@article {pmid41477949,
year = {2025},
author = {Li, W and Song, X and Wang, Y and Wen, D and Zhou, Y and Zhang, D},
title = {Iron-manganese inputs shape the coupling between deposit morphology and microbiome during the early-stage corrosion on cement mortar-lined pipe walls under drinking-water conditions.},
journal = {Journal of environmental management},
volume = {398},
number = {},
pages = {128468},
doi = {10.1016/j.jenvman.2025.128468},
pmid = {41477949},
issn = {1095-8630},
abstract = {Maintaining water quality in drinking water distribution systems (DWDSs) requires resilient pipe-wall interfaces, yet the build-up of iron (Fe) and manganese (Mn), the most common metals in DWDSs, often initiates deposit growth and triggers discoloration events. However, the physicochemical impacts of early Fe-Mn deposition on pipe-wall surfaces have not been systematically elucidated. To elucidate their mechanistic role in the onset of scale development, self-designed electrodes were employed to monitor the electrochemical behavior of cement mortar-lined pipe surfaces under controlled Fe-Mn dosing (50-200 μg/L Fe with 10 μg/L Mn). Results showed that a dosing condition of 100 μg/L Fe with 10 μg/L Mn produced compact and adherent deposits with high charge-transfer resistance (Rct = 1.33 × 10[6] Ω) and low corrosion current density (icor = 3.68 × 10[-5] mA/cm[2]). This condition was attributed to cohesive biofilms dominated by Pseudomonas with co-dominant Hydrogenophaga and Sphingomonas, which, through assimilation-centered carbon and nitrogen pathways, secreted abundant extracellular polymeric substances, associated with minimized particulate metal accumulation in bulk water. In contrast, excessive Fe input (200 μg/L) generated scale-like, metal-oxide-bearing deposits accompanied by elevated Fe-Al contents, reduced Rct = 2.97 × 10[5] Ω, higher icor = 1.70 × 10[-4] mA/cm[2] and metabolically diverse but weakly coordinated microbial communities. These results demonstrate that Fe-Mn-regulated morphology-microbiome coupling shapes early-stage corrosion behavior and that appropriate Fe-Mn levels are essential for promoting stable deposits and supporting long-term drinking-water safety.},
}

@article {pmid41477864,
year = {2026},
author = {Favela, A and Kent, AD and Sible, CN and Flint-Garcia, S and Klimasmith, IM and Mujjabi, C and Raglin, SS and Below, FE and Bohn, MO},
title = {Lost and found: Rediscovering microbiome-associated phenotypes that reshape agricultural sustainability.},
journal = {Science advances},
volume = {12},
number = {1},
pages = {eaed3360},
pmid = {41477864},
issn = {2375-2548},
mesh = {*Microbiota ; Phenotype ; *Agriculture/methods ; *Zea mays/microbiology/genetics/growth & development ; Rhizosphere ; Soil Microbiology ; Plant Roots/microbiology ; Crops, Agricultural/microbiology ; Nitrogen/metabolism ; Nitrification ; },
abstract = {Modern agriculture faces an urgent need to improve nutrient use efficiency while reducing environmental impacts. Here, we show that ancestral traits controlling rhizosphere microbiome functions can be reintroduced into elite maize through targeted teosinte introgressions. Using near-isogenic lines, we mapped microbiome-associated phenotypes (MAPs) derived from teosinte that suppress nitrification and denitrification-key microbial processes contributing to nitrogen loss. These introgressions altered root exudate chemistry, resulting in distinct microbial assemblies and enhanced nitrogen retention. We identified candidate loci and exudate metabolites responsible for suppressive activity and demonstrated their functional effects in vitro. These findings reveal a genetic and biochemical basis for rewilding microbiome-mediated ecosystem services in crops, offering a scalable path toward sustainable nutrient management in global agriculture.},
}

*Microbiota
Phenotype
*Agriculture/methods
*Zea mays/microbiology/genetics/growth & development
Rhizosphere
Soil Microbiology
Plant Roots/microbiology
Crops, Agricultural/microbiology
Nitrogen/metabolism
Nitrification

@article {pmid41477781,
year = {2025},
author = {Garashchenko, NE and Smurova, NE and Semenova, NV and Belkova, NL and Nemchenko, UM and Klimenko, ES and Zugeeva, RE and Kolesnikov, SI and Madaeva, IM and Kolesnikova, LI},
title = {[Gut microbiome and sleep disturbances in menopause.].},
journal = {Advances in gerontology = Uspekhi gerontologii},
volume = {38},
number = {4},
pages = {562-570},
pmid = {41477781},
issn = {1561-9125},
mesh = {Humans ; Female ; *Gastrointestinal Microbiome/physiology ; Middle Aged ; *Menopause/physiology ; *Sleep Wake Disorders/microbiology/diagnosis/physiopathology ; Surveys and Questionnaires ; Sleep Quality ; },
abstract = {The paper presents the results of the gut microbiota study in menopausal women with sleep disorders based on different assessments of sleep quality. The study involved 96 menopausal women. Sleep quality was assessed using three questionnaires: the Insomnia Severity Index (ISI), the Pittsburgh Sleep Quality Index (PSQI), and the Epworth Sleepiness Scale. The qualitative and quantitative composition of the microbiota was assessed using microbiological and molecular genetic methods. In the group with sleep disorders (according to PSQI), molecular genetic analysis of the microbiome revealed an increased content of Enterococcus spp. (p=0,03), Clostridium perfringens (p=0,01), and Shigella spp. (p=0,04). Compared to the control, with moderate sleep disorders (according to the ISI questionnaire), the content of Clostridium perfringens was increased (p=0,02). According to the Epworth scale, a higher content of Bifidobacterium spp. (p=0,04), Prevotella spp. (p=0,02) and Eubacterium rectale (p=0,04) was noted in the group with excessive daytime sleepiness compared to the control. Thus, in menopausal women, the composition and structure of the gut microbiota are associated with sleep disorders.},
}

Humans
Female
*Gastrointestinal Microbiome/physiology
Middle Aged
*Menopause/physiology
*Sleep Wake Disorders/microbiology/diagnosis/physiopathology
Surveys and Questionnaires
Sleep Quality

@article {pmid41477766,
year = {2025},
author = {Mirji, G and Bhat, SA and El Sayed, M and Reiser, SK and Gavara, SP and Ye, Y and Miyamoto, T and Zhang, W and Vogel, P and Cassel, J and Liu, Q and Goldman, AR and Kossenkov, A and Zhang, N and Shinde, RS},
title = {Aromatic microbial metabolite hippuric acid enhances inflammatory responses in macrophages via TLR-MyD88 signaling and lipid remodeling.},
journal = {Cell reports},
volume = {45},
number = {1},
pages = {116749},
doi = {10.1016/j.celrep.2025.116749},
pmid = {41477766},
issn = {2211-1247},
abstract = {The gut microbiome produces diverse metabolites shaping immunity, yet their pro-inflammatory potential remains unclear. Using untargeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) metabolomics, we identified hippuric acid-an aromatic, microbe-derived metabolite-as a potent enhancer of inflammatory responses during Escherichia coli infection. Hippuric acid administration heightened inflammation, activated innate immune cells, and reduced survival in infected mice. In vitro, hippuric acid selectively potentiated M1-like (lipopolysaccharide [LPS] or LPS+interferon gamma [IFNγ]) macrophage pro-inflammatory responses but had no effect on M2-like (interleukin [IL]-4) polarization. It enhanced responses to myeloid differentiation primary response 88 (MyD88)-dependent Toll-like receptor (TLR) ligands but not TRIF-, STING-, or NOD2-mediated stimuli. Genetic deletion of MyD88 abolished hippuric-acid-induced pro-inflammatory responses. Transcriptomic and lipidomic analyses revealed increased cholesterol biosynthesis and lipid accumulation, while reducing cellular cholesterol blunted the pro-inflammatory effects of hippuric acid. Notably, hippuric acid also enhanced pro-inflammatory responses in human macrophages, and its elevated levels correlated with sepsis mortality, linking microbial metabolism, lipid remodeling, and innate immunity.},
}

@article {pmid41477725,
year = {2026},
author = {Chan, NSL and Cross, C and Prestidge, CA and Wardill, HR and Bowen, J and Joyce, P},
title = {The resilient microbiome: how baseline gut microbial composition influences response to cancer treatment.},
journal = {Critical reviews in microbiology},
volume = {},
number = {},
pages = {1-18},
doi = {10.1080/1040841X.2025.2610215},
pmid = {41477725},
issn = {1549-7828},
abstract = {The human gut microbiome is increasingly recognized as a key modulator of health and disease, with growing evidence supporting its influence on responses to cancer therapy. An important aspect of this relationship is gut microbial resilience, defined as the ability of the microbiome to recover its ecological equilibrium following disruption. Individual variations in microbial composition significantly influence resilience and, consequently, personalized responses to cancer treatments. However, the underlying functional characteristics of a resilient microbiome remain incompletely understood. Identifying specific microbial profiles with greater resilience to cancer therapies could improve the ability to predict treatment responses and mitigate adverse events. However, despite growing interest, a lack of longitudinal and mechanistic studies currently limits their clinical translation. This review examines current literature on gut microbiome compositions and individual treatment response to cancer therapy, with a focus on microbial features linked to resilience which could enable prediction of adverse response. While the use of microbial metabolites as predictive biomarkers (e.g. short-chain fatty acids and bile acids) is promising, further longitudinal and interventional studies are essential to support clinical application. Establishing specific microbial and metabolite profiles that promote resilience is essential to advance this emerging field of personalized gut-microbiome therapy.},
}

@article {pmid41477720,
year = {2025},
author = {Kurnosov, AS and Linde, NN and Molodtsova, PA and Glazunova, EV and Moskalenko, AM and Sheptulina, AF and Bodunova, NA and Zlobovskaya, OA},
title = {[Comparative Evaluation of DNA Extraction Methods from Fecal Samples: Statistical Analysis of Commercial Kits and Laboratory Protocols Using Real-Time PCR Data].},
journal = {Molekuliarnaia biologiia},
volume = {59},
number = {6},
pages = {1002-1021},
doi = {10.7868/S3034555325060104},
pmid = {41477720},
issn = {0026-8984},
mesh = {*Feces/microbiology/chemistry ; Humans ; *DNA, Bacterial/isolation & purification/genetics ; *Real-Time Polymerase Chain Reaction/methods ; *Gastrointestinal Microbiome/genetics ; Reagent Kits, Diagnostic ; *Gram-Negative Bacteria/genetics/isolation & purification ; *Gram-Positive Bacteria/genetics/isolation & purification ; },
abstract = {The emergence of new data on the association between the composition of the intestinal microbiota and various human diseases has generated increasing interest in microbiome research. In this context, selection of the DNA extraction method represents a critical stage in the design of the experiment, significantly affecting the reliability and reproducibility of results. This study presents a comparative analysis of 12 DNA extraction methods, including nine commercial kits and three laboratory protocols. We evaluated the taxonomic representation, including Gram-positive (Lactobacillaceae, Coprococcus spp., Streptococcus sp., Clostridium leptum) and Gram-negative bacteria (Enterobacteriaceae, Akkermansia muciniphila, Fusobacterium nucleatum, Bacteroides fragilis). The extraction efficiency was assessed by the DNA yield, expressed in GE/pL of eluate or in GE/-µL of feces, as well as by the frequency of low-abundance taxa loss. Clustering of the methods according to the type of lysis was demonstrated: mechanical lysis provided stable and high DNA yields, particularly for Gram-positive bacteria, while chemical and enzymatic methods showed lower efficiency. We determined that the lysis type and pre-processing of intact fecal samples are the key factors affecting the DNA extraction efficiency and preservation of the native taxonomic profile. The best results were demonstrated by the QIAamp® PowerFecal® Pro DNA Kit (Qiagen) and the combination of AmpliTest UniProb + AmpliTest RIBO-prep kits (Center for Strategic Planning, Federal Medical-Biological Agency, Russia), both of which outperformed other methods in terms of DNA yield. The QIAamp® Fast DNA Stool Mini Kit (Qiagen) showed minimal losses of low-abundance taxa. These findings can be used for the standardization of gut microbiota DNA extraction methodologies and the development of domestic protocols.},
}

*Feces/microbiology/chemistry
Humans
*DNA, Bacterial/isolation & purification/genetics
*Real-Time Polymerase Chain Reaction/methods
*Gastrointestinal Microbiome/genetics
Reagent Kits, Diagnostic
*Gram-Negative Bacteria/genetics/isolation & purification
*Gram-Positive Bacteria/genetics/isolation & purification

@article {pmid41477712,
year = {2025},
author = {Glazunova, EV and Kurnosov, AS and Molodtsova, PA and Moskalenko, AM and Makarov, VV and Zlobovskaya, OA},
title = {[Gut Microbiota in Colorectal Cancer Carcinogenesis: The Evolution of Hypotheses].},
journal = {Molekuliarnaia biologiia},
volume = {59},
number = {6},
pages = {891-908},
doi = {10.7868/S3034555325060029},
pmid = {41477712},
issn = {0026-8984},
mesh = {*Colorectal Neoplasms/microbiology/pathology ; Humans ; *Gastrointestinal Microbiome ; *Carcinogenesis/pathology/genetics ; Animals ; *Dysbiosis/microbiology ; },
abstract = {Colorectal cancer remains one of the leading causes of cancer-related mortality, highlighting the importance of optimizing approaches for its early diagnosis and therapy. One promising area in this field is the investigation of the role of the gut microbiome in the initiation and progression of colorectal cancer. This review examines three principal hypotheses explaining the contribution of microbiota to carcinogenesis: the "Alpha-bug", the "Keystone pathogen", and the "Driver-Passenger" models. We analyze data on the mechanisms of microbiota-tumor cells interactions, including the induction of inflammation, genotoxicity, and disruption of the intestinal barrier function. Findings are also presented indicating that certain microorganisms previously considered markers of the advanced stages may possess pro-oncogenic properties, thereby refining existing carcinogenesis models. Overall, the data suggest that the microbiota and its dysbiotic alterations can be considered potential targets for colorectal cancer diagnosis and therapy.},
}

*Colorectal Neoplasms/microbiology/pathology
Humans
*Gastrointestinal Microbiome
*Carcinogenesis/pathology/genetics
Animals
*Dysbiosis/microbiology

@article {pmid41477689,
year = {2026},
author = {Chen, F and Sun, T and Song, H},
title = {Advances in Chemically Modified Polysaccharides with Enhanced Hypoglycemic Bioactivity.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c08511},
pmid = {41477689},
issn = {1520-5118},
abstract = {Polysaccharides are natural biopolymers with diverse bioactivities, but their clinical use in diabetes is restricted by poor solubility and bioavailability. Chemical modification provides an effective strategy to optimize polysaccharide structures, thereby enhancing their physicochemical properties and biological functions. This review summarized major chemical modification methods, focusing on introducing functional groups to sites such as hydroxyl, carboxyl, aldehyde, and amino groups. These modifications influence molecular weight distribution, monosaccharide composition, glycosidic linkage, solubility, and thermal stability, thereby modulating biological activities. Enhanced hypoglycemic effects of chemically modified polysaccharides were extensively discussed, emphasizing mechanisms such as suppression of digestive enzyme activities and the prevention of advanced glycation end-product generation, improvement of oxidative stress, improvement of gut microbiome and maintenance of gut health, and anti-inflammatory actions. This review underscored the potential of chemically modified polysaccharides as functional antidiabetic agents and advocated for further mechanistic studies and scalable, environmentally friendly modification techniques to advance their applications.},
}

@article {pmid41477501,
year = {2025},
author = {Govindharaj, GP and Choudhary, JS and Panda, RM and Basana-Gowda, G and Annamalai, M and Patil, N and Khan, RM and Banra, S and Srivastava, K and Mohapatra, SD},
title = {Bacterial communities in Nilaparvata lugens (Stål) (Hemiptera: Delphacidae) showed significant variation among the developmental stages with functional diversity.},
journal = {Heliyon},
volume = {11},
number = {4},
pages = {e42776},
pmid = {41477501},
issn = {2405-8440},
abstract = {Nilaparvata lugens, a major rice pest, hosts an essential microbiome, yet its dynamic changes across developmental stages remain poorly understood. This study analyzed the bacterial community across developmental stages using V3-V4 amplicon sequences of 16S rRNA gene. The microbiome was classified into 20 phyla, 38 classes, 77 orders, 155 families, and 273 genera, with Proteobacteria, Firmicutes, and Bacteroidetes dominating phyla. Families Morganellaceae, Enterobacteriaceae, and Moraxellaceae were prevalent across all stages, while Anaplamataceae was dominant in all the developmental stages except males. Key genera included Arsenophonous (5 %), Bacillus (5 %), and Acinetobacter (3 %), with Wolbachia (11 %) abundant in all developmental stages except in males. The shared operational taxonomic units (OTUs) between the developmental stages of N. lugens were only 40 OTUs, and higher unique OTUs were found in the late instar stage (89 OTUs), and the lowest unique OTUs were found at the male stage (64 OTUs). Functional prediction indicated roles in carbohydrate, amino acid, and energy metabolism, as well as membrane transport, signaling, DNA replication and repair. These findings highlight stage-specific microbiome variations, laying the foundation for microbiome-based pest management techniques.},
}

@article {pmid41477359,
year = {2025},
author = {Lee, YR and Park, JH and Yoo, HH and Choi, I and Park, HY},
title = {Standardization of Fecal Metabolomics Using Microbiome Preservation Kits: Implications for Multiomics Integration.},
journal = {International journal of analytical chemistry},
volume = {2025},
number = {},
pages = {8551545},
pmid = {41477359},
issn = {1687-8760},
abstract = {With the advancement of multiomics technologies and cohort study designs, integrative omics research is increasingly applied to human health and nutrition. However, optimal storage and preprocessing of labile biological samples, particularly feces, remain challenging. In this study, we systematically evaluated three normalization methods-wet weight, dry weight, and protein quantification-for quantitative metabolomic profiling of fecal samples, using 41 metabolites. Fresh fecal samples from three healthy individuals showed high reproducibility, with 24 metabolites exhibiting a coefficient of variation (CV) below 30 for both wet and dry weight normalization. Fecal samples from 20 obese patients collected using the OMNIgene·GUT kit demonstrated improved reproducibility with wet weight normalization (20 metabolites, CV < 30) and protein quantification normalization (19 metabolites, CV < 30), whereas dry weight normalization yielded no metabolites meeting the CV < 30 criterion. Direct analysis of the kit solution without a drying step further enhanced chromatographic clarity, highlighting practical considerations for large-scale studies. Overall, wet weight normalization consistently minimized variation across sample types, providing a robust and standardized framework for fecal metabolite profiling. These findings demonstrate that the OMNIgene·GUT kit is compatible with broad-spectrum metabolomic analyses and support its integration into multiomics workflows. By establishing reproducible normalization protocols, this study provides the foundation for accurate, comparable, and scalable fecal metabolomics in both clinical and nutritional research settings.},
}

@article {pmid41477198,
year = {2025},
author = {Feng, X and Song, W and Ren, X and Xu, Z and Li, C and Feng, M and Wang, N},
title = {Microbial influences on HPV infection and cervical carcinogenesis: emerging evidence from the vaginal microbiome.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1733315},
pmid = {41477198},
issn = {1664-302X},
abstract = {Microbial communities play a vital role in the human defense system, existing symbiotically with us, contributing to metabolic processes, and strengthening immune defenses against pathogens. A diverse bacterial population in the vagina contributes to maintaining dynamic homeostasis, with their interactions playing a critical role in determining health or disease status. The balanced vaginal microbiota, dominated by Lactobacilli, helps maintain vaginal pH, converts glycogen to lactic acid, and produces bacteriocins and hydrogen peroxide (H2O2), all contributing to its protective functions. On the other hand, an abnormal vaginal microbial composition, characterized by a decrease in beneficial microorganisms, heightens the risk of gynecological diseases such as bacterial vaginosis (BV), sexually transmitted infections, human papillomavirus (HPV) infections, and cervical cancer due to persistent infections. Variation in microbial composition is influenced by factors such as racial background, ethnicity, pregnancy, hormonal fluctuations, sexual behavior, personal hygiene practices, and various physiological conditions. This review aims to offer a detailed overview of the existing literature, focusing on the complex interplay between vaginal microbiota and gynecological conditions such as HPV infection. Our goal is to provide valuable insights that can inform future clinical strategies and interventions.},
}

@article {pmid41477061,
year = {2025},
author = {Zhong, D and Sun, Y and Zhao, L and Hu, Z and Li, G and Li, H and Xie, Z},
title = {Interplay between aging and metabolic diseases: from molecular mechanisms to therapeutic horizons.},
journal = {Medical review (2021)},
volume = {5},
number = {6},
pages = {477-489},
pmid = {41477061},
issn = {2749-9642},
abstract = {Aging and metabolic diseases are intricately linked through bidirectional molecular mechanisms that foster a harmful cycle of physiological decline. This cycle is driven by several key factors, including altered nutrient sensing, mitochondrial dysfunction, cellular senescence, chronic inflammation, epigenetic modifications, circadian rhythm disruptions, and imbalances in the gut microbiota. Emerging interventions targeting this aging-metabolism axis hold significant promise for extending healthspan. These approaches include the use of pharmacological mimetics, senolytics, multi-omics strategies, and microbiome modulation, all of which aim to restore metabolic homeostasis and mitigate age-related pathologies. However, several challenges remain in translating these strategies into clinical practice. These include the need for tissue-specific targeting, ensuring the long-term safety of interventions, and addressing socioeconomic disparities in healthcare access. Future research efforts are focusing on integrating multi-omic technologies, organoid and human cellular models, and developing equitable precision medicine frameworks. These initiatives aim to extend healthspan and reduce the global impact of aging-related metabolic diseases.},
}

@article {pmid41477025,
year = {2025},
author = {Miao, H and Wang, Z and Chen, S and Wang, J and Ma, H and Liu, Y and Yang, H and Guo, Z and Wang, J and Cui, P},
title = {Application of machine learning in the discovery of antimicrobial peptides: exploring their potential for ulcerative colitis therapy.},
journal = {eGastroenterology},
volume = {3},
number = {4},
pages = {e100253},
pmid = {41477025},
issn = {2976-7296},
abstract = {BACKGROUND: Ulcerative colitis (UC) is a chronic, relapsing inflammatory bowel disease with complex aetiology and limited treatment options. Antimicrobial peptides (AMPs), as endogenous immune effectors, have recently emerged as promising therapeutic agents in UC. However, systematic identification and functional evaluation of AMPs remain underexplored. We aimed to discover novel AMPs with potential therapeutic efficacy in UC by leveraging machine learning-based prediction and validating their impact in an experimental colitis model.

METHODS: We established a machine learning-driven pipeline to predict candidate AMPs based on their structural and functional features. Top-ranked peptides were synthesised and subjected to in vitro antibacterial assays and proteolytic stability tests. Their therapeutic potential was evaluated using a dextran sulfate sodium (DSS)-induced colitis mouse model, assessing clinical indicators, histopathology, inflammatory markers and gut microbiota alterations. Metagenomic and metabolomic analyses provided insights into microbial community dynamics and metabolic pathways. To probe the role of gut microbes in AMP-mediated gut homeostasis, we conducted Akkermansia (A.) muciniphila replenishment experiments.

RESULTS: Several AMPs identified by machine learning exhibited potent antimicrobial activity and resistance to proteolytic degradation. In vivo, AMP administration ameliorated DSS-induced colitis symptoms, including body weight loss, Disease Activity Index and histological damage. Treatment also modulated the gut microbiome, increasing the abundance of A. muciniphila and restoring microbial balance. Functional metagenomic profiling revealed enrichment of genes involved in mucosal barrier protection and immunoregulation. These findings were supported by improved inflammatory cytokine profiles and enhanced epithelial integrity.

CONCLUSIONS: Our findings demonstrate that machine learning-guided discovery of AMPs is a viable approach to identify promising therapeutic agents for UC. By integrating multi-omics analyses, we reveal potential microbiota-mediated mechanisms underlying AMP efficacy. These insights provide a strong foundation for advancing AMP-based strategies in UC management.},
}

@article {pmid41476963,
year = {2025},
author = {Ma, S and Zheng, L and Zhuang, X and Wang, M and Zou, Y},
title = {Pathogenic mechanisms and therapeutic potential of the microbiome in premature ovarian insufficiency.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1734367},
pmid = {41476963},
issn = {1664-3224},
mesh = {Humans ; *Primary Ovarian Insufficiency/therapy/microbiology/metabolism/etiology ; Female ; Animals ; *Microbiota ; Ovary/metabolism/microbiology ; Probiotics/therapeutic use ; },
abstract = {The postponement of childbearing age has become a global issue. Factors such as increased work pressures on women and environmental changes have led to a rising incidence and younger onset of premature ovarian insufficiency (POI). POI not only impacts patients' reproductive function but also heightens the risk of depression, anxiety, cognitive decline, premature mortality, osteoporosis, and cardiovascular disease. Exploring effective prevention and treatment strategies for POI can slow ovarian ageing and safeguard female reproductive health. Microbiome research confirms that most human tissues and organs form dynamic, interactive systems with symbiotic microbes that play a crucial role in female reproductive function. Previous studies on the microbiome and female reproductive health have rarely focused on POI. The proposed 'Microbiota-Ovary Axis' aims to establish an integrated regulatory framework. This theoretical model systematically elucidates how microbial signals influence ovarian function through four core pathways: the hypothalamic-pituitary-ovarian (HPO) axis, metabolism and endocrine regulation, immunoregulation, and oxidative stress. Evaluating the efficacy of dietary modifications, probiotics, and microbiota transplantation in animal models and preliminary clinical studies will establish a robust theoretical foundation for developing microbiota-targeted innovative diagnostic and therapeutic strategies for POI, thereby enhancing reproductive health throughout the female lifespan.},
}

Humans
*Primary Ovarian Insufficiency/therapy/microbiology/metabolism/etiology
Female
Animals
*Microbiota
Ovary/metabolism/microbiology
Probiotics/therapeutic use

@article {pmid41476768,
year = {2025},
author = {Dommer, AC and Amaro, RE and Prather, KA},
title = {Understanding Aerosol-Mediated Disease Transmission.},
journal = {ACS central science},
volume = {11},
number = {12},
pages = {2319-2328},
pmid = {41476768},
issn = {2374-7943},
abstract = {This Outlook aims to update the longstanding treatment of airborne disease transmission through an interdisciplinary lens combining biology, surface chemistry, and aerosol physics, drawing parallels between environmental and human-generated infectious aerosols and examining their effects on human and ecosystem health. By recasting the lung surface as a dynamic interface akin to the ocean surface, this Outlook illustrates the importance of a multidisciplinary approach to elucidate the mechanisms of disease transmission at a depth that enables practical mitigation strategies. The urgency of this analysis is motivated by the evolving nature of airborne pathogens of concern, such as SARS-CoV-2 and influenza, and the global impact of dynamic environments on the poorly understood airborne microbiome.},
}

@article {pmid41476253,
year = {2025},
author = {Kvitne, KE and Zuffa, S and Charron-Lamoureux, V and Mohanty, I and Patan, A and Mannochio-Russo, H and Zemlin, J and Burnett, LA and Zhang, LS and Cecala, MC and Ersoz, C and Connelly, JA and Halasa, N and Nicholson, M and Dorrestein, PC and Tsunoda, SM and Markle, J},
title = {Fecal microbial and metabolic signatures in children with very early onset inflammatory bowel disease.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-025-00899-0},
pmid = {41476253},
issn = {2055-5008},
support = {5P30HD106451-03//NICHD/NIH/ ; 5P30HD106451-03//NICHD/NIH/ ; 5P30HD106451-03//NICHD/NIH/ ; P50HD106463/HD/NICHD NIH HHS/United States ; },
abstract = {Very early onset inflammatory bowel disease (VEO-IBD) is a clinically distinct form of IBD manifesting in children before the age of six years. Disease in these children is especially severe and often refractory to treatment. While previous studies have investigated changes in the fecal microbiome and metabolome in adult and pediatric IBD, insights in VEO-IBD remain limited. This multi-omics analysis reveals changes in the fecal microbiome and metabolome in children diagnosed with VEO-IBD compared with age- and sexmatched healthy controls. Untargeted metabolomics analysis identified a depletion of short-chain N-acyl lipids and an enrichment of dipeptides, tripeptides, and oxo bile acids in children with VEO-IBD. Differential abundance analysis of 16S rRNA sequencing data showed lower abundance of beneficial bacteria such as Bifidobacterium and Blautia, and higher abundance of Lachnospira, Veillonella, and Bacteroides in VEO-IBD. Multi-omics integration revealed associations between the altered gut microbiome composition and metabolic dysregulation, specifically for the N-acyl lipids. This study offers unique insight into fecal microbial and metabolic signatures in VEO-IBD, paving the way for a better understanding of disease patterns and thereby more effective treatment strategies.},
}

@article {pmid41476057,
year = {2025},
author = {Wu, Y and Wong, O and Chen, S and Wang, Y and Lu, W and Cheung, CP and Ching, JYL and Cheong, PK and Chan, S and Leung, P and Chan, FKL and Su, Q and Ng, SC},
title = {Distinct diet-microbiome associations in autism spectrum disorder.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-67711-7},
pmid = {41476057},
issn = {2041-1723},
abstract = {Autism spectrum disorder (ASD) is linked to both altered gut microbiota and unhealthy diets; however, the mechanistic connections remain elusive. In this study, we conducted a systematic analysis of fecal microbiome metagenomic data, paired with granular dietary assessments and phenotypic profiles, across a cohort of 818 children (462 with ASD, 356 without ASD; mean age = 8.4 years; 27.3% female). By integrating dietary indices, nutrient intake, and food additive exposures, we uncovered ASD-specific linkages to the microbiome. Poor dietary quality correlated with aggregated core autistic symptoms, gastrointestinal complications, and atypical eating behaviors. Notably, children with ASD exhibited a more pronounced diet-microbiome interaction network compared to neurotypical peers, suggesting heightened microbial sensitivity to nutritional inputs. Furthermore, synthetic emulsifiers-specifically polysorbate-80 and carrageenan-were associated with disrupted microbial connectivity in ASD, a phenomenon attenuated in neurotypical children. Our findings elucidate the mechanistic links between dietary factors-particularly synthetic food additives-and microbiome dysregulation in ASD, urging a re-evaluation of dietary guidelines for ASD populations and laying the groundwork for personalized nutritional strategies.},
}

@article {pmid41475989,
year = {2025},
author = {Liu, YH and Peng, P and Hung, WC and Wu, PH and Kao, CY and Wu, PY and Huang, JC and Chen, SC and Kuo, CH},
title = {Gut microbiota profiles by LDL-C target achievement in statin-treated patients: A cross-sectional study.},
journal = {Nutrition, metabolism, and cardiovascular diseases : NMCD},
volume = {},
number = {},
pages = {104465},
doi = {10.1016/j.numecd.2025.104465},
pmid = {41475989},
issn = {1590-3729},
abstract = {BACKGROUND AND AIMS: Hyperlipidemia is linked to gut microbiota alterations, but the impact of statins on the gut microbiome remains unclear, especially concerning different low-density lipoprotein cholesterol (LDL-C) targets. This study explores gut microbiome changes in chronic disease patients under varying LDL-C targets with statin therapy.

METHODS AND RESULTS: A total of 125 patients (77 males and 48 females) diagnosed with chronic diseases, specifically diabetes mellitus (87 %), hypertension (74 %), and chronic kidney disease (48 %), were recruited. Fecal samples were collected from the participants to analyze the composition of the gut microbiota using Illumina sequencing of the 16S ribosomal ribonucleic acid gene. The patients were divided into two groups according to LDL-C level, including 57 patients in the LDL-C target-achieved group (LDL-C < 70 mg/dL), and 68 in the LDL-C target-not-achieved group (LDL-C ≥ 70 mg/dL). There were no significant differences in microbial species diversity (Chao1 index and Shannon index), beta diversity and microbial dysbiosis index between the two groups. However, a distinct microbial community structure was found in the LDL-C target-achieved group, with decreased abundances at the genus level of Barnesiella, Coprococcus 1, Flavonifractor, Odoribacter and Coprobacter.

CONCLUSION: No significant difference in alpha diversity, beta diversity, and microbial dysbiosis index were found between the LDL-C target-achieved and target-not-achieved groups. However, the LDL-C target-achieved group was associated with a significant reduction in short-chain fatty acid-producing bacteria, including taxa Barnesiella, Coprococcus 1, Flavonifractor and Odoribacter.},
}

@article {pmid41475718,
year = {2026},
author = {Zavagna, L and Alfano, A and Bianchi, M and Di Meo, C and Fusco, A and Esin, S and Batoni, G and Donnarumma, G and Schiraldi, C and Danti, S},
title = {Gellan gum electrohydrodynamic microencapsulation of probiotics for intestine-targeted delivery.},
journal = {Carbohydrate polymers},
volume = {375},
number = {},
pages = {124742},
doi = {10.1016/j.carbpol.2025.124742},
pmid = {41475718},
issn = {1879-1344},
mesh = {*Probiotics/chemistry/pharmacology/administration & dosage ; *Polysaccharides, Bacterial/chemistry ; Humans ; Caco-2 Cells ; Limosilactobacillus fermentum/chemistry ; Drug Compounding/methods ; Escherichia coli/drug effects ; Intestines/microbiology ; Particle Size ; *Anti-Bacterial Agents/pharmacology/chemistry ; Microspheres ; Drug Delivery Systems ; Hydrogen-Ion Concentration ; },
abstract = {Microencapsulation is a promising strategy to improve time-stability, viability and targeted delivery of probiotics, thus enhancing their beneficial roles in the intestine. However, areas of improvement persist, including optimal viability protection during storage and gastrointestinal (GI) transit, control over encapsulation and targeted release. Due to pH-responsiveness, gellan gum (GG) could be ideal to face some of these criticalities. In this study, we set-up a robust electrohydrodynamic (EHD) microdripping process to produce GG microparticles (GGMs) encapsulating Limolactobacillus fermentum. By varying GG concentration, flow rate and applied voltage, the optimized EHD parameters led to highly monodisperse microbeads with controlled morphology. Successful encapsulation of L. fermentum in GGMs was obtained at concentrations of 10[6] CFU/mL and 10[9] CFU/mL, leading to 300 ± 40 μm and 450 ± 100 μm particle sizes, with encapsulation efficiency of 94 ± 6 % and 99 ± 1 %, respectively. GGMs demonstrated post-encapsulation probiotic viability with lactic acid production. Freeze-dried formulations were lasting under storage until 3 months and resulted stable under GI-simulated conditions. Their bioactive properties were demonstrated by antimicrobial efficacy against Escherichia coli and enhanced defensin expression in Caco-2 intestinal cells. Overall, EHD microdripping was a versatile and robust platform useful in functional foods and gut microbiome engineering.},
}

*Probiotics/chemistry/pharmacology/administration & dosage
*Polysaccharides, Bacterial/chemistry
Humans
Caco-2 Cells
Limosilactobacillus fermentum/chemistry
Drug Compounding/methods
Escherichia coli/drug effects
Intestines/microbiology
Particle Size
*Anti-Bacterial Agents/pharmacology/chemistry
Microspheres
Drug Delivery Systems
Hydrogen-Ion Concentration

@article {pmid41475684,
year = {2025},
author = {Yamoah, JAA and Kwofie, KD and Akorli, J and Ladzekpo, D and Kawada, H and Boateng, KY and Beyuo, J and Keleve, A and Danquah, JB and Tawiah-Mensah, C and Ansah-Owusu, J and Dadzie, SK and Wallace, PA and Tsuji, N and Hatta, T},
title = {Beyond the usual suspects: Uncovering less-recognized pathogenic bacteria in Ghanaian blood-feeding Amblyomma variegatum ticks using 16S rRNA amplicon sequencing.},
journal = {Parasitology international},
volume = {112},
number = {},
pages = {103228},
doi = {10.1016/j.parint.2025.103228},
pmid = {41475684},
issn = {1873-0329},
abstract = {Ticks are important vectors of bacterial pathogens affecting both human and animal health. In Ghana, Amblyomma variegatum is the predominant cattle-infesting tick, yet most studies have focused on a limited range of well-characterized pathogens, potentially overlooking a broader diversity of less-recognized, emerging, or opportunistic bacteria. In this study, we used 16S rRNA amplicon sequencing to characterize the bacteriome of partially blood-fed Am. variegatum ticks, with emphasis on underexplored taxa. As ticks were blood-fed at the time of collection, some detected microorganisms may represent transient, host-derived bacteria rather than endogenous tick microbiota; therefore, findings should also be interpreted within the context of xenosurveillance. Partially-fed ticks were collected from cattle across three ecological zones within Ghana's Greater Accra Region. 11 Am. variegatum ticks, confirmed through both morphological and molecular analyses, were subjected to high-throughput sequencing, and bacterial diversity and composition were analysed using established bioinformatics tools. Sequencing generated over 1.75 million high-quality reads and 3172 amplicon sequence variants. Five dominant bacterial phyla were detected, with Actinomycetota and Bacillota being the most abundant. While Rickettsia spp. were prevalent in some samples, Anaplasma and Coxiella, two commonly studied tick-borne bacteria, were not detected. Several less-recognized or opportunistic species, including multidrug-resistant Corynebacterium resistens and bovine-associated Porphyromonas levii, were identified at high relative abundance. These findings suggest that Am. variegatum may harbor a broader range of bacterial taxa than previously recognized. Incorporating such neglected microorganisms into a One Health tick-surveillance framework may improve disease risk assessment and guide public and animal health interventions in the region.},
}

@article {pmid41475679,
year = {2025},
author = {Morel, C and Li, R and Luces, CF and Brougham, MFH and Pascual-Gazquez, JF and Iniesta, RR and Torquati, L},
title = {Interventions targeting the gut microbiome to improve cancer treatment outcomes and their gastrointestinal side effects: a systematic review and meta-analysis.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {101300},
doi = {10.1016/j.tjnut.2025.101300},
pmid = {41475679},
issn = {1541-6100},
abstract = {BACKGROUND: Improvements in cancer treatment are essential to reduce premature mortality. Emerging evidence highlights the role of the gut microbiome (GM) in influencing treatment responses and modulating gastrointestinal adverse events (GIAEs). Because cancer therapy disrupts GM composition, restoring gut health may help mitigate side effects and support gut-associated immunity.

OBJECTIVE: This study aims to systematically evaluate and assess the effectiveness of GM interventions on the occurrence of GIAEs and clinical responses to cancer treatment.

METHODS: Three databases (PubMed, Web of Science, Cochrane Library) were systematically searched up to February 2025 for studies assessing gut microbiome interventions during cancer treatment. Risk of bias was evaluated using the EPHPP Quality Assessment Tool. Meta-analyses were conducted in Stata 18® using random-effects models to estimate the pooled relative risk of GM interventions on GIAEs (primary outcome) and objective disease response rates (secondary outcome).

RESULTS: Fifty-six studies were included in the systematic review and forty were meta-analysed (n=37 for GIAE outcomes, n=8 for treatment response). GM interventions reduced the overall risk of GIAEs (RR = 0.59, 95% CI = 0.53, 0.65, I[2] = 76.8%; 95% PI = 0.32, 1.08), including diarrhoea, constipation, nausea, and vomiting, but with considerable heterogeneity between studies. There was insufficient evidence to suggest improvements in objective disease response rates (RR = 1.06, 95% CI = 0.93, 1.20; I[2] = 0%; 95% PI = 0.93, 1.20).

CONCLUSION: GM interventions show promise in improving cancer care by reducing GIAEs, though evidence for direct effects on treatment response remains limited. Standardising intervention protocols and outcome reporting in future RCTs is essential to strengthen the evidence base and guide clinical recommendations.

PROSPERO REGISTRATION: Registration number: CRD42023443332 LINK TO PROTOCOL: Https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42023443332.},
}

@article {pmid41475610,
year = {2025},
author = {Xie, Y and Jiang, C and Xu, S and Zhou, H and Wang, P and Yang, Y and Hou, X and Zheng, X and Zhuang, X},
title = {Application and mechanisms of wastewater load regulation for enhanced partial denitrification in constructed wetlands: From microbiome structure to single-cell functional validation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133899},
doi = {10.1016/j.biortech.2025.133899},
pmid = {41475610},
issn = {1873-2976},
abstract = {Achieving robust nitrogen removal in constructed wetlands (CWs) is often hindered by the inhibitory effects of high pollutant loads on microbial activity. This study validates that influent load regulation is a pivotal strategy for engineering a partial denitrification (PD)-dominant microbial ecosystem, effectively overcoming such limitations. Comparing low-load (LL), medium-load (ML), and high-load (HL) conditions, the LL group achieved superior total nitrogen removal (up to 97.11%), outperforming the ML and HL groups by 9.28% and 16.21%, respectively. The underlying mechanism involves the alleviation of free ammonia (FA) inhibition at lower loads, which permitted the enrichment of crucial PD-related genera like Pseudomonas and Flavobacterium. This engineered community structure facilitated the stable production of nitrite, a key substrate that subsequently fueled downstream processes such as anammox and DAMO, thereby creating a synergistic nitrogen removal network. Consequently, our findings confirm that managing influent load is a critical and practical method for engineering a stable, PD-dominant microbial ecosystem to achieve robust and sustainable nitrogen removal in CWs.},
}

@article {pmid41475548,
year = {2025},
author = {Borgini, S and Pasveer, E and Petre, C and Iorga, BI and Vertommen, D and Remaut, H and Collet, JF and Lauber, F},
title = {Identification of receptor-binding domains of Bacteroidales antibacterial pore-forming toxins.},
journal = {The Journal of biological chemistry},
volume = {},
number = {},
pages = {111113},
doi = {10.1016/j.jbc.2025.111113},
pmid = {41475548},
issn = {1083-351X},
abstract = {Bacteroidales are abundant Gram-negative bacteria present in the gut microbiota of most animals, including humans, where they carry out vital functions for host health. To thrive in this competitive environment, Bacteroidales use sophisticated weapons to outmatch competitors. Among these, BSAPs (Bacteroidales Secreted Antimicrobial Proteins) represent a novel class of bactericidal pore-forming toxins that are highly specific to their receptor, typically targeting only a single membrane protein or lipopolysaccharide. The molecular determinants conferring this high selectivity remain unknown. In this study, we therefore investigated the model protein BSAP-1 and determined which of its domains is involved in providing receptor specificity. We demonstrate that receptor recognition is entirely driven by the C-terminal domain (CTD) of BSAP-1 using a combination of in vivo competition assays, in vitro protein binding studies and mutational analysis. Specifically, we show that deletion of the CTD abrogates BSAP-1 bactericidal activity by preventing receptor binding, while grafting the CTD to unrelated carrier proteins enables CTD-driven interaction with the BSAP-1 receptor. Combining structural investigation of a BSAP-1-receptor complex with mutational analysis, we unveil that this interaction is driven by electrostatic interactions. Building upon this discovery, we show that BSAPs can be categorized according to the structure of their CTD, suggesting a strong CTD structure/receptor type correlation. In summary, our research demonstrates that BSAP receptor recognition is driven by their CTD and paves the way for future applications.},
}

@article {pmid41475542,
year = {2025},
author = {Nayak, A and Bera, S and Purohit, S and Jain, CK},
title = {Gut Microbiota Mediated Neuroinflammation in Psychiatric Disorders: Current Perspectives and Challenges.},
journal = {Behavioural brain research},
volume = {},
number = {},
pages = {116019},
doi = {10.1016/j.bbr.2025.116019},
pmid = {41475542},
issn = {1872-7549},
abstract = {Psychiatric disorders remain a major global health concern, with complex diagnostic criteria and a lack of clear biological markers that continue to challenge therapeutic strategies. Current treatment methods, such as psychotherapy, brain stimulation therapy, and pharmacological interventions, often come with their own set of side effects, thus warranting the need to explore alternative approaches. Emerging research highlights the gut brain axis (GBA) and gut microbiota (GM) as key modulators of brain health and disease. Dysbiosis, a disruption in gut microbial composition, can influence blood brain barrier (BBB) integrity, immune signaling, and microbial metabolite production, collectively modulating neuroimmune homeostasis and contributing to the onset of neuroinflammation. While growing preclinical and clinical evidence links altered GM to depression, anxiety, schizophrenia, bipolar disorder (BD), and autism spectrum disorder (ASD), causal relationships remain incompletely defined. This review examines the established and emerging mechanisms connecting the GM to neuroinflammation underlying psychiatric disorders and evaluates current microbiome targeted interventions, such as diet based strategies, probiotics, next generation probiotics (NGPs), and fecal microbiota transplantation (FMT). We also discuss speculative microbiome engineering approaches and highlight translational limitations that must be addressed before clinical implementation. A holistic approach integrating these strategies with conventional psychiatric treatments could facilitate more effective and personalized interventions.},
}

@article {pmid41475424,
year = {2025},
author = {Ranson, HJ and Ye, Y-S and Petukhova, VZ and Green-Saxena, A and He, R and Sun, J and Godugu, B and Sanchez, LM and Wu, Q and Rowley, DC},
title = {Lipopeptides and antibiotics from a marine Bacillus pumilus mediate a potential "catch and kill" effect on pathogenetic Vibrio parahaemolyticus.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0144025},
doi = {10.1128/msystems.01440-25},
pmid = {41475424},
issn = {2379-5077},
abstract = {UNLABELLED: Bacteria produce a diverse range of specialized metabolites that influence the health and behavior of neighboring cells and, therefore, have potential applications in treating diseases. Deciphering the intended ecological functions of specialized metabolites is challenging due to the small scales at which these interactions occur and the complexity of unraveling simultaneous responses to multiple signals. In this study, we investigated the chemical interactions between two marine bacterial colonies, Vibrio parahaemolyticus PSU5429 and Bacillus pumilus YP001. When the two bacteria were grown in proximity on agar, V. parahaemolyticus exhibited swarming motility toward B. pumilus, but close approach to the B. pumilus colony was impeded by a zone of inhibition. Matrix-assisted laser desorption/ionization time-of-flight imaging mass spectrometry (MALDI-TOF IMS) suggested that lipopeptides produced by Bacillus induced swarming motility, a finding corroborated by genomic and chemical analyses of YP001. Based on activity and metabolomics guidance, the antibiotic amicoumacin B was found to be responsible for the observed antibiosis, while swarming motility by V. parahaemolyticus was induced by lipopeptides and two lipoamides. In this scenario, lipopeptide production by the Bacillus colony induces the Vibrio colony to swarm toward a lysis zone, resulting in a possible "catch and kill" effect. These results demonstrate the complexity of behaviors and outcomes exhibited by microbes under the simultaneous influence of different allelochemicals, suggesting possible interplays between antibiotics and compounds that induce motility.

IMPORTANCE: Microbes communicate and compete using small molecules, yet linking specific metabolites to visible behaviors is difficult. We combine imaging mass spectrometry, genomics, analytical chemistry, and bioassays to decode an interaction between a marine Bacillus and the pathogen Vibrio parahaemolyticus. Surfactin-like lipopeptides act at a distance to stimulate Vibrio swarming and draw cells toward the colony. Amicoumacin B accumulates at the interface and halts growth, yielding a simple "catch and kill" outcome. This study shows that the spatial localization of natural products shapes microbial behavior on surfaces and provides a general, scalable workflow that maps chemistry to phenotype. Beyond this case, the approach can be applied broadly to understand and, ultimately, tune microbial interactions relevant to marine ecosystems, aquaculture health, and microbiome engineering.},
}

@article {pmid41475279,
year = {2025},
author = {Singh, G and Ansari, S and Yadav, S and Aran, KR},
title = {Gut microbiota's role in NAFLD- and HBV/HCV-related hepatocellular carcinoma: Mechanisms and therapeutic implications.},
journal = {Microbial pathogenesis},
volume = {211},
number = {},
pages = {108273},
doi = {10.1016/j.micpath.2025.108273},
pmid = {41475279},
issn = {1096-1208},
abstract = {Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related mortality globally and has been closely linked to chronic liver conditions, such as viral hepatitis and non-alcoholic fatty liver disease. Recent research has demonstrated that the gut microbiota significantly impacts the gut-liver axis, a crucial aspect of the pathophysiology of HCC. This review emphasizes the mechanisms by which gut dysbiosis contributes to liver inflammation, fibrosis, and tumor formation. In NAFLD-related HCC, modification in the microbiota composition facilitates intestinal barrier dysfunction, endotoxemia, and metabolic disturbances. In HCC associated with HBV/HCV, the microbiome modulates immune surveillance and viral persistence. Shared pathogenic pathways, such as LPS-TLR4 signaling, bile acid dysregulation, and immunosuppressive microenvironments, highlight the role of microbial imbalance across varied etiologies. We also discuss how antibiotics, diet, probiotics, and postbiotics influence gut-liver homeostasis, as well as their therapeutic potential in primary and secondary prevention and treatment of HCC. Short-chain fatty acids and valeric acid are examples of postbiotics with anti-inflammatory and pro-apoptotic anti-IBD effects, while fecal microbiota transplantation and dietary modulation have shown potential in improving outcomes. The review also identifies significant research gaps, particularly in establishing causality, understanding intrahepatic metastasis, and investigating the roles of the fungal and viral microbiome (mycobiome and virome). Finally, the incorporation of microbiome-based interventions into clinical practice could represent an effective future strategy for risk stratification, prevention, and adjuvant therapy of HCC. Future studies focusing on longitudinal analysis, mechanistic validation, and multi-kingdom profiling are essential for translating microbiome research into effective clinical applications.},
}

@article {pmid41475232,
year = {2025},
author = {Lehmann, K and Arachchige, DE and Lehmann, R and Overholt, WA and Küsel, K and Totsche, KU},
title = {Neglected but pivotal: Complex matter dynamics in the aeration zone contribute to groundwater quality evolution.},
journal = {Water research},
volume = {291},
number = {},
pages = {125287},
doi = {10.1016/j.watres.2025.125287},
pmid = {41475232},
issn = {1879-2448},
abstract = {Fluid and matter dynamics in thick aeration zones of topographic highs are insufficiently understood, particularly in their role for groundwater quality evolution and subsurface ecosystem functioning. We apply novel drainage collectors, installed in sub-horizontal boreholes, to fill the observational gap of bedrock percolates. In the Hainich Critical Zone Exploratory, 20 spatially distributed collectors act as a super-collector for percolates from the highly geodiverse aeration zone, complementing a lysimeter and well network. For over 3 years, we investigated percolate volume, quality, and controlling factors. 65% of the annual percolation flux occurred during winter. Of this, extreme rainfall (33%) and snowmelt events (25%) together accounted for 58%, depending on the recent past of subsurface moisture conditions. Collectors captured 13% of topsoil seepage, with soil thickness, sub-season, slope, and fracture properties as major factors. The mobile percolate inventory showed strong seasonality, driven by weather conditions. The solute signature differed markedly from that of soil seepage, more closely resembling groundwater. Winter high-flows translocated most of the organic carbon and a broad spectrum of mineral particles, up to 160 µm large mineral-organic aggregates, and bioparticles. Bacterial diversity suggests a distinct aeration-zone microbiome adapted to fluctuating habitat conditions, serving as a dispersal source for phreatic communities. Our findings showcase complex dynamics between matter sources, transformations, and sinks. Weather extremes affect the formation and transport of matter through regolith and bedrock. Increasing above- and belowground effects of climate change could thus impair subsurface services, including the provision of high-quality groundwater. We advocate considering thick recharge-area aeration zones as key compartments for subsurface life and for the evolution of groundwater quality.},
}

@article {pmid41475022,
year = {2025},
author = {Chen, N and Pang, D and Shang, H},
title = {Akkermansia muciniphila: A double-edged sword in life-stage-specific nutritional modulation of Parkinson's disease via the gut-brain axis.},
journal = {Microbiological research},
volume = {305},
number = {},
pages = {128436},
doi = {10.1016/j.micres.2025.128436},
pmid = {41475022},
issn = {1618-0623},
abstract = {The gut mucin specialist Akkermansia muciniphila (A. muciniphila) exhibits a paradoxical duality in PD, showing both positive and negative correlations with motor and non-motor symptoms across distinct PD subtypes. This enigmatic role is further complicated by its dynamic lifespan trajectory: colonizing early life, peaking in adulthood, declining with aging, yet resurging in longevity cohorts. This review synthesizes evidence on A. muciniphila's structural components, its divergent associations with PD phenotypes, and the dietary and host factors shaping its abundance from gestation to senescence. We propose a lifespan-targeted intervention model that strategically modulates A. muciniphila, which could concurrently mitigate PD progression and promote healthy aging. We suggest suppressing its neurotoxic pathways in susceptible individuals while enhancing its beneficial functions in the aging process. Reconciling this microbial Janus face may pave the way for novel microbiome-based precision therapeutics against neurodegeneration.},
}

@article {pmid41474788,
year = {2025},
author = {Wong, KX and Chen, ST and Ong, JJ and Gan, WY and Abdul Murad, NA and Chong, CW and Ramzi, NH},
title = {Exploring gut microbiome and nutritional status among children with Autism Spectrum Disorder (MY-ASD Microbiome): A study protocol.},
journal = {PloS one},
volume = {20},
number = {12},
pages = {e0338801},
pmid = {41474788},
issn = {1932-6203},
mesh = {Humans ; *Autism Spectrum Disorder/microbiology ; *Gastrointestinal Microbiome ; Child ; Male ; Child, Preschool ; *Nutritional Status ; Case-Control Studies ; Feces/microbiology ; Saliva/microbiology ; Malaysia ; Female ; },
abstract = {BACKGROUND: Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder characterised by persistent deficits in social communication and the presence of restricted, repetitive behaviours or interests. Previous literature has identified a link between the gut and ASD; however, the underlying mechanisms remain unclear. Gut microbiota dysbiosis has been extensively reported in cohort studies of ASD, and specific microbial metabolites or by-products may serve as potential biomarkers for ASD. Additionally, children with ASD often exhibit food refusal, have a limited food repertoire and display a tendency to consume the same foods frequently; thus, these behaviours increase their risk of malnutrition (over-nutrition or under-nutrition) compared to typically developing (TD) healthy children. This study primarily aims to identify oral and gut microbiota among children with ASD and TD healthy children. The secondary aim is to determine the associations between oral and gut microbiota with nutritional status among children with ASD. The findings will enhance understanding of the aetiology of ASD and inform early intervention strategies to mitigate disease severity and early identification of malnutrition in genetically at-risk children.

METHODS AND ANALYSIS: This observational, age-matched, case-control study is conducted in Malaysia among 40 male children with ASD and age-matched with 40 TD healthy controls aged 4-10 years. The dependent variables include the microbiota profile, identified through metagenomic sequencing analysis of saliva and faecal samples, and autism severity, assessed through validated questionnaires. Independent variables include nutritional status, determined through Subjective Global Nutrition Assessment (SGNA), anthropometry and dietary measurements, gastrointestinal symptoms, eating behaviour, behavioural profile, and sleep quality. Data collection is expected to be completed by June 2026. The study nature may limit causality establishment. Analyses will use chi-square/ANOVA for group comparisons, SparCC for microbiota correlations, and mixed-effects logistic regression to model associations.

CONCLUSION: This study advances understanding of ASD-related microbiota, guiding personalised nutrition and precision healthcare in Malaysia.},
}

Humans
*Autism Spectrum Disorder/microbiology
*Gastrointestinal Microbiome
Child
Male
Child, Preschool
*Nutritional Status
Case-Control Studies
Feces/microbiology
Saliva/microbiology
Malaysia
Female

@article {pmid41474687,
year = {2025},
author = {Abulaiti, A and Yu, H and Ma, J and Wuji, A and Chi, H},
title = {Advancement on the Association between Gut Microbiota and Autism Spectrum Disorder in Children.},
journal = {Annals of nutrition & metabolism},
volume = {},
number = {},
pages = {1-24},
doi = {10.1159/000549716},
pmid = {41474687},
issn = {1421-9697},
abstract = {Autism Spectrum Disorder (ASD) is a complex neurodevelopmental disorder characterized by deficits in social interaction, communication, and the presence of restricted, repetitive behaviors. The rising global prevalence of ASD suggests a multifactorial etiology involving genetic, environmental, and neurodevelopmental factors. This review explores the establishment of the early-life microbiome, highlighting rapid microbial colonization from maternal and environmental sources. Emerging evidence indicates that delivery mode and infant feeding practices may influence ASD susceptibility. Although the concept of a sterile intrauterine environment remains debated, its investigation is valuable. The bidirectional "microbiota-gut-brain axis" has emerged as a critical pathway linking gut microbiota and brain function, offering potential therapeutic targets for ASD. Dietary patterns in children with ASD are often characterized by selectivity and restriction, which may disrupt gut microbiota composition and exacerbate gastrointestinal symptoms, thereby increasing ASD risk. Nutritional interventions and early behavioral therapies are thus essential. The gluten-free, casein-free (GFCF) diet remains controversial, with inconsistent evidence regarding its efficacy. Probiotic supplementation shows strain-specific effects, necessitating rigorous evaluation before clinical application. Given the heterogeneity of ASD, pharmacological treatments have shown limited universal efficacy. This review provides a comprehensive analysis of the interplay between diet, gastrointestinal symptoms, and ASD, evaluates the gut-brain axis as a mechanistic framework, and assesses the therapeutic potential of microbial interventions, including probiotics, prebiotics, and fecal microbiota transplantation (FMT). While promising findings have emerged, further well-designed clinical studies are needed to elucidate the complex etiology of ASD and validate therapeutic strategies.},
}

@article {pmid41474588,
year = {2025},
author = {Rattanapitoon, NK and Thanchonnang, C and Rattanapitoon, SK},
title = {Exploring the gut-biliary microbiome axis in Opisthorchis viverrini-associated cholangiocarcinoma: An overlooked pathogenic interface.},
journal = {Journal of cancer research and therapeutics},
volume = {21},
number = {7},
pages = {1464-1465},
doi = {10.4103/jcrt.jcrt_1012_25},
pmid = {41474588},
issn = {1998-4138},
}

@article {pmid41474487,
year = {2025},
author = {Mukhanbetzhanov, N and Zhetkenev, S and Vinogradova, E and Sergazy, S and Jarmukhanov, Z and Issilbayeva, A and Kossumov, A and Kassenova, A and Mukhametuly, B and Kenessarin, M and Zhumadilov, K and Stepanenko, V and Bogacheva, V and Petukhov, A and Sato, H and Endo, S and Fujimoto, N and Hoshi, M},
title = {Multicompartmental analysis of microbiome alterations under radiation stress.},
journal = {AMB Express},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13568-025-02002-4},
pmid = {41474487},
issn = {2191-0855},
support = {(Grant No. AP09057915)//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; (Grant No. AP09057915)//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; (Grant No. AP09057915)//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; (Grant No. AP09057915)//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; (Grant No. AP09057915)//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; (Grant No. AP09057915)//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; (Grant No. AP09057915)//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; (Grant No. AP09057915)//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; },
}

@article {pmid41474484,
year = {2025},
author = {Kinkpe, L and Solomon, AI and Niu, Y and Goswami, N and Ikele, CM and Hu, D and Abdessan, R and Zhigang, H and Xia, W},
title = {A guide to network analysis, multi-omics integration, and applications in livestock microbiome research.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {1},
pages = {17},
pmid = {41474484},
issn = {1573-0972},
support = {2023YFD1300300//National Key Research and Development Program of China/ ; (CARS-42-2)//China Agriculture Research System of MOF and MARA/ ; },
mesh = {Animals ; *Livestock/microbiology ; *Gastrointestinal Microbiome ; *Genomics/methods ; *Microbiota ; Computational Biology/methods ; Machine Learning ; Multiomics ; },
abstract = {The function of the livestock gut microbiome in driving animal growth, health, and methane emissions is controlled by networks of interactions among microbes. A major challenge is to move beyond simply listing microbial members to understanding these interaction networks, which determine how the community functions as a whole. This review synthesizes how network analysis, combined with multi-omics data, can meet this challenge. We focus on the critical task of identifying keystone species, the disproportionately influential microbes that direct processes like fiber digestion and immune function, yet are often missed by standard surveys. We evaluate a progression of methods, from identifying correlated species to building models that integrate genomic, metabolic, and host data. This integration is key to separating true ecological relationships from statistical noise and to linking microbial presence to function. We highlight how computational techniques like metabolic modeling and machine learning are turning networks into predictive tools. Finally, we outline the path forward: field-ready studies that track microbiomes over time, the development of livestock-specific metabolic models, and analytical standards that will allow research to translate into practical strategies. The goal is to provide a framework for using network science to actively manage the microbiome, enhancing sustainable livestock production.},
}

Animals
*Livestock/microbiology
*Gastrointestinal Microbiome
*Genomics/methods
*Microbiota
Computational Biology/methods
Machine Learning
Multiomics

@article {pmid41474336,
year = {2025},
author = {Vazquez-Munoz, R and Ranjan, A and Bertolini, M and Thompson, A and Mosharaf Ghahfarokhy, P and Harnden, A and Nobile, CJ and Sobue, T and Vera-Licona, P and Dongari-Bagtzoglou, A},
title = {Enterococcus faecalis induces H2O2-mediated epithelial cell death and enhances Candida albicans virulence in oropharyngeal candidiasis.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0082225},
doi = {10.1128/msphere.00822-25},
pmid = {41474336},
issn = {2379-5042},
abstract = {UNLABELLED: In immunosuppressed humans with oropharyngeal candidiasis (OPC) and in mice with experimental OPC, Candida albicans infection is associated with a bacterial imbalance characterized by significantly reduced oral microbiome diversity and the expansion of enterococcal and streptococcal species, which may exacerbate oral mucosal pathology. In this study, we applied an unbiased genome-wide transcriptomic profiling approach to shed further mechanistic light on the role of indigenous enterococcal communities in mucosal infection in a mouse model of cancer chemotherapy-associated OPC. Transcriptomic profiling of tongue tissues revealed a wide-ranging, barrier-compromising molecular activity of resident enterococci that explains the previously observed attenuation of fungal mucosal invasion with antibiotic treatment in this mouse model. Mechanistically, we validated the pathogenic potential of resident bacteria by showing that enterococci isolated from mice with OPC produce hydrogen peroxide (H2O2) and induce oral epithelial cell death through apoptosis and necrosis in vitro. We also discovered that C. albicans increased enterococcal H2O2 production. These findings uncover a novel mechanism of pathogenic synergy between C. albicans and Enterococcus faecalis, which may be responsible for increased epithelial barrier damage and mucosal invasion by C. albicans hyphae during cancer chemotherapy.

IMPORTANCE: Chemotherapy-induced mucosal barrier injury and immune suppression increase susceptibility to oropharyngeal candidiasis (OPC), a debilitating fungal infection. Our study uncovers a previously unknown pathogenic interaction between Candida albicans and Enterococcus faecalis, by showing that indigenous enterococci produce H2O2, which contributes to oral epithelial cell death during fungal infection. By integrating transcriptomics with functional assays, we demonstrate that enterococci compromise epithelial integrity independently of fungal burdens, highlighting the role of the bacterial microbiota in driving tissue damage. These findings emphasize the need to consider bacterial-fungal interactions in managing OPC and suggest that targeting the microbial crosstalk could be a promising adjunctive strategy in immunocompromised hosts.},
}

@article {pmid41474178,
year = {2025},
author = {Yang, XG and Yan, YW and Zhang, XX and Su, Y and Chen, MX and Li, XY},
title = {Decoding Plant-Microbe Interactions through the Kiwifruit Microbiome in Bacterial Canker Disease.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c12587},
pmid = {41474178},
issn = {1520-5118},
abstract = {Numerous communities of bacteria, fungi, viruses, and other microorganisms live inside plants and colonize their internal and external tissues, having a significant impact on the health and functionality of the plants. Studies on infection specific microbiome interactions remain restricted in spite of broad studies of plant microbiome interactions. An excellent model for examining these interactions is kiwifruit bacterial canker (KBC), which is caused by Pseudomonas syringae pv actinidiae (Psa). The present understanding of Psa pathogenicity and kiwifruit-associated microbiomes in various ecological niches is summarized in this review with a focus on their dual functions of either promoting or suppressing disease. We identify important microbial taxa and interaction mechanisms that serve as ecological leverage points for KBC control mediated by the microbiome by incorporating recent findings. This perspective advances the conceptual shift from pathogen elimination to microbiome balance restoration, offering new insights into sustainable KBC management.},
}

@article {pmid41473794,
year = {2025},
author = {Han, EJ and Ganley, JG and Winner, CB and An, JS and Seyedsayamdost, MR},
title = {Tetracycline Antibiotics Induce Biosynthesis of Pro-Inflammatory Metabolites in the Immunobiotic Bacteroides dorei.},
journal = {ACS central science},
volume = {11},
number = {12},
pages = {2421-2432},
pmid = {41473794},
issn = {2374-7943},
abstract = {The human gut microbiome consists of diverse microbes that communicate through small molecules. Numerous recent studies have demonstrated links between gut microbiota and host physiological processes; however, the underlying metabolites remain elusive in part because laboratory conditions do not replicate the native environment of these bacteria. Herein, we focused on Bacteroides dorei, a predominant and representative member of human gut microbiota, to interrogate the chemical composition and possible biological functions of its secondary metabolome. Using UPLC-MS-guided high-throughput elicitor screening (HiTES), we examined how the metabolome of this commensal bacterium responds to hundreds of FDA-approved drug molecules that the host may intake. We identified low-dose tetracyclines as pleiotropic inducers of the B. dorei secondary metabolome, leading to the identification and structural elucidation of six serine-glycine dipeptide lipids, named doreamides A-F, and two 6-N-acyladenosines. The induced doreamides and N-acyladenosines exhibited pro-inflammatory activities, upregulating tumor necrosis factor α (TNFα), interleukin (IL)-1β, IL-6, and IL-10 in macrophages. Doreamides also triggered production of cathelicidin, which inhibits the growth of multiple bacteria tested but not B. dorei. Our results show that low-dose antibiotics can perturb the secondary metabolome of gut bacteria, and that these induced metabolites can exert immunomodulatory effects and restructure the microbiome.},
}

@article {pmid41473772,
year = {2025},
author = {Wang, T and Cao, H and Ma, S and Wang, Z and Liu, H and Zhang, H and Wang, Q},
title = {Periodontal disease and gastric and colorectal cancers: mechanisms and therapeutic perspectives.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1699738},
pmid = {41473772},
issn = {2235-2988},
mesh = {Humans ; *Colorectal Neoplasms/therapy/epidemiology/prevention & control/etiology ; *Periodontal Diseases/complications/therapy/epidemiology ; *Stomach Neoplasms/therapy/epidemiology/prevention & control/etiology ; },
abstract = {Periodontal disease (PD) is one of the most prevalent chronic oral diseases globally, characterized by chronic inflammatory responses in the gingiva and supporting periodontal tissues. Recent epidemiological and mechanistic studies have indicated that PD not only adversely affects oral health but is also significantly associated with gastric and colorectal cancers. This article reviews the potential link between PD and these gastrointestinal malignancies, exploring the underlying pathogenic mechanisms and potential strategies for preventing and treating gastric and colorectal cancers through the management of PD. Periodontal health management may represent an adjunct avenue for the prevention and control of gastrointestinal cancers; however, high-quality longitudinal and interventional studies are needed to clarify causality.},
}

Humans
*Colorectal Neoplasms/therapy/epidemiology/prevention & control/etiology
*Periodontal Diseases/complications/therapy/epidemiology
*Stomach Neoplasms/therapy/epidemiology/prevention & control/etiology

@article {pmid41473771,
year = {2025},
author = {Mao, X and Hu, X and Fang, J},
title = {Gut microbiota-metabolite interactions in drug-induced liver injury: mechanisms, biomarkers, and therapeutic perspectives.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1737234},
pmid = {41473771},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Chemical and Drug Induced Liver Injury/microbiology/metabolism/therapy ; Biomarkers/metabolism ; Dysbiosis ; Animals ; Liver/metabolism ; },
abstract = {Drug-induced liver injury (DILI) remains a major obstacle in clinical pharmacotherapy and a leading cause of acute liver failure and drug withdrawal worldwide. Conventional mechanistic models centered on hepatic xenobiotic metabolism, oxidative stress, and immune injury cannot fully account for the substantial interindividual variability and the unpredictable nature of idiosyncratic DILI. Increasing evidence shows that the gut microbiota and its metabolites critically shape hepatic susceptibility through modulation of drug metabolism, inflammatory signaling, and intestinal barrier integrity. This review summarizes current understanding of the gut-liver axis in DILI pathogenesis, with a focus on microbial enzymes such as β-glucuronidase that reactivate detoxified drug conjugates, microbial dysbiosis that disrupts bile acid homeostasis, and depletion of short chain fatty acids and indole derivatives that normally support epithelial defenses and immunologic tolerance. Drug-specific microbial patterns are discussed, including acetaminophen, amoxicillin-clavulanate, anti-tuberculosis regimens, and immune checkpoint inhibitors. We introduce the concept of metabotype-dependent hepatotoxicity, which emphasizes that individual microbial metabolic profiles influence DILI risk. Advances in metagenomics, metabolomics, and integrative multi-omics enable the identification of microbial biomarkers and functional pathways associated with DILI susceptibility. Emerging therapeutic strategies include restoration of microbial homeostasis, selective inhibition of microbial enzymes, and supplementation of hepatoprotective metabolites. Finally, we outline key challenges and future directions toward translating microbiome-based insights into clinical prediction and precision prevention of DILI. Importantly, this review integrates microbial metabolic functions with precision hepatology concepts, highlighting how metabotype-driven variability can be leveraged for individualized DILI risk assessment.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Chemical and Drug Induced Liver Injury/microbiology/metabolism/therapy
Biomarkers/metabolism
Dysbiosis
Animals
Liver/metabolism

@article {pmid41473770,
year = {2025},
author = {Machado, A and Foschi, C and Liao, Q and Xiao, B and Marangoni, A},
title = {Editorial: Advances in vaginal microbiome and metabolite research: genetics, evolution, and clinical perspectives.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1755233},
pmid = {41473770},
issn = {2235-2988},
}

@article {pmid41473686,
year = {2025},
author = {Yao, X and Zou, X and Cao, B},
title = {The Human Respiratory Virome in Health and Disease: Interactions, Dysbiosis, and Methodological Challenges.},
journal = {Advanced genetics (Hoboken, N.J.)},
volume = {6},
number = {4},
pages = {e00022},
pmid = {41473686},
issn = {2641-6573},
abstract = {The human respiratory virome is an underexplored component of the microbiome that includes diverse DNA and RNA viruses such as eukaryotic viruses, bacteriophages, and archaeal viruses. Recent advances in metagenomics have revealed the complexity and dynamic nature of the human respiratory virome, which interacts closely with the host and the bacterial microbiome to influence respiratory health and disease. In healthy individuals, the virome is characterized by low biomass and high temporal variability, with Anelloviruses predominant in the upper airways, whereas Streptococcus phages and herpesviruses are most commonly detected in the lower airways. Common respiratory viruses, such as respiratory syncytial virus, human rhinovirus, and influenza A virus, can persist after acute infection and modulate host immunity. The respiratory virome also plays a significant role in chronic respiratory diseases. Despite its importance, research on the respiratory virome is hampered by technical challenges, including low viral abundance and limited reference databases. This review summarizes current understanding of the composition and determinants of the respiratory virome in healthy individuals, describes its interactions with the host and respiratory microbiota, including the potential modulatory roles of bacteriophages, outlines virome alterations in respiratory diseases, examines methodological challenges, and highlights potential clinical applications and future research directions.},
}

@article {pmid41473682,
year = {2025},
author = {Fu, X and Wu, F and Liu, X},
title = {Bio-Archive of Cultural Heritage Microbiomes for Sustainable Conservation in the Multi-Omics Era.},
journal = {Advanced genetics (Hoboken, N.J.)},
volume = {6},
number = {4},
pages = {e00046},
pmid = {41473682},
issn = {2641-6573},
abstract = {Cultural heritage sites are commonly exposed to outdoor environments, resulting in severe damage to heritage objects from biotic and abiotic processes. Control of outdoor environments is impossible for heritage conservation, and we cannot prevent the abiotic processes. However, a variety of mitigation management can be developed for biotic damage, such as microbial colonization and biodeterioration. Over the past few decades, both conventional cultivation-dependent and modern cultivation-independent techniques have been employed to elucidate the microbiomes associated with the biodeterioration of cultural heritage. However, many studies are limited to segmentary analyses or simply stop at examining the community composition of the microbiomes, lacking solid evidence of microbial metabolism and biochemical reactions between microorganisms and heritage materials to support the core microbiomes associated with the biodeterioration. Here, we recommend thoroughly exploring the benefits of more advanced multi-omics techniques for analyzing cultural heritage microbiomes. We propose establishing a professional open-access database to standardize analytical procedures, integrating both culture-dependent and culture-independent approaches, and bio-archive valuable information on the core microbiomes, including their biodeterioration mechanisms, timelines, causes, and environmental conditions. This bio-archive of cultural heritage microbiomes will empower conservators and researchers worldwide to develop evidence-based, sustainable approaches for cultural heritage conservation under environmental change.},
}

@article {pmid41473651,
year = {2025},
author = {Damoulaki, E and Sioutis, D and Sarli, V and Trakakis, E and Mastorakos, G and Katoulis, A and Kastrinakis, K and Koratzanis, C and Machairiotis, N and Panagopoulos, P and Christodoulaki, C},
title = {Polycystic Ovary Syndrome-Associated Acne: The Interplay of Hyperandrogenism, Insulin Resistance, and Therapeutic Strategies.},
journal = {Cureus},
volume = {17},
number = {11},
pages = {e98103},
pmid = {41473651},
issn = {2168-8184},
abstract = {Acne vulgaris is one of the most prevalent dermatologic disorders in adolescent and adult women. Beyond classic pathogenic factors, such as sebaceous hypersecretion, follicular hyperkeratinization, Cutibacterium acnes overgrowth, and inflammation, endocrine drivers are pivotal. Polycystic ovary syndrome (PCOS) is common across reproductive ages and frequently presents with dermatologic manifestations, notably acne, through mechanisms dominated by hyperandrogenism and compounded by insulin resistance (IR). This narrative review synthesizes current evidence linking PCOS with acne, explains the interrelated roles of hyperandrogenism and IR, and outlines evidence-based management strategies tailored to women with PCOS. The Rotterdam diagnostic framework remains the globally favored standard for PCOS, emphasizing combinations of oligo-/anovulation, clinical/biochemical hyperandrogenism, and polycystic ovarian morphology. PCOS pathophysiology involves dysregulation of the hypothalamic-pituitary-ovarian axis with increased gonadotropin-releasing hormone pulsatility, elevated luteinizing hormone, and suppression of follicle-stimulating hormone, promoting thecal androgen excess and impaired folliculogenesis. IR, prevalent in PCOS, augments ovarian/adrenal androgen synthesis and lowers sex hormone-binding globulin levels, increasing free testosterone and sebum production; IGF-1 signaling further amplifies sebogenesis and follicular hyperkeratinization. Emerging data implicate genetic/epigenetic determinants, endocrine-disrupting chemicals, gut microbiome dysbiosis, and endoplasmic reticulum stress as modulators of the PCOS-acne phenotype. Epidemiologic studies and meta-analyses report higher acne prevalence and severity in PCOS, particularly among adolescents. First-line therapy includes combined oral contraceptive pills with antiandrogenic progestins; spironolactone is an effective adjunct. Where indicated, metformin addresses IR and may improve acne and ovulatory function. Judicious use of standard acne modalities such as topical retinoids, benzoyl peroxide, and oral/topical antibiotics remains essential; oral isotretinoin is reserved for refractory disease with careful risk management. PCOS-associated acne reflects converging endocrine and metabolic disturbances. Integrating androgen-targeted therapy, IR mitigation, and guideline-based acne care provides the most durable control. Future research should refine phenotype-directed treatment and clarify the contributions of microbiome, environmental exposures, and cellular stress pathways.},
}

@article {pmid41473600,
year = {2025},
author = {Zhang, Z and Chang, C and Xiao, L and Su, H and Lyu, Y and Zhao, J and Chen, J and Gou, K and Zhou, J and Wang, C and Zhu, X and Fu, S and Lu, M and Shi, L},
title = {The Neuroimmune Axis in Atopic Dermatitis: From Pathogenic Mechanisms to Targeted Neuroimmunotherapy.},
journal = {Journal of inflammation research},
volume = {18},
number = {},
pages = {18079-18113},
pmid = {41473600},
issn = {1178-7031},
abstract = {Atopic dermatitis (AD) is a chronic, relapsing inflammatory skin disease in which intense pruritus and eczematous lesions arise from tightly coupled disturbances of the nervous and immune systems. Emerging evidence indicates that a dysregulated neuroimmune axis-as reflected by peripheral neuronal sensitization, epidermal barrier dysfunction, and central itch processing-plays a central role in disease onset, persistence, and clinical heterogeneity. In this review, we synthesize current knowledge on the neuroimmune mechanisms that drive AD, focusing on how cytokines such as IL-31, IL-4/IL-13, TSLP and IL-33, together with neuropeptides including substance P, CGRP and VIP, establish self-reinforcing itch-scratch and inflammation loops at the level of the skin and the central nervous system. We then highlight recent multi-omics and systems biology approaches, including single-cell and spatial transcriptomics, neuroimaging, and microbiome profiling, that have reshaped the understanding of neuroimmune "neighbourhoods" and the gut-skin-brain axis in AD. Building on these mechanistic insights, we summarize key neuroimmune biomarkers-such as NGF, IL-31, TARC/CCL17, S100 proteins, barrier-related lipids, neurofunctional readouts from fMRI, and microbial signatures-and discuss their potential for improving diagnosis, patient stratification, and treatment monitoring within a precision medicine framework. Finally, we review established and emerging neuroimmune-targeted therapies, including IL-4/IL-13 and IL-31 pathway inhibitors, JAK inhibitors, OX40/OX40L-directed biologics, TRP and NK1R antagonists, phototherapy, and microbiome-based interventions, with a particular emphasis on biomarker-guided sequencing and combination strategies. Overall, we propose that positioning the neuroimmune axis at the core of AD pathogenesis provides a conceptual basis for developing stratified, durable, and patient-centred neuroimmunotherapy, while also outlining the remaining challenges regarding clinical validation of biomarkers, long-term safety, accessibility, and implementation across diverse patient populations.},
}

@article {pmid41473328,
year = {2025},
author = {Primov, K and Scott, C and Huzar, A and Peterson, C and Kirkpatrick, M and Matz, M},
title = {Acropora millepora 's microbiome is predicted by algal symbionts, host genetics, and environment.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2025.12.15.694400},
pmid = {41473328},
issn = {2692-8205},
abstract = {The coral microbiome is a critical component of coral health and resilience, yet it is unclear what factors drive coral microbiome composition, especially within the context of coral bleaching. Here, we use whole genome sequencing data combined with a machine learning approach (RDAforest) to assess predictors of the microbiome in 208 colonies of Acropora millepora from 12 reef sites in the Central Great Barrier Reef during a 2016 bleaching event. We characterized microbiome variation using k-mers. While some environmental variables, such as chlorophyll seasonal range and maximum degree heating weeks, were associated with microbiome composition, we find that host genetics and dominant photosymbionts were more powerful predictors. In contrast, bleaching score had negligible predictive power. The coral's microbiome therefore correlates with dominant photosymbiont identity even during a bleaching event. The association of the microbiome with the environment suggests that the coral microbiome can serve as a proxy for environmental variation when environment cannot be measured directly, which may be especially useful in ancient DNA studies.},
}

@article {pmid41473293,
year = {2025},
author = {Estrada, KB and Azamar, KMM and Wang, C and Sudi, SD and Friday-Saunders, K and Márquez, V and Quintanilla-Carvajal, MX and Acosta-González, A and Conde-Martinez, N and Porras, AM and Alviña, K},
title = {Supplementation with a Limosilactobacillus fermentum K73 synbiotic modulates gut microbiota function and behavior in gnotobiotic mice transplanted with microbiota from children diagnosed with autism spectrum disorder.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2025.12.16.694732},
pmid = {41473293},
issn = {2692-8205},
abstract = {BACKGROUND: Gut dysbiosis has been implicated in numerous pathological conditions, including neurodevelopmental and neurodegenerative disorders. Recently, dietary interventions targeted at restoring microbial balance have therefore gained attention as potential therapeutic strategies. We recently demonstrated that an encapsulated synbiotic containing high-oleic palm oil and Limosilactobacillus fermentum K73 can modulate the metabolic activity and composition of human-derived gut microbiota in an in vitro batch bioreactor. Here, we extended this work through an in vivo supplementation pilot study using gnotobiotic mice colonized with gut microbiota from Colombian pediatric patients diagnosed with autism spectrum disorder (ASD) or age-matched neurotypical (NT) donors. Behavioral assessments and analyses of gut microbiota composition and function were performed before and after synbiotic supplementation.

RESULTS: First, we found that the gut microbiota from Colombian ASD patients exhibited significantly reduced richness relative to NT donors, consistent with reports from other geographical regions, and displayed distinct compositional features unique to this population. Humanization of the gnotobiotic mice with this donor microbiota was successful, with murine gut communities reflecting features of their corresponding donor microbiota. Notably, synbiotic supplementation induced significant increases in the abundance of beneficial taxa and the production of short chain fatty acids that were more pronounced in mice colonized with ASD-derived microbiota, with concurrent behavioral changes associated with beneficial modulation of gut microbiota.

CONCLUSIONS: Overall, we provide evidence that supports synbiotic supplementation as a viable strategy to positively modulate gut microbiome in conditions of dysbiosis. Our study also expands the body of knowledge of gut microbiome to understudied populations such as Latin America.},
}

@article {pmid41473253,
year = {2025},
author = {Wagner, ES and Oliphant, K and D'Souza, M and Cruz-Ayala, W and Azzam, RK and Andrews, B and Claud, EC},
title = {Fecal Microbiome and Bile Acid Profiles Differ in Preterm Infants with Parenteral Nutrition-associated Cholestasis.},
journal = {Journal of clinical and translational hepatology},
volume = {13},
number = {12},
pages = {1036-1045},
pmid = {41473253},
issn = {2310-8819},
abstract = {BACKGROUND AND AIMS: Parenteral nutrition (PN)-associated cholestasis (PNAC) is frequently diagnosed in premature infants; however, not all PN-exposed infants develop PNAC. We propose that, in premature infants receiving PN and varying amounts of enteral feeds, differences in the gut microbiome and fecal bile acid content are associated with PNAC development. This study aimed to examine the fecal microbiome and bile acid content of premature infants on PN to determine if there is a relationship with the development of PNAC.

METHODS: Twenty-two preterm infants had serial bilirubin measurements and fecal samples collected during their neonatal intensive care unit admission. Fecal samples underwent 16S rRNA gene sequencing and bile acid analysis. Binomial regression, adjusting for postmenstrual age with feed amount as a moderator, was used to assess the impact of the fecal microbiome and bile acids on PNAC development.

RESULTS: Cholestatic patients (n = 11) had greater PN and antibiotic exposure (p = 0.020; p = 0.010) and longer neonatal intensive care unit stays (p = 0.0038) than non-cholestatic patients. Microbiome richness was higher in non-cholestatic infants (p < 2E-16), with no difference in β diversity (p = 1.0). Cholestatic infants had a significantly higher abundance of Proteobacteria and Fusobacteriota and a lower abundance of Bacteroidota (p < 2E-16). Akkermansia was abundant in all infants on low feeds; as feed volume increased, Akkermansia abundance significantly increased in non-cholestatic infants (p < 2E-16). Bile acid analysis demonstrated significantly lower deoxycholic acid concentrations in cholestatic infants (p < 2E-16). Metagenomic analysis revealed an increase in Proteobacteria requiring augmented stress responses in non-cholestatic infants.

CONCLUSIONS: This is the first study to directly explore the relationship between PNAC susceptibility, the microbiome, and fecal bile acids in preterm infants. The microbiome and bile acid patterns identified here may inform the development of targeted therapeutics for this vulnerable population.},
}

@article {pmid41473248,
year = {2025},
author = {Zhang, Y and Cao, J and Wang, Y and Fan, X and Deng, R and Mi, J},
title = {Effects of fecal microbiota transplantation on glycemic and lipid profiles in overweight or obese patients with metabolic disorders: a systematic review and meta-analysis.},
journal = {Frontiers in endocrinology},
volume = {16},
number = {},
pages = {1737543},
pmid = {41473248},
issn = {1664-2392},
mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; *Obesity/therapy/blood/complications ; *Metabolic Diseases/therapy/blood ; *Overweight/therapy/blood ; *Lipids/blood ; *Blood Glucose/metabolism ; Gastrointestinal Microbiome ; Randomized Controlled Trials as Topic ; Lipid Metabolism ; },
abstract = {UNLABELLED: Obesity and its associated metabolic disorders (such as type 2 diabetes, metabolic syndrome, and NAFLD/MASLD) represent a global health challenge. Fecal microbiota transplantation (FMT), as a therapy regulating the gut microbiome, has demonstrated inconsistent clinical efficacy. This systematic review aims to evaluate the impact of FMT on key indicators of glucose and lipid metabolism in overweight/obese adults with metabolic diseases. We systematically searched PubMed, Embase, Cochrane, and Web of Science databases up to September 28, 2025, to identify randomized controlled trials evaluating FMT for obesity and metabolic disorders. Data were pooled using a random-effects model, with primary outcomes being changes in BMI, HOMA-IR, and HbA1c relative to baseline. A total of 11 RCTs (320 participants) were included. The primary analysis showed that FMT intervention demonstrated a trend toward improvement in the primary outcome measures, BMI (MD: -0.65, p = 0.070) and HOMA-IR (MD: -0.64, p = 0.062), but these trends did not reach statistical significance. There was no significant effect on HbA1c (MD: 0.06, p = 0.742). However, this negative conclusion based on the conventional assumption (Corr = 0.5) exhibited high instability: sensitivity analysis revealed that FMT's improvement effects on BMI became statistically significant (p = 0.010) when the correlation coefficient (Corr) used to estimate the standard deviation of change was adjusted to 0.75. Furthermore, meta-regression analysis revealed that treatment regimen, follow-up duration, and patient baseline characteristics were significantly associated with HbA1c efficacy. Based on the current "low" certainty evidence, the overall improvement of metabolic parameters in overweight or obese patients with metabolic diseases following FMT did not reach statistical significance in the primary analysis. However, the robustness of this negative finding is limited, exhibiting high sensitivity to statistical hypotheses and likely being significantly confounded by methodological factors (e.g., administration protocols) and donor variability. Consequently, the true efficacy of FMT for treating systemic metabolic disorders remains uncertain. Future trials should shift toward precision medicine, prioritizing the standardization of donor selection and optimization of administration protocols.

https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD420251172011, identifier CRD420251172011.},
}

Humans
*Fecal Microbiota Transplantation/methods
*Obesity/therapy/blood/complications
*Metabolic Diseases/therapy/blood
*Overweight/therapy/blood
*Lipids/blood
*Blood Glucose/metabolism
Gastrointestinal Microbiome
Randomized Controlled Trials as Topic
Lipid Metabolism

@article {pmid41473189,
year = {2025},
author = {Duysburgh, C and Verstrepen, L and Van Meulebroek, L and Marzorati, M},
title = {Tributyrin (CoreBiome[®]) enhances butyrate levels and modulates the gut microbiota, barrier function, and immune response in vitro.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1712993},
pmid = {41473189},
issn = {2296-861X},
abstract = {BACKGROUND/OBJECTIVES: Oral butyrate is unstable during upper gastrointestinal tract (GIT) transit and very little reaches the colon. Tributyrin, a butyrate precursor, resists gastric acid and is converted to butyrate by pancreatic lipases. This study aimed to quantify tributyrin stability during upper GIT passage and to uncover the effects of tributyrin supplementation on the human gut microbiome and cellular responses.

METHODS: In vitro upper GIT simulations were used to evaluate the stability of a capsule and softgel formulation of tributyrin (CoreBiome[®]). The effects of tributyrin supplementation on the human gut microbiome and cellular responses were evaluated using the Simulator of the Human Intestinal Microbial Environment (SHIME[®]) model and Caco-2/THP1 co-cultures.

RESULTS: The upper GIT simulations showed that 40.9 and 48.7% of the tributyrin dose administered via the capsule or softgel, respectively, was hydrolyzed to butyrate in the small intestine; 59.1 and 51.3% remained stable and was available to enter the colon. Using the SHIME[®] model, it was shown that 3 weeks of daily tributyrin supplementation increased butyrate levels and enhanced the abundance of several bacterial species, including Bifidobacterium spp. and Akkermansia mucinophila. Metabolic impacts on the gut microbiome were also observed. Assessment of cellular responses revealed that tributyrin fermentation had a protective effect on the intestinal barrier and exerted immunomodulatory properties.

CONCLUSION: Enhanced butyrate concentrations and beneficial impacts on the gut microbial community composition were observed in an in vitro simulation of the human intestinal environment, suggesting that tributyrin could be considered as a solid alternative to butyrate supplementation.},
}

@article {pmid41472866,
year = {2025},
author = {Namasivayam, S and Romero-Soto, HN and Bacorn, M and Perez-Chaparro, PJ and Burns, AS and Mistry, S and Brandes, N and Chong, A and Cooper, G and LaCroix, IS and LaPoint, P and Banks, K and Chen, Q and Patel, A and Mueller, NT and Dominguez-Bello, MG and Maxwell, GL and Levy, S and Schwarz, B and Belkaid, Y and Hourigan, SK},
title = {The pioneering gut microbiome acquired via different delivery modes in neonates shapes distinct immune and metabolic environments.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.09.30.25337005},
pmid = {41472866},
abstract = {BACKGROUND: Cesarean section (CS) delivery is associated with an increased risk of inflammatory diseases, hypothesized to be driven by differences in the microbiome acquired at birth compared to vaginally delivered (VD) infants. How delivery mode associated differences in initial colonizers directly modulate early life immune education and metabolic development is poorly understood.

OBJECTIVE: First, to investigate how differences in pioneering colonizers associated with delivery mode directly modulate early life immune education and metabolic programming. Second, to examine the effect of vaginal seeding, an intervention aimed to restore the microbiome of CS infants to a VD state.

DESIGN: Germ-free mice were colonized with transitional stool from VD, CS or CS-delivered and vaginally seeded neonates. Immune cell populations, serum immunoglobulin levels, and fecal microbiome and metabolome profiles were analyzed.

RESULTS: Mice colonized with stool from VD neonates displayed increased numbers of myeloid cells at barrier tissues, whereas CS microbiome colonized mice exhibited decreased Th1/Th2 ratios and increased serum IgE levels. Key amino-acid pathways including tryptophan metabolism, riboflavin co-enzymes and carbohydrate metabolites were significantly enriched in the murine VD fecal metabolome and correlate with the increased abundance of Escherichia typically observed in the VD microbiome. Mice colonized with stool from CS neonates who received vaginal seeding, resulted in increased regulatory T cells and serum IgA in mice, suggesting potential benefits of vaginal seeding.

CONCLUSION: Collectively, our studies demonstrate the ability of pioneering colonizers to set the immune and metabolic tone that could have long-lasting effects and provide avenues for microbiome-mediated interventions.},
}

@article {pmid41472856,
year = {2025},
author = {Qi, C and Zhang, Y and Qing, W and Chen, R and Zhou, Z and Liu, Y and Chen, E and Chen, W and , and Zhou, H and Chen, M},
title = {Nationwide profiling of vaginal microbiota in Chinese women reveals age-dependent shifts and predictive biomarkers for reproductive health.},
journal = {iMeta},
volume = {4},
number = {6},
pages = {e70088},
pmid = {41472856},
issn = {2770-596X},
abstract = {The vaginal microbiome is central to reproductive health, yet large-scale studies in East Asian populations remain scarce. Here, we characterized the vaginal microbiota of 6423 Chinese women of reproductive age across 18 provinces and assessed associations with 33 host factors. We observed a striking compositional transition around age 40, marked by declining Lactobacillus crispatus and enrichment of dysbiosis-associated taxa including Gardnerella vaginalis, independent of lifestyle or sociodemographic influences. Sexual behavior, contraceptive use, and educational attainment emerged as key determinants of community structure, differentially shaping Lactobacillus crispatus and Lactobacillus iners. Despite these associations, host factors explained less than 2% of overall variation, highlighting the resilience and individuality of the vaginal microbiome. To quantify vaginal health, we derived a microbiome balance score, validated it in external cohorts, and demonstrated its predictive power for incident bacterial vaginosis and sexually transmitted infections. Our findings establish a national-scale reference for the vaginal microbiome in Chinese women, reveal a midlife inflection point in microbial composition, and introduce a clinically actionable metric for risk stratification. These insights advance mechanistic understanding of host-microbiome interactions and inform strategies for precision interventions to preserve vaginal health.},
}

@article {pmid41472855,
year = {2025},
author = {Wu, D and Wang, AJ and Bu, DC and Sun, YY and Li, CH and Hong, YM and Zhang, S and Chen, SY and Zhou, JA and Zhang, TY and Yu, MH and Ma, YJ and Wang, XL and Xu, J and He, W and Heeschen, C and Chen, JF and Mao, WJ and Ding, H and Wu, WJ and Zhao, Y and Wang, H and Liu, NN},
title = {The interplay between tissue-resident microbiome and host proteins by integrated multi-omics during progression of colorectal adenoma to carcinoma.},
journal = {iMeta},
volume = {4},
number = {6},
pages = {e70090},
pmid = {41472855},
issn = {2770-596X},
abstract = {The intratumoral microbiome is an emerging hallmark of cancer, yet its multi-kingdom host-microbiome ecosystem in colorectal cancer (CRC) remains poorly characterized. Here, we conducted an integrated analysis using deep shotgun metagenomics and proteomics on 185 tissue samples, including adenoma (A), paired tumor (T), and para-tumor (P). We identified 4057 bacterial, 61 fungal, 108 archaeal, and 374 viral species in tissues and revealed distinct intratumor microbiota dysbiosis, indicating a CRC-specific multi-kingdom microbial ecosystem. Proteomic profiling uncovered four CRC subtypes (C1-C4), each with unique clinical prognoses and molecular signatures. We further discovered that host-microbiome interactions are dynamically reorganized during carcinogenesis, where different microbial taxa converge on common host pathways through distinct proteins. Leveraging this interplay, we identified 14 multi-kingdom microbial and 8 protein markers that strongly distinguished A from T samples (area under the receiver operating characteristic curve (AUROC) = 0.962), with external validation in two independent datasets (AUROC = 0.920 and 0.735). Moreover, we constructed an early- versus advanced-stage classifier using 8 microbial and 4 protein markers, which demonstrated high diagnostic accuracy (AUROC = 0.926) and was validated externally (AUROC = 0.659-0.744). Functional validation in patient-derived organoids and murine allograft models confirmed that enterotoxigenic Bacteroides fragilis and Fusobacterium nucleatum promoted tumor growth by activating Wnt/β-catenin and NF-κB signaling pathways, corroborating the functional potential of these biomarkers. Together, these findings reveal dynamic host-microbiome interactions at the protein level, tracing the transition from adenoma to carcinoma and offering potential diagnostic and therapeutic targets for CRC.},
}

@article {pmid41472853,
year = {2025},
author = {Xu, J and Hu, P and Liu, M and Zhang, W and Xie, K},
title = {Cultivar-specific preference of bacterial communities and host immune receptor kinase modulate the outcomes of rice-microbiota interactions.},
journal = {iMeta},
volume = {4},
number = {6},
pages = {e70098},
pmid = {41472853},
issn = {2770-596X},
abstract = {Deciphering how plant-microbiota interactions achieve beneficial outcomes for crops will provide innovative strategies for sustainable agriculture. Here, we dissected rice-microbiota dynamics using a tailored gnotobiotic cultivation system that models the semiaquatic environment in a paddy field. Inoculation with native soil microbiota resulted in root-growth-promotion (RGP) and root-growth-inhibition (RGI) phenomena in different cultivars. This preference persisted in a simplified synthetic community and individual bacterial strains, indicating that cultivar-specific growth promotion is an intrinsic property of microbial inocula. Though stochastic process dominated the assembly of root microbiome in gnotobiotic cultivation, absolute quantification revealed that imbalance of detrimental and beneficial bacterial loads in roots correlated with RGP or RGI outcomes in different rice cultivars. From the host perspective, genetic screening identified that receptor-like kinase mutants, including OsFLS2 (FLAGELLIN-SENSITIVE 2), inverted microbiota functionality, converting RGP to RGI. In particular, over 4534 rice genes responded to microbiota inoculation and 46.1% of them were reprogrammed in osfls2 mutants, demonstrating the prominent regulatory role of OsFLS2 in rice-microbiota signaling. On the basis of these results, we propose that the rice-microbiota relationships are gated by cultivar-specific preferences of the bacterial microbiota and host immune receptor kinase, which provides a useful framework for crop microbiome engineering in the future.},
}

@article {pmid41472849,
year = {2025},
author = {Xiao, Z and Ding, K and Guo, X and Zhao, Y and Li, X and Jiang, D and Zhu, D and Chen, Q and Jong, MC and Graham, DW and Li, G and Zhu, YG},
title = {Soil-borne legacy facilitates the dissemination of antibiotic resistance genes in soil-plant continua.},
journal = {iMeta},
volume = {4},
number = {6},
pages = {e70094},
pmid = {41472849},
issn = {2770-596X},
abstract = {Antimicrobial resistance (AMR) disseminates throughout the soil-plant continuum via complex microbial interactions. Plants shape root- and leaf-associated microbiomes that sustain plant health; however, soil-borne legacies-enriched with antibiotic-producing microbes and resistance genes-govern AMR dynamics across agroecosystems. Using 16S rRNA gene sequencing, shotgun metagenomics, and high-throughput quantitative PCR, we profiled antibiotic resistance genes (ARGs), mobile genetic elements, and virulence factor genes across bulk soil, rhizosphere, phyllosphere, and root endosphere within soil-tomato and soil-strawberry continua. Recurrent bacterial wilt amplified the resistome, particularly polypeptide resistance genes, thereby establishing the rhizosphere as a major hotspot of ARG accumulation. Multidrug-resistant Ralstonia solanacearum (R. solanacearum) strains acted as major ARG reservoirs, harboring resistance determinants on both chromosomes and megaplasmids. Collectively, these findings demonstrate that pathogen-driven restructuring of the plant microbiome accelerates ARG dissemination, establishing soil-borne diseases as critical amplifiers of AMR across agricultural ecosystems.},
}

@article {pmid41472817,
year = {2025},
author = {Zhao, Z and Mao, Z and He, D and Wang, H and Wu, Q},
title = {Host specificity and uniqueness of shell microbiome in freshwater mollusks.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1702047},
pmid = {41472817},
issn = {1664-302X},
abstract = {INTRODUCTION: Mollusk shells represent a major substrate for the colonization of microbial communities and the functioning of aquatic ecosystems. However, our knowledge of the shell microbiome is very limited.

METHODS: Here, we selected Bellamya aeruginosa and Corbicula fluminea as two types of snails and clams, respectively, to explore their shell epiphytic bacteria by 16S amplicon sequencing.

RESULTS: We found different shell bacterial communities between snails and clams, which were also distinct from those in the surrounding environment. Source tracking analysis indicated that snail-shell bacteria were mostly derived from sediments, whereas clamshells originated from tissues. There was a site-specific difference in the shell bacteria within the habitat. Temporal variation in clamshell bacteria was observed, but not in snail shells, which corresponds to their source dynamics in the water column and stable surface sediment bacterial communities, respectively. The genus Nitrospira is mostly enriched in shell bacteria, particularly in eutrophic lakes. Taxa related to carbon, nitrogen, and sulfur cycling were recognized as the keystone species in the co-occurrence network associated with the shell surface. Our results demonstrate that mollusk shells represent a unique ecological niche for microbiomes in aquatic ecosystems and may serve as hotspots for biogeochemical cycling.},
}

@article {pmid41472812,
year = {2025},
author = {Xie, X and Tao, H and Li, Y and Feng, X and Li, K and Zhang, Z and Yan, J and Wang, X},
title = {Microbial fertilizer for improving maize yield, straw decomposition and soil microbiome structure.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1670118},
pmid = {41472812},
issn = {1664-302X},
abstract = {Microbial fertilizers represent a promising strategy to sustainably produce crops by enhancing the biological function of soil and availability of nutrients. However, there is a lack of study on their performance across diverse agroecological zones. In this study, we conducted a 3-year, two-site field experiment to assess the effects of a composite microbial fertilizer (Bacillus subtilis and Trichoderma harzianum) on the yield of maize (Zea mays), soil properties, straw degradation, and composition of the microbial community. The results showed that the microbial fertilizer treatment (MF) increased the yield of maize by 11.4 and 6.9% in Qingfeng Country (QF) and Xun Country (Xun), China, respectively, compared to normal chemical fertilizer (CF). These gains coincided with an enhanced straw degradation rate (SDR; +8.4-8.6%) and a tendency toward higher available phosphorus (AP; +15.4-19.7%), alongside shifts in bacterial and fungal composition. High-throughput sequencing revealed that Proteobacteria, Actinobacteriota, Acidobacteriota, and Chloroflexi dominated the bacterial communities at both sites, whereas the fungal communities were mainly composed of Sordariomycetes, Dothideomycetes, and Eurotiomycetes-taxa whose abundances displayed pronounced site specificity. Application of the microbial fertilizer was associated with higher relative abundance of Acidobacteriota by 22.7% (QF) and 60.8% (Xun) and that of Sordariomycetes by 13.7% (QF) and 30.9% (Xun), underscoring its strong, selective impact on the dominant bacterial and fungal assemblages. These regional differences underscore the influence of site-specific microbial assemblages on the performance of fertilizer. Partial least squares path modeling supported a plausible pathway in which changes in community structure and straw decomposition are linked to improved soil nutrient status, which in turn predicted yield (β = 0.846, R [2] = 0.715). Together, the field data indicate that microbial fertilizers may act through multi-step, microbiome-associated pathways, with success depending on compatibility with native microbial assemblages and environmental context.},
}

@article {pmid41472811,
year = {2025},
author = {Liao, J and Duan, L and Wang, G and Yu, S and Shen, X and Jiang, M and Shen, K and Singla, RK and Shen, B and Zhou, Y},
title = {Gut microbiome associated with melanin deposition by supporting energy metabolism in Sichuan mountainous black-bone chickens.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1682376},
pmid = {41472811},
issn = {1664-302X},
abstract = {INTRODUCTION: Variation in melanin deposition profoundly influences the economic value of Sichuan mountainous black-boned chickens; however, the contribution of the gut microbiome in modulating this process remains poorly understood. This study aimed to characterize the gut microbiome in Sichuan mountainous black-boned chickens with distinct skin color brightness (quantified by colorimeter) and to explore its association with melanin deposition.

METHODS: Cecal microbiota composition was profiled using 16S rRNA sequencing in dark-skinned (BlackD) and light-skinned (BlackL) groups. Serum metabolic profiles were determined via untargeted metabolomics. Differential abundance of bacterial genera was assessed, followed by pathway enrichment analysis (KEGG and MetaCyc). Associations between microbiome, metabolites, and melanin-related pathways were evaluated.

RESULTS: The BlackD group exhibited higher alpha diversity and significant alterations in 10 bacterial genera (primarily linked to short-chain fatty acid metabolism and melanin-related metabolites) compared to the BlackL group. Pathway enrichment showed upregulation of energy metabolism-related KEGG pathways (AMPK signaling, insulin signaling, thyroid hormone signaling) and MetaCyc pathways in BlackD. Untargeted serum metabolomics revealed elevated melanin-related metabolites in BlackD, including L-Tyrosine, L-DOPA, and Dopaquinone. Gut microbiome and serum metabolite profiles in BlackD were strongly correlated with enhanced energy metabolism.

DISCUSSION: The gut microbiome may influence melanin deposition by modulating host metabolic activity, with microbiome-derived metabolites supporting the high energy demands of melanocyte activity. These findings uncover a potential mechanism linking microbial composition to phenotypic variation in melanin deposition.},
}

@article {pmid41472810,
year = {2025},
author = {Lan, B and Liang, Y and Zhou, Z and Liu, J},
title = {Gut microbiome dysbiosis implicates the gut-bone axis in Modic changes: a metagenomic case-control study.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1702357},
pmid = {41472810},
issn = {1664-302X},
abstract = {INTRODUCTION: Modic changes (MCs) are vertebral endplate lesions strongly associated with discogenic low back pain (LBP), though their pathogenesis remains poorly understood. Emerging evidence implicates gut microbial dysbiosis in systemic inflammation and musculoskeletal disorders, yet its potential role in MCs has not been investigated. This study aimed to characterize the gut microbiome in patients with MCs and identify microbial and metabolic features linked to disease severity.

METHODS: In a case-control study, shotgun metagenomic sequencing was performed on fecal samples from 31 patients with MCs (16 Type 1, 15 Type 2) and 25 age- and sex-matched healthy controls. Microbial community structure was assessed via alpha and beta diversity analyses. Differential taxa and predictive biomarkers were identified using linear discriminant analysis effect size (LEfSe) and Random Forest modeling. Functional potential was evaluated via Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Associations between microbial features and clinical markers (C-reactive protein [CRP], Pfirrmann grade) were also examined.

RESULTS: Patients with MCs showed significantly reduced gut microbial alpha diversity compared to controls (Chao1 index: p = 0.005; Shannon index: p = 0.034; Simpson index: p = 0.042), with the most pronounced reduction in Type 1 MCs. Beta diversity analysis revealed distinct microbial communities between groups (PERMANOVA, p = 0.001). Key discriminative taxa included unclassified_Parabacteroides (AUC = 0.895) and Bacteroides uniformis (AUC = 0.889). Metabolic pathway analysis identified 52 differentially abundant pathways, with significant enrichment of quorum sensing (p < 0.001) and glycerolipid metabolism (p < 0.001) in MC patients, both strongly correlated with elevated CRP and higher Pfirrmann grade (p < 0.001).

DISCUSSION: Gut microbial dysbiosis is associated with MCs, marked by reduced diversity, specific bacterial biomarkers, and altered metabolic pathways related to inflammation and tissue degeneration. These results suggest a potential role of the gut-bone axis in MC pathogenesis and highlight novel targets for diagnostic and therapeutic strategies in LBP.},
}

@article {pmid41472807,
year = {2025},
author = {Zhang, Q and Ding, L and Xie, X and Ru, L and Li, Q and Yao, C and Solkner, J and Jiang, R},
title = {Third-generation sequencing reveals the spatial variation of microbial composition of airborne bacteria in an intensive dairy farm.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1688472},
pmid = {41472807},
issn = {1664-302X},
abstract = {INTRODUCTION: The intensification of livestock farming has led to increased bacterial bioaerosol emissions, posing potential health risks to both animals and humans. This study aimed to investigate the bacterial community composition, abundance, diversity, and variation in different functional zones of cattle farms to assess their impact on public health and environmental quality.

METHODS: We employed third-generation sequencing on the PacBio platform to analyze 16S ribosomal RNA (rRNA) sequences from air samples, identifying a diverse range of bacterial phyla, including Proteobacteria, Firmicutes, Verrucomicrobia, Bacteroidetes, Fusobacteria, Actinobacteria, Deinococcus-Thermus, Cyanobacteria, and Acidobacteria. The phylogenetic tree was built using the microbiome abundance of these samples.

RESULTS: Notably, Firmicutes and Proteobacteria were predominantly enriched in the samples, with genera such as Staphylococcus, Acinetobacter, Enterococcus, and Bacillus, and the family Enterobacteriaceae, which was unknown, being particularly abundant. These bacteria are known to be associated with various infections and chronic diseases. Correlation and canonical correspondence analysis (CCA) revealed that environmental factors, particularly ultraviolet (UV) radiation and global horizontal irradiance (GHI), significantly influence microbial species distribution, with R [2] values of 0.774 (p < 0.05) and 0.769 (p < 0.05), respectively. We further calculated the alpha and beta diversity of microbiome in these samples and observed that fermenting manure (F1), fresh manure (X2), and piled-up manure after fermentation (D3) samples have the highest alpha diversity, while PC1 from beta diversity, that is, weighted principal coordinates analysis (PCoA), explained 32.66% of the variance in the data. Interestingly, the relative abundance of the Kocuria genus was significantly different between the waste management area (FW) and the milking parlor (NT) (t-test, p < 0.013).

DISCUSSION: Our findings underscore the importance of understanding the complex microbial ecosystems in livestock farming environments and highlight the need for targeted interventions to mitigate public health risks associated with bacterial bioaerosols.},
}

@article {pmid41472804,
year = {2025},
author = {Zhao, R and Liu, P and Wu, Y and Bi, H and He, J and Zhang, J and Qu, Y and Chen, X and Chen, Z},
title = {Triclocarban exposure at environmentally relevant concentrations perturbs the gut microbiota and metabolic profile in Rana taihangensis (Anura, Ranidae) tadpoles.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1740880},
pmid = {41472804},
issn = {1664-302X},
abstract = {INTRODUCTION: The antibacterial agent triclocarban (TCC) poses a significant threat to aquatic ecosystems and its impact on amphibians remain poorly understood.

METHODS: Here, we investigated its acute and chronic effects on Rana taihangensis tadpoles at environmentally relevant concentrations (i.e., 5, 15 and 45 μg/L) using an integrated approach combining morphology, gut microbiome, and non-targeted metabolomic analyses.

RESULTS AND DISCUSSION: The acute toxicity tests for 96 h revealed that TCC had a lethal concentration (LC50) value of 169.863 μg/L for R. taihangensis tadpoles. Chronic exposure resulted in reduced body condition score across all the three TCC-treated groups compared to the control. Gut microbiome analysis revealed that TCC exposure significantly altered the community composition at both phylum (e.g., Pseudomonadota and Fusobacteriota) and genus (e.g., Cetobacterium and Citrobacter) levels. In addition, several metabolites (e.g., 20-carboxy-leukotriene B4, 11b-PGF2a, and leukotriene E4) associated with immune response and neural signaling were significantly perturbed in TCC-exposed tadpoles. Interestingly, correlation analysis indicated a significant relationship between specific metabolite changes and shifts in gut microbiota. Overall, our findings demonstrated that TCC exposure adversely affects the growth indexes, gut microbial composition and metabolites in R. taihangensis tadpoles, and the present study will provide new insights into the ecotoxicological risks of TCC and enhance the understanding of its mechanisms of toxicity in aquatic organisms.},
}

@article {pmid41472773,
year = {2025},
author = {Charoenwai, O and Tanpichai, P and Sukkarun, P and Jeon, HJ and Kim, B and Han, JE and Piamsomboon, P},
title = {Emergence of decapod hepanhamaparvovirus genotype V and its co-infection with Enterocytozoon hepatopenaei in cultured Penaeus vannamei in Thailand: Evidence from epidemiological, pathogenicity, and microbiome analyses.},
journal = {Veterinary world},
volume = {18},
number = {11},
pages = {3496-3508},
pmid = {41472773},
issn = {0972-8988},
abstract = {BACKGROUND AND AIM: Growth retardation syndrome in cultured Penaeus vannamei has been associated with Enterocytozoon hepatopenaei (EHP) and a recently identified decapod hepanhamaparvovirus (DHPV) genotype V. However, data on its prevalence, pathogenicity, and interaction with the shrimp hepatopancreatic microbiome in Thailand remain limited. This study aimed to determine the incidence and co-infection rate of DHPV genotype V with EHP, evaluate its pathogenic potential, and explore microbiome alterations associated with infection.

MATERIALS AND METHODS: Between 2022 and 2023, 1,270 shrimp from 127 grow-out ponds across 46 farms in eastern Thailand and post-larvae 12 from five hatcheries in the south were screened for DHPV and EHP by polymerase chain reaction. Six representative isolates underwent phylogenetic analysis based on non-structural protein 1 (NS1) and NS2 genes. Pathogenicity was evaluated by immersion challenge bioassays in specific pathogen-free P. vannamei. Hepatopancreatic microbiomes of naturally infected and healthy shrimp were compared using 16S ribosomal RNA gene sequencing and Quantitative Insights Into Microbial Ecology 2-based analysis.

RESULTS: DHPV was detected in 54.33% (69/127) of ponds and 4% (1/25) of hatchery tanks. Co-infection with EHP occurred in 40.16% of ponds. Phylogenetic analysis showed 97.99%-98.82% similarity with DHPV genotype V from South Korea, confirming transboundary genetic relatedness. Experimental infection caused low mortality (20%) but resulted in viral replication (10[1]-10[3] copies/μL) and characteristic intranuclear inclusion bodies in hepatopancreatic cells. DHPV-infected shrimp exhibited distinct microbiome profiles with elevated Firmicutes, Planctomycetota, and Actinobacteriota abundances, supporting a pathobiome shift during infection.

CONCLUSION: This is the first report of DHPV genotype V in P. vannamei from Thailand and its frequent co-infection with EHP. Despite its low experimental virulence, the widespread occurrence and microbiome dysbiosis suggest that it may have subclinical impacts that could exacerbate growth retardation. Routine molecular screening in hatcheries and farms, coupled with integrated viral-microbiome surveillance, is essential for sustainable aquaculture biosecurity and aligns with the United Nations Sustainable Development Goal 14 (Life Below Water) by promoting resilient aquatic food systems.},
}

@article {pmid41472726,
year = {2025},
author = {Jani, CT and Edwards, K and Bhanushali, C and Zheng, X and Salazar, AS and Lopes, G and Watson, DC},
title = {Leveraging beneficial microbiome-immune interactions via probiotic use in cancer immunotherapy.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1713382},
pmid = {41472726},
issn = {1664-3224},
mesh = {*Probiotics/therapeutic use ; Humans ; *Neoplasms/therapy/immunology/microbiology ; *Gastrointestinal Microbiome/immunology ; Animals ; *Immunotherapy/methods ; Immune Checkpoint Inhibitors/therapeutic use ; },
abstract = {The gut microbiome is a critical regulator of systemic immunity and a major modulator of response to cancer immunotherapy with immune checkpoint inhibitors (ICIs). However, the clinical implementation of microbiome-inspired therapies that leverage these associations have proven challenging. Probiotics-live microorganisms thought to confer health benefits as part of food or food supplements-have gained increasing attention as readily testable, low-toxicity agents with potential of favorably influencing host-microbiome-immune interactions in the context of cancer immunotherapy. In this review, we critically evaluate the growing body of evidence supporting the role of probiotics in enhancing ICI efficacy and summarize published and ongoing clinical trials formally testing their role as adjuncts to cancer immunotherapy. Probiotics have been shown in preclinical murine models to exert immunomodulatory effects, including activation and maturation of dendritic cells, enhancement of MHC-I-mediated antigen presentation, modulation of cytokine profiles, and promotion of pro-inflammatory macrophage polarization. Probiotics also regulate adaptive immunity via microbial metabolites such as short-chain fatty acids (SCFAs), inosine, and tryptophan derivatives that support effector T cell activation and reduce T cell exhaustion. Cross-reactivity between microbial and tumor-associated antigens (molecular mimicry) further underscores the potential of probiotic strains to stimulate antitumor responses. In these models, supplementation with specific bacterial strains such as Bifidobacterium spp., Lactobacillus spp., Clostridium butyricum, and Akkermansia muciniphila enhanced ICI responses across tumor types including melanoma, lung cancer, and colorectal cancer. These findings are in part supported by early-phase clinical studies and retrospective cohorts, particularly in lung and renal cancers, where probiotic use has been associated with improved progression-free and overall survival. However, most clinical data are observational, and the field lacks standardized probiotic formulations and dosing protocols. To transition probiotics from food supplements to clinically validated immunotherapy adjuncts, rigorous mechanistic, translational, and clinical studies are necessary. These approaches have the potential to define mechanism-of-action, identify immunologically active strains, and inform rational clinical trial design. With careful development, probiotics hold promise as cost-effective, scalable, and personalized tools to optimize the efficacy and safety of cancer immunotherapy.},
}

*Probiotics/therapeutic use
Humans
*Neoplasms/therapy/immunology/microbiology
*Gastrointestinal Microbiome/immunology
Animals
*Immunotherapy/methods
Immune Checkpoint Inhibitors/therapeutic use

@article {pmid41472687,
year = {2025},
author = {Loke, P and Smith, A and Kiwanuka, K and Pessenda, G and Rahmberg, A and Flynn, J and Herbert, R and Brenchley, J},
title = {Hematological Consequences of Environmental Change During Dewilding of Rhesus Macaques.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-7767375/v1},
pmid = {41472687},
issn = {2693-5015},
abstract = {The environment shapes immune system development and the regulation of inflammatory responses, which may affect the prevalence of immune mediated inflammatory diseases. However, the hematological consequences of a major environmental change, such as those experienced during migration, remain poorly understood. Here, we used cellular and molecular approaches to assess the immunological consequences in rhesus macaques as they transitioned from an outdoor provisioned environment to an indoor laboratory facility in a process we term 'dewilding.' Dewilding led to a sharp decrease in neutrophils and increased lymphocytes in the peripheral blood, a skewing toward a proinflammatory TH1 response, and increased T cell activation. Concurrently, we observed changes in the microbiome, with fungal abundance decreasing while bacterial abundance increased during dewilding. In the bone marrow, we observed increased granulopoiesis, reduced lymphocytes, and reduced hematopoietic stem cells and progenitors, with their shift toward less committed progenitor states. Single-cell nuclear RNA sequencing of the bone marrow revealed increased erythrocyte progenitors in the bone marrow during dewilding, with upregulation of genes involved in hemoglobin control and erythropoiesis. Notably, the vaccination response against measles varied based on vaccination period during the dewilding process. Together, our findings illustrate how dewilding alters immune homeostasis, with implications for understanding immune adaptation in migrants from rural to urban environments and for optimizing immunization strategies during environmental change.},
}

@article {pmid41472620,
year = {2025},
author = {Zhang, D and Xu, X and Zhang, Z},
title = {Effect of Social Rank on Gut Microbes and Their Metabolites of Greater Long-Tailed Hamsters (Tscherskia triton).},
journal = {Integrative zoology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1749-4877.70049},
pmid = {41472620},
issn = {1749-4877},
support = {RZ2300002832//Hainan University research start-up fund project/ ; },
abstract = {Although the effects of social rank on behavior and physiology are well established, their relationship with gut microbiota is not yet fully understood. We investigated how social rank affects physiological responses, gut microbiota, and metabolites in the greater long-tailed hamster (Tscherskia triton), a naturally solitary rodent. Dominant male hamsters displayed a "high-vigilance, metabolically activated" phenotype, characterized by increased aggression, elevated serum corticosterone (CORT) and serotonin (5-HT) levels, and activation of the paraventricular nucleus, a key regulator of the hypothalamic-pituitary-adrenal axis. In contrast, subordinates exhibited lower CORT and 5-HT levels, with increased activation of the arcuate nucleus (ARC), suggesting a more energy-conserving and stress-resilient phenotype. Social rank strongly shaped gut microbiota and metabolic output: dominants were enriched in energy-harvesting taxa (e.g., Limosilactobacillus and Alistipes) and had higher fecal queuine levels, a metabolite derived from gut microbiota. Conversely, subordinates were enriched in immunomodulatory taxa (e.g., Faecalibacterium and Butyrivibrio). These findings suggest that dominance in solitary species may be supported by coordinated host-microbiome interactions, which meet high energetic demands while maintaining stress resilience. This provides a novel framework for understanding the gut-brain-microbiome axis in social dominance.},
}

@article {pmid41472585,
year = {2025},
author = {Orhan, F and Bektaş, M and Bariş, Ö},
title = {Elucidating environmental reservoir of antimicrobial resistance - a phenotypic characterization of gut microbiota from aquatic coleoptera in a low-anthropogenic impact zone.},
journal = {Annals of agricultural and environmental medicine : AAEM},
volume = {32},
number = {4},
pages = {504-510},
doi = {10.26444/aaem/210421},
pmid = {41472585},
issn = {1898-2263},
mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; *Gastrointestinal Microbiome/drug effects ; *Coleoptera/microbiology ; *Bacteria/drug effects/isolation & purification/genetics/classification ; *Drug Resistance, Bacterial ; Turkey ; *Gram-Negative Bacteria/drug effects/isolation & purification/genetics ; Drug Resistance, Multiple, Bacterial ; },
abstract = {INTRODUCTION AND OBJECTIVE: This study investigated the antibiotic resistance of bacterial isolates obtained from the gut microbiota of certain insects (Coleoptera: Hydrophilidae and Helophoridae), which were collected from aquatic areas in Erzurum Province, Türkiye. This area is characterised by a low level of human impact, thereby providing a unique opportunity to investigate the baseline microbial diversity and ecological roles within relatively pristine aquatic environments.

MATERIAL AND METHODS: The antimicrobial susceptibility of the isolates was assessed using disc diffusion and minimum inhibitory concentration (MIC) methods. The analysis encompassed 30 Gram-negative bacteria belonging to the genera Aeromonas, Acinetobacter, Vibrio, Pseudomonas, Escherichia and Yersinia.

RESULTS: The results indicated that the most resistant bacteria were Aeromonas, Pseudomonas and Acinetobacter, while enteric bacteria demonstrated greater sensitivity. It is noteworthy that nitrofurantoin, a commonly used antibiotic for treating urinary tract infections, exhibited the highest level of resistance among the antibiotics tested by disc diffusion, followed by cephalosporins and penicillins.

CONCLUSIONS: The MIC testing with DKGM and NF kits demonstrated high resistance to cephalosporins, sulfonamides, polymyxins and monobactams. Furthermore, two multidrug-resistant (MDR) isolates exhibited resistance to at least two antibiotic classes. These findings underscore the necessity for expanded antimicrobial resistance surveillance beyond clinical settings, extending into environmental samples, and contributing to ongoing research on resistance mechanisms.},
}

Animals
*Anti-Bacterial Agents/pharmacology
Microbial Sensitivity Tests
*Gastrointestinal Microbiome/drug effects
*Coleoptera/microbiology
*Bacteria/drug effects/isolation & purification/genetics/classification
*Drug Resistance, Bacterial
Turkey
*Gram-Negative Bacteria/drug effects/isolation & purification/genetics
Drug Resistance, Multiple, Bacterial

@article {pmid41472545,
year = {2026},
author = {Chen, W and Lai, X and Tang, X and Ye, Q and Zhang, C and Yang, Y and Wang, Z and Li, M and Wang, Z and Li, Z and Yuan, C and Zhang, X and Li, L and Wang, B and Wang, R and Yan, Y},
title = {Dysbiosis in Acne Vulgaris and Hidradenitis Suppurativa: A Comparative Microbiome Analysis.},
journal = {Experimental dermatology},
volume = {35},
number = {1},
pages = {e70198},
doi = {10.1111/exd.70198},
pmid = {41472545},
issn = {1600-0625},
support = {82073471//National Natural Science Foundation of China/ ; CFH-2022-2-4043//Capital's Funds for Health Improvement and Research/ ; },
mesh = {Humans ; *Hidradenitis Suppurativa/microbiology ; *Acne Vulgaris/microbiology ; *Dysbiosis/microbiology ; Male ; Female ; Adult ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Skin/microbiology ; Young Adult ; Mouth Mucosa/microbiology ; Case-Control Studies ; Feces/microbiology ; Gastrointestinal Microbiome ; Adolescent ; },
abstract = {Acne and hidradenitis suppurativa (HS) are inflammatory disorders of the pilosebaceous unit that exhibit distinct clinical manifestations, indicating that they likely differ in their underlying pathophysiology. Microbial dysbiosis is implicated in both diseases, yet direct comparisons using unified methods and analyses incorporating the oral microbiome are lacking. In this study, we collected lesional and nonlesional skin, buccal mucosa and faecal samples from 28 HS patients, 29 acne patients and 40 healthy controls, and profiled microbial communities using 16S rRNA V3-V4 sequencing with qPCR validation. HS lesions showed a pronounced enrichment of anaerobic Gram-negative taxa, including Prevotella, Porphyromonas and Fusobacterium, whereas acne lesions were dominated by Cutibacterium and Pseudomonas. Oral microbiome diversity was increased in both diseases, with HS showing distinct enrichment of Prevotella and Veillonella. HS patients also exhibited reduced gut microbial diversity. Correlation analyses revealed coordinated microbial alterations across the oral-gut-skin axis, and qPCR confirmed elevated concentrations of key anaerobes in HS. By directly comparing acne and HS across multiple anatomical sites, our study helps differentiate general inflammatory microbiome changes from those more specific to HS. The findings also suggest a potential oral-gut-skin microbial axis that may contribute to the chronic and destructive phenotype of HS, providing insights that could inform future microbiome-targeted therapeutic approaches.},
}

Humans
*Hidradenitis Suppurativa/microbiology
*Acne Vulgaris/microbiology
*Dysbiosis/microbiology
Male
Female
Adult
RNA, Ribosomal, 16S/genetics
*Microbiota
Skin/microbiology
Young Adult
Mouth Mucosa/microbiology
Case-Control Studies
Feces/microbiology
Gastrointestinal Microbiome
Adolescent

@article {pmid41472301,
year = {2025},
author = {Yagi, K and Ethridge, AD and Asai, N and Malinczak, CA and Arzola Martinez, L and Rasky, AJ and Morris, SB and Falkowski, NR and Fonseca, W and Huffnagle, GB and Lukacs, NW},
title = {Changes in Microbiome Correspond with Diminished Lung Pathophysiology Following Early-Life Respiratory Syncytial Virus Infection or Antibiotic Treatment: Microbiome Following RSV Infection.},
journal = {Viruses},
volume = {17},
number = {12},
pages = {},
pmid = {41472301},
issn = {1999-4915},
mesh = {*Respiratory Syncytial Virus Infections/microbiology/physiopathology/drug therapy/virology ; Animals ; *Lung/physiopathology/microbiology/virology/drug effects ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Mice ; Mice, Inbred BALB C ; Dysbiosis ; *Microbiota/drug effects ; Gastrointestinal Microbiome/drug effects ; Animals, Newborn ; Disease Models, Animal ; Ampicillin/pharmacology ; Respiratory Syncytial Viruses ; Humans ; Female ; },
abstract = {Early-life respiratory syncytial virus (EL-RSV) infection has been implicated in long-term pulmonary disease in children. In these studies, neonatal BALB/c mice were infected at day 7 of life, leading to >35% losses in critical lung function, airway mucus metaplasia, and transcriptional hallmarks of mucus hypersecretion four weeks after RSV infection. While EL-RSV minimally reshaped the resident lung microbiota, it led to significant gut dysbiosis, including a long-term reduction of Proteobacteria that can be a source of protective metabolites related to barrier and immune function. Subsequent studies assessing whether a common infant antibiotic (ampicillin) could mitigate EL-RSV-induced lung alterations revealed further severe gut microbiome alterations and, on its own, later in life, recapitulated the full spectrum of RSV-associated alterations in lung function. Metagenomic inference showed that both RSV and ampicillin administered during early life reduced biosynthetic pathways for microbiome-derived metabolites, which are known to reinforce tight junctions, regulate inflammation, and preserve extracellular matrix elasticity. The shared loss of these metabolic programs provides a mechanistic bridge linking distinct early-life exposures to the microbiome changes and airway mechanical deficits later in life. Collectively, the data suggest that RSV and/or antibiotic-triggered gut dysbiosis is the primary insult that likely promotes improper lung maturation/repair through a metabolite-mediated mechanism and may suggest metabolite restoration as a strategy to promote proper developmental lung function.},
}

*Respiratory Syncytial Virus Infections/microbiology/physiopathology/drug therapy/virology
Animals
*Lung/physiopathology/microbiology/virology/drug effects
*Anti-Bacterial Agents/pharmacology/therapeutic use
Mice
Mice, Inbred BALB C
Dysbiosis
*Microbiota/drug effects
Gastrointestinal Microbiome/drug effects
Animals, Newborn
Disease Models, Animal
Ampicillin/pharmacology
Respiratory Syncytial Viruses
Humans
Female

@article {pmid41472294,
year = {2025},
author = {Mandal, E and Noirungsee, N and Disayathanoowat, T and Kil, EJ},
title = {TSWV Infection Differentially Reshapes the Symbiotic Microbiome of Two Frankliniella Thrips Species.},
journal = {Viruses},
volume = {17},
number = {12},
pages = {},
pmid = {41472294},
issn = {1999-4915},
support = {0//Gyeongkuk National University/ ; },
mesh = {*Thysanoptera/microbiology/virology ; Animals ; *Symbiosis ; *Microbiota ; *Tospovirus/physiology ; Serratia/genetics ; Bacteria/classification/genetics/isolation & purification ; Insect Vectors/virology/microbiology ; Metagenomics ; Plant Diseases/virology ; Wolbachia/genetics ; },
abstract = {Vectoring tomato spotted wilt virus (TSWV) by two well-known thrips species, Frankliniella occidentalis Pergande and F. intonsa Trybom (Thysanoptera: Thripidae), is facilitated in different ways. Symbiotic bacteria positively influence thrips fitness, but the interaction between these bacteria and tospovirus inside the thrips' body remains unknown. Metagenomic profiling of symbionts in nonviruliferous and viruliferous Frankliniella thrips was performed to elucidate the interactions between symbiotic bacteria and the virus. A total of 97 operational taxonomic units (OTUs) were identified by profiling the microbes, where Proteobacteria was the most abundant phylum, with a high richness in Serratia spp. F. occidentalis showed lower variation in bacterial diversity between nonviruliferous and viruliferous treatments than F. intonsa. RT-qPCR validation for Serratia and Escherichia revealed opposite abundance patterns between the two thrips species. In contrast, Enterobacteriaceae and Pantoea showed similar patterns with higher abundance in nonviruliferous conditions. Wolbachia was detected exclusively in F. intonsa, with a higher bacterial titer in the viruliferous sample. Our findings suggest that TSWV association may influence the abundance of different bacterial symbionts within the thrips' body, potentially via induction of antimicrobial peptides in response to viral invasion, and to our knowledge this is the first report addressing this tripartite interaction. These findings improve our understanding of how virus-symbiont association contributes to thrips vector competence.},
}

*Thysanoptera/microbiology/virology
Animals
*Symbiosis
*Microbiota
*Tospovirus/physiology
Serratia/genetics
Bacteria/classification/genetics/isolation & purification
Insect Vectors/virology/microbiology
Metagenomics
Plant Diseases/virology
Wolbachia/genetics

@article {pmid41472213,
year = {2025},
author = {Abdelbary, ER and Ramadan, M and Amin, IA and Abd-Elsamea, FS and Elsaghier, AM and Abd-Alrahman, EA and Ozbak, HA and Hemeg, HA and Almutawif, YA and Zakai, SA and Abdelrahman, AA and Salah, M},
title = {Early-Life Demographic Factors Shape Gut Microbiome Patterns Associated with Rotavirus Gastroenteritis Severity.},
journal = {Viruses},
volume = {17},
number = {12},
pages = {},
doi = {10.3390/v17121542},
pmid = {41472213},
issn = {1999-4915},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Gastroenteritis/microbiology/virology/epidemiology ; *Rotavirus Infections/microbiology/epidemiology/virology ; Infant ; Female ; Male ; Case-Control Studies ; Infant, Newborn ; Severity of Illness Index ; RNA, Ribosomal, 16S/genetics ; Rotavirus ; Bacteria/classification/genetics/isolation & purification ; Feces/microbiology ; Sociodemographic Factors ; },
abstract = {BACKGROUND: Rotavirus gastroenteritis (RVGE) remains a leading cause of severe infant diarrhea worldwide, with growing evidence supporting the role of the gut microbiome in modulating the disease. However, the interplay between early-life demographic factors, the gut microbiome, and their combined impact on RVGE clinical severity remains inadequately characterized, particularly in specific geographic populations.

AIM: We aimed to investigate how demographic determinants shape gut microbiome composition and function in RVGE and how these features relate to clinical severity.

METHODS: In our comprehensive case-control study of 165 infants (120 RVGE cases and 45 healthy controls, aged 0-12 months), we utilized 16S rRNA sequencing combined with advanced statistical modeling and machine learning to investigate how demographic factors influence microbiome composition and clinical outcomes.

RESULTS: RVGE cases exhibited significantly reduced bacterial diversity (Kruskal-Wallis, Static = 14.85, p < 0.001) and distinct patterns, with community structure most strongly associated with dehydration severity (PERMANOVA; R[2] = 0.15, p < 0.001). Substantial taxonomic alterations were identified characterized by depletion of beneficial commensals including Akkermansia (LDA score = 3.8, p < 0.001), Faecalibacterium (Random Forest AUC = 0.82, p < 0.001), and Bifidobacterium (r = -0.42 with breastfeeding, p < 0.001), alongside enrichment of inflammation-associated taxa such as Escherichia-Shigella (WBC; r = 0.49, p < 0.001, and CRP; r = 0.56, p < 0.001), Streptococcus (LDA score = 4.2, p < 0.001), and Staphylococcus. Proteobacteria was the top potential biomarker of severe outcomes (Random Forest AUC = 0.85), with abundance positively correlated with systemic inflammation (CRP: r = 0.51, p = 0.003). Functional predictions revealed increased lipopolysaccharide biosynthesis (ko00540) and reduced butanoate metabolism (ko00650, p < 0.001) in severe disease. Importantly, demographic factors significantly modulated clinical outcomes: cesarean-delivered, formula-fed infants presented the most dysbiotic profiles and experienced 3.2-fold longer hospitalization (95% CI: 1.8-5.6, p < 0.001) than vaginally delivered, breastfed infants did.

CONCLUSIONS: Collectively, these findings demonstrate that early-life demographic factors potentially shape the gut microbiome composition and function, may influence RVGE severity and recovery trajectories, thus providing candidate biomarkers for risk stratification and identifying targets for microbiota-based interventions.},
}

Humans
*Gastrointestinal Microbiome
*Gastroenteritis/microbiology/virology/epidemiology
*Rotavirus Infections/microbiology/epidemiology/virology
Infant
Female
Male
Case-Control Studies
Infant, Newborn
Severity of Illness Index
RNA, Ribosomal, 16S/genetics
Rotavirus
Bacteria/classification/genetics/isolation & purification
Feces/microbiology
Sociodemographic Factors

@article {pmid41472186,
year = {2025},
author = {Lu, Y and Li, Z and Yang, Z and Zhu, R and Yan, M and Liu, Z and Liu, M and Wang, Y and Wang, J and Wang, Q and Liu, J and Zhang, C and Wang, X and Cui, H},
title = {Effects of Combined Oregano Essential Oil and Macleaya cordata Extract on Growth, Antioxidant Capacity, Immune Function, and Fecal Microbiota in Broilers.},
journal = {Veterinary sciences},
volume = {12},
number = {12},
pages = {},
pmid = {41472186},
issn = {2306-7381},
support = {YJ2023038；246Z6604G；HBCT2024270204；CARS-41-13；KY2024006//This research was funded by the special project of introducing talents for scientific research in Hebei Agricultural University；Central government guided local science and technology development fund projects；Hebei Agriculture Research System；China Agricu/ ; },
abstract = {With the growing demand for antibiotic-free and sustainable poultry production, plant-derived antimicrobials have emerged as promising alternatives. However, a systematic understanding of the combined effects of oregano essential oil (OEO) and Macleaya cordata extract (MCE) on the broiler gut microbiome remains lacking. This study employed an integrated "structure-function-phenotype" framework to investigate the individual and combined (OMS) effects of OEO and MCE on gut microecological remodeling and its coupling with host growth, metabolic, and immune phenotypes. A total of 960 one-day-old broiler chicks were individually weighed and then randomly allocated to four treatments using body-weight-stratified randomization, with 6 replicate pens per treatment and 40 birds per pen, to ensure similar initial body weight across groups. Over a 42-day trial, we evaluated growth performance, serum biochemistry, antioxidant status, and immune parameters. Compared to the control, the OMS treatment significantly enhanced average daily feed intake (ADFI) and average daily gain (ADG), increased serum total protein (TP), and decreased blood urea nitrogen (BUN), triglycerides (TG), total cholesterol (TC), and alkaline phosphatase (ALP). However, the feed-to-gain ratio (F/G) was also higher in the OMS group, indicating that the improvement in growth rate did not translate into enhanced feed efficiency but was primarily driven by increased feed consumption. OMS also improved overall antioxidant capacity and key enzyme activities, elevated immunoglobulin levels, and reduced pro-inflammatory cytokines. Notably, OMS maintained Lactobacillus dominance, enriched Bacteroides, Enterococcus, and Butyricicoccus, and reduced Escherichia-Shigella. Functional predictions via PICRUSt2 suggested enhanced metabolic pathways related to antioxidant and immune functions; however, these results represent inference-based predictions and should be interpreted cautiously. Overall, the combination of OEO and MCE exerted synergistic benefits on growth, physiological health, and gut microbiota, supporting its potential as a phytogenic strategy for antibiotic-free broiler production.},
}

@article {pmid41472081,
year = {2025},
author = {Urga, and Wang, X and Wei, H and Zhao, G},
title = {Mechanisms and Applications of Gastrointestinal Microbiota-Metabolite Interactions in Ruminants: A Review.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41472081},
issn = {2076-2607},
support = {2025YJRC077//Research Foundation for Advanced Talents of InnerMongolia Normal University/ ; },
abstract = {The gastrointestinal microbiota of ruminants constitutes a complex invisible organ, which converts plant fibers into volatile fatty acids (VFAs) and microbial protein through fermentation, serving as the primary energy and protein sources for the host. While substantial progress has been made in characterizing this system, critical gaps remain in understanding causal mechanisms and translating knowledge into scalable interventions. This review systematically synthesizes current knowledge on the composition, function, and metabolite profiles of gastrointestinal microbial communities in ruminants, with emphasis on interaction mechanisms, methodological advances, and intervention strategies. We highlight persistent challenges, including the uncultured majority of microbes, causal inference limitations, and translational bottlenecks. The review further evaluates strategies for targeted microbiome modulation aimed at improving production performance and reducing environmental emissions. Finally, we propose integrated research priorities for developing efficient, low-carbon, and sustainable ruminant production systems.},
}

@article {pmid41472077,
year = {2025},
author = {Xu, L and Long, K and Zhang, Y and Zhou, G and Liu, J},
title = {Responses of Soil Microbial Communities and Anthracnose Dynamics to Different Planting Patterns in Dalbergia odorifera.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41472077},
issn = {2076-2607},
abstract = {Anthracnose is one of the major diseases affecting Dalbergia odorifera T. Chen. However, the soil microbial mechanisms underlying D. odorifera responses to anthracnose remain largely unexplored. This study investigated three planting systems: a Dalbergia odorifera monoculture (J); a mixed plantation of D. odorifera and Pterocarpus macrocarpus (JD); and a composite mixed plantation of D. odorifera, P. macrocarpus, and Clinacanthus nutans (JDY). Using amplicon sequencing technology for soil microbial analysis and combining soil physical and chemical properties with disease severity, we comprehensively analyzed changes in soil microbial community structure and function across different planting modes. The results showed that the diverse mixed mode (JD, JDY) significantly improved soil physicochemical properties and promoted soil nutrient cycling. Redundancy analysis (RDA) indicated that soil organic matter (SOM) and disease severity, quantified by the area under the disease progress curve (AUDPC), were the primary environmental drivers of microbial community variation. Genera positively correlated with SOM and negatively correlated with AUDPC were significantly enriched in JDY and JD, whereas genera showing opposite relationships were predominantly enriched in J. Functional predictions revealed enhanced nutrient-cycling capacities in JD and JDY, with JDY uniquely harboring functional groups such as Arbuscular Mycorrhizal, Epiphyte, and Lichenized taxa. In contrast, microbial functions in the J plantation were mainly limited to environmental amelioration. Co-occurrence network analysis further showed that as planting patterns shifted from J to JDY, microbial communities evolved from competition-dominated networks to cooperative defensive networks, integrating efficient decomposition with strong pathogen suppression potential. The study demonstrates that complex mixed planting systems regulate soil properties, enhance the enrichment of key functional microbial taxa, reshape community structure and function, and ultimately enable ecological control of anthracnose disease. This study provides new perspectives and theoretical foundations for ecological disease management in plantations of rare tree species and for microbiome-based ecological immunization strategies.},
}

@article {pmid41472044,
year = {2025},
author = {Hu, C and Wu, Y and Li, Z and Wang, Z and Huang, F and Fan, Z and Peng, M},
title = {Ecological Modulation of Soil Microbial Communities by Fertilization Regimes: Insights from Castor Bean Cake, Chemical Fertilizers, and Organic Fertilizer.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41472044},
issn = {2076-2607},
support = {S202510517029//Student Innovation and Entrepreneurship Training Program of Hubei Minzu University/ ; KYPT012305//Open Fund of Hubei Key Laboratory of Biological Resources Protection and Utilization (Hubei Minzu University)/ ; },
abstract = {Fertilization plays a vital role in replenishing soil nutrients, shaping microbial community composition, and enhancing agricultural productivity. Castor bean cake (CBC) is a nitrogen- and carbon-rich by-product increasingly used as an organic amendment, yet its effects on soil microbiomes remain unclear. Here, we compared CBC with a compound chemical fertilizer (CF) and a manure-based organic fertilizer (OF) across dose gradients using 16S rRNA sequencing and multi-level ecology analyses (α/β diversity, co-occurrence networks, and community assembly models). The results revealed that CBC increased bacterial richness and phylogenetic breadth relative to the unfertilized cultivated control, whereas OF showed dose-dependent declines in richness and CF maintained relatively stable richness with slight reductions in evenness at higher doses. Phylum-level composition shifted strongly with fertilizer identity: Bacillota decreased, whereas Pseudomonadota and Acidobacteriota increased under fertilization, with the largest compositional changes under CBC. CBC strengthened nutrient-enzyme-microbe coupling and generated increasingly complex, highly connected, and robust co-occurrence networks along the dose gradient, outperforming high-dose OF in network complexity and robustness, while OF maintained higher modularity. Null-model partitions (βNTI/RC_bray, NST, NCM, iCAMP) indicated that stochastic processes dominated community assembly across treatments; along the CBC gradient, dispersal limitation decreased from CBC1 to CBC2 and drift remained dominant, indicating increasing stochastic stabilization at moderate-high doses. Together, CBC promoted microbiome recovery and ecological resilience and represents a promising amendment for soil health.},
}

@article {pmid41472041,
year = {2025},
author = {Sharma, SB and Raverkar, KP and Wani, SP and Bagyaraj, DJ and Kannepalli, A and Kandula, DRW and Mikaelyan, A and Ansari, MA and Stock, SP and Davies, KG and Sharma, R},
title = {Role of the Plant-Microbiome Partnership in Environmentally Harmonious 21st Century Agriculture.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41472041},
issn = {2076-2607},
abstract = {The 21st century calls for a paradigm shift in agricultural practices to address the pressing issues of regeneration of soil health, climate change, environmental degradation, sustainability under growing population pressures, and food security challenges. This article reviews the potential of the plant-microbiome approach as a key driver for eco-conscious green farming. The focus is on the diverse roles of microbial communities in close association with plants in improving plant health, crop productivity, and soil ecosystem functions, and in enhancing environmental sustainability, with focus on four key areas: (1) Soil health and fertility through microbial partnerships; (2) Ecosystem sustainability through microbial functions; (3) Plant health, productivity and food security through microbial innovations emphasising the potential of microbial applications (biofertilisers, bioprotectants, and biostimulants) in sustainable agriculture; (4) Standardisation and stewardship in microbial agriculture highlighting the need for standardisation and quality control in microbial product development and use, and the concept of microbial stewardship and its importance in long-term agricultural sustainability. By synthesising current knowledge and identifying future challenges, this review underscores the transformative potential of the plant-associated microbiome approach in creating resilient, productive, and environmentally harmonious agricultural systems. We highlight current research gaps and future directions, arguing that embracing microbial solutions is not just an option but a necessity for ensuring food security and environmentally benign sustainability in the face of global challenges.},
}

@article {pmid41472037,
year = {2025},
author = {Aschalew, ND and Liu, J and Liu, Y and Sun, W and Yin, G and Cheng, L and Wang, H and Zhao, W and Zhang, L and Wang, Z and Jiang, H and Wang, T and Qin, G and Zhen, Y and Sun, Z},
title = {Enhancing Sheep Rumen Function, and Growth Performance Through Yeast Culture and Oxalic Acid Supplementation in a Hemicellulose-Based Diet.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41472037},
issn = {2076-2607},
support = {20230202075NC//the Scientific and Technological Development Scheme of Jilin Province/ ; 20230202075NC//the Scientific and Technological Development Scheme of Jilin Province/ ; },
abstract = {Yeast culture (YC) is a microbial product that enhances ruminal fiber breakdown and improves nutrient digestion and utilization. Our previous research showed that oxalic acid (OA) is a crucial metabolite in YC that enhances rumen function. This study aimed to investigate the effects of YC, OA, and their combination (YO) on rumen function, growth, and fattening in sheep. Twenty lambs were divided into 4 groups (ctrl, YC, OA, and YO; n = 5 each) and fed a diet supplemented with 2 levels of YC and 2 doses of OA for 60 days in a 2 × 2 factorial design. Growth and fattening performance, rumen microbiome analysis, serum indices and anti-oxidant levels, and metabolomic profiling were performed. Individual supplementation with YC and OA significantly increased the digestibility of dry matter (DM), organic matter (OM), and crude protein (CP) (p < 0.001); neutral detergent fiber (NDF) (p < 0.05); and acid detergent fiber (ADF) (p < 0.001) and their interaction significantly increased dry matter intake (DMI) (p = 0.05). Serum IgA and IgM levels were higher in the supplemented groups (p < 0.05). Serum calcium levels were higher in the OA and YO groups (p < 0.001). The supplemented groups showed significantly higher growth hormone and superoxide dismutase levels (p < 0.05). The longissimus dorsi muscle had higher levels of iron in the OA and YO groups; zinc in the OA, YO, and YC groups (p < 0.01); and selenium in the YC group (p < 0.05). The OA group had a higher total antioxidant capacity. All supplemented groups showed higher bacterial richness and diversity. Ruminococcus, Succinivibrio, and Fibrobacter were positively correlated with the fermentation and digestibility parameters. The supplementation also altered metabolite levels and types in key physiological pathways. In conclusion, this supplementation improved bacterial composition, nutrient digestibility, weight gain, carcass weight and quality, serum indices, antioxidant levels and metabolomic profiles. This suggests potential for the development of dietary supplements for ruminants.},
}

@article {pmid41472035,
year = {2025},
author = {Mntambo, N and Arumugam, T and Pramchand, A and Pillay, K and Ramsuran, V},
title = {A Review of Global Patterns in Gut Microbiota Composition, Health and Disease: Locating South Africa in the Conversation.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41472035},
issn = {2076-2607},
abstract = {The gut microbiota plays an essential role in human health through its contributions to immune regulation, metabolism, pathogen defence and disease susceptibility. Despite this significance, most gut microbiome research remains disproportionately focused on high-income countries, resulting in a limited and underrepresented view of global microbial diversity. This bias is evident in Africa, where populations, including those in South Africa, show unique combinations of genetic variation, dietary patterns and environmental exposures that are insufficiently captured in current datasets but offer opportunities to uncover novel insights into microbial evolution and its influences on health across diverse settings. In response to this gap, this review synthesises global patterns in gut microbiota composition and diversity while situating South African findings within this broader context. We examine evidence across microbial domains, including bacteria, fungi, viruses, archaea, protozoa and helminths, and highlight the impact of dietary transitions and environmental exposures on microbial community structure. Although still emerging, research on the gut microbiome of South African populations consistently reports contrasts between rural and urban populations, with rural groups enriched in fibre-fermenting and anti-inflammatory taxa, whereas urban communities often exhibit reduced diversity and features of dysbiosis linked to Westernisation. However, limited sample sizes, heterogeneous methodologies and absence of multi-omic approaches constrain robust interpretation. These lacunae in current knowledge emphasise the urgent need for large-scale, longitudinal studies that reflect South Africa's demographic and geographic diversity. Strengthening this evidence will not only help identify microbial signatures linked to modifiable lifestyle factors but will also guide nutrition, prevention and screening programmes to improve health in African populations.},
}

@article {pmid41472032,
year = {2025},
author = {Li, M and Chen, P and Liu, C and Wang, S and Zhang, H and Li, J and Karrow, NA and Mao, Y and Yang, Z},
title = {Gut Microbiome and Metabolome Signatures Associated with Heat Tolerance in Dairy Cows.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41472032},
issn = {2076-2607},
support = {2022YFF1001200//National Key Research and Development Program of China/ ; BK20241934//Natural Science Foundation of Jiangsu Province/ ; 32172686//National Natural Science Foundation of China/ ; },
abstract = {Heat stress significantly impairs dairy cow health and productivity, highlighting the need to understand the gut microbiome-metabolite interactions that contribute to heat tolerance. Here, we integrated metagenomic sequencing and untargeted metabolomics in twelve holstein cows selected from a previously phenotyped herd of 120 individuals, including six heat-tolerant (HT) and six heat-sensitive (HS) cows identified using entropy-weighted TOPSIS scoring. HT cows were enriched in genera such as Faecalimonas and UBA737, which were functionally linked to pathways of energy and lipid metabolism, whereas, HS cows harbored taxa associated with bacterial lipopolysaccharide and glycosphingolipid biosynthesis. A total of 135 metabolites were differentially abundant between groups. Among them, glycerol 2-phosphate and 24(28)-dehydroergosterol showed perfect classification performance (AUC = 1.000), and were mainly involved in membrane lipid remodeling and redox regulation. Integrated analysis revealed coordinated microbial-metabolite networks, exemplified by the Faecalimonas-LysoPS (16:0/0:0) and UBA737-Glycerol 2-phosphate axes, suggesting functional coupling between microbial composition and metabolic adaptation. Together, these findings demonstrate that HT cows harbor gut microbiota and metabolites favoring energy balance, membrane remodeling, and oxidative stress resilience, while HS cows display stress-related metabolic patterns. This study elucidates the microbial-metabolic mechanisms underlying thermal resilience and highlights potential biomarkers and metabolic pathways that could be applied in heat-tolerance breeding and precision management of dairy cattle.},
}

@article {pmid41472025,
year = {2025},
author = {Yun, Y and Ying, Y and Sun, J and Zhao, J and Wang, W and Kang, B},
title = {Effects of Adding Astragali Radix and Inulae Radix on Fermentation Quality, Nutrient Preservation, and Microbial Community in Barley Silage.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41472025},
issn = {2076-2607},
support = {Science and Technology Project from Inner Mongolia//2021GG0068/ ; Ordos Science and Technology Program//2022EEDSKJXM002/ ; },
abstract = {Chinese herbal medicine (CHM) residues represent a promising and sustainable category of silage additives, with the potential to modulate fermentation and enhance nutrient preservation. This study investigated the effects of two CHMs, Astragalus membranaceus L. (Astragali Radix, AR) and Inula helenium L. (Inulae Radix, IR), on the fermentation profile, nutritional composition, and bacterial community structure in barley silage. The forage was ensiled without additive (control, CK), or with 1% or 2% (w/w) of AR or IR for 75 days. The results showed that all additive treatments significantly improved fermentation quality, as evidenced by lower pH and reduced ammonia-nitrogen (NH3-N) content compared to CK. The 2% IR treatment was most effective in promoting homolactic fermentation, yielding the highest lactic acid content and lactic acid-to-acetic acid ratio. Nutritionally, additives significantly increased dry matter, starch, and water-soluble carbohydrates, while decreasing neutral and acid detergent fiber contents. High-throughput sequencing of the 16S rRNA gene revealed that both herbal additives profoundly reshaped the microbial community. They suppressed undesirable bacteria and significantly enriched beneficial Lactobacillus species. Principal component analysis confirmed a distinct separation in microbial community structure between control and treated silages. These findings underscore the potential of these herbal residues as natural modulators of the silage microbiome for improved forage conservation.},
}

@article {pmid41471992,
year = {2025},
author = {Wang, J and Li, D and Lu, D and Chen, C and Zhang, Q and Fu, R and Huang, F},
title = {Differential Assembly of Rhizosphere Microbiome and Metabolome in Rice with Contrasting Resistance to Blast Disease.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471992},
issn = {2076-2607},
support = {SCCXTD-2024-SD-4 & SCCXTD-2024-SD-8//Sichuan Rice Innovation Team Project/ ; 2021YFYZ0021//Sichuan Provincial Science and Technology Planning Project/ ; 5+1QYGG002//Sichuan Academy of Agricultural Sciences Financial Guidance Fund Project/ ; },
abstract = {Rice blast, caused by Magnaporthe oryzae, is one of the most devastating diseases threatening global rice production. Although host resistance represents a sustainable control strategy, the underlying mechanisms mediated by the rhizosphere microbiome remain poorly understood. In this study, we selected four rice varieties with varying resistance to blast and demonstrated, through an integrated approach of 16S rRNA/ITS amplicon sequencing, untargeted metabolomics, and soil physicochemical analysis, that the rice genotype reprograms the genotype-root exudate-rhizosphere microbiome system. Results showed that the resistant variety P104 significantly decreased the soil pH while increasing the contents of total nitrogen, ammonium nitrogen, and nitrate nitrogen. On the other hand, the susceptible variety P302 exhibited higher pH and available phosphorus content. Furthermore, the rhizosphere of P104 was enriched with specific beneficial microbes such as Desulfobacterota, Ascomycota, and Pseudeurotium, and activated defense-related metabolic pathways including cysteine and methionine metabolism and phenylpropanoid biosynthesis. In contrast, susceptible varieties showed reduced bacterial diversity and fostered a microecological environment more conducive to pathogen proliferation. Our findings indicate that blast-resistant rice genotypes are associated with a protective rhizosphere microbiome, potentially mediated by alterations in root metabolism, thereby suppressing pathogen establishment. These insights elucidate the underground mechanisms of blast resistance and highlight the potential of microbiome-assisted breeding for sustainable crop protection.},
}

@article {pmid41471991,
year = {2025},
author = {Qiao, S and Wang, Z and Zhang, R and Wang, Y and Wang, C and Gao, G and Pan, J},
title = {Microbial Community Analysis and Environmental Association in Cave 6 of the Yungang Grottoes.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471991},
issn = {2076-2607},
abstract = {The Yungang Grottoes, a World Heritage Site, face biodeterioration risks. This study analyzed microbial communities in five microenvironments within Cave 6 using high-throughput sequencing (16S/18S rRNA). Communities showed high microenvironment specificity. Ascomycota and Proteobacteria dominated fungi and bacteria, respectively. Areas near the lighting window, with high external interaction, showed the highest diversity, while red pigment areas, likely under heavy metal stress, had the lowest diversity. Human-associated microbes (e.g., Escherichia-Shigella, Malassezia) indicated anthropogenic pollution on statue surfaces. Core microbiome and functional prediction (PICRUSt2) suggested high biodegradation risk in dust accumulation and inter-statue areas, enriched with organic-degrading and acid-producing taxa (e.g., Rubrobacter, Cladosporium). Microbial distribution and function were driven by openness, substrate, and human impact. This study identifies key risk zones and informs targeted conservation strategies for the Yungang Grottoes.},
}

@article {pmid41471974,
year = {2025},
author = {Tu, Y and Chen, B and Wei, Q and Xu, Y and Peng, Y and Li, Z and Liang, J and Zhuo, L and Zhong, W and Huang, J},
title = {Biochar-Urea Peroxide Composite Particles Alleviate Phenolic Acid Stress in Pogostemon cablin Through Soil Microenvironment Modification.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471974},
issn = {2076-2607},
support = {2023B0202010027//Key-Area Research and Development Program of Guangdong Province/ ; 42177337//National Natural Science Foundation of China/ ; 2022A1515020753//Natural Science Foundation of Guangdong Province/ ; },
abstract = {The continuous-cropping obstacles of Pogostemon cablin (patchouli) is severely constrained by autotoxic phenolic acids accumulated in the rhizosphere soil. Biochar adsorption and chemical oxidation are common remediation strategies; they often fail to simultaneously and efficiently remove phenolic allelochemicals while improving the soil micro-ecological environment. To address this issue, this study developed a novel biochar-urea peroxide composite particle (BC-UP). Batch degradation experiments and electron paramagnetic resonance (EPR) analysis confirmed the synergistic adsorption-oxidation function of BC-UP. A pot experiment demonstrated that application of BC-UP (5.0 g/kg) significantly alleviated phenolic acid stress. Specifically, BC-UP application significantly enhanced shoot biomass by 28.8% and root surface area by 49.3% compared to the phenolic acid-stressed treatment and concurrently reduced the total phenolic acid content in the rhizosphere soil by 37.3%. This growth promotion was accompanied by the enhanced accumulation of key bioactive compounds (volatile oils, pogostone, and patchouli alcohol). BC-UP amendment also improved key soil physicochemical properties (e.g., pH, and organic matter) and enhanced the activities of critical enzymes. Furthermore, BC-UP reshaped the microbial community, notably reducing the fungi-to-bacteria OTU ratio by 49.7% and enriching the relative abundance of Firmicutes and Nitrospirota but suppressing the Ascomycota phylum abundance. Redundancy analysis identified soil sucrase and catalase activity, total phenolic acid content, and Ascomycota abundance as key factors influencing patchouli biomass. In conclusion, BC-UP effectively mitigates phenolic acid stress through combined adsorption and radical oxidation, subsequently improving soil properties and restructuring the rhizosphere microbiome, offering a promising soil remediation strategy for patchouli and other medicinal crops.},
}

@article {pmid41471968,
year = {2025},
author = {Huang, X and Huang, J and Zhong, CC and Wong, MCS},
title = {Cell-to-Cell and Patient-to-Patient Variability in Antimicrobial Resistance.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471968},
issn = {2076-2607},
abstract = {Antimicrobial resistance (AMR) remains a global health crisis, yet treatment outcomes cannot be explained by resistance genes alone. Increasing evidence highlights the importance of variability at two levels: within bacterial populations and across patients. At the microbial level, cell-to-cell variability including genetic mutations, stochastic gene expression, persister cell formation, heteroresistance, and spatial heterogeneity within biofilms creates phenotypic diversity that allows subsets of bacteria to survive antimicrobial stress. At the host level, patient-to-patient variability including differences in genetic background, immune competence, comorbidities, gut microbiome composition, and pharmacokinetics shapes both susceptibility to resistant infections and the likelihood of treatment success. Together, these dimensions explain why infections with the same pathogen can lead to divergent clinical outcomes. Understanding and integrating both microbial and host variability offers a path toward more precise diagnostics, personalized therapy, and novel strategies to counter AMR.},
}

@article {pmid41471964,
year = {2025},
author = {Jotic, A and Cirkovic, I and Jovicic, N and Bukurov, B and Krca, N and Savic Vujovic, K},
title = {Biofilm Formation and Its Relationship with the Microbiome in Pediatric Otitis Media.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471964},
issn = {2076-2607},
support = {451-03-65/2025-03/200110//Ministry of Science, Technological Development and Innovation, Republic of Serbia/ ; },
abstract = {Otitis media is among the most common pediatric illnesses globally, constituting a leading cause of antimicrobial prescriptions, recurrent medical consultations, and preventable hearing loss in early childhood. Traditionally regarded as a sterile cavity intermittently invaded by pathogens, the middle ear is now recognized as a dynamic ecological niche influenced by anatomical immaturity of the Eustachian tube, host immune development, and the composition of resident microbial communities. Increasing evidence demonstrates that microbial dysbiosis and the establishment of biofilms are central to the persistence and recurrence of disease. This review synthesizes current knowledge of the pediatric middle ear microbiome, highlighting how commensal organisms contribute to mucosal resilience and colonization resistance, whereas pathogenic bacteria exploit ecological disruption to establish biofilm communities. Biofilm formation provides bacteria with enhanced survival through immune evasion, altered microenvironments, and antibiotic tolerance, thereby transforming acute otitis media into recurrent or chronic states. Furthermore, studies demonstrate how adenoids act as reservoirs of biofilm-forming organisms, seeding the middle ear and perpetuating infection. The emerging ecological perspective emphasizes the limitations of conventional antibiotic-centered management and directs attention toward innovative strategies, including microbiome-preserving interventions, probiotic or live biotherapeutic approaches, and antibiofilm agents. By defining pediatric otitis media as a disorder of disrupted host-microbe equilibrium, future research may pave the way for precision-based preventive and therapeutic strategies aimed at reducing the global burden of this pervasive disease.},
}

@article {pmid41471956,
year = {2025},
author = {Xue, N and Liu, D and Feng, Q and Zhu, Y and Cheng, C and Wang, F and Su, S and Xu, J and Tao, J},
title = {Comparison of Gut Microbiome Profile of Chickens Infected with Three Eimeria Species Reveals New Insights on Pathogenicity of Avian Coccidia.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471956},
issn = {2076-2607},
support = {No. 31972698 to JT//National Natural Science Foundation of China/ ; },
abstract = {Avian coccidiosis is an intestinal disease caused by Eimeria spp. infection. A deeper understanding of the interaction between host gut microbiota and the Eimeria parasite is crucial for developing alternative therapies to control avian coccidiosis. Here, we used full-length sequencing of 16S ribosomal RNA amplicons to compare changes in the gut microbiota of chickens infected with Eimeria tenella, Eimeria maxima, and Eimeria necatrix, aiming to identify both species-specific and common alterations in gut microbiota at 4 and 10 days post-infection. The result revealed that infection with all three Eimeria species led to a decrease in the abundance of the microbial genera Limosilactobacillus, Streptococcus, Alistipes, Lactobacillus and Phocaeicola, while the abundance of Bacteroides, Escherichia and Ligilactobacillus increased. Escherichia and Enterococcus were most abundant in the jejunum of the E. necatrix-infected group and in the cecum of the E. tenella-infected group, whereas Megamonas abundance was highest in the E. maxima-infected group. LEfSe analysis showed that infection with all three Eimeria species significantly reduced the abundance of 13 bacterial species, including Acetilactobacillus jinshanensis, Bacteroides ndongoniae, Barnesiella viscericola, Christensenella minuta, Enterocloster clostridioformis, Gemella haemolysans_A, Granulicatella adiacens, Lawsonibacter sp000177015, Limosilactobacillus reuteri, Limosilactobacillus reuteri_D, Limosilactobacillus vaginalis_A, Limosilactobacillus caviae, Limosilactobacillus vaginalis. Infection with E. tenella significantly increased the abundance of five bacterial species, including Bacteroides fragilis, Enterococcus cecorum, Helicobacter pylori, Methylovirgula ligni, and Phocaeicola sp900066445. Infection with E. maxima significantly increased the abundance of seven bacterial species, including Clostridioides difficile, Faecalibacterium prausnitzii, Mediterraneibacter torques, Muribaculum intestinale, Mediterraneibacter massiliensis, Phascolarctobacterium faecium, and Phocaeicola plebeius. Infection with E. necatrix significantly increased the abundance of seven bacterial species, including Alistipes sp900290115, Anaerotignum faecicola, Bacteroides fragilis_A, Escherichia coli, Harryflintia acetispora, Pseudoclostridium thermosuccinogenes, and Tidjanibacter inops_A. The results showed that Eimeria infection causes significant species- and time-dependent changes in the gut microbiota of chickens. These findings enhance our understanding of coccidiosis pathogenesis and offer potential targets for developing probiotics.},
}

@article {pmid41471952,
year = {2025},
author = {Li, TP and Li, HX and Bao, JS and Wang, CH and Wang, KL and Hao, BR and Wang, ZH and Hu, JH and Zhao, LQ},
title = {Geographical Variation in Bacterial Community Diversity and Composition of Corythucha ciliata.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471952},
issn = {2076-2607},
support = {32301594//National Natural Science Foundation of China/ ; 32171803//National Natural Science Foundation of China/ ; },
abstract = {The sycamore lace bug, Corythucha ciliata, a globally invasive pest that damages Platanus spp., harbors a bacterial microbiome that may help it adapt to different geographical environments. However, the geographical differentiation patterns of its bacterial community and the underlying driving mechanisms remain unclear. In this study, we standardized rearing of three C. ciliata populations (collected from Beijing, Lianyungang, and Nanjing) for three generations to reduce immediate environmental interference, then analyzed their bacterial communities via 16S rRNA gene amplicon sequencing. The principal coordinate analysis revealed a significant separation of the bacterial community in the Nanjing population, while the Beijing and Lianyungang populations were more similar. Bacterial alpha diversity followed the gradient of "Nanjing > Lianyungang > Beijing", with the Nanjing population exhibiting significantly higher species richness and evenness than the Beijing population. All three populations shared core bacterial taxa (e.g., phyla Proteobacteria, Bacteroidota; genera Cardinium, Serratia), but their relative abundances differed significantly: Cardinium dominated the Beijing population (50.1%), Serratia dominated the Lianyungang population (45.86%), and the Nanjing population harbored unique dominant genera such as Sphingomonas. For the three target populations, monthly average temperature and wind speed were positively correlated with bacterial diversity, while latitude was negatively correlated (Pearson correlation coefficient: 0.6564 < |r| < 0.7010, p < 0.05). Core bacterial functions (e.g., substance transport) were conserved across populations, whereas differential functions (e.g., detoxification, lipid metabolism) were linked to geographical adaptation. This study confirms the climate-driven geographical differentiation of the C. ciliata bacterial community provides insights into the "insect-microbiome" interactive invasion mechanism that is present here.},
}

@article {pmid41471933,
year = {2025},
author = {Frizon, L and Rocchetti, TT and Frizon, A and de Alcântara, RJA and de Paiva, CS and Gomes, JÁP},
title = {The Gut Microbiome in Stevens-Johnson Syndrome and Sjögren's Disease: Correlations with Dry Eye.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471933},
issn = {2076-2607},
abstract = {Changes in gut microbial composition may influence mucosal immune responses and contribute to systemic autoimmune manifestations. In this pilot exploratory study, we investigated and compared the gut microbiome in patients with Stevens-Johnson syndrome (SJS), patients with Sjögren's disease (SjD), and healthy controls, using next-generation sequencing (NGS), and assessed correlations with dry eye parameters. The study included 10 patients with SJS matched by age and sex to 10 healthy controls, and 10 patients with SjD matched to an additional set of 10 healthy controls. Dry eye parameters were employed to evaluate dry eye disease (DED). Microbiome profiles were determined using next-generation sequencing of the 16S V3-V4 region and analyzed using the Silva database. The gut microbiome exhibited significant differences in the SJS group, including a reduced Chao1 index (p = 0.01) that was progressively correlated with increased ocular severity and a decrease in Faecalibacterium (p = 0.048) compared to the healthy control group. In the SJS group, strong correlations were observed between increased Christensenellaceae with decreased DED DEWS (Dry Eye Workshop score) (p = 0.04), increased Subdoligranulum with decreased NEI (National Eye Institute) score (p = 0.04), and increased Clostridia and longer TBUT (tear break-up time) (p = 0.009). In contrast, the gut microbiome of SjD patients was similar to that of healthy controls. Patients with SJS exhibited distinct alterations in gut microbial composition, characterized by reduced microbial richness and depletion of Faecalibacterium. Furthermore, a significant association was found between specific bacterial taxa and milder dry eye severity, suggesting a possible link between changes in the gut microbiome and inflammation of the ocular surface.},
}

@article {pmid41471929,
year = {2025},
author = {Han, D and Zhao, R and Yang, X and Wang, T and Li, Z and Zhu, M and Yang, Q and Qu, Y and Chen, X and Chen, Z},
title = {Comparative Analysis of Environmental and Host-Associated Microbiome in Odorrana schmackeri (Auran: Ranidae): Insights into Tissue-Specific Colonization and Microbial Adaptation.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471929},
issn = {2076-2607},
support = {ZC (Grant no. 32270440), XHC (Grant no. U21A20192) and YFQ (32171498)//National Natural Science Foundation of China/ ; },
abstract = {Amphibian microbial communities are known to be shaped by host physiology and environmental factors, yet the relative roles of sexual dimorphism and tissue specialization remain poorly understood. Using 16S rRNA gene sequencing, we compared the gastrointestinal and integumentary microbiomes of a monomorphic Chinese frog population, Odorrana schmackeri, inhabiting identical montane streams. Our results showed distinct phylogenetic stratification between niches: Proteobacteria dominated both environmental microbiota and O. schmackeri gut and skin microbiotas but with differential sub-phylum specialization. The soil microbiota was dominated by unclassified_Vicinamibacteraceae, the water microbiota was Limnohabitans-dominated, the skin microbiota was dominated by Bordetella, and the gut microbiota was led by Acinetobacter. Alpha diversity analysis revealed significant tissue- and environmental-based divergences but no sexual differentiation, a pattern confirmed by beta diversity assessments showing stronger microbial community separation by tissue and environmental compartmentalization than by sex. Functional metagenomic prediction indicated convergent enrichment of metabolic pathways across host-associated and environmental communities. These results suggest that microbial community structure in O. schmackeri is principally governed by tissue-specific ecological selection pressures rather than host sexual characteristics. Our findings enhance understanding of microbiome assembly rules in vertebrate ectotherms and identify potential connections between microbiota in different ecological niches.},
}

@article {pmid41471926,
year = {2025},
author = {Presutti, L and Gueningsman, MC and Fredericksen, B and Smith, A and Taylor, R and Tuckett, A and Folsom, C and Wainwright, R and Klena, C and Ericsson, AC and Zapata, I and Brooks, AE},
title = {Exploring the Interplay Between Fatigue and the Oral Microbiome: A Longitudinal Approach.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471926},
issn = {2076-2607},
abstract = {Fatigue is a pervasive burden for emerging medical professionals, often impacted by stress and lifestyle factors, yet insufficiently explained by these aspects alone. Considering the profound immediate and long-term consequences for physician well-being and patient care, exploring the interplay between biological factors, such as the oral microbiome and fatigue, emerges as a critical area of investigation. This exploratory longitudinal study investigates the relationship between oral microbiome diversity and fatigue in first-year medical students across four timepoints, where they provided buccal swabs and completed lifestyle and standardized stress, sleep, and fatigue assessments (PSQI, FAS, PSS). Microbiome analysis was performed using 16S rRNA sequencing and QIIME2-based bioinformatics to identify genus-level profiles and core microbiome composition. Forty-five healthy participants were assessed. Significant increases in fatigue and fluctuations in oral microbiome diversity were observed, with alpha diversity peaking mid-year before declining. Illness frequency and antibiotic use also rose, potentially influencing microbial shifts. These fluctuations may be indicative of an adaptation process where oral microbial diversity adjusts to changes in the subject's environment, which in this case is entering medical school. Despite no clear clustering in biodiversity metrics, associations between fatigue and microbiome richness were noted, suggesting that physiologic fatigue and environmental stressors may contribute to microbial variability. Limitations of the study include a small sample size, attrition, and representativeness of the study population. This study presents a longitudinal baseline that may serve as a reference for future investigations. These findings may support the development of targeted interventions designed to modulate microbial composition as a novel approach to alleviating fatigue.},
}

@article {pmid41471906,
year = {2025},
author = {Yang, Z and Duan, Y and Wei, R and Yuan, Y and Yan, H and Tang, T and Shang, H},
title = {Rhizosphere Microbiome and Nutrient Fluxes Reveal Subtle Biosafety Signals in Transgenic Cotton.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471906},
issn = {2076-2607},
support = {2023ZD04062//Biological Breeding-Major Projects/ ; 32201828//National Natural Science Foundation of China/ ; 241111114200//Key R&D Program of Henan Province/ ; 2022M722899//China Postdoctoral Science Foundation/ ; 1610162019010101, 1610162023002//Central Public-interest Scientific Institution Basal Research Fund/ ; CB2025C12, CB2024C05//Independent Fund of State Key Laboratory of Cotton Bio-breeding and Integrated Utilization/ ; CAASASTIP-2016-ICR//National Agricultural Science and Technology Innovation Project for CAAS/ ; },
abstract = {Genetically modified crops have transformed agriculture, but their long-term ecological impacts remain incompletely understood. Here we investigate how herbicide-tolerant transgenic cotton affects rhizosphere microbial communities and nutrient cycling over a 28-day growth period using 16S rRNA amplicon sequencing and multivariate analyses. We sampled rhizosphere soil from greenhouse-grown transgenic and wild-type cotton plants at five time points, analyzing microbial diversity, community structure, and nutrient dynamics. Despite initial concerns about transgenic modifications disrupting soil ecosystems, we found no significant differences in microbial α-diversity or β-diversity between genotypes. Only minor, transient changes occurred at the genus level, including <5% shifts in Flavobacterium and Ramlibacter abundance on day 14, alongside brief nutrient flux variations that normalized by day 28. Notably, transgenic plants showed enhanced above-ground biomass accumulation without compromising rhizosphere stability or soil moisture content. These results demonstrate that herbicide-tolerant cotton maintains rhizosphere homeostasis while improving agronomic performance, supporting the environmental safety of this biotechnology for sustainable agricultural intensification.},
}

@article {pmid41471878,
year = {2025},
author = {Qi, X and Han, Z and Meng, J and Zhao, H and Zhou, M and Wang, M and Kang, S and Shi, Q and Li, H and Lu, F and Zhao, H},
title = {Integrated Metagenomic and Lipidomic Profiling Reveals Dysregulation of Facial Skin Microbiome in Moderate Acne Vulgaris.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471878},
issn = {2076-2607},
support = {32402248//the National Natural Science Foundation of China/ ; No. 24JCQNJC00880//the Natural Science Foundation of Tianjin/ ; },
abstract = {Acne vulgaris is a prevalent chronic inflammatory dermatosis primarily affecting the pilosebaceous units. Current therapeutic approaches often exhibit limited efficacy and high recurrence rates. To investigate the microbiome-related mechanisms of acne vulgaris, facial skin samples from 19 patients with moderate acne and 20 healthy individuals were analyzed using an integrated metagenomic and lipidomic profiling strategy. Metagenomic analysis revealed a significant reduction in microbial diversity (Chao index) in acne-affected skin compared to healthy controls (p < 0.001). The relative abundance of Staphylococcus, particularly Staphylococcus epidermidis, was significantly elevated in acne group (p < 0.05), while Cutibacterium acnes levels remained unchanged. Carbon metabolism pathways were enriched in the acne group (p < 0.05), predominantly driven by Cutibacterium, whereas other enriched metabolic pathways, such as ABC transporters and glycine, serine, and threonine metabolism (p < 0.05), showed a greater contribution from Staphylococcus. Virulence factors enriched in acne samples were primarily offensive in nature and largely attributed to Staphylococcus. Moreover, acne-associated microbiome exhibited a significantly higher prevalence of resistance genes against fluoroquinolones, fosfomycin, and triclosan (p < 0.05). Untargeted lipidomic analysis demonstrated significantly elevated total serum and triglyceride levels, along with a reduction in fatty acid chain length and a higher degree of saturation compared to the healthy group (p < 0.01). Specific triglycerides significantly enriched in the acne group, such as TG (15:0_14:0_16:0) + NH4, exhibited a significant positive correlation with Staphylococcus. This correlation is associated with elevated clinical erythema and melanin indices, suggesting that Staphylococcus is implicated in the development of acne-related inflammation. Additionally, Thermus exhibits negative correlations with acne-associated lipids and inflammatory parameters, potentially exerting a protective role. These findings suggest that Cutibacterium and Staphylococcus play differential yet synergistic roles in acne pathogenesis. The observed skin microbiome dysbiosis and lipid metabolic alterations provide novel insights into the pathophysiology of acne vulgaris, which may inform the development of targeted therapeutic strategies.},
}

@article {pmid41471876,
year = {2025},
author = {Wang, Y and Gong, L and Gao, Z and Dong, D and Li, X},
title = {Comparative Analysis of Sponge-Associated, Seawater, and Sediment Microbial Communities from Site F Cold Seep in the South China Sea.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471876},
issn = {2076-2607},
support = {42176114//National Natural Science Foundation of China/ ; ZR2023MD100//the Shandong Provincial Natural Science Foundation/ ; CAS-TAX-24-30//Biological Resources Programme, Chinese Academy of Sciences/ ; },
abstract = {Microbial communities at Site F cold seep, ubiquitous in both the environment and the associated fauna, demonstrate clear habitat-specific partitioning. Metagenomic sequencing and binning demonstrated a striking partitioning of microbial taxa at the cold seep: whereas the sponge-associated microbiome was distinctly enriched with specialized sulfur- and methane-oxidizing bacteria that were rare in the environment, it simultaneously exhibited a significantly reduced archaeal content, lower α-diversity, and a simpler overall community structure compared to the sediment and seawater communities. Distinct evolutionary lineages and varying abundances were observed among the microbiomes from seawater, sediment, and sponges. Furthermore, their Metagenome-Assembled Genomes (MAGs) exhibited significant differences in genomic features, including genome size and GC content. The sponge-associated microbiome exhibits lower diversity but maintains a high abundance of key functional genes, particularly those involved in sulfur cycling (e.g., apr, dsr, metZ), indicating enhanced metabolic efficiency in energy conservation and nutrient acquisition. This study reveals that the seawater, sediment, and sponge-associated microbiomes exhibit genome simplification and functional specialization in the cold seep environment, with varying lifestyles driving structural optimization and functional remodeling of the symbiotic microbiomes.},
}

@article {pmid41471874,
year = {2025},
author = {Song, S and Iino, K and Nakamura, M and Sato, M and Oishi, M and Ito, A and Yokoyama, Y},
title = {Comparative Characterization of Vaginal and Gut Microbiota in Late-Pregnancy Women with or Without Group B Streptococcus Colonization.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471874},
issn = {2076-2607},
support = {JMWH Bayer Grant, 2022//JMWH Bayer Grant/ ; },
abstract = {Group B Streptococcus (GBS) colonization during pregnancy is a major cause of neonatal infection, yet its microbial determinants remain unclear. This pilot study compared the vaginal and gut microbiota of late-pregnancy women with and without GBS colonization to explore potential microbial cues for peripartum risk stratification. Forty-three Japanese pregnant women (GBS-Negative = 34; GBS-Positive = 9) were enrolled at 35-37 weeks of gestation. Vaginal secretions and stool were analyzed by 16S rRNA (V3-V4) sequencing using QIIME 2 with SILVA annotation and community state type (CST) classification. Vaginal communities were mainly Lactobacillus-dominant. GBS-Positive women showed a non-significant tendency toward more L. iners-dominant CST III and fewer L. crispatus-dominant CST I compared with GBS-Negative women. Prevotella, Atopobium, and Gardnerella were significantly enriched in the GBS-Positive group (false discovery rate < 0.05), whereas gut microbial diversity and composition showed no significant differences between groups. Cross-site gut-vagina genus-level correlations were generally weak and non-significant. These findings suggest that, in late pregnancy, GBS colonization is linked to subtle shifts within Lactobacillus-dominant vaginal communities, with more L. iners and bacterial vaginosis-associated genera, rather than global microbiota disruption. The apparent shift from L. crispatus- to L. iners-dominant communities is hypothesis-generating and should be confirmed in larger cohorts.},
}

@article {pmid41471873,
year = {2025},
author = {Zang, B and Xu, L and Huang, H and Liu, Q and Yao, Y and Li, J and Yang, Y and Zhao, C and Liu, B and Liu, B},
title = {Decoding the Gut Microbiome in Primary Sjögren's Syndrome and Primary Biliary Cholangitis: Shared Dysbiosis, Distinct Patterns, and Associations with Clinical Features.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471873},
issn = {2076-2607},
support = {81671600//National Natural Science Foundation of China/ ; 81241094//National Natural Science Foundation of China/ ; ZR2016HM13 /ZR2023MH066//Natural Science Foundation of Shandong Province/ ; 2024-WJKY160//Qingdao Medical and health scientific research project/ ; },
abstract = {This study aimed to analyze gut microbiome similarities and differences between primary biliary cholangitis (PBC) and primary Sjögren's syndrome (pSS), exploring potential associations with disease pathogenesis. High-throughput sequencing of the 16S rRNA gene was performed on fecal samples from 100 subjects (PBC: 38; pSS: 42; HC: 20) to compare the composition, diversity, and key microbial markers, examining associations with clinical indicators. The gut microbiome of PBC and pSS patients exhibited reduced alpha diversity (p < 0.05) and decreased abundance of the Bacteroides genus (both p < 0.001). While the majority of differentially abundant species were similar in PBC and pSS, unique imbalances were noted: Actinobacteria was elevated in pSS, whereas Proteobacteria was higher in PBC (p < 0.05). At the species level, a higher relative abundance of Ruminococcus torques, Clostridium celatum, and Lactobacillus vaginalis was identified in PBC patients, with positive correlations observed with key clinical indicators such as liver enzymes and TBA. In pSS patients, Faecalibacterium prausnitzii showed a negative correlation with GGT and ALT. Although PBC and pSS shared many similarities in their gut microbiome's composition and diversity, indicating common mechanistic microbial influences on their pathogenicity, distinct microbial profiles correlated with clinical indicators in each disease, highlighting specific microbiome-disease interactions that may underlie their differential pathogenesis.},
}

@article {pmid41471872,
year = {2025},
author = {Yang, B and Zhong, S and Wang, J and Yu, W},
title = {Dietary Modulation of the Gut Microbiota in Dogs and Cats and Its Role in Disease Management.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471872},
issn = {2076-2607},
support = {No. 20242BAB20315//Natural Science Foundation for Youth of Jiangxi Province/ ; GJJ2200410//The Science and Technology Program of Jiangxi Provincial Department of Education/ ; },
abstract = {Food has a massive influence on the gut microbiota and is one of the most useful therapeutic levers in disease. Recent developments have highlighted how macronutrient balance, food format, and functional ingredients can regulate microbial diversity, metabolism, and host physiology in companion animals such as dogs and cats. This narrative review condenses evidence on the bidirectional gut microbiota-diet connection and on nutritional therapy for gastrointestinal, metabolic, renal, hepatic, and immune-mediated disorders. Protein-based diets including high or hydrolyzed protein, omega-3 acids, fermentative fiber, and probiotics can positively affect microbial composition, stimulate short-chain fatty acid synthesis, and enhance intestinal barrier functions. Conversely, excess fats or refined carbohydrates may cause dysbiosis, inflammation, and metabolic imbalances. Numerous studies have shown that therapeutic nutrition-e.g., low-protein renoprotective, hepatoprotective antioxidants, and allergen-elimination diets-holds enormous potential for treatment. In addition, fecal microbiota transplantation (FMT) can be used as an additive therapy for resistant gastrointestinal illnesses. Despite these developments, constraints remain in terms of standardization, study duration, and species-specific data, especially for cats. This review underscores dietary modification as a clinically actionable tool for microbiota-targeted therapy and calls for integrative, multi-omics research to translate microbiome modulation into precision nutrition for companion animals.},
}

@article {pmid41471858,
year = {2025},
author = {Long, N and Zuo, Y and Li, J and Yao, R and Yang, Q and Deng, H},
title = {Thuja sutchuenensis Franch. Essential Oil Ameliorates Atopic Dermatitis Symptoms in Mice by Modulating Skin Microbiota Composition and Reducing Inflammation.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471858},
issn = {2076-2607},
support = {zlg2021-cq20211210, zlg2022-cq20220907//National Key Wildlife Conservation Project of Central Forestry Reform and Development Funds/ ; CSTB2024NSCQ-MSX1297//the Chongqing Natural Science Foundation/ ; 25MSZX555//the Sichuan Provincial Administration of Traditional Chinese Medicine/ ; CYZYB24-08//the Chengdu Medical College Natural Science Foundation/ ; },
abstract = {Atopic dermatitis (AD) is a chronic inflammatory skin disorder characterized by dysregulated immunity, skin barrier dysfunction, and cutaneous microbiome dysbiosis. While current therapies face limitations, Thuja sutchuenensis essential oil (TEO) shows promise due to its multi-target potential. We sought to explore the beneficial effects of TEO and delve into its mechanistic actions in a mouse model of AD. We combined network pharmacology with in vivo validation to evaluate the therapeutic efficacy and mechanisms of TEO in an AD model, and confirmed network-predicted targets in an in vitro inflammatory cell model. In AD mice, TEO alleviated pruritus and epidermal hyperplasia, suppressed systemic IL-4/TNF-α and IgE, and partially normalized serum ALB, LDL-C, and HDL-C. Microbial diversity increased after treatment, although potentially pathogenic taxa (Arthrobacter sp. and Corynebacterium mastitidis) remained enriched. Machine-learning analysis indicated the highest predicted metabolic activity in CK controls, whereas the AD and TEO groups showed elevated pathogenic phenotype scores. Network pharmacology prioritized active compounds [(E)-ligustilide, senkyunolide A, 3-butylisobenzofuran-1(3H)-one, butylated hydroxytoluene, Z-buthlidenephthalide, and β-Myrcene] and core targets (TNF, PTPRC, CCR5, JAK1), implicating T-cell receptor signaling, Staphylococcus aureus infection, and STAT3 pathways. Docking and molecular dynamics supported strong, stable binding of major constituents to JAK1, and Western blotting confirmed TEO-mediated inhibition of the JAK1/STAT3 axis. TEO effectively alleviates atopic dermatitis symptoms by modulating immune responses and enhancing microbial diversity. It targets key signaling pathways, such as JAK1/STAT3, highlighting its potential as a therapeutic option for AD.},
}

@article {pmid41471710,
year = {2025},
author = {Oliveira, MB and Maurício, AC and Barros, AN and Botelho, C},
title = {Rebalancing the Skin: The Microbiome, Acne Pathogenesis, and the Future of Natural and Synthetic Therapies.},
journal = {Molecules (Basel, Switzerland)},
volume = {30},
number = {24},
pages = {},
pmid = {41471710},
issn = {1420-3049},
support = {LA/P/0059/2020//Fundação para a Ciência e Tecnologia/ ; UIDB/00211/2020//Fundação para a Ciência e Tecnologia/ ; UID/04033/2025//Fundação para a Ciência e Tecnologia/ ; },
mesh = {Humans ; *Acne Vulgaris/microbiology/drug therapy/pathology/etiology ; *Microbiota/drug effects ; *Skin/microbiology/drug effects/pathology ; *Biological Products/therapeutic use/pharmacology ; Anti-Bacterial Agents/therapeutic use/pharmacology ; Dysbiosis ; Animals ; },
abstract = {The skin serves as a primary interface between the human body and the external environment, functioning both as a protective barrier and as a habitat for a complex and diverse microbiome. These microbial communities contribute to immune regulation, barrier integrity, and defence against pathogens. Disruptions in this equilibrium can precipitate dermatological disorders such as acne vulgaris, which affects millions of adolescents and adults worldwide. This chronic inflammatory disorder of the pilosebaceous unit is driven by microbial dysbiosis, hyperkeratinisation, sebum overproduction, and inflammation. This review synthesizes data from over 100 sources to examine the interplay between the skin microbiome and acne pathogenesis, and to compare synthetic treatments, including retinoids, antibiotics, and hormonal therapies, with natural approaches such as polyphenols, minerals, and resveratrol. The analysis highlights the therapeutic convergence of traditional pharmacology and bioactive natural compounds, proposing microbiome-conscious and sustainable strategies for future acne management.},
}

Humans
*Acne Vulgaris/microbiology/drug therapy/pathology/etiology
*Microbiota/drug effects
*Skin/microbiology/drug effects/pathology
*Biological Products/therapeutic use/pharmacology
Anti-Bacterial Agents/therapeutic use/pharmacology
Dysbiosis
Animals

@article {pmid41471248,
year = {2025},
author = {Shi, X and Bi, N and Liu, W and Ma, L and Liu, M and Xu, T and Shu, X and Gao, L and Wang, R and Chen, Y and Li, L and Zhu, Y and Li, D},
title = {Identification of Oral Microbiome Biomarkers Associated with Lung Cancer Diagnosis and Radiotherapy Response Prediction.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/pathogens14121294},
pmid = {41471248},
issn = {2076-0817},
support = {NCC202416006//National High Level Hospital Clinical Research Funding and National Cancer Center Climbing Fund/ ; 2023ZD0502100//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; },
mesh = {Humans ; *Microbiota/genetics ; *Lung Neoplasms/radiotherapy/diagnosis/microbiology ; Male ; Female ; Middle Aged ; *Mouth/microbiology ; RNA, Ribosomal, 16S/genetics ; Aged ; Biomarkers ; *Bacteria/classification/genetics/isolation & purification ; Prognosis ; Biomarkers, Tumor ; },
abstract = {The oral cavity acts as the anatomical gateway to the respiratory tract, sharing both microbiological and pathophysiological links with the lower airways. Although radiotherapy is a cornerstone treatment for lung cancer, reliable oral microbiome biomarkers for predicting patient outcomes remain lacking. We analyzed the oral microbiome of 136 lung cancer patients and 199 healthy controls across discovery and two validation cohorts via 16S rRNA sequencing. Healthy controls exhibited a significantly higher abundance of Streptococcus compared to patients (p = 0.049, p < 0.001, p < 0.001, respectively). The structure of the microbial community exhibited substantial dynamic changes during treatment. Responders showed enrichment of Rothia aeria (p = 0.027) and Prevotella salivae (p = 0.043), associated with prolonged overall survival (OS) and progression-free survival (PFS), whereas non-responders exhibited elevated Porphyromonas endodontalis (p = 0.037) correlating with shorter OS and PFS. According to Analysis of Compositions of Microbiomes with Bias Correction 2 (ANCOM-BC2) analysis, Akkermansia and Alistipes were nearly absent in non-responders, while Desulfovibrio and Moraxella were virtually absent in responders. A diagnostic model based on Streptococcus achieved area under the curve (AUC) values of 0.85 (95% CI: 0.78-0.91) and 0.99 (95% CI: 0.98-1) in the validation cohorts, and a response prediction model incorporating Prevotella salivae and Neisseria oralis yielded an AUC of 0.74 (95% CI: 0.58-0.90). Furthermore, in small cell lung cancer, microbiota richness and diversity were inversely correlated with Eastern Cooperative Oncology Group (ECOG) performance status (p = 0.008, p < 0.001, respectively) and pro-gastrin-releasing peptide (ProGRP) levels (p = 0.065, p = 0.084, respectively). These results demonstrate that lung cancer-associated oral microbiota signatures dynamically reflect therapeutic response and survival outcomes, supporting their potential role as non-invasive biomarkers for diagnosis and prognosis.},
}

Humans
*Microbiota/genetics
*Lung Neoplasms/radiotherapy/diagnosis/microbiology
Male
Female
Middle Aged
*Mouth/microbiology
RNA, Ribosomal, 16S/genetics
Aged
Biomarkers
*Bacteria/classification/genetics/isolation & purification
Prognosis
Biomarkers, Tumor

@article {pmid41471188,
year = {2025},
author = {Nikolić, N and Pucar, A and Tomić, U and Petrović, S and Mihailović, Đ and Jovanović, A and Radunović, M},
title = {Oral Microbiota and Carcinogenesis: Exploring the Systemic Impact of Oral Pathogens.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/pathogens14121233},
pmid = {41471188},
issn = {2076-0817},
support = {2019-191//eklund foundation/ ; 451-03-137/2025-03/200129//Ministry of Science, Technological Development and Innovations of the Republic of Serbia/ ; 03-136/2025-03/200129//Ministry of Science, Technological Development and Innovations of the Republic of Serbia/ ; },
mesh = {Humans ; *Mouth/microbiology ; *Microbiota ; *Carcinogenesis ; *Neoplasms/microbiology/etiology ; *Dysbiosis/microbiology/complications ; Fusobacterium nucleatum/pathogenicity ; Animals ; },
abstract = {For decades, cancer risk has been explained mainly by local factors. However, emerging evidence shows that the oral microbiome acts as a systemic modifier of oncogenesis well beyond the head and neck. This review synthesizes clinical and mechanistic data linking dysbiotic oral communities, especially Porphyromonas gingivalis, Fusobacterium nucleatum, and Treponema denticola, to malignancies across gastrointestinal, respiratory, hepatobiliary, pancreatic, breast, and urogenital systems. We summarize organ-specific associations from saliva, tissue, and stool studies, noting the recurrent enrichment of oral taxa in tumor and peri-tumoral niches of oral, esophageal, gastric, colorectal, lung, pancreatic, liver, bladder, cervical, and breast cancers. Convergent mechanisms include the following: (i) persistent inflammation (lypopolysacharide, gingipains, cytolysins, and collagenases); (ii) direct genotoxicity (acetaldehyde, nitrosation, and CDT); (iii) immune evasion/suppression (TLR/NLR signaling, MDSC recruitment, TAN/TAM polarization, and TIGIT/CEACAM1 checkpoints); and (iv) epigenetic/signaling rewiring (NF-κB, MAPK/ERK, PI3K/AKT, JAK/STAT, WNT/β-catenin, Notch, COX-2, and CpG hypermethylation). Plausible dissemination along an oral-gut-systemic axis, hematogenous, lymphatic, microaspiration, and direct mucosal transfer enables distal effects. While causality is not yet definitive, cumulative data support oral dysbiosis as a clinically relevant cofactor, motivating biomarker-based risk stratification, saliva/stool assays for early detection, and microbiome-targeted interventions (periodontal care, antimicrobials, probiotics, and microbiota modulation) alongside conventional cancer control.},
}

Humans
*Mouth/microbiology
*Microbiota
*Carcinogenesis
*Neoplasms/microbiology/etiology
*Dysbiosis/microbiology/complications
Fusobacterium nucleatum/pathogenicity
Animals

@article {pmid41471163,
year = {2025},
author = {Ziaka, M},
title = {Targeting Gut-Lung Crosstalk in Acute Respiratory Distress Syndrome: Exploring the Therapeutic Potential of Fecal Microbiota Transplantation.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/pathogens14121206},
pmid = {41471163},
issn = {2076-0817},
mesh = {*Respiratory Distress Syndrome/therapy/microbiology ; Humans ; *Fecal Microbiota Transplantation/methods ; *Gastrointestinal Microbiome ; *Lung/microbiology/immunology ; Animals ; *Gastrointestinal Tract/microbiology ; },
abstract = {The gastrointestinal (GI) tract contributes significantly to the pathogenesis of acute respiratory distress syndrome (ARDS) by influencing systemic inflammation and sepsis, which are key factors in the development of multiple organ dysfunction syndrome (MODS), while the significant impact of gut microbiota in critically ill patients, including those with sepsis and ARDS, further underscores its importance. The intestinal microbiota is vital to immune system function, responsible for triggering around 80% of immune responses. Therefore, it may be hypothesized that modifying fecal microbiota, such as through fecal microbiota transplantation (FMT), could serve as a valuable therapeutic approach for managing inflammatory diseases like lung injury (LI)/ARDS. Indeed, emerging experimental research suggests that FMT may have beneficial effects in ARDS models by improving inflammation, oxidative stress, LI, and oxygenation. However, well-designed randomized clinical trials in patients with ARDS are still lacking. Our study seeks to examine how therapeutic interventions such as FMT might benefit LI/ARDS patients by exploring the interactions between the gut and lungs in this context.},
}

*Respiratory Distress Syndrome/therapy/microbiology
Humans
*Fecal Microbiota Transplantation/methods
*Gastrointestinal Microbiome
*Lung/microbiology/immunology
Animals
*Gastrointestinal Tract/microbiology

@article {pmid41471117,
year = {2025},
author = {Shuvo, MSH and Kim, S and Jo, S and Rahim, MA and Barman, I and Hossain, MS and Yoon, Y and Tajdozian, H and Ahmed, I and Atashi, A and Jeong, G and Suh, HS and You, J and Sung, C and Kim, M and Seo, H and Song, HY},
title = {Flavonifractor plautii as a Next-Generation Probiotic Enhancing the NGP F/P Index in a Simulated Human Gut Microbiome Ecosystem.},
journal = {Pharmaceutics},
volume = {17},
number = {12},
pages = {},
doi = {10.3390/pharmaceutics17121603},
pmid = {41471117},
issn = {1999-4923},
support = {No. RS-2023-00219563//Ministry of Science and ICT/ ; Bio Workforce Training Program//Ministry of Trade, Industry, and Energy/ ; Soonchunhyang University Research Fund//Soonchunhyang University/ ; },
abstract = {Background/Objectives: Traditionally consumed fermented foods and lactic acid bacteria (LAB)-based products have primarily been investigated for their nutritional and health-promoting benefits as dietary supplements. More recently, research has advanced toward exploring their therapeutic potential in pharmaceutical development. However, reliance on conventional LAB strains despite their established safety and efficacy has led to saturation at the strain level, underscoring the need for next-generation probiotics (NGPs) with novel therapeutic potential. In this context, we identified Flavonifractor plautii from human feces as a candidate NGP and investigated its effects on the human gut microbiota. Methods: Whole-genome sequencing revealed distinct genetic features that supported its uniqueness, and the strain was designated PMC93. A human gut microbial ecosystem simulator was used to administer F. plautii daily for one week, after which microbial community changes were evaluated using 16S rRNA gene-based metagenomic sequencing. Results: The administration did not induce significant changes in alpha or beta diversity, suggesting that F. plautii does not disrupt overall bacterial community structure, thereby supporting its microbial community safety. Taxonomic analysis demonstrated a significant increase in the Firmicutes-to-Proteobacteria ratio (NGP F/P index). The improvement surpassed that of conventional LAB treatments and was consistently maintained under supplementation with commonly encountered pharmaceutical compounds and nutrients. The shift was associated with an increase in short-chain fatty acid (SCFA)-producing beneficial taxa and a decrease in pro-inflammatory and potentially pathogenic groups. Functional outcomes, including elevated SCFA levels and downregulation of inflammation-related gene expression, further corroborated these compositional changes. The strain also demonstrated safety in in vivo models. Conclusions: Collectively, these findings suggest that strain PMC93 is a promising NGP candidate with substantial therapeutic potential for microbiota-associated health and disease modulation, particularly due to its ability to enhance the NGP F/P index.},
}

@article {pmid41471111,
year = {2025},
author = {Holler, N and Ruseska, I and Schachner-Nedherer, AL and Zimmer, A and Petschacher, C},
title = {Oral Treatment of Obesity by GLP-1 and Its Analogs.},
journal = {Pharmaceutics},
volume = {17},
number = {12},
pages = {},
doi = {10.3390/pharmaceutics17121596},
pmid = {41471111},
issn = {1999-4923},
abstract = {Obesity is a multifaceted disease that significantly increases the risk of various chronic conditions. GLP-1R (co)-agonists first emerged as therapeutics for treatment of type 2 diabetes mellitus and have since become an established drug class for improving glycemic control. The interest in GLP-1 for obesity treatment has surged in 2015 after the approval of Saxenda[®] (liraglutide). To date, GLP-1 analogs are primarily administered by s.c. injection, which poses a significant burden on patient compliance. To address this challenge, research has focused on oral delivery. This review provides a concise overview of the techniques explored to enhance the oral delivery of GLP-1 analogs for the treatment of obesity. Relevant strategies include the following: (1) the use of permeation enhancers to increase gastrointestinal absorption of peptides; (2) micro- and nanocarriers loaded with GLP-1, including targeted delivery systems and general techniques for active drug targeting; (3) GLP-1 gene delivery; and (4) advanced microbiome systems for GLP-1 delivery. The potential for misuse and side-effects of GLP-1 analogs are also discussed.},
}