@article {pmid41240715,
year = {2025},
author = {Zheng, Z and Wang, X and Su, Z and Li, S and Qin, J and Ren, N and He, L and Zhang, W},
title = {Melatonin alleviates intestinal damage in neonate mice following Salmonella Typhimurium and LPS challenges involving gut microbiota remodeling.},
journal = {International immunopharmacology},
volume = {168},
number = {Pt 1},
pages = {115761},
doi = {10.1016/j.intimp.2025.115761},
pmid = {41240715},
issn = {1878-1705},
abstract = {Neonates exhibit heightened susceptibility to intestinal barrier disruption induced by Salmonella Typhimurium (ST) and its virulence factor lipopolysaccharide (LPS), while antibiotic-independent interventions remain scarce. Here, we demonstrate that melatonin, administered via discrete perinatal and postnatal regimens, ameliorates ST- and LPS-induced intestinal injury in neonatal mice through gut microbiota remodeling. In perinatal studies, maternal melatonin supplementation in drinking water (100 μg/mL; gestational day 13 to postnatal day 21) enhanced intestinal maturation in healthy neonates, upregulated tight junction proteins (Claudin-3, ZO-1), and enriched beneficial taxa (e.g., Candidatus Arthromitus, Lachnospiraceae NK4A136). In infection models, postnatal intraperitoneal melatonin administration (10 mg/kg; 7 days) attenuated ST- and LPS-induced pathology: suppressing pathogens (Salmonella enterica, Escherichia-Shigella), elevating commensals (Ligilactobacillus), restoring villus architecture, and balancing inflammatory mediators (decreased TNF-α, increased IL-10). Collectively, these findings identify melatonin as a microbiota-targeted therapy for neonatal enteropathies, supporting its therapeutic potential against Salmonella-induced intestinal injury.},
}

@article {pmid41240707,
year = {2025},
author = {Fonseca, A and Kenney, S and Boney, J and Ganda, E},
title = {Mycobiome temporal and functional dynamics in broilers: Ecological perspective on bacterial-fungal correlations and the effect of feed additives.},
journal = {Poultry science},
volume = {104},
number = {12},
pages = {106092},
doi = {10.1016/j.psj.2025.106092},
pmid = {41240707},
issn = {1525-3171},
abstract = {The gut mycobiome (the fungal component of the microbiome) of chickens, though less abundant than bacterial populations, plays a vital role in gut ecology, yet remains underexplored. This study investigated the temporal, dietary, and ecological factors shaping the broiler chicken excreta-associated fungal communities and their correlation with bacterial microbiota. A total of 320 Cobb 500 (1-day-old) chicks were raised for 21 days in 32 randomly allocated cages. Treatments consisted of four experimental diets: a Basal Diet, a Basal Diet with an Antibiotic (bacitracin methylene disalicylate), an Essential oils blend (oregano oil, rosemary, and red pepper), or a Probiotic (Bacillus subtilis). Shotgun metagenomic sequencing was performed on excreta samples collected at days 1, 10, and 21 to evaluate fungal diversity, composition, cross-kingdom correlation and functional profiling. The fungal community was dominated by Ascomycota and Basidiomycota across all treatments and time points. While alpha diversity metrics did not differ significantly between treatments (P > 0.05), fungal richness and evenness increased significantly over time (P < 0.05), indicating age-driven ecological succession. Beta diversity analysis revealed distinct age-related clustering patterns, with early dominance by Candida albicans and later shifts toward genera such as Fusarium and Malassezia. Feed additives exerted limited influence on fungal composition or diversity metrics, although clustering patterns suggested subtle treatment-specific effects over time. Cross-kingdom correlation analysis identified co-occurring temporal dynamics between the two microbial communities. Candida was positively correlated with Streptococcus and Escherichia/Shigella but negatively associated with beneficial genera like Bifidobacterium and Faecalibacterium. Additionally, microbial functional characteristics were observed in each treatment exhibiting metabolic features. Overall, this study demonstrates that excreta fungal succession in the broiler gut is primarily driven by host age and highlights the temporal plasticity of concurrent changes in fungal and bacteria communities. The findings underscore the importance of multi-kingdom ecological approaches to better understand gut health in poultry production.},
}

@article {pmid41240551,
year = {2025},
author = {Cecil, A and Gentschev, I and Prehn, C and Hauck, S and Witting, M and Petrov, I and Ye, M and Othman, EM and Szalay, AA},
title = {Endogenous gut microbiome and implanted intranasal E. coli-Nissle modulate cancer tissues metabolism in 4T1 syngeneic tumor bearing mice.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {193},
number = {},
pages = {118750},
doi = {10.1016/j.biopha.2025.118750},
pmid = {41240551},
issn = {1950-6007},
abstract = {Despite recent progress in the diagnosis and treatment of advanced cancers, the overall patient treatment outcome did not substantially improve over the last years. Therefore, developing novel therapies, which may also work synergistically in combination with the conventional therapies is crucial. One promising new therapeutic approach is bacterium-mediated cancer therapy. In the current work, we describe the influence of the gut microbiome and intranasal E. coli Nissle applications on the metabolism in cancer tissues of 4T1 syngeneic tumor bearing mice. Here we found that after gut microbiome depletion and/or E. coli Nissle treatment the ratios of ADMA/Arginine, Putrescine/Ornithine and Kynurenine/Tryptophan as well as the total concentration of Carnosine, Kynurenine and H1 (synonymus for all sugars detectable) are significantly altered in tumor tissues of as the result of treatment. In conclusion, our current data show that E. coli Nissle bacteria facilitating metabolic modulation of tumors, a finding could be important for improved cancer therapy in patients.},
}

@article {pmid41240439,
year = {2025},
author = {Thoniyot, S and Balakrishnan, V},
title = {Integrating multi-omics data for personalized nutrition using knowledge graphs and graph neural networks: A comprehensive review.},
journal = {Computational biology and chemistry},
volume = {120},
number = {Pt 1},
pages = {108772},
doi = {10.1016/j.compbiolchem.2025.108772},
pmid = {41240439},
issn = {1476-928X},
abstract = {This comprehensive review focuses on the use of knowledge graphs and Graph Neural Networks (GNNs) to integrate multi-omics data in the field of personalized nutrition. It investigates how different biological datasets-like genomics, proteomics, metabolomics, and gut microbiome profiles-can be combined to create customized dietary plans. By reviewing scientific literature from 2015 to 2025, the study highlights how knowledge graphs help map complex biological interactions and how GNNs effectively analyze and interpret graph-based multi-omics information. The review demonstrates that knowledge graphs provide an elastic and scalable model for representing multi-relational biological information; however, GNNs enable the identification of complex non-local relationships between omics layers that cannot be detected using conventional statistics. The most significant benefits include improved forecast accuracy of individual responses to diet, enhanced biomarker discovery, and the potential for the development of customized nutritional therapy based on detailed characterization of the individual through comprehensive biological profiling. Nevertheless, several issues require further attention, including the quality and standardization of data across omics platforms, scalability uncertainty in computational models, interpretability shortcomings of models, and the ethical challenges associated with the use of personal genetic information. In this review, case studies are provided for comparing the graph-based approach with traditional methods and demonstrating how these methods outperform in terms of their capability to capture biological complexity. Future directions emphasize the importance of international cooperation, the utilization of technology in computational processes with potential for scalability, the development of models that are easier to interpret, and adherence to acceptable ethical standards: knowledge graphs and GNNs. KG and GNNs can couple multi-omics data, providing a paradigm shift towards precision nutrition by enabling unprecedented capabilities to optimize personal health outcomes through scientifically augmented, customized dietary interventions.},
}

@article {pmid41240269,
year = {2025},
author = {Israr, G and Qiao, Q and An, Y and Liu, F and Li, Z},
title = {From Mycobiome Remodeling to Therapeutic Candidate: Aspergillus ruber and 3-methyldioxyindole, Acknowledged as a Novel Modulator Via BPIS Treatment and Alleviating MASLD.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41240269},
issn = {1867-1314},
support = {nos.2022ZDYF121//The Key Research and Development (R&D) Program of Shanxi Province/ ; },
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is a leading significant public health concern, affecting 25-30% of the population globally. Recent advances in gut microbiome research are increasingly recognized. Studies exploring the gut-liver axis have mostly focused on bacteriomes. There are limited studies about commensal fungi. Our earlier research on the anti-inflammatory properties of bound polyphenols of the inner shell (BPIS) extracted from Foxtail millet in the mouse colitis model revealed that BPIS significantly increased the abundance of Aspergillus ruber (A. ruber) and remodeled the gut mycobiome. The present study demonstrated that BPIS mitigated MASLD caused by a high-fat diet (HFD), significantly enhancing A. ruber fungi in the gut microbiome. Further investigation exhibited that the administration of A. ruber and its metabolite 3-methyldioxyindole alleviated disordered lipid metabolism, abnormal weight gain, oxidative stress, low ATP synthesis, and histological complications in HFD-fed mice. A. ruber and 3-methyldioxyindole also improved HFD-induced breakage of the intestinal barrier by enhancing the expression of tight junction proteins (Occludin, ZO-1, and claudin) in the colon. The study suggests that the metabolite 3-methyldioxyindole demonstrates more promising effects in lipid metabolism homeostasis. A. ruber or 3-methyldioxyindole has great potential to be developed as an effective probiotic agent for treating MASLD.},
}

@article {pmid41240244,
year = {2025},
author = {Jayathilaka, NS and Weththasinghe, AV and Amarasekara, CI and Amasha, EADH and Wijekoon, KJ and Firdous, SM},
title = {Targeting the Gut-Brain Axis Through Insulin-like Growth Factors: Therapeutic Implications and Future Directions.},
journal = {Journal of molecular neuroscience : MN},
volume = {75},
number = {4},
pages = {150},
pmid = {41240244},
issn = {1559-1166},
mesh = {Humans ; Animals ; *Brain/metabolism ; Gastrointestinal Microbiome ; *Somatomedins/metabolism ; *Neurodegenerative Diseases/metabolism/drug therapy/therapy ; *Insulin-Like Growth Factor I/metabolism ; *Brain-Gut Axis ; *Gastrointestinal Tract/metabolism ; Insulin-Like Peptides ; },
abstract = {The gut-brain axis represents a sophisticated bidirectional communication network connecting the gastrointestinal tract and central nervous system through neural, endocrine, and immune pathways. Insulin-like growth factors (IGFs), particularly IGF-1 and IGF-2, function as pivotal mediators within this communication framework. These polypeptide growth factors regulate intestinal barrier integrity, microbiota homeostasis, neurogenesis, and synaptic plasticity mechanisms. Clinical evidence from 1989 to 2024 demonstrates that gut microbiota-derived short-chain fatty acids enhance IGF-1 production through novel molecular mechanisms. This narrative review examines IGF roles in gut-brain communication and evaluates therapeutic potential for neurodegenerative diseases including Alzheimer's disease, Parkinson's disease, and depression, as well as inflammatory bowel disorders. Current clinical trials investigating IGF-based interventions show preliminary promising results, though studies remain limited in scope and patient numbers. Key therapeutic challenges include delivery mechanisms across biological barriers, oncogenic safety concerns related to cell proliferation, and substantial individual variability in treatment responses. Future directions emphasize development of tissue-specific IGF modulators, microbiome-targeted interventions, and precision medicine approaches utilizing advanced biomarkers. Understanding IGF-mediated gut-brain communication presents therapeutic opportunities for complex pathological conditions simultaneously affecting gastrointestinal and neurological systems.},
}

Humans
Animals
*Brain/metabolism
Gastrointestinal Microbiome
*Somatomedins/metabolism
*Neurodegenerative Diseases/metabolism/drug therapy/therapy
*Insulin-Like Growth Factor I/metabolism
*Brain-Gut Axis
*Gastrointestinal Tract/metabolism
Insulin-Like Peptides

@article {pmid41240124,
year = {2025},
author = {Jiao, Y and Xu, Y and Liu, Y and Li, X and Li, X and Liu, S and Liu, Y and Hou, Y and Guo, L},
title = {Microbial changes in different parts of the oral cavity during the early stage of clear aligner treatment: a preliminary study.},
journal = {Clinical oral investigations},
volume = {29},
number = {12},
pages = {569},
pmid = {41240124},
issn = {1436-3771},
mesh = {Humans ; Male ; Female ; *Dental Plaque/microbiology ; *Microbiota ; *Mouth Mucosa/microbiology ; *Orthodontic Appliances, Removable ; *Mouth/microbiology ; Adult ; Adolescent ; },
abstract = {OBJECTIVES: More and more patients choose clear aligners to improve their appearance and masticatory function. However, there is no study on whether clear aligner treatment affects the microecology of oral mucosal plaque. Therefore, we analyzed flora changes in different parts of patients' mucosa at various time points during the early stage of clear aligner treatment.

METHODS: Plaque samples were collected from the buccal, palatal, and dorsal lingual mucosa of 10 subjects before and 1, 3, 6, and 12 months post clear orthodontic treatment. Microbial community changes were analyzed by 16 S rRNA gene sequencing.

RESULTS: At 6 months, buccal plaque showed a significant decrease in alpha diversity and distinct microbial separation. By 12 months, diversity had recovered, and the community structure had returned to baseline levels. Genus-level changes varied by site: the periodontal pathogen Fusobacterium increased at 6 months and declined at 12 months; the periodontally relevant Prevotella showed a temporary increase at 3 months (palatal) and 1 month (dorsal lingual).

CONCLUSIONS: The clear aligner altered the microbial community of buccal mucosal plaque by 6 months, and the microbial community returned to the basal composition by 12 months.

CLINICAL RELEVANCE: This study highlights that clear aligner treatment transiently disrupts the oral mucosal microbiome, with a significant but reversible shift toward periodontal pathogen-associated flora within 6 months, suggesting the need for enhanced oral hygiene monitoring during early orthodontic therapy to mitigate potential periodontal risks.},
}

Humans
Male
Female
*Dental Plaque/microbiology
*Microbiota
*Mouth Mucosa/microbiology
*Orthodontic Appliances, Removable
*Mouth/microbiology
Adult
Adolescent

@article {pmid41240073,
year = {2025},
author = {Berkhout, MD and de Ram, C and Boeren, S and Plugge, CM and Belzer, C},
title = {Probiotic Engraftment of Akkermansia muciniphila in an In Vitro Synthetic Microbial Community.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {123},
pmid = {41240073},
issn = {1432-184X},
support = {0.24.002.002//Ministerie van Onderwijs, Cultuur en Wetenschap/ ; },
mesh = {*Probiotics ; *Gastrointestinal Microbiome ; Humans ; Mucins/metabolism ; *Verrucomicrobia/physiology ; Akkermansia ; Polysaccharides/metabolism ; Bacteroides thetaiotaomicron ; },
abstract = {Akkermansia muciniphila is a specialist mucin glycan-degrader that is common in the human gut. A. muciniphila is associated with host health and therefore proposed as a next-generation probiotic. However, it is unknown if consumption of live and active A. muciniphila will be effective in terms of survival and engraftment in the gut microbiome. Furthermore, it is of interest whether introduction of A. muciniphila would influence the resident mucosal microbiota. To this end, we investigate the addition of live A. muciniphila to a stable in vitro microbial mucin glycan-degrading synthetic community. A. muciniphila engrafted in this synthetic community and actively degraded mucin using essential mucin glycan-degrading enzymes. Addition of A. muciniphila did not induce major compositional changes, except that Bacteroides thetaiotaomicron increased in relative abundance at the expense of Bacteroides caccae. At the metaproteomic level, community function was not significantly affected, as peptidase, fucosidase, galactosidase and sulfatase expression remained stable. However, sialidase was significantly enriched after A. muciniphila addition, which can be explained by the relative increase of generalist glycan-degrader B. thetaiotaomicron. Overall, we show that a community without A. muciniphila still harbours a niche for this bacterium, but that A. muciniphila did not induce major changes in the in vitro mucosal synthetic community. This suggests that A. muciniphila applied as a probiotic can engraft and exert its beneficial effects on the host, without major impact on the human gut mucosal microbiota composition and function and warrants further research into A. muciniphila engraftment in vivo.},
}

*Probiotics
*Gastrointestinal Microbiome
Humans
Mucins/metabolism
*Verrucomicrobia/physiology
Akkermansia
Polysaccharides/metabolism
Bacteroides thetaiotaomicron

@article {pmid41239974,
year = {2025},
author = {Reichart, NJ and Bell, S and Garayburu-Caruso, VA and Sadler, N and Zhao, S and Hofmockel, KS},
title = {Impact of Moisture on Microbial Decomposition Phenotypes and Enzyme Dynamics.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf250},
pmid = {41239974},
issn = {1751-7370},
abstract = {Soil organic matter decomposition is a complex process reflecting microbial composition and environmental conditions. Moisture can modulate the connectivity and interactions of microbes. Due to heterogeneity, a deeper understanding of the influence of soil moisture on the dynamics of organic matter decomposition and resultant phenotypes remains a challenge. Soils from a long-term field experiment exposed to high and low moisture treatments were incubated in the laboratory to investigate organic matter decomposition using chitin as a model substrate. By combining enzymatic assays, biomass measurements, and microbial enrichment via activity-based probes, we determined the microbial functional response to chitin amendments and field moisture treatments at both the community and cell scales. Chitinolytic activities showed significant responses to the amendment of chitin, independent of differences in field moisture treatments. However, for other measurements of carbon metabolism and cellular functions, soils from high moisture field treatments had greater potential enzyme activity than soils from low moisture field treatments. A cell tagging approach was used to enrich and quantify bacterial taxa that are actively producing chitin-degrading enzymes. By integrating organism, community, and soil core measurements we show that 1) a small subset of taxa compose the majority (>50%) of chitinase production despite broad functional redundancy, 2) the identity of key chitin degraders varies with moisture level, and 3) extracellular enzymes that are not cell-associated account for most potential chitinase activity measured in field soil.},
}

@article {pmid41239968,
year = {2025},
author = {Kim, MS and Bisanz, JE},
title = {Design and application of synthetic human gut microbial communities.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2575923},
doi = {10.1080/19490976.2025.2575923},
pmid = {41239968},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; Fecal Microbiota Transplantation/methods ; Dysbiosis/therapy/microbiology ; Inflammatory Bowel Diseases/therapy/microbiology ; Host Microbial Interactions ; Bacteria/genetics/classification ; Animals ; },
abstract = {The gut microbiome shapes host health through a complex network driven by both host‒microbe and microbe‒microbe interactions. Disruption of these interactions, often referred to as dysbiosis, is associated with a range of infectious and chronic diseases. Owing to the success of fecal microbiota transplantation (FMT) for the treatment of recurrent Clostridioides difficile infection, FMT has been explored as a therapeutic option for a range of microbiota-associated conditions, including inflammatory bowel disease and obesity. However, the microbial diversity that is the greatest strength of FMT is also its greatest liability. Concerns relating to reliance on human donors, potential for transmission of multidrug-resistant organisms or undesirable phenotypes demonstrate a need for alternate approaches, including the generation of synthetic alternatives to FMT, which can be built in the laboratory from individual strains. Furthermore, these communities are powerful tools for conducting mechanistic research allowing for the generation of 'knockout' communities, which are not possible when working with undefined fecal transplants. This review examines strategies for designing synthetic microbial communities that represent a new generation of microbiome-derived therapies. We highlight how synthetic microbial communities are being used to answer mechanistic questions about host-microbiome interactions relevant to health and disease. Finally, we examine the current clinical translation of these communities as live biotherapeutic products (LBPs). While the regulatory frameworks for LBPs continue to evolve, early clinical successes illuminate the potential for synthetic microbial communities to treat complex human diseases through targeted manipulation and restoration of the gut microbiome.},
}

Humans
*Gastrointestinal Microbiome
Fecal Microbiota Transplantation/methods
Dysbiosis/therapy/microbiology
Inflammatory Bowel Diseases/therapy/microbiology
Host Microbial Interactions
Bacteria/genetics/classification
Animals

@article {pmid41239524,
year = {2025},
author = {Hashem, HR and Yehia, T and Azab, M and Abdellah, A and Amin, IA and Salah, M and Ramadan, M},
title = {Gut microbiome dysbiosis in hepatocellular carcinoma patients with persistent HCV viremia versus viral clearance: a cross-sectional study.},
journal = {Gut pathogens},
volume = {17},
number = {1},
pages = {88},
pmid = {41239524},
issn = {1757-4749},
abstract = {BACKGROUND: Hepatocellular carcinoma (HCC) remains a lethal complication of chronic hepatitis C virus (HCV) infection, even after successful direct-acting antiviral (DAA) therapy. The gut microbiome influences hepatocarcinogenesis through the gut‒liver axis; however, the microbial signatures associated with HCC in DAA-treated patients are poorly defined. This study aimed to elucidate the patterns of microbiomes in HCV-treated patients who developed HCC, with a focus on bacterial diversity, differentially represented taxa, and their associations with clinical markers (FIB-4) and metabolic profiles as potential biomarkers.

RESULTS: A total of 138 participants were enrolled: 46 HCC patients with persistent HCV viremia (RHCC), 46 HCC patients with HCV eradication (THCC), and 46 healthy controls. RHCC patients exhibited pronounced dysbiosis, characterized by reduced alpha diversity (Kruskal-Wallis; H = 14.37, p = 0.00076) and an elevated Firmicutes/Bacteroidetes (F/B) ratio (1.55 vs. 1.05 in controls; Mann-Whitney U test, U = 87.32, padj = 0.00079). At the genus level, Asteroleplasma was significantly enriched in RHCC (log₂FC = + 2.8, padj = 0.008), whereas the butyrate-producing genus Faecalibacterium was depleted (log₂FC = - 2.1, padj = 0.006). Machine learning identified Asteroleplasma, Moryella, Lachnoclostridium, Fournierella, Eubacterium xylanophilum, Succinivibrio, and Faecalibacterium as the top classifiers of RHCC (AUC = 0.81). Functional profiling revealed a 58% reduction in butyrate synthesis (padj = 0.0032) and increased lipopolysaccharide biosynthesis (log₂FC = + 3.2, padj = 0.002) in RHCC, both of which correlated with clinical deterioration (FIB-4 scores, r = 0.62).

CONCLUSIONS: Distinct gut microbial signatures distinguish HCC patients with persistent HCV viremia from those who achieve viral clearance, with implications for risk stratification and therapeutic targeting. The F/B ratio, abundance of Asteroleplasma, and functional pathway disruption (butyrate depletion) could serve as potential biomarkers for HCC progression. These findings underscore the influential role of the gut microbiome in hepatocarcinogenesis and its potential utility in personalized HCC management.},
}

@article {pmid41239321,
year = {2025},
author = {Alkuwaiti, SH and Skrabulyte-Barbulescu, J and Yassin, LK and Almazrouei, S and Aldhaheri, D and Alderei, M and BaniYas, S and Alshamsi, SH and Alnuaimi, A and Saeed, S and Alawadhi, M and Rutkowska-Gauvry, P and Ismail, FY and Hamad, MIK},
title = {Harnessing the microbiota-gut-brain axis to prevent and treat pediatric neurodevelopmental disorders: translational insights and strategies.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {1286},
pmid = {41239321},
issn = {1479-5876},
}

@article {pmid41239215,
year = {2025},
author = {Soliman, S and Rezk, A and Rocha, FI and Rodriguez-Ramos, JC and Manoharan, B and Wang, Y and Han, Z and Hale, L and El-Kereamy, A},
title = {Strigolactone GR24 modulates citrus root architecture and rhizosphere microbiome under nitrogen and phosphorus deficiency.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {1569},
pmid = {41239215},
issn = {1471-2229},
mesh = {*Rhizosphere ; *Phosphorus/deficiency/metabolism ; *Plant Roots/drug effects/growth & development/microbiology/anatomy & histology ; *Nitrogen/deficiency/metabolism ; *Microbiota/drug effects ; *Lactones/pharmacology ; *Citrus/microbiology/drug effects/growth & development/metabolism/anatomy & histology ; *Heterocyclic Compounds, 3-Ring/pharmacology ; Soil Microbiology ; *Plant Growth Regulators/pharmacology ; Soil/chemistry ; },
abstract = {Nutrient deficiencies, especially nitrogen (N) and phosphorus (P) deficiencies, are among the most critical challenges for sustainable crop production. Excessive use of chemical fertilizers contributes to environmental degradation and climate change, highlighting the need for alternative strategies to improve nutrient uptake. Strigolactones (SLs), a class of plant hormones, have emerged as key regulators of root development and plant-microbe interactions under nutrient-limited conditions. In this study, we investigated the effects of the SL analog GR24 on citrus rootstock C-32 under full nutrition, nitrogen deficiency, and phosphorus deficiency conditions. Plants were treated with five GR24 concentrations (0, 1, 2.5, 5, and 10 µM) and evaluated for changes in root architecture, biomass, soil nutrient content, and rhizosphere microbiomes. The results showed that SL application had a concentration-dependent effect on root morphology. The 2.5 µM SL treatment enhanced fine root initiation, proliferation, and lateral branching under nutrient deficiency, whereas higher concentrations (5 and 10 µM) generally had inhibitory effects. Root surface area and volume were modulated differently across diameter classes, depending on nutrient status and SL dose. Soil nutrient analyses indicated minor alleviating effects of SL on N and P starvation; however, SL significantly affected Cu and Mn. Microbiome analysis revealed that SL reduced bacterial ASV richness but increased dispersion in community structure, particularly under N and P deficiency. Functional annotation indicated changes in denitrification and methanotrophy pathways. Overall, SLs modulated both the root architecture and rhizosphere microbiome composition of citrus plants under nutrient stress. These findings suggest a dual role for SLs in enhancing root plasticity and microbial recruitment, with potential applications in sustainable crop nutrition and soil health.},
}

*Rhizosphere
*Phosphorus/deficiency/metabolism
*Plant Roots/drug effects/growth & development/microbiology/anatomy & histology
*Nitrogen/deficiency/metabolism
*Microbiota/drug effects
*Lactones/pharmacology
*Citrus/microbiology/drug effects/growth & development/metabolism/anatomy & histology
*Heterocyclic Compounds, 3-Ring/pharmacology
Soil Microbiology
*Plant Growth Regulators/pharmacology
Soil/chemistry

@article {pmid41239210,
year = {2025},
author = {Bódis, KB and Florea, DI and Goh, S and Kramser, N and Wienemann, T and Binsch, C and Stern, M and Pfeffer, K and Kelm, M and Roden, M and Wagner, R and Busch, L and Wischmann, P and , },
title = {PTA-DFS study: design of a randomised controlled trial assessing the effects of early percutaneous transluminal angioplasty on the healing of diabetic foot ulcers in persons with type 2 diabetes.},
journal = {BMC cardiovascular disorders},
volume = {25},
number = {1},
pages = {811},
pmid = {41239210},
issn = {1471-2261},
mesh = {Humans ; *Diabetic Foot/therapy/diagnosis/etiology/microbiology/physiopathology ; *Wound Healing ; *Diabetes Mellitus, Type 2/diagnosis/complications ; Time Factors ; Treatment Outcome ; Randomized Controlled Trials as Topic ; Male ; Amputation, Surgical ; *Peripheral Arterial Disease/therapy/physiopathology/diagnosis/diagnostic imaging ; Female ; *Angioplasty/adverse effects ; Risk Factors ; Aged ; Middle Aged ; },
abstract = {BACKGROUND: Peripheral arterial disease (PAD) and local infections increase the risk of non-healing diabetic foot ulcers (DFU) and limb amputations but are treatable by percutaneous transluminal angioplasty (PTA), local wound care and antibiotic therapy. The exact time to treat chronic leg artery stenosis (LAS) and the role of microbiome composition in DFU remain unclear. This study aims to assess whether an early PTA within 48 h after diagnosing a LAS offers advantages over standard care.

METHODS: The PTA-DFS Study is a randomised controlled monocentric trial including individuals with T2D and DFU, aged > 18 years with haemodynamically relevant chronic LAS. The primary study endpoint is to investigate the impact of the early PTA within 48 h on wound-healing assessed by wound area changes after PTA using a 3D-camera with artificial intelligence (AI)-based wound-analysis-system. The secondary endpoint is the effect of early PTA on the combined occurrence of major adverse limb (MALE) and safety-related cardiac events (MACE) over 12 month post-angioplasty using time-to-event analysis. Additional secondary outcomes are time to complete wound healing, major amputation rate and the need for new revascularization. Explanatory variables for wound healing are wound microbiome changes using whole-genome sequencing and oxygen saturation of the wound environment measured using near-infrared spectroscopy. Data will be collected at baseline, 24 h, 1, 2, 3, 6, and 12 months after PTA. Diabetic kidney disease, distal symmetric polyneuropathy, retinopathy, cardiomyopathy, LAS will be assessed by laboratory analyses, clinical scores, AI-based fundus photography, echocardiography, duplex sonography, and pulse oscillography.

DISCUSSION: The PTA-DFS aims to improve diagnostic and therapeutic algorithms, risk assessment and enable tailored therapies for persons with T2D and ischemic DFU.

TRIAL REGISTRATION: Trial Registration Number: NCT06124586 (Registration Date: 2023-08-2).},
}

Humans
*Diabetic Foot/therapy/diagnosis/etiology/microbiology/physiopathology
*Wound Healing
*Diabetes Mellitus, Type 2/diagnosis/complications
Time Factors
Treatment Outcome
Randomized Controlled Trials as Topic
Male
Amputation, Surgical
*Peripheral Arterial Disease/therapy/physiopathology/diagnosis/diagnostic imaging
Female
*Angioplasty/adverse effects
Risk Factors
Aged
Middle Aged

@article {pmid41239201,
year = {2025},
author = {Akanmu, AM and Lawal, IB and Ibrahim, SL and Marle-Köster, EV and Hassen, A},
title = {Metagenomic data from the rumen of South African Mutton Merino sheep supplemented with crude or encapsulated Acacia tannin extracts.},
journal = {BMC genomic data},
volume = {26},
number = {1},
pages = {86},
pmid = {41239201},
issn = {2730-6844},
support = {SRUG2204254606//National Research Foundation/ ; },
mesh = {Animals ; *Rumen/microbiology ; *Tannins/pharmacology/administration & dosage ; *Acacia/chemistry ; Sheep/microbiology ; *Metagenomics ; Gastrointestinal Microbiome ; *Plant Extracts/pharmacology ; Animal Feed ; Dietary Supplements ; },
abstract = {OBJECTIVES: This dataset was generated as part of a study investigating the impact of crude and encapsulated Acacia mearnsii tannin extracts on the rumen microbiota of South African Mutton Merino sheep. The aim was to provide high-quality metagenomic data to support methane mitigation strategies through dietary interventions targeting rumen microbial communities.

DATA DESCRIPTION: Rumen fluid was collected from 24 rams (six per treatment) fed a total mixed ration (TMR) supplemented with either distilled water (control), monensin (positive control), crude tannin, or microencapsulated tannin. However, one sample did not yield sufficient sequencing depth, resulting in 23 usable datasets. DNA was extracted and subjected to shotgun metagenomic sequencing on the Illumina NovaSeq 6000 platform. The dataset comprises paired-end reads deposited in the NCBI SRA under accession SRP480487. Taxonomic profiling reveals dominant phyla such as Bacteroidetes and Firmicutes, and the presence of archaeal genera such as Methanobrevibacter. This dataset provides insights into the structural and functional composition of the rumen microbiome and may be useful for comparative studies and biotechnology applications.},
}

Animals
*Rumen/microbiology
*Tannins/pharmacology/administration & dosage
*Acacia/chemistry
Sheep/microbiology
*Metagenomics
Gastrointestinal Microbiome
*Plant Extracts/pharmacology
Animal Feed
Dietary Supplements

@article {pmid41239036,
year = {2025},
author = {Casanova-Hernández, D and Pinacho-Pinacho, CD and Calixto-Rojas, M and Rubio-Godoy, M and Hernández-Velázquez, IM and Guevara-Avendaño, E and Méndez, O and Velázquez-Velázquez, E and Zamora-Briseño, JA},
title = {Challenging the paradigm: the Asian fish tapeworm (Schyzocotyle acheilognathi, Yamaguti 1934) lacks an intrinsic symbiotic bacterial community.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {41239036},
issn = {1618-1905},
abstract = {Schyzocotyle acheilognathi is an invasive generalist cestode with a high capacity for adaptation to multiple hosts and freshwater environments. Recent reports suggest that this parasite possesses an intrinsic symbiotic microbiota distinct from that of its fish hosts, and its presence induces gut dysbiosis in the host. In this study, we reassessed these ideas. For this, we collected naturally parasitized fish specimens from different locations in Mexico, encompassing different host species, including Cyprinus carpio, Pseudoxiphophorus bimaculatus, Tlaloc hildebrandi, and Vieja hartwegi. We also tested whether this parasite induces a dysbiotic process in the gut bacterial community of Tlaloc hildebrandi. Parasites were identified based on morphological and molecular criteria, and their bacterial communities were characterized using metataxonomy. Our results revealed that S. acheilognathi does not harbor a consistent microbial community among the different host species surveyed. We also did not detect any dysbiotic effect on the gut microbiota of Tlaloc hildebrandi. These findings contradict previous data and provide evidence of the loose relationship between this parasite and bacteria, which we propose could be a part of its successful generalist strategy. The results presented herein offer a novel perspective on the quest for understanding the microbial ecology in generalist cestodes of freshwater fish.},
}

@article {pmid41238775,
year = {2025},
author = {Gigi, E and Gavert, N and Raijman-Nagar, L and Zwang, Y and Zemach, H and Livyatan, I and Levy-Barda, A and Laviv, Y and Kanner, AA and Amiel, A and Siegal, T and Leibovici, A and Selezen, I and Badran, O and Zohar, Y and Safadi, E and Prather, LL and Helfer, CR and Castro, P and Barshack, I and Dadosh, T and Levin-Zaidman, S and Goliand, I and Golani, O and Horn, S and Mandel, JJ and Shental, N and Shai, A and Yust-Katz, S and Straussman, R},
title = {Characterization of the tumor microbiome of brain metastases and glioblastoma reveals tumor-type-specific and location-specific microbial signatures.},
journal = {Nature cancer},
volume = {},
number = {},
pages = {},
pmid = {41238775},
issn = {2662-1347},
support = {22-109-PG//Israel Cancer Research Fund (Israel Cancer Research Fund, Inc.)/ ; 2927/21//Israel Science Foundation (ISF)/ ; 818086//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; },
abstract = {Brain tumors, including glioblastoma multiforme (GBM) and brain metastases, present a notable clinical challenge. Recent research highlights the presence of intratumor bacteria across many tumor types, yet the microbiome of brain tumors remains largely underexplored. Here we show that the microbiome of 322 brain tumors differs markedly by tumor type and location. Using multiple approaches to visualize, culture and sequence bacterial communities, we found that brain metastases harbor higher bacterial richness and diversity than GBM, with distinct microbial compositions. Moreover, metastases in posterior brain regions exhibited greater diversity than those in anterior regions. Pathway analysis revealed enrichment of bacterial metabolic pathways associated with tumor spread and metastasis in brain metastases while GBM was enriched with pathways supporting alternative phosphorus use. These findings provide valuable insights into the microbial landscape of brain tumors, highlighting tumor-type-specific and location-specific variation and suggesting potential roles for bacteria in brain tumor biology.},
}

@article {pmid41238755,
year = {2025},
author = {Griffiths, JA and Nirmalkar, K and Wu, WL and Krajmalnik-Brown, R and Mazmanian, SK},
title = {The gut microbiome shapes social behaviour across animal species.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {41238755},
issn = {1740-1534},
abstract = {The gut microbiome has profound influences on brain activity and complex behaviours. Research across diverse animal species, in both natural environments and laboratory settings, has identified biological mechanisms that underlie gut-brain interactions. An emerging central theme is that the gut microbiome is shaped by, and actively contributes to, sociability throughout the lifespan. In this Review, we highlight recent literature revealing the effects of the microbiome on early neurodevelopment, immune modulation, stress responses and microorganism-mediated metabolism that affect social behaviour. Studies investigating the cellular and molecular pathways that underlie microbial influences on social behaviour have implicated brain regions and circuits that mediate critical aspects of animal behaviours, including bonding, mating, defence, aggression and social learning. Gut microbiome-brain research using animal models of social deficits and ecological studies in the wild, as well as investigations of human conditions comorbid with impaired social behaviour, could offer new and natural avenues for improved quality of life in individuals and social groups.},
}

@article {pmid41238743,
year = {2025},
author = {Zhang, L and Tan, X and Guo, Z and Liang, L and Yi, B and Liu, X and Li, F and Wang, Y and Wang, Y},
title = {Effects of gestational diabetes mellitus on the intestinal microbiota of the offspring.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {39934},
pmid = {41238743},
issn = {2045-2322},
support = {24JRRA938//Gansu Provincial Science and Technology Project/ ; NCRCCHD-2022-GP-17//General Project of Clinical Medical Research of National Center for Clinical Medical Research on Child Health and Diseases/ ; },
mesh = {Humans ; Female ; *Diabetes, Gestational/microbiology ; Pregnancy ; *Gastrointestinal Microbiome ; Infant, Newborn ; Adult ; Meconium/microbiology ; Dysbiosis/microbiology ; Case-Control Studies ; Male ; },
abstract = {Gestational diabetes mellitus (GDM) significantly impacts maternal and neonatal health, yet its influence on the neonatal intestinal microbiota remains poorly characterized. This study investigated the effects of maternal GDM on offspring microbiota by analyzing meconium samples from newborns of GDM-affected mothers (n = 16) and healthy controls (n = 16). Microbiome analysis revealed distinct composition alterations in the intestinal microbiota of GDM-exposed neonates. Significant differences in microbial abundance were observed between groups: at the phylum level, the GDM group exhibited a significant increase in Bacteroidetes but significant reductions in Actinobacteria and Proteobacteria. At the genus level, opportunistic pathogens including Bacteroides and Escherichia-Shigella were significantly enriched in the GDM group. These findings demonstrate that maternal GDM perturbs the initial colonization of the neonatal intestinal microbiota. Interventions targeting maternal glycemic control during gestation may mitigate offspring microbiota dysbiosis and its potential clinical implications.},
}

Humans
Female
*Diabetes, Gestational/microbiology
Pregnancy
*Gastrointestinal Microbiome
Infant, Newborn
Adult
Meconium/microbiology
Dysbiosis/microbiology
Case-Control Studies
Male

@article {pmid41238729,
year = {2025},
author = {Lee, KY and Shin, SH and Park, G and Kang, SH and Kang, HJ and Kim, J and Lee, JJ and Son, GH and Hong, JY},
title = {Shotgun metagenomics of the vaginal microbiome in cervical shortening and preterm birth risk.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {39988},
pmid = {41238729},
issn = {2045-2322},
support = {HI21C1624//Korea Health Industry Development Institute (KHIDI)/ ; HI21C1624//Korea Health Industry Development Institute (KHIDI)/ ; RS-2023-00252948//Korea government (the Ministry of Science and ICT, the Ministry of Trade, Industry and Energy, the Ministry of Health & Welfare, the Ministry of Food and Drug Safety)/ ; },
mesh = {Female ; Humans ; *Vagina/microbiology ; *Premature Birth/microbiology ; *Microbiota/genetics ; Pregnancy ; *Metagenomics/methods ; Adult ; *Cervix Uteri/microbiology/pathology ; Risk Factors ; },
abstract = {Preterm birth (PTB), a leading cause of neonatal morbidity and mortality, is frequently associated with premature cervical remodeling and vaginal microbiome dysbiosis. Cervical shortening in mid-pregnancy is a well-established risk factor for spontaneous PTB (sPTB), yet the microbial signatures underlying this condition remain underexplored, especially in Asian populations. In this study, we conducted shotgun metagenomic analysis of vaginal samples from 35 East Asian pregnant women with a short cervix and 12 with normal cervical length. Species-level taxonomic profiling and functional pathway analysis revealed reduced Lactobacillus dominance, increased microbial diversity, and enrichment of non-optimal CST IV species, such as Fannyhessea vaginae, Bifidobacterium breve, and Mycobacterium canetti in the short cervix group. Functional profiling showed group differences in pathways related to folate biosynthesis, carbohydrate metabolism, and epithelial barrier regulation. Among women with a short cervix, those who delivered preterm had vaginal microbiomes enriched in opportunistic pathogens, including Peptoniphilus equinus, Treponema spp., and Staphylococcus hominis. Conversely, B. breve, Lactobacillus gasseri, and Lactobacillus paragasseri were associated with full-term delivery. Functions related to glycosylation, structural stability, and degradation of cervical mucin were enriched in the sPTB group. Network analysis identified distinct microbial interactions between Lactobacillus-dominated clusters and CST IV-associated taxa, providing ecological insights that may reflect competitive dynamics and potential influences on cervicovaginal barrier integrity. These findings enhance our understanding of the taxonomic and functional profiles of the vaginal microbiome linked to cervical shortening and sPTB, contributing to improved risk stratification and management strategies for PTB, particularly in women with cervical shortening.},
}

Female
Humans
*Vagina/microbiology
*Premature Birth/microbiology
*Microbiota/genetics
Pregnancy
*Metagenomics/methods
Adult
*Cervix Uteri/microbiology/pathology
Risk Factors

@article {pmid41238692,
year = {2025},
author = {Singhal, R and Qaissi, Z and Zheng, H and Hua, Y and Hardesty, JE and Rouchka, EC and Merchant, ML and Kong, M and Wahlang, B},
title = {Sex-dependent modulation of PCB-mediated toxicity from a proteomic and microbiome perspective.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {39903},
pmid = {41238692},
issn = {2045-2322},
support = {P20GM113226, P20GM103436/GM/NIGMS NIH HHS/United States ; K01ES033289, P42ES023716, P30ES030283/ES/NIEHS NIH HHS/United States ; HT94252310949//U.S. Department of Defense/ ; },
mesh = {Animals ; *Polychlorinated Biphenyls/toxicity ; Male ; Female ; *Gastrointestinal Microbiome/drug effects ; Mice ; Proteomics/methods ; *Liver/drug effects/metabolism ; Mice, Inbred C57BL ; *Proteome/drug effects/metabolism ; Receptors, Aryl Hydrocarbon/metabolism ; Sex Factors ; Sex Characteristics ; Liver X Receptors/metabolism ; },
abstract = {Polychlorinated biphenyls (PCBs) have been associated with sex-dependent liver disease outcomes. Current mechanisms only partially explain these sex differences and alternative mechanisms including gut-liver toxicity warrant investigation. This study aims to identify PCB-induced changes in the hepatic proteome and gut microbiome and determine their contributions to sex-specific PCB toxicity. Male and female C57BL/6J mice were exposed to Aroclor1260 (20 mg/kg) and PCB126 (20 μg/kg) via oral gavage. After two weeks, hepatic and intestinal tissues were collected for peptide measurements (LC/MS) and 16S sequencing respectively. Proteomic analysis revealed that biological sex largely drove differences seen in the hepatic proteome and dictated PCB liver responses. PCB-exposed females manifested higher abundance of aryl hydrocarbon receptor (AHR) targets including CD36 vs. PCB-exposed males. Computational analysis also demonstrated enhanced AHR and liver-X-receptor (LXR) activation (higher z-scores) in PCB-exposed females vs. males. With regards to gut microbiome, both exposure and sex impacted the composition of microbial communities. Intriguingly, only PCB-exposed males exhibited increased Dehalobacterium abundance, and decreased mRNA levels for genes encoding gut barrier and antimicrobial proteins (Ocln, Reg3g). Overall, PCB-exposed females exhibited an altered proteome relevant to AHR and LXR responses, while PCB-exposed males exhibited more distinct changes in gut microbiota coupled with altered ileal gene expression. The findings suggest that, in addition to biological sex, organ-organ interactions should be considered when predicting toxicity outcomes, particularly for persistent compounds such as PCBs that can impact multiple organs simultaneously yet have tissue-specific toxic effects.},
}

Animals
*Polychlorinated Biphenyls/toxicity
Male
Female
*Gastrointestinal Microbiome/drug effects
Mice
Proteomics/methods
*Liver/drug effects/metabolism
Mice, Inbred C57BL
*Proteome/drug effects/metabolism
Receptors, Aryl Hydrocarbon/metabolism
Sex Factors
Sex Characteristics
Liver X Receptors/metabolism

@article {pmid41238653,
year = {2025},
author = {Wielkopolan, B and Szabelska-Beręsewicz, A and Obrępalska-Stęplowska, A},
title = {Bacteria associated with the cereal leaf beetle act as the insect's allies in adapting to protease inhibitors, but impair its development in laboratory condition.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {39944},
pmid = {41238653},
issn = {2045-2322},
support = {UMO-2020/37/N/NZ9/02577//Narodowe Centrum Nauki/ ; },
mesh = {Animals ; *Coleoptera/microbiology/growth & development/drug effects ; Larva/microbiology/growth & development/drug effects ; *Protease Inhibitors/pharmacology ; *Bacteria ; Microbiota ; *Adaptation, Physiological ; Edible Grain/parasitology ; },
abstract = {Oulema melanopus [L.] (cereal leaf beetle, CLB) is one of the most serious cereal pests. Plant protease inhibitors (PIs) are known for their insecticidal properties. The role of CLB-associated bacteria in insect adaptation to PIs is not yet known. We investigated the role of CLB-associated bacteria in adaptation to PIs, and whether the reduction of bacteria will affect the CLB development. We found a decrease in proteases activity in insects with a diminished bacterial community compared to those with an intact bacterial community. Thus, the study showed that the CLB-associated bacteria participate in the adaptation of CLB larvae to PIs. On the other hand, regardless of the type of PI used, ultimately a higher survival rates were recorded for larvae with a reduced bacterial community compared to insects with a natural microbiome in laboratory conditions. In such conditions, higher larval survival rates and a higher percentage of larvae reaching the pupal and imago stages were recorded in insects whose bacterial community was reduced. Since the CLB bacterial microbiome showed a negative impact on the development of the insect's host and its survival in response to PIs in laboratory conditions, it can be concluded that CLB-associated bacteria can be an ally of its insect host, but also an adversary when conditions are not optimal for symbiosis.},
}

Animals
*Coleoptera/microbiology/growth & development/drug effects
Larva/microbiology/growth & development/drug effects
*Protease Inhibitors/pharmacology
*Bacteria
Microbiota
*Adaptation, Physiological
Edible Grain/parasitology

@article {pmid41238551,
year = {2025},
author = {Chen, M and Qi, C and Qing, W and Zhou, Z and Zhang, Y and Chen, R and Hou, Y and Ou, J and , and He, Y and Zhou, H},
title = {Vaginal microbiome and sexually-transmitted pathogens in Chinese reproductive-age women: a multicentre cross-sectional and longitudinal cohort study.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10002},
pmid = {41238551},
issn = {2041-1723},
support = {82002201//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82302610//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82205157//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81925026//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Female ; Humans ; *Vagina/microbiology ; Longitudinal Studies ; *Microbiota/genetics ; Adult ; Cross-Sectional Studies ; China/epidemiology ; RNA, Ribosomal, 16S/genetics ; *Sexually Transmitted Diseases/microbiology/epidemiology/virology ; Young Adult ; Dysbiosis/microbiology ; Coinfection/microbiology ; Middle Aged ; Papillomavirus Infections/microbiology ; Adolescent ; East Asian People ; },
abstract = {Sexually transmitted infections (STIs) are associated with vaginal dysbiosis, and co-infections are common but understudied. In this study, 6217 reproductive-age women are recruited from 38 study centres across China at baseline and 2738 participants are followed up at 6 months. We profile the vaginal microbiota by 16S rRNA gene sequencing in conjunction with measurement of nine common STIs. The primary outcome of this study is STI status, and secondary outcome is the risk of cervical lesions. Mycoplasmas hominis (MH) far exceeds other STIs in the association with vaginal microbiota, whereases previously reported associations between Human papillomavirus (HPV) and vaginal dysbiosis might be confounded by the co-infected MH in this study. Both MH infection and increased bacterial diversity are independently associated with increased risk of cervical lesion in HPV-negative women (Shannon, OR (odds ratio) = 1.71, 95% CI (confidence interval) = 1.23-2.36; MH, OR = 2.42 95% CI = 1.36-4.30). These associations are also identified in longitudinal analyses (Shannon, HR (hazard ratio) = 1.72, 95% CI = 1.04-2.86; MH, HR = 2.37, 95% CI = 0.98-5.72). Our findings highlight the importance of considering MH status when studying vaginal microbiota in cervical lesions, and suggest the need for further investigation of microbiota-associated mechanisms in HPV-negative cervical lesions. (ClinicalTrials.gov. NCT04694495).},
}

Female
Humans
*Vagina/microbiology
Longitudinal Studies
*Microbiota/genetics
Adult
Cross-Sectional Studies
China/epidemiology
RNA, Ribosomal, 16S/genetics
*Sexually Transmitted Diseases/microbiology/epidemiology/virology
Young Adult
Dysbiosis/microbiology
Coinfection/microbiology
Middle Aged
Papillomavirus Infections/microbiology
Adolescent
East Asian People

@article {pmid41238500,
year = {2025},
author = {Choi, HS and Park, EJ and Pang, EK},
title = {Comparative analysis of the microbial profiles in supragingival and subgingival plaques obtained from different dental prostheses.},
journal = {The Journal of prosthetic dentistry},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.prosdent.2025.10.021},
pmid = {41238500},
issn = {1097-6841},
abstract = {STATEMENT OF PROBLEM: The oral microbial ecosystem significantly influences periodontal and peri-implant health. Although various studies have investigated the microbial influence of specific dental restorative materials, studies that directly compared the microbial diversity across different restoration types within the same oral cavity are sparse, limiting the identification of consistent, material-specific microbial profiles.

PURPOSE: The purpose of this clinical study was to analyze and compare the supragingival and subgingival microbial diversity and composition associated with an unrestored natural tooth, a gold crown-restored tooth, a zirconia crown-restored tooth, and an implant-supported restoration within the same participant. A secondary objective was to evaluate whether specific restorative materials induced reproducible microbial profiles across individuals.

MATERIAL AND METHODS: Thirty participants possessing all 4 types of restorations (unrestored natural tooth, gold crown, zirconia crown, and implant) in their oral cavity were enrolled. Supra- and subgingival biofilm samples were collected by using sterile swabs. Deoxyribonucleic acid (DNA) was extracted, and microbial identification was conducted via 16S rRNA sequencing targeting the V3-V4 regions. Alpha diversity was quantified by using Shannon, npShannon, and Simpson indices; beta diversity was assessed by using Bray-Curtis and UniFrac distances. Taxonomic classification and biomarker identification were performed by using the EzBioCloud software program (CJ Bioscience) and linear discriminant analysis effect size (LEfSe). Statistical significance was determined with Kruskal-Wallis and permutational multivariate analysis of variance tests (α=.05). Sample collection was standardized and conducted by a single calibrated examiner. DNA extraction, sequencing, and bioinformatics analyses were completed at a single laboratory facility to ensure methodological consistency.

RESULTS: Gold crown- and zirconia crown-restored teeth exhibited significantly higher alpha diversity than unrestored natural teeth orimplant-supported restorations (Shannon: Gold, 4.3 ±0.6; Zirconia, 4.1 ±0.5; Natural tooth, 3.5  ±0.4; Implant, 3.0 ±0.6, P<.05). The lowest microbial diversity was noted in implant-supported restorations, predominantly characterized by anaerobic taxa, including Clostridiales. Beta diversity analysis revealed distinct and significant microbial clustering based on restorative types (PERMANOVA, pseudo-F=2.8, R²=.04, P<.01). LEfSe analysis identified Actinomyces spp. predominance in unrestored teeth, Prevotella and Spirochaetes in gold crowns, Porphyromonas and Atopobium in zirconia crowns, and Clostridiales in implants. These microbial signatures remained consistent within individuals and across the study population.

CONCLUSIONS: Restorative materials significantly influenced the supragingival and subgingival microbiome composition within the same oral environment. Implant-supported restorations displayed lower microbial diversity and a higher prevalence of pathogenic taxa. Thus, restorative material selection may critically impact long-term periodontal and peri-implant health outcomes.},
}

@article {pmid41238428,
year = {2025},
author = {Elkourashy, SA and Abu-El-Ruz, R and Askar, MZ and Hamdan, A and Zughaier, SM},
title = {The microbiome-lymphoma Axis: A systematic review and Meta-analysis of gut Dysbiosis pattern in diffuse large B-cell lymphoma.},
journal = {Blood reviews},
volume = {},
number = {},
pages = {101341},
doi = {10.1016/j.blre.2025.101341},
pmid = {41238428},
issn = {1532-1681},
abstract = {BACKGROUND: Gut microbiota has emerged as a critical mediator of immune homeostasis and cancer biology. Increasing evidence suggests that gut dysbiosis may play a significant role in the pathogenesis of diffuse large B-cell lymphoma (DLBCL), the most common and aggressive subtype of non-Hodgkin lymphoma (NHL). However, a comprehensive synthesis of the microbial alterations associated with DLBCL remains poorly defined.

METHODS: We systematically reviewed and meta-analyzed thirteen studies (n = 4087 cases) to assess gut microbiota alterations in DLBCL. Both observational and Mendelian randomization designs were included. Pooled odds ratios (OR) were calculated for mendelian randomization studies using random-effects models, and microbial shifts were analyzed at the species level to contextualize biological relevance. Observational studies were used for qualitative assessment.

RESULTS: Meta analysis was done for the mendelian randomization studies (n = 3737 cases). The overall pooled OR was 0.96 (95 % CI: 0.93-1.00), suggested a slight shift towards depletion, with considerable heterogeneity (I[2] = 78.7 %). Species-level analysis revealed significant enrichment of pro-inflammatory or potentially oncogenic taxa in DLBCL, including Bilophila (OR = 1.78), Desulfovibrionaceae (OR = 1.58), and Coprobacter (OR = 1.37). Conversely, beneficial commensals with anti-inflammatory and metabolic regulatory roles such as Eubacterium coprostanoligenes group (OR = 0.19), Alistipes (OR = 0.57), Ruminococcaceae UCG011 (OR = 0.75) were significantly depleted.

CONCLUSIONS: This first comprehensive synthesis demonstrates a reproducible species-level microbial signature in DLBCL, characterized by depletion of protective commensals and enrichment of pro-tumorigenic taxa. Mechanistically, these shifts may promote lymphomagenesis via inflammatory, metabolic, and immune-modulatory pathways. Our findings highlight the gut microbiota as a latent biomarker source and therapeutic target, supporting microbiota-modulating strategies in precision lymphoma care.},
}

@article {pmid41238281,
year = {2025},
author = {Masthan, A and Strople, J and Runde, J},
title = {Dietary Therapy in the Management of Inflammatory Bowel Disease: A Lasting Legacy and a New Frontier.},
journal = {Gastroenterology clinics of North America},
volume = {54},
number = {4},
pages = {875-889},
doi = {10.1016/j.gtc.2025.07.004},
pmid = {41238281},
issn = {1558-1942},
mesh = {Humans ; *Inflammatory Bowel Diseases/diet therapy ; Gastrointestinal Microbiome ; Enteral Nutrition ; Child ; Diet, Gluten-Free ; *Diet ; },
abstract = {This article highlights the evolving role of dietary strategies in the management of pediatric inflammatory bowel disease (IBD). Advances in understanding diet's influence on IBD pathogenesis and disease progression have renewed interest in the role of diet in the treatment of IBD. Exclusive enteral nutrition remains the gold standard, but whole food diets that mimic the composition of EEN or eliminate foods that negatively impact the intestinal microbiome and immune response have shown promise. Additional research that includes larger patient populations and objective data is needed to expand applicability and develop patient-centered recommendations.},
}

Humans
*Inflammatory Bowel Diseases/diet therapy
Gastrointestinal Microbiome
Enteral Nutrition
Child
Diet, Gluten-Free
*Diet

@article {pmid41238277,
year = {2025},
author = {Pai, N and Sainath, NN},
title = {Diagnosis and Management of Small Intestinal Bacterial Overgrowth in Pediatric Short Bowel Syndrome.},
journal = {Gastroenterology clinics of North America},
volume = {54},
number = {4},
pages = {805-821},
doi = {10.1016/j.gtc.2025.07.005},
pmid = {41238277},
issn = {1558-1942},
mesh = {Humans ; *Short Bowel Syndrome/microbiology/complications/therapy ; *Intestine, Small/microbiology ; Child ; Anti-Bacterial Agents/therapeutic use ; Gastrointestinal Microbiome ; Breath Tests ; *Blind Loop Syndrome/diagnosis/therapy ; },
abstract = {This article explores the diagnosis and management of small intestinal bacterial overgrowth in children with short bowel syndrome, a population affected by altered anatomy, dysmotility, and medication-related risk factors. Diagnostic accuracy is limited by the feasibility, and specificity of breath testing and small bowel aspirates. While antibiotics are commonly used, concerns about recurrence and antibiotic resistance remain significant. Emerging nutritional strategies and precision-based, microbiome-targeted therapies offer promising adjunctive treatment options.},
}

Humans
*Short Bowel Syndrome/microbiology/complications/therapy
*Intestine, Small/microbiology
Child
Anti-Bacterial Agents/therapeutic use
Gastrointestinal Microbiome
Breath Tests
*Blind Loop Syndrome/diagnosis/therapy

@article {pmid41238276,
year = {2025},
author = {Ayala-Germán, AG and Pandey, A and Duro, D},
title = {The Role of Functional Nutrition in Disease Prevention and Management.},
journal = {Gastroenterology clinics of North America},
volume = {54},
number = {4},
pages = {791-803},
doi = {10.1016/j.gtc.2025.08.011},
pmid = {41238276},
issn = {1558-1942},
mesh = {Humans ; Gastrointestinal Microbiome ; *Functional Food ; },
abstract = {This article provides a comprehensive overview of culinary interventions, like food as medicine, which can potentially transform health care. It explores the integration of evidence-based nutritional science with the culinary arts, to help patients maintain health, prevent disease, and manage chronic conditions. This article highlights the impact of bioactive compounds in food on metabolic pathways, inflammation reduction, and gut microbiome modulation.},
}

Humans
Gastrointestinal Microbiome
*Functional Food

@article {pmid41238191,
year = {2025},
author = {Yang, Y and Wang, Q and Wang, Z and Wang, Y and Liu, B and Zhang, Y and Mao, X and Sun, H},
title = {The Role of Fatty Acids in Neurodegenerative Diseases: Mechanistic Insights and Therapeutic Strategies.},
journal = {Journal of lipid research},
volume = {},
number = {},
pages = {100944},
doi = {10.1016/j.jlr.2025.100944},
pmid = {41238191},
issn = {1539-7262},
abstract = {Fatty acids (FAs) play multifaceted roles in neurodegenerative diseases (NDDs), including Alzheimer's disease (AD), Parkinson's disease (PD), and amyotrophic lateral sclerosis (ALS). This review systematically summarizes current understanding of fatty acid metabolism and its diverse implications in NDD pathology. Short-chain fatty acids (SCFAs), primarily generated by gut microbiota, regulate neuroinflammation, gut-brain communication, and blood-brain barrier (BBB) integrity via epigenetic modifications and immune modulation. Medium-chain fatty acids (MCFAs) exhibit therapeutic potential by improving energy metabolism and neuromuscular function, particularly in ALS models. Long-chain polyunsaturated fatty acids (PUFAs), notably docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA), contribute to neuronal membrane integrity, synaptic plasticity, and antioxidant defense, mitigating oxidative stress and neuroinflammation. Conversely, saturated and certain n-6 fatty acids may exacerbate neurodegeneration through pro-inflammatory and oxidative pathways. Emerging evidence highlights fatty acid involvement in key pathological processes such as lipid peroxidation, mitochondrial dysfunction, ferroptosis, and BBB disruption. Therapeutically, targeted supplementation, dietary modification, microbiome manipulation, and advanced nanotechnology-based delivery systems are promising strategies. Nevertheless, precise therapeutic efficacy depends critically on disease stage, dosage, genetic background, and individual metabolic context. Integrating personalized medicine with precision nutritional strategies and novel drug-delivery platforms offers promising avenues to translate fatty acid-based interventions into clinical practice, potentially improving patient outcomes in the aging global population.},
}

@article {pmid41238092,
year = {2025},
author = {Ye, M and Ju, H and Ren, G and Hu, J},
title = {The Role of Microbiome in Immunotherapy: Insights and Perspectives.},
journal = {Seminars in cancer biology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.semcancer.2025.11.001},
pmid = {41238092},
issn = {1096-3650},
abstract = {The intricate interplay between the gut microbiome and the host immune system has been recognized as a pivotal determinant of clinical outcomes in cancer immunotherapy. Mounting evidence suggests that specific microbial communities are associated with both the efficacy and toxicity of immune checkpoint inhibitors in diverse malignancies, underscoring the microbiome's role in modulating systemic and tumour-localized immunity. Mechanistically, the microbiome shapes antitumour immunity by affecting antigen presentation, activation of effector cells, immunosuppression and adverse effects. Key microbial components and metabolites present in distinct anatomical niches have been identified as promoters or inhibitors of therapeutic responsiveness via multiple pathways. Harnessing this knowledge, microbiome-targeted strategies such as antibiotic, probiotic, fecal microbiota transplantation, and dietary modulation are regarded as potential adjuvant therapies to enhance the efficacy of anti-tumour therapies. Although significant progress has been achieved in preclinical studies, challenges persist in translating these findings into standardized clinical applications.},
}

@article {pmid41237939,
year = {2025},
author = {Devarajan, B and Sharma, S and Mills, B and Prajna, L and Venkatesh, PN and Dharmalingam, K},
title = {Dysbiosis of Bacterial and Fungal Microbiomes Affects the Disease Process and Treatment Outcome in Fungal Keratitis.},
journal = {Experimental eye research},
volume = {},
number = {},
pages = {110745},
doi = {10.1016/j.exer.2025.110745},
pmid = {41237939},
issn = {1096-0007},
abstract = {Fungal keratitis (FK) is a severe eye infection mainly caused by Aspergillus flavus and Fusarium solani. We examined the changes in bacterial and fungal microbiome profiles over a week of disease progression, treatment, and clinical status using targeted next-generation sequencing (NGS). Samples were collected from infected and healthy contralateral eyes of 25 FK patients and one eye of 10 healthy, non-infected cataract controls. QIIME (Quantitative Insights into Microbial Ecology) and MicrobiomeAnalyst were utilised for the data analysis. There was a reduction in beneficial bacteria like Prevotella, Lactobacillus, and Leuconostoc in FK patients compared to the control samples. On the other hand, opportunistic bacteria including Clostridium, Bifidobacterium, and Pseudomonas increased in FK patients. Aspergillus, Colletotrichum, and Basidiobolus were more abundant in keratitis patients, whereas Malassezia and Trichoderma were less abundant. This dysbiosis was also evident in the uninfected contralateral eyes of FK patients. Treatment resulted in significant changes in bacterial genera like Dolosigranulum, Sutterella, and Akkermansia, and fungal genera such as Myrothecium, Corynespora, and Penicillium. Further, treatment returned them to the control group levels, except for Akkermansia and Corynespora. Among the treated patients, a large subset remains nonresponsive to treatment. This treatment outcome, responder versus non-responder, was reflected in the abundance of bacterial genera such as Tannerella, Sutterella, Odoribacter, and fungal genera such as Coprinellus and Volutella. This study highlights the clinical relevance of microbiome signatures in FK, demonstrating bilateral dysbiosis, integrated bacterial-fungal profiling, and correlations with treatment outcomes. These findings suggest potential for microbiome-informed diagnostics, prognostic biomarkers, and risk stratification.},
}

@article {pmid41237903,
year = {2025},
author = {Mulet, M and Sánchez Milán, JA and Lorca, C and Fernández-Rhodes, M and Adrados-Planell, A and Bejarano Castillo, MC and Saiz, L and Mateos-Moreno, MV and Hase, Y and Mira, A and Rábano, A and Ser, TD and Kalaria, RN and Lagunas, A and Mir, M and Crespo, A and Samitier, J and Gallart-Palau, X and Serra, A},
title = {Oral microbiome-derived proteins in brain extracellular vesicles circulate and tie to specific dysbiotic and neuropathological profiles in age-related dementias.},
journal = {Molecular & cellular proteomics : MCP},
volume = {},
number = {},
pages = {101464},
doi = {10.1016/j.mcpro.2025.101464},
pmid = {41237903},
issn = {1535-9484},
abstract = {The involvement of the oral microbiome (OM) in the pathophysiology of Alzheimer's disease (AD) and vascular dementia (VaD) has been recognized epidemiologically, but the molecular mechanisms remain elusive. In this study, we uncovered the presence of oral microbiome-derived proteins (OMdPs) in brain extracellular vesicles (bEVs) from post-mortem AD and VaD subjects using unbiased metaproteomics. OMdPs circulation in blood extracellular vesicles was also confirmed in an independent cohort. Our findings also reveal that specific OMdPs are present in bEVs, with their levels varying with disease progression. Peptidome-wide correlation analyses further explored their exchange dynamics and composition within bEVs. Additionally, we validated the ability of OM-derived EVs (OM-EVs) to cross the blood-brain barrier (BBB) using a BBB-on-a-chip model, confirming a potential route for bacterial-derived molecules to reach the CNS. Bioinformatics-driven interaction analyses indicated that OMdPs engage with key neuropathological proteins, including amyloid-beta and tau, suggesting a novel mechanism linking dysbiotic OM to dementia. These results provide new insights into the role of the OM in neurodegeneration and highlight OMdPs as potential biomarkers and therapeutic targets.},
}

@article {pmid41237775,
year = {2025},
author = {Van Hul, M and Cani, PD},
title = {From microbiome to metabolism: Bridging a two-decade translational gap.},
journal = {Cell metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmet.2025.10.011},
pmid = {41237775},
issn = {1932-7420},
abstract = {The mapping of the human genome sparked high expectations for biomedical breakthroughs, yet attention has since shifted toward the human microbiome as a key player in health and disease. Pioneering studies revealed striking inter-individual variability and numerous associations between gut microbiota and a wide range of conditions (i.e., obesity, diabetes, cardiovascular and inflammatory bowel diseases, autism, allergies, neurodegenerative diseases, and cancers). However, the field has faced a deluge of correlative "dysbiosis" studies with limited causal evidence. Although animal models have provided crucial mechanistic insights, translating these findings to humans has proven challenging. Interventions such as fecal microbiota transplantation, prebiotics, probiotics, and postbiotics often yield inconsistent or modest effects in clinical trials. This gap highlights the need for precision, functional profiling, and integration of multi-omics , for instance, through artificial intelligence. In this perspective, we discuss what microbiome research offers as a transformative shift and how we conceptualize disease, favoring systems biology and personalized interventions over reductionist approaches.},
}

@article {pmid41237768,
year = {2025},
author = {Mitchell, KJ and Dahly, DL and Bishop, DVM},
title = {Conceptual and methodological flaws undermine claims of a link between the gut microbiome and autism.},
journal = {Neuron},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.neuron.2025.10.006},
pmid = {41237768},
issn = {1097-4199},
abstract = {The idea that the gut microbiome causally contributes to autism has gained currency in the scientific literature and popular press. Support for this hypothesis comes from three lines of evidence: human observational studies, preclinical experiments in mice, and human clinical trials. We critically assessed this literature and found that it is beset by conceptual and methodological flaws and limitations that undermine claims that the gut microbiome is causally involved in the etiology or pathophysiology of autism.},
}

@article {pmid41237685,
year = {2025},
author = {Kandel, SE and Lampe, JN},
title = {The anti-inflammatory drug celecoxib is metabolized by Pseudomonas aeruginosa CYP107S1 in vitro and in vivo.},
journal = {Drug metabolism and disposition: the biological fate of chemicals},
volume = {53},
number = {12},
pages = {100184},
doi = {10.1016/j.dmd.2025.100184},
pmid = {41237685},
issn = {1521-009X},
abstract = {The significance of the gut microbiome on drug metabolism has been demonstrated, yet much less is known about the pathobiome's potential impact on systemic drug metabolism outside of the β-lactam antibiotics, especially for bacterial species prone to multidrug resistance, which often leads to acute or chronic infections. CYP107S1, a cytochrome P450 (P450) from the opportunistic pathogen Pseudomonas aeruginosa, which exhibits substrate promiscuity and allosteric features, was able to tightly bind (Kd, app of 0.755 μM) and rapidly metabolize with high affinity (Km of 1.63 μM) the nonsteroidal anti-inflammatory drug celecoxib. It formed the same hydroxy metabolite as human CYP2C9, the primary enzyme responsible for the metabolism of this selective cyclooxygenase-2 inhibitor. In liquid cultures of the P. aeruginosa PAO1 strain expressing a relatively high level CYP107S1 during the initial bacterial growth phase, dosing of celecoxib resulted in an increase in the hydroxyl product formation over time, attesting to translation from the P450 in vitro recombinant drug-metabolizing activity to live bacterial cultures. Furthermore, the celecoxib metabolite formation by the CYP107S1 recombinant enzyme or in PAO1 culture was partially inhibited by the pan-CYP inhibitor 1-aminobenzotriazole and exhibited preincubation time-dependency characteristics. Thus, P. aeruginosa CYP107S1 capability to metabolize drugs continues to expand, driving new knowledge and potential for new useful substrate probes to study P450 function and regulation in P. aeruginosa. SIGNIFICANCE STATEMENT: This study provides further insights into the metabolic ability of CYP107S1, a cytochrome P450 enzyme belonging to the azetidine biosynthetic gene cluster of Pseudomonas aeruginosa, which is capable of metabolizing the nonsteroidal anti-inflammatory drug celecoxib, further widening the promiscuity feature of the enzyme and offering a novel probe to study its regulation in the PAO1 strain of P. aeruginosa.},
}

@article {pmid41237622,
year = {2025},
author = {Liu, B and Wang, S and Ren, J and Zhang, Z and Ma, J and Li, T and Zhou, Q and Sun, J},
title = {Impacts of non-spherical polyethylene nanoplastics on microbial communities and antibiotic resistance genes in the rhizosphere of pea (Pisum sativum L.): An integrated metagenomic and metabolomic analysis.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140425},
doi = {10.1016/j.jhazmat.2025.140425},
pmid = {41237622},
issn = {1873-3336},
abstract = {The ecological effects of nanoplastics (NPs) has become a growing concern; however, the influence of non-spherical NPs-which better represent real-world morphologies-remains poorly understood. This study investigated the impact of non-spherical polyethylene (PE) NPs on the growth of pea (Pisum sativum L.) and its rhizosphere microenvironment across different concentration levels (0, 20, and 200 mg/kg) using integrated metagenomics and metabolomics. Results showed that high-dose (200 mg/kg) exposure significantly inhibited plant growth. Although soil physicochemical properties remained unchanged, the rhizosphere microbial communities experienced significant restructuring, characterized by a marked enrichment of Pseudomonas and a reduction in beneficial Rhizobium populations. Metagenomic analysis revealed a concurrent increase in the abundance and diversity of antibiotic resistance genes (ARGs) under non-spherical PE-NP stress. This was accompanied by a shift in bacterial host composition, with a trend toward a higher prevalence of potentially pathogenic taxa such as Pseudomonas aeruginosa. Metabolomics analysis further revealed that non-spherical PE-NPs altered the rhizosphere metabolite profile, thereby significantly driving the succession of ARG hosts. Our integrated analysis enhances the understanding of how non-spherical PE-NPs disrupt microbial communities and elevate the risks of ARGs in rhizosphere soil, highlighting the significance of incorporating environmentally relevant NPs into environmental risk assessments.},
}

@article {pmid41237539,
year = {2025},
author = {Karisola, P and Sinkko, H and Nieminen, A and Laatikainen, T and Yang, Y and Paalanen, L and Jousilahti, P and Vartiainen, E and Mäkelä, MJ and Fyhrquist, N and Haahtela, T and Alenius, H},
title = {Serum metabolites link immune-microbiota interaction in children and young adults from Russian Karelia and Finnish Karelia with contrasting lifestyle and environment.},
journal = {Environment international},
volume = {205},
number = {},
pages = {109911},
doi = {10.1016/j.envint.2025.109911},
pmid = {41237539},
issn = {1873-6750},
abstract = {BACKGROUND: Environmental exposureregulates the immune, circulatory, and nervous systems, thereby affecting health. We investigated the associations between serum metabolite profiles, skin microbiota, and immune-related gene expression of peripheral blood mononuclear cells in children and young adults from Russian Karelia (RUS) and Finnish Karelia (FIN), two regions with contrasting environmental exposures and lifestyles.

METHODS: Serum metabolites (n = 278) from 15 to 20-year-old participants from RUS (n = 162) and FIN (n = 116) were profiled. Using integrative analysis, a subset of metabolomics was combined with skin microbiota (n = 143) and blood transcriptomics (n = 144) to characterize environment-linked metabolic and immune signatures.

RESULTS: Serum metabolite profiles differed significantly between the RUS and FIN subjects, reflecting divergent metabolic states. Citrulline and glutamate/glutamine metabolism were prominent in the RUS subjects while tryptophan catabolism was enhanced in the FIN subjects. Transcriptomic network analysis identified co-expression modules associated with metabolites, skin microbial taxa and key immune traits. A strongly RUS-associated module was dominated by epigenetic long non-coding RNAs and associated positively with anti-inflammatory metabolites such as circulating short-chain fatty acids (SCFAs) and betaine - both present at reduced levels in the FIN subjects. In contrast, FIN-associated modules were linked to inflammatory metabolites such as xanthurenic acid and L-cystine, as well as gene pathways involved in interferon (anti-viral) signaling and neutrophil responses. Across all omics layers, RUS subjects exhibited a more tightly integrated molecular network, with stronger correlations between circulating metabolites, microbial taxa and immune-related gene regulation.

CONCLUSIONS: Multi-omics integration revealed a more coordinated and responsive immune-metabolic network in RUS youth, potentially shaped by environmental exposures typical of their living context. In contrast, the FIN cohort exhibited metabolic patterns more closely linked to inflammatory gene expression.},
}

@article {pmid41237512,
year = {2025},
author = {Ma, X and Wang, A and Li, L and Li, X and Liu, J and Kan, H and Li, A and Sun, Z},
title = {Phosphorus availability affects the efficiency of plant-white rot fungus remediation of soil contaminated with polycyclic aromatic hydrocarbons by altering microbial community structure and functions.},
journal = {Ecotoxicology and environmental safety},
volume = {307},
number = {},
pages = {119396},
doi = {10.1016/j.ecoenv.2025.119396},
pmid = {41237512},
issn = {1090-2414},
abstract = {White rot fungi and soil microbial communities at the hyphosphere influence phosphorus availability through their interactions. However, the mechanisms underlying the effects of different phosphorus forms on polycyclic aromatic hydrocarbons (PAHs) during plant-white rot fungus remediation remain unclear. Therefore, this study aimed to investigate the effects of different forms of phosphorus supplementation on the diversity of soil microbial community during plant-white rot fungus remediation and their correlation with PAH biodegradation through amplicon high-throughput sequencing. Salix viminalis was cultivated under two fungal (inoculated and non-inoculated with Crucibulum laeve) and three phosphorus levels (no phosphorus addition, potassium dihydrogen phosphate addition, and calcium phytate addition) to remediate phenanthrene (PHE)-contaminated soil. Among the treatments, two potassium dihydrogen phosphate addition treatments exhibited the highest PHE removal rates (74.0 % and 79.4 %) on day 60. Inoculation with C. laeve significantly increased the relative abundance of Pseudomonas but antagonized other putative indigenous PAH-degrading taxa. The addition of potassium dihydrogen phosphate alleviated the antagonistic effect of C. laeve and indigenous microorganisms and synergistically promoted PHE degradation in soil with C. laeve, whereas calcium phytate addition did not significantly improve soil PHE removal rates. The simultaneous addition of phosphorus and C. laeve inoculation created a unique microbial community structure that facilitated organic phosphorus activation and accelerated phosphorus turnover. However, PHE degradation varied depending on the phosphorus form. Therefore, the addition of soluble phosphorus should be prioritized over organic phosphorus to optimize plant-white rot fungus remediation.},
}

@article {pmid41237249,
year = {2025},
author = {Fan, Y and Ye, J and Niu, G and She, Y and Li, R and Shi, J and Yang, Y and Wang, L and Kang, Y and Ji, X},
title = {Biohybrid nanorobots induce lactate isomer conversion to reverse the immune environment and promote tumor therapy.},
journal = {Science advances},
volume = {11},
number = {46},
pages = {eadz8419},
doi = {10.1126/sciadv.adz8419},
pmid = {41237249},
issn = {2375-2548},
mesh = {Animals ; *Tumor Microenvironment/immunology/drug effects ; Mice ; *Lactic Acid/metabolism/chemistry ; Humans ; Palladium/chemistry ; *Metal Nanoparticles/chemistry ; *Neoplasms/immunology/metabolism/therapy/pathology/drug therapy ; Gold/chemistry ; Cell Line, Tumor ; },
abstract = {Tumor cell glycolysis produces high levels of l-lactate (l-LA), creating an immunosuppressive microenvironment that enhances tumor stemness and impairs the efficacy of cancer therapies. Current strategies to reduce l-LA are limited by physical barriers in solid tumors and resource waste. This study presents an intelligent nanorobot that not only enhances tumor targeting and deep penetration but also reprograms the tumor immune microenvironment to convert l-LA into immunostimulatory d-lactate (d-LA). The nanorobot uses gold nanoparticles to bridge palladium (Pd) nanozymes and Lactobacillus crispatus-derived outer membrane vesicles (CMVs). Pd nanozymes catalyze H2O2 into O2, facilitating deep tumor penetration, whereas the acidic tumor microenvironment activates Pd nanozymes to produce hydroxyl radicals (·OH), inducing immunogenic cell death. CMVs, which are rich in d-lactate dehydrogenase and artificially introduce lactate oxidase, catalyze the conversion of l-LA to d-LA, reversing its immunosuppressive effects. Preclinical models demonstrate potent antitumor effects, enhancing the immune response and reshaping the tumor microbiome.},
}

Animals
*Tumor Microenvironment/immunology/drug effects
Mice
*Lactic Acid/metabolism/chemistry
Humans
Palladium/chemistry
*Metal Nanoparticles/chemistry
*Neoplasms/immunology/metabolism/therapy/pathology/drug therapy
Gold/chemistry
Cell Line, Tumor

@article {pmid41236809,
year = {2025},
author = {Shuvo, MSH and Kim, S and Jo, S and Rahim, MA and Barman, I and Hossain, MS and Jeong, Y and Jeong, H and Kim, S and Seo, H and Song, HY},
title = {Characterization of Gut Microbiota of Honey Bees in Korea.},
journal = {Polish journal of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.33073/pjm-2025-025},
pmid = {41236809},
issn = {2544-4646},
abstract = {Korea's unique climate and agricultural environment suggest that the gut microbiome of honey bees may possess distinctive compositions influenced by regional factors. With the decline in honey bee populations and rising health challenges, understanding the role of gut microbiomes is essential for enhancing honey bee health and their resilience to environmental stressors. To explore caste-specific gut microbiota and identify microbial signatures associated with honey bee health, this study examined the gut microbial composition of worker bees, queen bees, and drones of Apis mellifera using 16S rRNA gene amplicon sequencing. Analysis of beta diversity and species richness demonstrated significant differences between worker bees and both drones and queens, with no significant differences identified between drones and queens. Notably, Lactobacillus dominated all groups, comprising 98.6% of the drones, 95.4% of the queens, and 68.3% of the workers. Additionally, Bombella was prominent in queens (4%), whereas Gilliamella (23%) and Frischella (4.7%) were notably enriched in workers. Drones and queens exhibited similar gut microbiome profiles, while workers displayed distinctly different compositions. These findings underscore the variation in gut microbiota composition and potential functional roles across honey bee castes. Such microbial distinctions may reflect caste-specific roles and physiological demands within the colony. Future research should investigate the physiological roles of gut microbiota and their contributions to environmental resilience, paving the way for microbiome-based strategies to promote honey bee health. This study lays a crucial scientific foundation for conserving the honey bee ecosystem and promoting sustainable agriculture.},
}

@article {pmid41236788,
year = {2025},
author = {Artale, S and Filiali, F and Beretta, E and Arosio, F and Cazzaniga, F and Tersalvi, C and Sofia, M and Tagliabue, P and Pozzi, P and Colombo, A and Carbone, C and Pietrogiovanna, L and Verga, M and Nova, P and Calori, R and Renso, R and Rota, S and Aglione, S and Manfrida, I and Facendola, G and Trojani, A and Dazzani, MC and Basciani, S and Valsecchi, MG and Capitoli, G and Cocola, C and Consolandi, C},
title = {The Effects of a Modified Mediterranean Diet on Gut Microbiota and Chemotherapy Side Effects in Patients With Metastatic Colorectal Cancer Undergoing First-Line Chemotherapy With or Without Either Antiepidermal Growth Factor Receptor or Antivascular Endothelial Growth Factor Agent: Protocol for a Randomized Pilot Study in Italy.},
journal = {JMIR research protocols},
volume = {14},
number = {},
pages = {e72950},
doi = {10.2196/72950},
pmid = {41236788},
issn = {1929-0748},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Colorectal Neoplasms/drug therapy/pathology ; *Diet, Mediterranean ; Pilot Projects ; Italy ; Female ; Male ; Prospective Studies ; ErbB Receptors/antagonists & inhibitors ; *Antineoplastic Agents/adverse effects/therapeutic use ; Middle Aged ; Aged ; Randomized Controlled Trials as Topic ; Adult ; },
abstract = {BACKGROUND: The gut microbiota is attracting increasing interest as a factor possibly impacting colorectal cancer risk, therapy toxicity, and, as a consequence, patient's quality of life. It has been observed that microbial imbalance in the gut and in cancer tissue is facilitated by a Western type of diet, rich in meat, sugars, and refined grains, while a Mediterranean diet, rich in low saturated fat and fibers, promotes gut eubiosis, and results in reduced risk of developing colorectal cancer. Specifically, a high fiber content diet has been associated with a reduced incidence of therapy related adverse events in patients with malignant melanoma.

OBJECTIVE: This study aimed to analyze and compare the gut microbiota of patients with metastatic colorectal cancer undergoing first-line chemotherapy with or without a biological agent (antiepidermal growth factor receptor or antivascular endothelial growth factor), and receiving either a free standard Western diet, or a modified Mediterranean diet, and the impact of microbiota on chemotherapy toxicity.

METHODS: This is a pilot nondrug, interventional prospective, randomized, controlled, single-center (Italian), open-label trial. Patients (n=40) living in Italy, and with a local style of life, will be randomized 1:1 to either a modified Mediterranean diet or a free Western-type diet. Blood and fecal samples will be collected at baseline and control visits, for metagenomic and metabolomic analysis. The primary endpoint is the Firmicutes:Bacteroidetes ratio after completion of the third cycle of first-line chemotherapy (time T1). Secondary endpoints are (1) the percentage of patients experiencing gastrointestinal side effects at T1, (2) the percentage of patients experiencing grade 3/4 gastrointestinal side effects at T1, and (3) changes in the Firmicutes:Bacteroidetes ratio, overall microbiome composition, and metabolome at T1, and after the sixth chemotherapy cycle (T2) versus baseline.

RESULTS: This pilot trial received ethics approval on July 24, 2024. By July 2025, a total of 17 participants have been recruited. The study will conclude with the visit at T2 for the last enrolled patient. Results are expected to be published in October 2028.

CONCLUSIONS: This study has the potential to provide critical insights into the role of diet in modifying the gut microbiota, diminishing chemotherapy-related side effects, and possibly enhancing the therapeutic efficacy in metastatic colorectal cancer by improving tolerability. In addition, data may pave the way for future research in immunotherapy, potentially influencing both clinical practice and public health strategies.

TRIAL REGISTRATION: Clinicaltrial.gov NCT06794931; https://clinicaltrials.gov/search?term=NCT06794931.

DERR1-10.2196/72950.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Colorectal Neoplasms/drug therapy/pathology
*Diet, Mediterranean
Pilot Projects
Italy
Female
Male
Prospective Studies
ErbB Receptors/antagonists & inhibitors
*Antineoplastic Agents/adverse effects/therapeutic use
Middle Aged
Aged
Randomized Controlled Trials as Topic
Adult

@article {pmid41236711,
year = {2025},
author = {Li, YK and Li, WR and Ren, H and Xiao, CL and Guo, Z and Luo, JQ},
title = {Gut microbiome-targeted therapeutics for chronic kidney disease: comparative efficacy of probiotic and microbial preparations.},
journal = {Inflammopharmacology},
volume = {},
number = {},
pages = {},
pmid = {41236711},
issn = {1568-5608},
support = {82474016//National Natural Science Foundation of China/ ; 82404778//National Natural Science Foundation of China/ ; CPA-Z05-ZC-2024002//Research Project established by Chinese Pharmaceutical Association Hospital Phamacy department/ ; W20243164//Health Research Project of Hunan Provincial Health Commission/ ; 2025JGB077//Degree & Postgraduate Education Reform Project of Central South University/ ; },
abstract = {BACKGROUND: Probiotics supplements may be a solution to improve and delay chronic kidney disease (CKD), but their anti-inflammatory and other effects remain unclear. Our study conducted network meta-analysis (NMA) to appraise the efficacy of supplementary probiotic and microbial preparations for CKD patients.

METHODS: Searches for eligible trials were performed until January 30, 2025. The relative efficacy of various interventions was assessed using surface under the cumulative ranking (SUCRA).

RESULTS: This NMA included 53 studies and evaluated 4 aspects of the outcomes: renal markers and uremic toxins, glucolipid metabolism, inflammation and oxidative stress indices, and dietary intake. Multi-combination of three probiotics (Mix1) and four or more probiotics (Mix2) intervention were associated with significantly higher efficacy. For example, Mix2 intervention was the highest effecacy in reducing creatinine (SUCRA: 79.1%) and glucose (SUCRA: 97.1%). Moreover, Mix1 yielded the best ranking in decreasing uric acid (SUCRA: 82.5%), fasting blood sugar (FBS) (SUCRA: 92.0%), and malondialdehyde (MDA) (SUCRA: 78.7%).

CONCLUSION: Multi-combination of three or more probiotics may be the best choice for improving renal function, glucolipid metabolism, inflammation, oxidative stress, and dietary intake in CKD patients.},
}

@article {pmid41236361,
year = {2025},
author = {Markfeld, M and Titcomb, G and Randriamoria, TM and Sehgal, G and Baksh, N and Kerrigan, A and Soarimalala, V and Nunn, CL and Pilosof, S},
title = {Differential Assembly of Core and Non-Core Host-Microbe Network Structures Along a Land-Use Change Gradient.},
journal = {Ecology letters},
volume = {28},
number = {11},
pages = {e70255},
doi = {10.1111/ele.70255},
pmid = {41236361},
issn = {1461-0248},
support = {1281/20//Israel Science Foundation/ ; 2308460//National Science Foundation/ ; R01-TW011493//NIH-NSF-NIFA Ecology and Evolution of Infectious Diseases program/ ; 2022721//United States-Israel Binational Science Foundation/ ; Provost's Collaboratory Award//Duke University/ ; RGY0064/2022//Human Frontier Science Program/ ; //Duke Lemur Center/ ; },
mesh = {Animals ; Rats/microbiology ; Madagascar ; *Microbiota ; *Host Microbial Interactions ; },
abstract = {Microbial communities are fundamental to host health, yet their assembly dynamics under environmental change remain poorly understood. We analysed individual-level host-microbe networks in the non-native wild black rats (Rattus rattus) across a land-use gradient in Madagascar. By applying a moving prevalence threshold, we distinguished between core and non-core microbes and compared the assembly drivers shaping their network structures. Non-core microbes formed fragmented, modular networks shaped mainly by heterogeneous selection, reflecting environmental filtering. In contrast, core microbes exhibited stable, less modular networks driven primarily by stochastic ecological drift. These distinct assembly processes persisted across thresholds, highlighting fundamental differences in microbial structuring. Land-use change significantly influenced the modular structure of non-core microbes but had minimal effects on core microbes, demonstrating the differential sensitivity of microbial groups to environmental variation. This study advances our understanding of host-microbe interactions and provides a framework for assessing microbiome assembly under anthropogenic change.},
}

Animals
Rats/microbiology
Madagascar
*Microbiota
*Host Microbial Interactions

@article {pmid41236248,
year = {2025},
author = {Bal Bayazıtlı, EC and Aksoy Saraç, G and Uzdoğan, A and Acar, O and Karaman, HB and Külhan, A and Aktaş, A},
title = {Association Between Altered Gut Microbiota and Acne Vulgaris: A Comparative Study of Trimethylamine N-Oxide Levels in Patients and Healthy Controls.},
journal = {Dermatology practical & conceptual},
volume = {15},
number = {4},
pages = {},
doi = {10.5826/dpc.1504a5486},
pmid = {41236248},
issn = {2160-9381},
abstract = {INTRODUCTION: Microbiota refers to the microorganisms inhabiting specific environments, while the microbiome encompasses these organisms, their metabolites, and environmental factors. Variations in microbiota composition across body regions influence physiological processes, including metabolism, immunity, and skin health. Trimethylamine N-oxide (TMAO), a metabolite linked to gut dysbiosis, inflammation, and systemic diseases, has not been previously investigated in acne patients.

OBJECTIVE: We aimed to investigate the potential relationship between gut dysbiosis and acne vulgaris by assessing serum TMAO levels in acne patients compared to healthy controls.

METHODS: This case-control, cross-sectional study involved 70 acne patients and 70 age- and sex-matched healthy controls. Serum TMAO levels were measured, and acne severity was graded using the Global Acne Grading System (GAGS). Statistical analysis was performed using SPSS 20.0, with p-values <0.05 considered significant.

RESULTS: Acne patients exhibited significantly higher serum TMAO levels (16.74 ± 10.10 ng/ml) compared to controls (13.11 ± 4.28 ng/ml, P=0.007). While no significant correlation was found between TMAO levels and acne severity, a weak negative trend was observed (P=0.062). Similarly, TMAO levels showed no significant correlation with body mass index (BMI) (P=0.933).

CONCLUSION: This study identified elevated serum TMAO levels in acne vulgaris patients, suggesting a potential link between gut dysbiosis, diet, and acne pathogenesis. While these findings emphasize the role of systemic inflammation and microbiota, further research is necessary to establish causal relationships and to evaluate the impact of dietary and microbial interventions in acne management.},
}

@article {pmid41236047,
year = {2025},
author = {Ma, ZS},
title = {Anna Karenina Principle, Immune-Oncology-Microbiome Trio and Cancer Microbiome Therapy.},
journal = {WIREs mechanisms of disease},
volume = {17},
number = {6},
pages = {e70004},
doi = {10.1002/wsbm.70004},
pmid = {41236047},
issn = {2692-9368},
support = {//Bullard Felllowship from Harvard University/ ; 72274192//National Natural Science Foundation (NSFC)/ ; },
mesh = {Humans ; *Neoplasms/microbiology/therapy/immunology ; *Microbiota/immunology ; Immunotherapy/methods ; },
abstract = {The immune-oncology-microbiome (IOM) trio highlights the significant role of microbiomes in cancer progression by modulating immune evasion, genomic instability, and inflammation-key hallmarks of cancer. While microbiomes can exert both protective and detrimental effects on tumor development and treatment response, the mechanistic underpinnings-particularly those involving intratumoral microbiomes-remain poorly understood. To elucidate these dynamics, we frame the interplay between cancer, immune cells, and microbiomes through the lens of the Anna Karenina Principle (AKP)-using Leo Tolstoy's aphorism: "All happy families are alike; each unhappy family is unhappy in its own way." In biomedical terms, this translates to: all healthy systems including intratumoral microbiomes are alike, but each dysfunctional system fails in its own way. We hypothesize that either AKP or its inverse (anti-AKP) may govern microbial interactions that influence cancer progression. Analyzing four published cancer tissue microbiome datasets (Nejman 2020, Science), we identified two distinct patterns: AKP-driven increased microbial heterogeneity in lung and ovarian cancers, and anti-AKP-driven decreased heterogeneity in breast and colon cancers. We further propose cancer microbiome therapy (CMT) as an emerging frontier in microbiome-based therapeutics. The CMT may include the following strategies: (i) Restoring a healthy microbiome (including barrier tissue, tumor, blood microbiomes) to enhance immune function through ecosystem engineering; (ii) Developing specific microbial agents (species or their metabolites) to modulate crossroads of cancer immunotherapy; (iii) Engineering microbial agents to suppress cancer-causing microbes (oncomicrobes and complicit) and halt cancer progression; (iv) Reviving historical approaches like Coley's toxin and oncolytic viruses for direct cancer cell targeting. This article is categorized under: Cancer > Genetics/Genomics/Epigenetics Cancer > Computational Models.},
}

Humans
*Neoplasms/microbiology/therapy/immunology
*Microbiota/immunology
Immunotherapy/methods

@article {pmid41236031,
year = {2025},
author = {Kim, JR and Byun, JS and Jung, JK and Hong, SH and Lee, HJ},
title = {Altered oral microbiome diversity in patients with oral candidiasis.},
journal = {Archives of oral biology},
volume = {180},
number = {},
pages = {106430},
doi = {10.1016/j.archoralbio.2025.106430},
pmid = {41236031},
issn = {1879-1506},
mesh = {Humans ; *Candidiasis, Oral/microbiology/drug therapy ; *Microbiota/drug effects ; Male ; Saliva/microbiology ; Female ; *Fluconazole/therapeutic use/pharmacology ; Middle Aged ; *Antifungal Agents/therapeutic use/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Mouth/microbiology ; Aged ; Adult ; Streptococcus salivarius/drug effects ; Real-Time Polymerase Chain Reaction ; },
abstract = {OBJECTIVE: Oral candidiasis is a common opportunistic infection caused by Candida albicans, particularly in individuals with local or systemic risk factors. This study aimed to investigate how antifungal therapy affects the composition of the oral bacterial microbiome.

DESIGN: Unstimulated saliva samples were collected from ten patients diagnosed with acute pseudomembranous oral candidiasis before and after fluconazole treatment. Microbiome profiles were assessed using 16S rRNA gene sequencing. Quantitative PCR was performed to validate changes in specific bacterial species.

RESULTS: Alpha diversity did not change significantly, whereas beta-diversity analyses indicated modest compositional shifts. Antifungal therapy was associated with an increase in Streptococcus salivarius, a commensal linked to mucosal health. The signal was confirmed by species-specific qPCR in paired samples.

CONCLUSIONS: Fluconazole treatment for oral candidiasis induces modest shifts in the oral bacterial community, particularly increasing the abundance of S. salivarius. These changes may reflect partial recovery of microbial homeostasis, supporting the role of microbiome monitoring and probiotic approaches in post-treatment care.},
}

Humans
*Candidiasis, Oral/microbiology/drug therapy
*Microbiota/drug effects
Male
Saliva/microbiology
Female
*Fluconazole/therapeutic use/pharmacology
Middle Aged
*Antifungal Agents/therapeutic use/pharmacology
RNA, Ribosomal, 16S/genetics
*Mouth/microbiology
Aged
Adult
Streptococcus salivarius/drug effects
Real-Time Polymerase Chain Reaction

@article {pmid41235977,
year = {2025},
author = {Kolodkin-Gal, I and Murugan, PA and Mahapatra, S and Zanditenas, E and Ankri, S},
title = {Differential coping strategies exerted by biofilm and planktonic cells of Bacillus subtilis in response to a protozoan predator.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0159725},
doi = {10.1128/spectrum.01597-25},
pmid = {41235977},
issn = {2165-0497},
abstract = {UNLABELLED: The human protozoan parasite Entamoeba histolytica causes amebiasis and interacts with both beneficial and harmful members of the microbiome. In previous studies, it was shown that E. histolytica can break down pre-established biofilms of Bacillus subtilis in a time- and dose-dependent manner. Inhibiting parasitic cysteine proteases impairs biofilm degradation. However, it is still unknown whether bacteria can sense this process and respond to the degradation of the biofilms. Here, our research demonstrates a multilayered response of probiotic bacteria to the parasite, which differs between planktonic bacteria and pre-established biofilms. Sensing the activity of cysteine proteases from E. histolytica, the bacteria activate the general stress response and, to a lesser extent, the cell wall stress response. This activation helps the surviving members of the biofilm become more resistant to mild stressors such as ethanol, hydrogen peroxide, and sub-mic concentrations of ampicillin. On the other hand, planktonic cells exposed to the predators' lysate deactivate the expression of genes associated with biofilm formation while inducing their motility to avoid predation. Overall, our results indicate that bacteria have evolved to recognize amoeba predators capable of degrading biofilms. Furthermore, the partially digested biofilm cells may have unexpected disadvantages over bacteria that did not encounter a predator. These findings may be useful in developing more efficient probiotic strains that are resilient to amebiasis.

IMPORTANCE: The human protozoan parasite Entamoeba histolytica feeds on intestinal microbiota to survive. To enhance the effectiveness of probiotics, we characterized how they respond to amoeba predators. We found that probiotics decrease the expression of biofilm-related genes to avoid predation while simultaneously inducing their stress response and increasing their motility. Our results can provide novel directions for engineering probiotic bacteria to overcome gastrointestinal-associated parasitic diseases. Additionally, it highlights a fundamental mechanism through which bacterial prey can evade predation in the gastrointestinal tract.},
}

@article {pmid41235932,
year = {2025},
author = {Zhao, M and Liu, Y and Lv, S and Mi, T and Wang, N and Zhang, S and Liu, H},
title = {Prevotella copri facilitates wound healing in mice through the sphingosine-CerS1-ceramide metabolic pathway.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0158725},
doi = {10.1128/spectrum.01587-25},
pmid = {41235932},
issn = {2165-0497},
abstract = {Skin wound repair constitutes a sophisticated biological process involving spatiotemporally coordinated molecular cascades, with emerging evidence highlighting the dynamic regulatory role of skin microbiota. Utilizing a broad-spectrum antibiotic (ABX)-treated murine model, we identified Prevotella copri as a core functional commensal in the wound microecosystem that orchestrates tissue regeneration through metabolite-host crosstalk. ABX-induced microbial remodeling significantly enriched P. copri relative abundance, accelerated wound closure, and upregulated pro-regenerative factors vascular endothelial growth factor and epidermal growth factor. Metabolomic profiling revealed that P. copri-secreted sphingosine undergoes bioconversion to C18-ceramide via the non-canonical CerS1 pathway, driving keratinocyte hyperproliferation and neoangiogenesis. Pharmacological inhibition of CerS1 with P053 suppressed ceramide synthesis and delayed healing, mechanistically validating the sphingosine-CerS1-ceramide axis. Crucially, P. copri exhibits dual regulatory modalities: ecologically, β-lactamase-mediated antibiotic resistance establishes microbial dominance, while metabolically, sphingolipid-driven spatiotemporal signaling remodels the regenerative microenvironment. These findings align with and extend the evolving perspective of a functional wound microbiota and propose a potential synergistic strategy that combines targeted enrichment of beneficial commensals like P. copri with metabolic axis modulation to promote healing. Our findings elucidate a microecology-metabolism circuit that transitions wound management from passive anti-infection to precision intervention, providing a molecular blueprint for developing microbiome-reprogramming therapies in regenerative medicine.IMPORTANCETraditional wound repair research often focuses on microbial diversity, neglecting the critical role of specific taxa in tissue regeneration. Our study challenges this by highlighting Prevotella copri as a key species in wound healing, operating through the Prevotella copri-sphingosine-CerS1-ceramide signaling pathway. This discovery reshapes the understanding of microbiome-host interactions and paves the way for precision microbial therapies. By showing that a single bacterium can replace complex community dynamics, we connect ecological theory with regenerative applications, offering a strategy to use microbial metabolism for precise wound healing.},
}

@article {pmid41235927,
year = {2025},
author = {Huang, M and Afzal, M and Liang, Q and Chen, Y and Tian, J and Tan, X and Tan, Z},
title = {The application of Rhizobium subbaraonis TY15 increased soybean growth and disease resistance by modifying rhizosphere microbial communities.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0115525},
doi = {10.1128/spectrum.01155-25},
pmid = {41235927},
issn = {2165-0497},
abstract = {Microbial biofertilizers present a sustainable approach to enhancing agricultural productivity by reducing reliance on chemical inputs. A total of 193 bacterial strains were isolated from the soybean rhizosphere using culture-dependent methods and high-throughput sequencing. Genetic diversity analysis via IS-PCR fingerprinting identified 19 representative strains, followed by 16S rRNA sequencing that delineated Bacillus, Rhizobium, and Paenibacillus as dominant genera. We chose Rhizobium subbaraonis TY15 on the basis of its dominant position and plant growth-promoting rhizobacteria characteristics. Functional screening highlighted strains exhibiting phosphate and potassium solubilization, plant growth-promoting traits (e.g., auxin production and enzyme synthesis), and antagonistic activity against phytopathogens such as Fusarium oxysporum, Rhizoctonia solani, and Pseudomonas solanacearum. Notably, Rhizobium subbaraonis TY15 demonstrated dual benefits in promoting soybean growth and modulating rhizosphere microbial communities, significantly increasing the abundance of beneficial genera like Bacillus and Rhizobium. These findings underscore the potential of targeted microbial inoculants to improve crop resilience and nutrient efficiency, offering insights for developing sustainable biofertilizers through plant-microbe interaction optimization.IMPORTANCEPersistent challenges in soybean production demand sustainable solutions leveraging plant growth-promoting rhizobacteria. While biofertilizers enhance crop resilience, understanding how elite strains reconfigure rhizosphere microbiomes remains limited. Our study demonstrates that Rhizobium subbaraonis TY15 uniquely enriches beneficial genera (e.g., Bacillus and Rhizobium) while suppressing oligotrophic taxa, synergistically boosting nutrient mobilization and pathogen resistance-effects overlooked by conventional screening methods. By integrating culture-dependent isolation with high-throughput sequencing, we expose limitations of standard protocols in capturing strain-specific microbiome modulation. These insights establish a framework for precision microbial consortia design, advancing biofertilizer development to sustainably address global food security challenges.},
}

@article {pmid41235624,
year = {2025},
author = {Salah, EM and Bedair, NI and Farid, AS and Sharara, MA},
title = {Antifungal Monotherapy in Acne: Topical Ketoconazole 2% Cream Versus Adapalene Gel in Treating Acne Vulgaris: A Comparative Study.},
journal = {Journal of cutaneous medicine and surgery},
volume = {},
number = {},
pages = {12034754251386690},
doi = {10.1177/12034754251386690},
pmid = {41235624},
issn = {1615-7109},
abstract = {BACKGROUND: Acne is a widely prevalent disorder, with a largely negative impact on the patient's quality of life. Bacterial etiology and the role of Cutibacterium acne have always been incriminated in in acne pathogenesis. However, in the last decade, deeper understanding of skin microbiome postulates a possible role of other pathogens like Malassezia spp. ketoconazole has shown efficacy to both pathogens.

OBJECTIVES: To study the efficacy of topical ketoconazole 2% in the treatment of acne vulgaris (AV) compared to the standard treatment with adapalene.

METHODS: Fifty-eight acne patients in 2 groups were asked to blindly apply ketoconazole cream or adapalene gel to the face for 12 weeks. Acne lesion count was performed at baseline, and at the end of the 12 weeks.

RESULTS: At the end of the treatment period, both groups showed significantly similar improvement of comedones, papules, and pustules. Mild side effects were reported that were significantly less among the ketoconazole group.

CONCLUSION: Topical ketoconazole 2% can provide very promising results as monotherapy in acne comparable to topical retinoid.},
}

@article {pmid41235517,
year = {2025},
author = {Shestakova, EA and Nosova, AV and Dzgoeva, FK and Nurmamedova, SA and Frolkova, NV and Mishina, EE and Shestakova, MV},
title = {[The effect of AntiAGE-Biom probiotic on metabolic features in individuals with type 2 diabetes].},
journal = {Terapevticheskii arkhiv},
volume = {97},
number = {10},
pages = {859-866},
doi = {10.26442/00403660.2025.10.203462},
pmid = {41235517},
issn = {0040-3660},
mesh = {Humans ; *Diabetes Mellitus, Type 2/drug therapy/metabolism/microbiology/therapy/blood ; *Probiotics/administration & dosage ; Male ; Middle Aged ; Female ; Glycated Hemoglobin/analysis/metabolism ; Double-Blind Method ; *Gastrointestinal Microbiome/drug effects/physiology ; Treatment Outcome ; Hypoglycemic Agents/administration & dosage ; Body Composition/drug effects ; Blood Glucose ; },
abstract = {BACKGROUND: Despite the variety of antidiabetic therapies, many patients with type 2 diabetes (T2D) do not achieve optimal glycemic control. Therefore, there is a need to develop additional methods for managing T2D, including ones that regulate the gut microbiome.

AIM: To assess the effect of AntiAGE-Biom probiotic on metabolic parameters in T2D patients during 3 months of therapy.

MATERIALS AND METHODS: A randomized, double-blind, placebo-controlled, single-center study included patients with T2D with glycated hemoglobin - HbA1c<7,5% on stable antidiabetic therapy. Patients were randomized into groups receiving AntiAGE-Biom and placebo. The primary endpoint was the change in HbA1c from baseline, secondary endpoints included the dynamics in biochemical and anthropometric parameters, body composition, as well as HOMA-IR index.

RESULTS: The study included 40 patients with T2D (n=20 in each group). There was a trend towards a decrease in HbA1c in AntiAGE-Biom group, that did not reach statistical significance. The use of the probiotic improved the body composition after 3 months: reduced the percentage of fat in men and a subgroup of patients with an initial HbA1c≥ 6.5%; also increased skeletal muscle mass and lean mass in the trunk segment in men (р<0,05).

CONCLUSION: AntiAGE-Biom probiotic helps to maintain metabolic control and significantly improve body composition in T2D patients with initial HbA1c<7.5%.},
}

Humans
*Diabetes Mellitus, Type 2/drug therapy/metabolism/microbiology/therapy/blood
*Probiotics/administration & dosage
Male
Middle Aged
Female
Glycated Hemoglobin/analysis/metabolism
Double-Blind Method
*Gastrointestinal Microbiome/drug effects/physiology
Treatment Outcome
Hypoglycemic Agents/administration & dosage
Body Composition/drug effects
Blood Glucose

@article {pmid41235333,
year = {2025},
author = {Reytor-González, C and Cevallos-Fernández, E and Jácome, B and Simancas-Racines, D},
title = {From meal to malfunction: exploring molecular pathways, biomarkers and interventions in postprandial cardiometabolic health.},
journal = {Frontiers in cardiovascular medicine},
volume = {12},
number = {},
pages = {1655889},
pmid = {41235333},
issn = {2297-055X},
abstract = {Cardiometabolic diseases-including type 2 diabetes, cardiovascular disease, and metabolic dysfunction-associated steatotic liver disease-are increasingly driven by near-continuous after-meal exposure to glucose and lipid surges that traditional fasting tests often miss. This review prioritizes human studies from 2020 to 2025 and uses earlier work only as foundational anchors; non-English reports were excluded and preclinical findings are cited solely for mechanistic context. Evidence converges on six processes that amplify risk within hours after eating: impaired insulin signaling, delayed clearance of dietary lipids, mitochondrial and oxidative stress, loss of endothelial nitric oxide, inflammasome-mediated inflammation, and microbiome-hormone interactions. Dynamic, after-meal markers and simple composites such as the triglyceride-glucose index outperform fasting measures for identifying risk and guiding care. Practical strategies to shorten the "damage window" include Mediterranean-style meals with low glycemic index swaps and unsaturated fats, earlier distribution of daily energy and early time-restricted eating, a small pre-meal protein portion, and brief post-meal walking. Fast-acting medicines-glucagon-like peptide 1 and glucose-dependent insulinotropic polypeptide receptor agonists, rapid-acting insulin analogues, sodium-glucose cotransporter 2 inhibitors taken before meals, and proprotein convertase subtilisin/kexin type 9 inhibitors-further blunt peaks, while continuous glucose monitoring with algorithmic feedback enables timing-aware, person-specific adjustments. A tiered workflow-screen, stratify, and personalize-reframes prevention and treatment around after-meal physiology, with particular relevance to settings where resources are limited.},
}

@article {pmid41235258,
year = {2025},
author = {Fan, H and Fu, D and Tian, M and Li, Z and Liu, S and Ye, C and Wu, K and Zhu, C},
title = {Targeting the LPS-STING axis: neomycin restores STING-mediated anti-tumor immune suppression and inhibits tumor growth.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1637667},
pmid = {41235258},
issn = {1664-3224},
mesh = {Animals ; *Lipopolysaccharides/immunology/pharmacology ; *Membrane Proteins/agonists/metabolism/immunology ; Mice ; *Neomycin/pharmacology ; Signal Transduction/drug effects ; Macrophages/immunology/drug effects/metabolism ; Tumor Microenvironment/immunology/drug effects ; Immunity, Innate/drug effects ; Cell Line, Tumor ; Mice, Inbred C57BL ; *Melanoma, Experimental/immunology/drug therapy/pathology ; Interferon-beta/metabolism ; Female ; },
abstract = {INTRODUCTION: The interplay between microbial metabolites and host immunity within the tumor microenvironment (TME) critically modulates anti-tumor immune responses. The role of Gram-negative bacteria and their cell wall component lipopolysaccharide (LPS) in this context warrants further investigation.

METHODS: We assessed the impact of low-dose LPS pretreatment on macrophage function by measuring type I interferon (IFN-β) secretion in response to tumor cell debris. Mechanistic insights were gained by analyzing endogenous signaling pathways in macrophages. The therapeutic potential of targeting LPS was evaluated in melanoma-bearing mice treated with neomycin, alone or in combination with STING agonists.

RESULTS: Low-dose LPS pretreatment significantly suppressed IFN-β secretion by macrophages, indicating LPS-mediated immunosuppression. Mechanistically, LPS disrupted endogenous signaling pathways, blunting the ability of macrophages to sense tumor-derived damage signals. In vivo, neomycin treatment markedly inhibited melanoma growth and synergized with STING agonists.

DISCUSSION: Our findings demonstrate that elevated LPS in the TME inhibits anti-tumor innate immunity by impairing macrophage function. The combination of LPS modulation via neomycin with innate immune activation via STING agonists presents a potential strategy to enhance tumor immunotherapy.},
}

Animals
*Lipopolysaccharides/immunology/pharmacology
*Membrane Proteins/agonists/metabolism/immunology
Mice
*Neomycin/pharmacology
Signal Transduction/drug effects
Macrophages/immunology/drug effects/metabolism
Tumor Microenvironment/immunology/drug effects
Immunity, Innate/drug effects
Cell Line, Tumor
Mice, Inbred C57BL
*Melanoma, Experimental/immunology/drug therapy/pathology
Interferon-beta/metabolism
Female

@article {pmid41235192,
year = {2025},
author = {Liu, S and Greenhut, IV and Moe, LA},
title = {Bacterial community structure associated with smokeless tobacco reference products under different storage conditions and durations.},
journal = {Frontiers in public health},
volume = {13},
number = {},
pages = {1693267},
pmid = {41235192},
issn = {2296-2565},
mesh = {*Tobacco, Smokeless/microbiology ; *Bacteria/isolation & purification/classification/genetics ; Humans ; Time Factors ; Kentucky ; },
abstract = {The microbiology of smokeless tobacco products (STPs), such as moist snuff, snus, and loose-leaf chewing tobacco, has recently received significant interest owing to the impact of microbes on product storage and safety. Tobacco leaf-associated microbes, as well as microbes introduced during product manufacturing, may play a role in formation of carcinogenic nitrosamine compounds during manufacturing and product spoilage upon storage. The Center for Tobacco Reference Products at the University of Kentucky has, since 1968, provided tobacco reference products for non-clinical research purposes. These products, including cigarettes, cigars, and STPs, are commercially produced and meant to be representative of off-the-shelf products. Reference products provide the opportunity to enhance reproducibility and reduce batch-to-batch variability. In this study, the microbial communities of smokeless tobacco reference products 3S1 (loose-leaf chewing tobacco), 3S3 (moist snuff), 1S4 (Swedish-style snus), and 1S5 (American snus) were analyzed using culture-based and culture-independent analysis. Bacterial and fungal loads were assessed on three media types, and 16S rDNA amplicon sequencing was used to track the bacterial community structure as a function of time and product storage temperature. Culturable loads were consistently highest with moist snuff (~10[6]-10[7] CFU/g) and lowest with the snus products (~10[2]-10[3] CFU/g). Bacterial community structure varied according to product, with Firmicutes and Proteobacteria the primary phyla observed. At the genus level, the most commonly observed operational taxonomic units (OTUs) belonged to Tetragenococcus and Staphylococcus, but their relative abundances differed according to product. The moist snuff product showed the most significant shift in microbial community structure according to storage temperature, with an increase in Atopostipes, Staphylococcus, and Carnobacteriacea OTUs at room temperature and an increase in Lentibacillus at 37 °C. From these studies, we conclude that elevated storage temperatures will alter STP microbial communities but that storage at -20 °C is sufficient for long-term storage of the reference products.},
}

*Tobacco, Smokeless/microbiology
*Bacteria/isolation & purification/classification/genetics
Humans
Time Factors
Kentucky

@article {pmid41235136,
year = {2025},
author = {Wu, Y and Pan, S and Yin, C and Kong, Y and Huo, W and Wang, Q and Wu, J and Li, L and Wei, J and Lu, C and Han, L and Lu, Y},
title = {PSORI-CM02 Restores Epidermal Differentiation in Psoriasis via the Gut Microbiota-Sphingolipid Axis.},
journal = {Drug design, development and therapy},
volume = {19},
number = {},
pages = {9993-10010},
pmid = {41235136},
issn = {1177-8881},
mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Psoriasis/drug therapy/metabolism/pathology ; Mice ; Humans ; *Cell Differentiation/drug effects ; *Sphingolipids/metabolism ; *Epidermis/drug effects/pathology/metabolism ; Keratinocytes/drug effects/metabolism ; },
abstract = {BACKGROUND: Psoriasis is linked to gut dysbiosis and disturbed sphingolipid metabolism. PSORI-CM02 improves epidermal differentiation, yet its impact on the microbiota-sphingolipid axis remains unknown.

METHODS: Transcriptomics of patient keratinocytes, Carmofur inhibition in IMQ mice, and multi-omics (metabolomics, metagenomics) of skin, lymph nodes and gut were combined. SPF, PGF and GF mice underwent FMT to test microbiota dependency.

RESULTS: Psoriatic lesions showed sphingolipid pathway enrichment. Carmofur enhanced differentiation. PSORI-CM02 lowered PASI, spleen index, and tissue levels of ceramide, S1P, C1P and sphingomyelin while restoring Flg, Krt10 and Krt14. It reduced Turicibacter, Bacteroides, Bifidobacterium and Acetobacter. PSORI-CM02-derived microbiota reproduced therapeutic effects in all FMT settings.

CONCLUSION: PSORI-CM02 reshapes gut microbiota, normalizes sphingolipid metabolism and improves epidermal differentiation to treat psoriasis.},
}

*Gastrointestinal Microbiome/drug effects
Animals
*Psoriasis/drug therapy/metabolism/pathology
Mice
Humans
*Cell Differentiation/drug effects
*Sphingolipids/metabolism
*Epidermis/drug effects/pathology/metabolism
Keratinocytes/drug effects/metabolism

@article {pmid41234866,
year = {2025},
author = {Liang, Z and Gao, J and Zheng, Q},
title = {Multi-omics analysis reveals intratumoral microbiota as modulators of the immune environment within thyroid cancer.},
journal = {Translational cancer research},
volume = {14},
number = {10},
pages = {6681-6693},
pmid = {41234866},
issn = {2219-6803},
abstract = {BACKGROUND: Recent studies indicate that intratumoral microbiota play a crucial role in tumor development. While research on microbiota and thyroid cancer (TC) has primarily focused on gut microbiota, studies on intratumoral microbiota are limited. This study utilizes multi-omics analysis to investigate the effects and mechanisms of intratumoral microbiota on TC.

METHODS: We analyzed the microbial profile in the TC tumor microenvironment using data from published The Cancer Genome Atlas (TCGA) program. The impact of microbes on TC signaling pathways and the immune environment was examined through a combined analysis of the microbiome, transcriptome, and immune infiltration.

RESULTS: Significant differences in microbial diversity were observed between TC tumor tissue and adjacent non-tumor tissue. Specifically, there were notable differences in the relative abundance of 12 microbial species at the genus level. Additionally, there were marked differences in the infiltration scores of 11 immune cell species in the tumor microenvironment compared to adjacent tissues. Nine of these immune cell species were correlated with eight differentially expressed genes, and these genes were associated with differential bacterial abundance at the genus level.

CONCLUSIONS: Our findings reveal that the diversity and relative abundance of intratumoral microbiota are associated with tumorigenesis in TC.},
}

@article {pmid41234847,
year = {2025},
author = {Chen, Y and Wang, Y and Shen, S and Lu, J and Peng, Q and Yan, X and Peng, H and Xu, Z},
title = {Comparative microbiome profiling reveals unique signatures in multiple primary lung cancers.},
journal = {Translational cancer research},
volume = {14},
number = {10},
pages = {6388-6402},
pmid = {41234847},
issn = {2219-6803},
abstract = {BACKGROUND: Lung cancer is the leading cause of cancer-related mortality worldwide, with a rising incidence of multiple primary lung cancer (MPLC). However, the mechanisms underlying MPLC, including its early clinical diagnosis, pathogenesis and clinical management, remain poorly understood. The intratumoral microbiome is recognized to modulate the immune landscape within the tumor microenvironment (TME), potentially enhancing or suppressing antitumor immunity, thereby influencing tumor progression and therapeutic efficacy. The role of the intratumoral microbiome in MPLC development is an emerging area of research, yet its specific relationship with MPLC remains largely unexplored. This study aims to profile microbial communities in lung cancer tissues and elucidate differences between patients with MPLC and non-MPLC (NMPLC). This study aimed to profile the microbial communities in lung cancer tissues and investigate their potential relationships with MPLC.

METHODS: 16S ribosomal RNA (rRNA) gene sequencing was performed on tumor and adjacent tissues from MPLC and NMPLC patients. Bioinformatics analysis, including alpha diversity (Chao1, Shannon, Simpson), beta diversity (Bray-Curtis, UniFrac), and taxonomic profiling, was performed via QIIME2 and R. Microbial functions were predicted via PICRUSt2, and specific microbial signatures associated with MPLC were identified to explore their potential as biomarkers for early diagnosis and therapeutic strategies.

RESULTS: No significant difference in microbial diversity was observed between tumor and adjacent nontumor tissues. However, tumor tissues in the MPLC group presented higher α diversity than those in the NMPLC group. Functional analysis of the differential microbiota revealed that the tetracycline biosynthesis and naphthalene degradation pathways were upregulated in MPLC, whereas riboflavin metabolism was upregulated in NMPLC. Random forest analysis revealed Faecousia and Burkholderia as key genera with significantly greater abundances in MPLC tumor and paracancerous tissues.

CONCLUSIONS: For the first time, we demonstrate a potential association between the microbiota and MPLC, revealing distinct microbial profiles in MPLC tumors and their adjacent tissues compared to those in NMPLC. These findings establish a novel diagnostic framework based on microbial biomarkers that enhances early differentiation between MPLC and NMPLC, thereby facilitating timely and subtype-specific therapeutic decisions.},
}

@article {pmid41234824,
year = {2025},
author = {Liu, H and Liu, Y and Dai, Y and Zhang, L and Long, M},
title = {Integrated multi-omic analysis unravels the characteristics of the metabolism-related intratumoral microbes and establishes a novel signature for predicting prognosis and therapeutic response in lung adenocarcinoma.},
journal = {Translational cancer research},
volume = {14},
number = {10},
pages = {6771-6790},
pmid = {41234824},
issn = {2219-6803},
abstract = {BACKGROUND: Cellular metabolic irregularities are intricately associated with the initiation and progression of tumors. Emerging evidence suggests that interactions between intratumoral microbiomes and host mediate this process. However, a comprehensive understanding of the role of metabolism-related intratumoral microbes (MRIMs) in lung adenocarcinoma (LUAD) is still lacking. This study aimed to investigate the characteristics and prognostic significance of MRIMs, as well as elucidate their potential implications in relation to the microenvironment in LUAD.

METHODS: Integrated analyses were conducted using accessible datasets of the microbiome, bulk and single-cell transcriptomes. Spearman's coefficient between metabolic activity score and microbial abundance was used to identify MRIMs. An unsupervised clustering approach was utilized to distinguish the MRIMs-featured subtypes in LUAD samples. The Scissor algorithm was executed to select the cell subpopulations featured by MRIMs, and the underlying regulatory network in MRIMs-featured cells was explored. Additionally, a prognostic signature based on the microbial abundance of MRIMs was developed, and comprehensive analyses were subsequently carried out to reveal the correlation between MRIMs and LUAD microenvironment.

RESULTS: Ten microbial species were identified as MRIMs, enabling the classification of LUAD samples into two distinct subtypes that showed significantly associated with clinical features and survival outcomes. The scRNA-seq analysis revealed notable differences in T cells, ciliated cells, mast cells, endothelial cells, and fibroblasts between MRIM+ and MRIM- subpopulations. BCL3, KLF3, and NFKB2 were the regulons in the regulatory network of MRIM-featured cells. Additionally, a microbial prognostic-predictive signature was established comprising Succinimonas, Collimonas, and Marichromatium, which also exhibited potential for indicating immunotherapeutic benefit and predicting drug sensitivity to cisplatin, cytarabine, pyrimethamine, olaparib, bicalutamide and vorinostat in LUAD treatment.

CONCLUSIONS: This study identified intratumoral microbes associated with metabolism, revealed distinct subtypes and their roles in LUAD, and established a predictive signature for the prognosis and therapeutic responsiveness of LUAD.},
}

@article {pmid41234775,
year = {2025},
author = {Wolf, M and Wasinger, D and Donhauser, V and Moliterno, P and Keppler, BK and Gerner, C and Widhalm, K and Meier-Menches, SM},
title = {Eccrine sweat reveals normalization of artificial sweetener levels in children with overweight after nutritional education.},
journal = {iScience},
volume = {28},
number = {11},
pages = {113736},
pmid = {41234775},
issn = {2589-0042},
abstract = {Determining metabolic parameters associated with childhood obesity is challenging due to the invasive nature of most sampling methods. Using a non-invasive eccrine sweat collection, 134 metabolomes were obtained from 54 children, of which 20% had overweight, including obesity. This cohort is part of the preventive EDDY program aiming to promote healthy lifestyles in school-aged children from Vienna, Austria. The abundance of the artificial sweetener cyclamate in eccrine sweat correlated with body mass index in the overweight group at baseline. Cyclamate was also found to be elevated in the overweight group at baseline compared to the normal weight group, but normalized after the intervention, indicating a positive impact of the EDDY program. Furthermore, dynamic changes in metabolites originating from the gut microbiome were observed. Sweat metabotyping thus represents a valuable approach to accessing metabolic parameters in children in the context of overweight and obesity and promises broad applicability in pediatric research.},
}

@article {pmid41234773,
year = {2025},
author = {Levé, M and Manghi, P and Bredon, M and Lefevre, A and Manara, S and Armanini, F and Emond, P and Planchais, J and Rolhion, N and Segata, N and Sokol, H},
title = {Metabolomics and metagenomics in mice reveal the role of the gut microbiota in tryptophan metabolism.},
journal = {iScience},
volume = {28},
number = {11},
pages = {113751},
pmid = {41234773},
issn = {2589-0042},
abstract = {Tryptophan metabolism plays a key role in host-microbiota interactions, producing a wide array of bioactive metabolites. However, our understanding of the interactions between tryptophan metabolites and the gut microbiota is still limited. Using targeted quantitative metabolomics and metagenomics in mice across various compartments, we showed that the cecal microbiota massively impacts tryptophan metabolism both in the gut and systemically. Grouping bacterial taxa in co-abundance guilds better reflected the links between gut microbes and tryptophan metabolites than single taxa taken individually and suggested the involvement of complex microbial interactions in tryptophan metabolism regulation. Finally, analyzing functional data, we shed light on the potential links between tryptophan metabolism and bacterial enzymes or metabolic pathways.},
}

@article {pmid41234770,
year = {2025},
author = {Wang, IC and Swanson, JL and Waters, JL and Kochukov, MY and Buffington, SA and Dooling, SW and Arenkiel, BR and Costa-Mattioli, M},
title = {Alteration of gut microbial ecology by the direct activation of the brain: Inverse gut-microbiome-brain dynamics.},
journal = {iScience},
volume = {28},
number = {11},
pages = {113709},
pmid = {41234770},
issn = {2589-0042},
abstract = {The gut-microbiome-brain axis is a bidirectional communication system influencing host physiology and overall fitness. While "bottom-up" effects-where gut microbes influence brain function and behavior-are well established, direct evidence for "top-down" modulation-where the brain shapes the gut microbial ecology-remains elusive. Here, we show that the selective expression of the bacterial ion channel mNaChBac in glutamatergic lateral habenula (LHb) neurons increases their bursting activity and leads to endophentypes associated with depression. Importantly, this chronic activation leads to changes in the gut microbiome composition over time, as reflected by shifts in alpha-diversity and alterations in specific microbial taxa. These findings provide direct evidence that the persistent activation of the brain acts as a selective pressure that affects the stability and diversity of the gut microbiome, providing a new dimension by which gut-microbiome-brain interactions may cooperate to modulate host physiology and health.},
}

@article {pmid41234769,
year = {2025},
author = {Elhady, A and Hirt, H},
title = {Harnessing plant-soil-microbiome synergy for resilient desert restoration.},
journal = {iScience},
volume = {28},
number = {11},
pages = {113748},
pmid = {41234769},
issn = {2589-0042},
abstract = {Deserts cover one-third of Earth's land and support life forms uniquely adapted to extreme climatic and environmental conditions. Restoring these ecosystems remains difficult and costly, yet knowledge of native plants, soils, and their associated microbiomes offers promising solutions. This review outlines the drivers and consequences of desertification feedback loops and explains how microbial adaptations sustain soil functions under stress. We highlight the role of plant-microbe-soil interactions in shaping functional networks that support restoration and the development of synergistic plant communities. We also highlight how the integration of ecological frameworks such as niche differentiation, network theory, and stoichiometric balance reveals new directions for restoration efforts. In this framework, emerging microbiome-based strategies can offer a path to transform barren or degraded landscapes into diverse, resilient vegetative islands.},
}

@article {pmid41234743,
year = {2025},
author = {Dai, S and He, S and Zhao, S and Li, Q and Mao, H and Wu, D},
title = {Feeding regimens reshape rumen microbiota and metabolome in Shorthorn cattle: a multi-omic insight into microbial diversity and metabolic pathway dynamics.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1657402},
pmid = {41234743},
issn = {1664-302X},
abstract = {The rumen microbiome plays a central role in ruminant nutrition and health. To investigate the effects of different feeding regimens on it, this study employed multi-omics analysis to reveal how natural grazing versus intensive feeding alters the rumen microbiota and metabolites in Shorthorn cattle. A total of 18 male shorthorn cattle of about 17 months of age and similar body weight were selected and randomly divided into 3 groups: natural grazing bull group (DJCF), intensive feeding bull group (DJCY) and intensive feeding steer group (DJC). The experiment period was 361 days. After the fattening trial, rumen fluid was collected at slaughter. Microbiota and metabolites were analyzed by 16S rRNA sequencing and LC-MS, and correlations were assessed. The results indicate that different feeding regimens were strongly associated with shifts in rumen microbial diversity and community composition. The ACE and Shannon indices of DJCF group were significantly higher than those of DJCY and DJC group (p < 0.05). Bacteroidetes and Firmicutes were the dominant phyla, with relative abundances of 57.62% (DJCF), 54.11% (DJCY), 48.84% (DJC) and 34.07, 38.31, 43.08%, respectively, showing no significant differences (p > 0.05). At the genus level, Prevotella and Rikenellaceae_RC9_gut_group were dominant. The abundance of Prevotella was highest in DJCY (22.52%), significantly differing from DJC (12.43%; p < 0.05), while Rikenellaceae_RC9_gut_group abundances were 12.56% (DJCF), 9.92% (DJCY), and 11.89% (DJC). In the fungal community, Neocallimastigomycota and Ascomycota were the dominant phyla, and there were no significant differences among the three groups. At the genus level, Caecomyces, the highest in the DJC group, with a significant difference from the DJCF group (p < 0.05). Orpinomyces, the highest in the DJCF group, with significant differences from the DJCY and DJC groups (p < 0.05). There were significant differences in rumen metabolites between different groups, and a variety of different metabolites were identified, involving sucrose and starch metabolism, purine metabolism and other pathways (p < 0.05). In addition, there was a significant correlation between rumen microbes and metabolites (p < 0.05). Thus, an intensive feeding system altered the rumen microbiome, resulting in improvements of Shorthorn cattle growth. Nevertheless, the specific causal relationships and underlying regulatory mechanisms governing the interplay between rumen microbiota and metabolic processes remain to be further elucidated through in-depth investigations.},
}

@article {pmid41234653,
year = {2025},
author = {Farzaneh, F and Hekmatnia, K and Sadat Hosseini, M and Arab, M and Talayeh, M and Vasef, M and Yavari, S and Keyvani, H},
title = {Investigating the correlation between oncogenic HPV, sexually transmitted disease, and vaginal microbiota in patients with normal Pap smear.},
journal = {Iranian journal of microbiology},
volume = {17},
number = {5},
pages = {835-840},
pmid = {41234653},
issn = {2008-3289},
abstract = {BACKGROUND AND OBJECTIVES: This study investigated the correlation between high-risk (HR) human papillomavirus (HPV), sexually transmitted disease (STD), and vaginal microbiota in patients with a normal Pap smear.

MATERIALS AND METHODS: For women who were referred for their routine cervical cancer screening, in addition to co-testing, some samples were taken from the vaginal and cervical environment to check the presence of the most common STD pathogens. The diagnosis of the organisms was done by means of PCR and microbial cultures.

RESULTS: HR HPV was detected in 67 women, and STD was positive in 80% of them, while in HR HPV negative women, this was 67%. The HPV positive group reported a significantly higher rate of STD history (92% vs. 82%) and frequency of intercourse weekly (86% vs. 3.96%) (p<0.05). Lactobacilli, streptococcus, and staphylococcus concentrations were significantly lower in the HPV positive group compared to the HPV negative group (p<0.007; OR = 4.17). Ureaplasma urealyticum and Ureaplasma parvum were significantly (p<0.001) more prevalent in the HPV positive group compared to the HPV negative group.

CONCLUSION: This study showed that the existence of other STDs and the composition of the vaginal and cervical microbiome play an important role in either the clearance or the progression of high-risk HPV.},
}

@article {pmid41234582,
year = {2025},
author = {Shen, M and Chen, Y and Chen, J and Yin, J and Xu, C and Wang, D and Lv, T},
title = {Immune-oncology-microbiome axis in lung cancer: from carcinogenesis to therapy-a narrative review.},
journal = {Translational lung cancer research},
volume = {14},
number = {10},
pages = {4638-4657},
pmid = {41234582},
issn = {2218-6751},
abstract = {BACKGROUND AND OBJECTIVE: Recent studies have increasingly highlighted the critical role of the microbiome in lung cancer initiation, progression, metastasis, and therapeutic resistance. Microbial dysbiosis has been identified as a significant risk factor for lung cancer progression. Beyond the gut, emerging evidence shows that microorganisms also colonize the lungs and even inside tumors, suggesting a broader role of the microbiome in the disease. This review explores the immune-oncology-microbiome (IOM) axis by examining microbial communities across different anatomical sites, their interactions with the tumor immune microenvironment, and their impact on immunotherapy efficacy in lung cancer.

METHODS: We conducted a systematic literature search using PubMed and Web of Science databases for English-language articles published between 2014 and 2025, using key terms related to lung cancer and microbiome.

KEY CONTENT AND FINDINGS: The microbiome associated with lung cancer encompasses gut microbiota, lower respiratory tract microbiota, and intratumor microbiota. Different microbial communities maintain microecological homeostasis and modulate antitumor immune responses by shaping the tumor immune microenvironment. Meanwhile, certain microbiota can enhance or hinder the effectiveness of immunotherapy.

CONCLUSIONS: The IOM axis reveals dynamic interactions between immune cells, cancer cells, and microbes. Specific microbe-derived metabolites show promise as lung cancer biomarkers. Current microbiome-based therapy shows great potential in lung cancer treatment.},
}

@article {pmid41234570,
year = {2025},
author = {Shivakumar, S and Parakh, S and Vukelic, N and Atashrazm, F and Naranbhai, V and Goh, NSL and Da Gama Duarte, J and Leong, TL},
title = {Utility of bronchoalveolar lavage in checkpoint inhibitor pneumonitis evaluation: a narrative review.},
journal = {Translational lung cancer research},
volume = {14},
number = {10},
pages = {4628-4637},
pmid = {41234570},
issn = {2218-6751},
abstract = {BACKGROUND AND OBJECTIVE: Checkpoint inhibitors have revolutionised cancer treatment over the past few decades; however, their successes in clinical trials and real-world settings have been tempered by immune-related adverse events (IrAEs). Checkpoint inhibitor pneumonitis (CIP), the leading cause of IrAE-related mortality, poses a significant challenge to clinicians due to non-specific clinical features and unpredictable disease trajectory. Bronchoalveolar lavage (BAL) is a diagnostic procedure that offers insight into the immune and molecular processes underlying CIP. This review presents the current role and application of BAL in the evaluation of CIP, explores current literature, and discusses how recent advances in research and technology may shape future approaches to its diagnosis and management.

METHODS: A comprehensive literature search using PubMed, EMBASE, and Cochrane databases was performed to identify recent literature evaluating BAL findings in CIP. This review synthesizes findings from these studies to provide an up to date and comprehensive overview of the role of BAL in CIP management.

KEY CONTENT AND FINDINGS: Current guidelines recommend BAL in symptomatic patients when the diagnosis of CIP remains uncertain, primarily to exclude infection and other disease processes. However, the unpredictable clinical course of CIP narrows the window of opportunity to safely perform BAL. Variable utilisation of BAL in clinical practice may also be attributed to the lack of clinically reliable and applicable biomarkers that could improve diagnostic clarity. Beyond lymphocytosis, a well-recognised finding in BALs of patients with CIP, the role of specific immune cell populations and molecular drivers in shaping a proinflammatory microenvironment has been highlighted in multiple emerging studies. Advances in molecular profiling, immunogenomics, and lung microbiome research hold promise for enhancing our understanding of CIP pathogenesis and guiding future approaches to its diagnosis and management.

CONCLUSIONS: In current clinical practice, BAL remains an important investigation to support a diagnosis of CIP; however, its diagnostic value remains uncertain. Enhanced understanding of the CIP immune landscape is fundamental to identifying robust diagnostic and predictive biomarkers that could improve diagnosis and patient outcomes in cancer patients treated with checkpoint inhibitors.},
}

@article {pmid41234504,
year = {2025},
author = {Guo, Y and Tian, M and Liu, Y and Ma, J and Li, Y and Hou, Y and Wang, Y},
title = {New Bitongling Ameliorates Joint Tissue Damage in Collagen-Induced Arthritis Mice by Suppressing Mapt Expression: A Genome-Wide Sequencing Study.},
journal = {Journal of inflammation research},
volume = {18},
number = {},
pages = {15597-15614},
pmid = {41234504},
issn = {1178-7031},
abstract = {OBJECTIVE: Rheumatoid arthritis (RA) affects 1% of the global population, with joint destruction leading to disability. While current biologics (eg, TNF-α inhibitors) and small-molecule therapies (eg, JAK inhibitors) have significantly improved symptom control and slowed radiographic progression in many patients, unresolved challenges remain in simultaneously addressing mitochondrial dysfunction and synovial inflammation-the core drivers of joint destruction. This study aimed to investigate the molecular mechanism by which New Bitongling (NBTL) mitigates joint damage in collagen-induced arthritis (CIA) mice through regulation of the microtubule-associated protein tau (Mapt).

METHODS: Male C57BL/6 mice (6 weeks old, specific pathogen-free) were used to establish the collagen-induced arthritis (CIA) model and randomly assigned to three groups: control, model, and NBTL intervention. Clinical symptoms were evaluated using the arthritis index (AI), paw swelling volume (measured by water displacement), and behavioral tests (sucrose preference test and open-field test). Histopathological changes were assessed via hematoxylin-eosin (HE) and Safranin O-Fast Green staining. Molecular mechanisms were analyzed using Western blotting, flow cytometry, and mitochondrial membrane potential (JC-1 staining) assays. Western blotting analyzed apoptosis-related proteins and the Sirtuin 1 (Sirt1)/Peroxisome proliferator-activated receptor γ coactivator 1α (PGC-1α) pathway, flow cytometry measured reactive oxygen species (ROS) levels, and JC-1 fluorescence staining evaluated mitochondrial membrane potential. Genome-wide sequencing identified Mapt as the key target, with functional validation conducted through siRNA knockdown and adeno-associated virus (AAV) Mapt overexpression. Statistical analyses included repeated-measures Analysis of Variance (ANOVA) with Tukey's post-hoc test and P<0.05 was considered significant.

RESULTS: NBTL treatment significantly reduced AI scores, paw swelling, and joint deformities while improving behavioral indicators. Histological analysis revealed attenuated synovial inflammation, pannus formation, and bone erosion in the NBTL group. Moreover, pro-inflammatory mediators were downregulated in NBTL-treated mice, accompanied by reduced Bax/cleaved-caspase3 and elevated Bcl-2 expression (P<0.05). NBTL restored mitochondrial membrane potential, activated the Sirt1/PGC-1α pathway, reduced ROS levels, and decreased oxidative stress damage (P<0.05). Mapt overexpression exacerbated joint damage, whereas Mapt silencing or NBTL intervention reversed these effects. Genome-wide sequencing confirmed that NBTL modulates mitochondrial homeostasis and inflammatory responses via Mapt inhibition.

CONCLUSION: This study demonstrates that New bitongling ameliorates joint damage in collagen-induced arthritis mice by suppressing microtubule-associated protein tau expression, restoring mitochondrial function, and modulating synovial inflammation. These findings provide preclinical evidence supporting further investigation of New bitongling as a novel therapeutic agent for rheumatoid arthritis.},
}

@article {pmid41234409,
year = {2025},
author = {Martini, SE and Oba, PM and Geary, EL and Bauer, LL and Dilger, RN and Swanson, KS},
title = {In vitro fermentation characteristics of dietary fibers using fecal inocula from dogs fed a canned diet and treated with metronidazole.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1670624},
pmid = {41234409},
issn = {2297-1769},
abstract = {INTRODUCTION: Metronidazole is a potent antibiotic often prescribed to treat gastrointestinal enteropathies; however, it is known to induce loose stools, negatively alter the fecal microbiome, and affect fecal metabolite production. Dietary intervention may aid in post-antibiotic recovery; however, little research has been conducted on the potential of fiber utilization for microbial recovery in canines.

METHODS: Using an in vitro fermentation assay, the objective of this study is to investigate the fermentation characteristics of dietary fibers using fecal inocula from dogs treated with metronidazole. Four healthy male beagles (age = 1.62 ± 0.02 year) were fed a commercial canned diet for 2 weeks, then administered metronidazole (20 mg/kg BW BID) for 2 weeks. Fresh fecal samples were collected at weeks 2 (before antibiotic treatment; ABX-) and 4 (after antibiotic treatment; ABX+), stabilized in a 20% glycerol solution, and then frozen. On the day of in vitro fermentation, feces from each time point were thawed and used to inoculate the tubes. At baseline and after 6, 12, and 18 h of fermentation, pH, short-chain fatty acids (SCFA), and microbiota were measured. Blank-corrected changes from the baseline data were analyzed using repeated measures and the MIXED procedure in SAS 9.4, with significance set at a p value <0.05.

RESULTS: Pectin fermentation reduced (p < 0.001) pH and increased (p < 0.001) SCFA over time, but the responses were lower (p < 0.001) in ABX+ than in ABX-. Beet pulp fermentation also reduced (p < 0.001) pH and increased (p < 0.001) SCFA over time. The pH change was small between inoculum sources, but SCFA were different (p < 0.001) between ABX+ and ABX-. Chicory pulp fermentation reduced (p < 0.001) pH over time, with greater (p < 0.01) reductions in ABX+ than in ABX-. Chicory pulp fermentation increased SCFA but had different patterns depending on the inoculum source. Metronidazole altered microbiota populations by reducing bacterial alpha diversity (p < 0.001). Analysis of bacterial beta diversity revealed separate clusters in dogs based on metronidazole administration. Beta diversity analysis also showed that tubes containing chicory pulp clustered separately from those containing other fibers. The relative abundance of over 50 bacterial genera differed (p < 0.05) among the inoculum sources.

DISCUSSION: In summary, interesting fermentation patterns were observed in response to varying fiber sources, allowing for improved insights into their potential abilities in antibiotic-treated dogs.},
}

@article {pmid41234306,
year = {2025},
author = {Xie, Z and Qin, Y and Xie, X and Li, J and Zheng, L and Jiang, Y and Tu, X and Liu, A and Zhou, Z},
title = {Straw mulching-driven microbial relay enhances soil C-N coupling and cotton yield-quality synergy.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1671192},
pmid = {41234306},
issn = {1664-462X},
abstract = {INTRODUCTION: Straw return is a widely endorsed sustainable agronomic practice. However, a systematic understanding of its carbon-nitrogen coupling mechanisms and their consequent impacts on the soil-microbe-plant continuum across the entire cotton growth cycle is critically lacking.

METHODS: We conducted a field experiment with five treatments: CK (no straw return), T1 (one-third shredded straw), T2 (two-thirds shredded straw), T3 (full shredded straw), and T4 (full straw left intact as surface mulch). This design enabled us to decipher how the amount and fragmentation of straw residues synchronize the soil-microbe-plant system to enhance sustainability.

RESULTS: Our findings reveal distinct mechanistic pathways. The T3 treatment (full shredding) triggered an early-season microbial "relay," where Gammaproteobacteria expansion was succeeded by Actinobacteria, elevating soil pH from 4.82 to 5.73 and boosting alkaline-hydrolysable N by 113.01% at the flower and boll stage. This enhanced nitrate reductase activity by 74.1% and increased bolls per plant by 35.0%. In contrast, the T4 treatment (surface mulch) provided a more gradual nitrogen release (+28.4% alkaline-hydrolysable N during boll opening), which prolonged the secondary cell wall deposition phase in fibers. This strategy achieved a lint yield of 2055.63 kg ha⁻¹ (+63.8%) and a 2.6% increase in fiber strength. Furthermore, T4 fostered a "microbial sanctuary" at boll opening, evidenced by a 130.5% explosion in OTU richness and an 18.7% suppression of pathogen populations.

DISCUSSION: We demonstrate that surface mulching (T4) is the superior strategy, as it optimally balances high yield with superior fiber quality by creating a resilient and suppressive soil microbiome. This work provides a novel carbon-nitrogen synergy framework for the resource-efficient utilization of crop residues in sustainable cotton production.},
}

@article {pmid41233937,
year = {2025},
author = {Zhang, P and Roque, B and Romero, P and Shapiro, N and Eloe-Fadrosh, E and Kebreab, E and Diamond, S and Hess, M},
title = {Red seaweed supplementation suppresses methanogenesis in the rumen, revealing potentially advantageous traits among hydrogenotrophic bacteria.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {231},
pmid = {41233937},
issn = {2049-2618},
mesh = {Animals ; *Rumen/microbiology/metabolism ; *Methane/metabolism/biosynthesis ; Cattle ; *Seaweed ; *Dietary Supplements ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Animal Feed/analysis ; *Gastrointestinal Microbiome ; Fermentation ; Metagenome ; Metagenomics ; Hydrogen/metabolism ; },
abstract = {BACKGROUND: Macroalgae belonging to the genus Asparagopsis have shown to reduce methane (CH4) production during rumen fermentation, while increasing feed efficiency when added to the feed of cattle. However, little is known about how the rumen microbiome responds to Asparagopsis supplementation, and how changes in the microbiome may contribute to changes in rumen function and host phenotype. Here, we generated and analyzed metagenomic and metatranscriptomic data from the rumen microbiome from cows receiving (treatment) and not receiving (control) an Asparagopsis armata supplemented diet.

RESULTS: Using a combination of metatranscriptome and metagenome analysis, we found that reduction of CH4 emission from animals receiving A. armata was coupled to a significant reduction in the transcription of methanogenesis pathways. Additionally, a significant decrease in the transcription of genes for carbon catabolism and a reorganization of carbon catabolic gene expression occurred at the species level within the rumen microbiome of animals that received red seaweed with their diet. Increased H2 production, a consequence of methanogenesis suppression, was coupled to a significant increase in the transcription of hydrogenases that mediate hydrogenotrophic metabolism in the treatment group. Metatranscriptome analysis identified a single metagenome assembled genome (MAG) of a Duodenibacillus sp., a hitherto uncultured hydrogenotrophic bacterial species, as the dominant driver of this transcriptional change.

CONCLUSIONS: Comparative genomic analysis between the Duodenibacillus sp. and other hydrogenotrophic rumen organisms revealed metabolic traits that may provide Duodenibacillus sp. with a competitive advantage in H2 scavenging. Our findings provide an initial understanding of how the rumen microbiome responds to a promising CH4 reducing feed additive and serve as a model for alternative stable rumen microbiome states that produce less methane and increase animal productivity. Ultimately, insights from the work presented here might enable the development of advanced microbiome-based strategies to reduce enteric methane production.},
}

Animals
*Rumen/microbiology/metabolism
*Methane/metabolism/biosynthesis
Cattle
*Seaweed
*Dietary Supplements
*Bacteria/genetics/metabolism/classification/isolation & purification
Animal Feed/analysis
*Gastrointestinal Microbiome
Fermentation
Metagenome
Metagenomics
Hydrogen/metabolism

@article {pmid41233921,
year = {2025},
author = {Naga, NG and Taha, RM and Hamed, EA and Nawar, EA and Jaheen, HO and Mobarak, AA and Radwan, YM and Faramawy, AG and Arayes, MA},
title = {The silent microbial shift: climate change amplifies pathogen evolution, microbiome dysbiosis, and antimicrobial resistance.},
journal = {Tropical diseases, travel medicine and vaccines},
volume = {11},
number = {1},
pages = {43},
pmid = {41233921},
issn = {2055-0936},
}

@article {pmid41233836,
year = {2025},
author = {Zhao, H and Tao, L and Tang, C and Cai, W and Shen, W},
title = {Do immune system and microbiome-gut-brain axis interactions associate with major depressive disorder?.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {1279},
pmid = {41233836},
issn = {1479-5876},
support = {Grant No. 2024QN087//Shanghai Municipal Health Commission/ ; },
mesh = {Humans ; *Depressive Disorder, Major/immunology/microbiology/pathology ; *Gastrointestinal Microbiome ; *Brain/pathology/immunology ; *Immune System/pathology ; Animals ; *Brain-Gut Axis ; Blood-Brain Barrier ; },
abstract = {Major depressive disorder (MDD) is a leading psychiatric disorder with increasing global prevalence, yet its underlying pathogenesis remains inadequately elucidated. Increasing evidence highlights the complex interplay between the immune system, gut microbiota, and their bidirectional crosstalk with the central nervous system. Gut microbiota dysbiosis affects neuroimmune and intestinal immune homeostasis, driving bidirectional peripheral-central immune responses through immune-to-brain and gut-to-brain communication. This process involves impaired intestinal barrier integrity (bacterial translocation), systemic low-grade inflammation, activation of innate immune signaling pathways (e.g., TLR4 and NLRP3 inflammasomes), glial cell activation, neuroinflammation, and blood-brain barrier (BBB) dysfunction, ultimately leading to neuronal injury and disturbances in mood, cognition, and behavior. Conversely, gut microbiota and their metabolites exert neuroprotective effects through facilitating neurotransmitter synthesis, regulating the hypothalamic-pituitary-adrenal axis activity, and modulating immune response. Collectively, these actions enhance synaptic plasticity, suppress hippocampal neuronal apoptosis, and maintain BBB integrity. Understanding these immune-mediated multidimensional mechanisms not only deepens our understanding of the pathophysiology of MDD but also provides new perspectives for identifying potential biomarkers and developing therapeutic targets.},
}

Humans
*Depressive Disorder, Major/immunology/microbiology/pathology
*Gastrointestinal Microbiome
*Brain/pathology/immunology
*Immune System/pathology
Animals
*Brain-Gut Axis
Blood-Brain Barrier

@article {pmid41233829,
year = {2025},
author = {Sieders, M and Candry, P and El Aidy, S},
title = {Hydrogel-based experimental models of the gastrointestinal tract.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {233},
pmid = {41233829},
issn = {2049-2618},
mesh = {*Hydrogels/chemistry ; Humans ; *Gastrointestinal Microbiome/physiology ; *Gastrointestinal Tract/microbiology ; *Models, Biological ; Animals ; Coculture Techniques ; },
abstract = {The gut microbiome plays a pivotal role in human health, yet its complexity has long eluded detailed study under physiologically relevant conditions. Hydrogel-based models are revolutionizing microbiome research by bridging the gap between traditional in vitro systems and the complexity of in vivo environments. These advanced systems replicate key physical and biochemical features of the gastrointestinal tract, offering unprecedented opportunities to study microbial behavior, adaptation, and interactions within three-dimensional, tunable architectures. Unlike suspension cultures, hydrogels provide porous, mucosa-like environments that enable the cultivation of mucosa-associated microbes, co-culturing with human cells, and mimicking healthy and disease-related states. This review explores the transformative potential of hydrogel matrices in unveiling the spatial organization, nutrient gradients, and community communication that define microbial ecosystems. By integrating the benefits of in vitro and in vivo models, hydrogel-based platforms promise to accelerate discoveries in microbiome science, with far-reaching implications for understanding human health and developing targeted therapeutics. Video Abstract.},
}

*Hydrogels/chemistry
Humans
*Gastrointestinal Microbiome/physiology
*Gastrointestinal Tract/microbiology
*Models, Biological
Animals
Coculture Techniques

@article {pmid41233799,
year = {2025},
author = {Orschanski, D and Rubén Dandeu, LN and Rivero, MN and Labovsky, V and Fernández, EA},
title = {Dermatological implications of alignment-based de-hosting and bioinformatics pipelines on shotgun microbiome analysis.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {1276},
pmid = {41233799},
issn = {1479-5876},
mesh = {*Microbiota/genetics ; Humans ; *Computational Biology/methods ; *Skin/microbiology ; Metagenomics ; *Dermatology/methods ; },
abstract = {BACKGROUND: The skin microbiome is a critical component of dermatological health, with its dysbiosis implicated in conditions ranging from atopic dermatitis to cancer. Shotgun metagenomics offers an unparalleled resolution for comprehensive taxonomic and functional profiling, yet its application in dermatology is hampered by the high proportion of host DNA and the lack of consensus on best-practice bioinformatic pipelines. While Illumina's proprietary DRAGEN platform is widely used, its closed-source nature and cost limitations necessitate the validation of robust, open-source alternatives to democratize access and enable customization.

METHODS: This study evaluates the performance of Kraken-based open-source pipeline as a viable alternative to the DRAGEN platform as well as the effect of currently available alignment-based de-hosting methods-Bowtie2, BWA, and Rsubread-to remove human DNA, assuring the use of highly-curated human reference genome thus avoiding the limitations of potentially incomplete or contaminated k-mer-based databases. By using shotgun metagenomic data from 83 healthy individuals we systematically compared the impact of these de-hosting procedures prior to Kraken2/DRAGEN taxonomic classification and functional profiling using HUMAnN 3.0 to assess the influence of methodological choices on skin microbial community composition and metabolic pathway abundance interpretation.

RESULTS: Our analysis revealed marked discrepancies arising from the choice of de-hosting tool and taxonomic classifier, leading to substantial variability in microbial and functional profiles that could compromise clinical interpretation. Among the pipelines tested, Bowtie2 de-hosting combined with Kraken2 taxonomic classification and HUMAN functional profiling efficiently recovered well-established sex- and age-related bacterial associations in healthy skin that were missed by all other methods, including DRAGEN. This superior performance, together with its customizable features, underscores the value of this workflow for robust and clinically relevant dermatological metagenomic studies.

CONCLUSIONS: Our findings underscore the decisive impact of bioinformatic pipeline selection on skin microbiome analysis and offer actionable guidance for reproducible and clinically meaningful research. We present a customizable workflow that enhances reproducibility and transparency while improving the translational value of metagenomic data. This approach strengthens the reliability of microbiome studies and supports the development of precision diagnostics and personalized therapeutic strategies in dermatology.},
}

*Microbiota/genetics
Humans
*Computational Biology/methods
*Skin/microbiology
Metagenomics
*Dermatology/methods

@article {pmid41233756,
year = {2025},
author = {Puhlmann, ML and Wegh, CAM and van der Zalm, SCC and Dam, V and Doolan, A and Meyer, D and Belzer, C and Vaughan, EE and Benninga, MA and Smidt, H},
title = {Inulin-induced improvements on bowel habit and gut microbiota in adults with functional constipation: findings of a randomized, double-blind, placebo-controlled study.},
journal = {BMC gastroenterology},
volume = {25},
number = {1},
pages = {806},
pmid = {41233756},
issn = {1471-230X},
mesh = {Humans ; *Inulin/therapeutic use/administration & dosage ; *Constipation/microbiology/drug therapy/physiopathology ; *Gastrointestinal Microbiome/drug effects ; Double-Blind Method ; Male ; Female ; Adult ; Middle Aged ; Quality of Life ; *Prebiotics/administration & dosage ; Feces/microbiology ; Cross-Over Studies ; *Defecation/drug effects ; },
abstract = {BACKGROUND: Functional constipation is a common disorder of the gut-brain interaction characterized by infrequent bowel movements and hard stools, which substantially affects patients' quality of life. Supplementation with gut microbiome-targeted prebiotics is a promising non-pharmacological alternative to current treatments.

METHODS: In a randomized, double-blind, placebo-controlled, cross-over trial, we investigated the effect of four-week daily 12 g chicory inulin intake in 39 individuals, with functional constipation according to Rome III criteria. We assessed stool frequency and consistency, constipation-related quality of life (PAC-QOL) and symptoms (PAC-SYM), and microbiota composition through 16S rRNA gene sequencing of fecal samples.

RESULTS: After inulin intake, we observed larger changes in stool frequency, abdominal symptoms, and particularly social and emotional well-being related to quality of life, compared to placebo. Additionally, relative abundances of putative butyrate-producing Anaerostipes spp. and Coprococcus 1 spp. were higher. Further investigation, however, pointed to a carry-over whereby half of the participants receiving inulin in the first period had the largest improvements in all outcomes during inulin intake. Moreover, these same participants had higher baseline relative abundances of butyrate-producing Faecalibacterium spp. and Roseburia spp., and lower baseline relative abundances of Bifidobacterium spp. In turn, these participants' microbiota responded more strongly to inulin intake through a stronger increase in the relative abundance of Bifidobacterium spp. and Anaerostipes spp. To address this apparent carry-over induced bias, we analyzed the first period alone as a parallel trial which supported the observed positive effect of inulin, also affirming its established bifidogenic effect.

CONCLUSIONS: Daily intake of 12 g inulin improves functional constipation by increasing stool frequency, positively affecting abdominal symptoms and well-being, and modulating the gut microbiota towards higher relative abundances of butyrate-producing genera.

TRIAL REGISTRATION: Ethical approval was obtained from the Cork Research Ethics Committee of the Cork Teaching Hospitals (Reference ECM 4 (v) 01/09/15), and the trial design was retrospectively registered at ClinicalTrials.gov (NCT05447481; 07/2022).},
}

Humans
*Inulin/therapeutic use/administration & dosage
*Constipation/microbiology/drug therapy/physiopathology
*Gastrointestinal Microbiome/drug effects
Double-Blind Method
Male
Female
Adult
Middle Aged
Quality of Life
*Prebiotics/administration & dosage
Feces/microbiology
Cross-Over Studies
*Defecation/drug effects

@article {pmid41233407,
year = {2025},
author = {Marchesini, VA and Town, J and Tenuta, M and Pereira, FG and Shaw, L and Sharpe, S and Schoenau, J and Hubbard, M},
title = {Spiral nematodes, soil microbiome and micronutrients increase chickpea drought susceptibility but do not induce symptoms of the emerging health issue.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {39823},
pmid = {41233407},
issn = {2045-2322},
mesh = {*Cicer/parasitology/growth & development/microbiology/physiology ; *Droughts ; Animals ; *Microbiota ; *Soil/chemistry/parasitology ; *Soil Microbiology ; *Plant Diseases/parasitology ; *Micronutrients/metabolism/analysis ; Saskatchewan ; *Nematoda ; },
abstract = {In 2019, an emerging health issue was noted in chickpea in Saskatchewan, Canada. Symptoms included apical wilting, branch chlorosis and necrosis. The causes remain unclear. In 2023 these symptoms appeared on one side ("unhealthy", UH), but not the other ("healthy", H), of a dry field in Redvers, Saskatchewan. To test the hypothesis that Helicotylenchus, or spiral nematodes, and differences in soil microbiome and nutrients, in combination with drought, contribute to these symptoms, chickpea were grown in H and UH soil, and well-watered, or exposed to drought. Plant height, number of nodes and pods, chlorophyll fluorescence (Fv/Fm), biomass, foliar and root-rot symptoms, soil nutrients, nematodes and soil microbiome were assessed. Symptoms more consistent with drought than the emerging health issue developed. When chickpea was exposed to drought, symptoms were more severe in UH soil. Height and Fv/Fm were lower in UH soils. Foliar symptoms were more severe and spiral nematodes more abundant in UH soils. All parameters were affected by drought. Concentrations of K[+] and Mg[+] were higher in H soil; Ca[+] concentration was higher in UH soil. Microbiome community composition, including bacteria, fungi and oomycetes, differed between H and UH soils, however, no pathogens that could be responsible for symptoms were more abundant in UH soils. Nematodes and other soil factors increase the impacts of drought but are not sufficient to induce the emerging chickpea health issue in pots. In the field, the root growth restrictions due to nematode feeding may lead to chickpea emerging health symptoms.},
}

*Cicer/parasitology/growth & development/microbiology/physiology
*Droughts
Animals
*Microbiota
*Soil/chemistry/parasitology
*Soil Microbiology
*Plant Diseases/parasitology
*Micronutrients/metabolism/analysis
Saskatchewan
*Nematoda

@article {pmid41233278,
year = {2025},
author = {Tanabe, N and Matsumoto, H and Morimoto, C and Hayashi, Y and Sunadome, H and Sato, A and Sato, S and Hirai, T},
title = {Sputum symptoms and microbiome in type 2 airway diseases with mucus plugs on computed tomography.},
journal = {Allergology international : official journal of the Japanese Society of Allergology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.alit.2025.10.002},
pmid = {41233278},
issn = {1440-1592},
}

@article {pmid41233211,
year = {2025},
author = {Martin, P and Wong, JKF and McGrouther, G},
title = {Unresolved challenges in wound healing: When science meets clinical need.},
journal = {Journal of plastic, reconstructive & aesthetic surgery : JPRAS},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bjps.2025.10.039},
pmid = {41233211},
issn = {1878-0539},
abstract = {Tissue damage is a natural consequence of mankind's interactions with the physical environment and leads to activation of endogenous repair mechanisms. Wound treatments developed over centuries, although largely empirical, have been incorporated into routine clinical practice while awaiting evidence of their efficacy. Based on a revisited and updated discussion from a 2013 Gordon Research Conference between basic scientists and clinicians, we outlined current knowledge of wound repair, emphasising the unique roles of diverse cell types including neutrophils, macrophages, keratinocytes, fibroblasts, and other previously overlooked lineages such as adipocytes and melanocytes. Five key clinical challenges remain unsolved: hypertrophic and keloid scarring, burns, wound infections, and chronic wounds. For each challenge, we reviewed recent basic science insights that offer potential therapeutic avenues, such as the role of inflammatory signals and mechanical cues in scarring, neutrophil dysfunction in burns, influence of the wound microbiome on infection, and epigenetic changes in chronic wounds. Although significant progress has been made, these topics remain problematic. We concluded by highlighting emerging research areas, including the overlooked roles of the nerves, fascia and fat tissue, and lessons from cancer biology, which may provide further opportunities to develop innovative strategies for wound care. By fostering greater collaboration and targeting a deeper understanding of mechanisms with unique models, the pathway to accelerate the translation of new therapies to improve patient outcomes is hopeful.},
}

@article {pmid41232906,
year = {2025},
author = {Kumar, S and Matra, S and Rajput, V and Ghode, H and Rathore, D and Kumar, S and Kamble, S and Dastager, S and Bajaj, A and Qureshi, A and Kapley, A and Dharne, M},
title = {Deciphering the antimicrobial resistomes and microbiome landscape of open drain wastewater using metagenomics in a progressive Indian state.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123287},
doi = {10.1016/j.envres.2025.123287},
pmid = {41232906},
issn = {1096-0953},
abstract = {Antimicrobial resistance (AMR) is a growing environmental and public health concern, with wastewater systems are acting as a critical reservoirs for resistant microorganisms and genes. Open drains in densely populated and industrialized regions can accelerate AMR dissemination into the environment. Despite Maharashtra's high urban density and industrial activity, comprehensive metagenomic surveillance of its wastewater resistome is lacking. This study applied high-throughput nanopore sequencing to 138 wastewater samples collected from 23 open-drain sites across three regions of Maharashtra (Western, Mumbai, and Central). Bioinformatic pipelines were used to characterize microbial communities, resistance genes, mobile genetic elements (MGEs), and resistome risk scores. Microbial composition varied significantly across regions, with Mumbai and Central regions explaining up to 13% of variance at the family level. Thirty indicator taxa were identified through LEfSe analysis. Resistome profiling revealed 28 drug classes and 808 ARGs, dominated by multidrug (40.49%), macrolide-lincosamide-streptogramin (15.84%), beta-lactam (7.95%), and tetracycline (6.52%). WHO-priority pathogens such as Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa harbored high-abundance ARGs including sul1, mdr(ABC), and acrB. Resistome risk scores were highest in Mumbai, indicating elevated ecological and human health risks. These findings underscore wastewater as a hotspot for AMR persistence and spread. Integrating wastewater-based surveillance within a One Health framework enables systematic tracking of resistance trends, comprehensive assessment of environmental risks, and evidence-driven regional interventions. This integrated approach supports the development of targeted mitigation strategies to curb the spread of antibiotic-resistant contaminants across ecosystems.},
}

@article {pmid41232654,
year = {2025},
author = {Angthong, P and Uengwetwanit, T and Arayamethakorn, S and Potibut, P and Phanthura, M and Rungrassamee, W and Chaiyapechara, S},
title = {A comparative analysis of the gut microbiome and immune gene expression in two Penaeus monodon populations.},
journal = {Developmental and comparative immunology},
volume = {172},
number = {},
pages = {105514},
doi = {10.1016/j.dci.2025.105514},
pmid = {41232654},
issn = {1879-0089},
abstract = {Maintaining intestinal homeostasis is important for shrimp health in aquaculture, particularly under the constant exposure to environmental and biological stressors. While much research has focused on disease-related dysbiosis, the fundamental mechanisms of homeostasis under normal conditions remain largely uncharacterized. To address this gap, postlarval black tiger shrimp (Penaeus monodon) from two distinct genetic lineages, domestic and imported broodstock, were reared in a shared aquaculture environment for three months to observe baseline interaction between intestinal microbiota and immune responses. Intestinal microbiota was examined using 16S rRNA gene (V3-V4) sequencing, and transcriptomic profiles of the intestines were analyzed using RNA sequencing. Average final weight was not significantly different (p = 0.66) between two sources. Microbiota from the intestines of shrimp from different sources showed significant differences at all sampling periods throughout the feeding trial (p < 0.05), based on PERMANOVA results. Vibrio, Colwellia, Pseudoalteromonas, Shewanella, and Tenacibaculum were the dominant bacterial genera in the intestines of shrimp from both groups. Several discriminant genera between the two groups were also identified, including Pseudoalteromonas, Mesoflavibacter, Maribacter, Spongiimonas, Desulfobulbus, and uncultured JGI o_JGI 0000069-P22 (Patescibacteria group). Transcriptomic analysis revealed that while both groups expressed immune-related genes across broad functional categories like pattern recognition proteins (PRPs), proteinase and protease inhibitors (PPIs), and antimicrobial peptides (AMPs), they appeared to employ different sets of individual genes or isoforms within these functional groups. These findings suggest that shrimp's immune systems during normal conditions can utilize different pathways within the same functional categories to control the intestinal microbiome. The pathways preference could be due to their genetic background and baseline microbiota. A better understanding of the unstressed host-microbiota interaction could help guide the microbiome management strategies to maintain gut homeostasis for sustainable disease control in shrimp aquaculture.},
}

@article {pmid41232540,
year = {2025},
author = {Wieringa, JW and Binyamin, D and Jankelowitz, IA and Schweitzer, R and Turjeman, S and Khatib, S and Esser, MJ and van der Woude, CJ and Fuhler, GM and Koren, O},
title = {Intestinal barrier alterations in mice following fecal microbiota transplant from children of IBD-affected mothers.},
journal = {Med (New York, N.Y.)},
volume = {},
number = {},
pages = {100915},
doi = {10.1016/j.medj.2025.100915},
pmid = {41232540},
issn = {2666-6340},
abstract = {BACKGROUND: Inflammatory bowel disease (IBD) carries a hereditary risk, which is higher through maternal, rather than paternal, inheritance. Like their mothers, children born to mothers with IBD have an altered microbiome shortly after birth.

METHODS: To investigate whether this altered microbiome persists later in life and affects the intestinal mucosa, the fecal microbiome was analyzed in samples from 44 infants ranging from 0 to 10 years of age born to 26 women with IBD. Forty-four age-matched children of 29 women without IBD served as controls. Fecal microbiota transplantation (FMT) to germ-free mice was carried out from 4-year-olds born to mothers with IBD and controls. Markers of inflammation, barrier function, and metabolic changes were investigated.

FINDINGS: Intestinal microbiomes were more similar between women with IBD and their children than between control mothers and their offspring. Microbial changes were noticeable in children from mothers with IBD from the age of 4 years compared to children of controls. No inflammatory response was present in the mucosa of mice receiving FMT from children of mothers with IBD; however, mesenteric lymph node enlargement and decreased expression of barrier genes Zo1 and Ocln were seen in mice receiving FMT from these children compared to controls. Additionally, reduced colonic expression of the immunological tolerance enzyme Ido1 coincided with decreased serum kynurenine/tryptophan ratios.

CONCLUSIONS: Fecal microbiomes of children of mothers with IBD exhibit characteristics that reduce epithelial tight junction barrier genes and tolerogenic tryptophan metabolism. Microbiome-induced gut barrier disruptions may contribute to an enhanced IBD predisposition in infants of mothers with IBD.

FUNDING: This work was funded by ZonMw.},
}

@article {pmid41232537,
year = {2025},
author = {Hu, B and Liu, R and Ramm, E and Tong, P and Dannenmann, M and Chen, Z and Zou, T and Shi, X and Chen, X and Haensch, R and Schloter, M and Rennenberg, H},
title = {Impaired sustainability of thawing permafrost peatland ecosystems by Siberian alder colonization.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.10.021},
pmid = {41232537},
issn = {1879-0445},
abstract = {Anthropogenic climate warming causes thawing of permafrost soil in pan-Arctic areas of the Northern Hemisphere, thereby triggering changes in ecosystem biodiversity and biogeochemistry. Here, we analyzed the consequences of Siberian alder colonization for the thawing of permafrost soil, soil microbial biodiversity, and the performance of neighboring peatland vegetation. We show, for the first time, that heat dissipation from biological nitrogen fixation (BNF) by alder-Frankia symbiosis in numerous nodule clusters accelerates the thawing of permafrost soil in alder forests. On an areal basis, a rough estimate of heat dissipation from BNF amounts to 4,330-34,630 MJ year[-1] per hectare. The maximum value of this estimate is of the same order of magnitude as the reported areal heat dissipation from microbial organic matter decomposition and accounts for ∼7.6% of the heat dissipation from this decomposition. Colonization by Siberian alder trees strongly modified microbial biodiversity in the top peat and organic soil layers and had nursing effects on dominant peatland plant species neighboring alder forests, as indicated by carbon and nitrogen stable isotope signatures. These results reveal the mechanism of permafrost soil thawing attributed to BNF-mediated heat dissipation by Siberian alder forests at both the site-specific and ecosystem levels. They complement present knowledge on microbial-decomposition-driven soil heating and carbon release in permafrost regions under global warming. In addition, they show that colonization by Siberian alder has significant feedback on climate-change-mediated thawing of permafrost soil, thereby impairing the sustainability of pan-Arctic peatland ecosystems.},
}

@article {pmid41232519,
year = {2025},
author = {Sempeck, CD and Olm, MR},
title = {Mapping the oral microbiome opens links to periodontitis.},
journal = {Cell host & microbe},
volume = {33},
number = {11},
pages = {1832-1833},
doi = {10.1016/j.chom.2025.10.009},
pmid = {41232519},
issn = {1934-6069},
mesh = {Humans ; *Periodontitis/microbiology ; *Microbiota ; *Mouth/microbiology ; *Bacteria/genetics/classification/isolation & purification ; Genome, Bacterial ; },
abstract = {Many microbiome analysis techniques can only detect the microbes present in the reference genome database used. In this issue of Cell Host & Microbe, Cha et al. establish an improved genome database of the human oral microbiome, which they use to discover a connection between periodontitis and an enigmatic bacterial phylum.},
}

Humans
*Periodontitis/microbiology
*Microbiota
*Mouth/microbiology
*Bacteria/genetics/classification/isolation & purification
Genome, Bacterial

@article {pmid41232506,
year = {2025},
author = {Leng, T and de la Fuente-Nunez, C},
title = {The gut's hidden arsenal: A genomics-guided atlas of class II bacteriocins.},
journal = {Cell genomics},
volume = {5},
number = {11},
pages = {101064},
doi = {10.1016/j.xgen.2025.101064},
pmid = {41232506},
issn = {2666-979X},
mesh = {*Bacteriocins/genetics/pharmacology ; Humans ; *Genomics/methods ; *Gastrointestinal Microbiome/genetics/drug effects ; Genome, Bacterial ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Unmodified class II bacteriocins promise precision antimicrobials that spare bystander microbes. Zhang and colleagues introduce IIBacFinder, a genomics-guided pipeline that detects precursor and context genes with a curated pHMM library, infers leader-peptide cleavage, and triages candidates by meta-omics signals. The authors apply it across bacterial genomes, including an atlas of ∼280,000 human-gut genomes, and recover a vast reservoir of narrow-spectrum peptides and prioritize gut-resident candidates for synthesis. Of the 26 synthesized, 16 display activity in vitro, largely via membrane perturbation and with additive effects alongside vancomycin, while ex vivo assays show minimal compositional disruption of fecal communities compared with antibiotic controls. These results position unmodified class II bacteriocins as tractable, microbiome-sparing agents and illustrate how genome-scale mining coupled to meta-omics can bridge sequence to function in complex ecosystems.},
}

*Bacteriocins/genetics/pharmacology
Humans
*Genomics/methods
*Gastrointestinal Microbiome/genetics/drug effects
Genome, Bacterial
Anti-Bacterial Agents/pharmacology

@article {pmid41232381,
year = {2025},
author = {Ozgun Acar, O},
title = {Probiotic modulation of energy metabolism ameliorates experimental autoimmune encephalomyelitis via Nrf2-associated pentose phosphate pathway activation.},
journal = {Biochemical and biophysical research communications},
volume = {791},
number = {},
pages = {152934},
doi = {10.1016/j.bbrc.2025.152934},
pmid = {41232381},
issn = {1090-2104},
abstract = {Alterations in the gut microbiome not only impact immune processes associated with the pathogenesis of multiple sclerosis (MS) but also affect the regulation of metabolic pathways. In MS and experimental autoimmune encephalomyelitis (EAE) models, probiotics are thought to contribute not only to immunomodulatory effects but also to the reprogramming of energy metabolism. In light of these findings, this study assessed the efficacy of the probiotic Lactobacillus acidophilus LA-5 (LA-5) in disorders of pentose phosphate pathway (PPP) energy metabolism during disease processes. LA-5 supplementation markedly improved disease severity in the EAE model, as reflected by reduced clinical scores and increased expression and activity of key pentose phosphate pathway enzymes, including glucose-6-phosphate dehydrogenase (G6PDH) and 6-phosphogluconate dehydrogenase (6-PGD). The treatment also restored diminished transaldolase (TALDO) expression and normalized the NADPH levels in the brain tissue. Moreover, LA-5 reactivated the Nrf2 pathway, which was suppressed under EAE conditions, indicating increased antioxidant capacity. In conclusion, the present findings establish a direct connection between PPP dysfunction and MS pathology, indicating the therapeutic potential of metabolic modulation. This study provides new insights that could inform future strategies for the treatment of MS.},
}

@article {pmid41232361,
year = {2025},
author = {Bishoyi, AK and Al-Hasnaawei, S and Salem, KH and Ganesan, S and Shankhyan, A and Nanda, A and Sinha, A and Ray, S and Nathiya, D and Hammady, FJ},
title = {Gut microbiome metabolites in lung cancer: The emerging importance of short-chain fatty acids.},
journal = {International immunopharmacology},
volume = {168},
number = {Pt 1},
pages = {115821},
doi = {10.1016/j.intimp.2025.115821},
pmid = {41232361},
issn = {1878-1705},
abstract = {Short-chain fatty acids (SCFAs), which are produced from the fermentation by the gut microbiota of dietary fiber, are now proven to play a vital role in the growth control of lung cancer and drug response. SCFAs have mechanisms of action, including the inhibition of histone deacetylases, activation of G-protein-coupled receptors, and metabolic reprogramming. SCFAs suppress tumor growth, induce apoptosis, suppress angiogenesis, and modulate epithelial-mesenchymal transition. Besides the above direct antitumor effects, SCFAs enhance the therapeutic effect of immune checkpoint inhibitors and reduce the toxicity of radiotherapy and chemotherapy by maintaining the mucosal barrier and restoring systemic immune homeostasis. Butyrate function is highly dualistic; it is usually protective but may confer multidrug resistance under certain therapeuticconditions. To reconcile these opposing effects is akey challenge in the translation of microbiota-based therapeutics and interventions. Therapies such as probiotics, fecal microbiota transplantation, and designed microbial consortia all target SCFAs as central mediators of microbiome-host communication. Overall, SCFAs are candidate metabolic co-adjuvants that can maximize therapeutic efficacy, suppress unacceptable side effects, and redirect therapeutic approaches to lung cancer.},
}

@article {pmid41232294,
year = {2025},
author = {Ateş, Ç and Dilbaz, B and Saçıntı, KG},
title = {Deciphering the relationship between adenomyosis and the microbiota: a systematic review.},
journal = {European journal of obstetrics, gynecology, and reproductive biology},
volume = {316},
number = {},
pages = {114823},
doi = {10.1016/j.ejogrb.2025.114823},
pmid = {41232294},
issn = {1872-7654},
abstract = {Adenomyosis is a benign displacement of endomerial tissue into the uterine myometrium, the exact pathogenesis of which has not yet been established. Recently, there has been increased research on the relationship between microbiota dysbiosis and adenomyosis; however, the details of this interaction are not yet clearly known. We have systematically reviewed all studies focusing on the relationship between microbiota and adenomyosis. The databases Pubmed, Scopus, GoogleScholar and Web of Science were queried up until June 2024. A total of 446 citations were obtained, resulting in the inclusion of a total of 7 papers, one of which was an animal experiment. There were 670 humans and 16 mice. There were 416 adenomyosis patients, 223 healthy controls, and 47 endometriosis-associated controls. 16S rRNA gene amplification and sequencing was used in 6 of 7 studies. Data was collected from the microbiomes of the endometrium, vagina, and gut. In adenomyosis, the abundance of Firmucites, Rhodospirillales, Ruminococcus gauvreauii, Citrobacter freundii, Prevotella copri, Burkholderia cepacia and the predominance of CST-III and CST-IV increase, while the abundance of Clostridiacea, Peptostreptococcaceae, Atopobiacea families and Fastidiosipila, Magasphaera sp. species decrease. This systematic review has revealed distinct bacterial species that are linked to adenomyosis, as well as the microbiome of the female genital tract and gut. Additional research is required to determine if these bacteria are the primary cause or a secondary result of adenomyosis.},
}

@article {pmid41232270,
year = {2025},
author = {Liu, B and Liu, C and Sunggip, C and Pu, G and Deng, D},
title = {Viruses in gastrointestinal cancers: Molecular pathogenesis, oncogenic mechanisms, and translational perspectives.},
journal = {Molecular aspects of medicine},
volume = {106},
number = {},
pages = {101415},
doi = {10.1016/j.mam.2025.101415},
pmid = {41232270},
issn = {1872-9452},
abstract = {Viral pathogens are one of the most significant causes of human carcinogenesis, contributing to up to 15-20 % of worldwide cancers. The gastrointestinal (GI) tract is one of the most vulnerable human organ system to virus-mediated tumorigenesis as a result of frequent exposure to viral infections and various immunological processes. The present review aims to describe the dual roles of viral infections in the development of gastrointestinal cancers (GICs), with a focus on Human Immunodeficiency Virus (HIV) and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). HIV represents an oncological challenge in the era of effective antiretroviral therapy (ART), where significant immune dysfunction, persistent inflammation, and gut microbiome disruption render infected patients more susceptible to various GICs. On the other hand, SARS-CoV-2 is an emerging viral pathogen whose potential role in oncogenesis remains controversial yet biologically plausible. In this context, SARS-CoV-2 tropism to the gastrointestinal tissues and its capacity to drive cytokine storms, profound dysbiosis, and immune exhaustion raise significant questions regarding its potential to act as a pro-tumorigenic factor. Discussing mechanistic insights from well-known oncogenic viral pathogens, the present review describes the direct and indirect mechanisms by which these two major viruses may affect GI tumorigenesis. Moreover, this review translates these mechanisms into clinical perspectives, underscoring implications for diagnostics, prevention, and therapeutic strategies, while highlighting urgent research priorities for long-term surveillance and biomarker discovery. It highlights the importance of continuous scientific awareness to address the increasing cancer risks presented by emerging and re-emerging viruses through bridging virology and oncology.},
}

@article {pmid41232242,
year = {2025},
author = {Y, K and Isukapatla, AR},
title = {Postmortem microbiome dynamics: Review of forensic microbial clock.},
journal = {Journal of forensic and legal medicine},
volume = {117},
number = {},
pages = {103024},
doi = {10.1016/j.jflm.2025.103024},
pmid = {41232242},
issn = {1878-7487},
abstract = {The postmortem interval (PMI) in Forensic science presents several challenges, including accurate investigation, estimation and reliance on a limited set of physical and microbial markers. However, while these methods have advantages, they are also limited by factors such as environmental variability and temporal constraints. Microbial succession during decomposition, commonly referred to as the "microbial clock", has emerged as a promising and potentially more precise indicator of PMI. It is clear from a thorough examination of more than 30 peer-reviewed studies involving human cadavers and animal models that microbial communities undergo predictable, time-dependent internal and external changes. Controlled studies using murine and porcine models have demonstrated strong temporal correlations between specific microbial taxa and distinct stages of decomposition, with some models capable of predicting PMI within a two-to-three-day accuracy range over several weeks. Similarly, studies on human cadavers have shown consistent patterns of microbial succession within postmortem organs, revealing organ-specific microbial signatures that change over time and can be influenced by variables such as the cause of death, the environment and the health of an individual. These findings suggest that microbial succession can serve as a powerful quantitative and biological tool for determining the time of death. However, to realize its full potential, further research is needed, using diverse datasets and incorporating multiple post-mortem indicators. This review provides a comprehensive summary of current knowledge on the microbial clock and discusses the ecological and practical considerations necessary to develop a robust and reliable post-mortem clock for forensic practice.},
}

@article {pmid41232227,
year = {2025},
author = {Sharma, V and Goel, S and Bisht, K and Kaura, T and Verma, S and Mewara, A and Grover, GS and Biswal, M},
title = {Unveiling the Presence of Coxiella-like bacteria in Rhipicephalus microplus Ticks from Punjab, North India: A 16S rRNA metagenomic study.},
journal = {Veterinary microbiology},
volume = {312},
number = {},
pages = {110783},
doi = {10.1016/j.vetmic.2025.110783},
pmid = {41232227},
issn = {1873-2542},
abstract = {In this study, using 16S rRNA gene-based metagenomics, we aimed to determine the presence of infectious bacteria in the ticks collected from Punjab state in north India. Tick samples were collected from the domesticated animals from the Patiala, Ropar, and Mohali districts of Punjab, India from February 2022- April 2022. DNA was extracted, and the library was prepared by targeting the V3-V4 hypervariable region of the 16S rRNA gene. The sequencing was conducted in Illumina using the 300 bp paired-end chemistry. Eight tick samples were analyzed from the Patiala, Ropar and Mohali districts of Punjab, India, revealing a diverse range of bacterial species within the tick microbiome. Seven out of eight samples were found to harbour Coxiella-like bacteria (46-181,607 reads; closely related to C. burnetii based on 16S rRNA [V3-V4] sequence similarity), indicating their abundance in the tick population. Furthermore, the analysis uncovered the presence of other pathogenic bacterial genera, including Staphylococcus, Streptococcus, Corynebacterium, Enterococcus, Pseudomonas, Bordetella, and Micrococcus in the tick microbiome, highlighting the abundance and diversity of infectious organisms within ticks. 16S rRNA gene-based metagenomics enables valuable insights into infectious agents in disease-transmitting vectors. Coxiella-like bacteria were found to be predominant bacterial species in the tick microbiomes in this study. The public health significance of this finding in animals and humans needs to be explored in this region. However, as 16S rRNA sequencing offers limited resolution for distinguishing closely related taxa, further confirmation using additional loci or whole-genome sequencing is warranted.},
}

@article {pmid41232211,
year = {2025},
author = {Bai, X and He, Y and Ge, Y and Gao, S and Li, A and Guo, T and Hu, H and Pan, H},
title = {Crosstalk between liver gene expression and enteric microbiome regulates laying performance and lipid metabolism in different breeds of layer hens during growing and pre-laying periods.},
journal = {Poultry science},
volume = {104},
number = {12},
pages = {106068},
doi = {10.1016/j.psj.2025.106068},
pmid = {41232211},
issn = {1525-3171},
abstract = {The present work was conducted to investigate the interaction between liver gene profile and enteric microbiome on regulation of laying performance and lipid metabolism in different breeds of layer hens during the growth and pre-laying periods. A total of 192 7-w-old laying hens (six replicates per breed, 16 hens per replicate), including 96 Jingfen-1 (JF-1) and 96 Jingfen-2 (JF-2) hens, were selected and fed the same feed under identical environments. The experiment lasted from 7 to 20 w-of-age. JF-1 initiated egg production at 16 w, whereas JF-2 started at 18 w. From 17 w, JF-1 exhibited higher egg production rates than JF-2 (P < 0.05). Compared with JF-2, egg weight, Haugh unit, egg shape index, albumen height, and yolk mass were higher in JF-1 eggs (P < 0.05). Hepatic triglyceride, cholesterol, fatty acid synthase, and acetyl-CoA carboxylase contents were higher, whereas lipoprotein lipase and total lipase levels were lower in JF-1 (P < 0.05). There were 363 downregulated and 385 upregulated genes in the liver of the JF-2. Kyoto Encyclopedia of Genes and Genomes analysis indicated that pathways enriched in the downregulated genes of JF-2 hens included fatty acid biosynthesis, elongation, and metabolism and peroxisome proliferator-activated receptor signaling. Lipid synthesis-related genes such as FASN, ACACA, ELOVL2, and ACSL5 were upregulated in JF-1 hens. The cecal Firmicutes abundance in JF-1 was higher, whereas the Bacteroidetes abundance was lower than that in JF-2 hens (P < 0.05). Firmicutes/Bacteroidetes ratio in the cecum of JF-1 hens was higher than in JF-2 hens (P < 0.05). Phocaeicola, Lactobacillus, Mediterraneibacter, and Phascolarctobacterium were more abundant (P < 0.05) in the cecum of JF-1 hens. Correlation analysis suggested that higher Firmicutes/Bacteroidetes ratio in the cecum might activate the liver gene expression associated with lipid synthesis, and then improved egg quality in JF-1 hens. Summary, the liver genes and intestinal flora coordinated to promote laying performance and egg quality by modulating physiological fat deposition in JF-1 during the growing and pre-lay periods.},
}

@article {pmid41232182,
year = {2025},
author = {Guo, P and Li, Z and Luo, J and Xu, X and Liu, H and Cao, Y and Wei, Y and Liu, Z and Qing, Y and Wu, Y},
title = {Synergistic Se/S functionalization of biochar for effective immobilization of multi-target heavy metals in water and soil.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140453},
doi = {10.1016/j.jhazmat.2025.140453},
pmid = {41232182},
issn = {1873-3336},
abstract = {Cadmium (Cd) and lead (Pb) contaminate aquatic environments and soil systems, threatening ecosystems and human health via bioaccumulation, while current remediation materials are often limited by insufficient adsorption capacity and restriction to a single medium. To address these challenges, a novel almond shell biochar co-functionalized with L-cysteine (L-Cys) and selenium (Se) was prepared (L-SeBC). This synergistic integration endows L-SeBC with abundant active sites for effective remediation. Adsorption thermodynamics demonstrated the maximum of 147.7 mg/g (Cd[2 +]) and 203.4 mg/g (Pb[2+]). Density functional theory (DFT) calculations indicated that the enhanced adsorption occurred via chemisorption-physisorption synergy. In soil remediation experiments (5 % w/wL-SeBC application), the available Cd and Pb decreased by 45.1 % and 52.1 %. The addition of L-SeBC promoted soybean growth in contaminated soil, and reduced Cd and Pb contents in leaves (by 55.6 % and 68.9 %) and roots (by 28.6 % and 29.0 %). Furthermore, L-SeBC increased the activities of plant enzymes and soil enzymes, enhancing nutrient cycling and stress resistance of plants. Microbial analysis revealed that L-SeBC reshaped the soil microbiome by enriching functional genera (e.g., Pseudomonas spp.). Overall, the waste-derived, multifunctional adsorbent L-SeBC is cost-effective and eco-friendly, enables multi-scenario remediation, and exhibits great practical potential in sustainable pollution control.},
}

@article {pmid41231980,
year = {2025},
author = {Gelsinger, DR and Ronda, C and Ma, J and Kar, OB and Edwards, M and Huang, Y and Mavros, CF and Sun, Y and Perdue, T and Vo, PL and Ivanov, II and Sternberg, SH and Wang, HH},
title = {Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases.},
journal = {Science (New York, N.Y.)},
volume = {390},
number = {6774},
pages = {eadx7604},
doi = {10.1126/science.adx7604},
pmid = {41231980},
issn = {1095-9203},
mesh = {Animals ; Mice ; *Gastrointestinal Microbiome/genetics ; *Gene Editing/methods ; *Bacteroides/genetics/growth & development ; Humans ; Metagenomics/methods ; *CRISPR-Cas Systems ; Symbiosis ; Mice, Inbred C57BL ; Metagenome ; Clustered Regularly Interspaced Short Palindromic Repeats ; },
abstract = {Although metagenomic sequencing has revealed a rich microbial biodiversity in the mammalian gut, methods to genetically alter specific species in the microbiome are highly limited. Here, we introduce Metagenomic Editing (MetaEdit) as a platform technology for microbiome engineering that uses optimized CRISPR-associated transposases delivered by a broadly conjugative vector to directly modify diverse native commensal bacteria from mice and humans with new pathways at single-nucleotide genomic resolution. Using MetaEdit, we achieved in vivo genetic capture of native murine Bacteroides by integrating a metabolic payload that enables tunable growth control in the mammalian gut with dietary inulin. We further show in vivo editing of segmented filamentous bacteria, an immunomodulatory small-intestinal microbial species recalcitrant to cultivation. Collectively, this work provides a paradigm to precisely manipulate individual bacteria in native communities across gigabases of their metagenomic repertoire.},
}

Animals
Mice
*Gastrointestinal Microbiome/genetics
*Gene Editing/methods
*Bacteroides/genetics/growth & development
Humans
Metagenomics/methods
*CRISPR-Cas Systems
Symbiosis
Mice, Inbred C57BL
Metagenome
Clustered Regularly Interspaced Short Palindromic Repeats

@article {pmid41231970,
year = {2025},
author = {Coelho, C and Taborda, A and Lorena, C and Frazão, T and Veríssimo, A and Borges, PT and Brissos, V and Tiago, I and Martins, LO},
title = {Shotgun metagenomic mining reveals a new FAD-dependent D-lactate dehydrogenase in an isopod gut microbiome.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0148025},
doi = {10.1128/aem.01480-25},
pmid = {41231970},
issn = {1098-5336},
abstract = {UNLABELLED: Shotgun metagenomic sequencing has emerged as a powerful tool for exploring microbial diversity and uncovering genes encoding novel biocatalysts from complex environments. Here, we report the discovery and characterization of a new FAD-dependent D-lactate dehydrogenase (PdG-D-LDH) from the gut microbiome of the isopod Porcellio dilatatus. The enzyme was identified through in silico screening using BLAST and AlphaFold3 and functionally characterized as a homodimeric, thermoactive, and thermostable protein, demonstrating the robustness required for biotechnological applications. PdG-D-LDH exhibits a strong catalytic preference toward D-lactate and preferentially reduces quinones over cytochrome c or molecular oxygen. X-ray crystallography revealed a VAO/PCMH-like fold with a solvent-accessible active site that harbors both a FAD cofactor and an Fe(II) ion. Molecular docking studies provided insights into the structural determinants of its stereoselective substrate recognition. Under mild conditions, the enzyme catalyzed the oxidation of D-lactate to pyruvate with a 90% yield after 24 h of reaction, using molecular oxygen as the electron acceptor.

IMPORTANCE: This study illustrates how metagenomics, structural biology, and computational tools can jointly drive the discovery of new enzymes with valuable biotechnological applications aligned with circular economic principles. The newly identified D-lactate dehydrogenase, PdG-D-LDH, exhibits thermostability, stereoselectivity, and high catalytic efficiency, providing new insights into the structure-function relationships of lactate-metabolizing enzymes.},
}

@article {pmid41231796,
year = {2025},
author = {Baral, T and Maile, A and Adimurthy, NH and Saravu, K and Kudru, CU and Singh, J and Mukhopadhyay, C and Rao, M and Manu, MK and Sekhar Miraj, S},
title = {Exploring gut microbiota and its predicted functions in pulmonary tuberculosis: A multi-regional study using public 16S datasets.},
journal = {PloS one},
volume = {20},
number = {11},
pages = {e0336337},
doi = {10.1371/journal.pone.0336337},
pmid = {41231796},
issn = {1932-6203},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics/drug effects ; *Tuberculosis, Pulmonary/microbiology/drug therapy ; Phylogeny ; *RNA, Ribosomal, 16S/genetics ; Antitubercular Agents/therapeutic use ; Male ; Female ; Mycobacterium tuberculosis/genetics ; Middle Aged ; Adult ; },
abstract = {BACKGROUND: Pulmonary tuberculosis, caused by the bacillus Mycobacterium tuberculosis, remains a major global health challenge, particularly in developing countries. In this study, we analyzed publicly available 16S amplicon sequencing datasets from four geographical locations using a single workflow.

METHODS: We employed Quantitative Insights Into Microbial Ecology v.2 for microbial diversity analysis and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States v.2 for functional pathway predictions of the gut microbiota in patients with PTB and antitubercular therapy.

RESULTS: Our analysis revealed statistically significant alpha diversity differences in West Africa with decreased microbial diversity in pulmonary tuberculosis patients after two months of antitubercular therapy. Additionally, there were no statistically significant differences observed in pairwise comparisons within the same location or in the aggregate beta diversity of the datasets. The predicted microbial metabolic pathways related to vitamin biosynthesis, amino acid synthesis, and energy production were depleted in pulmonary tuberculosis patients following antitubercular therapy.

CONCLUSIONS: The observed alterations of gut microbial diversity and predicted functional profile underscores the influence of antitubercular therapy on gut health, suggesting that longer treatment durations may aggravate these alterations in gut microbial function. Moreover, geographical location exerts a more significant impact on microbial diversity than the disease state in a specific location, highlighting the potential for precision medicine to tailor interventions based on individual or regional microbiome characteristics.},
}

Humans
*Gastrointestinal Microbiome/genetics/drug effects
*Tuberculosis, Pulmonary/microbiology/drug therapy
Phylogeny
*RNA, Ribosomal, 16S/genetics
Antitubercular Agents/therapeutic use
Male
Female
Mycobacterium tuberculosis/genetics
Middle Aged
Adult

@article {pmid41231731,
year = {2025},
author = {van Hout, NE and Nevot, G and Jansen, PAM and Mannan, AA and Zeeuwen, PLJM and Hijnen, DJ and Tanaka, RJ and Güell, M and van den Bogaard, EH},
title = {From prebiotics to engineered microbes: microbe-inspired therapies for atopic dermatitis.},
journal = {The British journal of dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1093/bjd/ljaf451},
pmid = {41231731},
issn = {1365-2133},
abstract = {Atopic dermatitis (AD) is a common chronic inflammatory skin disease with diverse clinical and histological features. While primarily immune-mediated, genetic studies have also highlighted the role of epithelium-expressed gene abnormalities (e.g., filaggrin mutations) as a key factor. The approaches to treat AD are multifaceted, involving barrier restoration, local anti-inflammatory treatment, and, if needed, systemic immunosuppressive therapy. Genetic variations in the stratum corneum and the immune system are linked to an unbalance between the host and its microbiota, known as dysbiosis. An impaired skin barrier and immune responses can alter the microbial composition, while the skin microbiota itself can influence skin immunity and barrier formation. A hallmark of AD is increased bacterial colonization with Staphylococcus aureus (S. aureus), which is found on lesional skin in over 90% of patients. It contributes to disease severity driving further breakdown of the skin barrier and immune stimulation. The most common treatment for S. aureus infections in AD is topical or systemic antibiotic administration. While these treatments are typically reserved for active infections, they are sometimes prescribed to AD patients without clear skin infection. However, these treatments can disrupt commensal skin and gut microbiota, which play a critical role in maintaining skin and gut health. In this review we describe various therapies targeting the skin microbiome to reduce infection and inflammation in AD, including transplantation of microbiota, and the use of prebiotics, probiotics, and postbiotics. In addition, we provide a perspective to engineer and to harness bacteria of the skin microbiome as next-generation probiotics, also known as engineered live biotherapeutic products (eLBPs), using synthetic biology to create strains that can sense skin signals, such as immune signals, and environmental factors, and produce therapeutic treatments for AD on demand.},
}

@article {pmid41231537,
year = {2025},
author = {Cao, H and de la Fuente-Nunez, C},
title = {Microbial Primer: Artificial intelligence for microbiologists.},
journal = {Microbiology (Reading, England)},
volume = {171},
number = {11},
pages = {},
doi = {10.1099/mic.0.001629},
pmid = {41231537},
issn = {1465-2080},
mesh = {*Artificial Intelligence ; Machine Learning ; Humans ; Anti-Bacterial Agents/pharmacology ; Microbiota ; Genomics ; Drug Discovery/methods ; Bacteria/genetics/drug effects ; *Microbiology ; Algorithms ; },
abstract = {Artificial intelligence (AI) and machine learning (ML) are reshaping microbiology, enabling rapid antibiotic discovery, resistance prediction and clinical diagnostics. For microbiologists, the goal is not to build new algorithms but to recognize when ML is appropriate, how to prepare data and how to interpret outputs responsibly. This primer takes that practical stance - driving the ML car rather than rebuilding the engine. At a high level, ML learns from complex patterns, often noisy data. In antibiotic discovery, ML models help identify compounds in biological data and design new ones from scratch using generative AI. In microbiome studies, where measurements are compositional, sparse and often confounded, ML helps uncover community structure and link taxa or functions to phenotypes. In pathogen genomics, supervised models map sequence-derived features (e.g. k‑mers, SNPs and gene presence/absence) to outcomes such as species identity, antimicrobial susceptibility or MIC. Unsupervised learning supports exploration, including clustering, latent gradients and dimensionality reduction for visualization. Across these settings, success hinges less on exotic architectures than on sound problem framing, careful preprocessing and experimental validation.},
}

*Artificial Intelligence
Machine Learning
Humans
Anti-Bacterial Agents/pharmacology
Microbiota
Genomics
Drug Discovery/methods
Bacteria/genetics/drug effects
*Microbiology
Algorithms

@article {pmid41231416,
year = {2025},
author = {McAlister, FA and Lin, M and Youngson, E and Lethebe, BC and Leslie, M},
title = {Prior antibiotic exposure is associated with worse outcomes in adults with COVID-19.},
journal = {Infectious diseases (London, England)},
volume = {},
number = {},
pages = {1-9},
doi = {10.1080/23744235.2025.2585984},
pmid = {41231416},
issn = {2374-4243},
abstract = {BACKGROUND: Antibiotic-induced perturbations of the gut microbiome impair immunologic responses but whether they influence disease severity is unknown. The COVID-19 pandemic provided a unique opportunity to explore this question given widespread testing for SARS-CoV-2 infections.

OBJECTIVE: To determine whether prior antibiotic exposure was associated with outcomes in patients with COVID-19.

METHODS: Retrospective cohort study of all community-dwelling adults in Alberta, Canada with COVID-19 between March 2020 and June 2023. Subjects with antibiotic dispensations in the prior 3 months were compared (using multivariable logistic regression and propensity score (PS)-matching) to those without antibiotic exposure for differences in 30-day outcomes.

RESULTS: Of 445,646 adults with COVID-19, 49,581 (11.1%) were exposed to at least one antibiotic course in the prior 3 months. Those exposed to antibiotics were more likely to present to an emergency department (13.4% vs. 7.4%, aOR 1.52, 95%CI 1.48-1.57, PS-matched OR 1.48, 1.42-1.54), be hospitalised (5.8% vs. 2.8%, aOR 1.40,1.33-1.46, PS-matched OR 1.37, 1.29-1.45), or die (1.7% vs. 0.6%, aOR 1.28, 1.18-1.40, PS-matched OR 1.27, 1.14-1.42) than patients without prior antibiotic exposure. The associations were similar whether the antibiotic prescriptions were appropriate or not or whether antibiotic exposure periods were 6 weeks, 6 months, or 12 months prior to the positive RT-PCR test. The associations were stronger in those individuals with the highest tertile of antibiotic exposure, or those exposed to broad-spectrum antibiotics, or younger patients.

CONCLUSION: Prior antibiotic exposure is associated with worsened disease severity in patients infected with SARS-CoV-2. These findings support efforts to reduce antibiotic use.},
}

@article {pmid41231387,
year = {2025},
author = {Miller, CA and Pirotta, E and Grim, S and Moore, MJ and Durban, JW and Tyack, PL and Fearnbach, H and Leander, SGM and Knowlton, AR and Warren, AM and Zani, MA and Asmutis-Silvia, R and Pettis, HM and Apprill, A},
title = {Respiratory microbiomes reflect whale health.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
doi = {10.1093/ismejo/wraf231},
pmid = {41231387},
issn = {1751-7370},
support = {NA19OAR4320074, NA24OARX432C0008//NOAA Cooperative Institute agreement/ ; N000142012697//Office of Naval Research/ ; N000142112096//Office of Naval Research/ ; RC20-1097//Strategic Environmental Research and Development Program/ ; RC20-7188//Strategic Environmental Research and Development Program/ ; RC21-3091//Strategic Environmental Research and Development Program/ ; },
mesh = {Animals ; *Microbiota ; *Whales/microbiology/physiology ; *Bacteria/classification/genetics/isolation & purification ; Male ; Female ; Archaea/classification/isolation & purification/genetics ; *Respiratory System/microbiology ; },
abstract = {As important members of the marine ecosystem, baleen whales are frequently managed and protected, but methodology to assess their health remains limited. Recent technological advances, such as the use of drones, support the non-invasive collection of promising health-associated data, including respiratory exhalant microbiota. Here, we considered five health metrics paired with respiratory exhalant samples to examine the utility of characterizing respiratory microorganisms for health diagnostics of North Atlantic right whales (Eubalaena glacialis), one of the most endangered baleen whale species. In 2016-2024, we used drones to collect 103 exhalant samples from 85 individuals to examine the associated microbiome, using amplicon sequencing methods targeting bacteria and archaea. The health status of sampled whales was characterized using an index of body condition derived from full-body vertical drone images, three qualitative assessments obtained from photo-identification imagery, and an existing health and vital rates model. Using an elastic net penalized regression approach, we demonstrate significant relationships between these health metrics and respiratory-associated microorganisms. Bacterial taxa that significantly contributed to the model for the body condition index differed between the thinnest and most robust males in the dataset. The thin whale harbored taxa belonging to the same genus as mammalian pathogens, Clostridium and Peptoniphilus, whereas the robust whale harbored taxa commonly observed in lipid-rich environments, Sediminispirochaeta and Candidatus Gracilibacteria. These differences warrant further investigation into the mechanisms by which bacteria contribute to whale health. Our findings demonstrate the utility of non-invasive multi-metric health models that include respiratory exhalant microbiota for whale health assessment and management.},
}

Animals
*Microbiota
*Whales/microbiology/physiology
*Bacteria/classification/genetics/isolation & purification
Male
Female
Archaea/classification/isolation & purification/genetics
*Respiratory System/microbiology

@article {pmid41231285,
year = {2025},
author = {Padur Sankaranarayanan, A and Dhanapal, S and Valliyappan, M and Shyu, DJH and Parthasarathy, TN},
title = {Intestinal microbiome diversity and disparity between wild and captive endangered Asian elephants (Elephas maximus indicus) in southern India.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {12},
pages = {191},
pmid = {41231285},
issn = {1572-9699},
support = {31950410559//National Natural Science Foundation [NSFC] of China/ ; },
mesh = {Animals ; *Elephants/microbiology ; *Gastrointestinal Microbiome/genetics ; India ; RNA, Ribosomal, 16S/genetics ; *Animals, Wild/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Endangered Species ; Biodiversity ; Phylogeny ; Animals, Zoo/microbiology ; Male ; DNA, Bacterial/genetics/chemistry ; Feces/microbiology ; Female ; },
abstract = {The gut microbiome affects the physical and mental wellbeing of an animal. Several factors, including diet, host physiology, age, sex, lifestyle, and environmental factors, influence the dynamic gut microbiome. We studied the gut microbiome composition of the endangered Asian elephants (Elephas maximus) kept under prolonged captive conditions (15.8 ± 3.9 years) and their wild counterparts, as both were exposed to two different environmental pressures. A total of 648,581 high-quality sequences were obtained, comprising 208 microbial families from 22 phyla and 97 orders, as determined by high-throughput 16S rRNA gene sequencing. Among them, 90% of the microbes belonged to the phyla Firmicutes, Proteobacteria and Bacteroidetes. Our analysis revealed a distinct variation in the gut microbiome between captive and wild elephants. The captive elephants had a higher abundance of the microbial phyla Kiritimatiellaeota, Tenericutes, Euryarchaeota, and Verrucomicrobia, which suggests that captivity alters the gut microbiome. These findings reveal distinct patterns of gut microbiome diversity between captive and wild elephants, underscoring the role of diet and environmental conditions in shaping the elephant gut microbiome.},
}

Animals
*Elephants/microbiology
*Gastrointestinal Microbiome/genetics
India
RNA, Ribosomal, 16S/genetics
*Animals, Wild/microbiology
*Bacteria/classification/genetics/isolation & purification
Endangered Species
Biodiversity
Phylogeny
Animals, Zoo/microbiology
Male
DNA, Bacterial/genetics/chemistry
Feces/microbiology
Female