@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.},
}

@article {pmid41471101,
year = {2025},
author = {Tauser, RG and Vasincu, IM and Iacob, AT and Apotrosoaei, M and Profire, BȘ and Lupascu, FG and Chirliu, OM and Profire, L},
title = {A State-of-the-Art Overview on (Epi)Genomics and Personalized Skin Rejuvenating Strategies.},
journal = {Pharmaceutics},
volume = {17},
number = {12},
pages = {},
doi = {10.3390/pharmaceutics17121585},
pmid = {41471101},
issn = {1999-4923},
abstract = {This article aims to point out new perspectives opened by genomics and epigenomics in skin rejuvenation strategies which target the main hallmarks of the ageing. In this respect, this article presents a concise overview on: the clinical relevance of the most important clocks and biomarkers used in skin anti-ageing strategy evaluation, the fundamentals, the main illustrating examples preclinically and clinically tested, the critical insights on knowledge gaps and future research perspectives concerning the most relevant skin anti-ageing and rejuvenation strategies based on novel epigenomic and genomic acquisitions. Thus the review dedicates distinct sections to: senolytics and senomorphics targeting senescent skin cells and their senescent-associated phenotype; strategies targeting genomic instability and telomere attrition by stimulation of the deoxyribonucleic acid (DNA) repair enzymes and proteins essential for telomeres' recovery and stability; regenerative medicine based on mesenchymal stem cells or cell-free products in order to restore skin-resided stem cells; genetically and chemically induced skin epigenetic partial reprogramming by using transcription factors or epigenetic small molecule agents, respectively; small molecule modulators of DNA methylases, histone deacetylases, telomerases, DNA repair enzymes or of sirtuins; modulators of micro ribonucleic acid (miRNA) and long-non-coding ribonucleic acid (HOTAIR's modulators) assisted or not by CRISPR-gene editing technology (CRISPR: Clustered Regularly Interspaced Short Palindromic Repeats); modulators of the most relevant altered nutrient-sensing pathways in skin ageing; as well as antioxidants and nanozymes to address mitochondrial dysfunctions and oxidative stress. In addition, some approaches targeting skin inflammageing, altered skin proteostasis, (macro)autophagy and intercellular connections, or skin microbiome, are very briefly discussed. The review also offers a comparative analysis among the newer genomic/epigenomic-based skin anti-ageing strategies vs. classical skin rejuvenation treatments from various perspectives: efficacy, safety, mechanism of action, evidence level in preclinical and clinical data and regulatory status, price range, current limitations. In these regards, a concise overview on senolytic/senomorphic agents, topical nutrigenomic pathways' modulators and DNA repair enzymes, epigenetic small molecules agents, microRNAs and HOTAIRS's modulators, is illustrated in comparison to classical approaches such as tretinoin and peptide-based cosmeceuticals, topical serum with growth factors, intense pulsed light, laser and microneedling combinations, chemical peels, botulinum toxin injections, dermal fillers. Finally, the review emphasizes the future research directions in order to accelerate the clinical translation of the (epi)genomic-advanced knowledge towards personalization of the skin anti-ageing strategies by integration of individual genomic and epigenomic profiles to customize/tailor skin rejuvenation therapies.},
}

@article {pmid41470907,
year = {2025},
author = {Sekikawa, A and Weaver, A and Mroz, K and Heilmann, NZ and Madrid Fuentes, DA and Koltun, KJ and Carlson, LJ and Cattell, KL and Li, M and Li, J and Hughes, TM and Strotmeyer, E and Nindl, B and Cauley, JA},
title = {S-Equol as a Gut-Derived Phytoestrogen Targeting Estrogen Receptor β: A Promising Bioactive Nutrient for Bone Health in Aging Women and Men: A Narrative Review.},
journal = {Nutrients},
volume = {17},
number = {24},
pages = {},
doi = {10.3390/nu17243962},
pmid = {41470907},
issn = {2072-6643},
support = {R01 AG074971/AG/NIA NIH HHS/United States ; P30 AG021332/AG/NIA NIH HHS/United States ; P30 AG024827/AG/NIA NIH HHS/United States ; 1S10AG030295-01A1/NH/NIH HHS/United States ; 5UM1TR004929-02/NH/NIH HHS/United States ; },
mesh = {Humans ; *Equol/pharmacology/metabolism ; *Phytoestrogens/pharmacology ; *Estrogen Receptor beta/metabolism/agonists ; Male ; Female ; *Osteoporosis/prevention & control/drug therapy ; Animals ; *Bone and Bones/drug effects/metabolism ; Gastrointestinal Microbiome ; Isoflavones/metabolism ; Bone Density/drug effects ; *Aging ; Aged ; },
abstract = {Background/Objectives: Osteoporosis is highly prevalent and contributes substantially to morbidity and mortality, yet long-term concerns about pharmacologic therapies leave a major treatment gap. Soy isoflavones have been investigated as safer alternatives, but results across trials are inconsistent. A key unresolved issue is the equol-producer phenotype, the gut microbial ability to convert daidzein to S-equol, the most bioactive isoflavone metabolite, which may explain much of this variability. This narrative review synthesizes mechanistic, translational, and clinical evidence to clarify the potential skeletal relevance of S-equol. Methods: Literature was identified through PubMed and Scopus searches (January 2000-October 2025) for experimental, mechanistic, and clinical studies examining S-equol, estrogen receptor β (ERβ), and bone metabolism, with emphasis on equol-producing status, bone strength and bone microarchitecture. Results: S-equol acts as a high-affinity ERβ agonist with antioxidant and anti-inflammatory properties but lacks the carcinogenic or thrombotic risks linked to ERα activation. In estrogen-deficient rodent models, S-equol improves trabecular bone volume by 10-20%, increases trabecular number, and enhances biomechanical strength. These findings align with preclinical evidence demonstrating that S-equol preserves trabecular microarchitecture, enhances bone strength, and reduces bone turnover. A limited number of human trials show reductions in bone resorption by 20% at a daily dose of 10 mg S-equol. In contrast, trials of soy isoflavones in humans have produced inconsistent findings, partly because of substantial variability in equol-producer phenotype among participants and the reliance on dual-energy X-ray absorptiometry, which cannot distinguish trabecular from cortical compartments. Advanced bone imaging and microbiome-informed approaches enable the precise evaluation of S-equol's skeletal effects on trabecular bone and cortical bone, separately. Conclusions: S-equol represents a promising model for "precision nutrition," where microbiome, hormonal, and host factors converge with potential to prevent age-related bone fragility. Rigorous trials that integrate microbiome phenotyping and advanced imaging are needed to validate this approach, translate mechanistic promise into clinical benefit, and better define safety.},
}

Humans
*Equol/pharmacology/metabolism
*Phytoestrogens/pharmacology
*Estrogen Receptor beta/metabolism/agonists
Male
Female
*Osteoporosis/prevention & control/drug therapy
Animals
*Bone and Bones/drug effects/metabolism
Gastrointestinal Microbiome
Isoflavones/metabolism
Bone Density/drug effects
*Aging
Aged

@article {pmid41470885,
year = {2025},
author = {Jung, SH and Hwang, S and Seo, KH and Park, Y and Kim, MJ and Kim, H},
title = {Bioconversion-Based Postbiotics Enhance Muscle Strength and Modulate Gut Microbiota in Healthy Individuals: A Randomized, Double-Blind, Placebo-Controlled Trial.},
journal = {Nutrients},
volume = {17},
number = {24},
pages = {},
doi = {10.3390/nu17243937},
pmid = {41470885},
issn = {2072-6643},
support = {Otoki Ham Taiho Foundation//Otoki Ham Taiho Foundation/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Double-Blind Method ; Male ; Adult ; Female ; *Muscle Strength/drug effects ; *Whey Proteins/administration & dosage ; Young Adult ; Feces/microbiology ; Hand Strength ; Healthy Volunteers ; Dietary Supplements ; Biomarkers/blood ; },
abstract = {BACKGROUND: Postbiotics produced by kefir lactic acid bacteria through bioconversion of polyphenol-rich extract and whey protein are emerging as promising modulators of gut microbiota and muscle health. This study investigated whether Lentilactobacillus kefiri DH5-derived postbiotics, prepared with Cucumis melo L. and whey protein (KP, Kefir lactic acid bacteria-derived postbiotics), improve muscle strength and gut microbiota composition in healthy adults.

METHODS: In this 12-week, randomized, double-blind, placebo-controlled trial, participants consumed either KP (6 g/day) or placebo. Handgrip strength, circulating biomarkers, and fecal microbiota profiling (using 16S rRNA sequencing) were analyzed. Correlations between microbial taxa and muscle-related biomarkers were assessed.

RESULTS: KP supplementation significantly increased dominant-hand grip strength and plasma irisin and reduced IL-1β concentrations after 12 weeks, whereas IGF-1, lean mass, and non-dominant grip strength showed no significant changes. Gut microbiota profiling revealed enrichment of Bifidobacterium adolescentis, Latilactobacillus sakei, Lentihominibacter hominis, Mediterraneibacter gnavus, Streptococcus anginosus and Phocaeicola plebeius, with concomitant reductions in Lachnospira eligens, Roseburia inulinivorans, Ruthenibacterium lactatiformans and Vescimonas fastidiosa. Notably, relative abundance of Faecalibacterium prausnitzii was positively correlated with plasma irisin concentration.

CONCLUSIONS: KP supplementation produced a modest within-group improvement in grip strength, potentially through gut-muscle axis modulation involving irisin and anti-inflammation pathways. These preliminary findings suggest that kefir-derived postbiotics may have potential relevance for muscle health.},
}

Humans
*Gastrointestinal Microbiome/drug effects
Double-Blind Method
Male
Adult
Female
*Muscle Strength/drug effects
*Whey Proteins/administration & dosage
Young Adult
Feces/microbiology
Hand Strength
Healthy Volunteers
Dietary Supplements
Biomarkers/blood

@article {pmid41470864,
year = {2025},
author = {Torres-Mejías, J and Arriaza, K and Mena, F and Rivarola, E and Paredes, P and Ahmad, H and López, I and Soza, D and Pino-Villalón, JL and López-Espinoza, MÁ and Duran-Agüero, S and Merellano-Navarro, E},
title = {Body Composition, Microbiome and Physical Activity in Workers Under Intermittent Hypobaric Hypoxia.},
journal = {Nutrients},
volume = {17},
number = {24},
pages = {},
doi = {10.3390/nu17243919},
pmid = {41470864},
issn = {2072-6643},
mesh = {Humans ; *Body Composition/physiology ; *Exercise/physiology ; Adult ; Male ; *Gastrointestinal Microbiome/physiology ; *Hypoxia/physiopathology/microbiology ; Nutritional Status ; Energy Metabolism ; Female ; Electric Impedance ; Body Mass Index ; Middle Aged ; Feces/microbiology ; },
abstract = {Background/Objectives: Intermittent hypobaric hypoxia (IHH) induces various physiological and metabolic adaptations. This study aimed to investigate the effects of a seven-day IHH exposure on nutritional status, body composition, gut microbiota, movement intensity, and energy expenditure in 10 workers. Methods: A pre-post comparative design was employed, with measurements taken at the beginning and end of the exposure period. Nutritional status, body composition, and phase angle (PhA) were assessed via bioelectrical impedance analysis (BIA). Gut microbiota composition was analyzed through fecal DNA extraction and qPCR for specific bacterial families. Movement intensity and energy expenditure were monitored using accelerometry. An initial statistical analysis was performed, which included paired t-tests and Wilcoxon signed-rank tests. Results: A significant increase in PhA (mean difference: 0.40; p = 0.0053 for t-test, p = 0.0136 for Wilcoxon) and a significant decrease in BMI (mean difference: -0.38; p = 0.0311 for t-test, p = 0.0546 for Wilcoxon). Conclusions: While the original paper reported no significant changes in nutritional status or body composition, our re-analysis suggests a significant change in BMI. The original paper also reported significant changes in specific gut bacterial families (butyrate-producing bacteria, p = 0.037; Lactobacillus species, p = 0.006). Physical activity levels remained consistently low.},
}

Humans
*Body Composition/physiology
*Exercise/physiology
Adult
Male
*Gastrointestinal Microbiome/physiology
*Hypoxia/physiopathology/microbiology
Nutritional Status
Energy Metabolism
Female
Electric Impedance
Body Mass Index
Middle Aged
Feces/microbiology

@article {pmid41470852,
year = {2025},
author = {Stumpf, KA and Green, M and Niu, X and Lu, D and Gan, S and Zhan, X and Maxey, MN and Boren, M and Nayak, SP and Jaleel, S and Brown, LS and Foster, JA and Mirpuri, J},
title = {Gut Microbiome Composition and Variance Are Modified by Degree of Growth Failure in Preterm Infants: A Prospective Study.},
journal = {Nutrients},
volume = {17},
number = {24},
pages = {},
doi = {10.3390/nu17243907},
pmid = {41470852},
issn = {2072-6643},
support = {R01 DK121975/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Prospective Studies ; Infant, Newborn ; *Infant, Premature/growth & development ; Feces/microbiology ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; Case-Control Studies ; Infant ; Clostridium/isolation & purification ; Gestational Age ; Bifidobacterium/isolation & purification ; *Growth Disorders/microbiology ; Intensive Care Units, Neonatal ; },
abstract = {Background/Objectives: Preterm infants often require increased caloric intake to maintain appropriate growth while in the neonatal intensive care unit (NICU). Emerging evidence suggests that alterations of the gut microbiome may play a role in infant and childhood growth patterns. The fecal microbiome patterns in infants with normal and poor growth patterns were classified in this study. Methods: We conducted a prospective trial of infants of less than 29 weeks' gestation with an embedded case-control analysis of infants with normal or poor growth patterns. Fecal samples were collected weekly from infants on full enteral feeds and analyzed blindly using 16s rRNA next-generation sequencing. The relationship between gut microbial diversity and composition and growth pattern and trajectory were assessed. Results: A total of 115 infants were enrolled in the trial with 263 fecal samples selected from 87 enrolled infants for analysis. In total, 37 samples were available from the normal growth cohort, 56 samples from the poor growth cohort, and 170 samples were available for analysis from the very poor growth cohort. Analysis of relative abundance revealed increased representation of Veillonella, Bifidobacterium, and Clostridium in very poor growth infants compared to normal growth infants. Variation in specific taxa was also found to vary significantly across post-menstrual age depending on the degree of growth failure. Conclusions: Gut microbiome composition and variance was modified by the degree of growth failure in our cohort of preterm infants. Our study adds to the growing body of evidence that alteration of the microbiome is associated with poor growth in preterm infants. This may ultimately represent a therapeutic target for growth failure in preterm infants.},
}

Humans
*Gastrointestinal Microbiome
Prospective Studies
Infant, Newborn
*Infant, Premature/growth & development
Feces/microbiology
Male
Female
RNA, Ribosomal, 16S/genetics
Case-Control Studies
Infant
Clostridium/isolation & purification
Gestational Age
Bifidobacterium/isolation & purification
*Growth Disorders/microbiology
Intensive Care Units, Neonatal

@article {pmid41470806,
year = {2025},
author = {Black, EG and Bugarcic, A and Lauche, R and El-Omar, E and El-Assaad, F},
title = {The Effects of Kefir on the Human Oral and Gut Microbiome.},
journal = {Nutrients},
volume = {17},
number = {24},
pages = {},
doi = {10.3390/nu17243861},
pmid = {41470806},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Kefir/microbiology ; *Mouth/microbiology ; Probiotics ; Functional Food ; },
abstract = {Kefir, a fermented probiotic drink made from milk, water, or plant-based ingredients, has gained significant attention as a dietary supplement. Originating from the Caucasus Mountains over three thousand years ago, kefir is believed to harbor a range of health benefits through its ability to alter the composition of microbial niches within the human body. These microbial niches are called microbiomes and encompass the collective community of microbial organisms, their genomes and environment. The modern commercialization of kefir has driven the need for high-quality research into its impact on the human microbiome and associated health outcomes; however, there is currently very limited scientific evidence supporting effects of kefir consumption on the human oral and gut microbiome. High-quality human clinical trials are essential to establish the safety and effectiveness of kefir before it can be advised for use in treating conditions linked to the oral and gut microbiota or metabolic health. This literature review aims to critically analyze recent studies investigating the effect of kefir consumption on the oral and gut microbiome, as well as its potential implications for human health. By examining kefir's effects on these interconnected microbial ecosystems, we can better understand its potential and limitations as a functional food for promoting systemic health.},
}

Humans
*Gastrointestinal Microbiome
*Kefir/microbiology
*Mouth/microbiology
Probiotics
Functional Food

@article {pmid41470796,
year = {2025},
author = {Zhu, W and Edirisuriya, P and Ai, Q and Yang, F and Tang, J and Nie, K and Ji, X and Soltanieh, S and Musarrat, M and Alim, MA and Liao, Z and Zhou, K},
title = {C. cochlearium 2316 Ameliorates High-Fat Diet-Induced Obesity and Metabolic Syndrome Risk Factors via Enhanced Energy Expenditure and Glucose Homeostasis.},
journal = {Nutrients},
volume = {17},
number = {24},
pages = {},
doi = {10.3390/nu17243848},
pmid = {41470796},
issn = {2072-6643},
mesh = {Animals ; *Diet, High-Fat/adverse effects ; *Obesity/etiology/metabolism ; *Energy Metabolism/drug effects ; Mice, Inbred C57BL ; *Metabolic Syndrome/etiology/prevention & control ; *Probiotics/pharmacology/administration & dosage ; Mice ; Male ; Homeostasis ; *Blood Glucose/metabolism ; Risk Factors ; Insulin/blood ; Insulin Resistance ; },
abstract = {OBJECTIVES: This study investigated the potential beneficial effects of a probiotic candidate, Clostridium cochlearium 2316, in modulating physiological and metabolic markers in mice with high-fat diet-induced obesity (DIO).

METHODS: C57BL/6 DIO mice were assigned to three groups (ad libitum): standard low-fat control (LF, 10% fat), high-fat diet (HF, 60% fat), and high-fat diet supplemented with approximately one billion CFU/day of CC2316 via daily oral gavage for 16 weeks.

RESULTS: After 16 weeks, the CC group exhibited 17.3% lower body weight gain (p < 0.001) and significant fat mass decrease (p < 0.0001) compared to HF mice. Serum biochemistry showed that CC2316 supplementation resulted in a 27.7% reduction in fasting blood glucose (p < 0.05), a 58.4% reduction in fasting insulin (p < 0.01), and an 89.4% improvement in HOMA-IR score (p < 0.05). Furthermore, serum total cholesterol level decreased dramatically by 40.2% in the CC group (p < 0.001). Despite a higher caloric absorption rate (p < 0.001), CC mice demonstrated a significant beneficial shift in energy expenditure, characterized by an increased basal metabolic rate (p < 0.05), higher energy expenditure (p < 0.05), and an elevated respiratory quotient (RER) (p < 0.05), alongside increased physical activity (p < 0.05).

CONCLUSIONS: This investigation strongly suggests that CC2316 supplementation mitigates the adverse effects of HFD-induced obesity by modulating whole-body energy metabolism, positioning it as a potential aid to lower risk factors associated with metabolic syndrome. The precise mechanisms linking the gut microbiome to altered energy substrate utilization are discussed and suggested for further investigation.},
}

Animals
*Diet, High-Fat/adverse effects
*Obesity/etiology/metabolism
*Energy Metabolism/drug effects
Mice, Inbred C57BL
*Metabolic Syndrome/etiology/prevention & control
*Probiotics/pharmacology/administration & dosage
Mice
Male
Homeostasis
*Blood Glucose/metabolism
Risk Factors
Insulin/blood
Insulin Resistance

@article {pmid41470771,
year = {2025},
author = {Polyzou, M and Goules, AV and Tzioufas, AG},
title = {The Role of Nutrition in the Development, Management, and Prevention of Rheumatoid Arthritis: A Comprehensive Review.},
journal = {Nutrients},
volume = {17},
number = {24},
pages = {},
doi = {10.3390/nu17243826},
pmid = {41470771},
issn = {2072-6643},
mesh = {Humans ; *Arthritis, Rheumatoid/prevention & control/etiology ; Diet, Mediterranean ; *Diet/adverse effects ; *Nutritional Status ; Risk Factors ; Fatty Acids, Omega-3/administration & dosage ; },
abstract = {Background: Rheumatoid arthritis (RA) is a chronic autoimmune disease, with key features being synovial hyperplasia, autoantibody production, and ultimately cartilage and bone destruction. The pathogenesis of rheumatoid arthritis (RA) is not fully understood, but it is estimated that genetic factors account for 50-60% of the risk, with the remainder attributed to environmental factors, including infectious agents, smoking, gut microbiota, and diet. Given that most current clinical trials on RA and nutrition are limited in sample size and duration, there is an unmet need for higher-quality studies in the future, a need that EULAR has already recognized. Objective: This article aims to investigate the impact of diet and nutritional factors on the development, progression, and potential prevention of RA. Specifically, it provides a comprehensive review of certain foods, such as alcohol, gluten, red meat, and saturated and trans fats, and their contribution to the onset and progression of rheumatoid arthritis (RA). In addition, it examines the effect of key anti-inflammatory nutrients in reducing the risk of RA, including olive oil, fatty fish, juices, and certain fruits. Finally, it discusses the potential protective effects of certain dietary patterns, such as the Mediterranean diet (MD) and diets rich in omega-3 polyunsaturated fatty acids (PUFAs). Methods: A comprehensive literature search was conducted in the PubMed/Medline, Science Direct, and Scopus databases (1990-2025). English-language observational studies, clinical trials, and systematic reviews addressing the relationship between diet and dietary patterns and RA were included. Results: High consumption of red and processed meat, saturated and trans fats, sugary drinks, and gluten (in vulnerable individuals) is associated with increased RA risk and greater disease activity, partly through pro-inflammatory pathways and gut dysbiosis. In contrast, regular intake of olive oil, fatty fish rich in omega-3 polyunsaturated fatty acids, fruit juices, cocoa, certain fruits, and vitamin D appears protective and may reduce disease activity and symptom severity. Adherence to anti-inflammatory dietary patterns, particularly the Mediterranean diet and diets rich in omega-3 fatty acids, is consistently associated with a lower incidence of RA, reduced inflammatory markers, and improved clinical outcomes. However, most available studies are limited by small sample sizes, short duration, heterogeneous methodologies, and potential confounding by other lifestyle factors (e.g., smoking, obesity). Conclusions: Although an appropriate diet and dietary habits cannot replace pharmacological therapy, current knowledge supports the inclusion of an anti-inflammatory diet as an adjunct strategy in the prevention and management of RA. The relatively limited studies that have been conducted suggest that high-quality, large-scale, prospective studies are needed to prevent and treat RA. These studies should incorporate genetic, microbiome, and long-term clinical endpoints, so as to establish definitive dietary recommendations and allow for personalized nutritional interventions for patients with RA.},
}

Humans
*Arthritis, Rheumatoid/prevention & control/etiology
Diet, Mediterranean
*Diet/adverse effects
*Nutritional Status
Risk Factors
Fatty Acids, Omega-3/administration & dosage

@article {pmid41470606,
year = {2025},
author = {Karpova, D and Belkina, D and Porotikova, E and Yurchenko, E and Vinogradova, S},
title = {Metagenomic Study of the Grapevine Decline Detected a Cocktail of Fungi Associated with Grapevine Trunk Diseases.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {24},
pages = {},
pmid = {41470606},
issn = {2223-7747},
support = {23-16-00232//Russian Science Foundation/ ; 00000//Ministry of Education and Science of Russian Federation/ ; },
abstract = {This study analyzed the microbiome of three varieties differing in genotype and technical purpose: Cristal, Riesling, and Avgustin, all exhibiting decline symptoms of unknown etiology. A total of 92 symptomatic and asymptomatic grapevines were analyzed using ITS and 16S rRNA amplicon sequencing and molecular genetic methods. Phytoplasmas and the pathogenic bacteria Xylella fastidiosa and Xylophilus ampelinus were not present in the samples. The decline symptoms were associated with a cocktail of fungal pathogens that cause grapevine trunk diseases. In particular, the analysis revealed the causative agents of Botryosphaeria dieback (Sphaeropsis spp. and Botryosphaeria spp.), fungi associated with the Esca complex (Phaeomoniella spp., Phaeoacremonium spp., Inonotus spp., Seimatosporium spp., Stereum spp., and Cadophora spp.), and the causative agents of Phomopsis dieback (Diaporthe spp.). The symptoms of decline may be increased by several facultative grapevine pathogens that have been identified in microbiome (genera Stemphylium, Alternaria, Aspergillus, Penicillium, Talaromyces, and Fusarium). The metagenomic data of the grapevine microbiome provides opportunities for developing disease control strategies, which is important for the sustainable management of vineyards.},
}

@article {pmid41470243,
year = {2025},
author = {Kayer, A and Özen, A and Dinleyici, EÇ},
title = {Urinary Microbiota Composition in Treatment-Naïve Bladder Cancer: A Case-Control Study with Tumor Invasiveness Stratification.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {61},
number = {12},
pages = {},
pmid = {41470243},
issn = {1648-9144},
support = {2599//Eskişehir Osmangazi University/ ; },
mesh = {Humans ; *Urinary Bladder Neoplasms/microbiology/urine/pathology ; Male ; Female ; Case-Control Studies ; Middle Aged ; Aged ; *Microbiota/physiology ; RNA, Ribosomal, 16S/analysis ; *Urine/microbiology ; Neoplasm Invasiveness ; },
abstract = {Background and Objectives: Emerging evidence suggests that the genitourinary microbiota may influence the development and progression of urological malignancies, including bladder cancer. This study aimed to characterize the urinary microbiota at diagnosis in patients with bladder cancer and compare findings with healthy controls. Materials and Methods: Urine samples were collected from 30 patients with treatment-naïve bladder cancer and 20 age- and sex-matched healthy individuals. Microbiota composition was analyzed using 16S rRNA sequencing, and subgroup comparisons were made between muscle-invasive bladder cancer (MIBC) and non-muscle-invasive bladder cancer (NMIBC). Differentially abundant taxa were identified using linear discriminant analysis effect size (LEfSe) with an LDA threshold > 2 and p < 0.05. Results: No significant differences were observed in alpha or beta diversity between patients and controls or between MIBC and NMIBC. At the phylum level, Firmicutes was dominant in both groups but relatively more abundant in bladder cancer cases. Enterococcus was the most abundant genus in the cancer group (35.0%) and especially in MIBC (58.0%), while Lactobacillus was more prevalent in healthy controls (19.8% vs. 9.5%). At the species level, Veillonella dispar was notably enriched in MIBC cases (70.9%) compared to NMIBC (3.9%). LEfSe analysis revealed significant enrichment of Ralstonia, Microbacterium, and Facklamia in patients with bladder cancer, while Parvimonas, Sneathia, Gemella, and Acinetobacter guillouiae were more abundant in controls. Conclusions: These findings highlight preliminary microbiota differences associated with bladder cancer and tumor invasiveness; however, the results are exploratory and larger studies are required to evaluate their diagnostic or clinical relevance.},
}

Humans
*Urinary Bladder Neoplasms/microbiology/urine/pathology
Male
Female
Case-Control Studies
Middle Aged
Aged
*Microbiota/physiology
RNA, Ribosomal, 16S/analysis
*Urine/microbiology
Neoplasm Invasiveness

@article {pmid41470224,
year = {2025},
author = {Tatarciuc, D and Ghica, DC and Darnea, M and Esanu, IM and Vasluianu, RI and Stamatin, O and Indrei, L and Antohe, M and Lupu, IC and Bobu, L and Dima, AM},
title = {Beyond H. pylori: Re-Examining the Oral Microbiome's Role in Gastric Health and Disease, a Narrative Review.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {61},
number = {12},
pages = {},
pmid = {41470224},
issn = {1648-9144},
mesh = {Humans ; Helicobacter pylori/pathogenicity ; *Helicobacter Infections/complications/microbiology ; *Microbiota/physiology ; Dysbiosis/microbiology/complications ; Oral Health/standards ; Gastritis/microbiology ; Periodontitis/microbiology/complications ; *Mouth/microbiology ; Risk Factors ; },
abstract = {Background: The separation between oral and systemic health is increasingly challenged. Globally prevalent inflammatory diseases such as gastritis, often caused by Helicobacter pylori (H. pylori), and oral pathologies like periodontitis may be interconnected through microbial and inflammatory pathways. Objective: This review synthesizes evidence on the dental-gastric link, examining mechanistic pathways and clinical implications. Methods: A structured literature search identified key studies from 2000 to 2025, prioritizing systematic reviews and high-quality human research. Findings: Three key mechanistic pathways link oral dysbiosis with gastric pathology: (1) the direct translocation of oral pathogens to the stomach, including H. pylori and the broader dysbiotic oral microbiome; (2) the systemic inflammatory spillover from the periodontium, which primes the host immune system and exacerbates gastric inflammation; and (3) ancillary mechanisms such as the disruption of beneficial nitrate-nitrite-nitric oxide metabolism. Epidemiological studies show strong associations, and initial interventional trials indicate periodontal therapy may improve H. pylori eradication rates and reduce recurrence. However, the evidence is tempered by methodological limitations, including profound confounding by shared risk factors (e.g., smoking, socioeconomic status), the challenge of reverse causality, and inconsistent results from interventional studies. Conclusion: While confounding factors require consideration, oral health is a promising modifiable risk factor for gastritis. Interdisciplinary collaboration between dentistry and gastroenterology is essential to advance research and integrate oral care into gastrointestinal disease management.},
}

Humans
Helicobacter pylori/pathogenicity
*Helicobacter Infections/complications/microbiology
*Microbiota/physiology
Dysbiosis/microbiology/complications
Oral Health/standards
Gastritis/microbiology
Periodontitis/microbiology/complications
*Mouth/microbiology
Risk Factors

@article {pmid41470214,
year = {2025},
author = {Kahraman, T and Ayaz, A},
title = {Dietary Phytonutrients in Fibromyalgia: Integrating Mechanisms, Biomarkers, and Clinical Evidence-A Narrative Review.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {61},
number = {12},
pages = {},
pmid = {41470214},
issn = {1648-9144},
mesh = {Humans ; *Fibromyalgia/diet therapy/physiopathology ; Biomarkers/analysis/blood ; *Phytochemicals/therapeutic use/pharmacology ; Oxidative Stress/drug effects ; },
abstract = {Background and Objectives: Fibromyalgia (FM) is associated with chronic pain, oxidative stress, low-grade inflammation, and disturbances in signalling along the gut-brain axis. These pathways may be modulated by plant-derived phytonutrients. This narrative review summarises mechanistic and clinical evidence on phytonutrient-based strategies in FM. Materials and Methods: Following SANRA guidelines, we searched PubMed, Web of Science, Scopus and ScienceDirect for human and relevant preclinical studies published between 2005 and October 2025 that evaluated phytonutrient-rich dietary patterns or isolated bioactives in relation to FM symptoms or underlying mechanisms. Results: There is a consistent association between FM and increased oxidative damage and reduced antioxidant defences. Adopting plant-based diets, particularly Mediterranean-type and low-FODMAP diets, has been linked to improvements in pain, fatigue, sleep, and gastrointestinal symptoms, as well as modest gains in quality of life. However, the effects on inflammatory markers are conflicting. Trials of selected bioactive compounds, such as coenzyme Q10, curcumin-based formulations, L-carnitine and certain probiotics, suggest beneficial effects on symptoms, whereas others show little or no effect. Studies of the microbiome indicate a loss of butyrate-producing bacteria and altered microbial metabolites. Early dietary or probiotic interventions may partially mitigate these changes to some extent. Preclinical studies have identified SIRT1 as a potential mediator, but there is a lack of human data. Reporting on safety, dosage and formulation is often inadequate. Conclusions: Given the narrative design of this review and the methodological heterogeneity of the included studies, the overall certainty of the evidence cannot be formally graded and should be regarded as limited and heterogeneous. Nevertheless, current data supports phytonutrient-rich, food-based approaches as adjuncts rather than alternatives to standard FM care. Well-designed randomised trials with standardised outcomes and reporting of dose, formulation and relevant biomarkers are needed to identify the most effective strategies and the patient subgroups most likely to benefit.},
}

Humans
*Fibromyalgia/diet therapy/physiopathology
Biomarkers/analysis/blood
*Phytochemicals/therapeutic use/pharmacology
Oxidative Stress/drug effects

@article {pmid41470154,
year = {2025},
author = {Tjiu, JW and Lu, CF},
title = {Oral Probiotics in Acne vulgaris: A Systematic Review and Meta-Analysis of Double-Blind Randomized Clinical Trials.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {61},
number = {12},
pages = {},
pmid = {41470154},
issn = {1648-9144},
mesh = {Humans ; *Probiotics/therapeutic use/administration & dosage ; *Acne Vulgaris/therapy/drug therapy ; Randomized Controlled Trials as Topic ; Double-Blind Method ; Administration, Oral ; Adolescent ; },
abstract = {Background and Objectives: Acne vulgaris is a prevalent chronic inflammatory skin condition affecting adolescents and young adults worldwide. Increasing concern regarding antimicrobial resistance has renewed interest in microbiome-modulating therapies, including oral probiotics. This systematic review and meta-analysis evaluated the efficacy and safety of oral probiotic supplementation for acne vulgaris using contemporary random-effects methods. Materials and Methods: Following PRISMA 2020 guidelines, we searched PubMed, Embase, Web of Science, and ClinicalTrials.gov through November 2025 without language restrictions. Eligible studies were double-blind randomized controlled trials (RCTs) comparing oral probiotics with placebo or standard therapy for ≥4 weeks and reporting quantitative acne severity outcomes. Risk of bias was assessed using RoB 2.0. Standardized mean differences (SMDs) were pooled using restricted maximum likelihood (REML) with Hartung-Knapp adjustment. Heterogeneity was summarized using I[2], τ[2] (95% CI), and 95% prediction intervals. Adverse events were extracted. Results: Three RCTs (n = 231) met eligibility criteria. Pooled analysis suggested a modest reduction in inflammatory lesion counts favoring probiotics (SMD -0.57; 95% CI -0.94 to -0.21), although heterogeneity was substantial (I[2] = 72%; τ[2] = 0.11). The 95% prediction interval (-1.25 to 0.11) indicated that future studies may plausibly observe no meaningful effect. Sensitivity analyses using the DerSimonian-Laird estimator produced comparable results. All trials reported good short-term tolerability with no serious adverse events. Risk of bias was low in two trials and of some concern in one. Certainty of evidence was rated low to moderate. Conclusions: Oral probiotics may modestly reduce acne severity as a generally safe, antibiotic-sparing adjunct; however, the current evidence base is small and heterogeneous, and the certainty of effect remains low-to-moderate. Larger, standardized RCTs are required before firm clinical recommendations can be made. Registration: PROSPERO CRD420251181388. Funding: This research received no external funding.},
}

Humans
*Probiotics/therapeutic use/administration & dosage
*Acne Vulgaris/therapy/drug therapy
Randomized Controlled Trials as Topic
Double-Blind Method
Administration, Oral
Adolescent

@article {pmid41469665,
year = {2025},
author = {Zheng, SH and Li, KZ and Feng, G and Wang, YT and Wang, JN and Li, SQ and Sun, YD},
title = {Gut microbiota reshaping the pancreatic cancer immune microenvironment: new avenues for immunotherapy.},
journal = {Molecular cancer},
volume = {24},
number = {1},
pages = {313},
pmid = {41469665},
issn = {1476-4598},
mesh = {Humans ; *Tumor Microenvironment/immunology ; *Gastrointestinal Microbiome/immunology ; *Pancreatic Neoplasms/therapy/immunology/etiology/pathology/microbiology/metabolism ; *Immunotherapy/methods ; Animals ; Fecal Microbiota Transplantation ; },
abstract = {Pancreatic cancer remains one of the deadliest malignancies, primarily due to its highly immunosuppressive tumor microenvironment (TME) and poor response to conventional therapies. Increasing evidence highlights the gut microbiota as a pivotal regulator of antitumor immunity, modulating T cell activation, macrophage polarization, and dendritic cell function. Microbial communities and their metabolites can either inhibit or enhance immune surveillance, thereby influencing the efficacy of immunotherapies such as immune checkpoint inhibitors (ICIs) and CAR-T cell therapy. Approaches including dietary modulation, probiotics, fecal microbiota transplantation (FMT), and microbial metabolite supplementation show promise in restoring immune homeostasis and improving treatment outcomes. Additionally, gut microbiome profiling has emerged as a potential source of biomarkers for predicting therapeutic response and immune-related adverse events. This review summarizes current insights into microbiota-immune interactions in pancreatic cancer, emphasizes microbiome-targeted therapeutic strategies, and explores future opportunities for precision immunotherapy guided by microbial modulation.},
}

Humans
*Tumor Microenvironment/immunology
*Gastrointestinal Microbiome/immunology
*Pancreatic Neoplasms/therapy/immunology/etiology/pathology/microbiology/metabolism
*Immunotherapy/methods
Animals
Fecal Microbiota Transplantation

@article {pmid41469598,
year = {2025},
author = {Mbabazi, M and Kateete, DP and Nakazzi, F and Wandera, JN and Mutesi, N and Ocan, M and Biraro, IA and Abaasa, A and Johnson, WE and Wee, B and Muwonge, A},
title = {The impact of tuberculosis and its treatment on the lung and gut microbiota: a global systematic review, meta-analysis, and amplicon-based metagenomic meta-analysis.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-025-12369-1},
pmid = {41469598},
issn = {1471-2334},
}

@article {pmid41469399,
year = {2025},
author = {Fang, J and Wang, G and Zhang, C and Liu, G and Xu, J and Gao, Y and Guo, Y and Wang, X and Qiu, T},
title = {Conserved genotype-independent rhizobacteria promote maize growth.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-025-00895-4},
pmid = {41469399},
issn = {2055-5008},
support = {TSXM202525//Exploratory Research Project of Beijing Academy of Agriculture and Forestry Sciences/ ; KJCX20251102//Special Program for Creative Ability of Beijing Academy of Agriculture and Forestry Sciences/ ; KJCX20230113//Special Program for Creative Ability of Beijing Academy of Agriculture and Forestry Sciences/ ; },
abstract = {Rhizosphere microbiomes play an essential role in promoting plant growth and health. Although host genotype is known to shape rhizosphere microbial communities, it remains unclear whether core microbial taxa can persist across genetically diverse hosts and contribute to plant performance. Here, we conducted a large-scale analysis of 1005 rhizosphere samples from 335 maize populations to investigate the effects of host genetic variation on rhizosphere microbiota. We observed significant genotype-dependent variation in both bacterial and fungal community diversity and composition. However, community assembly was predominantly governed by stochastic processes, suggesting an evolutionary conservation of rhizosphere microbiota across genotypes. Based on the hypothesis that core microbes may consistently associate with maize independent of genotypes, we identified a core bacterial taxon, ASV245 (Pseudomonas sp.), which was consistently enriched across all maize genotypes. The corresponding strain, designated as WY16, was isolated from maize roots and significantly promoted both stem and root growth by activating maize hormone signaling pathways. These findings highlight the persistence and functional roles of genotype-independent core microbes, deepening our understanding of plant-microbiome interactions and providing new insights for microbiome-based strategies in sustainable agriculture.},
}

@article {pmid41469282,
year = {2025},
author = {Grover, BT and Docimo, S and Shin, TH and Shope, T and Albaugh, VL and Byers, R and Passerini, H and Northup, CJ and Vosburg, RW},
title = {American Society of Metabolic and Bariatric Surgery review of gut microbiome and alterations related to weight loss treatment, by the Clinical Issues Committee.},
journal = {Surgery for obesity and related diseases : official journal of the American Society for Bariatric Surgery},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.soard.2025.11.021},
pmid = {41469282},
issn = {1878-7533},
abstract = {The gut microbiome is a critical mediator of metabolic health including obesity and type 2 diabetes. Microbial composition variation - driven by diet, genetics, environment, and host physiology - can influence insulin sensitivity, energy absorption, fat storage, and systemic inflammation. Metabolic and bariatric surgery (MBS) is associated with distinct shifts in gut microbiota that may contribute to weight loss and metabolic improvements. Changes in microbial diversity, bile acid metabolism, and enrichment of beneficial taxa have all been linked to favorable metabolic outcomes. Furthermore, the gut microbiome may interact with molecular signaling pathways including glucagon-like peptide-1 signaling. Despite probiotics and prebiotics showing potential modulation of the gut microbiota, their clinical impact on obesity management remains inconsistent. Understanding the complex interplay between MBS, the gut microbiome, and host metabolism may offer novel insights into future therapeutic targets. As the field advances, microbiome-based strategies may enhance procedure selection, improve patient outcomes after MBS, and contribute to more personalized, durable treatment approaches for obesity and its related diseases.},
}

@article {pmid41469211,
year = {2025},
author = {Munteanu, C and Dhanasekaran, DN},
title = {Obesity as a Systems-Level Driver of Cancer: Mechanisms and Nutritional Reprogramming.},
journal = {Obesity reviews : an official journal of the International Association for the Study of Obesity},
volume = {},
number = {},
pages = {e70075},
doi = {10.1111/obr.70075},
pmid = {41469211},
issn = {1467-789X},
support = {W81XWH-22-1-0415//Department of Defense Ovarian Cancer Research Program Award/ ; P30CA225520//National Cancer Institute of the National Institutes of Health/ ; P30GM154635//National Institutes of General Medical Sciences of the National Institutes of Health/ ; },
abstract = {Obesity has emerged as a global health crisis and a potent driver of cancer incidence and mortality, yet its mechanistic impact on tumor biology remains underappreciated. Far from being a passive risk factor, obesity acts as a systems-level oncogenic stressor, reshaping hormonal signaling, immunometabolism, and epigenetic stability across the body. This review synthesizes current knowledge on the physiological, cellular, and molecular cascades linking obesity to carcinogenesis, with emphasis on chronic inflammation, metabolic reprogramming, tumor microenvironment remodeling, and microbiome dysbiosis. We also examine how dietary patterns modulate these cancer-associated processes, positioning nutrition not merely as a preventive tool but as a programmable interphase with cancer biology through soft epigenetic reprogramming. Emerging frameworks in precision nutritional oncology, driven by nutrigenomics, metabolomics, and patient-specific molecular profiling, offer promising avenues for personalized cancer prevention and metabolic targeting. By integrating epidemiological trends, mechanistic insights, and translational strategies, we propose a paradigm shift: treating obesity not just as a comorbid risk factor but also as a modifiable oncogenic ecosystem-one that can be reprogrammed through informed, individualized precision dietary interventions.},
}

@article {pmid41469026,
year = {2025},
author = {Yao, L and Solania, A and Luissint, AC and Balana, AT and Zhang, H and Sangaraju, D and Lai, Z and Kuo, J and Storek, KM and Wolan, DW},
title = {The Secreted Metabolite Isopentenyladenine from Faecalibacterium prausnitzii Is Anti-inflammatory with Barrier-Protective Properties.},
journal = {ACS infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsinfecdis.5c00771},
pmid = {41469026},
issn = {2373-8227},
abstract = {Colonic microbiome dysbiosis is correlated with inflammatory bowel disease (IBD), and depletion of the commensal bacterium Faecalibacterium prausnitzii (F. prausnitzii) is routinely observed in the metagenomic analyses of IBD patient microbiome samples. F. prausnitzii is likely beneficial to hosts, as oral administration of F. prausnitzii strain A2-165 has anti-inflammatory properties in murine models of colitis. Previous studies attribute the anti-inflammatory effects of F. prausnitzii A2-165 to production of the short-chain fatty acid butyrate, as well as a secreted protein known as microbial anti-inflammatory molecule (MAM). Here, we verified that oral dosing of strain A2-165 protects against DSS-induced murine colitis and further showed that the aqueous-soluble secreted fraction of overnight cultures from a collection of F. prausnitzii strains inhibits inflammatory signatures, including the activation of the host's NF-κB pathway, production of IL-8, and differentiation of naïve T cells into the TH17 lineage. Our findings against a panel of in vitro assays suggested that the anti-inflammatory responses were attributable to secreted small-molecule or peptide metabolites, as both heat-inactivated and proteinase K-treated F. prausnitzii culture supernatants retained activity. Untargeted and targeted mass spectrometry metabolomics analyses on the soluble anti-inflammatory secretome yielded several unique F. prausnitzii metabolites, including isopentenyladenine. We demonstrated that isopentenyladenine independently modulates host cellular signaling and immune responses and suggest that this newly identified metabolite with human immunomodulatory properties may be useful toward the discovery of IBD-focused therapeutics.},
}

@article {pmid41468854,
year = {2025},
author = {Chatterjee, S and Basak, C and Basak, G and Karjee, A and Mukherjee, S and Barman, P and Khan, NB and Sarkar, P and Majumdar, S and Chakraborty, R and Barman, C},
title = {Mitigating cadmium-induced stress in Capsicum annuum L. by Pseudomonas aeruginosa strain CD3: Impacts on morpho-physiology, reproductive traits, capsaicin content and soil microbiome.},
journal = {The Science of the total environment},
volume = {1013},
number = {},
pages = {181229},
doi = {10.1016/j.scitotenv.2025.181229},
pmid = {41468854},
issn = {1879-1026},
abstract = {Cadmium (Cd[2+]) contamination poses a major challenge to agricultural productivity and food safety by impairing plant physiology, inducing oxidative stress, and facilitating toxic metal accumulation in plants. Capsicum annuum, a widely cultivated crop, is highly susceptible to heavy metal toxicity, which hampers its growth, reproduction, and physiochemical balance. Although several studies have documented Cd[2+]-induced phytotoxicity in chili, mitigation strategies, particularly involving beneficial microbes, remain underexplored. This study investigates the role of Pseudomonas aeruginosa strain CD3 to alleviate cadmium stress in chili plants under controlled conditions. Morphological, physiological, biochemical, and reproductive traits were analyzed along with rhizospheric microbiome profiling in monsoon and winter seasons. CD3 inoculation significantly enhanced plant height (74.51 %), shoot biomass (73.08 %), relative water content (21.31 %), and antioxidant enzyme activity at 100 ppm Cd[2+] stress in both the season. Reactive oxygen species accumulation was reduced, while photosynthetic pigment content was restored. Our results verify that Cd[2+] severely disrupts chili reproductive biology, while strain CD3 markedly mitigates these effects by improving pollen viability, fruit yield, and seed production. Importantly, this study demonstrates the novel role of CD3 in regulating capsaicin accumulation under Cd[2+] stress, where microbial application alleviated stress-induced capsaicin enrichment. Cd[2+] accumulation was found to be below detectable levels in fruits of CD3-treated plants. Metataxonomic analysis demonstrated that CD3 successfully persisted in the soil, and its central role in the microbial network with strengthened interactions indicated a stabilizing and resilience-enhancing effect under cadmium stress. This research emphasizes the potential of P. aeruginosa strain CD3 as a green, sustainable bioremediation agent to improve crop yield, minimize metal translocation to edible tissues, and stabilize soil integrity in contaminated agricultural soils.},
}

@article {pmid41468691,
year = {2025},
author = {Leduc, F and Barko, PC and de Souza, CP and Reinhart, JM},
title = {Oral itraconazole may alter the gastrointestinal microbiome in healthy cats.},
journal = {American journal of veterinary research},
volume = {},
number = {},
pages = {1-13},
doi = {10.2460/ajvr.25.09.0338},
pmid = {41468691},
issn = {1943-5681},
abstract = {OBJECTIVE: To determine if and how oral itraconazole alters the gastrointestinal microbiome of cats.

METHODS: This was a single-arm, longitudinal exploratory study performed in a university setting. Healthy cats were administered 5 mg/kg/day of itraconazole solution orally with food during alternating weeks over a 5-week time period. Rectal swabs were collected at 2 time points before treatment and serially during and after treatment over 31 weeks. Bacterial and fungal populations were quantified by 16S and internal transcribed spacer 3 and 4 sequencing, respectively. Changes in α diversity, β diversity, and differential abundance were evaluated over time.

RESULTS: There were no significant changes in bacterial α diversity, β diversity (R2 = 0.0077; P = .550), or relative abundance between the 2 pretreatment time points indicating stable microbial populations before itraconazole exposure in 16 cats. Time was a significant determinant of β diversity during and after itraconazole treatment (R2 = 0.0181; P = .002), and several α-diversity indices significantly decreased in the posttreatment timeframe. Ruminococcus torques (-1.916; 95% CI, -2.971 to -0.861), Acidaminococcus spp (-1.291; 95%, CI -1.866 to -0.716), and Blautia hansenii (-1.475, 95% CI, -2.295 to -0.691) relative abundances were significantly decreased at weeks 1, 5, and 9, respectively. The final fungal internal transcribed spacer dataset only included 5 taxa limiting analysis and interpretation.

CONCLUSIONS: These findings provide preliminary evidence for possible dysbiosis in the feline gastrointestinal tract during itraconazole treatment. However, many changes in differential abundance were small and no longer significant posttreatment.

CLINICAL RELEVANCE: Itraconazole administration might induce gastrointestinal bacterial dysbiosis in cats. Alternate methods for fungal microbiome assessment should be used in future feline studies.},
}

@article {pmid41468674,
year = {2025},
author = {Feng, W and Ma, R and Guo, Y and Zhang, B and Lan, J and Liu, J and Chen, S},
title = {Rhizosphere metagenomics and metabolomes provide new insights into the relationship between rhizosphere microecology and early bolting of Angelica dahurica.},
journal = {Microbiological research},
volume = {305},
number = {},
pages = {128435},
doi = {10.1016/j.micres.2025.128435},
pmid = {41468674},
issn = {1618-0623},
abstract = {Angelica dahurica is a medicinal and edible plant with a wide range of pharmaceutical and food applications. However, the early bolting, which leads to reduced yield and loss of bioactive constituents, has become a major obstacle to the industrial development of A. dahurica. Rhizosphere microecology affects plant growth and secondary metabolite accumulation, but the association of rhizosphere microecology with the early bolting of A. dahurica is not fully understood. This study integrated metagenomic and metabolomic analyses to systematically characterize the differences in rhizosphere microecology of non-bolting and early bolting A. dahurica plants. Results revealed significant disparities in soil physicochemical properties, root exudate profiles, and microbial community composition between two groups, all of which exhibited correlations with the coumarin compounds content, the primary pharmacologically active constituents of A. dahurica. Integrated analysis suggested that root-derived acyl-homoserine lactone (AHL) quorum-sensing signals, as the primary chemical signals of the prevalent Gram-negative bacteria, may participate in regulating the microbial community structure and soil properties, thereby influencing the bolting and flowering process. This study proposes a potential complex regulatory network of "rhizosphere microbiome - quorum-sensing signals - soil nitrogen cycle - bolting and flowering" linking the rhizosphere microecology to early bolting in A. dahurica, thereby addressing a key knowledge gap in this area. The findings offer a scientific foundation and innovative strategy for the simultaneous prevention of early bolting and quality improvement in A. dahurica through soil microecological management, which is of significant importance for promoting the sustainable commercial development of the A. dahurica industry.},
}

@article {pmid41468549,
year = {2025},
author = {Ye, L and Wu, Y and Guo, J and Wang, H and Cai, J and Chen, K and Dong, N and Yu, J and Chao, S and Zhou, H and Chen, G and Chen, S and Zhang, R},
title = {Elucidation of population-based bacterial adaptation to antimicrobial treatment by single-cell sequencing analysis of the gut microbiome of a hospital patient.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0163124},
doi = {10.1128/msystems.01631-24},
pmid = {41468549},
issn = {2379-5077},
abstract = {In this study, we used single-cell sequencing to analyze the gut microbiome of an adult male patient with acute cerebral hemorrhage undergoing antibiotic treatment. We identified 92 bacterial species, including 23 Firmicutes and one archaeon from Methanobacteriota, along with 69 unclassified strains. Single-cell sequencing effectively detected bacteria carrying antibiotic resistance genes (ARGs), particularly in unclassified species, and traced the evolution of these genes across diverse bacterial taxa. Notably, the cfr(C) gene was detected in 11 bacterial species following antimicrobial treatment, with mutation patterns characterized in Enterococcus faecalis, Klebsiella pneumoniae, Ruthenibacterium UN-1, and four unclassified species. In total, 29 ARG subtypes across eight types were identified in 13 known, five unknown, and 18 unclassified species, allowing us to trace their evolution routes. In addition, we detected a total of 309 horizontal gene transfer (HGT) events, in which several genes like folE and queE were frequently involved. The products of these genes are known to enhance the ability of the recipient bacterial strains to repair DNA damage and maintain genomic stability, especially following prolonged antibiotic treatment. Comparison between isolated strain genomes (IS-KP1) and single-cell analysis confirmed the presence of at least two K. pneumoniae strains in the patient, with one exhibiting a larger extent of involvement in ARG co-evolution. This strain was found to contain the cfr(C) and fosXCC genes, which were absent in IS-KP1. Klebsiella strains were also found to participate actively in HGT events. In conclusion, the study identified a wide range of ARGs and HGT events within the microbiome. The detection of K. pneumoniae strains with distinct ARG evolution patterns underscores the gut microbiome's adaptability to environmental changes. These findings facilitate the development of novel antimicrobial strategies by fine-tuning the gut microbiome composition.IMPORTANCEThis study highlights the power of single-cell sequencing to unravel the diversity and dynamics of the gut microbiome during antibiotic treatment in a patient with acute cerebral hemorrhage. By identifying antibiotic resistance genes (ARGs) in both known and unclassified bacterial species, we reveal the intricate evolution and horizontal transfer of resistance traits across taxa. The discovery of distinct ARG patterns, including the emergence of the cfr(C) gene in multiple species and its co-evolution in K. pneumoniae, underscores the gut microbiome's adaptability to antimicrobial pressures. These findings provide critical insights into the mechanisms driving resistance dissemination and offer potential pathways for developing precision microbiome-based therapies to combat antibiotic resistance.},
}

@article {pmid41468410,
year = {2025},
author = {Molina, MA},
title = {From dysbiosis to mechanisms: Why cervicovaginal microbiome-HPV studies must catch up with biology.},
journal = {PLoS pathogens},
volume = {21},
number = {12},
pages = {e1013830},
pmid = {41468410},
issn = {1553-7374},
}

@article {pmid41468125,
year = {2025},
author = {Kirschen, GW and Gerson, KD},
title = {Performance Characteristics of Current Biomarkers for the Prediction of Spontaneous Preterm Birth.},
journal = {Clinical chemistry},
volume = {72},
number = {1},
pages = {71-81},
doi = {10.1093/clinchem/hvaf141},
pmid = {41468125},
issn = {1530-8561},
mesh = {Humans ; *Premature Birth/diagnosis/metabolism ; *Biomarkers/analysis/blood ; Female ; Pregnancy ; },
abstract = {BACKGROUND: Preterm birth (PTB), or birth occurring before 37 weeks' gestation, remains a significant public health burden, accounting for 10% of live births annually in the United States and incurring substantial healthcare expenditures. Our understanding of the molecular mechanisms underlying spontaneous preterm birth (sPTB) has advanced across the previous 4 decades, yet precise prediction tools and prevention strategies are lacking.

CONTENT: Numerous studies have identified potential anatomical and molecular risk factors for sPTB, including sonographic characteristics of the cervix; maternal serum circulating RNA and proteins; maternal urine metabolic byproducts; cervicovaginal cytokine, microbiome, and metabolome composition; amniotic fluid cytokines; umbilical cord blood leukocyte DNA methylation status; and placental transcriptome profiles. This review focuses on recent developments in sPTB biomarker determination among singleton gestations.

SUMMARY: Herein, we synthesize and evaluate the test characteristics of candidate biomarkers of sPTB, concluding that no single biomarker can accurately predict sPTB. However, several individual or combined panels of biomolecules, including some commercially available, carry clinically significant predictive information. These biomarkers include cervical ultrasonography, the ratio of insulin-like growth factor-binding protein 4 to sex-hormone binding globulin, panels of urinary metabolites and amniotic fluid proteins, and maternal circulating cell-free RNA. Future integration of select biomarkers drawn from prospective validation cohorts into existing risk stratification strategies may enhance sPTB prediction, thereby identifying patients at greatest risk.},
}

Humans
*Premature Birth/diagnosis/metabolism
*Biomarkers/analysis/blood
Female
Pregnancy

@article {pmid41468056,
year = {2025},
author = {Karikis, I and Arda, Y and Sanyal, R and DeWane, MP and Luckhurst, CM and Kaafarani, HM and Hwabejire, JO and Velmahos, GC and Paranjape, CN},
title = {Acute Appendicitis and the Microbiome: A Review of Microbial Signatures.},
journal = {Surgical infections},
volume = {},
number = {},
pages = {},
doi = {10.1177/10962964251408687},
pmid = {41468056},
issn = {1557-8674},
abstract = {Introduction: Acute appendicitis remains one of the most common surgical emergencies, yet its pathogenesis is incompletely understood. Although mechanical luminal obstruction has traditionally been considered the initiating factor, emerging evidence suggests that the appendix hosts a unique microbial community that may influence disease onset and severity. Methods: We conducted a narrative review that summarizes current data on the role of microbiota in appendicitis, while focusing on differences between complicated and uncomplicated presentations. Results: High-throughput sequencing studies have identified key taxa associated with inflamed appendices, including Fusobacterium, Prevotella, and oral cavity genera such as Gemella and Parvimonas. On the contrary, protective commensals such as Faecalibacterium prausnitzii and Akkermansia muciniphila appear depleted. Studies suggest that there is significant variation regarding the microbial composition of complicated and uncomplicated cases. We also examine the role of the appendix as a microbial reservoir and the potential health consequences of its removal. Finally, we discuss how microbiome-based approaches may improve treatment, particularly antibiotic agent selection both in operative and non-operative management. Conclusion: Current evidence supports that appendicitis may represent a disease spectrum carrying multiple rather than a single microbial signature that dictates different pathophysiologic processes.},
}

@article {pmid41467904,
year = {2026},
author = {Maruyama, D and Tian, X and Doan, TNM and Liao, WI and Chaki, T and Taenaka, H and Maishan, M and Matthay, MA and Prakash, A},
title = {Gut microbiome-derived propionate reprograms alveolar macrophages metabolically and regulates lung injury responses in mice.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2606486},
doi = {10.1080/19490976.2025.2606486},
pmid = {41467904},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Macrophages, Alveolar/metabolism/immunology ; Mice ; *Lung Injury/microbiology/metabolism/immunology ; Dietary Fiber/metabolism/administration & dosage ; Fatty Acids, Volatile/metabolism ; *Propionates/metabolism ; Mice, Inbred C57BL ; Male ; Bacteria/metabolism/classification/genetics/isolation & purification ; Lung/metabolism/immunology ; },
abstract = {Responses to lung injury can vary between individuals with the diet and gut microbiome representing two underappreciated sources for this variability. The gut microbiome can influence lung injury outcomes through the gut‒lung axis, but exactly how diet and its effects on the microbiota are involved remains unclear. We hypothesized that dietary fiber interventions would favor the presence of short-chain fatty acid (SCFA)-producing fermentative bacteria presence in the gut microbiome, thereby influencing the resting lung immunometabolic tone as well as influencing downstream responses to lung injury and infection. To test this hypothesis, we fed mice fiber-rich (FR) and fiber-free (FF) diets, and observed changes in the steady-state transcriptional programming of alveolar macrophages (AM). Next, we examined the effects of the FR and FF diets on murine responses to sterile and infectious lung injury in vivo while simultaneously profiling the gut microbiota and SCFA levels transmitted along the gut‒lung axis. Finally, we validated our in vivo observations with mechanistic studies of the metabolic, signaling, and chromatin-modifying effects of specific SCFAs on lung AM ex vivo and in vitro. Overall, our fiber-rich diet reprogrammed AMs and attenuated lung inflammation after sterile injury while exacerbating lung infection. This effect of FR diets could be transferred to germ-free (GF) mice by fecal microbiome transplantation (FMT) and depended on the ability of the microbiota to produce propionate. Mechanistically, SCFAs altered the metabolic programming of AMs and lung tissue ex vivo without a clear role for free fatty acid receptors (FFAR) or chromatin remodeling. These findings demonstrate that the gut‒lung axis can regulate resting lung metabolic tone through dietary fiber intake and the enrichment of SCFA-producing gut bacteria, as well as influence sterile and non-sterile lung injury responses. These results provide evidence to support the development of therapeutic dietary interventions to preserve or enhance specific aspects of host pulmonary immunity.},
}

Animals
*Gastrointestinal Microbiome/physiology
*Macrophages, Alveolar/metabolism/immunology
Mice
*Lung Injury/microbiology/metabolism/immunology
Dietary Fiber/metabolism/administration & dosage
Fatty Acids, Volatile/metabolism
*Propionates/metabolism
Mice, Inbred C57BL
Male
Bacteria/metabolism/classification/genetics/isolation & purification
Lung/metabolism/immunology

@article {pmid41467862,
year = {2025},
author = {van Straalen, KR and Gudjonsson, JE},
title = {Hidradenitis suppurativa: Why dose escalation often fails and what biology tells us about next steps.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2025.11.012},
pmid = {41467862},
issn = {1097-6825},
}

@article {pmid41467811,
year = {2025},
author = {Ha, LH and On, YY and Pohan, C and Lee, J and How, SHC and Teo, Y-Y and Seedorf, H and Gounot, J-S and Nagarajan, N},
title = {High-throughput single-cell isolation of Bifidobacterium strains from the human gut microbiome.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0303325},
doi = {10.1128/spectrum.03033-25},
pmid = {41467811},
issn = {2165-0497},
abstract = {UNLABELLED: Bifidobacterium represents a diverse genus of commensal gut bacteria with key roles in human health, from metabolizing indigestible fibers to protecting against pathogens. While metagenomic studies have highlighted significant strain diversity for Bifidobacterium species within individuals, their systematic isolation and phenotypic characterization can be hampered by the significant effort and biases inherent in traditional culturomics. Here, we explored the utility of a high-throughput single-cell dispensing system (B.SIGHT)-based workflow for accelerating the process of isolating diverse Bifidobacterium strains from fecal samples. Systematic assessment of this workflow revealed a high single-cell dispensing frequency (>88%) and the ability to preserve species diversity when a pool of Bifidobacterium strains was dispensed. Culturing-related factors including the use of an effective selection medium, such as the Bifidus Selective Medium supplemented with mupirocin, and the length of pre-dispensing incubation were found to be critical in determining isolation success. Leveraging this workflow, we obtained a total of 622 viable isolates from five Singaporean fecal samples, of which >98% were found to be from Bifidobacterium species. Whole-genome sequencing of 96 isolates identified six different Bifidobacterium species with both inter- and intra-subject strain and lineage diversity, and the majority (>66%) were novel relative to large public genomic databases. Our findings highlight the ability of this high-throughput culturomics workflow to accelerate the recovery of diverse and novel Bifidobacterium strains, enabling further interrogation of their functional characteristics and advancing our understanding of important bacterial species in the gut microbiome.

IMPORTANCE: The field of high-throughput microbial culturomics is still in its early stages. Enhancing our ability to isolate and phenotypically test bacterial strains from complex communities is crucial for advancing microbiome research and healthcare development. Given the time and cost inefficiencies of traditional culturing methods, a more efficient, high-throughput approach to obtain isolates is needed. In the present study, we assessed a single-cell dispensing platform and developed a workflow to isolate diverse Bifidobacterium strains from fecal samples. We demonstrated here the capability of this novel technology to efficiently obtain hundreds of isolates of a targeted group, covering both species and strain diversities. This generalizable and scalable method can potentially allow for the high-throughput recovery of microbes from other taxonomic groups, providing a fundamental step in improving the culturomics framework to complement metagenomic approaches and enable isolate-level functional studies of important microbes.},
}

@article {pmid41467444,
year = {2025},
author = {Wang, R and Hatano, T and Hattori, N and Cossu, D},
title = {Interplay of GBA1 with lysosomal dysfunction and inflammation in Parkinson's disease.},
journal = {Neural regeneration research},
volume = {},
number = {},
pages = {},
doi = {10.4103/NRR.NRR-D-25-01082},
pmid = {41467444},
issn = {1673-5374},
abstract = {Mutations in the glucocerebrosidase (GBA1) gene, encoding the lysosomal enzyme glucocerebrosidase, represent the most significant genetic risk factor for Parkinson's disease. These variants define a distinct clinical subtype characterized by earlier onset, accelerated motor decline, and pronounced cognitive impairment. This review synthesizes current insights into the molecular mechanisms linking GBA1 dysfunction to lysosomal failure, α-synuclein aggregation, and neuroinflammation. Pathogenic alleles such as N370S and L444P disrupt sphingolipid metabolism, resulting in toxic accumulations of glucosylceramide and glucosylsphingosine, endoplasmic reticulum stress, and impaired clearance of misfolded proteins. This initiates a self-reinforcing cycle in which glucocerebrosidase deficiency promotes α-synuclein aggregation, which subsequently impairs glucocerebrosidase trafficking. We explore the convergence of GBA1 mutations on the lysosomal-mitochondrial-autophagy axis, where impaired autophagic flux and disrupted organelle crosstalk amplify oxidative stress and activate the NLR family pyrin domain containing 3 inflammasome. The contribution of microglia, astrocytes, and oligodendrocytes to the neuroinflammatory cascade is eamined, along with the emerging influence of the microbiome-gut-brain axis in disease progression. Finally, we evaluate emerging therapeutic strategies, including pharmacological chaperones, NLRP3 inhibitors, adeno-associated virus-based gene therapy, and microbiome modulation, highlighting both promises and translational challenges such as blood-brain barrier penetration and mutation-specific efficacy. We conclude by advocating for precision medicine approaches, supported by robust biomarker development and advanced disease models, to guide tailored interventions for this aggressive Parkinson's disease subtype.},
}

@article {pmid41467389,
year = {2025},
author = {Stahlke, S and Theiss, C},
title = {Sex hormones, the gut microbiome, and neurodegenerative diseases: Lifespan perspective.},
journal = {Neural regeneration research},
volume = {},
number = {},
pages = {},
doi = {10.4103/NRR.NRR-D-25-00932},
pmid = {41467389},
issn = {1673-5374},
abstract = {The gut-brain axis represents a highly integrated communication network, connecting the gastrointestinal tract and the central nervous system via neural, immune, endocrine, and metabolic pathways. Steroid hormones, such as estrogens, androgens, and glucocorticoids, play a pivotal role in modulating these interactions across the lifespan. These hormones influence the composition of microbiota, intestinal permeability, and neuroimmune responses, thereby shaping brain function and behavior. Emerging evidence suggests a correlation between disruptions in the gut-brain axis and the onset and progression of neurodegenerative diseases, including Parkinson's disease, Alzheimer's disease, and multiple sclerosis. The diseases exhibit distinct sex-specific patterns in terms of prevalence, symptomatology, and progression. These patterns are often the consequence of differences in steroid hormone levels, receptor distribution, and immune responses. Despite these differences, the role of sex as a biological variable remains underrepresented in experimental and clinical research. This review synthesizes current evidence on how steroid hormones modulate gut-brain axis interactions and how these mechanisms contribute to neurodegeneration in a sex-specific manner. We highlight recent findings on hormonal regulation of the gut microbiome and its impact on neuroinflammation and neuronal vulnerability. This overview focuses not only on Parkinson's disease, in which genetic variations in the gene for brain-derived neurotrophic factor have been observed among others as triggers for dopaminergic neurodegeneration. In addition, Alzheimer's disease and multiple sclerosis are also considered, in which the prevalence of intestinal dysbiosis and impaired intestinal barrier function have been identified as significant influencing factors. This review provides a comprehensive framework for understanding the gender-specific neurobiology of gut-brain axis by integrating perspectives from the fields of endocrinology, neuroimmunology, and microbiome research. It is argued that a targeted investigation of the interactions between hormones and gut-brain axis is essential for the development of sex-specific therapeutic strategies for neurodegenerative diseases.},
}

@article {pmid41467356,
year = {2025},
author = {Vadillo Gonzalez, S and Jongen, R and Thomas, T and Marzinelli, EM and Gribben, PE},
title = {Seagrass-microbe interactions: a systematic review of current research trends and mapping of the core microbiome.},
journal = {Biological reviews of the Cambridge Philosophical Society},
volume = {},
number = {},
pages = {},
doi = {10.1002/brv.70126},
pmid = {41467356},
issn = {1469-185X},
support = {LP200200220//Australian Research Council/ ; DP240100556//Australian Research Council/ ; },
abstract = {Seagrass-microbe interactions are crucial for seagrass performance and the coastal ecosystem services they support. However, significant variation in experimental and analytical approaches has hindered our broader understanding of seagrass-microbe interactions and the potential existence of a functional core microbiome, i.e. microbial taxa that are consistently present on hosts and likely exert a disproportionate impact on host function. Through a systematic review, we aimed first to understand current trends and knowledge gaps in seagrass-microbe research. Additionally, we conducted a systematic mapping of global 16S ribosomal RNA (rRNA) gene sequencing data to characterise core bacterial taxa in three plant microenvironments (leaves, roots and rhizosphere) across multiple species and within a highly studied seagrass species, Zostera marina. The results revealed a growing number of studies since the 2010s manipulating environmental variables and/or seagrass microbes to investigate their roles in seagrass performance and responses to stressors. Most studies have primarily focused on seagrass leaves, examined a limited number of species, and investigated only bacteria via 16S rRNA gene amplicon sequencing. A few studies attempted to characterise seagrass core microbiomes, often using highly variable approaches to define core taxa. Our systematic mapping based on global sequencing data allowed the identification of prevalent bacterial taxa belonging to the families Desulfocapsaceae and Sulfurovaceae in the seagrass rhizosphere, which may play an important role in the performance of Z. marina and other seagrass species. The results also showed that many other bacterial families were prevalent across different seagrass microenvironments, such as Rhodobacteraceae and Flavobacteriaceae, with substantial taxonomic variability and functional metabolic redundancy. We identified key challenges stemming from available data and variable methodologies and provided insights to guide future experimental work and deepen our understanding of seagrass-microbe interactions. We argue that such knowledge may improve seagrass management outcomes, especially by informing restoration strategies based on core microbial taxa.},
}

@article {pmid41467315,
year = {2025},
author = {Sun, Y and Li, P and Wang, X and Jiang, D and Shao, Y},
title = {Gut dysbiosis in early severe burns contributes to acute lung injury by impairing neutrophil chemotaxis.},
journal = {Journal of leukocyte biology},
volume = {118},
number = {1},
pages = {},
doi = {10.1093/jleuko/qiaf169},
pmid = {41467315},
issn = {1938-3673},
support = {82302800//National Natural Science Foundation of China/ ; 2024M751108//China Postdoctoral Science Foundation/ ; SDCX-ZG-202400032//Postdoctoral Innovation Program in Shandong Province/ ; },
mesh = {Animals ; *Dysbiosis/complications/immunology/microbiology ; *Gastrointestinal Microbiome/immunology ; *Acute Lung Injury/etiology/pathology/microbiology/immunology ; *Neutrophils/immunology/pathology ; Humans ; Mice ; *Burns/complications/microbiology/pathology/immunology ; *Chemotaxis, Leukocyte ; Male ; Female ; Mice, Inbred C57BL ; Butyrates/pharmacology ; Disease Models, Animal ; Neutrophil Infiltration ; Chemotaxis ; },
abstract = {Severe burns complicated by acute lung injury are critical causes of respiratory failure and multiple organ dysfunction syndrome. Neutrophils extensively infiltrate lung tissues early postburn to mediate pulmonary damage, but the underlying mechanisms remain unclear. We analyzed gut microbiota of severe burn patients via metagenomics and metabolomics, assessed neutrophil chemotaxis using a self-developed in vitro agarose model, and validated Faecalibacterium prausnitzii and butyrate's effects on restoring neutrophil chemotaxis in gut microbiota-depleted mice via oral gavage (plus in vivo validation with small animal imaging). Bronchoalveolar lavage fluid biomarkers and pulmonary function tests evaluated pulmonary injury from impaired neutrophil chemotaxis. Early postburn, F. prausnitzii and its metabolite butyrate were significantly depleted in patients, concurrent with impaired neutrophil chemotaxis-restored by butyrate supplementation. In murine burn models, F. prausnitzii or butyrate rescued neutrophil chemotaxis, reduced pulmonary neutrophil infiltration, and attenuated lung injury. Mechanistically, butyrate restored neutrophil function in a severe burn patient plasma-stimulated model by downregulating P2X1 receptor expression and suppressing myosin light chain phosphorylation. Our findings indicate postburn gut microbiota dysbiosis and metabolite alterations disrupt neutrophil chemotaxis, causing excessive pulmonary neutrophil infiltration/activation. This highlights gut microbiota-derived metabolites as potential therapeutics for mitigating neutrophil-driven lung injury early postsevere burns.},
}

Animals
*Dysbiosis/complications/immunology/microbiology
*Gastrointestinal Microbiome/immunology
*Acute Lung Injury/etiology/pathology/microbiology/immunology
*Neutrophils/immunology/pathology
Humans
Mice
*Burns/complications/microbiology/pathology/immunology
*Chemotaxis, Leukocyte
Male
Female
Mice, Inbred C57BL
Butyrates/pharmacology
Disease Models, Animal
Neutrophil Infiltration
Chemotaxis

@article {pmid41467213,
year = {2025},
author = {Wang, S and Carroll-Portillo, A},
title = {Editorial: Genetic modulation of gut microbiome: effects on neurological health and aging.},
journal = {Frontiers in genetics},
volume = {16},
number = {},
pages = {1760164},
pmid = {41467213},
issn = {1664-8021},
}

@article {pmid41466840,
year = {2025},
author = {Hendesi, H and Godfrey, DA and Ruble, AF and Tran, AM and Villani, DA and Landgrave, SH and Hasan, NA and Adams, DJ and Zuscik, MJ},
title = {Intermittent fasting alleviates obesity-associated impairments in bone fracture healing: Exploring the role of gut microbiome.},
journal = {Bone reports},
volume = {27},
number = {},
pages = {101876},
pmid = {41466840},
issn = {2352-1872},
abstract = {Intermittent Fasting (IF) is a dietary strategy with metabolic benefits that can reverse certain obesity-related pathologies. This study aimed to investigate whether IF can mitigate delayed bone fracture healing associated with obesity. Using cohorts of mice on high-fat or control diets, we applied either an ad libitum feeding or an alternate-day fasting regimen to animals from both diet groups. We assessed bone healing outcomes by evaluating callus mineralization and adipocyte accumulation within the callus through micro computed tomography (micro-CT), histology, and immunohistochemical analyses. Since IF is known to modulate gut microbiome composition, often associated with improvement in various metabolic and inflammatory processes, particularly in high-fat-fed mice, we also explored the microbial community changes in IF mice through 16S rRNA sequencing of cecal samples. Metabolically, IF led to reduced body weight and improved glucose tolerance in obese mice. Regarding fracture healing outcomes, reduced/delayed mineralization and adipocyte accumulation in fracture callus tissue in the high-fat-fed cohort were significantly attenuated when the high-fat-fed mice were subjected to alternate-day fasting. These benefits of IF were not observed in lean mice fed a control diet. Furthermore, IF significantly altered the gut microbiota of mice on a high-fat diet, including an increased abundance of short-chain fatty acid producing bacteria, known for their positive effect on bone density, and a reduction in various pro-inflammatory taxa. While the mechanistic role remains unknown, these findings suggest that the improved fracture healing observed in obese mice following IF may be associated with alterations in gut microbiome composition and function.},
}

@article {pmid41466681,
year = {2025},
author = {Gupta, PS and Padmakumar, VM and Usmani, OI},
title = {Cross-sectional analysis of gut microbiome diversity with progression of Alzheimer's disease.},
journal = {Bioinformation},
volume = {21},
number = {9},
pages = {3329-3332},
pmid = {41466681},
issn = {0973-2063},
abstract = {The relationship between gut microbiome diversity and stages of Alzheimer's disease (AD) progression is of interest. Hence, a total of 124 participants, including cognitively normal controls and patients with mild, moderate, and severe AD, were assessed for microbiome composition using 16S rRNA sequencing. Results revealed significantly reduced microbial diversity and altered bacterial profiles, notably lower levels of Bifidobacterium and Faecalibacterium and increased Proteobacteria, in advanced AD stages. Correlations were observed between cognitive declines and reduced alpha diversity. Thus, we show gut dysbiosis may play a contributory role in Alzheimer's pathology.},
}

@article {pmid41466653,
year = {2025},
author = {Arvindssinh, RN and Patel, TG and Karthik Raj, MRM},
title = {Cross-sectional study on ethnic variations in gut microbiome diversity and hypertension severity.},
journal = {Bioinformation},
volume = {21},
number = {9},
pages = {3043-3046},
pmid = {41466653},
issn = {0973-2063},
abstract = {Stool samples were analyzed using 16S rRNA sequencing and blood pressure measurements were categorized per AHA guidelines. Hence, 130 adults from three ethnic groups to assess differences in gut microbiome diversity and their association with hypertension severity were studied. Significant ethnic variations were observed in microbial composition, particularly in Firmicutes-to-Bacteroidetes ratios. Greater microbial diversity was associated with lower hypertension severity in certain ethnicities. Thus, we show ethnic-specific microbiome patterns may influence hypertension outcomes.},
}

@article {pmid41466512,
year = {2025},
author = {Merz, E and Hale, RJ and Saberski, E and Kenitz, KM and Carter, ML and Bowman, JS and Barton, AD},
title = {Temperature alters interactions and keystone taxa in the marine microbiome.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf287},
pmid = {41466512},
issn = {1751-7370},
abstract = {Marine microbes shape global biogeochemical cycles and marine food webs. Although biotic interactions underpin microbial community dynamics, most interactions between wild marine microbes are unknown. Here, we used empirical dynamic modeling to examine a six-year record of coastal microbial community composition to quantify microbial interactions and their changes through time. We found that, on average, marine microbes interact with 20% of other taxa in the community, most interactions are weak (80%), and that positive interactions are more common than negative interactions. Keystone taxa, defined as having disproportionally strong and frequent interactions, were not generally the most abundant taxa. The strength and sign of interactions, as well as the identity of the keystone taxa, varied through time and with changes in water temperature. An increase of 13°C, the dynamic range in water temperature at this location during the observational period, led to a 33% less interactive microbial community and an 11% shift towards more positive interactions. Only a few of the keystone taxa are the most interactive in the community at all times, and we found a temporal succession of keystone taxa. These results reveal that interactions in the marine microbiome are common, more facilitative than previously thought, and highly variable through time.},
}

@article {pmid41466423,
year = {2025},
author = {Chen, L and Tang, C and Hu, D and Yu, S and Liao, P},
title = {Brevilin a reverses colitis of inflammatory bowel disease via modulation of TNF-α signaling and microbiome dysregulation.},
journal = {Gut pathogens},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13099-025-00792-3},
pmid = {41466423},
issn = {1757-4749},
support = {2024000003-09//Middle-aged Backbone Talents in the Province/ ; },
abstract = {BACKGROUND: Brevilin A (Br) has shown potential in modulating inflammatory bowel disease (IBD). Our study aims to explore its mechanism of anti-inflammatory action.

METHODS: Colitis was induced in C57BL/6 mice with dextran sulfate sodium (DSS), followed by treatment with or without Br(20 mg/kg). Fecal microbiota and metabolites were profiled by metagenomic sequencing and liquid chromatography-mass spectrometry (LC-MS), respectively. Furthermore, to delineate the essential role of the gut microbiota, we employed antibiotic-treated (microbiota-depleted) mice in our investigation of Br's mechanism of action.

RESULTS: Br significantly alleviated DSS-induced colitis and modulated the gut microbiota profile. Specifically, Br enriched beneficial bacteria such as Lactobacillus, while suppressing pathogenic bacteria including Escherichia coli and Clostridium perfringens. Metabolomic analysis revealed that Br significantly altered bacterial metabolites, including 7-Oxolithocholic Acid, Kudinoside A, Veratrine, and Soyasaponin. These metabolites were linked to key pathways such as GPCR signaling, DNA damage response, aminoacyl-tRNA biosynthesis, riboflavin metabolism, and central carbon metabolism in cancer. Transcriptomic profiling indicated that Br inhibited the TNF-α signaling pathway, and this inhibition was confirmed as TNF-α overexpression reversed its anti-inflammatory effects. Furthermore, the therapeutic effects of Br were partially recapitulated in microbiota-depleted mice through fecal microbiota transplantation from Br-treated donors.

CONCLUSION: Br's ability to regulate gut microbiota and metabolites, improve gut barrier function, and eliminate inflammation by inhibiting TNF-α highlights its potential as a novel therapeutic medicine for IBD. Future research should focus on further exploring its mechanisms and clinical applications.},
}

@article {pmid41466331,
year = {2025},
author = {Li, J and Zhang, X and Zhao, X and Gong, G and Li, J and Dalai, B and Mo, Z and Xu, X and Jia, X and Li, Y and Lai, J and Wang, P and Sun, L and Liu, Y and Luo, X},
title = {Characterising gut microbiome dysbiosis in diarrhoea calves from multiple farms in Inner Mongolia using 16S and metagenomics.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {259},
pmid = {41466331},
issn = {2049-2618},
support = {2021GG0171//Key Technology Project of Inner Mongolia Science and Technology Department/ ; 2021GG0171//Key Technology Project of Inner Mongolia Science and Technology Department/ ; 2021GG0171//Key Technology Project of Inner Mongolia Science and Technology Department/ ; 2021GG0171//Key Technology Project of Inner Mongolia Science and Technology Department/ ; 2021GG0171//Key Technology Project of Inner Mongolia Science and Technology Department/ ; 2021GG0171//Key Technology Project of Inner Mongolia Science and Technology Department/ ; 2021GG0171//Key Technology Project of Inner Mongolia Science and Technology Department/ ; 2020ZD0006//Inner Mongolia Autonomous Region Major Science and Technology Special Project/ ; 2020ZD0006//Inner Mongolia Autonomous Region Major Science and Technology Special Project/ ; 2020ZD0006//Inner Mongolia Autonomous Region Major Science and Technology Special Project/ ; 2020ZD0006//Inner Mongolia Autonomous Region Major Science and Technology Special Project/ ; 2020ZD0006//Inner Mongolia Autonomous Region Major Science and Technology Special Project/ ; 2022LJRC0009//Science and Technology Leading Talent Team in Inner Mongolia Autonomous Region/ ; 2022LJRC0009//Science and Technology Leading Talent Team in Inner Mongolia Autonomous Region/ ; 2022LJRC0009//Science and Technology Leading Talent Team in Inner Mongolia Autonomous Region/ ; 2022LJRC0009//Science and Technology Leading Talent Team in Inner Mongolia Autonomous Region/ ; 2022LJRC0009//Science and Technology Leading Talent Team in Inner Mongolia Autonomous Region/ ; },
mesh = {Animals ; Cattle ; *Gastrointestinal Microbiome/genetics ; *Diarrhea/microbiology/veterinary/epidemiology ; RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; China/epidemiology ; *Dysbiosis/microbiology/veterinary ; *Cattle Diseases/microbiology/epidemiology ; Feces/microbiology ; Escherichia coli/genetics/isolation & purification/pathogenicity ; *Bacteria/classification/genetics/isolation & purification ; Farms ; },
abstract = {BACKGROUND: The pathogenesis of neonatal calf diarrhoea (NCD), a critical disease that contributes to neonatal mortality in calves, remains nebulous.

RESULTS: Inner Mongolia, a key region for cattle farming in China, was selected as a study area to provide a comprehensive overview of the epidemiology and treatment of calf diarrhoea. No significant correlation was found between the incidence of diarrhoea and sampling points or medications. The severity of diarrhoea cases was stratified into five levels based on faecal characteristics. To elucidate the pathogenesis of NCD, 16S rRNA gene and metagenomic sequencing analyses were performed across severity levels. Microbial diversity analyses revealed distinct variations in microbial communities at different severity levels. Employing binning and LEfSe methodologies, two potential bacterial pathogens were identified: Escherichia coli (bin.216), leveraging non-canonical virulence mechanisms; and Streptococcus ruminantium (bin.338), an uncharacterised diarrhoeagenic bacterium. Furthermore, the viral agent Escherichia phage VpaE1_ev108 was significantly associated with disease progression. Gene function enrichment analysis revealed a broad spectrum of antibiotic resistance genes even in farms without direct antibiotic treatment, underscoring the pervasive prevalence of drug resistance.

CONCLUSIONS: The findings of this study revealed significant gut microbial dysbiosis in calves with severe diarrhoea, through which two putative NCD-associated pathogens were identified: E. coli (bin.216) and S. ruminantium (bin.338). Marked enrichment of Bacteroides spp. and Methanobrevibacter_A sp. 900313645 was observed in healthy cohorts, suggesting their potential protective roles. Therapeutic strategies employing phage-mediated pathogen targeting combined with probiotic transplantation have demonstrated dual benefits, potentially reducing antimicrobial dependency and preserving microbial homeostasis through ecological network reconstruction. Video Abstract.},
}

Animals
Cattle
*Gastrointestinal Microbiome/genetics
*Diarrhea/microbiology/veterinary/epidemiology
RNA, Ribosomal, 16S/genetics
*Metagenomics/methods
China/epidemiology
*Dysbiosis/microbiology/veterinary
*Cattle Diseases/microbiology/epidemiology
Feces/microbiology
Escherichia coli/genetics/isolation & purification/pathogenicity
*Bacteria/classification/genetics/isolation & purification
Farms

@article {pmid41466317,
year = {2025},
author = {Subberwal, M and Giles, M and Neilson, R and Roberts, D and Caul, S and Mitchell, S and Ijaz, UZ},
title = {From farm to microbe: organic amendments and soil texture as drivers of soil Microbiome composition.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {158},
pmid = {41466317},
issn = {2524-6372},
support = {BB/T010649/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
abstract = {BACKGROUND: Understanding how agricultural practices affect soil bacterial communities is vital to mitigating the negative impacts of intensive agriculture on soil health and preventing further deterioration of arable land. Increasing pressure on agricultural land necessitates careful management of our productive soil. This study investigates the interaction between organic amendments and soil texture in agricultural soils (n = 93) used for arable production, using a 16S rRNA-sequencing based microbial community analysis. Amendments include slurry, digestate, and farmyard manure. Additionally, soil physicochemical parameters were collected to explore the drivers of patterns of soil microbial diversity.

RESULTS: Microbial community composition was significantly influenced by organic amendments and soil texture, which both exerted distinct selective pressures. Analysis using 16S rRNA-sequencing and advanced modelling identified significant factors affecting community structure, including soil calcium levels, the crop grown one year previously, loss on ignition (LOI), and farm ID. The genus Candidatus Nitrosotalea was found to be positively associated with application of farmyard manure, while genus AD3 (phyla Chloroflexi) was found to be negatively associated with application of digestate and slurry.

CONCLUSIONS: The results highlight the importance of considering multiple, interacting factors when trying to establish how agricultural practice affects soil microbial communities. Our findings underscore the need for tailored management strategies - specific to the local environment and available resources - to promote soil health.},
}

@article {pmid41466108,
year = {2025},
author = {Sarafraz, F and Seo, H and Tajdozian, H and Atashi, A and Yoon, Y and Kim, S and Song, HY},
title = {Microbiome Therapeutic Lactiplantibacillus plantarum PMC105 for Systemic Carbapenem-Resistant Enterobacteriaceae Infections: Oral and Inhalation Efficacy In Vivo.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2508009},
doi = {10.4014/jmb.2508.08009},
pmid = {41466108},
issn = {1738-8872},
mesh = {Animals ; Mice ; Administration, Oral ; *Carbapenem-Resistant Enterobacteriaceae/drug effects ; Disease Models, Animal ; *Probiotics/administration & dosage/therapeutic use ; Klebsiella pneumoniae/drug effects ; *Enterobacteriaceae Infections/therapy/microbiology ; Anti-Bacterial Agents/pharmacology ; Gastrointestinal Microbiome ; Administration, Inhalation ; *Lactobacillus plantarum/physiology ; Female ; Dysbiosis ; Microbial Sensitivity Tests ; Klebsiella Infections/microbiology/therapy ; Humans ; Carbapenems/pharmacology ; },
abstract = {Carbapenem-resistant Enterobacteriaceae (CRE), particularly Klebsiella pneumoniae, are major causes of severe systemic infections due to their resistance to most antibiotics and the high associated mortality, representing a growing global health concern. In this study, we report the in vivo efficacy of a novel probiotic strain, Lactiplantibacillus plantarum PMC105, against systemic CRE infections. In a mouse model characterized by neutropenia and antibiotic-induced gut dysbiosis, infection with carbapenem-resistant K. pneumoniae (CRKP) resulted in 60% mortality within two weeks. However, oral administration of PMC105 significantly reduced intestinal CRKP colonization, minimized body weight loss, and resulted in 100% survival. This therapeutic effect is presumed to result from enhanced gut barrier function, driven by upregulation of the tight junction protein ZO-1 in the ileum, thereby preventing bacterial translocation and subsequent systemic dissemination. In a therapeutic model of systemic infection following translocation, intranasal administration of PMC105 reduced bacterial loads in the stool, liver, kidneys, and lungs, improved clinical symptoms, and maintained body weight, thereby increasing survival rates. Comprehensive safety evaluations, including antibiotic susceptibility testing, hemolysis, bile salt deconjugation, D-lactate production, and cytotoxicity assays, confirmed the strain's safety. These findings support the potential of PMC105 as a dual-route microbiome-based therapeutic candidate for the treatment of systemic CRE infections and warrant further clinical investigation.},
}

Animals
Mice
Administration, Oral
*Carbapenem-Resistant Enterobacteriaceae/drug effects
Disease Models, Animal
*Probiotics/administration & dosage/therapeutic use
Klebsiella pneumoniae/drug effects
*Enterobacteriaceae Infections/therapy/microbiology
Anti-Bacterial Agents/pharmacology
Gastrointestinal Microbiome
Administration, Inhalation
*Lactobacillus plantarum/physiology
Female
Dysbiosis
Microbial Sensitivity Tests
Klebsiella Infections/microbiology/therapy
Humans
Carbapenems/pharmacology

@article {pmid41466080,
year = {2025},
author = {Thng, KX and Mac Aogáin, M and Chotirmall, SH},
title = {Fungal-Associated Endotypes as a Treatable Trait in Bronchiectasis.},
journal = {Pulmonary therapy},
volume = {},
number = {},
pages = {},
pmid = {41466080},
issn = {2364-1746},
support = {MOH-001636//National Medical Research Council/ ; MOH-001356//National Medical Research Council/ ; MOH-000955//National Medical Research Council/ ; AcRF Tier 1 Grant (RT1/22)//Ministry of Education - Singapore/ ; },
abstract = {Emerging evidence demonstrates the evolving role of fungi in the pathophysiology and disease progression observed in bronchiectasis. Fungal-associated traits are linked to disease severity, exacerbation frequency and airway inflammation. Structural abnormalities and impaired mucociliary clearance, characteristic of bronchiectasis, predispose to fungal colonisation, with subsequent immunopathogenic responses dependent on underlying host immunity. The diagnosis of fungal infection remains challenging in clinical settings, owing to the limitations of existing diagnostic modalities; however, the development of culture-independent molecular techniques shows promise. The use of next-generation sequencing has significantly advanced our understanding of the fungal microbiome in bronchiectasis, identifying fungi that are challenging to culture. Integrative microbiomics further elucidates the intricate and dynamic role of fungi in relation to other microbial kingdoms, and across distant organs such as the gut, revealing important relationships with bacterial pathogens including Pseudomonas aeruginosa. Airway inflammatory profiling has shown fungal-associated inflammatory endotypes which may serve as treatable traits. Environmental influences on fungi and bronchiectasis-exacerbated by air pollution and climate change-underscore the key role of the exposome in fungal-associated endotypes in bronchiectasis. This review outlines the clinical significance of fungi in bronchiectasis, the current diagnostic and treatment challenges, and emerging fungal-associated endotypes in the context of environmental influence on disease.},
}

@article {pmid41466065,
year = {2025},
author = {Ebrahim, NAA and Soliman, SMA and Farghaly, TA},
title = {Saliva-based molecular diagnostics in oral squamous cell carcinoma (OSCC): a non-invasive frontier in oncology.},
journal = {European archives of oto-rhino-laryngology : official journal of the European Federation of Oto-Rhino-Laryngological Societies (EUFOS) : affiliated with the German Society for Oto-Rhino-Laryngology - Head and Neck Surgery},
volume = {},
number = {},
pages = {},
pmid = {41466065},
issn = {1434-4726},
support = {25UQU4350477GSSR10//Umm Al-Qura University/ ; },
abstract = {PURPOSE: Saliva is increasingly recognized as a powerful, noninvasive biofluid for the diagnosis and monitoring of oral squamous cell carcinoma (OSCC), serving as a practical alternative to conventional liquid biopsy. Salivary circulatory DNA (ctDNA) detection in OSCC may exceed plasma levels. emphasizing saliva's susceptibility to local illness. Saliva collection is simple, non-invasive, and inexpensive, allowing for regular monitoring.

METHODS: Current evidence demonstrates its potential through a wide spectrum of salivary biomarkers.

RESULTS: Identified salivary biomarkers include viral nucleic acids such as human papillomavirus (HPV), host-derived molecules such as proteins and cytokines (IL-6, IL-8, VEGF), regulatory microRNAs (e.g., miR-21, miR-31, miR-184), and extracellular vesicles containing tumor-specific cargo. Moreover, oral microbiome dysbiosis has been linked to malignant transformation and progression, highlighting saliva's ability to reflect complex tumor-host interactions. Technological progress in multi-omics profiling and artificial intelligence (AI) has enhanced the interpretation of these multidimensional datasets, supporting the design of more robust and individualized biomarker panels. Concurrently, point-of-care technologies, particularly microfluidic chips and biosensor platforms, are driving the development of rapid and portable saliva-based diagnostics.  CONCLUSION: The path toward clinical implementation is constrained by several factors: the absence of FDA-approved salivary assays for OSCC, reliance on relatively small and retrospective studies, and the lack of standardized protocols for collection, processing, and analysis. Despite these challenges, salivary diagnostics are advancing as a highly promising adjunct to established modalities such as histopathology and radiologic imaging. They hold potential in early disease detection, patient stratification, therapeutic monitoring, and surveillance of recurrence. Integrative models, such as liquid TNM staging-which combine salivary and blood-based biomarkers-may ultimately redefine cancer diagnostics and follow-up. To date, no saliva-based assay has received FDA approval for oral cancer, highlighting regulatory and validation shortcomings. For translation into practice, further validation through large-scale trials, regulatory endorsement, and demonstration of cost-effectiveness remain essential. Nonetheless, saliva-based assays stand out as accessible, patient-centered tools with significant implications for the future of head and neck oncology.},
}

@article {pmid41465981,
year = {2025},
author = {He, Y and You, G and Qian, Y and Long, Y and Wang, B and Zhou, Y},
title = {Role of cathepsin in mediating the effect of oral flora on myocardial infarction: A multi-omics and mediation Mendelian randomization study.},
journal = {Medicine},
volume = {104},
number = {52},
pages = {e46859},
pmid = {41465981},
issn = {1536-5964},
support = {gzwkj 2021-102, gzwkj2021-111//Guizhou Provincial Health and Wellness Commission/ ; gzwkj2023-299//Guizhou Provincial Health and Wellness Commission/ ; No. 82260084//The National Natural Science Foundation of China/ ; No. 82460059//The National Natural Science Foundation of China/ ; No.82260061//The National Natural Science Foundation of China/ ; Qian Ke He Foundation ZK [2023] General 217, Qian Ke He Basic-ZK (2022) 262//Guizhou Provincial Science and Technology Agency Project/ ; Qian Ke He Foundation ZK [2022] General 268//Guizhou Provincial Science and Technology Agency Project/ ; Qian Ke He Basic-ZK (2021) 358//Guizhou Provincial Science and Technology Agency Project/ ; Gzwjrs2023-011//Guizhou High-level Innovative Talents Programme/ ; },
mesh = {Humans ; Mendelian Randomization Analysis ; *Myocardial Infarction/microbiology/genetics ; *Microbiota/physiology ; *Cathepsins/metabolism ; *Mouth/microbiology ; *Cathepsin H/genetics/metabolism ; Multiomics ; },
abstract = {The association between oral microbiome (OM) and myocardial infarction (MI) has become a noteworthy topic in recent years, yet the role played by cathepsin in this association remains unclear. The main objective of this study was to elucidate the role of cathepsin in mediating the effect of OM on MI. The mutual causality among OM, cathepsins, and MI was analyzed using two-sample Mendelian randomization (TSMR), and the mediating role of cathepsins between OM and MI was evaluated using mediation MR analysis. Furthermore, we conducted a meta-analysis to verify the causal relationship between Cathepsin H and MI. Subsequently, we employed summary-data-based MR (SMR) method to examine the potential causal genes and proteins for Cathepsin H and acute myocardial infarction. The meta analysis result indicated that each standard deviation increase in the exposure factor of Cathepsin H was associated with a reduction in the MI risk (OR = 0.9991; 95% CI = 0.9984-0.9998; P = .0089). Our study confirmed that 3 salivary flora, including Lancefieldella_unclassified_mgs_1257, Fusobacterium_unclassified_mgs_3185, Oribacterium_asaccharolyticum_mgs_3324, and one tongue dorsal flora, named Saccharimonadaceae_unclassified_mgs_1355, can regulate the development of MI via Cathepsin H. The results of the SMR analysis indicated a statistically significant negative correlation between the Cathepsin H (CTSH) gene and coronary artery disease (P-SMR < .05, P-HEIDI > .01). Conversely, a significant positive correlation was observed between the MST1 protein and MI risk (P-SMR < .05, P-HEIDI > .01). Reverse transcription polymerase chain reaction and ELISA tests on clinical samples showed a significant decrease in Cathepsin H levels - both protein and messenger ribonucleic acid - in the blood of MI patients (P < .05), while MST1 expression was notably increased (P < .05). We identified 3 salivary bacteria and one tongue dorsum bacterium that may influence MI development, with Cathepsin H playing a key mediating role. These findings strengthen the evidence linking OM to MI and clarify the role of cathepsins in this relationship. The study highlights how Cathepsin H may mediate the impact of oral flora on MI and proposes new therapeutic directions and targets for MI prevention and treatment.},
}

Humans
Mendelian Randomization Analysis
*Myocardial Infarction/microbiology/genetics
*Microbiota/physiology
*Cathepsins/metabolism
*Mouth/microbiology
*Cathepsin H/genetics/metabolism
Multiomics

@article {pmid41465974,
year = {2025},
author = {Chen, C and Yang, Z and Guo, J and Liu, Y and Yang, X and Deng, W and Yu, H and Yang, S},
title = {Causal genetic link between gut microbiome, metabolites, and autism spectrum disorder in a European cohort.},
journal = {Medicine},
volume = {104},
number = {52},
pages = {e46526},
pmid = {41465974},
issn = {1536-5964},
mesh = {Humans ; *Autism Spectrum Disorder/genetics/microbiology/epidemiology/metabolism ; *Gastrointestinal Microbiome/genetics ; Genome-Wide Association Study ; Male ; Female ; Mendelian Randomization Analysis ; Europe/epidemiology ; Child ; Cohort Studies ; Child, Preschool ; },
abstract = {Recent studies have illuminated a significant relationship between the gut microbiota and the development and progression of autism spectrum disorder (ASD), mediated through the complex gut-brain axis, where metabolic pathways are crucial. Nevertheless, the exact causal link remains to be elucidated. This study aims to assess the potential causal relationship between the gut microbiota, metabolites, and ASD, utilizing Mendelian randomization methodology. The exposure variable of gut microbiota was ascertained using instrumental variables derived from a genome-wide association study that included a cohort of 18,340 individuals. The outcome variable comprised genome-wide association study data from 14,759 individuals diagnosed with ASD and 1,55,327 controls. The primary method of analysis was the inverse-variance weighted method. Multivariable multiple regression analysis was conducted to examine the impact of gut microbial metabolites on the established correlations. Inverse-variance weighted analyses revealed that Methanobacteria[c] (odds ratio [OR] = 1.17 [1.03-1.33]), Methanobacteriaceae[f] (OR = 1.17 [1.03-1.33]), Prevotellaceae[f] (OR = 1.29 [1.04-1.60]), Holdemania[g] (OR = 1.23 [1.03-1.45]), Lachnospiraceae[g] (OR = 1.29 [1.06-1.57]), Ruminiclostridium[g] (OR = 1.63 [1.27-2.10]), Terrisporobacter[g] (OR = 1.28 [1.00-1.63]), Methanobacteriales[o] (OR = 1.17 [1.03-1.33]), and Euryarchaeota[p] (OR = 1.16 [1.02-1.32]) serve as risk factors for ASD, while Eisenbergiella[g] (OR = 0.80 [0.68-0.94]) and Ruminococcaceae[g] (OR = 0.79 [0.63-1.00]) exhibit protective roles against ASD. Adjustments for neurotransmitter and amino acid metabolites effects diminished these associations. However, Prevotellaceae and Lachnospiraceae remained significantly associated with increased ASD risk. Reverse Mendelian randomization analyses did not establish a causal relationship between ASD and gut microbiota composition. Sensitivity tests showed no evidence of heterogeneity or pleiotropy. Alterations in metabolites induced by the gut microbiota may contribute to ASD susceptibility. Prevotellaceae and Lachnospiraceae are implicated as potential risk factors. Investigating these associations further could unveil novel therapeutic targets and provide deeper insights into ASD's etiological mechanisms.},
}

Humans
*Autism Spectrum Disorder/genetics/microbiology/epidemiology/metabolism
*Gastrointestinal Microbiome/genetics
Genome-Wide Association Study
Male
Female
Mendelian Randomization Analysis
Europe/epidemiology
Child
Cohort Studies
Child, Preschool

@article {pmid41465904,
year = {2025},
author = {Fan, Y and Chen, J and Zhuang, Y and Chang, L and Wang, W and Zhang, Y},
title = {Casual roles of gut microbiota, immune cells, and inflammatory cytokines in acute respiratory distress syndrome: A Mendelian randomization study.},
journal = {Medicine},
volume = {104},
number = {52},
pages = {e46736},
pmid = {41465904},
issn = {1536-5964},
support = {320.6750.2025-6-20//Wujieping Medical Foundation Clinical Research Special Fund/ ; },
mesh = {Humans ; Mendelian Randomization Analysis ; *Gastrointestinal Microbiome/immunology ; *Respiratory Distress Syndrome/immunology/microbiology/genetics ; *Cytokines/immunology/blood ; Dysbiosis/immunology ; },
abstract = {Gut dysbiosis and aberrant immune activation are increasingly recognized as critical determinants of acute respiratory distress syndrome (ARDS). However, the causal contributions of specific gut taxa, immune-cell phenotypes, and their interactive pathways remain incompletely understood. In this study, we conducted a comprehensive two-sample Mendelian randomization (MR) analysis to elucidate the individual and combined effects of the gut microbiome and immune milieu on ARDS susceptibility. Using 5 combined methodologies, the primary causal estimates were primarily derived through the Inverse-Variance Weighted approach. Heterogeneity was evaluated using Cochrane's Q test, while horizontal pleiotropy was assessed via the MR-Egger intercept, and robustness was confirmed through leave-one-out and reverse MR analyses. Following adjustments for the false discovery rate (FDR), our findings indicated that, although the overall effects of exposures on ARDS were not statistically significant (PFDR < 0.2), there were causal associations identified for 12 gut microbiota taxa, 24 immune cells, and 6 circulating inflammatory cytokines with ARDS (P < .05). Initial mediation analyses indicated that EIF4EBP1, caspase-8, IL-6, and IL-8 might partly mediate these effects, but 1000 BCa bootstrap iterations rejected all indirect pathways. These findings underscore the pivotal roles of gut microbiota and immune factors, both individually and interactively, in the pathogenesis of ARDS, offering a genetically informed basis for future treatments targeting the microbiome and immune system.},
}

Humans
Mendelian Randomization Analysis
*Gastrointestinal Microbiome/immunology
*Respiratory Distress Syndrome/immunology/microbiology/genetics
*Cytokines/immunology/blood
Dysbiosis/immunology

@article {pmid41465881,
year = {2025},
author = {Kukaev, E and Krogh-Jensen, O and Starodubtseva, N and Tokareva, A and Nikitina, I and Lenyushkina, A and Frankevich, V and Sukhikh, G},
title = {Longitudinal Fecal Short-Chain Fatty Acid Trajectories in Preterm Infants with Early-Onset Neonatal Sepsis: A Pilot Study.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {12},
pages = {},
pmid = {41465881},
issn = {2075-1729},
support = {24-25-00068//Russian Science Foundation/ ; },
abstract = {BACKGROUND: Early-onset neonatal sepsis (EONS), defined as systemic infection occurring within the first 72 hours of life, remains a major cause of morbidity and mortality in preterm infants. Increasing evidence indicates that the gut may play an active role in systemic inflammation, yet the temporal behavior of fecal short-chain fatty acids (SCFAs) during EONS has not been characterized. SCFAs and branched-chain fatty acids (BCFAs) are key microbial metabolites involved in epithelial maturation and immune regulation and may provide a non-invasive window into early inflammatory vulnerability.

METHODS: This pilot prospective longitudinal cohort study enrolled 49 preterm infants (≤32 weeks' gestation) originally identified as at high risk for necrotizing enterocolitis (NEC) and subsequently stratified into EONS and non-sepsis groups. Serial stool samples were collected at predefined timepoints (TPs; TP1 ≈ 3 days of life [DoL], TP2 ≈ 7 DoL, TP3 ≈ 14 DoL, TP4 ≈ 21 DoL, and TP5 ≈ 28 DoL). Samples were analyzed using gas chromatography-mass spectrometry (GC-MS) to quantify a panel of 12 SCFAs, including BCFAs and medium-chain fatty acids (MCFAs). Both absolute concentrations and relative fractions were evaluated, with emphasis on ratio-based metrics (e.g., acetic/propionic acid ratio) and timepoint-specific group contrasts, complemented by partial least squares discriminant analysis (PLS-DA).

RESULTS: At the earliest sampling window (TP1), infants with EONS exhibited distinct early changes in SCFA composition, including a significantly lower median relative fraction of acetic acid (86.6% vs. 94.5% in non-sepsis), while several non-acetate components-including propionic, valeric, and branched-chain acids-were relatively enriched. Acetate-to-non-acetate ratios were markedly reduced in EONS (e.g., acetic/propionic and acetic/isobutyric ratios), indicating an early shift away from acetate dominance. PLS-DA at TP1 demonstrated partial separation between groups, with acetic-acid depletion and non-acetate enrichment among the strongest contributors to discrimination. By later TPs, these early differences narrowed to a small subset of BCFA-related ratios and largely attenuated by the end of the first month.

CONCLUSIONS: In this pilot cohort of preterm infants, EONS was associated with early, structured alterations in fecal SCFA profiles, characterized by reduced acetic-acid dominance and relative enrichment of non-acetate acids. Dynamic, ratio-based assessment proved more informative than absolute concentrations alone, revealing transient intestinal metabolic signatures accompanying systemic infection. These findings provide the first longitudinal evidence of gut metabolic involvement in EONS and lay the groundwork for larger, multi-center studies integrating SCFA trajectories with microbiome and immune profiling to refine early risk stratification for systemic infection in high-risk neonatal populations.},
}

@article {pmid41465859,
year = {2025},
author = {Angelova, B and Boteva, S and Traykov, I and Tsvetkov, M and Kenarova, A},
title = {Bacterial Community Composition and Structure in the Littoral of Rila Mountains Glacial Lakes.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {12},
pages = {},
pmid = {41465859},
issn = {2075-1729},
support = {KP-06-M71/2//The Bulgarian National Science Fund/ ; },
abstract = {High-mountain lakes are biodiversity hotspots sensitive to increasing regional and global climate warming. However, their microbial communities remain insufficiently characterized due to their remoteness and limited accessibility. This study aimed to determine how seasonal environmental parameters shape the composition, structure and diversity of littoral bacterial communities in three glacial lakes in Rila Mountains (Bulgaria). Water samples were collected during ice-free periods in 2023 and 2024, and bacterial taxonomic composition was analysed by Next-generation sequencing. A total of 1158 bacterial OTUs were identified encompassing 18 phyla and 165 families. Actinomycetota, Pseudomonadota, and Bacteroidota were dominant at the phylum level, and Sporichthyaceae, Comamonadaceae, Chitinophagaceae and Mycobacteriaceae were most abundant among the families. Community richness and diversity peaked in June, immediately after ice melting, particularly in the highest-altitude lake (Sulzata Lake), and declined during the warm season (August), when the relative abundances of Sporichthyaceae and Mycobacteriaceae (Actinomycetota) increased. Seasonal restructuring occurred across phyla and families even in a single taxon, with water temperature and organic carbon availability identified as the main environmental drivers. The findings have improved our understanding of temperature-driven bacterial responses. They have also highlighted the vulnerability of cold-adapted taxa to regional climate warming which may contribute to more effective biodiversity conservation strategies for these unique ecosystems.},
}

@article {pmid41465800,
year = {2025},
author = {Messina, BM and Polizzi, A and Panuzzo, C and Belmonte, A and Angjelova, A and Fuochi, V and Annunziata, M and Isola, G},
title = {Impact of Periodontal Host-Modulation Therapies on Oral-Gut Microbiome Axis in Periodontitis Patients with Hematological Diseases: A Narrative Review.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {12},
pages = {},
pmid = {41465800},
issn = {2075-1729},
abstract = {Host-modulating therapies and oral microbiome-targeted approaches are emerging options in periodontal care and are especially relevant for patients undergoing immunotherapy for hematologic malignancies. Immune dysregulation induced by immune checkpoint inhibitors or CAR-T cell therapy may worsen periodontal inflammation and alter the composition and functions of the oral microbiota. Beyond these, other immunomodulatory treatments commonly employed in hematologic malignancies-including monoclonal antibodies (e.g., rituximab, daratumumab), immunomodulatory drugs (e.g., lenalidomide, thalidomide), cytokine-based therapies (e.g., interferon-α), and targeted small-molecule inhibitors (e.g., BTK inhibitors, JAK inhibitors) may also influence periodontal homeostasis and oral microbial ecology by altering neutrophil function, cytokine profiles, and mucosal immune surveillance. The oral microbiota is functionally connected with the intestinal microbial ecosystem through the oral-gut axis, by periodontal pathogens may colonize the gut and modulate systemic immune responses, with potential repercussions on the efficacy and safety of immunotherapy. This narrative review examines the mechanisms and clinical applicability of host-modulating therapies, including subantimicrobial-dose doxycycline, omega-3 fatty acids, and microbiome-targeted interventions, such as oral probiotics, prebiotics and other antimicrobials in patients treated with immunotherapy.},
}

@article {pmid41465793,
year = {2025},
author = {Popova, N and Safonov, A},
title = {Diversity of Groundwater Microbial Communities near Sludge Repositories with Different Types and Levels of Pollution.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {12},
pages = {},
pmid = {41465793},
issn = {2075-1729},
support = {no//The Ministry of Science and Higher Education of the Russian Federation/ ; },
abstract = {Multicomponent pollution of groundwater with nitrates and sulfates is a common issue associated with mining and ore-processing operations. This work presents the first large-scale comparative study of groundwater microbial communities from six geographically distant sites in the Russian Federation with varying levels of nitrate and sulfate pollution. Based on high-throughput 16S rRNA sequencing data and hydrochemical analysis, a statistically significant influence of the pollution type on the structural and functional diversity of the microbiome was established. Nitrates act as a stimulating factor, increasing alpha-diversity, while sulfates have an inhibitory effect. Principal component and correlation analysis revealed spatial grouping of samples according to the predominant pollution type. Microbiome representatives common to all sites under unpolluted conditions were identified: Bacteroides, Iamia, and Paenibacillus; and under high pollution levels: Acidovorax, Pseudomonas, Sphingomonas, Acinetobacter, and Limnohabitans. Based on the obtained data, it is concluded that representatives of these genera are the most promising and universal for isolation and use in bioremediation.},
}

@article {pmid41465751,
year = {2025},
author = {Zhang, X and Li, Y and Zhang, F and Zhou, G},
title = {Exercise and Diet Reshape Athletes' Gut Microbiota: Countering Health Challenges in Athletes.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {12},
pages = {},
pmid = {41465751},
issn = {2075-1729},
support = {82304144//National Natural Science Foundation of China/ ; 32372334//National Natural Science Foundation of China/ ; },
abstract = {With the advancement of modern competitive sports, specialized training regimens and tailored dietary patterns collectively shape a distinctive gut microbiota in athletes. This unique ecosystem exhibits high microbial diversity and is enriched with beneficial bacteria-such as short-chain fatty acid-producing strains-that contribute to enhanced athletic performance, support energy homeostasis and neural coordination, and mitigate exercise-induced injuries, thereby improving competitive outcomes. This review elaborates on the characteristics of the athlete gut microbiome across different exercise modalities, examines how microbial changes may benefit or pose risks to athlete health, and provides a unique perspective for developing microbiota-driven personalized nutrition strategies aimed at optimizing athletic performance.},
}

@article {pmid41465727,
year = {2025},
author = {Maresca, E and Carbone, M and Gallo, G and Fusco, S and Aulitto, M},
title = {Extremophile-Derived Bioactives in Cosmeceuticals: Bridging Nutraceuticals and Skincare for Holistic Wellness.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {12},
pages = {},
pmid = {41465727},
issn = {2075-1729},
abstract = {The integration of extremophile-derived bioactives into cosmeceuticals and nutricosmetics offers a novel strategy to enhance skin health through both topical and systemic approaches. Extremophile microorganisms, adapted to extreme conditions, produce unique compounds such as ectoine, extremozymes, carotenoids, exopolysaccharides (EPSs), and mycosporine-like amino acids (MAAs). These molecules exhibit antioxidant, anti-inflammatory, photoprotective, and regenerative properties. This review analyzes the molecular adaptations that enable extremophiles to synthesize these compounds, and explores their cosmetic applications, including enzymatic exfoliation, UV protection, hydration, and anti-pollution effects. This paper examines their nutraceutical potential, highlighting systemic benefits such as improved skin elasticity, reduced photoaging, and modulation of the gut-skin axis via prebiotic EPSs. Industrial strategies for sustainable production, such as microbial fermentation, synthetic biology, and green extraction, are discussed. Examples of commercial ingredients like PlusXanthin™, Antarctic-G, and Desertica. Extremophile-derived ingredients combine biological efficacy with environmental sustainability, positioning them as key assets for next-generation skincare. Future directions include clinical validation, regulatory harmonization, and the development of personalized, microbiome-friendly formulations.},
}

@article {pmid41465696,
year = {2025},
author = {Jin, JX and Wang, Y and Zhang, GF and Ye, ZC and Liu, B and Yao, DD and Jiang, ZC and He, YF},
title = {Diversity and Functional Analysis of Gut Microbiota in the Adult of Lissorhoptrus oryzophilus (Coleoptera: Curculionidae) by Metagenome Sequencing.},
journal = {Insects},
volume = {16},
number = {12},
pages = {},
pmid = {41465696},
issn = {2075-4450},
abstract = {The gut microbiota of insects plays a fundamental role in modulating host physiology, including nutrition, development, and adaptability to environmental challenges. The rice water weevil, Lissorhoptrus oryzophilus Kuschel (Coleoptera: Curculionidae), is a major invasive pest of rice worldwide, yet the composition and functional profile of its gut microbial community remain poorly characterized. Here, we employed metagenome sequencing on the Illumina NovaSeq X Plus platform to explore the gut microbial diversity and predicted functions in adults of L. oryzophilus. Our results revealed a rich microbial community, comprising 26 phyla, 42 classes, 72 orders, 111 families, and 191 genera. The bacterial microbiota was overwhelmingly dominated by the phylum Proteobacteria (85.13% of total abundance). At the genus level, Pantoea (48.86%) was the most predominant taxon, followed by Wolbachia (14.57%) and Rickettsia (11.81%). KEGG analysis suggested that the gut microbiota is primarily associated with metabolic pathways such as membrane transport, carbohydrate and amino acid metabolism, cofactor and vitamin metabolism, energy metabolism, and signal transduction. eggNOG annotation further highlighted significant gene representation in amino acid and carbohydrate transport and metabolism, while CAZy annotation revealed glycosyl transferases (GTs) and glycoside hydrolases (GHs) as the dominant carbohydrate-active enzymes. This study provides the first comprehensive insight into the gut microbiome of L. oryzophilus adults, highlighting its potential role in the ecological success of this invasive pest. Our findings lay groundwork for future research aimed at developing novel microbial-based strategies for the sustainable management of L. oryzophilus.},
}

@article {pmid41465624,
year = {2025},
author = {Remmal, I and El Yamlahi, Y and Bel Mokhtar, N and Galiatsatos, I and Loukovitis, D and Dionyssopoulou, E and Britel, MR and Stathopoulou, P and Maurady, A and Tsiamis, G},
title = {Analysis of the Bacterial Microbiota in Wild Populations of Prickly Pear Cochineal, Dactylopius opuntiae in Morocco.},
journal = {Insects},
volume = {16},
number = {12},
pages = {},
pmid = {41465624},
issn = {2075-4450},
support = {FAO/IAEA Contract 22662//FAO/IAEA/ ; },
abstract = {Dactylopius opuntiae (Cockerell) (Hemiptera: Dactylopiidae), the wild cochineal scale, is a major pest of prickly pear crops worldwide. This study characterized the bacterial community structure of D. opuntiae from four Moroccan regions using targeted PCR and full-length 16S rRNA MinION sequencing. We report the first detection of Wolbachia (16.6% prevalence) in D. opuntiae, with infection rates varying geographically from 0% (Rabat) to 53.3% (Ouazzane). Spiroplasma was detected at a lower prevalence (3.3%) and exclusively in males. Phylogenetic analysis showed that Wolbachia sequences likely belong to supergroup B, based on their similarity to reference sequences, while Spiroplasma sequences were placed within the poulsonii-citri complex. MinION sequencing revealed Candidatus Dactylopiibacterium as the dominant taxon (97.7%), consistent with its role as an obligate symbiont. After removing this dominant species, we uncovered a diverse bacterial community, including Flavisolibacter, Pseudomonas, Phyllobacterium, Acinetobacter, and Brevibacillus. Beta diversity analysis showed significant geographic variation (PERMANOVA p < 0.008), with distinct communities across regions. Females harbored a more specialized microbiome dominated by Flavisolibacter (except in Agadir), whereas males and nymphs showed Pseudomonas dominance. Core microbiome analysis revealed no universal genera across all groups, with females displaying a more restricted core than males and nymphs. The detection of reproductive symbionts, combined with geographic and sex-specific microbiome patterns, provides valuable insights into the potential roles of these bacteria in host adaptation and their implications for microbiome-based pest management strategies. The complementary use of targeted and untargeted sequencing methods is essential for comprehensive microbiome characterization in this economically important pest.},
}

@article {pmid41465599,
year = {2025},
author = {Borowik, A and Wyszkowska, J and Zaborowska, M and Kucharski, J},
title = {The Importance of Humic Acids in Shaping the Resistance of Soil Microorganisms and the Tolerance of Zea mays to Excess Cadmium in Soil.},
journal = {International journal of molecular sciences},
volume = {26},
number = {24},
pages = {},
pmid = {41465599},
issn = {1422-0067},
support = {30.610.006-110//University of Warmia and Mazury in Olsztyn, Faculty of Agriculture and Forestry, Department of Soil Science and Microbiology/ ; "the Regional Initiative of Excellence Program"//Minister of Science/ ; },
mesh = {*Zea mays/drug effects/growth & development/microbiology ; *Cadmium/toxicity ; *Soil Microbiology ; *Humic Substances/analysis ; *Soil Pollutants/toxicity ; *Bacteria/drug effects/genetics/classification ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; Microbiota/drug effects ; },
abstract = {Contamination with cadmium (Cd[2+]) poses a severe threat to the soil environment due to its toxic effect on bacteria, being of key importance to soil fertility and plant health. The present study aimed to evaluate the effect of a humic preparation, Humus Active (HA), on the structure, diversity, and functional potential of soil bacteria under conditions of cadmium stress during Zea mays cultivation. A model study was conducted to analyze the response of bacteria to soil contamination with 60 mg Cd kg[-1] under conditions of soil fertilization with humic acid at doses of 2 g (HA2) and 4 g (HA4) kg[-1] of soil. Microbiological analyses were carried out with both culture and non-culture (16S rRNA gene amplicon sequencing method) methods. Bacteria function prediction was also performed using FAPROTAX software. The study results demonstrated that Cd caused a 92% reduction in Zea mays biomass and a significant decrease (by 52%) in the abundance of organotrophic bacteria. The NGS analysis showed that it also reduced the population of the Neobacillus bacteria in the soil (by 50%), simultaneously causing an over twofold increase in the population of the Nocardioides genus bacteria. The application of HA (particularly in the HA4 dose) substantially mitigated Cd phytotoxicity. In the Cd-contaminated soil, HA4 stimulated the growth of culturable actinobacteria. The soil bacteria community was predominated by chemoheterotrophic bacteria and the nitrogen cycle bacteria, driven by tolerant, Cd[2+]-resistant bacteria from the following genera: Bacillus, Nocardioides, and Arthrobacter. The study results enable concluding that even though Humus Active does not restore the original microbiome structure, it promotes the development of a new stress-resistant bacterial community exhibiting high bioremediating potential, thereby directly translating into improved plant condition. Subsequently, humic acids provide an innovative approach that not only extends knowledge about the mechanisms behind bacterial resistance but also enables developing practical methods for diminishing cadmium mobility in the soil.},
}

*Zea mays/drug effects/growth & development/microbiology
*Cadmium/toxicity
*Soil Microbiology
*Humic Substances/analysis
*Soil Pollutants/toxicity
*Bacteria/drug effects/genetics/classification
RNA, Ribosomal, 16S/genetics
Soil/chemistry
Microbiota/drug effects

@article {pmid41465559,
year = {2025},
author = {Shen, CL and Liu, X and Cao, JJ and Neugebauer, V and Miranda, JM and Elmassry, MM and Dunn, DM and Dufour, JM},
title = {Dietary Geranylgeraniol Mitigates Pain-Associated Behaviors via Improving Mitochondrial Function and Colon Integrity and Suppressing Neuroinflammation in Male Diabetic Neuropathy Rats.},
journal = {International journal of molecular sciences},
volume = {26},
number = {24},
pages = {},
pmid = {41465559},
issn = {1422-0067},
support = {B1-0028, JMD//Robert A. Welch Foundation/ ; #3062-10700-002-000D//USDA-ARS/ ; R01NS038261 (VN)/GF/NIH HHS/United States ; },
mesh = {Animals ; Male ; Rats ; *Mitochondria/drug effects/metabolism ; *Colon/drug effects/metabolism/pathology ; Gastrointestinal Microbiome/drug effects ; Rats, Sprague-Dawley ; *Diabetic Neuropathies/drug therapy/metabolism ; Diabetes Mellitus, Experimental/complications ; *Diterpenes/pharmacology ; *Neuroinflammatory Diseases/drug therapy ; Behavior, Animal/drug effects ; *Pain/drug therapy ; },
abstract = {Growing evidence highlights the links between diabetic neuropathy (DNP), gut dysbiosis, mitochondrial dysfunction and neuroinflammation in colon and bone microstructure deterioration. Geranylgeraniol (GG) shows neuroprotective and osteoprotective capacity. Our study examines GG's effects on pain-associated behaviors, glucose homeostasis, gut microbiota, mitochondrial homeostasis, and bone microstructure in DNP rats. We randomly assigned 27 male Sprague Dawley rats to three groups (n = 8-10/group): a control group (regular low-fat diet), a DNP group (high-fat diet + a single dose of 35 mg/kg streptozotocin), and a GG-treated DNP group (a single dose of 35 mg/kg streptozotocin + GG at 800 mg/kg in diet) for 6 weeks. Nocifensive response was assessed via the von Frey test and an open field test, and the elevated plus maze was used to assess anxio-depressive behaviors. The mRNA expression levels of tight junction protein, mitochondrial homeostasis, and neuroinflammation were measured in the colon using qRT-PCR. We collected fecal samples for microbiota composition analysis with 16S rRNA gene sequencing and analyzed by QIIME 2. All other data were analyzed via one-way ANOVA followed by post hoc Tukey's multiple comparison. p < 0.05 was defined as statistical significance. Our study showed GG's ability to mitigate mechanical hypersensitivity and anxio-depressive behavior in rats with DNP. GG supplementation did not improve glucose homeostasis (i.e., glucose intolerance, insulin sensitivity, pancreatic β-cell dysfunction) and bone microstructure. GG increased alpha-diversity without changing microbial abundance. DNP rats exhibited elevated Clostridium sensu stricto and reduced Eubacterium coprostanoligenes, Lachnospiraceae, Oscillospiraceae, and Peptococcaceae compared with controls. GG did not reverse DNP-induced gut dysbiosis but increased colonic claudin-3 (tight junction), MFN1 (mitochondria fusion), and TFAM (mitochondria biogenesis), while reducing FIS1 (mitochondria fission), GFAP (glial activation), P62 and PINK1 (mitophagy), and TNFα (inflammation). Functionally, GG reduced pain behaviors, improved intestinal integrity and mitochondrial homeostasis, increased alpha-diversity, and suppressed neuroinflammation, but did not improve glucose homeostasis or bone microstructure in obese DNP rats.},
}

Animals
Male
Rats
*Mitochondria/drug effects/metabolism
*Colon/drug effects/metabolism/pathology
Gastrointestinal Microbiome/drug effects
Rats, Sprague-Dawley
*Diabetic Neuropathies/drug therapy/metabolism
Diabetes Mellitus, Experimental/complications
*Diterpenes/pharmacology
*Neuroinflammatory Diseases/drug therapy
Behavior, Animal/drug effects
*Pain/drug therapy

@article {pmid41465485,
year = {2025},
author = {Du, L and Cheng, X and Liu, B and Hao, Y and Long, Z and Hu, Q and Huo, B and Xie, T and Cheng, Q and Zhou, Y and Chen, J},
title = {A New Perspective on Nasal Microbiota Dysbiosis-Mediated Allergic Rhinitis: From the Mechanism of Immune Microenvironment Remodeling to Microbiota-Targeted Therapeutic Strategies.},
journal = {International journal of molecular sciences},
volume = {26},
number = {24},
pages = {},
pmid = {41465485},
issn = {1422-0067},
support = {2023YFC2507900//National Key Research/ ; 2022YFC2504100//National Key Research/ ; 82371124//National Nature Science Foundation of China/ ; },
mesh = {Humans ; *Dysbiosis/microbiology/immunology/therapy ; *Rhinitis, Allergic/microbiology/immunology/therapy ; *Microbiota/immunology ; Probiotics/therapeutic use ; Nasal Mucosa/microbiology/immunology ; Animals ; },
abstract = {Allergic rhinitis (AR) is a common heterogeneous chronic disease characterized by high prevalence, complex pathogenesis, and susceptibility to multiple contributing factors. Currently, its prevalence ranges from 20% to 30% in adults and reaches up to 40% in children. Extensive research has confirmed significant differences in nasal microbiota composition between AR patients and healthy individuals, most notably alterations in the abundance of four dominant phyla: Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. Among these, the most striking abundance alterations occur in Staphylococcus aureus and Streptococcus salivarius within the nasal mucosa of AR patients, suggesting a critical role of nasal microbiota in AR initiation and progression. In response, researchers have proposed microbiome-targeted therapeutic strategies. For example, nasal local administration of probiotics (e.g., Lactobacillus and Bifidobacterium) aims to reshape the nasal microbiota. Additionally, protective bacteria such as Corynebacterium accolens and Dolosigranulum pigrum can inhibit pathogenic bacteria, thereby correcting microbial dysbiosis and alleviating AR symptoms. This review summarizes the composition of the nasal microbiota, the latest research progress on its association with AR, and the underlying potential mechanisms. It provides novel insights and potential therapeutic strategies for the prevention and treatment of AR.},
}

Humans
*Dysbiosis/microbiology/immunology/therapy
*Rhinitis, Allergic/microbiology/immunology/therapy
*Microbiota/immunology
Probiotics/therapeutic use
Nasal Mucosa/microbiology/immunology
Animals

@article {pmid41465484,
year = {2025},
author = {Kim, HB and Kim, G and Park, E and Kim, H and Yu, BS and Lee, DG and Park, CH and Jo, H and Park, H},
title = {Functional Expansion of the Skin Microbiome: A Pantothenate-Producing Rothia Strain Confers Anti-Inflammatory and Photoaging-Protective Effects.},
journal = {International journal of molecular sciences},
volume = {26},
number = {24},
pages = {},
pmid = {41465484},
issn = {1422-0067},
mesh = {Humans ; *Pantothenic Acid/metabolism/pharmacology/biosynthesis ; *Skin/microbiology/radiation effects/metabolism ; *Skin Aging/drug effects/radiation effects ; *Microbiota ; *Anti-Inflammatory Agents/pharmacology/metabolism ; Keratinocytes/metabolism/drug effects ; *Micrococcaceae/metabolism/genetics ; Fibroblasts/metabolism/drug effects ; Ultraviolet Rays/adverse effects ; Skin Microbiome ; },
abstract = {The functional landscape of the skin microbiome is largely defined by dominant genera such as Cutibacterium and Staphylococcus, whereas rare commensals remain poorly understood. In this study, we identified Rothia kristinae BF00107, a skin-resident strain with a complete pantothenate biosynthesis pathway, as a novel postbiotic candidate with distinct dermatological benefits. BF00107 fermentation filtrate suppressed pro-inflammatory cytokines (IL-1β and TNF-α) in keratinocytes and restored extracellular matrix homeostasis in UVB-irradiated fibroblasts by upregulating COL1A1 expression and reducing MMP-1 levels. Consistent with the observed phenotypes, transcriptomic profiling revealed a strain-specific signature characterized by downregulation and upregulation of the expression of inflammatory mediators and barrier- and ECM-associated genes, respectively. Comparative genomics and metabolite profiling confirmed BF00107 as a unique high-pantothenate producer. Supplementation with pantothenic acid reproduced the anti-inflammatory and barrier-supporting effects of the strain, confirming its role as a key effector metabolite. Furthermore, BF00107 passed standard safety assessments, including the Human Repeat Insult Patch Test (HRIPT), Ames, and irritation tests, supporting its suitability for human applications. These findings establish the pantothenate-producing R. kristinae BF00107 as the first functionally validated Rothia strain with anti-inflammatory and photoaging-protective properties. This study expands the functional scope of the skin microbiome and highlights rare commensals as valuable reservoirs for safe, strain-specific postbiotic development.},
}

Humans
*Pantothenic Acid/metabolism/pharmacology/biosynthesis
*Skin/microbiology/radiation effects/metabolism
*Skin Aging/drug effects/radiation effects
*Microbiota
*Anti-Inflammatory Agents/pharmacology/metabolism
Keratinocytes/metabolism/drug effects
*Micrococcaceae/metabolism/genetics
Fibroblasts/metabolism/drug effects
Ultraviolet Rays/adverse effects
Skin Microbiome

@article {pmid41465447,
year = {2025},
author = {Duda-Madej, A and Viscardi, S and Łabaz, JP and Topola, E and Szewczyk, W and Gagat, P},
title = {Berberine in Bowel Health: Anti-Inflammatory and Gut Microbiota Modulatory Effects.},
journal = {International journal of molecular sciences},
volume = {26},
number = {24},
pages = {},
pmid = {41465447},
issn = {1422-0067},
mesh = {*Berberine/pharmacology/therapeutic use ; Humans ; *Gastrointestinal Microbiome/drug effects ; Animals ; *Anti-Inflammatory Agents/pharmacology/therapeutic use ; *Inflammatory Bowel Diseases/drug therapy/microbiology ; },
abstract = {Disruption of the gut-microbiome-brain axis contributes to the development of chronic inflammation, impaired intestinal barrier integrity, and progressive tissue damage, ultimately reducing quality of life and increasing risk of comorbidities, including neurodegenerative diseases. Current therapies are often limited by adverse effects and insufficient long-term efficacy, highlighting the need for more comprehensive therapeutic approaches. Berberine (BRB), a plant-derived isoquinoline alkaloid, has attracted growing attention due to its pleiotropic immunomodulatory, neuroprotective, and gut-homeostasis-modulating properties, which involve reshaping the gut microbiota and underscore its therapeutic relevance within the gut-microbiome-brain axis. The aim of this review is to synthesize current scientific evidence regarding the anti-inflammatory mechanisms of BRB in inflammatory bowel disease (IBD). We compare its activity with first-line therapies and discuss its impact on microbial composition, including the bidirectional regulation of specific bacterial taxa relevant to intestinal and systemic disorders that originate in the gut. Furthermore, we emphasize that gut bacteria convert BRB into bioactive metabolites, contributing to its enhanced intraluminal activity despite its low systemic bioavailability. By integrating molecular and microbiological evidence, this review fills a critical knowledge gap regarding the comprehensive therapeutic potential of BRB as a promising candidate for future IBD interventions. The novelty of this work lies in unifying fragmented findings into a framework that explains how BRB acts simultaneously at the levels of host immunity, microbial ecology, and neuroimmune communication-thus offering a new conceptual model for its role within the gut-microbiome-brain axis.},
}

*Berberine/pharmacology/therapeutic use
Humans
*Gastrointestinal Microbiome/drug effects
Animals
*Anti-Inflammatory Agents/pharmacology/therapeutic use
*Inflammatory Bowel Diseases/drug therapy/microbiology

@article {pmid41465322,
year = {2025},
author = {Rzeczycki, P and Pęciak, O and Plust, M and Droździk, M},
title = {Gut Microbiota in the Regulation of Intestinal Drug Transporters: Molecular Mechanisms and Pharmacokinetic Implications.},
journal = {International journal of molecular sciences},
volume = {26},
number = {24},
pages = {},
pmid = {41465322},
issn = {1422-0067},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Animals ; *Intestinal Mucosa/metabolism ; Multidrug Resistance-Associated Protein 2 ; *Membrane Transport Proteins/metabolism ; },
abstract = {Gut microbiota, through both its species composition and its metabolites, impacts expression and activity of intestinal drug transporters. This phenomenon directly affects absorption process of orally administered drugs and contributes to the observed inter-individual variability in pharmacotherapeutic responses. This review summarizes mechanistic evidence from in vitro and animal studies and integrates clinical observations in which alterations in gut microbiota are associated with changes in oral drug exposure, consistent with potential regulation of key intestinal drug transporters-such as P-glycoprotein (P-gp, ABCB1), Breast Cancer Resistance Protein (BCRP, ABCG2), MRP2/3 proteins (ABCC2/3), and selected Organic Anion-Transporting Polypeptides (OATPs, e.g., SLCO1A2, SLCO2B1)-by major bacterial metabolites including short-chain fatty acids (SCFAs), secondary bile acids, and tryptophan-derived indoles. The molecular mechanisms involved include activation of nuclear and membrane receptors (PXR, FXR, AhR, TGR5), modulation of transcriptional and stress-response pathways (Nrf2, AP-1) with simultaneous suppression of pro-inflammatory pathways (NF-κB), and post-translational modifications (e.g., direct inhibition of P-gp ATPase activity by Eggerthella lenta metabolites). The review also highlights the pharmacokinetic implications of, e.g., tacrolimus, digoxin, and metformin. In conclusion, the significance of "drug-transporter-microbiome" interactions for personalized medicine is discussed. Potential therapeutic interventions are also covered (diet, pre-/probiotics, fecal microbiota transplantation, modulation of PXR/FXR/AhR pathways). Considering the microbiota as a "second genome" enables more accurate prediction of drug exposure, reduction in toxicity, and optimization of dosing for orally administered preparations.},
}

Humans
*Gastrointestinal Microbiome/physiology
Animals
*Intestinal Mucosa/metabolism
Multidrug Resistance-Associated Protein 2
*Membrane Transport Proteins/metabolism

@article {pmid41465299,
year = {2025},
author = {Paduraru, DN and Palcau, AC and Dinca, VG and Ciuc, DM and Constantinescu, A},
title = {The Role of Gut Microbiota in Colorectal Cancer Pathogenesis: A Comprehensive Literature Review.},
journal = {International journal of molecular sciences},
volume = {26},
number = {24},
pages = {},
pmid = {41465299},
issn = {1422-0067},
mesh = {Humans ; *Colorectal Neoplasms/microbiology/pathology/etiology ; *Gastrointestinal Microbiome ; Dysbiosis/microbiology/complications ; Animals ; Carcinogenesis ; },
abstract = {Colorectal cancer (CRC) represents a significant global health burden, ranking as the third most frequently diagnosed malignancy worldwide. Emerging evidence has established a compelling association between gut microbiota dysbiosis and CRC pathogenesis, revealing complex mechanisms through which specific bacterial communities modulate carcinogenesis. This comprehensive review synthesizes current knowledge on the mechanistic contributions of gut microbiota to CRC development, with particular emphasis on key pathogenic bacteria including Fusobacterium nucleatum, Bacteroides fragilis, and Escherichia coli. We examine the molecular pathways through which these microorganisms promote tumorigenesis, including chronic inflammation induction, immune response modulation, metabolic reprogramming, and direct genotoxic effects. Furthermore, we discuss the therapeutic implications of microbiota-targeted interventions and the potential utility of microbial biomarkers for early CRC detection. Understanding the intricate host-microbiota interactions in CRC pathogenesis may facilitate the development of novel preventive strategies and therapeutic approaches for this devastating disease.},
}

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

@article {pmid41465291,
year = {2025},
author = {Chaudhuri, RK and Meyer, TA},
title = {Isosorbide Diesters: Mechanistic Insights and Therapeutic Applications in Skin and Neuroinflammatory Disorders.},
journal = {International journal of molecular sciences},
volume = {26},
number = {24},
pages = {},
pmid = {41465291},
issn = {1422-0067},
support = {None//Hallstar Beauty (United States)/ ; },
mesh = {Humans ; *Isosorbide/therapeutic use/pharmacology/chemistry/analogs & derivatives ; Animals ; *Neuroinflammatory Diseases/drug therapy ; *Esters/therapeutic use/chemistry ; *Anti-Inflammatory Agents/therapeutic use/pharmacology ; Skin/drug effects ; *Skin Diseases/drug therapy ; },
abstract = {Isosorbide fatty acid diesters constitute a novel class of bioactive compounds with emerging therapeutic applications in inflammatory and barrier-compromised disorders. Among them, isosorbide dicaprylate (IDC) and isosorbide di-linoleate/oleate (IDL) synergistically strengthen epidermal barrier integrity, enhance stratum corneum hydration, regulate keratinocyte differentiation, suppress proinflammatory signaling, and beneficially modulate the skin microbiome. Randomized, double-blind clinical trials in both pediatric and adult populations with atopic dermatitis (AD) demonstrate that topical IDC + IDL formulations significantly reduce pruritus, corticosteroid dependence, and Staphylococcus aureus colonization while improving sleep quality, disease severity scores, and overall quality of life. Extending applications within and even beyond dermatology, isosorbide dimethyl fumarate (IDMF)-a next-generation fumarate derivative designed to mitigate sensitization risk-exhibits potent anti-inflammatory and antioxidant activities through NRF2 activation and NF-κB/IRF1 suppression. Preclinical studies in psoriasis and neuroinflammatory models, including multiple sclerosis, reveal robust modulation of oxidative stress and immune pathways with improved safety and mechanistic precision compared to conventional fumarates, although its systemic use remains exploratory and requires clinical validation. Collectively, isosorbide diesters emerge as multifunctional therapeutic agents offering barrier repair, immune modulation, and inflammation control, representing promising alternatives to corticosteroids and systemic immunosuppressants across dermatologic and systemic inflammatory disorders.},
}

Humans
*Isosorbide/therapeutic use/pharmacology/chemistry/analogs & derivatives
Animals
*Neuroinflammatory Diseases/drug therapy
*Esters/therapeutic use/chemistry
*Anti-Inflammatory Agents/therapeutic use/pharmacology
Skin/drug effects
*Skin Diseases/drug therapy

@article {pmid41465268,
year = {2025},
author = {Goriuc, A and Luchian, I},
title = {Special Issue "Dental Health and Disease: From the Molecular and Pathological Perspectives".},
journal = {International journal of molecular sciences},
volume = {26},
number = {24},
pages = {},
pmid = {41465268},
issn = {1422-0067},
mesh = {Humans ; *Oral Health ; Microbiota ; },
abstract = {Oral health extends beyond aesthetics; it represents an integral component of overall health, sustained through a delicate balance among host defense mechanisms, the oral microbiome, and environmental influences [...].},
}

Humans
*Oral Health
Microbiota

@article {pmid41462374,
year = {2025},
author = {Zou, Q and Fu, B and Gou, Y and Zhong, G and Liu, Y},
title = {Vitamin D metabolites and the gut microbiota dietary index are associated with reduced all-cause mortality in US adults: a prospective cohort study.},
journal = {BMC nutrition},
volume = {11},
number = {1},
pages = {222},
pmid = {41462374},
issn = {2055-0928},
abstract = {BACKGROUND: Vitamin D and the gut microbiota are known to influence immune function, inflammation, and long-term health outcomes, including mortality. However, the interplay among vitamin D metabolites, microbiota-related dietary patterns, and mortality risk remains unclear.

METHODS: This prospective cohort study was conducted with data from 19,278 subjects enrolled in the National Health and Nutrition Examination Survey of 2005–2018. DI-GM, a surrogate measure derived from 24-h dietary recall data rather than direct microbiome sequencing, was used to evaluate the impacts of diet on the gut microbiota. The relationships and potential mediating effects were determined through Cox proportional hazards regression, restricted cubic splines, and mediation analysis. In addition, subgroup analyses were conducted to investigate the effect modifications based on age, diabetes status, and cancer or malignancy history. The study results were analyzed to gain a comprehensive understanding of the relationships under investigation.

RESULTS: Higher contents of vitamin D and its metabolites were related to a decreased risk of all-cause mortality (HR for 25-hydroxyvitamin D3: 0.60, 95% CI: 0.53–0.68; epi-25-hydroxyvitamin D3: 0.62, 95% CI: 0.54–0.71). DI-GM was inversely related to mortality risk (HR: 0.80, 95% CI: 0.71–0.91). In the mediation analysis, DI-GM accounted for less than 10% of the total effect.

CONCLUSIONS: The present study revealed the inverse relationships of vitamin D and DI-GM with mortality and that DI-GM partially mediated these relationships. The. results highlighted the potential effects of vitamin D and the gut microbiota in terms of improving survival outcomes, although further longitudinal studies are warranted to validate these relationships.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s40795-025-01211-1.},
}

@article {pmid41291108,
year = {2025},
author = {Eom, JH and Cho, MY and Choi, EM and Kim, JW and Yang, SJ and Hwang, J and Hwang, I and Lee, D and Kim, YY and Kim, HS and Baek, H and Kim, SJ},
title = {Comparative genomic analysis of hydrogen peroxide and nitric oxide metabolic pathways in Limosilactobacillus fermentum.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {45320},
pmid = {41291108},
issn = {2045-2322},
support = {2024ER050700//Korea National Institute of Health research project/ ; },
abstract = {UNLABELLED: Limosilactobacillus fermentum strains influence human health through distinct metabolic pathways; however, the genetic basis of these strain-specific functions remains unclear. This study investigated phenotypic divergence between two L. fermentum strains isolated from the human oral microbiome. Despite 98.2% average nucleotide identity, comparative genomics revealed substantial strain-specific gene repertoires (485 and 542 unique genes in DM072 and DM075, respectively). Functional characterization demonstrated that DM072 synthesizes hydrogen peroxide via pyruvate oxidase (EC 1.2.3.3; K00158), conferring strong antimicrobial efficacy against the Streptococcus mutans. Conversely, DM075 lacks this oxidative pathway but exhibits six-fold elevated nitrate reductase activity during the stationary phase. Transcriptomic profiling revealed significant temporal upregulation of glutamate synthase (gltB, p < 0.05) and alkyl hydroperoxide reductase (ahpC, p < 0.05) in DM075, indicating coordinated nitrogen assimilation and oxidative stress responses. Bioinformatic analyses identified strain-specific enzymatic profiles, including differential distributions of glycosyl hydrolases and transferases, alongside disparate acid tolerance (pH 2.5 for DM075 vs. pH 3.0 for DM072). These findings demonstrate functional specialization at the strain level within closely related taxa, highlighting the potential of DM072 as an antimicrobial probiotic for dental caries prophylaxis and DM075 as a potential cardiovascular homeostasis modulator via the nitrate–nitrite–nitric oxide pathway.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-025-29368-6.},
}

@article {pmid41467030,
year = {2025},
author = {Li, F and Wang, X and Cai, Y and Lin, Y and Tang, Y and Wang, S},
title = {Gut microbiota-derived metabolites as novel therapies for inflammatory bowel diseases: Role of nuclear receptors.},
journal = {Fundamental research},
volume = {5},
number = {6},
pages = {2622-2625},
pmid = {41467030},
issn = {2667-3258},
abstract = {Inflammatory bowel diseases (IBDs) are increasingly recognized as a pressing global health concern. The gut microbiome emerges as both a potential therapeutic target and a repository for pharmacological interventions in IBDs management. This perspective aims to elucidate the pivotal findings from recent studies concerning the anti-inflammatory properties of gut microbiota-derived metabolites (GMDMs), dissect the strengths and challenges of GMDMs as treatment strategies for IBDs, and highlight the integral role of nuclear receptors in mediating the interplay between IBD pathogenesis and GMDMs. Through the integration of these perspectives, our objective is to deepen the understanding of the therapeutic promise of nuclear receptor-targeted GMDMs, thus propelling forward the exploration and formulation of new pharmacological treatments for IBDs.},
}