; *Bacterial Infections/microbiology/therapy/prevention & control ; *Drug Resistance, Bacterial ; Phage Therapy ; *Bacteria/drug effects ; Antimicrobial Peptides/therapeutic use ; },
abstract = {Infections caused by antimicrobial-resistant bacteria represent a significant global health crisis that continues to worsen, creating an urgent need for alternative treatment and prevention strategies. A major source of drug-resistant bacteria is the human gut. The gut microbiota consists of bacteria that are frequently exposed to antibiotics, leading to selective pressure that promotes the development of resistant strains such as carbapenem-resistant Enterobacterales (CRE) and vancomycin-resistant enterococci (VRE). These drug-resistant bacteria can spread from the gut to other body sites, leading to hard-to-treat and potentially life-threatening infections such as bacteremia, surgical site infections, and urinary tract infections. Targeting the gut reservoir is essential in the fight against antimicrobial resistance. In this review, we focus on emerging non-antibiotic strategies aimed at eliminating drug resistant bacteria from the gut before they cause invasive infections, with particular emphasis on clinical evidence. Approaches discussed include fecal microbiota transplantation, bacteriophage therapy, antimicrobial peptides, probiotics, and dietary interventions. Optimizing these strategies, while continuing to explore newer approaches, will be essential to combat the growing threat of drug-resistant infections.},
}

Humans
*Gastrointestinal Microbiome/drug effects
Anti-Bacterial Agents/pharmacology/therapeutic use
Fecal Microbiota Transplantation
Probiotics/therapeutic use
*Bacterial Infections/microbiology/therapy/prevention & control
*Drug Resistance, Bacterial
Phage Therapy
*Bacteria/drug effects
Antimicrobial Peptides/therapeutic use

@article {pmid41267737,
year = {2025},
author = {Surendranath, A and Gupta, A and Singhal, S},
title = {Impact of Dementia on Patients Admitted With Complicated Diverticular Disease: A U.S. Nationwide Analysis.},
journal = {Cureus},
volume = {17},
number = {10},
pages = {e94971},
pmid = {41267737},
issn = {2168-8184},
abstract = {Background Emerging research has suggested a link between diverticular disease and dementia, potentially mediated by alterations in the gut microbiome and chronic systemic inflammation. This study aimed to evaluate in-hospital outcomes in patients admitted with complicated diverticular disease (CDD) and pre-existing dementia. Methods We used the 2021 National Inpatient Sample (NIS), which reflects 97% of the U.S. population. Patients admitted with CDD, defined as diverticulitis, abscess, perforation, or bleeding, were identified and stratified by the presence or absence of a prior dementia diagnosis. In-hospital mortality was compared between groups. Subgroup analysis evaluated the impact of specific complications (perforation/abscess vs. diverticulitis/bleeding) on mortality among patients with dementia. Multivariable logistic regression was used to adjust for potential confounders. Results Of 221,460 patients admitted with CDD, 9,160 (4.1%) had a comorbid dementia diagnosis. Patients with dementia were older (mean age 82.5 years), predominantly female (64.9%), and more likely to have multiple comorbidities. Overall, in-hospital mortality was higher in the dementia group (unadjusted OR 3.41; 95% CI: 2.38-4.90; p < 0.01), though this was not statistically significant after adjustment (aOR 1.45; 95% CI: 0.97-2.16; p = 0.07). Subgroup analysis revealed that dementia was significantly associated with increased mortality among patients with perforation or abscess (aOR 2.07; 95% CI: 1.07-4.04; p = 0.03), but not in those with diverticulitis or bleeding alone. Conclusion Pre-existing dementia was associated with higher unadjusted mortality, but it was not statistically significant after adjustment, except in patients with CDD who presented with perforation or abscess.},
}

@article {pmid41267628,
year = {2025},
author = {Chamedjeu, RR and Jani, K and Jetter, K and Wilhelm, K and Schäfer, P and Wilfert, L and Sommer, S and Riedel, CU},
title = {Impact of Fertilisation on the Bacterial Core Microbiome of Grassland Soils: Abundance in the Field and Growth In Vitro.},
journal = {Environmental microbiology reports},
volume = {17},
number = {6},
pages = {e70235},
doi = {10.1111/1758-2229.70235},
pmid = {41267628},
issn = {1758-2229},
support = {ID-18 IMPALA//Baden-Württemberg Stiftung/ ; },
mesh = {*Soil Microbiology ; *Grassland ; *Bacteria/genetics/growth & development/classification/isolation & purification ; *Microbiota ; *Fertilizers/analysis ; RNA, Ribosomal, 16S/genetics ; Animals ; DNA, Bacterial/genetics/chemistry ; Soil/chemistry ; Swine ; Phylogeny ; },
abstract = {Anthropogenic activities may have profound impacts on the soil microbiome with consequences for soil health, agriculture and food production. Here, we investigated the impact of different fertilisation regimes on the composition of the bacterial soil microbiome in grassland ecosystems by 16S rRNA gene amplicon sequencing and in vitro growth experiments with culturable representatives of the bacterial core microbiota. We observed a large proportion of taxa shared across fertilisation regimes without significant differences in their evenness, but shifts in the composition of the bacterial core microbiome by fertilisation. These effects were most pronounced for fertilisation with pig slurry (PS). Analysis of microbiome multivariable association with linear models identified bacterial biomarker taxa for different fertilisation regimes. This enabled the selection of several culturable representatives for in vitro growth experiments. Consistent with the relative abundances of Bradyrhizobium, Nocardioides, and Solirubrobacter in field samples, the growth of Bradyrhizobium japonicum was inhibited by PS, while Nocardioides albus and Solirubrobacter pauli exhibited enhanced growth in its presence. Our results suggest that culturable representatives of the bacterial core soil microbiota can be identified and used to investigate the effects of specific parameters linked to anthropogenic impacts under controlled laboratory conditions.},
}

*Soil Microbiology
*Grassland
*Bacteria/genetics/growth & development/classification/isolation & purification
*Microbiota
*Fertilizers/analysis
RNA, Ribosomal, 16S/genetics
Animals
DNA, Bacterial/genetics/chemistry
Soil/chemistry
Swine
Phylogeny

@article {pmid41267490,
year = {2025},
author = {Sharma, P and Dagariya, S and Sharma, S and Singh, M},
title = {Uncovering the nexus of human health hazards of nanoplastics, gut-dysbiosis and antibiotic-resistance.},
journal = {Journal of environmental science and health. Part C, Toxicology and carcinogenesis},
volume = {},
number = {},
pages = {1-60},
doi = {10.1080/26896583.2025.2578871},
pmid = {41267490},
issn = {2689-6591},
abstract = {Nanoplastics (1-1000 nm) (NPs) represent a novel and insidious class of emerging contaminants with the potential to profoundly disrupt gut microbial ecology and accelerate the spread of antibiotic resistance two critical and converging threats to global health. While prior studies have examined the toxicokinetics of NPs and their general microbial interactions, this review provides the first comprehensive synthesis specifically focused on the nexus between NPs, gut dysbiosis, and the propagation of antibiotic resistance genes (ARGs). This review highlights how NPs alter gut microbiota composition, suppressing beneficial microbes while fostering opportunistic pathogens and how such imbalances may contribute to human health issues. Importantly, emerging evidence also suggests that NPs may serve as unrecognized vectors for horizontal gene transfer (HGT), enabling the rapid dissemination of ARGs via conjugation, transformation, transduction, and extracellular vesicles within the gastrointestinal tract. In addition, this review also identifies urgent methodological gaps in detecting NPs in biological matrices and the environment, as well as assessing their mechanistic impacts, calling for innovation in analytical approaches. By presenting an interdisciplinary perspective that bridges nanotoxicology, microbiome science, and antimicrobial resistance, this article sheds light on an underexplored yet urgent frontier in environmental health, offering novel insights to guide future research, risk assessment, and policy development.},
}

@article {pmid41267409,
year = {2025},
author = {van der Hulst, R and Borra, LCP and Verschoor, SP and Hundscheid, IHR and Nienaber, WC and Quaak, FCA and Verschraagen, M and Oostra, RJ and Touw, DJ},
title = {The influence of 13 weeks of burial on morphine and metabolite distribution in human remains.},
journal = {Journal of forensic sciences},
volume = {},
number = {},
pages = {},
doi = {10.1111/1556-4029.70233},
pmid = {41267409},
issn = {1556-4029},
abstract = {When human remains are in an advanced stage of decomposition, drug concentrations are altered. In five decedents morphine, morphine-3-glucuronide (M3G), and morphine-6-glucuronide (M6G) concentration changes and bacterial DNA were investigated after 13 weeks of burial. Femoral blood (FB), musculus quadriceps femoris (QM), adipose tissue (AT), synovial fluid (SF), and vitreous humor (VH) were collected on arrival at the morgue (t1), 15-24 h later (t2), and after burial of 13 weeks (t3). At t3 FB, QM, AT, and BM were sampled during autopsy, along with additional samples. Morphine, M3G, and M6G concentrations were determined. The median morphine concentration change, expressed as t2/t1 ratios in FB, VH, SF, QM, and AT was 0.96 (0.87->1.1), 1.1 (0.90-1.2), 0.92 (0.86-1.02), 1.1 (0.90-1.6), and 1.4 (1.2-1.8), respectively. At t3 the concentrations showed wide variability, with the least in QM. The median(range) morphine to FB (t1) ratios in matrices collected at t3 from the torso (central) and outside the torso (peripheral) were 4.8 (1.0-70) and 1.3 (0.02->3.1), respectively, and were significantly different. The central and peripheral median M3G to morphine t3/t1 ratios were 0.31 (0.01-1.2) and 1.4 (range 0.34-13), respectively, suggesting postmortem deconjugation of M3G. Bacterial DNA was detected in all matrices. At t3 most matrices examined had a higher bacterial DNA concentration compared to t1. The measured t2/t1 morphine ratios suggest stability of morphine concentrations between t1 and t2. At t3 morphine concentrations in peripheral matrices are lower than in central matrices, where QM and BT are possible alternatives to analyze at extended PMIs.},
}

@article {pmid41267291,
year = {2025},
author = {Wang, X and Ma, X and Su, D and Zhang, Y and Miao, J and Liu, X and Yu, Y and Leng, K},
title = {The effect of short-term storage on Antarctic krill (Euphausia superba) quality: Insights into microbial characteristics, volatile flavor compounds, trimethylamine oxide and its derivatives.},
journal = {Food research international (Ottawa, Ont.)},
volume = {222},
number = {Pt 1},
pages = {117709},
doi = {10.1016/j.foodres.2025.117709},
pmid = {41267291},
issn = {1873-7145},
mesh = {Animals ; *Euphausiacea/microbiology/chemistry ; *Methylamines/analysis/metabolism ; *Food Storage/methods ; *Volatile Organic Compounds/analysis ; Microbiota ; Antarctic Regions ; Odorants/analysis ; Bacteria/classification/metabolism ; *Seafood/microbiology/analysis ; *Food Quality ; Taste ; Food Microbiology ; },
abstract = {Under suboptimal storage conditions, the conversion of trimethylamine oxide (TMAO) into undesirable metabolites seriously impairs the edible quality, safety, and market value of aquatic foods. This study aims to assess the microbiome variations related to spoilage and its relationship with volatile flavor compounds and TMAO metabolites in Antarctic krill simulated deck environment storage by bio-chemical examination and correlation analysis. Compared to storage at 4 °C and 0 °C, Antarctic krill stored at -20 °C maintained better freshness, with significant reductions in L*, a*, lipid oxidation, carotenoid degradation, texture deterioration, and excessive proteolysis. A total of 60 volatile compounds flavor were identified, of which 12 were identified as important flavor contributors with relative odor active value (ROAV) greater than 1. Bacterial diversity indicated that Proteobacteria, Actinobacteriota and Firmicutes were dominant bacterial phyla. According to Pearson correlation analysis, dominant bacterial genera may mediate changes in volatile compounds through amino acid and fatty acid metabolism. Concurrently, they synergistically drove quality deterioration during storage via multiple pathways, including altered nitrogenous compound metabolism, accelerated lipid oxidation, and induced pigment degradation. These findings offer critical insights into the relationships between quality indicators, volatile flavor compounds, TMAO/its derivatives and bacterial diversity, providing theoretical support for optimizing storage conditions to enhance the flavor and quality of Antarctic krill.},
}

Animals
*Euphausiacea/microbiology/chemistry
*Methylamines/analysis/metabolism
*Food Storage/methods
*Volatile Organic Compounds/analysis
Microbiota
Antarctic Regions
Odorants/analysis
Bacteria/classification/metabolism
*Seafood/microbiology/analysis
*Food Quality
Taste
Food Microbiology

@article {pmid41267258,
year = {2025},
author = {Tiwari, S and Shah, IA and Devi, PB and Suryavanshi, MV and Rani, PU and Rawat, A and Harini Nivedhitha, M and Kondepudi, KK and Bhanuprakash Reddy, G and Kavitake, D and Shetty, PH},
title = {Evaluating the prebiotic potential of a glucan EPS from Enterococcus hirae OL616073: Digestive resistance, probiotic growth stimulation, and gut microbiome modulation.},
journal = {Food research international (Ottawa, Ont.)},
volume = {222},
number = {Pt 1},
pages = {117649},
doi = {10.1016/j.foodres.2025.117649},
pmid = {41267258},
issn = {1873-7145},
mesh = {*Gastrointestinal Microbiome/drug effects ; *Prebiotics ; *Probiotics ; *Glucans/metabolism/pharmacology ; Fermentation ; Feces/microbiology ; *Enterococcus hirae/metabolism/chemistry ; Lacticaseibacillus rhamnosus/growth & development ; *Digestion ; Oligosaccharides ; Bifidobacterium breve/growth & development ; Escherichia coli/growth & development ; Humans ; *Polysaccharides, Bacterial/pharmacology ; },
abstract = {Earlier we have reported extraction, purification and characterization of glucan exopolysaccharide (EPS) from Enterococcus hirae OL616073. In this study, we investigate the potential of glucan EPS as a prebiotic biomolecule through in vitro gastrointestinal (GI) digestion, probiotic growth promotion, and fecal fermentation studies. The glucan EPS showed higher resistance (11.5 % hydrolysis) compared to standard fructooligosaccharide (FOS;18.5 % (p ≤ 0.05)). The impact of various growth media on the viability of Bifidobacterium breve, Lacticaseibacillus rhamnosus, and Escherichiacoli was examined. Glucose stimulated the growth of commensal bacteria, such as E. coli (log 8.69 ± 0.06), whereas with glucan EPS and FOS, the growth of E. coli was lower compared to probiotics. The growth viability for E.coli in the presence of EPS and FOS was log 7.97 ± 0.05 and log 7.85 ± 0.02, respectively while the values were log 8.2 ± 0.05 (p ≤ 0.05) for both the probiotics (B. breve and L. rhamnosus). During in vitro fecal fermentation glucan EPS showed a significant drop in pH from 7.56 to 4.60 after 48 h. Further, fermentation of glucan has produced high concentrations of key short chain fatty acids (SCFAs) that have several health benefits. Microbiome analysis after fecal fermentation demonstrated that glucan EPS impacts gut microbiota modification differently than FOS and a non-sugar control. A substantial increase in Bacillota abundance (33.94 to 54.32 % over 24 h) was observed with glucan EPS, indicating improved nutrition utilization and energy metabolism. Together, these findings highlight glucan EPS as a promising prebiotic agent with the potential to modulate gut microbiota and support metabolic health.},
}

*Gastrointestinal Microbiome/drug effects
*Prebiotics
*Probiotics
*Glucans/metabolism/pharmacology
Fermentation
Feces/microbiology
*Enterococcus hirae/metabolism/chemistry
Lacticaseibacillus rhamnosus/growth & development
*Digestion
Oligosaccharides
Bifidobacterium breve/growth & development
Escherichia coli/growth & development
Humans
*Polysaccharides, Bacterial/pharmacology

@article {pmid41267246,
year = {2025},
author = {Huang, X and Li, R and Zhang, L and Chen, X and Gong, X and Kang, J},
title = {Exploring the rare and abundant bacterial community structures and their metabolic differences in various types of qula cheese.},
journal = {Food research international (Ottawa, Ont.)},
volume = {222},
number = {Pt 1},
pages = {117633},
doi = {10.1016/j.foodres.2025.117633},
pmid = {41267246},
issn = {1873-7145},
mesh = {*Cheese/microbiology ; *Bacteria/classification/metabolism/genetics ; *Microbiota ; *Food Microbiology ; Animals ; Tibet ; Fermentation ; Metabolomics ; Cattle ; Milk/microbiology ; },
abstract = {Qula is a fermented cheese-like product made from yak milk. Although the bacterial communities in qula have been well documented, the diversity and functions of both abundant and rare bacterial subcommunities are still unclear. Here, our study examines the community structures of abundant and rare taxa, as well as their metabolite profiles, in the distinct qula samples from Tibet, China, employing high-throughput sequencing and untargeted metabolomics. Our results indicate that rare bacterial taxa account for 98.15 % of total operational taxonomic units and 48 % of total sequences. Dominant bacteria from abundant taxa consist of Lactococcus, Lactobacillus, and Acetobacter, while rare taxa contain Prevotella, Ruminococcus, and Butyrivibrio. Furthermore, we show that stochastic processes predominantly influence bacterial assembly in qula microbial communities. Specifically, stochastic processes have a more significant impact on community assembly for rare taxa, while deterministic processes are more important for abundant taxa. Moreover, we evaluate the contributions of rare taxa to network complexity and community stability, identifying potential keystone species. By analyzing metabolic profiles, we further compared the differences in metabolic functions between rare and abundant taxa in the qula microbiome. Our study shows that, along with abundant taxa, rare taxa in the qula microbiome play a significant role in community assembly and interactions, offering valuable insights into the microbial ecosystems of traditional fermented foods.},
}

*Cheese/microbiology
*Bacteria/classification/metabolism/genetics
*Microbiota
*Food Microbiology
Animals
Tibet
Fermentation
Metabolomics
Cattle
Milk/microbiology

@article {pmid41267138,
year = {2025},
author = {Zafari, R and Goudarzi, N and Kamroo, A and Tafti, MF and Ghorbani, A and Talebian, N and Najafi, S and Shahbazian, S and Rahmanian, M and Parvardeh, S and Dargahi, L and Nassiri-Asl, M},
title = {The effects of polyphenols on gut microbial metabolites and composition in neurodegenerative diseases: a systematic review.},
journal = {Nutrition & metabolism},
volume = {22},
number = {1},
pages = {142},
pmid = {41267138},
issn = {1743-7075},
}

@article {pmid41267120,
year = {2025},
author = {Ahannach, S and Gehrmann, T and Spacova, I and Wittouck, S and Hiers, J and Bron, PA and Vander Donck, L and Cromphout, M and Swayambhu, M and Arora, N and Schuh, L and Tournoy, I and Smeers, I and Wuestenbergs, J and Bekaert, B and Decorte, R and Jehaes, E and Lebeer, S},
title = {Microbial and seminal traces of sexual intercourse and forensic implications.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {237},
pmid = {41267120},
issn = {2049-2618},
support = {Lacto-Be 26850/ERC_/European Research Council/International ; DOCPRO 37054//Universiteit Antwerpen/ ; 1277222N//Fonds Wetenschappelijk Onderzoek/ ; 11A0620N//Fonds Wetenschappelijk Onderzoek/ ; 1SD0622N//Fonds Wetenschappelijk Onderzoek/ ; FN701000004//Fonds Wetenschappelijk Onderzoek/ ; },
mesh = {Humans ; Female ; *Vagina/microbiology ; *Coitus ; *Semen/microbiology ; *Microbiota ; Male ; Adult ; Sex Offenses ; Retrospective Studies ; Rape ; Longitudinal Studies ; Young Adult ; Machine Learning ; },
abstract = {BACKGROUND: The increasing numbers of sexual violence and unresolved rape cases require alternative approaches with higher evidential value to complement existing forensic tools. Predicting recent intercourse is crucial in forensic casework on sexual assaults. In this work, we assessed whether sexual intercourse can be predicted based on the vaginal microbiome and compared it to the gold standard method of semen detection.

RESULTS: Using a prediction model based on microbiome of 3043 women, intercourse was predicted with 71% accuracy in a balanced cross-validation machine learning setting. This prediction model was validated in a longitudinal intervention study and tested on forensic sexual assault cases. The developed predictor could accurately establish intercourse in 82% of the studied cases. Yet, underwear was found to hold an even greater evidential value and replace the more invasive vaginal sampling for semen detection in some cases with an accuracy of 95%. This was substantiated through a retrospective analysis of 207 forensic sexual assault cases.

CONCLUSIONS: Taken together, this study revealed that the vaginal microbiome is better at predicting recent sexual intercourse, while the victim's underwear has a clear value as additional biological trace evidence for semen detection. These findings are particularly useful in cases with delayed reporting and are obtained with less invasive sampling. Video Abstract.},
}

Humans
Female
*Vagina/microbiology
*Coitus
*Semen/microbiology
*Microbiota
Male
Adult
Sex Offenses
Retrospective Studies
Rape
Longitudinal Studies
Young Adult
Machine Learning

@article {pmid41266962,
year = {2025},
author = {Patridge, E and Gorakshakar, A and Molusky, MM and Ogundijo, O and Julian, C and Hu, L and Antoine, G and Vuyisich, M and Wohlman, R and Banavar, G},
title = {Altered gut microbial functional pathways in people with irritable bowel syndrome enable precision health insights.},
journal = {BMC gastroenterology},
volume = {25},
number = {1},
pages = {823},
pmid = {41266962},
issn = {1471-230X},
mesh = {Humans ; *Irritable Bowel Syndrome/microbiology ; *Gastrointestinal Microbiome/genetics/physiology ; Adult ; Female ; Male ; Middle Aged ; Feces/microbiology ; Transcriptome ; Precision Medicine ; },
abstract = {BACKGROUND: Functional gastrointestinal disorders present diagnostic and therapeutic challenges, and there is a strong need for molecular markers that enable early health insights and intervention. Herein, we present an approach to assess the gut microbiome with stool-based gut metatranscriptome data from a large adult human population (n = 80,570), using irritable bowel syndrome as an example that features both an abnormal gut microbiome and a spectrum of distinct conditions.

METHODS: We develop a suite of eight gut microbial functional pathway scores, each of which represents the activity of a set of interacting microbial functional features (based on KEGG orthology) relevant to known gut biochemical activities. We use a normative approach within a subpopulation (n = 9,350) to define "Good" and "Not Optimal" activities for these transcriptome-based gut pathway scores.

RESULTS: We hypothesize that Not Optimal scores are associated with irritable bowel syndrome (IBS) and its subtypes (i.e., IBS-Constipation, IBS-Diarrhea, IBS-Mixed Type). We show that Not Optimal functional pathway scores are associated with higher odds of IBS or its subtypes within an independent cohort (n = 71,220) using both the Rome IV Diagnostic Questionnaire as well as self-reported phenotypes.

CONCLUSIONS: Rather than waiting to diagnose IBS after symptoms appear, these functional pathway scores can help to provide early health insights into molecular pathways that may contribute to IBS. These molecular endpoints could also assist with measuring the efficacy of practical interventions, developing related algorithms, providing personalized nutritional recommendations, diagnostic support, and treatments for gastrointestinal disorders like IBS.},
}

Humans
*Irritable Bowel Syndrome/microbiology
*Gastrointestinal Microbiome/genetics/physiology
Adult
Female
Male
Middle Aged
Feces/microbiology
Transcriptome
Precision Medicine

@article {pmid41266961,
year = {2025},
author = {Wang, L and Qi, G and Shi, Y and Ma, Y and Gao, J},
title = {A systematic longitudinal study of microbiome: integrating temporal-spatial dimensions with causal and deep learning models.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {1068},
pmid = {41266961},
issn = {1471-2164},
support = {Grant No. 12271216, 11831015, 92370131//National Natural Science Foundations of China/ ; },
mesh = {*Deep Learning ; Humans ; Biomarkers ; Longitudinal Studies ; *Microbiota ; Gastrointestinal Microbiome ; },
abstract = {Longitudinal microbiome data provide a unique opportunity to explore dynamic interactions between microbial communities and disease progression. However, these data are often characterized by missing values, sparse signals, and limited interpretability, which impede effective biomarker discovery and accurate disease modeling. Therefore, we propose SysLM, a comprehensive deep learning framework for systematic analysis of longitudinal microbiome data. It comprises two synergistic modules: SysLM-I and SysLM-C. SysLM-I focuses on the task of missing-value inference, combines metadata and three feature enhancement strategies, and comprehensively captures temporal causality and long-term dependence through Temporal Convolutional Network and Bi-directional Long Short-Term Memory modules. SysLM-C integrates deep learning with causal inference modeling to construct three causal spaces to accomplish the tasks of classification and screening of multiple types of biomarkers, including differential biomarkers of microbiomes, network biomarkers, core biomarkers, dynamic biomarkers, disease-specific biomarkers, and shared biomarkers. SysLM demonstrates superior performance in imputation, classification, and biomarker discovery across multiple datasets. Importantly, it uncovers novel microbial mechanisms underlying ulcerative colitis, highlighting its value for precision medicine. By integrating deep learning with causal modeling, SysLM offers a promising approach to advance microbiome-based disease research and facilitate the development of targeted therapeutic strategies.},
}

*Deep Learning
Humans
Biomarkers
Longitudinal Studies
*Microbiota
Gastrointestinal Microbiome

@article {pmid41266917,
year = {2025},
author = {Huang, JS and Zhang, ZY and Zhong, QH and Guo, FL and Wu, JY and Chen, S and Lin, WW and Lin, JB},
title = {Tumor-Intrinsic Microbiome-Based Subtyping of Esophageal Cancer as Predictive Biomarkers for Postoperative Survival.},
journal = {Annals of surgical oncology},
volume = {},
number = {},
pages = {},
pmid = {41266917},
issn = {1534-4681},
abstract = {OBJECTIVE: This study aims to investigate the impact of different treatment regimens on the intratumoral microbiota (ITM) composition in esophageal cancer patients and its association with prognosis.

METHODS: Tumor tissue samples from 107 esophagectomy patients were analyzed by using 5R 16S rRNA sequencing. Patients were classified into esophagotype A and B via hierarchical clustering, and the relationship between microbiota and prognosis was assessed through Kaplan-Meier survival analysis and Cox regression.

RESULTS: Significant differences in ITM diversity and composition were observed between the neoadjuvant chemoimmunotherapy (nCIT) and surgery alone groups. Esophagotype A was enriched with Firmicutes and Lactobacillus, while esophagotype B with Proteobacteria and Fusobacterium. Survival analysis revealed that patients with esophagotype B had significantly worse outcomes compared with esophagotype A. The 3- and 5-year overall survival rates for esophagotype A were 73 and 69.2%, respectively, significantly higher than those for esophagotype B (57 and 37.5%; p < 0.05 and p < 0.01, respectively). Similarly, the 3- and 5-year recurrence-free survival rates for esophagotype A were both 80.7% compared with 64 and 50.1% for esophagotype B. Multivariable Cox regression confirmed microbial clustering within esophageal cancer subtypes as an independent prognostic factor.

CONCLUSIONS: This study classifies esophageal cancer based on ITM signatures, highlighting the microbiota's prognostic significance and supporting the potential of microbiome-based strategies for personalized treatment.},
}

@article {pmid41266864,
year = {2025},
author = {Tan, H and Li, S and Yan, H and Li, F and Yao, Y and Li, Y and Feng, Q},
title = {Mendelian Randomization Unlocks Stroke Therapeutics: Dioscin Inhibits CD27-Driven Neuroinflammation via Gut Microbiota Modulation.},
journal = {Molecular neurobiology},
volume = {63},
number = {1},
pages = {110},
pmid = {41266864},
issn = {1559-1182},
support = {2022ZL20//the hospital-level research project of the affiliated Hospital of Xuzhou Medical University/ ; XWKYHT20230067//the medical science and technology innovation project of Xuzhou Municipal Health Commission/ ; LCZX202412//the Construction Project of High Level Hospital of Jiangsu Province/ ; XZSYSKF2022020//the Project Funded by Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD)/ ; KC22243//the Xuzhou Science and Technology Program/ ; },
mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Stroke/drug therapy/genetics/microbiology ; *Mendelian Randomization Analysis/methods ; *Tumor Necrosis Factor Receptor Superfamily, Member 7/metabolism/antagonists & inhibitors ; *Neuroinflammatory Diseases/drug therapy/genetics ; },
abstract = {Research on the gut-brain-immune axis shows it plays a critical role in ischemic stroke, but the exact causal links between gut bacteria imbalance, immune system problems, and brain blood vessel damage remain unclear. To investigate this, we combined multiple types of biological data using a statistical method called Bayesian weighted Mendelian randomization (BWMR). We analyzed large genetic datasets covering 731 immune cell traits, 91 inflammatory proteins, 412 gut microbes and their pathways, and ischemic stroke cases. Shared genetic variants were confirmed using colocalization, and we used computer simulations to explore potential treatments. The analysis found that genetically predicted higher levels of the protein CD27 on specific memory B cells (CD24[+] CD27[+] and IgD[-] CD38[dim]) directly increased the risk of stroke caused by large-artery atherosclerosis. Computer modeling indicated that a compound called Dioscin could potentially block CD27 effectively. Conversely, bacteria from the order Burkholderiales (specifically at the family, genus, and species level Burkholderiales_bacterium_1_1_47) showed strong protective effects against small-vessel stroke. Further analysis revealed that about 12.6% of the protective effect of the gut bacterium g_Odoribacter worked through the signaling protein FGF19. This study identifies CD27-positive B cells as key drivers of brain inflammation in stroke and suggests Dioscin as a promising treatment candidate. It also demonstrates a protective mechanism where specific gut microbes communicate with blood vessels in the brain via FGF19, providing a foundation for new stroke therapies targeting the microbiome and immune system.},
}

*Gastrointestinal Microbiome/drug effects
Humans
*Stroke/drug therapy/genetics/microbiology
*Mendelian Randomization Analysis/methods
*Tumor Necrosis Factor Receptor Superfamily, Member 7/metabolism/antagonists & inhibitors
*Neuroinflammatory Diseases/drug therapy/genetics

@article {pmid41266809,
year = {2025},
author = {Docter-Loeb, H},
title = {Waste not: how researchers harness pee and poo for science.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {41266809},
issn = {1476-4687},
}

@article {pmid41266796,
year = {2025},
author = {Weng, Y and Guccione, C and McDonald, D and Oles, R and Devkota, S and Kopylova, E and Sepich-Poore, GD and Salido, RA and Din, MO and Song, SJ and Curtius, K and Chu, H and Bartko, A and Hasty, J and Knight, R},
title = {Calculating fast differential genome coverages among metagenomic sources using micov.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1624},
pmid = {41266796},
issn = {2399-3642},
mesh = {*Metagenomics/methods ; *Genome, Bacterial ; *Metagenome ; *Microbiota/genetics ; Humans ; },
abstract = {Breadth of coverage, the proportion of a reference genome covered by at least one sequencing read, is critical for interpreting metagenomic data, informing analyses from genome assembly to taxonomic profiling. However, existing tools typically summarize coverage breadth at the whole-genome or aggregate-sample level, missing informative variation along genomes and between sample groups. Here we introduce MIcrobiome COVerage (micov), a tool that computes and compares per-sample breadth of coverage across many genomes and samples. micov offers two key advances: (1) rapid cumulative coverage breadth calculations specific to each sample type, and (2) detection of differential coverage breadth along genomes. Applying micov to three metagenomic datasets, we show that it identifies a genomic region in Prevotella copri that explains variation in community composition independent of host country of origin, uncovers dietary association with a partially annotated region in an uncharacterized Lachnospiraceae genome, enabling hypothesis generation for genes of unknown function, and improves sensitivity in low-biomass settings by detecting a single genomic copy of enteropathogenic Escherichia coli (EPEC) in wastewater and distinguishing Mediterraneibacter gnavus across specimen types.},
}

*Metagenomics/methods
*Genome, Bacterial
*Metagenome
*Microbiota/genetics
Humans

@article {pmid41266667,
year = {2025},
author = {Horseman, TS and Parajuli, B and Murthy, V and Holmes-Hampton, GP and Sukumar, G and Dalgard, CL and Anderson, JA and Burmeister, DM},
title = {A multi-omics approach exploring the gut-liver axis following combined radiation exposure and burn injury in a Sinclair minipig model.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {41111},
pmid = {41266667},
issn = {2045-2322},
support = {RHE-24-01//United States Army Medical Research and Development Command's Combat Casualty Care Program/ ; RHE-24-01//United States Army Medical Research and Development Command's Combat Casualty Care Program/ ; RHE-24-01//United States Army Medical Research and Development Command's Combat Casualty Care Program/ ; RHE-24-01//United States Army Medical Research and Development Command's Combat Casualty Care Program/ ; },
mesh = {Animals ; *Burns/metabolism/pathology/genetics/microbiology/complications ; Swine ; *Liver/metabolism/radiation effects/pathology ; Swine, Miniature ; *Gastrointestinal Microbiome/radiation effects ; Disease Models, Animal ; Transcriptome ; *Radiation Exposure/adverse effects ; *Radiation Injuries, Experimental ; Multiomics ; },
abstract = {While radiation and burn injury have distinct local and systemic effects, they both negatively impact intestinal permeability/function. In a nuclear attack, combined thermal burns and radiation exposure (e.g., combined injury (CI)) would be a dominant injury pattern. Despite this, how burns affect gastrointestinal acute radiation syndrome, and vice versa, has been largely unstudied. Next-generation sequencing has revealed a strong bidirectional link between the liver and gut. Here, we used a porcine model to evaluate the impact of burn, radiation, and CI on the gut microbiota and liver transcriptomics to determine if this link exists in these injury patterns. Sinclair minipigs were randomly divided into three groups: burn (n = 8), hemibody radiation (n = 7), and CI (n = 8). Animals were monitored for 14 days with longitudinal rectal swab and blood collection. CI increased weight loss, diarrhea, inappetence and lethargy compared to either injury pattern alone. Jejunum histology revealed increased mucosal apoptosis in burn and CI groups compared to radiation. CI led to elevated levels of NLRP3 and IL1β in the jejunum. Intestinal barrier disruption was indicated by decreasing circulating l-citrulline in CI which correlated inversely with intestinal-Fatty Acid Binding Protein. Bacteremia was elevated post-burn on day 1 and again from day 7-14 in burn and CI groups. Microbiome analysis showed phylogenetic shifts and differential abundance across groups with CI animals exhibiting distinct microbial signatures linked to intestinal dysfunction and liver injury. Liver RNA-seq revealed group-specific gene expression changes, with CI-altered pathways implicating immune responses and lipid metabolism, which were correlated with gut microbiota such as Bacteroidaceae and Lachnospiraceae. Taken together, we present a first-of-its kind large animal model of radiation combined injury to highlight the interplay between gut-liver axis disruptions and systemic injury responses.},
}

Animals
*Burns/metabolism/pathology/genetics/microbiology/complications
Swine
*Liver/metabolism/radiation effects/pathology
Swine, Miniature
*Gastrointestinal Microbiome/radiation effects
Disease Models, Animal
Transcriptome
*Radiation Exposure/adverse effects
*Radiation Injuries, Experimental
Multiomics

@article {pmid41266339,
year = {2025},
author = {Muletz-Wolz, CR and Urrutia-Carter, J and Osborne, O and Kutos, S and Meneses Montano, J and Madison, JD and Gratwicke, B and Racharaks, R and Roncal, NE and Jimenez, RR and Ellison, A and Cleland, TP},
title = {Novel antimicrobial peptides and peptide-microbiome crosstalk in Appalachian salamander skin.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {213},
pmid = {41266339},
issn = {2055-5008},
support = {IOS-2131060//National Science Foundation/ ; IOS-2131060//National Science Foundation/ ; IOS-2131060//National Science Foundation/ ; IOS-2131060//National Science Foundation/ ; IOS-2131060//National Science Foundation/ ; IOS-2131060//National Science Foundation/ ; IOS-2131060//National Science Foundation/ ; BB/W013517/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/W013517/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MI210200//Walter Reed Army Institute of Research/ ; MI210200//Walter Reed Army Institute of Research/ ; },
mesh = {Animals ; *Skin/microbiology ; *Caudata/microbiology ; *Microbiota ; *Antimicrobial Peptides/pharmacology/metabolism/genetics ; Bacteria/drug effects/classification/genetics ; Proteomics ; Batrachochytrium/drug effects ; Humans ; *Antimicrobial Cationic Peptides/pharmacology ; Gene Expression Profiling ; },
abstract = {Using multi-omics tools, we discovered new antimicrobial peptides (AMPs) and examined AMP-microbial interactions in three Appalachian salamander species (Plethodon cinereus, Eurycea bislineata and Notophthalmus viridescens). We conducted skin transcriptomics (n = 13) and proteomics (n = 91) to identify 200+ candidate AMPs. With candidate AMPs, we identified correlations with skin microbiomes and synthesized 20 peptides to challenge against pathogens of amphibians (Batrachochytrium dendrobatidis: Bd) and humans (ESKAPEE). Using transcriptomics, candidate AMPs were detected in all individuals with Cathelidicins being most common. Using proteomics, AMPs were found in 34% of individuals (31/91)-predominately E. bislineata-with Kinin-like peptides being most common. Candidate AMP composition generally predicted skin bacterial composition, suggesting that AMPs influence host-microbial symbioses. Crude and synthesized peptides showed limited activity against Bd. Two synthesized Cathelicidins (Pcin-CATH3 and Pcin-CATH5) inhibited human pathogens, Acinetobacter baumannii, Pseudomonas aeruginosa and Escherichia coli. Our findings inform the potential usage of AMPs in conservation and translational applications.},
}

Animals
*Skin/microbiology
*Caudata/microbiology
*Microbiota
*Antimicrobial Peptides/pharmacology/metabolism/genetics
Bacteria/drug effects/classification/genetics
Proteomics
Batrachochytrium/drug effects
Humans
*Antimicrobial Cationic Peptides/pharmacology
Gene Expression Profiling

@article {pmid41266305,
year = {2025},
author = {Fouladi, F and Chen, Y and Bera, S and Jarmusch, AK and Van Tyne, D and Palella, FJ and Margolick, JB and Chew, KW and Sun, J and Martinson, J and Rinaldo, CR and Peddada, SD},
title = {A taxon-specific measurement of disruption in a multi-modal study of microbiomes and metabolomes reveals system-wide dysbiosis preceding HIV-1 infection.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10204},
pmid = {41266305},
issn = {2041-1723},
support = {ZIA ES103400/ImNIH/Intramural NIH HHS/United States ; ZIA ES103389/ImNIH/Intramural NIH HHS/United States ; ZIA ES 103400//U.S. Department of Health & Human Services | NIH | National Institute of Environmental Health Sciences (NIEHS)/ ; ZIA ES 103389//U.S. Department of Health & Human Services | NIH | National Institute of Environmental Health Sciences (NIEHS)/ ; },
mesh = {Humans ; *HIV Infections/microbiology/metabolism ; Male ; *HIV-1 ; *Dysbiosis/microbiology/metabolism ; Adult ; Feces/microbiology ; *Metabolome ; *Microbiota ; Homosexuality, Male ; Gastrointestinal Microbiome ; Purines/metabolism ; Middle Aged ; },
abstract = {The microbiome plays an important role in immune responses and inflammation in HIV-1 infection. Hence, a deeper understanding of the changes in the microbiome, its function and metabolites, and their interactions prior to HIV-1 infection is potentially important for HIV-1 prevention strategies. Using stool, oral washes, and plasma biospecimens obtained from men who have sex with men (MSM) and who were without HIV-1, we found several differences in microbial ecologies, gene functions, and metabolites between MSM who became HIV-1 infected (Pre-HIV) within six months and those who remained HIV-1 uninfected (Non-HIV). The Pre-HIV group had an enrichment of enzymes involved in purine metabolism, lower amino acid metabolism, and higher oxidative stress before the infection compared to the Non-HIV group. We also introduced a novel and broadly applicable taxon-specific measure of DISruption in COrrelations (DISCO) with other features, such as microbial taxa and metabolites in a given group (e.g., Pre-HIV group) relative to a reference group (e.g., Non-HIV group). Using DISCO, we identified several gut and oral species with disrupted correlations prior to HIV-1 infection. Application of DISCO to external datasets revealed that Prevotella spp. are consistently disrupted in their correlations across multiple cohorts prior to or following HIV-1 infection.},
}

Humans
*HIV Infections/microbiology/metabolism
Male
*HIV-1
*Dysbiosis/microbiology/metabolism
Adult
Feces/microbiology
*Metabolome
*Microbiota
Homosexuality, Male
Gastrointestinal Microbiome
Purines/metabolism
Middle Aged

@article {pmid41266190,
year = {2025},
author = {Wang, Y and Li, J and Lian, Z and Hao, H and Zheng, X},
title = {Tryptophan metabolites at the service of neuroimmune sensing of microbes.},
journal = {Trends in molecular medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.molmed.2025.10.009},
pmid = {41266190},
issn = {1471-499X},
abstract = {Hosts have evolved multifaceted, intricate mechanisms to sense and respond to the microbes they coexist with, and these mechanisms play an important role in health and disease. The co-metabolism of dietary components by hosts and their microbiomes produces a myriad of signaling molecules, which are increasingly recognized in pathophysiology regulation via their engagement with the neuro-immune network. In this review, we focus on the emerging role of tryptophan (Trp) metabolites in host-microbe crosstalk through the lens of neuroimmune sensing in the gut and beyond. We highlight how Trp metabolites orchestrate the immune and neural networks to mediate the local and trans-organ effects of the microbiome. We also consider how a neuroimmunometabolic perspective could offer valuable insights into the pathogenesis of, and treatment strategies for, chronic diseases.},
}

@article {pmid41266021,
year = {2026},
author = {Rutledge, S and Brown, RS},
title = {Acute Alcoholic Hepatitis: New and Experimental Medications.},
journal = {Clinics in liver disease},
volume = {30},
number = {1},
pages = {71-92},
doi = {10.1016/j.cld.2025.09.005},
pmid = {41266021},
issn = {1557-8224},
mesh = {Humans ; *Hepatitis, Alcoholic/therapy/drug therapy/genetics ; Liver Regeneration/drug effects ; Interleukins/therapeutic use ; Granulocyte Colony-Stimulating Factor/therapeutic use ; Interleukin-22 ; Acute Disease ; Acyltransferases ; Phospholipases A2, Calcium-Independent ; },
abstract = {Severe alcohol-associated hepatitis (AH) is associated with high mortality and is rising in incidence but there are limited treatment options. Therapies being studied for AH include those targeting systemic cytokine-mediated inflammation, hepatic regeneration, reactive oxygen species, the microbiome, and genetics. Regenerative agents (such as granulocyte colony-stimulating factor, interleukin-22, and stem cell therapies) and therapies targeting the dysregulated microbiome hold the most promise and warrant larger trials. Manipulating the underlying genetics (eg, by gene editing of PNPLA3 or HSD17B13) is a lofty goal in personalized targeted therapy for AH but is many years from primetime.},
}

Humans
*Hepatitis, Alcoholic/therapy/drug therapy/genetics
Liver Regeneration/drug effects
Interleukins/therapeutic use
Granulocyte Colony-Stimulating Factor/therapeutic use
Interleukin-22
Acute Disease
Acyltransferases
Phospholipases A2, Calcium-Independent

@article {pmid41266019,
year = {2026},
author = {Maddur, H and Flamm, S},
title = {Alcohol-Related Liver Disease: Novel Insights into Mechanism.},
journal = {Clinics in liver disease},
volume = {30},
number = {1},
pages = {45-54},
doi = {10.1016/j.cld.2025.08.004},
pmid = {41266019},
issn = {1557-8224},
mesh = {Humans ; *Liver Diseases, Alcoholic/metabolism/etiology/genetics ; Oxidative Stress ; Gastrointestinal Microbiome ; MicroRNAs/metabolism ; Epigenesis, Genetic ; Lipid Metabolism ; Receptors, G-Protein-Coupled/metabolism ; },
abstract = {Alcohol-related liver injury is complex and remains poorly understood. Research to date has pinpointed the role of oxidative stress, hepatic inflammation, and derangements in lipid metabolism as drivers of disease pathogenesis. More recent research has identified alterations in the gut microbiome, epigenetics, G protein-coupled receptors, and microRNA's as possible drivers of disease pathogenesis and may serve as potential new treatment targets.},
}

Humans
*Liver Diseases, Alcoholic/metabolism/etiology/genetics
Oxidative Stress
Gastrointestinal Microbiome
MicroRNAs/metabolism
Epigenesis, Genetic
Lipid Metabolism
Receptors, G-Protein-Coupled/metabolism

@article {pmid41265701,
year = {2025},
author = {Wijesundara, SH and Weeraratne, TC and Noordeen, F and de Silva, WAPP},
title = {Microbiome and physicochemical properties of breeding waters of Aedes albopictus mosquitoes in Sri Lanka.},
journal = {Parasitology international},
volume = {},
number = {},
pages = {103199},
doi = {10.1016/j.parint.2025.103199},
pmid = {41265701},
issn = {1873-0329},
abstract = {Aedes albopictus is a key vector of arboviral transmission, and its widespread adaptability to diverse breeding habitats makes control efforts challenging. This study aimed to evaluate the bacterial communities and physicochemical characteristics of Ae. albopictus breeding sites across selected localities in Sri Lanka and to assess their potential influence on adult mosquito fitness using adult body size as an indicator. A total of 133 positive breeding sites were surveyed across eight districts. Breeding sites were categorized by premise type, container type, nature (natural or artificial), and as indoor or outdoor. From a subset of 73 representing breeding sites, microbial cultures were isolated, and bacterial diversities were assessed. Adult emergence rate was recorded under standardized rearing conditions, and female body size was estimated using wing length measurements. Physicochemical parameters, including temperature, pH, dissolved oxygen, electrical conductivity, and total dissolved solids, were reported for each breeding site. Each breeding site consisted of 2-6 distinct bacterial morphotypes, with Aeromonas hydrophila, Acinetobacter proteolyticus, and Bacillus subtilis as the most frequently reported species. The physicochemical properties of the breeding water (temperature, conductivity, TDS, and DO) were significantly different between sites (P < 0.05). There was a strong correlation between the diversity of bacteria and the wing length of mosquitoes. A relatively weak correlation was noted between the body size measurements and the bacterial abundance. A moderate explanatory power was present between water quality parameters, microbial composition, and the adult Ae. albopictus body size (R[2] = 27.7 %).},
}

@article {pmid41256617,
year = {2025},
author = {Surve, SV and Valls, RA and Barrack, KE and Gwilt, LL and Gardner, TB and O'Toole, GA},
title = {The Regional Landscape of the Human Colon Culturome in Health and Cystic Fibrosis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41256617},
issn = {2692-8205},
abstract = {Cystic fibrosis (CF) alters gut physiology, yet its impact on microbial communities across colonic regions (ascending, transverse, descending colon) and microhabitats (lumen, mucosa) remains incompletely understood. Here, we applied culturomics to characterize gut microbiota in 32 individuals (22 nonCF, 10 CF). Persons with CF (pwCF) exhibited significantly higher viable bacterial loads than nonCF individuals, particularly in mucosal samples. Anaerobes predominated overall, with relative enrichment of aerobes in the mucosa of pwCF. Alpha diversity was reduced in mucosal samples and aerobic cultures for pwCF, whereas beta diversity was influenced by all the tested variables except the colonic region. Phylum-level analyses revealed enrichment of Proteobacteria and depletion of Actinobacteria, Bacteroidota, and Firmicutes in samples from pwCF, consistent with stool analysis. Random forest models identified selected oral-associated microbes as key predictive taxa and accurately classified polyp status with very high accuracy. Whole-genome sequencing of Bacteroides fragilis (n=21) and Escherichia coli (n=15) isolates, representing a subset of 109 gut bacterial genomes sequenced from this cohort, revealed minimal genomic variation across colonic regions and sample types, indicating intra-individual strain stability. The understandings from this pilot culturome study may help in developing targeted microbial therapeutic approaches to address the gut dysbiosis of CF.},
}

@article {pmid41265504,
year = {2025},
author = {McKee, KS and Bassis, CM and Golob, J and Palazzolo, B and Comstock, SS and Rosas-Salazar, C and Stanford, JB and Ananda, S and O'Connor, T and Gern, JE and Paneth, N and Dunlop, AL and , },
title = {Vaginal microbiome structure in pregnancy and host factors predict preterm birth: Results from the ECHO Cohort.},
journal = {Annals of epidemiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.annepidem.2025.11.003},
pmid = {41265504},
issn = {1873-2585},
abstract = {PURPOSE: The vaginal microbiome is dynamic, typically shifting during pregnancy toward enrichment of Lactobacillus. However, proliferation of Lactobacillus may be absent among women with preterm births (PTBs). We sought to identify robust vaginal microbiota signatures along with host factors that predicted PTB across diverse U.S. cohorts.

METHODS: We meta-analyzed 16S rRNA gene amplicon sequence data from the Environmental influences on Child Health Outcomes Cohort. We classified community state types (CSTs) and employed penalized logistic regression models to assess the association between vaginal CST and PTB. We generated supervised random forest models and validated them using a train-and-test approach to identify the most predictive vaginal taxa and host factors.

RESULTS: Of 683 births, 12% were preterm. Overall, 26% had a non- L. iners Lactobacillus-dominant CST (I, II, V), 43% had a L. iners-dominant CST (III), and 30% had a diverse, non-Lactobacillus-dominant (IV-B, IV-C) CST. Vaginal CST was strongly associated with PTB (adjusted odds ratio [aOR], 3.86, 95% confidence interval [CI], 1.57-11.3 for diverse, non-Lactobacillus-dominant communities and aOR, 3.03, 95% CI, 1.25-8.78 for L. iners-dominant compared to L. crispatus-dominant communities). The model with the highest area under the curve (AUC=.77) included Gardnerella vaginalis, age, Prevotella timonensis, and L. crispatus.

CONCLUSIONS: Along with host factors, vaginal microbiota could be used for predictive risk scoring for PTB across different U.S. cohorts.},
}

@article {pmid41265489,
year = {2025},
author = {Akhirini, N and Suprayogi, WPS and Saraswati, PN and Ratriyanto, A and Irawan, A},
title = {Fermented soybean meal using Bacillus subtilis and Aspergillus oryzae positively enhances cecal microbial composition and broiler performance.},
journal = {Animal bioscience},
volume = {},
number = {},
pages = {},
doi = {10.5713/ab.250400},
pmid = {41265489},
issn = {2765-0189},
abstract = {OBJECTIVE: This study investigated the effect of fermented SBM (FSBM) prepared through solid-state fermentation using Bacillus subtilis (BS) and Aspergillus oryzae (AO) to replace SBM in broiler chickens' diets on production, digestibility, and cecal microbial profile.

METHODS: In total, 160 sex-mixed day-old chicks of Cobb 500 broiler chickens were randomly assigned to four groups, four pens (replicates; 10 birds each pen), and were raised for 35 days under tropical conditions. The treatments were control (basal diet; CON) or SBM replaced by FSBM produced using AO (AO group), BS (BS group), and their combination (AO+BS group).

RESULTS: Birds fed AO+BS diet resulted in higher (p=0.003) BW while BS diet tended (p=0.063) to have higher final BW than CON or AO. Similarly, birds fed FSBM prepared under either BS or AO+BS had higher feed intake (p<0.01) than the CON group. No difference was found on feed conversion ratio (FCR). Relative organ weights including heart, liver, abdominal fat, and total inner organs were lower (p<0.01) on birds fed AO+BS diet than CON, but relative carcass weight was unaffected (p>0.05). Treatments with BS or AO+BS increased dry matter (DM) (p=0.032), organic matter (OM) (p=0.016), and crude protein (CP) (p=0.044) digestibility, while AO did not affect DM and CP digestibility. Broilers fed AO+BS diet showed greater abundance of Firmicutes phylum and Bacteroides genus than CON group. Several microbial taxa biomarkers were identified via LEfSE analysis, including higher abundance of Enterococcus and Bacillus in AO+BS group but lower abundance of Erysipelatoclostridium, Odoribacter, Ruminococcaceae bacterium, Staphylococcus, and Clostridium methylpentosum group in CON group.

CONCLUSION: B. subtilis and A. oryzae could synergistically enhance the nutritional quality of SBM, positively alter cecal microbiota, and improve the production performance of broiler chickens.},
}

@article {pmid41265441,
year = {2025},
author = {Xu, Y and Wang, Z and Wu, J and Yue, Y and Ren, Y and Pan, Y and Li, J and Liu, C and Borriss, R and Liu, X and Qiao, J and Lee, YW and Wu, H and Dini-Andreote, F and Shen, Q and Xiong, W and Gao, X and Berendsen, RL and Gu, Q},
title = {Keystone Pseudomonas species in the wheat phyllosphere microbiome mitigate Fusarium head blight by altering host pH.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.10.016},
pmid = {41265441},
issn = {1934-6069},
abstract = {Phyllosphere microbiota play crucial roles in supporting host performance. However, the dynamic changes of phyllosphere-associated microbiome during pathogen infections and their impacts on plant health remain unknown. Here, we found phyllosphere microbes can mitigate wheat Fusarium head blight (FHB), a severe disease caused by Fusarium graminearum (F. graminearum) pathogen that promotes infection by inducing host alkalinization. Using wheat head microbial community profiling and metatranscriptomics, we found Pseudomonas spp. significantly enriched on infected wheat heads. Through isolating 595 bacterial strains from infected wheat heads-including 196 Pseudomonas isolates-we identified certain enriched Pseudomonas isolates capable of producing organic acids that counteract pathogen-induced pH upshift. In vitro experiments confirm the selective promotion of specific host-acidifying Pseudomonas in wheat heads. Field trials confirmed that host-acidifying Pseudomonas strains effectively controlled FHB. These findings highlight the pivotal role of plant-beneficial microbes in host pH regulation and offer innovative avenues for sustainable plant disease control.},
}

@article {pmid41265342,
year = {2025},
author = {Uyeda, KS and Borovik, AS},
title = {Forged in O2: Transition metal ions and the rise of aerobic life.},
journal = {Journal of inorganic biochemistry},
volume = {275},
number = {},
pages = {113147},
doi = {10.1016/j.jinorgbio.2025.113147},
pmid = {41265342},
issn = {1873-3344},
abstract = {The evolution of oxidative metabolism has shaped life on Earth, from ancient anaerobic microorganisms to modern eukaryotes. Central to aerobic life is the ability of metalloproteins to regulate and utilize dioxygen through tightly controlled biochemical processes. Beginning with the emergence of oxygenic photosynthesis and aerobic respiration, the pivotal roles of metalloenzymes in dioxygen activation, utilization and detoxification are then highlighted. Bridging perspectives from bioinorganic chemistry, enzymology, synthetic biology and microbiome science, we discuss how studies of biomimetic molecular complexes and natural and artificial metalloproteins illuminate the structural and functional strategies used to manage dioxygen reactivity. We further consider the systemic roles of metal ions in maintaining redox balance, shaping host-microbe interactions, and contributing to pathological outcomes when misregulated. A foundation is established for understanding the critical roles that metal ions play in dioxygen chemistry that underpins both healthy metabolism and oxidative stress related diseases.},
}

@article {pmid41265278,
year = {2025},
author = {Tian, Y and Hao, F and Xu, G and Qian, Y and Liu, J and Pan, N and Yang, T},
title = {Causal effects of gut microbiome on aortic dissection: A mendelian randomization study.},
journal = {Clinics (Sao Paulo, Brazil)},
volume = {80},
number = {},
pages = {100811},
doi = {10.1016/j.clinsp.2025.100811},
pmid = {41265278},
issn = {1980-5322},
abstract = {INTRODUCTION: Aortic Dissection (AD) is a severe vascular disease with high mortality. While its progression is rapid, the development of AD is a chronic disease process. The gut microbiome may play a crucial role in this process. This study aims to explore the potential causal association between gut microbiome and AD using Mendelian Randomization (MR).

METHODS: This study employed a two-sample MR approach using Genome-Wide Association Study (GWAS) data from the Finnish population to investigate the causal association between gut microbiota and AD. Single Nucleotide Polymorphisms (SNPs) associated with 473 gut microbiota taxa were selected as instrumental variables, and various MR methods were applied to evaluate the causal effects. Sensitivity analyses were conducted to assess the robustness of the results, and a reverse MR analysis was performed to validate the directionality of the associations.

RESULTS: The MR analysis confirmed that Actinomycetales, Bacillales A, Lawsonibacter sp002161175, Prevotella sp002933775, Saccharomonospora, Acidaminococcus fermentans, CAG-110, CAG-177 sp002451755, CAG-177 sp003514385, and Eisenbergiella sp900066775 may exert protective effects, whereas koll11, Magnetospirillum A, Poseidoniaceae, Pseudomonas aeruginosa, Bacteroides eggerthii, CAG-269 sp002372935, and Dorea phocaeense may increase the risk of AD. Sensitivity analyses confirmed the robustness of these findings.

CONCLUSION: This study provides new insights into the role of gut microbiome in AD, identifying specific taxa that may serve as protective or risk factors. Further research is needed to validate these findings in broader populations.},
}

@article {pmid41265274,
year = {2025},
author = {Eichinger, J and Seifert, J and Sáenz, JS and Amin, N and Lorenz, S and Eckel, F and Zollfrank, C and Windisch, W and Brugger, D},
title = {The interaction of microplastics with the ruminal ecosystem in vitro.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140481},
doi = {10.1016/j.jhazmat.2025.140481},
pmid = {41265274},
issn = {1873-3336},
abstract = {Mismanaged plastic waste contaminates marine and terrestrial environments, so farm animals are increasingly exposed to microplastics (MP) in feed. Yet their interactions with the rumen microbiome are largely unknown. We evaluated these interactions in vitro with the Hohenheim Gas Test. Five MP chemical species - polylactide, polyhydroxybutyrate, high‑density polyethylene, polyvinyl chloride and polypropylene - were tested in two particle‑size classes (<125 µm and 125-500 µm) and six doses (0-70 mg per incubation cylinder). Each MP variant was incubated with rumen fluid plus hay or barley. We recorded cumulative gas production, pH and dry‑matter (DM) disappearance, followed by volatile‑fatty‑acid profiling, metaproteomics and metabolomics. MP consistently reduced cumulative gas output independent of polymer type, particle size or dose, but enhanced total DM degradation dose-dependently. In barley incubations, metaproteomics revealed a shift from Bacteroidetes toward Firmicutes and higher abundance of protein categories "replication & repair" and "translation", while "carbohydrate metabolism & transport" and "amino‑acid metabolism" declined. The results show that MPs interact with, and are at least partly degraded by, the ruminal microbiota. Progressive size reduction in the rumen could facilitate MP translocation into animal tissues, underscoring the need for in‑vivo studies on animal health and food‑safety implications.},
}

@article {pmid41265266,
year = {2025},
author = {Fernández-Triana, I and Rubilar, O and Fincheira, P and Fernández-Baldo, MA and Saldivar-Diaz, M and Lora-Peña, OA and Benavides-Mendoza, A and Schoebitz, M and Tighe-Neira, R and Leiva, S and Tortella, GR},
title = {Abiotic multi-stressor co-exposure to hazardous pollutants reveals drought as the primary driver of soil microbiome shifts.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140515},
doi = {10.1016/j.jhazmat.2025.140515},
pmid = {41265266},
issn = {1873-3336},
abstract = {Soil microbial communities are essential for ecosystem functioning, yet their responses to combined abiotic stressors remain unclear, as most studies focus on single-stressor effects. In this work, the combined effects of different drought levels and co-contamination with copper nanoparticles and the fungicide carbendazim on microbial community structure and function in an agricultural soil over 120 days were evaluated. Enzymatic activities, potential nitrification rate, and functional gene abundances (16S and amoB) were measured. Moreover, 16S rRNA metabarcoding was applied to explore microbial diversity and community dynamics comprehensively. Pesticide dissipation kinetics were also assessed. General metabolic and nutrient-cycling enzymes were susceptible to combined stress under SD and ED. Although alpha and beta diversity showed limited differences at the end of the experiment, co-occurrence networks revealed progressive increases in microbial connectivity and negative correlations, indicating structural reorganization. Functional predictions highlighted a shift from nitrogen and phosphorus cycling toward carbon-degradation pathways, suggesting stress-induced trade-offs. Significantly, pesticide dissipation was markedly reduced under SD, with prolonged half-lives and higher residues, reflecting impaired microbial degradation capacity. Collectively, our results demonstrate that drought is the dominant driver of microbial reorganization, amplifying the effects of emerging contaminants on microbial interactions, functional potential, and pollutant fate.},
}

@article {pmid41265168,
year = {2025},
author = {Jiang, Y and Xie, Y and Liu, F and Qin, Y and Zhang, Y and Tang, L and Dong, X and Li, L and Chen, S and Yuan, B and You, Y and Qiu, R},
title = {Biological Validation of the PSC-MCAT: Analyzing Dental Plaque Microbiota Across Caries Risk Levels in Preschoolers.},
journal = {International dental journal},
volume = {76},
number = {1},
pages = {104007},
doi = {10.1016/j.identj.2025.104007},
pmid = {41265168},
issn = {1875-595X},
abstract = {OBJECTIVE: Although Caries Risk Assessment (CRA) tools are widely recognised in preventive dentistry for predicting dental caries risk in children, there is a notable lack of studies addressing CRA within the Chinese population. This study aimed to evaluate the biological validity of the modified caries-risk assessment tool for preschool children (PSC-MCAT) by analysing the oral microbiome of children stratified by caries risk.

MATERIALS AND METHODS: A comprehensive analysis of the oral microbiome was conducted on 72 preschool children categorised into low- (L), moderate- (M), and high-risk (H) groups based on the PSC-MCAT criteria. Next-generation sequencing was employed to assess microbial diversity and structure. Statistical analyses were performed to identify significant differences among the risk groups.

RESULTS: The analysis revealed statistically significant differences in microbial diversity and structure among the caries risk groups (P < .05). Specific caries risk biomarkers, including Scardovia, Prevotella, and Megasphaera, were significantly enriched in the H group (P < .05). Co-occurrence network analysis showed that the M group exhibited a more complex microbial network compared to the H group, while the L group displayed sparse ecological interactions. KEGG pathway analysis identified 8 differentially abundant metabolic pathways among the risk groups. Furthermore, certain biomarkers in the H group, such as Scardovia and Megasphaera, were associated with D-arginine and D-ornithine metabolic pathways (P < .05) and were closely linked to children's oral health behaviours, including sweet food intake frequency and regular fluoride application (P < .05).

CONCLUSION: This study provides the first biological validation of the PSC-MCAT's risk stratification capacity, establishing a mechanistic link between clinical risk tiers and the dynamics of acidogenic pathobionts as well as host-microbe metabolic interactions. These findings offer valuable insights for prognostic predictions and targeted caries management strategies.},
}

@article {pmid41264973,
year = {2025},
author = {See, MS and Ching, XL and Razali, N and Asri, IS and Abdullah, MM and Bidai, J and Rusli, MU and Ma, NL},
title = {Blood heavy metals content and gut microbiota profile in immature and nesting wild green turtles (Chelonia mydas).},
journal = {Marine environmental research},
volume = {213},
number = {},
pages = {107688},
doi = {10.1016/j.marenvres.2025.107688},
pmid = {41264973},
issn = {1879-0291},
abstract = {Sea turtles live in habitats where they experience chronic exposure to pollutants, such as heavy metals, over the course of their long lifespan. This makes them valuable model organisms for studying the long-term biological impacts of persistent environmental contaminants. Morphological changes are often insufficient to capture the impacts of low-dose exposures, whereas gut microbiota profiling can offer critical insights into host health and adaptive responses to environmental stressors. This study investigated the relationship between heavy metal exposure and gut microbiota composition in green turtles (Chelonia mydas) at immature (IM, n = 10) and nesting (NT, n = 9) stages. Metal concentrations in whole blood were measured using inductively coupled plasma mass spectrometry (ICP-MS), while gut microbiota were characterized via 16S rRNA gene sequencing. The blood of immature turtles exhibited significantly higher concentrations of manganese (Mn), whereas nesting turtles had elevated arsenic (As), lead (Pb), barium (Ba), and strontium (Sr). Analysis of gut microbiota revealed significant differences in both α-Shannon and β-diversity associated with different pollutants, indicate restructuring of microbial communities. PICRUSt2 revealed alteration of carbohydrate, nucleotide, vitamin, and xenobiotic metabolisms among growth stages. Correlation analysis (LEfSe and CCA) further showed that bacterial genera such as Methylophaga and Thermomonas were positively associated with Cd, Pb, and Sr, whereas Lactobacillus and Rodentibacter displayed negative correlations with these metals. Collectively, this highlights the potential of pollutants to compromise host health through microbiome-mediated mechanisms.},
}

@article {pmid41264968,
year = {2025},
author = {Yang, C and Bao, L and Shi, Z and Xv, X and Li, J and Jiang, D and You, L},
title = {Jingning formula alleviates ADHD by restoring gut microbiota dysbiosis and tryptophan metabolic dysfunction.},
journal = {Journal of pharmaceutical and biomedical analysis},
volume = {269},
number = {},
pages = {117256},
doi = {10.1016/j.jpba.2025.117256},
pmid = {41264968},
issn = {1873-264X},
abstract = {Jingning Fang (JNF), a clinically used herbal medicine for attention deficit hyperactivity disorder (ADHD), demonstrates significant efficacy in alleviating core symptoms such as hyperactivity and impulsivity in pediatric patients. To systematically investigate its therapeutic mechanisms, we implemented an integrated approach encompassing UPLC-Q-TOF/MS-based untargeted metabolomics profiling of brain, serum, and fecal specimens, targeted quantification of tryptophan pathway metabolites across these biological compartments, and gut microbiome characterization via 16S rRNA sequencing. Our analysis revealed a prominently dysregulated metabolic pathway in ADHD, characterized by perturbations in tryptophan metabolism that were particularly pronounced in feces (P < 0.05). Notably, the kynurenic acid (KYNA)/quinolinic acid (QUINA) ratio, a pivotal indicator of kynurenine pathway homeostasis, exhibited robust correlations with both behavioral manifestations and gut microbial ecology. These findings provide a mechanistic basis for JNF's clinical efficacy in ADHD management by highlighting its role in restoring gut microbiome balance and tryptophan metabolic homeostasis.},
}

@article {pmid41264233,
year = {2025},
author = {Yun, Y and Duan, C and He, X and Tang, R and Lan, Y and Lu, M and Liu, T and Fan, X and Fan, Z and Ran, J},
title = {Gut microbiome plasticity explains the altitudinal distribution pattern and adaptability in a small mammal species (Apodemus draco).},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0238825},
doi = {10.1128/spectrum.02388-25},
pmid = {41264233},
issn = {2165-0497},
abstract = {Altitudinal distribution patterns of species, a central focus of ecology, predominantly focus on environmental factors and only rarely on the host's intrinsic adaptive capacity. Particularly, the role of gut microbiota has not yet been studied. Here, we used the wild South China Field Mouse (Apodemus draco), a widely distributed small mammal species, as the study subject to investigate the altitudinal distribution pattern of the species and assess how gut microbiota contributes to the formation of this pattern. A total of 219 wild samples were captured in the middle section of the Qionglai Mountains, China, and 121 adult individuals were selected for metagenomic sequencing (e.g., gut microbial diversity, network topology, composition, and functional profiles). Vegetation cover of each sampling quadrat was assessed using Normalized Difference Vegetation Index. Our results indicate that A. draco exhibited a hump-shaped altitudinal distribution, but the peak abundance of A. draco corresponds to lower vegetation cover of habitats. Gut microbial diversity, complexity, robustness, energy harvesting ability, and carbohydrate utilization capacity all peaked at the mid-altitude zone, matching the host's spatial distribution pattern. Furthermore, the gut microbiome in high-altitude A. draco populations facilitates host acclimatization in extreme high-altitude niches by enhancing energy harvesting, hypoxia tolerance, and pathogen resistance.IMPORTANCEWe propose for the first time that the gut microbiome serves as a pivotal factor in structuring the altitudinal distribution pattern of species and further reveal a gut microbiota-mediated adaptive strategy underlying mammalian high-altitude adaptation. These results demonstrate that the gut microbiome fundamentally facilitates host adaptation to ecological niches. The study provides a novel insight into the factors of species' spatial distribution from a gut microbiota perspective.},
}

@article {pmid41264189,
year = {2025},
author = {Mohamad Zain, N and Mohd Amin, I and Abdul Razak, F and Abu Hassan, MI},
title = {Preliminary screening of pomegranate-derived compounds for antimicrobial and anti-virulence effects against cariogenic streptococci.},
journal = {The Saudi dental journal},
volume = {37},
number = {10-12},
pages = {84},
pmid = {41264189},
issn = {1013-9052},
abstract = {As a biofilm-mediated disease, dental caries is primarily attributed to the activity of Streptococcus mutans and Streptococcus sobrinus, key contributors to enamel mineral loss under acidic conditions. Current broad-spectrum antimicrobials disrupt the oral microbiota and carry undesirable side effects, prompting interest in targeted, microbiome-friendly alternatives. This study evaluated the antimicrobial, anti-cariogenic, and cytotoxic properties of pomegranate (Punica granatum) derived compounds, corilagin, ellagic acid, gallocatechin, kaempferol-7-O-glucoside, punicalagin, punicalin, and rutin against cariogenic S. mutans and S. sobrinus, and the commensal S. gordonii. Antibacterial activity was assessed using disc diffusion, minimum inhibitory concentration (MIC), and minimum bactericidal concentration (MBC) methods. Anti-virulence effects were evaluated through glycolytic pH drop and cell surface hydrophobicity assays. Cytotoxicity was determined using the brine shrimp lethality assay. Punicalagin, punicalin, and ellagic acid showed strong, selective bactericidal activity against S. mutans and S. sobrinus, with low MICs and MBC/MIC ratios, while sparing S. gordonii. These compounds significantly suppressed acid production, maintaining pH above the critical demineralisation threshold, and reduced surface hydrophobicity in cariogenic strains without affecting the commensal. Most compounds exhibited low toxicity (LC50 > 500 µg/mL), indicating a favourable safety profile. Overall, punicalagin and punicalin demonstrated dual antimicrobial and anti-virulence activity with selective targeting of cariogenic pathogens. These findings support the potential inclusion of punicalagin and punicalin in oral care formulations aimed at preventing dental caries while preserving beneficial oral microbiota. As this is a preliminary screening study, the results should be interpreted cautiously, and further biofilm and host-cell assays are needed to confirm translational potential.},
}

@article {pmid41264167,
year = {2025},
author = {Baek, KW and Yun, K and He, MT and Kim, NK and Kim, JS and Ahn, K and Kim, JH},
title = {Integrated transcriptomic and 16S rRNA analyses reveal colon and brain barrier-preserving effects of red radish (Raphanus sativus L.) sprout supplementation in high-fat diet-fed mice.},
journal = {Genes & genomics},
volume = {},
number = {},
pages = {},
pmid = {41264167},
issn = {2092-9293},
abstract = {BACKGROUND: Radish sprouts (Raphanus sativus L.) are rich in dietary fibers and phytochemicals with antioxidant and anti-inflammatory activities. However, their whole-food effects on the gut-brain axis remain poorly defined.

OBJECTIVE: This study examined the preventive potential of whole-food red radish sprout (RS) powder against high-fat diet (HFD)-induced obesity and cognitive decline in mice, focusing on its effects on barrier integrity, inflammation, oxidative stress, and gut microbiota.

METHODS: Male C57BL/6 mice were fed an HFD for 16 weeks with or without RS powder (low or high dose). Assessments included body and tissue indices, oral glucose tolerance, serum leptin, cognitive performance, oxidative stress in brain, gene expression of tight junction and inflammatory markers in colon and brain, and fecal microbiota profiling using 16S rRNA sequencing.

RESULTS: RS supplementation attenuated HFD-induced weight gain, improved glucose tolerance, and reduced leptin levels, with stronger effects at the higher dose. Cognitive deficits were rescued by RS, accompanied by alleviation of brain oxidative stress and reduced expression of neuroinflammatory genes (Tnf, Il6, Il1b, Aif1, Gfap). RS restored tight-junction genes (Tjp1, Ocln, Cldn1, Jam2, Cdh5) while simultaneously decreasing Cldn2 and pro-inflammatory transcripts, and upregulating Il10. Although alpha diversity was unchanged, beta diversity differed significantly; RS reduced the Firmicutes/Bacteroidota ratio, enriched Akkermansia and Lactobacillus, and suppressed Oscillibacter and Desulfovibrio.

CONCLUSION: Whole-food RS powder prevents HFD-induced obesity and cognitive decline by reinforcing barrier integrity, reducing inflammation and oxidative stress, and reshaping gut microbiota. These findings support RS as a practical functional food for early obesity intervention via gut-brain axis regulation.},
}

@article {pmid41263968,
year = {2025},
author = {Brennan, AA and Renshaw, CP and Tata, SC and Campanella, A and Hartman, R and Carlotz, R and Downs, M and Yurtola, A and Baum, J and Rodriguez, KM and Bertucci, MA and Tal-Gan, Y},
title = {The Quorum Sensing-Controlled Competence Regulon Drives H2O2 Production in Streptococcus gordonii.},
journal = {ACS infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsinfecdis.5c00926},
pmid = {41263968},
issn = {2373-8227},
abstract = {Streptococcus gordonii sp. firmicutes is an early colonizer of the oral microbiome and contributes positively to oral health. While this species has been found to produce hydrogen peroxide by spxB expression, the relationship of this expression to the competence regulon has not yet been explored. To this end, this study sought to investigate the connection of the S. gordonii competence regulon quorum sensing (QS) circuitry with downstream proliferative phenotypic expression resulting from competence-stimulating peptide (CSP) exposure, with specific attention to peroxide formation. Following confirmation of the native CSP, RNA-seq was completed to gain insights into transcriptomic variations resulting from CSP incubation. Later, structure-activity relationship (SAR) analyses of the native CSP were completed. The results revealed residues integral to CSP:ComD binding and activation, while indicating which residues were considered dispensable to this process. Phenotypic assessment revealed that peroxide formation was modulated via the competence regulon. Finally, interspecies competition assays were carried out to understand the interactions between S. gordonii and S. mutans, with S. gordonii demonstrating a profound capability of antagonizing S. mutans growth and proliferation. Our results support that this antagonism is mainly attributed to hydrogen peroxide production by S. gordonii. This finding suggests that S. gordonii may be exploited for its beneficial proliferative phenotypes downstream of the competence regulon.},
}

@article {pmid41263913,
year = {2025},
author = {Merrick, B and Prossomariti, D and Kertanegara, M and Wyatt, D and Goldenberg, S},
title = {Facilitators and barriers to recruitment and retention in a feasibility trial of encapsulated faecal microbiota transplant to eradicate carriage of antibiotic-resistant bacteria at an academic hospital in central London: a nested qualitative study.},
journal = {BMJ open},
volume = {15},
number = {11},
pages = {e104783},
doi = {10.1136/bmjopen-2025-104783},
pmid = {41263913},
issn = {2044-6055},
mesh = {Humans ; London ; *Fecal Microbiota Transplantation/methods ; Male ; Female ; Feasibility Studies ; Middle Aged ; Qualitative Research ; Adult ; Focus Groups ; *Patient Selection ; COVID-19/epidemiology ; Aged ; *Carrier State/therapy ; },
abstract = {OBJECTIVES: This nested qualitative study (NQS) aimed to identify facilitators and barriers to the delivery of a substantive randomised controlled trial investigating the eradication of gastrointestinal tract carriage of antibiotic-resistant organisms using encapsulated faecal microbiota transplant (FMT).

DESIGN: NQS within a participant-blinded, randomised, placebo-controlled, single-centre, feasibility trial (RCT)-Feasibility of ERadicating gastrointestinal carriage of Antibiotic-Resistant Organisms (FERARO) (ISRCTN reg. no. 34 467 677)-with data collected via focus groups and analysed using thematic analysis.

SETTING: RCT participants were recruited from a large academic tertiary referral hospital in central London. Focus groups were held at the hospital or via videoconferencing for those unable to travel.

PARTICIPANTS: This study included 13 FERARO study participants across two focus groups. 11 participants were under RCT follow-up and unaware of their treatment allocation, two participants had completed 6-month follow-up and knew whether they had received FMT or matched placebo. Additional data were opportunistically collected on reasons for declining RCT participation.

RESULTS: Participants found FMT to be an acceptable and holistic management strategy and noted positive impacts from RCT participation including enhanced personal health awareness and valuable support from the research team. The time and travel commitment presented the most substantial barrier to RCT participation. Many participants were motivated by a desire to give something back to the UK National Health Service and/or research. Patients' current health status also influenced the decision-making process, and, while infrequently cited, the COVID-19 pandemic added extra complexity likely impacting individuals' willingness to participate.

CONCLUSIONS: While FMT is generally acceptable to participants, logistical barriers such as the time and travel commitment associated with RCT participation need consideration. Effective communication, personal connections and participant education on antimicrobial resistance are likely to be crucial for enhancing recruitment and retention in future trials.

TRIAL REGISTRATION NUMBER: ISRCTN registration number 34 467 677 and EudraCT number 2019-001618-41.},
}

Humans
London
*Fecal Microbiota Transplantation/methods
Male
Female
Feasibility Studies
Middle Aged
Qualitative Research
Adult
Focus Groups
*Patient Selection
COVID-19/epidemiology
Aged
*Carrier State/therapy

@article {pmid41263680,
year = {2025},
author = {Jakubczyk-Słabicka, A and Kasprzak, J and Skonieczna-Żydecka, K and Sławek, J and Górska-Ponikowska, M},
title = {Gut and skin microbiome profiles as promising biomarkers in Parkinson's disease - preliminary results.},
journal = {Neurologia i neurochirurgia polska},
volume = {},
number = {},
pages = {},
doi = {10.5603/pjnns.108273},
pmid = {41263680},
issn = {0028-3843},
}

@article {pmid41263597,
year = {2025},
author = {Ku, M and Taibi, A and Wu, D and Chen, YT and Lopez-Dominguez, L and Yang, Y and Chen, S and Liang, F and Liu, R and Tsao, R and Power, KA and Thompson, LU and Comelli, EM},
title = {Altered mouse cecal microbiome-serum enterolignans relationships in response to dietary lignans ingested through whole flaxseed or flaxseed hull.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo03558a},
pmid = {41263597},
issn = {2042-650X},
abstract = {Flaxseed (FS) is rich in bioactive compounds, including fiber and lignans, which provide health benefits largely mediated by gut microbial metabolism. However, gut microbiota responses, including their relationship with fiber- and lignan-derived microbial metabolites (short chain fatty acids (SCFA) and enterolignans enterodiol and enterolactone), remain unclear. We addressed this through administration of an isocaloric flaxseed (FS) or flaxseed hull (FH) diet to female mice, where FH provided a higher amount of fiber and lignan secoisolariciresinol diglucoside compared to FS. Both diets increased cecal SCFA and serum enterolignans concentrations compared to the basal control diet (BD). Compared to FS, FH increased serum secoisolariciresinol, enterodiol, and total lignans, but not SCFA concentrations. FS and FH increased α- and β-diversity and altered microbiota composition and functional potential compared to BD, but no differences were observed between FS and FH, except for altered abundance of select taxa and a limited number of functions. However, the two diets altered the microbial network structure, including keystone species shifts from Intestinimonas in FS to Carnobacterium in FH, and taxa relationships with enterolignans and SCFA. Our findings suggest that while intestinal microbiota composition responses to whole flaxseed result in increased circulating enterolignans and intestinal SCFA production, FH can further elevate serum enterolignans via reorganization of interactions among taxa.},
}

@article {pmid41263574,
year = {2025},
author = {Tang, L and Xie, P and Wang, H and Hong, X and Gong, Z and Zhao, G and Yue, M},
title = {The sex hormone-gut microbiome axis: mechanistic drivers of sex-disparate bacterial infection outcomes and precision clinical interventions.},
journal = {Clinical microbiology reviews},
volume = {},
number = {},
pages = {e0023625},
doi = {10.1128/cmr.00236-25},
pmid = {41263574},
issn = {1098-6618},
abstract = {SUMMARYSex disparities in bacterial infections pose significant challenges in clinical microbiology, influencing diagnostic approaches, antimicrobial stewardship, and patient outcomes. Males frequently exhibit heightened severity in conditions like Helicobacter pylori-associated gastritis and Vibrio cholerae outbreaks, whereas females face amplified risks during reproductive phases for pathogens, such as Listeria monocytogenes and Salmonella spp. Beyond genetic and behavioral factors, the bidirectional sex hormone-gut microbiome axis emerges as a key mechanistic driver: estrogens bolster innate immunity and microbial diversity (e.g., enriching short-chain fatty acid-producing taxa like Bifidobacterium), while androgens and progesterone impose immunosuppressive effects, altering colonization resistance and virulence modulation. Microbial contributions-via β-glucuronidase-mediated hormone deconjugation, bile acid biotransformations, and metabolite signaling-further calibrate host responses, as evidenced in Clostridioides difficile recurrence and enterohemorrhagic Escherichia coli virulence upregulation. This review synthesizes epidemiological, preclinical, and emerging clinical data, highlighting the axis's role in pathogen-specific immune evasion and dysbiosis-driven exacerbations. Clinically, these insights advocate for sex-stratified microbiome diagnostics (e.g., 16S rRNA sequencing for risk profiling) and targeted therapies, including hormone-modulated probiotics to restore barrier function, fecal microbiota transplantation to curb antibiotic-associated vulnerabilities, and selective estrogen receptor modulators to enhance clearance in high-risk cohorts. Despite advances, gaps in human longitudinal studies and pathogen-strain interactions limit translation. Future research integrating multi-omics with clinical trials could refine precision interventions, optimizing infection management in diverse populations and aligning with evolving demands for personalized microbiology.},
}

@article {pmid41263569,
year = {2025},
author = {Ding, W and Ling, Z and Liu, X and Zhang, J and Cheng, Y and Zhu, Z and Wu, L and Xu, X and Gao, Y and Hu, X},
title = {Impact of carbapenem-resistant Klebsiella pneumoniae infection on gut microbiota and host immunity: a case-control study.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0297525},
doi = {10.1128/spectrum.02975-25},
pmid = {41263569},
issn = {2165-0497},
abstract = {Carbapenem-resistant Klebsiella pneumoniae (CRKP) represents a critical global health threat with limited treatment options. While the gut microbiota is a reservoir for opportunistic pathogens and a regulator of host immunity, the reciprocal impact of systemic CRKP infection on gut microbial ecology and immune responses remains poorly defined. In a prospective case-control study, 38 patients with confirmed CRKP infection and 38 matched hospitalized controls without CRKP were enrolled. Fecal samples underwent 16S rRNA gene sequencing to characterize microbial profiles, and serum cytokine levels were quantified using multiplex immunoassays. CRKP infection was associated with significantly reduced microbial diversity and a distinct shift in community structure, characterized by depletion of beneficial commensals (Bacteroides, Faecalibacterium, Roseburia) and enrichment of pathobionts (Klebsiella, Enterococcus). Enterotype analysis revealed a predominance of a Klebsiella/Enterococcus-dominated enterotype in CRKP patients. Functional predictions indicated impaired carbohydrate and butyrate metabolism alongside increased virulence- and resistance-associated pathways. Systemically, patients exhibited elevated pro-inflammatory cytokines (IL-6, TNF-α, IFN-γ) and chemokines (IP-10, MCP-1, RANTES). Correlation analyses linked opportunistic taxa with heightened inflammatory markers, while beneficial short-chain fatty acid producers showed inverse associations. Systemic CRKP infection is associated with profound gut dysbiosis and a hyper-inflammatory immune response. The strong microbiota-immune correlations suggest that the gut microbiota may serve as a biomarker and a potential therapeutic target for mitigating CRKP-associated immune dysfunction, though the directional relationship (cause vs. consequence) between dysbiosis and CRKP infection remains to be elucidated.IMPORTANCECarbapenem-resistant Klebsiella pneumoniae (CRKP) is a critical global threat with limited therapeutic options. This study reveals that systemic CRKP infection is associated with profound gut dysbiosis-characterized by loss of beneficial commensals (e.g., Faecalibacterium) and expansion of pathobionts (e.g., Klebsiella, Enterococcus)-as well as a hyperinflammatory immune response. We demonstrate strong correlations between specific microbial taxa and host cytokines, suggesting that the gut microbiome may hold potential as a biomarker and therapeutic target. These findings enhance our understanding of host-microbe interactions in CRKP infection and support the exploration of microbiota-based therapies. However, further studies, including longitudinal and animal models, are needed to clarify whether gut dysbiosis directly influences CRKP outcomes or is a secondary consequence.},
}

@article {pmid41263392,
year = {2025},
author = {Zhao, R and Lu, Y and Xu, Q and Ren, H and Li, H and Gao, J and Cui, H and Yuan, Z and Cao, B and Wei, B},
title = {Gut blautia coccoides-derived 5Z-dodecenoic acid attenuates chronic psychological stress-induced gastric cancer progression.},
journal = {International journal of surgery (London, England)},
volume = {},
number = {},
pages = {},
doi = {10.1097/JS9.0000000000004080},
pmid = {41263392},
issn = {1743-9159},
abstract = {BACKGROUND: Chronic psychological stress is a critical oncogenic factor of gastric cancer (GC). However, the mechanisms underlying stress-induced malignant progression remain largely unknown. Gut microbiota dysregulation is tightly associated with cancer development and metabolism.

MATERIALS AND METHODS: Chronic unpredictable mild stress (CUMS) modeling was used to prepare mice suffering from chronic psychological stress. 16s rRNA sequencing and Q300 targeted metabolite quantification were jointly conducted to depict landscapes of gut microbiome and metabolomics of CUMS mice. Fecal microbiota transplantation was employed to investigate the functions of gut microbial communities in regulating CUMS-mediated GC growth. Drug affinity responsive target stability, surface plasmon resonance and molecular docking assays were performed to screen direct target proteins of 5Z-dodecenoic acid. The interactions between RIOK2 and BYSL were verified with co-immunoprecipitation and GST pull-down and fluorescent co-localization analysis. A series of experiments for malignant behaviors and glycolysis and subcutaneous tumor transplantation were employed to detect alterations of GC cell phenotypes ex vivo and in vivo, respectively.

RESULTS: Microbiome and metabolomics collectively demonstrated disrupted gut microbial communities and metabolic patterns. Particularly, Blautia coccoides-derived 5Z-dodecenoic acid was predominately declined by CUMS. Supplementation with Blautia coccoides or 5Z-dodecenoic acid effectively mitigated the negative effects of CUMS on glycolysis and malignancy. Mechanistically, 5Z-dodecenoic acid directly inhibits the functions of RIOK2, which maintained ectopic glycolysis and malignant behaviors. RIOK2 further interacted with BYSL and maintained its properties of potentiation of GC progression and metabolism.

CONCLUSION: Our findings advance the insights of Blautia coccoides-derived 5Z-dodecenoic acid implicated in chronic psychological stress-induced GC progression and provide novel strategies for dampening GC progression.},
}

@article {pmid41263210,
year = {2025},
author = {Zhukova, NG and Sayfitdinkhuzhaev, ZF and Israilova, GM and Bustonov, OY and Nasriddinova, NA and Gaponova, OV and Zhukova, IA and Masenko, AY},
title = {[«Brain-gut-microbiome» axis in patients with Parkinson's disease].},
journal = {Zhurnal nevrologii i psikhiatrii imeni S.S. Korsakova},
volume = {125},
number = {11. Vyp. 2},
pages = {18-23},
doi = {10.17116/jnevro202512511218},
pmid = {41263210},
issn = {1997-7298},
mesh = {Humans ; *Parkinson Disease/microbiology/metabolism/physiopathology ; *Gastrointestinal Microbiome ; *Brain/metabolism ; alpha-Synuclein/metabolism ; *Brain-Gut Axis ; },
abstract = {Parkinson's disease (PD) is one of the most common motor neurological diseases. The clinical presentation of PD includes both motor symptoms (hypokinesia, muscle rigidity, and tremor) and non-motor manifestations (asthenia, depression, hyposmia), as well as cognitive disorders. The primary link in PD pathogenesis is considered to be the accumulation of pathological α-synuclein; however, neuroinflammation, oxidative stress, mitochondrial dysfunction, and dysregulation of the Brain-gut microbiome axis also contribute to the pathological processes. This review of modern medical literature, encompassing domestic and foreign authors, summarizes recent studies on the significance of gastrointestinal tract changes in PD patients. The analysis revealed the involvement of the microbiome and specific bacterial taxonomic groups in the development of PD. In addition, the accumulation of α-synuclein, according to recent data, begins specifically in the nerve plexuses of the intestine and then spreads along the nerves upward into the central nervous system, affecting the substantia nigra, in particular.},
}

Humans
*Parkinson Disease/microbiology/metabolism/physiopathology
*Gastrointestinal Microbiome
*Brain/metabolism
alpha-Synuclein/metabolism
*Brain-Gut Axis

@article {pmid41263129,
year = {2025},
author = {Mesiha, M and Cumbermack, M and Kim, J and White, R and Lin, T and Rubin, J and Jotwani, R},
title = {How pro-inflammatory diets influence perioperative outcomes.},
journal = {Pain management},
volume = {},
number = {},
pages = {1-6},
doi = {10.1080/17581869.2025.2591598},
pmid = {41263129},
issn = {1758-1877},
abstract = {Recent evidence shows that pro-inflammatory diets-high in saturated fats, added sugars, and ultra processed foods-have been linked to elevated levels of cytokines like interleukin-6 (IL-6) and tumor necrosis factor (TNF), showing a marked increase in systemic inflammation, disrupted immune function and altered anesthetic drug metabolism. These effects have been linked to prolonged recovery, impaired wound healing, and increased complication rates. Additionally, a pro-inflammatory diet changes the gut microbiome, impacting pain perception, opioid sensitivity and stress response by the gut-brain axis. On the contrary, an anti-inflammatory diet reduces inflammatory markers and is associated with a shorter hospital stay. This review synthesizes data from randomized controlled trials (RCT), meta-analyses, and mechanistic studies from 2000-2025, emphasizing literature on omega-3 fatty acids, specialized pro-resolving mediators (SPMs), and short-chain fatty acids (SCFAs). Targeted interventions such as education on nutrition and dietary assessment risk could enhance surgical recovery. Perioperative interventions discussed include pre/probiotic supplementation, omega-3 fatty acid administration, and also dietary counseling as part of Enhanced Recovery After Surgery (ERAS) pathways.},
}

@article {pmid41263038,
year = {2025},
author = {Wang, M and Sun, H and Wang, X and Zhang, X and Huang, Y and Cui, R and Sun, Y and Yao, H and Wan, JY},
title = {Tangerine Peel-Based Herbal Formula Ameliorates Metabolic Syndrome via Gut Microbiota-Mediated Bile Acid Remodeling and TGR5 Activation.},
journal = {The American journal of Chinese medicine},
volume = {},
number = {},
pages = {1-19},
doi = {10.1142/S0192415X25500946},
pmid = {41263038},
issn = {1793-6853},
abstract = {The growing global burden of metabolic syndrome (MetS), a key driver of multiple chronic diseases, highlights the limited treatment options for its multifactorial pathophysiology. Tanshi-Tiaoti Decoction (TTD), a Chinese herbal formula comprised of Citri Reticulatae Pericarpium (Tangerine peel), Coicis Semen (Raw coix seed/Job's tears), Raphani Semen (Radish seed), Nelumbinis Folium (Lotus leaf), Eckloniae/Laminariae thallus (Kelp), and Crataegi Fructus (Raw hawthorn fruit), demonstrates efficacy in the clinical management of MetS. However, its underlying molecular mechanisms remain incompletely elucidated. This study indicates that TTD restored gut microbiota homeostasis and bile acid (BA) profiles in high-fat diet (HFD)-induced MetS mice. TTD significantly attenuated body weight gain, fasting glucose levels, serum triglycerides, and hepatic steatosis. TTD corrected gut microbiota dysbiosis, most notably by reducing the Firmicutes/Bacteroidetes ratio. Fecal microbiota transplantation (FMT) validated the fact that the gut microbiome mediates TTD's therapeutic effects. TTD regulated BA biosynthesis through this microbial modulation, and thus specifically increased hyodeoxycholic acid (HDCA). HDCA, which has been identified as the signature BA during TTD treatment, phenocopied TTD's therapeutic effects against MetS by both activating the BA receptor TGR5 and subsequently promoting beige adipocyte browning. Collectively, TTD ameliorates MetS by reshaping microbial-mediated BA pools, and in particular elevates HDCA levels to thereby activate TGR5 and induce beige adipocyte browning. These findings support TTD as a promising herbal-based therapeutic strategy for the treatment of MetS.},
}

@article {pmid41262934,
year = {2025},
author = {Herath Dissanayakalage, SS and Kaur, J and Mann, RC and Sawbridge, TI},
title = {Host genotype-driven shifts in the Medicago seed microbiome reveal domestication-linked diversity loss in lucerne (Medicago sativa).},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1660250},
pmid = {41262934},
issn = {1664-302X},
abstract = {Seed microbiomes represent a critical yet underexplored dimension of plant-associated microbial communities, with potential to enhance crop resilience and sustainability. While plant microbiomes have gained prominence, the diversity and composition of seed-associated bacteria-especially across wild and domesticated lineages-remain poorly characterised. Here, we profiled the bacterial seed microbiome of lucerne (Medicago sativa L.) and its crop wild relatives using an integrative approach combining amplicon sequencing, culture-based recovery, and whole-genome analysis of representative isolates. Amplicon profiling revealed a conserved core microbiome across all accessions, alongside host-genotype-specific patterns and markedly higher bacterial diversity in wild relatives. Culture-based methods recovered over half of the abundant amplicon sequence variants (ASVs), validating the representativeness of the isolate library. The whole genome sequencing of selected isolates uncovered substantial intra-species variation, including genomically distinct strains within the same species. Core taxa such as Pantoea, Paenibacillus, and Pseudomonas were consistently recovered, while several genera enriched in wild relatives-Massilia, Duganella, Sphingomonas-were absent or rare in domesticated lines. Comparative microbiome analysis revealed that domestication has reduced both taxonomic richness and microbial variability in the lucerne seed microbiome. The dominance of conserved taxa alongside the exclusion of wild-enriched groups suggests that breeding history influences microbial assembly and may constrain microbiome function. The consistent presence of core taxa across accessions is consistent with the possibility that, vertical transmission, together with host genotype, contributes to seed microbiome structure. By linking plant genotype with seed microbiome composition and culturability, this study provides a high-resolution view of seed microbial assembly shaped by evolutionary history. The resulting culture-based microbial resource, supported by genome-level characterisation of representative taxa, offers a robust foundation for microbiome-informed strategies in lucerne breeding and pasture improvement.},
}

@article {pmid41262932,
year = {2025},
author = {Meng, F and Zhao, Y and Guo, Y and Guo, X and Zhang, Q and Li, S and Chi, Y and Li, L and Hui, F and Tong, M and Yan, S},
title = {Optimization of Artemisia ordosica crude polysaccharides on milk fatty acid composition in lactating donkeys and their effects on rectal microbiome and lactation performance.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1682805},
pmid = {41262932},
issn = {1664-302X},
abstract = {INTRODUCTION: This study evaluated the effects of dietary Artemisia ordosica crude polysaccharides (AOCP; 0.5 g/kg DM) supplementation on milk fatty acid profiles, rectal microbiota, enzymes related to lipid metabolism, and lactation performance in lactating Dezhou donkeys.

METHODS: A single-factor completely randomized design was used, with 14 lactating Dezhou donkeys (6.16 ± 0.67 years old, 250.06 ± 25.18 kg, parity 2.82 ± 0.48, 39.11 ± 7.42 days in lactation, each with a foal) randomly divided into two groups (n = 7/group). The CON group was fed a diet with a concentrate to forage ratio of 3:7, while the AOCP group received the same diet supplemented with 0.5 g/kg DM of AOCP. The trial lasted 10 weeks (including a 2-week adaptation period).

RESULTS AND DISCUSSION: Compared with the CON group, AOCP supplementation significantly enhanced lactation performance (milk yield, fat, lactose) and the digestibility of DM, ADF, NDF, and elevated oleic acid, linoleic acid, eicosapentaenoic acid, as well as the unsaturated-to-saturated (U/S) and polyunsaturated-to-saturated (P/S) fatty acid ratios, while reducing saturated fatty acids and the c index. AOCP elevated acetate and butyrate in the rectum and the activity of enzymes related to lipid metabolism such as stearoyl-CoA desaturase, and increased the relative abundance of beneficial bacteria (Eubacterium hallii group, Prevotella, Ruminococcus), while decreasing potentially pathogenic bacteria Streptococcus and norank_f_Lachnospiraceae. In summary, AOCP may optimize the fatty acid composition of donkey milk and enhance lactation performance by modulating rectal bacteria structure, enzymes related to lipid metabolism, and nutrient utilization.},
}

@article {pmid41262931,
year = {2025},
author = {Trunfio, M and Scutari, R and Fox, V and Vuaran, E and Dastgheyb, RM and Fini, V and Granaglia, A and Balbo, F and Tortarolo, D and Bonora, S and Perno, CF and Di Perri, G and Alteri, C and Calcagno, A},
title = {The cerebrospinal fluid virome in people with HIV: links to neuroinflammation and cognition.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1704392},
pmid = {41262931},
issn = {1664-302X},
abstract = {INTRODUCTION: Despite durable viral suppression, neuroinflammation and neurocognitive complications remain common yet poorly understood in people with HIV (PWH). HIV alters human viromes, and virome perturbations have been linked to neurocognitive issues in people without HIV. Recently characterized, the brain and cerebrospinal fluid (CSF) viromes represent a new avenue to understand brain and mental health in PWH.

METHODS: This cross-sectional study analyzed 85 CSF samples (74 from PWH on suppressive antiretroviral therapy, and 11 from controls without HIV, CWH) through shotgun metagenomics for DNA and RNA viruses. Taxonomic composition (reads and contigs), diversity, and relative abundance (RA) of prokaryotic (PV), human eukaryotic (hEV), and non-human eukaryotic viruses (nhEV) were evaluated in relation to HIV status, markers of neuroinflammation/neurodegeneration, cognitive functions, and depressive symptoms. Sensitivity analyses and post-hoc cluster analysis on the RA of hEV, non-human viruses (NHV) and blood-brain barrier permeability were performed. Multivariable models assessed the relationship between cognition and clusters.

RESULTS: Of 46 read-positive CSF samples, 93.5% contained PV sequences, 47.8% hEV, and 45.6% nhEV. PWH displayed lower α diversity, although p > 0.05. At β diversity analysis, HIV status explained 3.4% of the variation in viral composition (p = 0.016). Contigs assembly yielded 13 samples positive for 8 hEV, 2 nhEV, and 6 PV. Higher RA of PV was correlated with higher CSF S100β (rho 0.36, p = 0.002) and β-Amyloid 1-42 fragment (βA-42, rho 0.27, p = 0.026), whereas higher RA of nhEV with poorer cognitive performance (rho 0.26, p = 0.022). Conversely, higher RA of hEV correlated with better cognition (rho -0.38, p = 0.003) and lower βA-42 (rho -0.30, p = 0.012). Sensitivity analyses restricted to only CSF samples with detectable reads confirmed these findings. Three CSF clusters were identified and showed differences in astrocytosis, βA-42, tau protein, and cognitive functions. Participants with hEV-enriched CSF showed better cognitive performance compared to those with virus-devoid and NHV-enriched CSF (all p < 0.05).

CONCLUSION: This study provides the first comprehensive description of the CSF virome in PWH, revealing associations with neuroinflammation and cognition. These findings highlight the potential involvement of the CSF virome in brain health and inform about its composition, origin, and potential clinical implications in people with and without HIV.},
}

@article {pmid41262929,
year = {2025},
author = {Asatulloev, T and Yusupov, Z and Cai, L and Chen, Q and Gurung, B and Tojibaev, KS and Sun, W},
title = {Comparative root associated microbial community analysis of Oreocharis mileensis, a resurrection plant species with extremely small populations.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1692695},
pmid = {41262929},
issn = {1664-302X},
abstract = {Plants dynamically interact with their microbiomes through phytohormonal signaling and defense responses, shaping microbial diversity and ecosystem function. While resurrection plants host growth-promoting and drought associated microbes, prior studies on different resurrection plants have been limited to localized sampling, potentially underestimating microbial diversity. We analyzed bacterial and fungal communities across five populations of Oreocharis mileensis, a resurrection plant, during hydrated and dehydrated states to examine population-level microbiome differences or affinity, identify microorganisms that may assist during plant desiccation, and assess their conservation across populations. We found that microbial composition was strongly influenced by compartment (bulk soil, rhizosphere, and endosphere) but exhibited only moderate drought-induced changes, suggesting that O. mileensis maintains a stable microbiome under stress. Core phyla (e.g., Proteobacteria, Actinobacteriota, Ascomycota) were conserved across populations, but genus-level core taxa varied relatively between populations, reflecting niche specialization and host genotype. Drought increased bacterial alpha diversity while reducing beta diversity, indicating homogenization driven by stress-tolerant taxa such as Actinobacteriota. Fungal responses differed, with increased beta diversity suggesting drought-enhanced compositional turnover. Key bacterial genera (e.g., Burkholderia-Caballeronia-Paraburkholderia, Bacillus, Rhizobium) dominated hydrated states, while drought enriched Actinobacteria (e.g., Microlunatus, Rubrobacter) and other drought-resistant taxa. Fungal communities shifted from saprotroph-dominated hydrated states to symbiotic taxa (e.g., Paraboeremia, Helotiales) under drought conditions. Functional profiling revealed compartment-specific metabolic specialization, with drought enriching stress-response pathways (e.g., secondary metabolite biosynthesis, signal transduction). These findings demonstrate that O. mileensis microbiomes are structured by compartmental filtering and exhibit drought-driven functional plasticity, with conserved stress-adapted taxa potentially supporting host resilience. Overall, this study expands our understanding of microbiome assembly in resurrection plants and highlights candidate microbes for microbiome engineering to enhance crop stress tolerance.},
}

@article {pmid41262927,
year = {2025},
author = {González-Chávez, SA and Alvarado-Jáquez, MF and Salas-Leiva, JS and Mohl, JE and Chaparro-Barrera, E and Prieto-Carrasco, R and Loya-Rivera, M and Pacheco-Silva, C and Pacheco-Tena, C},
title = {Joint Microbiota Suggests Articular Dysbiosis in Experimental Murine Spondyloarthritis and Histological Detection of Bacteria in Human SpA Joints.},
journal = {International journal of inflammation},
volume = {2025},
number = {},
pages = {9982583},
pmid = {41262927},
issn = {2090-8040},
abstract = {BACKGROUND: Recent studies have provided evidence supporting the presence of a commensal joint microbiome; however, its role in the pathogenesis of spondyloarthritis (SpA) remains unclear. This study aimed to characterize the joint microbiome and assess its role in bacterial dissemination and systemic involvement.

METHODS: DBA/1 mice with spontaneous arthritis (SpAD) and healthy BALB/c mice, as well as biopsies from SpA patients, were analyzed by histology (Gram staining and IHC), short-read next-generation sequencing of the 16S rRNA gene amplicons, and transcriptomics. Shared bacterial species were evaluated across tissues, including the liver and heart, and the colocalization of bacterial and inflammatory markers was assessed using double indirect immunofluorescence (IIF).

RESULTS: Bacteria were detected in the joints of healthy and SpAD mice, with significantly greater abundance in the latter. Microbiome analysis revealed distinct bacterial communities, with genera, such as Pelomonas and Aerococcus uniquely identified in the joints of SpAD mice, indicating a state of dysbiosis. Several bacterial species, including Prevotella sp., Ruminococcus gnavus, Lactobacillus johnsonii, and Limosilactobacillus reuteri, were detected in both the gut and joints of SpAD mice. Additionally, bacterial DNA from these taxa was also amplified from liver and heart tissues, indicating systemic dissemination. Transcriptomic analysis revealed dysregulated bacterial response pathways in SpAD joints, with an inflammatory profile distinct from that observed in gut tissues. Double IIF confirmed the colocalization of bacterial components with proinflammatory cytokines in joint cells. In human SpA biopsies, Gram staining and IHC also identified bacteria in sacroiliac and tarsal tissues.

CONCLUSIONS: These findings confirm the presence of bacteria in the joints of healthy and SpAD mice, as well as SpA patients. The joint microbiome differs between healthy and diseased mice, contributing to inflammation through dysregulated bacterial responses. Additionally, the identification of shared bacterial species between the gut and joints, as well as their detection in the liver and heart, supports the hypothesis of bacterial dissemination consistent with translocation and systemic involvement.},
}

@article {pmid41262831,
year = {2025},
author = {Murthy D, K and Soman, RJ and Soman, D and Pv, K},
title = {Testing the Immunomodulatory Effects of Probiotic Bacillus coagulans SNZ 1969® in Healthy Adults: A Randomized, Double-Blind, Placebo-Controlled Trial.},
journal = {Cureus},
volume = {17},
number = {10},
pages = {e94845},
pmid = {41262831},
issn = {2168-8184},
abstract = {BACKGROUND: The immune system and the gastrointestinal tract are intricately linked. The intestinal barrier, microbiome, and immune system are in constant communication, shaping immune responses and maintaining homeostasis. Imbalances in the gut microbiome can affect the intestinal barrier and increase susceptibility to infections, along with a decline in immune function (both innate and adaptive immunity). Maintaining optimal immune function is crucial for protecting against infections and supporting overall health, particularly in populations that may be more vulnerable to seasonal respiratory and gastrointestinal infections. Probiotics, particularly spore-forming strains, demonstrate potential for improving natural killer (NK) cell function and mucosal immunity through gut-associated lymphoid tissue interactions. This study evaluated the immunomodulatory effects of Bacillus coagulans SNZ 1969[®] in adults.

METHODS: This randomized, double-blind, placebo-controlled clinical trial enrolled adults aged 60-65 years who were susceptible to seasonal infections. Participants were randomized 1:1 to receive either B. coagulans SNZ 1969[®] (2 billion CFU/day) or placebo for 12 weeks. Primary endpoints included NK cell activity, absolute NK cell count (CD3⁻/CD16⁺/CD56⁺), and immunoglobulin levels (serum IgM, IgG, and IgA and salivary IgA). Secondary outcomes assessed respiratory and gastrointestinal infection incidence, inflammatory markers (C-reactive protein), and safety parameters.

RESULTS: Of 60 enrolled participants, 50 completed the study (25 per group). B. coagulans SNZ 1969[®] significantly enhanced NK cell activity compared to placebo, with a net increase of 42.07% between groups (44.59% versus 2.52% increase from baseline; p = 0.0002). NK cell activity improvements were consistent across both genders in exploratory subgroup analyses (limited by small female n = 7-8 per arm; males: 36.75% versus 2.52%; p = 0.00004; females: 63.64% versus 2.71%; p = 0.01155). Significant improvements were observed in serum IgA (25.00% versus 2.30% change; p = 0.0016) and salivary IgA (27.70% versus 0.60% change; p = 0.0002). No significant changes occurred in absolute NK cell counts, serum IgM, IgG, or C-reactive protein levels. Secondary analyses showed numerical reduction trends in upper respiratory tract infections (20% versus 32%; p = 0.11), gastrointestinal infections (8% versus 28%), and total illness days (23 days versus 35 days), favoring the probiotic group, though statistical significance was not achieved. The probiotic was well-tolerated with no serious adverse events.

CONCLUSIONS:  B. coagulans SNZ 1969[®] supplementation significantly enhanced NK cell activity and mucosal IgA production in adults, suggesting its potential role in strengthening the innate immune defense mechanisms. These findings support the role of B. coagulans SNZ 1969[®] as a safe dietary supplement for augmenting innate cellular immune function and thereby potentially contributing to a reduced trend to infection susceptibility; however, these preliminary findings require more extensive investigation in a larger study population.},
}

@article {pmid41262520,
year = {2026},
author = {Yang, X and Jin, Y and Wu, Y and Zhou, F and Qu, Z and Zhou, Q and He, J and Tao, Y and Zhuang, J and Han, S},
title = {Gut microbiome-metabolome-ionome network spectrum mapping of colorectal cancer.},
journal = {Genes & diseases},
volume = {13},
number = {1},
pages = {101566},
pmid = {41262520},
issn = {2352-3042},
}

@article {pmid41262449,
year = {2025},
author = {Huang, X and Mo, W and Wang, X},
title = {Metabolomics in autoimmune hepatitis: progress and perspectives.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1667391},
pmid = {41262449},
issn = {2296-858X},
abstract = {This review summarizes recent advances in applying metabolomics to autoimmune hepatitis (AIH). AIH is a chronic liver disease characterized by immune-mediated hepatocellular injury, with complex pathogenesis involving genetic, immunological, and environmental factors. Metabolomics, a system-wide approach analyzing small molecule metabolites, offers potential in early diagnosis, prognosis, and therapeutic evaluation of AIH. Current studies identify alterations in amino acid, lipid, carbohydrate, and bile acid metabolism, as well as changes in the gut microbiome and specific metabolite markers that distinguish AIH from other liver diseases. Techniques such as liquid chromatography-mass spectrometry (LC-MS), and bioinformatics facilitate biomarker discovery and enhance understanding of disease mechanisms. Despite challenges such as standardization and data integration, metabolomics holds promise for developing personalized treatment strategies and advancing disease management. Future prospects include combining multi-omics approaches, large-scale cohort studies, and artificial intelligence (AI)-based data analysis to deepen insights into AIH pathology and improve clinical outcomes.},
}

@article {pmid41262252,
year = {2025},
author = {Pang, X and Huang, P and Huang, S and Liu, X},
title = {The gut-lung axis: a new perspective on the impact of atmospheric particulate matter exposure on chronic obstructive pulmonary disease.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1657675},
pmid = {41262252},
issn = {1664-3224},
mesh = {Humans ; *Particulate Matter/adverse effects ; *Pulmonary Disease, Chronic Obstructive/etiology/metabolism/microbiology/immunology ; *Gastrointestinal Microbiome/drug effects/immunology ; *Lung/immunology/metabolism/drug effects ; Oxidative Stress ; Animals ; *Environmental Exposure/adverse effects ; *Air Pollutants/adverse effects ; },
abstract = {Environmental pollution is a serious public health problem closely related to various chronic respiratory diseases, such as chronic obstructive pulmonary disease (COPD), bronchial asthma, and lung malignancies. Atmospheric particulate matter (PM) is an important component of environmental pollution, and its influence on COPD has been shown to be related to inflammation, oxidative stress, immune imbalance, abnormal cell death, and cell aging. A growing body of evidence has shown that an imbalance of the lung and intestinal microbiota, as well as changes in metabolites, is closely related to the occurrence and development of PM-induced COPD. PM exposure damages the respiratory system and alters the structure and activity of the gut microbiome. The metabolites produced by the gut microbiome, in turn, disrupt airway immunity and exacerbate respiratory inflammation. Therefore, the bidirectional influence of PM on the gut-lung axis has attracted widespread attention. This review explores the mechanisms by which PM causes oxidative stress damage to the lungs and intestines, as well as the characteristics of the resultant immune imbalance and changes in the microbiota and metabolite products. It also describes how PM disrupts barrier function through microecological imbalance and how it participates in the progression of COPD via the gut-lung axis. These mechanisms highlight the potential of targeting the microbial flora as a new approach for treating COPD caused by environmental pollution.},
}

Humans
*Particulate Matter/adverse effects
*Pulmonary Disease, Chronic Obstructive/etiology/metabolism/microbiology/immunology
*Gastrointestinal Microbiome/drug effects/immunology
*Lung/immunology/metabolism/drug effects
Oxidative Stress
Animals
*Environmental Exposure/adverse effects
*Air Pollutants/adverse effects

@article {pmid41262070,
year = {2025},
author = {Ganamurali, N and Sabarathinam, S},
title = {Integrative Network Analysis of Antioxidant Nutrients Targeting 7-Ketocholesterol-Induced Lipotoxicity via Sterol Metabolism and Organelle Protection Pathways.},
journal = {Lipids},
volume = {},
number = {},
pages = {},
doi = {10.1002/lipd.70024},
pmid = {41262070},
issn = {1558-9307},
abstract = {7-Ketocholesterol (7-KC), a cytotoxic oxysterol, contributes to atherosclerosis, neurodegeneration, and metabolic disorders by promoting oxidative stress, inflammation, and dysfunction of organelles including mitochondria, peroxisomes, lysosomes, and the endoplasmic reticulum, ultimately leading to cell death. Nutritional biomedicine offers potential strategies to counteract these effects using antioxidant nutrients and probiotics. In this study, genes associated with 7-KC toxicity were retrieved from GeneCards, and targets of quercetin, luteolin, butyrate, Docosahexaenoic Acid (DHA), and vitamin E were predicted using SwissTargetPrediction. Overlapping targets were identified via an interactive Venn tool and analyzed through STRING protein-protein interaction networks, CytoHubba hub ranking, and Gene Ontology (GO)/ClueGO pathway enrichment. Twenty shared genes were identified, with Peroxisome Proliferator-Activated Receptor Gamma (PPARG), AKT Serine/Threonine Kinase 1 (AKT1), Amyloid Precursor Protein (APP), and Matrix Metalloproteinase-9 (MMP9) as key hubs. Enriched processes included sterol metabolism, cholesterol efflux, inflammatory regulation, and organelle protection, indicating multi-target modulation. These findings support that combinatorial nutrient interventions can restore sterol homeostasis, mitigate oxidative stress, and attenuate 7-KC-induced pathologies.},
}

@article {pmid41261931,
year = {2025},
author = {Lindner, N and Leibman-Markus, M and Gupta, R and Anand, G and Marash, I and Dolgov, T and Kleiman, M and Bar, M},
title = {Leaf Developmental Stage Influences Disease Resistance in Tomato.},
journal = {Molecular plant pathology},
volume = {26},
number = {11},
pages = {e70162},
doi = {10.1111/mpp.70162},
pmid = {41261931},
issn = {1364-3703},
support = {1759/20//Israel Science Foundation/ ; },
mesh = {*Plant Leaves/growth & development/microbiology/immunology/metabolism ; *Solanum lycopersicum/microbiology/growth & development/immunology/metabolism ; *Disease Resistance/physiology ; *Plant Diseases/microbiology/immunology ; Cyclopentanes/metabolism ; Oxylipins/metabolism ; Salicylic Acid/metabolism ; },
abstract = {The processes of morphogenesis and differentiation are crucial for leaf development, with the duration of the morphogenetic window influencing final leaf shape. Leaves at different developmental stages exhibit distinct morphological and physiological characteristics that may influence their ability to resist pathogens, and disease resistance has been linked to developmental stage in many plant species. To understand how leaf development impacts disease resistance, we examined the immunity of leaves at distinct developmental stages, exploring the role of hormonal pathways and the impact of leaf structure and microbial interactions on disease resistance. Our findings reveal that leaves of different developmental stages exhibit distinct disease responses to various pathogens, determined primarily by the ratio between salicylic acid and jasmonic acid. Higher relative jasmonic acid content in later developing leaves was found to result in increased disease resistance to necrotrophs, while higher relative salicylic acid content in earlier developing leaves rendered them more resistant to biotrophs. This phenomenon occurred across plant ages, in several species, and also impacted the plants' response to biocontrol agents, depending on the pathway being primed. We found that structural variations among leaves can also affect disease response, due to differential recognition by the invading pathogen, and possibly also due to alterations in the leaf microbiome. Our results uncover some of the factors influencing developmental immunity in tomato, and highlight the importance of considering plant development when managing disease resistance.},
}

*Plant Leaves/growth & development/microbiology/immunology/metabolism
*Solanum lycopersicum/microbiology/growth & development/immunology/metabolism
*Disease Resistance/physiology
*Plant Diseases/microbiology/immunology
Cyclopentanes/metabolism
Oxylipins/metabolism
Salicylic Acid/metabolism

@article {pmid41261800,
year = {2025},
author = {},
title = {Yuting Liang.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70754},
pmid = {41261800},
issn = {1469-8137},
}

@article {pmid41261325,
year = {2025},
author = {Miková, E and Krčmářová, E and Černý, V and Sklenářová, L and Avramová, P and Protivová, E and Slunéčková, B and Akhtar, M and Věcek, J and Procházka, J and Kubik-Zahorodna, A and Petrásková, P and Novotná, O and Pelantová, H and Kuzma, M and Schabussova, I and Hrdý, J},
title = {The Ability of Probiotic Strain Escherichia coli O83:K24:H31 to Modulate Gut Homeostasis and Immune Function After Antibiotic-Induced Dysbiosis.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41261325},
issn = {1867-1314},
support = {6121//GAUK/ ; CZ.02.01.01/00/22_010/0008115//MSCA fellowship CZ/ ; CZ 04/2024 and CZ 07/2023//OeAD-GmbH/ ; IMMU207032//Cooperatio/ ; },
abstract = {A healthy microbiome and a homeostatic interaction between the microbiome and the host immune system are essential for proper nutrition and overall health. Excessive use of antibiotics (ATB) can disrupt the healthy gut microenvironment, leading to dysbiosis, a condition linked to a wide range of disorders and diseases. Alterations in the composition and function of the microbiota have been associated with a broad spectrum of pathological conditions. In this work, we investigated the effect of ATB administration on microbiota composition and immune modulation, with a particular focus on neutrophil dynamics. We evaluated the capacity of the probiotic strain Escherichia coli O83:K24:H31 (EcO83) to mitigate ATB-induced dysbiosis and restore immune function. As expected, ATB treatment reduced microbiota diversity, which was partially restored by EcO83 supplementation. Furthermore, ATB administration affected the expression of tight junction proteins in the small intestine, an effect reversed by EcO83 treatment. Notably, our data indicate that ATB-induced dysbiosis accelerates neutrophil aging and reduces the release of neutrophils from the bone marrow. EcO83 supplementation counteracts these effects by promoting the influx of newly generated neutrophils into circulation. Overall, our findings confirm that ATB treatment disrupts gut microbiota homeostasis, adversely affecting immune function, including neutrophil turnover. However, probiotic supplementation with EcO83 can at least partially restore microbiome composition and immune homeostasis, highlighting its potential therapeutic application in mitigating ATB-induced dysbiosis.},
}

@article {pmid41261182,
year = {2025},
author = {Prusty, G and Prasad, BR and Polaki, S and Mereddy, S},
title = {Integrative multi-omics characterization of the gut microbiome in Pila globosa: functional insights into nutrient cycling and detoxification potential.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {12},
pages = {464},
pmid = {41261182},
issn = {1573-0972},
mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Metagenomics/methods ; Proteomics/methods ; *Snails/microbiology ; Phylogeny ; Metagenome ; Multiomics ; },
abstract = {Pila globosa, a freshwater snail endemic to Indian aquatic ecosystems, plays a pivotal role in nutrient cycling and organic matter turnover. In this study, we present the first integrative multi-omics characterization of its gut microbiome using shotgun metagenomics, metaproteomics, and genome-resolved analyses. The gut microbiota was taxonomically diverse yet compositionally stable, dominated by Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, with core genera including Pseudomonas, Clostridium, Bacillus, and Streptomyces. Alpha diversity metrics (Shannon = 4.22 ± 0.15; Simpson = 0.90 ± 0.01) and low Bray-Curtis dissimilarity (0.12-0.15) indicated a conserved core microbiome across replicates. Functional profiling through HUMAnN2 and metaproteomic validation revealed enrichment of pathways related to carbohydrate metabolism, short-chain fatty acid (SCFA) synthesis, amino-acid biosynthesis, and oxidative phosphorylation, reflecting the community's contribution to host nutrition and metabolic balance. Genes and proteins associated with xenobiotic degradation (benzoate, toluene metabolism) and oxidative stress response (superoxide dismutase, catalase, glutathione S-transferase) were abundant, suggesting microbial support for redox regulation and detoxification. Twelve high-quality metagenome-assembled genomes (MAGs) reconstructed from dominant taxa encoded traits for secondary metabolite production, metal resistance, and stress tolerance, underscoring their ecological versatility. Together, these results establish a foundational reference for understanding the functional potential of the P. globosa gut microbiome and its possible role in nutrient transformation and pollutant processing in freshwater systems. The study provides baseline data for future comparative and ecotoxicological investigations of gastropod holobionts.},
}

*Gastrointestinal Microbiome/genetics
Animals
*Bacteria/classification/genetics/metabolism/isolation & purification
Metagenomics/methods
Proteomics/methods
*Snails/microbiology
Phylogeny
Metagenome
Multiomics

@article {pmid41260935,
year = {2025},
author = {Peláez-Vico, MÁ and Rillig, MC and Mittler, R},
title = {Plant-to-plant signaling: building networks for resilience to stress, or merely eavesdropping?.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2025.10.021},
pmid = {41260935},
issn = {1878-4372},
abstract = {The overall function of an ecosystem is determined by the richness of its biodiversity and the complex interactions formed between the different species that inhabit it. Understanding how global change factors (including climate change), and their combinations, are affecting the intricate species-to-species relationships formed within different ecosystems and agro-ecosystems is becoming therefore increasingly important to our future. Here, we discuss how improved plant-to-plant and plant-to-microbiome signaling, achieved via research, intervention, and altered practices, can be used to form resilient plant communities that will help us shape our environment and successfully address some of our current and future anthropogenically generated critical challenges.},
}

@article {pmid41260765,
year = {2026},
author = {Rojanasopondist, P and Kaz, A and Yu, M and Grady, WM},
title = {Emerging Biomarkers for Managing Barrett's Esophagus.},
journal = {Gastrointestinal endoscopy clinics of North America},
volume = {36},
number = {1},
pages = {149-170},
doi = {10.1016/j.giec.2025.05.005},
pmid = {41260765},
issn = {1558-1950},
mesh = {Humans ; *Barrett Esophagus/genetics/metabolism/diagnosis/pathology/therapy ; *Adenocarcinoma/genetics/metabolism/diagnosis ; *Esophageal Neoplasms/genetics/diagnosis/metabolism ; *Biomarkers, Tumor/metabolism/genetics ; DNA Methylation ; Biomarkers ; MicroRNAs ; },
abstract = {Comparative analyses of normal esophageal tissue, Barrett's Esophagus (BE), and esophageal adenocarcinoma have identified distinctive molecular alterations in genomic DNA, epigenetics, non-coding RNA, and proteins that have shown promise as disease-specific biomarkers. Some of the best characterized and promising biomarkers for managing BE are multi-target esophageal cytology DNA assays based on methylated-DNA and immunohistochemical staining of Trefoil factor 3. Additional biomarkers including microRNA, measures of genomic instability, mixed-method panels, and other novel biomarkers (e.g. volatile organic compounds and saliva microbiome) remain in early development and will need further validation in large, prospective studies prior to clinical use.},
}

Humans
*Barrett Esophagus/genetics/metabolism/diagnosis/pathology/therapy
*Adenocarcinoma/genetics/metabolism/diagnosis
*Esophageal Neoplasms/genetics/diagnosis/metabolism
*Biomarkers, Tumor/metabolism/genetics
DNA Methylation
Biomarkers
MicroRNAs

@article {pmid41260570,
year = {2025},
author = {Deb, S and Zhang, Y and An, Y and Xia, Y and Sun, J},
title = {Loss of intestinal endosome associated protein sorting nexin 27 disrupts epithelial barrier and promotes inflammation.},
journal = {Cellular and molecular gastroenterology and hepatology},
volume = {},
number = {},
pages = {101682},
doi = {10.1016/j.jcmgh.2025.101682},
pmid = {41260570},
issn = {2352-345X},
abstract = {BACKGROUNDS AND AIMS: SNX27, member of the sorting nexin (SNX) family, carries a unique PDZ domain and mediates recycling of endocytosed transmembrane proteins. SNX27 is critical for neurodevelopmental processes, however its role in intestine remains unexplored. We aim to determine the previously unknown roles of SNX27 in regulating intestinal homeostasis, epithelial barrier integrity, and inflammatory responses.

METHODS: We used available NCBI GEO and Single Cell RNA Sequencing datasets to analyze SNX27 expression in human IBD. We generated a novel mouse model of SNX27 conditional deletion from intestinal epithelial cells (SNX27[ΔIEC]) and challenged these mice with Dextran Sulfate Sodium (DSS).

RESULTS: SNX27 expression was significantly lower in human IBD, including UC and CD. SNX27[ΔIEC] mice had significantly lower bodyweight and exhibited increased proliferation and poor differentiation of secretory Paneth and Goblet cells. We found reduced mucin layer and downregulation of crucial epithelial barrier proteins β-catenin, E-cadherin, ZO-1, ZO-2, and Claudin10 in SNX27[ΔIEC] mice. SNX27[ΔIEC] mice showed high intestinal permeability and spontaneously developed intestinal inflammation. Moreover, SNX27[ΔIEC] mice were more susceptible towards DSS-induced colitis, compared to the SNX27[Loxp] mice.

CONCLUSION: Overall, deletion of intestinal epithelial SNX27 weakens barrier functions and promotes inflammation. Our results indicate a novel role of SNX27 in regulating intestinal physiology and protecting against intestinal disorders. Thus, understanding the mechanisms of SNX27 downregulation in IBD will provide insights into new prevention and targets against chronic inflammation.},
}

@article {pmid41260531,
year = {2025},
author = {Siracusano, M and Arturi, L and Riccioni, A and Medoro, A and Savino, R and Scapagnini, G and Davinelli, S and Mazzone, L},
title = {Feeding Difficulties, Eating Disorders and Therapeutic Approaches in Autism Spectrum Disorder: An Overview.},
journal = {Pharmacological research},
volume = {},
number = {},
pages = {108040},
doi = {10.1016/j.phrs.2025.108040},
pmid = {41260531},
issn = {1096-1186},
abstract = {Feeding problems are highly prevalent in individuals with autism spectrum disorder (ASD) from early developmental stages. Difficulties during the transition to solid foods, limited dietary variety, and reluctance to try new foods since infancy, combined with gastrointestinal disorders, represent significant concerns for both parents and clinicians from diagnostic and, more importantly, therapeutic perspectives. The primary clinical link between atypical eating behaviors and core autistic symptoms lies in aberrant sensory processing and an insistence on sameness, which have important implications for intervention strategies. Additionally, the increased risk of gastrointestinal disorders and altered gut microbiome composition in individuals with ASD constitute another critical factor, opening avenues for novel therapeutic approaches. Therefore, the aim of this review is to summarize the existing literature on therapeutic approaches for feeding problems in ASD, with a focus on evidence-based practices across pharmacological, psychological, and nutritional domains.},
}

@article {pmid41260454,
year = {2025},
author = {Tarique, I and Haider, A and Nawazish, F},
title = {Complementary Therapeutic Actions of Shikonin and Indolepropionic Acid Ameliorate Diabetic Infertility via Distinct Antioxidant and Metabolic Pathways.},
journal = {F&S science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.xfss.2025.11.001},
pmid = {41260454},
issn = {2666-335X},
abstract = {OBJECTIVE: To evaluate the effect of Shikonin, a potent direct ROS scavenger, and Indolepropionic acid (IPA), a microbiome-derived metabolite, on epididymis and sperm morphology and function in diabetic rats.

DESIGN: A rat model of Type 2 diabetes mellitus (T2DM) was induced in male Wistar rats using a high-fat diet and streptozotocin (50 mg/kg). The animals were subsequently divided into seven groups: Control, T2DM, T2DM + IPA (50 mg/kg), T2DM + Shikonin (0.5 mg/kg), T2DM + Metformin (50 mg/kg), IPA-only, and Shikonin-only. Treatments were administered orally for four weeks. We assessed histological integrity, sperm motility and viability (via CASA), serum lipid profiles, epididymal antioxidant activity (SOD, MDA, catalase), and apoptotic marker (cytochrome C, caspase-9, caspase-3) and metabolic signature (FGF21) expression via qRT-PCR.

SETTING: University ANIMAL(S): Male Wistar albino rats (n = 42, Age: 8-12 weeks old, 200 ± 2.4 g) INTERVENTION(S): Streptozotocin, Shikonin, Indolepropionic Acid MAIN OUTCOME MEASURE(S): T2DM profoundly impairs male fertility, with oxidative stress in the epididymis being a key driver of sperm damage.

RESULT(S): Streptozotocin-induced diabetic rats exhibited increased oxidative damage, characterized by an impaired antioxidant system, high expression of apoptotic markers, and reduced metabolic gene expression. These effects ultimately damaged epididymis tissue and resulted in poor sperm quality. Shikonin and Indolepropionic Acid treatments significantly attenuated oxidative stress and apoptosis, restored antioxidant activity and lipid profiles, and improved sperm parameters. Both treatments enhanced metabolic balance, as indicated by improved FGF-21 expression, and restored epididymal histoarchitecture. Shikonin was superior in improving the epididymal somatic index and sperm motility, whereas IPA was more effective in normalizing FGF21 expression and lipid profiles, highlighting its primary metabolic role.

CONCLUSION(S): Our findings reveal that Shikonin and IPA protect against diabetic reproductive damage through complementary pathways. This work not only introduces promising natural therapeutic strategies but also provides a mechanistic framework for their combined or targeted use in managing diabetic infertility.},
}

@article {pmid41260449,
year = {2025},
author = {Chen, YF and Fan, CS and Hung, YC and Chien, PJ and Tsai, WH and Yeh, YT and Jhong, JH and Hsieh, YN and Huang, YH and Jan, MS and Chang, CF and Yang, CY and Chang, WW},
title = {Heat-killed Lacticaseibacillus paracasei GMNL-346 exerts anti-oral cancer effect by suppressing cancer stem cell activity and rebalancing gut microbiota dysbiosis.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {149033},
doi = {10.1016/j.ijbiomac.2025.149033},
pmid = {41260449},
issn = {1879-0003},
abstract = {Oral squamous cell carcinoma (OSCC) presents a major therapeutic challenge, necessitating novel treatments. This study investigated heat-killed Lacticaseibacillus paracasei GMNL-346 as a potential therapeutic agent for OSCC, targeting tumor progression and gut microbiota dysbiosis. In OSCC cell lines, GMNL-346 selectively inhibited proliferation by disrupting the cell cycle and suppressing cancer stemness proteins, while sparing normal gingival epithelial cells. In OSCC xenograft mouse models, the treatment enhanced survival rates and reversed tumor-induced gut microbiota dysbiosis, increasing beneficial metabolites such as propionic and isobutyric acids, which are associated with reduced OSCC progression. Whole-genome sequencing identified a heat-stable antimicrobial peptide that replicated GMNL-346's ability to suppress OSCC cell proliferation and cancer stemness protein expression. These findings suggest that heat-killed L. paracasei GMNL-346 may represent a promising and safe therapeutic candidate for OSCC, potentially acting through direct tumor suppression and microbiota modulation, which supports further exploration of its role in microbiome-based cancer therapy.},
}

@article {pmid41260222,
year = {2025},
author = {Wang, Y and Wu, J and Yao, J and Chen, J and Cheng, KKY and Ho, MY and Lee, CH and Lam, KS and Tse, MA and Panagiotou, G and Xu, A},
title = {Gut microbiome-adipose crosstalk modulates soluble IL-6 receptor influencing exercise responsiveness in glycemic control and insulin sensitivity.},
journal = {Cell metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmet.2025.10.013},
pmid = {41260222},
issn = {1932-7420},
abstract = {Exercise is an effective intervention for the prevention and management of diabetes, but the high interpersonal variability in response to exercise impedes its widespread implementation. Herein, we identify adipocyte-derived soluble interleukin-6 receptor (sIL-6R) as a key exerkine determining exercise efficacy in improving metabolic health. In individuals with obesity who underwent a 12-week exercise intervention, circulating sIL-6R level exhibits dichotomous changes between exercise responders (Rs) and non-responders (NRs), in close association with exercise-mediated alterations in insulin sensitivity and glycemic control. Mechanistically, elevated gut microbiome-mediated leucine in NR acts on white adipocytes to promote disintegrin and metalloproteinase 17 (ADAM17)-mediated sIL-6R production via the mammalian target of rapamycin (mTOR)-hypoxia-inducible factor 1α (HIF1α) pathway, which in turn impairs the metabolic benefits of exercise through interleukin (IL)-6 trans-signaling-induced adipose inflammation. Adipocyte-selective ablation of ADAM17 prevents the effects of fecal microbiota transplantation from NR on elevation of sIL-6R, thereby restoring the efficacy of exercise-shaped gut microbiome in counteracting glucose intolerance and insulin resistance in obese mice. Thus, therapeutic interventions targeting adipocyte-derived sIL-6R represent a promising strategy for maximizing exercise efficacy in personalized diabetes prevention.},
}

@article {pmid41260126,
year = {2025},
author = {Sójka, O and van der Mei, HC and van Veelen, HPJ and van Rijn, P and Gagliano, MC},
title = {Investigating the role of physicochemical surface properties of polymeric pipe materials and a nanogel-based coating on microbial adhesion in unchlorinated drinking water.},
journal = {Water research},
volume = {289},
number = {Pt B},
pages = {124941},
doi = {10.1016/j.watres.2025.124941},
pmid = {41260126},
issn = {1879-2448},
abstract = {Past research focused on the effect that different polymeric pipe materials have on biofilm formation in drinking water distribution systems (DWDS), to determine the best one to deliver safe drinking water to customers. However, results are often contradictory. Here, we studied the influence of five polymeric pipe materials and a surface modification with the anti-adhesive poly(N-isopropylmethacrylamide)-based nanogel coating on early-stage biofilms formation in unchlorinated drinking water in simulated DWDS conditions. Coupons made from two high-density polyethylene (HDPE-1 and HDPE-2), two unplasticized polyvinyl chloride (PVC-1 and PVC-2), and a molecularly oriented polyvinyl chloride (PVCO) were characterized in terms of surface topography, roughness, chemistry, and hydrophilicity. Biofilms were grown from real drinking water on the selected materials in a flow-chamber setup simulating DWDS conditions, with and without nutrient supplementation. Biofilm growth for 72 h with nutrient addition led to the same extensive biofilm formation on all surfaces. Without nutrients supplementation, 35-days experiments showed significant biofilm development on HDPE-1 only, despite comparable surface properties and chemistry to HDPE-2, and smoother and more homogeneous topography than PVCs. Application of the nanogel coating on HDPE-1 resulted in an average reduction of 87 % in biofilm development regardless under which condition. Microbial community analysis of biofilms by means of 16S rRNA gene sequencing showed a common core microbiome on all included materials in both nutrient-rich and oligotrophic conditions, with a high variability even within duplicates of the same material. Presented findings in combination with multiple studies available in the literature suggest that no conclusion can be made of whether PVC or PE is ultimately better in preventing biofilm formation in DWDS, because it is mainly due to the manufacturer. The suggested application of a surface modification with the anti-adhesive nanogel coating could uniform materials behaviour, acting as a localized biofilm control strategy for DWDS sections (hotspots) especially prone to biofilm development.},
}

@article {pmid41260114,
year = {2025},
author = {Ahmad, W and Ray, R and Khan, AL},
title = {Can silicate types regulate plant defense and rhizospheric microbiome diversity differently during heat stress conditions?.},
journal = {The Science of the total environment},
volume = {1007},
number = {},
pages = {180812},
doi = {10.1016/j.scitotenv.2025.180812},
pmid = {41260114},
issn = {1879-1026},
abstract = {Silicates (Si) improve plant growth; however, how different types of silicate sources influence plant growth and rhizosphere microbiome remains underexplored. We compare two Si types (pure and bioavailable silicic acid (Si) and mineral magnesium silicate (MgSi)) applied to the soybean (Glycine max L.) rhizosphere to determine whether two silicate types (Si-types) differently impact plant growth, defense responses, and microbiome diversity and function during heat stress. Under heat stress, Si-type treatments improved biomass (86 % with Si and 82 % with MgSi), reduced H2O2 (26 % phyllosphere; 33 % rhizosphere), and enhanced β-glucosidase activity (2.6-fold rhizosphere) compared to heat-only treatment and increased Proteobacteria relative abundance from ∼65 % (heat-only) to ∼74 % in Si-type-treated rhizospheric soil. Si-types showed downregulation of heat shock transcription factors, suggesting regulatory defense effects during heat stress. Metagenome-assembled genomes (MAGs) analysis revealed significant bacterial shifts across the Si-treatments, with Proteobacteria and Bacteroidetes being the dominant phyla in the rhizospheric soil. Under heat stress, the core microbiome comprised 14 rhizosphere genera (including Pelomonas, Achromobacter, Paracoccus, Nocardioides), whereas Pelomonas was the sole core root genus, and Pelomonas puraquae core species in both compartments. MAGs analysis revealed Si-based shifts in microbial metabolic pathways and enrichment of auxin biosynthesis in Si-treated roots during heat stress. Because MgSi supplies both Mg and Si, effects observed with MgSi are interpreted as combined Si + Mg effects. In conclusion, both Si-types caused shifts in microbiome diversity and function, and impacted plant growth and defense responses under heat stress, providing a foundation for improving thermotolerance in plants.},
}

@article {pmid41256388,
year = {2025},
author = {King, AC and Seiler, K and Swanson, K and Ciorba, MA and Alvarado, DM},
title = {IBD risk locus rs1077773 is a pharmacogenomic eQTL for aryl hydrocarbon receptor activity and modulates immune cell function.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41256388},
issn = {2692-8205},
abstract = {INTRODUCTION: The inflammatory bowel diseases (IBD) Crohn's disease (CD) and ulcerative colitis (UC) are disorders that cause chronic inflammation of the gastrointestinal tract. Both genetic and environmental factors contribute to the pathogenesis of IBD. There are currently >200 known genetic susceptibility loci for the development of IBD. The physiological impact of the majority of these loci remain a gap in our knowledge. One such locus is the single nucleotide polymorphism rs1077773, located ~56kbp downstream from the aryl hydrocarbon receptor (AHR) gene. AHR is a ligand-activated transcription factor that is crucial to maintaining intestinal homeostasis. We hypothesized that rs1077773 enhances AHR activity to regulate mucosal immune response and maintain intestinal homeostasis.

METHODS: All study procedures and reagents were approved by the Washington University Institutional Review Board (#202011003). Patient biopsies were collected at Barnes Jewish Hospital and genotyped using the IBD Genetics Consortium custom GSA SNP chip (Broad Institute) followed by imputation using TopMed Imputation Server at University of Michigan. Patient derived organoids (PDOs; N=3 G/G, N=4 G/A, N=5 A/A) were derived and maintained in 3D culture and supplemented with 50% L-WRN conditioned medium with passage every 3-4 days as previously described. PDOs were treated with AHR agonist 6-Formylindolo[3,2-b]carbazole (FICZ) or vehicle for 48h. Expression of AHR and its transcriptional targets Cytochrome P450 1A1 (CYP1A1) and CYP1B1 was assessed by RT-qPCR. Blood was collected from pediatric patients undergoing intestinal resection at St. Louis Children's Hospital and was genotyped with custom TaqMan SNP assay (N=3 G/G, N=5 G/A). Peripheral blood monocyte-derived macrophages (MDMϕs) were treated with lipopolysaccharide in the presence or absence of AHR ligands FICZ or indole-3-carboxaldehyde for 24h. Cytokine levels in culture supernatant were measured via using the ProcartaPlex human cytokine, chemokine, and growth factor 45-plex (ThermoFisher) on a Luminex FLEXMAP3D instrument.

RESULTS: AHR expression was similar across genotypes and treatments. PDOs homozygous for rs1077773 demonstrate enhanced CYP1A1 expression in response to AHR activation. In PBMϕs, cytokine secretion was stimulated by LPS treatment and was abrogated by FICZ treatment. PBMϕs with rs1077773 alternate allele demonstrated significant reduction in secretion of 17 cytokines and chemokines.

CONCLUSIONS: This work demonstrates that rs1077773 is an expression quantitative trait locus (eQTL) for AHR activity and modulates epithelial and immune cell function in vitro. Further mechanistic understanding of this locus and its correlates could improve our understanding of the molecular mechanisms of IBD susceptibility and may lead to novel personalized therapeutic approaches in IBD.},
}

@article {pmid41260033,
year = {2025},
author = {Zhang, Q and Zhang, S and Cao, X and Zhi, Y and Guo, Y},
title = {The gut microbiota in post-stroke depression: A systematic review of microbial mechanisms and therapeutic targeting of neuroinflammation.},
journal = {Microbiological research},
volume = {303},
number = {},
pages = {128391},
doi = {10.1016/j.micres.2025.128391},
pmid = {41260033},
issn = {1618-0623},
abstract = {Post-stroke depression (PSD), a frequent and debilitating complication after stroke, severely hinders rehabilitation. Emerging evidence underscores the role of neuroinflammation and the gut microbiota in PSD pathogenesis. This review systematically elaborates the mechanisms by which gut dysbiosis contributes to PSD-related neuroinflammation via immune cell regulation (e.g., Treg/Th17 balance), microbial metabolites (e.g., SCFAs, tryptophan derivatives), and neural pathways (vagus nerve, HPA axis). A key focus is the comparative analysis of the gut microbiota in PSD against major depressive disorder (MDD) and Alzheimer's disease (AD), revealing a unique, stroke-induced microbial signature characterized by a loss of protective symbionts and a bloom of pro-inflammatory taxa. We further discuss the translational potential of microbiota-targeted interventions (e.g., probiotics, prebiotics) for PSD. By integrating clinical microbial ecology with mechanistic insights, this review synthesizes evidence suggesting that the gut microbiome may represent a promising diagnostic and therapeutic target for PSD, offering a distinct perspective from previous literature.},
}

@article {pmid41259916,
year = {2025},
author = {Shi, R and Liu, W and Shi, X and Li, X and Ge, Y and Liu, J and Zeb, A and Zhao, Y and Sun, Y and An, J},
title = {Earthworm intestine orchestrates dual host-microbiome detoxification of 6PPD-quinone.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140527},
doi = {10.1016/j.jhazmat.2025.140527},
pmid = {41259916},
issn = {1873-3336},
abstract = {The highly toxic tire-derived compound N-(1,3-dimethylbutyl)-N'-phenyl-p-phenylenediamine-quinone (6PPD-Q) poses emerging environmental risks, yet its fate within soil invertebrates remains unclear. Here, we investigate the tissue distribution, elimination kinetics, biotransformation, and detoxification of 6PPD-Q in earthworms. 6PPD-Q showed tissue-specific accumulation, with the highest levels in the lipid-rich intestine (48.30 ± 4.06 ng/g; bioaccumulation factor (BAF) = 0.489 ± 0.156). We identified 17 metabolites generated through classical phase I and II detoxification pathways, mainly mediated by cytochrome P450 (CYP450) enzymes. 6PPD-Q exposure enriched detoxifying microbes (e.g., Paenibacillus and Pseudarthrobacter) and shifted microbial dynamics from deterministic to stochastic processes. Network analysis revealed enhanced microbial connectivity and functional resilience, which correlated strongly with degradation efficiency (p < 0.001). In vitro assays further confirmed microbial transformations yielding unique hydroxylated, acetylated, and methylated products. These findings highlight the intestine as both a reservoir and a bioreactor, emphasizing host-microbiota synergy in 6PPD-Q detoxification and offering new insights into contaminant bioremediation in soil invertebrates.},
}

@article {pmid41259824,
year = {2025},
author = {Fan, X and Wei, Y and Zang, T and Tu, Y and Liu, L and Tian, H and Li, X and Cheng, H and Bai, J and Liu, Y},
title = {Gut feelings: Dysbiosis of gut microbiota and short-chain fatty acids associated with prenatal depression, pregnancy-related anxiety, and prenatal combined depression and anxiety.},
journal = {Psychoneuroendocrinology},
volume = {184},
number = {},
pages = {107686},
doi = {10.1016/j.psyneuen.2025.107686},
pmid = {41259824},
issn = {1873-3360},
abstract = {OBJECTIVES: The role of the gut microbiota and short-chain fatty acids (SCFAs) in psychiatric disorders in pregnant women has not been fully elucidated. Therefore, this study aimed to investigate the association between the gut microbiota and its metabolite SCFAs and prenatal depression, pregnancy-related anxiety, and prenatal combined depression and anxiety.

METHODS: In total 200 pregnant women in the third trimester were recruited for this study. The Edinburgh Postnatal Depression Scale and Pregnancy-Related Anxiety Questionnaire Revised-2 were used to evaluate pregnant women's anxiety and depression, and stool samples were collected for gut microbiome and SCFAs.

RESULTS: This study found that reduced abundance of Allobaculum and Cetobacterium were associated with pregnancy-related anxiety in women. Furthermore, the enrichment of Anaerofustis, Gemella, and Staphylococcus and the reduction of Tyzzerella and unclassified_f_UCG-011 were associated with prenatal depression. This study was the first to indicate that women with comorbid prenatal anxiety and depression share similarities in gut microbiota and SCFAs with women with prenatal depression (Anaerofustis, Gemella, Staphylococcus, Tyzzerella, and isohexanoic acid). This study also found that certain gut microbial profiles were associated with prenatal comorbid anxiety and depression. While receiver operating characteristic analysis suggests a limited ability of the gut microbiota alone to predict prenatal psychological distress problems, the integration of phenotypic variables into the model significantly improved the model's predictive ability.

CONCLUSION: Our findings suggested that dysbiosis of gut microbiota and SCFAs are associated with prenatal psychiatric disorders. Alterations of the gut microbiota may have the potential as biomarkers for distinguishing prenatal psychiatric disorders.},
}

@article {pmid41259688,
year = {2025},
author = {Alizon, S and Tamarelle, J},
title = {[The scientific, health et social significance of the vaginal microbiome].},
journal = {Medecine sciences : M/S},
volume = {41},
number = {10},
pages = {760-769},
doi = {10.1051/medsci/2025139},
pmid = {41259688},
issn = {1958-5381},
mesh = {Humans ; Female ; *Microbiota/physiology ; *Vagina/microbiology/physiology ; Sexually Transmitted Diseases/microbiology/epidemiology ; },
abstract = {The vaginal microbiome is an ideal study system given the diversity of bacteria it harbors, its communities that can be structured into large, stable types, the ease of sampling, and the well-characterized environment. The microbiome is also dynamic and varying according to life stage, biological mechanisms such as hormonal cycles or menstruation, and specific exposures (e.g.; antibiotics, sexual practices). The associations between vaginal microbiota and health are strong, including its role in sexually transmitted infections, fertility, and general well-being. This raises questions about prevention and therapies, while avoiding the risk of excessive pathologization.},
}

Humans
Female
*Microbiota/physiology
*Vagina/microbiology/physiology
Sexually Transmitted Diseases/microbiology/epidemiology

@article {pmid41259558,
year = {2025},
author = {Issilbayeva, A and Jarmukhanov, Z and Kozhakhmetov, S and Bakytgul, Y and Chulenbayeva, L and Muniz-Terrera, G and Furukawa, M and Nikawa, H and Supiyev, A and Kushugulova, A and Zhumadilova, A},
title = {Oral microbiome patterns of dental caries in Kazakhstani adolescents.},
journal = {Journal of applied oral science : revista FOB},
volume = {33},
number = {},
pages = {e20250476},
doi = {10.1590/1678-7757-2025-0476},
pmid = {41259558},
issn = {1678-7765},
mesh = {Humans ; *Dental Caries/microbiology ; Adolescent ; Male ; *Microbiota/genetics ; Female ; Child ; RNA, Ribosomal, 16S/genetics ; *Mouth/microbiology ; DMF Index ; Reference Values ; },
abstract = {OBJECTIVE: The oral microbiome is one of the most complex microbial ecosystems in the host. This study aimed to investigate and characterize the oral microbiome composition in Kazakhstani adolescents associated with dental caries.

METHODOLOGY: The study included 312 adolescents, with 241 individuals presenting with caries and 71 caries-free, aged 12-15 years. Dental caries assessment was performed using DMFT (Decayed, missed, filled teeth) index. Oral samples were collected, and 16S rRNA (16S ribosomal ribonucleic acid) gene sequencing targeting the V3-V4 hypervariable regions on an Illumina MiSeq platform was performed to profile the microbial communities. Functional metagenomic predictions were generated using PICRUSt2 v2.5.0, using the KEGG database for bacterial pathway abundance estimation. Data analysis was conducted using Python 3.9.16 and R 4.2.2.

RESULTS: The alpha diversity was insignificant, while beta diversity analysis demonstrated clear distinctions by Bray-Curtis (F=2.5, p=0.003) and weighted UniFrac distances (F=4.4, p=0.002). The Neisseria and Prevotella genera, and Gammaproteobacteria class showed significant associations with dental caries (MaAsLin2 p≤0.05, LDA≥2), stronger predictive power (AUC=0.65, F1=0.83), and higher predicted functional activity through glutathione metabolism, RNA degradation, and unsaturated fatty acid metabolism pathways.

CONCLUSIONS: This study identified specific oral microbiome patterns associated with dental caries in Kazakhstani adolescents, revealing interactions between key bacterial taxa and metabolic pathways.},
}

Humans
*Dental Caries/microbiology
Adolescent
Male
*Microbiota/genetics
Female
Child
RNA, Ribosomal, 16S/genetics
*Mouth/microbiology
DMF Index
Reference Values

@article {pmid41259413,
year = {2025},
author = {Triadafilopoulos, G},
title = {Lessons learned: endoscopy with 96-hour ambulatory esophageal pH monitoring as a tool to avoid proton pump inhibitor use in cancer patients with refractory gastroesophageal reflux.},
journal = {Diseases of the esophagus : official journal of the International Society for Diseases of the Esophagus},
volume = {38},
number = {6},
pages = {},
doi = {10.1093/dote/doaf102},
pmid = {41259413},
issn = {1442-2050},
mesh = {Humans ; *Proton Pump Inhibitors/therapeutic use/adverse effects ; *Gastroesophageal Reflux/drug therapy/etiology/complications/diagnosis ; Male ; Female ; Retrospective Studies ; Middle Aged ; *Esophageal pH Monitoring/methods ; Aged ; *Neoplasms/complications ; *Heartburn/etiology/drug therapy ; *Esophagoscopy/methods ; Adult ; },
abstract = {The proton pump inhibitors (PPIs) are extensively prescribed for the empirical treatment of epigastric pain and heartburn in cancer patients. However, they carry the potential for drug interactions with antineoplastic agents during active cancer therapy, and osteopenia, opportunistic infections, adverse cardiovascular outcomes, and altered gut microbiome in long-term users in survivorship. Herein, we examined the use of endoscopy with esophageal 96-hour ambulatory pH monitoring in guiding clinicians in safely prescribing PPI in 21 such patients. We retrospectively studied patients with active cancer or in survivorship, presenting with PPI-refractory heartburn. All underwent an endoscopy with esophageal ambulatory pH monitoring performed "off" PPI therapy for 96 hours, following a "liberal diet" for the first 48, and a "restrictive diet" for the latter 48 hours. Acid exposure time (AET) ≥ 6% per 24 hours was defined as abnormal. For each patient, the average AET from the first 2 days was considered as baseline and was compared with that from the latter 2 days (on restrictive diet). We concluded that ambulatory 96-hour pH monitoring, identifies 48% of patients with normal AET, who may not need PPI. Esophageal pH monitoring on restrictive diet normalizes AET in 73% of patients, thereby allowing esophageal acid control to be achieved with diet alone.},
}

Humans
*Proton Pump Inhibitors/therapeutic use/adverse effects
*Gastroesophageal Reflux/drug therapy/etiology/complications/diagnosis
Male
Female
Retrospective Studies
Middle Aged
*Esophageal pH Monitoring/methods
Aged
*Neoplasms/complications
*Heartburn/etiology/drug therapy
*Esophagoscopy/methods
Adult

@article {pmid41259398,
year = {2025},
author = {Yadav, A and Ali, R and Devi, P and Kumari, P and Soni, J and Garima, and Tarai, B and Budhiraja, S and Shamim, U and Pandey, R},
title = {Non-canonical Metatranscriptomic analysis of COVID-19 and Dengue reveals an expanded microbial and AMR landscape in COVID-19 mortality patients.},
journal = {PLoS pathogens},
volume = {21},
number = {11},
pages = {e1013703},
doi = {10.1371/journal.ppat.1013703},
pmid = {41259398},
issn = {1553-7374},
mesh = {Humans ; *COVID-19/mortality/microbiology ; *Dengue/microbiology/mortality ; *Microbiota/genetics ; SARS-CoV-2 ; Female ; Male ; Middle Aged ; Transcriptome ; Adult ; Anti-Bacterial Agents/pharmacology/therapeutic use ; *Drug Resistance, Bacterial/genetics ; },
abstract = {AMR is a growing concern in viral infections, where microbiome shifts contribute to resistance gene dissemination. While dengue and COVID-19, caused by ssRNA viruses, are not bacterial-driven, their resistome and microbial communities influence disease progression and AMR burden. This study analyzes the resistome and microbiome in 251 COVID-19 and 112 dengue patients using non-canonical metatranscriptomics. By mapping antimicrobial resistance genes (ARGs) and their transcriptionally active microbes (TAMs) hosts, we uncover greater ARG burden in COVID-19, particularly during mortality, with a diverse set of associated TAMs compared to dengue. MDR genes were prevalent, with beta-lactamase ARGs commonly detected in both infections. COVID-19 exhibited higher carbapenemase resistance genes (NDM, OXA, VIM), while dengue was associated with TEM variants. Escherichia coli and Klebsiella pneumoniae were dominant ARG hosts, with Acinetobacter baumannii in COVID-19 mortality and Bacillus cereus in severe dengue. These findings highlight resistome dynamics and emphasize the need for AMR surveillance in high-burden infections.},
}

Humans
*COVID-19/mortality/microbiology
*Dengue/microbiology/mortality
*Microbiota/genetics
SARS-CoV-2
Female
Male
Middle Aged
Transcriptome
Adult
Anti-Bacterial Agents/pharmacology/therapeutic use
*Drug Resistance, Bacterial/genetics

@article {pmid41259328,
year = {2025},
author = {Custodio, R and Alseth, EO and Brockhurst, MA and Brown, SP and Westra, ER},
title = {Bacterial immune systems as causes and consequences of microbiome structure.},
journal = {PLoS biology},
volume = {23},
number = {11},
pages = {e3003489},
doi = {10.1371/journal.pbio.3003489},
pmid = {41259328},
issn = {1545-7885},
mesh = {*Microbiota/immunology/genetics ; *Bacteria/immunology/genetics ; Humans ; Interspersed Repetitive Sequences ; Animals ; },
abstract = {Attacks from molecular parasites such as mobile genetic elements (MGEs) have driven the evolution of defense systems in bacterial genomes. Yet, despite significant advances in understanding the molecular mechanisms of these bacterial immune systems, we have only a rudimentary understanding of their ecology and evolution. Bacteria exist as part of complex microbiomes, but community ecology and microbiome research has yet to characterize the impacts of interactions between MGEs and defense mechanisms upon the structure, dynamics and evolution of microbiomes. This Essay introduces and discusses the interplay between bacterial community dynamics and bacterial immune systems, speculating about how these reciprocal interactions may shape microbial community structure and function.},
}

*Microbiota/immunology/genetics
*Bacteria/immunology/genetics
Humans
Interspersed Repetitive Sequences
Animals

@article {pmid41259124,
year = {2025},
author = {Todt, T and van Bussel, I and Afman, L and Brennan, L and Ivanova, DG and Kiselova-Kaneva, Y and Thomas, EL and Rühl, R},
title = {Transcriptome-driven Health-status Transversal-predictor Analysis for health, food, microbiome and disease markers for understanding of lifestyle diseases.},
journal = {Physiological genomics},
volume = {},
number = {},
pages = {},
doi = {10.1152/physiolgenomics.00026.2025},
pmid = {41259124},
issn = {1531-2267},
support = {EU FP7 nutritech//all except Tilman/ ; },
abstract = {We developed a novel artificial intelligence (AI) approach based on machine-learning to predict general health and food-intake parameters. This approach, named Transcriptome-driven Health-status Transversal-predictor Analysis (THTA) is relevant for markers of diabesity and is based on a non-transcriptomic, mathematics-driven approach. The prediction was based on values derived from food consumption, dietary lipids and their bioactive metabolites, peripheral blood mononuclear cell (PBMC) mRNA-based transcriptome signatures, magnetic resonance imaging (MRI), energy metabolism measurements, microbiome analyses, and baseline clinical parameters, as determined in a cohort of 72 subjects. Our novel machine learning approach incorporated transcriptome data from PBMCs as a "one-method" approach to predict 77 general health-status markers for the broad stratification of the diabesity phenotype. These markers would usually necessitate measurements using 16 different methods. The PBMC transcriptome was used to determine these 77 basic and background health markers with very high accuracy in a transversal-predictor establishment group (Pearson correlations are r = 0.98 ranging from 0.94 to 0.99). These collected variables provide valuable insides into which individual factor(s) are mainly target diabesity. Based on the "establishment group" prediction approach a further "confirmation group" prediction approach was performed, achieving a predictive potential r = 0.59 (ranging from 0.19 to 0.98) for these 77 variables. This "one-method" approach enables the simultaneous monitoring of a large number of health-status variables relevant to diabesity and may facilitate the monitoring of therapeutic and preventive strategies. In summary, this novel technique, which is based on PBMC transcriptomics from human blood, can predict a wide range of health-related markers.},
}

@article {pmid41258884,
year = {2025},
author = {Ni, D and Pinget, G and Santner-Nanan, B and Tan, J and Reyes, JGA and Lai, CL and Wang, Y and Tran, C and Clarke, JM and Macia, L and Campbell, DE and Hsu, P and Nanan, R},
title = {Effects of Butyrylated High Amylose Maize Starch (HAMSB) as an Adjuvant for Oral Immunotherapy.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.70161},
pmid = {41258884},
issn = {1398-9995},
support = {//National Health and Medical Research Council/ ; //Norman Ernest Bequest Fund/ ; },
}

@article {pmid41258872,
year = {2025},
author = {Scheelings, TF and Kodikara, S and Beale, DJ and Van, TTH and Moore, RJ and Skerratt, LF},
title = {Unravelling the impacts of captivity on saltwater crocodile (Crocodylus porosus) cloacal bacterial communities and physiology.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf114},
pmid = {41258872},
issn = {1574-6941},
abstract = {This study addresses a significant research gap in understanding the impacts of captivity on the bacteriome and physiology of saltwater crocodiles (Crocodylus porosus). Despite their ecological and cultural significance, crocodilians are a taxon that remains underexplored in microbiome research. We investigated cloacal bacteriome samples from both wild and captive populations to identify compositional and functional differences resulting from captivity. Our findings reveal significant alterations in bacterial diversity and community structure in captive crocodiles, with notable shifts at both phylum and family levels; specifically, Bacteroidota and Fusobacteriota dominate in captivity, whereas wild crocodiles exhibit a higher prevalence of Pseudomonadota and Bacillota. The Shannon diversity index indicates a significant reduction in bacterial diversity among captive individuals, likely due to husbandry practices that foster a microbially depauperate environment. Additionally, serum metabolomics analysis shows an enrichment of alcohol sugars in captive crocodiles, alongside a decrease in pantothenic acid. While this is the first study to characterize these traits in saltwater crocodiles, further research is necessary to determine the physiological consequences of these bacterial and metabolic changes on host fitness and adaptability. Longitudinal studies are essential for understanding how bacterial communities evolve over time and in response to environmental factors, which will inform conservation strategies and improve the management of captive populations of crocodilians intended for reintroduction into the wild.},
}

@article {pmid41258857,
year = {2025},
author = {Wang, M and Hou, H and Sang, W and Li, P and Yang, X and Qi, P and Ma, Y},
title = {Bile Microbiome and Metabolic Characteristics in Primary Common Bile Duct Stone Patients with Juxtapapillary Duodenal Diverticula: A Clinical Investigation.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf280},
pmid = {41258857},
issn = {1365-2672},
abstract = {OBJECTIVE: This study aimed to characterize the bile microbiome and metabolome in patients with common bile duct stones (CBDs), with versus without juxtapapillary duodenal diverticulum (JPDD), to identify potential factors associated with stone formation.

METHODS: From January to May 2024, CBDs patients undergoing endoscopic retrograde cholangiopancreatography at our hospital were prospectively enrolled. Bile samples were collected for 16SrRNA sequencing and LC-MS/MS metabolomics analysis. Patients were divided into JPDD (n = 15) and CBDs (n = 15) groups.

RESULTS: The JPDD group had larger stone and bile duct diameters (P < 0.05). Although Proteobacteria dominated the bile microbiota in both groups, the JPDD group showed higher abundances of Escherichia-Shigella, Enterococcus, and Escherichia coli. Beta diversity differed significantly between groups (P < 0.05), and LEfSe identified 25 differentially abundant bacterial taxa. Enterococcus, Klebsiella, and Gemellaceae were more abundant in the JPDD group, while Peptococcaceae, Roseburia, and Alistipes were more prevalent in the CBDs group. Enterococcaceae and Enterococcus abundances were positively correlated with stone and duct sizes in the JPDD group (P < 0.05), whereas Peptococcaceae and Acinetobacter showed negative correlations. Metabolomic analysis identified ten differentially enriched pathways-including phenylalanine and alanine metabolism-and higher levels of bilirubin glucuronide and taurochenodeoxycholic acid in the JPDD group. Enterococcus abundance was correlated with bile acid metabolites such as chenodeoxycholylasparagine (P < 0.05).

CONCLUSIONS: JPDD is associated with distinct microbial and metabolic profiles in bile. Enrichment of Enterococcus and Klebsiella in the JPDD group, along with changes in metabolic pathways and bile acid metabolites, suggests a potential link to CBD stone formation and growth.},
}