@article {pmid41482468,
year = {2026},
author = {Xiao, Y and Zhao, S and Wang, W and Asante, KA and Habib, A and Bong, CW and Syed, JH and Bartilol, S and Weber, R and Jones, KC and Li, J and Njeru, M and Zhang, G},
title = {Highly Volatile POPs in Urban Air across Asia and Africa: Dominance of Volatile Methylsiloxanes.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c16890},
pmid = {41482468},
issn = {1520-5851},
abstract = {Highly volatile persistent organic pollutants (HV-POPs) are characterized by high volatility, environmental persistence, bioaccumulative potential, toxicity, and ability for long-range transport, posing environmental and health concerns. However, research on HV-POPs remains limited, particularly in rapidly urbanizing regions, constraining understanding of their sources, environmental fate, and risks. This study investigated 52 HV-POPs, including Stockholm Convention-listed POPs like hexachlorobutadiene (HCBD) and hexa-/pentachlorobenzene (HCB/PeCB), and nonlisted HV-POPs such as volatile methylsiloxanes (VMS) and chlorinated nitrobenzenes (CNBs), using active air samplers in six major cities across Asia and Africa. The median total concentrations of HV-POPs were highest in Guangzhou (351 ng/m[3]), followed by Kuala Lumpur (167 ng/m[3]), Accra (82.4 ng/m[3]), Dhaka (73.3 ng/m[3]), Nairobi (44.9 ng/m[3]), and Islamabad (33.5 ng/m[3]). VMS dominated at all sites, accounting for 84 ± 18% of total HV-POPs, up to 2-5 orders of magnitude higher than other compounds. Source analysis showed VMS emissions in Guangzhou were mainly from industrial activities, while in the other cities, they were from usage of personal care products. Inhalation risk assessments indicated negligible noncarcinogenic and carcinogenic risks at all sites. This study provides the first multiregional HV-POPs data set in urban air, supporting chemical risk assessment efforts and broader international regulatory initiatives.},
}

@article {pmid41482032,
year = {2025},
author = {Wu, D and Zhang, L and Zhang, Z and Xu, M},
title = {Early-life high-dose sodium butyrate supplementation in milk inhibits growth via sterol metabolism in 15-month-old dairy cattle: Insights from gastrointestinal microbiota and host metabolism.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-27618},
pmid = {41482032},
issn = {1525-3198},
abstract = {Sodium butyrate (SB) is a common feed additive used in calf nutrition to support early growth and gastrointestinal health; however, its long-term programming effects remain poorly characterized. This study examined the dose-dependent effects of preweaning SB supplementation in milk on long-term growth, metabolic profiles, and gastrointestinal microbiota in dairy cattle. Eighty Holstein calves were assigned to one of 4 treatments beginning at 2 to 4 d of age: milk supplemented with 0 (CON), 4.4 (LSB), 8.8 (MSB), or 17.6 (HSB) g/d of SB. The same animals were evaluated later as heifers at 15 mo of age for performance, metabolic parameters, and microbial communities. Ruminal fluid, fecal, and plasma samples were collected from 8 animals per group and analyzed via 16S rRNA sequencing (V3-V4 regions) and liquid chromatography-tandem MS-based metabolomics. The HSB group showed a significant reduction in withers height compared with CON, although no significant differences were detected in BW, heart girth, or reproductive measures. Metabolomic and biochemical profiling indicated disrupted sterol metabolism and signs of hepatic stress in HSB heifers, reflected by increased alanine aminotransferase and total bilirubin, alongside decreased total cholesterol and creatine. Ruminal microbiota in the HSB group exhibited reduced diversity, richness, and evenness, accompanied by a decline in beneficial bacteria such as Rikenellaceae_RC9_gut_group. Predicted microbial function indicated inhibited steroid biosynthesis in the rumen. In contrast, the intestinal microbiota composition remained largely unchanged, though steroid degradation function was suppressed. Correlation and network analyses linked these changes, suggesting that early high-dose SB disrupts ruminal microbial ecology, resulting in lasting impairments in host metabolic health and growth. Key biomarkers included Rikenellaceae_RC9_gut_group, steroid biosynthesis, and plasma creatine. Collectively, these results indicate that milk-supplemented high-dose SB in early life leads to long-term inhibitory effects on growth and metabolic homeostasis in dairy heifers, largely mediated through rumen microbiota-driven alterations in sterol metabolism.},
}

@article {pmid41481725,
year = {2026},
author = {Shi, T and Van de Peer, Y},
title = {Revisiting ancient whole-genome duplications in the seed and flowering plants through the lens of dosage-sensitive genes.},
journal = {Science advances},
volume = {12},
number = {1},
pages = {eaea9797},
pmid = {41481725},
issn = {2375-2548},
mesh = {*Gene Duplication ; *Magnoliopsida/genetics ; *Genome, Plant ; *Gene Dosage ; *Seeds/genetics ; Phylogeny ; Evolution, Molecular ; *Genes, Plant ; },
abstract = {Whole-genome duplication (WGD) has been proposed as a catalyst for evolutionary innovation in seed plants and angiosperms, yet their occurrence remains contentious. By integrating gene dosage balance principles with phylogenomic reconciliation and probabilistic modeling, we revisit the debated ancestral seed and angiosperm WGDs. Leveraging dosage-sensitive orthologous gene groups (OGs) as evolutionary markers across representative plants for gene tree/species tree reconciliation, we demonstrate that gene retention patterns in Amborella and Aristolochia-early-diverging plants lacking post-angiosperm origin WGDs-reveal a single gene duplication peak predating the seed plant diversification, with no signal of ancestral angiosperm WGD. Correlation analyses of observed and expected OG copy numbers, given proposed WGD(s), further refute an angiosperm WGD. Probabilistic retention modeling analysis corroborates these findings and shows that retention rates of dosage-sensitive genes from the putative angiosperm WGD are extremely low. Besides, our study establishes that genes inferred to have higher dosage sensitivity based on their sequential retention following WGD events may have increased utility in resolving ancestral polyploidy.},
}

*Gene Duplication
*Magnoliopsida/genetics
*Genome, Plant
*Gene Dosage
*Seeds/genetics
Phylogeny
Evolution, Molecular
*Genes, Plant

@article {pmid41480114,
year = {2025},
author = {Robayo-Cuevas, C and Junca, H and Uribe, S and Gómez-Palacio, A},
title = {Detection of endosymbiotic, environmental, and potential bacterial pathogens in diverse mosquito taxa from Colombian tropical forests using RNAseq.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1727830},
pmid = {41480114},
issn = {1664-302X},
abstract = {INTRODUCTION: Mosquitoes of the subfamily Culicinae transmit pathogens of major medical and veterinary importance, particularly in tropical regions where urbanization and ecological change promote arbovirus circulation. In Colombia, rural Culicinae species are diverse and harbor microbiomes that may influence vector competence, yet their bacterial communities remain poorly characterized.

METHODS: We characterized the bacterial microbiota of multiple Culicinae species and morphotypes collected from two rural localities in Antioquia, Colombia, using an integrated metagenomic approach. Ribosomal 16S rRNA sequences were extracted from total RNA-seq datasets to infer bacterial community composition and assess α- and β-diversity. Diversity metrics (Chao1 and Shannon indices), Discriminant Analysis of Principal Components (DAPC), and Bray-Curtis ordination were used to evaluate community structure. In parallel, de novo assembled contigs were taxonomically annotated against the NCBI NR bacterial database to obtain complementary taxonomic and functional insights.

RESULTS: Culex morphotypes exhibited the highest richness and evenness, whereas Aedes and Trichoprosopon showed lower diversity. Ordination and DAPC analyses revealed partial clustering by species and tribe. Both the 16S and assembly-based analyses showed complex bacterial assemblages dominated by Wolbachia (up to 60% of reads in several Aedes and Culex morphotypes), followed by environmental genera such as Pseudomonas and Acinetobacter (10-20%). Lower-abundance taxa of medical and veterinary importance-including Salmonella, Borrelia, and Clostridium (<5%)-were also detected. Bacterial community structure differed among mosquito species; Aedes albopictus was enriched in lactic acid bacteria, while Culex morphotypes exhibited broader environmental and endosymbiotic profiles.

DISCUSSION: This study provides the first comprehensive metagenomic description of bacterial communities associated with rural Culicinae mosquitoes in Colombia. The predominance of symbionts such as Wolbachia and Spiroplasma, coupled with distinct bacterial signatures among host species, highlights the ecological complexity of these microbiomes and their potential relevance for microbiome-based strategies in sustainable arboviral disease management.},
}

@article {pmid41479530,
year = {2025},
author = {Guo, T and Wang, M and Chen, Y and Yue, K and Ma, L and Huang, S and Xu, X and Song, X and Su, S and Zhang, Z and Zhang, Q and Zhang, K},
title = {Nitrogen addition accelerated straw in-situ decomposition by promoting specific microbial taxa growth and straw decomposing enzyme activities.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1703916},
pmid = {41479530},
issn = {1664-462X},
abstract = {INTRODUCTION: Crop residue represents the largest input of organic carbon in agricultural ecosystems and its decomposition is fundamentally mediated by soil microbial communities. However, the mechanism of N fertilization regulating decomposition of the plant residue especially the associated key microbial taxa remain unclear.

METHODS: To address this gap, we conducted a 100-day field decomposition experiment using the litterbag method to track temporal shifts in straw physicochemical properties and associated microbial communities under three N regimes: no nitrogen (N0), 200 kg N ha[-1] (N200), and 300 kg N ha[-1] (N300).

RESULTS AND DISCUSSIONS: Results showed that nitrogen addition significantly accelerated the decomposition of wheat straw, increasing mass loss and the degradation rates of cellulose, hemicellulose, and lignin relative to N0 treatment. Enzyme activities linked to carbon acquisition, including α-glucosidase (AG), β-glucosidase (BG), cellobiohyrolase (CBH), and β-xylosidase (XYL), were consistently elevated under N-amended treatments during mid- to late-stage decomposition. Similarly, activities of N-acquiring enzymes (β-N-acetyl-glucosaminidase, NAG; leucine aminopeptidase, LAP) and oxidative enzymes (polyphenol oxidase, PPO; laccase) were significantly enhanced, particularly after Day 14. Microbial community succession was tightly coupled with decomposition progression. Random forest modeling identified key bacterial biomarkers (e.g., Terribacillus, Bacillus, Solibacillus, Oceanobacillus, and Cellulosimicrobium) and fungal biomarkers (e.g., Neocosmospora, Actinomucor, Fusarium, Chaetomium, and Aspergillus), all of which are known for their capacity to degrade lignocellulosic and recalcitrant substances. Variation partitioning revealed that straw properties, especially the C/N ratio, TN content, and CBH activity, collectively explained the majority of microbial community variation. These findings support a mechanistic pathway in which nitrogen fertilization reduces residue C/N, thereby reshaping microbial community composition and stimulating enzyme production, which in turn accelerates decomposition. Our study provides novel insights into how nitrogen management influences the coupling of microbial ecology and biogeochemical cycling during straw decomposition, with direct implications for optimizing N fertilization management and sustaining soil fertility in agroecosystems.},
}

@article {pmid41478687,
year = {2026},
author = {Wang, G and Liu, Y and Ma, F and Qiu, W},
title = {Insights into meat-microbiome interactions: from community assembly to meat spoilage.},
journal = {Food microbiology},
volume = {136},
number = {},
pages = {105010},
doi = {10.1016/j.fm.2025.105010},
pmid = {41478687},
issn = {1095-9998},
mesh = {*Meat/microbiology ; *Microbiota ; Animals ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Food Microbiology ; Microbial Interactions ; Ecosystem ; },
abstract = {Meat spoilage represents a critical challenge in food security and sustainability. Although extensive research has characterized meat microbiota composition and identified specific spoilage organisms, comprehensive understanding of the complex ecological dynamics within meat microbiomes remains limited. This review critically examines current knowledge of meat-associated microbiomes by applying an ecological perspective to address four key questions: the functional roles assigned to microorganisms during community assembly, microbial colonization and adaptation mechanisms in meat ecosystems, nutrient utilization patterns driving metabolic activities and ecological interactions, and microbial interaction effects on community ecology and functional outcomes. Through systematic exploration of these questions, we reveal that meat spoilage is determined by community dynamics and functional activities of entire microbial ecosystems rather than individual species alone. Our analysis identifies critical research gaps including inadequate understanding of core and keystone taxa contributions, limited exploration of microbial interactions, and insufficient integration of multi-omics approaches with ecological modeling. Based on these findings, future practical applications should focus on ecology-guided preservatives that target key spoilage pathways and predictive models integrating metabolic fluxes with environmental parameters. This comprehensive paradigm shift from composition-focused to function-oriented research will enhance theoretical understanding and provide practical insights for more effective spoilage control in the food industry.},
}

*Meat/microbiology
*Microbiota
Animals
*Bacteria/classification/genetics/isolation & purification/metabolism
Food Microbiology
Microbial Interactions
Ecosystem

@article {pmid41478108,
year = {2025},
author = {Idbella, M and Abelouah, MR and Djebaili, R and Idbella, A and Raho, O and Nouj, N and Iacomino, G and Bonanomi, G and Hazzoumi, Z},
title = {Microplastic pollution drives soil bacterial community shifts and alters phosphorus cycling across land use gradients.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140968},
doi = {10.1016/j.jhazmat.2025.140968},
pmid = {41478108},
issn = {1873-3336},
abstract = {Microplastics (MPs) pollution is increasingly recognized as a pervasive threat to terrestrial ecosystems, yet its functional impacts on soil processes remain poorly understood under field conditions. Here, we conducted a landscape-scale study across four land-use types, urban, mining, agricultural, and rural, to quantify environmentally accumulated MP and assess their effects on phosphorus (P) cycling and microbial communities. High-resolution spectroscopy revealed that urban and mining soils contained the highest MP loads (600-1000 particles/kg), with distinct polymer types linked to anthropogenic activities. MP abundance was negatively correlated with P solubilization (R = -0.59, p < 0.01) and soil enzymatic activity, and positively with P immobilization (R = 0.53, p < 0.05), indicating impaired nutrient availability. Amplicon sequencing showed that MP-rich soils were enriched in certain taxa within Firmicutes and Actinobacteria often associated with stress tolerance, while low-MP soils supported functionally important groups, including specific Acidobacteria and nitrifying archaea (e.g., Candidatus Nitrososphaera). Co-occurrence network analysis revealed simplified and cooperative microbial structures in MP-polluted soils. Multivariate analyses confirmed that MP are independent drivers of microbial beta-diversity beyond land use. Overall, our findings provide in situ evidence that MP, even at moderate levels, alter microbial ecology and disrupt soil nutrient cycling, posing a potential risk to biogeochemical resilience in human-impacted landscapes.},
}

@article {pmid41475142,
year = {2025},
author = {Gallego-Cartagena, E and Morillas, H and Maguregui, M},
title = {Biodeterioration of built heritage in the context of climate change and atmospheric pollution: Toward transdisciplinary conservation strategies.},
journal = {The Science of the total environment},
volume = {1013},
number = {},
pages = {181313},
doi = {10.1016/j.scitotenv.2025.181313},
pmid = {41475142},
issn = {1879-1026},
abstract = {The built heritage -encompassing monuments, historic buildings and sculptural ensembles- is increasingly threatened by the synergistic impacts of climate change, atmospheric pollution and biological activity. This review critically analyses current understanding of the mechanisms driving the biodeterioration of built heritage, focusing on calcareous materials (e.g., limestone, marble and lime-based mortars), which are both widespread in built heritage and highly susceptible to degradation. We examine how environmental drivers -such as elevated humidity, temperature fluctuations, and pollutant deposition (SOₓ, NOₓ, particulate matter)-trigger complex physicochemical and biochemical reactions that compromise structural stability and aesthetic integrity. The review explores the metabolic strategies of biodeteriative organisms (fungi, algae, cyanobacteria), the interactions of pollutants and mineral substrates, and the consequent formation of salts, black crusts and corrosion products. We highlight the role of biomonitoring as a methodological and interpretive bridge linking atmospheric pollution to biodeterioration processes. In addition, we discuss emerging interdisciplinary methodologies - including functional metagenomics, microbial network analysis, and metabolomic profiling -and introduce the Function-Based Biodegradation Risk Assessment model, extended into a Multi-Level Risk Assessment Framework that connects microbial functionality, material diagnostics, and climate modeling. We contend that safeguarding built heritage in a changing climate requires transitioning from static, material-centred diagnostics to integrated, predictive frameworks that link microbial ecology, materials science, and climate dynamics, providing the basis for adaptive and anticipatory conservation strategies.},
}

@article {pmid41472882,
year = {2025},
author = {Gómez-Pérez, D and Keller, A},
title = {Integrating natural language processing and genome analysis enables accurate bacterial phenotype prediction.},
journal = {NAR genomics and bioinformatics},
volume = {7},
number = {4},
pages = {lqaf174},
pmid = {41472882},
issn = {2631-9268},
mesh = {*Natural Language Processing ; Phenotype ; *Genome, Bacterial ; *Bacteria/genetics ; *Genomics/methods ; Machine Learning ; },
abstract = {Understanding microbial phenotypes from genomic data is crucial for studying co-evolution, ecology, and pathology. This study presents a scalable approach that integrates literature-extracted information with genomic data, combining natural language processing and functional genome analysis. We applied this method to publicly available data, providing novel insights into predicting microbial phenotypes. We fine-tuned transformer-based language models to analyze 3.83 million open-access scientific articles, extracting a phenotypic network of bacterial strains. This network maps relationships between strains and traits such as pathogenicity, metabolism, and biome preference. By annotating their reference genomes, we predicted key genes influencing these traits. Our findings align with known phenotypes, reveal novel correlations, and uncover genes involved in disease and host associations. The network's interconnectivity provides deeper understanding of microbial communities and allowed identification of hub species through inferred trophic connections that are difficult to infer experimentally. This work demonstrates the potential of machine learning for uncovering cross-species gene-phenotype patterns. As microbial genomic data and literature expand, such methods will be essential for extracting meaningful insights and advancing microbiology research. In summary, this integrative approach can accelerate discovery and understanding in microbial genomics. Ultimately, such techniques will facilitate the study of microbial ecology, co-evolutionary processes, and disease pathogenesis to an unprecedented depth.},
}

*Natural Language Processing
Phenotype
*Genome, Bacterial
*Bacteria/genetics
*Genomics/methods
Machine Learning

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

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

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

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

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

@article {pmid41472031,
year = {2025},
author = {Yuan, W and Shang, Y and Bai, M and Sun, M and Su, Z and Yang, X and Riaz, L and Guo, Y and Lu, J},
title = {Occurrence and Distribution of Antibiotics and Antibiotic Resistance Genes in the Water and Sediments of Reservoir-Based Drinking Water Sources in Henan, China.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41472031},
issn = {2076-2607},
support = {241111320200//the Key R&D projects in Henan Province/ ; 42407404//the National Natural Science Foundation of China/ ; },
abstract = {The improper use of antibiotics accelerates the emergence of resistance via environmental selection pressures, jeopardizing public health and ecosystems by promoting the worldwide dissemination of antibiotic resistance genes (ARGs). Reservoirs, as crucial water supplies, have been recognized as primary reservoirs of ARGs, particularly those that originate from the Yellow River, necessitating further investigation. This study analyzed 9 ARGs, 3 mobile genetic elements (MGEs), 16 antibiotics, and 10 heavy metals in water/sediments from three reservoirs originating from the Yellow River in Henan Province, China. The findings indicated that antibiotic concentrations in water exceeded those in sediment, with quinolones detected at 100% frequency (5.47-116.03 ng/L) and enrofloxacin predominating (3.36-107.71 ng/L). Redundancy analysis revealed that MGEs exert greater control over ARG dissemination than antibiotics, with intI1 showing strong positive correlations with sul1 (p < 0.05). Conversely, heavy metals (Zn, As, Cd) suppress ARG proliferation through negative selection pressures. A network study indicated Mycobacterium, Pseudarthrobacter, and Massilia as critical hosts for ermB, tetA, and qnrA, respectively. Of the three reservoirs, Jian'gang Reservoir, driven by synergistic effects of unique microbial ecology, water self-purification capacity, and flow dynamics, exhibited the best removal effectiveness of ARGs from input to outflow, with 71.75% in the water and 97.91% in the sediment. These findings provide critical insights into the prevalence, migration, and self-purification processes of ARGs in reservoirs originating from the Yellow River, integrating environmental factors and microbial data to clarify the complex dynamics affecting ARG behavior and inform targeted pollution control strategies.},
}

@article {pmid41472029,
year = {2025},
author = {Dhakal, R and Guo, W and Vieira, RAM and Guan, L and Neves, ALA},
title = {Advances in Lignocellulose-Degrading Enzyme Discovery from Anaerobic Rumen Fungi.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41472029},
issn = {2076-2607},
abstract = {Anaerobic fungi (phylum Neocallimastigomycota) play a crucial role in degrading forages and fibrous foods in the gastrointestinal tract of mammalian herbivores, particularly ruminants. Currently, they are classified into twenty-two genera; however, recent research suggests the occurrence of several novel taxa that require further characterization. Anaerobic rumen fungi play a pivotal role in lignocellulose degradation due to their unique enzymatic capabilities. This review explores the enzymatic systems of rumen anaerobic fungi, highlighting their ability to produce a diverse array of carbohydrate-active enzymes (CAZymes), such as cellulases, hemicellulases, and pectinases. These enzymes facilitate the breakdown of complex plant polymers, making anaerobic fungi essential contributors to fiber degradation in the rumen ecosystem and valuable resources for biotechnological applications. This review summarizes the structural and functional diversity of fungal CAZymes, and the mechanical disruption of plant cell walls by fungal rhizoidal networks is discussed, showcasing the ability of fungi to enhance substrate accessibility and facilitate microbial colonization. Recent studies using genomic, transcriptomic, and biochemical approaches have uncovered several novel CAZymes in anaerobic fungi, including multifunctional xylanases, β-glucosidases, and esterases. These findings highlight the continued expansion of fungal enzyme repertoires and their potential for biotechnology and feed applications. Continued research in this field will enhance our understanding of microbial ecology and enzyme function, paving the way for applications that address global challenges in energy, food security, and environmental sustainability.},
}

@article {pmid41472008,
year = {2025},
author = {Leal, G and Canals, JM and Beltran, G and Peña-Neira, Á and Jara, C and Romero, J and Ramírez, C and Sanz, R},
title = {From Soil to Wine: Influence of Vegetative Covers on Microbial Communities and Fermentative Dynamics in Cabernet Sauvignon.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41472008},
issn = {2076-2607},
abstract = {The implementation of vegetative cover crops in vineyards is a sustainable alternative to chemical weed control, potentially influencing both soil fertility and grape-associated microbiota. This study evaluated the impact of six groundcover management strategies under vines-white clover (Trifolium repens), red clover (Trifolium pratense), burr medic (Medicago polymorpha), lupine (Lupinus albus), spontaneous weeds, and an herbicide-treated control-on the microbial dynamics and physicochemical properties of Cabernet Sauvignon must and wine from the Maipo Valley, Chile. Amplicon sequencing of bacterial (16S rRNA) and fungal (ITS) communities was combined with spontaneous fermentation trials and chemical analyses of must and wine. Fungal and bacterial communities on grape surfaces were dominated by Ascomycota and Proteobacteria, respectively, with no significant compositional differences among treatments. During fermentation, Metschnikowia and Tatumella were the most abundant non-Saccharomyces and bacterial genera, respectively, showing dynamic shifts across fermentation stages. Legume-based covers, particularly red clover, increased wine total acidity and polyphenol index while reducing pH. Correlation analyses revealed associations between specific microbial taxa (Metschnikowia, Cohnella, Saliterribacillus) and key enological parameters. Overall, these findings demonstrate that leguminous cover crops subtly modulate vineyard microbial ecology and fermentation outcomes, offering an environmentally sustainable pathway to enhance enological differentiation in semi-arid viticultural regions.},
}

@article {pmid41471996,
year = {2025},
author = {Zhang, X and Mao, G and Pei, Z and Sun, Y and Cen, J and Zhang, S and Li, S and Meng, W and Xiao, K and Xu, Q and Sun, M},
title = {Microbial Ecology of Sulfur Mustard Toxicity: From Dysbiosis to Restoration.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471996},
issn = {2076-2607},
support = {82103885//National Natural Science Foundation of China/ ; 82273672//National Natural Science Foundation of China/ ; 20ZR1470300//Natural Science Foundation of Shanghai Municipality/ ; 21ZR1477700//Natural Science Foundation of Shanghai Municipality/ ; GWV-10.2-YQ48//Shanghai Municipal Health Commission-Outstanding Youth Foundation of Public Health/ ; },
abstract = {Sulfur mustard (SM) causes multi-organ toxicity, yet its impact on intestinal tissue and the associated gut microbiota remains poorly characterized. This study demonstrates that in a mouse model of SM exposure, gut microbial ecological collapse occurs, characterized by depletion of protective taxa (Bifidobacteriales, Gordonibacter, and Lachnospiraceae UCG010) while promoting a 302-fold expansion of inflammation-associated Escherichia/Shigella. Mendelian randomization analysis established causal relationships between these SM-perturbed taxa and human inflammatory bowel disease. Fecal microbiota transplantation effectively restored microbial diversity (Simpson index: 0.85 to 0.95), suppressed Escherichia/Shigella by 97.4%, and ameliorated intestinal pathology. Longitudinal tracking revealed persistent vulnerability of Bifidobacteriales compared to other depleted taxa. Our findings establish the gut microbiota as a key mediator in SM intestinal toxicity and provide new insights for microbiota-targeted interventions against chemical injuries.},
}

@article {pmid41469005,
year = {2025},
author = {Cao, ZW and Zhang, LK and Fang, B and Zhang, X},
title = {[Risk management and clinical strategies for early enamel demineralization in orthodontic patients].},
journal = {Zhonghua kou qiang yi xue za zhi = Zhonghua kouqiang yixue zazhi = Chinese journal of stomatology},
volume = {61},
number = {1},
pages = {30-38},
doi = {10.3760/cma.j.cn112144-20251020-00418},
pmid = {41469005},
issn = {1002-0098},
support = {2022YFC2405900, 2022YFC2405902//National Key Research and Development Program of China/ ; 82171007//National Natural Science Foundation of China/ ; },
abstract = {Early enamel demineralization, one of the common side effects of orthodontic treatment, occurs when dental plaque accumulation disrupts the balances of demineralization-remineralization and the oral microbial ecology. Clinically, the existence of orthodontic appliances can make oral hygiene more challenging. At the same time, patient adherence to oral hygiene appointments may be inconsistent. The combination of these factors often leads to inadequate plaque control and increases the risk of enamel demineralization. Presently, there is a lack of standardized guidelines for the clinical intervention and management for early enamel demineralization. Moreover, the associated risk assessment and prevention systems require further improvement. This article provides a review of the etiology, risk factors, and preventive and treatment strategies for managing early enamel demineralization in orthodontic patients. The aim is to provide references for clinicians to promote the early detection, early intervention, and standardized management of early enamel demineralization, thereby effectively controlling the incidence and progression of these lesions during orthodontic treatment.},
}

@article {pmid41468165,
year = {2025},
author = {Benner, SA and Schulze-Makuch, D and Spacek, J and Abraham, C},
title = {Viking Mars, Now 50 Years Old, Still Needs a Scientific Analysis.},
journal = {Astrobiology},
volume = {},
number = {},
pages = {},
doi = {10.1177/15311074251404929},
pmid = {41468165},
issn = {1557-8070},
abstract = {A scientific back-and-forth, a half century overdue, is needed to develop an understanding of the possibility of life on the near surface of Mars before crewed missions complicate the search for indigenous extant martian life.},
}

@article {pmid41466397,
year = {2025},
author = {Alimata, B and Ablassé, R and Moussa, C and Eli, C and Leila, KWME and Noufou, O and Emmanuelle, HA and Martin, K and Marie-Geneviève, DF},
title = {Anti-biofilm, anti-quorum sensing potential, cytotoxicity, and UPLC-UV/DAD-MS/MS/QTOF profiling of Prosopis Africana (Guill. & Perr.) Taub. leaves and stems extracts: benefits of a traditional medicine in dental care.},
journal = {BMC complementary medicine and therapies},
volume = {25},
number = {1},
pages = {445},
pmid = {41466397},
issn = {2662-7671},
abstract = {BACKGROUND: Prosopis africana is traditionally used in folk medicine in Burkina Faso for oral diseases. Leaves and stems are used in rural areas to treat dental caries, and the bark is used to treat green diarrhea in infants. In the context of a better understanding of Prosopis africana’s bioactivity and toxicity, the present study deals with the chemical profiling of the different botanical parts of P. Africana used in phytomedicine. The impact of herbal medicine on various factors contributing to oral infections and caries, specifically with its anti-biofilm and anti-quorum sensing properties have been little investigated.

METHODS: The anti-biofilm effect of methanolic extracts of leaves and stems of P. africana was evaluated on Streptococcus mutans, Staphylococcus aureus, and Pseudomonas aeruginosa by using the crystal violet assay. The anti-quorum sensing effect on Chromobacterium CV026 and Pseudomonas aeruginosa was assessed spectrophotometrically by using the violacein, rhamnolipids and pyocyanin quantification assay. The cytotoxicity of the leaves and stems extracts was also evaluated by using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide method. The chemical composition of the extracts was characterized by UPLC-UV/DAD-MS[2]/ESI-QTOF analysis.

RESULTS: The extracts (100 µg/ml), without affecting cells viability, significantly reduced the biofilm formation of S. mutans with the best inhibition rates of 56.7% and 47.6% for stem and leaf extracts respectively. In Chromobacterium CV026, the violacein inhibition rate was 37.9 ± 3.7% for leaves methanol extract and 42.6 ± 1.4% for the stem methanol extract. In P. aeruginosa inhibition rates of 49.03%, 40.2%, and 46.7% were obtained for pyocyanin, elastase, and rhamnolipids respectively, with leaf extracts. UPLC-UV-MS[2] analysis identified sixteen compounds which are mainly polyphenols and alkaloids. They could be related to the activities.

CONCLUSION: The present study provides evidence of the efficacy and basic scientific justification for the traditional uses of P. africana in the treatment of dental caries.},
}

@article {pmid41465800,
year = {2025},
author = {Messina, BM and Polizzi, A and Panuzzo, C and Belmonte, A and Angjelova, A and Fuochi, V and Annunziata, M and Isola, G},
title = {Impact of Periodontal Host-Modulation Therapies on Oral-Gut Microbiome Axis in Periodontitis Patients with Hematological Diseases: A Narrative Review.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {12},
pages = {},
doi = {10.3390/life15121862},
pmid = {41465800},
issn = {2075-1729},
abstract = {Host-modulating therapies and oral microbiome-targeted approaches are emerging options in periodontal care and are especially relevant for patients undergoing immunotherapy for hematologic malignancies. Immune dysregulation induced by immune checkpoint inhibitors or CAR-T cell therapy may worsen periodontal inflammation and alter the composition and functions of the oral microbiota. Beyond these, other immunomodulatory treatments commonly employed in hematologic malignancies-including monoclonal antibodies (e.g., rituximab, daratumumab), immunomodulatory drugs (e.g., lenalidomide, thalidomide), cytokine-based therapies (e.g., interferon-α), and targeted small-molecule inhibitors (e.g., BTK inhibitors, JAK inhibitors) may also influence periodontal homeostasis and oral microbial ecology by altering neutrophil function, cytokine profiles, and mucosal immune surveillance. The oral microbiota is functionally connected with the intestinal microbial ecosystem through the oral-gut axis, by periodontal pathogens may colonize the gut and modulate systemic immune responses, with potential repercussions on the efficacy and safety of immunotherapy. This narrative review examines the mechanisms and clinical applicability of host-modulating therapies, including subantimicrobial-dose doxycycline, omega-3 fatty acids, and microbiome-targeted interventions, such as oral probiotics, prebiotics and other antimicrobials in patients treated with immunotherapy.},
}

@article {pmid41465447,
year = {2025},
author = {Duda-Madej, A and Viscardi, S and Łabaz, JP and Topola, E and Szewczyk, W and Gagat, P},
title = {Berberine in Bowel Health: Anti-Inflammatory and Gut Microbiota Modulatory Effects.},
journal = {International journal of molecular sciences},
volume = {26},
number = {24},
pages = {},
doi = {10.3390/ijms262412021},
pmid = {41465447},
issn = {1422-0067},
mesh = {*Berberine/pharmacology/therapeutic use ; Humans ; *Gastrointestinal Microbiome/drug effects ; Animals ; *Anti-Inflammatory Agents/pharmacology/therapeutic use ; *Inflammatory Bowel Diseases/drug therapy/microbiology ; },
abstract = {Disruption of the gut-microbiome-brain axis contributes to the development of chronic inflammation, impaired intestinal barrier integrity, and progressive tissue damage, ultimately reducing quality of life and increasing risk of comorbidities, including neurodegenerative diseases. Current therapies are often limited by adverse effects and insufficient long-term efficacy, highlighting the need for more comprehensive therapeutic approaches. Berberine (BRB), a plant-derived isoquinoline alkaloid, has attracted growing attention due to its pleiotropic immunomodulatory, neuroprotective, and gut-homeostasis-modulating properties, which involve reshaping the gut microbiota and underscore its therapeutic relevance within the gut-microbiome-brain axis. The aim of this review is to synthesize current scientific evidence regarding the anti-inflammatory mechanisms of BRB in inflammatory bowel disease (IBD). We compare its activity with first-line therapies and discuss its impact on microbial composition, including the bidirectional regulation of specific bacterial taxa relevant to intestinal and systemic disorders that originate in the gut. Furthermore, we emphasize that gut bacteria convert BRB into bioactive metabolites, contributing to its enhanced intraluminal activity despite its low systemic bioavailability. By integrating molecular and microbiological evidence, this review fills a critical knowledge gap regarding the comprehensive therapeutic potential of BRB as a promising candidate for future IBD interventions. The novelty of this work lies in unifying fragmented findings into a framework that explains how BRB acts simultaneously at the levels of host immunity, microbial ecology, and neuroimmune communication-thus offering a new conceptual model for its role within the gut-microbiome-brain axis.},
}

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

@article {pmid41463564,
year = {2025},
author = {Zi, Y and Yang, Y and Li, M and Li, Y and An, Z and Liu, M and Ma, C and Gao, F and Li, C},
title = {Rumen Microbial Diversity and Metabolome Analysis Reveals the Effects of Alkaline Metal Ion Complexes on Muscle Quality of Lambs.},
journal = {Biology},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/biology14121791},
pmid = {41463564},
issn = {2079-7737},
support = {CARS38//China Agriculture Research System/ ; BRS231402//Interdisciplinary Research Fund of Inner Mongolia Agricultural University/ ; },
abstract = {This study investigated the effects of dietary supplementation with an alkaline metal ion complex (AMIC) on growth performance, meat quality, rumen microbiota, and metabolome in Hu lambs. Fifty lambs were randomly assigned to either a control group (basal diet) or an AMIC group (basal diet + 0.15% AMIC) for 60 days. The results showed that AMIC significantly increased carcass weight, Longissimus dorsi area, crude protein, intramuscular fat, ash content, and meat luminosity (L*). Amino acid profiles and key flavor compounds were elevated, while off-flavor hydrocarbons were reduced. 16S rRNA sequencing revealed that AMIC altered rumen microbiota composition, enriching butyrate-producing genera such as Butyrivibrio and Saccharofermentans. Metabolomic analysis identified 398 differentially expressed metabolites, with upregulated pathways including butanoate metabolism and xylene degradation. Correlation analyses indicated strong associations between specific microbial taxa, metabolites, and meat quality traits. These findings suggest that AMIC enhances meat quality by modulating rumen microbial ecology and metabolic pathways, leading to improved nutrient deposition and flavor development. This study provides novel insights into the microbe-metabolite-muscle axis in ruminants and supports the use of AMIC as a dietary strategy for quality lamb production.},
}

@article {pmid41463403,
year = {2025},
author = {Sun, X and Li, P and Chen, B and Chen, C and Zhao, J and Sun, S},
title = {Fucoidan Therapy for Extraintestinal Diseases: Targeting the Microbiota-Gut-Organ Axes.},
journal = {Biomolecules},
volume = {15},
number = {12},
pages = {},
doi = {10.3390/biom15121750},
pmid = {41463403},
issn = {2218-273X},
support = {82374218//National Natural Science Foundation of the People's Republic of China/ ; 82405310//National Natural Science Foundation of the People's Republic of China/ ; 2023DYPLHGG-09//The First Batch of Joint Research Projects of the China Association of Traditional Chinese Medicine/ ; MS2021002//Jiangsu Province Traditional Chinese Medicine Science and Technology Development Project/ ; 1020241792//Natural Science Foundation of the Jiangsu Higher Education Institutions of China/ ; },
mesh = {*Polysaccharides/therapeutic use/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Humans ; Animals ; Prebiotics ; Obesity/drug therapy/microbiology ; },
abstract = {The microbiota-gut-organ axis is widely recognized as a pivotal mediator of systemic health, primarily through gut-derived immune, metabolic, and inflammatory signaling. Fucoidans, a class of fucose-containing sulfated polysaccharides predominantly composed of L-fucose and exclusively found in brown seaweeds, have been demonstrated to modulate gut microbiota composition and function, resulting in the enrichment of beneficial bacteria and the suppression of harmful species. They enhance the production of beneficial metabolites, such as short-chain fatty acids and specific bile acids, while suppressing harmful metabolites, including lipopolysaccharide, thereby ameliorating organ damage via key mechanisms such as the mitigation of oxidative stress and inhibition of inflammatory responses. Furthermore, fucoidan supplementation was found to restore intestinal barrier integrity. Using disease models including Parkinson's disease, alcoholic liver disease, diabetic kidney disease, and obesity, the mechanisms through which fucoidans ameliorate extraintestinal diseases via the microbiota-gut-organ axis were elucidated. Microbiota-dependent mechanisms have been confirmed via experimental approaches such as fecal microbiota transplantation and specific bacterial strain supplementation. Fucoidans represent promising prebiotic agents for the restoration of microbial ecology and the treatment of extraintestinal diseases, highlighting the need for further clinical investigation.},
}

*Polysaccharides/therapeutic use/pharmacology
*Gastrointestinal Microbiome/drug effects
Humans
Animals
Prebiotics
Obesity/drug therapy/microbiology

@article {pmid41462375,
year = {2025},
author = {Zhang, Y and Zhou, K and Chen, X and Zhang, H and Han, J and Ning, K},
title = {A temporal-aware machine learning framework enables microbial community dynamics prediction with personalized precision.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {261},
pmid = {41462375},
issn = {2049-2618},
support = {Grant No. 2023YFA1800900 and 2018YFC0910502//National Key R&D Program of China/ ; Grant Nos. 32071465, 31871334, 81827901//the National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Machine Learning ; *Precision Medicine/methods ; *Gastrointestinal Microbiome ; *Microbiota ; Infant ; Bacteria/classification/genetics ; },
abstract = {BACKGROUND: Accurately forecasting the dynamic behavior of microbial communities from sparse longitudinal data remains a critical challenge for microbiome-based precision medicine and ecological monitoring. Most existing models depend on data interpolation and assume population-level dynamics, which limits their ability to capture personalized microbial changes in real-world scenarios.

RESULTS: We propose MicroProphet, a personalized temporal-aware framework capable of accurately forecasting microbial abundance trajectories from incomplete longitudinal observations without requiring data imputation. Powered by a time-aware Transformer architecture, MicroProphet reconstructs subject-specific microbial trajectories using only the initial 30% of observed time points, capturing critical transitional states through an attention mechanism. We demonstrated its robust cross-ecosystem generalizability across synthetic communities, human gut microbiomes, infant gut development, and corpse decomposition. The framework consistently achieves high predictive accuracy and biological interpretability. In clinical contexts, the framework enables early detection of disease-associated microbial shifts and supports timing optimization for microbiome-targeted interventions. In forensic settings, it accurately infers decomposition timelines from early microbial signals.

CONCLUSIONS: By transforming incomplete, noisy microbiome data into actionable, individualized forecasts, MicroProphet lays the foundation for a new class of temporal-aware systems in microbial ecology and precision health.},
}

Humans
*Machine Learning
*Precision Medicine/methods
*Gastrointestinal Microbiome
*Microbiota
Infant
Bacteria/classification/genetics

@article {pmid41461510,
year = {2026},
author = {Chen, B and Hao, Z and Luo, L and Wu, N and Liu, W and Zhu, D and Ge, Y and Chen, W and Jiao, W and Zhang, X and Liu, S and Shen, J and Xiao, KQ and Fu, W and Wu, S and Zhu, YG},
title = {Soil science research in Research Center for Eco-Environmental Sciences: Review and outlook.},
journal = {Journal of environmental sciences (China)},
volume = {161},
number = {},
pages = {64-74},
doi = {10.1016/j.jes.2025.09.065},
pmid = {41461510},
issn = {1001-0742},
mesh = {*Soil/chemistry ; *Environmental Science ; Soil Microbiology ; Ecosystem ; China ; Soil Pollutants/analysis ; Environmental Monitoring ; Environmental Pollution ; Research ; },
abstract = {Soil science research involves the composition, properties, processes, and functions of soil under natural conditions and anthropogenic utilization, and provides scientific basis for the utilization, protection, and sustainable management of soil resources. This review summarizes the significant contributions of Research Center for Eco-Environmental Sciences (RCEES), Chinese Academy of Sciences, to the advances of soil science. Over past decades, RCEES has conducted innovative research in areas such as soil pollution and remediation, biogeochemical cycling of macro and trace elements and soil microbial ecology. Groundbreaking discoveries have been achieved in research directions such as metal transformation and translocation in the soil-plant continuum, soil microbial diversity and biogeography, and the environmental and health risk of soil contamination. In recent years, on-going projects also involves cutting-edge hotspots, including the environmental behavior of emerging pollutants, and soil organic matter dynamics. The soil lab in RCEES has undertaken important research projects and trained a group of dynamic young scientists, and has also been instrumental in establishing international collaborations, enhancing its global impact through participation in global soil research initiatives and conferences. Concurrently, soil science at RCEES is moving forward to the resilience of soil ecosystems to global changes, integrating soil health into the One Health framework, and sustainable soil management practices. RCEES remains a key player in shaping the future of soil science, contributing to both scientific advances and the sustainable management of soil resources in China.},
}

*Soil/chemistry
*Environmental Science
Soil Microbiology
Ecosystem
China
Soil Pollutants/analysis
Environmental Monitoring
Environmental Pollution
Research

@article {pmid41461285,
year = {2025},
author = {Bharathi, S and Soundara Rajan, YAPA and Prakash, S and Immanuel, G and Ramasubburayan, R},
title = {Pathobionts in the microbiome: Drivers of disease and targets for treatment.},
journal = {Microbial pathogenesis},
volume = {211},
number = {},
pages = {108268},
doi = {10.1016/j.micpath.2025.108268},
pmid = {41461285},
issn = {1096-1208},
abstract = {Pathobionts are commensal inhabitants of the human microbiome that can transition to a pathogenic state under specific genetic or environmental conditions. They have recently gained attention for their impact on various clinical conditions. This review discusses the key factors behind pathobiont emergence, including microbial dysbiosis, antibiotic use, dietary influences, immune dysfunction and host genetics. It provides a comprehensive overview of pathobionts associated with the gut, oral cavity, and vaginal microbiomes highlighting their roles in disease pathogenesis. A significant focus is also placed on the involvement of pathobiont in immune-related disorders. Furthermore, current and advanced therapeutic strategies aimed at mitigating the effects of pathobionts, such as faecal microbiota transplantation, phage therapy, probiotics and prebiotics, along with their advantages and limitations, were highlighted. Thus, the integrated perspective combining microbial ecology, host immunity, and therapeutic strategies outlines the need for targeted, microbiome-based interventions to address the complex behaviour of pathobionts.},
}

@article {pmid41460347,
year = {2025},
author = {Zhang, Y and Zheng, C and Wang, S and Zhu, F},
title = {Variations in Nodule Microbial Communities and Their Association with Root-Colonizing Arbuscular Mycorrhizal Fungi in Medicago Sativa.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02687-x},
pmid = {41460347},
issn = {1432-184X},
support = {2022YFF1302801//National Key Research and Development Program of China/ ; 2022YFD1900301//National Key Research and Development Program of China,China/ ; },
abstract = {Alfalfa (Medicago sativa L.), known as "Queen of forages", is valued to its high-nutritional quality and is a key member of Leguminosae family. Its productivity is largely attributed to mutualistic symbioses with arbuscular mycorrhizal fungi (AMF) and rhizobia, which facilitate nutrient exchange and plant growth. However, the coexistence and mutualistic interactions between rhizobia and AMF across alfalfa genotypes with differing yields in native soil remain poorly understood. In this study, we investigated the community composition of rhizobia and AMF colonizing alfalfa roots across different-yield varieties. Our results showed variations in dominant microbial taxa and the structural complexity of root-associated microbial networks among genotypes. Moreover, rhizobia exhibited no significant associations with AMF on genus level, however, negative correlations were observed among genera within the AMF community, and a comparable trend was identified among rhizobial taxa. In summary, our findings offer new insights into how native soil microbiota influence the dual symbiotic relationships of alfalfa, with implications for leveraging native microbial communities to enhance sustainable forage production.},
}

@article {pmid41459044,
year = {2025},
author = {Wu, X and Shao, T and Huang, Y and Cui, X and Luo, Y and Ji, Q and Hu, Z and Teng, S and Bao, G and Liu, Y},
title = {Effects of dietary nisin supplementation on the growth performance, serum biochemistry, digestive enzyme activities, intestinal morphology, and intestinal microbiota in rabbits.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1726365},
pmid = {41459044},
issn = {2297-1769},
abstract = {INTRODUCTION: This study evaluated the impact of dietary supplementation with varying doses of nisin (NI) on the growth performance, serum biochemical parameters, intestinal digestive enzyme activity, short-chain fatty acid (SCFA) profiles, mucosal morphology, and the cecal microbiota composition in rabbits.

METHODS: Healthy female New Zealand white rabbits (5 weeks old; n = 90) of comparable body weight were randomly allocated to five groups: a positive control (PC) group receiving a basal diet supplemented with kitasamycin (300 mg/kg), three NI groups supplemented with nisin at 600 (NI600), 800 (NI800), or 1,000 (NI1000) mg/kg, and a negative control (NC) group receiving the basal diet without additives. Each treatment was comprised of three replicates (n = 6 per replicate), and the trial lasted 42 days.

RESULTS: The results showed that the rabbits administered NI displayed significantly enhanced final body weights as compared to the NC group (P < 0.05), with a dose-dependent effect. Notably, the NI800 and NI1000 groups exhibited a superior average daily gain (ADG) and average daily feed intake (ADFI). Serum analyses showed improved lipid profiles and elevated antioxidant enzyme activities concomitant with reduced lipid peroxidation in the NI-supplemented groups. Enzymatic assays indicated elevated duodenal a-amylase activity in the NI800 group as compared to the PC (P < 0.05) and enhanced ileal trypsin activity in the NI800 as compared to NI1000 and PC (P < 0.05). Histological evaluation confirmed that the NI800 group displayed optimal intestinal villi morphology, characterized by increased density, height, and structural integrity relative to the PC and NC controls. Metagenomic analysis of the cecal microbiota further revealed dose-dependent shifts in the diversity and composition of the microbiota, with the NI800 group exhibiting pronounced restructuring. Enriched functional pathways in the NI groups, including cofactor/vitamin metabolism, amino acid biosynthesis, energy homeostasis, and environmental adaptation.

DISCUSSION: Collectively, these findings highlight that NI supplementation enhances digestive efficiency, augments systemic antioxidant defenses, fortifies intestinal barrier function, and modulates microbial ecology and SCFA production, there by promoting growth and metabolic health in rabbits. Nisin, especially at 800 mg/kg, demonstrates significant potential as an antibiotic alternative.},
}

@article {pmid41458128,
year = {2025},
author = {Qin, Y and Wang, Y and Huang, Y and Chen, H and Zhuang, Y and Liu, Q and Soteyome, T and Zhu, B and Brennan, C},
title = {Antimicrobial EU@Ag-MOF/PLA composite films enhance postharvest quality of strawberries by mitigating oxidative stress and modulating microbial communities.},
journal = {Food chemistry: X},
volume = {32},
number = {},
pages = {103377},
pmid = {41458128},
issn = {2590-1575},
abstract = {Strawberries are highly perishable fruits susceptible to rapid postharvest deterioration. This study investigated the efficacy of EU@Ag-MOF/PLA composite films for postharvest strawberry preservation. The 3EU@Ag-MOF/PLA formulation demonstrated optimal performance in maintaining physicochemical properties, reducing reactive oxygen species accumulation, and enhancing antioxidant enzyme activities. Notably, this composite film suppressed hydrogen peroxide, superoxide anion, and malondialdehyde content by 28.44 %, 37.33 %, and 29.91 %, respectively, compared to control packaging after 10 days. Pathogen challenge studies with Botrytis cinerea and Rhizopus stolonifer revealed that this composite effectively balances reactive oxygen species production and scavenging mechanisms during storage. High-throughput sequencing showed that 3EU@Ag-MOF/PLA packaging preserved more balanced microbial community structures and dramatically reduced the relative abundance of pathogenic fungi by day 10. These findings demonstrate that 3EU@Ag-MOF/PLA composite film represent a promising active packaging solution for extending the shelf life of highly perishable fruits by simultaneously addressing fungal proliferation, oxidative stress, and microbial ecology.},
}

@article {pmid41457489,
year = {2025},
author = {Silbiger, NJ and Fields, JB and Nelson, CE and Kelly, LW},
title = {Foundation Species Modulate Microbial Benthic-Pelagic Coupling in the Rocky Intertidal.},
journal = {Ecology letters},
volume = {28},
number = {12},
pages = {e70301},
doi = {10.1111/ele.70301},
pmid = {41457489},
issn = {1461-0248},
support = {2044837//NSF Biological Oceanography/ ; 2513325//NSF Biological Oceanography/ ; COAST-GDP-2020-006//Council on Ocean Affairs Science and Technology, California State University/ ; //Uehiro Foundation on Ethics and Education/ ; },
mesh = {Animals ; *Ecosystem ; Oregon ; *Bacteria/growth & development ; *Bivalvia/physiology ; Nitrogen/metabolism ; Seawater/microbiology ; },
abstract = {Benthic-pelagic coupling, the reciprocal exchange of materials between benthic and pelagic habitats, has traditionally emphasised pelagic influences on benthic systems. Yet, the role of benthic biological processes in shaping pelagic microbial dynamics remains underexplored. We investigated how surfgrass and mussels regulate nitrogen and dissolved organic matter (DOM) cycling and their cascading effects on heterotrophic bacteria in Oregon tide pools. We quantified biogeochemical fluxes and bacterial responses before and after foundation species removal during contrasting upwelling regimes. Mussel-dominated pools released high concentrations of ammonium and nitrate, while surfgrass pools transformed DOM that fueled bacterial growth; upwelling intensified these benthic-pelagic linkages. Removing foundation species dampened nutrient release in mussel pools and reduced DOM-fueled bacterial growth in surfgrass pools, ultimately decoupling benthic productivity from pelagic microbial growth. Our results demonstrate the critical role of foundation species to pelagic microbial processes and underscore the vulnerability of coastal microbial dynamics to their global decline.},
}

Animals
*Ecosystem
Oregon
*Bacteria/growth & development
*Bivalvia/physiology
Nitrogen/metabolism
Seawater/microbiology

@article {pmid41457317,
year = {2025},
author = {Anbo, M and Otani, S and Ivanova, M and Nielsen, HN and Jensen, JD and Svendsen, CA and Pang, C and Aarestrup, FM},
title = {Contrasting pH optima of β-lactamases CTX-M and CMY influence Escherichia coli fitness and resistance ecology.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0177525},
doi = {10.1128/aem.01775-25},
pmid = {41457317},
issn = {1098-5336},
abstract = {Antimicrobial resistance is one of the largest and most pressing global health threats. This is not only a huge burden on the global economy but also a growing threat to animal, environmental, plant, and human health, and new strategies are needed to avoid resistance and improve treatment. Novel antimicrobial resistance genes are normally first detected once they cause problems in clinical infections, and we have limited knowledge on their evolutionary trajectories. Current antimicrobial susceptibility testing and research have a limited focus on key environmental factors in pathogen-reservoir-host interactions, possibly leading to inaccurate results that do not reflect the in vivo conditions. Focusing on differences in pH, we determined the MIC of a panel of isogenic strains expressing CTX-M-15 and CMY-2 β-lactamases. We found that pH has a large impact on the activity of β-lactamases, and treatment of these resistant isolates could be possible if the pH of the environment is modified. We verified this using enzyme kinetics, co-cultures, and growth experiments, suggesting that exposure to different environmental conditions may lead to distinct evolutionary trajectories for specific β-lactamases. Exploring the effect of different temperatures, we also observed a differential effect of avian and mammal host temperatures. Environmental factors such as pH and temperature may have a large unnoticed effect on antimicrobial resistance, and we might use this knowledge to renew and extend the use of old antibiotics for certain infections.IMPORTANCEAntimicrobial resistance is a huge burden to global health and economy. We need new options for avoiding selection of resistance and improved treatment. Overlooked aspect: current susceptibility testing does not take pH into account. With this study, we show that pH and temperature can have large and contrasting effects on the activity (and therefore MIC) of specific β-lactamases. This might help to explain the phenomenon of bacteria often harboring multiple β-lactamases seemingly with the same function as well as be utilized to enable treatment of genotypically resistant strains under very specific conditions, that is, treatment of CTX-M-15, the most prevalent ESBL in healthcare, under alkaline conditions.},
}

@article {pmid41456824,
year = {2025},
author = {Quan, H and Ouyang, J and Fu, X and Lin, D and Wu, Q and Li, D and Li, Y and Yang, F and Wu, S and Li, C and Mao, W},
title = {Elucidating the Therapeutic Mechanism of Orthosiphon aristatus in Hyperuricemic Nephropathy: An Integrated Microbiome-Metabolomics Approach.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {121115},
doi = {10.1016/j.jep.2025.121115},
pmid = {41456824},
issn = {1872-7573},
abstract = {Hyperuricemic nephropathy (HN) remains challenging to treat due to the limitations, including variable efficacy and side effects, of conventional drugs. Orthosiphon aristatus (O. aristatus), used for over 2000 years in Dai medicine to treat kidney disorders by "clearing heat and promoting diuresis," shows strong potential for HN management. However, its mechanisms of action against HN remain unclear.

AIM OF THE STUDY: This study aimed to elucidate the nephroprotective effects and underlying mechanisms of O. aristatus against HN using an integrated strategy focusing on the gut-kidney axis.

METHODS: A rat model of HN was established by combined oral administration of potassium oxonate (750 mg/kg) and uric acid (300 mg/kg) daily for 7 weeks. Model rats were treated with a low- or high-dose aqueous extract of O. aristatus (3.125 or 6.25 g/kg/day), using allopurinol (5 mg/kg/day) as a positive control. Renal function was assessed by measuring serum levels of uric acid, creatinine, and urea nitrogen. Renal pathological injury and fibrosis were evaluated through histopathological examination (H&E and Masson's trichrome staining), immunohistochemistry (α-SMA, vimentin), and transmission electron microscopy. To elucidate the underlying mechanisms, an integrated multi-omics approach was employed: gut microbiota composition was profiled by metagenomic sequencing, and metabolic alterations in cecal content and kidney tissue were characterized using UPLC-MS-based metabolomics. Furthermore, the protein expression of key targets involved in intestinal barrier function (Occludin, Claudin-1) and the IDO1/AhR signaling pathway was validated by Western blot analysis.

RESULTS: O. aristatus treatment significantly ameliorated renal dysfunction and pathological injury, as demonstrated by marked reductions in serum uric acid (sUA), creatinine (Scr), and blood urea nitrogen (BUN) levels (all p < 0.001), alongside attenuated tubular injury and fibrosis. Concurrently, it restored gut microbiota diversity (e.g., increased Shannon index, p < 0.05) and composition, characterized by an enrichment of beneficial Prevotella and a reduction in Bacteroides. Integrated metabolomics analysis further linked these effects to the rectification of tryptophan metabolism, manifested by decreased renal kynurenine levels (p < 0.01) and enhanced intestinal barrier integrity (e.g., elevated Occludin and Claudin-1, p < 0.05). Collectively, our results delineate that the renoprotective effect of O. aristatus is mediated through the suppression of the renal IDO1/kynurenine/AhR pro-fibrotic signaling axis, unveiling a novel gut microbiota-metabolite-kidney interaction mechanism.

CONCLUSION: This study elucidates that the renoprotective effect of O. aristatus against HN is mediated through modulation of the gut-kidney axis, by restoring microbial ecology, reprogramming host tryptophan metabolism, and subsequently inhibiting the IDO1/kynurenine/AhR pro-fibrotic pathway.},
}

@article {pmid41455542,
year = {2025},
author = {Mariën, Q and Regueira, A and Petrognani, C and Scarborough, M and Ganigué, R},
title = {Enhancing carbon capture and utilization: mixotrophic growth of Clostridium luticellarii using methanol and hydrogen for efficient CO2 reduction.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133886},
doi = {10.1016/j.biortech.2025.133886},
pmid = {41455542},
issn = {1873-2976},
abstract = {Carbon capture and utilization remains a major challenge in mitigating climate change. Carbon dioxide (CO2) fixing microorganisms offer promising routes to convert CO2 emissions into valuable products. Clostridium luticellarii is a recently discovered acetogen capable of converting CO2 to acetic, butyric and isobutyric acids using H2 or methanol as electron donors. Both routes can use renewable electricity as primary energy input, but each has its limitations: While H2-based processes suffer from poor gas-to-liquid mass transfer and low product selectivity beyond acetic acid, methanol requires a preliminary energy-intensive catalytic reduction of CO2. This study investigated the growth of C. luticellarii on both substrates to compensate their respective drawbacks. Combining methanol and H2 resulted in mixotrophic growth and enhanced CO2 assimilation up to four-fold compared to conversion of methanol alone, while producing similar product spectra. Thermodynamic pathway analysis suggested that high H2 pressures inhibit the H2-producing formate oxidation, while pathways with alternative electron carriers remain favorable. Subsequently, a metabolic model of the one-carbon catabolism was constructed and used to perform flux balance analysis. This revealed that H2 oxidation during mixotrophic growth augments the intracellular pool of reducing equivalents, reducing the need for methanol oxidation and increasing net CO2 assimilation into products. These findings highlight the potential of combining methanol and H2 as electron donors to improve CO2 conversion efficiency for the sustainable production of butyric and isobutyric acids.},
}

@article {pmid41455317,
year = {2025},
author = {Caly-Simbou, E and Ramin-Mangata, S and Poussier, S and Pecrix, Y},
title = {Bacteriocins in plant pathology: current knowledge, application, challenges and perspectives.},
journal = {Biochemical and biophysical research communications},
volume = {797},
number = {},
pages = {153203},
doi = {10.1016/j.bbrc.2025.153203},
pmid = {41455317},
issn = {1090-2104},
abstract = {To address the growing emergence of multi-resistant phytopathogenic bacteria, innovative solutions are being explored in the field of plant health. Among them, bacteriocins, antimicrobial peptides or proteins secreted by bacteria, characterized by a highly specific spectrum of activity and involved in intra-specific competition, are gaining increasing interest. Bacteriocins can confer a positive selective advantage in both natural and agricultural environments, thereby contributing to microbiome modulation. Bacteriocin-producing rhizobacteria and lactic acid bacteria are already used as biocontrol agents against phytopathogenic bacteria, as well as plant growth stimulators. Bacteriocins can be produced in situ by using avirulent strains, or ex situ through industrial synthesis and applied as biopesticides. Nowadays, genetic engineering enables production of chimeric bacteriocins and their direct production in transgenic plants, avoiding the need for repeated treatments and limiting emergence of resistances. The selection of promising bacteriocins can be guided by omics-based approaches, notably metagenomics, which involve the direct extraction and sequencing of DNA from environmental samples and provides access to the genetic diversity in complex soil or plant-associated microbiomes. Combined with open-access databases and recently developed integrated tools, this approach not only facilitates the identification of known structures of bacteriocins, but also enables the prediction of potentially active peptides even those never experimentally characterized. Bacteriocin-based strategies, at the crossroads of molecular biology, microbial ecology and agronomy, hold significant potential for promoting sustainable agriculture through highly specific pathogen targeting. However, their large-scale implementation still faces several challenges, including standardization of strain screening protocols, compliance with regulatory frameworks and farmer acceptance.},
}

@article {pmid41455041,
year = {2025},
author = {Sarkar, P and Das, S and Bandyopadhyay, S and Gopi, P and Biswas, S and Tribedi, P and Pandya, P and Mandal, S and Bhadra, K},
title = {Beta Carboline Alkaloid Harmine as Biofilm Inhibitor: In vitro, in Silico and in Vivo Studies Suppressing Growth and Virulence-Related Factors Against Resistant Staphylococcus Aureus.},
journal = {Applied biochemistry and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {41455041},
issn = {1559-0291},
support = {2025-2026//PRG University of Kalyani/ ; 2025-2026//DST PURSE/ ; },
abstract = {Screening plant-based alkaloids is one of the alternate therapeutic approaches to control antibiotic-resistant micro-pathogens. Our research highlighted beta carboline alkaloids as one of the most promising small molecules to established anti-virulent and anti-biofilm efficacy to regulate resistant bacterial infection. In vitro, in vivo assay and molecular docking were employed. Result Among six different bacterial strains, harmine showed 160 ± 2.07 µg/ml as the minimum inhibitory concentrations (MIC), followed by harmalol (190 ± 2.46) and harmaline (270 ± 3.04) against Staphylococcus aureus 96 (SA 96). Methicillin-resistant Staphylococcus aureus MRSA strain also showed inhibition of growth (MIC) by harmine, harmalol and harmaline at 250 ± 3.10, 320 ± 3.39 and 390 ± 4.90 µg/ml, respectively. MRSA is a prominent source of nosocomial infections, forming biofilms. The growth of biofilm got decreased with exposure to the sub-MIC concentrations (60, 80 and 100 µg/mL) of harmine, suppressing protein, targeting EPS and inhibiting extracellular protease. Harmine promote biofilm cell detachment by targeting cell surface hydrophobicity. Harmine causes depolarization of bacteria's cell membrane. Bacterial cell viability was further studied by propidium iodide (PI), DNA leakage and Acridine Orange (A/O)-Ethidium Bromide (EtBr) assay. Harmine treatment leads to increased reactive oxygen species (ROS) levels in biofilm cells. The binding affinities by molecular docking and dynamics indicated highest affinity with AgrC (-6.17 kcal/mol). Harmine treatment (32.0 mg/ kg bw, IP for five days) further recovered MRSA infected lungs in BALB/c mice. The findings revealed that among the three beta carboline alkaloids, harmine might be employed as a potential antibiofilm and antimicrobial agent for successful control of clinical S. aureus infection.},
}

@article {pmid41454163,
year = {2025},
author = {Bovio-Winkler, P and Orellana, E and Campanaro, S and de Jesús Montoya-Rosales, J and Fuess, LT and Carrillo-Reyes, J and Castelló, E and Muñoz-Páez, KM and Moreno-Andrade, I and Buitrón, G and Razo-Flores, E and Etchebehere, C},
title = {Unraveling the biological mechanisms of biohydrogen production through dark fermentation using assembled genomes from metagenomic data.},
journal = {Bioprocess and biosystems engineering},
volume = {},
number = {},
pages = {},
pmid = {41454163},
issn = {1615-7605},
support = {project A1-S-37174//Fondo Sectorial SEP-CONACYT/ ; },
abstract = {Dark fermentation represents a sustainable and promising approach for biohydrogen generation. However, achieving high yields depends on understanding the complex microbial interactions driving the process. This study used genome-centric metagenomics to analyze microbial communities from 11 hydrogen-producing reactors. In total, 44 metagenome-assembled genomes (MAGs) were analyzed in detail. High-yield reactors demonstrated a strong synergy between hydrogen-producing bacteria (HPB) and lactic acid bacteria (LAB), particularly Clostridium butyricum and Clostridium beijerinckii. These species encode the electron-transferring flavoprotein-lactate dehydrogenase complex (EtfAB-ldh complex), enabling hydrogen production from lactic acid. In contrast, reactors with lower hydrogen yields exhibited a higher prevalence of hydrogenotrophic microorganisms, including homoacetogens and methanogens, which redirected electron flow toward competing pathways, thereby decreasing hydrogen output. These results emphasize the importance of promoting HPB while suppressing hydrogen consumers to maintain an optimal microbial community. By linking community composition with metabolic potential, this study provides a framework for improving reactor performance, increasing hydrogen yields, and advancing sustainable hydrogen production from organic waste streams.},
}

@article {pmid41452003,
year = {2025},
author = {Sun, B and Sun, T and Ji, K and Yang, Z and Wang, J and Zhao, Y and Yu, X and Tang, X and Xiao, H},
title = {Effects of the tidal dehydration stress on epiphytic bacterial community of the intertidal macroalga Sargassum thunbergii.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0194825},
doi = {10.1128/spectrum.01948-25},
pmid = {41452003},
issn = {2165-0497},
abstract = {UNLABELLED: Intertidal macroalgae and their epiphytic bacteria experience periodic dehydration-rehydration cycles due to tidal fluctuations. The influence of tidal dehydration on algal epiphytic bacteria remains poorly understood. This study investigated the effect of tidal dehydration on epiphytic bacterial communities of macroalga Sargassum thunbergii. While tidal dehydration had a small impact on the composition of the epiphytic bacterial community of S. thunbergii, it significantly influenced community diversity, abundance of dominant taxa, and some predicted functional genes. Specifically, the abundance of Proteobacteria and Granulosicoccus increased markedly, whereas that of Cyanobacteria, Litoreibacter, and Sva0996_marine_group decreased significantly. The abundance of Marinomonas exhibited a trend of initial decrease, followed by subsequent increase. Predictive functional analysis suggested that the bacterial community adapted to dehydration stress by regulating genes involved in energy, nitrogen, and sulfur metabolism. The shifts in the bacterial community following dehydration stress may result from the inherent differential stress tolerance among bacterial taxa and host-mediated facilitation through algal metabolic adjustments that selectively favored specific groups. This study revealed the structural and functional response of the epiphytic bacterial community of macroalgae in intertidal zones to dehydration stress.

IMPORTANCE: The adaptive mechanisms of the intertidal macroalgal-epiphytic bacterial symbiotic system to periodic tidal dehydration stress play a crucial role in maintaining coastal ecosystem stability. Although numerous studies have investigated the effects of tidal dehydration on intertidal macroalgae, the impact of dehydration on the epiphytic bacteria has received much less attention. Our investigation revealed that tidal dehydration stress significantly alters both the community structure and metabolic functions of the epiphytic bacteria on Sargassum thunbergii. Notably, dehydration stress selectively enriched stress-tolerant bacterial taxa and induced metabolic reprogramming, particularly in energy, nitrogen, and sulfur cycling pathways. These microbial responses demonstrate not only bacterial stress adaptation strategies but also suggest potential host-mediated regulation within the algal-bacterial symbiotic system. These findings provide novel insights into the ecological adaptability mechanisms of intertidal ecosystems under environmental stress.},
}

@article {pmid41450949,
year = {2025},
author = {Perzon, O and Ilan, Y},
title = {Understanding gut microbial diversity using systems based on the Constrained-Disorder Principle provides a novel approach to targeting gut microbiome therapies.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1713775},
pmid = {41450949},
issn = {1664-302X},
abstract = {BACKGROUND/AIMS: The diverse composition of the gut microbiome is vital for human health, influencing digestion, immune regulation, and disease resistance. While higher diversity is generally associated with resilience, reduced and excessive diversity can lead to health issues.

METHODS: This paper introduces the Constrained Disorder Principle (CDP) as a new framework for understanding microbial diversity.

RESULTS: The CDP emphasizes the significance of maintaining variability within certain boundaries to sustain ecosystem stability and promote health. It considers intra- and inter-individual variability, illustrating how microbial ecosystems adapt throughout different life stages, genetic backgrounds, and environmental exposures. Integrating CDP-based artificial intelligence systems may enable the establishment of personalized diversity thresholds, predict dysbiosis, and refine interventions such as probiotics, prebiotics, fecal microbiota transplantation, and customized dietary strategies. CDP-driven platforms enhance therapeutic precision by utilizing variability induction, feedback loops, and microbial signature analysis to optimize diversity goals and identify actionable biomarkers.

CONCLUSION: This platform can pave the way for adaptive, individualized disease prevention and treatment strategies, bridging the gap between microbial ecology and precision medicine. It provides a powerful tool for harnessing the therapeutic potential of gut microbial diversity to enhance human health.},
}

@article {pmid41445807,
year = {2025},
author = {Wang, XW and Wang, T and Liu, YY},
title = {Artificial Intelligence for Microbiology and Microbiome Research.},
journal = {ArXiv},
volume = {},
number = {},
pages = {},
pmid = {41445807},
issn = {2331-8422},
abstract = {Advancements in artificial intelligence (AI) have transformed many scientific fields, with microbiology and microbiome research now experiencing significant breakthroughs through machine learning applications. This review provides a comprehensive overview of AI-driven approaches tailored for microbiology and microbiome studies, emphasizing both technical advancements and biological insights. We begin with an introduction to foundational AI techniques, including primary machine learning paradigms and various deep learning architectures, and offer guidance on choosing between traditional machine learning and sophisticated deep learning methods based on specific research goals. The primary section on application scenarios spans diverse research areas, from taxonomic profiling, functional annotation \& prediction, microbe-X interactions, microbial ecology, metabolic modeling, precision nutrition, clinical microbiology, to prevention \& therapeutics. Finally, we discuss challenges in this field and highlight some recent breakthroughs. Together, this review underscores AI's transformative role in microbiology and microbiome research, paving the way for innovative methodologies and applications that enhance our understanding of microbial life and its impact on our planet and our health.},
}

@article {pmid41443232,
year = {2025},
author = {Dissanayaka, S and Jayasingh, T and Sohrabi, HR and Rainey-Smith, SR and Scott, K and Martins, RN and Fernando, WMADB and , },
title = {Basic Science and Pathogenesis.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {21 Suppl 1},
number = {Suppl 1},
pages = {e105512},
doi = {10.1002/alz70855_105512},
pmid = {41443232},
issn = {1552-5279},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; *Alzheimer Disease/metabolism/microbiology ; Aged ; *Cognitive Dysfunction/metabolism/microbiology ; *Fatty Acids, Volatile/metabolism ; Feces/microbiology/chemistry ; Amyloid beta-Peptides/metabolism ; Brain/metabolism ; Positron-Emission Tomography ; Aged, 80 and over ; Middle Aged ; },
abstract = {BACKGROUND: Gut microbiota and their metabolites, particularly short-chain fatty acids (SCFAs), play a vital role in the gut-brain axis, and have been associated with neurodegenerative diseases like Alzheimer's disease (AD). However, the changes in gut microbiota composition and SCFA levels during the progression of AD are not yet well understood. This study seeks to investigate these variations to gain deeper insights into their potential role in disease development.

METHOD: This study examined changes in gut microbiota and SCFA across three groups; Cognitively unimpaired individuals with low amyloid-beta ((CU) Aβ Low (n =  71)), CU Aβ High (n =  19), and those diagnosed with mild cognitive impairment (MCI) or AD (Disease Group (DG), n = 10). Participants were selected from well characterised cohorts and underwent Pittsburg compound B-positron emission tomography to determine cerebral amyloid status. Faecal microbiota composition was assessed using shotgun metagenomics, while faecal SCFA concentrations were quantified via Gas Chromatography-Mass Spectrometry (GC-MS). Associations between taxa and SCFAs were assessed using Spearman correlation and MaAsLin2.

RESULT: Firmicutes, Proteobacteria, and Bacteroidetes exhibited significant correlations with SCFAs across all groups. In the CU Aβ Low and Disease Group (DG), Firmicutes showed Positive correlations with butyric acid. Group-specific patterns included negative correlations between Bacteroidetes and propionic acid in the DG group, a positive correlation between Firmicutes and total SCFAs in the CU Aβ Low group, and a positive correlations between Proteobacteria and Actinobacteria with butyric acid in the CU Aβ High group, alongside notable interactions with isovaleric acid. Furthermore, specific taxa such as Corynebacterium falsenii (Phylum: Actinobacteria), Ruthenibacterium lactatiformans (Phylum: Firmicutes), and Streptomyces capitiformicae (Phylum: Actinobacteria) showed significant associations with SCFAs, particularly propionic acid and butyric acid.

CONCLUSION: These findings suggest that changes in gut bacteria and their metabolites vary at different stages of AD. Key results show that certain bacteria, such as Firmicutes, Bacteroidetes, and Proteobacteria, are linked to SCFAs, especially butyric acid, which plays a role in gut and brain health. This suggests that modifying gut bacteria could help regulate SCFA levels and potentially slow the progression of AD. However, more research is needed to fully understand this connection.},
}

Humans
*Gastrointestinal Microbiome/physiology
Male
Female
*Alzheimer Disease/metabolism/microbiology
Aged
*Cognitive Dysfunction/metabolism/microbiology
*Fatty Acids, Volatile/metabolism
Feces/microbiology/chemistry
Amyloid beta-Peptides/metabolism
Brain/metabolism
Positron-Emission Tomography
Aged, 80 and over
Middle Aged

@article {pmid41441004,
year = {2025},
author = {Alabi, JO and Kholif, AE and Ike, KA and Okedoyin, DO and Adelusi, OO and Wuaku, M and Anotaenwere, CC and Enikuomehin, JM and Oderinwale, OA and Adebayo, JO and Gentry-Apple, AR and Anele, UY},
title = {Rumen Fluid Metabolomics and Microbiome Profiling of Dairy Cows Fed Combinations of Prebiotics, Essential Oil Blend, and Onion Peel Using the RUSITEC System.},
journal = {Metabolites},
volume = {15},
number = {12},
pages = {},
pmid = {41441004},
issn = {2218-1989},
support = {NC.X338-5-21-120-1//United States Department of Agriculture/ ; },
abstract = {BACKGROUND AND OBJECTIVES: Dairy products provide vital energy, high-quality protein, and micronutrients for over six billion people worldwide, with dairy cows contributing nearly 81% of global milk production. Sustainable strategies to enhance productivity are therefore critical. Feed additives such as essential oil blends (EOB), onion peel (OPE), and prebiotics including mannan oligosaccharides (MOS) and galacto-oligosaccharides (GOS) have been proposed to improve rumen fermentation, modulate microbial ecology, and mitigate greenhouse gas emissions. This study evaluated the combined effects of EOB, OPE, MOS, and GOS on rumen metabolism using the rumen simulation technique (RUSITEC).

MATERIALS AND METHODS: Rumen inoculum from three cannulated Holstein Friesian cows was incubated across 16 vessels (four treatments × four replicates) for nine days. Treatments included a control (CON; TMR only), GEO (TMR + GOS + EOB + OPE), MEO (TMR + MOS + EOB + OPE), and OLEO (TMR + a 1:1 mixture of GOS and MOS + EOB + OPE). Additives were included at 3 µL/g TMR for EOB and 30 mg/g TMR (3% w/w) for OPE, GOS, MOS, or OLG. Rumen effluents were collected for untargeted metabolomic profiling by liquid chromatography-mass spectrometry, identifying 661 metabolites.

RESULTS: Partial least squares-discriminant analysis revealed clear separation between CON and additive groups, confirming distinct metabolic shifts. GEO primarily enhanced tryptophan, tyrosine, and purine metabolism; MEO stimulated phosphonate and pyrimidine pathways and bile acid biosynthesis; OLEO promoted phosphonate, nicotinamide, and taurine metabolism. Microbial analysis showed enrichment of taxa such as Lachnospira, Succinivibrionaceae, Macellibacteroides, Lysinibacillus, and Christensenellaceae, indicating complementary effects on fermentation and microbial stability.

CONCLUSIONS: These results demonstrate that dietary supplementation with GEO, MEO, or OLEO modulates rumen metabolism and microbial ecology without impairing fermentation, supporting improved nutrient utilization, antioxidant defenses, and metabolic resilience in dairy cows, with potential benefits for productivity and sustainability.},
}

@article {pmid41439189,
year = {2025},
author = {Ghotbi, M and Ghotbi, M and D'Agostino, E and Kanitz, M and Needham, DM},
title = {From microscale to microbial insights: validating high-throughput microvolume extraction (HiMEx) methods for marine microbial ecology.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf218},
pmid = {41439189},
issn = {2730-6151},
abstract = {Extracting and directly amplifying DNA from small-volume, low-biomass samples would enable rapid, ultra-high-throughput analyses, facilitating the study of microbial communities where large-volume sample collection is challenging. This can aid where 'conventional' filtrater-based methods miss capturing smaller microbes, or where microscale variability matters, such as the ocean. Here, we develop and validate physical and chemical-based DNA extractions from microvolumes with universal rRNA gene amplicons and metagenomic sequencing of all domains and viruses, on natural surface seawater and experimentally manipulated marine waters. Compared to 500-mL filter-based extraction, direct PCR of 3 μL of lysate from seawater microvolume extractions ranging from 100-1000 μL consistently captured comparable microbial community composition and diversity, with reliable amplification and little to no contamination. Metagenomic results of 10 μL lysates from 15 microvolume samples (100 μL) captured 83 high- and draft-quality, diverse bacterial genomes and 430 complete, high and medium quality viral contigs. Our approach enables scaling of rRNA gene sequencing and metagenomic library prep for high-throughput experimentation for a fraction of the cost of conventional methods and builds upon existing microvolume approaches by removing unnecessary expenses, like excess plasticware and expensive bead clean-up. The method expands opportunities for more comprehensive microbial community monitoring and controlled laboratory experiments by facilitating higher sample numbers and lowering sample volume needs. However, its potential bias against Gram-positive bacteria should be considered when applying to environments where these taxa are abundant.},
}

@article {pmid41439181,
year = {2025},
author = {Yang, M and He, T and Moukarzel, R and Li, M and Li, M and Zhang, Z and He, Y and Liu, Y and Yu, L and Zhu, S and Du, F},
title = {Phyllosphere microbiome responses to nano-berberine and chemical fungicides in powdery mildew infected strawberry.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1712123},
pmid = {41439181},
issn = {1664-462X},
abstract = {Strawberry powdery mildew, caused by the obligate biotroph Podosphaera aphanis, is a major threat to commercial strawberry production, reducing both yield parameters and fruit quality. While chemical fungicides remain a standard control method, their non-target effects on phyllosphere microbial communities have raised important ecological and environmental concerns. Nano-pesticides are increasingly applied in plant disease management, however, their influence on the composition and functional potential of phyllosphere microbial communities remains poorly understood. The nano-berberine formulation (BBR-M) used in this study was provided by a collaborative group, with synthesis and physicochemical characteristics consistent with those previously reported for this material. In this study, we compared the field-level effects of a nano-berberine formulation (BBR-M) and conventional chemical fungicides (e.g., bupirimate) on the strawberry phyllosphere microbiota using high-throughput sequencing, bioinformatics analysis, and microbial isolation techniques. The results showed that nano-fungicide application significantly reduced the disease index of powdery mildew and markedly decreased its incidence in field-grown strawberries, ultimately lowering leaf disease incidence to 5.06% with a control efficacy of 96.81%. Furthermore, nano-fungicides and conventional chemical fungicides treatments were associated with distinct impacts on the phyllosphere microenvironment of strawberry. Application of BBR-M was associated with a more structured and potentially stable microbial community, characterized by increased fungal diversity and higher modularity in co-occurrence networks. In contrast, bupirimate treatment increased microbial complexity but coincided with reduced network stability. A strain of Bacillus siamensis-a genus identified as a core taxon within the BBR-M phyllosphere network-was subsequently isolated from nano-berberine-treated leaves and exhibited strong antagonistic activity against Colletotrichum nymphaeae. Field assays showed that this strain effectively suppressed strawberry powdery mildew with 98.18% control efficacy. Collectively, these findings provide important insights into the ecological safety and functional implications of novel pesticide technologies, underscoring the potential of nano-fungicides and native biocontrol agents for sustainable strawberry disease management.},
}

@article {pmid41438540,
year = {2025},
author = {Zhou, L and Lin, X and Guo, R and Li, T and Brennan, C and Fu, X and Liu, RH},
title = {Phytochemical compounds, antioxidant activity, and antiproliferative activity of sesame seeds as affected by simulated digestion.},
journal = {Food chemistry: X},
volume = {32},
number = {},
pages = {103317},
pmid = {41438540},
issn = {2590-1575},
abstract = {Antioxidant and antiproliferative activities in white and black sesame seeds were investigated during a simulated in vitro digestion. The levels of phenolic compounds, flavonoids and oxygen radical absorbance capacity (ORAC) values of sesame seeds increased by over 50 % after simulated stomach, small and large intestine digestion. A higher cellular antioxidant activity (CAA) and a higher inhibition of HepG2 cell proliferation were found in the extract from small intestine digestion phase. In comparison with Aijiao Bawangbian (white color), the phenolics, flavonoids, ORAC values, CAA values and antiproliferative activity of Changzhi II (black color) were higher both before and after simulated digestion. In tested phenolics, sesamol and ferulic acid showed better antioxidant and antiproliferative activities than pinoresinol diglucoside, pinoresinol, sesamolin, and sesamin in cellular level. Sesame seed has considerable cellular antioxidant and antiproliferative activities both before and after simulated digestion, which merits further investigation in vivo studies.},
}

@article {pmid41438070,
year = {2025},
author = {Brandt, A and Yergaliyev, T and Halibasic, E and Cyba, A and Jaeger, JW and Gong, R and Hernández-Arriaga, A and Schneider, CV and Sjöland, W and Molinaro, A and Trauner, M and Trautwein, C and Camarinha-Silva, A and Bergheim, I and Schneider, KM},
title = {Fiber enrichment is not superior to dietary monitoring in MASLD: A dual-center, double-blind, placebo-controlled trial.},
journal = {iScience},
volume = {28},
number = {12},
pages = {114019},
pmid = {41438070},
issn = {2589-0042},
abstract = {Dietary fiber enrichment may modulate intestinal microbiota and positively impact metabolic dysfunction-associated steatotic liver disease (MASLD). This randomized, double-blind, placebo-controlled dual-center study evaluated the effects of dietary fiber (oat bran and spelt bran) on MASLD. After a 3-week Run-in phase during which dietary intake was assessed, 48 patients (CAP >280 dB, no fibrosis) were assigned to oat bran (4.5 g oat β-glucan, total fiber 11.7 g/day), spelt bran (11.7 g fiber/day), or placebo (2.1 g fiber/day) for 12 weeks. During the Run-in phase, dietary assessment alone significantly decreased BMI and liver enzymes (ALT, AST, γ-GT) while increasing microbiota diversity. Improvements were maintained in all three intervention groups. However, no significant changes were observed in hepatic steatosis (CAP), overall microbiota composition, and serum bile acid profiles. Dietary assessment alone improved MASLD biomarkers, with the fiber supplementation offering no additional benefit. This highlights the importance of dietary counseling in MASLD management. (clinical trials: NCT03897218).},
}

@article {pmid41436102,
year = {2025},
author = {Hild, K and Kwarkye, N and Huang, C and Harms, H and Chatzinotas, A and Ritschel, T and Totsche, KU and Wick, LY},
title = {Transport and Survival of Marine Tracer Phages in Topsoil at Field Conditions.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c12252},
pmid = {41436102},
issn = {1520-5851},
abstract = {Phages are ubiquitous in soil, shaping microbial diversity and nutrient cycling. Phage replication requires maintaining infectivity and finding the right host. Yet, there are limited data on phage persistence and transport in soil under field conditions. The potential presence of hosts enabling phage replication impedes the assessment of the mobility of autochthonous phages in soils. In lysimeters installed in forest and pasture topsoil, we elucidated the transport of the tailed marine Pseudoalteromonas phage HS2 in comparison to deuterium. Transport of infectious phages as well as numbers of tracer phage genomes and tracer capsid-bound genomes were quantified to account for phage retention and inactivation. Phages were transported up to 4 times faster than the simultaneously applied deuterium tracer, which was attributed to pore size exclusion. Retention in immobile regions and remobilization during precipitation caused pronounced tailing in tracer breakthroughs. High phage survival in pasture soil resulted in mass recoveries of infectious phages that were up to 6 times higher than those in forest soil. However, long-term observations showed that the infectivity was also preserved in forest soil, enabling event-driven remobilization. This remobilization underscores the importance of distinguishing between phage retention and inactivation, which is crucial for accurately predicting phage transport dynamics and their ecological impact in terrestrial environments.},
}

@article {pmid41435658,
year = {2025},
author = {Ho, L and Pham, K and Debognies, A and Bodé, S and Vermeir, P and Boeckx, P and De Vrieze, J and Goethals, P},
title = {Unveiling the important roles of sludge worms (Tubifex tubifex) in wetland carbon and nitrogen cycling: Implications for greenhouse gas emissions in a warming climate.},
journal = {Water research},
volume = {291},
number = {},
pages = {125230},
doi = {10.1016/j.watres.2025.125230},
pmid = {41435658},
issn = {1879-2448},
abstract = {Wetland greenhouse gas (GHG) emissions represent a major component of global climate feedbacks, driven by complex biogeochemical processes that regulate carbon and nitrogen cycling. However, how bioturbating invertebrates, such as sludge worms (Tubifex tubifex), regulate these underlying microbial and physicochemical mechanisms remains poorly understood. Here, we conducted controlled microcosm incubations at 15, 25, and 35°C to examine how increasing temperatures modulate the influence of these sludge worms on wetland carbon and nitrogen cycling, combining biogeochemical flux measurements with microbial functional gene analysis. We discovered four synergistic mechanisms by which T. tubifex influences wetland biogeochemistry: 1) physical bioturbation creating distinct biogeochemical conditions; 2) respiratory and feeding activities modifying redox conditions; 3) specialized gut microbiomes directly producing GHGs; and 4) continuous microbial inoculation of sediments through excretion. These mechanisms collectively enhanced CH4 and N2O emissions, with N2O fluxes showing a fourfold increases at elevated temperatures. Worm gut microbiomes were primarily regulated by temperature, organic matter, and nitrogen compounds, with the main controlling factors shifting from nutrient availability at lower temperatures to direct thermal stress effects at higher temperatures. Strong metabolic intensity of worm gut microbiomes, with gene expression-to-abundance ratios being up to 2000 times higher than in sediment communities, resulted in their indirect impacts on wetland GHG emissions. At cooler temperatures (15°C), denitrifier genes (nirK and nirS) prevailed in worm guts, whereas higher temperatures (35°C) favored nitrifier genes (amoA AOA and amoA AOB). These findings provide the first comprehensive framework revealing previously underappreciated mechanisms by bioturbating invertebrates amplifying wetland GHG emissions under warming, creating overlooked positive feedback loops in wetland ecosystems.},
}

@article {pmid41432929,
year = {2025},
author = {Garcia, M and Sadler, NC and Stohel, I and Zhao, S and Krishnamoorthy, S and Farris, Y and Reichart, NJ and Bagwell, CE and Zambare, N and McClure, R},
title = {Community Dynamics Drive Calcium Carbonate Production in an Enriched Consortium of Soil Microbes.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02632-y},
pmid = {41432929},
issn = {1432-184X},
abstract = {Recently, there has been a focus on using soil microbes as a means to store carbon in the soil in the form of calcium carbonate, outcomes of which include soil stabilization and biocementation. The molecular processes involved in microbially induced calcium carbonate formation are known, but there is still a significant knowledge gap regarding how community interactions, emergent processes that are distinct from the roles of individual members, may drive the formation of carbonate. To answer these questions, we describe the development and application of a consortium of soil microbes consisting of one species each of the Rhodococcus, Microbacterium, and Curtobacterium genera and two species from the Bacillus genus. We term these five species cultivated together carbon storing consortium A (CSC-A). Growth assays show that only a subset of CSC-A members produces CaCO3 with Rhodococcus producing the most CaCO3 but the complete CSC-A produces significantly higher amounts of CaCO3 compared to the sum total carbonate produced by all member species. The development of CSC-A shows that CaCO3 production may be as much a community process as it is the contribution of individual species, requiring us to move beyond single species analysis to fully understand carbonate formation by microbial communities in nature. CSC-A will allow the scientific community to ask and answer key questions about the molecular interactions surrounding inorganic carbon formation in soil, an important knowledge gap that must be filled if we wish to stabilize soils and harness microbial processes for materials production.},
}

@article {pmid41432792,
year = {2025},
author = {Basile, A and Spagoni, L and Visaggio, D and Riggio, FP and Bologna, MA and Mancini, E and Visca, P and Riccieri, A},
title = {The Putative Involvement of Bacterial Symbionts in Cantharidin Biogenesis: An Explorative Study in Meloidae Insects.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02683-1},
pmid = {41432792},
issn = {1432-184X},
abstract = {Insect-microbes holobionts integrate host and microbial functions, with symbionts supporting nutrition, immunity, and defence, while producing metabolites, including beetle-derived compounds with therapeutic potential. Cantharidin is a toxic terpene produced by blister beetles (Coleoptera: Meloidae), endowed with defensive and pharmacological properties. Male insects produce and contain cantharidin in large quantities and transfer it to females upon mating. This study is aimed to gain information about the involvement of insect-associated bacteria in cantharidin biogenesis. To support the possibility that bacteria participate in cantharidin biogenesis, cantharidin antibacterial activity was assessed against six reference strains of representative species of Bacillota and Pseudomonadota from publicly available culture collections. All bacterial strains tolerated concentrations up to 600 µg/ml cantharidin in a standard antibacterial susceptibility test. To identify candidate bacterial lineages, 16S rRNA metataxonomic profiling of the V5-V6 region was performed in males and females from different Meloidae subfamilies and tribes. Analysis of the insect-associated microbiomes of the five cantharidin-producing species (Lydus trimaculatus, Meloe proscarabaeus, Mylabris variabilis, Hycleus polymorphus, Zonitis flava) revealed communities dominated by Pseudomonadota, with secondary contributions from Actinomycetota in Z. flava and M. proscarabaeus and Cyanobacteriota in the other host insects. Although overall community structure and composition did not differ significantly between sexes, a few taxa displayed consistent male-associated patterns, with Staphylococcus, Cutibacterium and one Enterobacteriaceae ASV resulting more abundant in males across all species. The intrinsic bacterial resistance to cantharidin, with both quantitative and qualitative differences in microbiome structure between male and female insects, makes the hypothesis of a putative involvement of bacteria in cantharidin biogenesis still viable.},
}

@article {pmid41432418,
year = {2025},
author = {Weiss, AS and Santos-Santiago, JA and Keenan, O and Smith, AB and Knight, M and Zackular, JP and Tamayo, R},
title = {Enterococcus faecalis modulates phase variation in Clostridioides difficile.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0037425},
doi = {10.1128/jb.00374-25},
pmid = {41432418},
issn = {1098-5530},
abstract = {To adapt and persist in the gastrointestinal tract, many enteric pathogens, including Clostridioides difficile, employ strategies such as phase variation to generate phenotypically heterogeneous populations. Notably, the role of the gut microbiota and polymicrobial interactions in shaping population heterogeneity of invading pathogens has not been explored. Here, we show that Enterococcus faecalis, an opportunistic pathogen that thrives in the inflamed gut during C. difficile infection, can impact the phase-variable CmrRST signal transduction system in C. difficile. The CmrRST system controls multiple phenotypes, including colony morphology, cell elongation, and cell chaining in C. difficile. Here, we describe how interactions between E. faecalis and C. difficile on solid media lead to a marked shift in C. difficile phenotypes associated with phase variation of CmrRST. Specifically, E. faecalis drives a switch of the C. difficile population to the cmr-ON state, leading to chaining and a rough colony morphology. This phenomenon is most pronounced with E. faecalis, as other enterococcal species and select Gram-negative enteric bacteria do not show a similar effect. These results suggest that the composition of the polymicrobial environment in the gut is critical to influencing C. difficile population heterogeneity. Our findings shed light on the complex role that microbial ecology and polymicrobial interactions can have in the phenotypic heterogeneity of invading pathogens.IMPORTANCEClostridioides difficile is an enteric pathogen with critical implications for public health. The microbial ecosystem in which C. difficile resides shapes the behavior and fitness of C. difficile; however, the mechanisms underlying these interactions are not well defined. Here, we demonstrate that Enterococcus faecalis, an opportunistic pathogen known to co-colonize the gut with C. difficile, influences phase variation and downstream growth phenotypes in C. difficile. This phenomenon represents a new paradigm by which co-residing bacteria can modulate phase variation dynamics in C. difficile or other enteric pathogens. Understanding factors that influence C. difficile behavior may elucidate new therapeutic strategies, especially in complex polymicrobial infections.},
}

@article {pmid41432242,
year = {2025},
author = {Xie, X and Chen, L and Yuan, J and Zheng, H and Zhang, L and Yu, X and Liu, X and Wei, C and Qiu, G},
title = {Metagenomic characterization of the metabolism, evolution, and global distribution of Candidatus Accumulibacter members in wastewater treatment plants.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf278},
pmid = {41432242},
issn = {1751-7370},
abstract = {Deciphering the genomic basis of ecological diversification in activated sludge microbiomes is essential for optimizing treatment technology and advancing microbial ecology. Here, we present a global genome-resolved investigation of Candidatus Accumulibacter, the primary functional agent of enhanced biological phosphorus removal, based on 828 metagenomes from wastewater treatment plants across six continents. We recovered 104 high-quality Candidatus Accumulibacter metagenome-assembled genomes, discovering a new clade (Clade IV), substantially expanding the known phylogenetic diversity and revealing a ubiquitous yet geographically heterogeneous global distribution. Phylogenomic and pangenome analyses uncovered extensive clade-specific gene gain and loss, particularly in nitrogen metabolism, suggesting divergent evolutionary trajectories shaped by relaxed selection and niche adaptation. Genome-wide patterns of convergent streamlining and enriched antiviral defense systems indicate selective pressures from strong competition and viral predation. Constraint-based metabolic modeling revealed pervasive amino acid autotrophies and metabolic complementarity, coupled with distinct carbon utilization strategies that support ecological specialization across operational settings. Experimental validation reconciled model-phenotype discrepancies, highlighting the importance of transporter promiscuity and gene regulation in carbon substrate assimilation. Collectively, our findings redefine Candidatus Accumulibacter as a dynamic model of microbial genome plasticity, metabolic adaptation, and ecological resilience, providing an insight for understanding how microbial communities adapt and respond under engineered environmental conditions.},
}

@article {pmid41430825,
year = {2025},
author = {Gao, ZL and Li, JJ and Ai, BQ},
title = {Activity-driven demixing and sustained temperature gradients in inertial active-passive mixtures.},
journal = {Physical review. E},
volume = {112},
number = {5-1},
pages = {054103},
doi = {10.1103/5lm1-h83g},
pmid = {41430825},
issn = {2470-0053},
abstract = {While traditional thermodynamic equilibrium requires uniform temperature across coexisting phases, underdamped active matter systems can sustain nonequilibrium hot-cold coexistence through motility-induced phase separation. We investigate particle demixing and emergent temperature gradients in binary mixtures of inertial active and passive particles. Remarkably, within specific parameter ranges of intermediate particle inertia and self-propulsion strength, the system simultaneously achieves pronounced particle demixing and sustains significant hot-cold coexistence. Activity differences drive rapid species separation, which is further enhanced over time by persistent rotational diffusion. The synergy between inertia and activity significantly amplifies temperature differences both between particle species and across coexisting gas-liquid phases. These temperature disparities originate from inertia-enabled energy storage, collision-mediated energy transfer, propulsion-driven acceleration, and weakened liquid-phase cohesion. Unlike equilibrium systems, active-passive mixtures circumvent thermal homogenization by maintaining kinetic temperature gradients through continuous energy injection and dissipation. These findings elucidate fundamental principles of nonequilibrium self-organization in hybrid systems, with implications for bio-inspired materials, microbial ecology, and energy transport in active composites.},
}

@article {pmid41430013,
year = {2025},
author = {Wolfgang, A and Temme, N and Tilcher, R and Schumann, M and Berg, G},
title = {Wireworm-Associated Microbial Communities and their Implications on Biological Control.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02672-4},
pmid = {41430013},
issn = {1432-184X},
abstract = {Wireworms (larvae of different click beetles, Elateridae) are significant soil-borne pest species that can cause severe crop losses. They are difficult to control, and biocontrol using entomopathogenic fungi (EPF) display variable field efficacy. To understand microbial interactions and improve biological control, we studied the interplay between insect and soil microbiota in four wireworm species (Agriotes spp.) at temporal and spatial scales. We found that microbiota associated with wireworms are species-specific and primarily soil-derived. Our results further indicate that ectosymbiotic bacterial community composition on wireworm cuticles is relatively stable over time in specimens not deceasing from spontaneous entomopathogen infection. Therefore, successful microbiome homeostasis on cuticles appears to be correlated with long-term survival of wireworms in soil. Interestingly, EPF were prevalent but low-abundant in all wireworm species as well as in soils. Therefore, we analyzed immune priming effects by low-abundant EPF in soil. Mortality was higher in naïve wireworms than in wireworms pre-exposed to EPFs, and molting frequency increased, indicating both developmental adaptations and immune priming as strategies for EPF avoidance in wireworms. This work disentangles the key components of wireworm microbiomes and highlights the importance of microbial interactions for biocontrol. Biocontrol of wireworms could be improved by considering their species-dependency in microbiome homeostasis as well as physiological and behavioral adaptations to soil-borne pathogens. The potential functional synergies between EPF and soil microbes need further exploration.},
}

@article {pmid41429876,
year = {2025},
author = {Galbán, S and Almela, P and Quesada, A and Justel, A},
title = {Exploring local and regional contribution to airborne bacterial communities in the Antarctic Peninsula.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-32162-z},
pmid = {41429876},
issn = {2045-2322},
support = {PIPF-2022/ECO-25833//Comunidad de Madrid/ ; CTM2016-79741-R//European Regional Development Fund/ ; CTM2016-79741-R//European Regional Development Fund/ ; PID2020-116520RB-I00//Agencia Estatal de Investigación/ ; },
abstract = {Understanding microbial dispersion in the atmosphere is essential for studying microbial biogeography and ecosystem dynamics under global change. Airborne bacterial communities, shaped by exchanges between atmosphere and Earth's surface, can originate from diverse sources and vary with meteorological conditions and air mass trajectories. In this study, we assessed airborne microbial communities in Antarctica at regional and local scales. Air samples were collected during the austral summer at two Antarctic Specially Protected Areas (ASPAs): Byers Peninsula (Livingston Island, South Shetland Islands) and Avian Island (Marguerite Bay). Bacterial composition was analysed through 16S rRNA gene sequencing using amplicon sequence variants (ASVs). Additionally, back-trajectories of the sampled air parcels were simulated with HYSPLIT. A core community was identified in 80% of Byers Peninsula samples, representing 57.91% of total ASVs. Notably, 79.4% of ASVs matched soil bacteria from the same location, suggesting a strong influence of local sources. Communities from Byers Peninsula and Avian Island showed low overall similarity. However, one sample from Byers resembled the Avian sample, likely due to similar air mass back-trajectories. These findings suggest that airborne bacterial communities are shaped by both local ecosystems, and broader regional or continental processes, such as long-range trajectories carrying microorganisms from distant locations.},
}

@article {pmid41427997,
year = {2025},
author = {Lebrun, S and Crevecoeur, S and Taminiau, B and Everaert, N and Marzorati, M and Leenders, J and de Tullio, P and Korsak, N and Daube, G and Stiernon, B and Delcenserie, V and Gonza, I},
title = {Gut Microbiota Modulation by Pomegranate Extract: Insights from a Controlled Supplementation Study.},
journal = {Plant foods for human nutrition (Dordrecht, Netherlands)},
volume = {81},
number = {1},
pages = {5},
pmid = {41427997},
issn = {1573-9104},
support = {NUTRIGUTIOR under grant convention 6918//Walloon Agri-Food innovation cluster Wagralim/ ; NUTRIGUTIOR under grant convention 6918//Walloon Agri-Food innovation cluster Wagralim/ ; NUTRIGUTIOR under grant convention 6918//Walloon Agri-Food innovation cluster Wagralim/ ; NUTRIGUTIOR under grant convention 6918//Walloon Agri-Food innovation cluster Wagralim/ ; NUTRIGUTIOR under grant convention 6918//Walloon Agri-Food innovation cluster Wagralim/ ; NUTRIGUTIOR under grant convention 6918//Walloon Agri-Food innovation cluster Wagralim/ ; NUTRIGUTIOR under grant convention 6918//Walloon Agri-Food innovation cluster Wagralim/ ; },
mesh = {*Pomegranate/chemistry ; *Gastrointestinal Microbiome/drug effects ; *Plant Extracts/pharmacology ; Humans ; *Dietary Supplements ; Male ; Fatty Acids, Volatile/metabolism ; Colon/microbiology/drug effects/metabolism ; Polyphenols/pharmacology ; Adult ; Female ; Lactic Acid/metabolism ; Bacteria/metabolism/drug effects ; Fruit/chemistry ; },
abstract = {Regular consumption of pomegranate, a polyphenol-rich fruit, is associated with multiple health benefits. As polyphenols reach the colon, they interact with the gut microbiota, influencing both its composition and metabolic activity. This study investigated the impact of a one-week supplementation with two doses of the commercial pomegranate extract Oxylent[®] (1.3 and 2.6 g/day) on gut microbiota and metabolite production using the SHIME[®] system. Bacterial metabolite production, including short-chain fatty acids (SCFA), urolithins, succinate, and lactate, was assessed using chromatographic and enzymatic assays. The bacterial composition across colonic sections, represented by different fermenters in the SHIME, was investigated using 16 S rRNA amplicon sequencing. Pomegranate extract did not significantly alter SCFA or succinate levels, but reduced L- and D-lactate in the transverse colon; the higher dose (2.6 g/day) also decreased D-lactate in the ascending colon. Microbiota profiling revealed a higher bacterial diversity following pomegranate extract supplementation. However, Prevotella abundance decreased in the ascending and transverse colonic sections, potentially explaining the reduced propionate levels observed in the transverse colon with 2.6 g/day of pomegranate extract. Interestingly, contrasting effects were noted for Mitsuokella genus, which decreased in the descending colon at 1.3 g/day but increased at 2.6 g/day in the transverse and descending colons. Furthermore, the higher dose reduced Enterocloster abundance in the descending colon. Overall, Oxylent[®] pomegranate extract influenced both microbial composition and metabolite production, particularly taxa associated with health-related metabolites. These results highlight the potential of pomegranate compounds to beneficially influence the gut microbiota, supporting their role in promoting intestinal health.},
}

*Pomegranate/chemistry
*Gastrointestinal Microbiome/drug effects
*Plant Extracts/pharmacology
Humans
*Dietary Supplements
Male
Fatty Acids, Volatile/metabolism
Colon/microbiology/drug effects/metabolism
Polyphenols/pharmacology
Adult
Female
Lactic Acid/metabolism
Bacteria/metabolism/drug effects
Fruit/chemistry

@article {pmid41427744,
year = {2025},
author = {Burnside, M and Helliwell, E and Treerat, P and Rozendal, T and Merritt, J and Baker, JL and Kreth, J},
title = {Comparative characterization reveals conserved and divergent ecological traits of oral corynebacteria.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0297325},
doi = {10.1128/spectrum.02973-25},
pmid = {41427744},
issn = {2165-0497},
abstract = {Corynebacteria are abundant members of the oral microbiome and increasingly recognized as key structural organizers of supragingival biofilms. Despite their prevalence, the ecological roles and phenotypic traits of many oral corynebacterial species remain poorly defined. Here, we isolated and characterized two new strains, Corynebacterium durum JJ2 and Corynebacterium argentoratense MB1, and compared them with previously characterized and published Corynebacterium durum JJ1 and reference strain Corynebacterium matruchotii ATCC 14266. Phenotypic assays revealed that C. durum strains displayed robust aggregation, thick biofilm formation, and extensive extracellular polymeric substance (EPS) networks, whereas C. argentoratense MB1 and C. matruchotii ATCC 14266 formed thinner biofilms with minimal EPS production. All four strains secreted extracellular membrane vesicles capable of inducing chain elongation in Streptococcus sanguinis, underscoring a conserved interspecies signaling function. Genomic analysis demonstrated close relatedness between C. durum and C. matruchotii, while C. argentoratense MB1 was more distantly related, with a reduced genome, fewer metabolic pathways, and the absence of nitrate reductase genes, consistent with its inability to grow under anaerobic conditions. These findings suggest that C. argentoratense MB1 may represent a less specialized or transient inhabitant of the oral cavity, whereas C. durum and C. matruchotii are well adapted to the oral niche. Together, this study expands our understanding of phenotypic diversity, metabolic capacity, and interspecies interactions among selected oral corynebacteria, highlighting their potential importance as biofilm organizers and contributors to oral microbial ecology.IMPORTANCEOral corynebacteria contribute to the structural and ecological stability of supragingival communities. Yet, their species-level functions remain poorly defined. By isolating and characterizing new strains of Corynebacterium durum and Corynebacterium argentoratense, and comparing them with reference strains including Corynebacterium matruchotii, we provide new insight into their phenotypic diversity, metabolic capacity, and ecological roles. Our results demonstrate that C. durum strains form robust biofilms enriched in extracellular polymeric substances, while C. argentoratense produces thinner biofilms and lacks the genomic features required for anaerobic growth, suggesting a less specialized or transient role in the oral cavity. Importantly, we show that extracellular membrane vesicles secreted by all tested strains promote chain elongation in Streptococcus sanguinis, highlighting a conserved mechanism of interspecies communication. These findings advance our understanding of how oral corynebacteria contribute to biofilm organization and microbial homeostasis and position them as critical but understudied players in oral microbial ecology.},
}

@article {pmid41424705,
year = {2025},
author = {Charria Girón, E and Toshe, R and Khonsanit, A and Kobmoo, N and Kwanthong, P and Gorelik, TE and Luangsa-Ard, JJ and Ebada, SS and Stadler, M},
title = {Chemical clues to infection: A pilot study on the differential secondary metabolite production during the life cycle of selected Cordyceps species.},
journal = {IMA fungus},
volume = {16},
number = {},
pages = {e172651},
pmid = {41424705},
issn = {2210-6340},
abstract = {Cordyceps species are widespread entomopathogens and promising biocontrol agents that produce diverse secondary metabolites, yet the roles of these molecules during the infection process remain unclear. To interpret how fungal chemistry contributes to host colonization, we compared the metabolomes and virulence traits of two strains of phylogenetically distinct Cordyceps species (C. javanica and C. blackwelliae) and assessed their effects on beet armyworms (fungiSpodoptera exigua). Virulence assays revealed species-dependent pathogenicity, with C. javanica showing the highest virulence. Combining untargeted metabolomics, feature-based molecular networking (FBMN), 3D electron-diffraction crystallography and comprehensive 1D/2D NMR, we gained insights into their metabolomic traits. For instance, C. javanica displayed notable beauveriolide diversity, including three previously undescribed derivatives (1-3), while C. blackwelliae produced mainly diketopiperazines in vitro. The FBMN results revealed putative beauveriolide analogs in the C. blackwelliae extracts, unlike the cadaver analysis, revealing beauvericins in infected corpses. Remarkably, the crude extracts obtained from authentic insect cadavers contained beauveriolides and beauvericins, providing in vivo chemical evidences of their production during infection for the first time. Moreover, bioassays with purified compounds showed that insecticidal activity cannot be attributed across all beauveriolides but depends on amino-acid composition, implying multifunctional roles beyond direct toxicity. Altogether, these results reveal context-dependent metabolic reprogramming and species-specific chemical strategies in entomopathogenic fungi, with implications for microbial ecology, host specificity, and the rational development of fungal biocontrol agents. The results of this study also give rise to the need for more intensified study on the chemical composition of the insect cadavers that are colonized by other entomopathogens.},
}

@article {pmid41422804,
year = {2025},
author = {Tabuteau, S and Hervé, V and Irlinger, F and Monnet, C},
title = {Metagenomic Profiling and Genome-Centric Analysis Reveal Iron Acquisition Systems in Cheese-Associated Bacteria and Fungi.},
journal = {Environmental microbiology},
volume = {27},
number = {12},
pages = {e70218},
doi = {10.1111/1462-2920.70218},
pmid = {41422804},
issn = {1462-2920},
support = {//ABIES Doctoral School/ ; //MICA Department of INRAE/ ; },
mesh = {*Cheese/microbiology ; *Iron/metabolism ; Siderophores/biosynthesis/metabolism/genetics ; Metagenomics ; *Bacteria/genetics/metabolism/classification/isolation & purification ; *Fungi/genetics/metabolism/classification/isolation & purification ; *Metagenome ; Genome, Bacterial ; },
abstract = {Cheese microbial communities are composed of diverse interacting microorganisms, including both inoculated and non-inoculated strains. One limiting factor for microbial growth on cheese surfaces is iron availability. To better understand the role of iron acquisition in cheese microbial ecology, we investigated the diversity and distribution of iron uptake systems across a wide range of cheeses. We analysed 136 metagenomes and 1400 genomes and Metagenome-Assembled Genomes (MAGs) from 44 French Protected Designation of Origin (PDO) cheeses. Using an updated set of Hidden Markov Models targeting iron acquisition genes, we identified a wide diversity of iron uptake systems. Siderophore biosynthesis and import systems were more prevalent in surface-associated species than in those from the cheese core. About 20 different siderophore biosynthesis pathways were detected, with desferrioxamine and enterobactin-type being the most prevalent. Genomic analyses revealed the main bacterial and fungal producers, including Glutamicibacter, Corynebacterium, Staphylococcus, and Penicillium. While siderophore biosynthesis pathways were found in a minority of MAGs, iron/siderophore import systems were widespread, suggesting the potential for cross-feeding interactions involving siderophores. These findings enhance our understanding of microbial interactions in cheese and open perspectives for improving ripening cultures by considering iron acquisition traits.},
}

*Cheese/microbiology
*Iron/metabolism
Siderophores/biosynthesis/metabolism/genetics
Metagenomics
*Bacteria/genetics/metabolism/classification/isolation & purification
*Fungi/genetics/metabolism/classification/isolation & purification
*Metagenome
Genome, Bacterial

@article {pmid41422362,
year = {2025},
author = {Kuuri-Riutta, O and Palacios Ganoza, B and Ylänne, H and Mitchell, EAD and Väliranta, MM and Tuittila, ES},
title = {Assessing the Value of Testate Amoebae and their Functional Traits in Detecting Climate Change-Induced Peatland Drying.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02682-2},
pmid = {41422362},
issn = {1432-184X},
support = {00240717//Suomen Kulttuurirahasto/ ; 20230925//OLVI-Säätiö/ ; 3825//Maj ja Tor Nesslingin Säätiö/ ; 338631//Research Council of Finland/ ; 30840//Research Council of Finland/ ; },
}

@article {pmid41422133,
year = {2025},
author = {Chang, CY and Topping-Brown, T and Rud, JL and Calvert, MB and Bencosme, G and Wood, CW},
title = {Biogeographic and Genomic Signatures of Thermal Adaptation in Facultative Symbionts.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02678-y},
pmid = {41422133},
issn = {1432-184X},
support = {The Data-Driven Discovery Postdoctoral fellowship//University of Pennsylvania/ ; DEB2118397//National Science Foundation/ ; DEB2118397//National Science Foundation/ ; DEB2118397//National Science Foundation/ ; DEB2118397//National Science Foundation/ ; DEB2118397//National Science Foundation/ ; DEB2118397//National Science Foundation/ ; },
}

@article {pmid41421681,
year = {2025},
author = {Fu, Q and Shi, JS and Lai, JL and Zhang, Y and Huang, Y and Luo, XG},
title = {Maize adaptation to low-dose nanoplastic-lead co-contamination: Foliar metabolic reprogramming and phyllospheric microbiome restructuring.},
journal = {NanoImpact},
volume = {},
number = {},
pages = {100606},
doi = {10.1016/j.impact.2025.100606},
pmid = {41421681},
issn = {2452-0748},
abstract = {Nanoplastics (NPs) and lead (Pb), as emerging environmental pollutants, have been rarely studied in terms of their combined effects on crop growth and metabolic processes under low-dose co-exposure conditions. This study simulated rain-mediated co-exposure of maize seedlings to NPs and Pb at environmentally relevant concentrations (400 μg/L) to elucidate the metabolic responses in leaves and the dynamics of phyllosphere microbial communities. Short-term exposure (45 days) to NPs and Pb did not significantly impair maize seedling growth; however, it induced the accumulation of essential macronutrients in leaves. The metabolic adaptation of maize leaves to NPs and Pb exposure was characterized by a reduction in carbon metabolic flux coupled with an enhancement in lipid metabolic flux. Furthermore, plants responded to co-exposure by activating key metabolic pathways such as those involving ABC transporters, nucleotide metabolism, and amino acid metabolism. Concurrently, the phyllosphere microbiome exhibited structural reorganization, with enrichment of stress-tolerant microbial taxa (e.g., Acidobacteria, Chloroflexi), activation of microbial redox systems, and enhanced capacity of the leaf microbiota to adapt to NPs and Pb exposure. The findings offer theoretical insights into assessing agricultural environmental impacts associated with combined exposure to emerging pollutants, phyllosphere microbial ecology, and plant stress resistance.},
}

@article {pmid41421210,
year = {2025},
author = {De Munck, J and Grootaert, C and Magdalenic, K and Deveci, D and Gansemans, Y and Van Nieuwerburgh, F and Boon, N and Skirtach, A and Rajkovic, A and D'hooghe, M and Van Camp, J},
title = {Curcumin-based benzothiazepane analogues exhibit selective anti-cancer activity in HCT-116 cells via precipitated particle formation and internalisation.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {194},
number = {},
pages = {118926},
doi = {10.1016/j.biopha.2025.118926},
pmid = {41421210},
issn = {1950-6007},
abstract = {Despite extensive investigation into the anti-cancer activity of the natural polyphenol curcumin, its therapeutic application is restricted by its inherent physicochemical properties. Synthetic curcumin analogues, however, offer a promising strategy to improve the drug-like potential of curcumin. In this study, we evaluated three curcumin-based benzothiazepane analogues for their ability to selectively target colon cancer cells. Their cytotoxicity was assessed on intestinal cancerous HCT-116 and non-cancerous IPEC-J2 cells using cell viability assays and microscopic imaging. Two analogues, AT007 and AT096, demonstrated enhanced anti-cancer selectivity compared to curcumin. Interestingly, this effect correlated with the aggregation of these compounds in cell medium, which was influenced by compound concentration and medium composition (particularly the presence of albumin). Confocal microscopy confirmed the presence of particles up to 12 µm inside both cell lines, yet downstream metabolic and transcriptomic responses revealed distinct coping mechanisms that may underlie the higher survival of IPEC-J2 cells. Rather than direct molecular interactions typical of soluble compounds, the observed selectivity appears to result from indirect, particle-driven physical effects, potentially involving (intracellular) membrane disruption. Our findings suggest that aggregation behaviour can be a key determinant in improving the potency and selectivity of bioactive compounds, opening new opportunities for the design and screening of more selective anti-cancer therapeutics.},
}

@article {pmid41420099,
year = {2025},
author = {Stansfield, AR and Booth, RK and Nelson, DM and Johnson, J},
title = {Recent Changes in the Use of Phototrophy by a Mixotrophic Testate Amoeba Inferred from δ[13]C Measurements from an Arctic Peat Core.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02681-3},
pmid = {41420099},
issn = {1432-184X},
support = {College of Arts & Sciences Dean's Research Fellowship//Lehigh University/ ; DEB-1802810//Division of Environmental Biology/ ; },
abstract = {High-latitude ecosystems are undergoing rapid ecological changes in response to climate warming. While some changes are well studied, the responses of microbial communities remain less understood. Testate amoebae, shell-producing protists well preserved in peat, provide a means to reconstruct past microbial dynamics. Mixotrophic taxa such as Archerella flavum host algal endosymbionts (zoochlorellae), allowing both heterotrophic and phototrophic energy acquisition. Previous work has demonstrated that these pathways result in different δ[13]C values. We applied a novel stable isotope approach to a peat core from the North Slope of Alaska to reconstruct changes in phototrophy by Archerella flavum. δ[13]C values were measured on Archerella flavum tests (i.e. shells) and Sphagnum, and a two-endmember mixing model was used to estimate relative usage of phototrophy through time. δ[13]C values were compared with testate amoeba community composition, test size, vegetation, and historical climate. Archerella flavum δ[13]C values were consistently more positive than Sphagnum δ[13]C values in the peat core, and patterns indicated greater phototrophy use after the late 1980s CE. This shift was followed by expansion of Archerella flavum populations and a trend of decreasing test length in several testate amoeba taxa. Increased phototrophy was associated with higher peat C:N ratios, indicating more oligotrophic conditions. From 2007 to 2019 CE, the length of the snow-free growing season was correlated with estimates of phototrophy usage, with more phototrophy during longer growing seasons. δ[13]C analyses of mixotrophic testate amoebae are a powerful tool for reconstructing microbial nutritional strategies and responses to past environmental change.},
}

@article {pmid41416826,
year = {2025},
author = {Wang, B and Zhu, C and Wang, X and Yang, T and Zhang, B and Hu, Y},
title = {The assembly of microbial communities on red sandstone surfaces was shaped by dispersal limitation and heterogeneous selection.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0160025},
doi = {10.1128/msystems.01600-25},
pmid = {41416826},
issn = {2379-5077},
abstract = {Understanding the role of microbiota on stone surface is essential for developing effective grottoes conservation strategies. However, the ecological feature of microbial communities on stone surfaces has been rarely investigated systematically. In this study, we explored diversity, assembly, and functional profiles of microbial communities on the red sandstone surface of the Leshan Giant Buddha from a microbial ecology perspective. The results show that Proteobacteria, Actinobacteria, Cyanobacteria, and Ascomycota are the dominant phyla. Fundamental metabolic pathways are maintained during the formation of visually distinguishable microbial communities, but gene profiles vary across microbial communities of different colors. Ecological modeling suggests that selective pressure from the harsh stone surface environment fostered the interplay of dispersal limitation and heterogeneous selection during community assembly. The assembly of visually distinct microbial communities is linked to a narrower ecological niche, a higher proportion of habitat specialists, and a sparser network structure. Microbial-mediated ammonium assimilation and nitrogen mineralization might be the two prominent processes that contribute to stone biodeterioration. This study deepens our understanding of the assembly mechanisms and functional potentials of microbial communities on stone cultural heritage surfaces, provides microbial ecological insights for the conservation of these cultural treasures.IMPORTANCEMinimal systematic research on the ecological interpretation of stone biodeterioration. This study reports dispersal limitation and heterogeneous selection shape the microbial community assembly responsible for the biodeterioration of red sandstone. Furthermore, fundamental metabolic processes of microbial communities, such as ammonium assimilation and nitrogen mineralization, are identified as contributors to stone biodeterioration. This study improves our understanding of microbial community assembly and their functional roles, providing a microbial ecological basis for developing effective strategies for the conservation of stone cultural heritage.},
}

@article {pmid41413692,
year = {2025},
author = {Carrascosa-Robles, Á and Pascual, JA and Trinchera, A and Testani, E and Fontaine, S and Sanchez-Moreno, S and Supronienė, S and Sail, S and Rasmussen, J and Hanegraaf, M and Ros, M},
title = {The Influence of Agroecological Intensification on Dominant and Rare Microbial Communities Across Diverse European Countries.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02655-5},
pmid = {41413692},
issn = {1432-184X},
}

@article {pmid41410463,
year = {2025},
author = {Xie, Y and Cidan, Y and Cisang, Z and Ciwang, R and Liu, G and Wu, D and Cideng, D and Chilie, J and Kang, J and Zhu, Y and Basang, W},
title = {Effect of altitudes on serum parameters, metabolome, and gut microbiota in yaks on the Qinghai-Tibet Plateau.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0254925},
doi = {10.1128/spectrum.02549-25},
pmid = {41410463},
issn = {2165-0497},
abstract = {Yaks (Bos grunniens), native to the Qinghai-Tibet Plateau, have evolved extraordinary physiological resilience to chronic hypoxia, cold, and nutritional scarcity. However, the integrated metabolic and microbial mechanisms underlying these adaptations remain poorly defined. Here, a comprehensive multi-omics analysis was performed on thirty grazing heifer yaks (2.5 years old) from three altitudes-3,600 m (low altitude [LA]), 4,000 m (middle altitude [MA]), and 4,500 m (high altitude [HA])-to investigate how altitude affects host physiology, metabolism, and gut microbial ecology. Increasing altitude significantly reduced serum total protein, globulin, blood urea nitrogen, and alkaline phosphatase, indicating suppressed anabolic metabolism and nitrogen-sparing strategies. Antioxidant capacity (total superoxide dismutase, total antioxidant capacity) and pro-inflammatory cytokines (interleukin-2 [IL-2], IL-6, tumor necrosis factor-α, interferon-γ) increased (P < 0.05), while glutathione peroxidase, IL-4, IL-10, growth hormone, insulin-like growth factor-1, and growth hormone-releasing hormone declined (P < 0.05), reflecting energy reallocation from growth toward antioxidation and immune maintenance under hypoxia. Plasma metabolomics revealed distinct altitude-dependent reprogramming, with enrichment of retinol metabolism at 4,000 m and α-linolenic acid metabolism, tricarboxylic acid (TCA) cycle, and branched-chain amino acid biosynthesis at 4,500 m. These pathways link lipid remodeling, oxidative balance, and oxygen utilization. The gut microbiota displayed altitude-specific shifts, characterized by enrichment of Christensenellaceae_R-7_group and Monoglobus and reduced UCG-005 and Rikenellaceae_RC9_gut_group, accompanied by lower fecal volatile fatty acids (P < 0.05). Correlation analyses confirmed tight associations between fermentative taxa and volatile fatty acids production. Collectively, our results establish a serum-metabolome-microbiota axis as a central mechanism supporting yak adaptation to high altitude.IMPORTANCEThis study demonstrates that the gut microbiota plays a crucial role in how yaks adapt to high-altitude hypoxia. Rising altitude not only alters the composition of gut microbes but also shifts their metabolic activity toward improving fermentation efficiency and antioxidant capacity. These microbial changes are closely linked with host metabolism, forming a coordinated serum-metabolome-microbiota network that helps maintain energy balance and immune stability when oxygen is limited. The enrichment of retinol and α-linolenic acid metabolism as altitude-responsive pathways further highlights the metabolic interplay between host and microbes in supporting physiological resilience. Overall, our findings show that microbial flexibility and metabolic cooperation are key factors enabling ruminants to survive in extreme environments, providing a scientific basis for microbiome-informed strategies to enhance yak health and productivity on the Qinghai-Tibet Plateau.},
}

@article {pmid41410364,
year = {2025},
author = {Mancini, L and Saliekh, L and Claydon, R and Kotar, J and Bernadett Benyei, E and A Munro, C and N Shendruk, T and Brown, A and Welch, M and Cicuta, P},
title = {Hyphal growth determines spatial organization and coexistence in a pathogenic polymicrobial community in a spatially structured environment.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf279},
pmid = {41410364},
issn = {1751-7370},
abstract = {The bodies of macroorganisms host microbes living in multi-species communities. Sequencing approaches have revealed that different organs host different microbiota and tend to be infected by different pathogens, drawing correlations between environmental parameters at the organ level and microbial composition. However, less is known about the microscale dimension of microbial ecology, particularly during infection. In this study, we focus on the role of microscale spatial structure, studying its influence on the ecology of a polymicrobial infection of P. aeruginosa, S. aureus, and C. albicans. Although these pathogens are commonly found together in the lungs of chronically ill patients, it is unclear whether they coexist or compete and segregate in different niches. We find that, whereas P. aeruginosa quickly outcompetes C. albicans and S. aureus on large surfaces, robust spatial organization and coexistence emerges in spatially structured microenvironments. In confined spaces, slowly growing C. albicans is able to leverage rapid radial hyphal growth to conquer boundaries, where it establishes itself displacing the other pathogens. Similar outcomes are observed when the P. aeruginosa strain carries mexT-inactivating mutations, which are often found in clinical isolates. The observed spatial organization enables coexistence and potentially determines infection severity and outcomes. Our findings reveal a previously unrecognized role of mechanical forces in shaping infection dynamics, suggesting that microenvironmental structure might be a critical determinant of pathogen coexistence, virulence, and treatment outcomes. Because adaptations, such as changes in morphology, are widespread among microbes, these results are generalizable to other ecologies and environments.},
}

@article {pmid41410209,
year = {2025},
author = {Vidal, E and Lindsay, MR and Bradley, JA and Osburn, MR and Ruff, SE},
title = {Subsurface Life on Earth as a Key to Unlock Extraterrestrial Mysteries.},
journal = {Microbial biotechnology},
volume = {18},
number = {12},
pages = {e70286},
doi = {10.1111/1751-7915.70286},
pmid = {41410209},
issn = {1751-7915},
support = {https://doi.org/10.52044/HFSP.RGEC342023.pc.gr.168586//Human Frontier Science Program/ ; https://doi.org/10.52044/HFSP.RGY00582022.pc.gr.153592//Human Frontier Science Program/ ; ANR23-CPJ1-0172-01//Agence Nationale de la Recherche/ ; 101115755/ERC_/European Research Council/International ; //CIFAR Earth 4D/ ; 80NSSC23K1355//NASA Exobiology/ ; EAR-2042249//National Science Foundation/ ; EAR-2120912//National Science Foundation/ ; OCE-1450528//National Science Foundation/ ; //United States Science Support Program/ ; //David and Lucile Packard Foundation/ ; },
mesh = {*Earth, Planet ; *Extraterrestrial Environment ; *Exobiology/methods ; Bacteria/metabolism/genetics ; },
abstract = {The first forms of life on Earth were microbial, preceding the evolution of multicellular life by more than two billion years. Based on our current understanding of the origin of life, it is likely that the first life forms on any extraterrestrial world would also be microbial. Due to the extreme temperatures, radiation or aridity on most planetary surfaces, such extraterrestrial microbes would most likely dwell in subsurface environments. Earth's subsurface features a wide range of environments, including deep marine sediments, crustal aquifers, rock fracture fluids, hydrocarbon reservoirs, caves and permafrost soils. These environments are known to host an immense diversity of life forms, predominantly microbes that survive or even thrive under extreme conditions and energy scarcity. Life's ability to endure and possibly evolve in Earth's subsurface lends credence to the possible existence of life beyond our planet and provides a blueprint for the extraterrestrial life forms and biosignatures we might expect. The exploration of space via extraterrestrial samples analysed on Earth, in situ extraterrestrial analyses, and remote sensing continue to advance our search for and understanding of potential biosignatures on other planetary bodies. But by investigating Earth's deep, dark and isolated ecosystems, we not only broaden our understanding of life's adaptability but also refine our strategies and technologies for detecting life on other planets and moons. Subsurface exploration is not just a frontier of Earth science-it is a cornerstone of astrobiology and in the pursuit of understanding the multitude of processes that could create and sustain life anywhere. In this opinion article, we discuss the latest highlights in subsurface research and technology, how Earth's subsurface environments serve as models for potential environments on other planetary bodies, why insights into subsurface microbiomes inform the search for life elsewhere, and which technologies and developments will advance the field in the future.},
}

*Earth, Planet
*Extraterrestrial Environment
*Exobiology/methods
Bacteria/metabolism/genetics

@article {pmid41408796,
year = {2025},
author = {Rojas-Preciado, N and Stockmans, I and Everaert, EA and De Jonghe, K and Wauters, A and Lievens, B and Jacquemyn, H},
title = {Incidence and environmental drivers of beet mild yellowing virus, beet chlorosis virus and beet yellows virus in sugar beet fields in Flanders.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-08-25-1626-RE},
pmid = {41408796},
issn = {0191-2917},
abstract = {Since the ban on neonicotinoids, aphid-transmitted yellowing viruses have increasingly reduced sugar beet yields, leading to substantial economic losses. With limited sustainable alternatives, understanding virus incidence and its drivers is essential for effective disease prevention. This study examined the prevalence and incidence of major yellowing viruses in sugar beet crops across Flanders and assessed the influence of aphid abundance and environmental factors to identify key drivers of infection. We evaluated the incidence of beet mild yellowing virus (BMYV), beet chlorosis virus (BChV), and beet yellows virus (BYV) in 25 sugar beet fields and investigated the influence of aphid abundance, soil nutrients, weather conditions, and landscape features on virus incidence. BMYV was the most prevalent virus detected. Higher incidences of BMYV and BYV were associated with earlier sowing dates and increased early-season abundance of Myzus persicae. BMYV incidence increased under warmer, wetter conditions, while BYV showed the opposite trend. Incidences of BChV and BYV increased in areas dominated by sugar beet cultivation. Elevated soil concentrations of phosphorus and potassium were only associated with higher BMYV incidence. The incidence of yellowing viruses in Flanders was primarily driven by early-season aphid pressure and environmental conditions that facilitate virus transmission and establishment. The increasing occurrence of yellowing viruses poses a significant threat to sugar beet production and calls for better insights into the factors driving virus infection and spread. Effective preventive management strategies should integrate pest dynamics, weather forecasting, landscape structure, and soil health into informed decision-making to limit further spread of yellowing viruses.},
}

@article {pmid41408749,
year = {2025},
author = {Zuccaro, A},
title = {Effector biology and immunometabolic (re)programming: microbial strategies for compatibility.},
journal = {Molecular plant},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.molp.2025.12.016},
pmid = {41408749},
issn = {1752-9867},
abstract = {Root immunometabolism: balancing defense and accommodation Plant health depends on balanced immune defense and microbial accommodation. As constant contact zones, roots must exclude pathogens while fostering beneficial symbionts. Classical, leaf-based immunity models fail to capture the spatial and metabolic complexity of roots, which contain functionally distinct zones and cell types with diverse immune sensitivities and responses (Tsai et al., 2023). Unlike broad immune responses in leaves, root defense is often confined to a few neighboring cells where cellular damage signals coincide with microbial cues. This localized activation likely prevents excessive immunity that could disrupt root development or beneficial colonization (Tsai et al., 2023), shaping microbiome assembly by determining which taxa persist in specific root niches. Beyond immunity, metabolic cues also influence niche formation, collectively defining the physicochemical landscape that selects specific microbial consortia (Loo et al., 2024). Microbial effector proteins from both pathogens and mutualists act individually or cooperatively to reprogram host immune and metabolic pathways, modulating compatibility and plant health. This integrated regulation, known as immunometabolism, is well established in animals, where defined metabolic pathways govern immune cell fate and function. In plants, immunometabolic control is emerging as a conceptual frontier, with host transporters, receptors, and microbial effectors increasingly recognized as key modulators along the mutualism-pathogenesis continuum. Central to this molecular dialogue are extracellular and intracellular signaling metabolites, or infochemicals, produced by both plants and microbes. These small molecules coordinate immune-metabolic states and shape community composition, with purine-derived signals and iron-mediated redox exchanges representing conserved regulatory axes across plant and animal systems (Dangol et al., 2019; Dunken et al., 2024). Together, these cross-kingdom principles offer conceptual and practical leverage for predictive microbiome engineering. Because this opinion piece spans immunity, metabolism, and microbial ecology, INFOBOX 1 defines key terms to establish a shared conceptual framework.},
}

@article {pmid41408715,
year = {2025},
author = {Pérez-Lorente, AI and Molina-Santiago, C and Vela-Corcía, D and Stincone, P and Hierrezuelo, J and Grifé, M and Pakkir Shah, AK and de Vicente, A and Petras, D and Romero, D},
title = {Offensive role of the Bacillus extracellular matrix in driving metabolite-mediated dialogue and adaptive strategies with the fungus Botrytis.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf277},
pmid = {41408715},
issn = {1751-7370},
abstract = {Bacterial-fungal interactions have traditionally been attributed to secondary metabolites, but the role of the bacterial extracellular matrix in shaping these relationships has remained unclear. Here, we demonstrate that the extracellular matrix protein TasA is a key mediator in the antagonistic interaction between Bacillus subtilis and Botrytis cinerea. TasA enables Bacillus to tightly adhere to fungal hyphae, disrupts the β-glucan layer, and compromises fungal cytoskeletal integrity synergistically with fengycin, which causes cytological damage. Additionally, TasA acts as a carrier for bacillaene, amplifying its fungistatic activity. In response, Botrytis mounts a multifaceted defense, enzymatically degrading fengycin, producing antibacterial oxylipins, and activating adaptive programs such as hyphal branching and chlamydospore formation. Our findings reveal the previously unrecognized role of extracellular matrix components in fungal suppression and the modulation of fungal adaptive responses. This study reveals the complex interplay between microbial aggression and defense, providing new insights into the ecological dynamics of microbial competition and coexistence.},
}

@article {pmid41407993,
year = {2025},
author = {Cota Ortega, LE and Quiroz-Guzmán, E and Balcázar, JL},
title = {Ecological Drivers of Plasmid-Mediated Antimicrobial Resistance in Aquaculture.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02684-0},
pmid = {41407993},
issn = {1432-184X},
abstract = {Antimicrobial resistance (AMR) is a growing global challenge that compromises the effectiveness of disease control and increases risks for both human and animal health. Aquaculture systems are particularly vulnerable, as extensive and often inappropriate antimicrobial use has driven the emergence and persistence of multidrug-resistant bacteria. This mini-review summarizes the ecological and genetic mechanisms underlying AMR in aquaculture, with emphasis on plasmid-mediated resistance and its role in horizontal gene transfer. It also addresses the broader environmental and public health implications of these processes and calls for sustainable management, enhanced surveillance, and coordinated international policies to curb resistance dissemination and safeguard global food security.},
}

@article {pmid41405607,
year = {2025},
author = {Satterwhite, RS and Bergelson, J},
title = {Adaptation without Dominance in Pseudomonas syringae Pathovars.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02675-1},
pmid = {41405607},
issn = {1432-184X},
support = {Hutchinson Fund//University of Chicago Department of Ecology and Evolution/ ; NSF MCB 0603515//National Science Foundation, United States/ ; },
abstract = {Understanding local adaptation of phytopathogens has significant practical and economic implications. The opportunistic pathogen Pseudomonas syringae exemplifies this challenge, causing regular epidemics in diverse host plants. Many pathogenic microbes, including P. syringae, are divided into intraspecific lineages, or pathovars, based on their host-of-isolation. However, whether pathovar classifications reflect adaptation of the pathogen to the host (local adaptation) or a competitive advantage of the pathogen in the host (local dominance), often goes untested. In this study, we performed in vitro growth assays and factorial controlled infections to test whether a suite of five P. syringae pathovars are locally adapted to, and/or locally dominant in, their hosts-of-isolation. We found evidence of local adaptation in three of five pathogens, only one of which was also locally dominant. Several strains performed as well or better than the locally adapted strain in that strain's host-of-isolation, consistent with cost-free generalism. Thus, pathovar designations do not reliably delineate pathogenic phenotypes. Moreover, we found that in vitro growth was not predictive of in planta growth. To contextualize phenotypes, we compared pathogen gene content, identifying unique phytotoxins, secreted effectors, and general virulence factors. In all, we found that local adaptation is common but not universal, and that locally adapted strains are not necessarily constrained from performing competitively in multiple hosts. Thus, neither host-of-isolation nor in vitro performance is reliable for strain classification. Our findings highlight the vast intraspecific variation in P. syringae, and the coexistence of multiple successful adaptive strategies.},
}

@article {pmid41404415,
year = {2025},
author = {Sakarika, M and Brancart, J and Gujar, SA and De Meester, S and Allegue, LD and Bastiaens, L and Ragaert, P and Vlaeminck, SE and De Wever, H and Rabaey, K},
title = {Microbial protein-derived bioplastics from renewable substrates: pathways, challenges, and applications in a circular economy.},
journal = {Environmental science and ecotechnology},
volume = {28},
number = {},
pages = {100635},
pmid = {41404415},
issn = {2666-4984},
abstract = {Microbial protein (MP)-the protein-rich biomass derived from recovered or virgin resources-is attracting interest as a source of food and feed. However, its potential as a feedstock for protein-based bioplastics remains underexplored. Proteins offer desirable properties, including superior oxygen-barrier capabilities and complete biodegradability, making them ideal for applications from food packaging to agricultural mulches. Currently, most protein-based bioplastics derive from crops such as wheat, restricting applications and competing with food production. MP can overcome these limitations by supplying diverse proteins from various inputs, including CO2, biomass, and liquid side-streams. In this review, we evaluate bioprocessing pathways for producing MP from renewable and waste-derived substrates from an interdisciplinary viewpoint. We also examine the technical, regulatory, market, and environmental factors to address, delineating the pathway from substrate to MP-based plastics and highlighting key challenges throughout the production chain. Novel strategies-such as efficient co-recovery of proteins with other cellular products like polyhydroxyalkanoates or direct use of microbial biomass without extraction-are essential to maximize environmental and economic sustainability. Carefully chosen processing methods for recovered proteins, including wet and dry blending or extrusion with other biopolymers, can yield diverse products. Concurrently, policy and market developments are vital for adopting MP-based bioplastics. Addressing these challenges will enable MP-based bioplastics to propel the shift toward a circular economy, diminishing dependence on fossil-derived plastics and alleviating plastic pollution.},
}

@article {pmid41403705,
year = {2025},
author = {Paccagnella, D and Bağcı, C and Gavriilidou, A and Ziemert, N},
title = {PanBGC: a pangenome-inspired framework for comparative analysis of biosynthetic gene clusters.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf225},
pmid = {41403705},
issn = {2730-6151},
abstract = {Bacterial secondary metabolites are a major source of therapeutics and play key roles in microbial ecology. These compounds are encoded by biosynthetic gene clusters (BGCs), which show extensive genetic diversity across microbial genomes. While recent advances have enabled clustering of BGCs into gene cluster families (GCFs), there is still a lack of frameworks for systematically analysing their internal diversity at a population scale. Here, we introduce "PanBGC", a pangenome-inspired framework that treats each GCF as a population of related BGCs. This enables classification of biosynthetic genes into core, accessory, and unique categories and provides openness metrics to quantify compositional diversity. Applied to over 250 000 BGCs from more than 35 000 genomes, PanBGC maps biosynthetic diversity of more than 80 000 GCFs. Our analysis reveals that gene composition reshuffling, rather than acquisition of new genes, is the dominant driver of diversity within GCFs, with most families exhibiting closed gene repertoires but high compositional variability. Additionally, transporter-related domains were commonly identified among core genes, reflecting the fundamental importance of compound export in BGC function. To facilitate exploration, we present PanBGC-DB (https://panbgc-db.cs.uni-tuebingen.de), an interactive web platform for comparative BGC analysis. PanBGC-DB offers gene- and domain-level visualizations, phylogenetic tools, openness metrics, and custom query integration. Together, PanBGC and PanBGC-DB provide a scalable framework for exploring BGCs at population resolution and for contextualizing newly discovered BGCs within the global landscape of secondary metabolism.},
}

@article {pmid41402555,
year = {2025},
author = {Lakhlifi, T and El Oirdi, S and Kaddouri, AC and Belhaj, A},
title = {Factors influencing antifungal activity of selected lactic acid bacteria strains and characterization of their active compounds.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {1},
pages = {13},
pmid = {41402555},
issn = {1572-9699},
support = {PPR2/2016/07//Centre National pour la Recherche Scientifique et Technique/ ; },
mesh = {*Antifungal Agents/pharmacology/metabolism/chemistry ; *Lactobacillales/chemistry/metabolism ; Hydrogen-Ion Concentration ; Temperature ; Carbon/metabolism ; Culture Media/chemistry ; Microbial Sensitivity Tests ; },
abstract = {Lactic acid bacteria (LAB) are known to possess potent antifungal activity; however, the factors that affect this activity remain poorly investigated. In this study, we explored the influence of physicochemical and nutritional factors on the antifungal activity of five LAB strains namely Lactiplantibacillus pentosus 22B, Leuconostoc mesenteroides 8C2, Lactiplantibacillus plantarum 21B, Enterococcus faecium LC2V5 and Enterococcus faecium LC2P8. These factors included incubation period, medium initial pH, incubation temperature, long-term storage and carbon source. Results showed that these factors significantly influenced the antifungal activity of the studied LAB strains (p < 0.0001). The optimal conditions yielding the most potent inhibition (21 ± 0.4 mm to 19 ± 0.4 mm) were identified. Specifically, maximum activity was achieved after a 48-h incubation (late stationary phase), at 25-30 °C, an initial pH of 3-4, and with sucrose, galactose, or mannose as the carbon source, depending on the strain. Moreover, long-term storage at - 80 °C led to complete loss of activity in two strains (8C2 and LC2P8), while the other three remained stable. Furthermore, HPLC and GC-MS analyses were used to identify the antifungal compounds produced by these three stable strains. The results revealed the presence of various organic acids (lactic, acetic, formic, malic, and fumaric acids) and fatty acids, such as 9-octadecenoic acid, 11-dodecenoic acid, 10-hydroxy. Scanning electron microscopy confirmed that these compounds caused significant structural damage to fungal mycelia, supporting their demonstrated fungicidal effects. This study improves our understanding of the key factors and mechanisms underlying LAB antifungal activity, contributing to the optimization of their use as natural antifungal agents.},
}

*Antifungal Agents/pharmacology/metabolism/chemistry
*Lactobacillales/chemistry/metabolism
Hydrogen-Ion Concentration
Temperature
Carbon/metabolism
Culture Media/chemistry
Microbial Sensitivity Tests

@article {pmid41402426,
year = {2025},
author = {Wauquier, F and Chavanelle, V and Bouchard-Mercier, A and Boutin-Wittrant, L and Otero, YF and Krisa, S and Valls, J and Le Joubioux, F and Pereira, B and Roux, V and Macian, N and Pickering, G and Sapone, V and Cazaubiel, M and Bron, A and Peltier, S and Blanquet, S and Sirvent, P and Wittrant, Y},
title = {Bioavailable human metabolites from TOTUM-448 (plant-based formulation) maintain liver cell functionality in a hyperlipidic context that drives MASLD onset.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-32556-z},
pmid = {41402426},
issn = {2045-2322},
support = {Labcom MIMETiv (ANR, ANR-22-LCV1-0003-01)//Agence Nationale de la Recherche/ ; Labcom MIMETiv (ANR, ANR-22-LCV1-0003-01)//Agence Nationale de la Recherche/ ; Labcom MIMETiv (ANR, ANR-22-LCV1-0003-01)//Agence Nationale de la Recherche/ ; Labcom MIMETiv (ANR, ANR-22-LCV1-0003-01)//Agence Nationale de la Recherche/ ; Labcom MIMETiv (ANR, ANR-22-LCV1-0003-01)//Agence Nationale de la Recherche/ ; Labcom MIMETiv (ANR, ANR-22-LCV1-0003-01)//Agence Nationale de la Recherche/ ; Labcom MIMETiv (ANR, ANR-22-LCV1-0003-01)//Agence Nationale de la Recherche/ ; Labcom MIMETiv (ANR, ANR-22-LCV1-0003-01)//Agence Nationale de la Recherche/ ; Labcom MIMETiv (ANR, ANR-22-LCV1-0003-01)//Agence Nationale de la Recherche/ ; Labcom MIMETiv (ANR, ANR-22-LCV1-0003-01)//Agence Nationale de la Recherche/ ; Labcom MIMETiv (ANR, ANR-22-LCV1-0003-01)//Agence Nationale de la Recherche/ ; Labcom MIMETiv (ANR, ANR-22-LCV1-0003-01)//Agence Nationale de la Recherche/ ; Labcom MIMETiv (ANR, ANR-22-LCV1-0003-01)//Agence Nationale de la Recherche/ ; Pack Ambition Recherche 2021 MICROMETiv//Région Auvergne-Rhône-Alpes/ ; Pack Ambition Recherche 2021 MICROMETiv//Région Auvergne-Rhône-Alpes/ ; Pack Ambition Recherche 2021 MICROMETiv//Région Auvergne-Rhône-Alpes/ ; Pack Ambition Recherche 2021 MICROMETiv//Région Auvergne-Rhône-Alpes/ ; Pack Ambition Recherche 2021 MICROMETiv//Région Auvergne-Rhône-Alpes/ ; Pack Ambition Recherche 2021 MICROMETiv//Région Auvergne-Rhône-Alpes/ ; Pack Ambition Recherche 2021 MICROMETiv//Région Auvergne-Rhône-Alpes/ ; Pack Ambition Recherche 2021 MICROMETiv//Région Auvergne-Rhône-Alpes/ ; Pack Ambition Recherche 2021 MICROMETiv//Région Auvergne-Rhône-Alpes/ ; Pack Ambition Recherche 2021 MICROMETiv//Région Auvergne-Rhône-Alpes/ ; ANR11-INBS-0010//Bordeaux Metabolome Facility and the MetaboHUB/ ; ANR11-INBS-0010//Bordeaux Metabolome Facility and the MetaboHUB/ ; },
abstract = {Lipotoxic and inflammatory environment drives metabolic dysfunction-associated steatotic liver disease (MASLD) onset. As most conventional treatments present adverse side effects, alternative options such as preventive nutritional interventions have been developed, though further clinical validation is needed. In this study, we conducted an innovative ex vivo clinical investigation to examine how circulating metabolites generated after oral intake of TOTUM-448 (a plant-based, polyphenol-rich formulation) may influence hepatocyte function. UHPLC-MS/MS analysis confirmed and characterized the bioavailable polyphenol metabolites present in human serum. This metabolite-enriched serum was further used to treat HepG2 hepatocytes, with or without palmitate pretreatment (250 µM). The effects of TOTUM-448-derived metabolites on hepatocytes were evaluated by monitoring cell viability, lipid metabolism, inflammation, oxidative stress, and endoplasmic reticulum (ER) stress, all of which are central features of MASLD. Treated hepatocytes exhibited resistance to palmitate-induced lipotoxic stress, showing reduced intracellular lipid accumulation. TOTUM-448-derived metabolites also prevented the palmitate-induced upregulation of inflammatory gene expression. Additionally, while palmitate strongly upregulated CHOP and XBP1 mRNA expression as well as ATF6 and Caspase-3 activities, the presence of TOTUM-448-derived metabolites restored these ER stress markers to normal levels.},
}

@article {pmid41400860,
year = {2025},
author = {Zander, S and von Friesen, LW and Gonçalves-Araujo, R and Grosso, O and Benavides, M and Granskog, MA and Riemann, L},
title = {Contrasting Nitrogen Fixation Between Arctic and Atlantic Waters in the Fram Strait.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02673-3},
pmid = {41400860},
issn = {1432-184X},
support = {730965//European Union H2020/ ; NE/W004933/1//Natural Environment Research Council/ ; 2032-00001B//Danmarks Frie Forskningsfond/ ; 6108-00013//Danish Council for Independent Research/ ; },
abstract = {Nitrogen availability limits primary production in the Arctic Ocean, making it vital to understand its sources and sinks to predict future productivity. Although nitrogen fixation has been reported in the Arctic Ocean, data remain scarce, especially in the Atlantic sector. Here, we measured nitrogen fixation rates and examined diazotroph community composition across the Fram Strait, targeting Polar waters in the East Greenland Current, Atlantic waters in the West Spitsbergen Current, and their frontal zone. Nitrogen fixation was mainly low (< 1 nmol N L[-1] d[-1]) in Polar waters, however, elevated at the one station in the Atlantic water sector (up to 10.15 nmol N L[-1] d[-1]). Rates were only detectable in the epipelagic layer (0-100 m) across the strait and positively correlated with temperature, primary production, and chlorophyll-a fluorescence, and negatively correlated with coloured dissolved organic matter and silicate. The diazotrophs were dominated by non-cyanobacterial diazotrophs (NCDs; 77% of nifH amplicon reads), with an Arctic Betaproteobacterial group (order Rhodocyclales) accounting for 11% of sequence reads. This group was quantifiable (up to 6700 nifH gene copies L[-1]) within the West Spitsbergen Current and the frontal zone, where the highest nitrogen fixation and primary production occurred, and its prevalence was positively correlated with temperature. We propose that temperature and freshly produced dissolved organic matter influence the NCD-dominated nitrogen fixation in Fram Strait. Our study suggests that NCDs are key diazotrophs in Fram Strait, and that nitrogen fixation rates and their potential importance for primary production vary across the contrasting water masses entering and exiting the Arctic Ocean. We encourage future studies to quantify these nitrogen fluxes and evaluate their importance for productivity in the Arctic Ocean.},
}

@article {pmid41400345,
year = {2025},
author = {Yuan, W and Xu, EG and Zhu, D and Zhang, W and Liu, W and Abdolahpur Monikh, F and Lin, L and Li, L and Grossart, HP and Yang, Y and Rillig, MC and Peijnenburg, WJGM},
title = {Nanoplastics in Duckweed: Single-Cell Responses and Recovery.},
journal = {ACS nano},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsnano.5c15989},
pmid = {41400345},
issn = {1936-086X},
abstract = {Micro- and nanoplastics have emerged as critical contaminants in aquatic ecosystems due to their small size, persistent nature, and potential for bioaccumulation. Nanoplastics are particularly concerning because they can be widespread in aquatic environments and ingested by aquatic organisms, posing potential risks to ecological health and environmental sustainability. However, the response and recovery of aquatic plants to nanoplastics, as well as the cell-specific molecular mechanisms underlying these processes, remain unclear. By integrating single-cell transcriptomics, enzymatic assays, and europium-doped nanoplastic tracing, we comprehensively investigated the response of duckweed to polystyrene nanoplastics at environmentally relevant and high doses over exposure and recovery phases. Nanoplastics exposure reduced plant reproduction and root length by inducing oxidative damage, with partial recovery after removal. Single-nucleus RNA sequencing revealed cell-type-specific responses of duckweed to nanoplastics, particularly in mesophyll, mestome sheath, epidermis, and parenchyma cells. Interestingly, recovery triggered a greater number of differentially expressed genes mechanistically linked to carbon metabolism, membrane transport, and stress-responsive pathways. Nanotracer quantification demonstrated root/frond absorption and 36.8-51.4% postrecovery excretion. These multiscale lines of evidence decipher the molecular strategies of duckweed to nanoplastics at single-cell resolution, providing mechanistic insights into the interactions between aquatic plants and nanoplastics contamination.},
}

@article {pmid41398214,
year = {2025},
author = {Sari, SP and Soylu, A and Peker, KD and Adas, G and Akgul, O and Sapmaz, B and Oner, YA and Mayda, PY and Caliskan, R},
title = {Comparative gastric microbiota profiles in non-ulcer dyspepsia and peptic ulcer patients.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04607-y},
pmid = {41398214},
issn = {1471-2180},
support = {Project number: 2018/05//Istanbul Aydın University Scientific Research Projects Coordination Unit/ ; },
abstract = {BACKGROUND: Recent evidence suggests that the human stomach hosts a diverse microbiota beyond Helicobacter pylori, and that shifts in microbial composition may influence gastric health. In particular, oral-origin bacteria may dominate the gastric niche in the absence of H. pylori, yet their specific roles in different gastroduodenal disorders remain unclear. This study aimed to profile and compare the gastric microbiota composition in Turkish patients with non-ulcer dyspepsia (NUD) and peptic ulcer disease (PUD), in order to better understand microbial profiles potentially associated with gastroduodenal disease.

METHODS: Ninety-eight patients underwent endoscopic evaluation and were divided into two groups according to the presence or absence of ulcers. Group 1 (n = 52) included individuals with NUD, while Group 2 (n = 46) comprised patients with PUD. Gastric biopsy samples from both groups were analyzed for the relative abundance of H. pylori using quantitative real-time PCR (qPCR), and next-generation sequencing was employed for a comprehensive analysis of the gastric microbiota.

RESULTS: In total, H. pylori DNA was detected in 71.4% (70/98) of the samples, with a significantly higher prevalence in PUD patients (82.6%) compared to NUD patients (61.5%) (p = 0.02). Distinct microbial profiles were observed based on H. pylori status. In NUD patients, Alloprevotella showed significantly higher relative abundance in H. pylori-negative samples (p < 0.05). Among PUD patients, the absence of H. pylori was associated with increased levels of Porphyromonas and Neisseria compared to NUD patients without H. pylori (p < 0.05). These genera, typically associated with the oral cavity, appeared to expand opportunistically when H. pylori was absent.

CONCLUSIONS: The absence of H. pylori in gastric disorders was linked to a notable shift in microbiota composition, with increased representation of oral-origin bacteria such as Alloprevotella, Porphyromonas, and Neisseria. These findings, observed in a Turkish patient cohort, may reflect a potentially compensatory or opportunistic microbial shift in H. pylori-negative gastroduodenal disease. As exploratory findings, this study represents the first analysis from Türkiye comparing gastric microbiota profiles in NUD and PUD patients and provides novel regional insight into gastric microbial ecology.},
}

@article {pmid41398058,
year = {2026},
author = {},
title = {Microbial ecology and evolution in the genomics era.},
journal = {Nature reviews. Genetics},
volume = {27},
number = {1},
pages = {1-2},
pmid = {41398058},
issn = {1471-0064},
}

@article {pmid41396129,
year = {2025},
author = {Timmis, K and Baquero, F and Lal, R and Amorim, LRP and Nikel, PI and Kaur, J and Sood, U and Lata, P and Singh, S and Robinson, JM and Chavarria, M and Verstraete, W and Bernal, P and Banciu, H and Steward, K and Frey, J and Danchin, A and Karnkowska, A and Kotsyurbenko, O and Pereira, CS and Boyd, ES and Hallsworth, JE and Nunes, O and Udaondo, Z and Huang, W and Wang, Y and Karahan, ZC and Junier, P and Ron, E and Ramos, JL},
title = {Scientists' Warning to Humanity: The Need to Begin Teaching Critical and Systems Thinking Early in Life.},
journal = {Microbial biotechnology},
volume = {18},
number = {12},
pages = {e70270},
doi = {10.1111/1751-7915.70270},
pmid = {41396129},
issn = {1751-7915},
mesh = {Humans ; Decision Making ; },
abstract = {We live in a time of global crises: a deteriorating environment that is struggling to provide all the resources and services we demand of it, changing climate and its consequences for the biosphere, its habitats, inhabitants and biodiversity, conflicts-divisive ideologies-competition for resources, increasing societal inequalities and human deprivations, and a youth mental health pandemic, to name but just a few. Most of these crises are self-made, the result of human decisions, and their acceptance/toleration by society. Policies and practices at all levels of society that created, exacerbate and launch new crises are, at worst, self-serving and, at best, faulted through a lack of understanding. In democracies, citizens can hold decision-makers to account but, to do this, they must understand the issues and be able to imagine better policies. We also live in a digital world in which a flood of mostly inconsequential information and misinformation pollutes our brains, enhancing pre-existing biases and creating new ones, and numbing our mental ability to think clearly and reach sensible decisions. But sensible decisions are urgently needed at all levels to fix problems and reduce future self-harm. Sensible decisions require sourcing the best available relevant information, and a process to convert information into understanding, understanding into clear decision options, and the choice of a decision option that leads to an action that represents best practice. Critical thinking is the enabling cognitive process of this decision pathway, because it selects the best available information through demanding evidence-basing, seeks critical discourse between experts and stakeholders that agnostically explores solution space to find plausible options, and whittles down options inter alia through plausibility, due diligence, bottleneck analysis, cost-benefit analysis, and benchmarking filtering. Crucially, it rejects biases, influencing factors, and other constraints on options, and is an effective barrier to the information flood. The problem is that critical thinking capacity is not widely available among either decision makers or stakeholders. There is an urgent need to rapidly roll out effective education programmes in which critical thinking teaching is solidly embedded. Since biases accumulate with age, the teaching of critical thinking must begin with the very young. However, the very young are not able to comprehend the complex abstract issues underpinning critical thinking. Embedding the teaching of critical thinking in a suitable educational context, and integrating it into curricula, is another challenge. To address these two challenges, the International Microbiology Literacy Initiative is developing a storytelling programme for children, called the Critical Thinking MicroChats Gallery, within the curriculum of societally relevant microbiology it is creating. MicroChats illustrate the principal practical elements of critical thinking, like bottlenecks, cost: benefit, benchmarking, the need for discussions and other points of view, employing readily relatable, relevant microbially centric scenarios. MicroChats suggest class discussion topics to encourage children to imagine the application of each element in other contexts to reinforce principles and hone critical thinking skills. Critical thinking, and especially the cultivation of the habit of asking 'why' and requiring plausible justification for policies/actions, is a shield against bias, prejudice, propaganda, misinformation and the incessant pressures of social media. It promotes a healthy mind and the attainment of the developmental potential of individuals. Increasing critical thinking in society will raise the quality of decision making at all levels and thereby improve sustainability/reduce the human footprint on our planet, and promote the individual sense of responsibility and global citizenship necessary for the improvement of the condition of humanity and its relationship with Planet Earth.},
}

Humans
Decision Making

@article {pmid41395947,
year = {2025},
author = {Bouchali, R and Sentenac, H and Bates, KA and Fisher, MC and Schmeller, DS and Loyau, A},
title = {Unraveling the disease pyramid: the role of environmental micro-eukaryotes in amphibian resistance to the deadly fungal pathogen Batrachochytrium dendrobatidis.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0143625},
doi = {10.1128/msystems.01436-25},
pmid = {41395947},
issn = {2379-5077},
abstract = {The disease pyramid conceptualizes the predictors of host infection risk, linking the host, the pathogen, environmental conditions, and both host and environmental microbiomes. However, the importance of the interaction between environmental and host-associated microbiomes in shaping infectious disease dynamics remains poorly understood. While the majority of studies have focused on bacteria, the role of micro-eukaryotes has been seldom investigated. Here, we explore three axes of the disease pyramid using an 18S rRNA gene metabarcoding approach to analyze the micro-eukaryotic assemblages of biofilm, water, and skin samples from three European amphibian species. Skin bacterial communities of the investigated amphibian populations have already been shown to be impacted by the presence of the lethal fungal pathogen Batrachochytrium dendrobatidis (Bd), with a higher abundance of protective bacteria in infected populations and a greater environmental microbial contribution to the skin microbiota in Bd-positive lakes. Here, we explored the relationships between the micro-eukaryotic skin communities of these tadpole populations with their surrounding environment. Tadpoles were sampled at 22 mountain lakes located in the Pyrenees (France), 8 of which harbored amphibian populations infected by Bd. We found that biofilms from Bd-negative lakes had higher environmental micro-eukaryotic diversity and a greater abundance of putative anti-Bd fungi, both in the environment and on the skin microbiota of Bufo spinosus and Rana temporaria, but not of Alytes obstetricans. Bayesian SourceTracker analysis further showed that the environmental contribution from biofilms to amphibian skin micro-eukaryotic assemblages was higher in Bd-positive lakes for B. spinosus and R. temporaria, but not for A. obstetricans.IMPORTANCEResearch on host-associated microbiomes and infectious diseases has mostly focused on bacteria, overlooking the potential contributions of micro-eukaryotes to infection dynamics. Here, we show that environmental and skin-associated micro-eukaryotes-especially putative anti-Batrachochytrium dendrobatidis (Bd) fungi-differ between Bd-positive and Bd-negative amphibian populations in mountain lakes. Our results suggest that micro-eukaryotes influence disease resistance and microbiome assembly, similarly to bacteria. Importantly, environmental reservoirs of micro-eukaryotes appear to contribute differently across infection contexts. These findings demonstrate the importance of adopting a broader microbiome perspective that includes micro-eukaryotes when investigating the ecological mechanisms underlying infectious disease risk.},
}

@article {pmid41395872,
year = {2025},
author = {Mason, AR and Taylor, LS and Gilbert, NE and Wilhelm, SW and DeBruyn, JM},
title = {Soil Microbial Gene Expression Over One Year of Human Decomposition.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf126},
pmid = {41395872},
issn = {1574-6941},
abstract = {During terrestrial vertebrate decomposition, host and environmental microbial communities work together to drive biogeochemical cycling of carbon and nutrients. These mixed communities undergo dramatic restructuring in the resulting decomposition hotspots. To reveal the succession of the active microbes (bacteria, archaea, and fungi) and the metabolic pathways they use, we generated metatranscriptomes from soil samples collected over one year from below three decomposing human bodies. Soil microbes increased expression of heat shock proteins in response to decomposition products changing physiochemical conditions (i.e. reduced oxygen, high salt). Increased fungal lipase expression identified fungi as key decomposers of fat tissue. Expression of nitrogen cycling genes was phased with soil oxygen concentrations: during hypoxic soil conditions, genes catalyzing N-reducing processes (e.g. hydroxylamine to nitric oxide and nitrous oxide to nitrogen gas during reduced oxygen conditions) were increased, followed by increased expression of nitrification genes once oxygen diffused back into the soil. Increased expression of bile salt hydrolases implicated a microbial source for the high concentrations of taurine typically observed during vertebrate decomposition. Collectively, microbial gene expression profiles remained altered even after one year. Together, we show how human decomposition alters soil microbial gene expression, revealing both ephemeral and lasting effects on soil microbial communities.},
}

@article {pmid41395225,
year = {2025},
author = {Mortier, L and Vanhoomissen, R and Davies, L and Kirk, PM and Maciá-Vicente, JG and Piepenbring, M and Haelewaters, D},
title = {The first checklist of fungi known for Honduras: revealing taxonomic, geographical, and functional trends.},
journal = {MycoKeys},
volume = {126},
number = {},
pages = {93-117},
pmid = {41395225},
issn = {1314-4049},
abstract = {Fungi play pivotal roles in ecosystem functioning and the provision of ecosystem services. Despite their ecological importance, fungal research remains limited, particularly in tropical regions. Many tropical countries, including Honduras, still lack a comprehensive fungal checklist. To address this gap, we compiled the first fungal checklist for Honduras by collating data from Index Fungorum, MyCoPortal, the Kew Data Portal, and published literature. The resulting dataset contains 1365 species across 4011 records, of which 96.6% are true fungi and 3.4% are fungus-like organisms. Among the true fungi, 69.8% belong to Basidiomycota and 29.4% to Ascomycota. A large percentage of the records refer to plant pathogens (42.4%), reflecting a relatively high number of phytopathological studies and a focus on fungal associations with plant species. Species accumulation curves indicate that all administrative divisions (departments) of Honduras remain understudied, as none have reached saturation. This checklist is a fundamental resource tool for fungal identification and conservation planning and contributes to a broader understanding of fungal biodiversity in the region.},
}

@article {pmid41394253,
year = {2025},
author = {Fadum, J and Sun, X and Zakem, E},
title = {Redox-constrained microbial ecology dictates nitrogen loss versus retention.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf219},
pmid = {41394253},
issn = {2730-6151},
abstract = {Microorganisms drive biogeochemical cycling. Therefore, examining environmental change through the lens of microbial ecology is particularly useful for developing a mechanistic understanding of the biogeochemical consequences and feedbacks of perturbations to ecosystems. When aquatic systems with deep anoxic waters undergo eutrophication, the resulting surface productivity impacts the anaerobic microbial community below. The increase in sinking organic carbon can shift the anaerobic community function from inorganic nitrogen (N) loss to N retention, amplifying eutrophication as a positive feedback. However, we lack a mechanistic understanding of this transition, which is critical for anticipating these impacts in aquatic environments where microbial community composition is unknown. Here, we provide a first-principles, quantitative model of this transition from N loss to retention by linking ecological dynamics to the energetics underlying microbial metabolisms. We develop and analyze an ecosystem model in which redox chemistry constrains the traits of key anaerobic N-cycling microbial functional types: denitrification, dissimilatory nitrate reduction to ammonium, and anaerobic ammonium oxidation (anammox). The model captures the transition from N loss to N retention with increasing organic carbon supply, consistent with observations for specific systems and species. Results identify characteristics of the microbial community composition at the "net zero N loss" point at which N loss balances N retention, providing testable hypotheses for sequencing data and other observations. By tying microbial ecological dynamics to environmental chemical potential, results provide a broadly applicable framework for better predicting the biogeochemical impacts of eutrophication, deoxygenation, and other perturbations.},
}

@article {pmid41393217,
year = {2025},
author = {Xu, Z and Premarathna, M and Li, Y and Yin, X and Soteyome, T and Liu, J and Seneviratne, G},
title = {Current knowledge on the polymicrobial interaction and biofilm between Saccharomyces and Lactobacillaceae: regulatory mechanisms and applications.},
journal = {Biofilm},
volume = {10},
number = {},
pages = {100336},
pmid = {41393217},
issn = {2590-2075},
abstract = {The family Lactobacillaceae plays a crucial role in food fermentation and probiotic applications, and exhibiting metabolic versatility and adaptability to diverse nutrient-rich environments. They are abundant in nutrient-rich environments like fermented food, vegetables, and the vaginal and gastrointestinal tracts of animals, where they metabolize carbohydrates to produce lactic acids. They also produce bioactive compounds and exhibit anti-inflammatory, antibacterial, and antifungal properties. Saccharomyces yeasts are also widely applied in food, medicine, and biofuel industries. Some species, such as S. boulardii, are recognized for their probiotic benefits, particularly in promoting gut health and alleviating intestinal disorders. This review focuses on the polymicrobial interactions between Lactobacillaceae and Saccharomyces species, highlighting their synergistic roles in improving fermentation efficiency, product quality, and microbial stability through mechanisms such as biofilm formation, metabolic exchange, and nutrient sharing. We also discuss competitive interactions observed in certain systems, such as sugarcane fermentation, which demonstrate the complexity of microbial ecology and the need for precise microbial management strategies. By synthesizing current research, this review aims to provide a comprehensive understanding of how microbial interactions influence fermentation outcomes, and to identify existing knowledge gaps and future directions for optimizing industrial applications.},
}

@article {pmid41392918,
year = {2025},
author = {Cianetti, S and Marchianò, S and Wijeratne, DF and Carino, A and Biagioli, M and Bordoni, M and Roselli, R and Di Giorgio, C and Bellini, R and Valenti, C and Coniglio, M and Lomurno, G and Lomurno, AP and Pagano, S},
title = {Analysis of Oral and Gut Microbiota Composition in Children with Dental Caries by NGS Approaches.},
journal = {Recent advances in inflammation & allergy drug discovery},
volume = {19},
number = {3},
pages = {413-427},
doi = {10.2174/0127722708335159241117062704},
pmid = {41392918},
issn = {2772-2716},
mesh = {Humans ; *Dental Caries/microbiology ; *Gastrointestinal Microbiome ; Male ; Female ; *Mouth/microbiology ; Child ; *Probiotics/administration & dosage/therapeutic use ; Feces/microbiology ; High-Throughput Nucleotide Sequencing ; Child, Preschool ; Streptococcus salivarius ; Saliva/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {OBJECTIVES: This study aimed to characterize oral and gut microbiota of children with high dmft index and caries-free children at phylum, family and species levels as well as to evaluate the effect of Streptococcus salivarius M18 DSM 14685 (Carioblis) administration on microbiota composition of caries active children.

MATERIALS AND METHODS: Ten children with active caries and nine caries-free children have been recruited. Four samples from different oral niches and stools were collected from each patient for the NGS sequencing of 16s Microbiota rDNA by S5 Ion Torrent.

RESULTS: Our results revealed modifications in the microbiota composition of teeth, saliva and vestibular regions of the oral cavity and faecal samples in the presence of dental caries. These changes were evident at the family and species levels, with no significant differences found at the phylum composition level. In particular, Streptococcaceae were positively correlated to the high degree of caries in all niches, and the analysis at the species level led to the identification of 39 bacterial species significantly modulated in the analyzed groups. The use of probiotic seemed to exert beneficial effects on oral but not on faeces dysbiosis. The intestinal tract was confirmed to have a different microbiota composition compared to the oral cavity.

CONCLUSION: Dental caries mainly lead to modifications in the oral microbiota composition. Streptococcus salivarius M18 DSM 14685 administration determines a shift in the oral microbiota composition towards a healthier state. Concerning the gastrointestinal tract, our study found for the first time that caries cause the increase of two bacterial species, related to other disorders: Bifidobacterium adolescentis and Ruminococcus torques.},
}

Humans
*Dental Caries/microbiology
*Gastrointestinal Microbiome
Male
Female
*Mouth/microbiology
Child
*Probiotics/administration & dosage/therapeutic use
Feces/microbiology
High-Throughput Nucleotide Sequencing
Child, Preschool
Streptococcus salivarius
Saliva/microbiology
RNA, Ribosomal, 16S/genetics

@article {pmid41391312,
year = {2025},
author = {Wang, T and Roschke, C and Sánchez, N and Duncan, AH and Namayandeh, A and Fendorf, S and da Rocha, UN and Muehe, EM},
title = {Temporal decoupling of metal(loid) binding and microbial adaptation in arsenic and cadmium contaminated soils under changing climates.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140787},
doi = {10.1016/j.jhazmat.2025.140787},
pmid = {41391312},
issn = {1873-3336},
abstract = {Soil contamination with metals and metalloids is a growing environmental concern, impacting soil ecosystems. Exogenous metal(loid)s are retained in the soil matrix via adsorption, structural incorporation, and precipitation, imposing stress on soil microbiomes, potentially influenced by climate. It remains unclear whether introduced metal(loid)s bind similarly to native ones and how quickly soil microbiomes adapt under today's and future climate conditions. We incubated soils spiked with 0.7 mg kg[-1] cadmium or 15 mg kg[-1] arsenic under today's and future climate scenarios (IPCC SSP 3-7.0: +400 ppmv CO2, +4°C). After 38 days, spiked As and Cd did not integrate into soil minerals like native counterparts but preferentially associated with more reactive minerals. Spiked As became more recalcitrant over time, an effect enhanced under future conditions. Spiked Cd remained reactive during incubation, independent of climate conditions. Prokaryotic abundances increased faster in metal(loid)-spiked soil under future conditions with distinct soil prokaryotic community structures emerging in response to metal(loid)s and climate. Despite this, key functions like Fe(III) reduction were maintained. Communities nearly stabilized within 38 days across climate conditions. These findings suggest that exogenous metal(loid)s may require years to achieve native-level binding, while soil microbes adapt functionally within weeks, even under climate change.},
}

@article {pmid41391222,
year = {2025},
author = {García-Carmona, M and Sulbaran-Bracho, Y and Marín, C and Maldonado, JE and García-Orenes, F and Rojas, C},
title = {Organic amendments as a tool to restore soil microbial diversity after wildfires in native Mediterranean forests.},
journal = {Journal of environmental management},
volume = {397},
number = {},
pages = {128261},
doi = {10.1016/j.jenvman.2025.128261},
pmid = {41391222},
issn = {1095-8630},
abstract = {Wildfires are intensifying under climate change and increasingly compromising the resilience of Mediterranean ecosystems. Soil restoration through organic amendments has been proposed as an effective tool to mitigate soil degradation after fires, yet there is limited knowledge on how different typologies of organic amendments influence soil microbial communities and the recovery of microbial-mediated functions. This study evaluated contrasting organic amendments-straw mulch, compost, and fresh swine and poultry manures-on soil microbial diversity and enzymatic activity in burned native sclerophyllous, Mediterranean forest in central Chile, the earliest in its type experiencing effects of climate change. The study took place six months after amendment application and two years after a wildfire occurrence. Enzyme activities showed different responses according to organic amendments type: while manures strongly stimulate enzymes (urease, glucosidase, and phosphatase activities), compost and mulch promoted a gradual effect on nutrient cycling. Fungal biomass, reduced by fire, recovered best under compost and swine manure. However, organic amendments significantly reduced eukaryotic alpha diversity and differentiated communities from unburned soils and burned soils with no amendment. In contrast, only manures reduced alpha diversity in prokaryotes, while beta diversity analyses revealed that compost amended soils maintained communities closer to reference conditions. Overall, manures provided short-term functional improvements in burned soils, but compost supported a more balanced recovery, preserving microbial communities closer to unburned soils. Therefore, the compost amendment can represent a practical and ecologically safer strategy to accelerate post-fire soil restoration. Targeted application, for example through "fertile islands" in the most degraded areas, may enhance soil resilience while minimizing ecological risks in fire-sensitive landscapes.},
}

@article {pmid41389787,
year = {2025},
author = {Pei, J and Gong, J and Liu, Z and Jin, W and Hou, M and Abd El-Aty, AM and Deng, Q},
title = {High-throughput sequencing reveals microbial transitions in refrigerated sturgeon meat: Implications for quality assurance.},
journal = {International journal of food microbiology},
volume = {448},
number = {},
pages = {111542},
doi = {10.1016/j.ijfoodmicro.2025.111542},
pmid = {41389787},
issn = {1879-3460},
abstract = {This study investigated the microbially driven spoilage mechanism of sturgeon (Acipenser baerii) under refrigerated (4 °C) aerobic storage. High-throughput sequencing analysis revealed that Pseudomonas and Shewanella dominated late-stage spoilage, which was strongly positively correlated with volatile base nitrogen (VBN) accumulation and microbial metabolic shifts toward amino acid degradation pathways. By applying machine learning (random forest coupled with SHAP analysis, AUROC = 0.96) and graph neural networks (GAT, recall = 89.7 %), we pinpointed key spoilage-associated taxa and their interaction dynamics. Furthermore, numerous chemical descriptors have revealed that spoilage-associated enzymes present elevated molecular electrostatic potential (MEPs >25 kcal/mol), which facilitates the nucleophilic attack of amino acids and accelerates spoilage reactions. Time series forecasting (multivariate Prophet model) accurately predicted critical spoilage thresholds (96.5 ± 4.2 h postprocessing) with high accuracy (MAPE = 12.3 %). Additionally, metabolic modeling has demonstrated microbial cold-adapted energy strategies, including a significant increase in succinate fermentation flux (3.8 ± 0.5 mmol·g[-1] DW·h[-1]) and the suppression of TCA cycle activity. This study establishes a multiscale framework linking microbial ecology, enzymatic quantum mechanics, and metabolic dynamics, offering mechanistic insight into spoilage and providing a foundation for precise sturgeon preservation strategies in cold chain logistics.},
}

@article {pmid41389460,
year = {2025},
author = {Balaberda, AL and Escolástico-Ortiz, D and Martineau, C and Heshka, NE and Lindsay, MBJ and Degenhardt, D},
title = {Biogeochemical characterization of froth treatment tailings.},
journal = {Chemosphere},
volume = {394},
number = {},
pages = {144800},
doi = {10.1016/j.chemosphere.2025.144800},
pmid = {41389460},
issn = {1879-1298},
abstract = {Froth treatment tailings (FTT) are byproducts of bitumen extraction at oil sands mines in northern Alberta. Produced during froth treatment, where diluent such as naphtha is added to separate bitumen from water and solids, FTT contain residual hydrocarbons and sulfide minerals like pyrite, potentially posing reclamation challenges. This study investigated the spatial and vertical distribution of hydrocarbons and microbial communities across a transect of an FTT deposit at Syncrude's Mildred Lake Settling Basin. Residual naphtha and petroleum hydrocarbon (PHC) concentrations reflected deposition history, with higher concentrations near the pond and in deeper, older tailings at the dyke. Microbial diversity was lower in FTT than in underlying coarse tailings, with the lowest diversity observed at ∼30 m depth, likely due to moderate to high PHC concentrations, anoxic conditions, and nutrient limitations. Microbial community composition varied with depth, material type, and location, and FTT were enriched in taxa involved in hydrocarbon degradation (Pseudomonas), sulfur cycling (Thiobacillus, Desulfovibrio, Desulfotomaculales), and methanogenesis (Methanosaeta). Among hydrocarbons, toluene and ethylbenzene were strong predictors of microbial variation. Pyrite content also emerged as an important driver, likely due to its role in redox processes. These results highlight the close links between residual diluent, tailings geochemistry, and microbial ecology, emphasizing the importance of accurate FTT characterization to support closure landform design and inform future reclamation monitoring.},
}

@article {pmid41389450,
year = {2025},
author = {Mittal, A and Sharma, S},
title = {Gut microbiota and nutritional interventions in alcohol-associated liver disease: Mechanisms and therapeutic advances.},
journal = {Nutrition research (New York, N.Y.)},
volume = {145},
number = {},
pages = {8-24},
doi = {10.1016/j.nutres.2025.11.004},
pmid = {41389450},
issn = {1879-0739},
abstract = {Alcohol-associated liver disease (ALD) is a leading cause of liver-related morbidity and mortality worldwide. Despite growing awareness of its burden, treatment options remain limited, with abstinence as the only widely accepted intervention. Recent research underscores the critical role of the gut-liver axis and nutritional status, particularly dietary protein, in modulating ALD pathogenesis and progression. This review aims to integrate current knowledge on the interplay between gut microbiota, dietary protein, and alcohol-induced liver injury, and to evaluate microbiota-targeted therapeutic strategies, including fecal microbiota transplantation (FMT), within this context. We examine how chronic alcohol intake reshapes the gut microbiome, impairs barrier function, and alters microbial metabolism. We discuss how dietary protein, based on source, quantity, and amino acid composition, influences microbial ecology and metabolite profiles, with plant and dairy proteins emerging as beneficial. The review also highlights advances in FMT, which shows promise in improving outcomes in severe alcoholic hepatitis. However, its efficacy is modulated by donor microbial composition and recipient compatibility, both of which may be influenced by diet. Furthermore, we address emerging evidence on the role of fungal and viral communities, which remain understudied contributors to ALD. Despite substantial progress, significant knowledge gaps persist. These include the need for clinical validation of preclinical findings, deeper exploration of nonbacterial microbiota, and a lack of personalized, nutrition-based interventions. Addressing these gaps through integrative, multiomic approaches will be essential to advancing precision therapeutics in ALD.},
}

@article {pmid41388438,
year = {2025},
author = {Chiriac, MC and Layoun, P and Fernandes, C and Szőke-Nagy, T and Kasalicky, V and Okazaki, Y and Woodhouse, JN and Grossart, HP and Piwosz, K and Znachor, P and Sonntag, B and Callieri, C and Orlić, S and Sommaruga, R and Lepère, C and Biderre-Petit, C and Tammert, H and Herlemann, DPR and Ślusarczyk, M and Bednarska, A and Banciu, HL and Zalewski, M and Woźniczka, A and Ghai, R and Salcher, MM and Haber, M},
title = {Ecological success in freshwater lakes: insights from novel cultivated lineages of the abundant Nanopelagicales order.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02272-x},
pmid = {41388438},
issn = {2049-2618},
support = {24-12912M//Grantová Agentura České Republiky/ ; 22-03662S//Grantová Agentura České Republiky/ ; 22-33245S//Grantová Agentura České Republiky/ ; 20-12496X//Grantová Agentura České Republiky/ ; 21-21990S//Grantová Agentura České Republiky/ ; 022/2019/P//Grant Agency of the University of South Bohemia/ ; 017/2022/P//Grant Agency of the University of South Bohemia/ ; JPMJFR2273//JST FOREST/ ; 25K18161//Japan Society for the Promotion of Science/ ; GR1540/37-1//Leibniz-Institut für Gewässerökologie und Binnenfischerei/ ; KK.01.1.1.01.0003//European Regional Development Fund - the Operational Programme Competitiveness/ ; HRZZ IP-2020-02-9021//Croatian Science Foundation/ ; 760010/30.12.2022//Ministerul Cercetării şi Inovării/ ; },
abstract = {BACKGROUND: The order Nanopelagicales is the most abundant bacterioplankton lineage in freshwater lakes and exhibits typical streamlined genomic characteristics such as small cell volumes (<0.1 μm[3]), reduced genome sizes (<1.5 Mbp), and low GC content. These characteristics reflect adaptations to a free-living life strategy in oligotrophic environments. While many Nanopelagicales metagenome-assembled genomes and single-amplified genomes are available in public databases, strain-level microdiversity within this lineage remains poorly understood. This is mainly attributed to the incomplete nature of these genomes and the difficulty in isolating and maintaining pure cultures, with only 20 genome-sequenced cultures available to date.

RESULTS: Here, we report the isolation and genome analysis of 72 new Nanopelagicales strains, including members of Planktophila and a novel, previously uncultured genus, Aquilimus. High interspecific diversity and microdiversity were observed in the genus Planktophila, which likely facilitates the coexistence of closely related species within the same habitats by allowing fine-scale niche partitioning. The unusually high diversity of transporters for small organic compounds, along with carbohydrate-active enzymes, suggests that Planktophila members can degrade plant and algal polymers and import the resulting products to support growth. A notable finding is the repeated, independent loss of the oxidative phase of the pentose phosphate pathway in abundant Nanopelagicales species, which may represent an energy-saving adaptation in oligotrophic waters. Two species (Planktophila vernalis and Nanopelagicus abundans) seem to be equally abundant on a global scale, with water pH likely being the most significant factor influencing the predominance of one group over the other in different water bodies. Additionally, P. vernalis may tolerate periods of anoxia due to genomic encoding of respiratory nitrate reductase and nitrate/nitrite antiporters.

CONCLUSIONS: In conclusion, this work increased to a great degree the cultivated diversity of the abundant Nanopelagicales order. Analysis of over 1700 metagenomes showed that only a few cultivated species are globally dominant, and time-series analyses revealed consistent spring and autumn peaks. Key metabolic adaptations, such as loss of the oxidative phase of the pentose phosphate pathway and a high microdiversity of genes involved in cell surface biosynthesis and modifications, are likely to help these species survive periods of starvation and avoid predation. These findings highlight the ecological importance of Nanopelagicales and suggest that microdiversity underpins their adaptability. This work lays a foundation for studying their physiology, ecology, and strain-specific functional variation. Video Abstract.},
}

@article {pmid41388368,
year = {2025},
author = {Chen, Y and Nguyen, AD and Lunjani, N and Ndhlovu, G and Kaul, D and De Pessemier, B and Nakatsuji, T and Madzinga, M and Sovershaeva, E and Hlela, C and Levin, M and Mankahla, A and Hightower, G and Callewaert, C and Knight, R and Gallo, RL and Dupont, CL and Dube, F},
title = {Environmental and skin-nasal microbiome variation in South African children with atopic dermatitis.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04589-x},
pmid = {41388368},
issn = {1471-2180},
support = {HREC/REF: 451/2014/GF/NIH HHS/United States ; },
abstract = {BACKGROUND: Atopic dermatitis (AD) in early childhood is associated with microbial dysbiosis. Skin and nasal microbiomes have been linked to AD severity; this relationship has not yet been studied in an African cohort. Here, we aimed to explore how urban and rural stratification, disease severity, and inter-site bacterial overlap shape the skin and nasal microbiomes of South African children with AD.

METHODS: Children were recruited from urban Cape Town (CT) and rural Umtata (UM), South Africa. We profiled the skin and nasal microbiomes of 183 children (84 healthy controls and 99 with AD; ages 9-37 months), totaling 462 samples, including both lesional and non-lesional skin sites in children with AD, in a cross-sectional study design. Using 16S rRNA V4-V5 sequencing for its accessibility, we applied random forest (RF) models to classify AD status based on amplicon sequence variants (ASVs) and analyzed microbiome composition and diversity by region.

RESULTS: We found that RF models could predict AD status using both skin and nasal microbiomes (AUCs: skin = 0.69-0.79; nasal = 0.65), strongly driven by both Streptococcus and Staphylococcus. The correlations between skin and nasal microbiomes were significantly stronger in children with AD compared to controls, with higher correlations observed in rural UM (healthy r = 0.45 to AD r = 0.67) compared to urban CT (healthy r = 0.27 to AD r = 0.65). The skin microbiome diversity was higher in children from rural UM with healthy skin than in those from urban CT (p = 0.004). However, children with AD in both groups showed significant alterations in their microbiome, with those in rural UM exhibiting greater beta diversity changes (p = 0.001-0.002) than their urban CT counterparts (p = 0.002-0.349).

CONCLUSION: In South African children with AD, skin-nasal microbiomes reflect shared reservoirs, and differences in the AD microbiome were observed between environmental regions. These findings highlight the need for geographically diverse studies incorporating skin and mucocutaneous sampling to better understand pediatric AD.},
}

@article {pmid41387715,
year = {2025},
author = {Fundora, MP and Dressner, L and Calamaro, C and Brown, AM and John, AS and Keiffer, R and Alexander, N and Huang, H and Gillespie, S and Denning, PW and Sanders-Lewis, K and Bai, J},
title = {Association between the gut microbiome and neurodevelopmental outcomes in infants with congenital heart disease: A prospective cohort study.},
journal = {JPEN. Journal of parenteral and enteral nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1002/jpen.70038},
pmid = {41387715},
issn = {1941-2444},
support = {UL1-TR002378//The Imagine, Innovate and Impact (I3) Award from the Emory University School of Medicine, Georgia CTSA NIH award/ ; },
abstract = {BACKGROUND: Children with congenital heart disease are at risk for poor neurodevelopment. The gut microbiome may influence neurodevelopmental outcomes through the gut-brain axis. This study investigated the association of early-life gut microbiome with neurodevelopmental outcomes.

METHODS: A prospective cohort study was conducted in the cardiac intensive care unit. Fecal samples were collected before surgery, after surgery, and before discharge. Neurodevelopmental testing used Bayley Scales of Infant and Toddler Development between 9 and 12 months. Microbial data of the 16S ribosomal RNA V4 region were processed. Microbiome data were analyzed using Quantitative Insights Into Microbial Ecology 2 and MicrobiomeAnalyst 2.0.

RESULTS: Twenty-four patients were analyzed: 15 (62.5%) were male and 12 (50%) were White. Children with lower cognitive (Chao1 P = 0.024) and language scores (Chao1 P = 0.018) had lower alpha diversity; beta diversity showed marginally significant dissimilarities (Jaccard P = 0.102 and P = 0.051, respectively). Lower cognitive scores were associated with less Parabacteroides (P = 0.031), Bacteroides (P = 0.041), and Bifidobacterium (P = 0.047), and lower language scores were associated with less Bifidobacterium (P = 0.044) and Enterococcus (P = 0.024). Lower motor scores were associated with less Rothia (P = 0.017) but a higher abundance of Serratia (P < 0.001), Acinetobacter (P = 0.016), and Proteus (P = 0.013).

CONCLUSION: Children with congenital heart disease with lower cognitive and language scores had lower diversity and less anti-inflammatory flora (eg, Bifidobacterium), whereas those with lower motor scores had a higher abundance of pro-inflammatory flora (eg, Serratia, Acinetobacter, and Proteus). Further studies are needed to understand the longitudinal effect of gut microbial dysbiosis on neurodevelopment in children with congenital heart disease.},
}

@article {pmid41387646,
year = {2025},
author = {Crucitti, D and Carimi, F and Caruso, T and Pacifico, D},
title = {Microbial Allies in the Olive Canopy: Endophyte Composition, Drivers, and their Role in Plant Protection.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02676-0},
pmid = {41387646},
issn = {1432-184X},
abstract = {The olive tree (Olea europaea L.) hosts diverse endophytic microbial communities that contribute to its resilience, productivity, and adaptation to environmental stressors. Since the temperature increases caused by global climate change primarily affects the aerial part of the plant, this review synthesizes current knowledge on the diversity, composition, and ecological drivers of olive phyllosphere endophytes, with a focus on bacterial and fungal communities. We highlight the role of host-related factors-including plant genotype, organ specificity, age, and phenological stage-in shaping microbiota structure across spatial and temporal scales. Genotype consistently emerges as a major determinant of microbial composition, while leaves and twigs harbor distinct yet overlapping communities. Geographic location, environmental variables, and seasonal shifts significantly influence microbial assemblages, with closer sites often supporting more similar communities. We also discuss the impact of agricultural practices and biotic and abiotic stressors on microbiota stability and function. Notably, several cultivable taxa-including Bacillus, Paenibacillus, Pantoea, Aureobasidium, and Penicillium-exhibit antagonistic activity against key olive pathogens, underscoring their potential as biological control agents. We conclude by emphasizing the need for functional studies to elucidate the roles of keystone endophytes and to inform microbiome-based strategies for sustainable olive cultivation.},
}

@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.},
}