@article {pmid41386516,
year = {2025},
author = {Drabesch, S and Mueller, S and Leon Ninin, JM and Planer-Friedrich, B and Kappler, A and Muehe, EM},
title = {Rising temperature and atmospheric CO2 combine to antagonistically alter Cd mobility and biogeochemistry in an agricultural soil.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {127508},
doi = {10.1016/j.envpol.2025.127508},
pmid = {41386516},
issn = {1873-6424},
abstract = {Soil cadmium (Cd) contamination threatens ecosystems and crop safety. Understanding how individual climate change factors influence soil Cd bioavailability is essential for mechanistic understanding and future risk assessments. This study examined individual and combined effects of elevated temperature (+4°C) and doubled atmospheric CO2 (800 ppmv) on soil Cd bioavailability, biogeochemistry, and greenhouse gas emissions in agricultural soils with native (0.13 mg Cd kg-[1]) and high Cd (1.5 mg Cd kg[-1]). Elevated temperature increased porewater Cd up to 50% relative to ambient, while doubled atmospheric CO2 did not alter porewater Cd. Combined future conditions increased porewater Cd by 30% relative to ambient indicating an antagonistic interaction. Doubled atmospheric CO2 enhanced microbial nitrogen fixation and reduced ammonium oxidation, increasing ammonium concentrations up to 10-fold relative to ambient. Elevated temperature stimulated microbiome activity and ammonium oxidation, leading to 1.7-fold more CO2 and 5.5-fold more N2O compared to ambient, both exceeding levels observed under combined future climate. These contrasting single-factor responses highlight the non-additive nature of combined climate factor effects. Warming alone overestimated and CO2 alone underestimated the combined impact on Cd mobility and soil biogeochemistry. Simulating multiple climate drivers is therefore essential for accurate environmental prediction and sustainable Cd management under climate change.},
}

@article {pmid41387206,
year = {2025},
author = {Wang, Z and Li, Q and Shi, M and Leite, MFA and Chen, X and Kuramae, EE and Cordovez, V and Cao, T and Zhu, C and Zhou, L and Yu, W and Tang, Z and Peng, C and Song, X},
title = {Compartmentalized Homeostasis Drives High Bamboo Forest Productivity under Nutrient Imbalance.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e17442},
doi = {10.1002/advs.202517442},
pmid = {41387206},
issn = {2198-3844},
support = {32125027//National Natural Science Foundation of China/ ; 32361143866//National Natural Science Foundation of China/ ; 32401673//National Natural Science Foundation of China/ ; LQ23C030005//Natural Science Foundation of Zhejiang Province/ ; },
abstract = {Stoichiometric homeostasis, the ability to maintain internal nutrient balance, is central to plant fitness under soil nutrient variability. While traditionally viewed as static, emerging theory posits that it is a conditionally flexible trait, though empirical evidence is scarce. Through large-scale field investigations, nutrient additions, and data synthesis, this study shows that Moso bamboo (Phyllostachys edulis), a fast-growing plant species, employs a unique compartmentalized homeostasis strategy by decoupling nitrogen (N) and phosphorus (P) regulation across tissues. It achieves strict N:P homeostasis in leaves while allowing P flexibility in woody tissues to serve as reservoirs that buffer leaves from soil P limitation and microbial competition. This mechanism, consistently observed in bamboo across wide geographical and soil nutrient gradients, yields lower leaf N:P variability than 75 out of 91 co-occurring tree species, can be one of the critical factors for sustaining ≈25% higher annual productivity than other forests (including evergreen-broadleaf, deciduous-broadleaf, and coniferous forests). These findings reconcile classical views of stoichiometric homeostasis and plasticity by demonstrating a flexible, compartmentalized mechanism that resolves growth-stability conflicts. Recognizing such flexible strategy advances the understanding of eco-evolutionary feedbacks in ecosystem stoichiometry and improves predictions of species adaptability, nutrient cycling, and carbon sequestration under global change.},
}

@article {pmid41387111,
year = {2025},
author = {Araujo, ASF and Pereira, APA and de Medeiros, EV and Mendes, LW},
title = {Root-driven microbiome memory enhances plant disease resistance.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2025.12.002},
pmid = {41387111},
issn = {1878-4372},
abstract = {Root-driven microbiome memory imprints biological and chemical legacies in soil, boosting plant disease resistance across generations. In a recent study, Wu et al. found flavonoids acting as key mediators, recruiting protective microbes and lowering pathogen severity beyond one crop cycle. Here, we highlight this concept, its limitations, and opportunities for sustainable disease resistance in agriculture.},
}

@article {pmid41386888,
year = {2025},
author = {Wu, Q and Su, S and Han, Y and Deng, S and Wang, B and She, Y and Zhang, F},
title = {Full genome sequences of two strains of Pseudomonas stutzeri isolated from oil reservoirs and their adaptation mechanisms to harsh environments.},
journal = {Journal, genetic engineering & biotechnology},
volume = {23},
number = {4},
pages = {100623},
doi = {10.1016/j.jgeb.2025.100623},
pmid = {41386888},
issn = {2090-5920},
abstract = {Pseudomonas stutzeri is a type of microorganism widely present in nature, particularly in petroleum-contaminated environments, where it exhibits a high capacity for biodegradation. In this study, two strains of Pseudomonas stutzeri 1W1-1A and DW2-1A, were isolated from oil-water samples from Dagang Oilfield and their whole genomes were sequenced. The whole genome of 1W1-1A is 4,454,378 bp in size, with a GC content of 64.23 % in its single circular chromosome; the whole genome of DW2-1A is 3,967,155 bp in size, with a GC content of 62.98 % in its single circular chromosome. Comparing these two strains with Pseudomonas sp. in the NCBI database, we counted the strains with genes related to hydrocarbon oxidation, nitrate, sulfite, and oxygen reduction in the genome and their global distribution. Genes related to hydrocarbon oxidation, nitrate, sulfite, and oxygen reduction were found in the genome, revealing the survival strategies and adaptation mechanisms of Pseudomonas in extreme oil reservoir environments, including its genomic characteristics, functional gene distribution, and tolerance to different environmental conditions. These findings enrich our understanding of the ecological adaptability and functional evolution of Pseudomonas, providing a new perspective for research in microbial ecology and environmental microbiology. The results of this study offer new strain resources and a scientific basis for microbial enhanced oil recovery (MEOR). Utilizing the hydrocarbon degradation capabilities and biosurfactant production characteristics of these strains is of great significance for microbial industrial applications such as MEOR and the remediation of petroleum-contaminated environments.},
}

@article {pmid41385904,
year = {2025},
author = {Pan, X and Elsayed, SS and van Wezel, GP and Raaijmakers, JM and Carrión, VJ},
title = {Disentangling the molecular mechanisms of disease suppression by endophytic Flavobacterium sp. 98.},
journal = {Microbiological research},
volume = {304},
number = {},
pages = {128415},
doi = {10.1016/j.micres.2025.128415},
pmid = {41385904},
issn = {1618-0623},
abstract = {Endophytic microorganisms colonize internal plant tissues and enhance host resistance to pathogens. We previously showed that endophytic Flavobacterium sp. 98 (Fl98) protects sugar beet against the fungal root pathogen Rhizoctonia solani via biosynthetic gene cluster 298 (BGC298). However, the molecular mechanisms underlying this protection remained poorly understood. Here, comparative metabolomic analyses revealed that knockout of BGC298 led to reduced production of the antifungal compound 5,6-dimethylbenzimidazole (DMB) in Fl98. We hypothesized that BGC298 is involved in regulating DMB biosynthesis and therefore contributes to Fl98's disease suppression as a novel protective mechanism. Subsequent site-directed mutagenesis of the DMB-synthase gene bluB abolished DMB production by Fl98, and both ΔBGC298 and ΔbluB mutants were compromised in protecting sugar beet seedlings in greenhouse bioassays. Bioinformatic analyses further indicated that bluB is widespread across Flavobacterium, while BGC298 is limited to a small subset of plant-associated strains. Together, our findings highlight the pivotal role of BGC298 and DMB biosynthesis in plant protection by endophytic Flavobacterium sp. 98.},
}

@article {pmid41384736,
year = {2025},
author = {Madrid-Restrepo, MA and León-Inga, AM and Peñuela-Martínez, AE and Cala, MP and Reyes, A},
title = {Metagenomic, metabolomic, and sensorial characteristics of fermented Coffea arabica L. var. Castillo beans inoculated with microbial starter cultures.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0136425},
doi = {10.1128/msystems.01364-25},
pmid = {41384736},
issn = {2379-5077},
abstract = {UNLABELLED: Coffee is one of the most important and widely consumed drinks around the world, and fermentation plays a pivotal role in shaping its quality. This research explores the impact of co-fermentation with "starter cultures" on the sensory and metabolic profiles, as well as on the dynamics of microbial communities involved in coffee processing. Freshly harvested Arabica coffee beans were subjected to two wet-fermentation processes, one inoculated with a microbial starter culture and the other undergoing spontaneous fermentation. Quantitative descriptive analysis revealed that the inoculated coffee outperformed the spontaneous fermentation in all sensory attributes, boasting higher sweetness, reduced acidity and bitterness, and the presence of consumer-preferred notes. Untargeted metabolomic analysis identified over a hundred differential metabolites distinguishing both fermentation processes in green and roasted beans. Inoculated coffee displayed elevated levels of compounds such as sucrose, mannitol, methyl phenylacetate, and organic acids like malic, citric, and quinic acid, compounds likely associated with improved sensory perception. The inoculated process was characterized by shifts in the abundance of lactic acid bacteria and Kazachstania yeasts, groups linked to desirable metabolites such as lactic, acetic, isobutyric, and hexanoic acids. Our results strongly suggest that the use of starter cultures can enhance coffee beverage quality, as reflected by standardized cupping, metabolic profiles, and microbial community dynamics. Future studies should focus on disentangling microbial contributions and metabolite pathways to inform the design of commercially viable starter cultures for coffee fermentation.

IMPORTANCE: Our study demonstrates that inoculating coffee fermentation alters the sensory qualities of coffee and reshapes the dynamics of bacterial and fungal communities during this process. We identified distinct changes in microbial diversity and metabolite composition associated with inoculation, which correlated with improved sensory attributes. In addition, we detected aminophenol and phenol at higher levels in spontaneously fermented coffees, compounds that are likely responsible for phenolic defects. To our knowledge, this is the first report directly linking these compounds to defective flavor notes in coffee. Together, these findings show that inoculation not only enhances desirable flavor profiles but may also serve as a strategy to reduce the risk of cup defects by modulating the fermentation microbiota. Our work advances the understanding of community-level microbial processes in coffee fermentation and opens opportunities for developing techniques to produce coffee with unique, high-quality, and reproducible sensory characteristics.},
}

@article {pmid41383741,
year = {2025},
author = {Song, J and He, Q and Cao, K and Song, X and Zeng, Q},
title = {Effects of continuous cropping on soil metabolomics and rhizosphere bacterial communities in Panax quinquefolius L.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1698779},
pmid = {41383741},
issn = {1664-302X},
abstract = {INTRODUCTION: Continuous cropping obstacles (CCOs) due to long-term monoculture have emerged as a pervasive challenge in contemporary agriculture worldwide. The practices of CCOs are the primary causes of restraining the Panax quinquefolius L. (P. quinquefolius) growth, whereas its underlying microbial mechanisms have not been fully elucidated.

METHODS: We investigated the effects of CCOs on soil physicochemical properties, enzyme activities, microbial community composition, and metabolite profiles in the rhizosphere of P. quinquefolius cultivated continuously for one, two, three, and four consecutive years (designated as CC1, CC2, CC3, and CC4, respectively) without crop rotation. Rhizosphere soil samples were collected from fields with different years of CCOs and analyzed for physicochemical properties and enzyme activities. Microbial community composition was assessed using Illumina high-throughput sequencing, and metabolite profiles were analyzed using non-targeted metabolomics (UPLC-MS/MS).

RESULTS: Significant decreases were observed in soil pH (12.2-28.0%), cation exchange capacity (42.6-65.5%), organic matter (8.7-27.3%), total nitrogen (7.6-27.8%), and ammonium (NH4 [+]) content (16.9-56.6%) with an increasing number of continuous cropping years. Enzymatic activities, including urease, invertase, alkaline phosphatase, catalase, protease, and polyphenol oxidase, were also reduced. The occurrence of CCOs decreased bacterial richness and number but increased bacterial diversity. Key microbial biomarkers were shifted from Gemmatimonadota, Actinobacteriota, and Proteobacteria to Acidobacteriota, Chloroflexi, and WPS-2 with P. quinquefolius CCOs. Consequently, the number of beneficial microorganisms decreased, whereas the number of pathogenic microorganisms increased. Non-targeted metabolomic profiling showed significant enantioselectivity in phenylpropanoid biosynthesis and pyrimidine metabolism. Time-series analysis revealed a decrease in metabolites classified as lipids and lipid-like molecules and an increase in organic acids, derivatives, phenylpropanoids, and polyketides with continuous cropping. Partial least squares-path modeling identified reduced soil enzymatic activity due to CCOs as the primary factor regulating soil bacterial communities and metabolites.

SIGNIFICANCE: These findings offer new insights into the microecological mechanisms of CCOs in P. quinquefolius, aiding in controlling pathogenic bacteria and maintaining soil health in agricultural systems.

CONCLUSION AND PROSPECTS: P. quinquefolius CCOs significantly alter soil physicochemical properties, microbial community structure, and metabolite profiles, leading to reduced soil fertility and increased prevalence of soil-borne diseases. Future research should focus on exploring sustainable agricultural practices, such as crop rotation and soil amendments, to mitigate these adverse effects and improve the long-term viability of P. quinquefolius cultivation.},
}

@article {pmid41383635,
year = {2025},
author = {Zhu, W and Ni, R and Cai, B and Ma, S and Jiang, J and Wang, B},
title = {In-situ diet-microbiota associations across taxonomic scales in desert-dwelling amphibians and reptiles.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf213},
pmid = {41383635},
issn = {2730-6151},
abstract = {Understanding how host and environmental factors shape gut microbiota is central to microbial ecology and evolution. However, the extent to which gut microbes covary with diet and how such variation reflects host phylogeny, remains unclear under natural conditions. Here, we used DNA metabarcoding of gut contents to analyze the dietary arthropod composition and gut microbiota of four amphibian and three reptile species from the Tarim Desert, Xinjiang, China. These species showed pronounced differences in both diet and microbial profiles. Dominant dietary arthropod families exhibited generally low overlap among species, and dietary variation did not align with host phylogeny. Interestingly, Bufotes pewzowi (amphibian) and Teratoscincus przewalskii (reptile)-the most common species in their respective groups-both primarily consumed ants (Formicidae). Conversely, gut microbial composition more closely reflected host phylogeny than diet, with a clear separation between amphibians and reptiles, particularly in the relative abundances of Bacteroidetes and the genera Bacteroides and Blautia. These findings suggest that the previously reported phylosymbiosis in these species is not primarily driven by dietary overlap. Significant diet-microbiota correlations were observed across all species and within each taxonomic class but were largely absent within species. This highlights taxonomic-level differences in the diet-microbiota relationship, indicating that diet-microbiota covariation is more pronounced over evolutionary timescales than in response to real-time dietary variation. Taken together, our results show that gut microbiota and diet exhibit distinct phylogenetic patterns, with microbiota showing both associations with diet and resilience to short-term dietary changes, underscoring the importance of considering timescales in diet-microbiota studies.},
}

@article {pmid41381925,
year = {2025},
author = {González-Villalobos, E and Aranda, A and de Almeida, ACM and Balcázar, JL},
title = {Global Transcriptomic Profiling Reveals Conserved and Phage-specific Responses to Phage Infection in Escherichia Coli.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02665-3},
pmid = {41381925},
issn = {1432-184X},
support = {792686//EU Horizon 2020 Programme (Marie Skłodowska-Curie)/ ; },
abstract = {Although phages shape bacterial evolution and physiology, the specificity of host transcriptomic responses to phage infection remains incompletely understood. Here, we performed global transcriptomic profiling of Escherichia coli exposed to two lytic phages, ΦX174 and T4, and the temperate phage λ, to explore both conserved and phage-specific host responses. All infections induced stress-related genes, including SOS and general stress pathways, along with repression of anabolic processes such as purine and amino acid biosynthesis, suggesting a metabolic shift to conserve resources. Notably, ΦX174 strongly activated the phage shock protein operon, while both ΦX174 and λ selectively induced soxS, a regulator of oxidative stress. Despite infecting the same host, each phage triggered distinct transcriptional signatures. These findings highlight the complexity of bacterial responses and the value of transcriptomics in decoding host-phage interactions, offering insights into resistance, survival, and co-evolution.},
}

@article {pmid41381498,
year = {2025},
author = {Dong, Z and Zhou, H and Cao, R and Zhang, O and Zhao, S and Lyu, P and Alcalde, R and Yang, C},
title = {Analytic Fourier ptychotomography for aberration-free and high-resolution volumetric refractive index imaging.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-67460-7},
pmid = {41381498},
issn = {2041-1723},
abstract = {Three-dimensional (3D) refractive index tomography offers label-free quantitative volumetric imaging. However, existing tomography approaches are limited by optical aberrations, limited resolution, and computational complexity. To overcome these issues, we propose Analytic Fourier Ptychotomography (AFP), a computational microscopy technique that analytically reconstructs aberration-free, complex-valued 3D refractive index distributions without iterative optimization or axial scanning. AFP employs a unique prior based on the finite sample thickness to recast the inverse scattering problem into analytically solvable linear equations. Unlike iterative methods, AFP does not require parameter tuning and computationally intensive optimizations, and can achieve efficient, robust, and generalizable image reconstructions across diverse samples and systems. We experimentally demonstrated that AFP greatly enhanced image quality and resolution under various aberration conditions across a range of applications. AFP corrected aberrations associated with 25 Zernike modes (with maximal phase difference of 2.3π and maximal Zernike coefficient value of 4), extended the synthetic numerical aperture from 0.41 to 0.99, and provided a two-fold resolution enhancement in all directions. With its simplicity, robustness, and broad applicability, AFP offers a user-friendly imaging platform for quantitative 3D analysis in biology, microbial ecology, and clinical science.},
}

@article {pmid41378987,
year = {2025},
author = {Niu, S and Al, MA and Zhang, D and Ming, Y and Liu, H and Zhu, W and Li, M and Yu, X and Niu, M and Wu, K and Xie, W and He, Z and Yan, Q},
title = {Assembly and interactions of denitrifying and anammox communities in a typical eutrophic lake.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnaf139},
pmid = {41378987},
issn = {1574-6968},
abstract = {Nitrogen removal is crucial for controlling nitrogen levels in eutrophic lakes and depends on the high transformation capacity of nitrogen-cycling microorganisms. However, the assembly mechanisms and interactions of nitrogen removal microbial communities in lake water remain unclear. This study aimed to clarify how nitrogen levels influence the diversity, interactions, and assembly of denitrifying and anaerobic ammonia oxidation (anammox) communities. We collected lake water from different areas in a typical eutrophic lake and investigated the nitrogen removal bacterial communities by high-throughput sequencing of two representative functional genes (nirS and hzsB). Our results indicated that the α-diversity of anammox bacteria was higher in sites with high concentration of nitrogen (> 1.5 mg/L) than in sites with low concentration of nitrogen (< 1.5 mg/L). Anammox bacteria in high-nitrogen sites were dominated by the potential keystone taxon Candidatus Brocadia. Co-occurrence network analysis revealed that low-nitrogen sites had more negative connections between denitrifying and anammox communities. Moreover, total nitrogen and electrical conductivity were key factors determining community structure. Microbial community assembly analysis indicated that both denitrifying and anammox communities were primarily governed by stochastic processes across different nitrogen levels. This study enhanced our understanding of microbial community dynamics in nitrogen removal processes in eutrophic lakes.},
}

@article {pmid41377758,
year = {2026},
author = {Benjamin, K and Yuan, Q and Boyer, J},
title = {Increased gut Saccharomyces and decreased pathogenic fungi associated with food protein-induced enterocolitis syndrome resolution.},
journal = {The journal of allergy and clinical immunology. Global},
volume = {5},
number = {1},
pages = {100598},
pmid = {41377758},
issn = {2772-8293},
abstract = {BACKGROUND: Food protein-induced enterocolitis syndrome (FPIES) is a non-IgE-mediated allergy, primarily affecting infants and children, with potentially severe gastrointestinal impacts. As with other allergic diseases, the cause of FPIES is unknown. Preliminary research suggests that the gut microbiome may play a role in FPIES, as well as other allergy, yet data on the mycobiome are limited.

OBJECTIVE: We sought to examine the role of the gut mycobiome in FPIES by comparing the stool mycobiome of children with FPIES to that of children who have outgrown FPIES.

METHODS: Caregivers of children with FPIES and children who had outgrown FPIES completed a demographic and lifestyle survey. DNA was extracted and sequenced from stool samples of 23 children with FPIES and 17 children with resolved FPIES. Fungal diversity and composition between the 2 groups were compared using QIIME2 (Quantitative Insights Into Microbial Ecology 2).

RESULTS: Children with resolved FPIES had significantly more Saccharomyces than children with current FPIES. Children with current FPIES had significantly more diverse samples and included opportunistic pathogens, such as Candida spp. Children with resolved FPIES reported significantly less infant antibiotic usage and proton pump inhibitor usage.

DISCUSSION: This study identified distinct mycobiome profiles in children with current versus resolved FPIES. Resolved FPIES was associated with Saccharomyces enrichment, whereas children with current FPIES had more diverse, opportunistic pathogen-associated communities and greater infant antibiotic and proton pump inhibitor usage. Although these associations do not establish causality, they underscore the need for larger, longitudinal studies to determine whether the mycobiome and early-life exposures influence FPIES outcomes, because it could have implications for treatment and prevention.},
}

@article {pmid41376875,
year = {2026},
author = {Yadav, BNS and Sharma, P and Maurya, S and Yadav, A and Tiwari, N and Reddy, MS and Yadav, RK},
title = {Spatial and seasonal variations of active micro-eukaryotic community structure in heavy metal-contaminated soils.},
journal = {3 Biotech},
volume = {16},
number = {1},
pages = {6},
pmid = {41376875},
issn = {2190-572X},
abstract = {UNLABELLED: Heavy metal contamination of soil poses a significant hazard to the environment. However, numerous eukaryotic microbes can sustain themselves and thrive in such polluted soils, playing a pivotal role in transforming heavy metal contaminants into more stable and less toxic forms. This study employed an amplicon-based metatranscriptomic approach to investigate the active micro-eukaryotic community structure in heavy metal-contaminated soils across two locations in India, KJ (Jajmau) and UZ (Zawar Mines), during two different seasons (spring and autumn). The diversity assessment targeted the V4 hypervariable region of the 18S rRNA gene, amplified from reverse-transcribed RNA. The supergroup Opisthokonta was found to be dominant across all soil samples, constituting a significant proportion of the eukaryotic community. The microbial communities exhibited clear seasonal variation. In UZ, the genera Aplanochytrium and Colpoda dominated in spring, whereas Hypocreales prevailed in autumn. In KJ, Chlorella, Acari, and Colpoda dominated in spring, while Acari remained dominant in autumn. Regardless of seasonal or spatial fluctuations, 44 genera were found to be common across all samples. Alpha and beta diversity measures, along with hierarchical clustering, network analysis, heatmap visualization, and Principal Component Analysis (PCA), provided strong support for the variations in biodiversity and community organization across the datasets. The ecological significance of these findings lies in demonstrating how micro-eukaryotic communities reorganize spatially and seasonally to maintain resilience in contaminated soils. Such adaptive associations highlight their potential role in natural attenuation and provide a foundation for developing targeted bioremediation strategies by leveraging stress-adapted micro-eukaryotes.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-025-04605-x.},
}

@article {pmid41373555,
year = {2025},
author = {Zhang, J and Shen, J and Ji, L and Tan, P and Liu, C and Zhang, X and Ma, X},
title = {Lacticaseibacillus rhamnosus MS27 Potentially Prevents Ulcerative Colitis Through Modulation of Gut Microbiota.},
journal = {International journal of molecular sciences},
volume = {26},
number = {23},
pages = {},
doi = {10.3390/ijms262311397},
pmid = {41373555},
issn = {1422-0067},
mesh = {Animals ; *Colitis, Ulcerative/prevention & control/microbiology/chemically induced ; *Gastrointestinal Microbiome/drug effects ; *Lacticaseibacillus rhamnosus/physiology/isolation & purification ; *Probiotics/pharmacology/therapeutic use ; Mice ; RNA, Ribosomal, 16S/genetics ; Disease Models, Animal ; Dextran Sulfate ; Male ; },
abstract = {(1) This study explored Lacticaseibacillus rhamnosus MS27, a newly isolated strain, as a potential probiotic candidate for alleviating the onset and severity of ulcerative colitis (UC). (2) L. rhamnosus MS27 was isolated and subjected to biochemical identification, antibiotic sensitivity testing, and antibacterial activity assessment. Dextran sulfate sodium (DSS) colitis model mice were used to evaluate its alleviating effects. In this study, 16S rRNA microbiome and eukaryotes reference transcriptome analyses were conducted to investigate its impact on intestinal microbial ecology and potential molecular mechanisms. (3) L. rhamnosus MS27 exhibits high acid tolerance at pH 3.23 and maintains a high viable bacterial count for 24 h. It can utilize sucrose, lactose, maltose, inulin, esculin, salicin, and mannitol but not raffinose, and it is sensitive to carbenicillin, erythromycin, tetracycline, chloramphenicol, clindamycin, and penicillin. It effectively increases the abundance of beneficial microbes, particularly Akkermansia, Muribaculaceae, and Limosilactobacillus reuteri (p < 0.05), while significantly reducing microorganisms linked to human pathogens causing diarrhea and gastroenteritis (p < 0.05). Transcriptomic analysis demonstrated that the expression levels of Igkv16-104 and C1qtnf3 were significantly downregulated in the presence of L. rhamnosus MS27 treatment compared to DSS treatment alone (p < 0.05). Further analysis revealed significant differences in genes related to immune functions, antigen presentation, and immune cell markers, indicating potential protein-protein interaction networks, particularly among genes of the major histocompatibility complex (MHC). (4) L. rhamnosus MS27, as a novel strain, demonstrates a significant capacity to alleviate inflammatory phenotypes. L. rhamnosus MS27 exhibits distinctive metabolic characteristics in lactic acid utilization, acetic acid and oleic acid production. Furthermore, it contributes to systemic homeostasis regulation by modulating Turicibacter to link intestinal microbiota composition with host immune function.},
}

Animals
*Colitis, Ulcerative/prevention & control/microbiology/chemically induced
*Gastrointestinal Microbiome/drug effects
*Lacticaseibacillus rhamnosus/physiology/isolation & purification
*Probiotics/pharmacology/therapeutic use
Mice
RNA, Ribosomal, 16S/genetics
Disease Models, Animal
Dextran Sulfate
Male

@article {pmid41373452,
year = {2025},
author = {Mehelleb, D and Ghidouche, A and Baldi, S and Djoudi, F and Bertorello, S and Di Gloria, L and Ramazzotti, M and Niccolai, E and Madaoui, M and Takbou, I and Tliba, S and Amedei, A},
title = {Specific Intratumoral Microbiome Signatures in Human Glioblastoma and Meningioma: Evidence for a Gut-Brain Microbial Axis.},
journal = {International journal of molecular sciences},
volume = {26},
number = {23},
pages = {},
doi = {10.3390/ijms262311290},
pmid = {41373452},
issn = {1422-0067},
support = {THE-Tuscany Health Ecosystem-ECS00000017-CUP B83C22003920001; #NEXTGENERA-TIONEU (NGEU)//European Union/ ; National Recovery and Resilience Plan (NRRP), project MNESYS (PE0000006) - A Multiscale in-tegrated approach to the study of the nervous system in health and disease (DR. 1553 11.10.2022)//Ministero dell'università e della ricerca/ ; },
mesh = {Humans ; *Meningioma/microbiology/pathology ; *Glioblastoma/microbiology/pathology ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; *Brain Neoplasms/microbiology/pathology ; *Meningeal Neoplasms/microbiology ; Aged ; Adult ; Bacteria/genetics/classification ; Case-Control Studies ; },
abstract = {Brain tumors (BTs), including glioblastoma (GBM) and meningioma (MGM), contribute significantly to the global cancer burden. The microbiome has been implicated in carcinogenesis, yet its role in BTs remains underexplored. We performed 16S rRNA gene sequencing of the gut microbiota (GM) and intratumoral microbiome (ItM) from fresh tissue samples of 9 patients with GBM and 18 with MGM. 12 age- and sex-matched healthy controls (HCs) were also enrolled. GM profiling revealed reduced alpha diversity and distinct microbial communities in BT patients versus HCs. Notably, Verrucomicrobiota and Synergistaceae were enriched, while Lachnospiraceae, Peptostreptococcaceae, and Muribacter spp. were depleted. GBM patients showed reductions in Peptostreptococcaceae and the Eubacterium hallii group, while MGM patients had increased Synergistia and Erysipelatoclostridium. Compared with MGM, GBM patients were enriched in Peptostreptococcales-Tissierellales, Coprobacillus, and Peptoniphilus but depleted in Weissella. Venn analysis revealed 176 genera shared across groups with unique taxa distinguishing tumor patients and HCs. ItM profiling revealed enrichment of Proteobacteria, Actinomycetota, and Campylobacterota in GBM, while MGM contained higher levels of Bacillota and Bacteroidota. GBM tissues harbored Burkholderia-Caballeronia-Paraburkholderia, Helicobacter, and Leifsonia, whereas MGM tissues were dominated by Bacteroides and Blautia. Notably, stool and tumor samples shared 91 genera in GBM and 105 in MGM. This study provides novel insights by (i) characterizing ItM from fresh samples, (ii) comparing ItM profiles of GBM and MGM, (iii) linking GM and ItM within the same patients, and (iv) suggesting potential clinical implications for BT management.},
}

Humans
*Meningioma/microbiology/pathology
*Glioblastoma/microbiology/pathology
*Gastrointestinal Microbiome/genetics
Female
Male
Middle Aged
RNA, Ribosomal, 16S/genetics
*Brain Neoplasms/microbiology/pathology
*Meningeal Neoplasms/microbiology
Aged
Adult
Bacteria/genetics/classification
Case-Control Studies

@article {pmid41369196,
year = {2025},
author = {Gundrum, J and Ramirez-Puebla, ST and Mark Welch, JL and Borisy, GG},
title = {Slicing overcomes the bacterial cell wall barrier to fluorescence in situ hybridization.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0200125},
doi = {10.1128/spectrum.02001-25},
pmid = {41369196},
issn = {2165-0497},
abstract = {UNLABELLED: Simultaneous visualization of all bacterial species in a polymicrobial biofilm by fluorescence in situ hybridization (FISH) remains a challenge because bacterial taxa respond differently to the hybridization procedure. This heterogeneity is due, in part, to the cell wall barrier of Gram-positive taxa. Enzymatic procedures required to permeabilize the cell walls of Gram-positive microbes can result in the disruption or loss of Gram-negative bacteria. Here, we demonstrate a procedure that enables the hybridization of difficult-to-hybridize bacteria while preserving the microarchitecture of all bacteria within a biofilm. The key feature of the procedure is to physically cut through the cell wall, thus allowing probe entry. We first embed the sample in a covalently crosslinked, glycol methacrylate resin to preserve the structure of the biofilm. Embedment is followed by sectioning and hybridization of material with the methacrylate still in place. We tested the procedure on common oral species, including difficult Gram-positive taxa, and found marked improvement in hybridization; both average signal intensity and homogeneity of hybridization were improved as compared to standard whole cell mount procedures. Our results confirm that the cell wall is the major barrier preventing efficient hybridization in whole mount samples. By physically overcoming the cell wall barrier, our protocol provides a universal procedure to visualize all bacteria in a polymicrobial community.

IMPORTANCE: It has long been recognized that the major barrier to efficient in situ hybridization of bacteria is the cell wall, with Gram-positive bacteria generally being the most problematic. Because enzymatic methods that facilitate hybridization of Gram-positive bacteria can result in the loss of Gram-negative bacteria, visualization of both kinds of bacteria simultaneously is often not feasible. In this study, we use embedding and sectioning to establish a universal approach for the simultaneous visualization of all bacteria within a microbial community while preserving its microarchitecture. We show that the mechanism underlying the approach is the physical slicing of the bacterial cell, thus obviating the barrier posed by the cell wall. These findings will benefit researchers within the microbiology community interested in complex microbial communities.},
}

@article {pmid41368505,
year = {2025},
author = {Di Leo, D and Nilsson, E and Krinos, A and Pinhassi, J and Lundin, D},
title = {The Nextflow nf-core/metatdenovo pipeline for reproducible annotation of metatranscriptomes, and more.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20328},
pmid = {41368505},
issn = {2167-8359},
mesh = {*Software ; Reproducibility of Results ; Workflow ; *Transcriptome ; *Computational Biology/methods ; *Molecular Sequence Annotation/methods ; *Metagenomics/methods ; },
abstract = {Metatranscriptomics-the sequencing of community RNA-has become a popular tool in microbial ecology, proving useful for both in situ surveys and experiments. However, annotating raw sequence data remains challenging for many research groups with limited computational experience. Standardized and reproducible analyses are important to enhance transparency, comparability across studies, and long-term reproducibility. To simplify metatranscriptome processing for biologists, and to promote reproducible analyses, we introduce nf-core/metatdenovo, a Nextflow-based workflow. Nextflow pipelines run on different computing platforms, from standalone systems to high-performance computing clusters and cloud platforms (e.g., AWS, Google Cloud, Azure) and use container technology such as Docker or Singularity to reproducibly provision software. Biologists can access the pipeline using either the command line or the Seqera platform, which provides a web browser-based interface to Nextflow pipelines. Collaborating with nf-core ensures high-quality, documented, reproducible workflows. Our nf-core/metatdenovo pipeline adheres to these established standards, enabling FAIR metatranscriptome de novo assembly, quantification, and annotation.},
}

*Software
Reproducibility of Results
Workflow
*Transcriptome
*Computational Biology/methods
*Molecular Sequence Annotation/methods
*Metagenomics/methods

@article {pmid41367422,
year = {2025},
author = {Yu, H and Guo, Y and Li, J and Fu, R and Zhang, Y and Guo, W},
title = {Disruption of the gut bile acid-microbiota axis precedes severe bronchopulmonary dysplasia in preterm infants.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1705965},
pmid = {41367422},
issn = {1664-302X},
abstract = {BACKGROUND: Bronchopulmonary dysplasia (BPD) remains a major cause of morbidity in preterm infants, yet current diagnostic criteria are delayed and underlying mechanisms are incompletely defined. Evidence suggests that intestinal dysbiosis may influence pulmonary outcomes via the gut-lung axis, but the metabolic mediators of this interaction remain unclear.

METHODS: We conducted a prospective cohort study of 50 preterm infants (≤ 32 weeks gestation), stratified by BPD severity at 36 weeks. Stool samples collected on postnatal day 7 underwent 16S rRNA sequencing and targeted bile acid metabolomics. Differential features were identified via multivariate statistics and LEfSe. Spearman correlation analysis explored bile acid-microbiota interactions. An interpretable machine learning model (XGBoost) incorporating bile acid and microbial features was developed and validated using five-fold cross-validation and an independent test set.

RESULTS: Infants with severe BPD showed significantly reduced levels of 16 bile acids-including primary, secondary, and sulfated species-compared to non-BPD controls. Gut microbiome β-diversity differed significantly among groups, with enrichment of opportunistic Proteobacteria (e.g., Brevundimonas) in severe BPD. Negative correlations were observed between depleted bile acids and enriched bacterial genera. The XGBoost model predicted BPD severity with 80% accuracy (AUC = 0.91), leveraging key features such as chenodeoxycholic acid (CDCA), hyocholic acid (HCA), and Brevundimonas.

CONCLUSIONS: Preterm infants who develop severe BPD exhibit early disruption of the bile acid-microbiota axis, characterized by reduced bile acid levels and enrichment of opportunistic taxa. Integrating these features within interpretable machine-learning models enables accurate early risk stratification and provides mechanistic insights beyond traditional inflammation-based frameworks. Validation in larger, multicenter cohorts is warranted to refine biomarker panels and explore targeted interventions that modulate bile acid signaling or microbial ecology to prevent or attenuate BPD.},
}

@article {pmid41366526,
year = {2025},
author = {Zhang, Y and Zhou, J and Wu, M and Wang, Z and Zhang, N and Wang, W},
title = {Impact of Different Aquaculture Densities on the Growth Performance and Intestinal Health of Triploid Rainbow Trout (Oncorhynchus mykiss) Fry in High-altitude Environments.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02653-7},
pmid = {41366526},
issn = {1432-184X},
abstract = {The high-altitude regions of the Tibet Autonomous Region possess abundant cold-water resources, with annual average water temperatures suitable for culturing triploid rainbow trout. However, environmental challenges-including low atmospheric pressure, hypoxic water conditions, and significant diurnal temperature fluctuations-necessitate precise optimization of stocking density. Inadequate densities result in suboptimal resource utilization, whereas excessive densities induce chronic stress, leading to suppressed growth, reduced survival, and intestinal microbiota dysbiosis. Currently, research on appropriate stocking densities under these specific conditions remains limited. This study investigated the effects of stocking density on growth performance, intestinal microbiota, and tissue health of triploid rainbow trout, to identify the optimal density to support sustainable aquaculture in high-altitude plateau areas. Three stocking densities were tested over a 60-day culture period in 0.25 m[3] cylindrical tanks (radius 0.45 m, water depth 0.45 m, adjusted for internal volume): Low-Density (LD, 100 fish/barrel), Medium-Density (MD, 200 fish/barrel), and High-Density (HD, 300 fish/barrel). Results demonstrated that the final body weight (Wt) and specific growth rate (SGR) in the LD treatment were significantly higher than those in the HD group (Wt: P ≤ 0.009; SGR: P ≤ 0.019). Survival rate was also significantly greater in the LD treatment compared to HD (P < 0.036), with values of 84.67%, 80.83%, and 72.67% for LD, MD, and HD, respectively. Alpha diversity of both water and gut microbial communities varied with stocking density. Principal component analysis (PCA) revealed differentiated clustering of microbial communities in water and the intestine across density treatments (Water: P = 0.35; intestinal microbiota: P = 0.7). The dominant phyla in aquatic and intestinal microbiomes were Proteobacteria, Firmicutes, and Bacteroidetes. In intestinal samples, the genus Pseudomonas was significantly more abundant in the HD and MD treatments than in the LD treatment. Co-occurrence network analysis revealed a higher average degree in LD and MD treatments, suggesting enhanced stability of microbial ecosystems in both the intestine and water under these conditions. In conclusion, low and medium stocking densities are more suitable for cultivating triploid rainbow trout in high-altitude plateau environments. These findings provide a scientific basis for ecologically sound, efficient, and healthy aquaculture practices for this species in alpine regions.},
}

@article {pmid41365804,
year = {2025},
author = {Thompson, AR and Adams, BJ and Hogg, ID and Yooseph, S},
title = {Evidence for Trace Gas Metabolism and Widespread Antibiotic Synthesis in an Abiotically Driven, Antarctic Soil Ecosystem.},
journal = {Environmental microbiology reports},
volume = {17},
number = {6},
pages = {e70249},
doi = {10.1111/1758-2229.70249},
pmid = {41365804},
issn = {1758-2229},
support = {ANT 2133685//National Science Foundation/ ; OPP-2224760//National Science Foundation/ ; DBI-2400009//National Science Foundation/ ; OAC-2408259//National Science Foundation/ ; OPP-1043681//National Science Foundation/ ; OPP-1559691//National Science Foundation/ ; OPP-2129685//National Science Foundation/ ; //Antarctica New Zealand (Event K024)/ ; //New Zealand Antarctic Research Institute (Event K024)/ ; //Monte L. Bean Life Science Museum, the Department of Biology, Brigham Young University/ ; //Kravis Department of Integrated Sciences, Claremont McKenna College/ ; },
mesh = {Antarctic Regions ; *Soil Microbiology ; *Bacteria/metabolism/genetics/classification/isolation & purification ; Metagenome ; *Anti-Bacterial Agents/biosynthesis ; Ecosystem ; Soil/chemistry ; *Gases/metabolism ; },
abstract = {The McMurdo Dry Valleys (MDVs) of Antarctica are a uniquely pristine, low-biodiversity model system for understanding fundamental ecological phenomena, the impact of a warming climate on ecosystem functioning, community structure and composition and the dynamics of adaptation. Despite the scientific value of this system, we still know little about the functional ecology of its biota, especially the bacteria. Here, we analysed the bacterial taxonomic and functional diversity of 18 shotgun metagenomes using the VEBA metagenome processing pipeline. We recovered 701 medium-to-high quality metagenome-assembled genomes (MAGs) (≥ 50% completeness and contamination < 10%) and 201 high-quality MAGs (≥ 80% completeness and < 10% contamination), almost 50% more than found in similar sites previously. We found that: (1) community composition shifts along environmental gradients correlated with soil moisture, elevation and distance to the coast; (2) many MDV bacteria are capable of performing trace gas metabolism; (3) genes associated with antibiotic-mediated competitive interactions (e.g., antibiotic biosynthesis and antibiotic resistance genes) are widespread; and (4) MDV bacteria employ survival strategies common to bacteria in similarly extreme environments. This study provides novel insight into microbial survival strategies in extreme environments and lays the groundwork for a more comprehensive understanding of the autecology of MDV bacteria.},
}

Antarctic Regions
*Soil Microbiology
*Bacteria/metabolism/genetics/classification/isolation & purification
Metagenome
*Anti-Bacterial Agents/biosynthesis
Ecosystem
Soil/chemistry
*Gases/metabolism

@article {pmid41364266,
year = {2025},
author = {Carrasco, N and Miranda, MH and Aristimuño Ficoseco, C and Nader-Macías, MEF and LeBlanc, JG},
title = {Lactic acid bacteria: potentials in canine formulas for puppies.},
journal = {Veterinary research communications},
volume = {50},
number = {1},
pages = {70},
pmid = {41364266},
issn = {1573-7446},
support = {PICT 2018-00473//MINCYT-ANPCYT:/ ; 2019-00942 and 2021-00071//Mincyt-Anpcyt/ ; },
mesh = {Animals ; Dogs/microbiology ; *Probiotics ; *Animal Feed/microbiology/analysis ; *Lactobacillales/physiology ; },
abstract = {The use of probiotics and natural nutraceuticals with demonstrated therapeutic effects for companion animals is becoming increasingly popular in the veterinary community. Probiotics are alternative to antibiotics, which produce adverse effects, such as promoting bacterial resistance and altering the intestinal microbial ecology and in turn affecting the animal's health. In this study, the in vitro safety and technological characteristics of previously isolated beneficial canine strains were evaluated for the design of a probiotic formulation for dogs. The screening of inhibitory substances production was performed in 100 isolates by plate diffusion technique. 30 strains were pre-selected to evaluate their in vitro safety and innocuity by phenotypic and genotypic antibiotic resistance and expression of pathogenicity enzymes related to virulence factors. Finally, 10 were selected to assay their tolerance to gastrointestinal conditions and stress situations such as high temperatures and solute concentrations by microplate assays. Compatibility between the selected strains was also determined in order to include them in a probiotic multi-strain formulation for canines. According to the results obtained, some strains showed inhibitory activity against common pathogens, and 38% were able to produce H2O2. Antibiotic resistance genes were detected in only one of the selected strains, none evidenced gelatinase or lecithinase activity and most isolates showed alpha and gamma hemolysis. Resistance to gastrointestinal tract and stress conditions was strain dependent. The compatible strains with complementary beneficial characteristics were: Lactobacillus johnsonii 67, Lactiplantibacillus plantarum 74, Ligilactobacillus salivarius 84 and Pediococcus acidilactici 81 and are being included in the design of a probiotic formulas to be evaluated in small dogs.},
}

Animals
Dogs/microbiology
*Probiotics
*Animal Feed/microbiology/analysis
*Lactobacillales/physiology

@article {pmid41364243,
year = {2025},
author = {Xie, T and Lin, Y and Jia, P and Li, X},
title = {Warming Promotes Deterministic Assembly of Bacterial and Fungal Communities in Drylands.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02668-0},
pmid = {41364243},
issn = {1432-184X},
support = {32061123006//National Natural Science Foundation of China/ ; },
abstract = {Warming is altering the functioning of desert ecosystems in global drylands. Microbial communities are crucial for maintaining these ecosystems, yet how their co-occurrence networks and assembly mechanisms respond to warming remains unclear. Using 16 S and ITS rRNA amplicon sequencing, we examined bacterial and fungal community composition and structure. Further, we investigated cross-trophic bacterial-fungal interactions via inter-domain ecological network analysis. Warming significantly altered the diversity, composition, and structure of both bacterial and fungal communities. It increased bacterial network complexity but simplified the fungal network. Notably, warming enhanced cross-trophic interactions between bacteria and fungi, facilitating the maintenance of microbial hierarchical interactions, particularly bacterial network complexity. However, microbial keystone taxa declined dramatically under warming, 41.18% of these belonged to Ascomycota. Neutral community models and normalized stochastic ratio-based analyses revealed that deterministic processes dominated community assembly, with warming increasing their relative importance by 8-46%. This suggests a potential deterministic environmental filtering induced by warming. Collectively, these findings advance our understanding of the ecological mechanisms and microbial interactions underpinning rhizospheric communities in drylands under future climate change.},
}

@article {pmid41363836,
year = {2025},
author = {Wang, B and Zhang, J and Zhu, X and Wang, Y and Teng, HH},
title = {Mineral substrates as evolutionary drivers of soil microbial diversity through the rare biosphere.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0201125},
doi = {10.1128/aem.02011-25},
pmid = {41363836},
issn = {1098-5336},
abstract = {UNLABELLED: Minerals are fundamental yet underappreciated drivers of microbial ecology. Traditionally viewed as passive nutrient sources or inert scaffolds, their broader ecological roles remain poorly defined. This study investigates the evolutionary influence of substrates (minerals and rocks) on soil bacterial communities through serial passage evolution experiments. Soil-derived microbial consortia from three distinct locations were exposed to nutritive (olivine, granite, diorite) and non-nutritive (quartz, kaolinite, montmorillonite) substrates under nutrient-rich conditions to isolate substrate-specific effects. Results revealed systemic variations of community structure across all treatments, characterized by elevated Firmicutes/Bacteroidetes ratio and taxonomic changes predominantly driven by rare taxa. These discoveries indicate that, under the influence of substrates, the communities shifted toward ones that preferentially utilize more labile carbon. Crucially, the acute responsiveness of rare taxa to mineral-induced environmental selection suggests that, although abundant taxa appeared to maintain core community functions, the rare biosphere facilitated niche specialization and functional diversification. These findings position minerals as dynamic drivers of microbial ecology and evolution, highlighting the mineralosphere as a critical microhabitat where abiotic properties govern biodiversity, functional redundancy, and evolutionary innovation in soil ecosystems.

IMPORTANCE: Even under nutrient-rich conditions, non-nutritive and chemically inert minerals, exemplified by quartz, actively reshape microbial community assembly. Through controlled serial-passage experiments, we show that distinct substrates selectively enrich rare biosphere members that expand functional potential and seed adaptation, while dominant taxa sustain core processes. These results reveal that mineral surface properties and physical interfaces, rather than nutrient supply, govern microbial diversification and evolutionary trajectories. Accordingly, the mineralosphere emerges as a dynamic microhabitat where abiotic complexity regulates biodiversity, metabolism, and long-term community succession. This reframes minerals and rocks as active ecological and evolutionary agents, bridging geomicrobiology and evolutionary ecology, with implications for soil health, biogeochemical cycling, and the origin and maintenance of microbial diversity.},
}

@article {pmid41363449,
year = {2025},
author = {Meyer, KM and Lindow, SE},
title = {Microbial dispersal from surrounding vegetation influences phyllosphere microbiome assembly of corn and soybean.},
journal = {mBio},
volume = {},
number = {},
pages = {e0333525},
doi = {10.1128/mbio.03335-25},
pmid = {41363449},
issn = {2150-7511},
abstract = {Non-crop plants surrounding agricultural fields provide numerous ecological services to crops but have rarely been considered a source of microorganisms during the early stages of crop growth. In this study, we test whether crops in close proximity to surrounding woodland habitat fragments develop a denser microbiome that more closely resembles the microbiome composition of the surrounding vegetation than plants farther away. We sampled epiphytic bacteria from corn and soybean plants weekly for 4 (corn) and 3 (soybean) weeks during early development using a spatially explicit design, and on the final time point, we sampled additional cohorts of younger leaves. To contextualize the source strength of the surrounding vegetation, we also sampled soil at each sampling location. Both crop species exhibited a microbiome density gradient and a decay of microbiome similarity to the surrounding vegetation over a distance of 100 m from the vegetation at many time points. Phyllosphere microbiome similarity to the soil tended to increase into the field interior. The strength of host microbiome filtering also depended on the proximity to the surrounding vegetation, with intermediate to most distant locations exhibiting the highest values of host filtering. Last, the microbiomes of younger leaves tended to more closely resemble those of the older surrounding conspecific leaves than the soil or surrounding woodland vegetation. Overall, our study demonstrates that dispersal of bacteria from nearby leaves can shape the abundance and composition of developing crop phyllosphere microbiomes and highlights the diminishing role that soil plays when plant sources are closer or more abundant.IMPORTANCEA central concern in microbial ecology is understanding the sources of microbial colonists and how proximity to such sources impacts community assembly. This area of research is especially important for plants during early stages of development, where the arrival of leaf-specialized bacteria plays an influential role in priming plant immunity and consequently promoting disease resistance. In this study, we test the effect of dispersal from surrounding vegetation on the phyllosphere assembly of corn and soybean using a time series over the early stages of growth. Our work demonstrates that at these early developmental stages, non-crop vegetation surrounding croplands acts as a meaningful source of phyllosphere microorganisms. We further show that the influence of soil on the phyllosphere depends on host proximity to surrounding vegetation and that microbiomes of young leaves emerging on more mature plants tend to be more influenced by older surrounding crop leaves than soil or non-crop leaves.},
}

@article {pmid41359884,
year = {2025},
author = {Zhang, Q and Zhou, Z and Cheung, YM and Yeung, HW and Li, M and He, C and Tian, XY and Li, C and Wong, WT},
title = {Hydroxylation-Driven Microbial and Metabolic Reshaping: Coumarin Derivatives as Novel Prebiotics for Aging Gut Health.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c10344},
pmid = {41359884},
issn = {1520-5118},
abstract = {This study aimed to investigate the therapeutic potential of three naturally occurring coumarin derivatives─coumarin, umbelliferone, and esculetin, which exhibit distinct hydroxylation patterns in mitigating age-related gut dysbiosis through in vitro colonic fermentation models. By integrating antioxidant profiling, short-chain fatty acid (SCFA) profiling, 16S rRNA sequencing, and metabolomics, we assessed their structural specificity in modulating microbial ecology and metabolic pathways. Results demonstrated a hydroxylation-dependent hierarchy in antioxidant capacity and differential regulation of SCFA production. Coumarin partially enriched g__Turicimonas but showed limited SCFA induction, whereas umbelliferone selectively enhanced butyrate synthesis and enriched g__Bacteroides. Esculetin exhibited the broadest impact, characterized by both increased acetate and propionate levels and the concurrent enrichment of g__Ileibacterium and g__Enterococcus. Metabolomic profiling further revealed that three coumarins released antioxidant metabolites, correlating with microbiota-driven detoxification. These findings highlight hydroxylated coumarins as promising prebiotics that counter age-related dysbiosis via multitarget microbiota-metabolite modulation, providing a mechanistic basis for antiaging strategies.},
}

@article {pmid41359033,
year = {2025},
author = {ElKhouri-Vidarte, N and Useros, F and Lara, E},
title = {Beneath the Cedars: Exploring the Water-Energy Balance on Arcellinida Biodiversity in Lebanon's Cedar Forests.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02666-2},
pmid = {41359033},
issn = {1432-184X},
abstract = {The distribution of diversity in function of climate has been largely studied in plants and animals, leading to a large body of literature on macroecological rules applied to large geographic scales. However, the applicability of these rules to microbes has almost never been tested at local scales. Arcellinida are a diverse group of protists known to be narrow ecological specialists and constitute therefore an excellent group to test general rules validated on "macrobes", like the water-energy balance that stipulates that biodiversity peaks with humidity and temperature. In order to test that hypothesis, we collected 122 samples from four cedar forests situated along an elevation gradient in Lebanon, spanning different local climates. We evaluated their diversity using an Arcellinida-specific metabarcoding approach based on the cytochrome oxidase subunit I gene. Our study shows that Arcellinida richness and phylogenetic diversity follow a unimodal distribution, peaking at mid-elevations. β-diversity was chiefly the product of turnover, illustrating the high spatial heterogeneity of the forests. Precipitation and actual evapotranspiration were identified as key drivers of diversity, thus supporting the water-energy balance hypothesis. Communities situated at higher or lower elevation were, to a large extent, subsets of more diverse mid-elevation assemblages, which designates the latter as biodiversity sources. These results suggest that, under the increasing aridification of the Middle East due to climate change, Arcellinida communities will lose diversity and will undergo a process of homogenisation, with possible consequences on ecosystem functioning.},
}

@article {pmid41358850,
year = {2025},
author = {Winther-Have, CS and Rasmussen, JA and Zhai, X and Nielsen, DS and Sicheritz-Pontén, T and Gopalakrishnan, S and Clokie, MRJ and Middelboe, M and Limborg, MT},
title = {Ecological strategies of bacteria shape inherent phage diversity in Atlantic salmon gut microbiomes.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf272},
pmid = {41358850},
issn = {1751-7370},
abstract = {Understanding host-specific phage diversity is essential for deciphering the complex dynamics shaping microbial ecology and evolution. However, the lack of inherent host associations between uncultivated bacteria and their viruses remains a major limitation to understanding the drivers of viral diversity and its role in bacterial ecology, particularly given the intricate specificity of phage-host interactions. The naturally low complexity of the gut microbiota within piscivorous fish, such as Atlantic salmon (Salmo salar), makes it a valuable model for unravelling ecological patterns of viral diversity in the context of a limited bacterial species composition, and to explore the impact of an invading pathogen on the "steady-state" viral community. The intestinal microbiota of the salmon studied here, was in some cases dominated by a salmon-associated Mycoplasma or increasing levels of an opportunistic Aliivibrio, the latter observed in response to a disease outbreak. The two bacteria are distinctively different in their ecological strategies and their overall genomic and functional properties. A pronounced difference was observed in the gut viral communities and diversity, depending on whether it was dominated by a commensal or an invading bacterial species. Samples dominated by Mycoplasma sp. had few to no viruses, whereas samples dominated by Aliivibrio sp. had viral communities comprising up to 22 viral taxonomic operational units. This study provides unique insights into the significance of bacterial ecological trade-offs linked to niche adaptation and how these affect the associated viral communities in a natural host-controlled environment.},
}

@article {pmid41358825,
year = {2025},
author = {Kumar, C and Bertani, I and Chaouachi, M and Myers, MP and Garbeva, P and Bez, C and Venturi, V},
title = {AHL quorum sensing regulates T6SS and volatiles production in rice root-colonizing Enterobacter asburiae AG129.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf120},
pmid = {41358825},
issn = {1574-6941},
abstract = {Pseudomonadota (formerly Proteobacteria) commonly use a contact independent cell-cell communication system known as quorum sensing (QS) mediated by N-acyl-homoserine lactone (AHL) signal molecules. The canonical AHL QS system involves a luxI-family gene which encodes an AHL synthase, and a luxR-family gene, which encodes a transcriptional regulator responsive to the cognate AHL(s). This study involves the AHL QS system of Enterobacter asburiae AG129, a root associated strain isolated from rice (Oryza sativa). E. asburiae AG129 produces the N-butanoyl homoserine lactone (C4-AHL) signal molecule. Genome sequencing of strain AG129 revealed the presence of a canonical AHL QS system, comprising genetically adjacent easI-like and easR-like genes. A genomic easI knockout mutant was no longer able to produce AHLs, but the in-trans complementation with a plasmid carrying the easI gene restored the AHL production. QS mediated by AHLs in AG129 was found to influence rice root colonization, and secretome analysis highlighted a significant regulatory role in the expression of Type VI secretion system (T6SS) proteins. GC-MS analysis identified sixteen volatile organic compounds (VOCs) that were more abundantly emitted by the wild-type strain compared to the easI mutant. Overall, our findings suggest that AHL-based QS in E. asburiae AG129 positively regulates T6SS expression and VOC production, while negatively affecting root colonization. This study is among the first to explore the role of QS signaling in a bacterial root-endophyte, providing evidence of a connection between QS activity and the ability of the bacterium to inhabit, compete and colonize the plant endosphere.},
}

@article {pmid41358465,
year = {2025},
author = {Tang, X and Wang, R and Yang, S and Wang, G and Luo, J and Peng, S and Liang, K and Yang, J},
title = {Species-Specific Antibacterial Materials: From Design to Application.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {},
number = {},
pages = {e07114},
doi = {10.1002/smll.202507114},
pmid = {41358465},
issn = {1613-6829},
support = {SKLOD-2025RD002//State Key Laboratory of Oral Diseases/ ; 2023YFSY0048//Sichuan Science and Technology Program/ ; 82170949//National Natural Science Foundation of China/ ; 82270970//National Natural Science Foundation of China/ ; 82470967//National Natural Science Foundation of China/ ; 51903169//National Natural Science Foundation of China/ ; },
abstract = {Traditional broad-spectrum antibacterial strategies are known to contribute to the increase in drug-resistant microorganisms and the disruption of microbial ecological balance. To break this stalemate, researchers have begun to explore selective antibacterial strategies that minimize the impact on normal flora and maintain microbial ecological balance. Species-specific antibacterial materials, which can target particular bacterial species or even specific strains, offer innovative perspectives and methodologies for the prevention and treatment of infectious diseases. This review first explores the selective mechanisms that underpin species-specific antibacterial strategies, summarizes the main classifications of species-specific antibacterial strategies, investigates the engineering techniques employed in the development of such materials, and emphasizes the importance of structure-activity relationships in the design of species-specific antibacterial materials. It explores techniques like peptide modification, nanoparticle engineering, and genetic manipulation, highlighting that a thorough understanding of the structure and function of antibacterial materials is essential for improving their efficacy and specificity. Ultimately, it anticipates the potential applications of species-specific antibacterial materials in disease diagnosis and treatment, while addressing the challenges associated with clinical translation. It is expected that this comprehensive review will offer novel perspectives for the development of species-specific antibacterial materials.},
}

@article {pmid41358355,
year = {2025},
author = {Shen, S and Xu, Y and Liu, Z and Luo, Y and Wang, R and Li, G and Liu, Y},
title = {Combined application of biochar and halophyte intercropping enhances cucumber yield and quality by ameliorating soil properties in a continuous cropping system.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1711099},
pmid = {41358355},
issn = {1664-462X},
abstract = {Biochar amendment and halophyte intercropping are viable strategies for alleviating soil degradation in greenhouse systems, specifically the secondary salinization and autotoxicity induced by continuous cropping. Nevertheless, the potential synergistic effects of combining these practices remain poorly understood. This study investigated their synergistic effects on soil properties, microbial communities, and cucumber performance. A pot experiment was conducted with the following treatments: soil without amendment (CK), biochar (B), Paspalum vaginatum intercropping (S), and biochar combined with Paspalum vaginatum intercropping. The results showed that BS treatment led to the highest increases in soil organic carbon content, pH, total nitrogen content, available phosphorus content, and available potassium content compared to CK (p<0.05). Concurrently, BS significantly reduced available nitrogen, electrical conductivity, Na[+], SO4 [2-], and Cl[-] levels, while total phosphorus remained unaffected. Cucumber yield increased significantly by 11.50% and 27.12% under B and BS treatments, respectively, whereas S showed no significant effect. BS also achieved the highest fruit quality enhancement, followed by B and S. Notably, B and S treatments displayed the highest and lowest K[+], Ca[2+]and Mg[2+] accumulation, respectively, whereas the BS treatment led to K[+] and Ca[2+] concentrations that were significantly lower than those in the B treatment. Soil bacterial diversity was significantly enhanced under BS. The PLS-PM identified the alleviation of soil salinity and acidity, along with improved nutrient availability, as the primary drivers for enhanced crop performance, with soil bacterial diversity playing a secondary yet significant role. These findings suggest that biochar combined with intercropping (BS) effectively mitigates continuous cropping obstacles in greenhouse systems by synergistically improving soil health and microbial ecology.},
}

@article {pmid41358162,
year = {2025},
author = {Nicolas-Asselineau, L and Speth, DR and Zeller, LM and Woodcroft, BJ and Singleton, CM and Liu, L and Dueholm, MKD and Milucka, J},
title = {Occurrence and temporal dynamics of denitrifying protist endosymbionts in the wastewater microbiome.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf209},
pmid = {41358162},
issn = {2730-6151},
abstract = {Effective wastewater treatment is of critical importance for preserving public health and protecting natural environments. Key processes in wastewater treatment, such as denitrification, are performed by a diverse community of prokaryotic and eukaryotic microbes. However, the diversity of the microbiome and the potential role of the different microbial taxa in some wastewater treatment plant setups is not fully understood. We aimed to investigate the presence and diversity of denitrifying bacteria of the candidate family Azoamicaceae that form obligate symbioses with protists in wastewater treatment plants. Our analyses showed that denitrifying endosymbionts belonging to the Ca. Azoamicus genus are present in 20%-50% of wastewater treatment plants worldwide. Time-resolved amplicon data from four Danish WWTPs showed high temporal fluctuations in the abundance and composition of the denitrifying endosymbiont community. Twelve high-quality metagenome-assembled genomes of denitrifying endosymbionts, four of which were circular, were recovered. Genome annotation showed that a newly described, globally widespread species, Ca. Azoamicus parvus, lacked a nitrous oxide reductase, suggesting that its denitrification pathway is incomplete. This observation further expands the diversity of metabolic potentials found in denitrifying endosymbionts and indicates a possible involvement of microbial eukaryote holobionts in wastewater ecosystem dynamics of nitrogen removal and greenhouse gas production.},
}

@article {pmid41357478,
year = {2025},
author = {Ni, J and Tang, Y and Zhou, F and Hu, Y and Liu, L and Huang, M and Ouyang, H and Xie, C},
title = {Association between serum total cholesterol levels and Crohn's clinical disease severity: a retrospective cross-sectional study.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1708838},
pmid = {41357478},
issn = {2296-858X},
abstract = {BACKGROUND: This retrospective cross-sectional study aimed to investigate the relationship between serum total cholesterol (TC) levels and the clinical activity of Crohn's disease (CD).

METHODS: One hundred and four patients with Crohn's disease (CD) and twenty healthy volunteers were included in the analysis. Serum uric acid (SUA) levels and indicators related to lipid metabolism were measured within 1 week before undergoing endoscopic and CT enterography (CTE) examinations. Patients were divided into groups based on their Crohn's Disease Activity Index (CDAI) scores.

RESULTS: Patients were categorized into mild and moderate groups, with no patients meeting the criteria for severe CD. The serum uric acid (SUA) and triglyceride (TG) levels were similar between CD patients and the control group (p > 0.05). However, the levels of total cholesterol (TC), apolipoprotein A1 (apo A1), apolipoprotein B (apo B), high-density lipoprotein cholesterol (HDL-C), and low-density lipoprotein cholesterol (LDL-C) were higher in the control group (p < 0.05). The TC and LDL-C levels were lower in the moderate patients compared to those in mild group (p < 0.05). TC ≤ 3.5 mmol/L was identified as an independent risk factor for more severe disease (OR = 4.50, 95%CI 1.612-12.561, p = 0.004). TC levels were correlated to both CRP and CDAI scores negatively (p < 0.05).

CONCLUSION: TC may serve as a potential supplementary marker for clinical disease activity in CD, but further research, including longitudinal studies, is needed to confirm its reliability.},
}

@article {pmid41356477,
year = {2025},
author = {Chakraborty, A and Roy, A and He, S and Castellano-Hinojosa, A and Asiegbu, FO and Coutinho, TA},
title = {Editorial: Forest microbiome: dynamics and interactions in the anthropocene era.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1729625},
pmid = {41356477},
issn = {1664-302X},
}

@article {pmid41356467,
year = {2025},
author = {Castelli, L and García-Amado, MA and Rudolf, CA and Contreras, M and Espinosa-Blanco, AS and Godoy-Vitorino, F},
title = {Microbial diversity in the critically endangered Orinoco crocodile (Crocodylus intermedius): influence of body site and Helicobacter spp. on microbiota composition.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1697111},
pmid = {41356467},
issn = {1664-302X},
abstract = {INTRODUCTION: The Orinoco crocodile (Crocodylus intermedius), a critically endangered species from Colombia and Venezuela Llanos, continues to face significant threats despite existing legal protections. Understanding the microbial diversity associated with this species, particularly in captive populations, can offer valuable insights into its health status and inform conservation strategies. In this study, we characterized the bacterial microbiota of C. intermedius, focusing on the influence of body site and the presence of Helicobacter spp. on microbial diversity.

METHODS: We collected oral and cloacal samples from five captive C. intermedius individuals and analyzed their bacterial microbiota using high-throughput sequencing techniques. The study specifically investigated how microbial diversity varies by body site and how the presence of Helicobacter spp. influences community structure and composition.

RESULTS: Oral samples exhibited higher microbial diversity compared to cloacal samples. This difference is likely attributable to greater environmental exposure and dietary variation affecting the oral cavity. The presence of Helicobacter spp. was associated with a marked reduction in bacterial richness and significant shifts in community composition. Samples positive for Helicobacter spp. were notably enriched in potentially pathogenic genera, including Campylobacter and Escherichia, suggesting a dysbiotic effect on the microbiota.

DISCUSSION: Our findings indicate that both body site and Helicobacter spp. presence play significant roles in shaping the microbial communities of C. intermedius. These results have important implications for reptile health management and zoonotic disease surveillance, as dysbiosis could compromise host health and facilitate pathogen transmission. Furthermore, this study underscores the role of reptiles as potential reservoirs for Campylobacter spp. and Helicobacter spp., highlighting the need for continued research into the microbial ecology of endangered species to guide conservation strategies and inform public health policies.},
}

@article {pmid41356191,
year = {2026},
author = {Xiao, Y and Li, X and Fang, Y and Guo, M and Shui, M and Zhong, G and Zhou, H and Lin, C and Sun, B and Wang, S},
title = {Berberine suppresses colon inflammation via integrated modulation of host metabolism, microbial ecology, and innate immune signaling.},
journal = {Theranostics},
volume = {16},
number = {4},
pages = {2019-2036},
pmid = {41356191},
issn = {1838-7640},
mesh = {*Berberine/pharmacology ; Animals ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Immunity, Innate/drug effects ; *Colitis/drug therapy/chemically induced/microbiology ; RNA, Ribosomal, 16S/genetics ; Mice, Inbred C57BL ; Signal Transduction/drug effects ; Metabolomics ; *Anti-Inflammatory Agents/pharmacology ; Fatty Acids, Volatile/metabolism ; Male ; Inflammation/drug therapy ; Colon/drug effects/pathology ; Single-Cell Analysis ; Disease Models, Animal ; Dextran Sulfate ; Energy Metabolism/drug effects ; Interleukin-1beta/metabolism ; },
abstract = {Background: Berberine, a natural compound with unique bioactivity, has been widely used in the treatment of gastrointestinal inflammatory diseases. Despite its well-documented anti-inflammatory properties, the system-level regulatory network underlying its multifaceted mechanisms remains poorly understood. Methods: In this study, we employed a multi-level analytical approach, integrating single-cell RNA sequencing, targeted metabolomics, 16S rRNA gene sequencing, and drug-target analysis, to elucidate the integrative effects of berberine on gut microbiota-metabolism-immune interactions. Results: Single-cell RNA sequencing revealed that berberine enhances energy metabolism in intestinal cells of DSS-induced mice, thereby maintaining normal physiological functions. Targeted metabolomics analysis of short-chain fatty acids, combined with 16S rRNA gene sequencing, demonstrated that berberine supplementation significantly increases short-chain fatty acid (SCFA) levels in the intestinal environment and selectively enriches the abundance of Akkermansia. Furthermore, single-cell RNA sequencing data indicated that berberine inhibits fibroblast-to-lymphatic transformation and suppresses the expression of interleukin-1β, leading to reduced immune activation in innate immune cells. Drug-target analysis identified shared molecular targets between berberine and various immunotherapeutic agents. Conclusion: This study provides a comprehensive understanding of berberine's multi-target mechanisms and highlights its potential as a therapeutic agent for inflammatory diseases through the modulation of gut microbiota, host metabolism, and immune responses.},
}

*Berberine/pharmacology
Animals
Mice
*Gastrointestinal Microbiome/drug effects
*Immunity, Innate/drug effects
*Colitis/drug therapy/chemically induced/microbiology
RNA, Ribosomal, 16S/genetics
Mice, Inbred C57BL
Signal Transduction/drug effects
Metabolomics
*Anti-Inflammatory Agents/pharmacology
Fatty Acids, Volatile/metabolism
Male
Inflammation/drug therapy
Colon/drug effects/pathology
Single-Cell Analysis
Disease Models, Animal
Dextran Sulfate
Energy Metabolism/drug effects
Interleukin-1beta/metabolism

@article {pmid41356074,
year = {2025},
author = {Tsuji, K and Yoshida, H and Saba, M and Terauchi, Y and Kawauchi, M and Honda, Y and Tanaka, C and Yoshimi, A},
title = {Hydrophobins in Bipolaris maydis do not contribute to colony hydrophobicity, but their heterologous expressions alter colony hydrophobicity in Aspergillus nidulans.},
journal = {Frontiers in fungal biology},
volume = {6},
number = {},
pages = {1604903},
pmid = {41356074},
issn = {2673-6128},
abstract = {Hydrophobins are small amphiphilic proteins secreted by filamentous fungi. These proteins confer hydrophobic properties to the hyphae and conidia. Bipolaris maydis is the causal agent of southern corn leaf blight; the biological function of its hydrophobins is not clear. In the present study, we focused on the broad function of hydrophobins in the life cycle of this fungus. We found that the B. maydis genome encodes four hydrophobins-Hyp1 of class I, and Hyp2, Hyp3 and Hyp4 of class II-and all of them are expressed. We generated single disruptants of each gene, as well as triple and quadruple disruptants. No differences were detected between the wild type and any of disruptants in mycelial growth, conidiation, stress tolerance, virulence, or sexual reproduction. The colony hydrophobicity of all disruptant strains was similar to that of the wild-type strain. Complementation of a null Aspergillus nidulans mutant of dewA, which showed a significantly reduced colony hydrophobicity, with each of the four B. maydis hydrophobin genes restored the hydrophobic phenotype, although the degree of hydrophobicity varied among them. Despite the absence of any significant phenotypic changes in the B. maydis mutants generated, results strongly suggest that all four hydrophobins have retained their function in hydrophobicity. Furthermore, the results of this study suggest that the role of hydrophobins might change depending on the fungal species.},
}

@article {pmid41355978,
year = {2025},
author = {Oporto-Llerena, R and Huerto-Huánuco, R and Quispe-Hualpa, Y and Palomino-Kobayashi, LA and Soza, G and Rojas-Jaimes, J and Gonzales, P and Pollack, L and Gomez, AC and Salvador-Luján, G and Cuaresma, E and Luque, N and Casapia, M and Arteaga-Livias, K and Sáenz, Y and Pons, MJ and Ruiz, J},
title = {bla OXA-51-Negative Acinetobacter calcoaceticus-baumannii Complex as a Cause of Human Infection in Peru.},
journal = {Journal of tropical medicine},
volume = {2025},
number = {},
pages = {8851906},
pmid = {41355978},
issn = {1687-9686},
abstract = {BACKGROUND: Common identification techniques do not differentiate among members of the Acinetobacter calcoaceticus-baumannii (ACB) complex, and the presence of non-baumannii Acinetobacter is often misinterpreted. The bla OXA-51 gene is located within the chromosome of Acinetobacter baumannii. Despite its plasmid dissemination to other members of the genus, it may be considered in initial species screening. Thus, this study aimed to determine the presence of bla OXA-51-negative Acinetobacter spp. as a cause of infection in Peru.

METHODS: Two hundred ninety-eight ACB complex isolates from different regions of Peru were isolated between January 2018 and March 2024. Of these, 272 and 25 were confirmed as hospital-acquired and community infections, respectively. The presence of bla OXA-51 was determined by polymerase chain reaction, and the susceptibility levels to 12 antimicrobial agents were determined.

RESULTS: The results showed that 38 (12.7%) isolates were bla OXA-51-negative. These isolates were frequent among community infections (13/25, p < 0.0001), often causing urine infections. They showed significantly lower levels of resistance to almost all antimicrobial agents tested, and most of them were recovered from regions outside metropolitan Lima.

CONCLUSION: A relevant number of infections by non-baumannii Acinetobacter species in Peru is suggested, highlighting the need for systematic identification of these species in the country.},
}

@article {pmid41355197,
year = {2025},
author = {Yi, F and Shao, L and Wu, S and Cheng, K and Zhang, Z and Li, Y and Hu, S and Wan, J and Liu, Q and Guo, L and Zhang, X and Shang, B and Yu, J and Zheng, H and Liu, J and Cai, Y and Zhang, X},
title = {Cotton gland formation genes GbCGF2/3 positively regulate Verticillium wilt resistance through modulating suberin biosynthesis.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70809},
pmid = {41355197},
issn = {1469-8137},
support = {2022YFD1200303//National Key Research and Development Program of China/ ; 251111113800//Key Research and Development Project of Henan Province/ ; 32070262//National Natural Science Foundation of China/ ; 32401779//National Natural Science Foundation of China/ ; CB2024A16//State Key Laboratory of Cotton Bio-breeding and Integrated Utilization Open Fund/ ; CB2024A23//State Key Laboratory of Cotton Bio-breeding and Integrated Utilization Open Fund/ ; CB2023A14//State Key Laboratory of Cotton Bio-breeding and Integrated Utilization Open Fund/ ; CB2023A11//State Key Laboratory of Cotton Bio-breeding and Integrated Utilization Open Fund/ ; CB2025A26//State Key Laboratory of Cotton Bio-breeding and Integrated Utilization Open Fund/ ; 2024M760773//China Postdoctoral Science Foundation/ ; 234400510004//Project of Zhongyuan Scholars Workstation/ ; },
abstract = {Verticillium wilt, caused by Verticillium dahliae, is a serious vascular wilt disease in cotton (Gossypium spp.). However, the roles and mechanisms of cotton gland formation (CGF) genes in regulating cotton V. dahliae resistance remain elusive. Virus-induced gene silencing or CRISPR-/Cas9-mediated knockdown or knockout of GbCGF2/3 decreases cotton resistance to Verticillium wilt. RNA-sequencing (RNA-seq) shows lower transcript levels of the suberin biosynthetic gene fatty acyl-coenzyme A reductase 3.1 (FAR3.1) in GbCGF2/3-silenced cotton plants. Silencing or knocking out GbFAR3.1 impairs cotton resistance to V. dahliae and decreases suberin compositional monomer fatty acids (C16-C24) contents. GbCGF2/3 positively regulates GbFAR3.1 expression by binding to its promoter. Suberin deposition in the lamellae layer of the root cell wall decreases significantly in GbCGF2/3 Cas9-mediated knockout and GbFAR3.1-silenced cotton plants. Additionally, the expression of gossypol biosynthetic genes and defense-related genes PDF1.2 and PR4 in the phytohormone jasmonic acid (JA) pathway is also downregulated in GbCGF2/3-silenced or Cas9-mediated knockout plants. In conclusion, GbCGF2/3 positively regulates Verticillium wilt resistance through promoting suberin biosynthesis, gossypol accumulation and expression of JA signaling defense-related genes, providing a novel insight and strategy for breeding cotton cultivars resistant to Verticillium wilt.},
}

@article {pmid41353943,
year = {2025},
author = {Zheng, Y and Zhou, X and Deng, S and Zhao, H},
title = {Spatial pattern of spring dissolved organic matter and microbial communities under dual anthropogenic-natural forcing in a tropical semi-enclosed bay.},
journal = {Marine environmental research},
volume = {214},
number = {},
pages = {107739},
doi = {10.1016/j.marenvres.2025.107739},
pmid = {41353943},
issn = {1879-0291},
abstract = {Coastal zones serve as vital interfaces between continental and oceanic ecosystems, where anthropogenic inputs strongly influence dissolved organic matter (DOM) and associated microbial processes. However, the response of DOM-microbe interactions to various human activities remains inadequately understood. In this study, we examined physicochemical parameters, DOM optical properties, and microbial community structures in surface waters of Zhanjiang Bay, which is influenced by agricultural runoff, sewage, and industrial effluent. This pattern could be attributed to the impact of agricultural runoff and sewage input. Nutrient-rich terrestrial inputs were associated with enhanced humic-like and protein-like fluorescent DOM (FDOM) and high-molecular-weight, aromatic chromophoric DOM (CDOM), accompanied by the enrichment of Cyanobacteria and Thermoplasmatota. In contrast, in the lower bay, industrial activities, particularly effluent from a steel plant, resulted in an increased humic-like and protein-like FDOM alongside low-aromatic CDOM. Additionally, an increase in Verrucomicrobiota and humification index indicated that DOM may undergo decomposition processes in addition to in situ production. Multivariate analyses (PCA, RDA) confirmed strong correlations between physicochemical parameters, DOM properties, and microbial community composition. Collectively, these findings demonstrate that anthropogenic activities primarily shape DOM characteristics, which in turn structure microbial communities, highlighting the cascading effects of anthropogenic activities in regulating coastal biogeochemistry. This study elucidates the mechanistic pathway through which anthropogenically altered DOM composition shapes microbial community assembly, providing insights into the coupling between DOM dynamics and microbial ecology in anthropogenically impacted coastal ecosystems.},
}

@article {pmid41353355,
year = {2025},
author = {Todorović, I and Abrouk, D and Kyselková, M and Rey, M and López-Mondéjar, R and Raičević, V and Jovičić-Petrović, J and Moënne-Loccoz, Y and Muller, D},
title = {Fluorescent Pseudomonas spp. from suppressive and conducive soils share genomic and functional traits relevant to Fusarium graminearum disease suppression.},
journal = {BMC genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12864-025-12374-3},
pmid = {41353355},
issn = {1471-2164},
support = {grant numbers 670-00-573/1/372/2019-04, 670-00-2590/1/304/2020-04, 670-00-2551/1/298/2021-04 and 670-00-1/1/317/2022-01//Ministry of Youth and Sports, Belgrade, Serbia/ ; grant numbers 964308G, 972203C and 103939T//Campus France/ ; PHC DANUBE 2020: 45296XM//Programme for Multilateral Scientific and Technological Cooperation in the Danube Region/ ; Ministry of Education, Youth and Sports of the Czech Republic, project number 8X20052//Programme for Multilateral Scientific and Technological Cooperation in the Danube Region/ ; Ministry of Education, Youth and Sports of the Czech Republic, project number 8X20052//Programme for Multilateral Scientific and Technological Cooperation in the Danube Region/ ; The Ministry of Education, Science, and Technological Development of the Republic of Serbia, project number: 451-03-01086/2020-09/07//Programme for Multilateral Scientific and Technological Cooperation in the Danube Region/ ; PHC DANUBE 2020: 45296XM//Programme for Multilateral Scientific and Technological Cooperation in the Danube Region/ ; PHC DANUBE 2020: 45296XM//Programme for Multilateral Scientific and Technological Cooperation in the Danube Region/ ; SuppressSOIL ANR-19-EBI3-0007//BiodivERsA3 ERA-Net COFUND programme/ ; SuppressSOIL ANR-19-EBI3-0007//BiodivERsA3 ERA-Net COFUND programme/ ; SuppressSOIL ANR-19-EBI3-0007//BiodivERsA3 ERA-Net COFUND programme/ ; SuppressSOIL ANR-19-EBI3-0007//BiodivERsA3 ERA-Net COFUND programme/ ; project number CZ.02.01.01/00/22_008/0004635//the Ministry of Education, Youth and Sports of the Czech Republic/ ; The Ministry of Education, Science, and Technological Development of the Republic of Serbia, project number: 451-03-01086/2020-09/07//Programme for Multilateral Scientific and Technological Cooperation in the Danube Region, The Ministry of Education/ ; grant number 451-03-137/2025-03/200116//The Ministry of Education, Science, and Technological Development of the Republic of Serbia/ ; },
abstract = {BACKGROUND: Soils suppressive to fungal pathogens harbor microbiomes that can inhibit disease development despite the presence of virulent pathogens and susceptible hosts. Fluorescent Pseudomonas are often implicated in such suppressiveness, but their genomic determinants and distribution in suppressive vs. non-suppressive (i.e., conducive) soils remain unclear.

RESULTS: We investigated the taxonomic and functional diversity of Pseudomonas populations from wheat rhizospheres in four agricultural soils with contrasting suppressiveness to Fusarium graminearum-induced seedling disease. rpoD-based metabarcoding and culture-dependent isolation revealed distinct Pseudomonas community structures linked to soil suppressiveness. However, major phylogenetic groups were shared across soils. From 406 isolates, 29 representative strains spanning seven subgroups of the P. fluorescens group were selected for whole-genome sequencing. Comparative genomics revealed 14 putative novel Pseudomonas genomospecies (dDDH < 70% with closest described type strains). Genomic screening revealed wide distribution of genes linked to biocontrol and plant-growth promotion, including siderophore biosynthesis, hormone modulation, phosphate solubilization, and production of antimicrobial compounds. Biosynthetic genes for phenazine and pyrrolnitrin were detected exclusively in P. chlororaphis strains isolated from suppressive soils, and rpoD alleles corresponding to these strains were not found in conducive soils within our metabarcoding dataset. Other traits such as hydrogen cyanide, ACC deaminase, and auxin biosynthesis were broadly distributed across isolates from all soils. Functional assays demonstrated variable expression of predicted traits, indicating regulatory or environmental influence. Several strains inhibited F. graminearum mycelial growth via volatile organic compounds, while two strains also reduced conidia germination, including isolates from both suppressive and conducive soils.

CONCLUSIONS: This study demonstrates that Pseudomonas genomic traits important for biocontrol are not restricted to suppressive soils, and that functional redundancy and context-dependent expression may shape the contribution of Pseudomonas to disease suppression. Our results highlight the need for integrative analyses combining community profiling, genome-based prediction, and phenotyping to better understand microbiome-mediated plant protection. The identification of novel genomospecies and lineage-specific biosynthetic traits advances our knowledge of Pseudomonas diversity in agricultural soils and supports future development of targeted microbial consortia.},
}

@article {pmid41353279,
year = {2025},
author = {Stuehrenberg, J and Kitzinger, K and von Arx, JN and Graf, JS and Lavik, G and Littmann, S and Milucka, J and Orsi, WD and Schorn, S and Speth, DR and Vuillemin, A and Wu, S and Marchant, HK and Kuypers, MMM},
title = {Urea use drives niche separation between dominant marine ammonia oxidizing archaea.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-67048-1},
pmid = {41353279},
issn = {2041-1723},
support = {EXC-2077-390741603//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
abstract = {Ammonia-oxidizing archaea (AOA) are among the most abundant microorganisms in the ocean and play a critical role in marine nitrogen cycling. Recently, urea has been shown to serve as an additional substrate for marine AOA, with substantial urea use in the ammonium-depleted open-ocean. Yet, the mechanisms that control urea use and potentially maintain high AOA abundances remain unclear. Here, we investigate urea and ammonia use by AOA in three contrasting marine environments, from coastal, ammonium-rich to open-ocean, ammonium-poor waters. Our combined results indicate that distinct substrate utilization strategies of Nitrosopumilus and Nitrosopelagicus control their environmental distribution. The more coastal AOA genus, Nitrosopumilus, primarily uses ammonium. In contrast, enhanced urea utilization in ammonium-limited waters is linked to the activity and growth of Nitrosopelagicus. Thus, the use of urea, and potentially other organic-N compounds by Nitrosopelagicus plays a major role in fueling open-ocean nitrification and sustaining primary productivity in these vast regions.},
}

@article {pmid41352799,
year = {2026},
author = {Cheng, W and Jiang, C and Pan, T and Zhu, Q and Liu, G and Li, N and Wu, Z and Li, X},
title = {Effects of quinoa addition on physicochemical properties, microbiome profiles, and volatile organic compounds in medium-temperature Daqu.},
journal = {Food research international (Ottawa, Ont.)},
volume = {223},
number = {Pt 1},
pages = {117868},
doi = {10.1016/j.foodres.2025.117868},
pmid = {41352799},
issn = {1873-7145},
mesh = {*Volatile Organic Compounds/analysis ; *Chenopodium quinoa/chemistry ; *Microbiota ; Fermentation ; Food Microbiology ; Food Handling/methods ; Temperature ; },
abstract = {The selection of raw materials plays a pivotal role in shaping the microbial ecology and metabolic functions of Daqu, a fermentation starter widely used in Baijiu production. Quinoa (Chenopodium quinoa Willd.), a pseudocereal rich in proteins, polyphenols, and bioactive compounds, has recently gained attention as a functional food ingredient. In this study, Quinoa was used to replace a certain proportion of wheat and incorporated into the making process of medium-temperature Daqu (MTD), and its effects on the physicochemical properties, microbial community dynamics, and volatile organic compound (VOC) were investigated. Compared with traditional MTD, quinoa-supplemented Daqu (L-MTD) exhibited significantly higher starch (increased by 8.4 %), reducing sugar (increased by 12.7 %), and acidity (increased by 15.3 %) levels (p < 0.05), along with enhanced esterification and fermentation power of its central part (increased by 10.2 % and 9.5 %, respectively, p < 0.05). High-throughput sequencing revealed that quinoa addition reshaped the microbial community by enriching beneficial lactic acid bacteria (e.g., Lactobacillus and Weissella) and reducing potential spoilage fungi (e.g., Aspergillus and Rhizopus). In addition, Lactobacillus and Saccharomycopsis showed strong correlations with the accumulation of esters and aromatic compounds, including ethyl lactate, phenethyl acetate, DL-(-)-pantoyl lactone, and benzyl alcohol. Redundancy analysis (RDA) indicated strong correlations between Lactobacillus and Saccharomycopsis with the accumulation of esters (such as ethyl acetate and ethyl lactate) and aromatic compounds (such as benzyl alcohol and phenethyl acetate), providing a research basis for identifying functional microbial strains in MTD and conducting subsequent micro-fermentation experiments. These findings highlight the potential of quinoa as a functional additive that modulates the microbial ecology and enhances the aroma complexity of Daqu, thereby offering a novel strategy for improving the quality and potential health value of traditional fermented products.},
}

*Volatile Organic Compounds/analysis
*Chenopodium quinoa/chemistry
*Microbiota
Fermentation
Food Microbiology
Food Handling/methods
Temperature

@article {pmid41352467,
year = {2025},
author = {Nalladiyil, A and Khuntia, HK and Chanakya, HN and Babu, GLS},
title = {Treatment of ultra-high-strength compost leachate using an anaerobic biomass biofilm reactor.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133774},
doi = {10.1016/j.biortech.2025.133774},
pmid = {41352467},
issn = {1873-2976},
abstract = {Leachate produced during the composting of the organic fraction of municipal solid waste (OFMSW) is highly concentrated and acidic (chemical oxygen demand (COD) -125 g/L, pH 3-5). Its recalcitrant nature necessitates long hydraulic retention times for effective digestion, which, in turn, leads to high organic loads and, consequently, large reactor footprints. This study evaluated the treatment performance, bioenergy potential, and microbial ecology of the Anaerobic Biomass Biofilm Reactor (ABBR) for ultra-high strength leachate treatment. The reactor employed lignocellulosic wastes such as coir, ridge gourd, and dried acacia leaves as natural biofilm supports. Operated over 180 days with a gradually increasing organic loading rate from 1.1 to 11.2 kg COD/m[3]/d, the reactor achieved 92.9 % COD removal and a methane yield of 0.357 NL/g COD removed at the maximum loading rate. Moreover, the reactor also exhibited exceptionally high space utilization efficiency (3.5-4 L CH4/L/d), highlighting its enhanced volumetric productivity and effectiveness in treating high-strength leachate. Metagenomic analysis revealed a diverse microbial community, with Methanospirillum (3 %) and Methanosaeta (2.6 %) identified as dominant archaea contributing to methanogenesis. The high moisture content of OFMSW, coupled with tropical climatic conditions, leads to rapid fermentation and the generation of large volumes of leachate. Therefore, the ABBR represents a sustainable and high-rate alternative to conventional anaerobic systems, enabling efficient leachate treatment and enhanced bioenergy recovery in windrow composting facilities.},
}

@article {pmid41351873,
year = {2025},
author = {Pan, X and Hageman, JJ and Weits, DA and Caldas, L and Elsayed, SS and Bayona, LM and van Wezel, GP and Berendsen, RL and Carrión, VJ and Raaijmakers, JM},
title = {Hypoxia Induces Phenotypic and Metabolic Shifts in Endophytic Flavobacterium sp. 98.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf269},
pmid = {41351873},
issn = {1751-7370},
abstract = {Oxygen plays a crucial role in shaping microbial physiology, functions, and behavior. Endophytic bacteria, residing within plant tissues, inhabit microenvironments where oxygen availability can be limited. However, the magnitude of hypoxic conditions in the endosphere and how these affect functional microbial traits is largely unknown. Here, we showed with a microsensor that oxygen levels in roots of sugar beet seedlings drop drastically to variable, low oxygen levels when going from epidermal to endodermal root tissue into the vasculature. Subsequently, we investigated phenotypic and metabolic responses of endophytic Flavobacterium sp. 98 at oxygen levels of 100 ppm. Under these oxygen conditions, Flavobacterium sp. 98 showed reduced growth, enhanced motility, and an altered extracellular metabolite profile. Flavobacterium sp. 98 colonies spread out in response to oxygen limitation and more effectively restricted hyphal growth of the sugar beet root pathogen Rhizoctonia solani than Flavobacterium sp. 98 grown at ambient oxygen conditions. Exometabolome analysis revealed enhanced accumulation of lysophosphatidylethanolamine (lysoPE) and N-acetyl-phenylalanine under low-oxygen conditions, along with a reduced level of the antifungal compound 5,6-dimethylbenzimidazole. These responses reflect physiological and metabolic plasticity of Flavobacterium sp. 98, highlighting significant changes in the expression of specific traits under hypoxic conditions. Our findings provide insights into niche-adaptive strategies of endophytic bacteria and pinpoint functional traits in microbe-plant interactions operating inside plant tissue.},
}

@article {pmid41351708,
year = {2025},
author = {Campbell, KL and Armitage, AR and Labonté, JM},
title = {Microbial Communities Display Key Functional Differences between Reference and Restored Salt Marshes.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02661-7},
pmid = {41351708},
issn = {1432-184X},
abstract = {Salt marshes, despite their ecological importance (i.e., carbon sequestration) and rapid decline due to climate change and sea-level rise. Salt marsh ecosystems provide essential services such as removal of pollutants, carbon sequestration, and protection of coastal lands from storm surges. These services are strongly influenced by plant productivity, which is closely linked to microbial processes such as biogeochemical cycling of carbon, nitrogen, and sulfur. To retain carbon sequestration and other ecological functions, substantial efforts are currently directed towards coastal marsh restoration. Restoration efforts often lack comprehensive assessments of ecosystem functioning. Here, in an effort to assess ecosystem functions, we compared the microbial and viral community composition, as well as the genetic potential between reference and 10-year-old restored marshes in Galveston Bay, TX, USA. Duplicate bulk surface sediment in stands of Spartina alterniflora were sampled for metagenomic analysis. Metagenome assembled genomes analysis showed that while the microbial community composition was largely similar among sites, the overall metabolic potential was dissimilar. Restored sites displayed a higher abundance of carbon and nitrogen cycling functions compared to reference sites, which mainly consisted of sulfur cycling. Although the restored sites developed sediment microbial communities that approached reference microbial composition, the differences in the metabolic functions suggest that even after 10 years, the restored sites were still in a transitional stage of development. The differences between the reference and restored sites were even more differentiated in the viral community's predicted host composition. Additionally, viruses potentially play a variety of roles within the sediment community, including population control and biogeochemical cycles participation through auxiliary metabolic genes. These results highlight the prolonged timeline of functional development in restored salt marshes and highlight the need to develop approaches to boost the development of soil microbial communities in newly created habitats.},
}

@article {pmid41350753,
year = {2025},
author = {Kim, K and Park, S and Jinno, C and Ji, P and Liu, Y},
title = {Impact of dietary supplementation of Bacillus subtilis on the metabolic profiles and microbial ecology of weanling pigs experimentally infected with a pathogenic Escherichia coli.},
journal = {Journal of animal science and biotechnology},
volume = {16},
number = {1},
pages = {167},
pmid = {41350753},
issn = {1674-9782},
abstract = {BACKGROUND: Our previous study demonstrated that dietary supplementation of Bacillus subtilis enhanced growth performance and intestinal integrity in weaned pigs challenged with enterotoxigenic Escherichia coli (ETEC). Therefore, this study aimed to explore the impact of Bacillus subtilis on gut health and its role in modulating host-microbe interactions in post-weaning pigs.

RESULTS: ETEC infection disrupted key metabolic pathways in distal colon, including glutathione, beta-alanine, and pyrimidine metabolism, indicating increased oxidative stress, impaired nucleotide balance, and amino acid catabolic stress. Bacillus subtilis supplementation induced distinct metabolomic and microbiome profiles in colon digesta of weaned pigs challenged with ETEC. Bacillus subtilis-treated pigs under ETEC challenge exhibited significant enrichment in amino acid- and energy-related pathways such as arginine biosynthesis, phenylalanine metabolism, pantothenate and CoA biosynthesis. ETEC infection induced microbial dysbiosis in the distal colon, resulting in decrease (P < 0.05) in abundance of Streptococcaceae and Enterobacteriaceae compared to healthy controls. Bacillus subtilis supplementation mitigated the ETEC-induced disruptions by increasing the relative abundance of beneficial bacterial families, including Lachnospiraceae and Bacteroidaceae.

CONCLUSION: Supplementation of Bacillus subtilis improves intestinal health and resilience against ETEC challenge by mitigating infection-induced metabolic disruptions and gut dysbiosis in weaned pigs.},
}

@article {pmid41350118,
year = {2025},
author = {Fukase, S and Kouketsu, A and Tamahara, T and Saito, T and Ito, A and Higashi, Y and Kajita, T and Kurobane, T and Miyakoshi, M and Iikubo, M and Shimizu, R and Takahashi, T and Yamauchi, K and Sugiura, T},
title = {Differences in the Oral Microbiome Between Patients With and Without Oral Squamous Cell Carcinoma.},
journal = {Journal of oral pathology & medicine : official publication of the International Association of Oral Pathologists and the American Academy of Oral Pathology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jop.70099},
pmid = {41350118},
issn = {1600-0714},
abstract = {BACKGROUND: Although studies have demonstrated a relationship between pathogenic microorganisms and oral cancer, no study has demonstrated a relationship between changes in bacterial flora and oral squamous cell carcinoma (OSCC). Therefore, we investigated the association between oral microbiota and oral squamous cell carcinoma using metagenomic analysis.

METHODS: Saliva samples from 64 patients with OSCC and 50 healthy controls who visited the Department of Oral Surgery, Tohoku University Hospital, were collected, and bacterial genomic DNA was extracted using polymerase chain reaction amplification. Single-end sequencing was performed using the Illumina MiSeq platform, and sequence data were analyzed using the Quantitative Insights Into Microbial Ecology 2 platform. The Steel-Dwass test was used for between-group comparisons, and Analysis of Compositions of Microbiomes with Bias Correction was used to detect significant differences in microbiome composition.

RESULTS: Significant differences were observed in alpha-diversity indices of bacterial flora (richness, Faith- phylogenetic diversity, Shannon index) in the OSCC group compared to those in the control group. Among the OSCC group, patients with larger tumor diameters and lymph node metastases (T3/T4, N1 or greater) formed independent clusters in the beta diversity analysis of the bacterial flora. Bacteria of the Actinomycetia phylum, such as Actinomyces and Rothia, were significantly reduced in patients with higher stage and pathological grade. Conversely, bacteria of the phylum Spirochaetia and Proteobacteria, particularly those of the genus Treponema, were significantly elevated in advanced cancer cases.

CONCLUSIONS: Our results suggest that changes in the oral microbiota may play a role in OSCC development and progression.},
}

@article {pmid41348832,
year = {2025},
author = {Cervantes-Echeverría, M and Jimenez-Rico, MA and Manzo, R and Hernández-Reyna, A and Cornejo-Granados, F and Bikel, S and González, V and Hurtado Ramírez, JM and Sánchez-López, F and Salazar-León, J and Pedraza-Alva, G and Perez-Martinez, L and Ochoa-Leyva, A},
title = {Human-derived fecal virome transplantation (FVT) reshapes the murine gut microbiota and virome, enhancing glucose regulation.},
journal = {PloS one},
volume = {20},
number = {12},
pages = {e0337760},
doi = {10.1371/journal.pone.0337760},
pmid = {41348832},
issn = {1932-6203},
mesh = {Animals ; *Gastrointestinal Microbiome ; Humans ; Mice ; *Fecal Microbiota Transplantation/methods ; *Virome ; Male ; Diet, High-Fat/adverse effects ; Obesity/therapy/microbiology ; *Feces/virology ; Mice, Inbred C57BL ; *Glucose/metabolism ; Metabolic Syndrome/therapy/microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; },
abstract = {The gut microbiome, comprising bacteria, viruses, archaea, fungi, and protists, plays a crucial role in regulating host metabolism and health. This study explored the effects of fecal virome transplantation (FVT) from healthy human donors on metabolic syndrome (MetS) in a diet-induced obesity (DIO) mouse model, without diet change. Mice received a single oral dose of human-derived virus-like particles (VLPs) and continued on a high-fat diet (HFD) for 17 weeks. Despite persistent dietary stress, FVT significantly improved glucose tolerance. Longitudinal profiling by virome shotgun metagenomics and bacterial 16S rRNA sequencing revealed marked, durable shifts in both viral and bacterial community composition. Notable bacterial changes included a decrease in Akkermansia muciniphila and Peptococcaceae and increases in Allobaculum and Coprococcus; A. muciniphila positively correlated with glucose levels and negatively correlated with body weight. Together, these results suggests that human-derived virome can durably reshape gut microbial ecology and improve glucose metabolism in mice with obesity, even without dietary modification, offering a novel avenue for developing phage-based therapies. This proof-of-concept study provides foundational observations for using human-derived VLPs for FVT in standard laboratory mouse models, and provides a foundation for elucidating bacteria-phage interactions and their role in host metabolic health.},
}

Animals
*Gastrointestinal Microbiome
Humans
Mice
*Fecal Microbiota Transplantation/methods
*Virome
Male
Diet, High-Fat/adverse effects
Obesity/therapy/microbiology
*Feces/virology
Mice, Inbred C57BL
*Glucose/metabolism
Metabolic Syndrome/therapy/microbiology
RNA, Ribosomal, 16S/genetics
Bacteria/genetics

@article {pmid41348222,
year = {2025},
author = {Soto-Pozos, ÁF and Rebollar, EA and Rovito, SM and Parra-Olea, G},
title = {Imprints of Land Use History on the Cutaneous Microbiota of Mexican Cloud Forest Salamanders.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02671-5},
pmid = {41348222},
issn = {1432-184X},
support = {CF-2019/373914//Secretaría de Ciencia, Tecnología e Innovación del Distrito Federal/ ; IN208024//Universidad Nacional Autónoma de México/ ; },
abstract = {The cloud forest harbors the highest amphibian diversity in Mexico, particularly among plethodontid salamanders. However, the expansion of agricultural and cattle ranching activities has significantly impacted this ecosystem and their native species. Beyond direct effects on cloud forest-dwelling species, effects of land-use change on free-living and salamander skin associated bacterial assemblages are underexplored in the cloud forest and in plethodontid salamanders specifically. This study examines how historical land-use changes may influence environmental and salamander skin bacterial communities, focusing on two types of previous land-use and six sympatric plethodontid salamanders from the cloud forest. Furthermore, we explored the presence of the pathogenic fungus Batrachochytrium dendrobatidis (Bd), due to its potential interaction with salamander skin bacterial communities. We found that skin bacterial communities varied with land-use history: in habitats formerly used for agriculture salamanders exhibited higher bacterial diversity, and communities' dispersion varied depending on the previous land-use. We found a very low Bd prevalence throughout the study area. Our findings suggest that bacterial communities associated with the skin of plethodontid salamanders may be influenced by land-use history in cloud forest fragments.},
}

@article {pmid41345535,
year = {2025},
author = {Guijosa-Ortega, JL and Romaní, AM and Grau, O and Pla-Rabés, S and Margalef, O and Salminci, JG and Zarroca, M and Pastor, A},
title = {Effects of Acid Rock Drainage on Microbial Communities in Alpine Streams of the Pyrenees.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02667-1},
pmid = {41345535},
issn = {1432-184X},
abstract = {Weathering of sulphur-bearing rocks leads to acid rock drainage (ARD), which decreases water pH, mobilizes heavy metals, and forms coloured coatings of metal precipitates on riverbeds. This study assessed the effects of ARD on microbial biofilm biodiversity and community structure in alpine streams across two Pyrenean regions (Núria and Chistau). Biofilms were sampled from acidic (pH < 5.5) and non-acidic (pH > 6.5) streams, and at their confluence, where metal precipitates occur (white-coated streams). We characterised bacterial and eukaryote communities by molecular tools and specifically analysed the diatom communities by morphology approach. Their respective community composition varied with stream category for both bacteria and eukaryotes, but only bacteria exhibited a loss in diversity in acidic and white-coated streams. Diatom communities and diversity differences were driven mainly by region. In acidic and white-coated streams, bacteria which can use metals and sulphurs in their metabolic processes increased, together with fungi and some photosynthetic groups (Chlorophyta, Streptophyta) among eukaryotes. Amplicon Sequence Variants (ASVs) assigned to acidophilic and psychrotolerant bacteria were highly associated with acidic streams, and Cyanophyceae ASVs were highly associated with white-coated ones. As for eukaryotes, ASVs of Chrysophyceae were associated with both acidic and white-coated streams. Nonetheless, the regional factor remained consistently significant across microbial communities. This study indicates that ARD-affected streams can support microbial communities adapted to their extreme conditions, with the communities in white-coated rivers differing markedly from those in acidic rivers.},
}

@article {pmid41345364,
year = {2025},
author = {Zhai, L and Yang, J and Lu, M and Sun, T and Wang, Y and Tang, G and Wu, D and Xu, L},
title = {Effects of Leaf Structure, Physiological Characteristics, and Chemical Properties on Phyllosphere Microorganisms Associated with Four Forage Crops in Fallow Land.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02638-6},
pmid = {41345364},
issn = {1432-184X},
support = {2023//Xingzhao Talent Support Program/ ; QKHJCQN[2025]265//Guizhou Provincial Basic Research Program (Natural Sciences) Youth Guidance Project/ ; 52020-2024-PT-02//Liupanshui Municipal-Level Science and Technology Innovation Platform Construction Project/ ; LPSSYKYJJ202306//High-Level Talents Introduction Project of Liupanshui Normal University/ ; },
abstract = {Phyllosphere microorganisms promote plant health, facilitate plant growth, and support ecosystem function. In this study, we compared the effects of leaf anatomy, physiological properties, and chemical composition on the diversity and abundance of epiphytic microorganisms across four forage species: wheat (Triticum aestivum), rye (Secale cereale), barley (Hordeum vulgare), and Italian ryegrass (Lolium multiflorum). The results showed that crop type significantly influenced microbial abundances on leaf surfaces and in whole leaves (P < 0.05). Specifically, wheat exhibited higher abundances of aerobic bacteria, lactic acid bacteria, molds, and yeasts in whole leaves and on leaf surfaces than those of the other three forage species. Microbial abundance on leaf surfaces was lower than that in whole leaves among the four crops. The stomatal density on the abaxial leaf surface was significantly higher than that on the adaxial surface (P < 0.0001) among the four crops. The main drivers of whole-leaf microbial abundance included soluble sugars, stomatal density, intercellular CO2 concentration, and total water vapor conductance. Conversely, the key factors influencing surface microbial abundance were reducing sugars (affecting lactic acid bacteria and molds) and stomatal density on the adaxial surface (affecting yeasts). In conclusion, the morphology, physiology, and chemical composition of forage leaves collectively shape the colonization patterns and abundance of epiphytic microorganisms. Wheat exhibited larger microbial numbers than those of the other three forages. Soluble sugars and stomatal density emerged as key determinants of microbial community structure, whereas epidermal structure influenced the formation of specific functional microbial communities through a dual mechanism of physical selection and microenvironmental regulation.},
}

@article {pmid41345336,
year = {2025},
author = {Antoł, W and Surmacz, B and Ostap-Chec, M and Stec, D and Miler, K},
title = {Do Shifts in Honeybee Crop Microbiota Enable Ethanol Accumulation? A Comparative Analysis of Caged and Foraging Bees.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02627-9},
pmid = {41345336},
issn = {1432-184X},
support = {Sonata 17 grant 2021/43/D/NZ8/01044//National Science Center in Poland/ ; },
abstract = {Honeybees encounter low environmental doses of ethanol, primarily through fermenting nectar, which can have both beneficial and detrimental effects on their functioning. Yet, ethanol traces can also be detected in the crop of caged bees with no access to environmental food sources. This raises the possibility that endogenous ethanol accumulation could occur under restricted conditions, with microbial contributions as a potential mechanism. The crop microbiota, although less diverse than that in other gut segments, plays important roles in food fermentation and pathogen defense. We hypothesized that captivity-induced shifts in crop microbiota may facilitate fermentation, resulting in measurable ethanol. To test this, we compared the crop contents of naturally foraging hive bees and caged bees reared without access to the natural environment. Ethanol levels were low in both groups and did not differ significantly, but non-zero measurements were more frequently observed in caged bees. Microbial community structure differed strongly in α- and β-diversity. Caged bees showed reduced abundance of nectar-associated genera (e.g., Apilactobacillus) and an increase in genera that include known ethanol-producing strains, such as Gilliamella and Bifidobacterium. While we did not directly assess metabolic activity, our results suggest that captivity alters microbial communities in ways that may influence ethanol levels. This raises broader questions about how microbe-host interactions modulate host phenotypes under different environmental conditions.},
}

@article {pmid41345266,
year = {2025},
author = {Zhao, Z and Klawonn, I and Baltar, F and Grossart, HP},
title = {Size-fractionated fungal communities in the sunlit ocean.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-025-09314-y},
pmid = {41345266},
issn = {2399-3642},
abstract = {Marine fungi play key roles in organic matter cycling, yet their distribution across particle size fractions remains understudied. We analyze 18S rDNA data from four size fractions (0.8-5, 5-20, 20-180, and 180-2000 μm) collected across the global sunlit ocean. Here, we show fungal diversity and relative abundance decline with increasing particle size. Fungal community structure is influenced by eukaryotic diversity and chlorophyll levels. Fungi co-occur with other eukaryotes, especially zooplankton, hinting at potential predator-prey interactions. Generalist fungi dominate smaller fractions, while specialists dominate larger fractions, likely due to stronger microenvironmental selection. Co-occurrence networks are dominated by positive interactions and driven by fungal specialists. Dispersal limitation emerges as the main ecological process shaping community assembly. Our findings reveal strong niche differentiation among marine fungi along the particle continuum and emphasize the role of particle size and biological interactions in structuring fungal diversity and biogeography.},
}

@article {pmid41345123,
year = {2025},
author = {Tucker, SJ and Füssel, J and Freel, KC and Kiefl, E and Freel, EB and Ramfelt, O and Sullivan, CES and Gajigan, AP and Mochimaru, H and de Souza, MR and Quinn, M and Ratum, C and Tran, LL and Sobczyk, M and Miller, SE and Trigodet, F and Lolans, K and Morrison, HG and Fallon, B and Huettel, B and Pan, T and Rappé, MS and Eren, AM},
title = {A high-resolution diel survey of surface ocean metagenomes, metatranscriptomes, and transfer RNA transcripts.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1913},
pmid = {41345123},
issn = {2052-4463},
support = {687269//Simons Foundation/ ; 989028//Simons Foundation/ ; 989028//Simons Foundation/ ; 2019589//NSF | GEO | Division of Ocean Sciences (OCE)/ ; },
mesh = {*Metagenome ; Pacific Ocean ; *Transcriptome ; *RNA, Transfer/genetics ; *Seawater/microbiology ; Ecosystem ; Microbiota ; },
abstract = {The roles of marine microbes in ecosystem processes are inherently linked to their ability to sense, respond, and ultimately adapt to environmental change. Capturing the nuances of this perpetual dialogue and its long-term implications requires insight into the subtle drivers of microbial responses to environmental change that are most accessible at the shortest scales of time. Here, we present a multi-omics dataset comprising surface ocean metagenomes, metatranscriptomes, tRNA transcripts, and biogeochemical measurements, collected every 1.5 hours for 48 hours at two stations within coastal and adjacent offshore waters of the tropical Pacific Ocean. We expect that this integrated dataset of multiple sequence types and environmental parameters will facilitate novel insights into microbial ecology, microbial physiology, and ocean biogeochemistry and help investigate the different mechanisms of adaptation that drive microbial responses to environmental change.},
}

*Metagenome
Pacific Ocean
*Transcriptome
*RNA, Transfer/genetics
*Seawater/microbiology
Ecosystem
Microbiota

@article {pmid41344775,
year = {2026},
author = {Zhu, J and Liao, Y and Zhao, Y and Liu, J and Li, Z and Kong, X and Zhang, S and Song, C and Fu, Q and Wang, X and Xue, R and Shi, X and Tian, Y and Cao, R and You, J and Li, L},
title = {Functional division of labor within defined yeast consortia drives flavor formation during early solid-state fermentation of sichuan shai vinegar.},
journal = {Food microbiology},
volume = {135},
number = {},
pages = {104983},
doi = {10.1016/j.fm.2025.104983},
pmid = {41344775},
issn = {1095-9998},
mesh = {*Acetic Acid/metabolism/analysis ; Fermentation ; *Flavoring Agents/metabolism ; Saccharomyces cerevisiae/metabolism ; Taste ; *Microbial Consortia ; Pichia/metabolism ; Saccharomycetales/metabolism ; *Yeasts/metabolism/classification ; Ethanol/metabolism ; Fermented Foods/microbiology/analysis ; Food Microbiology ; Brettanomyces ; },
abstract = {Sichuan Shai vinegar (SSV) is a traditional fermented product with complex microbial ecology. This study elucidated the functional division of labor within the yeast microbiota during the early stage (days 1-5) of solid-state fermentation in SSV. Investigating of four key yeast strains (Saccharomyces cerevisiae, Pichia kudriavzevii, Kazachstania humilis, and Brettanomyces bruxellensis) via co-culturing, metabolomics, and simulated fermentation revealed distinct roles: Pichia kudriavzevii dominated ester synthesis, Brettanomyces bruxellensis primarily produced characteristic flavor compounds (e.g., acetaldehyde, 4-ethylguaiacol), Kazachstania humilis efficiently produced acids accelerating acidification, and Saccharomyces cerevisiae produced ethanol, which served as a precursor for ester synthesis by other yeasts. The triple-strain combination of Pichia kudriavzevii, Kazachstania humilis, and Brettanomyces bruxellensis exhibited optimal synergy, achieving peak total acid (10.96 g/100 g DW) and acetic acid (3.54 g/100 g DW) content while significantly enhancing characteristic flavor profiles. Untargeted metabolomics indicated that this combination efficiently regulated multiple flavor biosynthesis pathways through pyruvate-mediated metabolic hubs. This systematic clarification of functional roles within the yeast community provides an experimental foundation for designing synthetic microbial starters to modulate flavor profiles and advance the standardization of fermented food production.},
}

*Acetic Acid/metabolism/analysis
Fermentation
*Flavoring Agents/metabolism
Saccharomyces cerevisiae/metabolism
Taste
*Microbial Consortia
Pichia/metabolism
Saccharomycetales/metabolism
*Yeasts/metabolism/classification
Ethanol/metabolism
Fermented Foods/microbiology/analysis
Food Microbiology
Brettanomyces

@article {pmid41344333,
year = {2025},
author = {Cao, Y and Bowker, MA and Feng, Y and Delgado-Baquerizo, M and Xiao, B},
title = {The Great Wall of China harbors a diverse and protective biocrust microbiome.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.10.087},
pmid = {41344333},
issn = {1879-0445},
abstract = {The Great Wall of China, one of the most emblematic human heritage sites ever built, is largely covered by a living skin that has a potentially distinct microbiome compared with bare wall surfaces. However, the structure and function of this microbiome remain virtually unknown, which hampers any effort to understand the impacts of this microbiome on the long-term conservation of the Great Wall. Here, we investigated the microbiome of the Great Wall at six sampling sites along a 600-km section, which stretches across arid and semiarid climates and is covered by a mosaic of biological soil crusts (biocrusts) and exposed wall surfaces. We hypothesized that these biocrusts could establish a unique microhabitat and support a microbiome with a community structure and function potentially distinct from those on bare walls, thereby modulating the biodeterioration processes affecting the Great Wall. Our findings revealed that biocrust-covered sections exhibited a 12%-62% increase in abundance, diversity, and co-occurrence network complexity for bacterial and fungal communities compared with bare walls. Further metagenomic analyses indicated that the biocrust cover enhanced the abundance of overall functional genes and stress-resistance pathways within the microbiome by 4%-15%, while decreasing the metabolic pathways linked to heritage biodeterioration. Aridity was an additional determinant of the microbiome. Our work serves as a critical step toward understanding the microbiome of the Great Wall, which contributes to conserving this unparalleled human monument for future generations.},
}

@article {pmid41344264,
year = {2025},
author = {Li, C and Li, S and Ma, L and Wang, H and Li, X and Li, M and Yang, Q},
title = {Allantoin enhances growth and nutrient accumulation in Dioscorea opposita under saline-alkali stress through regulation of ion homeostasis and antioxidant capacity.},
journal = {Plant physiology and biochemistry : PPB},
volume = {229},
number = {Pt E},
pages = {110819},
doi = {10.1016/j.plaphy.2025.110819},
pmid = {41344264},
issn = {1873-2690},
abstract = {Saline-alkali stress (SAS) significantly impairs crop growth, yield and quality, while allantoin plays a crucial role in enhancing plant tolerance to this stress. Yam (Dioscorea opposita Thunb.) has substantial nutritional and medicinal value. However, the regulatory mechanism of allantoin in regulating yam growth and nutritional quality under SAS remains largely unclear. In this study, we found that SAS severely inhibited the growth and root development of yam bulbil seedlings. Specifically, in leaves, the contents of osmotic regulators (e.g., proline, soluble sugar) and malondialdehyde (MDA), along with the activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), were significantly increased. Additionally, leaf Na[+] content was increased, K[+] content was decreased, and the Na[+]/K[+] ratio was significantly elevated. Meanwhile, the contents of allantoin, diosgenin, and polysaccharides in tubers were significantly increased. Overexpression of the allantoin synthase gene DoAS in Arabidopsis thaliana further enhanced its tolerance to SAS. Furthermore, compared with the SAS-only group, allantoin treatment significantly improved yam seedling growth, reduced leaf proline and MDA contents, enhanced SOD and POD activities, decreased the Na[+]/K[+] ratio, increased tuber yield and contents of major active components, and lowered tuber Na[+] content. Taken together, allantoin significantly improves ionic balance and antioxidant capacity in yam bulbil seedlings under SAS, thereby promoting seedling growth and nutrient accumulation in tubers. This study thus highlights the critical role of allantoin in regulating the growth and nutrient accumulation in tuber crops under SAS.},
}

@article {pmid41342921,
year = {2025},
author = {Taurozzi, D and Scalici, M},
title = {Regional γ Diversity of Diatoms in Mediterranean and Alpine Temporary Ponds.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02670-6},
pmid = {41342921},
issn = {1432-184X},
abstract = {Temporary ponds, characterized by periodic or intermittent hydroperiods, are globally widespread in all the biogeographical regions and host peculiar biotic communities. Here we investigated shifts in diatom community assemblages across two contrasting biogeographical regions in Italy, the Mediterranean and the Alpine. The study focused on 24 temporary ponds, with 12 ponds sampled at Castelporziano (CP) and 12 at Campo Imperatore (GS). Our results highlighted that γ diversity varied significantly between the two study sites, indicating a notably greater species richness in GS compared to CP. In GS, functional richness values were generally higher, whereas no significant differences were detected for functional distance and functional divergence. Species composition differed significantly between CP and GS indicating that the two sites host distinct communities, with species turnover (0.904) which contributed most to total beta diversity (0.926), while nestedness (0.021) was negligible. CP communities were characterized by pronounced functional clustering in specific sites while GS exhibited both clustering and slight overdispersion. However, although GS communities occupy slightly larger trait space, both regions shared most functional strategies, reflecting substantial redundancy in functional traits across the two environments. Overall, diatom communities in the GS were characterized by higher frequencies of small, mobile, low-profile, and mucilaginous-tube taxa, whereas CP ponds displayed relatively higher representation of larger or motile forms. Although our study is a starting point, large-scale analyses of diatom communities are crucial, as climate change may rapidly and irreversibly alter taxonomic and functional diversity, profoundly affecting the ecology of these temporary habitats and surrounding landscapes.},
}

@article {pmid41342600,
year = {2025},
author = {Bauchinger, F and Berry, D},
title = {Metatranscriptomic-driven insights into mucosal glycan degradation by the human gut microbiota.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf118},
pmid = {41342600},
issn = {1574-6941},
abstract = {The secreted mucus layer in the human gastrointestinal tract constitutes both a protective boundary between gut lumen and epithelium as well as an important nutrient source for members of the gut microbiota. While many gut microbes possess the genetic potential to degrade mucin it is still unclear which species transcribe the respective genes. Here, we systematically analyzed publicly available metagenome and metatranscriptome datasets to characterize the gut microbial community involved in mucosal glycan degradation. We utilized co-occurrence network analysis and linear regression to elucidate the ecological strategies of, and relationship between, mucus degraders. We found that although approximately 60% of species carrying genes encoding for mucosal-glycan-degrading enzymes have detectable transcription of these genes, only 21 species prevalently transcribe more than 1 gene. Furthermore, the transcription of individual genes was frequently dominated by single species in individual samples. Transcription patterns suggested the presence of competitive mucosal glycan degraders characterized by abundance-driven transcription that were negative predictors for the transcription of other degraders as well as opportunistic species with decoupled abundance and transcription profiles. These findings provide insights into the ecology of the mucosal glycan degradation niche in the human gut microbiota.},
}

@article {pmid41341498,
year = {2025},
author = {Sun, D and Šmilauer, P and Pjevac, P and Rozmoš, M and Forczek, ST and Kotianová, M and Hršelová, H and Bukovská, P and Jansa, J},
title = {Arbuscular mycorrhiza suppresses microbial abundance, and particularly that of ammonia oxidizing bacteria, in agricultural soils.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1671859},
pmid = {41341498},
issn = {1664-302X},
abstract = {Interactions between arbuscular mycorrhizal (AM) fungi and ammonia-oxidizing (AO) microorganisms, two important microbial guilds contributing to soil-plant mineral nutrient cycling, are complex, given the high variability of soil biological, physical, and chemical properties. In addition, AO microorganisms are generally slow growing and require ample time to establish. Their communities are thus difficult to reconstruct under laboratory conditions, for example after soil sterilization. Therefore, in this study, we investigated quantitative and compositional responses of indigenous microorganisms occurring in 50 different field soils (collected from grasslands and arable fields) to actively growing mycelium of the AM fungus Rhizophagus irregularis. To this end, we quantified the abundance of various microbial guilds including AO bacteria (AOB), AO archaea (AOA), and comammox Nitrospira in pot-incubated soils exposed or not to actively growing AM fungus. Across the variety of soils, we observed systematic suppression by the AM fungus of different microbial groups including bacteria, protists, and fungi. The strongest suppression was noted for AOB and comammox Nitrospira, whereas the abundance and community structure of AOA remained unaffected by the AM fungal activity. Mycorrhizal suppression of AOB abundance was accompanied by changes in AOB community structure and correlated with soil pH. Contrary to the expected competition between AM fungus and AO microorganisms for available ammonium (NH4 [+]) in the soil solution, the presence of the actively growing AM fungus significantly increased soil NH4 [+] levels as compared to the non-mycorrhizal control, at least upon the final destructive harvest. Thus, the interaction between the AM fungi and AO microorganisms likely goes beyond the simple competition for the free ammonium ions and might involve microorganisms active in other pathways of soil nitrogen cycle (e.g., mineralization) or temporarily different trajectories of nutrient use in mycorrhizal vs. non-mycorrhizal systems. Alternatively, elusive biological nitrification inhibitors may have contributed to the observed effect, produced by the AM fungus or its host plant, and subsequently transported to the root-free soil via the AM fungal hyphae.},
}

@article {pmid41339548,
year = {2025},
author = {Singleton, CM and Jensen, TBN and Delogu, F and Knudsen, KS and Sørensen, EA and Jørgensen, VR and Karst, SM and Yang, Y and Sereika, M and Petriglieri, F and Knutsson, S and Dall, SM and Kirkegaard, RH and Kristensen, JM and Overgaard, CK and Woodcroft, BJ and Speth, DR and Aroney, STN and , and Wagner, M and Dueholm, MKD and Nielsen, PH and Albertsen, M},
title = {The Microflora Danica atlas of Danish environmental microbiomes.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {41339548},
issn = {1476-4687},
abstract = {Over the past 20 years, there have been considerable advances in revealing the microbiomes that underpin processes in natural and human-associated environments. Recent large-scale metagenome surveys have recorded the variety of microbial life in the oceans[1], in the human gut[2] and on Earth[3], with compilations encompassing thousands of public datasets[4,5]. However, despite their broad scope, these studies often lack functional information, and their sample locations are frequently sparsely distributed, limited in resolution or lacking metadata. Here we present Microflora Danica-an atlas of Danish environmental microbiomes encompassing 10,683 shotgun metagenomes and 450 nearly full-length 16S and 18S rRNA datasets, linked to a five-level habitat classification scheme. We show that although human-disturbed habitats have high alpha diversity, species reoccur, revealing hidden homogeneity. This underlines the role of natural systems in maintaining total species (gamma) diversity and emphasizes the need for national baselines for tracking microbial responses to land-use and climate change. Consequently, we focused our dataset exploration on nitrifiers, a functional group closely linked to climate change and of major importance for Denmark's primary land use: agriculture. We identify several lineages encoding nitrifier key genes and reveal the effects of land disturbance on the abundance of well-studied, as well as uncharacterized, nitrifier groups, with potential implications for N2O emissions. Microflora Danica offers an unparalleled resource for addressing fundamental questions in microbial ecology about what drives microbial diversity, distribution and function.},
}

@article {pmid41338824,
year = {2025},
author = {Guo, M and Chen, C and Wang, W and Zhang, C and Ma, J and Sadike, M and Niyazi, M and Feng, X and Zhu, K},
title = {Research on the relationship between HPV infection and alterations in vaginal microbial ecology.},
journal = {Enfermedades infecciosas y microbiologia clinica (English ed.)},
volume = {43},
number = {10},
pages = {688-697},
doi = {10.1016/j.eimce.2025.07.006},
pmid = {41338824},
issn = {2529-993X},
mesh = {Female ; Humans ; *Vagina/microbiology/virology ; Adult ; *Papillomavirus Infections/microbiology ; *Microbiota ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Young Adult ; },
abstract = {OBJECTIVE: To investigate the changes in vaginal microbiota under different HPV infection statuses and explore the correlation between vaginal microbiota alterations and HPV infection.

METHODS: 151 cervical samples from gynecological outpatients were grouped into HPV-negative (HN, N=51), transient infection (HTI, N=42), and persistent infection (HPI, N=58). Vaginal secretions were collected to assess microecology (pH, vaginal cleanliness, hydrogen peroxide, leukocyte esterase) via genital secretion analyzer. 16S ribosomal RNA (rRNA) sequencing analyzed vaginal microbiota characteristics, community state types (CST), richness, diversity, and biomarkers.

RESULTS: 16S rRNA sequencing identified 5 CST II, 52 CST III, and 94 mixed CST IV samples, showing diverse microbiota. Compared with HN, HTI and HPI had lower vaginal cleanliness, higher sialidase activity, elevated pH, and fewer Lactobacilli (P<0.05). Lactobacillus iners dominated all groups, while Sneathia amnii was significantly higher in HPI (P<0.05). HPV infection increased vaginal microbiota richness (HPI>HTI/HN, P<0.05), with distinct group compositions (P<0.05). Linear Discriminant Analysis Effect Size identified Lactobacillus gasseri, Atopobium vaginae, and Lactobacillus jensenii as biomarkers.

CONCLUSION: This study found significant differences in microbial community characteristics under different HPV infection statuses. The identification of biomarkers in vaginal microbiota under different infection statuses could provide new targets for clinical screening and prevention of cervical cancer.},
}

Female
Humans
*Vagina/microbiology/virology
Adult
*Papillomavirus Infections/microbiology
*Microbiota
Middle Aged
RNA, Ribosomal, 16S/genetics
Young Adult

@article {pmid41335295,
year = {2025},
author = {Jayanandan, M and Veeraraghavan, VP and Govindarajan, S and Mariyappa Subramani, S},
title = {Development of oral dysbiosis following use of antimicrobial mouthwashes: a systematic review.},
journal = {Odontology},
volume = {},
number = {},
pages = {},
pmid = {41335295},
issn = {1618-1255},
abstract = {The oral microbiome maintains the oral and systemic health. The extensive use of antimicrobial mouthwashes to control biofilm-related diseases has increased the concerns about their effect on microbial ecology. Specific formulations may cause microbial shifts which influences both the oral and systemic physiology in an individual. This systematic review evaluates the oral dysbiosis development after antimicrobial mouthwash use and correlates the microbial changes with clinical and systemic outcomes. A comprehensive search in various databases like PubMed, Scopus, etc. (till March 2025) was done. It identified 14 relevant studies from a total of 681 screened records. Risk of bias was assessed using ROB2, ROBINS-I, CRIS, and NOS tools, with data extracted on microbial diversity, taxonomic changes, nitrate reduction capacity, and antibiotic resistance. The findings showed that chlorhexidine caused the greatest dysbiosis and reduces the microbial diversity by 40-60%, with increasing Streptococcus spp. two-to-threefold, and elevating antibiotic resistance gene prevalence. Cetylpyridinium chloride and polyhexamethylene biguanide showed milder effects, thus preserving 70-80% of commensals, while herbal and plant-based rinses (o-cymen-5-ol, StellaLife®, Rosella) reduced pathogens by 25-40% without disrupting the balance. Fluoride-arginine formulations promote beneficial bacteria by 30-50% but marginally upregulated resistance genes, whereas mechanical hygiene methods maintained over 90% microbial diversity. Suppression of nitrate-reducing bacteria was associated with reduced nitric oxide bioavailability, potentially increasing vascular and cognitive risks. Hence, antimicrobial mouthwashes especially chlorhexidine induces significant dysbiotic shifts, while herbal, postbiotic, and mechanical alternatives demonstrate safer, microbiome thereby preserving the effects which is suitable for long-term oral health maintenance.},
}

@article {pmid41333479,
year = {2025},
author = {Ni, Z and Zhou, W and Gao, Y},
title = {A social-architecture perspective on gut microbiota dynamics and host physiology.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1642080},
pmid = {41333479},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/immunology ; Animals ; *Host Microbial Interactions ; Homeostasis ; },
abstract = {The human gut microbiota, a dynamic consortium of trillions of microorganisms, is increasingly recognized not merely as a metabolic entity but as a structured "microbial society" exhibiting hierarchical organization, cooperative networks, and competitive exclusion. This hypothesis posits that gut microbiota communities operate under principles analogous to social structures, with emergent behaviors that directly impact host health. By integrating recent advances in microbial ecology, spatial omics, and neurogastroenterology, this paper proposes those microbial social dynamics-such as division of labor, territorial specialization, and collective decision-making-mediate critical host functions, including immune regulation, metabolic homeostasis, and cognitive processes. In research or therapy targeting the gut microbiota, safeguard the stability of the microbial society and eschew simplistic, blunt approaches. In short, the gut microbiota behaves like a collective mind, showing tight unity and rapid, fine-tuned adaptation to external cues. Its imbalance breeds disease; its vigor enhances human life.},
}

Humans
*Gastrointestinal Microbiome/physiology/immunology
Animals
*Host Microbial Interactions
Homeostasis

@article {pmid41330424,
year = {2025},
author = {Zöhrer, J and Ascher-Jenull, J and Prem, EM and Wagner, AO},
title = {State-Specific Extraction of Environmental DNA: Spike-and-Recovery Controls to Validate and Optimise Extraction Protocols.},
journal = {Environmental microbiology},
volume = {27},
number = {12},
pages = {e70209},
doi = {10.1111/1462-2920.70209},
pmid = {41330424},
issn = {1462-2920},
support = {P36711//Austrian Science Fund/ ; },
mesh = {*DNA, Environmental/isolation & purification ; *DNA, Bacterial/isolation & purification ; *Bacteria/genetics/isolation & purification/classification ; Polymerase Chain Reaction ; *Environmental Microbiology ; },
abstract = {Getting insights into the quantitative and qualitative contribution of different DNA states, i.e., extracellular (exDNA) and intracellular DNA (iDNA), to the total environmental DNA (eDNA) pool requires reliable methods for their separation. Even though a multitude of respective extraction protocols has been published, their validation is often missing. Here, we selected four protocols for the state-specific extraction of eDNA and traced the separation of exDNA and iDNA within natural environments using previously designed spike-and-recovery controls. Besides accounting for the different eDNA states, the spike-ins also distinguished different bacterial origins (gram-positive, gram-negative). Following their quantification by digital PCR, the recovery of exDNA and iDNA spike-ins in both the target as well as nontarget eDNA states differed among the selected extraction protocols and environmental matrices, albeit the effect of the former was far more decisive. While the recovery of exDNA spike-ins was mainly affected by the chemical composition of the washing buffer and the duration of each washing step, the lysis method determined the recovery of spiked iDNA. These aspects were further combined within an optimised protocol, providing a valuable step towards a more concise understanding of factors governing the state-specific extraction of eDNA and hence their relevance in molecular microbial ecology.},
}

*DNA, Environmental/isolation & purification
*DNA, Bacterial/isolation & purification
*Bacteria/genetics/isolation & purification/classification
Polymerase Chain Reaction
*Environmental Microbiology

@article {pmid41325059,
year = {2025},
author = {Zhang, Y and Walker, RW and Kaplan, RC and Qi, Q},
title = {Added sugars, gut microbiota, and host health.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2592431},
doi = {10.1080/19490976.2025.2592431},
pmid = {41325059},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Animals ; Bacteria/classification/metabolism/genetics/isolation & purification ; *Dietary Sugars/adverse effects/metabolism ; Fatty Acids, Volatile/metabolism ; Obesity/microbiology ; },
abstract = {Excessive intake of added sugars is a global public health concern, given its established links with cardiometabolic disease and other chronic conditions. Emerging evidence suggests that the gut microbiota might mediate the harms of high sugar intake. In this review, we summarize evidence from animal and human studies regarding the impact of added sugar intake on gut microbiota diversity and composition, and discuss potential mechanisms linking sugar-induced microbial changes to health outcomes. Added sugars, including glucose, fructose, and sucrose, can alter gut microbial diversity, enrich sugar-utilizing taxa, and deplete short-chain fatty acid-producing bacteria. These microbial changes may impair gut barrier integrity, increase luminal oxygen and alternative electron acceptors under inflammatory conditions, reduce short-chain fatty acid production, alter bile acid and amino acid metabolism, and promote translocation of endotoxin across the gut barrier into the bloodstream. Collectively, these pathways may link added sugar intake to irritable bowel syndrome, obesity, liver steatosis, diabetes, and cardiovascular diseases. However, inconsistent results on alterations in the gut microbiota related to added sugar intake were observed across studies, which may be due to differences in sugar dose and form (liquid vs. solid), as well as population variation in background diet, host genetics, and gut microbial ecology. Future research should focus on mechanistic investigations, characterization of inter-individual variability in response to added sugar intake, and clinical studies to assess whether dietary or therapeutic interventions can reverse sugar-induced gut microbial changes and improve host health outcomes.},
}

Humans
*Gastrointestinal Microbiome/drug effects
Animals
Bacteria/classification/metabolism/genetics/isolation & purification
*Dietary Sugars/adverse effects/metabolism
Fatty Acids, Volatile/metabolism
Obesity/microbiology

@article {pmid41321823,
year = {2025},
author = {Zheng, Z and Xie, D and Han, Y and Li, G and Wang, S and Zhang, X and Huang, T and Xu, W and Wu, G},
title = {Deciphering the urinary microbiome and urological cancers: from correlation to mechanisms and treatment.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1699308},
pmid = {41321823},
issn = {1664-302X},
abstract = {Given that the sterility of urine and the urinary tract has been questioned by research, urinary microbiome dysbiosis has been recognized as one of the potential cancer-promoting factors. The composition of the urinary microbial community in healthy individuals has a relatively high similarity at the phylum level, with factors like age and gender influencing the expression and distribution. In contrast, the urinary microbiome of patients with urologic cancers shows significant variability and diversity depending on the type of cancer. Most of the early studies focused on the distribution, aggregation, and expression of microbiota in urologic cancers, warranting advanced studies on the causal relationship between microbes and urologic cancers. Bladder and prostate cancer tumorigenesis and progression can be influenced by microbes through chronic inflammatory or immunomodulatory pathways making them cancer models strongly associated with the urinary microbiome. Here, we summarize the expression characteristics of the microbiomes associated with these cancers and analyze the pathophysiological mechanisms and signaling pathways of the microbiome in the tumor promotion or suppression. By examining the role played by the urinary microbiome in the pathogenesis of urologic cancers, we assess the potential of specific microbial groups as biomarkers for diagnosis and surveillance. Additionally, involving the microbiome or using adjunctive participation in tumor therapy is becoming an emerging cancer treatment option. Improving urinary microbial homeostasis in urinary cancers by direct treatment with microbial products, microbial co-immunotherapy, probiotic-assisted therapy, and fecal microbial transplantation may broaden the scope of therapy and enhance the efficacy of conventional medicines.},
}

@article {pmid41321415,
year = {2025},
author = {Horstmann, L and Lipus, D and Bartholomäus, A and Oses, R and Kitte, A and Friedl, T and Wagner, D},
title = {Microbial ecology of subsurface granitic bedrock: a humid-arid site comparison in Chile.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf199},
pmid = {41321415},
issn = {2730-6151},
abstract = {Subsurface microorganisms face extreme challenges such as anoxic, xeric, and oligotrophic conditions. In igneous systems, nutrient limitation is critical, as biomass input relies on surface-derived fluids via tectonic fractures. Despite growing interest in subsurface habitats, little is known about ecosystems beneath arid landscapes, where surface water input is limited by the low annual precipitation. This study compares granitic subsurface environments beneath arid and humid surface ecosystems, highlighting the link between surface climate and subsurface biodiversity. DNA was extracted from granitic subsurface rocks recovered from two endmember sites along a north-south climate gradient in Chile's Coastal Cordillera. Microbial communities inhabiting down to 55 m deep subsurface rocks were characterized using 16S rRNA amplicon and shotgun metagenomic sequencing. We identified an abundant and potentially active subsurface community below both climates dominated by heterotrophic bacteria, including Pseudarthrobacter, Janthinobacterium, and Pseudomonas. However, rare taxa affiliated with common chemolithoautrophs, e.g. Thiobacillus, Sulfuriferula, and Sulfuricurvum, were only observed in the arid subsurface, indicating increased oligotrophic conditions and reliance on inorganic electron donors in the deeper subsurface of the desert. Functional analysis revealed sulphur, hydrogen, and carbon monoxide as potential inorganic electron donors. These findings expand the current understanding of microbial life in the subsurface of granite rocks showing the influence of surface climate on nutrient conditions in the deeper subsurface, providing new insights into the extent and functional capacity of terrestrial subsurface habitats and their role in global biogeochemical processes.},
}

@article {pmid41320393,
year = {2026},
author = {Wang, S and De Paepe, K and Onyango, SO and Zhang, B and Huang, Q and Wang, S and Van de Wiele, T},
title = {Starch-entrapped microspheres selectively promote propionate or butyrate production through individual-specific modulation of the human fecal microbiome.},
journal = {Carbohydrate polymers},
volume = {373},
number = {},
pages = {124614},
doi = {10.1016/j.carbpol.2025.124614},
pmid = {41320393},
issn = {1879-1344},
mesh = {Humans ; *Starch/chemistry/pharmacology ; *Feces/microbiology ; *Microspheres ; Prebiotics ; *Butyrates/metabolism ; *Propionates/metabolism ; *Gastrointestinal Microbiome/drug effects ; Adult ; Male ; Zea mays/chemistry ; Female ; Inulin/chemistry ; Fermentation ; Young Adult ; },
abstract = {Starch microspheres encapsulated with chitosan synergistically and beneficially modulate the microbiota composition and metabolic activity of a pooled fecal slurry compared to starch, suggesting a superior prebiotic potential. Interindividual differences in prebiotic potential are, however, unexplored. Therefore, we incubated starch-entrapped microspheres (MS), high amylose maize starch (HAMS) and the reference prebiotic inulin with the separate fecal microbiota derived from six healthy individuals. The variation in microbial community composition was largely driven by inter-individual variability (effect size of 71.7 %). Despite the inter-individual variability, the different prebiotic substrates significantly affected the microbiota composition (effect size of 9.5 %) and metabolic activity over the course of fermentation. MS delayed the fermentation and reduced the gas production and acidification in all donors compared to HAMS and inulin. Furthermore, compared to HAMS, MS more effectively promoted propionate or butyrate production in a donor-dependent manner. MS increased butyrate levels with 0.1 ± 0.72 mM per unit of starch across all donors. Additional, MS increased the propionate production with 0.52 ± 0.71 mM per unit of starch in donors 1, 2, 4, 6. The donor-specific propiogenic and butyrogenic effects of MS were linked to the enrichment of Bacteroides and Agathobacter species. Our findings confirm the superior prebiotic effect of MS and provide directions for the design and manufacture of starch-based functional foods to enhance gut health.},
}

Humans
*Starch/chemistry/pharmacology
*Feces/microbiology
*Microspheres
Prebiotics
*Butyrates/metabolism
*Propionates/metabolism
*Gastrointestinal Microbiome/drug effects
Adult
Male
Zea mays/chemistry
Female
Inulin/chemistry
Fermentation
Young Adult

@article {pmid41318730,
year = {2025},
author = {González-Pimentel, JL and Cuecas, A and Álvarez, C and Mariscal, V},
title = {Soil Bacteriome Shifts along a Cultivation Gradient in Southwestern Spanish Wetlands.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02660-8},
pmid = {41318730},
issn = {1432-184X},
abstract = {Understanding how long-term agricultural practices affect soil bacteriome is essential for sustainable land management. In the Guadalquivir Marshes of southwestern Spain, which encompass both Doñana National Park and one of Europe's most productive rice cultivation areas, decades of rice farming have transformed natural wetlands into artificial agroecosystems. Although bacterial degradation in cultivated soils has been previously suggested, comparative analyses between rice paddies and adjacent natural wetlands remain scarce.Here, we characterized the soil bacteriome across a cultivation gradient by comparing undisturbed natural marshes, within Doñana National Park, with rice fields cultivated for 25 years (Cantarita) and 80 years (Mínima 2). Using full 16S rRNA gene via long-read metabarcoding and standardized soil physicochemical assays, we analysed taxonomic composition, environmental associations, and predicted functional profiles.Our results reveal a progressive restructuring of bacterial communities with increased cultivation time, notably a significant enrichment of Chloroflexota (especially Anaerolineae) and a decline in Actinomycetota and Planctomycetota in paddy soils. Functional predictions indicated a higher potential for denitrification in cultivated soils-likely involving Chloroflexota taxa-compared to more diverse nitrogen pathways in natural sites. These shifts were strongly associated with changes in pH, electrical conductivity, calcium carbonate, and nitrate levels. Remarkably, most bacterial differences were already evident within the first 25 years of cultivation, underscoring the rapid ecological impact of intensive rice cultivation.Notably, we identified specific bacterial groups (Anaerolineae and Nocardioides in paddy soils; Euzebya, Rubrobacter, and Planctomycetota in natural wetlands), whose enrichment was associated with soil type. This approach highlights the value of integrating bacterial-based assessments into sustainable wetland management strategies.},
}

@article {pmid41318612,
year = {2025},
author = {Rivera, DS and Beltrán, V and Hoepfner, C and Del Pilar Fernández, M and Oliva, CA and Vera, MJ and Farías, C and Valenzuela, R and Pérez, I and Correa, LA and Urbina, F},
title = {Nutritional modulation of host physiology, behavior, and gut microbiome in the captive rodent Octodon degus.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-26991-1},
pmid = {41318612},
issn = {2045-2322},
support = {11190603//Fondo Nacional de Desarrollo Científico y Tecnológico/ ; },
abstract = {Diet is a key determinant of health by affecting nutrient metabolism, energy balance, body weight regulation, and mental health. The gut-brain axis is a critical pathway through which dietary factors influence cognitive function and behavior via microbial metabolites. While this relationship has been extensively studied in traditional laboratory models, diet-microbiome-cognition interactions remain largely unexplored in Octodon degus, an emerging model for aging, neurodegeneration, and cognitive research. Here, we compared two widely used rodent diets-LabDiet and Champion-to evaluate their effects on digestive efficiency, behavior, and gut microbiome composition. We also examined the relationships between these variables using piecewise structural equation modeling (pSEM). Our results indicated that LabDiet-fed degus exhibited enhanced nutrient absorption, higher fecal acetic acid levels, and a higher abundance of Actinobacteria (particularly Bifidobacterium), likely driven by its vitamin C supplementation. These animals also showed improved working memory and social motivation, but they displayed increased anxiety-like behavior. In contrast, Champion-fed degus, which consumed a more fiber-diverse, plant-based diet, showed lower anxiety traits and significantly greater gut microbial richness, with higher abundance of Bacteroidota and Tenericutes. Innate behaviors, such as burrowing and nesting, remained unaffected by the diet. SEM analysis revealed that diet explained most of the variance in microbial activity and identified a positive association between acetic acid levels and cognitive performance. This emphasizes a strong relationship among diet, microbiome, and brain function. Overall, our results suggest that dietary composition is a key factor influencing experimental outcomes in degus, with important implications for physiology, cognition, and microbial ecology. Standardizing dietary inputs is essential to ensure reproducibility in behavioral and biomedical studies using this model. Additionally, our results reinforce the microbiome's role as a mediator of diet-driven brain function via SCFAs, underscoring degus as a powerful system for investigating diet-microbiome-neurobehavioral interactions relevant to aging and mental health.},
}

@article {pmid41317466,
year = {2025},
author = {Belarbi, H and Kebede, F and De Leyn, I and Van Bockstaele, F and Van De Wiele, T and Lambrecht, F and Cakmak, I and Du Laing, G},
title = {Enhancing iodine delivery through sourdough wheat bread: influence of biofortified flour and iodized salt on iodine concentration and bioaccessibility.},
journal = {Food chemistry},
volume = {498},
number = {Pt 2},
pages = {147232},
doi = {10.1016/j.foodchem.2025.147232},
pmid = {41317466},
issn = {1873-7072},
abstract = {Iodine deficiency remains a critical health concern, particularly in populations with limited access to iodized salt or shifting dietary patterns. This study assessed the impact of iodine-biofortified wheat flour (IBF), alone or combined with iodized salt (IS), on iodine content and bioaccessibility in sourdough bread. In vitro digestion showed that IBF increased iodine content to 158 μg/kg, and to 340 μg/kg with IS, compared to 1.63 μg/kg in control bread. This corresponds to an estimated intake of 68 μg/day. The IBF + IS formulation demonstrated the highest iodine bioaccessibility (224 μg/kg; 65 %). Interestingly, while iodine-fortified breads showed reduced values for selenium, potassium, and calcium, breads made with plain salt exhibited higher bioaccessibility for these minerals. These findings confirm the efficacy of IBF in enhancing iodine intake and its potential as an alternative or complement to salt iodization. They also indicate the importance of fortification approaches, considering the broader nutritional matrix over individual nutrients.},
}

@article {pmid41315866,
year = {2025},
author = {Engelberts, JP and Tyson, GW},
title = {Understanding microbial ecology and evolution with single-cell genomics.},
journal = {Nature reviews. Genetics},
volume = {},
number = {},
pages = {},
pmid = {41315866},
issn = {1471-0064},
}

@article {pmid41315055,
year = {2025},
author = {Gallardo-Becerra, L and Cornejo-Granados, F and Bikel, S and Arenas, I and López-Leal, G and Alvarado-Gonzalez, C and Sánchez-López, F and Manzo, R and Corzo, G and Espino-Solis, GP and Canizales-Quinteros, S and Ochoa-Leyva, A},
title = {Bioactive Plasmid- and Phage-Encoded Antimicrobial Peptides (AMPs) in the Human Gut: A Metatranscriptome-Virome Profiling Reveals Exploratory Links to Metabolic Human Diseases.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02620-2},
pmid = {41315055},
issn = {1432-184X},
abstract = {Microbe-derived antimicrobial peptides (AMPs) can shape gut community structure; however, their contribution to disease-associated dysbiosis remains poorly understood. We assembled fecal metatranscriptomes from individuals with normal weight (NW), obesity (O), and obesity with metabolic syndrome (OMS), yielding 51,087 non-human transcripts. We screened 1,095 small open reading frames (smORFs) using AMP-prediction algorithms combined with stringent post-hoc bioinformatics filters identifying 51 high-confidence AMP candidates. Most matched bacterial homologs, predominantly Faecalibacterium prausnitzii, while eight mapped to plasmids or bacteriophages. Differential expression identified two and four AMPs overexpressed in O and OMS, respectively. Two of them were originated from chromosomes, three from phages, and one from plasmid. Notably, the over-expression of these AMPs was negatively correlated with healthy-associated bacteria and positively correlated with obesity-enriched taxa. Furthermore, these AMPs were broadly detectable across 372 external gut metatranscriptomes (prevalence up to 94% of the samples) indicating conservation within the human gut microbiome and highlighting mobile elements as an overlooked reservoir of transcriptionally active AMPs. Using DNA virome sequencing and prophage analyses, we suggested phage origin of the transcribed AMPs. We further synthesized a phage-encoded AMP (AMP-3020), demonstrating broad-spectrum activity against Gram-positive and Gram-negative bacteria, without detectable cytotoxicity toward human immune T cells. This supports the idea that phages could encode functional AMPs capable of shaping gut community structure by suppressing diverse bacteria without harming host immune cells. Our gut metatranscriptome-virome profiling revealed a conservative core of actively transcribed, plasmid- and phage-encoded AMPs with exploratory associations to obesity/MetS. These findings support mobile-element AMPs as candidate ecological regulators and motivate validation in larger cohorts and mechanistic models.},
}

@article {pmid41314076,
year = {2025},
author = {Md Ali, SA and Saito, S and Nishiyama, M and Phung, LD and Watanabe, T},
title = {Composted sewage sludge reshapes soil resistome connectivity and enhances antibiotic resistance gene dissemination in paddy fields.},
journal = {The Science of the total environment},
volume = {1009},
number = {},
pages = {181049},
doi = {10.1016/j.scitotenv.2025.181049},
pmid = {41314076},
issn = {1879-1026},
abstract = {The reuse of organic waste streams, such as composted sewage sludge (CSS), provides agronomic benefits, but also represents a critical pathway for the environmental dissemination of antibiotic resistance genes (ARGs). The consequences of CSS application for soil resistome dynamics and microbial ecology remain insufficiently understood. Here, we investigated paddy soils in Tsuruoka, Japan, under three fertilization treatments: CSS, chemical fertilizer (CF), and their combination (CSS + CF). Quantitative PCR targeted total bacterial (16S rRNA), fecal indicators (E. coli, Enterococcus spp.), mobile genetic element (MGE) (inlt1), and five ARGs (sul1, blaTEM, blaCTX-M Groups 1, 2, and 9). CSS amended soils showed elevated levels of intI1, sul1, and blaTEM in 2023, with blaTEM persisting into 2024. Although both E. coli and Enterococcus spp. showed weak correlations with ARGs, only Enterococcus spp. (ρ = 0.37, p < 0.05) showed statistically significant associations with intI1. Network analysis demonstrated that CSS fostered a highly interconnected resistome with sul1 emerging as a central hub linking multiple bacterial families. In contrast, CF maintained a sparse modular structure while CSS + CF generated an intermediate network. Collectively, these results demonstrate that CSS amplifies the potential for ARG dissemination by fostering a highly connected resistome, whereas co-application with chemical fertilizers partially disrupts this connectivity, thereby reducing dissemination risk in the soil environment. Our findings provide field-based evidence of the environmental impacts of waste-derived fertilization and underscore the need for integrated fertilization strategies and ARG surveillance to promote sustainable soil management and safeguard environmental health.},
}

@article {pmid41313007,
year = {2025},
author = {Fletcher, JR and Hansen, LA and Hoyser, JR and Hanna, AE and Martinez, R and Freeman, CD and Thorns, NT and Penningroth, MR and Villarreal, AR and Vogt, GA and Tyler, MA and Hines, KM and Hunter, RC},
title = {Commensal-derived short-chain fatty acids disrupt lipid membrane homeostasis in Staphylococcus aureus.},
journal = {mBio},
volume = {},
number = {},
pages = {e0139225},
doi = {10.1128/mbio.01392-25},
pmid = {41313007},
issn = {2150-7511},
abstract = {The role of commensal anaerobic bacteria in chronic respiratory infections is unclear, yet they can exist in abundances comparable to canonical pathogens in vivo. Their contributions to the metabolic landscape of the host environment may influence pathogen behavior by competing for nutrients and creating inhospitable conditions via toxic metabolites. Here, we show that the anaerobe-derived short-chain fatty acids (SCFAs) propionate and butyrate negatively affect Staphylococcus aureus physiology by disrupting branched-chain fatty acid (BCFA) metabolism. In turn, alterations to BCFA abundance impair S. aureus growth, compromise membrane integrity, diminish expression of the accessory gene regulator quorum-sensing system, and increase sensitivity to membrane-targeting antimicrobials. Disrupted BCFA metabolism also reduced S. aureus fitness in competition with Pseudomonas aeruginosa, suggesting that airway microbiome composition and the metabolites they exchange can directly impact pathogen succession over time. The pleiotropic effects of SCFAs on S. aureus fitness and their ubiquity as metabolites in the human host also suggest that they may be effective as adjuvants to traditional antimicrobial agents when used in combination.IMPORTANCEStaphylococcus aureus is a primary pathogen of chronic airway disease yet is also found in the upper airways of 30%-50% of the population to no obvious detriment. Thus, identifying the host and/or microbial factors that tip the balance between its commensal and pathogenic states may be key to its control. Here, we reveal that short-chain fatty acids produced by commensal microbiota promote a marked remodeling of the S. aureus lipid membrane that, in turn, sensitizes the pathogen to antimicrobials, disrupts accessory gene regulator quorum signaling, and reduces its competitive fitness. Altogether, these data suggest that co-colonizing microbiota and the metabolites they exchange with S. aureus may be key players in the microbial ecology of airway disease.},
}

@article {pmid41311479,
year = {2025},
author = {Gao, Y and Zhang, L and Zhang, Y and Huang, J and Wu, C and Zhou, R},
title = {Synthetic microbial community SMC-L1 optimizes flavor chemistry in reduced salt soy sauce via targeted metabolic reprogramming.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1701479},
pmid = {41311479},
issn = {1664-302X},
abstract = {The high sodium content in traditional soy sauce presents significant public health concerns, particularly related to hypertension and cardiovascular diseases. However, reducing salt content often disrupts microbial ecology and impairs flavor formation during fermentation. To overcome this challenge, we developed synthetic microbial communities (SynMCs) for reduced-salt (13% NaCl) moromi fermentation under traditional sun-brewing conditions. Using integrated multi-omics analyses, we identified an optimal consortium (SMC-L1) incorporating Tetragenococcus halophilus T10 as a key lactic acid bacterium alongside functional yeast strains. This defined community maintained fermentation stability while significantly enhancing flavor-relevant biochemical profiles. SMC-L1 inoculation markedly improved key quality parameters, increasing total nitrogen by 40.8% and amino acid nitrogen by 56.7%. Furthermore, it elevated critical metabolites including organic acids, particularly succinate, free amino acids, and short-chain esters. Network analysis revealed robust ecology-metabolite relationships: Tetragenococcus abundance correlated with succinate production and ester synthesis, while Aspergillus dynamics corresponded with free amino acid accumulation. These findings highlight how targeted microbial consortia can reprogram metabolic networks under salt-reduced conditions. From a food microbiology perspective, this study demonstrates that rational design of microbial communities can effectively decouple salt reduction from flavor deterioration in fermented foods. The metabolic pathways observed, particularly the anaerobic TCA cycle activity connecting Tetragenococcus to succinate accumulation, provides mechanistic insights into microbial adaptation to reduced-salt environments. This approach offers a viable strategy for developing healthier fermented products without compromising their sensory characteristics, advancing both fundamental knowledge and practical applications in food biotechnology.},
}

@article {pmid41307726,
year = {2025},
author = {Ferreira, CM and de Affonseca, DB and Barbosa, FAS and Campos, AB and Menezes, R and Brait, L and Viana, PAB and Trindade-Silva, AE and Loiola, M and Azevedo, AR and Coutinho, FH and Assis, APA and Bruce, T and Ramos, PIP and Ara, A and Brouns, R and Andrade, RFS and Guimarães, PR and Meirelles, PM},
title = {Rare Phyla, Such as CPR and DPANN, Shape Ecosystem-Level Microbial Community Structure Dissimilarities.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {135},
pmid = {41307726},
issn = {1432-184X},
support = {88887-468244-2019-00//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 114693/2022-6//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; RYC2022-037094-I//Ministerio de Ciencia e Innovación/ ; Serra-1709-17818//Instituto Serrapilheira/ ; },
mesh = {*Bacteria/classification/genetics/isolation & purification ; *Archaea/classification/genetics/isolation & purification ; *Microbiota ; *Ecosystem ; Metagenome ; Biodiversity ; Phylogeny ; Soil Microbiology ; },
abstract = {Rare microbial lineages, such as members of the candidate phyla radiation (CPR) bacteria and Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) archaea, are increasingly recognized as key components of microbial communities in natural systems. Yet, their global distribution, biogeographic patterns, and broader role in shaping microbial community structure across diverse ecosystems remain poorly characterized. Here, we analyzed 2860 metagenomes spanning nine ecosystems using a curated reference database and a bias-aware taxonomic filtering approach to quantify the richness, relative abundance, and structural influence of low-abundance microbial taxa on community structure across a wide range of ecosystems. Our findings reveal that rare taxa, primarily CPR and DPANN, disproportionately shape microbial community dissimilarities across global ecosystems. We observed that the richness of these two groups, that drives community structure variation, increases with latitude, peaking in temperate regions, thereby contrasting classical latitudinal diversity patterns and suggesting unique biogeographic drivers. CPR and DPANN were predominantly enriched in free-living environments, particularly groundwater and soil, then in host-associated habitats, consistent with niche specialization shaped by environmental filtering and dispersal constraints. These findings challenge abundance-centric assumptions in microbial ecology and highlight the need to integrate low-abundance taxa into macroecological frameworks. Fully resolving their ecological functions, however, will require targeted experimental and multi-omics investigations.},
}

*Bacteria/classification/genetics/isolation & purification
*Archaea/classification/genetics/isolation & purification
*Microbiota
*Ecosystem
Metagenome
Biodiversity
Phylogeny
Soil Microbiology

@article {pmid41304320,
year = {2025},
author = {Tawidian, P and Tucker, BJ and Zembsch, TE and Ip, HS and Bartholomay, LC},
title = {Infection-Mediated Shifts in the Microbial Communities of Deer-Fed Ixodes scapularis Ticks.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
pmid = {41304320},
issn = {2076-2607},
support = {cooperative agreement U01CK000505/CC/CDC HHS/United States ; G21AC10134//United States Department of Agriculture/ ; },
abstract = {The holobiont of the blacklegged tick (Ixodes scapularis) includes maternally inherited rickettsial endosymbionts and environmentally acquired microbes that may influence tick fitness and vector competence. While previous studies have focused on characterizing the microbiota of I. scapularis ticks, less is known about the influence of tick infection status on microbial assemblages. Here, we collected engorged female I. scapularis ticks from hunter-harvested white-tailed deer (Odocoileus virginianus) across 11 counties in Wisconsin during fall 2022. The ticks were maintained in laboratory conditions for oviposition and then frozen for nucleic acid extraction. The infection status of each tick was determined using qPCR, targeting Borrelia spp., Babesia spp., and Powassan virus. Bacterial and fungal communities were characterized through amplicon-based sequencing targeting the 16S rRNA gene and ITS2 region, respectively. Our targeted pathogen testing revealed that 14.1% of the collected ticks were infected with Babesia odocoilei and 23.3% with Borrelia burgdorferi. The microbial community composition of ticks was significantly influenced by infection status and pathogen identity. Notably, Borrelia-infected ticks exhibited distinct microbiota profiles and increased microbial network connectivity. These findings provide new insights into the microbial ecology of deer-fed I. scapularis ticks and highlight the role of infection in shaping both microbiota and mycobiota communities.},
}

@article {pmid41304309,
year = {2025},
author = {Paoli, JE and Thongthum, T and Bassett, M and Beardsley, J and Tagliamonte, MS and Cash, MN and Spertus Newman, J and Smith, LM and Anderson, BD and Salemi, M and Subramaniam, K and von Fricken, ME and Braun de Torrez, E and Mathis, V and Mavian, CN},
title = {Virome and Microbiome of Florida Bats Illuminate Viral Co-Infections, Dietary Viral Signals, and Gut Microbiome Shifts.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112625},
pmid = {41304309},
issn = {2076-2607},
support = {Department of Pathology EPIG RAS 2021-2022//University of Florida/ ; Florida Informatics Institute SEED 2022-2023//University of Florida/ ; Biodiversity Institute SEED 2022-2023//University of Florida/ ; },
abstract = {Florida's bat virome remains poorly characterized despite the state's high bat species diversity and conservation importance. We characterized viral metagenomes from rectal tissues, anal swabs, and feces of Myotis austroriparius and Tadarida brasiliensis sampled across north Florida. We recovered a near-complete Hubei virga-like virus 2 (HVLV2) genome from T. brasiliensis feces, a finding consistent with an arthropod-derived dietary signal rather than active bat infection. An Alphacoronavirus (AlphaCoV) was detected in two M. austroriparius specimens, including one with a putative co-infection involving an Astrovirus (AstV), the first detection of AstV in Florida bats to date. Parallel profiling of the M. austroriparius gut microbiome highlighted compositional differences in the co-infected individual relative to AlphaCoV-only and virus-negative bats, suggestive of potential associations between viral detection and gut microbial shifts. Our study expands the known viral diversity in Florida bat populations, and demonstrates how metagenomics can simultaneously illuminate host diet, viral exposure, and gut microbial ecology. This approach provides a scalable framework for monitoring how diet, microbiome composition, and environmental pressures shape the bat virome, and inform conservation and zoonotic risk assessments.},
}

@article {pmid41304257,
year = {2025},
author = {Ma, R and Chen, Y and Chen, X and Zhang, J and Liu, C and Yang, L and Song, Y and Sun, Z and Lin, X and Ai, T and Ren, D and Chen, S},
title = {The Dominant Role of Dietary Differences in Shaping the Intestinal Microbial Communities of Grass Carp, Carp, and Crucian Carp in a Saline-Alkali Lake in Xinjiang During Winter.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112572},
pmid = {41304257},
issn = {2076-2607},
support = {Grant No. 2023YFD2401000;Grant No.2023TSYCCX0128;2024AB019;Grant No. XJARS-08-14//The Key R & D plan of Ministry of Science and Technology;The Tianshan Talent Training Project of Xinjiang;The Key Scientific and Technological Research Projects of Xinjiang Production and Construction Corps;Xinjiang Agriculture Research System/ ; },
abstract = {In this study, gut microorganisms of herbivorous grass carp, omnivorous carp, crucian carp, and aquatic microorganisms were collected from natural salt-alkali lakes and ponds in Xinjiang in winter to analyze their community structures. We sequenced 16S rRNA amplicons to investigate the composition and function of the microorganisms in the gut. PCoA analysis revealed that the gut microbiota of herbivorous and omnivorous fish formed two distinct clusters. Proteobacteria, Actinobacteria, Desulfobacterota, Firmicutes, and Chloroflexia are the dominant bacteria in the gut of fish. Proteobacteria, Bacteroidetes, Actinobacteria, Cyanobacteria, and Gram-negative bacteria are the dominant bacteria in the water. Carbohydrate- and protein-degrading bacteria, such as Desulfofustis, Lactiplantibacillus, and Vibrio, were predominant in omnivorous fish (CC and GRC), while cold-resistant bacteria, such as Shewanella and Psychromonas, were colonized in grass carp. This suggests that the same environment does not lead to similar gut bacteria, and that specific endogenous factors play a far more important role in shaping the microbiota composition than environmental factors.},
}

@article {pmid41304168,
year = {2025},
author = {Ouyang, H and Grześkowiak, Ł and Vahjen, W and Zentek, J and Martínez-Vallespín, B},
title = {Effects of Fibrous By-Products on Growth Performance, Ileal Nutrient Digestibility, Intestinal Morphology, and Microbiota Composition in Weaned Piglets.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112482},
pmid = {41304168},
issn = {2076-2607},
abstract = {Three fibrous by-products were evaluated over a 35-day feeding period in 64 weaned piglets, randomly assigned to four groups: a control without by-products (CON) and three others with diets containing 8% carrot pomace (CRT), 8% brewers' spent grain (BSG), or 8% carob pods (CRB). The growth performance, feed intake, feed conversion ratio, and apparent ileal digestibility of protein and amino acids were not affected. The jejunal and colonic morphology showed no statistical differences, although small numerical increases in the villus height and villus height-to-crypt ratio were noted with the by-products. Total short-chain fatty acid concentrations were stable, but their profile shifted: acetate increased in CRT and CRB (p < 0.001) mainly at the expense of propionate (p = 0.005). The microbiota composition in the proximal colon showed modest changes, with the highest Bifidobacterium spp. abundance in CRT and lowest in CRB (p = 0.042), reduced Ruminococcaceae UCG 005 with all the by-products (p = 0.008), and greater microbial richness in CRB (p = 0.009). These results suggest that a moderate inclusion of fibrous by-products may influence intestinal microbial ecology and fermentation patterns without negatively affecting performance or nutrient digestibility in weaned piglets, with no source appearing superior, thereby highlighting their potential as sustainable feed ingredients.},
}

@article {pmid41304165,
year = {2025},
author = {Tong, F and Feng, X and Yuan, H and Chen, Y and Chen, P},
title = {Oyster Aquaculture Impacts on Environment and Microbial Taxa in Dapeng Cove.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112480},
pmid = {41304165},
issn = {2076-2607},
support = {SML2023SP237//Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai)/ ; 2023TD06//Central Public-interest Scientific Institution Basal, Research Fund, CAFS/ ; 2024YFD2401405; 2024YFB4206600//National Key Research and Development Program of China/ ; },
abstract = {Environmental physicochemical factors and microorganisms play critical roles in the health of oysters. However, the impact of high-density oyster farming-a highly efficient filter-feeding bivalve system-on environmental conditions and microbial community structure and function remains poorly understood. This study conducted four-season monitoring of the water and sediment parameters in a semi-enclosed bay commercial oyster aquaculture (OA) system and a control area (CT), coupled with 16S rRNA amplicon sequencing of the environmental microbiota. Oyster aquaculture caused negligible disruption to water column parameters but significantly increased the concentrations of total organic carbon (TOC, annual mean OA vs. CT:1.15% vs. 0.56%), sulfides (annual mean OA vs. CT:67.72 vs. 24.99 mg·kg[-1]), and heavy metals (Cd, Pb, Cu, Zn, and Cr) in the sediment. α-diversity (Shannon and Chao indices) exhibited minimal overall perturbation, with significant inter-regional differences observed only in winter for both water and sediment. The bacterial community structure of the water column was significantly altered only in winter, whereas sediment communities showed structural shifts in spring, summer, and autumn. Water microbiota were primarily influenced by turbidity, dissolved oxygen, salinity, the Si/N ratio, and silicates. Sediment microbiota were correlated with Pb, Cu, Zn, TOC, Cr, and sediment particle size. Water bacterial functions displayed only four significantly divergent biogeochemical processes annually (sulfur compound respiration; OA vs. CT). In contrast, sediment bacteria exhibited 29 significantly disrupted functions annually, with the greatest seasonal divergence in winter (11/67 functions). Spring, summer, and autumn sediment functions showed distinct patterns. Understanding these environmental-microbial interactions is essential for sustainable oyster aquaculture and ecological optimization.},
}

@article {pmid41304129,
year = {2025},
author = {Zhong, Y and Wu, C and E, J and Gu, Y and Chi, H and Du, X},
title = {Bioavailability, Ecological Risk, and Microbial Response of Rare Earth Elements in Sediments of the Remediated Yitong River: An Integrated DGT and Multi-Parameter Assessment.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112443},
pmid = {41304129},
issn = {2076-2607},
abstract = {The expanding use of rare earth elements (REEs) in high-tech industrials has increased their environmental release, raising concerns about their ecological risks. This study employed the Diffusive Gradients in Thin Films (DGT) technique to assess REE bioavailability, spatial distribution, and ecological risks of REEs in sediments of the Yitong River, a historically polluted urban river in Changchun, China. Sediment characteristics (organic matter, pH, salinity), nutrient dynamics (N, P), and metal concentrations (Fe, Mn, As, etc.) were analyzed alongside REEs to evaluate their interactions and environmental drivers. Results revealed that REE concentrations (0.453-1.687 μg L[-1]) were dominated by light REEs (50.1%), with levels an order of magnitude lower than heavily industrialized regions. Ecological risk quotients (RQ) for individual REEs were below thresholds (RQ < 1), indicating negligible immediate risks, though spatial trends suggested urban runoff influences. Probabilistic risk assessment integrating DGT data and species sensitivity distributions (SSD) estimated a low combined toxic probability (2.26%) for REEs and nutrients. Microbial community analysis revealed correlations between specific bacterial (e.g., Clostridium, Dechloromonas) and fungal genera (e.g., Pseudeurotium) with metals and REEs, highlighting microbial sensitivity to pollutant shifts. This study provides a multidimensional framework linking REE bioavailability, sediment geochemistry, and microbial ecology, offering insights for managing REE contamination in urban riverine systems.},
}

@article {pmid41304117,
year = {2025},
author = {Guo, M and Liu, D and Xia, Z and Xie, T and Su, L and Pérez-Moreno, J and Yu, F},
title = {Geographic Provenances Outweigh Tissue Compartments in Bacteriome Assembly of the Ectomycorrhizal, Edible, and Hallucinogenic if Undercooked, Lanmoa asiatica (Boletaceae, Boletales) Mushroom from Yunnan China.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112431},
pmid = {41304117},
issn = {2076-2607},
support = {KCXFZJ-DDBF-202403//Designated Support Project of Chinese Academy of Sciences/ ; Guike AB22080097//the Key Research and Development Program of GuangXi/ ; 202205AD160036//the Yunnan Technology Innovation Program/ ; },
abstract = {Ectomycorrhizal fungal sporomes represent complex microuniverses harboring structurally and functionally eclectic microbiomes with significant ecological roles and potential anthropogenic applications. Nevertheless, the factors governing the assembly of these microbial communities remain poorly understood, and numerous fungal taxa, including many ectomycorrhizal species, remain uninvestigated. This study characterizes the bacteriome of the socioculturally and economically important yet hallucinogenic-if-raw ectomycorrhizal bolete Lanmoa asiatica. We analyzed 36 basidiomata from four geographic locations within China, partitioning each into pileus, stipe, and hymenophore tissues, and sequenced the V5-V7 region of the bacterial 16S rRNA gene. Proteobacteria dominated (>85%), with Pantoea, Sphingomonas, and the Burkholderia complex identified as core genera. Contrary to expectations, α-diversity was highest in the stipe (Chao1 index up to 1934) rather than the exposed hymenophore. PERMANOVA indicated that geographic origin (R[2] = 0.46, p < 0.001) was a stronger structuring force than tissue type (R[2] = 0.28, p < 0.01). Functional prediction via PICRUSt2 revealed enrichments in lipid metabolism, antimicrobial resistance, and apoptosis pathways across sites, while tissue-specific functions involved carbohydrate and nitrogen metabolism. These findings support a hierarchical model of bacteriome assembly where broad-scale environmental filters override micro-niche differentiation, providing a biogeographic framework for the conservation of this highly valued edible mushroom.},
}

@article {pmid41301533,
year = {2025},
author = {Sabharwal, A and Haase, EM and Scannapieco, FA},
title = {Amylase Binding to Oral Streptococci: A Key Interaction for Human Oral Microbial Ecology, Adaptation and Fitness.},
journal = {Biomolecules},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/biom15111616},
pmid = {41301533},
issn = {2218-273X},
support = {1R01DE022673-01/NH/NIH HHS/United States ; 1C06DC022673-18/NH/NIH HHS/United States ; },
mesh = {Humans ; *Mouth/microbiology ; *Streptococcus/metabolism/enzymology ; Biofilms/growth & development ; *Amylases/metabolism ; Bacterial Adhesion ; Adaptation, Physiological ; Microbiota ; },
abstract = {The interaction between human salivary alpha-amylase (HSAmy) and amylase-binding oral streptococci (ABS) helps determine the bacteria that colonize the oral cavity by establishing dental biofilms. Streptococci are important pioneer species of the oral cavity and influence oral health as well as common diseases such as dental caries. Various oral streptococcal species express distinct amylase-binding proteins, among which amylase-binding protein A (AbpA), encoded by the abpA gene in Streptococcus gordonii and several other species, which is the most extensively studied. Amylase binding facilitates microbial adhesion to host surfaces and biofilm formation and enables bacteria to harness the host's amylase enzymatic activity at their cell surface, enhancing their capacity to metabolize dietary starch for nutritional gain. Additionally, amylase binding may also influence bacterial cell division and stress tolerance by engaging novel bacterial signaling pathways. From an evolutionary perspective, both Neanderthals and modern humans exhibit functional adaptations in nutrient metabolism, including selection for salivary amylase-binding oral streptococci, highlighting the importance of microbial co-adaptation in response to host diet. Further research is warranted to elucidate the broader roles of amylase binding to bacteria in host-bacterial signaling, bacterial cell division and fitness and the evolutionary trajectory of the oral microbiome.},
}

Humans
*Mouth/microbiology
*Streptococcus/metabolism/enzymology
Biofilms/growth & development
*Amylases/metabolism
Bacterial Adhesion
Adaptation, Physiological
Microbiota

@article {pmid41301495,
year = {2025},
author = {Teslya, AV and Stepanov, AA and Poshvina, DV and Petrushin, IS and Vasilchenko, AS},
title = {From Lab to Field: Context-Dependent Impacts of Pseudomonas-Produced 2,4-Diacetylphloroglucinol on Soil Microbial Ecology.},
journal = {Biomolecules},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/biom15111578},
pmid = {41301495},
issn = {2218-273X},
support = {19-76-30005//Russian Science Foundation/ ; FEVZ-2024-0005//The Ministry of Science and Higher Education of the Russian Federation/ ; },
mesh = {*Soil Microbiology ; *Phloroglucinol/analogs & derivatives/pharmacology/metabolism ; *Pseudomonas/metabolism ; Fungi/drug effects/genetics ; Bacteria/drug effects/genetics ; Microbiota/drug effects ; },
abstract = {The secondary metabolite 2,4-diacetylphloroglucinol (2,4-DAPG), which is produced by Pseudomonas bacteria, is a potent antimicrobial agent with well-documented properties that suppress phytopathogens. However, its broader ecological impact on soil microbial communities is not understood. Through a combination of controlled microcosm and field trials, we have demonstrated that the effects of 2,4-DAPG are highly context-dependent. Laboratory exposure (10 mg kg[-1]) altered the abundance of 8.53% of bacterial and 6.91% of fungal amplicon sequence variants, and simplified the bacterial co-occurrence networks (reduced number of nodes and links). In contrast, field conditions amplified bacterial sensitivity (the Shannon index decreased from 4.77 to 4.17, p < 0.05) but maintained fungal stability (Shannon index varied from 3.93 to 3.97, p > 0.05); these conditions affected a smaller proportion of fungal ASVs (4.23%). Taxonomic analysis revealed consistent suppression of fungi of the Mucoromycota (e.g., Mortierella) and context-dependent shifts in bacteria, with an enrichment of Bacillota (e.g., Bacillus, Paenibacillus) in the laboratory but not in the field. Enzymatic responses revealed a dose-dependent activation of the C-cycle, with up to 7.4-fold increases in the laboratory and up to a 10.5-fold increase in the field. P- and N- cycles showed more complex dynamics, with acid phosphatase activity increasing 3.8-fold in laboratory conditions and recovering from initial suppression to an increase of 144% in field conditions, while N-acetylglucosaminidase activity increased and L-leucine aminopeptidase decreased under laboratory conditions. Our results suggest that the response of microorganisms to 2,4-DAPG in natural soils is reduced, probably due to functional redundancy and pre-adaptation to abiotic stresses. This difference between laboratory and field studies warns against extrapolating data from controlled experiments to predict outcomes in agricultural ecosystems, and emphasizes the need for a context-specific evaluation of biocontrol agents.},
}

*Soil Microbiology
*Phloroglucinol/analogs & derivatives/pharmacology/metabolism
*Pseudomonas/metabolism
Fungi/drug effects/genetics
Bacteria/drug effects/genetics
Microbiota/drug effects

@article {pmid41301464,
year = {2025},
author = {Cai, Y and Zhao, F and Cheng, X},
title = {Gut Microbiota and Ferroptosis in Colorectal Cancer: A Comprehensive Review of Mechanisms and Therapeutic Strategies to Overcome Immune Checkpoint Resistance.},
journal = {Biomolecules},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/biom15111546},
pmid = {41301464},
issn = {2218-273X},
mesh = {Humans ; *Ferroptosis/drug effects ; *Gastrointestinal Microbiome/drug effects ; *Colorectal Neoplasms/microbiology/immunology/therapy/drug therapy/pathology/metabolism ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; Animals ; *Drug Resistance, Neoplasm ; },
abstract = {Colorectal cancer (CRC) remains a leading cause of cancer-related mortality worldwide. Although immune checkpoint inhibitors (ICIs) have achieved striking clinical efficacy in the subset of CRCs with mismatch repair deficiency/high microsatellite instability (dMMR/MSI-H), the vast majority of patients-those with proficient mismatch repair/microsatellite-stable (pMMR/MSS) tumors-derive little benefit from current immunotherapies. Ferroptosis, an iron-dependent form of regulated cell death driven by lethal accumulation of lipid peroxides, has emerged as a promising antitumor mechanism that can interact with and modulate antitumor immunity. Concurrently, the gut microbiota exerts powerful control over host metabolism and immune tone through microbial community structure and metabolite production; accumulating evidence indicates that microbiota-derived factors can either sensitize tumors to ferroptosis (for example, via short-chain fatty acids) or confer resistance (for example, indole-3-acrylic acid produced by Peptostreptococcus anaerobius acting through the AHR→ALDH1A3→FSP1/CoQ axis). In this review we synthesize mechanistic data linking microbial ecology, iron and lipid metabolism, and immune regulation to ferroptotic vulnerability in CRC. We discuss translational strategies to exploit this "microbiota-ferroptosis" axis-including precision microbiome modulation, dietary interventions, pharmacologic ferroptosis inducers, and tumor-targeted delivery systems-and we outline biomarker frameworks and trial designs to evaluate combinations with ICIs. We also highlight major challenges, such as interindividual microbiome variability, potential collateral harm to ferroptosis-sensitive immune cells, adaptive antioxidant compensation (e.g., NRF2/FSP1 activation), and safety/regulatory issues for live biotherapeutics. In summary, this review highlights that targeting the microbiota-ferroptosis axis may represent a rational and potentially transformative approach to reprogramming the tumor microenvironment and overcoming immune checkpoint resistance in pMMR/MSS colorectal cancer; however, further research is essential to validate this concept and address existing challenges.},
}

Humans
*Ferroptosis/drug effects
*Gastrointestinal Microbiome/drug effects
*Colorectal Neoplasms/microbiology/immunology/therapy/drug therapy/pathology/metabolism
*Immune Checkpoint Inhibitors/therapeutic use/pharmacology
Animals
*Drug Resistance, Neoplasm

@article {pmid41300079,
year = {2025},
author = {Guo, X and Lin, M and Le, TN and Zhou, Z and Zhao, M and Cai, H},
title = {Impact of Aspergillus Species on Microbial Community Dynamics and Their Associations with Fermentation Properties in Fermented Walnut-Based Soy Sauce.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {22},
pages = {},
doi = {10.3390/foods14223921},
pmid = {41300079},
issn = {2304-8158},
support = {32172214, 31972079//National Natural Science Foundation of China/ ; },
abstract = {This study investigated microbial community dynamics and their links to fermentation traits in solid-state fermentation of walnut -based soy sauce (WSS) using walnut meal-soybean meal mixtures. Via 16S rRNA sequencing and molecular docking, it analyzed the effects of three distinct starter culture treatments-Aspergillus oryzae (AO), Aspergillus niger (AN), and mixed starter culture (A. oryzae + A. niger, ON)-as well as fermentation duration on microbial diversity and physicochemical properties, aiming to clarify microbial-driven quality mechanisms. Physicochemical analysis demonstrated superior fermentation performance in the AO group, showing significantly higher amino nitrogen (NH3-N) accumulation (0.23 g/100 mL) and protease activity (30.5 U/mL) compared to the AN group, with the mixed inoculation group (ON) exhibiting intermediate results, indicating A. oryzae's dominant role in mixed fermentation. Via PCA and Shannon index, microbial diversity analyses revealed starter cultures shaped microbial community structure: Enterococcus and Staphylococcaceae were enriched by AO starter, and Klebsiella dominated in AN group. Additionally, temporal succession of the microbiota occurred during post-fermentation of WSS, with Lactobacillales, Staphylococcus, and special flavor-producing functional flora dominating early, middle, and later stages, respectively. Staphylococcus positively correlated with protease activity and amino nitrogen, critical for quality. Molecular docking showed major walnut polyphenols significantly affected protease activity, aiding process optimization. This research provides theoretical foundations for improving WSS production and enriches understanding of solid-state fermentation microbial ecology.},
}

@article {pmid41299791,
year = {2025},
author = {Cheng, Q and Ma, J and Yang, Y and Ma, J and Grossart, HP and Xu, L and Lin, H},
title = {Enrichment of vitamin B12-producing Porphyrobacter in the phycosphere microbiome promotes microalgal stress adaptation to antibiotic exposure.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {240},
pmid = {41299791},
issn = {2049-2618},
support = {42207285//National Natural Science Foundation of China/ ; 42177002//National Natural Science Foundation of China/ ; LMS25C150001//Natural Science Foundation of Zhejiang Province/ ; 2021R52045//Leading talents in scientific and technological innovation, high-level Talents of Zhejiang Special Support Program/ ; 202204T14//Key Scientific Research and Development Program of Hangzhou/ ; },
mesh = {*Vitamin B 12/biosynthesis/metabolism ; *Microalgae/drug effects/microbiology/growth & development/physiology ; *Anti-Bacterial Agents/pharmacology ; *Microbiota ; Stress, Physiological ; Adaptation, Physiological ; },
abstract = {BACKGROUND: Planktonic microalgae deploy multifaceted responsive and adaptive strategies against anthropogenic pollutants; however, current understanding of antibiotic resistance mechanisms remains predominantly focused on intrinsic physiological adaptations. While microalgae maintain intimate relationships with the phycosphere microbiome, the ecological roles of these associated microbes in mediating host adaptation to polluted environments are inadequately characterized.

RESULTS: We identified a phycosphere microbiome-involved antibiotic resistance mechanism in Dictyosphaerium sp., a pollution-tolerant Chlorophyta microalgae exhibiting remarkable enrofloxacin (ENR) tolerance. Microalgal growth displayed initial inhibition followed by significant promotion under 5 mg/L ENR exposure. This resilience was associated with the restructuring of phycosphere microbiome, characterized by Porphyrobacter enrichment and functional enhancement of algal fitness-promoting pathways, including upregulation of cobalamin biosynthesis genes (log2FC = 7.76) and a 33.3-fold increase in extracellular B12 accumulation. Consequently, we isolated the ENR-selected microbial taxa to elucidate their roles in microalgal stress adaptation. Co-culturing axenic Dictyosphaerium sp. with Porphyrobacter enhanced microalgal growth by 36.5% after 8-day ENR exposure, whereas non-dominant bacteria exhibited negligible effects. Based on the transcriptomic and metabolomic analyses of the algal system when Porphyrobacter was dominant, we subsequently compared the growth of axenic microalgae with and without B vitamin (B1, B6, B7, B12) supplementation. Experimental validation demonstrated the pivotal role of B12-producing Porphyrobacter in enhancing microalgal ENR adaptation through (i) stimulating extracellular polymeric substances production and subsequently enhancing ENR removal via EPS-mediated adsorption and (ii) alleviating intracellular oxidative stress via elevating superoxide dismutase and peroxidase activities and reducing malondialdehyde levels. Additionally, this B12-producing bacteria/B12-mediated adaptability exhibited cross-species conservation, improving ENR resistance in Chlorella vulgaris and Scenedesmus quadricauda, with analogous protection observed under ciprofloxacin and norfloxacin exposures.

CONCLUSION: Collectively, our findings establish stress-induced enrichment of B12-producing Porphyrobacter within the phycosphere microbiome as a pivotal mechanism underlying microalgal antibiotic adaptation. This insight facilitates the rational development of microalgae-microbiome systems for enhanced wastewater treatment and sustainable bioproduction, with applications in aquatic feed supplementation, biofuel production, and biofertilizer development. Video Abstract.},
}

*Vitamin B 12/biosynthesis/metabolism
*Microalgae/drug effects/microbiology/growth & development/physiology
*Anti-Bacterial Agents/pharmacology
*Microbiota
Stress, Physiological
Adaptation, Physiological

@article {pmid41299662,
year = {2025},
author = {Jiménez, DJ and Jamil, T and Miliotis, G and Schultz, J and Patel, N and Aldakheel, L and Kontis, N and García, FC and Villela, HDM and Duarte, GAS and Barno, AR and Farran, A and Alsaggaf, A and Santoro, ÉP and Tumeo, A and Page, A and Wong, S and Kabza, A and Putra, A and Park, C and Angelov, A and Driguez, P and Peixoto, RS and Green, SJ and Tighe, S and Rosado, AS and Venkateswaran, K},
title = {Microbial community characterization in Red Sea-derived samples using a field-deployable DNA extraction system and nanopore sequencing.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-025-00819-x},
pmid = {41299662},
issn = {2524-6372},
support = {BAS/1/1096-01-0//King Abdullah University of Science and Technology/ ; },
abstract = {BACKGROUND: In this study, xTitan, a field-deployable, automated, and versatile nucleic acid extraction system was employed to characterize microbial communities in Red Sea-derived samples, including coral colonies, mangrove sediments, and seawater. The use of the xTitan in the field was intended to minimize sample transport bias, obtaining data that may be closer to "ground truth" for microbial diversity. The observed microbial communities from DNA extracted in the field using the xTitan system were compared to DNA extractions performed in a laboratory setting using both xTitan and a standard commercial kit (Qiagen) after approximately 24 h of sample transfer and storage.

RESULTS: Microbial community analyses conducted on DNA extracted using the xTitan system and the Qiagen kit yielded similar alpha diversity metric values, with a trend toward higher diversity observed in most samples extracted with the xTitan. The microbial community structure in samples from a Pocillopora verrucosa colony, mangrove sediments, and seawater was affected by the DNA extraction system. In the P. verrucosa colony, 16S rRNA gene sequences affiliated to Endozoicomonas acroporae were preferentially abundant when DNA was extracted in the field with the xTitan system rather than in the lab. In mangrove sediments, significant differences (P-value < 0.05) in beta diversity and functional gene profiles were observed when comparing in-field to in-lab xTitan DNA extracts. In seawater, a pronounced decrease in the relative abundance of cyanobacterial populations was observed when DNA was extracted with both methods after samples were transported to the lab on ice. In addition, hundreds of species in mangrove-associated samples were differentially abundant when DNA was extracted on-site with the xTitan system compared to in-lab extractions. Balneolaceae was one of the most abundant taxa in mangrove sediments and several genera from this family were detected in all replicates across all DNA extraction systems.

CONCLUSIONS: The usability of different field-deployable instruments for microbial community characterization in marine-derived samples was demonstrated. Moreover, differences in beta diversity were observed when DNA was extracted in-field versus in-lab using the xTitan system, particularly for mangrove-associated samples. These results highlight the value of on-site nucleic acid extraction for enhancing the detection of microbial taxa that can be sensitive to cold storage. This study enabled the testing of the xTitan on Red Sea-derived samples, generating comprehensive information on the effects of DNA extraction systems and transportation of samples on coral and mangrove-associated microbiomes.},
}

@article {pmid41299176,
year = {2025},
author = {Wirbel, J and Hickey, AS and Chang, D and Enright, NJ and Dvorak, M and Chanin, RB and Schmidtke, DT and Bhatt, AS},
title = {Long-read metagenomics reveals phage dynamics in the human gut microbiome.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {41299176},
issn = {1476-4687},
abstract = {Gut bacteriophages profoundly impact microbial ecology and health[1-3]; yet, they are understudied. Using deep long-read bulk metagenomic sequencing, we tracked prophage integration dynamics in stool samples from six healthy individuals, spanning a 2-year timescale. Although most prophages remained stably integrated into their hosts, approximately 5% of phages were dynamically gained or lost from persistent bacterial hosts. Within a sample, we found that bacterial hosts with and without a given prophage coexisted simultaneously. Furthermore, phage induction, when detected, occurred predominantly at low levels (1-3× coverage compared to the host region), in line with theoretical expectations[4]. We identified multiple instances of integration of the same phage into bacteria of different taxonomic families, challenging the dogma that phages are specific to a host of a given species or strain[5]. Finally, we describe a new class of 'IScream phages', which co-opt bacterial IS30 transposases to mediate their mobilization, representing a previously unrecognized form of phage domestication of selfish bacterial elements. Taken together, these findings illuminate fundamental aspects of phage-bacterial dynamics in the human gut microbiome and expand our understanding of the evolutionary mechanisms that drive horizontal gene transfer and microbial genome plasticity.},
}

@article {pmid41299132,
year = {2025},
author = {Zhang, J and Zhou, X and Rong, X and Salem, H and Zhang, J and Yin, B and Guo, X and Zhang, Y},
title = {Effects of Plant Phylogeny and Traits on the Composition of Phyllosphere Microbial Communities in a Typical Temperate Desert in Central Asia.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02635-9},
pmid = {41299132},
issn = {1432-184X},
support = {2022D01A351//The Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; Non//The Tianchi Talent Introduction Project of Xinjiang Uygur Autonomous Region/ ; 2022D01D083//The Key Project of Xinjiang Uygur Autonomous Region Natural Science Foundation/ ; 2022TSYCLJ0058//The Leading Talents in Sci-Technological Innovation Project of "Tianshan Talent" Training Plan of Xinjiang Uygur Autonomous Region/ ; },
abstract = {Phyllosphere microorganisms play a vital role in supporting host plant health and adaptability. Although previous research on the effects of host performance and their phylogenetic associations on phyllosphere microbial communities has predominantly focused on tropical, subtropical, and temperate forestry ecosystems, the responses of these microbial communities to plant phylogeny and functional traits in temperate desert environments remains poorly understood. In this study, we conducted a quantitative analysis of bacterial and fungal community structures in the phyllosphere of 39 plant species from the Gurbantunggut Desert, a typical temperate desert in Central Asia. Variation partitioning analysis revealed that plant phylogeny, leaf physicochemical properties, and leaf morphological characteristics collectively explained the variation in phyllosphere microbial communities. Specifically, these factors accounted for 19.26%, 14.53%, and 2.32% of the variance in bacterial communities, and 11.55%, 8.36%, and 2.19% of the variance in fungal communities, respectively. A significant hierarchical pattern emerged: plant phylogeny > leaf physicochemical properties > leaf morphological characteristics, highlighting the dominant role of plant filtering effects in community assembly. Linear mixed-effects model analysis further confirmed the significant influence of multiple plant attributes, including phylogeny and functional traits, on microbial community structure. Plant-microbe interaction analysis revealed distinct host preferences of microbial taxa across different plant taxonomic levels. Co-evolutionary analysis also indicated a significant phylogenetic association between host plants and their phyllosphere amplicon sequence variants (ASVs). Overall, our findings demonstrate that plant attributes, particularly plant phylogeny and functional traits, are key factors driving the assembly of phyllosphere microbial communities in deserts. This study provides new insights into species coexistence mechanisms in fragile habitats and enhances our understanding of plant-microbe interactions in global desert ecosystem.},
}

@article {pmid41297120,
year = {2025},
author = {Rajbhandari, RM and Shrestha, S and Manandhar, P and Napit, R and Sadaula, A and Chaudhary, A and Raut, R and Gortázar, C and Alves, PC and de la Fuente, J and Queirós, J and Forcina, G and Karmacharya, D},
title = {Comparing the respiratory tract microbiome in captive elephants and humans in Chitwan National Park: Implications for conservation medicine.},
journal = {Comparative immunology, microbiology and infectious diseases},
volume = {125},
number = {},
pages = {102422},
doi = {10.1016/j.cimid.2025.102422},
pmid = {41297120},
issn = {1878-1667},
abstract = {The study of gut microbiome in both animals and humans living in proximity has proven crucial in understanding their coevolution, the potential for microbial transfer and the dynamics behind various diseases. Similarly, the investigation of respiratory microbiomes has been gaining popularity due to its significance and impact on respiratory health. Here, we use 16S rRNA metabarcoding to explore the respiratory microbiome of captive Asian elephants (Elephas maximus) and their mahouts (i.e., trainers and handlers) in Chitwan National Park (Nepal), with local villagers residing out of the protected area acting as control. Sputum samples were collected to characterize their bacterial composition, while its functional profile was inferred with PICRUSt2. Additionally, the occurrence of genera hosting potentially pathogenic ESKAPE-E species was evaluated. Our findings revealed high similarity in the bacterial and functional composition of the respiratory microbiome of elephants and mahouts, with Bacillota and Pseudomonadota emerging as the most abundant phyla across all host categories and the controls displaying the highest diversity. A striking difference was observed in relation to the family Bacillaceae that dominated the microbial composition of both mahouts and elephants but not controls. Genera hosting potentially pathogenic ESKAPE-E bacteria were found in all host categories, which underscores the need for in-depth analyses to identify the species involved. Our study delivers valuable insights in the respiratory microbial community of both Asian elephants and humans, thus laying the basis for further investigations on their diversity and function, unveiling their role in respiratory health of both host species.},
}

@article {pmid41296916,
year = {2025},
author = {Rettura, F and Lambiase, C and Bottari, A and Filippini, F and Giacomelli, L and Pistello, M and Bellini, M},
title = {Gut Virome: What's the Role in Irritable Bowel Syndrome?.},
journal = {Reviews in medical virology},
volume = {35},
number = {6},
pages = {e70080},
doi = {10.1002/rmv.70080},
pmid = {41296916},
issn = {1099-1654},
support = {2022FRE3RH//Italian Ministry of University and Research/ ; CUP I53D23000480006//National Recovery and Resilience Plan/ ; },
mesh = {Humans ; *Irritable Bowel Syndrome/virology/microbiology/therapy ; *Virome ; *Gastrointestinal Microbiome ; Bacteriophages/physiology ; Dysbiosis/virology ; Animals ; },
abstract = {The gut virome, an integral but still poorly understood component of the gut microbiota, is emerging as an important player in the pathophysiology of irritable bowel syndrome (IBS). Recent evidence suggests that alterations in virome diversity and phage-bacteria interactions contribute to gut dysbiosis, immune modulation and gut barrier dysfunction in IBS. This review summarises current knowledge on virome alterations in IBS and emphasises the role of bacteriophages in shaping microbial ecology and host responses. Different virome signatures in the different subtypes of IBS highlight the potential of the virome for disease stratification and personalised therapeutic strategies. In addition, we discuss the analytical challenges in virome research and explore novel virome-targeted interventions, including phage therapy and dietary modulation. A deeper understanding of virome dynamics in the gut could open new avenues for precision medicine approaches to treat IBS.},
}

Humans
*Irritable Bowel Syndrome/virology/microbiology/therapy
*Virome
*Gastrointestinal Microbiome
Bacteriophages/physiology
Dysbiosis/virology
Animals

@article {pmid41296063,
year = {2025},
author = {Guo, M and Zhou, Z and Zheng, Y and Fu, D and Hou, L and Zhu, R},
title = {Ubiquity and Dominance of Comammox Over AOB and AOA and their Links To ARGs in Antarctic Lake Sediments.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02664-4},
pmid = {41296063},
issn = {1432-184X},
support = {2022YFF0801101//National Key Research and Development Program of China/ ; 42576267//National Natural Science Foundation of China/ ; },
abstract = {Complete ammonia oxidizers (comammox), oxidizing ammonia to nitrate directly, have been found to exist widely in multiple environments, but their distribution patterns are still under-explored in Antarctic environments. For the first time, the sediments were collected from West Antarctic lakes to investigate distribution patterns and community structure for comammox, ammonia oxidizing archaea (AOA) and bacteria (AOB), and nitrite-oxidizing bacteria (NOB), as well as the associations between ammonia oxidizers and antibiotic resistance genes (ARGs). Comammox clade B and AOB were dominant ammonia oxidizers, with the abundances of (1.62 ± 0.10) × 10[2] - (5.21 ± 0.74) × 10[6] and (0.17 ± 0.05) × 10[5] - (4.79 ± 0.65) × 10[5] copies g[- 1] sediment, respectively. Comammox clade B, instead of clade A, occurred in all sediments, exhibiting higher abundances than AOB and AOA in most of the sediments. The abundances for comammox clade B demonstrated significant positive correlation (p < 0.01) with NH4[+]-N levels, but negative correlation (p < 0.05) with C: N ratios. The coexistence of ammonia oxidizers in lake sediments was jointly structured by niche differentiation and environmental variables, and pH, modulated by penguin guano input, was found to be the most crucial factor in shaping their community structure. Co-occurrence network analyses revealed strong synergistic interactions between comammox and AOB, AOA, NOB, which played a critical role in nitrification processes. Our results further confirmed that comammox could act as important hosts for ARGs, hence stimulated their transmission and proliferation in the sediments. This study presented novel insights into the distribution patterns for ammonia oxidizers, their niche differentiation and the associations with ARGs in natural lake sediments of West Antarctica.},
}

@article {pmid41295040,
year = {2025},
author = {Abdul Rahiman, S and Qiblawey, H},
title = {Anammox-MBR Technology: Breakthroughs and Challenges in Sustainable Nitrogen Removal from Wastewater.},
journal = {Membranes},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/membranes15110337},
pmid = {41295040},
issn = {2077-0375},
support = {QUHI-CENG-25/26-747//Qatar University/ ; },
abstract = {Wastewater nitrogen pollution is a serious environmental problem, and traditional treatment techniques are frequently constrained by their high energy requirements and operational complexity. The anaerobic ammonium oxidation (anammox) process combined with membrane bioreactor (MBR) technology (anammox-MBR) offers a practical and energy-efficient solution for the sustainable removal of nitrogen, further enhanced by its potential to minimize emissions of nitrous oxide (N2O), a potent greenhouse gas with a global warming potential nearly 300 times that of carbon dioxide. This review outlines the most recent advancements in anammox-MBR systems, highlighting their ability to achieve nitrogen removal efficiencies of more than 70-90% and, in integrated systems with reverse osmosis, to recover up to 75% of the inflow as high-quality reusable water. Significant advancements such as high-rate activated sludge coupling, reverse osmosis integration, microaeration methods, and membrane surface modifications have decreased membrane fouling, accelerated startup times, and enhanced system stability. Despite these achievements, there are still issues that hinder widespread use, such as membrane fouling exacerbated by hydrophobic anammox metabolites, sensitivity to low temperatures (≤10 °C), and the persistent challenge of suppressing nitrite-oxidizing bacteria (NOB), which compete for the essential nitrite substrate. To enable cost-effective, energy-efficient, and environmentally sustainable large-scale applications, future research directions will focus on creating cold-tolerant anammox strains, advanced anti-fouling membranes, and AI-driven process optimization.},
}

@article {pmid41294522,
year = {2025},
author = {Špiljak, B and Andabak Rogulj, A and Lončar Brzak, B and Brailo, V and Škrinjar, I and Ozretić, P and Vidović Juras, D},
title = {Desquamative Gingivitis and the Oral Microbiome: Insights into Immune-Microbial Interactions in Mucosal Inflammation.},
journal = {Dentistry journal},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/dj13110541},
pmid = {41294522},
issn = {2304-6767},
abstract = {Desquamative gingivitis (DG) is a clinical presentation characterized by erythema, epithelial desquamation, and mucosal fragility, commonly associated with immune-mediated diseases such as oral lichen planus (OLP), mucous membrane pemphigoid (MMP), and pemphigus vulgaris (PV). While traditionally viewed as a manifestation of immune dysregulation, growing evidence suggests that the oral microbiome may modulate disease onset, persistence, and severity. This review summarizes current knowledge on the oral microbiota in DG and its underlying diseases, explores mechanistic links between dysbiosis and immune activation, and discusses clinical and research implications. A narrative literature review was conducted using PubMed and Scopus, focusing on studies analyzing the oral microbiome in OLP, MMP, and PV. Emphasis was placed on molecular microbiology techniques, immune profiling, and functional or longitudinal approaches. In OLP, microbial dysbiosis is consistently reported, including reduced diversity and increased abundance of pro-inflammatory genera such as Fusobacterium, Prevotella, and Capnocytophaga. These shifts correlate with epithelial barrier disruption and inflammatory cytokine production. Although data on MMP and PV are limited, early findings suggest microbial involvement in sustaining inflammation, delaying healing, and possibly amplifying autoimmune responses. Dysbiosis may activate Toll-like receptors, skew T cell responses, and contribute to the breakdown of immune tolerance. DG may reflect a dynamic interplay between immune mechanisms and microbial ecology. While evidence is strongest for OLP, preliminary data suggest broader microbial contributions across DG-associated diseases. Microbiome-informed approaches could enhance diagnostic accuracy and support the development of adjunctive therapies.},
}

@article {pmid41293856,
year = {2025},
author = {Schäfer, RB and Baikova, D and Bayat, HS and Beermann, AJ and Berger, SA and Boenigk, J and Brauns, M and Burfeid-Castellanos, A and Cardinale, BJ and David, GM and Feckler, A and Feld, CK and Fink, P and Gessner, MO and Hadziomerovic, U and Hering, D and Le, TTY and Macaulay, SJ and Madariaga, GM and Serge Mayombo, NA and Pimentel, IM and Orr, JA and Osakpolor, S and Schlenker, A and Sures, B and Vermiert, AM and Vos, M and Weitere, M and Schürings, C},
title = {Effects of Biodiversity Loss on Freshwater Ecosystem Functions Increase With the Number of Stressors.},
journal = {Global change biology},
volume = {31},
number = {11},
pages = {e70617},
doi = {10.1111/gcb.70617},
pmid = {41293856},
issn = {1365-2486},
support = {426547801//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Biodiversity ; *Fresh Water ; *Ecosystem ; *Stress, Physiological ; Biomass ; },
abstract = {A multitude of anthropogenic stressors drive biodiversity loss and alter ecosystem functioning. Freshwaters, which contribute disproportionally to global biodiversity and biogeochemical cycles, are particularly threatened. Although the relationship between biodiversity and ecosystem functions (BEF) is generally well-established, especially in terrestrial ecosystems, the role of multiple, co-occurring stressors in modulating the relationship remains unclear. We conducted a meta-analysis to address this knowledge gap by assessing the effect of multiple stressors on the relationship between taxon richness and four measures of ecosystem function. The relationship was generally positive, with the slope becoming steeper as the number of stressors increased, suggesting that exposure to multiple stressors exacerbates impacts of biodiversity loss on ecosystem function. Multiple stressor effects on both taxon richness and ecosystem functions were largely predictable from individual stressor effects, although antagonistic effects on ecosystem functions emerged in 14% of the considered cases. The type of stressor and ecosystem function, along with taxonomic group, exerted no influence on the BEF relationship, contrary to our expectations. Microbial production and biomass declined most strongly in response to stressors, despite notable variability. Overall, our findings imply that functional consequences of freshwater biodiversity loss are more severe under multifaceted environmental change than previously assumed.},
}

*Biodiversity
*Fresh Water
*Ecosystem
*Stress, Physiological
Biomass

@article {pmid41292685,
year = {2025},
author = {O'Brien, JM and Blais, ND and Holland-Moritz, H and Shek, KL and Douglas, TA and Barbato, RA and Ernakovich, JG},
title = {Consistent microbial responses during the aerobic thaw of Alaskan permafrost soils.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1654065},
pmid = {41292685},
issn = {1664-302X},
abstract = {Arctic systems are warming at four times the global average, causing permafrost-permanently frozen soil, ice, organic matter, and bedrock-to thaw. Permafrost thaw exposes previously unavailable soil carbon and nutrients to decomposition-a process mediated by microbes-which releases greenhouse gases such as carbon dioxide and methane into the atmosphere. While it is well established that thaw alters the composition and function of the permafrost microbiome, patterns revealing common responses to thaw across different permafrost soil types have not yet emerged. In this study, we address how permafrost thaw impacts microbiome diversity, alters species abundance, and contributes to carbon flux in the Arctic. We sampled peat-like, mineral, and organic-mineral permafrost from three locations in central and northern Alaska. We assessed their abiotic soil properties and microbiome characteristics before and after a 3-month laboratory microcosm incubation. Across all sites, prokaryotic biomass increased following thaw, measured as 16S rRNA gene copy number. This change in biomass was positively correlated with cumulative respiration, indicating an increase in microbial activity post-thaw. We evaluated the thaw response of microbial taxa across three sites, identifying taxa that significantly increased in abundance post-thaw. Common responders shared across all sites belonged to the families Beijerinckiaceae, Burkholderiaceae, Clostridiaceae, Oxalobacteraceae, Pseudomonadaceae, and Sporichthyaceae, indicating a common set of taxa that consistently respond to thaw regardless of site-specific conditions. Alpha diversity decreased with thaw across all sites, likely reflecting the increased dominance of specific thaw-responsive taxa that may be driving post-thaw biogeochemistry and increased respiration. Taken together, we deepen the understanding of different permafrost microbiomes and their response to thaw, which has implications for the permafrost-climate feedback and enables more accurate predictions of how Arctic ecosystem structure and function respond to change.},
}