@article {pmid41798180, year = {2026}, author = {Cakin, I and Millington, R and Pawar, S and Buckling, A and Smirnoff, N and Padfield, D and Duffy, J and Yvon-Durocher, G}, title = {A novel method to simultaneously estimate bacterial respiration and growth from oxygen dynamics.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag024}, pmid = {41798180}, issn = {2730-6151}, abstract = {Bacterial growth and respiration are fundamental metabolic processes that drive energy transformation and allocation within organisms and impact carbon sequestration at the ecosystem scale. However, these traits are usually measured independently; bacterial growth is quantified with endpoint biomass measurements, while respiration is determined by monitoring oxygen or carbon dioxide. Because the two physiological traits are collected at different temporal and volumetric scales (hours-to-days for growth versus minutes-to-hours for respiration), reconciling them is challenging and often introduces scale-mismatch bias, obscuring causal links between metabolism and environmental drivers. In this study, we develop a novel method for quantifying the rates of bacterial growth and respiration from a single dissolved-oxygen time series. Our approach introduces a model that couples exponential biomass growth with biomass-specific respiration, enabling simultaneous inference of growth rate and respiration rate from each oxygen trajectory. We applied our high-throughput method to 15 bacterial taxa isolated from natural environments. Our approach yielded growth estimates in close agreement with measurements based on popular methods using optical density or flow cytometry ([Formula: see text] > 0.9) with no evidence of taxon-specific bias. We also tested our approach in quantifying the effects of temperature on respiration, growth, and carbon use-efficiency in Pseudomonas sp. Our method yielded typical unimodal thermal response curves for growth and respiration where rates were highest at moderate temperatures, while carbon use efficiency increased with temperature, peaked around the growth thermal optimum (∼30°C-35°C), and declined at the highest temperature. By quantifying respiration and growth within a single assay and in high throughput, our approach effectively enables measurement of microbial metabolic strategies and adaptations to stress. It offers a noninvasive and scalable tool for high-throughput phenotyping and studies of environmental perturbations, enabling a new class of trait-based microbial ecology that links cellular physiology to broader ecosystem function.}, }
@article {pmid41797016, year = {2026}, author = {Ghannem, S and Labiadh, H and Ishak, S and Louiz, S and Derguini, A and Idres, T and Grassi, E and Semprucci, F and Badraoui, R and Ben Hamadi, N and Chaudhary, AA and Alsalamah, SA and Bendif, H and Rebai, A and Boufahja, F}, title = {Investigation of the impacts of second-generation antihistamines on free-living marine nematodes and their interaction with ZnS nanoparticles: Mechanistic insights from community and population approaches and molecular interactions modeling.}, journal = {Marine environmental research}, volume = {217}, number = {}, pages = {107969}, doi = {10.1016/j.marenvres.2026.107969}, pmid = {41797016}, issn = {1879-0291}, abstract = {The current research investigates the impact of loratadine and its active metabolite desloratadine, applied at environmentally relevant concentrations (40 and 80 ng/L), using community-level, population-based, and molecular modeling approaches, on meiofauna from the Dammam coast, Saudi Arabia. The results indicate a significant reduction in the abundance of meiobenthic organisms, accompanied by a marked decline in nematode diversity across treatments, especially under combined exposures at higher concentrations. Additionally, trophic groups 1B and 2B, characterized by clavate tail morphologies, were the main contributors to the observed dissimilarity patterns across treatments. The mixture of 40 ng/L of antihistamines with ZnS nanoparticles (4.1 nm) enhanced catalase and GST activities in Metoncholaimus pristiurus. An increase in growth rate was also observed, along with larger pharyngeal lumens, suggesting higher food pumping under stress. Locomotion issues and decreased fertility are also suggested, with signs of masculinization. This highlights the intensified toxic effects of antihistamines following the addition of ZnS NPs. Overall, the findings suggest synergistic or additive interaction between loratadine, desloratadine, and ZnS nanoparticles. Their toxicokinetic properties, along with strong binding affinities and stable molecular interactions with GLD-3 and SDP receptors, provide a mechanistic basis and support ecotoxicological impacts of these antihistamines and ZnS NPs on nematodes.}, }
@article {pmid41795790, year = {2026}, author = {Özkan Vardar, D and Ekmen, B and Çalı, A}, title = {Interactions between polystyrene-derived micro- and nanoplastics and the microbiota: a systematic review of multi-omics mouse studies.}, journal = {Journal of environmental science and health. Part C, Toxicology and carcinogenesis}, volume = {}, number = {}, pages = {1-19}, doi = {10.1080/26896583.2026.2636868}, pmid = {41795790}, issn = {2689-6591}, abstract = {Micro- and nanoplastics (MNPs), especially polystyrene-derived particles (PS-MPs/PS-NPs), have become a growing concern due to their increasing presence in the environment and their proven biological toxicity. Although PS particles have been identified in various human tissues, including feces, placenta, and blood, their impact on the gut microbiota and microbiota-driven metabolic pathways remains insufficiently synthesized. This systematic review aims to compile current in vivo evidence from mouse studies to assess how PS-MP/NP exposure influences gut microbial diversity, taxonomic composition, microbial metabolites, and subsequent physiological outcomes. A PRISMA-guided literature search identified 15 controlled mouse studies published between 2010 and 2024. Across these studies, PS exposure consistently induced gut dysbiosis, characterized by reductions or shifts in alpha-diversity, distinct beta-diversity clustering, loss of beneficial commensals such as Lactobacillus, Bifidobacterium, and members of Ruminococcaceae, and enrichment of opportunistic or pro-inflammatory taxa including Proteobacteria, Helicobacter, and Staphylococcus. Notably, MNPs particles induced more pronounced microbial disruption than micro-sized forms. Overall, current experimental evidence indicates that PS-MPs/PS-NPs induce multidimensional toxicity by simultaneously disrupting gut microbial ecology and host metabolic pathways. These findings emphasize the need for standardized methodologies in microplastic research and highlight the importance of clarifying the long-term health effects of human exposure to micro- and nanoplastics.}, }
@article {pmid41794478, year = {2026}, author = {Chiarini, E and Buzzanca, D and Devizia, A and Giordano, M and Dipietro, F and Zeppa, G and Alessandria, V}, title = {Kombucha meets circular economy: A microbiome and metabolite perspective on second fermentation with plant by-products.}, journal = {Food research international (Ottawa, Ont.)}, volume = {230}, number = {}, pages = {118597}, doi = {10.1016/j.foodres.2026.118597}, pmid = {41794478}, issn = {1873-7145}, mesh = {*Fermentation ; *Microbiota ; *Kombucha Tea/microbiology/analysis/economics ; Food Microbiology ; Bacteria/metabolism/classification ; Yeasts/metabolism ; Volatile Organic Compounds/analysis ; Gas Chromatography-Mass Spectrometry ; }, abstract = {Kombucha is a traditional fermented beverage produced through the fermentation of sugared tea by a symbiotic culture of bacteria and yeasts (SCOBY). In recent years, the valorisation of plant-based by-products as fermentation substrates has gained attention as a sustainable approach to improving both the nutritional and economic efficiency of fermented beverages. The present study investigated the production of kombuchas supplemented with pineapple, fennel, and carrot by-products during the secondary fermentation phase, aiming to evaluate their influence on fermentation dynamics, microbial ecology, and the chemical and aromatic profiles of the final products. The experimental design integrated culture-dependent and culture-independent approaches, including amplicon sequencing, to characterize microbial community composition and evolution throughout fermentation. Chemical profiling was carried out using gas chromatography coupled with quadrupole mass spectrometry (GC-qMS) and high-performance liquid chromatography equipped with diode-array and refractive index detectors (HPLC-DAD/RI). The fermentation process was monitored during both the primary and secondary stages, and a shelf-life assessment was conducted over 14 days of refrigerated storage (4 °C) to evaluate product stability. Microbiological results indicated a predominance of Schizosaccharomyces spp., while Komagataeibacter spp. was the only bacterial genus identified. A significant reduction in α-diversity was observed over time, suggesting selective adaptation of the microbial community to the fermentation environment. β-diversity analysis revealed clear differences among samples collected after 8 and 22 days, reflecting the combined influence of time and substrate composition on microbial succession. Chemical analyses demonstrated an increase in acetic acid concentration and a progressive decline in pH throughout fermentation, consistent with the metabolic activity of acetic acid bacteria. Among volatile organic compounds (VOCs), alcohols and organic acids were the most abundant chemical classes detected. Several VOCs were associated with minor yeast genera, including Hannaella, Galactomyces, Aureobasidium, and Millerozyma, whereas Schizosaccharomyces spp. showed a strong correlation with specific aroma-active compounds, highlighting its key role in defining the sensory characteristics of the beverage. Overall, this study provides new evidence on how different vegetable by-products and microbial consortia influence the development of chemical and aromatic compounds in kombucha. The findings highlight the potential of using by-products as a sustainable, value-added strategy for producing fermented beverages, while also supporting the principles of the circular economy and resource-efficient food systems.}, }
@article {pmid41794468, year = {2026}, author = {Wang, A and Qiu, C and Tang, J}, title = {Multidimensional synergy between yeast and lactic acid bacteria: mechanisms, quality formation, and precision fermentation strategies.}, journal = {Food research international (Ottawa, Ont.)}, volume = {230}, number = {}, pages = {118586}, doi = {10.1016/j.foodres.2026.118586}, pmid = {41794468}, issn = {1873-7145}, mesh = {*Fermentation ; *Lactobacillales/metabolism/physiology ; Biofilms/growth & development ; *Microbial Interactions ; *Food Microbiology ; Quorum Sensing ; *Fermented Foods/microbiology ; *Yeasts/metabolism ; }, abstract = {The complex functional characteristics of fermented foods stem from dynamic microbial interactions rather than the activities of individual microorganisms. Traditional research has primarily focused on single-strain cultures and metabolic functions, whereas contemporary studies increasingly emphasize the pivotal role of interactions between different species in shaping fermentative ecosystems. This review explores the multifaceted interactions between yeast-lactic acid bacteria (LAB), focusing on three key aspects: (1) nutritional interactions and cross-feeding mechanisms; (2) molecular communication via metabolite exchange and quorum sensing; (3) collective adaptation strategies encompassing biofilm formation and environmental remodeling. Synergistic interactions promote metabolic complementarity, thereby enhancing substrate utilization efficiency and biosynthetic capacity beyond the limitations of single-strain cultures. Competitive interactions maintain ecological equilibrium within microbial communities while suppressing undesirable microorganisms. Quorum sensing mechanisms synchronize gene expression across entire populations, coordinating metabolic pathways and optimizing collective behavior. Biofilm formation creates structured microenvironments that enhance microbial resilience and metabolic specialization. Advanced methodologies, particularly multi-omics technologies and synthetic microbial ecology approaches, have become indispensable tools for unravelling these intricate interaction networks. Integrating genome-scale metabolic modelling with experimental validation offers unprecedented insights into the molecular mechanisms underpinning microbial interactions. This systems-level understanding enables the purposeful design of synthetic microbial communities and precise fermentation processes, highlighting the imperative shift from single-species optimization towards ecological management strategies. Future research should translate laboratory discoveries into industrial applications through standardized evaluation systems and dynamic regulatory strategies.}, }
@article {pmid41794110, year = {2026}, author = {Wei, C and Hu, J and Wang, X and Chen, Y and Zhang, S and Peng, Y}, title = {Optimization of sulfate-reducing ammonium oxidation based on N/S: nitrogen and sulfur removal performance, microbial community, and response surface methodology.}, journal = {Environmental research}, volume = {}, number = {}, pages = {124143}, doi = {10.1016/j.envres.2026.124143}, pmid = {41794110}, issn = {1096-0953}, abstract = {Sulfate-reducing ammonium oxidation (Sulfammox) offers a novel strategy for simultaneous nitrogen and sulfur removal. However, the microbial-driven metabolic pathways under different N/S and the optimal operational conditions remain unclear. This study operated three anaerobic sequencing batch reactors at N/S of 2.5, 2.0, and 1.5 to investigate the removal performance and microbial ecology. The reactor with an N/S of 1.5 (R3) achieved the highest removal efficiencies of 91.82% for NH4[+]-N and 47.95% for SO4[2-]-S, while the reactor with an N/S of 2.5 (R1) showed efficiencies below 15% for both, indicating that a lower N/S is critical for efficient removal. X-ray photoelectron spectroscopy confirmed the formation of elemental sulfur, indicating active sulfur transformation that alleviated sulfide inhibition and enhanced system stability. Batch tests identified optimal operating conditions: pH 8.0, hydraulic retention time 48 h, and COD 50 mg/L. When COD is greater than 300 mg/L, sulfate reduction dominated and inhibited the sulfammox process. Response surface methodology models (R[2]>0.98) predicted the optimal parameters in N/S 1.57, pH 7.66, HRT 46.53 h, and COD of 48.61 mg/L, achieving NH4[+]-N and SO4[2-]-S removal efficiencies of 93.13% and 47.35%. This represents 9.5% enhancement in NH4[+]-N removal over the pre-optimization phase. Microbial analysis revealed that N/S of 1.5 abundance of Desulfobacterota increased by 1.67%, driving sulfate reduction, while Chloroflexi constituted 26.07% in R3, the anammox bacterium Candidatus-Brocadia was inhibited, exhibiting a relative abundance of less than 0.1%. By elucidating sulfammox interactions, this study offers a practical, low-carbon and synergistic framework for the effective co-treatment of high NH4[+]-N and SO4[2-]-S wastewater.}, }
@article {pmid41792903, year = {2026}, author = {Liang, MQ and Yuan, L and Liu, QH and Wu, J and Liu, DF and Sheng, GP}, title = {Membrane perturbation by the last-resort antibiotic polymyxin B drives biphasic regulation of horizontal gene transfer.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag046}, pmid = {41792903}, issn = {1751-7370}, abstract = {Although it is increasingly recognized that anthropogenic chemicals modulate horizontal gene transfer (HGT), the nature of these interactions is often more complex than a simple promotion or inhibition. The potential for a single chemical to exert opposing, concentration-dependent effects represent a critical and less-explored frontier in microbial ecology. Here, we investigate the last-resort antibiotic polymyxin B, a membrane-targeting peptide, and reveal a concentration-dependent, biphasic regulation of plasmid conjugation. Sub-inhibitory concentrations (0.125-0.5 mg/L) consistently inhibited the transfer of antibiotic resistance genes (ARGs) by up to 65.4%, whereas bactericidal concentrations (≥ 1 mg/L) strongly promoted it by up to 15.9-fold. This regulatory switch is driven by distinct physiological states: low-level exposure triggers defensive responses including reduced membrane permeability, whereas high-level exposure causes catastrophic membrane damage, inducing a synergistic stress response involving oxidative damage (>2-fold ROS increase) and a surge in cellular energy (up to 83.0% ATP increase) that facilitates HGT. High-concentration polymyxin B also promotes plasmid transfer in complex microbial communities derived from activated-sludge biofilms. Our findings reveal a new paradigm for the interaction between chemical stressors and microbial evolution, demonstrating that the ecological impact of contaminants on HGT cannot be predicted by monotonic models and highlighting the role of environmental hotspots in shaping the dissemination of antibiotic resistome.}, }
@article {pmid41791723, year = {2026}, author = {Raj, A and Pant, A and Kumar, A and Kumar, A and Kalamdhad, AS and Khwairakpam, M}, title = {Systems-Level Insights Into Microbial Naphthalene Biodegradation: An Integrated In Silico and Omics Perspective.}, journal = {Environmental microbiology}, volume = {28}, number = {3}, pages = {e70264}, doi = {10.1111/1462-2920.70264}, pmid = {41791723}, issn = {1462-2920}, support = {IITG/R&D/IPDF/2024-25/20240815P852//Indian Institute of Technology Guwahati/ ; }, mesh = {*Naphthalenes/metabolism ; Biodegradation, Environmental ; *Bacteria/metabolism/genetics ; Systems Biology ; Computer Simulation ; *Environmental Pollutants/metabolism ; Microbial Consortia ; }, abstract = {Naphthalene, a widely detected polycyclic aromatic hydrocarbon (PAH), is among the 16 priority PAHs identified as major environmental hazards due to its persistence, ubiquity, and toxicity to ecosystems and human health. Its occurrence in crude oil, combustion residues, vehicle emissions, and household products highlights the urgent need for sustainable remediation strategies. Microbial-based bioremediation stands out as an eco-friendly and cost-effective approach that harnesses the metabolic versatility of diverse microorganisms, their genes, and enzymes responsible for naphthalene degradation. Recent advances in omics technologies and high-throughput sequencing have expanded our understanding of novel microbial taxa, metabolic pathways, and stress responses under naphthalene exposure. Complementarily, computational modelling, in silico tools, machine learning, and systems biology have enabled the prediction of degradation dynamics and the design of synthetic microbial consortia optimised for field use. Despite these advances, challenges such as environmental fluctuations, co-contaminant effects, and the gap between laboratory and field outcomes remain. Overcoming these requires an integrative framework that connects microbial ecology, omics insights, and computational modelling. This review consolidates current knowledge on microbial degradation of naphthalene, emphasising key taxa, genes, and pathways, and highlights how omics, in silico tools and systems biology can drive sustainable remediation in the Anthropocene.}, }
@article {pmid41790321, year = {2026}, author = {Sahoo, A and Maity, A and Das, B and Paul, RC and Paul, P and Chakraborty, P and Chaudhuri, BN and Ghosh, MM and Das, S and Tribedi, P}, title = {Combined application of Vancomycin and Levofloxacin potentiates the antimicrobial activity against MRSA: a response surface methodology-based study.}, journal = {Folia microbiologica}, volume = {}, number = {}, pages = {}, pmid = {41790321}, issn = {1874-9356}, support = {TNU/R&D/MG/24/02//The Neotia University, India/ ; TNU/R&D/MP/2021/010//The Neotia University, India/ ; }, }
@article {pmid41789424, year = {2026}, author = {Katrak, C and Reed, S and Carter, M and Khatib, M and Peterson, A and Martin, K and Kajfasz, JK and Abranches, J}, title = {Oral hygiene agents at work: effects on Streptococcus mutans and caries risk.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1768512}, pmid = {41789424}, issn = {2235-2988}, mesh = {Humans ; *Dental Caries/prevention & control/microbiology ; *Streptococcus mutans/drug effects/physiology/growth & development ; Biofilms/drug effects/growth & development ; *Oral Hygiene/methods ; Probiotics/pharmacology ; Dental Plaque/microbiology/prevention & control ; Chlorhexidine/pharmacology/therapeutic use ; Hydrogen Peroxide/pharmacology ; Fluorides/pharmacology/therapeutic use ; Prebiotics ; Zinc/pharmacology ; }, abstract = {Dental caries remains one of the most prevalent chronic polymicrobial diseases worldwide, driven by acidogenic and aciduric bacteria, most notably Streptococcus mutans, that thrive within oral biofilms. Conventional strategies for caries prevention rely on mechanical plaque removal combined with agents that inhibit bacterial growth, disrupt biofilm formation, or enhance enamel remineralization. Here, we synthesize current evidence regarding a range of key agents that are incorporated into modern oral hygiene products. In addition to describing the mechanisms and efficacy of these agents, we describe their distinct biochemical and ecological effects on S. mutans metabolism, acid tolerance, and biofilm development. The agents that are relevant in the present day include fluoride, hydrogen peroxide, chlorhexidine, zinc, prebiotics (such as arginine and xylitol), and probiotics. Fluoride remains the cornerstone of caries prevention through its dual effects on enamel fluorapatite formation and inhibition of bacterial glycolysis, while chlorhexidine and hydrogen peroxide provide broad-spectrum antimicrobial activity. Zinc exhibits multifaceted roles in metabolic inhibition and plaque reduction, whereas pre- and probiotics aim to restore ecological balance by favoring health-associated commensal species. Finally, the review highlights evidence supporting combinatorial and synergistic use of these agents, particularly fluoride pairings, which may yield additive or enhanced protective effects. Understanding the molecular mechanisms that drive the efficacy of these compounds and gaining insight into cumulative influence on oral microbial ecology will drive the development of future treatment strategies.}, }
@article {pmid41788582, year = {2026}, author = {Wang, E and Chen, C and Li, Q}, title = {Current obstacles for continuous cropping of Panax species and mitigation strategies.}, journal = {Journal of ginseng research}, volume = {50}, number = {2}, pages = {100925}, pmid = {41788582}, issn = {1226-8453}, abstract = {Panax species-represented here by Panax ginseng Meyer, Panax quinquefolius L., and Panax notoginseng (Burk.) F. H. Chen-are valued for their saponins and polysaccharides and thus have significant clinical and commercial value. Rising global demand has driven intensive, large-scale cultivation, but repeated monoculture has produced persistent continuous cropping obstacles that now threaten the sustainability of the industry. These obstacles are not attributable to a single factor. Rather, they arise from interacting processes including degradation of soil physical and chemical properties, accumulation of plant-derived toxins that inhibit growth (allelopathic autotoxicity), and shifts in the soil microbial community that impair soil health and plant resilience. Together, these changes lead to stunted growth, reduced yields, and increased disease incidence. This review synthesizes recent advances in understanding continuous cropping obstacles in Panax species. It evaluates evidence for the primary causal factors, assesses current mitigation strategies, and highlights areas where findings are robust or still uncertain. By integrating soil science, plant physiology, and microbial ecology, the review identifies practical approaches already in use and emerging technologies with potential to improve outcomes. Finally, we identify critical knowledge gaps and outline priority directions for future research aimed at clarifying mechanisms and translating that knowledge into an effective management framework. The ultimate goal is to provide a theoretical basis to guide the development of scalable, evidence-based practices that alleviate continuous cropping obstacles in the cultivation of Panax species.}, }
@article {pmid41788258, year = {2026}, author = {Keles, E and Celik, O}, title = {Metagenomic and microbiological analyses of historical manuscripts for bacterial community profiling and bacteria-related biodeterioration assessment.}, journal = {Microbial cell (Graz, Austria)}, volume = {13}, number = {}, pages = {117-130}, pmid = {41788258}, issn = {2311-2638}, abstract = {Bacteria are important agents in the biodeterioration of cultural heritage objects, including historical manuscripts. Characterizing bacterial communities and generating robust microbiological data has therefore become crucial for conservation and restoration strategies. In this study, we investigated the bacterial communities associated with biodeterioration in six historical manuscripts using both culture-dependent and culture-independent (Illumina MiSeq) approaches. Culture-dependent methods yielded only 16 viable and culturable isolates, highlighting the limitations of traditional techniques. In contrast, metagenomic analysis revealed a far richer and more diverse bacterial community, capturing both living and non-living microbial traces accumulated over centuries. Bacterial genera with known cellulolytic and/or proteolytic activities, such as Bacillus, Stenotrophomonas, Pseudomonas and Acinetobacter, were identified as part of a core microbiome commonly associated with paper deterioration. High abundances of gut-associated bacteria (Prevotella, Faecalibacterium, Bacteroides, Porphyromonas) and human-related taxa (Staphylococcus, Streptococcus, Cutibacterium) indicated extensive historical human handling. A notable finding was the detection of Pseudonocardia broussonetiae, an endophytic bacterium associated with paper mulberry (Broussonetia papyrifera), suggesting the possible use of this plant as a papermaking material in one manuscript. This represents an important contribution to understanding Islamic paper production. Overall, our results demonstrate that effective conservation strategies require a detailed understanding of each manuscript's microbial ecology, together with evidence of past environmental conditions, handling history, and production materials.}, }
@article {pmid41787281, year = {2026}, author = {Van Rossum, U and Heyndrickx, M and Rasschaert, G and Demaître, N and Sadiq, FA and Boon, N and Cools, A and De Reu, K}, title = {Hidden threats: exploring biofilm communities in broiler houses and pig nursery units drinking water lines.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-04790-6}, pmid = {41787281}, issn = {1471-2180}, support = {HBC.2021.1060//VLAIO-LA/ ; }, }
@article {pmid41787131, year = {2026}, author = {Stanovcic, S and Milisavljevic, M and Azanjac, N and Kojic, S and Kojic, M}, title = {Biomolecules Generated During Programmed Cell Death (PCD) Enhance the Capacity of Proliferating Ustilago maydis Cells to Overcome the Negative Impacts of Non-PCD Necromass.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02736-z}, pmid = {41787131}, issn = {1432-184X}, support = {7730230//Science Fund of the Republic of Serbia/ ; }, }
@article {pmid41786226, year = {2026}, author = {Li, Y and Wang, WJ and Zhang, S and Luo, Q and Qian, NF and Chen, DZ and Jin, RC and Feng, LJ and Yang, GF}, title = {Chaotic effects in completely autotrophic nitrogen removal over nitrite process: how minor dissolved oxygen variations reshape microbial community and functional genes to drive divergent nitrogen removal.}, journal = {Bioresource technology}, volume = {448}, number = {}, pages = {134333}, doi = {10.1016/j.biortech.2026.134333}, pmid = {41786226}, issn = {1873-2976}, abstract = {To elucidate how dissolved oxygen (DO) regulates nitrogen removal in the completely autotrophic nitrogen removal over nitrite (CANON) process, three continuous-flow reactors were operated under micro-aerobic conditions. Results revealed that minor DO variations (0.36-0.51 mg/L) triggered dramatic bifurcation in performance and microbial ecology, demonstrating chaotic effects characterized by nonlinear dynamics and sensitive dependence on initial conditions. A superior total nitrogen removal rate of 0.38 kg/m[3]/d and a NH4[+]-N removal efficiency of 86.7% were achieved at 0.36 mg/L DO. However, a slight increase to 0.51 mg/L DO significantly enhanced nitrite-oxidizing bacteria (NOB) activity and nitrate accumulation. Lower DO favored anammox bacteria and their essential genes (hzs/hdh), while elevated DO promoted NOB competition and oxidative stress responses, evidenced by Fe-Mn SOD gene upregulation and altered extracellular polymers composition. Our findings establish a direct link between minor DO fluctuations and macro-scale functional outcomes, providing a mechanistic framework for predicting and controlling CANON process.}, }
@article {pmid41778806, year = {2026}, author = {Wasson, PA and McRose, DL}, title = {Nitrous oxide produced by denitrifying pseudomonads inhibits the growth of rhizosphere bacteria by inactivating the cobalamin-dependent methionine synthase.}, journal = {mBio}, volume = {}, number = {}, pages = {e0269925}, doi = {10.1128/mbio.02699-25}, pmid = {41778806}, issn = {2150-7511}, abstract = {Microbial communities are shaped by complex metabolic interactions, whereby the byproducts of one organism influence the physiology of others. This is exemplified in the microbial nitrogen cycle, where diffusion of free intermediates can drastically reshape the chemical landscape of the environment. One such intermediate, nitrous oxide (N2O), is often overlooked as biologically inert. However, emerging evidence suggests this gas may inhibit the activity of some cobalamin-dependent enzymes through a reaction with the cofactor. This raises the possibility that, through such an interaction, N2O-producing organisms may shape the microbial communities in which they reside, selecting against organisms that rely on these sensitive cobalamin enzymes. At the plant root, a hotspot of microbial activity, the impact of such interactions may be especially important. To investigate this, we focused on microbial N2O production and its effect on methionine biosynthesis, a ubiquitous bacterial process carried out by cobalamin-dependent (MetH) or independent (MetE) methyltransferases. In this study, we show that deleting metE and forcing reliance on MetH sensitizes the denitrifier Pseudomonas aeruginosa to exogenous and self-produced N2O. We extend these findings to plant-associated bacteria, where we find that a significant portion of an Arabidopsis thaliana rhizosphere culture collection relies exclusively on cobalamin-dependent methionine synthases and experimentally demonstrate their sensitivity to N2O. Finally, we show that the growth of one MetH-reliant rhizosphere isolate is suppressed in co-culture with N2O-producing P. aeruginosa. Together, these findings suggest that N2O producers can shape microbial ecology at the plant root.IMPORTANCEMicrobes that live on plant roots can make important contributions to plant health and often exist in tight-knit communities held together by chemical exchanges. This study investigates an interaction between two such metabolites: the climate-active gas nitrous oxide (N2O) and cobalamin. N2O can become toxic through a reaction with methionine synthase enzymes that use cobalamin as a cofactor. We asked whether the production of N2O by some bacteria curtails the growth of others that rely on these enzymes. Using genetic mutants of a model bacterium and natural isolates from the roots of the plant Arabidopsis thaliana, we showed that N2O-producing microbes suppress growth of their sensitive neighbors and that N2O sensitivity is common in rhizosphere bacteria. As natural and agricultural soils periodically experience bursts of N2O, our results suggest that exposure to this gas may shape the assembly of plant-beneficial microbial communities.}, }
@article {pmid41786065, year = {2026}, author = {Wang, X and Liu, R and Liu, J and Lin, Y and Zhou, M}, title = {Gut microbiota-derived indole metabolites in depression: mechanisms and therapeutic potential.}, journal = {European journal of pharmacology}, volume = {}, number = {}, pages = {178720}, doi = {10.1016/j.ejphar.2026.178720}, pmid = {41786065}, issn = {1879-0712}, abstract = {Depression, a prevalent neuropsychiatric disorder with complex pathophysiology and often insufficient treatment efficacy, is increasingly associated with disruptions in the gut-brain axis. This review focuses on the underappreciated role of the microbial indole pathway, a key route in tryptophan metabolism orchestrated by the gut microbiota. We synthesize recent evidence demonstrating that gut microbiota-derived indole metabolites, such as indole-3-propionic acid (IPA) and indole-3-aldehyde (IAld), are significantly reduced in depression. These metabolites exert multifaceted antidepressant effects by enhancing intestinal and blood-brain barrier integrity, suppressing neuroinflammation, and promoting neuroplasticity. Furthermore, we explore the therapeutic potential of targeting this axis through interventions like specific probiotics, prebiotics, dietary modifications, and fecal microbiota transplantation to restore microbial ecology and indole metabolite levels. By highlighting the microbiota-indole-brain pathway as a critical mechanistic and therapeutic frontier, this review provides a novel perspective on the pathogenesis and treatment of depression, moving beyond conventional monoaminergic theories.}, }
@article {pmid41785727, year = {2026}, author = {Wang, C and Luo, M and Chen, Q and Zheng, L and Jiang, T and Dai, M}, title = {Hedyotis diffusa Willd. extract alleviates CCl4-induced liver fibrosis via modulation of the gut microbiota and FXR/SHP/CYP7A1-mediated bile acid metabolism.}, journal = {Journal of ethnopharmacology}, volume = {363}, number = {}, pages = {121450}, doi = {10.1016/j.jep.2026.121450}, pmid = {41785727}, issn = {1872-7573}, abstract = {Liver fibrosis is a critical stage in the progression of chronic liver diseases, yet effective therapeutic agents are limited. Hedyotis diffusa Willd., a traditional Chinese medicine herb with heat-clearing and detoxifying properties, has long been used to treat inflammatory disorders, hepatic dysfunction and malignancies. Although accumulating studies suggest that Hedyotis diffusa Willd. Extract (HDW) possesses hepatoprotective and antifibrotic potential, the underlying mechanisms, particularly those involving gut microbiota and bile acid (BA) metabolism along the gut-liver axis, remain largely undefined.<br><br>AIM OF THE STUDY: To investigate the protective effects of HDW against carbon tetrachloride (CCl4)-induced liver fibrosis in mice, and to determine whether its antifibrotic efficacy is mediated by modulation of the gut microbiota-bile acid-FXR/SHP/CYP7A1 axis.<br><br>MATERIALS AND METHODS: Liver fibrosis was induced by intraperitoneal injection of 10% CCl4 in olive oil for five weeks. Histopathological changes were evaluated using H&amp;E, Sirius red and Masson staining. Liver function was assessed using serum levels of ALT, AST, ALP and &#x3b3;-GT. Collagen deposition was evaluated by measuring hepatic hydroxyproline (HYP) and fibrosis-related markers (HAase, IV-C, LN and PC-III). Activation of hepatic stellate cells was determined by &#x3b1;-SMA and Col1a1 expression. The composition of the gut microbial was profiled using 16&#xa0;S rRNA sequencing, and the necessity of gut microbiota for HDW efficacy was evaluated through an antibiotic (ABX) cocktail intervention. Targeted BA metabolomics quantified BA profiles, while RT-qPCR and Western blotting evaluated FXR/SHP/CYP7A1 pathway activity. Intestinal barrier integrity was assessed by villus morphology, tight junction protein levels (Claudin-1, ZO-1, Occludin), and serum lipopolysaccharide (LPS).<br><br>RESULTS: HDW treatment markedly alleviated CCl4-induced liver fibrosis, demonstrated by improved hepatic architecture, reduced serum transaminases and ALP/&#x3b3;-GT, decreased hydroxyproline levels, and downregulation of &#x3b1;-SMA and Col1a1. HDW reshaped the gut microbial composition by enriching beneficial taxa, whereas ABX treatment markedly attenuated its antifibrotic effects, indicating that the therapeutic action of HDW is largely microbiota-dependent. HDW restored BA homeostasis and significantly increased fecal odeoxycholic acid. Consequently, hepatic FXR/SHP/CYP7A1 signaling was upregulated at both the mRNA and protein levels. Furthermore, HDW strengthened the intestinal epithelial barrier by enhancing tight junction integrity and reducing serum LPS.<br><br>CONCLUSION: HDW exerts significant antifibrotic effects in CCl4-induced liver fibrosis via a gut microbiota-dependent mechanism involving the restoration of BA metabolism and the activation of the hepatic FXR/SHP/CYP7A1 axis. Given its ability to modulate gut microbial ecology, BA homeostasis and intestinal barrier integrity simultaneously, HDW is a promising therapeutic candidate for targeting the gut microbiota in the treatment of liver fibrosis.}, }
@article {pmid41785576, year = {2026}, author = {Poirier, S and Rondeau-Leclaire, J and Faticov, M and Roy, A and Lajeunesse, G and Lucier, JF and Tardif, S and Kembel, SW and Ziter, C and Laprise, C and Paquette, A and Girard, C and Laforest-Lapointe, I}, title = {Season and city shape urban bioaerosol composition beyond vegetation and socioeconomic gradients.}, journal = {The Science of the total environment}, volume = {1023}, number = {}, pages = {181623}, doi = {10.1016/j.scitotenv.2026.181623}, pmid = {41785576}, issn = {1879-1026}, abstract = {Urban vegetation varies with socio-economic gradients, as lower-income neighborhoods often host sparser and less diverse green spaces. This disparity may affect respiratory health by influencing exposure to bioaerosols. Understanding the characteristics of this aerobiome could help anticipate risks related to allergies and other respiratory conditions. Here, we hypothesized that urban vegetation cover and socio-economic status shape urban bioaerosol dynamics. We sampled bioaerosols at 65 sites across three Canadian cities of varying population size and density using an active air sampler over four months, and characterized their bacterial, fungal, and plant particles composition using amplicon sequencing. Seasonal alpha diversity varied significantly for fungi and plant particles. Based on beta diversity, sampling period alone explained up to 40% of plant particle, 29% of fungal, and 11% of bacterial bioaerosol composition variation. In contrast, vegetation cover explained only a minor portion of the variance in bioaerosol composition, and median household income, almost none. These findings provide a critical baseline for understanding the urban aerobiome and highlight the need to study how vegetation identity and diversity, rather than cover alone, may shape bioaerosol dynamics in cities. As cities grow and urban greening initiatives expand, demystifying the aerobiome dynamics becomes an urgent public health priority.}, }
@article {pmid41782409, year = {2026}, author = {Yang, J and Xiao, Y and Cui, J and Song, R and Ma, W and Liu, J and Miao, C and Sun, X and Kong, X and Zhang, ZS and Zhou, L and Yao, Z and Wang, Q}, title = {A 4-guanidinobutanoic acid-SLC36A1 axis drives a microbiota‒host feedback loop to regulate intestinal homeostasis.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2639216}, doi = {10.1080/19490976.2026.2639216}, pmid = {41782409}, issn = {1949-0984}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/physiology ; Humans ; Mice ; Homeostasis ; *Intestinal Mucosa/metabolism/microbiology/drug effects ; *Guanidines/metabolism/pharmacology ; Colitis, Ulcerative/microbiology/metabolism ; Mice, Inbred C57BL ; Bacteroides/metabolism ; *Butyrates/metabolism ; Disease Models, Animal ; Stem Cells/metabolism ; Feedback, Physiological ; *Amino Acid Transport System y+/metabolism/genetics ; Akkermansia ; }, abstract = {The role of gut microbiota‒derived metabolites in regulating the intestinal mucosal barrier remains poorly defined. Here, we identified 4-guanidinobutanoic acid (4-GBA), produced by Bacteroides stercorirosoris, as a critical regulator of intestinal homeostasis. Using untargeted metabolomics, organoid co-cultures, mouse models, and single-cell RNA sequencing, we demonstrated that 4-GBA enhances intestinal stem cells (ISCs) function and goblet cell differentiation. This promotes Akkermansia muciniphila enrichment through mucus-dependent niche expansion, establishing a microbiota‒host feedback loop. Mechanistically, 4-GBA upregulates the proton-coupled amino acid transporter SLC36A1 and activates the Hedgehog signaling pathway to drive epithelial reprogramming. Clinically, SLC36A1 expression inversely correlates with ulcerative colitis (UC) severity in human samples. Furthermore, the SLC36A1 agonist sarcosine enhances barrier homeostasis and attenuates colitis in mice, highlighting the diagnostic and therapeutic potential of this axis in UC. Our findings reveal a novel microbiome-host axis through which a microbial metabolite modulates epithelial function and microbial ecology, offering a potential therapeutic strategy targeting microbiota-epithelial crosstalk for UC management.}, }
@article {pmid41781688, year = {2026}, author = {Cinek, O and Hubáčková, K and Litošová, K and Hlináková, L}, title = {Heterogeneity Primer Spacers Improve the Performance of Massively Parallel Amplicon Sequencing of the V3-V4 Region of the 16 S rDNA as well as the 18 S Region for Blastocystis Subtyping.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02708-3}, pmid = {41781688}, issn = {1432-184X}, }
@article {pmid41779172, year = {2026}, author = {Roldán, DM and Carrizo, D and Sánchez-García, L and Menes, RJ}, title = {Temperature Response of Aerobic Methane-Oxidizing Bacteria in Lake Sediments from King George Island, Maritime Antarctica.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02717-2}, pmid = {41779172}, issn = {1432-184X}, }
@article {pmid41779071, year = {2026}, author = {Lygis, V and Marčiulynas, A and Plepytė, T and Šulčius, S and Menkis, A}, title = {Metabarcoding Reveals Rich and Diverse Aeromycobiota in Protected Oak Forests.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02714-5}, pmid = {41779071}, issn = {1432-184X}, abstract = {Old-growth oak (Quercus robur) forests in Europe are biodiversity hotspots, yet their airborne fungal diversity remains poorly studied. We investigated aeromycobiota in three Lithuanian oak stands (Punia, Dūkštos and Šilinė) using passive spore traps combined with DNA metabarcoding. Weekly sampling between August and September 2022 yielded 75 spore samples, producing 262,755 high-quality fungal sequences clustered into 1,881 operational taxonomic units (OTUs) representing six phyla and 36 classes. Ascomycota (53.1% of OTUs) and Basidiomycota (44.3%) dominated in richness, while Basidiomycota prevailed in relative sequence abundance (62.8%). Major taxa included Exobasidiaceae sp., Cladosporium sp., Melampsora sp., and Thelephora terrestris. Airborne fungal communities exhibited a substantial core assemblage shared among stands, accompanied by stand-associated differences in species richness and relative sequence abundance. The Punia stand showed the highest richness and the greatest proportion of stand-specific OTUs. Temporal variation was detectable but moderate relative to spatial differences among stands. Functional guild analysis revealed dominance of saprotrophs (46.5% of assigned OTUs), followed by pathotrophs (14.5%) and symbiotrophs (13.2%). Overall, our results demonstrate that passive spore traps-based airborne metabarcoding captures high fungal diversity and resolves both widespread and stand-associated community patterns in old-growth oak forests. This study provides the first characterization of aeromycobiota in old-growth Q. robur forests of Northern Europe and highlights the value of airborne metabarcoding for fungal biodiversity assessment and long-term forest monitoring.}, }
@article {pmid41777393, year = {2026}, author = {Zhang, B and Liu, Y and Zhou, D and Lv, Y and Cao, M and Li, H and Yang, Z and Liu, Z and Yin, H and Wang, X and Huang, Z and Meng, D}, title = {The role of quorum sensing in rhizosphere community regulation during bacterial wilt pathogen invasion.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1685007}, pmid = {41777393}, issn = {1664-462X}, abstract = {Bacterial wilt, caused by the soil-borne pathogen Ralstonia solanacearum is a major threat to solanaceous crops worldwide. The onset of this disease is frequently associated with disruptions in the rhizosphere microbial community. Quorum sensing (QS), a key mechanism for microbial communication, plays a critical role in regulating microbial interactions and maintaining community structure. However, whether and how QS is involved in reshaping the rhizosphere microbiome during R. Solanacearum infection remains poorly understood. In this study we compared QS-related genes, signaling pathways, and network structures in metagenomes of healthy and wilt-infected rhizospheres. The results show QS-related genes of the plant beneficial bacterial were significantly down-regulate, whereas QS-related genes of pathogenic R. Solanacearum were up-regulated in wilt-infected rhizosphere. The up-regulated QS genes of pathogens belong to eight QS signaling pathways (AI-1, GABA, PapR, NprX, Phr, cCF10, and DSF). Network analysis showed a simplified structure in the wilt-infected rhizosphere. It is also found the number of connectors in the QS gene co-occurrence network was reduced in wilt-infected rhizosphere network. This is due to the upregulation of QS system allows the pathogen to mediate the rhizosphere microbial ecology network, and leads to destabilization of rhizosphere community. These findings demonstrate that QS system contributes to bacterial wilt infection by suppressing the QS-based interactions among plant beneficial microbes, thereby triggering community function disruption.}, }
@article {pmid41776739, year = {2026}, author = {Tang, X and Liu, H and Qin, P and Wang, T and Du, W and Zhang, M and Zhu, M and Feng, J}, title = {Identification and Fungicide Efficacy of Leaf Spot on Euonymus fortunei Caused by Alternaria alternata in China.}, journal = {Plant disease}, volume = {}, number = {}, pages = {}, doi = {10.1094/PDIS-01-26-0167-RE}, pmid = {41776739}, issn = {0191-2917}, abstract = {Leaf spot disease has recently emerged on Euonymus fortunei in Shanxi Province, China, causing noticeable foliar lesions and reducing ornamental value. The causal agent was identified as Alternaria alternata based on morphological characteristics and multilocus phylogenetic analysis using five loci (Alt a1, gapdh, RPB2, ITS, and OPA10-2). Biological characterization showed that mycelial growth was optimal at 27 ℃ on oatmeal agar, whereas conidial germination was favored under alkaline conditions (pH 9.0). The pathogen was sensitive to NaCl stress but showed no significant response to different light regimes. In vitro fungicide sensitivity assays revealed marked differences in inhibitory efficacy between mycelial growth and conidial germination, indicating strong developmental stage-dependent responses. Certain fungicide mixtures exhibited enhanced inhibitory effects compared with single compounds, suggesting potential synergistic interactions. Microscopic observations further revealed fungicide-induced morphological abnormalities, including hyphae swelling, roughened surfaces, reduced sporulation, and deformation of conidial germ tubes. This study represents the first report of A. alternata causing leaf spot disease on E. fortunei in China and provides a basis for understanding pathogen biology and developing effective chemical management strategies for this emerging ornamental disease.}, }
@article {pmid41774190, year = {2026}, author = {Noirungsee, N and Pitaktham, T and Nakkaew, A and Chantanaorrapint, S and Klinnawee, L}, title = {Microbial Communities of the Mycoheterotrophic Plant Thismia Gardneriana in a Lowland Tropical Rainforest of Southern Thailand.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02727-0}, pmid = {41774190}, issn = {1432-184X}, support = {N25A650472//National Research Council of Thailand/ ; }, }
@article {pmid41773092, year = {2026}, author = {Lamanna, OK and Hu, R and Khemmani, M and Wolfe, AJ and Groah, SL and Forster, CS}, title = {Differential Effects of Uropathogenic and Non-Uropathogenic E. coli on the Mouse Urobiome and Urine NGAL Levels.}, journal = {Research and reports in urology}, volume = {18}, number = {}, pages = {580953}, pmid = {41773092}, issn = {2253-2447}, abstract = {OBJECTIVE: To determine whether urine neutrophil gelatinase-associated lipocalin (uNGAL) or urobiome alterations can differentiate urinary tract infections (UTI) from asymptomatic bacteriuria (ASB).<br><br>METHODS: Female 8-week-old C57BL/6 mice were instilled with either Escherichia coli CFT073 (UTI model, n=12), E. coli 83972 (ASB model, n=12), or saline (control, n=3). uNGAL was measured daily for 3 days post-instillation. Urobiome composition was assessed pre- and post-instillation using 16S rRNA sequencing. At day 3, kidneys were harvested for culture. Comparisons were made across groups for uNGAL levels and urobiome diversity.<br><br>RESULTS: Baseline &#x3b2; diversity did not differ between groups. Post-instillation, &#x3b2; diversity significantly differed across groups (p=0.01), driven by increased relative abundance of E. coli in UTI mice compared to ASB mice. Median uNGAL levels increased significantly in both UTI and ASB groups relative to controls, but no significant difference was observed between UTI and ASB groups.<br><br>CONCLUSION: Introduction of a uropathogenic E. coli strain reduced urobiome diversity, while a non-uropathogenic strain did not, suggesting strain-specific effects on microbial ecology. Bladder instillation itself also altered the urobiome. Elevated uNGAL levels were observed in both UTI and ASB models, indicating that while uNGAL reflects bacterial exposure, it does not distinguish between uropathogenic and non-uropathogenic E. coli. These findings highlight urobiome analysis as a potential tool for differentiating UTI from ASB, whereas uNGAL alone is insufficient.}, }
@article {pmid41772134, year = {2026}, author = {Sadiq, FA and Yang, N and Goeteyn, J and De Reu, K and Heyndrickx, M and Burmølle, M}, title = {Microbial Interactions Shape Spatial Organisation and Transcriptional Responses in a Model Mixed-Species Biofilm.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02701-w}, pmid = {41772134}, issn = {1432-184X}, abstract = {Dynamic social interactions within bacterial biofilms drive distinct spatial organisation and transcriptional responses. Here, we combine fluorescence in situ hybridisation (FISH), confocal laser scanning microscopy (CLSM), and RNA sequencing (RNA-Seq) to investigate a model three-species biofilm community derived from a dairy pasteuriser, comprising Stenotrophomonas rhizophila, Microbacterium lacticum, and Bacillus licheniformis. CLSM revealed species-specific biovolume dynamics and stratified 3D structures over 24 h, with S. rhizophila as the dominant species and M. lacticum exhibiting the lowest abundance yet playing an essential role as the initial coloniser. Spatial patterns reflected known pairwise interactions - commensalism, exploitation, and neutral interaction. Transcriptomic profiling of S. rhizophila revealed extensive gene expression changes in dual-species biofilms with M. lacticum, including upregulation of genes related to flagellar motility, nutrient acquisition, energy metabolism, and TonB-dependent transport. In contrast, co-culture with B. licheniformis induced minimal transcriptional changes in S. rhizophila, consistent with a neutral interaction among the two. Our findings demonstrate how interspecies interactions govern both spatial topology and functional specialisation in mixed-species biofilms which is of relevance to microbial ecology, industrial biofilm control, and the targeting of keystone biofilm species.}, }
@article {pmid41771260, year = {2026}, author = {Vaughn, SN and Pavlovsky, JC and Jackson, CR}, title = {Bacterial Communities in Sand and Seawater of Northern Gulf Coast Beaches: Temporal, Spatial, and Environmental Influences.}, journal = {Environmental microbiology reports}, volume = {18}, number = {2}, pages = {e70309}, pmid = {41771260}, issn = {1758-2229}, support = {//U.S. Department of the Treasury/ ; //Mississippi Department of Environmental Quality/ ; //Mississippi Based RESTORE Act Center of Excellence/ ; }, abstract = {Coastal microbial communities play critical roles in marine food webs and biogeochemical cycling, yet their diversity and function remain poorly characterised in many regions. This is especially evident along the northern Gulf coast, a dynamic system with substantial freshwater influences. We used high throughput 16S rRNA sequencing to characterise bacterial communities in sand and seawater collected every 3 months (March 2024 through March 2025) from 10 beaches along a 53 km stretch of the Mississippi coast. The diversity and composition of these communities were related to environmental variation and to biogeochemical function as determined from the activity of enzymes related to carbon, nitrogen, and phosphorus mineralisation. Our findings revealed distinct bacterial communities in sand and seawater, with the microbiome of each habitat showing greater temporal variation over the course of the study than spatial variation between beaches. Patterns in bacterial community structure and proportions of abundant taxa were strongly linked to physicochemical variables, while enzyme activities suggested how microbial communities may contribute to biogeochemical processes in these habitats. Collectively, these findings provide critical information for understanding microbial ecology in this system and highlight the central role of bacteria in mediating ecosystem function along a dynamic and understudied coastline.}, }
@article {pmid41770930, year = {2026}, author = {Bai, X and Li, Z and Chen, B and Qian, X and Guo, Y and Wang, Q and Chen, C and Chen, W and Shen, X and Liu, J and Jin, J and Zhang, W and Liu, Q and Chen, S and Yang, S and Xu, L and van der Heijden, MGA and Tiedje, JM and Jiao, S and Wei, G}, title = {High bacterial diversity drives the suppression of a soilborne plant disease.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {123}, number = {10}, pages = {e2509303123}, doi = {10.1073/pnas.2509303123}, pmid = {41770930}, issn = {1091-6490}, abstract = {The rhizosphere microbiome plays a crucial role in the resistance to soilborne plant diseases. However, the principles needed to explain and predict which microbiota will be effective against soilborne pathogens are still lacking due to the complexity of the soil microbial community. We hypothesized that, independent of particular microbial strains, a high diversity is associated with, or increases the probability of, effective suppression. We tested this hypothesis by demonstrating that random combinations of rhizosphere microbial isolates, with the same bacterial diversity, had an equal impact on suppressing root diseases. The incidence of root rot was significantly reduced when soil bacterial diversity was high. We further investigated how high-diversity bacterial communities suppress root rot by constructing synthetic bacterial communities (SynComs). The results suggest that high bacterial diversity suppresses pathogens through mechanisms potentially including nutrient competition and the formation of physical barriers on the root surface. Our study highlights that high bacterial diversity is beneficial for suppressing soilborne plant diseases, offering a nonchemical and sustainable approach for crop disease management.}, }
@article {pmid41770403, year = {2026}, author = {D'Souza, R and Pujare, K and Balu, SK and Kanojiya, D and Garg, Y and Ghag, SB}, title = {Differential Response of Banana Root Exudates and its Components on the Growth and Development of Banana Wilt Pathogen.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02693-z}, pmid = {41770403}, issn = {1432-184X}, }
@article {pmid41770335, year = {2026}, author = {Suarez-Silva, R and Saucedo-Bazalar, M and Ramirez Saenz, M and La Torre Ramirez, RD and Caycho Ortiz, E and Orjeda, G}, title = {Exploring the Algarrobo Decline in the Pómac Forest: Unraveling the Relationship between the Endomicrobiome of Neltuma Pallida and Enallodiplosis Discordis.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02711-8}, pmid = {41770335}, issn = {1432-184X}, support = {No. 042-2022-RFNP//Servicio Nacional de &#xc1;reas Naturales Protegidas Servicio Nacional de &#xc1;reas Naturales Protegidas/ ; R. R. No 009412-2021-UNMSM and Project number B2110006i - PINTERDIS - 2021//Universidad Nacional Mayor de San Marcos/ ; }, }
@article {pmid41770002, year = {2026}, author = {Feliu-Paradeda, L and Amorós-Espuña, Q and Perona-Vico, E and Casals, E and Esteve-Codina, A and Puig, S and Bañeras, L}, title = {Synergies revealed: RNA-seq study of C. acetobutylicum and C. carboxidivorans co-cultured in the presence of conductive materials.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0326225}, doi = {10.1128/spectrum.03262-25}, pmid = {41770002}, issn = {2165-0497}, abstract = {Co-cultures can improve substrate utilization and product yields, yet the dynamics between species remain highly variable and poorly understood. In this study, we investigated the metabolic and transcriptional interplay between Clostridium acetobutylicum and Clostridium carboxidivorans when co-cultured in the presence of activated carbon or magnetite, with the aim of evaluating these materials as metabolism enhancers. Fermentation profiling showed that magnetite accelerated glucose consumption and favored acid over alcohol production, with butyrate and acetate reaching yields of 0.65 and 0.62 mol/mol glucose, respectively. Alcohols (ethanol and butanol) accumulated in late fermentation and occurred concomitantly to a metabolic shift from acidogenesis to solventogenesis, potentially driven by interspecies dynamics as RNA-seq data suggested. RNA-seq analysis detected 7,369 genes and revealed C. carboxidivorans dominated in early fermentation, and C. acetobutylicum was activated later (in view of the number of reads detected for each species). Magnetite-treated samples displayed the most transcriptional variation, and species-specific patterns emerged. Changes in electron-active genes (e.g., hydA and rnf genes) suggest enhanced redox communication, highlighting the capacity of conductive materials to influence metabolic flow and regulatory pathways in microbial consortia, opening possibilities for improved bioproduction and carbon utilization.IMPORTANCEMicrobial co-cultures offer a promising strategy to expand metabolic capabilities beyond those of individual strains, yet their internal coordination remains poorly understood. This study demonstrates that conductive materials not only accelerate substrate utilization but also modulate cooperation in a co-culture of Clostridium carboxidivorans and Clostridium acetobutylicum. According to gene expression levels, we demonstrate a clear temporal division of labor between the two partners, with C. carboxidivorans initiating acidogenesis and C. acetobutylicum later driving solventogenesis. Magnetite and activated carbon addition had little effect, but changes in the expression pattern of electron-active genes (hydA and rnf) could be detected for the two species. Understanding and controlling these dynamics are key to optimizing co-cultures for industrial fermentation and biofuel production.}, }
@article {pmid41769348, year = {2026}, author = {Sun, M and Zang, D and Zhou, H and Che, YL and Chen, J}, title = {Epistemic compression in large language model explanations of the gut-liver axis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1773593}, pmid = {41769348}, issn = {2235-2988}, abstract = {BACKGROUND: The gut-liver axis integrates intestinal barrier function, microbial ecology, metabolism, immune regulation, and hepatic feedback, yet remains causally non-closed and strongly context dependent. As large language models (LLMs) increasingly mediate biomedical explanation, their ability to preserve evidentiary structure within such epistemically open frameworks requires systematic evaluation.<br><br>METHODS: We conducted a cross-platform, mixed-methods infodemiology analysis of five widely accessible LLMs. Twenty clinically grounded questions spanning five hierarchical domains from basic mechanisms to intervention and evaluation generated 100 single-turn responses. Linguistic accessibility was assessed using seven established readability indices, while epistemic integrity was evaluated using the Journal of the American Medical Association Benchmark Criteria, Global Quality Score, and a modified DISCERN framework.<br><br>RESULTS: Linguistic complexity increased as prompts progressed toward intervention and evaluation, without corresponding gains in transparency, reliability, or educational quality. Informational integrity clustered primarily by platform rather than domain. Readability indices showed strong internal concordance, whereas integrity metrics aligned only moderately and correlated weakly with readability. Item-level analysis revealed consistently high narrative clarity but systematic under-signaling of source attribution and uncertainty, resulting in over-coherent explanations that compressed conditional associations into mechanism-like claims.<br><br>CONCLUSIONS: LLM explanations of the gut-liver axis are susceptible to epistemic compression driven by narrative fluency rather than factual error. Readability does not reliably indicate epistemic robustness in decision-adjacent contexts. These findings support shifting evaluation and governance from platform comparison toward concept-conditioned requirement engineering that enforces provenance, calibrated uncertainty, and explicit separation of correlation, mechanism, and actionability as generative outputs approach clinical relevance.}, }
@article {pmid41769190, year = {2026}, author = {Al-Jamal, FF and Abuassaf, RA and Abusara, OH and Zihlif, M and Deeb, AA and Al-Rshaidat, MMD}, title = {Ethanolic extracts from deep marine sponges: A new frontier in antibacterial discovery from the Jordanian Gulf of Aqaba.}, journal = {Biomedical reports}, volume = {24}, number = {4}, pages = {44}, pmid = {41769190}, issn = {2049-9442}, abstract = {The urgent need for new antibiotics to counter bacterial resistance has led to renewed interest in marine natural products. The present study evaluated the antibacterial potential of ethanolic extracts from three deep-sea sponges: Stelletta sp., Dactylospongia cf. elegans (D. cf. elegans) and Axinella sp., which were collected from the Gulf of Aqaba off the coast of Jordan. Antibacterial activity was assessed against Gram-negative and Gram-positive bacteria using the well diffusion method, followed by determination of the Minimum Inhibitory Concentration (MIC) and Minimum Bactericidal Concentration (MBC). Only D. cf. elegans exhibited potent activity, which was limited to Gram-positive bacteria and showed inhibition zones of 7 to 21 mm and MIC and MBC values of 1 and 2 mg/ml, respectively. Stelletta sp. showed no detectable activity, and Axinella sp. displayed minimal effects. DNA barcoding (28S rRNA) confirmed that all three species belong to the class Demospongiae. LC-MS/MS analysis of the extract from D. cf. elegans identified bioactive constituents, including bolinaquinone, dactyloquinone, gallic acid and caffeic acid, which are compounds known for antibacterial properties and likely contributed to the observed activity. Thus, D. cf. elegans could be a promising source of antibacterial agents against Gram-positive pathogens and warrants further evaluation of the mechanisms involved, its toxicity, and its effects in vivo.}, }
@article {pmid41767570, year = {2026}, author = {Souza, JM and Silva, LAF and Casali, DM and Souza, JCSM and Wolfe, LA and Skarlupka, JH and Zuniga-Chaves, I and Steinberger, AJ and Deblois, CL and Scheftgen, AJ and Lelis, ALJ and Leiva, T and Rodrigues, MC and Barroso, JPR and Lasmar, PVF and Suen, G and Millen, DD}, title = {Rumen and cecum microbial dynamics following narasin inclusion in Nellore cattle diets.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1645979}, pmid = {41767570}, issn = {1664-302X}, abstract = {This study investigated the effects of narasin supplementation on the ruminal and cecal bacterial communities of feedlot Nellore cattle. We hypothesized that narasin would selectively modulate microbial populations in distinct gastrointestinal compartments without causing broad-scale disruption of overall community diversity. Sixty-four Nellore bulls (393 ± 24 kg) were assigned to a completely randomized block design and fed finishing diets containing either 0 or 20 ppm of narasin for 112 days. Rumen and cecal contents were collected at slaughter and analyzed using 16S rRNA gene sequencing to characterize bacterial community structure and composition. Overall, the rumen exhibited greater bacterial diversity and richness than the cecum, regardless of dietary treatment. Narasin supplementation did not affect Shannon diversity in either the rumen (p = 0.182) or the cecum (p = 0.298); however, Chao richness was reduced in the rumen of narasin-fed cattle (p = 0.028). Beta-diversity analyses based on Bray-Curtis and Jaccard dissimilarities revealed no significant differences in overall community structure between treatments in either compartment (p > 0.198). At the phylum level, narasin supplementation was associated with a reduction in Firmicutes and a concomitant increase in Bacteroidetes in the rumen. In contrast, Firmicutes predominated in the cecum, and narasin significantly increased the relative abundance of this phylum, particularly members of the order Clostridiales (p = 0.05). In conclusion, narasin exerts selective effects on specific bacterial populations rather than inducing widespread shifts in microbial diversity. These results provide novel insights into how narasin modulates microbial ecology in both the rumen and the understudied cecum, highlighting compartment-specific responses that may contribute to improved feed efficiency in beef cattle.}, }
@article {pmid41764142, year = {2026}, author = {Brayley, ODM and McCready, K and Liu, S and Convey, P and Chen, Y and Ullah, S and Teets, N and Hayward, SAL}, title = {The Microbiome of an Invasive Antarctic insect, Eretmoptera Murphyi (Diptera: Chironomidae), and its Potential Role in Nutrient Cycling.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02706-5}, pmid = {41764142}, issn = {1432-184X}, support = {NE/S007350/1//NERC CENTA2/ ; NE/S007350/1//NERC CENTA2/ ; NE/T009446/1//NSFGEO-NERC/ ; NE/T009446/1//NSFGEO-NERC/ ; NE/T009446/1//NSFGEO-NERC/ ; OPP-1850988//National Science Foundation/ ; 700545//USDA National Institute of Food and Agriculture Hatch Project/ ; RF-2024-396/2//Leverhulme Research Fellowship/ ; }, }
@article {pmid41763651, year = {2026}, author = {Angebault, C and Bardoul, M and Fillâtre, P and Bouju, P and Rieul, G and Fedun, Y and Launey, Y and Reizine, F}, title = {Clinical landscape and mortality risk in Intensive Care Unit peritonitis in a low-MultiDrug Resistant setting: A multicentre cohort study.}, journal = {Anaesthesia, critical care &amp; pain medicine}, volume = {}, number = {}, pages = {101783}, doi = {10.1016/j.accpm.2026.101783}, pmid = {41763651}, issn = {2352-5568}, abstract = {INTRODUCTION: Peritonitis is a frequent cause of sepsis in the intensive care unit (ICU) and is characterized by substantial microbiological variability, including multidrug-resistant organisms (MDROs).<br><br>METHOD: We conducted a retrospective, multicenter cohort study including ICU patients diagnosed with intra-abdominal infection across 4 hospitals 2020-2022). The primary objective was to describe clinico-biological features, and microbiological characteristics according to the setting of the peritonitis (Community peritonitis (CP), early nosocomial peritonitis (ENP), or late nosocomial peritonitis (LNP)). Additionally, we analyzed 90-day survival using Kaplan-Meier curves and multivariable Cox regression.<br><br>RESULTS: Among the 392 patients included in the study period, 195 experienced a CP, 88 an ENP, and 109 an LNP. Extended-spectrum beta-lactamase-producing bacteria were identified in 24 patients (6.1%), and carbapenem-resistant bacteria in 5 patients (1.3%). MDRO rates differed significantly: carbapenem-resistant bacteria were more frequent in LNP patients (3.7% vs. 0.0% in CP and 0.5% in ENP; p&#x2009;=&#x2009;0.03), and cephalosporinase-producing bacteria were more common in nosocomial settings (40.4% in LNP vs. 19.0% in CP; p&#x2009;<&#x2009;0.001). Ninety-day mortality was 34.7% overall and did not differ across settings (p&#x2009;=&#x2009;0.345). Age and SAPS II were independently associated with mortality. Finally, appropriate empirical antimicrobial therapy was not associated with improved 90-day survival (p&#x2009;=&#x2009;0.128).<br><br>CONCLUSION: Through this large cohort study of ICU patients with peritonitis, we observed a low prevalence of MDRO. Our findings challenge the relevance of broad-spectrum empirical therapy in low-MDRO regions and underscore the need for tailored antimicrobial stewardship strategies.}, }
@article {pmid41762238, year = {2026}, author = {Phauk, S and Sin, S and Terenius, O}, title = {Symbiotic Diversity of Sap-Feeding Auchenorrhyncha (Hemiptera) in the Upland Landscapes of Central Cardamom Mountains, Cambodia.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02724-3}, pmid = {41762238}, issn = {1432-184X}, }
@article {pmid41757148, year = {2025}, author = {Bektaş, A and Ulusoy, M}, title = {Gluten Tolerance through Microbial and Cultural Adaptation: A Holistic Model for Celiac Disease and Non-celiac Gluten Sensitivity.}, journal = {Euroasian journal of hepato-gastroenterology}, volume = {15}, number = {2}, pages = {185-189}, pmid = {41757148}, issn = {2231-5047}, abstract = {AIM AND BACKGROUND: Celiac disease (CD) and nonceliac gluten sensitivity (NCGS) are increasing in public and scientific focus. Interestingly, regions with traditionally high gluten consumption such as Turkey, Iran, and the Mediterranean show lower CD prevalence than the Western countries. This paradox indicates that genetic predisposition alone, such as HLA DQ2 or DQ8 carriage, does not fully explain gluten intolerance. Understanding environmental, microbial, and cultural contributors may clarify the development of gluten tolerance.<br><br>METHODS: This narrative review synthesizes current evidence from epidemiology, microbiology, immunology, and nutritional science to propose an integrative hypothesis. Relevant literature was examined to explore interactions among diet, gut microbiota, and immune tolerance mechanisms that influence responses to gluten exposure.<br><br>RESULTS: Findings suggest that early life gluten exposure, microbial diversity, and long-term dietary adaptation enhance mucosal tolerance to gluten. Specific microorganisms such as Lactobacillus, Bifidobacterium, and Prevotella can enzymatically degrade immunogenic gluten peptides including the 33-mer &#x3b1;2-gliadin fragments. Reduced microbial diversity and the consumption of ultra-processed foods may contribute to heightened gluten sensitivity and immune dysregulation.<br><br>CONCLUSION: Gluten is not inherently toxic; its immunogenicity depends on host microbiota composition, environmental exposures, and dietary context. A systems biology approach that integrates microbial ecology, evolutionary adaptation, and immunonutrition may better explain gluten tolerance variability across populations.<br><br>CLINICAL SIGNIFICANCE: Recognizing gluten tolerance as a modifiable, microbiota influenced process may guide more individualized dietary recommendations, reduce unnecessary gluten avoidance, and promote evidence-based clinical management of gluten-related disorders.<br><br>HOW TO CITE THIS ARTICLE: Bekta&#x15f; A, Ulusoy M. Gluten Tolerance through Microbial and Cultural Adaptation: A Holistic Model for Celiac Disease and Non-celiac Gluten Sensitivity. Euroasian J Hepato-Gastroenterol 2025;15(2):185-189.}, }
@article {pmid41757127, year = {2026}, author = {Saha, A and Jones, JM and Plummer, A and Larkin, JW}, title = {Formation of a swelling gel underlies a morphological transition in Bacillus subtilis biofilms.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.02.20.707077}, pmid = {41757127}, issn = {2692-8205}, abstract = {Microbes across species and environments form biofilms, living materials composed of cells and extracellular polymers. Biofilm-dwelling cells benefit from emergent soft matter physics that sculpts three-dimensional morphologies and osmotically absorbs nutrients. Although biofilms are modeled as viscoelastic gels, the physical origins of the phase transition underlying their conversion from groups of cells to living gels have not been systematically investigated. Here, we show that Bacillus subtilis biofilms use polymer composition to tune their physical properties and drive gel formation. Using imaging and water immersion experiments with matrix knockout strains, we demonstrate the complementary roles of two polymers in this developmental transition: hydrophilic poly- γ -glutamate swells colonies by absorbing water and exopolysaccharides serve as effective cross-linkers, causing a sol-gel-like phase transition that imparts structural integrity. With matrix knockout co-culture biofilms, we independently modulate the production of each polymer and reveal a phase space of biofilm morphologies. Colonies that produce both polymers develop macroscopic wrinkles. A thin-film model predicts biofilm wrinkling from swelling-generated internal strain coupled to elasticity. The model reproduces the shape of our observed morphological phase diagram. Our results demonstrate that bacteria leverage gelation to vary their material properties and morphologies, with implications for microbial ecology and engineering living matter.}, }
@article {pmid41754095, year = {2026}, author = {Mafe, AN and Büsselberg, D}, title = {The Diet-Microbiota-Polyamine Axis in Intestinal Aging: Microbial Pathways, Functional Foods, and Physiological Implications.}, journal = {Nutrients}, volume = {18}, number = {4}, pages = {}, pmid = {41754095}, issn = {2072-6643}, support = {NPRP 14S0311-210033//Qatar National Research Fund/ ; }, abstract = {Intestinal aging is characterized by a gradual decline in epithelial renewal capacity, barrier function, immune balance, and metabolic regulation, often accompanied by shifts in gut microbial composition. Polyamines, including putrescine, spermidine, and spermine, are vital microbial-host metabolites that support intestinal cell growth, autophagy, immune modulation, and mucosal repair. With advancing age, both host-derived and microbiota-mediated polyamine production declines, contributing to intestinal dysfunction and heightened vulnerability to inflammation and age-related disorders. This review explores the diet-microbiota-polyamine axis as a key biological framework influencing intestinal aging. It aims to integrate evidence on how dietary components and functional foods shape gut microbial ecology and, in turn, regulate microbial polyamine biosynthetic pathways that impact intestinal health. The review highlights major microbial contributors to polyamine metabolism, particularly lactic acid bacteria, and outlines mechanistic pathways linking polyamines to epithelial regeneration, inflammatory control, and gut barrier maintenance. It further discusses how age-associated dysbiosis disrupts these interactions and evaluates nutritional and microbial-based strategies such as fermented foods, prebiotics, and probiotics that may enhance polyamine availability and restore gut homeostasis. From the standpoint of food microbiology and human physiology, this synthesis underscores the translational potential of targeting microbial polyamine production through diet-based interventions. This article presents a narrative review synthesizing experimental, animal, and emerging human evidence on microbial and dietary polyamines in intestinal aging. In conclusion, modulating the diet-microbiota-polyamine axis represents a promising strategy to promote healthy intestinal aging, meriting deeper mechanistic exploration and validation through clinical studies.}, }
@article {pmid41753780, year = {2026}, author = {Palanisamy, V and Bosilevac, JM and Barkhouse, DA and Velez, SE and Dass, SC}, title = {Unraveling the Coevolutionary Dynamics of Phage and Bacterial Protein Warfare Occurring in the Drains of Beef-Processing Plants.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, pmid = {41753780}, issn = {2076-2607}, support = {2020-67017-30776//USDA-NIFA/ ; }, abstract = {Phages, the most abundant entities on Earth, exhibit a complex interplay with bacteria, especially within environmental biofilms, resulting in an ecological arms race. This study investigates the interaction between phages and bacteria in the drains of beef-processing plants using high-throughput sequencing and metagenomic analysis. Metagenomic data collected from 75 drain samples from beef-processing plants were analyzed to investigate phage-bacterial interactions. First, assembled contigs were screened to identify viral sequences, which were then taxonomically annotated to determine the viral composition, including phages. Functional annotation of these viral sequences provided information about the viral genes and their roles in bacterial interactions specifically associated with attack and counterattack of bacteria. In parallel, bacterial contigs were examined to identify genes associated with antiphage defense systems, providing insights into the strategies adapted by bacteria to resist phage infection. Taxonomic annotation of viral sequences from the bulk metagenomic data revealed the presence of phages targeting Pseudomonas, Klebsiella, and Enterococcus. The higher abundance of Pseudomonas phages aligns with our previous study, where Pseudomonas was identified as the dominant bacterial genus, suggesting potential copersistence of phages and their hosts. Functional annotation of phage contigs revealed infective and lysis-related genes, highlighting their potential role in bacterial attack. Conversely, bacterial contigs encoded antiphage defense systems, including CRISPR-Cas, restriction-modification, and other defense-related genes. The study also uncovered the presence of anti-CRISPR proteins in phages, suggesting a counterattack on the bacterial defense. These findings provide evidence for phage attack, bacterial defense, and phage counterattack and may showcase the ongoing coevolutionary arms race between phages and bacteria. While this evidence looks promising, these results remain preliminary and further studies are needed to validate these findings. Still, this study provides a foundational understanding of bacteria-phage coexistence in beef-processing plant drains and paves the way for further explorations of these intricate interactions and their possible applications in controlling pathogenic microorganisms within biofilms.}, }
@article {pmid41753774, year = {2026}, author = {Dobrzyński, J and Naziębło, A and Kulkova, I and Szpytma, M and Antosik, A and Sitarek-Andrzejczyk, M and Wróbel, B}, title = {Paenibacillus-Pseudomonas Consortium Improves Barley Performance with Minimal Impact on Native Rhizobacterial Community.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, pmid = {41753774}, issn = {2076-2607}, abstract = {The intensive use of mineral nitrogen fertilizers in cereal production contributes to environmental degradation, highlighting the need for more sustainable crop management strategies. Plant growth-promoting bacteria (PGPB) offer a promising alternative; however, their effects on native rhizosphere communities remain underexplored, particularly in barley. This study evaluates the impact of a bacterial consortium composed of Paenibacillus sp. Z15 and Pseudomonas sp. KR227 on barley growth, yield, and rhizosphere bacteria under field conditions in temperate climate (2025). Plant biometric traits, photosynthetic pigment content, and soil properties were measured, and rhizobacterial communities were analyzed using 16S rRNA gene (V3-V4) sequencing. The PGPB consortium significantly increased early root biomass (120%), shoot height (7.8%), and grain yield (15.5%), while no significant effects were observed on soil chemistry or photosynthetic pigments. Sequencing revealed no major changes in alpha or beta diversity; however, transient shifts in the relative abundance of specific taxa were detected relatively shortly after inoculation and mostly disappeared by harvest. These findings indicate that the Paenibacillus-Pseudomonas consortium can enhance barley performance without disrupting native rhizobacterial communities. Overall, the results support the potential of PGPB as a sustainable agronomic tool and provide new insights into PGPB-microbiome interactions in barley under field conditions.}, }
@article {pmid41753768, year = {2026}, author = {Frantz, CM and Crump, BC and Carpenter, S and Firth, E and Orellana, MV and Light, B and Junge, K}, title = {Microbial Ecology of Rotten Sea Ice: Implications for Arctic Carbon Cycling with Global Warming.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/microorganisms14020482}, pmid = {41753768}, issn = {2076-2607}, support = {1656026//USA National Science Foundation/ ; PLR-1304228//USA National Science Foundation/ ; }, abstract = {"Rotten" sea ice, ice in an advanced stage of melt, represents an important but understudied habitat in the rapidly changing Arctic. As Arctic warming accelerates, this late-season ice type will become more prevalent, yet little is known about its microbial inhabitants or their roles in Arctic marine biogeochemical cycles. We examined microbial communities (prokaryote and algal abundance, 16S and 18S rRNA gene and transcript sequencing) and biogeochemical properties of rotten sea ice and earlier-season ice near Utqiaġvik, Alaska, USA. Rotten ice was comparatively warm, isothermal, and largely drained of brine, with extensive, interconnected pore networks linked to melt ponds above and seawater below. Unlike earlier-season ice, fluids saturating rotten ice were vertically homogeneous in pH, dissolved inorganic carbon, prokaryote and phytoplankton abundance, and microbial community composition. However, particulate carbon and nitrogen exhibited strong vertical gradients, with the highest concentrations near the surface. Microbial communities in rotten ice were significantly different from those in earlier-season ice and varied between individual floes. These findings indicate that rotten ice constitutes a distinct microbial habitat and may serve as an important source of nutrient-rich particulate matter in the future Arctic Ocean during the summer melt season.}, }
@article {pmid41753753, year = {2026}, author = {Lerner, A and Lieber, AD and Nelson-Dooley, C and Leu, A and Perro, M and Koch, G and Benzvi, C and Smith, J}, title = {Genetically Modified Microorganisms: Risks and Regulatory Considerations for Human and Environmental Health.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/microorganisms14020467}, pmid = {41753753}, issn = {2076-2607}, abstract = {Advances in affordable genetic engineering have accelerated the creation and large-scale environmental release of genetically modified microorganisms (GMMs). While beneficial applications exist, GMMs may present unique, long-term risks to human and environmental health. Unlike static chemicals, GMMs are biologically active, self-replicating entities capable of rapid mutation and global dispersal. Current regulatory frameworks place responsibility on each country to regulate GMMs, without a clear, coordinated international policy. This review details critical risk scenarios, including horizontal gene transfer to native species and the possible disruption of vital human microbiomes (gut, oral, and infant), which could increase resistance to degradation, promote traits that expand a microbe's range of hosts or ecological niches, and enhance the production of novel metabolites with unexpected biological activity. In soil, GMMs may support the emergence of "super bugs" or destabilize carbon sequestration cycles, potentially impacting climate resilience. Engineered microbial enzymes in the food supply may also act as environmental drivers of autoimmunity. Given the limited understanding of microbial ecology, we propose a decision-based biosafety workflow emphasizing pre-release risk assessment and continuous post-release monitoring. We urge national and international regulators to adopt the precautionary principle to better protect human health and the environment from the potential negative outcomes of GMMs.}, }
@article {pmid41753641, year = {2026}, author = {Pérez-García, LA and Sáenz-Mata, J and Fortis-Hernandez, M and Preciado-Rangel, P}, title = {Plant Growth-Promoting Rhizobacteria as a Strategy to Enhance Enzymatic and Metabolic Tolerance of Cucumis sativus L. Under Salinity Stress.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/microorganisms14020351}, pmid = {41753641}, issn = {2076-2607}, abstract = {Cucumis sativus L., a salt-sensitive horticultural crop, is severely affected by soil salinity, which disrupts photosynthetic efficiency and metabolic homeostasis. This study quantified the effects of Plant Growth-Promoting Rhizobacteria (PGPR)-Pseudomonas paralactis, Bacillus cereus, Sinorhizobium meliloti, and Acinetobacter radioresistens-on key enzymatic indicators of cucumber seedlings exposed to 0, 50, 100, and 150 mM NaCl. PGPR inoculation significantly enhanced bacterial stress-mitigation and hormonal pathways, with ACC-deaminase activity increasing by up to 78.8% (A. radioresistens, 150 mM NaCl) and nitrilase activity by 50.5% (S. meliloti, 50 mM NaCl). Auxin-related pathways were strongly induced, as reflected by increases of up to 51.1% in the IAM pathway (P. paralactis) and 42.9% in the IPA pathway (A. radioresistens). In plant tissues, key metabolic enzymes exhibited high stability under salinity, with ProDH and NDPK activities increasing by up to 4.5% and 2.35%, respectively, while RuBisCO activity remained unaffected across treatments. These results demonstrate that PGPR function as effective bioestimulants by coordinating hormonal regulation and metabolic resilience, providing a sustainable biotechnological strategy to enhance cucumber tolerance to salinity stress.}, }
@article {pmid41751059, year = {2026}, author = {Tapingkae, W and Srinual, O and Srinual, P and Khamtavee, P and Pintalerd, N and Chaiyaso, T and Yachai, M and Tapingkae, T and Kanmanee, C}, title = {Dietary Coffee Silverskin Supplementation: Effect on Growth Performance, Carcass Traits, and Gastrointestinal Health of Broilers.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {4}, pages = {}, doi = {10.3390/ani16040598}, pmid = {41751059}, issn = {2076-2615}, support = {FF66/045//Fundamental Fund 2023, Chiang Mai University/ ; }, abstract = {Coffee silverskin (CSS) remains a neglected poultry additive; investigating its bioactive potential is essential for optimizing agricultural productivity and enhancing food security via advanced nutrition. This study analyzed how dietary CSS supplementation influences broiler growth, slaughter characteristics, meat quality, cecal microbial ecology, and intestinal histomorphology. A total of 400 one-day-old male Ross 308 broilers were randomly assigned to four dietary treatments with 10 replicates of 10 birds each. Experimental treatments consisted of a negative control (NC, basal diet) and CSS-supplemented groups (0.5, 1.0, and 2.0 g/kg, designated CSS0.5, CSS1.0, and CSS2.0, respectively). All data were subjected to one-way ANOVA using the procedure of SPSS 23.0. Coffee silverskin supplementation, specifically at 1.0-2.0 g/kg, optimized broiler growth performance, significantly elevating body weight and average daily gain (p < 0.05). While carcass yield improved in a dose-dependent manner, fundamental meat quality-pH and shear force-remained stable. Crucially, CSS inclusion reconfigured cecal ecology, selectively suppressing Escherichia coli and Salmonella sp. while enhancing Lactobacillus populations (p < 0.001). This microbial shift mirrored histological gains, notably enhanced villus height and villus height-to-crypt ratios (p < 0.05). These findings demonstrate that CSS, particularly at 1.0-2.0 g/kg, enhances broiler performance, carcass quality and gut health.}, }
@article {pmid41750824, year = {2026}, author = {Oh, SC and Lee, SJ and Ding, K and Shen, J and Huang, C and Kang, SN and Reaney, MJT and Kim, YJ and Shim, YY}, title = {Kimchi Fermentation-Driven Detoxification of Flaxseed: Impact on Physicochemical Quality and Antioxidant Potential.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {4}, pages = {}, doi = {10.3390/foods15040632}, pmid = {41750824}, issn = {2304-8158}, support = {RS-2023-00263064//Ministry of Science and ICT/ ; }, abstract = {Flaxseed (Linum usitatissimum L.) is a rich source of α-linolenic acid (ALA) and lignans but contains toxic cyanogenic glycosides (CGs) that limit its application in foods. This study investigated the efficacy of a specialized Lactobacillaceae consortium in detoxifying flaxseed and the subsequent effects of adding this cyanogenic glycoside-depleted flaxseed (CGDF) to a kimchi matrix. Ground flaxseed and CGDF were added to the kimchi seasoning mixture at concentrations of 0.5%, 1.0%, and 2.0% (w/w) and fermented at 4 °C for 8 weeks. Analytical results confirmed that the fermentation process reduced linustatin and neolinustatin to undetectable levels (<500 mg/kg) and reduced total hydrogen cyanide (HCN) to below the Japanese regulatory limit of 10 mg/kg established under the Food Sanitation Act. During fermentation, CGDF-supplemented groups exhibited a delayed decrease in pH and higher retention of free sugars and vitamin C compared to the control and raw flaxseed groups. Notably, the 2.0% CGDF group maintained high oxidative stability of ALA, which we attribute to a putative antioxidant protection mechanism driven by the bioconversion of lignan glycosides into bioactive aglycones. These findings suggest that incorporating biologically detoxified flaxseed into kimchi creates a functional food system that ensures safety while enhancing nutritional stability. Overall, this work provides foundational evidence for developing safe, nutritionally enhanced functional foods within the One Health framework, integrating food safety, microbial ecology, and improved bioactive compound availability.}, }
@article {pmid41750446, year = {2026}, author = {Magnano San Lio, R and Maugeri, A and Barchitta, M and Favara, G and La Rosa, MC and La Mastra, C and Ferrante, M and Agodi, A}, title = {The Wastewater Resistome: A Shotgun Metagenomics Analysis of Urban Treatment Plants in Sicily.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {2}, pages = {}, doi = {10.3390/antibiotics15020148}, pmid = {41750446}, issn = {2079-6382}, support = {MUR-PNRR project SAMOTHRACE (ECS00000022)//European Union (NextGeneration EU)/ ; }, abstract = {Background/Objectives: Antimicrobial resistance (AMR) in wastewater represents a valuable reservoir of information for wastewater-based epidemiology (WBE) and a major environmental and public health concern, as wastewater treatment plants (WWTPs) are recognized hotspots for the accumulation and dissemination of antimicrobial resistance genes (ARGs). Within the One Health framework, and to better understand the contribution to AMR spread and the potential of metagenomic surveillance, this study aimed to characterize the taxonomic, functional, and resistome profiles of three WWTPs in Sicily, specifically those located in Catania, Giarre, and Syracuse. Methods: Sixty-nine composite influent samples were collected between February 2022 and December 2023. Shotgun metagenomic sequencing was performed on the Illumina NovaSeq platform. Bioinformatic analyses were conducted to assess microbial community composition, functional pathways, and ARG prevalence across sites. Results: Dominant genera included Aliarcobacter, Bacteroides, and Acinetobacter. Site-specific taxonomic variations reflected differences in local microbial ecology. Functional profiling revealed enrichment in membrane-associated, ribosomal, and energy metabolism pathways, consistent with the expected functional redundancy of wastewater microbiomes. Resistome analysis detected a diverse and ubiquitous array of ARGs, dominated by β-lactam and macrolide resistance genes, followed by aminoglycoside, sulphonamide, and tetracycline classes. Conclusions: These findings highlight urban wastewater as a relevant reservoir and dissemination route for AMR and support the integration of metagenomic approaches into wastewater surveillance programs. By providing region-specific, integrated taxonomic, functional, and resistome data from Sicilian WWTPs, this study contributes to the growing body of evidence supporting WBE as a valuable tool for AMR monitoring and One Health-oriented risk assessment.}, }
@article {pmid41749772, year = {2026}, author = {Shang, J and Dong, C and Zhou, Q and Chai, J and Wei, Y}, title = {The Bacteriophage VMY 22 Has Enhanced the Stability of Its Functional Proteins via Adaptive Evolution in a Temperature-Varying Environment.}, journal = {Bioengineering (Basel, Switzerland)}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/bioengineering13020233}, pmid = {41749772}, issn = {2306-5354}, abstract = {Temperature fluctuations strongly affect microbial viability, often inducing adaptive responses. In this study, we employed the psychrophilic bacterium Bacillus mycoides 41-22 and its associated phage VMY22, originally isolated from the Mingyong Glacier, to investigate phage adaptability under varied temperature conditions. Through selective enrichment at 4 °C, 15 °C, 28 °C, and 32 °C, we observed clear differences in phage infectivity, as assessed by plaque assays, along with genomic mutations and protein structural changes. Notably, mutations predominantly occurred in functional genes (ATPase, endolysin), while the examined structural loci remained conserved. Homology modeling revealed distinct adaptations in protein tertiary structures corresponding to environmental temperatures, suggesting that phage evolution mainly affects post-adsorption processes. Our findings elucidate a novel mechanism of temperature-driven functional protein evolution among cold-adapted bacteriophages (phage) and providing insights into their potential applications in microbial ecology and biotechnology.}, }
@article {pmid41748761, year = {2026}, author = {de Lima, LVA and da Silva, MF and de Oliveira, LM and de Assis, MCT and Carvalho, ICO and Fuzinatto, IM and Semprebon, SC and de Oliveira Nocetti, RV and Lazarin-Bidoia, D and Nakamura, CV and Felicidade, I and Lepri, SR and Favaron, PO and Dealis, ML and Cabeça, LF and Filho, GA and Mantovani, MS}, title = {PEGylated liposomal fluopsin C triggers cuproptosis and ferroptosis pathways and suppresses 3D tumor spheroid growth in NCI-H460 cells.}, journal = {Archives of toxicology}, volume = {}, number = {}, pages = {}, pmid = {41748761}, issn = {1432-0738}, }
@article {pmid41747730, year = {2026}, author = {Matias Rodrigues, JF and Tackmann, J and Malfertheiner, L and Patsch, D and Perez-Molphe-Montoya, E and Näpflin, N and Gaio, D and Rot, G and Danaila, M and Peluso, ME and Dmitrijeva, M and Schmidt, TSB and von Mering, C}, title = {The MicrobeAtlas database: Global trends and insights into Earth's microbial ecosystems.}, journal = {Cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2026.01.021}, pmid = {41747730}, issn = {1097-4172}, abstract = {Environmental DNA sequencing has revolutionized our understanding of microbial diversity and ecology. Microbiomes have now been sequenced across the entire planet-from the deep subsurface to the mountaintops-covering a myriad of hosts, biomes, and conditions. Yet, the diversity of sequencing and processing strategies hampers universal insights. MicrobeAtlas unifies more than two million microbiome samples in a single resource, harmonized to facilitate discoveries across technologies. Communities are hierarchically quantified at adjustable small subunit rRNA marker gene resolution and feature detailed metadata, including rich geographic information. Connections to the genome, phenotype, and ecological resources enable multimodal insights. Microbial lineages can be reliably tracked across environments, including a "long tail" of rare, uncharacterized species. Recurring community structures and geographic preferences become apparent, and global, taxonomy-specific generalism trends emerge. With MicrobeAtlas (www.microbeatlas.org), known and newly described species and communities can readily be placed into their ecological context, taking full advantage of earlier work.}, }
@article {pmid41746386, year = {2026}, author = {Wang, Z and Wang, Q and Liu, Y and Du, W and Hong, L and Zhou, D and Asiegbu, FO and Wu, P and Ma, X and Wang, K}, title = {Soil Nutrient Availability By Beneficial Bacteria of Forest Trees: From Mechanisms To Applications.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02728-z}, pmid = {41746386}, issn = {1432-184X}, abstract = {As global environmental challenges intensify, enhancing forest health and soil quality has emerged as a crucial area of research. Understanding and application of beneficial bacteria in forestry industry is urgently needed as an environmentally friendly and sustainable approach. Although thousands of patents have been registered for microbial application in agriculture and forestry, the mechanisms and application of beneficial bacteria on the soil nutrient availability have not been well summarized. This review investigated the role of beneficial bacteria in tree growth, particularly their contributions to soil nutrient availability in forest trees. We summarized that beneficial bacteria significantly enhance the availability of essential elements such as nitrogen, phosphorus, potassium, and iron by promoting nutrient cycling and transformation within the soil. This process supports tree growth and improves soil quality. Additionally, beneficial bacteria facilitate plant growth by synthesizing plant hormones and inducing resistance to biotic and abiotic stresses. This review concludes by discussing practical implications of beneficial bacterial colonization and application for enhancing soil nutrient levels, along with potential future research directions. We have enriched the theoretical framework of forest-associated bacteria and provided a scientific basis that can inform forest management and ecological restoration.}, }
@article {pmid41745260, year = {2026}, author = {Christinaki, AC and Floudas, D and Myridakis, AI and Gonou-Zagou, Z and Kouvelis, VN}, title = {Cladobotryum rhodochroum sp. nov. (Hypocreales, Ascomycota): A New Fungicolous Species Revealed by Morphology, Phylogeny, and Comparative Genomics.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {12}, number = {2}, pages = {}, pmid = {41745260}, issn = {2309-608X}, support = {19620//Hellenic Foundation for Research and Innovation/ ; }, abstract = {Species of the ascomycetous genus Cladobotryum (Hypocreales, Hypocreaceae) are ecologically and economically important mycoparasites that cause cobweb disease in cultivated and wild mushrooms. Despite their significance as fungal pathogens and producers of bioactive metabolites, the taxonomy of Cladobotryum remains unresolved due to extensive morphological plasticity, complex teleomorph-anamorph connections, and the presence of cryptic species. This study employs an integrative approach combining micro- and macromorphological characterization, multi-locus phylogeny (ITS, rpb2, and tef-1a), and comparative genomics to clarify the taxonomic position of the Greek isolate Cladobotryum sp. ATHUM 6904, previously designated as an unclassified red-pigmented (URP) strain. Phylogenetic analyses demonstrated that URP strains form a distinct, well-supported clade closely related to C. tenue and C. rubrobrunnescens, yet genetically and morphologically distinct from both. Comparative genomic analyses of isolate ATHUM 6904 and the ex-type strains of C. tenue and C. rubrobrunnescens revealed pronounced divergence in transposable element content, mitochondrial genome architecture, gene order, orthologous gene composition, secondary metabolite biosynthetic potential, and overall genomic distance. Micro- and macromorphological comparisons further supported the differentiation of isolate ATHUM 6904 from both reference species. Based on the combined molecular, morphological, and genomic evidence, the Greek isolate ATHUM 6904 is described as a novel species, Cladobotryum rhodochroum sp. nov.}, }
@article {pmid41744634, year = {2026}, author = {Pérez, E and Sanjuán, E and Jůzl, M and Raposo, A and Saraiva, A and Jaber, JR and Carrascosa, C}, title = {Active Antimicrobial Packaging Systems: Mechanisms of Microbial Control and Applications in Food Preservation.}, journal = {Biology}, volume = {15}, number = {4}, pages = {}, pmid = {41744634}, issn = {2079-7737}, abstract = {Microbial spoilage and foodborne pathogens remain central challenges in food safety, driven by the metabolic resilience and ecological adaptability of bacteria, yeasts, and molds across diverse food matrices. Active antimicrobial packaging has emerged as a biologically informed strategy that directly targets microbial physiology through controlled release or contact-mediated mechanisms. These systems employ natural antimicrobials, bacteriocins, essential oils, and metal nanoparticles to disrupt cell membranes, inhibit enzymatic pathways, generate reactive oxygen species, or interfere with quorum sensing, resulting in substantial reductions in microorganisms such as Listeria monocytogenes, Salmonella spp., E. coli O157:H7, Pseudomonas spp., Brochothrix thermosphacta, and spoilage fungi. In real food environments, these interventions achieve multi-log reductions and attenuate microbial metabolism, though efficacy varies with pH, water activity, fat content, and storage temperature. Oxygen scavengers further reshape microbial ecology by suppressing aerobic spoilage organisms while inadvertently favoring anaerobic competitors. Despite promising outcomes, concerns regarding nanoparticle migration, microbial resistance potential, and matrix-dependent performance highlight the need for deeper microbiological validation. Future progress will require integrative research linking microbial ecology, packaging material science, and mechanistic toxicology. By aligning with microbial behavior at the cellular and ecosystem levels, active antimicrobial packaging represents a powerful, biologically grounded approach to mitigating foodborne risks.}, }
@article {pmid41744504, year = {2026}, author = {Firrman, J and Liu, L and Mahalak, K and Lemons, JMS and Narrowe, A and Friedman, ES and Wu, GD and Van de Weile, T}, title = {An in vitro model of the small intestinal microbiota provides key insights into interindividual variability in structure and function.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0137325}, doi = {10.1128/msystems.01373-25}, pmid = {41744504}, issn = {2379-5077}, abstract = {UNLABELLED: Although there is clear evidence demonstrating the importance of the small intestinal microbiota (SIM) for nutrient utilization within the upper gastrointestinal tract, research is limited by difficulties accessing this community in vivo. Additionally, the high level of interindividual variability in taxonomic structure, which is well documented for the SIM, raises the question of how such divergent communities fill the same physiological roles. Here, we designed and evaluated an in vitro model of the terminal ileum representative of four unique donors and utilized it to interrogate interindividual variability. Shotgun sequencing confirmed that the in vitro communities were representative of their specific inocula and composed of facultative and obligate anaerobic taxa typical of the SIM, such as Klebsiella, Escherichia, Streptococcus, and Enterococcus. Untargeted metabolomics revealed a high degree of similarity between communities in terms of which metabolites were produced. Combining metagenomics and metabolomics, a core set of genes, features, and metabolites was found shared across all communities despite the high degree of structural variability observed. These results indicated that while the taxonomic structure of the SIM was variable between individuals, there were similarities in functional outcome due to underlying gene representation in the microbiome. Moving forward, this model system may serve as a starting point to further elucidate the role of the SIM in nutrition and health.<br><br>IMPORTANCE: The small intestinal microbiota (SIM) plays a pivotal role in nutrient digestion and absorption and immune function, with researchers continuing to find connections between this community and human health. Expanding on the currently available methods within the field to study this community, here, an in vitro model of the SIM was developed and designed to mimic the terminal ileum. Metagenomic and metabolomic analysis confirmed that this model recapitulated the unique communities of four different donors while maintaining the interindividual variability canonical of the SIM. Despite variation in taxonomic structure, in-depth analysis found that there was a core set of genes shared among the four in vitro communities that correlated with a relatively consistent metabolomic signature. These significant findings provided unique insight into the relationship between structural and functional variability for the SIM and furthered the field's understanding of how such structurally variable communities have such similar physiological outcomes.}, }
@article {pmid41743866, year = {2025}, author = {Tarigan, MB and Saragih, RM and Tarigan, KA and Ginting, F}, title = {Antimicrobial resistance and empirical antibiotic use in diabetic foot infections: A retrospective study from Indonesia.}, journal = {Narra J}, volume = {5}, number = {3}, pages = {e2895}, pmid = {41743866}, issn = {2807-2618}, abstract = {Diabetic foot infection (DFI) represents a major complication of diabetes mellitus with significant morbidity, frequently leading to amputation if not optimally managed. The aim of this study was to analyze clinical, microbiological, and antibiotic susceptibility data from patients with type 2 diabetes who presented with foot infections in Indonesia. The retrospective study, conducted at St. Elisabeth Hospital in North Sumatra, Indonesia, predominantly comprised male farmers with a mean diabetes duration of 8.6 years, most of whom exhibited advanced ulcer severity (64.5% at Wagner grade III). Surgical debridement was performed in 79.0% cases, and amputation in 21.0% of cases. Laboratory investigations revealed poor glycemic control (mean HbA1c 10.12%) and biochemical markers indicative of systemic inflammation and renal impairment. Microbial cultures identified a predominance of Gram-negative bacteria (58.1%), primarily Klebsiella pneumoniae, Proteus mirabilis, and Escherichia coli, whereas Gram-positive isolates (41.9%) were dominated by Staphylococcus aureus, including methicillin-resistant strains. Empirical outpatient and inpatient antibiotic regimens commonly included amoxicillin, ciprofloxacin, metronidazole, and ceftriaxone; however, in vitro susceptibility testing demonstrated limited efficacy of β-lactams such as ampicillin and amoxicillin (<10% sensitivity). In contrast, linezolid, amikacin, vancomycin, carbapenems, and fosfomycin exhibited superior activity against the isolated pathogens. These findings emphasize the critical need for empirical antibiotic guidelines tailored to local microbial ecology and resistance profiles, integrated with early surgical management, stringent glycemic control, and multidisciplinary care. This comprehensive approach is essential to reduce the risk of amputation and improve clinical outcomes in tropical, resource-limited settings.}, }
@article {pmid41743643, year = {2026}, author = {Markfeld, M and Talpaz, I and Biton, B and Maheriniaina Randriamoria, T and Soarimalala, V and Goodman, SM and Nunn, CL and Titcomb, G and Pilosof, S}, title = {Host traits and environmental factors shape infection heterogeneity in wild rat-protozoa networks.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag026}, pmid = {41743643}, issn = {2730-6151}, abstract = {The occurrence of microbes in animal hosts is highly heterogeneous, shaped by interactions among host traits, environmental context, and microbial diversity. Understanding this heterogeneity is particularly critical for endoparasite infections, where some hosts harbor diverse, high-burden assemblages that elevate disease spread and spillover risk. Yet the mechanisms underlying such heterogeneity remain poorly understood in wild systems, especially at the individual-host level. We addressed this challenge by studying protozoan infections in introduced black rats (Rattus rattus) across environmental gradients in Madagascar. Using network-based stochastic block modeling, we identified three infection profiles capturing meaningful variation in protozoan richness and composition, providing a structured framework for understanding heterogeneity. To uncover the predictors of these profiles, we trained machine-learning models incorporating host traits with environmental variables. Our models consistently outperformed no-skill baselines, with host traits contributing [Formula: see text]40% more to predictions than environmental factors. Body mass and gut microbiome composition emerged as the strongest host predictors, while rat and other non-native species densities were the most influential environmental predictors. These results show that infection heterogeneity arises from the interplay of intrinsic host traits and extrinsic environmental conditions. Our approach illustrates how combining network analysis with predictive modeling can (i) uncover latent heterogeneity in host-microbe associations, (ii) identify the relative contribution of the factors driving this heterogeneity, and (iii) predict host infection profiles. Our framework advances microbial ecology by linking host traits, microbial communities, and environmental context, while also informing disease ecology at human-animal interfaces where zoonotic pathogens circulate.}, }
@article {pmid41743513, year = {2025}, author = {Hylling, O and Forero-Junco, LM and Ellegaard-Jensen, L and Dedon, PC and Cui, L and Nielsen, TK and Hansen, M and Neve, H and Johansen, A and Kot, W}, title = {Novel Modification Sites of dPreQ0 in Aminobacter niigataensis Phage Erebus Provide New Insights into the Role of 7-Deazaguanine Modifications in Bacteriophages.}, journal = {PHAGE (New Rochelle, N.Y.)}, volume = {6}, number = {4}, pages = {250-258}, pmid = {41743513}, issn = {2641-6549}, abstract = {BACKGROUND: Bacteriophages protect themselves against host-encoded defense systems through DNA modifications. This study introduces Erebus, a newly identified phage infecting Aminobacter niigataensis, a bacterium capable of mineralizing 2,6-dichlorobenzamide- a common pesticide metabolite. The use of such bacterial degraders has been proposed for the bioremediation of contaminated groundwater. However, the presence of bacteriophages targeting these degraders poses a potential challenge to the success of such strategies.<br><br>MATERIALS AND METHODS: The Erebus phage was isolated and subjected to whole-genome sequencing. Phylogenetic analysis was performed to determine its taxonomic placement and genomic synteny. DNA modifications were identified using a combination of liquid chromatography-mass spectrometry (LC-MS) and Oxford Nanopore Technologies sequencing. Transmission electron microscopy was used to determine the phage morphology.<br><br>RESULTS: Phylogenetic analysis revealed that Erebus belongs to an unclassified genus, showing high synteny with Rhizobium phages of the Kleczkowskaviridae family. The phage possesses a double-stranded DNA genome of 52,229 base pairs, which includes a functional 7-deazaguanine DNA-modification system. Nanopore sequencing and LC-MS analysis confirmed the presence of PreQ0 modifications at novel GG and AG motifs, conferring resistance against multiple restriction endonucleases.<br><br>CONCLUSIONS: This is the first report of a phage infecting the genus Aminobacter, highlighting the potential impact of bacteriophages on microbial biodegradation strategies. The findings underscore the importance of considering phage-host interactions when deploying bacterial degraders for environmental remediation.}, }
@article {pmid41743133, year = {2026}, author = {Zhang, W and Jiang, H and Zhu, Q and Shi, Z and Chen, W and Xu, X and Peng, F and Chi, Y}, title = {Microbial diversity and water quality changes in mangrove sediments in Quanzhou Bay.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1743704}, pmid = {41743133}, issn = {1664-302X}, abstract = {This study investigated the diversity, composition, and environmental drivers of bacterial communities in the mangrove sediments of Quanzhou Bay, a subtropical estuary under anthropogenic pressure. Using high-throughput sequencing of the 16S rRNA gene, we analyzed samples from four sites (Fengze-FZ, Jinjiang-JJ, Luojiang-LJ, and Shishi-SS) representing a gradient of terrestrial influence and environmental conditions. The bacterial communities were predominantly composed of Pseudomonadota and Chloroflexi, a pattern consistent with global mangrove ecosystems but with distinct local structuring. Beta-diversity analyses (NMDS/PCA) revealed a significant spatial divergence, with the FZ site forming a distinct cluster separate from JJ, LJ, and SS, correlating with its unique environmental profile. Redundancy analysis (RDA) identified dissolved oxygen (LDO) and salinity as the key environmental factors shaping community structure. Functional prediction indicated a conserved potential for core metabolic processes (e.g., amino acid biosynthesis, bacterial chemotaxis) across sites, suggesting functional redundancy, while differences in the relative abundance of these pathways pointed to adaptive metabolic adjustments along the environmental gradient. Our findings demonstrate that the sedimentary microbial community structure in Quanzhou Bay is primarily shaped by localized environmental heterogeneity, providing critical insights into the microbial ecology of mangroves in urbanized coasts and a baseline for assessing ecosystem health and biogeochemical functioning under anthropogenic influence.}, }
@article {pmid41740962, year = {2026}, author = {Scheuerl, T and Rivett, DW}, title = {A Concept Using α-Niche Evolution Within Bacterial Communities to Direct β-Niche Evolution of Focal Species.}, journal = {Environmental microbiology}, volume = {28}, number = {3}, pages = {e70255}, doi = {10.1111/1462-2920.70255}, pmid = {41740962}, issn = {1462-2920}, support = {316807//UIBK/ ; 325779//Tyrolian Science Foundation/ ; 101067338//MSCA Postdoctoral Fellowship/ ; EP/X024830/1//EPSRC Postdoc Fellowship/ ; ISS-2021-109666//Vertex Pharmaceuticals Research/ ; }, abstract = {The process of bacterial adaptation has a profound impact on human wellbeing and health, but our toolkit to modify evolution is limited. Here, we present a concept of how steering adaptation can be achieved by integration of bacterial evolution and microbial ecology. The fundamental question is how specific species bloom after community perturbation and subsequently evolve. We consider two kinds of traits-α-niche traits involved in partitioning resources (e.g., broadened resource consumption) and β-niche traits driven by changes in the abiotic environment (e.g., pH adaptation or resistance after antibiotic treatment). We suggest that the evolution of the second trait can be directed indirectly via the evolution of the first trait, exploiting specific interspecies interactions. Thus, understanding how these traits interact in co-evolving communities may offer unprecedented opportunities to deflect trait evolution. Summarising current knowledge, emphasising open questions and highlighting conceptual ideas, we hope to stimulate new studies that are needed to move this field forward.}, }
@article {pmid41739277, year = {2026}, author = {Silva, MLOM and Martins, AKS and Sandes, SHC and Alvim, LB and Nunes, &#xc1;C and Camargo, ILBC and Tinoco, HP and Nicoli, JR and Martins, FS}, title = {Isolation and evaluation of antagonistic activity against pathogenic bacteria by Lactobacillus and Enterococcus spp. from the saliva of Speothos venaticus and Chrysocyon brachyurus.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {57}, number = {1}, pages = {}, pmid = {41739277}, issn = {1678-4405}, abstract = {UNLABELLED: Saliva plays a crucial role in oral defense across mammals by combining host-derived antimicrobial factors with antagonistic indigenous microbiota. Understanding the composition of the oral lactic microbiota in wild canids may provide valuable insights into microbial ecology and animal health. In this study, Lactobacillus and Enterococcus spp. isolated from the saliva of South American bush dogs (Speothos venaticus) and maned wolves (Chrysocyon brachyurus) were enumerated, identified, and evaluated for their antagonistic activity against pathogenic bacteria. For bacterial isolation, MRS agar and BHI agar supplemented with sodium azide (BHI-SA) were used for Lactobacillus and Enterococcus, respectively. Identification of the bacterial isolates was performed using PCR-ARDRA and multiplex PCR. Antagonistic activity was assessed using a double-layer agar diffusion assay, which detects diffusible inhibitory effects without identifying the compounds involved. A total of 23 bacterial isolates were obtained from BHI-SA and 24 from MRS for bush dogs, while 15 were recovered from BHI-SA and 23 from MRS for maned wolves. Salivary bacterial counts ranged from 4.0 to 5.0 log10 CFU/mL. In bush dogs, Enterococcus faecalis and Enterococcus faecium were identified, while E. faecalis and Enterococcus hirae were found in maned wolves. Limosilactobacillus reuteri, Lactiplantibacillus paraplantarum, Lactiplantibacillus plantarum and Lactobacillus johnsonii were isolated from bush dogs, while Ligilactobacillus salivarius and Latilactobacillus curvatus were identified in maned wolves. Antagonistic activity against indicator pathogens was more frequent among Lactobacillus isolates. These results suggest that the antibacterial properties observed in the saliva of these wild canids may be partly attributed to indigenous Lactobacillus and Enterococcus species.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42770-026-01877-0.}, }
@article {pmid41739174, year = {2026}, author = {Sánchez-Astráin, B and Borrego-Ramos, M and Viso, R and de la Hoz, CF and Blanco, S and Juanes, JA}, title = {Unravelling Diatom-Microbiome Dynamics in the Red Alga Gelidium Corneum (Florideophyceae, Rhodophyta).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02723-4}, pmid = {41739174}, issn = {1432-184X}, }
@article {pmid41738851, year = {2025}, author = {Kim, M and Hakeem, WGA and Rothrock, MJ}, title = {Key Farm-to-Fork Factors Influencing E. coli Levels in Pastured Poultry Production.}, journal = {Avian diseases}, volume = {69}, number = {4}, pages = {395-406}, doi = {10.1637/aviandiseases-D-25-00033}, pmid = {41738851}, issn = {1938-4351}, mesh = {Animals ; *Escherichia coli/isolation &amp; purification/physiology ; *Animal Husbandry/methods ; *Chickens ; Feces/microbiology ; *Escherichia coli Infections/veterinary/microbiology/epidemiology ; Soil Microbiology ; *Poultry Diseases/microbiology/epidemiology ; Farms ; Southeastern United States ; }, abstract = {Pastured poultry farms offer a unique model for investigating microbial ecology in less controlled environments, presenting challenges and opportunities for food safety management. This study aims to identify the key factors that influence Escherichia coli levels with two complementary modeling approaches: a linear mixed-effect model (LMM) and a random forest (RF) model. Data were collected from 11 pastured poultry farms in the southeastern United States from 2014 to 2017. Five sample types were analyzed: soil (n = 812), feces (n = 817), ceca (n = 206), postprocessing whole carcass rinse (WCR-P; n = 235), and final product whole carcass rinse (WCR-F; n = 230). Two different sets of predictor variables were used separately: 1) 32 farming practices and 26 physicochemical properties and 2) 80 meteorological factors. The model performance was compared with the randomized mean squared error (RMSE) with a test dataset. LMM was not used for meteorological factors because of the multicollinearity. Significant differences (α = 0.05) in E. coli levels were observed between all sample types, with feces samples showing the highest level. Compared to LMMs, RF models generally showed higher predictive accuracy (lower RMSE) on the test dataset. For soil samples, higher pH and sodium levels were linked to higher E. coli levels. The same trend with pH was observed in fecal samples. WCR-P samples showed that the organic acid treatment in the rinse water led to lower E. coli levels than other treatments. In WCR-F samples, longer storage time led to lower E. coli levels. Meteorological factors showed a weaker relationship with E. coli levels compared to farming practices and physicochemical properties, but in soil samples, mild and stable temperature played an important role in E. coli survival. This study can help stakeholders develop data-driven management strategies targeting key factors to aid in the reduction of food safety and animal health risk.}, }
@article {pmid41736367, year = {2026}, author = {Keum, HL and Sul, WJ and Kim, S and Chung, IY and Koh, A and Kim, HS}, title = {Preliminary characterization of the skin microbiota in basal cell carcinoma: An exploratory pilot study in Korean patients.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {}, number = {}, pages = {}, doi = {10.71150/jm.2511012}, pmid = {41736367}, issn = {1976-3794}, abstract = {Basal cell carcinoma (BCC) is the most common form of skin cancer, with ultraviolet radiation recognized as the primary environmental driver; however, the potential contribution of alterations in the skin microbiota remains incompletely understood, particularly in Asian populations. This exploratory pilot study describes bacterial community patterns in BCC lesions compared with contralateral clinically normal skin in 20 Korean patients. Lesional and contralateral samples were obtained using paired skin swabs and punch biopsies and analyzed by full-length 16S rRNA gene sequencing, with targeted quantitative PCR (qPCR) of the roxP antioxidant gene of Cutibacterium acnes. Given the low-biomass nature of skin samples and the exploratory design, analyses focused on descriptive trends rather than confirmatory inference. Across available samples, C. acnes was the dominant taxon, with a trend toward lower relative abundance in BCC lesions, particularly in biopsy-derived datasets. Microbial evenness appeared higher in lesions than controls. Predictive functional profiling suggested reduced representation of vitamin B6 metabolism pathways in lesions, while qPCR analysis of swab samples showed a trend toward lower roxP/16S rRNA ratios in BCC-associated microbiota. These findings should be interpreted cautiously in light of methodological constraints, including sample heterogeneity, lidocaine exposure prior to biopsy, absence of sequencing-based negative controls, and reliance on predictive functional inference. Overall, this pilot study highlights potential differences in skin bacterial community structure between BCC lesions and contralateral skin in a Korean cohort. Larger, methodologically optimized studies incorporating metagenomic and functional validation will be required to determine whether these microbiota shifts contribute to, or result from, BCC-associated changes in the cutaneous environment.}, }
@article {pmid41735517, year = {2026}, author = {Piaszczyk, W and Lasota, J and Foremnik, K and Błońska, E}, title = {Tree species determine soil microbial diversity: variation in fungal and bacterial communities in temperate forests.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-41297-6}, pmid = {41735517}, issn = {2045-2322}, support = {2022/06/X/NZ9/00006//Narodowe Centrum Nauki/ ; }, abstract = {This study investigates the influence of three deciduous tree species: small-leaved linden (Tilia cordata), common beech (Fagus sylvatica), and sessile oak (Quercus petraea) on soil microbial diversity in temperate forest ecosystems. Conducted on loess soils in southern Poland, the research clarifies species-specific effects on soil microbiota and chemical properties, providing insights into tree-microbe-soil interactions in forest environments. Soil samples were collected from monospecific stands and analysed using next-generation sequencing (NGS). Fungal and bacterial DNA was extracted, and libraries targeting the ITS1 (fungi) and 16 S rRNA V3-V4 (bacteria) regions were sequenced using the Illumina MiSeq platform. Microbial communities were evaluated in relation to soil pH, nutrient content, and exchangeable cations. Linden soils had the highest pH (5.1-7.0) and calcium content (18.9 cmol(+)·kg[-1]), while beech soils were the most acidic (pH 3.8-5.7) with the lowest calcium (8.0 cmol(+)·kg[-1]). Fungal communities were dominated by Basidiomycota, Ascomycota, and Mortierellomycota, with varying proportions across species. Bacterial diversity was highest in linden and oak stands. Dominant bacterial phyla included Actinobacteriota, Proteobacteria, and Acidobacteriota. Each tree species hosted a distinct microbial community, reflecting its impact on soil properties and microbial structure. Tree species significantly shape soil microbial diversity and chemistry. Incorporating microbial data into forest management may enhance soil function, biodiversity conservation, and ecosystem resilience. Broader spatial sampling is recommended to generalize findings.}, }
@article {pmid41734518, year = {2026}, author = {Dhillon, A and Yadav, P and Gupta, S and Singh, SV and Sohal, JS and Rawat, KD}, title = {Microbiome alterations and host-pathogen interactions in paratuberculosis: A one health perspective.}, journal = {Veterinary microbiology}, volume = {315}, number = {}, pages = {110940}, doi = {10.1016/j.vetmic.2026.110940}, pmid = {41734518}, issn = {1873-2542}, abstract = {Paratuberculosis is a chronic ruminal-enteric infection caused by Mycobacterium avium subsp. paratuberculosis (MAP). It has significant economic, trade, and public health implications. In addition to evading host immunity, MAP modulates the gut microbiome, resulting in dysbiosis that exacerbates disease progression. A conceptual framework is proposed in which Johne's disease (JD) can serve as the paradigm of chronic infection, based on dysbiosis in microbial imbalance, immune escape, and pathogen survival in a self-sustaining loop, as in human tuberculosis and Crohn's disease. This review evaluates the evidence on MAP-induced microbiome alterations and their impact on host-pathogen relations, immune responses, and metabolic processes in cattle, sheep, goats, and other ruminants. JD-associated dysbiosis is characterized by reduced microbial diversity, depletion of butyrate-producing taxa (e.g., Ruminococcaceae and Lachnospiraceae), enrichment of pro-inflammatory Enterobacteriaceae, and disruption of short-chain fatty acid (SCFA) metabolic pathways. Recent studies suggest that such alterations in microbes can be the initial signs of diagnosis and pre-treatment components, such as probiotics, prebiotics, dietary modifications, and microbiome-based vaccinations. This summary bridges the research on the veterinary and human microbiome, revealing that MAP-Microbiome interactions reflect immunological evasion and microbial persistence schemes observed with other intracellular pathogens. Evidence across species and disciplines highlights the interdependence between host microbiome stability, pathogen persistence, and disease progression. However, variances between studies show the need to adopt standardized methodologies, longitudinal studies, and multi-omics designs to establish whether dysbiosis precedes or follows MAP infection. The review is the first to combine molecular, immunological, and microbiome-level data into the One Health concept of MAP persistence. Moreover, this review takes a One Health approach where the investigation of MAP-induced dysbiosis offers an understanding of chronic inflammation, microbial ecology, and persistence strategies applicable to veterinary as well as human health. This way, we can emphasize the diagnostic, therapeutic, and translational opportunities of microbiome-based interventions in JD using a One Health model that connects ruminant disease to human inflammatory bowel diseases, including Crohn's disease.}, }
@article {pmid41733768, year = {2026}, author = {Zhou, S and Yao, Y and Yuan, R and Chu, W}, title = {Comparative Microbiome Analysis of Rhodiola fastigiata Rhizosphere Versus Bulk Soil in Xizang with Targeted Isolation of Rhizosphere-Derived Functional Strains.}, journal = {Molecular biotechnology}, volume = {}, number = {}, pages = {}, pmid = {41733768}, issn = {1559-0305}, support = {PAPD//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; }, abstract = {Rhodiola fastigiata, a critically endangered medicinal plant of the Qinghai-Xizang Plateau, faces severe threats from habitat degradation. This study aimed to support its microbial-assisted conservation by characterizing the rhizosphere microbiome and isolating functional plant growth-promoting (PGP) bacteria. Using high-throughput sequencing of the 16S rRNA gene and ITS region, we found the rhizosphere community to be distinct and enriched in key taxa (e.g., Sphingomonas, Mortierella). Metabolic predictions suggested upregulated stress-adaptive pathways. Crucially, from 126 isolates, we obtained four Bacillus strains that concurrently produce protease, amylase, and cellulase and solubilize phosphate-quantifying a multifunctional PGP profile critical for nutrient-poor soils. These culturable, spore-forming strains provide direct resources for developing synthetic inoculants. Our work bridges microbial ecology with applied biotechnology, delivering both a foundational microbial map and candidate strains to enable the cultivation and conservation of this endangered species in extreme environments.}, }
@article {pmid41733363, year = {2026}, author = {Ziegert, ZA and Troester, A and Frebault, J and Goffredo, P and Gaertner, WB and Jahansouz, C and Staley, C}, title = {SparCC co-occurrence networking reveals intracommunity dynamics of the microbiome following colorectal surgery.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0397325}, doi = {10.1128/spectrum.03973-25}, pmid = {41733363}, issn = {2165-0497}, abstract = {The intestinal microbiota plays a critical role in post-surgical wound healing following bowel resection; however, perioperative, prophylactic antibiotic administration may deleteriously affect it. We previously used 16S rRNA amplicon sequencing of stool samples to assess perioperative and longitudinal changes in the microbiome through 6 months in patients undergoing (i) colonoscopy after mechanical bowel prep (MBP) alone, (ii) non-resectional colorectal surgery after MBP with oral antibiotics and prophylactic intravenous antibiotics no longer than 24 h post-operative (surgical bowel prep [SBP]), and (iii) resectional colorectal surgery with SBP. Our objective in this study was to investigate the translational utility of SparCC co-occurrence networking to uncover biologically relevant patterns. Network topological parameters and hub species were calculated using NetCoMi, and permutational statistical tests were used to compare parameters. Network similarity among cohorts and time points generally matched changes in beta diversity, except in the resectional cohort, where all networks could not be differentiated statistically. Similarity in centrality measures among hub species was frequently significantly less similar than expected by chance and corresponded to an increased edge density and modularity, suggesting the latter parameters may reflect re-stabilization of the microbiome following surgery. We further noted the infrequently reported genera Enterocloster and Ruthenibacter were hub species during time points associated with surgical recovery, suggesting potentially novel roles for these genera in wound healing. Streptococcus, frequently implicated in surgical site infections at our center, was also frequently positively associated with Blautia throughout all networks, suggesting an increasing abundance of commensal bacteria serves as a prophylactic strategy.IMPORTANCEThis study employs the emerging approach of co-occurrence networking to assess ecological dynamics in the microbiome following colonoscopy and colorectal surgery. We expand upon applications of this approach to determine hub species and investigate clinically translational interpretations of network topological parameters in the context of recovery across three different trajectories of perturbation. Our results provide a context in which to interpret these network parameters biologically and represent a foundational step in beginning to quantitatively leverage network-based approaches to study microbial ecology. Furthermore, we identify network hub taxa that may play previously unexplored roles in wound healing.}, }
@article {pmid41733159, year = {2026}, author = {Diab, E and Du, C and Tigani, W and Elsayed, SS and van Wezel, GP}, title = {Plant Coumarins Modulate Natural Product Biosynthesis in a Streptomyces Root Endophyte.}, journal = {Journal of natural products}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jnatprod.5c01626}, pmid = {41733159}, issn = {1520-6025}, abstract = {The plant microbiome plays a central role in regulating plant health and resilience, providing eco-friendly alternatives to agrochemicals. Plant-associated Streptomyces species are prolific producers of structurally diverse natural products with a demonstrated role in promoting plant growth. Coumarins are prevalent plant metabolites that shape the root microbiome, but their impact on microbial natural product biosynthesis is poorly understood. Here, we demonstrate that the coumarins scopoletin and its glucoside scopolin remodel specialized metabolism in the Arabidopsis root endophyte Streptomyces sp. ATMOS53. Multiomics analyses revealed that the coumarins activate the biosynthesis of the pyrrolizidine alkaloids bohemamines and alter the balance in anthracycline biosynthesis, with reduced production of late-stage anthracycline congeners and accumulation of shunt metabolites earlier in the pathway. These metabolic shifts resulted in a marked reduction of the antimicrobial activity of ATMOS53 against plant-associated Bacillus and Paenibacillus species. Notably, coumarin-mediated repression of anthracycline production was also observed in the established producers Streptomyces peucetius and Streptomyces galilaeus, indicating that the regulatory effect on anthracycline biosynthesis is conserved in streptomycetes. Our findings highlight coumarins as modulators of specialized metabolism of Streptomyces and show the significance of plant-derived chemicals for the control of the biosynthetic capacity of plant-associated microbes.}, }
@article {pmid41732360, year = {2026}, author = {Yash,  and Ghosh, A and Dey, A and Sinha, M and Bera, N and Chakraborty, S and Bhadury, P}, title = {Dataset on ecological health and microbial communities of coastal aquaculture ponds from surrounding region of Sundarban mangroves.}, journal = {Data in brief}, volume = {65}, number = {}, pages = {112542}, pmid = {41732360}, issn = {2352-3409}, abstract = {Integrated Mangrove Aquaculture (IMA) and Sustainable Aquaculture in Mangrove Ecosystem Fisheries (SAIME) are key activities undertaken across coastal regions globally to meet growing demand for brackish-water aquaculture products through sustainable practices. An in-depth biomonitoring study was conducted to map the ecological health of IMA and non-IMA aquaculture ponds in the surrounding region of the Indian Sundarbans mangroves located along the northeast coast of Bay of Bengal. Surface water samples were collected from six aquaculture ponds, four IMA (IMA_C1, IMA_C3, IMA_DB1, and IMA_DB4) and two non-IMA (C6_NM and DB5_NM) in the month of October 2022, for characterizing niche-specific biological communities using the environmental DNA (eDNA) approach. During sampling, in-situ environmental parameters were recorded. Mangrove litter-derived phenolics (tannic and gallic acids) and dissolved nutrients were estimated using a UV-Vis spectrophotometer, while dissolved organic carbon (DOC) was measured with the elemental analyzer. Metal and metalloid concentrations were determined by inductively coupled plasma mass spectrometry approach (ICP-MS). IMA ponds showed ideal conditions for shrimp aquaculture, with pH ranging from 7.913 to 8.633 and dissolved oxygen (DO) between 5.32 and 6.03 mg/L, indicating no hypoxic conditions despite higher concentrations of phenolics. High-throughput sequencing (HTS) based on Oxford Nanopore Technologies (ONT) sequencing chemistry was undertaken on the MinION platform, revealing the predominance of Proteobacteria among prokaryotes and Bacillariophyta as well as Chlorophyta among eukaryotes from extracted eDNA in each studied pond. Additionally, members of the family Cyprinidae were also detected, reflecting the biodiversity of fish population in these ponds. Functional gene profiling indicated signatures associated with nitrogen, phosphorus, sulphur, potassium and iron acquisition and metabolism, along with pathways related to aromatic compound degradation. Overall, dissolved nutrients, dissolved organic carbon (DOC), metal and metalloid ion concentrations as well as structure and functional profiles of biological communities provide a comprehensive basis for evaluating the ecological health of aquaculture ponds. This study generates important baseline information for long-term monitoring and represents the first eDNA-based high-throughput sequencing assessment of IMA and non-IMA aquaculture ponds from surface water in close proximity to the Sundarbans mangrove.}, }
@article {pmid41729252, year = {2026}, author = {Li, Y and Chen, D and Liu, X and Li, Y and Chen, F}, title = {Zooplankton-associated Bacterial Communities are Dominated by Host-Specific Rather than Environmentally Random Taxa.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02702-9}, pmid = {41729252}, issn = {1432-184X}, }
@article {pmid41725809, year = {2026}, author = {Zenati, K and Braun, SD and Belhadi, D and Moawad, AA and Müller, E and Diezel, C and Brandt, C and Mostefaoui, R and Monecke, S and Zaidi, FZ and Belmahdi, M and Touati, A and Ehricht, R}, title = {The oral cavity as a reservoir for resistance- and hypervirulence-associated genes of Klebsiella pneumoniae in hospitalized patients.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1751947}, pmid = {41725809}, issn = {1664-302X}, abstract = {INTRODUCTION: This study investigated the epidemiology and distribution of carbapenem resistance and virulence genes in Klebsiella pneumoniae strains isolated from the oral cavity of hospitalized patients, highlighting their role as reservoirs in non-epidemic contexts.<br><br>METHODS: Carbapenem-resistant Klebsiella spp. were isolated from the oral cavity of 180 hospitalized patients in medical wards at two hospitals in Bejaia, Algeria. Screening for carbapenem resistance was performed on oral mucosa and saliva using Carba-MTL broth. Antibiotic susceptibility was assessed with the Vitek2 system and interpreted according to EUCAST guidelines. Whole genome sequencing (WGS) was carried out using Oxford Nanopore Technologies, with ABRicate used for resistance/virulence gene detection and Kleborate for hypervirulence assessment. Whole-genome sequences were further examined to identify single-nucleotide polymorphisms (SNPs) and to reconstruct a SNP-based phylogenetic tree in order to assess the genetic relatedness among the isolates.<br><br>RESULTS: Twenty Klebsiella strains were identified as K. pneumoniae. Among these, 85% were carbapenem-resistant, carrying OXA-48 (80%) or NDM-5 (5%), and all harbored blaCTX-M-15. WGS of the 20 K. pneumoniae strains revealed a broad resistome, including &#x3b2;-lactamases (CTX-M-15, CMY-4, OXA-1, TEM-1), sulfonamide (sul1, sul2), aminoglycoside (aac(3)-IIa, aadA2, aph(3')-VI, armA, strA, strB), trimethoprim (dfrA12, dfrA5, dfrA14), and tetracycline (tetA). Quinolone resistance was linked to QRDR mutations (gyrA S83I, parC S80I) and plasmid-mediated genes (qnrS1, qnrB10, qnrS10, aac(6')-Ib-cr). Five distinct sequence types (STs) were identified, including high-risk clones ST13 and ST48. Virulence profiling revealed yersiniabactin (85%), frequently linked to ICEKp elements (ICEKp4, ICEKp10), and colibactin (40%) among OXA-48 isolates. Notably, a single K. pneumoniae isolate harboring NDM-5 (K21) carried both hypervirulence markers (ybt9/ICEKp3, iuc1, rmp1/kpvp-1) and carbapenem resistance, documenting, for the first time in Algeria, the convergence of these traits in oral isolates. ICEKp was identified as the key vehicle for dissemination of yersiniabactin and colibactin, and a novel association between ICEKp and kpvp-1 was observed. Capsular typing showed predominance of K57-O1/O2v2 among OXA-48 producers and K27/O4 among NDM-5 strains.<br><br>CONCLUSION: This study provides the first evidence in Algeria of OXA-48- and NDM-5-producing K. pneumoniae in the oral cavity of hospitalized patients. The coexistence of carbapenem resistance and hypervirulence underscores the oral cavity as a critical reservoir, potentially fueling nosocomial infections and the dissemination of high-risk clones within hospitals and the wider community.}, }
@article {pmid41720792, year = {2026}, author = {Mohammadzadeh, R and Mahnert, A and Zurabishvili, T and Wink, L and Kumpitsch, C and Habisch, H and Sprengel, J and Filek, K and Mertelj, P and Pernitsch, D and Hingerl, K and Durdevic, M and Gorkiewicz, G and Diener, C and Loy, A and Kolb, D and Trautwein, C and Madl, T and Moissl-Eichinger, C}, title = {Cross-domain metabolic interactions link Methanobrevibacter smithii to colorectal cancer microbial ecosystems.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-69711-7}, pmid = {41720792}, issn = {2041-1723}, support = {10.55776/P32697//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; 10.55776/CoE7//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; 10.55776/CoE7//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; }, abstract = {The human gut is colonized by trillions of microbes that influence the health of their human host. Whereas many bacterial species have now been linked to a variety of different diseases, the involvement of Archaea, an evolutionarily distinct group of microbes, in human disease remains elusive. By analyzing 19 independent clinical studies, we demonstrate that associations between Archaea and human diseases are widespread yet highly heterogeneous, with a pronounced and consistent enrichment of Methanobrevibacter smithii in colorectal cancer (CRC) patients. Metabolic modelling and in vitro co-culture identified distinct mutualistic interactions of M. smithii with CRC-causing bacteria such as Fusobacterium nucleatum, including metabolic enhancement. Metabolomics further reveal archaeal-derived compounds with tumor-modulating properties. Together, our results provide mechanistic insights into how the human gut archaeome may participate in CRC-associated microbial networks through metabolic cooperation with bacteria.}, }
@article {pmid41720095, year = {2026}, author = {Wang, T and George, AB and Maslov, S}, title = {Higher-order interactions in auxotroph communities enhance their resilience to resource fluctuations.}, journal = {Cell systems}, volume = {}, number = {}, pages = {101491}, doi = {10.1016/j.cels.2025.101491}, pmid = {41720095}, issn = {2405-4720}, abstract = {Auxotrophs are prevalent in microbial communities, enhancing their diversity and stability-a counterintuitive effect considering their dependence on essential resources from other species. To address the ecological roles of auxotrophs, our study introduced a consumer-resource model (CRM) to capture the complex higher-order interactions within these communities. We also developed an intuitive graphical and algebraic framework, which assesses the feasibility of auxotroph communities and their stability under resource fluctuations and biological invasions. Validated against experimental data from synthetic E. coli auxotroph communities, the model accurately predicted outcomes of community assembly. Our findings highlight the critical role of higher-order interactions and resource dependencies in maintaining the diversity and stability of microbial ecosystems dominated by auxotrophs. A record of this paper's transparent peer review process is included in the supplemental information.}, }
@article {pmid41716220, year = {2026}, author = {Gomes-Neto, JC and Crook, A and Hestrin, R and Li, G and Liew, CS and Rosa, G and Singh, KD and Tuggle, CK and Summers, KL and Valdes, C and Fahlgren, N and Clarke, J}, title = {Challenges and opportunities: computational biology and the future of agriculture.}, journal = {Bioinformatics advances}, volume = {6}, number = {1}, pages = {vbag003}, pmid = {41716220}, issn = {2635-0041}, abstract = {MOTIVATION: The world of agriculture is rapidly changing with advances in artificial intelligence and demands for greater feed and food security considering environmental and sustainability challenges. The 30th Conference on Intelligent Systems in Molecular Biology (ISMB) held in July 2022 featured an invited session on the role of computational biology in Digital and Precision Agriculture. This session featured presentations by experts from various subdisciplines on novel research discoveries and a panel discussion on Digital Agriculture at Scale. Topics discussed during the session included genetics, epigenetics, and genomics of agriculturally relevant species; foodborne pathogen genomics and epidemiology; plant and animal phenomics; AI/machine learning; image analysis; remote sensing; educational innovations; discoveries resulting from public-private partnerships; data sharing and findable, accessible, interoperable, and reproducible (FAIR) data standards; biotechnology; and soil microbial ecology and biogeochemistry.<br><br>RESULTS: We present several of the current and future challenges and opportunities for computational biology in agriculture including why these challenges are important to address, what barriers exist, and what skills and competencies are required to be successful as a computational biologist in agriculture. We intend this summary to engage the computational biology community and attract them to the opportunities available for interesting and impactful work toward ensuring sustainable food security.}, }
@article {pmid41715924, year = {2026}, author = {Marín, MDC and Konno, M and Rozenberg, A and Béjà, O and Inoue, K}, title = {Novel light-driven schizorhodopsins from Antarctic patescibacteria and cyanobacteria.}, journal = {Biophysical journal}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.bpj.2026.02.022}, pmid = {41715924}, issn = {1542-0086}, abstract = {Microbial rhodopsins represent a diverse superfamily of light-sensitive proteins composed of seven transmembrane helices with expanding phylogenetic diversity driven by advances in metagenomics. Among these, schizorhodopsins constitute a divergent family originally identified as inward proton pumps from Promethearchaeota (Asgard archaea). Here, we report that in addition to archaeal schizorhodopsins, many members of the family originate from bacteria and detail a comprehensive biophysical characterization of two schizorhodopsins from uncultured Antarctic bacteria: paSzR from Minisyncoccota (Patescibacteria) and psSzR from a Pseudanabaenacea cyanobacterium. Both proteins function as light-driven inward proton pumps, as confirmed through pH measurements in Escherichia coli cells. Laser-flash photolysis experiments identified multiple photointermediates (K, L, and M) characteristic of microbial rhodopsin photocycles, though with slower turnover rates compared to archaeal schizorhodopsins. Site-directed mutagenesis of conserved residues in the third and sixth transmembrane helices demonstrates differential structural requirements between paSzR and psSzR. Our phylogenetic reconstruction reveals that most bacterial schizorhodopsins cluster in a single lineage distinct from archaeal variants. These findings expand our understanding of microbial rhodopsin diversity and provide crucial insights into alternative molecular mechanisms for light-driven proton translocation, with implications for microbial ecology in extreme environments.}, }
@article {pmid41715245, year = {2026}, author = {Luna, N and Hernández, C and Ramírez, AL and Urbano, P and Barragán, K and Ariza, C and Muñoz, M and Patiño, LH and Ramírez, JD}, title = {Ecological insights into the cross-domain microbiome interactions in the hematophagous bat Desmodus rotundus.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {22}, pmid = {41715245}, issn = {2524-4671}, abstract = {BACKGROUND: Bats are recognised as reservoirs for a wide range of microorganisms, including viruses, bacteria, fungi, and parasites, some of which are of zoonotic concern. The common vampire bat (Desmodus rotundus) is particularly important due to its hematophagous feeding behaviour and ecological adaptability, both of which enhance its potential for cross-species pathogen transmission. Despite its well-established relevance to public health, the microbial communities associated with D. rotundus remain poorly characterised. This study aimed at investigating the composition, diversity, and interactions of prokaryotic, eukaryotic, and viral communities, alongside feeding sources, using high-throughput sequencing in 27 D. rotundus individuals from a rural area in Casanare, eastern Colombia.<br><br>RESULTS: We analysed a total of 81 samples (blood, faeces, and oral swabs) using long-read amplicon sequencing of the 16S- and 18S-rRNA genes and viral metagenomics via Oxford Nanopore Technologies. The microbial profiles revealed highly diverse assemblages, encompassing a wide range of bacterial, fungal, eukaryotic parasites, and viral taxa, with significant variation in community structure and diversity metrics across the three sample types collected from each bat. Taxa of public health concern were detected, including Enterococcus faecalis, Mycoplasma spp. Acanthamoeba spp. and viruses from the families Coronaviridae, Retroviridae, and Circoviridae. Correlation analyses suggested potential intra- and inter-domain interactions and co-occurrence dynamics among these microbes. Additionally, feeding source profiling, based on vertebrate assignments from faeces and swab samples, indicated evidence of livestock consumption, suggesting possible transmission pathways between bats and domestic animals.<br><br>CONCLUSIONS: The detection of multiple co-occurring pathogens across distinct sample types, coupled with their association with feeding sources, highlights the role of D. rotundus as a functionally specialised reservoir capable of harbouring and potentially disseminating zoonotic microbes. This study provides new insights into the cross-domain microbial ecology of hematophagous bats and underscores the need to integrate microbial community profiling with host behavioural data to enhance surveillance and mitigation strategies for zoonotic disease transmission.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-025-00504-x.}, }
@article {pmid41714654, year = {2026}, author = {Rabaey, JS and Lewis, ASL and Attermeyer, K and Aurich, P and Bansal, S and Bartosiewicz, M and Bertolet, BL and Bussmann, I and Cadieux, SB and Calamita, E and Capelli, C and Carey, CC and Cillero, C and Clayer, F and D'Ambrosio, SL and Davidson, TA and Deemer, BR and Denfeld, BA and Eckert, W and Esposito, C and Ford, P and Gorsky, A and Griffiths, NA and Grossart, HF and Hamilton, DP and Holgerson, MA and Huser, BJ and Iwata, T and Jansen, J and Jones, SE and Juutinen, S and Kortelainen, P and Koschorreck, M and Kragh, T and Laas, A and Larmola, T and Läubli, S and Laurion, I and Lehmann, MF and Liu, L and Martikainen, PJ and Matoušů, A and McCord, SA and Montes-Pérez, JJ and Nizzoli, D and Ordóñez, C and Peacock, M and Pilla, RM and Prėskienis, V and Pu, J and Riis, T and Saarela, T and Santoso, AB and Schubert, CJ and Sepulveda-Jauregui, A and Sherman, BS and Sø, JS and Stenehjem, KJ and Strock, KED and Tsuchiya, K and Wendt-Potthoff, K and Weyhenmeyer, GA and Znachor, P and Zopfi, J}, title = {Depth-resolved carbon dioxide and methane concentrations in 522 lakes, ponds, and reservoirs worldwide.}, journal = {Scientific data}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41597-026-06751-0}, pmid = {41714654}, issn = {2052-4463}, abstract = {Lakes, ponds, and reservoirs (hereafter: "lakes") are important sources of the greenhouse gases carbon dioxide (CO2) and methane (CH4). Emissions of CO2 and CH4 from lakes are regulated in part by in-lake processes, including the production and storage of gases in the lower parts of the water column (bottom waters). However, while substantial efforts have been made to improve estimates of greenhouse gas emissions from lakes, limited data on gas concentrations along depth profiles have prevented the incorporation of bottom-water processes in global emission estimates. Here, we present GHG-depths: the largest existing dataset of depth-profile CO2 and CH4 measurements worldwide, including 522 lakes across 38 countries and all seven continents. These data include contributions from 45 research teams and 56 published studies, totaling 2558 discrete sampling events. As global change continues to alter biogeochemical cycling in lakes, these data can help improve mechanistic models to better predict greenhouse gas production and emission from lakes worldwide.}, }
@article {pmid41714186, year = {2026}, author = {Wang, B and Gao, P and Zhang, P and Zheng, Y and Liu, X and Ling, N and Shan, J and Yao, R and Zhao, S and Zhang, Z and Zhu, G and Jung, MY and Zou, J and Yan, X and Lee, S and Hazard, C and Nicol, GW and Zhou, J and Yang, Y and Zhu, Y and Stahl, DA and Wagner, M and Gao, Y and Jiang, J and Qin, W}, title = {Elevated Temperature Simulating Heatwaves Restructures Active Nitrifying Communities and Associated Viruses in Tidal Flats and Agricultural Soils.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag037}, pmid = {41714186}, issn = {1751-7370}, abstract = {Global heatwave intensification under climate change will impact the nitrogen cycle, yet its effect on active nitrifier groups or their interactions with viruses remains unclear. Using 13CO2-DNA-based stable-isotope probing coupled with metagenomics, we show that elevated temperatures under heatwave conditions fundamentally restructure active nitrifying communities and their associated viruses in Yangtze River estuary upper tidal flats and adjacent agricultural soils. In tidal flats, sustained high temperature constrained nitrification by reducing the abundance of active ammonia-oxidizing archaea and bacteria (AOA, AOB) and canonical nitrite-oxidizing bacteria (NOB). This was accompanied by a shift in the active community from marine to more thermotolerant but less salt-tolerant terrestrial ecotypes. Conversely, heatwave conditions in agricultural soils suppressed AOB but enhanced nitrification activity in thermotolerant terrestrial AOA ecotypes. Across both ecosystems, inferred virus-nitrifier interactions were temperature dependent. 13C-labeled nitrifier-infecting viruses exhibited coordinated shifts in virus-to-host abundance ratios and predicted lifestyles with their hosts, with sustained high temperatures reducing virus-to-host abundance ratios and favoring temperate infections, relative to higher abundance ratios and a greater proportion of predicted lytic cycles at lower temperatures. We identified AOA-infecting viruses that carry plastocyanin (pcy), encoding a key copper-dependent electron carrier in the AOA respiratory chain, with conserved active sites and a predicted protein fold that supports its capacity for electron transfer, potentially augmenting host energy metabolism. Together, our findings demonstrate that prolonged heatwaves drive coupled shifts in nitrifier community composition and virus-host interaction strategies in a land-use-dependent manner, with implications for nitrogen transformations and ecosystem feedbacks under climate extremes.}, }
@article {pmid41713418, year = {2026}, author = {Shao, Y and Wang, S and Gichuki, BM and Stares, MD and Rozday, TJ and Kumar, N and Browne, HP and Dawson, NJR and Njunge, JM and Tigoi, C and Ngao, N and Chisti, MJ and Singa, BO and Kariuki, S and Diallo, AH and Saleem, AF and Ali, SA and Mupere, E and Mbale, E and Tickell, KD and Voskuijl, WP and Lancioni, CL and Bandsma, RHJ and Ahmed, T and Walson, JL and Berkley, JA and Lawley, TD}, title = {Genomic atlas of Bifidobacterium infantis and B. longum informs infant probiotic design.}, journal = {Cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2026.01.007}, pmid = {41713418}, issn = {1097-4172}, abstract = {Bifidobacterium longum and B. infantis are pioneer colonizers of the neonatal gut and are widely used as probiotics to support infant growth, development, and disease resistance. However, commercial strains derived largely from high-income countries (HICs) may be suboptimal for infants in low- and middle-income countries (LMICs). We assembled a global genomic atlas of more than 4,000 genomes from 48 countries, increasing representation from LMICs by 12- to 17-fold. High-resolution phylogenomic and functional analyses support delineating B. longum and B. infantis as distinct species with divergent functions and epidemiological patterns. B. infantis dominates early-life microbiota in LMICs but is rarely detected in HICs. Natural B. infantis strains show extreme biogeographic stratification and predicted adaptations to local plant-glycan-rich diets and breast-milk-derived substrates, including urea and B vitamins. This genomic resource enables genome-guided selection of geographically matched strains to inform more effective probiotics and precision microbiome therapeutics for diverse infant populations.}, }
@article {pmid41713400, year = {2026}, author = {Wang, XW and Wang, T and Liu, YY}, title = {Artificial intelligence for microbiology and microbiome research.}, journal = {Cell systems}, volume = {17}, number = {2}, pages = {101531}, doi = {10.1016/j.cels.2026.101531}, pmid = {41713400}, issn = {2405-4720}, mesh = {*Artificial Intelligence/trends ; *Microbiota/physiology ; Humans ; Machine Learning ; *Microbiology/trends ; }, 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 first introduce foundational AI techniques 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 and prediction, microbe-X interactions, microbial ecology, metabolic modeling, precision nutrition, and clinical microbiology to prevention and 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 {pmid41708342, year = {2026}, author = {Alfahl, Z and Lynch, R and O'Dwyer, C and Kelly, JP}, title = {Medical versus science students: Knowledge, perceptions and learning of core pharmacology concepts.}, journal = {British journal of clinical pharmacology}, volume = {}, number = {}, pages = {}, doi = {10.1002/bcp.70498}, pmid = {41708342}, issn = {1365-2125}, abstract = {AIMS: Pharmacology is a core discipline underpinning both medical and biomedical science education, essential for understanding drug action, safety and therapeutic efficacy. This study compared pharmacology knowledge, perceptions and learning experiences between second-year medical and science students to evaluate how effectively each curriculum supports acquisition of internationally defined core pharmacology concepts.<br><br>METHODS: A mixed-methods design was employed, involving pre- and post-module surveys and curriculum mapping against the global pharmacology core concept framework. Quantitative data were analysed using chi-squared tests, while qualitative responses were evaluated thematically. Participants included students enrolled in MD214 Introduction to Pharmacology (medical) and PM208 Fundamental Concepts in Pharmacology (science) at the University of Galway.<br><br>RESULTS: Medical students demonstrated stronger baseline and post-module understanding of pharmacokinetic and pharmacodynamic principles, particularly in applied pharmacokinetics such as drug-drug interactions and variability in drug response. Science students showed significant improvement over time, reflecting effective conceptual learning. Both cohorts reported positive perceptions of module relevance and teaching effectiveness (mean scores 7.7-8.9/10) and moderate to high confidence in mastering core concepts. YouTube and textbooks were the most common supplementary resources. Curriculum mapping showed alignment with 23 of 24 core concepts in the medical module and 20 in the science module.<br><br>CONCLUSIONS: Medical students exhibited greater initial competence and perceived relevance, whereas science students benefited substantially from targeted instruction. Findings highlight the value of concept-based, contextually integrated pharmacology teaching and support continued curriculum development guided by international core concept frameworks.}, }
@article {pmid41705859, year = {2026}, author = {Medeiros, WB and Centurion, VB and Silva, JB and Duarte, AW and Hidalgo-Martinez, KJ and Dos Santos, JA and Penna, DDPS and Bagci, C and Ziemert, N and Oliveira, VM}, title = {Antarctic soil prokaryotic diversity: a dataset of 319 metagenome-assembled genomes from Deception and Livingston Islands.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0134625}, doi = {10.1128/mra.01346-25}, pmid = {41705859}, issn = {2576-098X}, abstract = {A total of 319 bacterial metagenome-assembled genomes (MAGs) were recovered from soil samples collected on the Antarctic Peninsula (Deception and Livingston Islands). These MAGs reveal microbial life's phylogenetic diversity and functional potential in extreme polar environments, providing resources for advancing microbial ecology, evolution, and Antarctic biotechnology.}, }
@article {pmid41705204, year = {2026}, author = {Verbunt, J and Mennens, L and Jocken, J and Blaak, EE and Savelkoul, P and Stassen, FRM}, title = {From food to vesicle: nutritional influences on gut microbial inflammatory signaling.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1756462}, pmid = {41705204}, issn = {2296-861X}, abstract = {Diet is a pivotal determinant of gut microbial ecology, giving not only rise to specific bacterial compositionality but also its functional output. Studying functional readouts-such as microbial metabolite production-could provide a more accurate and mechanistically informative measure of intervention outcome than traditional compositional profiling alone. Bacterial membrane vesicles (bMVs) are gaining attention as mediators of microbial metabolism and output. These nanoparticles are selectively released as carriers of bioactive proteins, lipids, nucleic acids, and metabolites reflective of the activity of the parent bacteria. Importantly, bMVs are rigid, can efficiently be isolated from feces, and are able to stably transport their cargo to interact with the host. In interacting with immune cells or pathogen recognition receptors, they can potentiate inflammatory responses. Given their extensive, multifaceted involvement in inter-Kingdom communication, bMVs represent an important biomarker for evaluating dietary modulation of gut microbial function. We propose that characterization of gut-derived bMVs offers a highly sensitive, mechanistically grounded approach to titrating impact of dietary interventions. By capturing shifts in microbial metabolic activity and inflammatory potential, bMV-based assessments could complement or surpass traditional measures of microbiome compositional change. Integrating bMV profiling into dietary intervention studies may therefore provide new insight into the functional consequences of diet-microbiome interactions and help refine strategies aimed at reducing inflammation and promoting host health.}, }
@article {pmid41704769, year = {2026}, author = {Yinhang, W and Xueli, J and Zheng, W and Xiaojian, Y and Shu, X and Qingjie, Z and Ying, L and Shuwen, H}, title = {Gut fungal landscape in colorectal cancer and its cross-kingdom interplay with gut microbial ecology.}, journal = {iScience}, volume = {29}, number = {2}, pages = {114664}, pmid = {41704769}, issn = {2589-0042}, abstract = {The gut microbiota is a key hallmark of colorectal cancer (CRC), yet gut fungi remain understudied. We characterized the gut fungal landscape and its associations with bacteria, metabolites, and trace elements in CRC using fecal samples from healthy controls (n = 401), colorectal polyp patients (n = 162), and CRC patients (n = 253). Fungal annotation was performed using genomic data from NCBI (PRJNA833221) as reference. Fungal diversity increased in CRC patients, with seven genera showing differential abundance. Rhizopus was specifically enriched in CRC, while Sporisorium, etc. enriched in polyps. Ablation study identified an optimal 31-microbial-marker panel (28 bacteria and three fungi) that effectively distinguished intestinal disease groups (AUC = 0.89). Structural equation modeling revealed three fungal markers-Penicillium citrinum, Penicillium sp. PG10607D, and Rhizopus stolonifera-that influence bacterial-metabolite-trace element networks. This study delineates the gut fungal atlas in CRC and reveals complex cross-kingdom interactions, offering new insights into CRC pathogenesis.}, }
@article {pmid41703880, year = {2026}, author = {Mipun, P and Sarma, P and Dey, G and Terangpi, L and Hajong, B and Chakraborty, D and Kshetriya, D and Mandal, SM and Dinata, R and Baindara, P}, title = {Ethnic fermentation secrets of Northeast India and emerging functional food insights.}, journal = {Food research international (Ottawa, Ont.)}, volume = {228}, number = {}, pages = {118431}, doi = {10.1016/j.foodres.2026.118431}, pmid = {41703880}, issn = {1873-7145}, mesh = {India ; *Fermentation ; *Fermented Foods/microbiology ; Humans ; *Functional Food/microbiology ; *Food Microbiology ; *Ethnicity ; Probiotics ; }, abstract = {Northeast India is home to an incredible variety of ethnic fermented foods, shaped over centuries by cultural wisdom and adaptation to the local environment. From bamboo shoots, soybeans, and rice to fish, dairy, vegetables, and traditional beverages, these foods are deeply woven into daily life and are rich in beneficial microorganisms with probiotic potential. Understanding the microbial ecology, biochemical transformations, and functional metabolites of Northeast India's traditional fermented foods provides a scientific basis for improving safety, identifying bioactive ingredients, and guiding the development of next-generation fermented products. This review brings together insights from ethnomicrobiological surveys and culture-based studies to explore the microbes, fermentation pathways, and biochemical changes that give these foods their distinctive qualities, as well as their nutritional benefits and safety considerations. We highlight lesser-known products, examine toxin-producing pathogens, and profile antimicrobial peptides (AMPs), uncovering varying levels of pathogen risk across products. Additionally, fermentation space analysis reveals exciting opportunities to create new foods by creatively combining local ingredients. Finally, we look at how modern tools, including artificial intelligence (AI) and machine learning (ML), can help scale up production, standardize quality, and ensure safety. Overall, by blending traditional knowledge with modern biotechnology and AI, these unique fermentation foods could find their place globally while preserving their cultural roots.}, }
@article {pmid41568973, year = {2026}, author = {Downing, BE and Gupta, D and Shalvarjian, KE and Nayak, DD}, title = {Genus-specific remodeling of carbon and energy metabolism facilitates acetoclastic methanogenesis in Methanosarcina spp. and Methanothrix spp.}, journal = {Journal of bacteriology}, volume = {208}, number = {2}, pages = {e0044825}, doi = {10.1128/jb.00448-25}, pmid = {41568973}, issn = {1098-5530}, support = {F32GM150233/NH/NIH HHS/United States ; Packard Fellowship in Science and Engineering//David and Lucile Packard Foundation/ ; S589706//U.S. Department of Energy/ ; Sloan Research Fellowship//Alfred P. Sloan Foundation/ ; Early Career Investigator in Marine Microbial Ecology and Evolution//Simons Foundation/ ; Beckman Young investigator Award//Arnold and Mabel Beckman Foundation/ ; Searle Scholars Award//Kinship Foundation/ ; 202299857//National Science Foundation Graduate Research Fellowship Program/ ; }, mesh = {*Methane/metabolism/biosynthesis ; *Methanosarcina/metabolism/genetics ; *Energy Metabolism ; Acetates/metabolism ; *Carbon/metabolism ; Archaeal Proteins/metabolism/genetics ; Gene Expression Regulation, Archaeal ; Acetyl Coenzyme A/metabolism ; }, abstract = {UNLABELLED: Methanogenic archaea (methanogens) are microorganisms that obligately produce methane as a byproduct of their energy metabolism. While most methanogens grow on CO2+H2, isolates of the genera Methanosarcina and Methanothrix can use acetate as the sole substrate for methanogenesis. Methanogenic growth on acetate, i.e., acetoclastic methanogenesis, is hypothesized to require two distinct genetic modules: one for the activation of acetate to acetyl-CoA and another for producing a chemiosmotic gradient using electrons derived from ferredoxin. In Methanosarcina spp., the activation of acetate to acetyl-CoA is mediated by acetate kinase (Ack) and phosphotransacetylase (Pta), whereas Methanothrix spp. encode AMP-forming acetyl-CoA synthetases (Acs). The Rhodobacter nitrogen fixation complex (Rnf) or energy-converting hydrogenase (Ech) is critical for energy conservation in Methanosarcina spp. during growth on acetate, and a F420:methanophenazine oxidoreductase-like complex (Fpo') likely plays an analogous role in Methanothrix spp. Here, we tested the proposed modularity of these pathways to facilitate acetoclastic methanogenesis. First, we surveyed over 100 genomes within the class Methanosarcinia to show that the genomic potential for acetoclastic methanogenesis is widespread. We then used the genetically tractable strain, Methanosarcina acetivorans, to build all modular combinations that might support acetoclastic methanogenesis. Our results indicate that Acs, while functional, cannot replace Ack+Pta to rescue acetate growth in M. acetivorans. Similarly, the Fpo' bioenergetic complex cannot replace Rnf. As such, our work suggests that, in addition to horizontal gene transfer of core catabolic modules, acetoclastic metabolism in methanogens requires changes to core energy metabolism too.<br><br>IMPORTANCE: A large fraction of biogenic methane is derived from acetate, yet acetoclastic methanogens, i.e., methanogens that grow on acetate, remain poorly characterized due to their slow growth. Two groups of methanogens, Methanosarcina spp. and Methanothrix spp., perform acetoclastic methanogenesis using distinct sets of genes for acetate activation and energy conservation. It is widely hypothesized that these genetic modules from Methanosarcina spp. and Methanothrix spp. are functionally analogous and would thus be interchangeable. To test this hypothesis, we engineered different combinations of modules for acetoclastic growth in Methanosarcina acetivorans. Our results challenge this hypothesized paradigm of modularity, and we posit that other changes to the carbon and electron transfer pathways are crucial for the emergence of acetoclastic methanogenesis.}, }
@article {pmid41703847, year = {2026}, author = {Gil, MI and Tudela, JA and Illán, G and Hernández, N and Andújar, S and Sabater, D and Allende, A and Truchado, P}, title = {Industrial-scale application of bacteriophages on baby spinach: One-year study of Listeria control, quality and microbial community shifts.}, journal = {Food research international (Ottawa, Ont.)}, volume = {228}, number = {}, pages = {118384}, doi = {10.1016/j.foodres.2026.118384}, pmid = {41703847}, issn = {1873-7145}, mesh = {*Spinacia oleracea/microbiology ; *Bacteriophages ; *Food Microbiology/methods ; *Listeria/virology ; Listeria monocytogenes/virology ; Microbiota ; *Food Preservation/methods ; Food Handling/methods ; Food Contamination/prevention &amp; control ; }, abstract = {Bacteriophages have emerged as promising biocontrol agents against pathogenic bacteria due to their strong antimicrobial activity and host specificity. In this study, we evaluated a previously validated industrial bacteriophage cocktail (PhageGuard Listex™) for its performance on baby spinach, focusing on product quality and microbial community dynamics. Twenty industrial trials conducted over one year compared non-treated and phage-treated baby spinach samples after processing (day 0) and after 10 days of storage under commercial (3 d at 4 °C followed by 7 d at 7 °C) and abusive (continuous 10 °C) temperature conditions. Phage stability was confirmed in the application solution and persistence on the product surface after storage. Although Listeria monocytogenes was not detected in any sample (0/600), the proportion of samples positive for Listeria spp. was significantly lower in the phage-treated group (6%) than in the non-treated group (12%). The preventive phage application did not affect headspace gas composition, sensory attributes, or objective color parameters. Quality deterioration was observed only at 10 °C, regardless of phage treatment. Despite the reduction in Listeria spp. prevalence, microbial diversity and community structure were unaffected by phage application, consistent with the low relative abundance of Listeria spp. in the microbiota and the narrow host range of the phage cocktail; storage conditions, particularly temperature, were the most influential factor affecting bacterial taxonomic composition. The relative abundance of Pseudomonas and Flavobacterium increased during storage, while Bacillus and Exiguobacterium decreased. These findings support the feasibility of using this bacteriophage-based treatment as a preventive intervention that does not affect product quality and preserves the natural microbial ecology of baby spinach during storage.}, }
@article {pmid41703844, year = {2026}, author = {Fang, X and Pu, Q and Qu, A and Wang, C and Shen, T and Wu, S and Li, M and Sui, M and Ji, Z and Huang, Y}, title = {Mechanisms of phenolic conversion in anaerobic fermentation of tea leaves revealed by integrating microbiome and metabolome analysis.}, journal = {Food research international (Ottawa, Ont.)}, volume = {228}, number = {}, pages = {118381}, doi = {10.1016/j.foodres.2026.118381}, pmid = {41703844}, issn = {1873-7145}, mesh = {*Fermentation ; *Phenols/metabolism/analysis ; *Plant Leaves/microbiology/metabolism/chemistry ; *Microbiota ; *Tea/microbiology/chemistry/metabolism ; *Metabolome ; Anaerobiosis ; Metabolomics/methods ; Bacteria/metabolism ; *Camellia sinensis/microbiology ; Flavonoids/metabolism ; }, abstract = {To systematically investigate the phenolic transformation mechanisms during tea anaerobic fermentation, the changes in phenolics and microbial communities of pickled teas under varying extrusion degrees were analyzed by combining metabolomics and microbiomics. The changes in 118 differential phenolics (p < 0.05, variable importance in projection >1.0, and fold change >1.2 or < 1/1.2) revealed that anaerobic fermentation drives the bioconversion of bound phenolics into free phenolics and their derivatives in tea leaves. Additionally, the potential metabolic pathways of tea phenolics in anaerobic fermentation were comprehensively proposed, mainly including hydrolysis of polymerized/galloylated catechins, hydrolysis of flavonoid glycosides, and hydrolysis of galloylated phenolics to release gallic acid and its further derivatization. The degree of extrusion significantly influenced microbial community succession: high-extrusion enriched Enterobacter, Cladosporium, Setophoma, and Vishniacozyma, enhancing the hydrolysis of flavonoid glycosides and depsides, while light-extrusion promoted Candida, Cyberlindnera, Lactobacillus, and Pantoea, favoring the accumulation of free phenolics and their derivatives. These findings establish a mechanistic link between microbial ecology and phenolic biotransformation, providing a foundation for precision fermentation in tea processing.}, }
@article {pmid41700860, year = {2026}, author = {Machushynets, NV and Elsayed, SS and Du, C and Lysenko, V and de la Cruz, M and Sanchez, P and Genilloud, O and Martin, NI and Liles, MR and van Wezel, GP}, title = {Paenitracins, a novel family of bacitracin-type nonribosomal peptide antibiotics produced by plant-associated Paenibacillus species.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0149625}, doi = {10.1128/msystems.01496-25}, pmid = {41700860}, issn = {2379-5077}, abstract = {The growing threat of antimicrobial resistance necessitates the discovery of novel antibiotics with activity against drug-resistant pathogens. Members of the genus Paenibacillus are a rich source of nonribosomal peptides (NRPs), including well-known antibiotics such as polymyxins, paenibacterin, and tridecaptins. Here, we use a targeted mass spectrometry query language (MassQL)-based approach to identify the NRPs produced by a collection of 227 taxonomically diverse plant-associated Paenibacillus strains, providing detailed insights into their NRP-producing potential. Using MassQL to zoom in specifically on NRPs containing basic amino acids, we discovered a novel family of bacitracins, which we designated paenitracins. The paenitracins are the first bacitracin-type peptides reported in Paenibacillus and are distinguished from canonical bacitracins by three previously unseen amino acid substitutions. The paenitracins exhibit potent activity against gram-positive pathogens, including vancomycin-resistant Enterococcus faecium E155. Our work provides a novel metabolomics-guided and genomics-guided workflow for the discovery of bioactive NRPs as a strategy to prioritize natural product chemical space and accelerate antibiotic discovery.IMPORTANCEMembers of the genus Paenibacillus play an important role in soil ecology, producing a range of important nonribosomal peptides (NRPs). A collection of plant-associated Paenibacillus spp. were analyzed for their phylogenetic and metabolic diversity. We developed a novel discovery pipeline that combines feature-based molecular networking with mass spectrometry query language queries to systematically prioritize bioactive NRPs containing basic amino acids. Thus, we provide a comprehensive genus-wide inventory of NRPs produced by Paenibacillus spp. We thereby identified the paenitracins, a new sub-family of bacitracins active against multidrug-resistant gram-positive pathogens. Our pipeline enables the discovery of novel peptidic natural products to accelerate the prioritization of chemical space for antibiotics.}, }
@article {pmid41700805, year = {2026}, author = {Zhou, S and Bai, X and Xue, B and Chu, W}, title = {A Vaginal Microbiota-Ovary Axis in Chemotherapy-Accelerated Ovarian Aging: Single-Cell Insights into Cellular Dysregulation.}, journal = {Biology of reproduction}, volume = {}, number = {}, pages = {}, doi = {10.1093/biolre/ioag042}, pmid = {41700805}, issn = {1529-7268}, abstract = {BACKGROUND: Chemotherapy-induced premature ovarian failure (POF) represents a major challenge to female reproductive health, yet the potential regulatory role of vaginal microbiota in this process remains largely unexplored.<br><br>RESULTS: Using a well-established model of chemotherapy-induced ovarian aging, we observed significant disruptions in vaginal microbial ecology characterized by depletion of Lactobacillus species and concomitant enrichment of pathogenic bacteria. Microbiota transplantation effectively reversed these dysbiosis patterns and restored ovarian function. Single-cell transcriptomic analysis revealed that microbial intervention promoted the recovery of granulosa and luteal cell populations while simultaneously suppressing inflammatory activation in ovarian stromal cells, demonstrating the vaginal microbiota's capacity to maintain follicular integrity. Further mechanistic insights showed that microbiota transplantation upregulated key antioxidant defense systems and ribosomal protein networks within ovarian cells, suggesting coordinated actions to mitigate oxidative stress and enhance cellular repair capacity, although the specific microbial metabolites mediating these effects require further elucidation.<br><br>CONCLUSIONS: Our findings establish for the first time the existence of a functional vaginal microbiota-ovary axis and delineate its critical role in protecting against chemotherapy-induced ovarian damage. This work not only advances our fundamental understanding of microbial-endocrine crosstalk but also identifies concrete microbial targets for developing innovative strategies to preserve fertility in cancer patients.}, }
@article {pmid41697449, year = {2026}, author = {Zavřel, T and Pohland, AC and Pfennig, T and Matuszyńska, AB and Tóth, SZ and Bernát, G and Červený, J}, title = {Correction to: Estimating the redox state of the plastoquinone pool in algae and cyanobacteria via OJIP fluorescence: perspectives and limitations.}, journal = {Photosynthesis research}, volume = {164}, number = {2}, pages = {14}, doi = {10.1007/s11120-026-01203-7}, pmid = {41697449}, issn = {1573-5079}, }
@article {pmid41697388, year = {2026}, author = {Ding, Z and Guo, Y and Guo, L and Ren, B and Yang, J and Li, J and Bai, L}, title = {Reintroduction of Grassland Plant Species Shapes Soil Bacterial Ecological Groups and Contributes Differently To Bacterial Diversity.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02718-1}, pmid = {41697388}, issn = {1432-184X}, support = {LJKMZ20221053//Foundation of Liaoning Province Education Administration/ ; X2021012//Shenyang Agricultural University/ ; }, }
@article {pmid41696024, year = {2026}, author = {Pendleton, A and Schmidt, ML}, title = {Interpreting UniFrac with absolute abundance: a conceptual and practical guide.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycaf250}, pmid = {41696024}, issn = {2730-6151}, abstract = {[Formula: see text]-diversity is central to microbial ecology, yet commonly used metrics overlook changes in microbial load (or "absolute abundance"), limiting their ability to detect ecologically meaningful shifts. Popular for incorporating phylogenetic relationships, UniFrac distances currently default to relative abundance and therefore omit important variation in microbial abundances. As quantifying absolute abundance becomes more accessible, integrating this information into [Formula: see text]-diversity analyses is essential. Here, we introduce "Absolute UniFrac" ([Formula: see text]), a variant of Weighted UniFrac that incorporates absolute abundances. Using simulations and a reanalysis of four 16S rRNA metabarcoding datasets (from a nuclear reactor cooling tank, the mouse gut, a freshwater lake, and the peanut rhizospere), we demonstrate that Absolute UniFrac captures microbial load, composition, and phylogenetic relationships. While this can improve statistical power to detect ecological shifts, we also find Absolute Unifrac can be strongly correlated to differences in cell abundances alone. To balance these effects, we also incorporate absolute abundance into the generalized extension ([Formula: see text]) that has a tunable, continuous ecological parameter ([Formula: see text]) that modulates the relative contribution of rare versus abundant lineages to [Formula: see text]-diversity calculations. Finally, we benchmark GU[A] and show that although computationally slower than conventional alternatives, GU[A] is comparably sensitive to noise in load estimates compared to conventional alternatives like Bray-Curtis dissimilarities, particularly at lower [Formula: see text]. By coupling phylogeny, composition, and microbial load, Absolute Unifrac integrates three dimensions of ecological change, better equipping microbial ecologists to quantitatively compare microbial communities.}, }
@article {pmid41695957, year = {2026}, author = {Dobrzyński, J and Gradowski, M and Radkowski, A and Bujak, H}, title = {Chloroflexota in agricultural soils: current knowledge and future research directions.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1705889}, pmid = {41695957}, issn = {1664-302X}, abstract = {The review organizes current knowledge on the biofunctions, life-history strategies, and environmental responses of Chloroflexota in agricultural soils. Members of this phylum play key roles in carbon, nitrogen, and phosphorus cycling through a high degree of metabolic versatility, including photosynthesis, redox reactions, and the degradation of complex organic compounds such as cellulose and lignin. Chloroflexota contribute to major soil processes, including nitrification, denitrification, and nitrogen fixation. In agricultural soils, the predominant classes are Anaerolineae and Ktedonobacteria, each exhibiting distinct ecological strategies. Anaerolineae members, such as Leptolinea, Bellilinea, and Anaerolinea, are often associated with nutrient-enriched conditions, suggesting copiotrophic or competitor- and ruderal-like traits. In contrast, Ktedonobacteria show negative responses to increased soil carbon and nitrogen, suggesting that its members are oligotrophic. Despite these trends, responses to soil organic carbon, nitrogen, phosphorus, and pH vary substantially across studies, likely due to functional heterogeneity within the phylum and insufficient taxonomic resolution in metataxonomic datasets. Emerging evidence from metagenome-assembled genomes (MAGs) reveals that Chloroflexota harbor genes involved in carbon fixation, nitrogen transformations, and phosphorus solubilization, highlighting their previously underestimated ecological significance. However, most Chloroflexota remain uncultured, and available genomic data are still limited. Future research integrating high-resolution taxonomic profiling, metagenomics, and cultivation-based approaches is needed to clarify the ecological roles and life-history strategies of Chloroflexota members. Such advances may ultimately establish this phylum as an important microbial indicator of soil fertility and environmental change in agricultural soils.}, }
@article {pmid41695945, year = {2026}, author = {Kothe, CI and Mak, T and Julienne, A and Okazaki, K and Jahn, LJ and Evans, JD}, title = {Miso without kōji: nesashi miso ecology driven by spontaneous fermentation with Mucor plumbeus.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1759987}, pmid = {41695945}, issn = {1664-302X}, abstract = {Nesashi miso is a rare, traditionally fermented soybean paste from Japan, and unlike most misos is produced through spontaneous fermentation without the use of a kōji starter. Here we analyzed a nesashi miso alongside two other misos from the same producer (rice and black soybean) as well as a hatchō miso from another producer which, like the nesashi, is based only on soybeans. Shotgun metagenomics confirmed that while Aspergillus oryzae dominated the three kōji-based misos, nesashi miso lacked this starter culture, and revealed that it was instead dominated by other filamentous fungi, mainly Mucor spp. and Penicillium spp., and contained typical yeast and bacterial genera found in traditional misos such as Zygosaccharomyces and Tetragenococcus. Principal component analysis (PCA) of 65 publicly available metagenomes showed that the nesashi miso sample clustered with other spontaneous solid-state fermentations like Chinese qu rather than with traditional kōji-based misos. To further characterize this unique fermentation, we isolated the Mucor sp. from nesashi miso, and sequenced it using long-read genomic sequencing. Pangenomic analysis confirmed its identity as M. plumbeus, and revealed close relationships between food- and environment-derived strains, suggesting that some Mucor species may already be naturally equipped to grow, establish and function in food fermentation niches. The nesashi strain specifically shared a large core genome with M. racemosus C, a strain patented for use in food, suggesting the former's potential for use in and potentially even adaptation to food environments. Functional annotation highlighted unique genes in the food strain group associated with amino acid metabolism, which may contribute to flavor formation. Together, these findings bridge traditional fermentation practices with meta/genomic insights, highlighting the built fermentation environment as a reservoir of potential starter cultures and the genus Mucor as a worthy candidate for future food fermentation research and innovation.}, }
@article {pmid41695141, year = {2025}, author = {Uh, YR and Park, SN and Song, MJ}, title = {Characterization of the gut micro biota in Koreans and investigation of its association with probiotic consumption: implications for microbial ecology and host health.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1745533}, pmid = {41695141}, issn = {1664-302X}, abstract = {INTRODUCTION: The gut micro biota is reportedly closely related to human health, and its composition and diversity are determined by a variety of factors, including age, diet, and probiotic intake. Although many studies on the gut micro biota have been conducted, most have focused on Western populations or have been limited by small sample sizes, making it difficult to understand micro biota differences across populations and lifestyles. In this study, we analyzed a large Korean cohort of 3,450 individuals, focusing on gut micro biome differences according to age and host-related markers, as well as the impact of probiotic supplementation.<br><br>METHODS: Fecal samples from 3,450 Koreans were analyzed using 16S rRNA gene sequencing (V3-V4 region). Bioinformatics and taxonomic analyses were performed to compare microbial composition and diversity according to age and probiotic intake.<br><br>RESULTS: The data revealed a significant increase in microbial diversity with age and distinct shifts in taxonomic composition between younger and older participants. In addition, probiotic intake did not alter overall community diversity but increased the detection of probiotics, suggesting that they serve as moderators rather than direct drivers of diversity.<br><br>CONCLUSION: These findings emphasize the importance of population-specific micro biome research and suggest that diverse host-related and lifestyle factors jointly contribute to shaping gut microbial ecology in Koreans. Probiotic supplementation primarily increased the detection of specific lactic acid bacteria and bifidobacterial species without substantially altering overall alpha diversity, consistent with a modulatory role on targeted taxa rather than broad community restructuring. Together, these results provide a useful framework for future studies linking probiotic-responsive microbial features to human health outcomes and for developing precision nutrition and probiotic strategies in Korean and similar populations.}, }
@article {pmid41695122, year = {2026}, author = {Yash,  and Ghosh, A and Dey, A and Sinha, M and Bera, N and Chakraborty, S and Bhadury, P}, title = {Genomic insights into Brevibacterium sediminis strain IMA_C3 isolated from an integrated mangrove aquaculture pond.}, journal = {Access microbiology}, volume = {8}, number = {2}, pages = {}, pmid = {41695122}, issn = {2516-8290}, abstract = {Brevibacterium sediminis strain IMA_C3, a Gram-positive bacterium, was isolated from an integrated mangrove aquaculture pond near the Sundarbans mangrove. The bacterium was isolated from mangrove leaf litter and grown on Luria-Bertani medium at a salinity of 20. Phylogenetic analysis based on 16S rRNA sequencing showed a 99.67% identity with Brevibacterium linens AE038-8 from the International Nucleotide Sequence Database Collaboration DNA databases (GenBank/DDBJ/ENA). Whole-genome sequencing was carried out using long-read sequencing on the Oxford Nanopore MinION platform, with genome annotation performed against the NCBI Reference Sequence Database and The Genome Taxonomy Database databases. The genome is ~4.1 Mb in size, with a G+C content of 64.59 mol%. Functional analysis of the genome revealed genes related to complex carbon utilization, nitrogen and phosphate metabolism and metal transport. Additionally, the genome encodes secondary metabolites, including ε-poly-l-lysine, ectoine, terpene and phenazine, which could have potential applications in controlling viral infections in indigenous shrimp populations within integrated mangrove aquaculture systems.}, }
@article {pmid41695029, year = {2026}, author = {Qin, H and Zhang, L and Rao, Z and Wei, X and Táncsics, A and Sheng, R and Liu, Y and Chen, A and Fang, C and Huang, F and Long, P and Zhu, B}, title = {Decoding endophytic microbiome dynamics: engineering antagonistic synthetic consortia for targeted fusarium suppression in monoculture regimes.}, journal = {Horticulture research}, volume = {13}, number = {2}, pages = {uhaf286}, pmid = {41695029}, issn = {2662-6810}, abstract = {Biological control leveraging endophytic microbes represents a promising eco-friendly strategy to mitigate soil-borne diseases, yet the efficacy and mechanistic underpinnings of synthetic microbial communities (SynComs) derived from plant endophytes remain poorly understood. This study employed a holistic approach-integrating field sampling, microbial profiling, and functional validation-to investigate the dynamics of edible lily (Lilium) microbiomes under continuous cropping and develop targeted SynComs against Fusarium oxysporum. Metacommunity analysis revealed that prolonged monoculture co-enriched both potentially beneficial taxa (e.g. Pseudomonas, Bacillus) and pathogenic Fusarium, reflecting a dynamic equilibrium where naturally recruited antagonists were insufficient to prevent pathogen dominance, while increasing the complexity of endophytic co-occurrence networks. Keystone bacterial lineages, including Burkholderiaceae and Pseudomonas, emerged as critical stabilizers of the endosphere microbiome. Notably, 50% of endogenous bacterial taxa exhibited rhizospheric origins, contrasting with fungal communities where <10% derived from soil-a finding underscoring host-specific filtering mechanisms. Through systematic isolation and combinatorial testing, we engineered SynComs combining core antagonistic strains (Rhizobium, Methylobacterium, Talaromyces) with auxiliary microbes. Fungal-integrated SynComs outperformed bacteria-only consortia in plant growth promotion and pathogen suppression. By bridging fundamental microbial ecology with translational agriculture, our findings establish SynComs as scalable tools for sustainable soil health management, reducing reliance on synthetic fungicides while addressing the yield-limiting challenges in continuous cropping systems.}, }
@article {pmid41694331, year = {2026}, author = {Mourot, R and Lebert, S and Martinez-Rabert, E and Barani, A and Grégori, G and Nunige, S and Dufour, A and Guasco, S and Larose, C and Bradley, JA}, title = {SIESTA Project: Svalbard summer 2025 expedition report.}, journal = {Open research Europe}, volume = {6}, number = {}, pages = {23}, pmid = {41694331}, issn = {2732-5121}, abstract = {Microbial dormancy plays an important role in the persistence, dispersal, and functioning of microbial communities in moderate to extreme environments. The activity or inactivity of microbial communities also has implications for rates of biogeochemical transformations and thus elemental stocks and redox conditions. Microbial communities inhabiting glacier surface environments encounter harsh and variable environmental conditions including nutrient limitation, low temperatures, and light availability across various micro-habitats including cryoconite and the bare ice surface. The metabolic states of cells within these microhabitats and in relation to their environment is fundamental to the functioning of the ecosystem and has implications for ecosystem resilience, responses to environmental change, and biogeochemical cycling. This report describes an expedition to Brøggerhalvøya, north-west Svalbard, carried out in July 2025, within the framework of the ERC SIESTA project. A major objective of the project is to resolve microbial activity and dormancy on an individual cell basis, to characterise the adaptive and functional traits of active and dormant fractions of the native glacier microbial population, and to link microbial metabolic states to broader ecological and biogeochemical dynamics. Here we report the site characteristics, the samples collected, the analyses undertaken, and the future analyses planned. Two small valley glaciers near to Ny-Ålesund were selected for investigation during this summer campaign: Midtre Lovénbreen and Austre Brøggerbreen. The data collected in the field, combined with subsequent laboratory analyses, will provide insights into the spectrum of dormancy and activity in situ among glacier microbial communities, and the taxa and functions associated with active and inactive fractions of the communities. These findings will contribute to a deeper understanding of the impacts and role of both short- and long-term microbial dormancy in glacial environments.}, }
@article {pmid41692701, year = {2026}, author = {Keneally, C and Gaget, V and Chilton, D and Dornan, TN and Hensel, J and Keneally, AE and Kidd, SP and Brookes, JD}, title = {Extreme Salinity Change Governs Microbial Community Assembly and Interactions.}, journal = {Environmental microbiology reports}, volume = {18}, number = {1}, pages = {e70301}, doi = {10.1111/1758-2229.70301}, pmid = {41692701}, issn = {1758-2229}, support = {2024316//Medical Research Future Fund/ ; }, mesh = {*Salinity ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Microbiota ; *Geologic Sediments/microbiology/chemistry ; *Archaea/genetics/classification/metabolism/isolation &amp; purification ; South Australia ; Ecosystem ; Seawater/microbiology/chemistry ; Wetlands ; Sulfur/metabolism ; }, abstract = {Coastal wetlands are highly vulnerable to climate-driven salinisation, which reshapes critical microbial processes underpinning nutrient cycling and energy flow. We examined how sediment microbial communities vary with salinity across the Coorong Lagoon (South Australia), spanning estuarine (0-40 g L[-1]), intermediate (40-100 g L[-1]) and hypersaline (100-150 g L[-1]) waters. Salinity was found to be the dominant driver of sediment microbial community composition, diversity and assembly. High salinity favoured specialists and homogenous community structures, with generalist bacteria persisting across intermediate salinities and supporting ecosystem resilience. Sulfur and carbon cycling is likely dependent on salinity, as bacterial sulfur-oxidisers were abundant estuarine specialists, whereas methane producers (Archaeal methanogens) and sulfate-reducers were enriched at high salinity. Deterministic microbial community assembly (homogeneous selection) was dominant, increasing at extreme salinity, which acted as a strong environmental filter. Community complexity increased at both high and low salinity ranges, with intermediate salinity exhibiting less complexity, suggesting community reorganisation under osmotic stress. The varied roles of specialists and generalists at different salinities support ecosystem function, where increased heterogeneity and specialisation in hypersaline conditions suggest vulnerability of the community to disturbance. These findings provide insight into how microbially underpinned ecosystems may respond to future climate-driven salinisation, important for making predictions and informing mitigation strategies.}, }
@article {pmid41691943, year = {2026}, author = {Huang, J and Tan, Z and Sun, R and Dai, Z and He, L and Li, C}, title = {Vertical and spatial variations of microbial communities in sediment cores from the mangrove of Gaoqiao National Nature Reserve.}, journal = {Marine pollution bulletin}, volume = {226}, number = {}, pages = {119416}, doi = {10.1016/j.marpolbul.2026.119416}, pmid = {41691943}, issn = {1879-3363}, abstract = {Sediment microbial communities act as key regulators of mangrove ecosystem functions. However, systematic studies on the spatial distribution characteristics, potential functions, and environmental driving mechanisms of microbial communities within sediment cores in mangrove ecosystems remain scarce. In this study, fifteen sediment cores were obtained from the mangrove within the Gaoqiao National Nature Reserve. The microbial community composition within the sediment cores was investigated using 16S rRNA high-throughput sequencing. Significant differences in microbial community structure were observed among the three designated zones (Nearshore, Mangrove, and Offshore) and across different sediment depths ranging from 0 to 80 cm. The dominant bacterial phyla identified comprised Pseudomonadota, Actinomycetota, and Chloroflexota, along with the archaeal phylum Thermoplasmatota. Their distributions demonstrated clear biogeographic and vertical stratification patterns. Functional prediction revealed that microbial communities extensively involved in carbon, nitrogen, and sulfur cycles exhibited higher richness, as these communities demonstrated stronger expression of metabolic functional genes. Furthermore, the abundance of metabolic functional genes was found to be higher in the mid-depth sediments at depths of 30 to 45 cm. Redundancy analysis (RDA) and variation partitioning analysis (VPA)demonstrated that sediment pH, electrical conductivity (EC), and total organic carbon (TOC) content were identified as the primary environmental factors governing the succession of both microbial community structure and function. This study advances our understanding of mangrove sediment microbial ecology and provides a scientific basis for targeted conservation and restoration of the Gaoqiao mangrove ecosystem.}, }
@article {pmid41691853, year = {2026}, author = {Wei, Y and Chen, Y and Lv, S and Ou, D and Tao, Y and Zhou, Y and Yang, J and Song, X}, title = {Persistence of the coccidiostat robenidine in soil and its impacts on the soil microbiome and enzyme functions.}, journal = {Ecotoxicology and environmental safety}, volume = {311}, number = {}, pages = {119858}, doi = {10.1016/j.ecoenv.2026.119858}, pmid = {41691853}, issn = {1090-2414}, abstract = {Robenidine is a synthetic coccidiostat that is excreted from animals in its prototype form, leading to soil contamination. Despite its widespread use, comprehensive environmental risk assessments remain limited. Consequently, we initially constructed a manure-soil microcosm and investigated the degradation pattern of robenidine using a highly efficient HPLC-dSPE method. The degradation half-lives of robenidine in soil were 14.74 days at 0.8 mg/kg and 21.26 days at 8 mg/kg. Exposure to 8 mg/kg of robenidine significantly altered the soil microbial community, leading to a 140.0 % increase in the abundance of Proteobacteria. However, the Shannon index indicated that soil microbial diversity decreased by 32.4 % from 1 d to 60 d. Compared to the control check group, 8 mg/kg of robenidine significantly increased the abundance of harmful bacteria (e.g., unclassified_Intrasporangiaceae increased by 33.5 %) in the soil at 60 d, while simultaneously reducing the populations of beneficial bacteria such as Bacillaceae (decreased by 23.8 %), Pseudograilibacillus (decreased by 39.6 %), and Massilia (decreased by 31.7 %). Network correlation and FAPROTAX analyses indicated that long-term exposure to robenidine inhibited chitinolysis and aromatic compound degradation pathways. Furthermore, low-dose robenidine increased the activities of dehydrogenase, acid phosphatase, and β-glucosidase by 34.0 %, 24.7 %, and 21.6 % at 1 d, respectively, while these enzymes returned to control levels over time. These findings provide critical insights into the biological and metabolic impacts of robenidine exposure on soil microbial communities, which is crucial for clarifying the ecological concerns associated with robenidine.}, }
@article {pmid41691349, year = {2026}, author = {Fan, S and Liu, H and Yan, Y and Xu, M and Wan, X and Hao, Y and Gong, C and Wang, C and Zhang, Y and Liu, D and Zheng, J and Chen, J}, title = {Metatranscriptomic analyses of gut bacterial and viral communities in the critically endangered Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) under distinct environments.}, journal = {Animal microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42523-026-00528-x}, pmid = {41691349}, issn = {2524-4671}, }
@article {pmid41690572, year = {2026}, author = {Koffel, T and Grimaud, G and Litchman, E and Klausmeier, CA}, title = {Metabolically structured population models: a unifying framework for microbial ecology and evolution.}, journal = {Journal of theoretical biology}, volume = {}, number = {}, pages = {112410}, doi = {10.1016/j.jtbi.2026.112410}, pmid = {41690572}, issn = {1095-8541}, abstract = {Cells grow by acquiring external resources and transforming them internally, forming new cells as they divide. Metabolic networks focus on the flow of such resources within the cell as they undergo series of biochemical reactions. How population growth emerges from these complex dynamical networks remains unclear. Modeling the emergence of population growth, a central ecological concept, is thus essential to understand the forces shaping microbial communities. Here we present a novel theoretical framework that builds on structured population theory to model the growth of cell populations whose intracellular dynamics are driven by arbitrarily complex metabolic networks. Population growth is driven by limitation regimes, which capture how reaction-level limitations combine in the network to determine growth rate. Resource availability changes trigger switches between limitation regimes, capturing resource interaction and colimitation. We also discovered alternative metabolic states, where different regimes are reached depending on initial metabolite concentrations. We first use a minimal metabolic network of limitation by two essential resources to illustrate our framework, then apply it to E. coli's glycolysis pathway to showcase its capabilities on a more realistic, albeit still simplistic, network. By integrating metabolic networks into ecological theories, our work provides a mechanistic foundation for understanding the structure and evolution of microbial communities.}, }
@article {pmid41646430, year = {2026}, author = {Thompson, AW and Lamberson, K and Sutherland, KR}, title = {Coexisting salps exhibit distinct feeding selectivity on microorganisms in the North Pacific Subtropical Gyre.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {41646430}, issn = {2693-5015}, abstract = {Mortality mechanisms play an important role in how oceanic microorganisms contribute to global biogeochemical cycles. Salps are widespread pelagic tunicates known to remove phytoplankton from coastal and high-latitude waters, but their interaction with microorganisms in the vast tropical and subtropical gyres is not well quantified. Using quantitative measurements of six major marine microorganisms in the guts of six distinct but co-occurring salp species from the North Pacific Subtropical Gyre, we examined the impact and dynamics of salp feeding on marine microorganisms in a vast open ocean region. All salps preferentially removed prey greater than 1 μm in diameter, including marine Synechococcus, diatoms, Crocosphaera, and Chrysochromulina, while the smaller Prochlorococcus and SAR11 were not a major source of prey biomass. We also found that salp feeding varied between salp taxa with some salp guts dominated by both Crocosphaera and Chrysochromulina while others were dominated by Crocosphaera alone. Together, these results suggest that salp impacts are not uniform across taxa and their patterns of selective feeding among marine microbes requires consideration of species-specific feeding strategies and environmental context. Further, this work suggests that the mortality pressure of salp feeding on marine microorganisms may shape microbial community structure and that this pressure varies with the diversity and dynamics of macrozooplankton predators.}, }
@article {pmid41690245, year = {2026}, author = {Hu, J and Zhou, Y and Ishii, S and Ahmed, W and Sadowsky, MJ and Xia, X and Du, Z and Cytryn, E and Mwakalapa, EB and Rivera, WL and Zhou, Y and Rensing, C and Zhang, Q}, title = {Sources, contamination pathways, and monitoring of pathogens in urban estuaries.}, journal = {Marine pollution bulletin}, volume = {226}, number = {}, pages = {119415}, doi = {10.1016/j.marpolbul.2026.119415}, pmid = {41690245}, issn = {1879-3363}, abstract = {Urban estuaries are critical ecological and socio-economic interfaces but are increasingly impacted by microbial pathogen contamination driven by anthropogenic activities such as wastewater discharge, stormwater runoff, agriculture, and wildlife inputs. Despite extensive documentation of estuarine pathogens, effective risk assessment and management remain constrained by key knowledge gaps related to source apportionment, environmental fate, and monitoring relevance. This review synthesizes current understanding of pathogen sources and transmission pathways in urban estuaries and critically examines the physicochemical, hydrodynamic, and sediment-mediated processes that regulate pathogen persistence, redistribution, and exposure risk. We identify three interconnected challenges: (i) limited resolution in differentiating human and non-human contamination sources due to overlapping microbial signatures; (ii) inadequate incorporation of estuarine hydrodynamics and sediment reservoirs into fate-and-transport frameworks; and (iii) misalignment between conventional monitoring indicators and actual pathogen and antimicrobial resistance risks. Emerging approaches, including microbial source tracking, sequencing-based surveillance, biosensors, and hybrid predictive modelling, are evaluated for their capacity to support risk-relevant decision-making. Framed within a One Health perspective, this review integrates microbial ecology, environmental processes, and surveillance technologies to support evidence-based management and sustainable mitigation of pathogen risks in urban estuaries.}, }
@article {pmid41689629, year = {2026}, author = {Mohammadzadeh, MH and Asadollahpour, M and Sharbatdar, HR and Darbouy, MS and Fekrirad, Z}, title = {Voices of Eukaryotic Microbes: Chemical Communication Via Quorum Sensing.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02716-3}, pmid = {41689629}, issn = {1432-184X}, abstract = {Quorum sensing (QS) is a cell-cell communication mechanism mediated by secreted hormone-like signaling molecules that operates in both Gram-positive and Gram-negative bacteria, driving coordinated alterations in gene expression once a critical cell density is reached. In these prokaryotic systems, bacteria produce, release, detect, and respond to small autoinducers, such as acyl-homoserine lactones in Gram-negative bacteria, oligopeptides in Gram-positive bacteria, and the universal autoinducer-2, to regulate community behaviors including biofilm formation, virulence factor production, and stress adaptation. The concept of QS in eukaryotic microbes emerged decades ago, and later investigations confirmed that unicellular fungi and protozoa similarly measure population density to regulate collective activities. In Saccharomyces cerevisiae, aromatic alcohols (2-phenylethanol, tryptophol, tyrosol) serve as QS signals to control filamentous growth, biofilm assembly, and environmental stress responses. Candida albicans employs farnesol to suppress hyphal development while utilizing tyrosol to accelerate germ tube emergence and biofilm maturation. African trypanosomes, including Trypanosoma brucei and related species, generate oligopeptides via secreted peptidases that accumulate as stumpy induction factors (SIFs), triggering a density-dependent shift from proliferative slender forms to transmission-competent stumpy forms essential for tsetse fly infection. QS-based mechanisms influence virulence factors in fungal and protozoan pathogens, affecting their ability to colonize hosts. Exploring QS in eukaryotic organisms opens new possibilities for antifungal treatments and parasite management. By interfering with QS signaling, researchers can disrupt fungal biofilm formation and regulate protozoan development, paving the way for innovative disease control methods.}, }
@article {pmid41687498, year = {2026}, author = {Liao, B and Wang, Q and Zhang, T and Lu, X and Fang, N}, title = {Optimizing carbon source strategy for denitrification using food waste fermentation liquid: Synergistic mechanisms of butyrate and sucrose.}, journal = {Journal of environmental management}, volume = {401}, number = {}, pages = {128950}, doi = {10.1016/j.jenvman.2026.128950}, pmid = {41687498}, issn = {1095-8630}, abstract = {Food waste fermentation liquid, rich in volatile fatty acids (VFAs) and carbohydrates, serves as a sustainable electron donor for biological nitrogen removal. However, the compositional fluctuation of fermentation liquid often leads to unstable denitrification, and the mechanistic influence of mixed VFA-saccharide interactions on microbial ecology remains poorly understood. In this study, four carbon-source systems-three simulating typical mixed fermentation products (acetate + sucrose, propionate + sucrose, butyrate + sucrose) and one single-carbon control (acetate alone)-were systematically evaluated in sequencing batch reactors (SBRs). Results indicated that the butyrate-sucrose system (A3) exhibited superior performance, achieving a nitrate removal efficiency of 98.5%, which was 13.5% and 8.2% higher than that of the acetate-sucrose (A1) and propionate-sucrose (A2) systems, respectively. Furthermore, A3 maintained the lowest nitrite accumulation (<0.5 mg/L). Mechanistically, A3 facilitated the selective enrichment of functional genera Ferruginibacter and Terrimonas. PICRUSt2 functional predictions revealed that this specific combination significantly enhanced KEGG pathways related to membrane transport (ABC transporters) and energy metabolism, suggesting a synergistic effect that accelerates electron transfer and metabolic turnover. This study demonstrates that regulating acidogenic fermentation towards a butyrate-dominant composition is a promising strategy to maximize the utility of food waste as a carbon source, ensuring robust nitrogen removal in wastewater treatment.}, }
@article {pmid41687164, year = {2026}, author = {Kim, D and Yun, N and Du, H and Li, C and Preheim, S and Rossi, R}, title = {Enabling microbial electrolysis cell scale-up via electrochemistry-, hydrodynamic-, and microbial ecology-informed framework.}, journal = {Water research}, volume = {294}, number = {}, pages = {125503}, doi = {10.1016/j.watres.2026.125503}, pmid = {41687164}, issn = {1879-2448}, abstract = {Microbial electrolysis cells (MECs) can produce green hydrogen while removing organic contaminants from liquid waste streams by leveraging the metabolic activity of electroactive microorganisms. Despite their potential in a sustainable, circular economy, large-scale MECs that can treat relevant volumes of wastewater have failed to deliver performance proportional to their lab-scale counterparts. The reason behind this lower performance at scale remains unclear. In this study, we developed a combined electrochemistry-, hydrodynamic-, and microbial ecology-informed framework to analyze and optimize MEC performance during scale-up, enabling accurate quantification of major limitations and the identification of strategies to overcome them, ultimately facilitating equivalent performance at scale. Applying this framework to the scale-up of a zero-gap MEC from 9 cm[2] electrode area to 100 cm[2] electrode area, resulted in similar maximum current densities in a 100 cm[2] MEC (21.7 ± 1.1 A/m[2]) compared to a 9 cm[2] system (25.1 ± 2.7 A/m[2]), as well as equivalent hydrogen production rates of 69.3 L/L-d (100 cm[2]) and 67.7 ± 2.4 L/L-d (9 cm[2]). COMSOL flow dynamics simulations were used to scale up the reactor configuration without negatively affecting electrolyte velocity and distribution in the cell, minimizing the increase in internal resistances during scale-up (11.7 ± 0.5 mΩm[2] at 9 cm[2]; 19.7 ± 1.3 mΩm[2] at 100 cm[2]). Microbial community structures were assessed at both scales using high-throughput sequencing, highlighting the differences of populations across electrode dimensions and operational parameters. The framework presented here accelerates the development of effective strategies toward the scale-up of MECs by furthering the understanding of how electrochemical, hydrodynamic, and microbial ecology parameters change as the reactor dimension is increased. Ultimately, this approach contributes to advancing electrochemical biotechnology toward practical deployment in energy-efficient wastewater treatment systems.}, }
@article {pmid41686264, year = {2026}, author = {Wu, CY and Cheng, HY and Lin, YC and Wang, YC and Meng, YZ and Hsieh, YE and Liu, AC and Yang, SH}, title = {Role of Core Microbiome Shifts in Octocoral Litophyton Under Diurnal Temperature Fluctuations.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02715-4}, pmid = {41686264}, issn = {1432-184X}, support = {NSTC 112-2611-M-002 -020//National Science and Technology Council/ ; NTUCCP- 115L891306//National Taiwan University/ ; }, abstract = {Climate change is projected to raise sea surface temperatures and intensify diurnal temperature fluctuations (DTF), threatening the survival of both scleractinian corals and octocorals. Litophyton, a common octocoral in Taiwan's shallow reefs, is frequently exposed to large DTF and summer heat stress, making it a suitable model to study thermal resilience. Coral-associated bacterial communities are known to shift under thermal stress, and key bacterial taxa may play crucial roles in host acclimation. This study aimed to address two questions: (1) Can higher DTF mitigate cumulative heat stress in octocorals? (2) If so, what physiological and microbial community changes accompany this effect? To answer these questions, we conducted tank experiments under constant warming and two short-term DTF regimes (± 5 °C and ± 7 °C; baseline 25-27.8 °C), along with a no-fluctuation control. We measured physiological stress indicators, including superoxide dismutase (SOD) and catalase (CAT) activities, and monitored bacterial community dynamics. Our results show that DTF helped maintain stable photosynthetic efficiency (Fv/Fm) compared to constant warming. Notably, significant differences in ROS activity were only observed in the ± 5 °C group, rather than in the larger ± 7 °C group, indicating a measurable alleviation of thermal stress and greater plasticity in Litophyton coping with temperature changes. Moreover, 29.4% more significantly abundant in the ± 7 °C group compared to the control in the core microbiome Endozoicomonas preceded detectable physiological changes in the host, suggesting a potential role in early stress mitigation. These findings deepen our understanding of octocoral holobiont resilience under fluctuating thermal regimes and highlight Endozoicomonas diversity as a potential indicator of Litophyton health.}, }
@article {pmid41685888, year = {2026}, author = {Gilson, M and Bayon-Vicente, G and Krings, S and Toubeau, L and Wattiez, R and Leroy, B}, title = {Fundamental aspects of sucrose metabolism reveal a trophic link between Rhodospirillum rubrum and Rhodobacter capsulatus.}, journal = {mBio}, volume = {}, number = {}, pages = {e0371725}, doi = {10.1128/mbio.03717-25}, pmid = {41685888}, issn = {2150-7511}, abstract = {Purple non-sulfur bacteria (PNSB) are well known to have an exceptional metabolic versatility. However, while the growth of PNSB on sugar-rich streams has been extensively explored, their ability to metabolize sugars is poorly understood. Here, we explore the metabolic mechanisms of sucrose, glucose, and fructose utilization in two phototrophic PNSB, Rhodospirillum rubrum and Rhodobacter capsulatus. Our findings demonstrate distinct carbohydrate assimilation capacities, as well as the use of different metabolic strategies for each species. Moreover, a trophic link was identified between the two species during co-cultivation, resulting from the production of fermentation by-products by Rh. capsulatus, which are then reassimilated by Rs. rubrum. Finally, we demonstrate that the synergy observed between Rs. rubrum and Rh. capsulatus can be successfully scaled up in a photobioreactor system. Our study highlights how fundamental knowledge of metabolism and the establishment of a trophic link between two PNSB species might be useful for the development of biobased economy and resource recovery strategies.IMPORTANCEThe diverse metabolic capacities found in microbial communities expand the possibilities of microbial biotechnological exploitation. In this study, we demonstrate that Rhodospirillum rubrum and Rhodobacter capsulatus, two purple non-sulfur bacteria, adopt different metabolic strategies for sugar assimilation. These differences allow them to benefit from each other, resulting in enhanced carbon yield and productivity compared to pure cultures. We also showed that the trophic link between both species can be scaled up in a photobioreactor system. Understanding these interactions expands the potential for designing microbial consortia optimized for the valorization of carbohydrate-rich waste streams using purple non-sulfur bacteria.}, }
@article {pmid41683185, year = {2026}, author = {Song, D and Song, L and Zhong, X and Wu, Y and Zhang, Y and Yang, L}, title = {Integrated Molecular Informatics and Sensory-Omics Study of Core Trace Components and Microbial Communities in Sauce-Aroma High-Temperature Daqu from Chishui River Basin.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {3}, pages = {}, pmid = {41683185}, issn = {2304-8158}, support = {MTXYTD202501//Science and Technology Innovation Team of Moutai Institute/ ; QianKeHeJiChu-ZD[2025]018//Guizhou Provincial Basic Research Program (Natural Science)/ ; ZunShiKeHe HZ Zi[2023]112//The Fund of Zunyi Technology and Big data Bureau, Moutai Institute Joint Science and Technology Research and Development Project/ ; mygccrc[2022]011, mygccrc[2022]013//Research Foundation for Scientific Scholars of Moutai Institute/ ; XYNJ20240104//Moutai Institute &amp; Guangdong Li'er'an Chemical Industry Group Co., Ltd/ ; }, abstract = {Flavor-relevant trace volatiles and microbial communities were examined in six sauce-aroma high-temperature Daqu samples. Headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry (HS-SPME-GC-MS) quantified 210 trace volatile compounds across 14 chemical classes. Orthogonal partial least squares discriminant analysis (OPLS-DA) with variable importance in projection (VIP) screening was integrated with sensory scoring, correlation analysis, and molecular docking to an olfactory receptor model. Volatile profiles showed clear stratification in total abundance. Pyrazines dominated the high-total group. Tetramethylpyrazine served as a major driver. Sensory evaluation indicated that aroma explained overall quality best. (E)-2-pentenal and dimethyl trisulfide showed significant positive associations with aroma and overall scores. In the olfactory receptor, the polar residue module that provides directional constraints for Daqu odor activation was formed by Ser75, Ser92, Ser152, Ser258, Thr74, Thr76, Thr98, Thr200, Gln99, and Glu94. The hydrogen-bond or charge network was further reinforced by Arg150, Arg262, Asn194, His180, His261, Asp182, and Gln181. The core discriminant set comprised acetic acid, hexanoic acid, (E)-2-pentenal, nonanal, decanal, dimethyl trisulfide, trans-3-methyl-2-n-propylthiophane, 2-hexanone oxime, ethyl linoleate, propylene glycol, 2-ethenyl-6-methylpyrazine, 4-methylquinazoline, 5-methyl-2-phenyl-2-hexenal, and 1,2,3,4-tetramethoxybenzene. Sequencing revealed higher bacterial diversity than fungal. Bacillus and Kroppenstedtia were dominant bacterial genera. Aspergillus, Paecilomyces, Monascus, and Penicillium were major fungal genera. Correlation patterns suggested that Bacillus and Monascus were positively linked to acetic acid and 1,2,3,4-tetramethoxybenzene. Together, these results connected chemical fingerprints, sensory performance, receptor-level plausibility, and microbial ecology. Concrete targets are provided for quality control of high-temperature Daqu.}, }
@article {pmid41683077, year = {2026}, author = {Jiang, X and Li, X and Song, P and Dou, Y and Xue, J and Wu, Z and Ma, S and Wei, W and Zheng, W and Dou, S and Dong, L}, title = {Analysis of Microbial Interactions During the Production of Chinese Ethnic Fermented Foods.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {3}, pages = {}, pmid = {41683077}, issn = {2304-8158}, support = {No.2025-MSLH-016//Liaoning Provincial Science and Technology Plan Joint Plan (Natural Science Foundation-General Program)/ ; 2014020134//Natural Science Foundation of Liaoning Province/ ; JYTMS20230376//Liaoning Provincial Department of Education University Basic Scientific Research Surface Project/ ; }, abstract = {Food fermentation is an ancient bioprocess characterized by complex biochemical transformations driven primarily by microbial communities. Across the diverse regions of China, various ethnic groups have developed a rich array of traditional fermented foods through long-term practical experience. These foods are integral to local culinary heritage and provide valuable systems for studying microbial ecology and function. From the perspective of microbial interactions, this review summarizes key concepts and major interaction types-including mutualism, commensalism, and competition-and describes how bacteria, yeasts, and molds interact via metabolic division of labor to drive substrate conversion, flavor formation, preservation, and biosynthesis of functional compounds. Focusing on four representative ethnic fermented foods-Dong fermented fish, Mongoslian milk curd, Miao sour soup, and Manchurian kombucha-we analyze how microbial interactions contribute to product quality, safety, and sensory attributes. Given current challenges in industrializing traditional fermented foods, such as poor standardization and variable quality, we propose future research directions centered on modern microbiome tools, designed microbial consortia, and process optimization. This work aims to provide a scientific foundation and practical strategies for modernization and quality improvement of traditional fermented foods.}, }
@article {pmid41681446, year = {2026}, author = {Onbaşılar, EE and Yalçın, S and Batur, B and Yalçın, S and Kılıçlı, &#x130;B and Bakıcı, C and Bakır, B and Kartal, YK and Sel, T}, title = {Effects of Xylanase and Protease Supplementation on Growth Performance, Meat Quality, Gut Health, Cecal Fermentation, and Bone Traits in Broiler Chickens.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {3}, pages = {}, doi = {10.3390/ani16030465}, pmid = {41681446}, issn = {2076-2615}, abstract = {This study investigated the effects of dietary xylanase and protease supplementation, applied individually or in combination, on growth performance, intestinal characteristics, gut fermentation, meat quality, and skeletal traits in broiler chickens. A total of 540-day-old male broiler chicks were allocated to six experimental groups and fed a control corn-soybean meal-based diet or diets supplemented with xylanase, protease, or a xylanase-protease combination. Enzyme supplementation significantly improved body weight gain and feed efficiency, particularly between days 22 and 42, and reduced intestinal digesta viscosity. Improvements in gut morphology were reflected by increased villus height and villus-to-crypt ratios, accompanied by higher cecal total volatile fatty acid concentrations, increased Lactobacillus populations, and reduced coliform counts. In contrast, breast meat physicochemical composition and antioxidant status were not affected by dietary treatments. Skeletal development was positively influenced, with improvements observed in selected morphometric and structural bone traits. Overall, dietary xylanase and protease supplementation enhanced broiler performance and skeletal development primarily through improved digestive efficiency and favorable modulation of gut morphology, microbial ecology, and intestinal fermentation, without adverse effects on meat quality.}, }
@article {pmid41681371, year = {2026}, author = {Tang, D and Chen, S and Tang, C and Li, X and Li, M and Li, X and Zhang, K and Ma, J}, title = {The Analysis of Transcriptomes and Microorganisms Reveals Differences Between the Intestinal Segments of New Zealand Rabbits.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {3}, pages = {}, doi = {10.3390/ani16030390}, pmid = {41681371}, issn = {2076-2615}, support = {2021YFYZ0009//Main livestock and poultry molecular breeding platform (Breeding research project)/ ; CARS-43-A-3//Supported by the earmarked fund for China Agriculture Research System/ ; }, abstract = {This study systematically characterized functional compartmentalization along the intestinal tract of New Zealand rabbits by analyzing mucosal tissue and luminal contents from distinct segments, including the duodenum, jejunum, ileum, cecum, and colon, using RNA-seq and 16S rRNA sequencing. Transcriptomic analysis revealed that differentially expressed genes identified between the small and large intestines were mainly enriched in digestion, absorption, and immune functions. Genes associated with the transport of amino acids, sugars, vitamins, and bile salts showed significantly higher expression in the small intestine, whereas genes related to water absorption, short-chain fatty acids (SCFAs), nucleotides, and metal ion transport were preferentially expressed in the large intestine. From an immunological perspective, genes involved in fungal responses were enriched in the small intestine, while bacterial response pathways and pattern recognition receptor (PRR) signaling genes were upregulated in the large intestine. Microbiota analysis demonstrated significantly greater diversity and abundance in the large intestine compared with the small intestine. Specifically, Proteobacteria and Actinobacteria were enriched in the small intestine, whereas Firmicutes, Verrucomicrobia, and Bacteroidetes dominated the large intestine. Correlation analysis further identified significant associations between gut microbiota composition and host genes involved in nutrient digestion and absorption. Together, these findings provide transcriptome-based evidence for regional specialization of nutrient transport, immune responses, and microbial ecology along the rabbit intestine.}, }
@article {pmid41680172, year = {2026}, author = {Lu, Q and Wang, K and Gu, S and Ma, J and Cui, D and Chi, Z and Li, B and Zai, X and Wang, N and Wang, T and Dou, Z and Zhang, F and Geisen, S and Raaijmakers, JM and Song, C and Zuo, Y}, title = {Siderophore-producing Bacillus and free-living nematodes are associated with soil suppressiveness to banana root-knot nematodes.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-69647-y}, pmid = {41680172}, issn = {2041-1723}, support = {No. 32372810//National Natural Science Foundation of China (National Science Foundation of China)/ ; No. 32302668//National Natural Science Foundation of China (National Science Foundation of China)/ ; No. 42577142//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {The control of soil-borne diseases is crucial for ensuring global food security. Here, we investigate the impact of the root-knot nematode (Meloidogyne) on banana continuous cropping over a period of 11 years. The results show significant root infestation initially, but disease incidence declined markedly from the 7th cropping year onwards. Soil community profiling revealed that this intriguing onset of nematode suppressiveness was associated with changes in free-living nematode populations and rhizosphere microbiome composition. Rhizosphere microbiome analyses and strain isolation pinpointed Bacillus velezensis as a keystone taxon in soil suppressiveness to Meloidogyne. Genomics, metabolomics and bioassays validated the suppressive effects of B. velezensis against Meloidogyne and identified the siderophore bacillibactin as key metabolite with repellent and nematicidal activities. By integrating long-term field studies with multi-omics approaches, this study uncovered co-occurring increases in specific rhizobacterial genera and free-living nematodes associated with reduced root-parasitic nematode populations, offering valuable insights for sustainable agriculture.}, }
@article {pmid41679819, year = {2026}, author = {Ding, Y and Li, X and Hao, Y and Ding, P and Chen, N and Luo, L and Wan, C and Wu, M}, title = {Structural elucidation and effects on gut microbiota of soluble galactans from edible Boletus.}, journal = {Carbohydrate polymers}, volume = {378}, number = {}, pages = {124886}, doi = {10.1016/j.carbpol.2026.124886}, pmid = {41679819}, issn = {1879-1344}, mesh = {*Gastrointestinal Microbiome/drug effects ; *Galactans/chemistry/pharmacology/isolation &amp; purification ; Fermentation ; *Agaricales/chemistry ; Molecular Docking Simulation ; Fatty Acids, Volatile/metabolism ; Prebiotics ; }, abstract = {Edible Boletus mushrooms hold considerable development potential due to their exceptional nutritional and biological profiles. This study characterized two novel galactans, NBP and BRP, extracted from Neoboletus brunneissimus and Butyriboletus roseoflavus, respectively. Structural analysis revealed that both NBP and BRP possess a backbone composed of α-1,6-linked galactopyranosyl residues substituted at O-2, with structural diversity arising from variations in the side-chain substituents. Although both polysaccharides exhibit low viscosities, BRP forms a shear-stable elastic gel network, contrasting with the predominantly linear structure of NBP. In vitro fermentation demonstrated that both galactans markedly promoted the proliferation of beneficial probiotics, optimized gut microbiota composition, and enriched butyrate-producing bacteria including Faecalibacterium prausnitzii. Furthermore, they stimulated the production of lactic acid and short-chain fatty acids (SCFAs), leading to a reduction in fermentation pH and thereby modulating microbial ecology and host energy metabolism. Metagenomic annotation revealed that galactan degradation was driven by glycoside hydrolases (GHs) from Bacteroidaceae, and molecular docking analyses indicated that these GHs exhibit distinct binding preferences for specific structural regions of the polysaccharides. These results explain the basis for the microbiota-dependent improvement of gut health by Boletus galactans, providing a theoretical foundation for their development as precision prebiotics.}, }
@article {pmid41679575, year = {2026}, author = {Kovarova, A and Ryan, K and Tumeo, A and McDonagh, F and Clarke, C and Cormican, M and Miliotis, G}, title = {Emergence of dual β-lactam and Colistin resistance via blaFRI-8 and mcr-10.2 co-carriage on an IncFII family plasmid in Enterobacter vonholyi.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {}, number = {}, pages = {105899}, doi = {10.1016/j.meegid.2026.105899}, pmid = {41679575}, issn = {1567-7257}, abstract = {OBJECTIVES: Enterobacter vonholyi isolate E323169 represents a rare case of co-carriage of the antimicrobial resistance genes (ARGs) blaFRI-8, mcr-10.2, isolated from a clinical rectal swab. E323169 represents one of only 11 known E. vonholyi genomes. To date, within the NCBI Pathogen Detection resource, blaFRI-8 was identified in three assemblies and mcr-10.2 in two. In that dataset, blaFRI-8 co-occurred with an mcr-10 hit only once (Enterobacter asburiae). This study analyzes the genomic, phenotypic and epidemiological importance of this rare co-occurrence.<br><br>METHODS: Species identification for E323169 was initially assigned by MALDI-TOF and subsequently confirmed using a multifactorial genomic workflow. Antimicrobial susceptibilities were determined by MIC assay. The genome of E323169 was sequenced on an Illumina-NextSeq-1000, assembled, and annotated for ARGs, virulence factors, and plasmid replicons detection. Comparative phylogenomics used all canonical E. vonholyi RefSeq assemblies, and NCBI metadata were analysed for plasmid distributions of blaFRI-8 and mcr-10.2.<br><br>RESULTS: E323169 carried six ARGs: four chromosomally encoded (blaACT-91, fosA, oqxA10, oqxB9) and two plasmid-borne (blaFRI-8 and mcr-10.2) co-located on IncFII(p14)_1_p14 replicon. Additional plasmid replicons: Col(MG828)_1 and ColRNAI_1 were also identified. By mining the NCBI Pathogen Detection pipeline, we identified blaFRI-8 on IncFII replicon in E. asburiae JBIWA002, and mcr-10.2 on a multi-replicon (IncFIB/IncFII) plasmid in E. kobei 11,778-yvys.<br><br>CONCLUSION: This report, to our knowledge, represents the first E. vonholyi isolate co-harboring blaFRI-8 and mcr-10.2 on a single IncFII family plasmid in a non Enterobacter cloacae complex species, showing the widening host range of plasmid-mediated resistance to carbapenems/colistin. These findings suggest IncFII-family plasmids as recurrent scaffolds for the accumulation of high-impact resistance determinants in Enterobacter and suggest that monitoring IncFII backbones may provide an early warning signal for future convergence events.<br><br>IMPACT STATEMENT: The detection of Enterobacter vonholyi across human, animal, plant, and environmental sources underscore its relevance within a One Health framework, highlighting the potential for cross-sectoral circulation of antimicrobial resistance. The convergence of blaFRI-8 and mcr-10.2 on an IncFII plasmid in E. vonholyi exposes an unrecognized reservoir of last-line resistance in a species prone to misidentification. Together, these findings emphasize the importance of integrating genomic surveillance into routine diagnostics to identify hidden reservoirs of carbapenem and colistin resistance and to strengthen infection prevention strategies before wider dissemination occurs.}, }
@article {pmid41677726, year = {2026}, author = {Zeng, T and Zuo, L and Yu, Q and Wu, Q and Bao, Z and Xiong, H and Luo, M and Li, B}, title = {Role and Mechanisms of Gut Microbiota in Infectious Diseases: Recent Evidence from Animal Models.}, journal = {Biology}, volume = {15}, number = {3}, pages = {}, pmid = {41677726}, issn = {2079-7737}, support = {XGKJ2024010037//Xiaogan Municipal Bureau of Science and Technology (Hubei Province&#xff0c; China)/ ; 2025K009//Hubei Small Town Development Research Center, Hubei University of Engineering/ ; }, abstract = {Infectious diseases present persistent and complex challenges to global public health, with conventional antibiotic therapies increasingly limited by antimicrobial resistance, microbiota disruption, and adverse effects. There is a critical need to explore complementary strategies that augment host defense mechanisms without exacerbating these limitations. Accumulating evidence underscores the integral role of the gut microbiota-a diverse microbial ecosystem within the gastrointestinal tract-in regulating systemic immunity and pathogen susceptibility. This review synthesizes recent advances from animal models to delineate the multi-faceted mechanisms by which commensal microbes and their metabolites confer protection against enteric and respiratory infections. Key processes include competitive exclusion for nutrients and ecological niches, production of antimicrobial compounds, reinforcement of intestinal barrier integrity, and orchestration of local and systemic immunity via gut-lung axes. We further discuss the potential of microbiota-targeted interventions to enhance treatment efficacy and patient outcomes. By integrating mechanistic insights with translational applications, this review aims to inform the rational design of next-generation anti-infective strategies grounded in microbial ecology and host immunobiology.}, }
@article {pmid41674154, year = {2026}, author = {Măgălie, A and Marantos, A and O'Brien, JM and Schwartz, DA and Marchi, J and Lennon, JT and Weitz, JS}, title = {Phage infection fronts trigger early sporulation and viral entrapment in bacterial populations.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag023}, pmid = {41674154}, issn = {1751-7370}, abstract = {Bacteriophage (phage) infect, lyse, and propagate within bacterial populations. However, physiological changes in bacterial cell state can protect against infection even within genetically susceptible populations. One such example is the generation of endospores by Bacillus and its relatives, characterized by a reversible state of reduced metabolic activity that protects cells against stressors including desiccation, energy limitation, antibiotics, and infection by phage. Here we tested how sporulation at the cellular scale impacts phage dynamics at population scales when propagating amongst B. subtilis in spatially structured environments. Plaques resulting from infection and lysis were approximately 3-fold smaller on lawns of spore-forming bacteria vs. non-spore-forming bacteria. Analysis of plaque growth revealed that final plaque size was reduced due to an early termination of expanding phage plaques rather than the reduction of plaque growth speed. Microscopic imaging of the plaques revealed "sporulation rings", i.e., spores enriched around plaque edges relative to phage-free regions. We developed a series of mathematical models of phage, bacteria, spore, and small molecules that recapitulate plaque dynamics. We show evidence that phage infections trigger the formation of sporulation rings that reduce the productivity of phage infections and halt plaque spread even when resources are available for infection and lysis further away from plaque centers. Moreover, sporulation rings are also enriched in viable virospores, suggesting that although dormancy limits phage infections at population scales in the near-term, viruses may co-opt phage-avoidance strategies to re-emerge over the long-term, opening new avenues to explore the entangled fates of phages and their bacterial hosts.}, }
@article {pmid41673345, year = {2026}, author = {Lafont, A and Violle, C and Ranchou-Peyruse, M and Guignard, M and Mura, J and Fargetton, T and Cézac, P and Ranchou-Peyruse, A}, title = {Successional Trajectories of Deep Subsurface Microbiomes in Response To Experimental Dihydrogen Injection.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02697-3}, pmid = {41673345}, issn = {1432-184X}, support = {ANR-20-CHIN-0001//Agence Nationale de la Recherche/ ; ANR-20-CHIN-0001//Agence Nationale de la Recherche/ ; ANR-20-CHIN-0001//Agence Nationale de la Recherche/ ; }, abstract = {Converting pre-existing gas storage facilities to dihydrogen storage raises critical questions about storage quality and dihydrogen consumption by prokaryotes. To investigate biologically driven changes during such transitions, we analyzed data from five dihydrogen pulse experiments conducted in pressurized bioreactors that replicate deep aquifer pressure and temperature conditions. Our goal was to determine whether consistent community-level responses to dihydrogen injection could be identified. We found that dihydrogen exposure consistently led to a decline in fermentative ASVs, likely driven by environmental filtering. Hydrogenotrophic sulfate reducers initially dominated in some experiments, with total sulfate depletion observed in certain cases, followed by the emergence of methanogenic archaea. In some instances, a succession pattern involving Thermodesulfovibrio and Methanothermobacter appeared across taxonomically distinct communities, suggesting deterministic ecological processes. Additionally, we observed potential dispersal limitation and selection pressures, possibly linked to pH shifts caused by autotrophy. These findings underscore the importance of considering microbial dynamics in dihydrogen storage strategies in deep aquifers and suggest that, despite initial variability, predictable ecological succession may occur under specific geochemical conditions.}, }
@article {pmid41675503, year = {2025}, author = {Gu, S and Shao, J and He, R and Xiong, G and Qu, Z and Shao, Y and Yu, L and Zhang, D and Wang, F and Xu, R and Guo, P and Xi, N and Li, Y and Wu, Y and Wei, Z and Li, Z}, title = {Forging the iron-net: Towards a quantitative understanding of microbial communities via siderophore-mediated interactions.}, journal = {Quantitative biology (Beijing, China)}, volume = {13}, number = {2}, pages = {e84}, pmid = {41675503}, issn = {2095-4697}, abstract = {Iron is a critical yet limited nutrient for microbial growth. To scavenge iron, most microbes produce siderophores-diverse small molecules with high iron affinities. Different siderophores are specifically recognized and uptaken by corresponding recognizers, enabling targeted interventions and intriguing cheater-producer dynamics. We propose constructing a comprehensive iron interaction network, or "iron-net", across the microbial world. Such a network offers the potential for precise manipulation of the microbiota, with conceivable applications in medicine, agriculture, and industry as well as advancing microbial ecology and evolution theories. Previously, our successful construction of an iron-net in the Pseudomonas genus demonstrated the feasibility of coevolution-inspired digital siderophore-typing. Enhanced by machine learning techniques and expanding sequencing data, forging such an iron-net calls for multidisciplinary collaborations and holds significant promise in addressing critical challenges in microbial communities.}, }
@article {pmid41675709, year = {2025}, author = {Lin, W and Niu, M and Mu, C and Wang, C and Ye, Y}, title = {Key species drive community and functional stability of segment-specific gut microbiomes after the swimming crab molting.}, journal = {iMetaOmics}, volume = {2}, number = {1}, pages = {e51}, pmid = {41675709}, issn = {2996-9514}, abstract = {Molting is a crucial process for crab growth and development. However, the impacts of molting on the structure and function of the gut bacterial community in swimming crab Portunus trituberculatus are poorly understood. Then, dynamic changes in the microbiotas of gut segments (foregut, midgut, and hindgut) after molting were investigated using 16S rRNA gene amplicon and shotgun metagenomic sequencing. We highlight the segment-specific responses in bacterial community compositions, alpha-diversity, and co-occurrence patterns, emphasizing the significant impact of hindgut bacteria on the analysis of the whole gut. The identification of enriched and emerged species and their source, coupled with insights into functional stability and multifunctionality, adds granularity to our understanding of postmolt microbial ecology. We offer potential keys to driving microbial community succession. These findings provide essential insights into the stability and dynamics of gut microbiota, which are crucial for both ecological understanding and sustainable management of crab probiotic regulation.}, }
@article {pmid41673333, year = {2026}, author = {Lu, L and Wang, X and Qin, Y and Xiao, Y and Zhang, Y and Ma, H and Wang, D and Li, Z}, title = {Hydrological Fragmentation Driving Microbial Carbon Necromass Reduction in Columnar Sediments: Evidence from CAZyme Genomic Signatures in Cascade Reservoirs.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02705-6}, pmid = {41673333}, issn = {1432-184X}, support = {52470202//National Natural Science Foundation of China/ ; U2340222//National Natural Science Foundation of China/ ; NBWL202200489 and 202403005//China Three Gorges Corporation/ ; 309GJHZ2024110GC//Chinese Academy of Sciences/ ; }, abstract = {Microbial necromass carbon (MNC), a key component of soil organic carbon, plays a vital role in aquatic carbon sequestration. Its accumulation and transformation are highly sensitive to environmental changes, particularly in reservoir sediments-critical zones for organic matter storage and biogeochemical cycling. This study investigated the vertical distribution and regulatory mechanisms of MNC in cascade reservoir systems through sediment analysis and metagenomic sequencing. Our findings reveal that MNC constitutes 15 ~ 35% of total sediment organic carbon (SeOC) , with fungal-derived necromass consistently dominating over bacterial contributions. Metagenomic data highlight distinct functional potentials in carbon cycling, showing that bacterial necromass exhibits higher lability than fungal necromass, as evidenced by shifts in carbohydrate-active enzyme (CAZyme) gene abundances-particularly those involved in glucan and peptidoglycan degradation. Notably, cascade damming introduced spatial heterogeneity in MNC distribution , with downstream reservoirs experiencing reduced MNC accumulation due to altered hydrological connectivity and nutrient regimes. These results underscore the pivotal role of MNC in aquatic carbon storage while highlighting the complex interplay between environmental factors, microbial metabolic traits, and anthropogenic disturbances in regulated river systems. Therefore, our findings demonstrate that fungal necromass is a dominant and relatively stable component of sediment carbon, and its dynamics must be integrated to accurately assess and predict carbon sequestration in dammed rivers.}, }
@article {pmid41671169, year = {2026}, author = {Saati-Santamaría, Z and Pérez-Mendoza, D and Khashi U Rahman, M and de Sousa, BFS and Montero-Calasanz, MDC and Rey, L and Roy, S and Sanjuán, J and García-Fraile, P}, title = {Evolutionary mechanisms underlying bacterial adaptation to the plant environment.}, journal = {FEMS microbiology reviews}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsre/fuag005}, pmid = {41671169}, issn = {1574-6976}, abstract = {Plants and bacteria have coevolved over hundreds of millions of years, forming complex associations ranging from mutualism to pathogenicity that are essential for plant survival and ecosystem function. Bacterial adaptation to plant environments involves dynamic evolutionary mechanisms including horizontal gene transfer, gene regulation, and metabolic specialization, enabling bacteria to persist and specialize within diverse plant-associated niches. Here we review how evolutionary forces such as selection, drift, and gene flow shape bacterial genomes, regulatory networks, and ecological strategies in response to plant-imposed pressures, underpinning both beneficial and pathogenic lifestyles. Understanding these processes provides a unified evolutionary framework for bacterial adaptation to plants and highlights their implications for sustainable agriculture and microbiome-based innovations.}, }
@article {pmid41668299, year = {2026}, author = {Frings, DM and Mellinger, JM and Drace, KM}, title = {Microbial Diversity Across Chemolithotrophic and Phototrophic Biofilms in Cold Sulfur Springs.}, journal = {MicrobiologyOpen}, volume = {15}, number = {1}, pages = {e70223}, pmid = {41668299}, issn = {2045-8827}, mesh = {*Biofilms/growth &amp; development ; *Sulfur/metabolism ; RNA, Ribosomal, 16S/genetics ; Alabama ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Phototrophic Processes ; *Microbiota ; Phylogeny ; *Biodiversity ; DNA, Bacterial/genetics/chemistry ; DNA, Ribosomal/genetics/chemistry ; Chemoautotrophic Growth ; Cold Temperature ; *Natural Springs/microbiology ; Sequence Analysis, DNA ; Oxidation-Reduction ; }, abstract = {Sulfur-rich environments host specialized microbial communities that drive key biogeochemical processes, particularly sulfur cycling. While sulfur-oxidizing microbiota from hydrothermal vents and volcanic systems are well studied, microbial communities in cold terrestrial sulfur springs remain less understood. In this study, we used 16S rRNA gene sequencing to examine how sulfur availability and environmental conditions shape microbial assemblages across different biofilm types in a cold sulfur spring system at Blount Springs, Alabama (33.9301° N, 86.7928° W). Sulfur-oxidizing chemolithotrophs, including Sulfurovum and Halothiobacillus, represented the majority of the recovered reads in sulfur-rich white biofilms, while purple phototrophic biofilms were enriched with anoxygenic sulfur-oxidizing bacteria, such as Chromatium and Chlorobium. Nonsulfur biofilms from adjacent environments displayed greater microbial diversity, including a high abundance of photosynthetic diatoms, like, Melosira. Notably, Sulfurovum was abundant across both sulfur-rich and phototrophic niches, suggesting ecological flexibility and a central role in sulfur metabolism. These findings highlight the influence of sulfur chemistry and light availability in structuring microbial communities and contribute to a broader understanding of microbial adaptation and sulfur cycling in cold sulfur spring ecosystems.}, }
@article {pmid41668183, year = {2026}, author = {Zhang, Y and Jing, G and Chen, R and Gong, Y and Li, Y and Wang, Y and Wang, X and Zhang, J and Mao, Y and He, Y and Zheng, X and Wang, M and Yuan, H and Xu, J and Sun, L}, title = {RamEx: an R package for high-throughput microbial ramanome analyses with accurate quality assessment.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02339-3}, pmid = {41668183}, issn = {2049-2618}, abstract = {BACKGROUND: Microbial single-cell Raman spectroscopy (SCRS) has emerged as a powerful tool for label-free phenotyping, enabling rapid characterization of microbial diversity, metabolic states, and functional interactions within complex communities. However, high-throughput SCRS datasets often contain spectral anomalies from noise and fluorescence interference, which obscure microbial signatures and hinder accurate classification. Robust algorithms for outlier detection and microbial ramanome analysis remain underdeveloped.<br><br>RESULTS: Here, we introduce RamEx, an R package specifically designed for high-throughput microbial ramanome analyses with robust quality control and phenotypic classification. At the core of RamEx is the Iterative Convolutional Outlier Detection (ICOD) algorithm, which dynamically detects spectral anomalies without requiring predefined thresholds. Benchmarking on both simulated and real microbial datasets-including pathogenic bacteria, probiotic strains, and yeast fermentation populations-demonstrated that ICOD achieves an F1 score of 0.97 on simulated datasets and 0.74 on real datasets, outperforming existing approaches by at least 19.8%. Beyond anomaly detection, RamEx provides a modular and scalable workflow for microbial phenotype differentiation, taxonomic marker identification, metabolic-associated fingerprinting, and intra-population heterogeneity analysis. It integrates Raman-based species-specific biomarkers, enabling precise classification of microbial communities and facilitating functional trait mapping at the single-cell level. To support large-scale studies, RamEx incorporates C++&#x2009;acceleration, GPU parallelization, and optimized memory management, enabling the rapid processing of over one million microbial spectra within an hour.<br><br>CONCLUSIONS: By bridging the gap between high-throughput Raman-based microbial phenotyping and computational analysis, RamEx provides a comprehensive toolkit for exploring microbial ecology, metabolic interactions, and antibiotic susceptibility at the single-cell resolution. RamEx is freely available under the MIT license at https://github.com/qibebt-bioinfo/RamEx. Video Abstract.}, }
@article {pmid41667848, year = {2026}, author = {González-Azcona, C and Solano-González, F and Jiménez-Ruiz, S and Santos, N and Marañón-Clemente, I and Álvarez-Gómez, T and Eguizábal, P and Alonso, CA and Benito, D and Zarazaga, M and Torres, C and Lozano, C}, title = {High Nasal Carriage of MRSA-mecC in Wild Rabbits in the Iberian Peninsula: a Wildlife Reservoir?.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02713-6}, pmid = {41667848}, issn = {1432-184X}, }
@article {pmid41666926, year = {2026}, author = {Kim, CY and Podlesny, D and Schiller, J and Khedkar, S and Fullam, A and Orakov, A and Schudoma, C and Robbani, SM and Grekova, A and Kuhn, M and Bork, P}, title = {Planetary microbiome structure and generalist-driven gene flow across disparate habitats.}, journal = {Cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2025.12.051}, pmid = {41666926}, issn = {1097-4172}, abstract = {Microbes are ubiquitous on Earth, forming microbiomes that sustain macroscopic life and biogeochemical cycles. Microbial dispersal, driven by natural processes and human activities, interconnects microbiomes across habitats, yet most comparative studies focus on specific ecosystems. To study planetary microbiome structure, function, and inter-habitat interactions, we systematically integrated 85,604 public metagenomes spanning diverse habitats worldwide. Using species-based unsupervised clustering and parameter modeling, we delineated 40 habitat clusters and quantified their ecological similarity. Our framework identified key drivers shaping microbiome structure, such as ocean temperature and host lifestyle. Regardless of biogeography, microbiomes were structured primarily by host-associated or environmental conditions, also reflected in genomic and functional traits inferred from 2,065,975 genomes. Generalists emerged as vehicles thriving and facilitating gene flow across ecologically disparate habitat types, illustrated by generalist-mediated horizontal transfer of an antibiotic resistance island across human gut and wastewater, further dispersing to environmental habitats, exemplifying human impact on the planetary microbiome.}, }
@article {pmid41666603, year = {2026}, author = {Cristino, S and Caligaris, L and Salaris, S and Derelitto, C and Bonincontro, C and Marino, F and Grottola, A and Girolamini, L}, title = {Legionella petroniana sp. nov., a novel species isolated in Bologna, Italy: taxonomic, genomic and ecological insights in the era of environmental change.}, journal = {Systematic and applied microbiology}, volume = {49}, number = {2}, pages = {126694}, doi = {10.1016/j.syapm.2026.126694}, pmid = {41666603}, issn = {1618-0984}, abstract = {This study presents the characterization of a novel Legionella species isolated in Italy over three different years from one company and two hospitals. Starting from standard techniques such as culture of water samples, agglutination test, MALDI-TOF MS and gene sequencing analysis used to identify the isolates, genomic and metabarcoding approaches were subsequently employees to further characterize the species. Legionella contamination ranged from 400 to 700 CFU/L. The tiny colonies displayed atypical morphology compared to typical Legionella features, although they grew on BCYE medium supplemented with L-cysteine. Microscopic and phenotypic analyses revealed Gram-stain negative, Ziehl-Neelsen-negative, rod-shaped, motile cells capable of growing at 32-37 °C, including on selective media such as GVPC and MWY. The isolates tested positive for oxidase and gelatinase activity. Fatty acid profiling identified the dominant components as Summed Features 3 (C16:1 ω7c/C16:1 ω6c, 28.9%), C16:0 iso (18.4%), and C15:0 anteiso (15.4%). Ubiquinone Q13 was the major quinone. Sequence analysis of the mip and rpoB genes showed 98.2% and 95.1% similarity, respectively, to L. feeleii (WO-44C ATCC 35072[T]). Whole genome sequencing (WGS) revealed a GC content of 41.5%, a dDDH value of ≤54.9%, and an ANI of 94.06% with L. feeleii (WO-44C ATCC 35072[T]), supporting the classification of a novel species within the genus Legionella. Furthermore, taxonomic resolution of water samples revealed the presence of 168 bacterial genera, including several respiratory, opportunistic, and zoonotic pathogens, as well as seven Legionella species. The name Legionella petroniana sp. nov. is proposed, with strain 31fI33[T] (=DSM 114357[T]=CCUG 76442[T]) designated as type strain.}, }
@article {pmid41663799, year = {2026}, author = {Gao, S and Zhao, W and Guan, X and Zhao, Z and Wang, B and Xiao, Y and Zhang, G and Pan, Y and Sun, H and Jiang, P and Mi, R and Jiang, J and Zhou, Z}, title = {Stronger Adaptability of Eukaryotic Communities than Prokaryotes in Seawater across an Extensive Salinity Gradient.}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {28}, number = {1}, pages = {32}, pmid = {41663799}, issn = {1436-2236}, support = {U24A200104//National Natural Science Foundation of China/ ; XLYC2203191//Liaoning Revitalization Talents Program/ ; 2023JH1/10200007//Science and Technology Project of Liaoning Province/ ; 2023RJ007//Dalian Science and Technology Talent Innovation Support Program/ ; 2025HQ1304//Fundamental Research Funds of Liaoning Academy of Agricultural Sciences/ ; }, mesh = {*Salinity ; *Seawater/microbiology/chemistry ; *Eukaryota/physiology/genetics/classification ; *Prokaryotic Cells/physiology ; *Adaptation, Physiological ; *Microbiota ; Biodiversity ; }, abstract = {Researching microbial ecology in extreme environments is crucial for advancing the basic ecological theory and exploring their potential applications in biotechnology. The salt drying system provides an accessible but harsh environment that covers a maximum salinity gradient. In this study, we conducted a comparative analysis of the salinity adaptation and assembly mechanisms of prokaryotic and eukaryotic communities in several salt drying tanks using high-throughput amplicon sequencing and multiple ecological analyses. The beta diversity analysis, based on the unweighted and weighted Unifrac distances, revealed significant variations in microbial community compositions along the salinity gradient, with stronger influences on prokaryotes. Species turnover was the primary mechanism driving the beta diversity patterns, which was regulated by the local species pool. Further comparisons of multiple niche and adaptation indices indicated that seawater eukaryotic communities exhibited stronger salinity adaptability than prokaryotes. In addition, the beta deviation index suggested that heterogeneous processes shaped the microbial communities. Moreover, the neutral community model showed higher dispersal ability of eukaryotes than prokaryotes. Also, they were stochastic and deterministic dominant communities along the salinity gradient, respectively. Overall, our findings contributed significantly to understanding the microbial ecology in relation to salinity gradients.}, }
@article {pmid41661138, year = {2026}, author = {Bäcker, M and Doekes, HM and Garza, DR and Meijer, J and van Vliet, S and Allen, RJ and Hogeweg, P and Dutilh, BE and van Dijk, B}, title = {Spatial structure: Shaping the ecology and evolution of microbial communities.}, journal = {FEMS microbiology reviews}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsre/fuaf067}, pmid = {41661138}, issn = {1574-6976}, abstract = {Most microbes grow in spatially structured communities, and this profoundly shapes their ecology and evolution. At the microscale, short interaction ranges and steep nutrient gradients underlie cross-feeding, quorum sensing, and niche construction, generating spatial patterns that influence microbial behavior, community assembly, and stability. Here, we review theoretical and experimental evidence for how spatial organization drives eco-evolutionary processes, including founder effects during colonization, allele surfing during range expansion, emergent patterns that facilitate multilevel selection, and the exploration of rare epistatic genotypes. While the ecological and evolutionary consequences of spatial structure at the microscale are becoming clearer, linking these processes across scales to predict community- and ecosystem-level outcomes remains a major challenge. Addressing spatial interactions explicitly in microbiome research will be key. Recent advances in computational modeling, cultivation approaches, and omics now offer unprecedented opportunities to meet this challenge, providing fresh insights into how spatial structure governs the organization and dynamics of the microbial world across scales.}, }
@article {pmid41660022, year = {2026}, author = {Shaji, A and Ramachandran, AK and Chandrasekaran, N and Savarimalai, KC and Adhira, R}, title = {A cross-sectional metagenomic analysis of the microbial ecology in symptomatic apical periodontitis - An in vivo study.}, journal = {Journal of conservative dentistry and endodontics}, volume = {29}, number = {1}, pages = {60-64}, pmid = {41660022}, issn = {2950-4708}, abstract = {BACKGROUND: Symptomatic apical periodontitis (SAP) is a painful inflammatory disease driven by root canal infection. A detailed understanding of its microbial ecology, compared to a noninfectious baseline, is needed.<br><br>AIMS: This study aimed to characterize the microbial ecology of SAP using 16S ribosomal (RNA) 16S rRNA metagenomic sequencing and compare it to control teeth undergoing root canal treatment after trauma.<br><br>MATERIALS AND METHODS: This cross-sectional study included 10 patients with SAP and 10 control patients. Pulpal samples were collected aseptically. Microbial DNA was extracted, and the full-length 16S rRNA gene was sequenced through Oxford Nanopore Technology. Analysis was performed using QIIME2.<br><br>STATISTICAL ANALYSIS USED: Microbial abundances and diversity indices were compared using an independent samples t-test or Mann-Whitney U-test (P < 0.05 significant).<br><br>RESULTS: The SAP microbiome was dysbiotic and enriched in anaerobes. Veillonella parvula was highly abundant in SAP (mean 13.1%) but absent in controls. Species like Dialister pneumosintes and Prevotella melaninogenica were found almost exclusively in SAP. Commensals including Faecalibacterium prausnitzii were significantly reduced.<br><br>CONCLUSION: SAP is associated with a distinct microbial signature defined by the enrichment of anaerobic pathobionts and a loss of commensals, revealing a polymicrobial, dysbiotic community.}, }
@article {pmid41659429, year = {2026}, author = {Vallecillo-Zuniga, ML and Akeefe, A and Brown, DG and Wahlig, TA and Marchetti, M and Heiner, T and Davis, KL and Nieznanski, C and Flynn, A and Leung, DT}, title = {Longitudinal Changes in Nasal and Oral Microbiome and Antimicrobial Resistance Gene Profiles in Response to Human Fecal Microbiota Transplantation.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.01.27.701854}, pmid = {41659429}, issn = {2692-8205}, abstract = {The gut-lung axis describes interactions between intestinal and respiratory mucosal systems through microbial, metabolic, and immune pathways, but the systemic impact of gut-targeted therapies on upper respiratory tract (URT) communities remains underexplored. We conducted a longitudinal study in adult patients undergoing fecal microbiota transplantation (FMT) for recurrent Clostridioides difficile infection (CDI) alongside healthy controls. Fecal, nasal, and oral samples were collected at baseline (Day 0) and on Days 14 and 56 following FMT. Shotgun metagenomic sequencing was performed to quantify microbial diversity, taxonomic composition, and the abundance of antimicrobial resistance genes (ARGs). FMT was associated with increased gut diversity and decreased levels of key intestinal taxa commonly considered pathobionts, including Klebsiella spp., Escherichia spp., Shigella spp., and Klebsiella pneumoniae . At the phylum level, fecal Bacteroidota increased, while Mucoromycota decreased following treatment. Post-FMT nasal microbiome changes included reduced richness and diversity, expansion of Moraxella , and decreases in taxa linked with respiratory colonization, including Staphylococcus aureus and Streptococcus pneumoniae . By Day 56, nasal communities partially recovered toward healthy profiles. Baseline nasal ARG abundance decreased following FMT, particularly among β-lactam, aminoglycoside, and fluoroquinolone resistance genes, and remained comparable to healthy controls by Day 56. In contrast, the oral microbiome and oral resistome remained largely stable, with only minor fluctuations, and no consistent increases in respiratory pathobiont-associated taxa. In summary, FMT was associated with broader effects beyond the gut, including changes in the URT microbial ecology and antimicrobial resistance profiles. Together, these findings are consistent evidence of gut-lung microbial interactions, linking intestinal dynamics with respiratory microbial composition and antimicrobial resistance patterns.}, }
@article {pmid41655393, year = {2026}, author = {Tao, S and Gao, J and He, B and Zhang, T and Chen, B and Yin, Y and Shi, J and Mao, Y and Hu, L and Jiang, G}, title = {Understanding microbial mercury methylation via metabolic pathways: Processes associated with one-carbon metabolism.}, journal = {Journal of hazardous materials}, volume = {504}, number = {}, pages = {141373}, doi = {10.1016/j.jhazmat.2026.141373}, pmid = {41655393}, issn = {1873-3336}, abstract = {Microbial mercury methylation is the key step responsible for the high toxicity and bioaccumulation potential of mercury. Since metabolic pathways serve as a bridge between mercury methylation and microbial activity, studying mercury methylation from the perspective of metabolic pathways will offer valuable insights into its underlying mechanism and integration into microbial metabolism. This review aims to summarize current understanding of the metabolic pathways that supply methyl groups for mercury methylation and to elucidate the relationships between them. The acetyl-coenzyme A pathway is extensively studied and well recognized for its role in methyl group transfer. The Wolfe cycle, representing the methanogenesis pathway in methanogenic archaea, has recently been identified as a distinct source of methyl groups contributing to mercury methylation. In addition, at the chemical level, S-adenosyl-L-methionine from the methionine biosynthesis pathway has been shown to donate a methyl group to mercury via the HgcAB complex, although this process has not yet been validated in vivo. Finally, the dimethylsulfoniopropionate degradation pathway is proposed as a speculative and potential route for mercury methylation. By integrating these pathways, we provide a comprehensive overview of their interconnections, demonstrating that microbial mercury methylation is embedded within the broader framework of one-carbon metabolism. The close association between methylation and one-carbon flux suggests that mercury methylation may function as an interspecies competition strategy that enhances microbial survival in mercury-rich environments. This pathway-centered perspective advances our understanding of the biochemical basis of microbial mercury methylation and may inform future research into its environmental controls and microbial ecology.}, }
@article {pmid41654744, year = {2026}, author = {Wünschmann, T and Ghaderiardakani, F and Homeier-Bachmann, T and Quartino, ML and Wichard, T and Busch, A}, title = {Genomic and functional characterization of Pseudosulfitobacter pseudonitzschiae BPC-C4-2: a growth-promoting symbiont in Antarctic Ulva communities.}, journal = {BMC genomics}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12864-026-12626-w}, pmid = {41654744}, issn = {1471-2164}, }
@article {pmid41653958, year = {2026}, author = {Gamez, I and Fouladi, F and Gonzalez, A and Ward, J and Wang, Z and Beane Freeman, LE and Motsinger-Reif, A and Peddada, SD and Knight, R and Lee, M and London, SJ}, title = {Household Environmental Characteristics Influence House Dust Metagenome.}, journal = {Environmental research}, volume = {}, number = {}, pages = {123889}, doi = {10.1016/j.envres.2026.123889}, pmid = {41653958}, issn = {1096-0953}, abstract = {Environmental exposures can shape microbial community compositions inside homes. Metagenomic sequencing methods can further elucidate the role of household exposures like indoor moisture and the surrounding landscape. To identify household environmental exposures associated with the house dust metagenome. Microbial communities in vacuumed dust from 771 homes in the Agricultural Lung Health Study were characterized using whole metagenome shotgun sequencing (5,821 taxa across 45 phyla). Household characteristics (i.e. presence of leaks, de-humidifier, humidifier use) were assessed by questionnaires or field technicians. We evaluated associations between exposures and both overall microbial diversity and differentially abundant taxa (ANCOM-BC2). Additionally, we explored microbial networks based on Spearman correlations (SECOM). Microbial diversity was higher in homes with mold/mildew (p-value<0.05), leaks, humidifier use, or occupants removing shoes before entering (p-value<0.1). Examining individual species, <10 taxa were significantly differentially abundant (p-value<0.05 after Holm-Bonferroni correction) in relation to both mold/mildew and leaks. Greater than 10 species were significantly differentially abundant in relation to removing shoes and humidifier use. Additionally, the genera Clostridium, Prevotella, and Cryptobacteroides were positively associated with removing shoes. In this farming population, the house dust microbiome differed by moisture-related exposures, and removing shoes before entering the home. Many novel associations were identified between individual taxa and these exposures. Our findings further knowledge of the impact of environmental conditions inside the home on the indoor microbiome.}, }
@article {pmid41653300, year = {2026}, author = {Zenelt, W and Hoffmann, A and Sadowska, K and Krawczyk, K}, title = {Insects as a New Source of Plant Growth Promoting Bacteria - Review.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02692-0}, pmid = {41653300}, issn = {1432-184X}, }
@article {pmid41653280, year = {2026}, author = {Kalatehjari, P and Wolf, R and Jedlitschky, G and Tolksdorf, C and Rauch, BH and Müller, C}, title = {The great diversity: monomeric and oligomeric hirudins, hirudin-like factors and decorsins in the Asian medicinal leeches Hirudo nipponia and Hirudo tianjinensis.}, journal = {Parasitology research}, volume = {125}, number = {1}, pages = {18}, pmid = {41653280}, issn = {1432-1955}, mesh = {Animals ; *Hirudins/genetics/chemistry/metabolism ; *Leeches/genetics/classification/metabolism ; Phylogeny ; Platelet Aggregation/drug effects ; Amino Acid Sequence ; }, abstract = {Medicinal leeches express a broad variety of anticoagulants and other bioactive factors that are involved in the blood feeding process. For most of the anticoagulants, several genes exist that may encode isoforms of the respective proteins, including hirudins and decorsins. Decorsins negatively affect platelet aggregation, whereas hirudins are potent thrombin inhibitors. Both factors belong to the hirudin superfamily that also includes the group of hirudin-like factors, and all hematophagous leeches analyzed so far contain several gene copies that encode representatives of at least two of the three groups of these factors. Members of the hirudin superfamily may contain only one central globular domain, but others may contain two or more copies. Here we describe the molecular identification and partial functional characterization of a broad variety of putative mono-, bi and multimeric hirudins, decorsins and hirudin-like factors in two Asian medicinal leech species, namely Hirudo nipponia and H. tianjinensis. Some of the monomeric hirudins and decorsins have already been described before, but they represent only a small part of the overall diversity. For the first time, putative monomeric and one oligomeric decorsins of H. tianjinensis were expressed as recombinant proteins, functionally characterized and successfully verified as platelet aggregation inhibitors. In addition we have conducted phylogenetic analyses based on genomic and mitochondrial markers and found convincing evidence that H. nipponia and H. tianjinensis together with members of the genus Whitmania form a monophyletic clade that is clearly distinct from clades that are formed either by European members of the genus Hirudo or by members of the genus Hirudinaria.}, }
@article {pmid41652742, year = {2026}, author = {Van Meulebroek, L and Ghyselinck, J and Van Elst, D and Duysburgh, C and Gessner, A and Thas, O and Marzorati, M}, title = {The impact of Symprove™ multi-strain probiotic on enterotoxigenic Escherichia coli- or antibiotic-induced gut microbiome dysbiosis using high-throughput in vitro screening.}, journal = {Food research international (Ottawa, Ont.)}, volume = {227}, number = {}, pages = {118172}, doi = {10.1016/j.foodres.2025.118172}, pmid = {41652742}, issn = {1873-7145}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Probiotics/pharmacology ; *Dysbiosis/microbiology/chemically induced ; *Anti-Bacterial Agents/adverse effects ; Feces/microbiology ; *Enterotoxigenic Escherichia coli/drug effects ; Fatty Acids, Volatile/metabolism ; Adult ; Male ; High-Throughput Screening Assays ; Female ; Escherichia coli Infections/microbiology ; Fermentation ; Young Adult ; }, abstract = {The gut microbiome plays a significant role in host physiology, both in health and disease. Assessment of changes in microbial metabolites beyond short-chain fatty acids (SCFAs) following probiotic supplementation may identify additional metabolic pathways that are activated or suppressed in response to probiotics. This study assessed changes in microbial metabolites in healthy and dysbiosed microbiomes following supplementation with Symprove™, a multistrain probiotic, using the Colon-on-a-plate® miniaturized short-term batch fermentation system with a fractional factorial design. The fecal microbiome from 10 healthy human donors was evaluated under healthy and dysbiosed (enterotoxigenic Escherichia coli infection and/or low-, medium-, or high-dose antibiotics) conditions. Samples were supplemented with Symprove™ or water (control) and evaluated for microbial metabolites at 24 h and 48 h using untargeted metabolic fingerprinting, capillary gas chromatography, and targeted metabolic profiling. Favorable impacts were observed with Symprove™ supplementation across the different antibiotic doses. SCFA levels (acetate, propionate, butyrate) were significantly increased and levels of branched SCFAs were significantly decreased with Symprove™ supplementation versus control in both the healthy and dysbiosed populations. Significant increases and decreases in several other microbial metabolites were also observed with Symprove™, many of which could be considered to have beneficial effects on intestinal inflammation, intestinal barrier health, and the gut-brain axis. Symprove™ supplementation significantly affected microbial metabolism, with many of the observed changes being considered positive for human health. Importantly, these benefits were shown not only in healthy fecal microbiomes, but also in fecal microbiomes with in vitro antibiotic-induced dysbiosis, showing therapeutic potential.}, }
@article {pmid41652077, year = {2026}, author = {Jeong, YS and Jeon, BS and Park, MG}, title = {Dinopallor Comventus n. gen., n. sp., a Novel Parasitoid of Marine Dinoflagellates Representing a Sister Lineage to Seagrass Parasites and Expanding the Host Range of Phytomyxea (Rhizaria, Endomyxa).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02707-4}, pmid = {41652077}, issn = {1432-184X}, support = {RS-2025-00552993//National Research Foundation of Korea/ ; RS-2022-NR068504//National Research Foundation of Korea/ ; RS-2023-00256330//Korea Institute of Marine Science and Technology promotion/ ; }, abstract = {Phytomyxea (SAR: Rhizaria: Endomyxa) is a group of obligate biotrophic parasitic protists comprised of two orders: Plasmodiophorida, found in terrestrial or freshwater environments, and Phagomyxida, found in marine environments. While Plasmodiophorida has been extensively studied due to its economic importance as plant pathogens, Phagomyxida remains poorly investigated despite its ecological significance in marine ecosystems. During intensive sampling along the Korean coast from April to December 2023, novel parasitoids infecting dinoflagellates were discovered in seawater collected at 10 coastal stations. A total of 23 isolates were successfully established in culture, and the morphology of infected host cells resembled that of known Phagomyxa infections. The newly identified parasitoid exhibits a life cycle that includes zoospore penetration, multinucleate plasmodium development, and formation of a sporangiosorus composed of numerous zoosporangia. Each zoosporangium produces three biflagellate zoospores, and no resting spores were observed. A key morphological feature distinguishing this parasitoid from Phagomyxa species is the presence of a sporangiosorus wall enclosing the zoosporangia. Phylogenetic analysis based on small subunit (SSU) ribosomal DNA (rDNA) revealed that this parasitoid forms a distinct clade with Marinomyxa and the environmental sequence TAGIRI-5, suggesting a disparity between its morphological similarity to Phagomyxa and its molecular phylogenetic position. The SSU rRNA gene sequence of the new parasitoid showed 99.87% identity to the TAGIRI-5 sequence obtained from an anoxic sediment in Kagoshima Bay, Japan. Cross-infection experiments demonstrated that infections occurred only in five dinoflagellate genera among the taxa tested. Based on morphological and molecular data obtained in this study, we propose a new genus and species, Dinopallor comventus n. gen., n. sp., for this newly discovered parasitoid.}, }
@article {pmid41648583, year = {2026}, author = {Bald, S and Zhang, J and Nelson, R and Scott, DC and Dukovski, I and de Raad, M and Northen, TR and Segrè, D}, title = {Metabolic blueprints of monocultures enable prediction and design of synthetic microbial consortia.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.01.11.698878}, pmid = {41648583}, issn = {2692-8205}, abstract = {Synthetic microbial ecology aims at designing communities with desired properties based on mathematical models of individual organisms. It is unclear whether simplified models harbor enough detail to predict the composition of synthetic communities in metabolically complex environments. Here, we use longitudinal exometabolite data of monocultures for 15 rhizosphere bacteria to parametrize a consumer-resource model, which we use to predict pairwise co-cultures and higher order communities. The capacity to artificially "switch off" cross-feeding interactions in the model demonstrates their importance in ecosystem structure. Leave-one-out and leave-two-out experiments demonstrate that pairwise co-cultures do not necessarily capture inter-species interactions within larger communities and broadly highlight the nonlinearity of interactions. Finally, we demonstrate that our model can be used to identify new sub-communities of three strains with high likelihood of coexistence. Our results establish hybrid mechanistic and data-driven metabolic models as a promising and extendable framework for predicting and engineering microbial communities.}, }
@article {pmid41646503, year = {2025}, author = {Abjani, F and Er, YX and Lee, SC and Madhavan, P and Rhodes, A and Lim, YAL and Chong, PP and Chinna, K}, title = {Gut Microbiota of Sarawak's "Orang Ulu" Indigenous Community in East Malaysia Reveals Vanish Microbes: A Comparison With Urban Communities.}, journal = {British journal of biomedical science}, volume = {82}, number = {}, pages = {15378}, pmid = {41646503}, issn = {2474-0896}, mesh = {Humans ; Malaysia ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Adult ; Feces/microbiology ; Urban Population ; RNA, Ribosomal, 16S/genetics ; Cross-Sectional Studies ; Middle Aged ; Bacteria/genetics/classification ; Indigenous Peoples ; }, abstract = {INTRODUCTION: Urbanization often correlates with reduced diversity in human gut microbiota, with notable variations observed between the gut microbiota among the Indigenous communities in rural villages and urban citizens residing in modern settings. Although research has been conducted on the gut microbiota of healthy adults in Malaysia, there has been no study characterising the gut microbiota of Sarawak's Indigenous communities to date. This study aims to fill this gap by examining the gut microbiota profile of the Sarawak Indigenous groups (specifically Orang Ulu subethnic groups Kayan and Kenyah), comparing them with semi-urbanized Selangor Indigenous communities from Peninsular Malaysia (represented by Proto Malay subtribe Temuan) and Urban communities from Kuala Lumpur.<br><br>METHODS: We conducted a cross-sectional study and collected stool samples from 86 Indigenous participants from Sarawak and compared them with published data from 45 Malaysian Indigenous participants from Selangor and 18 Urban citizens living in Kuala Lumpur City. DNA was extracted from the stool samples, and subsequently, the V4 hypervariable region of the 16S rRNA gene was sequenced. The raw sequence data were analyzed using the Quantitative Insights into Microbial Ecology 2 (QIIME2) bioinformatics platform.<br><br>RESULTS AND DISCUSSION: Analysis revealed that the Sarawak Indigenous community exhibited the highest gut microbial diversity, followed by the Peninsular Indigenous and Urban groups. The Prevotella/Bacteroides (P/B) ratio revealed that the Sarawak Indigenous community showed the highest presence of Prevotella at 88.3%, while Kuala Lumpur Urban residents had a predominantly Bacteroides composition at 61%. The Selangor Indigenous community also exhibited a Prevotella-dominant profile at 75.5%. VANISH microbes (Prevotella, Faecalibacterium, and Succinivibrio) were identified as dominant genera in the Sarawak Indigenous gut microbiota, contrasting with the BIoSSUM microbe (Bacteroidaceae) found in the Kuala Lumpur cohort.<br><br>CONCLUSION: This study sheds light on the distinct gut microbiota composition of Sarawak's Indigenous community, which has not been previously explored. It highlights the impact of urbanization on gut microbiota composition during lifestyle transitions.}, }
@article {pmid41642996, year = {2026}, author = {Ma, W and Liu, Y and Wei, X and Zhang, X and Li, X and Liu, Z and Yuan, L and Li, G and Zhang, S and Yang, Q and Chang, X and Han, Z and Liang, H and Luan, Z and Wang, Q and Gu, Y and Wang, X and Zhao, X and Liu, Q and Sun, X and Liu, M and Feng, D and Lu, Y and Luo, S and Yang, L and Li, M and Allaby, R and Wang, K and Zhang, T and Shen, S and Van de Peer, Y and Hong, Y and Yuan, Y and Zhao, J}, title = {Gapless pangenome analyses reveal fast Brassica rapa subspeciation.}, journal = {Science (New York, N.Y.)}, volume = {391}, number = {6785}, pages = {eady7590}, doi = {10.1126/science.ady7590}, pmid = {41642996}, issn = {1095-9203}, mesh = {*Brassica rapa/genetics/classification/anatomy &amp; histology ; *Genome, Plant ; Genes, Plant ; Centromere/genetics ; Plant Leaves/anatomy &amp; histology/genetics/growth &amp; development ; Genome-Wide Association Study ; Plant Proteins/genetics ; Telomere/genetics ; Plant Breeding ; Genetic Variation ; }, abstract = {Brassica rapa (Br) encompasses many morphotypes and subspecies, so it is a good model with which to investigate plant diversification and subspeciation. Here, we resequenced the genomes of 1720 Br accessions and de novo assembled 11 representative telomere-to-telomere gapless genomes for seven elite subspecies that underwent intensive morphotypification and developed distinct agronomic traits valued to agriculture. We identified 6992 unknown genes, 110 complete (peri)centromeres, and five new satellites associated with Br morphotypes and subspecies and Brassica species evolution. The pangenome, built on 11 gapless and 20 published genomes, reveals structural variations and gene diversities among Br subspecies. Pangenome-wide association studies uncovered that the gene BrLH1 controls leaf-head formation. We show that structural changes have occurred in satellites, (peri)centromeres, and genes, contributing to fast subspeciation and morphotypification during the short history of Br cultivation, providing invaluable resources for Brassica breeding.}, }
@article {pmid41642984, year = {2026}, author = {Spohn, M and Arnillas, CA and Bakker, JD and Borer, ET and Bråthen, KA and Cadotte, MW and Carbutt, C and Catford, JA and DuPre, ME and Dwyer, C and Eisenhauer, N and Estrada, C and Hagenah, N and Haider, S and Harms, KE and Hautier, Y and Hersch-Green, EI and Knops, JMH and Laanisto, L and Laungani, R and Macek, P and Martinson, H and Millett, J and Pärtel, M and Pennings, SC and Peri, PL and Power, SA and Risch, AC and Roscher, C and Seabloom, EW and Smith, NG and Stevens, C and Virtanen, R and Wardle, GM and Zhang, P}, title = {Intense solar radiation constrains plant species richness in global grasslands.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {123}, number = {6}, pages = {e2527128123}, doi = {10.1073/pnas.2527128123}, pmid = {41642984}, issn = {1091-6490}, mesh = {*Biodiversity ; *Grassland ; *Plants/radiation effects/classification ; Biomass ; *Sunlight ; Poaceae/radiation effects ; Photosynthesis/radiation effects ; }, abstract = {The search for predictors of plant diversity has challenged scientists for decades. Here we identify intense photosynthetically active radiation (PAR) as a major factor constraining plant species richness in global grasslands. We show that the strength of the negative relationship between species richness and PAR increases with increasing elevation and that species richness is more strongly correlated with intense PAR than with UV-B radiation, climate variables, and atmospheric nitrogen deposition. In addition to species richness, plant biomass was also negatively correlated with PAR at higher elevations, indicating that intense PAR also constrains plant biomass in montane grasslands. Furthermore, we show that the decrease in plant species richness with increasing PAR is mainly caused by a decrease in species richness of forbs, sedges, and rushes. In contrast, species richness of grasses was only negatively correlated with PAR at high elevations, and species richness of legumes was not significantly correlated with PAR. Our results suggest that PAR constrains plant species richness in global grasslands and limits the extent to which plant species of specific functional groups can migrate uphill in response to climate warming.}, }
@article {pmid41640738, year = {2025}, author = {Zöhrer, PA and Unterberger, S and Aschauer, R and Draxler, A and Somloi, S and Kapeller, M and Bauer, T and Heinz, C and Reichstam, S and Franzke, B and Strasser, EM and Hausmann, B and Pjevac, P and Berry, D and Wessner, B and Wagner, KH}, title = {The impact of a high-protein diet with strength training on the gastrointestinal microbiota in community-dwelling older adults: subanalysis of a randomized controlled trial.}, journal = {Frontiers in nutrition}, volume = {12}, number = {}, pages = {1712451}, pmid = {41640738}, issn = {2296-861X}, abstract = {BACKGROUND: A balanced gastrointestinal (GI) microbiota is essential for healthy aging. Although high-protein diets and strength training are recommended for older adults to maintain muscle mass, their effects on GI microbiota remain unclear.<br><br>METHODS: This randomized controlled trial examined the effect of a habitual diet with recommended protein intake or high protein intake combined with strength training on the GI microbiota of 112 community-dwelling adults aged 65-85&#x202f;years. The participants were divided into three groups: no intervention control (CON), recommended protein intake plus strength training (RP&#x202f;+&#x202f;T), and high protein intake plus strength training (HP&#x202f;+&#x202f;T). Over 17&#x202f;weeks, protein intake increased significantly from 0.80 (IQR: 0.30-0.50) g/kg body weight at baseline, reaching 1.07&#x202f;&#xb1;&#x202f;0.25&#x202f;g/kg in RP&#x202f;+&#x202f;T, and 1.62&#x202f;&#xb1;&#x202f;0.37&#x202f;g/kg in HP&#x202f;+&#x202f;T groups. Stool samples collected at baseline, after dietary intervention, and after combined dietary and training intervention were analyzed using 16S rRNA gene amplicon sequencing.<br><br>RESULTS: Despite increased protein intake, microbiota richness, diversity, and composition showed no significant changes within or between groups. Residual energy and inflammatory markers indicated that higher protein intake was well tolerated.<br><br>CONCLUSION: The findings suggest that increasing protein intake via food sources up to 1.6&#x202f;g/kg body weight for more than 4&#x202f;months, with or without strength training, does not adversely affect the GI microbiota composition in older adults.}, }
@article {pmid41640304, year = {2026}, author = {Hart, DW and Ng, AS and Gazińska, P and Goldin, R and Gopal, P and O'Dell, N and Zargar, A and Pytowski, L and Montazid, S and Bardella, C and East, JE and Tomlinson, IP and Koch, N and Bennett, NC and Irshad, S}, title = {Characterisation of bacteria-induced colitis and its modulation by probiotics in naked mole rats: a new mammalian model for acute inflammatory disease.}, journal = {The Journal of pathology}, volume = {}, number = {}, pages = {}, doi = {10.1002/path.70034}, pmid = {41640304}, issn = {1096-9896}, support = {DST-NRF (GUN 64756)//Department of Science and Technology-National Research Foundation/ ; //The National Institute for Health and Care Research (NIHR) Oxford Biomedical Research Centre (BRC)/ ; }, abstract = {Enteropathogenic bacteria are a major cause of morbidity and mortality globally. While mouse models have been indispensable in advancing our understanding of infectious enteric diseases, key differences in intestinal microbiota and immunobiology between mice and humans underscore the need for alternative mammalian models that better recapitulate human disease states. The naked mole rat (NMR), the longest-lived rodent and a model of healthy ageing, presents a unique opportunity. It possesses an exceptionally robust intestinal barrier, an abundance of goblet cells, a thicker mucin layer, and reduced gut permeability compared to mice. Additionally, the NMR gut microbiome exhibits compositional and functional features shared with human centenarians and traditional-lifestyle populations (e.g. Hadza hunter-gatherers), including an enrichment of health-associated taxa and metabolic pathways. Here, we leverage this model to show that systemic Citrobacter braakii infection is associated with colonic inflammation and epithelial injury that closely mimics human haemorrhagic colitis. Infected NMRs develop mucosal erosions, ulcerations, depletion of goblet cells, expansion of proliferative compartments, and active inflammation in the lamina propria. Without intervention, systemic inflammation associated with sepsis ensues and results in high mortality. Furthermore, we demonstrate the utility of this model for therapeutic testing by showing a strong effect of a probiotic cocktail comprising lactobacilli, bifidobacteria, streptococci, and enterococci. Treatment with this cocktail promoted mucosal healing, restored intestinal homeostasis, and exerted an anti-inflammatory effect. Taken together, we establish the NMR as a translatable model for investigating disease mechanisms in infectious colitis, including disruptions in mucosal barrier permeability, gut microbial ecology, and local and systemic immune regulation, as well as for testing functional probiotic strains as potential therapeutics. © 2026 The Author(s). The Journal of Pathology published by John Wiley &amp; Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.}, }
@article {pmid41637059, year = {2026}, author = {Xiong, S and Liu, Z and Xiao, N and Hua, Y and Wan, X and Zhao, J}, title = {Vallisneria Invasion into Myriophyllum Community: Differential Responses of Comammox Community in Changing Rhizosphere Environment.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxag038}, pmid = {41637059}, issn = {1365-2672}, abstract = {AIMS: Species invasion is one of the key issues in global ecosystems. This study investigated the changes in the rhizosphere community structure of complete ammonia-oxidizing bacteria (Comammox) after the invasion of the long-rooted submerged macrophyte Vallisneria spiralis L. into the community of the short-rooted submerged macrophyte Myriophyllum spicatum L.<br><br>METHODS AND RESULTS: Different planting ratios simulated varying invasion intensities. Increasing invasion intensity significantly altered rhizosphere factors, increasing invasion intensity significantly reduced dissolved organic carbon (DOC) and lowered pH, thereby causing distinct alterations in the rhizosphere environment. Comammox Clade A remained dominant with stable abundance, indicating strong adaptability. In contrast, Clade B abundance increased under low-moderate invasion but declined sharply under high intensity, suggesting a preference for mixed roots or low-intensity invasion. Higher pH and dissolved organic carbon provided a stable niche for Clade A. High invasion intensities elevated NH&#x2084;&#x207a;-N and NO&#x2083;&#x207b;-N concentrations, which coupled with stronger oxidative conditions promoted ammonia-oxidizing bacteria (AOB) and certain Clade A subgroups, thereby suppressing the low-nitrogen-adapted Clade B.<br><br>CONCLUSIONS: This study demonstrates that submerged macrophyte invasion reshapes the rhizosphere environment and drives Comammox community differentiation, offering new insights into plant invasion's ecological effects and nitrogen cycling regulation.}, }
@article {pmid41635904, year = {2025}, author = {Fan, X and Wang, X and Chao, Y and Xu, E}, title = {Probiotic and prebiotic mechanisms in IBD-associated colorectal carcinogenesis: recent advances.}, journal = {Frontiers in nutrition}, volume = {12}, number = {}, pages = {1693875}, pmid = {41635904}, issn = {2296-861X}, abstract = {Inflammatory bowel disease (IBD), a chronic relapsing inflammatory disorder of the gastrointestinal tract, significantly increases the risk of progression to colorectal cancer (CRC). Emerging studies highlight the critical roles of gut microbial dysbiosis and sustained intestinal inflammation in driving this pathological transformation. Probiotics and prebiotics, as modulators of gut microbial ecology, have attracted considerable attention as potential interventions to restore microbial balance, regulate immune responses, and mitigate carcinogenic processes. In this review, we integrate the interplay mechanisms among inflammation, microbiota, and immunity in IBD-associated colorectal carcinogenesis (IBD-CRC), with a focus on the roles of probiotics and prebiotics in microbial remodeling, enhancement of epithelial barrier integrity, inhibition of inflammatory signaling, and activation of antitumor immunity. Furthermore, we discuss preclinical and clinical evidence supporting their efficacy in delaying or preventing IBD-CRC. The review also provides perspectives on future customized synbiotic strategies in microbiota-targeted therapy and cancer prevention.}, }
@article {pmid41635399, year = {2026}, author = {Morton, SG and Vucelic-Frick, G and Dickey, JR and Rajput, BS and Spiegel, CJ and Loomis, DA and Jackrel, SL and Burkart, MD and Shurin, JB}, title = {Microplastic pollution induces algae blooms in experimental ponds but bioplastics are less harmful.}, journal = {Communications sustainability}, volume = {1}, number = {1}, pages = {16}, pmid = {41635399}, issn = {3059-4308}, abstract = {An ever-growing sea of plastic waste permeates even the most remote ecosystems; however, its ecological impact is unclear. Less persistent bioplastic alternatives are available but also have unknown environmental effects. We conducted a three-month experiment exposing plankton in experimental ponds to 10 concentrations of three different thermoplastic polyurethane microplastics, including two biodegradable bioplastics. Algal blooms with dense chlorophyll occurred consistently at high concentrations of the petroleum-derived thermoplastic polyurethane, but only occasionally with the two bioplastics. Herbivorous zooplankton density was strongly reduced by typical thermoplastic polyurethane and only weakly by bioplastics, therefore the effect on algae is at least partly due to reductions in top-down grazing pressure. Microbial communities exhibited compositional shifts in response to all three plastic types, with petroleum-derived plastic associated with the most pronounced differences across both prokaryotic and eukaryotic domains. Our results show that plastic pollution may contribute to the growing global problems of eutrophication, coastal hypoxia and harmful algae blooms, and that biodegradable plastics may have smaller environmental footprints.}, }
@article {pmid41632325, year = {2026}, author = {Lyons, R and Chan, CM and Hodal, CME and Parry, AR and Lant, P and Pratt, S and Laycock, B and Dennis, PG}, title = {The Diversity of Plastisphere Bacterial and Fungal Communities Differs between Biodegradable Polymer Types in Soil.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02677-z}, pmid = {41632325}, issn = {1432-184X}, }
@article {pmid41632308, year = {2026}, author = {Gayithri, M and Singh, S and Pradhan, B and Boorla, V and Chand, S}, title = {Multifunctional Roles of Bacillus spp. in Sustainable Agriculture: Advances in Biocontrol, Omics, and Ecological Applications.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02709-2}, pmid = {41632308}, issn = {1432-184X}, }
@article {pmid41630783, year = {2026}, author = {Sachdeva, C and Prasad, SS and Shenoy, KR and Kudva, A and Badareesh, L and Veerabhadrappa, BS and Krishna, SM and Murali, TS}, title = {A longitudinal profiling of microbiome of diabetic foot ulcers shows functional role of microbial communities in wound worsening and chronicity.}, journal = {Current research in microbial sciences}, volume = {10}, number = {}, pages = {100544}, pmid = {41630783}, issn = {2666-5174}, abstract = {Microbial communities in infected diabetic foot ulcers (DFUs) play a critical role in wound morbidity and healing outcomes. While cross-sectional studies that profile the microbial communities using culture-independent approaches are available, we conducted a longitudinal microbiome analysis of 30 diabetic individuals to elucidate the relationship between microbial composition, host factors, and wound healing trajectories. Using a 16S rRNA-based metagenomic approach, we characterized the core microbial communities associated with DFU. Alpha diversity analysis revealed significant differences between DFU microbiome from same individuals across visits, and between DFU and non-DFU cohorts, while no significant differences in beta diversity was observed. Core microbiome analysis identified Pseudomonas to be consistently present across all cohorts, higher abundance of Escherichia and Prevotella in DFU samples across visits while Acinetobacter and Morganella were predominant in non-DFU wounds. Healed DFUs were enriched in Alcaligenes and Corynebacterium while worsened DFUs showed increased abundance of Enterococcus and Serratia. In amputated individuals, Escherichia was found in high abundance, while Staphylococcus was reduced. DFU subjects with high HbA1c levels (7.3-14.9%) had higher abundance of Pseudomonas and Acinetobacter, while Prevotella and Escherichia were abundant in individuals with lower HbA1c (<7.2%). Functional predictive profiling of microbiome communities using MicrobiomeAnalyst showed significant differences between healed and worsened DFUs, especially related to genes with roles in wound healing, drug resistance, biofilm formation, tissue invasion and pathogenicity. Our findings provide insights into the microbial ecology of DFUs, while the longitudinal screening of microbes associated with DFU revealed microbial dynamics and their probable role on wound outcome.}, }
@article {pmid41628729, year = {2026}, author = {Romeiro, K and Siqueira, JF and Rôças, IN and Gominho, LF and Villela, LB and Brisson-Suárez, K and Carmo, FL}, title = {Root Canal Microbiome in Patients Undergoing Antineoplastic Therapy: a Next-Generation Sequencing Study.}, journal = {Journal of endodontics}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.joen.2026.01.020}, pmid = {41628729}, issn = {1878-3554}, abstract = {INTRODUCTION: This study compared the intracanal microbiome of teeth with apical periodontitis in oncological and healthy patients using 16S rRNA gene-based next generation sequencing.<br><br>METHODS: Root canal samples were taken from 46 teeth with pulp necrosis and primary apical periodontitis (23 from oncological patients and 23 from healthy controls). DNA was extracted and sequenced using the Illumina MiSeq platform targeting the V3-V4 region of the 16S rRNA gene. Bioinformatics processing was conducted using QIIME2 and DADA2. Alpha and beta diversity analyses, genus-level abundance comparisons, and indicator species analyses were performed.<br><br>RESULTS: After quality filtering, 3,307,822 sequence reads were retained, averaging 68,912.96 reads/sample, and resulting in 3,241 unique amplicon sequence variants. Oncological patients exhibited significantly higher bacterial richness (p = 0.01), while Shannon diversity showed no significant difference between groups. Beta diversity analysis (Bray-Curtis, MDS stress = 0.14) did not reveal significant differences between groups. Indicator species analysis identified some specific taxa more associated with oncological patients, including the candidate endodontic pathogens Prevotella, Selenomonas, Alloprevotella, Rothia, and Fretibacterium.<br><br>CONCLUSIONS: The root canal microbiome of oncologic patients with apical periodontitis was broadly similar to that of healthy controls. The oncologic group showed higher species richness, but no significant differences in the overall bacterial diversity or community structure.}, }
@article {pmid41628277, year = {2026}, author = {Marrec, L and Lehtinen, S}, title = {Cluster dispersal shapes microbial diversity during community assembly.}, journal = {PLoS computational biology}, volume = {22}, number = {2}, pages = {e1013918}, doi = {10.1371/journal.pcbi.1013918}, pmid = {41628277}, issn = {1553-7358}, abstract = {Identifying the drivers of diversity remains a central challenge in microbial ecology. In microbiota, within-community diversity is often linked to host health, which makes it all the more important to understand. Since many communities assemble de novo, microbial dispersal plays a critical role in shaping community structure during the early stages of assembly. While theoretical models typically assume microbes disperse individually, this overlooks cases where microbes disperse in clusters, such as, for example, during host feeding. Here, we investigate how cluster dispersal impacts species richness, between-community dissimilarity, and species abundance in the initial steps of microbial community assembly. We developed a model in which microbes disperse from a pool into communities as clusters and then replicate locally. Using both analytical and numerical approaches, we show that cluster dispersal promotes community homogenization by increasing within-community richness and reducing dissimilarity across communities, even at low dispersal rates. Moreover, it modulates the influence of local selection on microbial community assembly and, consequently, on species abundance. Our results demonstrate that cluster dispersal has distinct effects from simply increasing the dispersal rate. This work reveals new evidence for the role of cluster dispersal in the early dynamics of microbial community assembly.}, }
@article {pmid41627727, year = {2026}, author = {Ginger, ML and Karnkowska, A and McCall, LI and Silber, AM and Michels, PAM}, title = {Why Euglenozoans.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3013}, number = {}, pages = {3-22}, pmid = {41627727}, issn = {1940-6029}, mesh = {*Euglenozoa/physiology/genetics/classification ; Animals ; }, abstract = {To accompany a new collection of methods and protocols, we discuss the relevance of the microbial eukaryotes belonging to the protist phylum Euglenozoa. For those interested by Euglena, applied biology is often relevant: as a starting point for useful natural products including biofuels, nutritional supplements, and metabolites with biomedical potential, or as an environmental agent for bioremediation. Arguably the most widely studied euglenozoans are the parasitic trypanosomatids. Collectively, trypanosomatids cause several serious neglected tropical diseases and economically important diseases of animals and plants; since the early 1900s, drug discovery and disease intervention have been prominent research areas. Yet for those interested in evolution, trypanosomatids and Euglena are host to all sorts of extreme biology either not seen or so pronounced in other eukaryotes. Euglenozoans are also relevant in an ecology context: free-living relatives of the trypanosomatids are abundant in freshwater environments. Moreover, the other major euglenozoan group, the diplonemids, are recently recognized as the most abundant heterotrophic protists in the world's oceans, their diversity and abundance at least comparable to major algal groups. Finally, the long history of euglenozoan study illustrates nicely the evolving nature of scientific discovery and reporting since Van Leeuwenhoek first saw Euglena in the pioneering days of microscopy.}, }
@article {pmid41627051, year = {2026}, author = {Shoemaker, WR and Grilli, J}, title = {The macroecological dynamics of sojourn trajectories in the human gut microbiome.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0122125}, doi = {10.1128/msystems.01221-25}, pmid = {41627051}, issn = {2379-5077}, abstract = {The human gut microbiome is a dynamic ecosystem. Host behaviors (e.g., diet) provide a regular source of environmental variation that induces fluctuations in the abundances of resident microbiota. Despite these displacements, microbial community members remain highly resilient. Population abundances tend to fluctuate around a characteristic steady-state over long timescales in healthy human hosts. These temporary excursions from steady-state abundances, known as sojourn trajectories, have the potential to inform our understanding of the fundamental dynamics of the microbiome. However, to our knowledge, the macroecology of sojourn trajectories has yet to be systematically characterized. In this study, we leverage theoretical tools from the study of random walks to characterize the duration of sojourn trajectories, their shape, and the degree that diverse community members exhibit similar qualitative and quantitative dynamics. We apply the stochastic logistic model as a theoretical lens for interpreting our empirical observations. We find that the typical timescale of a sojourn trajectory does not depend on the mean abundance of a community member (i.e., carrying capacity), although it is strongly related to its coefficient of variation (i.e., environmental noise). This work provides fundamental insight into the dynamics, timescales, and fluctuations exhibited by diverse microbial communities.IMPORTANCEMicroorganisms in the human gut often fluctuate around a characteristic abundance in healthy hosts over extended periods of time. These typical abundances can be viewed as steady states, meaning that fluctuating abundances do not continue towards extinction or dominance but rather return to a specific value over a typical timescale. Here, we empirically characterize the (i) length (i.e., number of days), (ii) relationship between length and height, and (iii) typical deviation of a sojourn trajectory. These three patterns can be explained and unified through an established minimal model of ecological dynamics, the stochastic logistic model of growth.}, }
@article {pmid41627043, year = {2026}, author = {Tan, Y and Liang, J and Yi, Q}, title = {Study on geographic differentiation and environment-host synergistic assembly mechanism of root-associated fungal communities in Paphiopedilum purpuratum.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0257325}, doi = {10.1128/spectrum.02573-25}, pmid = {41627043}, issn = {2165-0497}, abstract = {The orchid-fungus symbiosis is fundamental to orchid survival and reproduction; however, the diversity patterns and assembly mechanisms of the root-associated mycobiota in Paphiopedilum purpuratum remain inadequately characterized. We utilized high-throughput sequencing of the internal transcribed spacer 2 region to investigate the composition, diversity, sources, and assembly processes of the endophytic fungal communities across eight geographically distinct populations, with complementary profiling of rhizosphere soil fungi. Our results indicated that Ascomycota constituted the dominant phylum within the root mycobiota, while core taxonomic groups exhibited pronounced geographic differentiation at both family and genus levels. Significant inter-population disparities in α-diversity metrics reflected underlying community compositional divergence. Environmental variables, particularly longitude, exerted a stronger influence on community structure than biotic factors. Approximately 44.05% of root fungal operational taxonomic units were soil-derived, and the host plant selectively enriched fungal taxa, most of which possessed unknown trophic modes. Community assembly processes were compartment-specific: the root endophytic mycobiota was primarily governed by stochastic ecological drift, whereas the rhizosphere communities were predominantly shaped by deterministic dispersal limitation. This compartment-specific assembly was evidenced by the prevalence of stochastic processes (|βNTI| < 2) in the root endosphere, contrasting with the dominance of deterministic processes (|βNTI| > 2) in the rhizosphere. Co-occurrence network analysis revealed higher connectivity and robustness in the endophytic mycobiota. The interaction network between orchid mycorrhizal fungi and other root-associated soil fungi formed an efficient and stable functional system whose complexity showed population-specific differentiation. Collectively, our findings demonstrate clear geographic divergence in the root fungal communities of P. purpuratum and underscore a synergistic environment-host assembly mechanism, thereby providing critical ecological insights for informing conservation strategies for this endangered orchid.IMPORTANCEThis study investigates the root-associated fungal communities of the endangered orchid Paphiopedilum purpuratum across its geographical distribution. We identified clear geographical differentiation in community composition and diversity, predominantly driven by abiotic factors-particularly longitude-rather than biotic factors. A key finding reveals that 44% of root fungal taxa originate from the soil, indicating active host-mediated selection. A fundamental dichotomy in assembly mechanisms was observed: stochastic ecological drift dominated within roots, whereas deterministic dispersal limitation prevailed in the rhizosphere. Co-occurrence networks demonstrated that the root fungal community is highly connected and robust, suggesting a stable functional system. Our findings elucidate the synergistic roles of environment and host in shaping fungal assembly, providing novel insights into orchid-fungus symbiosis with theoretical implications for mycorrhizal ecology and practical relevance for conservation strategies.}, }
@article {pmid41626752, year = {2026}, author = {Demeter, K and Savio, D and Kirschner, AKT and Reischer, GH and Kolarevic, S and Parajka, J and Derx, J and Jakwerth, S and Wurzbacher, C and Blaschke, AP and Mach, RL and Blöschl, G and Farnleitner, AH and Eiler, A}, title = {Hydrological regime of a continental river system predicts bacterial macroecological patterns.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag013}, pmid = {41626752}, issn = {1751-7370}, abstract = {Modelling bacterial dynamics in large river systems is crucial for predicting continental-scale ecosystem functioning under anthropogenic pressures. Although the River Continuum and Metacommunity concepts have provided theoretical frameworks, quantitative parameters necessary for microbial macroecological models remain scarce. Here, we present results from two whole-river surveys, conducted six years apart along 2600 km of the Danube River. Using bacterial secondary production, cell counts, and 16S rRNA gene amplicon sequencing, we quantified carbon, cell, phylotype, and diversity turnover along the river. Carbon incorporation per cell declined with water travel time by 6,000 - 21,000 atoms per hour. Bacterial cells multiplied every eight days, resulting in four to six doublings during downstream transport. Growth responses at the level of individual phylotypes differed up to a hundredfold from these bulk community estimates. Bacterial diversity dynamics were dominated by phylotype turnover rather than phylotype loss. Turnover ranged 0.92 to 0.96 across the river, indicating an almost complete replacement of phylotypes with 2-11% of headwater-associated ASVs persisting under base-flow conditions. Richness declined gradually downstream at a rate of approximately 0.13 ASVs per hour. Variations in bacterial secondary production, cell abundance, and observed ASVs were best explained by models combining hydrological and water quality parameters, whereas beta diversity followed a gradual development primarily structured by water travel time. Together, these results identify water travel time as the key integrative parameter governing microbial macroecological dynamics along large rivers, with environmental conditions fine-tuning local responses. These models can help predict changes in microbial diversity and functioning under anthropogenic alterations.}, }
@article {pmid41626630, year = {2026}, author = {Lin, L and Neves, ALA and Ominski, KH and Guan, LL}, title = {Metatranscriptomics uncovers diet-driven structural, ecological, and functional adaptations in the rumen microbiome linked to feed efficiency.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycaf251}, pmid = {41626630}, issn = {2730-6151}, abstract = {The rumen microbiome plays a pivotal role in modulating feed efficiency in ruminants, yet the ecological mechanisms mediating the active interactions among microbial adaptations, dietary inputs, and host feed efficiency within the rumen remain poorly understood. To address this gap, we analyzed 120 metatranscriptomic datasets obtained from 30 purebred Angus bulls (each sampled four times) classified as high-feed-efficiency or low-feed-efficiency based on feed conversion ratio, and fed either forage-based (n = 15) or grain-based (n = 15) diets. We constructed a comprehensive active gene catalog comprising 1 744 067 non-redundant genes and compiled a reference set of 25 115 ruminant microbial genomes. Using integrated Neutral Community Model analysis and carbohydrate-active enzyme profiling, we examined how ecological processes and functional capacities differed across host phenotypes and diets. Neutral Community Model fits revealed that stochastic processes broadly governed rumen microbial community structures (R[2] = 0.779 for high-feed-efficiency; R[2] = 0.781 for low-feed-efficiency). Within the predominantly stochastic processes, however, high-feed-efficiency bulls exhibited strong positive selection for diet-responsive microbial lineages: Fibrobacter spp. (positively selected species-level genome bins: 61.3%-76.0%; negatively selected: 0%-1.3%), Butyrivibrio spp. (positively selected: 13.3%-46.0%; negatively selected: 1.0%-11.2%) under forage feeding, and UBA1067 spp. (positively selected: 33.3%-48.5%; negatively selected: 0%-8.3%) under grain feeding. These lineages encoded catalytic domains appended with carbohydrate-binding modules, such as tandem carbohydrate-binding modules linked to glycoside hydrolases, thereby enhancing substrate adhesion and degradation. In contrast, low-feed-efficiency bulls showed more random community structures and reduced functional specialization. Therefore, these suggest that cattle hosts with higher feed efficiency promote microbial populations functionally aligned with dietary inputs, a process we define as efficient host-mediated microbial amplification. These findings offer new insight into how ecological assembly and functional adaptation of the microbiome contribute to feed efficiency and lay the foundation for microbiome-informed strategies to enhance ruminant production sustainability.}, }
@article {pmid41624311, year = {2026}, author = {Marchal, C and Ballan, D and Azib, S and Innocent, M and Urien, B and Tamaro, A and Gall-Ely, ML and Coton, E and Picot, A and Mounier, J and Coroller, L and Gabriel, P}, title = {Participatory and multi-disciplinary science dataset and surveys for the assessment of the microbiological and behavioural factors influencing fresh fruits and vegetables' waste at home.}, journal = {Data in brief}, volume = {65}, number = {}, pages = {112434}, pmid = {41624311}, issn = {2352-3409}, abstract = {Fresh fruits and vegetables (FFV) represent the largest part of food waste at the consumer level. This waste directly results from FFV physiological and microbiological spoilage, itself intricately linked to behavioural factors such as consumer practices, including purchase, storage and hygiene practices, but also consumers' perceptions towards spoilage. Based on a dual approach combining microbiological and behavioural sciences, we examined the link between FFV waste produced by 49 volunteering French households, measured using connected bins, the microbial ecology of their storage compartments, using culture-dependent and -independent approaches, and their consumer behaviour, cleaning and storage practices, through in-depth interviews and a dedicated survey. An exploratory qualitative survey carried out on 17 individuals followed by two quantitative data collections on 1048 and 815 representative French consumers enabled us to identify anti-FFV waste practices and to cluster consumers according to their anti-FFV waste behaviours. Spoilage dynamics of commonly consumed FFV, according to storage temperature, microbial contamination level and the presence or absence of surface wounds, were also performed in controlled conditions. This citizen-science-based dataset covers a wide array of microbiological and behavioural factors related to domestic FFV waste, as well as real measurements of waste volumes thanks to the innovative use of connected bins. Altogether, this data could provide interesting insights into more effective and accessible guidelines for FFV waste reduction at the consumer level, and thus to a potential reduction of global food waste and its related costs.}, }
@article {pmid41624200, year = {2025}, author = {Xu, H and Liu, X and Sun, W and Dong, X and Liu, X and Xie, Y and He, J and Ali, A and Chen, M and Wu, L and Ma, J and Shao, K}, title = {Multi-omics elucidation of Lactiplantibacillus plantarum NKK20 in preventing PCOS via the gut-ovary axis: SCFAs-mediated microbiota-metabolite-immune crosstalk.}, journal = {Frontiers in nutrition}, volume = {12}, number = {}, pages = {1709581}, pmid = {41624200}, issn = {2296-861X}, abstract = {PURPOSE: Polycystic ovary syndrome (PCOS) is a clinically prevalent endocrine and metabolic disorder characterized by gut microbial disturbances and chronic low-grade inflammatory responses.<br><br>METHODS: This study explores the therapeutic potential and mechanistic insights of Lactiplantibacillus plantarum NKK20 (LP) in a PCOS murine model established through high-fat diet (HFD) and letrozole co-induction. By integrating multi-omics profiling (16S rRNA sequencing and untargeted metabolomics) with histopathological evaluation, we systematically assessed LP-mediated modulations of gut microbiota composition, metabolic signatures, ovarian function, and intestinal barrier integrity.<br><br>RESULTS: The results demonstrated that LP administration effectively counteracted metabolic dysregulation in PCOS mice, mitigating body weight gain, ameliorating lipid abnormalities (reduced total cholesterol, triglycerides, and LDL-C alongside elevated HDL-C), and lowering fasting glucose levels. Hormonally, LP suppressed hyperandrogenism, as evidenced by decreased testosterone, while rebalancing inflammatory mediators through IL-10 upregulation and concomitant reduction of TNF-&#x3b1;, IL-6, IL-1&#x3b2;, and MCP-1. Ovarian histomorphology revealed attenuated follicular cysts and enhanced luteinization. Critically, LP restored intestinal homeostasis by (i) augmenting short-chain fatty acid (SCFA) production-particularly butyrate-(ii) fortifying the gut barrier via increased ZO-1 and occludin expression, and (iii) diminishing circulating endotoxin. Microbial sequencing identified enrichment of Bacteroidetes and Muribaculum following LP treatment. Serum metabolomics further uncovered LP-induced normalization of steroid hormone biosynthesis and glycerophospholipid metabolism, coinciding with elevated anti-inflammatory mediators such as 6a-prostaglandin I1.<br><br>CONCLUSION: Collectively, these findings delineate a novel preventive axis through which LP inhibits PCOS progression&#x202f;-&#x202f;namely, via coordinated "gut microbiota-metabolite-ovarian" crosstalk involving SCFA-mediated barrier restoration, microbial ecology stabilization, and suppression of ovarian inflammatory onset. This work advances the translational rationale for probiotic-based strategies in PCOS prevention.}, }
@article {pmid41624197, year = {2025}, author = {Govaert, M and Duysburgh, C and Kesler, B and Marzorati, M}, title = {Effects of NatureKnit™ organic, a blend of organic fruit and vegetable fibers rich in naturally occurring bound polyphenols, on the metabolic activity and community composition of the human gut microbiome using the M-SHIME[®] gastrointestinal model.}, journal = {Frontiers in nutrition}, volume = {12}, number = {}, pages = {1740906}, pmid = {41624197}, issn = {2296-861X}, abstract = {OBJECTIVES: The effects of a proprietary blend of organic fruit and vegetable fibers rich in naturally occurring bound polyphenols (commercially known as NatureKnit™ Organic) on the human gut microbiome were assessed.<br><br>METHODS: Short-term (48&#x202f;h) in vitro colonic simulations using the validated Mucosal Simulator of the Human Intestinal Microbial Ecosystem (M-SHIME[&#xae;]) platform, with fecal inoculum from nine individual healthy human donors, were performed. Purified organic fibers (inulin and psyllium) were evaluated as comparators and a negative control was included. Primary measures included pH, gas pressure, short-chain fatty acid (SCFA) production, and microbial community composition.<br><br>RESULTS: All test products were well fermented with NatureKnit&#x2122; Organic showing slower fermentation kinetics than the purified fibers. SCFAs were significantly increased with all test products versus the negative control (p&#x202f;<&#x202f;0.0001 for all) and NatureKnit&#x2122; Organic reached significance versus both purified fibers (p&#x202f;<&#x202f;0.0001 for both). While relative abundances in the mucosal compartment were similar among all test conditions, luminal bacterial abundance increased with NatureKnit&#x2122; Organic and psyllium versus the negative control. The latter was mainly associated with statistically increased abundance (p&#x202f;<&#x202f;0.05) of the genera Eisenbergiella and Monoglobus, with an additional strong enrichment of Bacteroidaceae. Furthermore, bacterial species richness was significantly increased with NatureKnit&#x2122; Organic versus the negative control (p&#x202f;=&#x202f;0.0495), which was not observed for the purified organic fibers (p&#x202f;=&#x202f;0.0567 and p&#x202f;=&#x202f;0.4285 for inulin and psyllium, respectively).<br><br>CONCLUSION: Overall, the obtained results indicate that NatureKnit&#x2122; Organic may have a greater and gentler prebiotic effect compared with established purified prebiotic fibers.}, }
@article {pmid41621727, year = {2026}, author = {De Luca, D}, title = {FastqOrienter: A Python utility for the automated orientation and quality diagnostics of paired-end Illumina metabarcoding reads.}, journal = {Journal of microbiological methods}, volume = {}, number = {}, pages = {107413}, doi = {10.1016/j.mimet.2026.107413}, pmid = {41621727}, issn = {1872-8359}, abstract = {FastqOrienter is a Python tool that corrects inconsistent read orientations in Illumina paired-end metabarcoding reads using a primer-aware logic and IUPAC-compliant matching. In addition, it provides detailed diagnostics and actionable insights for discarded reads. It ensures data integrity for downstream pipelines like DADA2 and QIIME 2.}, }
@article {pmid41620541, year = {2026}, author = {Wang, Y and Han, S and Zhang, W and Shen, W and Dong, B and Wang, N}, title = {Microbial Mediators of Pine Defense Resistance: Stage-Specific Gut Symbionts Enable Acantholyda posticalis to Overcome Terpenoid Barriers.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02641-x}, pmid = {41620541}, issn = {1432-184X}, support = {SDAIT-24//Modern Agricultural Technology Industry System of Shandong province/ ; ZR2022MC198//Natural Science Foundation of Shandong Province/ ; 2023TSGC0345//Science and Technology of Small and Medium Enterprises Innovation Ability Enhancement in Shandong Province/ ; }, abstract = {Acantholyda posticalis (Matsumura) is a globally significant forest pest that inflicts substantial economic losses through its feeding activity on Pinus species. As an oligophagous insect, A. posticalis relies critically on its gut microbiota to overcome the defensive secondary metabolites of pine needles, particularly α- and β-pinene terpenoids. This study investigated the dynamic compositional changes of gut bacterial communities across different developmental stages of A. posticalis and characterized their functional roles in host adaptation. Through traditional culturing methods, two pinene-degrading bacterial strains-Klebsiella variicola and Enterobacter hormaechei-were isolated from the larval gut. In vitro assays demonstrated their significant capacity to degrade the two pinenes. High-throughput 16S rRNA sequencing revealed stage-specific bacterial enrichment patterns. Functional prediction suggested these microbial communities participate in critical metabolic processes, including phosphotransferase systems, GST activity, and detoxification pathways. This work advances understanding of insect-microbe symbiosis in oligophagous systems and proposes novel strategies for ecologically sustainable A. posticalis control through manipulation of its gut microbiota.}, }
@article {pmid41618023, year = {2026}, author = {Han, D and Hong, HW and Kim, H and Richter-Heitmann, T and Ryu, JS and Yoo, KC}, title = {Unraveling the Complex Planktonic Microbial Community in the Amundsen Sea, Southern Ocean.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02696-4}, pmid = {41618023}, issn = {1432-184X}, support = {NRF- 2022R1F1A1065719//National Research Foundation of Korea/ ; 2025-RISE-10-004//the Ministry of Education (MOE) and the Gangwon State (G.S.)/ ; KOPRI PE24090//Ministry of Oceans and Fisheries/ ; }, abstract = {Spatial differences in microbial community structure and function were examined across polynyas, sea ice zones (SIZ), and ice-free waters of the Amundsen Sea, Southern Ocean, using 16 S and 18 S rRNA gene-based eDNA metabarcoding and quantitative PCR targeting nitrogen cycling and dimethylsulfoniopropionate (DMSP) degradation genes. The SIZ exhibited enrichment of psychrophilic bacteria (Colwellia spp.) and dominant eukaryotic taxa such as Diatomea and Prymnesiophyceae, likely linked to sea-ice-driven shifts in nutrient stoichiometry (elevated N: P and positive N*). Network analysis revealed interactions among primary producers, bacteria, and zooplankton, highlighting complementary roles in trophic energy transfer and nutrient recycling. Metabolic pathway predictions implied active bacterial processes related to sulfur and nitrogen cycling in the SIZ, particularly dissimilatory nitrate reduction and DMSP demethylation, suggesting coupling between carbon, nitrogen, and sulfur pathways. Quantitative PCR showed higher copy numbers of nitrogen cycling genes and DMSP degradation genes in the SIZ than in other regions, consistent with enhanced microbial denitrification, nitrogen fixation, and sulfur cycling under cold conditions shaped by sea-ice-driven nutrient dynamics. These findings demonstrate that environmental variation in Antarctic waters influences microbial diversity, reshapes ecological interactions, and modulates biogeochemical functions, with implications for nutrient cycling, food web dynamics, and ecosystem resilience in this climate-sensitive region.}, }
@article {pmid41617658, year = {2026}, author = {Yan, Z and Liu, R and Zhang, ZA and Dai, T and Zhu, D and Zhang, Y}, title = {Intestinal Microplastic Retention Reshapes Gut Microbial Ecology through Surface-Associated Colonization and Additive Leaching.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c16988}, pmid = {41617658}, issn = {1520-5851}, abstract = {Microplastics (MPs) have attracted increasing attention due to their potential impacts on the human gut microbiota, yet the mechanisms governing MP-microbiota interactions remain insufficiently resolved. Here, we employed the Simulator of the Human Intestinal Microbial Ecosystem, a dynamic host-free in vitro model, to investigate how intestinally retained poly(ethylene terephthalate) MPs influence gut microbial communities. We show that MP retention is associated with two separable processes: surface-mediated spatial redistribution of microbes and additive-associated perturbations. Compared with additive-eluted MPs and inert SiO2 particles, MPs exhibited greater surface roughness and hydrophobicity, promoting selective colonization by hydrophobic, potentially pathogenic, and organic-degrading taxa. This surface-associated colonization coincided with the displacement of luminal keystone taxa and pronounced restructuring of microbial co-occurrence networks, reflected by reduced negative cohesion and altered community stability. In parallel, leachable MP-associated additives independently shifted microbial composition and predicted functional potential, including enrichment of pathways related to xenobiotic degradation. This work provides mechanistic insight into how retained MPs may condition gut microbial ecosystems and underscores the importance of considering MP-associated microbial perturbations in gut-relevant exposure assessments.}, }
@article {pmid41615200, year = {2026}, author = {Yang, J and Qin, X and Zhang, D and Dong, C}, title = {Microbial landscape: composition and health associations of environmental microbiome in key functional spaces of premium elderly care facilities.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0183725}, doi = {10.1128/spectrum.01837-25}, pmid = {41615200}, issn = {2165-0497}, abstract = {The environmental microbiome in elderly care facilities plays a crucial role in the health of aging populations with immunosenescence; however, its composition and health associations remain underexplored. This study characterizes the microbial ecology of premium elderly care facilities, focusing on key functional spaces, environmental drivers, and implications for resident health. We conducted 16S rRNA gene sequencing (V3-V4 regions) on 320 surface and air samples from six functional spaces (dining areas, medical facilities, bedrooms, bathrooms, recreational rooms, and corridors) across four premium elderly care facilities. Environmental parameters (temperature, humidity, CO2, and occupancy) were measured concurrently. Bioinformatics analysis (QIIME 2, DADA2, and Silva database) and statistical modeling (permutational multivariate analysis of variance, distance-based redundancy analysis, and PICRUSt2) were employed to assess microbial diversity, taxonomic composition, functional potential, and environmental correlations. Using 16S rRNA gene sequencing across four facilities in different geographic regions, we identified significant spatial heterogeneity in microbial diversity and composition, with dining areas and recreational rooms exhibiting higher richness (Shannon index: 6.07 ± 0.37) and human-associated taxa (e.g., Firmicutes), while medical facilities and bathrooms harbored lower diversity but elevated opportunistic pathogens (Pseudomonas and Klebsiella). Environmental parameters-particularly relative humidity (explaining 13.8% of community variation) and occupancy-strongly influenced the microbial structure. A core microbiome dominated by Proteobacteria, Firmicutes, and Actinobacteria was conserved across facilities, while functional predictions revealed space-specific traits, including predicted enrichment of antibiotic resistance genes in medical facilities (ARG Shannon diversity: 4.87 ± 0.42) and carbohydrate metabolism pathways in dining areas. Negative correlations between beneficial (Lactobacillus) and pathogenic taxa (Staphylococcus aureus) were consistent with potential ecological strategies for microbial balance, although validation with absolute quantification is needed. This study highlights the need for space-specific microbial management in elderly care environments, emphasizing humidity control, ventilation, and targeted hygiene to mitigate pathogen risks while preserving beneficial communities. Our findings suggest the potential value of ecologically informed stewardship over pathogen-centric approaches. Future research should integrate multi-omics and longitudinal health data to optimize microbiome-resident health interactions.IMPORTANCEAs people age, their immune systems weaken, making the elderly especially vulnerable to germs in their surroundings. This study reveals that the types and amounts of bacteria living on surfaces and in the air within premium elderly care facilities differ significantly depending on the room's purpose-such as dining areas, medical rooms, or bathrooms. We found that humidity and how many people use a space strongly influence these bacterial communities. Crucially, areas like medical rooms had more bacteria linked to infections and antibiotic resistance, while social spaces hosted more diverse and potentially beneficial bacteria. This shows that a "one-size-fits-all" cleaning approach is not ideal. Instead, tailoring hygiene practices and environmental controls (like managing humidity) to specific spaces could better protect residents' health by reducing harmful germs while supporting helpful ones, offering a smarter way to manage these critical living environments for our aging population.}, }
@article {pmid41615027, year = {2026}, author = {Jiménez, DJ and Marasco, R and Schultz, J and Rodríguez, CAD and Nogales, J and Rodriguez-R, LM and Overmann, J and Rosado, AS}, title = {Discovery and cultivation of prokaryotic taxa in the age of metagenomics and artificial intelligence.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag012}, pmid = {41615027}, issn = {1751-7370}, abstract = {Despite advances in sequencing, microbial genomics, and cultivation techniques, the vast majority of prokaryotic species remain uncultured, which is a persistent bottleneck in microbiology and microbial ecology. This perspective outlines a conceptual framework to improve the transition from genome-resolved metagenomics to the targeted isolation of yet-uncultured prokaryotic taxa. The proposed framework integrates the induced reshaping of microbiomes, genome-based inferences of physiological and phenotypic traits, culture media design, and targeted culturomics, enabling hypothesis-driven cultivation. In addition, this manuscript addresses the critical limitations in the field, including the sequence-to-function gap, and emphasizes the synergistic potential of experimental microbiology, microbial ecology, metagenomics, and artificial intelligence (AI)-based predictions to enhance rational and actionable roadmaps for discovering and cultivating novel prokaryotic lineages.}, }
@article {pmid41614284, year = {2026}, author = {Karmakar, R and Paul, P and Malik, M and Maity, A and Mishra, MC and Tribedi, P and Ghosh, MM}, title = {In Silico and In Vitro Investigations of Novel Strategies to Combat Drug-Resistant Comamonas aquatica.}, journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica}, volume = {134}, number = {2}, pages = {e70152}, doi = {10.1111/apm.70152}, pmid = {41614284}, issn = {1600-0463}, support = {BT/INF/22/SP41296/2020//Department of Biotechnology, Ministry of Science and Technology, India/ ; IMSXC2022-23/010//St. Xavier's College (Autonomous) Kolkata/ ; }, mesh = {*Biofilms/drug effects ; *Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; *Tetracycline/pharmacology ; Computer Simulation ; *Benzaldehydes/pharmacology ; Humans ; *Drug Resistance, Bacterial ; Reactive Oxygen Species/metabolism ; }, abstract = {Comamonas aquatica, an emerging nosocomial pathogen, poses significant clinical challenges through biofilm-mediated antimicrobial resistance. This study investigated the efficacy of cuminaldehyde combined with tetracycline against C. aquatica biofilms using an integrated approach. In silico predictions (PASS online, SwissADME, PROTOX 3.0, OSIRIS) indicated that cuminaldehyde exhibited favorable oral bioavailability with acceptable toxicity profiles, while tetracycline showed limited oral absorption due to molecular size and polarity constraints. Experimentally, individual minimum inhibitory concentrations (MICs) were determined as 300 μg/mL for cuminaldehyde and 0.2 μg/mL for tetracycline. The fractional inhibitory concentration index (FICI) of 0.66 demonstrated additive interactions between the compounds (cuminaldehyde and tetracycline). The result indicated that the combinatorial application of compounds exhibited enhanced antimicrobial potential against the test organism. Furthermore, co-application of cuminaldehyde and tetracycline was found to show increased antibiofilm potential against the same organism. The result showed that the biofilm inhibition under the influence of the combinatorial application could be attributed to the enhancement of bacterial cell membrane permeability and accumulation of intracellular reactive oxygen species. In a nutshell, the findings of this study highlight a promising strategy of using combinatorial therapy involving cuminaldehyde-tetracycline for dealing with biofilm-associated infections caused by C. aquatica.}, }
@article {pmid41614084, year = {2026}, author = {Kwarteng, SA and Mensah, JO and Obuam, PK and Odenteh, EA and Foriwaah, PD and Mbelede, AI and Dziwornu, E and Duker, EO and Boakye, JD and Agbotse, GD and Yanney, JN and Aba Aude Koffi, MC and DeWitt, ME and Addo, SO}, title = {Occurrence of Tick-Borne Pathogens in Rhipicephalus sanguineus Sensu Lato From Domestic Dogs in Kumasi, Ghana.}, journal = {Veterinary medicine international}, volume = {2026}, number = {}, pages = {8881048}, pmid = {41614084}, issn = {2090-8113}, abstract = {Tick-borne pathogens, transmitted by ticks, infect humans and animals worldwide. The brown dog tick, Rhipicephalus sanguineus sensu lato, is a significant vector of a number of pathogens, including Ehrlichia canis, Rickettsia and Anaplasma species. In Ghana, there is limited information on the pathogens carried by Rh. sanguineus s.l. As such, Rh. sanguineus ticks taken from domestic dogs in Kumasi were screened for tick-borne pathogens, including Coxiella burnetii, Rickettsia, Babesia, Theileria, Anaplasma, Ehrlichia and Hepatozoon species. A total of 204 ticks collected from 56 infested dogs were morphologically identified as Rh. sanguineus s.l. From the 88 pools screened, 36 (40.9%) were positive for pathogen DNA. The pathogens identified were Rickettsia africae (5 pools), Ehrlichia canis (10 pools) and uncultured Anaplasma sp. (21 pools) with maximum likelihood estimates as 2.48% (95% CI: 0.93, 5.38%), 5.22% (95% CI: 2.69, 9.15%) and 11.20% (95% CI: 7.32, 16.29%), respectively. There was no association between the detection of a pathogen and the tick sex or dog breed, age or sex. This study provides important baseline data on the circulation of tick-borne pathogens in Rh. sanguineus s.l. ticks in Kumasi, with implications for both veterinary and human health. The presence of uncultured Anaplasma sp. suggests a wider diversity of tick-borne bacteria with unknown pathogenicity. There is a need for integrated tick control, improved diagnosis and additional epidemiological studies to mitigate the impact of tick-borne diseases in Ghana.}, }
@article {pmid41613253, year = {2026}, author = {Samimi, A and Verdon, N and Allen, RJ and Rosenbaum, MA}, title = {Probing Antibiotic Inhibition in Small Bacterial Populations With Combinatorial Droplet Microfluidics.}, journal = {Small science}, volume = {6}, number = {1}, pages = {e202500421}, pmid = {41613253}, issn = {2688-4046}, abstract = {Bacterial infections often involve small, local populations of bacteria, yet antibiotic treatment decisions are generally based on bulk population susceptibility assays. Stochastic variability among local small populations can influence susceptibility, limiting the predictive capability of bulk assays. Therefore there is a need to better understand antibiotic response in small populations. Droplet-based microfluidics enables the high-throughput production of tens of thousands of picolitre droplets, in which small populations of bacteria (e.g., 8 cells) can be encapsulated and their responses to different environmental conditions tracked. Here, we use a combinatorial droplet-generation platform, combined with microscopy and image analysis, to interrogate the responses of small populations of Escherichia coli to different bulk-determined sub-inhibitory concentrations of the antibiotics tetracycline, streptomycin, and ampicillin within a single experiment. We observe qualitatively distinct small-population responses for these antibiotics. For the bacteriostatic ribosome-targeting antibiotic tetracycline, growth varies nonmonotonically at low antibiotic concentrations. For the bactericidal ribosome-targeting antibiotic streptomycin, we observe apparent bistability, some replicate populations growing while others die. For the bactericidal cell-wall targeting antibiotic ampicillin, we observe stochastic bacterial filamentation. Our study shows how distinct phenomena impacting antibiotic susceptibility may emerge in small bacterial populations, laying a foundation for deeper studies into potential treatment implications.}, }
@article {pmid41612472, year = {2026}, author = {Wang, Y and Shen, Y and Shen, J and Bi, J and Xu, J and Wei, T and Wang, R and Wu, X and Li, F and Bai, J and Jie, Z and Hou, D and Song, Y}, title = {Airway microbiome dysbiosis in severe pneumonia: metagenomic evidence of pathogen expansion and commensal depletion.}, journal = {European journal of medical research}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40001-026-03892-1}, pmid = {41612472}, issn = {2047-783X}, support = {ZD2021CY001//Shanghai Municipal Science and Technology Major Project/ ; GWVI-11.1-18//Shanghai Three-year Action Plan to Strengthen the Construction of Public Health System/ ; 82130001//National Natural Science Foundation of China/ ; 2024YFC3044400//National Key Research and Development Program of China/ ; GZNL2024A02003//R&amp;D Program of Guangzhou National Laboratory/ ; W2020-013//The Construction of Multi-Disciplinary Treatment System for Severe Pneumonia/ ; 22Y11900800//Science and Technology Commission of Shanghai Municipality/ ; shslczdzk02201//Shanghai Municipal Key Clinical Specialty/ ; }, abstract = {BACKGROUND: The pulmonary microbiome is increasingly recognized as a key determinant of pneumonia severity, yet its clinical implications remain incompletely understood. Disruption of microbial ecology, or dysbiosis, may impair host immune responses and exacerbate disease progression. This study aimed to characterize microbiome alterations associated with severe pneumonia and their correlation with host inflammatory and coagulative parameters.<br><br>METHODS: In this multicenter, prospective observational cohort study conducted across nine hospitals in Shanghai (2021-2025), bronchoalveolar lavage fluid (BALF) samples from 306 patients with clinically diagnosed pulmonary infections were analyzed using metagenomic next-generation sequencing (mNGS). Patients were stratified into severe (n&#x2009;=&#x2009;196) and non-severe (n&#x2009;=&#x2009;110) groups using WHO-derived severe pneumonia criteria at the time of bronchoalveolar lavage (BAL). Microbial taxonomic profiles, diversity indices, co-occurrence networks, and correlations with clinical markers were comprehensively assessed using standard bioinformatic and statistical approaches.<br><br>RESULTS: Severe pneumonia was associated with marked microbial dysbiosis, including reorganization of co-occurrence network topology with centrality shifting away from commensals toward opportunistic taxa in severe disease, characterized by reduced &#x3b1;-diversity, altered &#x3b2;-diversity, and enrichment of opportunistic Gram-negative pathogens including Acinetobacter and Klebsiella. In contrast, commensals such as Rothia and Prevotella were depleted. Co-occurrence network analysis revealed fragmentation of microbial interactions in severe cases, with centrality shifting from commensals to opportunists like Corynebacterium striatum. Shannon diversity negatively correlated with SOFA scores, and specific taxa positively associated with systemic inflammation (CRP, PCT) and coagulation abnormalities. Nearly all samples demonstrated polymicrobial infection, with distinct microbial patterns observed across monomicrobial and polymicrobial subgroups.<br><br>CONCLUSION: Our multicenter observational analysis suggests that severe pneumonia is associated with marked ecological disruption of the lower-airway microbiome, characterized by commensal loss, opportunist expansion, and fragmented interspecies networks, and with concurrent inflammatory and coagulative abnormalities. These hypothesis-generating findings warrant external validation in independent, multi-region cohorts and longitudinal sampling to test directionality and causality before informing clinical decision-making.}, }
@article {pmid41612032, year = {2026}, author = {Li, Q and Shen, J and Feng, J and Liu, Y and Huang, Z and Wang, X}, title = {Patterns of ARGs and VFs Driven by Short-Term Seasonal Hydro-Environmental Stress Interactions in a Eutrophic Plateau Lake.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02703-8}, pmid = {41612032}, issn = {1432-184X}, support = {No. 202303AC100016//the Key Research and Development Program of Yunnan/ ; Project No. 202301AT070001//the Yunnan Fundamental Research Projects/ ; No. 2024YFD1700100//the National Key Research and Development Program of China/ ; }, abstract = {With the intensification of human activities, large amounts of antibiotics, heavy metals, and disinfectants enter lakes, exerting continuous selective pressure and driving the enrichment and dissemination of ARGs and VFs in aquatic microbial communities. Previous studies have primarily focused on the occurrence and abundance of ARGs in extreme plateau environments. However, the diversity and abundance of ARGs and VFs in eutrophic plateau lakes under different seasons and environmental pressures remain underexplored. In this study, we analyzed the presence of ARGs and VFs in the eutrophic plateau lake Qilu Lake across different seasons. From the perspective of hydrology and water quality, there is no inflow into the lake during the dry season, while the wet season sees an inflow of 28.1724 million cubic meters. Organic matter and metal ions are significantly higher in the dry season, whereas total nitrogen and pH levels rise notably in the wet season. We found 29 types of ARGs and 601 types of VFs in the dry season, compared to 45 types of ARGs and 637 types of VFs in the wet season. In both seasons, glycopeptide antibiotic resistance genes were the most abundant ARGs. LPS was the most abundant VFs in the dry season, while Type IV pili dominated in the wet season. The primary microbial-driven resistance mechanism strategy in both seasons was Antibiotic target alteration. The microorganism with the highest abundance of ARGs and VFs in both seasons was Pseudomonadota. Correlation analysis showed a positive relationship between the abundance of ARGs and VFs in both seasons, with this relationship being more pronounced in the dry season. Our findings indicate that the increased diversity and abundance of ARGs during the wet season may be directly linked to the heightened input of exogenous antibiotic-resistant bacteria and the promotion of plasmid conjugation transfer by hydraulic disturbances. Although VFs diversity was higher in the wet season, the low-water concentration effect and metal ion stress during the dry season significantly elevated the relative abundance of core VFs (e.g., type IV pili), resulting in the abundance of VFs per unit volume surpassing that of the wet season.}, }
@article {pmid41611907, year = {2026}, author = {Capri, FC and Prazzi, E and Casamento, G and Alduina, R}, title = {Influence of Nest Microbiota on Hatching Success of Caretta Caretta on Lampedusa Island.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02699-1}, pmid = {41611907}, issn = {1432-184X}, abstract = {Egg hatching success in sea turtle nests can be influenced by multiple abiotic and biotic factors. Although interest in nest microbiota as a determinant of embryo development and viability is increasing, its role has not yet been fully elucidated. In this study, we profiled the bacterial communities of four Caretta caretta nests on Lampedusa Island: Cala Pisana (P1 and P2) and Spiaggia dei Conigli (C1 and C2), which showed different hatching success rates (P1 = 85.2%, P2 = 1.1%, C1 = 1.1%, C2 = 0.0%). Using 16S rRNA gene (V3-V4) sequencing, we analyzed different sample types, including sand from inside and outside the nest chamber, eggshells, and inner membranes. Alpha diversity was highest in sand and lower in eggshells and inner membranes. β-diversity clearly separated the only successful nest (P1) from the others (P2, C1, and C2) (PERMANOVA p < 0.001). Across all nests, the dominant phyla were Proteobacteria, Firmicutes, Actinobacteriota, and Bacteroidota; notably, the Firmicutes/Bacteroidota (F/B) ratio was lowest in P1 compared with P2, C1, and C2. Nests with low hatching success were Firmicutes-dominated, enriched in Bacillus and Pseudomonas, and harbored hydrocarbon-degrading genera (Pseudoxanthomonas and Devosia), suggesting environmental influences. Opportunistic pathogens (Ochrobactrum and Simkaniaceae), likely associated with vertical transmission, were detected exclusively in C1 and C2 nests. Overall, our findings highlight the potentially critical role of nest microbiota in reproductive success. Both vertical (maternal) and horizontal (environmental and anthropogenic) transmission appear to shape microbial composition, potentially affecting hatchling viability and offering useful insights for conservation monitoring.}, }
@article {pmid41611865, year = {2026}, author = {Ulloa, MA and Serrano, AV and Camelo, LC and Guyot, R and Vela, D and Muñoz, AR}, title = {Bacterial genome reconstruction and community profiling in Neotropical Drosophila.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-36282-y}, pmid = {41611865}, issn = {2045-2322}, abstract = {Drosophila species serve as key models for microbiota research due to their relatively simple microbial communities. However, microbial diversity and dynamics in Neotropical Andean Drosophila remain underexplored. Here we applied shotgun metagenomics to characterize the microbiota of 24 Neotropical Drosophila species from Ecuador, reconstructing 64 high-quality bacterial genomes predominantly from Acetobacteraceae and Enterobacterales. Microbial communities were consistently dominated by yeasts, lactic acid bacteria, acetic acid bacteria, and Wolbachia. Comparative analyses revealed no strong correlation between host phylogeny and microbial community composition, suggesting environmental factors and microbial interactions shape these communities. Notably, shifts in relative abundances indicate dynamic ecological succession and metabolic cooperation among microbes. These findings expand genomic resources for Drosophila-associated bacteria and highlight the complex ecological processes influencing host-microbiota relationships in natural populations.}, }
@article {pmid41611114, year = {2026}, author = {Young, RB and Correia, GDS and MacIntyre, DA}, title = {Host, microbial and environmental drivers of vaginal microbiota composition.}, journal = {Fertility and sterility}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.fertnstert.2026.01.020}, pmid = {41611114}, issn = {1556-5653}, abstract = {The human vagina harbours a microbial community that differs markedly in compositional structure from all mammals, including closely related primates. Lactobacilli are the most abundant vaginal species, and their dominance in this niche are associated with protection against adverse health outcomes including preterm birth, sexually transmitted infections and bacterial vaginosis. However, the vaginal environment can also support compositions of diverse anaerobic bacteria, which have been linked to poor reproductive health outcomes. Here, we review current knowledge on host and microbial determinants that influence microbial community structure within the vaginal niche, emphasising the interplay between host physiology, immune and metabolic interactions as well as lifestyle factors. This integrated understanding provides a foundation for linking vaginal microbiome compositions to clinically relevant phenotypes and highlights mechanisms that could be exploited to promote improved reproductive health.}, }
@article {pmid41610262, year = {2026}, author = {Wrightson, I and Man, M and Castañeda-Gómez, L and Srikanthan, N and Tong, H and Knorr, MA and Frey, SD and Nadelhoffer, KJ and Lajtha, K and Simpson, MJ}, title = {Three Decades of Litter Manipulation Distinctly Shifts Soil Organic Matter Composition and Constrains Soil Carbon Sequestration in Temperate Forest Soils.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c11996}, pmid = {41610262}, issn = {1520-5851}, abstract = {The capacity of forest soils to sequester carbon (C) is susceptible to shifts in the litter quantity and chemistry. Using measurements from the third decade of a long-term Detrital Input and Removal Treatment (DIRT) experiment at Harvard Forest (MA, USA), extending previously published work from 20 years, we examined how litter inputs shape soil organic matter (SOM) chemistry. Elemental analysis, targeted compound analysis, solid-state [13]C nuclear magnetic resonance (NMR) spectroscopy, and microbial biomass and community composition measurements were used. Despite doubled litter inputs over 30 years, no net soil C accumulation occurred, and the SOM decomposition stage was similar to the control, suggesting continuous microbial processing of added inputs. The exclusion of litter, roots, or both led to lower soil C and more advanced SOM decomposition in mineral soils. Shifts in microbial community composition, particularly an increase in Gram (+) to Gram (-) bacteria under exclusion treatments, point to microbial reorganization in response to altered substrate availability. This long-term study underscores the limited potential for long-term soil C sequestration due to sustained microbial decomposition and the role of continuous plant inputs in shaping SOM chemisty under changing detrital regimes in a temperate forest.}, }
@article {pmid41610138, year = {2026}, author = {Dubey, S and Shukla, S and Gupta, N and Dixit, R and Bhadury, P and Kumar, A}, title = {Effect of perchlorate on biocementation capable bacteria and Martian bricks.}, journal = {PloS one}, volume = {21}, number = {1}, pages = {e0340252}, pmid = {41610138}, issn = {1932-6203}, mesh = {*Perchlorates/pharmacology ; *Mars ; *Bacteria/drug effects/metabolism/genetics ; Calcium Carbonate/chemistry ; *Construction Materials/microbiology ; Urease/metabolism ; }, abstract = {With the recent discovery of perchlorate (0.5-1%) in Martian regolith, more experiments related to the impact of perchlorate on microbial life are crucial to understanding the possibility of earth life forms that could sustain on the Martian terrain. While we are familiar with the idea of bioconsolidated Martian bricks made via Microbially Induced Calcite Precipitation (MICP), studies on the effect of perchlorate on Martian bricks &amp; biocementation capable microbes have been obscure. In this work, we investigated the effect of perchlorate (MgClO4- salt) on a lab-isolated biocementation capable bacteria &amp; Martian bricks bioconsolidated by the same, with 1% perchlorate in Mars Global Simulant-1 (MGS-1). The screening of biocementation-capable bacteria involved phenol red assay for urease activity followed by Scanning Electron Microscopy (SEM) and X-ray diffraction (XRD) study of the precipitate formed through MICP via ureolytic pathway. The biocementation capable bacterium SI_IISc_isolate was found to be phylogenetically closest to Sporosarcina pasteurii strain S2135 with a draft genome size of 3.69 Mb. To understand the effect of perchlorate on SI_IISc_isolate, we majorly relied on Gram-staining &amp; SEM. The negative effect of perchlorate stress on the isolate was evident by its decreased growth in the presence of varying concentrations of perchlorate through plate assays, growth curve studies in broth &amp; live-dead staining. Gram-staining study and SEM both revealed that perchlorate induces the release of extracellular matrix (ECM) and promotes clustering of cells by the bacteria, which we termed as 'multicellularity-like behavior.' Further, we constructed Martian bricks with Martian Global Simulant (MGS-1) along with 1% perchlorate, utilizing the microbially induced calcite precipitation ability of the Sporosarcina sp. strain SI_IISc_isolate via ureolysis, following an established protocol at our lab. The bioconsolidation experiments showed that in the presence of a natural adhesive - guar gum, perchlorate tends to significantly improve the compressive strength of Martian bricks. However, the end result eventually relies on the overall effect of various additives in the regolith.}, }
@article {pmid41609879, year = {2026}, author = {Sánchez Espinosa, KC and Fernández-González, M and Dias-Lorenzo, DA and Rodríguez-Rajo, FJ}, title = {First Report of Alternaria in the Olive Agroecosystem of NW Spain: Aerobiological Characterization and Relationship with Meteorological Factors.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02700-x}, pmid = {41609879}, issn = {1432-184X}, abstract = {Alternaria spp. is one of the fungal genera affecting olive cultivation, and its temporal dynamics are influenced by climatic variations occurring throughout the crop's vegetative cycle. The aim of this study was to determine the presence of Alternaria spp. in an olive-growing area in northwestern Spain and to examine the relationship between its airborne concentrations and meteorological variables, in order to preliminarily predict its presence in the atmosphere during the olive tree's phenological cycle. To achieve this, a phenological, aeromycological, and meteorological study was conducted from 2021 to 2024. Alternaria spp. conidia were detected in the air throughout all major phenological stages, with peak concentrations occurring mainly during fruit development. The highest percentages of spores were recorded between 11:00 and 22:00, primarily influenced by temperature and sunlight. During the maturity of fruit stages in 2023 and 2024, isolates from the Alternaria section Alternaria were identified as the cause of olive rot. A predictive model was obtained that estimates the atmospheric concentrations of this type of fungus in the study area, based on average temperature values and hours of sunshine. This study constitutes the first report of Alternaria spp. in an olive-growing area of northwestern Spain and provides models that preliminarily predict its presence. These models can inform growers of the pathogen's presence in the air before visible symptoms appear, thereby reducing the likelihood of infection in susceptible plants when environmental conditions favor its development.}, }
@article {pmid41608689, year = {2025}, author = {Yan, W and Du, N and Zhang, K and Yang, P and Guo, J and Xu, L}, title = {Bilirubin-microbiota interaction: molecular mechanisms and therapeutic strategies in neonatal jaundice.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1749152}, pmid = {41608689}, issn = {1664-302X}, abstract = {Recent studies have revealed a complex interplay between bilirubin metabolism and the gut microbiota. Bilirubin functions as a potent antioxidant and signaling molecule in humans, and its concentration-dependent effects on distinct microbial taxa indicate that the compound exerts selective pressure on the gut ecosystem. The gut microbiota modulates bilirubin metabolism by altering intestinal pH, producing and activating Bilirubin metabolic enzyme, and bile acids. Because perturbations in bilirubin handling are especially common-and potentially neurotoxic-in neonates, a concise synthesis of recent progress is warranted. Here we review how microbial communities reshape bilirubin flux, how bilirubin and its conjugates, in turn, sculpt microbial ecology, and how the dynamic equilibrium between conjugated and unconjugated bilirubin in hyperbilirubinaemia is influenced by the microbiome. Regulating gut microbiota to accelerate bilirubin clearance or attenuate its toxicity may therefore offer a tractable therapeutic avenue.}, }
@article {pmid41607130, year = {2026}, author = {Stewart, JD and Ramirez, DX and Leon-Reyes, A and Barriga, N and Llerena, S and Manley, BF and Carpintero-Salvador, N and Ruiz-Uriguen, M and Raaijmakers, JM and Kiers, ET and Weedon, JT}, title = {Land Use Change Reshapes Climate-Driven Diversity Patterns of Tropical Arbuscular Mycorrhizal Fungi.}, journal = {Molecular ecology}, volume = {35}, number = {2}, pages = {e70253}, doi = {10.1111/mec.70253}, pmid = {41607130}, issn = {1365-294X}, support = {MICROP 024.004.014//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; //Jeremy and Hannelore Grantham Environmental Trust/ ; //Paul G. Allen Family Foundation/ ; //Schmidt Family Foundation/ ; }, mesh = {*Mycorrhizae/genetics/classification ; *Biodiversity ; *Soil Microbiology ; Agriculture ; Tropical Climate ; Temperature ; Ecosystem ; Soil ; Climate ; *Climate Change ; }, abstract = {Land use change and agricultural expansion threaten biodiversity yet the effects on soil life remain poorly understood, especially for microbes. Arbuscular mycorrhizal (AM) fungi are microbes that form associations with most plant species and are essential for plant nutrient uptake. The diversity of these fungi is also sensitive to both land use change and regional climatic conditions. We therefore asked whether variation in AM fungal diversity is driven by land use change, and whether these effects are further influenced by interactions with temperature and precipitation gradients. To test this, we quantified AM fungal biodiversity in cultivated and adjacent uncultivated soils across a 1700 m elevational gradient (temperature: 7.7°C-16.5°C and precipitation: 1000-3500 mm). We found that conversion of uncultivated soils to agriculture reduced AM fungal richness by 80%, on average. Richness in uncultivated soils increased with the temperature gradient, while richness in farms declined. A similar but inverted trend was found for precipitation, where richness in uncultivated sites declined as precipitation increased. Uncultivated soils contained approximately three-fold more unique AM fungal species compared to cultivated soils. Our findings demonstrate that interactions between climate and land use strongly influence AM fungal biodiversity patterns in tropical mountain ecosystems. Incorporating both factors into conservation and sustainable agriculture strategies will be critical to preserving belowground biodiversity under global change.}, }
@article {pmid41606790, year = {2026}, author = {Clutter, CH and Leung, DT}, title = {Tracing MR1 expression across tissues to find the perfect MAIT.}, journal = {Journal of leukocyte biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jleuko/qiag014}, pmid = {41606790}, issn = {1938-3673}, abstract = {Mucosal associated invariant T (MAIT) cells are part of a T cell subset that is activated upon presentation of B2 vitamin (riboflavin) metabolites by the major histocompatibility complex, class I related (MR1) protein. Though there is a clear relationship between microbial production of riboflavin and MAIT cell development and persistence, little is known about the cells that primarily communicate with MAIT cells and other MR1-restricted T cells. Elegant work by Deng et al demonstrates that it is macrophages from the lung and peritoneum that express the highest amount of MR1 and are the most efficient at presenting vitamin B antigens to MAIT cells. This landmark study not only definitively identifies and maps the key antigen presenting cell populations involved in MAIT cell activation, it also reveals a bidirectional relationship between MR1 expression and the host microbiome. While further work on how these findings translate to human MAIT cell biology is needed, this study has provided us with unprecedented insights into the mechanistic interplay and microbial ecology of MR1 presentation of riboflavin metabolites.}, }
@article {pmid41606115, year = {2026}, author = {Hao, YQ and Li, BH and Chen, JY and Shu, WS and Zhao, XF}, title = {Bacterial necromass recycling promotes diversity maintenance in bacterial communities via resource partitioning.}, journal = {Nature ecology &amp; evolution}, volume = {}, number = {}, pages = {}, pmid = {41606115}, issn = {2397-334X}, support = {32371597//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32271600//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Understanding how high species diversity is maintained in natural bacterial communities is a central question in microbial ecology. Due to the versatile heterotrophic capacities of bacteria and the rich nutrients released by deceased bacterial cells, necromass recycling plays an important role in sustaining bacterial growth. Such nutrient cycling within communities can provide additional resource niches for bacteria, but its potential effects on bacterial diversity maintenance have been neglected. Here we conducted two independent experiments and studied the assembly of 276 soil-derived bacterial communities sustained by a wide range of bacterial necromass combinations, from single-species necromass to combinations of up to nearly 1,000 species. Our results highlight the existence of a species-rich bacterial necrobiome in soil. We found that the composition of necromass-decomposing communities was determined by the various organic compounds in the different necromass combinations, and the increases in necromass-producing species constantly promoted species diversity of necromass-decomposing communities. Moreover, the average niche breadth and overlap of coexisting necromass-decomposing species in utilizing distinct single-species necromass decreased with increases in necromass diversity, supporting the hypothesis of resource partitioning in utilizing different single-species necromass. Our study provides insights into diversity maintenance in bacterial communities from a perspective of internal nutrient cycling.}, }
@article {pmid41605992, year = {2026}, author = {Dickerson, AL and Jechow, A and Nößler, M and Walles, TJW and Berger, SA and Hölker, F and Nejstgaard, JC}, title = {High-resolution in situ imaging reveals size-specific moonlight responses in zooplankton diel vertical migration.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {4086}, pmid = {41605992}, issn = {2045-2322}, mesh = {Animals ; *Zooplankton/physiology ; *Moon ; Copepoda/physiology ; Light ; *Animal Migration/physiology ; Body Size ; Germany ; Cladocera/physiology ; Lakes ; }, abstract = {Light is the primary cue driving zooplankton diel vertical migration (DVM), a strategy that balances predation risk with resource access. However, DVM is often oversimplified, with limited consideration of how light-driven risks and resource needs vary across taxa and life stages. This simplification is partly due to constraints on collecting high-resolution, size-resolved data -especially at night, when subtle shifts in illumination reshape nocturnal risk landscapes. To overcome these limitations, we deployed a high-resolution in situ modular Deep-focus Plankton Imager and an image-recognition approach to quantify fine scale DVM and body sizes of Cladocerans and Copepods in Lake Stechlin, Germany. Data was collected from day into night and across moonrise and was compared with environmental data from vertical profiling sondes. Typical DVM patterns emerged, with deeper daytime distributions, however, moonlight introduced additional behavioural complexity: larger individuals avoided illuminated layers, likely managing predation risk, while smaller individuals moved into these layers, possibly exploiting foraging opportunities and reduced risk. These light-mediated shifts were further shaped by ecological conditions; copepods tracked food-rich layers regardless of light levels at night, while cladocerans showed light-dependent responses to both temperature and food, such that light caused them to avoid otherwise favourable (warm, food-rich) layers. Our approach provides new insight into how zooplankton navigate nocturnal lightscapes, revealing size- and taxon-specific strategies. By establishing size-dependent responses to natural moonlight, this work provides a crucial baseline for predicting how artificial light at night may restructure zooplankton communities and destabilize freshwater food webs.}, }
@article {pmid41605068, year = {2026}, author = {Truswell, A and Jordan, D and Pang, S and Cherrington, T and Hampson, DJ and Blinco, J and Adsett, S and Abraham, R and Stegger, M and Abraham, S}, title = {Genomic analysis of a porcine exudative epidermitis outbreak caused by Staphylococcus hyicus.}, journal = {Veterinary microbiology}, volume = {314}, number = {}, pages = {110883}, doi = {10.1016/j.vetmic.2026.110883}, pmid = {41605068}, issn = {1873-2542}, abstract = {Exudative epidermitis (EE) causes substantial morbidity and mortality in piglets. This study investigated the microbial ecology, antimicrobial resistance (AMR), and genomic diversity of Staphylococcus hyicus associated with an EE outbreak in an Australian piggery. Lesion swabs from 20 affected piglets yielded 160 bacterial isolates (including S. hyicus and cohabiting species). Isolates underwent species identification, antimicrobial susceptibility testing, and whole-genome sequencing (WGS) of S. hyicus for AMR/virulence gene profiling and core-genome SNP analysis to assess genomic relatedness. S. hyicus predominated among lesion isolates. Phenotypic testing showed varied AMR, with frequent resistance to erythromycin and tetracycline. WGS of 27 S. hyicus isolates identified five distinct genotypic AMR profiles, including combinations spanning multiple drug classes. All S. hyicus carried the exfoliative toxin gene shetA, and 24 also carried exhD. Core-genome analysis indicated a highly clonal outbreak: 24/27 genomes differed by 0 core SNPs, with the remaining three closely related. Despite this clonality, resistance gene carriage varied across isolates. Consequently, reliance on a single colony to represent an outbreak could understate resistance and overstate treatability. These findings support routine multi-isolate sampling to capture within-clone AMR variability, bolster antimicrobial selection during EE management, and inform consideration of autogenous vaccines targeting dominant outbreak clones.}, }
@article {pmid41604921, year = {2026}, author = {De, J and Banerjee, G and De Leon, EV and Martinez, AG and Wong, C and Banerjee, P}, title = {Polystyrene nanoplastics and pathogen plasticity: Toxic threat or tolerated stressor in Salmonella enterica?.}, journal = {Journal of hazardous materials}, volume = {503}, number = {}, pages = {141264}, doi = {10.1016/j.jhazmat.2026.141264}, pmid = {41604921}, issn = {1873-3336}, abstract = {Polystyrene nanoplastics (PS-NPs), a group of increasingly common environmental pollutants, pose emerging risks to microbial ecology and food safety. This study examines the concentration- and time-dependent effects of PS-NPs (low exposure: 2.5-5 mg/L; moderate exposure: 10-20 mg/L; high exposure: 50-100 mg/L) on Salmonella enterica, a major foodborne pathogen. Under realistic environmental conditions, PS-NPs influenced bacterial viability, membrane integrity, and oxidative stress levels, with higher concentrations causing lipid peroxidation and membrane disruption. Gene expression analyses showed early upregulation of stress-related, biofilm-associated, virulence, and adhesion genes, indicating an adaptive response to PS-NP-induced stress. Biofilm formation increased with moderate to high PS-NP exposure, confirmed by exopolysaccharide measurement and confocal microscopy. However, prolonged or high-dose exposure resulted in downregulation of efflux systems (acrB, tolC), quorum-sensing regulators (lsrA, invF), and antimicrobial resistance genes (marR, tetC), suggesting stress-related trade-offs. Notably, transient activation of marA and acrA indicates potential NP-induced cross-resistance mechanisms. These results imply that PS-NPs act as environmental stressors capable of altering bacterial virulence and survival strategies, with significant implications for microbial behavior in plastic-contaminated ecosystems and food processing environments. Collectively, our results emphasize the urgent need to reevaluate NP exposure in the context of public health and antimicrobial resistance.}, }
@article {pmid41604057, year = {2026}, author = {Silveira, KA and Ramiro-Garcia, J and Lawless, C and Espinosa-Vazquez, JM and Fermoso, FG and Collins, G and O'Flaherty, V}, title = {Mutual dosing of tungsten, molybdenum and selenium impact anaerobic digestion microbiome.}, journal = {Biometals : an international journal on the role of metal ions in biology, biochemistry, and medicine}, volume = {}, number = {}, pages = {}, pmid = {41604057}, issn = {1572-8773}, support = {861088//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; }, abstract = {Metals are critical in anaerobic digestion, but their co-occurrence effects on microbiome structure and function are underexplored. This study hypothesized that exposure of methanogenic granules to a trace element (TE) mixture alongside molybdenum (Mo), tungsten (W) or selenium (Se)-would alter (i) extracellular polymeric substances (EPS) protein and carbohydrate content, (ii) microbial composition and function (iii) methanogenic pathways.To test this, anaerobic batch reactors (n = 35) were set up in a fed batch mode, with sacrificial reactors (n = 14) used to collect biomass for analyses, including DNA: RNA co-extraction, amplicon sequencing, and determination of the concentrations of total and soluble metals, Scanning Electron Microscopy- Energy Dispersive X-ray (SEM-EDX) and EPS extraction over a 24-day period.The results reveal that, Mo and W increased the concentration of soluble Fe in abiotic controls, enhancing Fe and S retention. The presence of W, Mo, W + Se, and Se had a positive effect on methane production, with W + Se and W enhancing acetoclastic methanogenesis. Additionally, Se increased EPS protein and carbohydrate contents in the biomass. Shifts in the microbiome composition were mainly driven by Mo and Se, with typically dominant Anaerolineacaeae, Capriciproducens, Macelibacteroides and Clostridium sensu stricto 5 taxa. Functional potential suggested an enrichment of nucleotide metabolism and, importantly, Vitamin (B12, B6 and B9) metabolic potential.These finding inform Anaerobic digestion (AD) stakeholders about the impacts of Fe, W, Mo, and Se co-dosing on process performance and microbiome structure and function, offering insights to optimize biogas production through tailored metal supplementation combinations, given demonstrations at lab and pilot scales.}, }
@article {pmid41603638, year = {2026}, author = {Kosztik, J and Baka, E and Táncsics, A and Ábrahám, R and Szabó, G and Nagy, I and Orsini, M and Bata-Vidács, I and Szalontai, H and Kukolya, J and Nagy, I}, title = {Genomic and proteomic analyses of the maize root isolate Rhodococcus erythropolis NI86/21 reveal extensive genome plasticity and parallel evolution of herbicide degradation.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0240725}, doi = {10.1128/aem.02407-25}, pmid = {41603638}, issn = {1098-5336}, abstract = {Rhodococcus erythropolis NI86/21, isolated from maize rhizosphere in Hungary, possesses one of the largest genomes (8.046 Mb) within the species. The genome comprises a 6.83 Mb chromosome and 1.22 Mb of extrachromosomal elements, including three circular and two fragmented linear plasmids. Comparative analysis identified five horizontally acquired genomic islands (HGTi), totaling 0.64 Mb with mosaic-like architecture derived from plasmids, phages, and chromosomal segments of other Nocardiaceae. Liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based proteomic analysis revealed a lower expression of genes located in HGT elements (53%) compared to core chromosomal genes (73%), indicating regulatory silencing of foreign DNA. Nevertheless, an inducible cytochrome P450 monooxygenase (CYP116) responsible for thiocarbamate and atrazine degradation is encoded on HGTi_V and actively expressed upon herbicide exposure. Strikingly, an identical CYP450 locus is present on a conjugative plasmid in Rhodococcus sp. TE1 isolated from thiocarbamate-treated soil in Canada, demonstrating independent acquisition of the same catabolic module from a high GC% content Rhodococcus, under similar selective pressure. Frequent recombination between chromosomal and mobile elements generates the observed mosaic-like HGT structures, which we found common for R. erythropolis strains. These results highlight extraordinary genomic plasticity and rapid adaptive evolution in Rhodococci, enabling efficient colonization of herbicide-contaminated agro-ecosystems.IMPORTANCERhodococcus erythropolis NI86/21 exemplifies how bacterial genomes evolve through horizontal gene transfer and mobile elements. Its unusually large, plastic genome contains extensive HGT islands and a high load of active transposons, which shape mosaic genomic architectures and hinder complete genome assembly. These horizontally acquired regions, although partially silenced, encode key adaptive functions such as an inducible CYP116 monooxygenase enabling thiocarbamate and atrazine degradation. Remarkably, an identical CYP116 module is present in Rhodococcus sp. TE1 from thiocarbamate-treated Canadian soil, demonstrating that similar environmental pressures can drive independent acquisition of the same biodegradation trait. Together, the dynamic transposon activity, mosaic HGT structure, and geographically convergent gene recruitment highlight the extraordinary genomic plasticity of R. erythropolis and underscore its rapid adaptive potential in agro-ecosystems, with implications for microbial evolution and bioremediation strategies.}, }
@article {pmid41601066, year = {2026}, author = {Chen, Y and Cai, S and Zhang, P and Sun, C and Huang, D and Zhang, M and Tian, S}, title = {Effects of soil covering on bacterial communities and C/N functional genes during phytoremediation of copper tailings.}, journal = {Ecotoxicology and environmental safety}, volume = {309}, number = {}, pages = {119639}, doi = {10.1016/j.ecoenv.2025.119639}, pmid = {41601066}, issn = {1090-2414}, mesh = {*Copper/metabolism ; Biodegradation, Environmental ; *Soil Pollutants/metabolism/analysis ; *Soil Microbiology ; *Soil/chemistry ; Mining ; Nitrogen/metabolism ; Carbon/metabolism ; *Bacteria/genetics/metabolism ; China ; Metals, Heavy/analysis ; Genes, Bacterial ; }, abstract = {Copper tailings, a mining waste, pose environmental threats, and phytoremediation commonly employs soil covering to improve substrate properties and promote vegetation recovery. This study was conducted at the Yangshanchong Tailings Reservoir in Tongling City, Anhui Province, to comprehensively evaluate changes in soil physicochemical properties, bacterial community structure, and carbon/nitrogen functional genes during copper tailings remediation. We compared areas with and without soil covering, which were vegetated by two dominant species, Imperata cylindrica and Miscanthus floridulus, across profile depths of 0-20 cm, 20-40 cm, and 40-60 cm. Results indicated that: (i) soil covering significantly modified substrate pH, elevated levels of organic matter, organic carbon, and ammonium nitrogen, decreased surface total nitrogen, total phosphorus, and selected heavy metals, and altered the depth-dependent distribution of copper, manganese, and cadmium, (ii) soil covering reduced bacterial richness and diversity in I. cylindrica areas, increased the relative abundance of phyla such as Deinococcota, and significantly enriched genera including Brevundimonas, Acidisoma, and Acinetobacter, while enhancing the influence of heavy metals on dominant genera, (iii) soil covering reduced the abundance of genes related to nitrogen cycling (nifH, amoA, nosZ) and methane metabolism (pmoA1), and altered their correlations with specific bacterial genera. Overall, soil covering shapes bacterial community structure and the dynamics of carbon/nitrogen functional genes by altering the physicochemical properties and heavy metal distribution in tailings substrates, thereby playing a key regulatory role in microbial ecology during copper tailings revegetation. This study provides valuable insights for the restoration management of mining areas.}, }
@article {pmid41601011, year = {2026}, author = {Staley, BT and DeWitt, ME and Wenner, JJ and Sanders, JW and Wierzba, TF and Poehling, K}, title = {Trusted Sources of COVID-19 Vaccine Information by County Characteristics in North Carolina.}, journal = {Vaccines}, volume = {14}, number = {1}, pages = {}, pmid = {41601011}, issn = {2076-393X}, support = {49927//NC Department of Health and Human Services/ ; }, abstract = {BACKGROUND/OBJECTIVES: The COVID-19 pandemic disproportionately impacted rural areas across the United States, including rural North Carolina (NC). Consistent with national patterns, COVID-19 vaccination coverage as of December 2022 was higher for non-rural (72%) than rural (58%) NC counties. The role of trusted sources of vaccine information used by rural and non-rural residents is unknown.<br><br>METHODS: Using data from two surveys distributed by the COVID-19 Community Research Partnership from 8 June 2021 through 21 December 2021, we compared self-reported sources of trusted COVID-19 vaccine information by non-rural and rural counties and by county-level predominant political vote in the 2020 Presidential election.<br><br>RESULTS: While NC respondents were highly vaccinated (94%), fewer residents from rural counties self-reported COVID-19 vaccination than those from non-rural counties (91% versus 95%). The most common reported source of trusted vaccine information was federal health agencies. The proportion citing a federal health agency was higher for respondents from non-rural (80%) than rural (72%) counties and was higher for vaccinated (75%) than unvaccinated (42%) rural respondents. The next two most trusted sources of vaccine information were state/local health officials (48%) and health care providers (42%). Among trusted resources reported by 10-15% of respondents, those from rural counties were less likely to use hospital websites, employers, or news sources than those from non-rural counties. More respondents from counties with >60% vote for the 2020 Democratic Presidential candidate cited federal health agencies, state and local officials, and new sources than respondents from counties with >60% vote for the 2020 Republican Presidential candidate.<br><br>CONCLUSIONS: By identifying the trusted sources of vaccine information for residents in non-rural and rural NC counties, future vaccine implementation efforts can tailor communication efforts to increase vaccine uptake and potentially reduce the rates of hospitalizations and death from vaccine-preventable diseases such as COVID-19 or other future pandemics.}, }
@article {pmid41503489, year = {2026}, author = {Goddard, TR and Carlson-Jones, JA and Judith, M and Ooi, CY and Andrew, T and Warner, MS and John, W and Evans, IE and Hopkins, E and Iredell, JR and Jersmann, HP and Whiteson, KL and Bouras, G and Doane, MP and Falk, NW and Green, R and Grigson, SR and Mallawaarachchi, V and Martin, B and Roach, MJ and Ryan, FJ and Tarasenko, A and Papudeshi, B and Drigo, B and Giles, SK and Harker, CM and Hesse, RD and Hodgson, RJ and Hussnain, A and Hutton, A and Inglis, LK and Keneally, C and Kerr, EN and Liddicoat, C and Peddle, SD and Watson, CD and Yang, Q and Decewicz, P and Speck, PG and Mitchell, JG and Dinsdale, EA and Edwards, RA}, title = {Microbial Ecological Signatures Predict Pathogen Emergence and Multidrug Resistance in Cystic Fibrosis Airways up to a Year in Advance.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {41503489}, abstract = {Chronic infections in cystic fibrosis (CF) emerge from gradual ecological transitions in the airway microbiome, yet early predictive markers remain poorly defined. We developed a new autoencoder-based framework that outperforms read-based or metagenome-assembled genome-based analyses at capturing the continuum from health-associated commensals to pathogen-dominated, antibiotic-tolerant communities. This improvement is achieved by integrating taxonomic and functional data from 127 sputum and bronchoalveolar lavage metagenomes from 64 people with CF into latent "Clusters of Phylogeny and Functions" (COPFs). Coupled with gradient-boosted random forests, COPFs predicted Pseudomonas aeruginosa colonisation, multidrug resistance, and impending infection up to a year before clinical detection. The multidrug-resistant P. aeruginosa signature showed the same resistance-mechanism evolution as found in laboratory experiments. The inclusion of eukaryotic markers revealed persistent Aspergillus fumigatus signatures even during culture-negative intervals. Applying our South Australian-trained model to over 1,000 global metagenomes from 22 independent CF datasets, we achieved 94% accuracy in predicting P. aeruginosa status across platforms and geographies, validating the model's universal utility. Our results demonstrate that combining datasets with deep learning reveals conserved ecological and metabolic mechanisms in disease progression, transforming metagenomics into a predictive framework for managing chronic infections.}, }
@article {pmid41600663, year = {2025}, author = {Polyorach, S and Suphalucksana, W and Klompanya, A and Yuangklang, C and Wanapat, M and Cheas, S and Cherdthong, A and Kang, S and Gunun, P and Gunun, N and Foiklang, S and Kongmun, P and Montri, N and Srikijkasemwat, K}, title = {Ensiling Time and Mixed Microbe Fermented Liquid Modulate In Vitro Digestibility and Rumen Fermentation of Fermented Total Mixed Rations.}, journal = {Veterinary sciences}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/vetsci13010006}, pmid = {41600663}, issn = {2306-7381}, support = {Grant No. 2561-01-04-006//Faculty of Agricultural Technology, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand/ ; }, abstract = {This study investigated how varying the ensiling period and the level of mixed microbes fermented liquid (MMFL) influences the chemical composition, in vitro degradability, rumen fermentation profile, and microbial ecology of fermented total mixed rations (FTMR). A completely randomized 4 × 4 factorial design was used, incorporating four fermentation durations (0, 7, 14, and 21 days) and four MMFL inclusion rates (0, 0.5, 1.0, and 1.5% of DM). Both factors exerted significant effects on FTMR quality (p < 0.05). The combination of a 14-day fermentation period with 0.5% MMFL consistently produced the most desirable outcomes. Under these conditions, crude protein concentration rose from 12.0% to 14.3% of DM, while neutral-detergent fiber declined from 54.2% to 49.1%. Improvements were also observed in in vitro digestibility, with DM and OM increasing by 9-12% relative to the untreated control (p < 0.05). Fermentation end-products were enhanced, as total volatile fatty acids increased by 15% (92.4 vs. 80.1 mmol/L), and the molar proportion of propionate increased from 24.5 to 29.2 mol/100 mol, thereby lowering the acetate-to-propionate ratio (2.4 vs. 3.0; p < 0.05). Estimated methane production declined by 18% (p < 0.01). Microbial counts reflected a shift toward a more efficient fermentative community, with bacterial and fungal populations increasing by 21% and 18%, and protozoa decreasing by 25% (p < 0.05). Overall, moderate MMFL supplementation during a 14-day ensiling phase enhanced nutrient conservation and fermentation efficiency, suggesting practical value for improving FTMR utilization in ruminant systems. Further in vivo and economic evaluations remain necessary.}, }
@article {pmid41600038, year = {2026}, author = {Shen, H and Liu, Z and Wang, C and Chu, Y and Zhang, C and Yu, Y and Yang, S}, title = {EDDS-Enhanced Phytoremediation of Cd-Zn Co-Contaminated Soil by Sedum lineare: Mechanisms of Metal Uptake, Soil Improvement, and Microbial Community Modulation.}, journal = {Plants (Basel, Switzerland)}, volume = {15}, number = {2}, pages = {}, doi = {10.3390/plants15020231}, pmid = {41600038}, issn = {2223-7747}, support = {32271705//National Natural Science Foundation of China/ ; }, abstract = {Soil co-contamination with cadmium (Cd) and zinc (Zn) poses serious threats to environmental safety and public health. This study investigates the enhancement effect and underlying mechanism of the biodegradable chelator Ethylenediamine-N,N'-disuccinic acid (EDDS) on phytoremediation of Cd-Zn contaminated soil using Sedum lineare. The results demonstrate that EDDS application (3.65 g·L[-1]) effectively alleviated metal-induced phytotoxicity by enhancing chlorophyll synthesis, activating antioxidant enzymes (catalase and dismutase), regulating S-nitrosoglutathione reductase activity, and promoting leaf protein synthesis, thereby improving photosynthetic performance and cellular integrity. The combined treatment significantly increased the bioavailability of Cd and Zn in soil, promoted their transformation into exchangeable fraction, and resulted in removal rates of 30.8% and 28.9%, respectively. EDDS also modified the interaction patterns between heavy metals and essential nutrients, particularly the competitive relationships through selective chelation between Cd/Zn and Fe/Mn during plant uptake. Soil health was substantially improved, as evidenced by reduced electrical conductivity, enhanced cation exchange capacity, and enriched beneficial microbial communities including Sphingomonadaceae. Based on the observed ion antagonism during metal uptake and translocation, this study proposes a novel "Nutrient Regulation Assisted Remediation" strategy to optimize heavy metal accumulation and improve remediation efficiency through rhizosphere nutrient management. These findings confirm the EDDS-S. lineare system as an efficient and sustainable solution for remediation of Cd-Zn co-contaminated soils.}, }
@article {pmid41599027, year = {2025}, author = {Maçin, S and Özden, &#xd6; and Samadzade, R and Saylam, E and Çiftçi, N and Arslan, U and Yormaz, S}, title = {Oral Microbiota Alterations and Potential Salivary Biomarkers in Colorectal Cancer: A Next-Generation Sequencing Study.}, journal = {Pathogens (Basel, Switzerland)}, volume = {15}, number = {1}, pages = {}, doi = {10.3390/pathogens15010043}, pmid = {41599027}, issn = {2076-0817}, support = {23401136//Sel&#xe7;uk University/ ; }, mesh = {Humans ; *Colorectal Neoplasms/microbiology/diagnosis ; Male ; Female ; *Saliva/microbiology ; Middle Aged ; *Microbiota/genetics ; High-Throughput Nucleotide Sequencing ; Aged ; RNA, Ribosomal, 16S/genetics ; Pilot Projects ; *Biomarkers, Tumor ; Phylogeny ; Bacteria/classification/genetics/isolation &amp; purification ; *Mouth/microbiology ; Biomarkers ; Case-Control Studies ; Gastrointestinal Microbiome ; }, abstract = {Colorectal cancer (CRC) has a high mortality rate worldwide. Oral and intestinal microbiota members may have an effect on gastrointestinal tumors' pathogenesis, particularly in CRC. Designed as a pilot study, this study's aim was to investigate the relationship between CRC and oral microbiota and to identify potential biomarkers for CRC diagnosis. Saliva samples were collected from recently diagnosed CRC patients (n = 14) and healthy controls (n = 14) between March 2023 and December 2023. Microbiota (16S rRNA) analyses were conducted on these saliva samples using a next-generation sequencing method. Phylogenetic analyses, including alpha diversity, principal component analysis (PCA), principal coordinate analysis (PCoA), beta diversity, biomarker, and phenotype analyses, were conducted using the Qiime2 (Quantitative Insights Into Microbial Ecology) platform. Alpha diversity indices (Shannon: p = 0.78, Cho1: p = 0.28, Simpson: p = 0.81) showed no significant difference between CRC and control groups. Beta diversity analysis using Bray-Curtis PCoA indicated significant differences in the microbial community between the two groups (p = 0.003). Examination of OTU distributions revealed that the Mycoplasmatota phylum was undetectable in the oral microbiota of healthy controls but was significantly elevated in CRC patients (CRC: 0.13 ± 0.30, Control: 0.00 ± 0.00, p < 0.05). Additionally, Metamycoplasma salivarium, Bacteroides intestinalis, and Pseudoprevotella muciniphila were undetectable in healthy controls but significantly more prevalent in CRC patients (p < 0.05 for all three species). LEfSe analysis identified eight species with an LDA score > 2, Granulicatella adiacens, Streptococcus thermophilus, Streptococcus gwangjuense, Capnocytophaga sp. FDAARGOS_737, Capnocytophaga gingivalis, Granulicatella elegans, Bacteroides intestinalis, and Pseudoprevotella muciniphila, as potential biomarkers. The results of this study contribute critical evidence of the role of oral microbiota in the pathogenesis of colorectal cancer. Alterations in the microbiota suggest potential biomarkers in understanding the biological mechanisms underlying CRC and developing diagnostic and therapeutic strategies.}, }
@article {pmid41597698, year = {2026}, author = {Mohammed, A and Negm, E and Amarin, N and Sayed, S and Soliman, A and Askar, H and Yusuf, S and Rayan, AA}, title = {Impact of Dietary Supplementation of Probiotics on Cecal Microbial Ecology, Immune Response, and Meat Quality of Muscovy Ducks.}, journal = {Microorganisms}, volume = {14}, number = {1}, pages = {}, doi = {10.3390/microorganisms14010182}, pmid = {41597698}, issn = {2076-2607}, support = {United Animal Health//United Animal Health (United States)/ ; }, abstract = {Probiotics represent a beneficial approach to boost the welfare, health, and meat quality of poultry. One hundred and twenty one-day-old male Muscovy ducklings were divided among 24 floor pens (five ducklings per pen). The pens were randomly distributed among one of four dietary treatments with six replicates (G-C) without any supplementation of probiotics; (G-A) was supplemented with 0.4 g/kg of Amnil[®]; (G-M) was supplemented with 0.5 g/kg of M-Mobilize[®]; and (G-A-M) was supplemented with 0.4 g/kg of Amnil[®] (1-30 day) and 0.5 g/kg of M-Mobilize[®] (31-60 day), respectively. The results indicated that BW at day 60 was improved in (G-A) birds compared with (G-C) ones, IL-6 was decreased in (G-A) and (G-A-M) in liver and spleen in comparison with (G-C) (p < 0.05), but no differences were observed between (G-C) and (G-M) (p > 0.05); IL-10 was decreased in all the probiotic-fed ducklings compared with (G-C) birds in the spleen (p < 0.05), and IL-10 was decreased in the (G-A) birds compared with the other treatments in the liver (p < 0.05). Probiotic-fed birds showed a higher enumeration of Lactobacillus spp. compared to (G-C) group (p < 0.05). In addition, the (G-M) group showed improved breast meat flavor, general acceptability, and water-holding capacity (WHC%) compared to (G-C) group (p < 0.05). These results suggest that the probiotic supplement (G-A), could be a good management tool for improving Muscovy ducks' health and production and further research is needed to improve meat quality traits.}, }
@article {pmid41597665, year = {2026}, author = {Khachatryan, A and Vardanyan, A and Zhang, R and Zhang, Y and Shi, X and Willscher, S and Nguyen, NHA and Vardanyan, N}, title = {Metagenome Insights into Armenian Acid Mine Drainage: A Novel Thermoacidophilic Iron-Oxidizing Bacterium with Perspectives for Copper Bioleaching.}, journal = {Microorganisms}, volume = {14}, number = {1}, pages = {}, doi = {10.3390/microorganisms14010146}, pmid = {41597665}, issn = {2076-2607}, support = {22rl-031//Higher Education Science Committee of Armenia/ ; 23-YSIP-012//Higher Education Science Committee of Armenia/ ; }, abstract = {The microbial ecology of acid mine drainage (AMD) systems in Armenia, with a long mining history, remains unexplored. This study aimed to characterize the microbial diversity and functional potential of AMD in the Syunik region and to isolate novel microorganisms with biotechnological value. A comprehensive analysis of the microbial communities' structure of Kavart abandoned, Kapan exploring mines effluent, and Artsvanik tailing was conducted. Metagenomics revealed bacterial-dominated communities, comprising Pseudomonadota (previously "Proteobacteria") (68-72%), with site-specific variations in genus abundance. A high abundance and diversity of metal resistance genes (MRGs), particularly for copper and arsenic, were identified. Carbohydrate-active enzyme (CAZy) analysis showed a dominance of GT2 and GT4 genes, suggesting a high potential for extracellular polymeric substances (EPS) production and biofilm formation. A novel strain of iron-oxidizing bacteria Arm-12 was isolated that shares only ~90% similarity with known Leptospirillum type species, indicating it may represent a new genus without culturable representatives. The strain exhibits enhanced copper extraction from concentrate. This study provides the first metagenomic insights into Armenian AMD systems and tailing, revealing a unique community rich in metal resistance and biofilm-forming genes. The isolation of a novel highly effective iron-oxidizer Arm-12 highlights the potential of AMD environments as a source of novel taxa with significant applications in biomining and bioremediation processes.}, }
@article {pmid41597639, year = {2026}, author = {Yin, Y and Xu, W and Xu, M and Wang, Y and Liu, H and Cao, H and Wang, F}, title = {Prokaryotic Microbial Diversity and Community Assembly in Reclaimed Coastal Agricultural Soils.}, journal = {Microorganisms}, volume = {14}, number = {1}, pages = {}, doi = {10.3390/microorganisms14010120}, pmid = {41597639}, issn = {2076-2607}, support = {32471725//National Natural Science Foundation of China/ ; 2021S018//Ningbo Municipal Bureau of Science and Technology/ ; 2022Z169//Ningbo Municipal Bureau of Science and Technology/ ; }, abstract = {Coastal reclamation profoundly alters soil physicochemical conditions and strongly influences soil microbial ecology; however, the millennial-scale successional patterns and assembly mechanisms of prokaryotic communities under such long-term disturbance remain insufficiently understood. In this study, we investigated archaeal and bacterial communities in the plow layer along a 0-1000-year coastal reclamation chronosequence on the southern shore of Hangzhou Bay. We analyzed community abundance, diversity, composition and assembly processes, and quantified the relative contributions of geographic distance, environmental factors and reclamation years to microbial biogeographic patterns. The results showed that reclamation markedly drove continuous soil desalination, acidification, nutrient accumulation, and particle-size refinement. Bacterial abundance exhibited a sharp decline during the early stages of reclamation, whereas archaeal abundance remained relatively stable. The α-diversity of both archaea and bacteria peaked at approximately 210-230 years of reclamation. Community assembly processes differed substantially between the two microbial domains: the archaeal communities were dominated by stochastic processes (77.78%) identified as undominated processes and dispersal limitation, whereas bacterial communities were primarily shaped by deterministic processes (70.75%) driven as variable selection. Distance-decay analysis indicated that bacterial communities were more sensitive to environmental gradients. Multiple regression and variance partitioning further demonstrated that soil pH and electrical conductivity were the key drivers of community structure. Overall, this study reveals the millennial-scale community dynamics and assembly mechanisms of archaea and bacteria in response to coastal reclamation, providing mechanistic insights into long-term microbial ecological succession and offering valuable guidance for sustainable agricultural management and ecological restoration in reclaimed coastal regions.}, }
@article {pmid41597573, year = {2025}, author = {Si, W and Zhang, J and Zhang, Y and Ji, Y and Khan, MZ and Chen, Y and Cheng, Z and Zhuang, J and Zhao, X and Liu, W}, title = {Characterization of Bacterial Communities in Air and Bedding Materials of Intensive Donkey Farms During Summer.}, journal = {Microorganisms}, volume = {14}, number = {1}, pages = {}, doi = {10.3390/microorganisms14010053}, pmid = {41597573}, issn = {2076-2607}, support = {SDAIT-27-11//Shandong Donkey Industry Technology System Fund/ ; }, abstract = {This study investigated the bacterial community composition and diversity in air and exercise yard bedding samples from large-scale donkey farms in Liaocheng, China, during summer using 16S rRNA high-throughput sequencing. Air samples were collected from five functional areas of donkey barns, while bedding samples were obtained from eight farms housing Dezhou donkeys. Sequencing analysis revealed 894 operational taxonomic units (OTUs) in air samples and 3127 OTUs in bedding samples. Alpha diversity indices indicated that the mare barn exhibited the highest microbial diversity in air, while the foal barn showed the lowest. Actinobacteriota, Proteobacteria, and Firmicutes were the dominant phyla across different functional areas. Rhodococcus was identified as the predominant airborne genus, representing a potential pneumonia risk in foals. In bedding materials, Firmicutes, Actinobacteriota, and Proteobacteria predominated, with Corynebacterium, Salinicoccus, and Solibacillus as dominant genera. Several potentially pathogenic bacteria were detected, including Rhodococcus, Corynebacterium, Clostridium, Streptococcus, and Escherichia-Shigella. These findings provide critical insights into the microbial ecology of intensive donkey farming environments and offer scientific evidence for developing targeted biosecurity strategies to safeguard animal health and promote sustainable livestock production.}, }
@article {pmid41597522, year = {2025}, author = {Tamahara, T and Kouketsu, A and Fukase, S and Sripodok, P and Saito, T and Ito, A and Li, B and Kumada, K and Shimada, M and Iikubo, M and Shimizu, R and Yamauchi, K and Sugiura, T}, title = {Ecological and Functional Landscape of the Oral Microbiome: A Multi-Site Analysis of Saliva, Dental Plaque and Tongue Coating.}, journal = {Microorganisms}, volume = {14}, number = {1}, pages = {}, doi = {10.3390/microorganisms14010002}, pmid = {41597522}, issn = {2076-2607}, support = {JP24K1310 and JP22K17150//JSPS KAKENHI/ ; }, abstract = {The oral cavity contains several microbial niches, including saliva, dental plaque and tongue coating, each shaped by distinct local environments and host factors. This study compared the ecological and functional characteristics of the microbiomes of these three oral sites within the same individuals and examined host conditions associated with their variation. Saliva, supragingival plaque and tongue coating samples were collected simultaneously from 31 adults without clinical oral lesions. The bacterial 16S rRNA gene (V3-V4 region) was sequenced using the Illumina MiSeq platform, and analyses included α and β diversity, Mantel correlations, differential abundance tests, network analysis and functional prediction. The three sites displayed a clear ecological gradient. Saliva and tongue coating were taxonomically similar but were influenced by different host factors, whereas plaque maintained a distinct, biofilm-like structure with limited systemic influence. Functional divergence was most pronounced on the tongue coating despite its taxonomic similarity to saliva, whereas functional differences between saliva and plaque were modest despite larger taxonomic separation. These findings indicate that microbial composition and function vary independently across oral niches and support the need for multi-site sampling to more accurately characterize oral microbial ecology.}, }
@article {pmid41596857, year = {2026}, author = {Tsouggou, N and Korozi, E and Pemaj, V and Drosinos, EH and Kapolos, J and Papadelli, M and Skandamis, PN and Papadimitriou, K}, title = {Advances in Shotgun Metagenomics for Cheese Microbiology: From Microbial Dynamics to Functional Insights.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {2}, pages = {}, doi = {10.3390/foods15020259}, pmid = {41596857}, issn = {2304-8158}, abstract = {The cheese microbiome is a complex ecosystem strongly influenced by both technological practices and the processing environment. Moving beyond traditional cultured-based methods, the integration of shotgun metagenomics into cheese microbiology has enabled in-depth resolution of microbial communities at the species and strain levels. The aim of the present study was to review recent applications of shotgun metagenomics in cheese research, underscoring its role in tracking microbial dynamics during production and in discovering genes of technological importance. In addition, the review highlights how shotgun metagenomics enables the identification of key metabolic pathways, including amino acid catabolism, lipid metabolism, and citrate degradation, among others, which are central to flavor formation and ripening. Results of the discussed literature demonstrate how microbial composition, functional traits, and overall quality of cheese are determined by factors such as raw materials, the cheesemaking environment, and artisanal practices. Moreover, it highlights the analytical potentials of shotgun metagenomics, including metagenome-assembled genomes (MAGs) reconstruction, characterization of various genes contributing to flavor-related biosynthetic pathways, bacteriocin production, antimicrobial resistance, and virulence, as well as the identification of phages and CRISPR-Cas systems. These insights obtained are crucial for ensuring product's authenticity, enabling traceability, and improving the assessment of safety and quality. Despite shotgun metagenomics' advantages, there are still analytical restrictions concerning data handling and interpretation, which need to be addressed by importing standardization steps and moving towards integrating multi-omics approaches. Such strategies will lead to more accurate and reproducible results across studies and improved resolution of active ecosystems. Ultimately, shotgun metagenomics has shifted the field from descriptive surveys to a more detailed understanding of the underlying mechanisms shaping the overall quality and safety of cheese, thus bringing innovation in modern dairy microbiology.}, }
@article {pmid41595487, year = {2026}, author = {Ucero-Carretón, A and Puente, H and Ithurbide, M and Estellé, J and Carvajal, A and Argüello, H}, title = {Factors Involved in Host Resilience to Enteric Infections in Pigs: Current Knowledge in Genetic, Immune, and Microbiota Determinants of Infection Resistance.}, journal = {Genes}, volume = {17}, number = {1}, pages = {}, doi = {10.3390/genes17010067}, pmid = {41595487}, issn = {2073-4425}, support = {PID2024-160714OB-I00//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; MICIU/AEI/10.13039/501100011033//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; LE088P23//Junta de Castilla y Le&#xf3;n/ ; JDC2023-051122-I//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; ULE-Predoc/2024//Universidad de Le&#xf3;n/ ; }, mesh = {Animals ; Swine/genetics ; *Gastrointestinal Microbiome/genetics/immunology ; *Disease Resistance/genetics ; *Swine Diseases/microbiology/genetics/immunology/virology ; *Host-Pathogen Interactions/genetics/immunology ; Quantitative Trait Loci ; }, abstract = {Enteric infections remain a major health and economic challenge in swine production, with outcomes determined not only by pathogen virulence but also by the complex interplay between host genetics, immune competence, and the intestinal microbiota. This review synthesises current knowledge on host-pathogen genomic interactions in pigs, with a focus on resilience mechanisms against enteric diseases in swine. For this purpose, 103 articles were used as information sources, retrieved through structured keyword searches in PubMed. The review first addresses host genetic factors, highlighting genomic variants and quantitative trait loci associated with resistance or resilience to viral and bacterial pathogens such as porcine epidemic diarrhoea virus (PEDV) or Escherichia coli. Next, the key factors of the immune system to confer protection are also reviewed, emphasising the role of innate and adaptive responses in controlling each pathogen and disclosing the contribution of regulatory networks that balance pathogen clearance. Finally, the last section of the review is devoted to exploring current knowledge in the involvement of the microbiota in resilience against enteric pathogens, mostly, but not exclusively, enteric bacteria. In this sense, competitive exclusion is a concept which has gained attention in recent years. The review pinpoints and discusses the state of the art about how the microbial community provides colonisation resistance, shapes immune development, and influences pathogen fitness within the intestinal niche. As final perspectives, the review explores future drivers in the genetic immune and microbiota resistance. By bridging host genomic data with functional insights into immunity and microbial ecology, this review underscores the potential of multi-omics approaches to enhance resilience against enteric infections in pigs and advance sustainable swine health management.}, }
@article {pmid41593721, year = {2026}, author = {Xi, J and Tao, H and Zhang, Z and Lian, B and Sun, W and Zhang, Y and Bu, S and Yang, X and Qian, X}, title = {Captive breeding of specialty animals represents an overlooked yet critical reservoir for spreading antibiotic resistance genes.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag009}, pmid = {41593721}, issn = {1751-7370}, abstract = {Driven by wildlife conservation and economic demands, captive breeding has expanded globally, intensifying wildlife-human interactions. In specialty animal breeding, particularly for species with short domestication histories and underdeveloped breeding protocols, clinically important antibiotics are commonly misused, posing potential ecological and health risks that remain largely unexplored. We collected fecal samples from three groups of musk deer (Moschus berezovskii): those exposed to clinically important antibiotics, those not exposed for six months, and wild musk deer, and analyzed their microbiomes and resistomes using metagenomic and culture-based methods. We found that captivity significantly expanded and reshaped the fecal resistome of musk deer. The antibiotic-exposed musk deer harbored a significantly higher diversity and abundance of antibiotic resistance genes (ARGs) compared to those non-exposed to antibiotics and wild deer. We observed a higher abundance of clinically important ARGs within Enterobacteriaceae in fecal samples of captive musk deer. This observation was further supported by the antibiotic susceptibility profiles of 124 Escherichia coli strains isolated from antibiotic-exposed musk deer. Seven identical mobile genetic element-associated ARGs were detected in distinct bacterial hosts across fecal samples from musk deer and farm workers, indicating potential conjugative transfer between the two groups. Our results suggest that captive breeding of specialty animals is an overlooked but significant reservoir for disseminating clinically important ARGs, and underscore the transmission risk at the animal-human interface.}, }
@article {pmid41592901, year = {2026}, author = {Pedreira, A and Vázquez, JA and García, MR}, title = {The mini revolution: application of mini-bioreactors in adaptive laboratory evolution.}, journal = {Critical reviews in biotechnology}, volume = {}, number = {}, pages = {1-19}, doi = {10.1080/07388551.2025.2608012}, pmid = {41592901}, issn = {1549-7801}, abstract = {Adaptive laboratory evolution (ALE) is a powerful tool for understanding and controlling the evolutionary trajectories of microorganisms. The scope of applications extends widely, including areas such as: biotechnology, synthetic biology, microbial ecology, and fundamental evolutionary research. In this work, we systematically explore the implementation and advantages of mini-bioreactors, defined as reactors with working volumes below 0.5 L, in ALE experiments. Mini-bioreactors offer substantial improvements over traditional large-scale reactors, including: reduced costs, enhanced parallelization capabilities, customizable configurations, and ease of automation. Through the utilization of illustrative case studies, which facilitate a comparative and critical evaluation of: batch, chemostat, turbidostat, and morbidostat operational modes, this review underscores the distinct capabilities of mini-bioreactors in enabling precise, dynamic control of evolutionary pressures. The novelty of this review lies in its comprehensive synthesis of recent advancements in mini-bioreactor technologies and operational strategies, particularly emphasizing innovations, such as: integrated automation, advanced sensors, and novel control algorithms adapted or specially designed for ALE. The ultimate objective is to provide both novices and experienced researchers with an updated, in-depth resource that addresses current technological limitations and future directions of mini-bioreactors in ALE.}, }
@article {pmid41592403, year = {2026}, author = {Zhang, B and Wang, M and Zheng, J and Yu, C and Wei, C and Ren, J and Sun, S and Wang, G and Wang, J and Lu, Y and Lin, L and Zhang, C}, title = {Strain-specific impacts of Pichia kudriavzevii on metabolite profiles and microbial community dynamics in Chinese Baijiu fermentation: Integrated metabolomics and metagenomics analysis.}, journal = {International journal of food microbiology}, volume = {450}, number = {}, pages = {111660}, doi = {10.1016/j.ijfoodmicro.2026.111660}, pmid = {41592403}, issn = {1879-3460}, abstract = {Pichia kudriavzevii is a dominant yeast species in Chinese baijiu fermentation, yet its intraspecific diversity remains underexplored. This study used metabolomics and metagenomics analysis to investigate the impact of four distinct P. kudriavzevii strains (PK12, PK25, PK97, and PK360) on the metabolite profiles and microbial community structure in a controlled baijiu solid-state fermentation. Metabolomics analysis identified 49 key volatile compounds and 2792 non-volatile metabolites. Strain PK97 exhibited exceptional capacity for butanoic acid metabolism, inducing a 55.27-fold increase in butanoic acid and a 30.54-fold enhancement in ethyl butanoate production. Strain PK25 specialized in acetoin biosynthesis, while PK360 maximized 2-phenylethanol production. Metagenomic analysis uncovered that strains PK12, PK25, and PK360 promoted Lactobacillus acetotolerans population, increasing its relative abundance to 67.39%, 58.57%, and 71.79%, respectively. In contrast, strain PK97 orchestrated a dramatic ecological shift, elevating Enterobacter mori abundance from 0.56% to 17.60%, transforming the community from Lactobacillus-dominated to Enterobacteriaceae-enriched. Integration of metabolomic and metagenomic data revealed that strain PK97's promotion of Enterobacter mori correlated with significant upregulation of key enzymes including α-amylase (EC 3.2.1.1), enoyl-CoA hydratase (EC 4.2.1.17), and succinyl-CoA synthetase (EC 6.2.1.5), creating a metabolic environment favoring enhanced starch hydrolysis, altered TCA cycle flux, and butanoic acid accumulation. Strain PK25 specifically upregulated acetyl-CoA hydrolase (EC 3.1.2.1), facilitating acetic acid and acetoin formation. Strain PK360 enhanced glucose pyrophosphorylase (EC 2.7.7.9) and asparagine synthetase (EC 6.3.1.1) activities, accelerating galactose metabolism and amino acid transformations. These findings illustrate the impact of P. kudriavzevii intraspecific diversity on reshaping microbial ecology and flavor chemistry in Chinese baijiu, offering novel insights for targeted fermentation control and quality enhancement strategies in baijiu production.}, }
@article {pmid41592132, year = {2026}, author = {Rathod, DR and Silverman, JD}, title = {PCR bias impacts microbiome ecological analyses.}, journal = {PLoS computational biology}, volume = {22}, number = {1}, pages = {e1013908}, doi = {10.1371/journal.pcbi.1013908}, pmid = {41592132}, issn = {1553-7358}, abstract = {Polymerase Chain Reaction (PCR) is a critical step in amplicon-based microbial community profiling, allowing the selective amplification of marker genes such as 16S rRNA from environmental or host-associated samples. Despite its widespread use, PCR is known to introduce amplification bias, where some DNA sequences are preferentially amplified over others due to factors such as primer-template mismatches, sequence GC content, and secondary structures. Although these biases are known to affect transcript abundance, their implications for ecological metrics remain poorly understood. In this study, we conduct a comprehensive evaluation of how PCR-bias influences both within-samples (α-diversity) and between-sample (β-diversity) analyses. We show that perturbation-invariant diversity measures remain unaffected by PCR bias, but widely used metrics such as Shannon diversity and Weighted-Unifrac are sensitive. To address this, we provide theoretical and empirical insight into how PCR-induced bias varies across ecological analyses and community structures, and we offer practical guidance on when bias-correction methods should be applied. Our findings highlight the importance of selecting appropriate diversity metrics for PCR-based microbial ecology workflows and offer guidance for improving the reliability of diversity analyses.}, }
@article {pmid41591842, year = {2026}, author = {Islam, H and Sharma, A and Blair, J and Lopatkin, AJ}, title = {PlasAnn: a curated plasmid-specific database and annotation pipeline for standardized gene and function analysis.}, journal = {Nucleic acids research}, volume = {54}, number = {3}, pages = {}, doi = {10.1093/nar/gkaf1507}, pmid = {41591842}, issn = {1362-4962}, support = {1R35GM150871-01/NH/NIH HHS/United States ; //Pew Charitable Trusts Foundation/ ; 2440082//National Science Foundation/ ; //Edward Mallinckrodt Jr. Foundation/ ; }, mesh = {*Plasmids/genetics ; *Molecular Sequence Annotation/methods ; *Databases, Genetic ; Genome, Bacterial ; Software ; DNA Transposable Elements ; Genes, Bacterial ; Bacteria/genetics ; }, abstract = {Conjugative plasmids are key drivers of bacterial adaptation, enabling the horizontal transfer of accessory genes within and across diverse microbial populations, yet annotating them remains challenging due to their highly mosaic genetic architectures and inconsistent gene naming conventions that complicate functional predictions and comparative analyses. To address this, we developed PlasAnn, a database designed specifically for genes encoded on natural plasmids, paired with a dedicated annotation pipeline (available via Bioconda or through the URL https://plasann.rochester.edu/). The curated database provides highly accurate, plasmid-type-specific gene names with standardized functional annotations, enabling direct comparison across plasmids without manual curation or specialized expertise, while the integrated annotation tool incorporates other common plasmid features for a fast, one-stop solution that outperforms broad prokaryotic genome annotation pipelines in both accuracy and efficiency. We demonstrate PlasAnn's utility by showing that plasmid accessory genes from different groups often share conserved repertoires, suggesting dynamic, modular networks of interconnected genes, and by revealing that plasmid-encoded transposable elements frequently carry genes related to bacterial adaptation beyond antibiotic resistance, including metabolism, virulence, and stress responses, emphasizing their broader contributions to fitness and adaptability. These insights, not captured by current field-standard tools, highlight how PlasAnn improves plasmid annotation and advances our understanding of plasmid biology, microbial ecology, and evolution.}, }
@article {pmid41590453, year = {2026}, author = {Zhang, K and Cai, Y and Shi, X and Yan, Z and Huang, Q and Perez-Moreno, J and Liu, D and Yang, Z and Yang, C and Yu, F and Liu, W}, title = {Symbiosis Among Naematelia aurantialba, Stereum hirsutum, and Their Associated Microbiome in the Composition of a Cultivated Mushroom Complex JinEr.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {12}, number = {1}, pages = {}, doi = {10.3390/jof12010041}, pmid = {41590453}, issn = {2309-608X}, support = {202205AD160036//Fuqiang Yu/ ; Yunnan Revitalization Talent Support Program//Jes&#xfa;s P&#xe9;rez-Moreno, Xinhua He/ ; }, abstract = {The JinEr mushroom ("Golden Ear"), a globally rare edible and medicinal macrofungus, comprises a symbiotic complex formed by the symbiotic association of Naematelia aurantialba (Tremellomycetes) and Stereum hirsutum (Agaricomycetes). However, the interactions between these fungi and their associated microbiome remain poorly understood. This study employed high-throughput amplicon sequencing, in situ microbial isolation and culture, and microbial confrontation assays to analyze microbial diversity, community structure, and potential functional roles of the endomycotic bacterial community within JinEr basidiomata and its cultivation substrate. Molecular analysis confirmed the heterogenous composition of the basidiomata, revealing N. aurantialba constitutes less than 20% of the fungal biomass, while S. hirsutum predominates, accounting for approximately 80%. Endomycotic fungi accounted for 0.33% (relative abundance) of the fungal community. Prokaryotic analysis identified Delftia and Sphingomonas as the dominant endomycotic bacterial genera within basidiomata, comprising 85.42% of prokaryotic sequences. Endomycotic bacterial diversity differed significantly (p < 0.05) between basidiomata and substrate, indicating host-specific selection. Cultivation-based approaches yielded 140 culturable bacterial isolates (spanning four families and seven genera) from basidiomata core tissues. In vitro co-culture experiments demonstrated that eight representative bacterial strains exhibited compatible growth with both hosts, while one Enterobacteriaceae strain displayed antagonism towards them. These findings confirm that the heterogeneous JinEr basidiomata harbor a specific prokaryotic assemblage potentially engaged in putative symbiotic or commensal associations with the host fungi. This research advances the understanding of microbial ecology in this unique fungal complex and establishes a culture repository of associated bacteria. This collection facilitates subsequent screening for beneficial bacterial strains to enhance the JinEr cultivation system through the provision of symbiotic microorganisms.}, }
@article {pmid41589897, year = {2026}, author = {Huang, J and Cai, M and Han, M and Fang, B and Dong, L and Zhang, G and Han, J-R and Li, S and Rustamova, N and Liu, Y and Li, W-J and Jiang, H}, title = {Habitat heterogeneity drives microbial community assembly and functional specialization in extremely arid ecosystems.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0258825}, doi = {10.1128/aem.02588-25}, pmid = {41589897}, issn = {1098-5336}, abstract = {UNLABELLED: Extreme arid ecosystems present significant environmental challenges, yet the mechanisms by which habitat heterogeneity (e.g., salinity gradients, soil-sediment contrasts) shapes microbial community assembly and functional specialization remain poorly understood. This study integrated culture-dependent and culture-independent approaches to investigate microbial diversity, assembly processes, and metabolic potential across wasteland soils, desert soils, and saline lake sediments in the Turpan-Hami Basin. High-throughput sequencing revealed habitat-specific patterns, with lake sediments exhibiting significantly greater OTU richness and Shannon diversity than wasteland and desert soils (P < 0.05). These shifts were driven by salinity-dependent taxonomic succession, notably the dominance of Gammaproteobacteria, Halobacteria, and Desulfobacteria in hypersaline lakes. Ecological assembly processes diverged across habitats, with deterministic processes (heterogeneous/homogeneous selection) dominated in deserts and moderate saline lakes, whereas stochastic processes (dispersal limitation, drift) prevailed in wastelands and hypersaline systems. Metabolic profiling highlighted habitat-specific functional specialization: terrestrial systems were characterized by nitrogen-cycling, while saline lakes displayed partitioned sulfur metabolism (e.g., sulfate respiration in high-salinity sediments). Co-occurrence network analyses revealed greater topological complexity in freshwater lakes than in extreme environments, reflecting contrasting resilience strategies. Cultivation strategies informed by sequencing results recovered 4.02% to 21.76% of the sequence-detected genera, significantly improving access to the uncultured majority. These findings demonstrate that habitat heterogeneity drives microbial community assembly and functional evolution in extremely arid ecosystems, underscoring the value of integrating omics with cultivation to uncover microbial dark matter.<br><br>IMPORTANCE: Understanding microbial adaptation in hyperarid environments is crucial for predicting ecosystem responses to extreme stressors. This study provides an integrative framework linking environmental heterogeneity to microbial community assembly and metabolic specialization across diverse habitats in one of Earth's driest basins. Our findings demonstrate that deterministic environmental filtering dominates community assembly in deserts and moderately saline lakes, whereas stochastic processes prevail in wastelands and hypersaline systems. Habitat&#x2011;specific metabolic specialization is evident, with nitrogen cycling being key in terrestrial soils and sulfur metabolism central to saline lakes. By significantly improving the recovery of uncultured diversity through targeted strategies, this study bridges a major gap between molecular surveys and cultivable microorganisms. These findings advance ecological theory on community assembly and offer a model for studying microbial resilience and functional evolution under extreme aridity.}, }
@article {pmid41589889, year = {2026}, author = {Wang, S and Su, Y}, title = {Challenging the paradigm of metabolic exclusivity: coexistence of methanogenesis and sulfate reduction in oil reservoirs.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0217225}, doi = {10.1128/aem.02172-25}, pmid = {41589889}, issn = {1098-5336}, abstract = {The prevailing dogma in microbial ecology holds that sulfate-reducing microorganisms (SRMs) outcompete methanogenic archaea for common substrates (e.g., H2/formate and acetate), leading to the mutual exclusion of sulfate reduction and methanogenesis in sulfate-rich anaerobic environments. This principle underpins models of organic carbon flow to sulfate-respiration-derived CO2 in ecosystems like oil reservoirs, where seawater injection introduces high concentrations of sulfate. In an Applied and Environmental Microbiology article by S. Beilig, L. Voskuhl, I. Geydirici, L. K. Tintrop, T. C. Schmidt, and R. U. Meckenstock (91:e00141-25, 2025, https://doi.org/10.1128/aem.00141-25), the authors challenge this view by demonstrating coexistence of methanogenesis and sulfate reduction in a sulfate-adapted enrichment culture from an oil reservoir. The authors employ incubation experiments and microbial activity assessment via the reverse stable isotope labeling (RSIL) method to argue for metabolic coexistence, even under conditions thought to favor complete competitive exclusion. This commentary discusses the mechanistic reasons underlying the coexistence and explores the broader implications for predicting microbial activities and interactions. The study compellingly argues that thermodynamic and kinetic arguments alone are insufficient to predict microbial community function, necessitating a more nuanced understanding of microbial interactions in complex environments.}, }
@article {pmid41588828, year = {2026}, author = {Shaw, D and Gentekaki, E and Tsaousis, AD}, title = {The Microbiome Within a Microbe: Rethinking Blastocystis Biology.}, journal = {The Journal of eukaryotic microbiology}, volume = {73}, number = {1}, pages = {e70056}, doi = {10.1111/jeu.70056}, pmid = {41588828}, issn = {1550-7408}, support = {CA21105//COST/ ; //University of Kent/ ; }, mesh = {*Blastocystis/physiology/microbiology/virology ; Humans ; *Microbiota ; Blastocystis Infections/parasitology ; *Gastrointestinal Microbiome ; }, abstract = {Blastocystis spp., one of the most prevalent microeukaryotes in the human gut, has long puzzled researchers with its ambiguous role in health and disease. Decades-old microscopy studies reported bacterial- and viral-like particles within Blastocystis spp. cells, but these findings have been mainly overlooked. Comparable associations in other protozoa, such as those between Trichomonas vaginalis and Mycoplasma, as well as protozoan-virus interactions, are known to influence metabolism, immune evasion, and ecological fitness. Here, we revisit these neglected observations in Blastocystis spp., framing them within the holobiont concept and proposing that this protist may host its own microbial consortium. We also propose potential mechanisms, ecological implications, and modern experimental strategies-from organ-on-a-chip to single-cell multi-omics-to rigorously test this hypothesis. Recognizing Blastocystis spp. as a possible "microbiome within a microbe" could transform our understanding of its biology and its place in gut microbial ecology.}, }
@article {pmid41588461, year = {2026}, author = {Zheng, H and Payne, L and He, W and Mestre, MR and Yang, L and Dechesne, A and Pinilla-Redondo, R and Nesme, J and Sørensen, SJ}, title = {Plasmids as persistent genetic reservoirs of bacterial defense systems in wastewater treatment.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-025-02297-2}, pmid = {41588461}, issn = {2049-2618}, abstract = {BACKGROUND: Bacterial antiphage defense systems play essential roles in microbial ecology, yet their dynamics within urban wastewater systems (UWS) remain poorly characterized.<br><br>RESULTS: In this study, we performed comprehensive metagenomic and plasmidome analyses on 78 wastewater samples collected during two seasons and four sampling points across UWS from three European countries. We observed a significant reduction in the abundance, diversity, and mobility potential of defense systems during biological treatment. However, these reductions were not directly correlated with changes in microbial abundance. Defense systems were significantly enriched on plasmids, particularly conjugative plasmids, where their gene density was approximately twice as high as on chromosomes and remained relatively stable across compartments. In contrast to chromosomal defense systems, plasmid-borne systems exhibited more frequent co-localization with a wide range of mobile genetic elements (MGEs)-associated genes, thereby facilitating multilayered dissemination networks. Furthermore, we detected a strong correlation between phage abundance and host defense system profiles, indicating ongoing phage-host co-evolutionary dynamics in these environments.<br><br>CONCLUSIONS: In summary, our results demonstrate that UWS reduce the abundance and diversity of bacterial defense system genes. However, plasmid-associated defense systems can persist through shared mobile genetic reservoirs. These findings underscore the critical role of plasmids in bacterial immunity and provide new insights into defense system dynamics within urban wastewater environments.}, }
@article {pmid41588066, year = {2026}, author = {Pániková, L and Ondreičková, K and Pánik, P and Janiga, M and Oxikbayev, B}, title = {Linkages Between Trace Elements and Bacterial Communities in Glacial Freshwater Systems of Zhongar Alatau National Park, Kazakhstan.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02674-2}, pmid = {41588066}, issn = {1432-184X}, abstract = {Glacial ecosystems of Central Asia represent extreme environments where microbial communities are shaped by both physicochemical conditions and hydrological dynamics. In this study, we analysed 21 surface and meltwater samples collected in September 2023 from a lake, river, glacier, glacial river, and sedimentary lake in the Zhongar Alatau National Park (Kazakhstan, 1 040-3 360 m a.s.l.). Bacterial community structure was assessed using ARISA profiling, while spectrometric methods determined concentrations of chemical elements. Alpha diversity indices revealed the highest richness and diversity in lake and sedimentary lake samples, moderate diversity in river samples, and the lowest values in glacier samples. The glacial river samples showed the strongest variability among the samples. Unique operational taxonomic units (OTUs) were most abundant in the lake, but the glacier exhibited the highest relative proportion of habitat-specific OTUs. Principal component analysis revealed that DNA yield, along with heavy metals and other elements (Rb, Fe, Mn, K, Ba), covaried along the major axes, primarily reflecting differences driven by habitat. Overall, our results demonstrate that glacial valley habitats host distinct bacterial assemblages and that the chemical environment is consistent with the observed spatial structuring of microbial communities. These findings highlight the vulnerability and sensitivity of mountain freshwater ecosystems to glacier retreat and associated changes in water chemistry.}, }
@article {pmid41587649, year = {2026}, author = {Shi, J and Li, LK and Lin, LH and Li, DK and Lu, J and Saleh, SM and Zhang, TY and He, H and Dong, ZY and Xiao, Q and Xu, B and Zeng, C}, title = {Magnetic properties driving nitrogen removal improvement in magnetite-enhanced activated sludge: Mechanistic insights and process validation.}, journal = {Environmental research}, volume = {294}, number = {}, pages = {123870}, doi = {10.1016/j.envres.2026.123870}, pmid = {41587649}, issn = {1096-0953}, abstract = {The magnetite-enhanced activated sludge (MEAS) process offers a promising in situ strategy for upgrading wastewater treatment plants (WWTPs) to meet increasing treatment demands and stricter discharge regulations. Unlike conventional materials, magnetite possesses intrinsic magnetic properties, yet their influence on biological treatment efficiency and microbial ecology remains underexplored. This study systematically evaluated three types of magnetite particles with varying properties, focusing on their roles in denitrification, sludge settling, and microbial responses. Batch experiments under low carbon-to-nitrogen conditions (C/N = 4.4) demonstrated that magnetite with high saturation magnetization (65.9 emu/g) achieved 79.3 ± 10.2 % nitrate removal, 3.3 times higher than the control. It reduced the sludge volume index (SVI) from 84.7 to 28.4 mL/g by promoting compact floc formation through extracellular polymeric substance (EPS) protein conformational changes and enhanced microbe-particle interactions. It also increased bio-capacitance of the sludge and achieved a 77.0 % increase in electron transport system activity (ETSA). Surface analysis confirmed that magnetite served as a passive electron mediator rather than actively participating in redox cycling. Metagenomic sequencing further demonstrated the selective enrichment of denitrifying and magnetotactic bacteria and enrichment of key nitrogen metabolism genes (narG, nirK, narK, narH). Validation in an anaerobic-anoxic-aerobic (AAO) reactor treating real municipal wastewater achieved NH4[+]-N and total nitrogen removal efficiencies of 98.7 % and 73.6 %, respectively, meeting stringent discharge limits. These results identify saturation magnetization as a critical parameter for selecting or engineering magnetite materials and provide mechanistic insights and engineering guidance for deploying MEAS as an efficient, retrofit-friendly technology for WWTP upgrading.}, }
@article {pmid41586525, year = {2026}, author = {Díaz-González, F and Rojas-Villalobos, C and Issotta, F and Reyes-Impellizzeri, S and Hedrich, S and Johnson, DB and Temporetti, P and Quatrini, R}, title = {Trait-based meta-analysis of microbial guilds in the iron redox cycle.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0148825}, doi = {10.1128/msystems.01488-25}, pmid = {41586525}, issn = {2379-5077}, abstract = {UNLABELLED: Microbial iron (Fe) redox cycling underpins key biogeochemical processes, yet the functional diversity, ecological roles, and trait architectures of iron-transforming microbes remain poorly synthesized across global environments. Here, we present a systematic review and trait-based meta-analysis of 387 microbial taxa spanning 314 studies and 76 years of research, integrating phenotypic, genomic, and environmental data to define ecologically coherent microbial iron redox cycle guilds. Rather than relying on taxonomy, our framework delineates first-order functional guilds-Fe(III) reducers, Fe(II) oxidizers, and dual-capacity Fe oxidizers/reducers-and resolves second-order guilds based on trait syndromes, such as acidophily, redox flexibility, or metabolic breadth. Trait profiling revealed that iron-cycling capacities frequently transcend phylogenetic boundaries, with multiple guilds converging in chemically stratified hotspots like hot springs, hydrothermal vents, and acid mine drainages. Dual-capacity Fe oxidizers/reducers (e.g., Acidithiobacillus ferrooxidans and Metallosphaera sedula) emerged as overlooked mediators of "cryptic" iron cycling, possessing genomic repertoires capable of toggling between oxidative and reductive modes in response to redox oscillations. Hierarchical clustering and kernel density analyses of ecophysiological traits highlighted niche partitioning along key environmental filters, including pH, iron availability, salinity, and temperature. Collectively, this work introduces the Guild Exploitation Pattern as a conceptual lens for understanding iron microbiome assembly, providing a data-driven foundation for predicting microbial contributions to iron cycling under changing environmental conditions.<br><br>IMPORTANCE: Iron redox reactions shape nutrient turnover, contaminant mobility, and primary productivity, yet the microbes driving these processes are often studied in isolation. By integrating decades of data into a trait-based guild framework, we reveal the ecophysiological diversity and niche differentiation of microbial iron redox cycling taxa across environments. Our synthesis exposes major gaps, such as limited trait data for >80% of dual-capacity Fe oxidizing/reducing species and highlights the need for functional trait surveys to complement metagenomics and cultivation efforts. The guild framework presented here advances predictive microbial ecology by linking metabolic traits with environmental gradients, offering a robust foundation for incorporating iron cycling into ecosystem models and biogeochemical forecasts.}, }
@article {pmid41586521, year = {2026}, author = {Wang, N and Liu, Q and Huo, F and Zhang, S and Lv, S and Mi, T and Liu, H}, title = {Intestinal epithelial Tet2 deficiency reprograms the gut microbiota through bile acid metabolic alterations.}, journal = {mBio}, volume = {}, number = {}, pages = {e0356225}, doi = {10.1128/mbio.03562-25}, pmid = {41586521}, issn = {2150-7511}, abstract = {Epigenetic mechanisms are increasingly recognized as critical regulators of host-microbiota interactions, yet their specific roles in gut homeostasis remain elusive. Here, we demonstrate that intestinal epithelial-specific deletion of the DNA demethylase Tet2 leads to structural abnormalities, impaired barrier function, and remarkable reprogramming of the gut microbiota. Mechanistically, Tet2 deficiency downregulated the apical sodium-dependent bile acid transporter ASBT/Slc10a2, resulting in altered bile acid homeostasis with luminal accumulation of hyocholic acid (HCA). This metabolic shift created a favorable niche for the selective expansion of bile salt hydrolase (BSH)-expressing Lactobacillus species. Furthermore, we identified an age-dependent regulatory role of HCA, which promoted Lactobacillus in young mice but enriched Akkermansia in aged animals. Our findings establish an epigenetic-metabolic-microbial axis centered on Tet2-mediated bile acid regulation, providing new insights into how host epigenetic factors shape the gut microbial ecosystem in an age-sensitive manner.IMPORTANCEWhile the gut microbiota is known to influence host physiology, the molecular mechanisms by which the host epigenetically regulates microbial composition remain largely unexplored. Our work reveals that the epigenetic enzyme Tet2 in intestinal epithelial cells acts as a master regulator of gut microbial ecology by modulating bile acid metabolism. The discovery that Tet2 deletion drives hyocholic acid (HCA) accumulation-which exerts age-dependent effects on Lactobacillus and Akkermansia-provides a novel principle for understanding host-microbe interactions across the lifespan. By linking epithelial DNA demethylation to bile acid transport and microbial phenotype, we establish a previously unrecognized Tet2-ASBT-HCA pathway that expands the conceptual framework for microbiota research. These insights open new avenues for therapeutic interventions aimed at reversing microbial dysbiosis through epigenetic or metabolic modulation.}, }
@article {pmid41586352, year = {2025}, author = {Pandey, A and Dhakar, K}, title = {Extreme thermal environments: reservoirs of industrially important thermozymes.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1739143}, pmid = {41586352}, issn = {1664-302X}, abstract = {Extreme thermal environments, both natural (e.g., hot springs, fumaroles, geysers, mud pots, deep-sea hydrothermal vents) and man-made (e.g., compost heaps, sawdust, coal refuse piles), are rich sources of thermophilic microorganisms, including Bacteria and Archaea. These organisms possess unique adaptations that allow survival and metabolic activity at elevated temperatures, making them valuable sources of thermostable and thermoactive enzymes. This review synthesizes current knowledge on thermophiles, including their phylogeny, adaptation mechanisms, and cultivation strategies. We discuss the industrial applications of thermozymes, such as DNA polymerases and other thermostable enzymes, and highlight the role of genomics, systems biology, and bioinformatics in accelerating enzyme discovery. The review also addresses the astrobiological relevance of thermophiles as models for life in extreme extraterrestrial environments and emphasizes the importance of conservation and sustainable use of natural thermal habitats. Collectively, this overview provides a comprehensive perspective on the ecological, biotechnological, and fundamental research significance of thermophiles and their enzymes.}, }
@article {pmid41584899, year = {2026}, author = {Zhou, H and Li, L and Gong, Y and Liu, H and Wu, H and Bravo, A and Soberón, M and Zheng, J and Peng, D and Sun, B and Sun, M}, title = {Geographic and seasonal variation of culturable bacteria associated with the diseased silkworm (Bombyx mori).}, journal = {Current research in microbial sciences}, volume = {10}, number = {}, pages = {100529}, pmid = {41584899}, issn = {2666-5174}, abstract = {The domesticated silkworm, Bombyx mori, is critically impacted by bacterial pathogens, yet the environmental and ecological drivers of their spatiotemporal dynamics remain poorly defined. In this study, 514 bacterial strains were isolated from diseased and healthy silkworm larvae across major sericultural regions in China. Through 16S rRNA gene sequencing and multi-tier pathogenicity assays, 51 isolates were identified as potential novel insect pathogens. Fulfilling Koch's postulates via oral infection tests, the pathogenicity of nine strains belonging to the genera Raoultella, Stenotrophomonas, and Citrobacter were confirmed, while the remaining isolates are considered putative pathogens. All isolates were classified into 33 genera within the phyla Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes, with Enterobacter, Bacillus, and Serratia being the most prevalent. Multivariate analysis indicated that geographic and climatic factors-specifically distance from the coastline and key thermal and radiative variables-collectively explained a significant though modest portion of the variance in bacterial community composition. Bacterial diversity correlated positively with cocoon yield. Guangxi presented the highest potential pathogen diversity and co-infection frequency, aligning with its intensive sericulture practices. Seasonal analyses indicated higher bacterial abundance and virulence in spring-summer compared to summer-autumn. Many isolates are taxonomically affiliated with genera containing insect gut microbiota, plant-associated bacteria, and human (opportunistic) pathogens, suggesting diverse environmental and anthropogenic origin. The detection of bacteria related to mulberry phyllosphere microbes underscore the role of host plant ecology in shaping the silkworm microbiome. These findings illuminate the ecological drivers of silkworm-associated bacterial communities and highlight the complex microbial connections within sericulture ecosystems, suggesting potential pathways relevant to a One Health perspective. Furthermore, the repository of 514 identified bacterial isolates from the model lepidopteran B. mori here provides a valuable resources for exploring novel biocontrol agents against other lepidopteran pests.}, }
@article {pmid41584691, year = {2026}, author = {Forte, L and Parabita, N and Santoro, M and Longobardi, F and Natrella, G and Quiñones, J and Ponnampalam, EN and Tomasevic, I and De Palo, P and Maggiolino, A}, title = {From rumen to milk: Dietary polyphenols in dairy cows-A critical review.}, journal = {Veterinary and animal science}, volume = {31}, number = {}, pages = {100569}, pmid = {41584691}, issn = {2451-943X}, abstract = {Polyphenols represent a large and structurally diverse family of plant secondary metabolites with bioactive properties. In ruminants, these compounds can influence rumen fermentation, microbial ecology, and nutrient metabolism, offering potential benefits for animal health, productivity, and environmental sustainability. This review synthesizes evidence on the fate of dietary polyphenols in dairy cows from ingestion to their possible secretion into milk. It outlines the main dietary sources and classes of polyphenols, their microbial biotransformations in the rumen, and subsequent host metabolism involving absorption, conjugation, and systemic circulation. Particular attention is given to the mechanisms of mammary uptake and secretion, where most compounds appear as conjugated metabolites such as glucuronides, sulfates, and urolithins rather than parent forms. Although the transfer efficiency from feed to milk is typically low, consistent detection of isoflavone derivatives, phenyl-γ-valerolactones, urolithins, and hippuric acid demonstrates the feasibility of diet-to-milk modulation. Factors affecting bioavailability and transfer include polyphenol structure, dietary matrix, dose, rumen microbiota composition, animal physiology, and feed processing. Advances in high-resolution analytical techniques have improved the characterization of these low-abundance metabolites, yet large variability among studies persists. In vivo studies indicate that polyphenol-derived metabolites in bovine milk occur at low ng/mL to low µg/mL levels, with compounds such as equol, enterolactone, urolithins, phenyl-γ-valerolactones and phenolic acids typically detected in the sub-micromolar range. Overall, dietary polyphenols offer promising opportunities to improve ruminant health and produce milk with enhanced functional quality, but quantitative and mechanistic research is still required to optimize feeding strategies and understand their contribution to milk bioactivity.}, }
@article {pmid41584621, year = {2026}, author = {Garcia-Rodriguez, AF and Moreno-Racero, FJ and Álvarez, R and Colmenero-Flores, JM and Knicker, H and Rosales, MA}, title = {Biochar enhances nitrogen use efficiency in lettuce by promoting its metabolic assimilation.}, journal = {Plant and soil}, volume = {518}, number = {1}, pages = {299-317}, pmid = {41584621}, issn = {0032-079X}, abstract = {BACKGROUND AND AIMS: Peat replacement with biochar (BC) offers a sustainable strategy in horticultural substrates but its effects on plant nitrogen (N) metabolism and N use efficiency (NUE) remain unclear. This study tested whether vineyard-pruning-derived BC can boost NUE and metabolic activity in lettuce, providing a pathway toward more productive and sustainable horticulture.<br><br>METHODS: Plant substrates (BC, peat and vermiculite) were prepared in the following proportions (v:v:v): B0 (0:70:30), B15 (15:55:30) and B30 (30:40:30) for growing lettuce (Lactuca sativa L. var. Batavia) under greenhouse conditions for 31&#xa0;days. We assessed plant growth and physiological traits, quantified N species and calculated NUE parameters and the activities of key N assimilation enzymes.<br><br>RESULTS: B30 plants produced 44.2% more biomass and 23.2% larger leaf area than B0, resulting in lower specific leaf area and greater succulence. BC addition decreased available NO&#x2083;&#x207b; and NH&#x2084;&#x207a; in substrate and roots without causing any plant stress symptoms, as chlorophyll content and PSII efficiency remained stable. B30 increased N uptake flux, N utilization efficiency, partial N balance, and N productivity by 31.8%, 34.8%, 27.8%, and 13.8%, respectively, relative to B0, coinciding with enhanced N-assimilation enzymatic activity. Despite lower total N in roots and shoots, protein accumulation increased, indicating more efficient N conversion into organic compounds.<br><br>CONCLUSION: These findings demonstrate the potential of BC-based substrates (especially 30% BC) to enhance lettuce productivity by improving NUE through the stimulation of N assimilation pathway, offering a promising strategy to optimize N-fertilizer needs to support more sustainable agriculture and soil management practices.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11104-025-07997-0.}, }
@article {pmid41582111, year = {2026}, author = {Afonso, AC and Botting, J and Simões, M and Simões, L and Liu, J and Saavedra, MJ}, title = {Ultrastructure Analysis by Cryo-Electron Tomography Revealed Mesosomes in the Gram-negative Delftia Acidovorans.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02698-2}, pmid = {41582111}, issn = {1432-184X}, abstract = {Delftia acidovorans, a Gram-negative bacterium commonly found in diverse environments, can occasionally cause infections in immunocompromised individuals. Despite its environmental prevalence and clinical relevance, there is a notable lack of studies on the cellular ultrastructure of D. acidovorans. Characterizing this aspect is essential for understanding the bacterium aggregation behavior, which significantly influences biofilm formation, environmental adaptability, and potential pathogenicity in clinical contexts. This study employs cryo-electron tomography to investigate the cellular ultrastructure of Delftia acidovorans. Our observations of D. acidovorans revealed a supercoiling pattern in flagellar filaments and diverse outer membrane projections. Our major finding was the observation of cytoplasmic membrane invaginations resembling mesosomes seen in Gram-positive bacteria, offering new insights into the cellular architecture and potential functions of these structures in Gram-negative bacteria. Together, these ultrastructural insights reveal adaptations potentially linked to environmental persistence and interspecies aggregation.}, }
@article {pmid41579275, year = {2026}, author = {Sasaki, K and Emoto, S and Yokoyama, Y and Ishihara, S}, title = {Circulating tumor DNA methylation and gut microbiota in colorectal cancer: diagnostic, prognostic, and therapeutic implications.}, journal = {International journal of clinical oncology}, volume = {}, number = {}, pages = {}, pmid = {41579275}, issn = {1437-7772}, abstract = {Colorectal cancer remains one of the leading causes of cancer-related mortality worldwide, and early detection is essential for improving outcomes. Advances in liquid biopsy technologies and microbiota research have shed new light on diagnostic and therapeutic strategies for colorectal cancer. Notably, circulating tumor DNA methylation has emerged as a sensitive and specific biomarker for early detection, recurrence surveillance, and treatment monitoring. Recent progress in methylation-based assays, including stool- and plasma-derived approaches, highlights their potential clinical utility; however, challenges remain in detecting minimal residual disease at the earliest stages. Parallel to these developments, the gut microbiota has been recognized as a critical modulator of colorectal carcinogenesis and treatment response. Specific bacterial species, such as Fusobacterium nucleatum, polyketide synthase-positive Escherichia coli, and enterotoxigenic Bacteroides fragilis, have been implicated in tumor initiation and progression through epigenetic reprogramming, including aberrant DNA methylation. Microbial metabolites, particularly short-chain fatty acids such as butyrate, influence DNA methyltransferase activity and histone modifications, linking microbial ecology to the host epigenome. Microbiota composition also affects responses to chemotherapy, radiotherapy, and immunotherapy, underscoring its potential as a predictive biomarker and therapeutic target. Integrating circulating tumor DNA methylation profiling with microbiota analysis provides a promising strategy for personalized colorectal cancer management, combining early detection with treatment outcome prediction. This review summarizes the current evidence and future directions at the interface of DNA methylation and the gut microbiota, emphasizing their synergistic role as composite biomarkers in precision oncology.}, }
@article {pmid41576057, year = {2026}, author = {Lagneaux, P and Widjaja, N and Lagneaux, B and Nguyen, TKC and Licandro, H and Winckler, P and Waché, Y}, title = {Optical photothermal infrared (OPTIR) spectroscopy assisted by machine learning for lactic acid bacteria identification at strain level.}, journal = {The Analyst}, volume = {}, number = {}, pages = {}, doi = {10.1039/d5an01093d}, pmid = {41576057}, issn = {1364-5528}, abstract = {Lactic acid bacteria (LAB) are widely used in food, health, and biotechnology sectors, where accurate strain level identification is critical. Conventional methods, such as 16S rRNA sequencing, PCR-based fingerprinting (RAPD, AFLP), and MALDI-TOF mass spectrometry are powerful tools to identify bacteria at species level but often fail to resolve closely related strains due to limited taxonomic resolution, protocol sensitivity, or database dependence. In this study, we evaluated the capacity of Optical photothermal infrared (OPTIR) spectroscopy, a single-cell vibrational imaging technique, combined with supervised neural networks, to classify LAB at both species and strain levels. A total of 13 strains were analysed, including five Lactiplantibacillus plantarum, one Lactiplantibacillus pentosus, one Limosilactobacillus fermentum, three Lacticaseibacillus casei/paracasei, and three Streptococcus thermophilus, covering both intra- and inter-species diversity. Spectral data from LAB were acquired using a mIRage LS OPTIR system, preprocessed, and used to train a fully connected neural network for each level. The models achieved macro F1-scores of 97% for species level and 91% for strain level classification. These results demonstrate the potential of OPTIR, when integrated with machine learning, as a robust tool for high-resolution bacterial classification, with promising applications in microbiological quality control, probiotic selection, and microbial ecology.}, }
@article {pmid41575584, year = {2026}, author = {Ma, Y and Xu, Q and Sun, F and Wang, X and Zhou, W and Yue, M and Gao, L and Li, W}, title = {Potassium-Solubilizing Bacteria Mediate Light-Potassium Synergy to Enable Native Pueraria lobata to Outcompete Invasive Mikania micrantha.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02695-5}, pmid = {41575584}, issn = {1432-184X}, support = {2022A1515011169//National Natural Science Foundation of China-Guangdong Joint Fund/ ; 2023S017084//Guangdong Province Science and Technology Innovation Strategic Special Project/ ; 2022s037//the Maoming City Science and Technology Plan Project/ ; 32172430//National Natural Science Foundation of China/ ; }, abstract = {The invasive vine Mikania micrantha H. B. K. poses severe threats to biodiversity and ecosystem stability in tropical and subtropical regions, calling for sustainable ecological approaches. This study explores how the native legume Pueraria lobata var. thomsonii Benth displaces M. micrantha in the field, with a focus on the synergistic roles of light capture advantage and rhizosphere potassium (K) dynamics driven by specialized bacteria. In competitive ecotones, P. lobata demonstrated superior growth and photosynthetic performance relative to M. micrantha. Its main stem length was 1.31 times greater, while net photosynthetic rate, stomatal conductance, and chlorophyll content were 80%, 110.7%, and 21.4% higher, respectively. Soils associated with P. lobata contained significantly higher available K, correlated with enhanced enzyme activities, indicating a "microbe-enzyme-K" activation cascade. P. lobata specifically enriched efficient potassium‑solubilizing bacteria (KSB), such as Pseudomonas and Acinetobacter. Isolated KSB strains exhibited K‑solubilizing and plant‑growth‑promoting capacities and increased the competitive balance index of P. lobata in inoculation assays. Partial least‑squares discriminant analysis confirmed that KSB‑mediated K mobilization boosted stem elongation primarily by improving photosynthetic potassium use efficiency (PKUE), forming a reinforcing "light-K-microbe" loop that drives competitive displacement. This work establishes a "microbe‑mediated invasion suppression" framework, demonstrating how a native plant can couple superior light‑use efficiency with a specialized rhizosphere microbiome to outcompete an invasive species. We propose that managing potassium‑solubilizing microbiomes offers a sustainable strategy for ecological restoration in K‑limited ecosystems.}, }
@article {pmid41574941, year = {2026}, author = {Lhoste, E and David, J and Ponsin, V and Maikel, R and Lazar, CS}, title = {Seasons and vertical dynamics influence community composition in a flooded and abandoned mica mine.}, journal = {FEMS microbiology ecology}, volume = {102}, number = {2}, pages = {}, pmid = {41574941}, issn = {1574-6941}, abstract = {Artificial lakes formed from past mining activities represent unique but underexplored ecosystems that support diverse microbial communities. This study examined how seasonal variation and depth influence bacterial, archaeal, and micro-eukaryotic assemblages in the stratified water column of the Blackburn Mine (Outaouais, Quebec, Canada). Water and biofilm samples were collected by technical divers from the surface to 52 m during spring, summer, and autumn of 2021-2022, and analyzed by 16S/18S rRNA gene sequencing. Seasonal changes had little effect on physicochemical parameters but strongly shaped microbial community composition, together with depth. Archaeal taxa displayed greater stability across depths compared to bacteria and eukaryotes. Oxygen profiles defined three ecological zones: an oxic layer dominated by Actinobacteria and the methanogen Methanosarcina; a transition zone enriched in Chlorobium and methanogens such as Methanospirillum and Methanosaeta; and an anoxic layer containing sulfur-reducing (Desulfomonile, Desulfobacca), sulfur-oxidizing (Sulfuricurvum), and methane-cycling archaea. Eukaryotic communities included algae, particularly Chrysophyceae, and diverse protists. These findings suggest that microbial communities in the mine are integral to sulfur and carbon cycling, emphasizing the ecological significance of such stratified, mining-associated aquatic systems. The Blackburn mine provides valuable insight into how anthropogenic legacies shape microbial diversity and ecosystem functioning in artificial aquatic environments.}, }
@article {pmid41571998, year = {2026}, author = {Cheng, C and Bennett, BD and Savalia, P and Asrari, H and Biel, C and Evans, KA and Tang, R and Thrash, JC}, title = {Cell cycle dysregulation of globally important SAR11 bacteria resulting from environmental perturbation.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {41571998}, issn = {2058-5276}, support = {Investigator in Aquatic Microbial Ecology Award//Simons Foundation/ ; Early Career Investigator in Marine Microbial Ecology and Evolution Award//Simons Foundation/ ; }, abstract = {Genome streamlining is hypothesized to occur in bacteria as an adaptation to resource-limited environments but can result in gene losses affecting fundamental aspects of cellular physiology. The most abundant marine microorganisms, SAR11 (order Pelagibacterales), exhibit canonical genome streamlining, but the consequences of this genotype on core cellular processes such as cell division remain unexplored. Here, analysis of 470 SAR11 genomes revealed widespread absence of key cell cycle control genes. Growth experiments demonstrated that although SAR11 bacteria maintain a normal cell cycle under oligotrophic conditions, they exhibit growth inhibition and aneuploidy when exposed to nutrient enrichment, carbon source shifts or temperature stress. Detailed growth measurements and antibiotic inhibition experiments showed that these phenotypes resulted from cell division disruption with continuing DNA replication, leading to heterogeneous subpopulations of normal and polyploid cells. This vulnerability raises questions about microbial genome evolution and the evolutionary trade-offs between adaptation to stable nutrient-limited conditions and physiological resilience.}, }
@article {pmid41571114, year = {2026}, author = {Han, H and Wang, S and Zhou, L and Li, S and Huang, J and Peng, X}, title = {Insights into impact of tire additives on activated sludge systems: Treatment performance, extracellular polymeric substances, and microbial community.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134049}, doi = {10.1016/j.biortech.2026.134049}, pmid = {41571114}, issn = {1873-2976}, abstract = {This study systematically investigated the impacts of seven common tire additives (TAs) and their derivatives on the performance and microbial ecology of an activated sludge system exposed to environmental concentrations (0.2-20.0 μg/L) over 160 days. While most individual TAs showed minimal effects, the mixture of TAs (MIX) and 2-((4-Methylpentan-2-yl)amino)-5-(phenylamino)cyclohexa-2,5-diene-1,4-dione (6PPD-Q) significantly inhibited nitrogen removal efficiency. At 20.0 μg/L, the abundances of key nitrification and denitrification genes (amoA, nirK, nirS, nosZ) were markedly suppressed, leading to reductions in NH4[+]-N (12-14%) and total nitrogen (18-23%) removal efficiencies. The impairment was associated with elevated oxidative stress level, as indicated by a sharp increase in reactive oxygen species (0.9-1.1 fold) and lactate dehydrogenase (1.5-2.1 fold) release, alongside suppressed adenosine triphosphate (ATP) synthesis. Concurrently, sludge settleability deteriorated and mixed liquor volatile suspended solids (MLVSS) decreased, which correlated with reduced sludge hydrophobicity and enhanced hydrogen bond intensity (3435 cm[-1]). Microbial community restructuring was observed, with tolerant genera (e.g., Comamonadaceae, Rhodobacteraceae) increasing, while key nitrogen-removing genera (e.g., Nitrosomonas, Thauera) decreased. Three-dimensional fluorescence spectroscopy analysis revealed a decline in tryptophan and tyrosine like proteins in tightly bound extracellular polymeric substances. Molecular docking demonstrated that 6PPD-Q exhibited the strongest binding affinity to tryptophan and tyrosine synthases, suggesting a high potential for enzymatic interference even at low concentrations. This study demonstrated that MIX and 6PPD-Q, at environmental concentrations, significantly affect activated sludge systems and investigated the mechanisms involved, thereby providing important evidence for the ecological risk assessment of such pollutants during wastewater treatment.}, }
@article {pmid41570927, year = {2026}, author = {Magalhães, AP and Jorge, P and Neiva, J and Sousa, AM and Cerca, N and Pereira, MO}, title = {Contribution of viable but non culturable cells and small colony variants in antibiotic insusceptibility and therapeutic failure against S. aureus and P. aeruginosa biofilm co-infections.}, journal = {Microbial pathogenesis}, volume = {212}, number = {}, pages = {108312}, doi = {10.1016/j.micpath.2026.108312}, pmid = {41570927}, issn = {1096-1208}, abstract = {P. aeruginosa and S. aureus are often co-isolated from biofilm-associated infections, such as those afflicting cystic fibrosis (CF) patients. Biofilms, along with the interspecies interactions, play a significant role in fostering antibiotic insusceptibility, contributing to infection chronicity. Previously, we showed that S. aureus adopts a viable but non-culturable (VBNC) state in biofilms with P. aeruginosa. Here, we aimed to gain insight into the impact of VBNC and phenomena such as phenotypic switching on antimicrobial treatment and vice-versa. Single- and dual-species biofilms of two isolates from each species were characterised in terms of viability, culturability, clonal diversification, and pathogenic potential, upon treatment with ciprofloxacin and vancomycin. Data show that S. aureus became less susceptible to antibiotics in its VBNC state induced by P. aeruginosa and by the treatments. P. aeruginosa's susceptibility to ciprofloxacin diminished in dual-species biofilms, suggesting mutual benefits. Following treatment, S. aureus persisted as VBNC in the dual-species biofilm and its tolerance to ciprofloxacin endured after planktonic regrowth. P. aeruginosa triggered S. aureus's small colony variants (SCV), but P. aeruginosa's rugose SCV probably explains S. aureus's protection due to enhanced biofilm formation. This work sheds light on P. aeruginosa and S. aureus' co-increased tolerance to antibiotics, with cooperative interactions, phenotypic diversification, and VBNC underpinning this and the persistence of S. aureus within P. aeruginosa biofilms. This work is the first relating S. aureus's decreased susceptibility in dual-species biofilms to its VBNC state. Findings highlight the importance of microbial ecology, viability and colony morphotyping studies when designing treatments for multispecies infections.}, }
@article {pmid41568955, year = {2026}, author = {Baborski, A and Rohland, O and Wuenschmann, T and Bauer, M and Allen, RJ and Busch, A}, title = {Biofilm-derived bile duct microbiota in liver transplantation: high-quality genomes of Klebsiella pneumoniae, Enterococcus faecalis, and Enterococcus faecium.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0088625}, doi = {10.1128/mra.00886-25}, pmid = {41568955}, issn = {2576-098X}, abstract = {We present draft genomes of Klebsiella pneumoniae (K. pneumoniae), Enterococcus faecalis (E. faecalis), and Enterococcus faecium (E. faecium) isolated from a bilioenteric catheter after liver transplantation. Genome sizes were 5.58 Mb, 2.95 Mb, and 2.78 Mb, with G+C contents of 57.25%, 37.6%, and 37.99%, respectively, highlighting biofilm-associated bile duct colonizers.}, }
@article {pmid41568039, year = {2025}, author = {Dong, W and Chen, S and Hu, Y}, title = {Editorial: Diversity, function, and application of microbes in the fermentation or production of traditional food.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1751159}, doi = {10.3389/fmicb.2025.1751159}, pmid = {41568039}, issn = {1664-302X}, }
@article {pmid41567175, year = {2026}, author = {Hussain, N and Ramadan, A and Al Haddad, AHI and Alfahl, Z}, title = {A Review of Emerging Biomarkers Connecting Diabetes and Ischemic Stroke: Implications for Early Detection and Risk Stratification.}, journal = {Journal of diabetes research}, volume = {2026}, number = {}, pages = {2719491}, pmid = {41567175}, issn = {2314-6753}, mesh = {Humans ; *Biomarkers/blood ; *Ischemic Stroke/diagnosis/blood/genetics ; Early Diagnosis ; Risk Assessment ; Risk Factors ; *Diabetes Mellitus/blood/diagnosis/genetics ; }, abstract = {Diabetes substantially increases the risk of ischemic stroke through complex metabolic, inflammatory, and vascular mechanisms, yet early identification of high-risk individuals remains challenging. This narrative review synthesizes emerging circulating and genomic biomarkers that illuminate the pathways linking diabetes and ischemic stroke and evaluates their potential for early detection and precise risk stratification. Systematic searches of PubMed, Scopus, and Web of Science identified 141 relevant studies examining biomarkers, genetic and epigenetic factors, or risk prediction models in adults with diabetes. Evidence highlights several biomarker domains. Inflammatory markers such as high-sensitivity C-reactive protein, interleukin-6, and tumor necrosis factor-α indicate immune activation driving atherogenesis and plaque instability. Endothelial markers, including endothelin-1, soluble vascular cell adhesion molecule-1, and asymmetric dimethylarginine, reflect endothelial dysfunction and a prothrombotic state. Metabolic indicators, notably glycated hemoglobin, adipokines, and lipoprotein(a), capture cumulative glycemic burden, adipose signaling, and inherited atherothrombotic risk. Genetic and epigenetic measures, including polygenic risk scores, microRNAs, long noncoding RNAs, and DNA methylation, quantify inherited susceptibility and molecular imprints of the diabetic environment. Renal markers such as albuminuria and reduced eGFR reflect microvascular injury and consistently associate with stroke risk. Multimarker panels and multi-omics integration using machine learning approaches show promise for improving predictive accuracy, though standardization, external validation, and demonstration of clinical utility are needed. Integrating these biomarkers with established clinical risk factors could transform stroke prevention in diabetes from reactive to proactive, enabling personalized, mechanism-informed strategies for early detection and risk stratification.}, }
@article {pmid41566387, year = {2026}, author = {Xu, M and Chen, S and Pei, H and Hu, L and Zhang, Y}, title = {Engineering bacteriophages for gut health: precision antimicrobials and beyond.}, journal = {Journal of nanobiotechnology}, volume = {24}, number = {1}, pages = {62}, pmid = {41566387}, issn = {1477-3155}, support = {12275192//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Bacteriophages/genetics ; Phage Therapy/methods ; *Gastrointestinal Microbiome/drug effects ; Animals ; Precision Medicine ; *Anti-Infective Agents/pharmacology ; Inflammatory Bowel Diseases/therapy/microbiology ; Colorectal Neoplasms/therapy/microbiology ; }, abstract = {Engineered bacteriophages are emerging as a promising class of precision antimicrobials at a time when gastrointestinal diseases are increasingly linked to microbial dysbiosis, antibiotic resistance, and disruptions in host-microbe interactions. Conventional antibiotics often provide limited benefit in these settings because they lack selectivity and fail to restore microbial ecology. Advances in synthetic biology and nanotechnology have made it possible to redesign phages with enhanced specificity, expanded functionality, and improved stability, positioning them as versatile tools for microbiota-centered therapies. This review summarizes the major engineering approaches, and examines their applications in inflammatory bowel disease (IBD), colorectal cancer (CRC), and infectious enteritis. Key mechanistic insights into pathogen targeting, immune modulation, and barrier protection are highlighted. Remaining challenges, such as ensuring long-term stability, avoiding resistance development, and enabling scalable manufacturing, are discussed together with emerging interdisciplinary strategies that may advance the clinical translation of personalized phage therapies.}, }
@article {pmid41565754, year = {2026}, author = {Solís-Marín, FA and Vergara-Ovando, C and Rojas-Oropeza, M and Calderón-Gutiérrez, F and Medina-Tanco, G and Cabirol, N}, title = {Asterinides sp. an endemic stygobitic seastar from an anchialine cave and its interactions among prokaryotic communities.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-36065-5}, pmid = {41565754}, issn = {2045-2322}, support = {PAPIIT-IN207021//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; PAPIIT-IN207021//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; Posgraduate grant//Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; }, abstract = {Anchialine caves house a vast variety of organisms that support complex ecological relationships among themselves and their environment. The following study was made in the anchialine karst cave El Aerolito, found on Cozumel Island, Quintana Roo, Mexico. It explores the relationship between wall microbial mats and the diet of Asterinides sp., an endemic stygobitic seastar. Wall microbial mats inside the cave were sampled and the stomach microbiome of Asterinides sp. was obtained through regurgitation. Asterinides sp. sampling was made through the Catcher Collection Chamber (CCC), an innovative technology for the exploration of these ecosystems. The obtained results suggest that microbial mats are part of the diet of Asterinides sp. The following results highlight the potential relevance of the microbial communities inside the trophic chain present in El Aerolito. Additionally, the methodology presented here provides a useful framework for future ecological research in El Aerolito cave.}, }
@article {pmid41563471, year = {2026}, author = {Luo, W and Liu, P and Qiu, Y and Li, M and Huang, Y}, title = {Diversity and Functional Analysis of Epiphytic and Endophytic Bacteria in Three Different Parts of Brasenia Schreberi.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02688-w}, pmid = {41563471}, issn = {1432-184X}, support = {24XJQN04//Nanchang Normal University 2024 Youth Science and Technology Talent Training Project/ ; NSBSJJ2023003//Nanchang Normal University Doctoral Research Start-up Fund/ ; 24FZZX13//Nanchang Normal University Funds for Improvement and Research/ ; }, }
@article {pmid41563055, year = {2026}, author = {Sadiq, S and Xue, P and Tang, Y and Du, M and Van Brussel, K and McBratney, AB and Holmes, EC and Minasny, B}, title = {Limited effect of short- to mid-term storage conditions on an Australian farmland soil RNA virome.}, journal = {Journal of virology}, volume = {}, number = {}, pages = {e0145925}, doi = {10.1128/jvi.01459-25}, pmid = {41563055}, issn = {1098-5514}, abstract = {Soils represent one of the largest and most diverse reservoirs of microbial life on Earth, yet their associated RNA viruses remain underexplored compared to animal and aquatic systems. Viral discovery in soils has been further limited by technical hurdles, particularly difficulties in obtaining sufficient yields of high-quality RNA for sequencing. To address this, we evaluated a range of storage and preservation strategies, including the use of commercial preservative solutions and ultra-cold snap-freezing, followed by standardized RNA extraction, sequencing, and virus discovery pipelines. This work aimed to establish minimum sample storage requirements that maintain RNA integrity, generate sufficient RNA sequencing data, and subsequently enable reliable soil virome characterization. While no preservative solution proved effective, "neat" soil samples were stable at 2°C-8°C and -30°C for at least 2 weeks, and at -80°C for at least 3 months, with no measurable reduction in RNA quality, sequencing data, or viral abundance and diversity. From 32 resulting libraries, we identified 1,475 putative novel RNA viruses, with the majority belonging to the microbe-associated phylum Lenarviricota. Several novel viruses formed divergent clusters with other environmentally derived sequences distantly related to traditionally animal-associated families, such as the Astroviridae and Picornaviridae. Furthermore, unique clusters within the Picobirnaviridae, Alsuvirucetes, Ghabrivirales, and Amabiliviricetes comprised exclusively Australian viruses, suggesting instances of region-specific evolution. Together, these findings highlight soils as rich reservoirs of RNA viral diversity and provide practical minimum standards for storage, expanding opportunities to investigate the ecological and evolutionary roles of RNA viruses in terrestrial systems.IMPORTANCERNA viruses are the most abundant and diverse biological entities on Earth and are likely present in all other organisms and ecosystems, including soil-dwelling invertebrates, microbes, and plants. Despite this, their diversity and role in soil systems remain largely unknown. Methodological challenges in preserving and extracting sufficient quantities of RNA from soils have hindered the study of these communities. Here, we identified 1,475 previously undescribed RNA viruses in Australian soils while systematically testing different preservation strategies. The significance of our research lies in the demonstration that snap-freezing soil is a viable and robust storage strategy for at least 3 months, while also highlighting the extraordinary scale of viral diversity present in terrestrial environments. This work establishes a foundation for reliable exploration of terrestrial RNA viruses, improving the accessibility of more remote environmental viromes and enabling future efforts to integrate them into broader models of microbial ecology and ecosystem function.}, }
@article {pmid41561919, year = {2026}, author = {Phyu, KK and Zhi, S and Liang, J and Yang, Z and Zhao, R and Liu, J and Cao, Y and Wang, H and Zhang, K}, title = {Dataset on microbial community structure in response to microalgal cultivation in dairy wastewater.}, journal = {Data in brief}, volume = {64}, number = {}, pages = {112407}, pmid = {41561919}, issn = {2352-3409}, abstract = {This data article describes a comprehensive dataset investigating the dynamics between microalgae, bacteria, and pollutant removal in dairy wastewater treatment. Data was collected from a 12-day laboratory-scale experiment employing three distinct cultivation systems: monoculture, co-culture, and sequential culture of four algal/cyanobacterial strains (Chlorella sorokiniana, Euglena gracilis, Synechocystis sp., and Desertifilum tharense). The generated dataset includes high-frequency measurements of water quality parameters (COD, NH4 [+]-N, TN, TP), algal physiological data (biomass production, total chlorophyll, biochemical compositions like proteins, lipids, and polysaccharides), and 16S rRNA gene sequencing data of the associated bacterial communities, which were fractionated into free-living and tightly bound phycosphere populations. The reuse potential of this data is significant. It provides a detailed profile of microbial community assembly driven by different cultivation strategies and environmental factors, offering a benchmark for future ecological studies in engineered systems. Researchers in the fields of wastewater biotechnology, microbial ecology, and synthetic ecology can reuse this data to validate microbial interaction models, optimize consortia design for bioremediation, and inform life-cycle assessments of algal-based treatment processes. The dataset generated in this study is publicly available in the NCBI BioProject repository under the accession number [PRJNA1265442].}, }
@article {pmid41558125, year = {2026}, author = {Armstrong, R}, title = {Biocatalytic surfaces in architecture.}, journal = {Current opinion in biotechnology}, volume = {97}, number = {}, pages = {103435}, doi = {10.1016/j.copbio.2025.103435}, pmid = {41558125}, issn = {1879-0429}, abstract = {This review explores the reconceptualisation of microbial colonisation on buildings: from a detrimental process (biofouling) to a source of beneficial, programmable biocatalysis. Strategies for embedding microbial and fungal communities into architectural materials to perform functions such as bioremediation, biomineralisation, and energy generation are explored. The analysis includes the multiscalar design of bioreceptive substrates, engineered living paints, mycelium composites, and probiotic surfaces, which transform passive structures into metabolically active interfaces. These approaches are regarded as Engineered Eco-Ornamentation, where surface design intentionally supports microbial ecology and urban metabolism. The integration of these living systems with computational modelling and digital fabrication to create adaptive building systems is considered. Key challenges include scaling biological processes for architectural application, ensuring long-term material durability, and aligning metabolic activity with practical construction constraints. Addressing these challenges positions functionally designed biocatalytic surfaces as a foundational research field for more regenerative and ecologically integrated architecture.}, }
@article {pmid41557960, year = {2026}, author = {Machushynets, NV and Terlouw, BR and Zhang, L and Du, C and Al Ayed, K and Schill, J and Trebosc, V and Elsayed, SS and Pieren, M and Liles, MR and Medema, MH and Martin, NI and van Wezel, GP}, title = {Diversification of Tridecaptin Chemical Space via a Chimeric Biosynthetic Pathway in Paenibacillus.}, journal = {Journal of natural products}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jnatprod.5c01298}, pmid = {41557960}, issn = {1520-6025}, abstract = {Paenibacillus species produce a wide array of bioactive nonribosomal peptides (NRPs). The structural diversity of NRPs is shaped by various diversification strategies that support bacterial ecological adaptation and create opportunities for new antibiotic discovery. Here, we show that chimeric biosynthesis occurs within the family of tridecaptin antibiotics. Genome mining revealed that 15 Paenibacillus strains harbored both a full tridecaptin BGC and a stand-alone tridecaptin-like NRPS predicted to encode a truncated decamer. The encoded NRPS domain architectures suggested the capability of these strains to produce multiple tridecaptin variants through collaborative action between this tridecaptin-like NRPS and a second NRPS homologous with TriE encoded within the complete tridecaptin BGC. Indeed, Paenibacillus sp. JJ-1683 produced both tridecaptin A5 and tridecaptin B1, while deletion of triE in the canonical BGC prevented the biosynthesis of all tridecaptins. This provides strong evidence for the existence of chimeric biosynthesis of lipopeptide antibiotics. Bioactivity testing revealed that the synthetic analogue of tridecaptin A5, Oct-TriA5, has unusual broad-spectrum activity against Gram-positive and Gram-negative ESKAPE pathogens, while Oct-TriB1 displays moderate activity against Gram-negative strains and is not active against Gram-positive bacteria. We hypothesize that chimeric biosynthesis is a strategy that enables bacteria to produce compounds with distinct chemistry and bioactivity profiles.}, }
@article {pmid41557197, year = {2026}, author = {Dos Santos, JFM and Mello, IS and da Cruz, ILS and Soares, MA}, title = {Non-Saccharomyces yeasts contribute to longevity, mitigated protein toxicity, and protection against abiotic stress in Caenorhabditis elegans.}, journal = {Archives of microbiology}, volume = {208}, number = {3}, pages = {128}, pmid = {41557197}, issn = {1432-072X}, support = {445388/2024-2//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {Animals ; *Caenorhabditis elegans/microbiology/physiology/genetics ; *Longevity ; Caenorhabditis elegans Proteins/genetics/metabolism ; Oxidative Stress ; Probiotics ; *Stress, Physiological ; *Cryptococcus/physiology/isolation &amp; purification ; Amyloid beta-Peptides/toxicity ; *Yeasts/physiology/isolation &amp; purification ; Saccharomyces/physiology/isolation &amp; purification ; DNA-Binding Proteins ; Receptor, Insulin ; Transcription Factors ; }, abstract = {The search for probiotic microorganisms that can be applied beyond gut health has advanced into areas that seek to promote longevity and to prevent neurodegenerative diseases. In this study, we have investigated non-Saccharomyces strains isolated from the Amazon, Cerrado, and Pantanal biomes and evaluated how they affect Caenorhabditis elegans. During our initial screening, based on increased body size and population, we selected eight yeast strains and characterized their cells. Then, we selected three of these strains for in vivo testing. Cryptococcus sp._T038 and Cryptococcus sp._T248 prolonged longevity and reduced the effects of thermal and oxidative stress in C. elegans. Hanseniaspora opuntiae_W164 and Saccharomyces boulardii_SB delayed beta-amyloid-induced paralysis in C. elegans CL4176. The antioxidant genes of the DAF-2/SKN-1 pathway were activated by Cryptococcus_T038 and _T248 and H. opuntiae_W164 in C. elegans strain LD1171 (GCS-1p::GFP) and by Cryptococcus_T038, H. opuntiae_W164, and S. boulardii_SB in C. elegans strain CF1553 (SOD-3p::GFP). These data reinforce that wild yeasts are potential functional probiotics.}, }
@article {pmid41554215, year = {2026}, author = {Mekureyaw, MF and Pandey, C and Sorty, AM and Hennessy, RC and Nicolaisen, MH and Liu, F and Nybroe, O and Roitsch, T}, title = {Biofilm formation by Pseudomonas putida KT2440 contributes to improve tomato drought stress resilience and priming for enhanced gene regulation.}, journal = {Journal of plant physiology}, volume = {317}, number = {}, pages = {154704}, doi = {10.1016/j.jplph.2026.154704}, pmid = {41554215}, issn = {1618-1328}, abstract = {Pseudomonas putida KT2440 is a plant growth-promoting rhizobacterium (PGPR), known to enhance tolerance to pathogen infection, but its role in drought stress mitigation remains largely unexplored. This study aimed to assess whether inoculation with KT2440 improves tomato tolerance to drought. Inoculation with the KT2440 wild type (WT) significantly improved ecophysiological drought stress responses by increasing leaf water potential and photosynthetic rate. It also resulted in an impact on the holobiont cell physiology through modulation of the activity signature of key enzymes of carbohydrate (e.g., PGM and vacInv) and antioxidant (e.g., GR, MDHAR, and cwPOX) metabolism under drought conditions. To functionally assess the role of biofilm formation in drought response, biofilm-deficient mutants KT2440 Alg, with only one gene cluster for the exopolysaccharide alginate deleted, and KT2440 Q, with four exopolysaccharide gene clusters (alg, bcs, pea and peb) deleted, were used. Inoculation with these two mutants led to reduced drought resilience, with partial or complete loss of protective effects in the Alg and Q mutants, respectively. This was reflected in lowered leaf water potential, photosynthetic rate, and reduced antioxidant and carbohydrate metabolism enzyme activities compared to inoculation with the corresponding wild type. Global RNA sequencing revealed that under drought conditions 360 % more genes were differentially regulated in the presence of KT2440 WT compared to the mock inoculated control, whereas this value decreased again to only 140 % more differentially regulated genes after recovery from the drought stress. Thus, KT2440 specifically primes the plant for a much more pronounced transcriptional response only during the impact of drought, thus providing resilience protection on demand. This priming for enhanced abiotic stress responsiveness was partially dependent on the ability to form biofilm. Both under well-watered and drought stress the number of differentially regulated genes was strongly reduced in plants inoculated with KT2440 Q compared to WT. Gene ontology and expression analyses showed significant upregulation of pathways involved in photosynthesis, phytohormone signaling, antioxidant metabolism, and drought resilience in KT2440-inoculated plants. Although KT2440 WT showed higher biofilm formation compared to the Alg and Q mutants, the strains did not differ in their ability for root colonization. These findings provide novel insights into the contribution of biofilm formation to PGPR-mediated drought tolerance and protection on demand via priming for enhanced transcriptional regulation under stress, supporting the potential of KT2440 for environmentally friendly mitigating of drought stress responses in crops.}, }
@article {pmid41553662, year = {2026}, author = {Sarkar, B and Bag, S and Mandal, A and Saha, D and Saha, S and Bhaduri, R and Chatterjee, S}, title = {Cresol Derivatives from Bacillus subtilis as Natural Oviposition Modulator of Culex quinquefasciatus: A Molecular Docking Approach.}, journal = {Applied biochemistry and biotechnology}, volume = {}, number = {}, pages = {}, pmid = {41553662}, issn = {1559-0291}, abstract = {Mosquitoes rely heavily on olfactory cues for locating suitable oviposition sites, with microbial communities in aquatic habitats playing a crucial role in producing volatile organic compounds (VOCs) that influence mosquito behaviour. In this study, we isolated Bacillus subtilis DHB13 from the breeding habitat of Culex quinquefasciatus, a major vector of several human diseases. The partial 16S rRNA gene sequence of the isolate has been submitted to NCBI GenBank with the accession number PV698100. The identity and resistance profile of the strain was confirmed through biochemical and antibiotic susceptibility tests. The bacterial suspension demonstrated a notable oviposition activity index (OAI) of 0.77 ± SE, with moderate variation among treatments (F(3, 8) = 3.631, p = 0.0642). Multiple comparison analysis (Tukey's test) showed that OAI values for DHB13-treated media did not differ significantly from natural habitat water but were significantly higher than the sterile control, indicating a biologically relevant attraction of gravid female mosquitoes. LC-MS analysis of the bacterial culture supernatant revealed the presence of three cresol derivatives: diisopropyl-m-cresol, 3-ethyl-p-cresol, and 6-ethyl-o-cresol. These compounds were evaluated through molecular docking against Cx. quinquefasciatus Odorant Binding Protein 1 (CxOBP1), a protein known to mediate olfactory-driven oviposition behaviour. However, mosquito olfaction involves several OBPs, receptors, and enzymes, so interaction with CxOBP1 represents only part of this complex sensory system. Molecular docking revealed strong binding of CxOBP1 with diisopropyl-m-cresol (-6.7 kcal/mol), 3-ethyl-p-cresol (-6.2 kcal/mol), and 6-ethyl-o-cresol (-5.9 kcal/mol), indicating potential oviposition attractant activity. All three ligands were found to bind within a conserved binding pocket of CxOBP1, behavioural assays confirmed the oviposition-stimulant properties of the bacterial suspension, indicating that the detected compounds mimic natural semio-chemicals such as p-cresol, previously recognized as an oviposition cue. These findings reinforce the role of microbiota in shaping mosquito reproductive behaviour through the production of volatile attractants. Moreover, they highlight the potential of using microbial VOCs as environmentally sustainable tools for mosquito surveillance and vector control. This integrative approach linking microbial ecology, chemical analysis, and mosquito behaviour provides novel insights for the development of attractant-based control strategies.}, }
@article {pmid41553583, year = {2026}, author = {Zavřel, T and Pohland, AC and Pfennig, T and Matuszyńska, AB and Tóth, SZ and Bernát, G and Červený, J}, title = {Estimating the redox state of the plastoquinone pool in algae and cyanobacteria via OJIP fluorescence: perspectives and limitations.}, journal = {Photosynthesis research}, volume = {164}, number = {1}, pages = {6}, pmid = {41553583}, issn = {1573-5079}, }
@article {pmid41551586, year = {2026}, author = {Rahlff, J and Amato, P}, title = {A look into the virosphere of clouds: A world yet to be explored.}, journal = {Current research in microbial sciences}, volume = {10}, number = {}, pages = {100545}, pmid = {41551586}, issn = {2666-5174}, abstract = {Clouds are aqueous atmospheric systems hosting diverse and active microorganisms. Viruses may also persist despite harsh conditions, support active viral infections, and contribute to microbial dynamics during aerial transport. However, assessing viruses, and even more, virus-bacteria interactions in the atmospheric environment is highly challenging, and knowledge remains very limited. Here, based on current knowledge in cloud microbiology, we estimate the cloud virome at ∼10[21] virus particles globally. One out of a million of cloud droplets is susceptible to host virus-bacteria interactions, which represents considerable volume at global scale, and we discuss potential implications for microbial ecology. We finally propose future research directions to explore further the cloud virosphere and its ecological roles.}, }
@article {pmid41222968, year = {2026}, author = {Le, OTH and Chu, LK and Pham, QV and Tran, HT and Nguyen, HN and Nguyen, HT and Dinh, HT}, title = {Enhancing compost maturity and nitrogen content through cocomposting of chicken feather waste with rice husk and vegetable residues.}, journal = {Journal of the Air &amp; Waste Management Association (1995)}, volume = {}, number = {}, pages = {1-13}, doi = {10.1080/10962247.2025.2587011}, pmid = {41222968}, issn = {2162-2906}, abstract = {Chicken feather waste is a potential low-cost nitrogen source for fertilizer production. However, due to its recalcitrant biodegradability, low C/N ratio, and high water content, composting chicken feather waste requires amendments. Optimizing the initial substrate composition plays a key role in improving composting performance. This study investigated the effects of varying chicken feather waste proportions, which altered the initial C/N ratio of the composting substrate, on the physicochemical evolution and final product quality of compost mixtures containing rice husk as a bulking agent and readily degradable vegetable residues. The substrates were composted in static compost bins of 20 L for 126 days under ambient conditions (~28°C). Significant differences were observed in physicochemical evolution and compost quality. A higher proportion of chicken feather waste or a lower initial C/N ratio led to increased total nitrogen (TN), extractable NH4[+], and SO4[2‒] concentrations during composting and in the final products. The addition of rice husk and vegetable residue improved the germination index of compost products from chicken feather waste. It was found that more-nutrient-rich compost could be produced by co-composting chicken feather waste with a low C/N ratio.Implications: This study highlights the interrelation of cosubstrates (rice husk, vegetable residue) in the decomposition of chicken feather waste. Nutrient-rich composts were obtained when chicken feather waste was cocomposted with low C/N ratios. Higher proportion of chicken feather waste or lower initial C/N ratio of composting substrate increased total N, extractable NH4[+], and SO4[2-] concentrations in compost product. Cocomposting of chicken feather waste with rice husk and vegetable residue enhanced compost maturity and germination index. The findings contribute a scientific basis for promoting the utilization of chicken feather waste to produce N-rich fertilizer.}, }
@article {pmid41549150, year = {2026}, author = {Negi, R and Sharma, B and Jyothi, RS and Gupta, A and Parastesh, F and Kaur, T and Jhamta, S and Thakur, N and Singh, S and Yadav, N and Yadav, AN}, title = {Phyllosphere microbiome: Exploring the unexplored frontiers for precision agricultural and environmental sustainability.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {2}, pages = {50}, pmid = {41549150}, issn = {1573-0972}, mesh = {*Microbiota ; *Agriculture/methods ; Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Fungi/metabolism/classification ; *Plant Leaves/microbiology ; *Plants/microbiology ; }, abstract = {The phyllosphere, encompassing the aerial surfaces of plants, represents one of the largest microbial habitats on Earth and plays a pivotal yet underutilized role in sustainable agriculture and environmental health. Colonized by diverse bacterial, fungal, and yeast communities, the phyllosphere microbiome significantly influences plant growth, disease resistance, nutrient dynamics, and abiotic stress tolerance. These microorganisms engage in complex interactions with host plants, often functioning as biofertilizers, biopesticides, and stress protectants by producing phytohormones, antimicrobial metabolites, and stress-responsive compounds. Importantly, phyllospheric microbes also contribute to atmospheric and ecological balance by participating in carbon and nitrogen cycling, degrading volatile organic compounds (VOCs), and mitigating air pollution. However, despite their immense potential, the practical application of phyllospheric microbes remains limited by challenges such as environmental instability, poor field persistence, and incomplete functional characterization. The highly variable microclimate of the leaf surface poses survival barriers to both native and introduced microbial inoculants. Moreover, the specificity of plant-microbe associations and the complexity of microbial interactions necessitate precision-based approaches for successful deployment. Recent advances in omics technologies, microbial consortia engineering, and nano-enabled delivery systems provide new opportunities to overcome these limitations. A deeper understanding of phyllosphere microbial ecology, combined with innovations in synthetic biology and ecological modeling, can facilitate the development of robust microbial tools tailored to specific crops and climates. Harnessing the potential of phyllospheric microorganisms is not merely an academic pursuit, it is a strategic imperative for transitioning toward climate-resilient, low-input, and ecologically sound agricultural systems.}, }
@article {pmid41548260, year = {2026}, author = {Ravikumar, BN and Carvajal-Arroyo, JM and Jia, M and Ganigué, R}, title = {Ecophysiological characterization of thermophilic anammox process: Impact of environmental conditions and wastewater constituents on the activity of a novel granular thermophilic anammox culture.}, journal = {Water research}, volume = {292}, number = {}, pages = {125402}, doi = {10.1016/j.watres.2026.125402}, pmid = {41548260}, issn = {1879-2448}, abstract = {Understanding the ecophysiology of thermophilic anammox bacteria is crucial for expanding anaerobic ammonium oxidation (anammox)-based nitrogen removal to warm (>45[0]C), nitrogen-rich and carbon-deficient wastewaters (bCOD/N < 3 g/g) such as, centrate from thermophilic anaerobic digesters. Despite recent enrichments of thermophilic anammox cultures, their ecophysiological responses to process variables remain largely unknown. This study provides the first systematic characterization of the short-term response of a granular thermophilic anammox culture, enriched in Candidatus Brocadia sp., to key environmental conditions (pH, temperature, salinity) and wastewater constituents (ammonium, nitrite, phosphate, sulfide, volatile fatty acids (VFAs)). The culture displayed an optimal pH range of 7.3-7.8 and a temperature optimum of 50-53 °C, the highest short-term activity temperature recorded for any anammox species, yet. Ammonium caused only slight inhibition (IC50>57 mM), and free ammonia was not the primary inhibitory species, in contrast to mesophilic observations. Thermophilic Ca. Brocadia culture showed higher salinity (IC50=159 mM NaCl) and phosphate tolerance (IC50=44.9 mM) tolerance than most mesophilic counterparts, whereas nitrite (IC50=25.9 mM) and sulfide (IC50=0.03 mM H2S) elicited strong inhibition. Among VFAs, propionate was the most inhibitory (IC50=22 mM), while low concentrations (2.5 mM) of acetate and formate slightly enhanced anammox activity. These results identify the inhibitory thresholds and operational boundaries of thermophilic anammox systems, demonstrating that the culture is sufficiently robust for application in warm nitrogenous wastewaters, paving the way for developing sustainable and cost-efficient wastewater treatment technologies for high temperatures.}, }
@article {pmid41547661, year = {2026}, author = {Dasgupta, M and Maity, A and Sarker, RK and Paul, P and Chakraborty, P and Sarkar, S and Roy, R and Malik, M and Das, S and Tribedi, P}, title = {Antibiotic-phytochemical combinations against Enterococcus faecalis: a therapeutic strategy optimized using response surface methodology.}, journal = {Antonie van Leeuwenhoek}, volume = {119}, number = {2}, pages = {41}, pmid = {41547661}, issn = {1572-9699}, support = {TNU/R&amp;D/MG/24/02//The Neotia University/ ; TNU/R&amp;D/MP/2021/010//The Neotia University/ ; }, mesh = {*Enterococcus faecalis/drug effects ; *Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; *Phytochemicals/pharmacology ; Vancomycin/pharmacology ; Ciprofloxacin/pharmacology ; Drug Synergism ; Benzoquinones/pharmacology ; }, abstract = {Enterococcus faecalis, a Gram-positive bacterium that causes nosocomial infections, has been reported to be resistant to several antibiotics, posing a significant threat to public healthcare. In the present study, we explored a combinatorial therapeutic approach involving conventional antibiotics alongside phytochemicals against E. faecalis. Vancomycin and ciprofloxacin were chosen for the current study due to their different modes of action. The minimum inhibitory concentration (MIC) of cuminaldehyde and thymoquinone was found to be 500 µg/mL and 30 µg/mL, respectively. Co-administering vancomycin with thymoquinone or cuminaldehyde reduced the MIC of vancomycin from 5 to 2 µg/mL, resulting in a 60% drop in MIC dose. Ciprofloxacin's MIC reduced from 1.5 to 1 µg/mL in the presence of the same phytochemicals, resulting in 33% reduction in its MIC dose. Furthermore, fractional inhibitory concentration indices (FICI) suggested additive interactions (FICI range: 0.66-1) between the antibiotics and phytochemicals against E. faecalis. Since precision dosing is important for any combinatorial application, we explored response surface methodology (RSM) to optimize dosing regimens of the selected compounds. It was observed that the predicted optimal concentrations of the test compounds (in different combinations) could closely match the actual observations when tested under the in-vitro laboratory conditions (R[2] range: 0.97-0.99). These findings suggested that combining conventional antibiotics with phytochemicals may offer a promising strategy to enhance the antimicrobial efficacy for effective control of infections caused by E. faecalis.}, }
@article {pmid41547536, year = {2026}, author = {Banik, M and Bashyal, S and Ahmed, KA and Banik, K and Dua, K and Choi, JP and Paudel, KR and Majumder, R}, title = {The Gut Microbiome of Australian Cats and Dogs: Dietary Influences, Health Impacts, and Emerging Research.}, journal = {Veterinary journal (London, England : 1997)}, volume = {}, number = {}, pages = {106566}, doi = {10.1016/j.tvjl.2026.106566}, pmid = {41547536}, issn = {1532-2971}, abstract = {The gut microbiome plays a pivotal role in the health, metabolism, and behaviour of companion animals, yet comprehensive syntheses of its composition and functional relevance in cats and dogs in Australia are overlooked and remain limited globally. This review synthesises current knowledge on the gut microbial communities inhabiting the gastrointestinal tracts of dog and cats, with a particular focus on taxonomic diversity, dietary modulation, and associations with disease states within Australian context. Core phyla including Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria dominate the canine and feline gut, but marked interspecies and individual variability is shaped by factors such as feeding practices, living environment, obesity, and chronic disease. Recent studies have elucidated functional signatures linked to conditions ranging from the influence of microplastics to pet gut health, as well as gut-microbiome transmission between pets and their owners, highlighting this area as a promising field of investigation. In parallel, this review contextualizes the broader landscape of pet ownership in Australia, where nearly 70% of households own pets, and significant resources are devoted to nutrition, veterinary care, and preventive health. Emerging evidence also suggests bidirectional influences between pets and their human companions' microbiota, highlighting opportunities for integrated approaches. We identify critical knowledge gaps, including the need for region-specific microbial baselines, standardized methodologies, and controlled intervention trials targeting microbiome modulation and transmission. By consolidating advances across microbial ecology, veterinary medicine, and translational research, this review provides a foundation for future studies that aim to harness the diagnostic and therapeutic potential of the pet microbiome, thereby improving health outcomes for animals and humans alike.}, }
@article {pmid41546932, year = {2026}, author = {Verduzco Garibay, M and Hernández-Guardado, I and Yebra-Montes, C and Díaz-Torres, O and Fernández Del Castillo, A and Díaz-Vázquez, D and Kreft, JU and Cortés-Aguilar, J and Senés-Guerrero, C and Gradilla-Hernández, MS}, title = {Exploring the resilience of playa lake ecosystems to climate change: A microbial perspective.}, journal = {Journal of environmental management}, volume = {399}, number = {}, pages = {128474}, doi = {10.1016/j.jenvman.2025.128474}, pmid = {41546932}, issn = {1095-8630}, abstract = {Playa lakes, ephemeral water bodies found in arid and semi-arid regions, are increasingly impacted by climate change. The Mexican playa Lake Atotonilco has experienced a significant decline in water volume, leading to increased salinity and making it a valuable model for assessing climate impacts. Using 16S rRNA sequencing, this study investigated the responses of microbial communities and their contributions to key biogeochemical cycles, including those related to greenhouse gas dynamics. Spatial differences in physicochemical parameters were observed: channels and wastewater treatment plant (WWTP) effluent showed elevated BOD5, COD, coliforms, and pH above regulatory limits, whereas the lake displayed higher DO but increased TP and TKN. Bacterial communities exhibited marked seasonal and depth-related shifts, reflecting strategies that support ecosystem resilience. To robustly identify differentially abundant taxa, two methods (ANCOM-BC2 and DESeq2) were implemented, which consistently detected significant differences across seasons. Despite strong environmental fluctuations, a core microbial community persisted, suggesting functional continuity in biogeochemical cycling. This study provides a comprehensive assessment of microbial dynamics in a playa lake, integrating community structure with physicochemical variability to reveal bacterial responses to climate-driven environmental change. Because playa and other shallow lakes worldwide are experiencing increasing desiccation, salinization, and nutrient imbalances, defining these microbial processes is essential for anticipating ecological change. This study provides a needed baseline for future research and offers key insights for managing climate-vulnerable aquatic ecosystems in arid regions.}, }
@article {pmid41545601, year = {2026}, author = {Shin, S and Bang, D and Lee, M and Kang, Y}, title = {Heavy Rain, Less Bloom Under Heat: Succession of Size-Structured Phytoplankton Community Without Biomass Increases in a Monsoonal Korean Coastal Ecosystem.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02680-4}, pmid = {41545601}, issn = {1432-184X}, support = {R2025011//National Institute of Fisheries Science/ ; NRF2022R1C1C1008380//National Research Foundation of Korea/ ; }, }
@article {pmid41545035, year = {2026}, author = {Eggestein, A and Rauer, D and Herrmann, SM and Kolek, F and Leier-Wirtz, V and Urban, S and Foesel, B and Schloter, M and Bhattacharyya, M and Pyrri, I and Reiger, M and Schwierzeck, V and Hülpüsch, C and Traidl-Hoffmann, C and Damialis, A and Gilles, S}, title = {A Walk in the Park: Influence of Natural Co-Exposure to Grass Pollen and Fungal Spores on Nasal Mycobiome and Cytokine Responses.}, journal = {Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology}, volume = {}, number = {}, pages = {}, doi = {10.1111/cea.70216}, pmid = {41545035}, issn = {1365-2222}, support = {//Christine K&#xfc;hne-Center for Allergy Research and Education (CK-Care)/ ; }, abstract = {BACKGROUND: During the grass flowering season, fungal spores are abundant in outdoor air. We tested for co-sensitisations to grass pollen and fungal spores, assessed the degree of co-exposure, and studied its impact on the nasal mycobiome and immune responses.<br><br>METHODS: Fungi-specific IgE-levels were studied in 277 individuals with and without grass pollen sensitisation. In a small cohort (n&#x2009;=&#x2009;7), exposure to grass pollen and fungal spores was monitored during 5 consecutive indoor and outdoor stays in a flowering meadow and correlated with changes in the nasal mycobiome. Cytokines of nasal epithelial cells were studied under stimulation with recombinant grass pollen allergens, with and without fungal spores derived from outdoor isolates.<br><br>RESULTS: IgE-sensitisation against the studied fungi was significantly more frequent among individuals with grass pollen sensitisation than among those without grass pollen sensitisation. Outdoor exposure resulted in changes in the nasal mycobiome, with a transitory enrichment of environmental fungi, for example, Cladosporium species. Most of the fungi cultivated from outdoor air samples belonged to the genera Fusarium, Cladosporium and Penicillium. Apical co-stimulation of nasal epithelial cells with grass pollen allergens and Fusarium, Cladosporium or Penicillium spores led to an increased loss of transepithelial electrical resistance and induction of pro-inflammatory cytokine release compared to mono-stimulation.<br><br>CONCLUSION: Frequent co-exposure to fungal spores and grass pollen may increase the chance of acquiring a co-sensitisation to both allergens. Environmental fungi interact with and transitorily change the local mycobiome. Under co-exposure, fungal spores induce nasal inflammation and foster immune responses to otherwise poorly immunogenic pollen allergens.}, }
@article {pmid41544570, year = {2026}, author = {Aminullah, N and Langar, H and Mahaq, O and Azizi, MN and Zahir, A}, title = {Microbial ecology, functional implications, and associated factors influencing poultry intestinal health.}, journal = {Veterinary immunology and immunopathology}, volume = {293}, number = {}, pages = {111065}, doi = {10.1016/j.vetimm.2026.111065}, pmid = {41544570}, issn = {1873-2534}, abstract = {Gut health is a dynamic phenomenon regulated by the balanced interaction among gastrointestinal tract morphological structure, resident microbiota, and available nutrients, producing an integrated barrier that ensures efficient physiological functions, enhanced immune competence and optimal productivity. Gut health is recognised as a crucial factor for optimum management, farming economy, and sustainable commercial poultry production. Poultry gut health has become a central focus, particularly following restrictions applied on the use of antimicrobial growth promoters in poultry production due to rising global concerns about microbial resistance. Intestinal integrity and health are being regulated by microbiota metabolites such as short-chain fatty acids (SCFAs), which modulate intestinal morphogenesis vis-à-vis villus size, crypt depth and physiological functions, including feed digestion, nutrients synthesis and absorption, and immune response. Any disturbances arising from nutritional imbalances, microbial infections, environmental stress, or poor management practices compromise epithelial health, barrier integrity, and physiological functions, leading to impaired growth performance and productivity. This review provides an overview of poultry gut health, highlighting the interdependence of gut microbiota, gut morphogenesis, physiology, environmental factors affecting gut health, and management approaches for sustainable poultry production.}, }
@article {pmid41540283, year = {2026}, author = {Bueno, RS and Catania, V and Auteri, M and Grilli, E and di Iorio, T and di Sarra, A and Castaldi, S and Quatrini, P}, title = {Patterns and Drivers of Plant Arbuscular Mycorrhizal Traits Across a Pedo-Climatic Gradient in Mediterranean Agroecosystems Under Desertification Risk.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02689-9}, pmid = {41540283}, issn = {1432-184X}, abstract = {Desertification is a global concern, reducing vegetation cover and soil fertility. Arbuscular mycorrhizal symbiosis (AM), the most common plant-fungi association, can enhance plant fitness and stress tolerance. Despite its significance, comprehensive data on community-wide patterns and drivers of plant AM traits are limited in the Mediterranean, one of the regions most vulnerable to desertification. We examined four traits: colonization frequency, intensity, arbuscule abundance, and spore density in the rhizosphere of 20 plant species across ten agroecosystems in desertification-prone areas of Italy, Spain, and Portugal. We analysed whether these traits varied across Raunkiær's plant life forms and were affected by vegetation cover, soil properties, precipitation, and temperature, both overall and regionally, to explore potential context-dependency. All plants showed a high frequency of AMF colonization, with an average intensity of 54%, indicating obligate AMF interactions, and arbuscule abundance was significantly correlated with spore density. These traits were significantly higher in microhabitats dominated by trees and shrubs compared to those dominated by herbaceous plants. Phanerophytes (perennials) presented lower trait values than therophytes (annuals), while the highest values were found in hemicryptophytes. Lampedusa, a region with hotter and drier climate conditions in Southern Europe, had significantly lower AMF trait levels, though Spanish site values resembled those in Sicily more than Portugal. Soil organic carbon, nitrogen, and the overall positive interaction between precipitation and temperature significantly influenced all AMF traits. However, the magnitude and direction of soil and climate related effects differed among regions, indicating strong context dependency. Our study contributes to better define indicators for monitoring desertification and evaluating restoration efforts while highlighting the need of site-specific evaluations and careful interpretation of broad generalisations.}, }
@article {pmid41537975, year = {2026}, author = {Sless, T and Chau, K and Nguyen, P and Rehan, S}, title = {Microbial communities of wild bees and comparative phylogenetics of key bacterial taxa across the bee tree of life.}, journal = {Proceedings. Biological sciences}, volume = {293}, number = {2062}, pages = {}, doi = {10.1098/rspb.2025.1823}, pmid = {41537975}, issn = {1471-2954}, support = {//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Animals ; Bees/microbiology ; Phylogeny ; *Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics/analysis ; *Microbiota ; *Fungi/classification/genetics/isolation &amp; purification ; DNA Barcoding, Taxonomic ; }, abstract = {Recent years have seen a rapidly growing interest in the study of microbiomes to understand the health and well-being of host animals. Within bees, much of this work has focused on managed species of agricultural importance, such as honeybees and bumblebees. However, unmanaged wild bees are also vital to both agricultural and natural systems, and studying their microbial associates is essential to understanding the impacts of microbiomes on bee health. We used metabarcoding based on 16S rRNA and internal transcribed spacer region (ITS1) loci to identify bacterial and fungal associates of adult bees from 16 species, 10 genera and 5 families, representing a diverse sampling of wild bees common to eastern North America. Overall, Apilactobacillus was the largest component of bacterial communities, while fungal communities were dominated by Cladosporium. Alpha diversity of both bacteria and fungi differed significantly across genera and species, while beta diversity varied at all taxonomic levels. Additionally, we conducted a broad phylogenetic comparison of bacterial communities across bees using previously published 16S rRNA datasets and contrasted these findings with functional traits across the bee tree of life. Several bacterial taxa showed evidence of strong phylogenetic signal in prevalence, while the presence of corbiculae was more strongly associated with bacterial community composition than sociality or nesting habit. This study provides expanded insights into the microbial associates of wild bees, as well as the broadest investigation to date into patterns of phylogenetic conservation in bacterial communities across a total of 42 species representing the five most diverse bee families.}, }
@article {pmid41536172, year = {2026}, author = {Carboni, S and Asangba, AE and Melin, AD}, title = {Microbial Contributions to Primate Reproduction.}, journal = {Evolutionary anthropology}, volume = {35}, number = {1}, pages = {e70023}, pmid = {41536172}, issn = {1520-6505}, mesh = {Animals ; *Primates/microbiology/physiology ; Female ; *Reproduction/physiology ; *Microbiota/physiology ; Male ; Humans ; Pregnancy ; Anthropology, Physical ; Sexual Behavior, Animal ; Biological Evolution ; Copulation/physiology ; }, abstract = {Reproduction is a complex process, and microbes play a far greater role than previously imagined. This review explores the ways that microbiomes influence the rich tapestry of reproductive processes and outcomes within the primate lineage, including pre-copulatory and post-copulatory mechanisms. We discuss microbiomes in a sexual selection framework, specifically how they might influence mate choice and sexual competition across multiple sensory modalities. We then consider how copulatory behavior and mating systems may in turn shape reproductive microbiomes. Moving to post-copulatory processes, we discuss the potential impact of microbes on cryptic choice and sperm competition and call for additional research in this area. Finally, we explore the influence of microbes on pregnancy outcomes, emphasizing evolutionary perspectives often overlooked in clinical research. Importantly, we compare human studies to those on nonhuman primates, bridging the two areas of inquiry and outlining future research directions. Our aim is to highlight the vast potential for microbes to contribute to all stages of reproduction, and to inspire creative, synthetic future research that moves forward this fascinating area of inquiry.}, }
@article {pmid41534871, year = {2026}, author = {Xie, Y and Artacho, A and Yu, X and Bi, M and Li, H and Li, Y and Roccuzzo, A and Mira, A and Rosier, BT and Tonetti, MS}, title = {Oral-Rinse-Sourced Microbiota in Oral Health and Diseases in a Representative US Adult Population: Implications for Diagnostics.}, journal = {Journal of clinical periodontology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jcpe.70101}, pmid = {41534871}, issn = {1600-051X}, support = {JYLJ202404//Clinical+ programme of the Ninth People's Hospital/ ; }, abstract = {AIMS: To investigate the associations between oral-rinse microbiota and distinct oral conditions, and further evaluate its potential ability to distinguish periodontitis severity.<br><br>METHODS: Oral-rinse-sourced microbiota with 16S ribosomal RNA sequencing from 3770 adults in US National Health and Nutrition Examination Survey 2009-2012 were analysed across oral health, caries, periodontitis, co-existing caries and periodontitis and edentulism. Diagnostic potential of the oral-rinse microbiota for periodontitis severity was evaluated using multi-class random forest (RF) model with internal validation and external validation in an independent cohort (n&#x2009;=&#x2009;392).<br><br>RESULTS: Oral condition accounted for substantial variance in oral-rinse microbiota, revealing disease or tooth loss-associated shifts. Increasing acidogenic/aciduric taxa (Veillonella, Lactobacillus, Atopobium) or periodontitis-associated taxa (Filifactor, Treponema, Tannerella) were identified in caries-only or periodontitis-only groups, respectively, while the co-existing disease group showed overlapping shifts. Taxa shifted dose-dependently with increasing periodontitis severity. The RF model achieved moderate performance in identifying severe periodontitis, with the area under the receiver operating characteristic curve (AUROC) of 0.81 (0.75-0.87) internally and 0.83 (0.77-0.88) externally. Key contributing taxa aligned with established periodontitis-associated genera, supporting model interpretability.<br><br>CONCLUSION: Based on our results, oral-rinse microbiota captures disease-specific signatures across oral conditions, supporting its potential as a non-invasive tool to monitor oral microbial ecology and assess periodontitis severity at the population level.}, }
@article {pmid41534410, year = {2026}, author = {Cardinali, F and Rampanti, G and Lucci, P and Ferrocino, I and Pacetti, D and Fanesi, B and Ismaiel, L and Milanović, V and Garofalo, C and Petruzzelli, A and Savelli, D and Gabucci, C and Aquilanti, L and Osimani, A}, title = {Novel insights into hákarl: A deep dive into the microbiological and physico-chemical features of Iceland's traditional fermented shark.}, journal = {International journal of food microbiology}, volume = {450}, number = {}, pages = {111629}, doi = {10.1016/j.ijfoodmicro.2026.111629}, pmid = {41534410}, issn = {1879-3460}, abstract = {Hákarl, the traditional Icelandic product obtained from the fermentation of Greenland shark (Somniosus microcephalus), represents a unique food item from both cultural and microbiological perspectives. This study investigated commercial samples of hákarl using an integrated approach, combining physico-chemical analyses, lipid and volatile profiling, metataxonomic sequencing, and microbial isolation. Results confirmed the alkaline nature of the product (pH ∼8) and a water activity (aw) of 0.96, sufficient to sustain an active and diverse microbial community. Lipid profiling revealed the predominance of monounsaturated fatty acids, with differences in PUFA and DHA levels between the analyzed producers, consistent with nutritionally favorable characteristics. Microbiological analysis highlighted bacterial communities dominated by Firmicutes, particularly Bacilli and Clostridia, with significant abundances of Tissierella creatinini and Atopostipes suicloacalis. Culture-dependent methods led to the isolation of Carnobacterium antarcticum cultures, which were subsequently characterized for their enzymatic activities. These findings suggest potential biotechnological applications of the isolates, especially in fermentation and aroma development. Volatile compound analysis identified thirteen VOCs including alcohols, aldehydes, ketones, phenols, sulfur- and nitrogen-containing compounds. Trimethylamine was the predominant metabolite responsible for the strong ammonia-like odor, followed by phenol and sulfur-containing compounds, which also contributed to the sensory profile. Overall, the results provide novel insights into the microbial ecology, physico-chemical traits, and volatile characteristics of hákarl, confirming its variability linked to artisanal production methods. The study emphasizes hákarl's role as a reservoir of pro-technological microorganisms and advances current understanding of the factors influencing its safety, quality, and identity as traditional fermented food.}, }
@article {pmid41533097, year = {2026}, author = {Huertas-Díaz, L and Hosek, J and Gram-Hansen, D and Frei, R and Roduit, C and Sasaki, M and Lauener, RP and Schwab, C and , }, title = {pH-Dependent Effects of Short-chain Carboxylic Acids and Buffer Systems On Clostridioides difficile in Vitro and in Vivo.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02694-6}, pmid = {41533097}, issn = {1432-184X}, abstract = {The spore-forming anaerobe Clostridioides difficile colonizes the highly dynamic gut environment early after birth, frequently without causing disease. In this study, we aimed to determine how environmental conditions indicative of the infant gut impacted prevalence and physiology of C. difficile. We examined the effect of pH, fermentation derived short-chain carboxylic acids (SCCA) and buffering systems combining in vitro and in vivo analysis, and experimental and modelling approaches. In vivo, the prevalence of Clostridioides significantly increased between 3 months (30.2%) and 12 months (56.2%) after birth. At 12 months, the occurrence of Clostridioides was the highest in feces with near neutral pH (6.7 (IQR 6.5‒7.3). In vitro, C. difficile showed pH-dependent growth and metabolic activity with an optimum around pH 5.8-6.3. Most SCCA conferred antimicrobial activity at pH 5.2 and 6.1 while at pH 6.5, high concentrations of SCCA promoted growth. The presence of phosphate buffer enhanced antimicrobial activity of SCCA, particularly at lower pH values (5.2-5.8). Two multilinear regression models indicated that ionic strength was inversely related to optical density in vitro, while in vivo, the abundance of Clostridioides was inversely linked to the presence of undissociated SCCA. Together, this study highlights that the that occurrence and performance of the opportunistic pathogen C. difficile was affected by chemical systems such as pH, the presence of buffer systems and concentration and chemical state of SCCA. Our results suggest novel targets that could be modulated to impact C. difficile colonization.}, }
@article {pmid41531331, year = {2026}, author = {Wu, H and Xu, S and Chen, Y and Yuan, Z and Yao, Y and Hao, J and Han, L}, title = {Phenazine-1-Carboxamide from Streptomyces Suppresses Phytophthora nicotianae via CDC48-Targeted Mitochondrial Disruption.}, journal = {Plant, cell &amp; environment}, volume = {}, number = {}, pages = {}, doi = {10.1111/pce.70383}, pmid = {41531331}, issn = {1365-3040}, support = {32272594//National Natural Science Foundation of China/ ; 2024QCY-KXJ-097//Technology Innovation Leading Program of Shaanxi/ ; }, abstract = {Phytophthora nicotianae is a plant-pathogenic oomycete, posing a serious threat to global agriculture due to its highly destructive infections and challenges in management. To explore a biologically based disease management strategy, we investigated Streptomyces ardesiacus HL-06, which produces phenazine-1-carboxamide (PCN), a potent anti-oomycete metabolite that effectively suppresses the growth of P. nicotianae in vitro and reduces tobacco black shank severity by over 80% under field conditions, surpassing the efficacy of commercial fungicides. Mechanistically, we identified CDC48, a AAA+ ATPase essential for mitochondrial homeostasis, as the direct molecular target of PCN. Drug affinity responsive target stability (DARTS), molecular docking, and isothermal titration calorimetry revealed that PCN binds to CDC48's ATPase domain, thereby disrupting mitochondrial protein quality control. This interaction leads to mitochondrial cristae loss, ATP synthase inhibition, and reactive oxygen species (ROS) accumulation, ultimately triggering oomycete apoptosis. This is the first report of a phenazine compound targeting a eukaryotic AAA+ ATPase, revealing a novel mode of action against oomycete pathogens. Our findings integrate microbial ecology with chemical biology, positioning PCN as a promising eco-friendly candidate for sustainable plant disease management.}, }
@article {pmid41531312, year = {2026}, author = {Boldt, J and Porten, C and Haeckl, FPJ and Hug, JJ and Panter, F and Steglich, M and Wink, J and Overmann, J and Göker, M and Krug, D and Müller, R and Nübel, U}, title = {Phylogeny-Aware Metabologenomics Accurately Assigns Natural Products to Biosynthetic Gene Clusters.}, journal = {Microbial biotechnology}, volume = {19}, number = {1}, pages = {e70298}, doi = {10.1111/1751-7915.70298}, pmid = {41531312}, issn = {1751-7915}, support = {09.720//Deutsches Zentrum f&#xfc;r Infektionsforschung/ ; }, mesh = {*Multigene Family ; *Biological Products/metabolism ; *Phylogeny ; *Biosynthetic Pathways/genetics ; *Metabolomics/methods ; Genomics/methods ; Mass Spectrometry ; }, abstract = {Tens of thousands of biosynthetic gene clusters (BGCs) have been identified in microbial genomes, but the vast majority of associated natural products (NPs) and their underlying biosyntheses remain unknown. Metabologenomics approaches integrate genomic and metabolomic datasets to statistically associate BGCs to their cognate NPs, yet often suggest many false links. Here, we show that incorporating information on the producer strains' phylogeny greatly improves accuracy. We sequenced 72 Sorangium spp. genomes (myxobacteria), predicting 2030 BGCs in 265 gene cluster families (GCFs). Mass spectrometry (MS[1]) revealed 99 metabolite families (MFs) from the same strains. Using a phylogeny-aware statistical analysis, we identified 43 high-confidence associations between GCFs and MFs, correctly including 89% of previously characterised links and reducing spurious associations by 33-fold, compared to simple correlational analysis. Our approach identified previously unknown BGCs for rowithocin and an undescribed poly-glycosylated NP. It also identified a distinct BGC associated with the production of chlorotonil C variants and refined the BGC for maracen. This study demonstrates the effectiveness of phylogeny-aware metabologenomics as a scalable strategy for NP discovery and biosynthetic pathway elucidation, and provides a roadmap to improved analyses of paired-omics data towards NP discovery.}, }
@article {pmid41528150, year = {2026}, author = {Guo, M and Xia, Z and He, X and Wan, S and Wang, Y and Fan, S and Pérez-Moreno, J and Yang, Z and Yang, C and Liu, D and Yu, F}, title = {High-throughput sequencing reveals endophytic bacterial differentiation of common truffles (Tuber spp.) in China: diversity, biogeographical patterns, and fungal health implications.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0186625}, doi = {10.1128/spectrum.01866-25}, pmid = {41528150}, issn = {2165-0497}, abstract = {UNLABELLED: As valuable hypogeous fungi, truffles depend on fruiting-body-associated microorganisms for lifecycle functions like growth and nutrient cycling. This study sampled fruiting bodies of 10 Tuber species from 16 sites across six major truffle-producing provinces in China, characterizing endophytic bacterial communities via high-throughput sequencing and multivariate analysis. Proteobacteria dominated the endophytic bacteria, with Bradyrhizobium as the prevalent genus. Significant genus-level compositional differences occurred across provenances and species: Bradyrhizobium reached 99.80% relative abundance in Tuber sinense from Mengzi, Yunnan, versus 7.90% in Tuber shii from Dali (12.6-fold difference). Shannon diversity indices (n = 48) revealed striking species- and altitude-related variations (P < 0.001): Tuber lijiangense (5.111) and T. shii (5.091) had the highest diversity, while T. sinense (1.336) had the lowest (3.8-fold gap). Subtropical Dali samples exhibited a sevenfold higher diversity compared to those from the Mengzi region, which is geographically closer to the tropics. Non-metric scaling and principal coordinates analysis identified environmental factors (soil, climate) and host species as primary drivers, with species effects potentially overriding environment. Five core taxa (all Rhizobiales) suggested nitrogen-fixing roles, while Variovorax (via linear discriminant analysis effect size) emerged as an external-disturbance-sensitive opportunist. This study clarifies endophytic bacterial variation patterns and drivers, identifies key taxa, and informs truffle ecological interactions, providing a scientific basis for sustainable resource management and conservation.<br><br>IMPORTANCE: This study underscores the critical importance of truffle endophytic bacteria in mediating fungal health and ecological resilience, addressing a major knowledge gap in hypogeous fungal microbiome research. By integrating high-throughput sequencing across 10 Tuber species in China, we reveal how bacterial communities (dominated by Bradyrhizobium) shape biogeographical patterns and functional roles like nitrogen fixation. These findings advance understanding of microbe-fungal symbioses, with direct applications for sustainable truffle cultivation (e.g., microbial inoculants) and climate-resilient management-aligning perfectly with AEM's focus on applied microbial ecology and biotechnological relevance.}, }
@article {pmid41524991, year = {2026}, author = {Ding, Q and Li, J and Xue, F and Cui, W and Hu, S and Yu, L and Huang, W and Li, L and Cheng, P}, title = {Distinct soil microbial community composition and structure: evidence from soil inside and outside the cattle farm.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {57}, number = {1}, pages = {31}, pmid = {41524991}, issn = {1678-4405}, support = {No. 32402941//National Natural Science Foundation of China/ ; No. 2308085QC108//Natural Science Foundation of Anhui Province/ ; No.rc392109//Talent research fund project of Anhui Agricultural University/ ; }, mesh = {*Soil Microbiology ; Cattle ; Animals ; Soil/chemistry ; *Bacteria/classification/genetics/isolation &amp; purification ; Manure/microbiology ; Farms ; *Fungi/classification/genetics/isolation &amp; purification ; *Microbiota ; Biodiversity ; }, abstract = {The contrast between the soils inside and outside the cattle farm may reflect the prolonged manure exposure within the farm, potentially creating distinct properties and microbial structure. However, comparative studies are scarce on the microbial composition and co-occurrence patterns between soils inside and outside the cattle farm. To address this gap, this study combined Illumina MiSeq sequencing with co-occurrence network analysis and soil physicochemical characterization to compare the microbial community structures between the two sites. The soil inside the cattle farm exhibited higher microbial alpha diversity than that outside the farm. Volcano plots revealed significant differences in the relative abundances of microbial taxa between sites. Notably, the relative abundances of Devosia was significantly higher inside the cattle farm, whereas Paenibacillus and Nitrospira were markedly higher outside the cattle farm (|log2FC| ≥ 1.2). The fungal network inside the cattle farm demonstrated higher complexity and stability than outside, with larger nodes and edges (Nodes: 194 vs. 153; Edges: 13231 vs. 8007) and superior topological characteristics. To elucidate the specific manure-induced environmental factors driving these differences, Mantel tests confirmed that soil organic carbon and alkali-hydrolyzable nitrogen significantly influenced the microbial communities. This study identifies the specific manure-derived drivers of microbial community structure and network stability, providing critical insights for utilizing cattle manure to improve soil microbial ecology and thereby contributing to sustainable agricultural management.}, }
@article {pmid41520335, year = {2026}, author = {Sang, J and Li, S and Xu, C and Pan, X and Zhu, Y and Li, Y and Ma, C and Zhang, Y and Chen, S and Qiu, Q and Si, H and Huang, Z and Wang, J and Jiao, J and Li, Z}, title = {Rumen microbiome biogeography and ventral epithelial architecture in three ruminant species.}, journal = {Cell reports}, volume = {45}, number = {1}, pages = {116779}, doi = {10.1016/j.celrep.2025.116779}, pmid = {41520335}, issn = {2211-1247}, abstract = {Ruminants thrive in diverse ecosystems by leveraging their rumen microbiome to ferment fibrous plants. However, the spatial biogeography of rumen microbiome and the genetic diversity of the ventral rumen epithelium remain unknown. Here, we present a multi-omics study in roe deer, sika deer, and sheep, integrating region-resolved microbiome and metabolome across 11 ruminal sacs, as well as single-cell RNA sequencing (scRNA-seq), assay for transposase-accessible chromatin using sequencing (ATAC-seq), and bulk RNA sequencing (RNA-seq) of ventral epithelium. We reveal species-specific microbial compositions and metabolic capacities contributing to differences in short-chain fatty acid and vitamin B production. We uncover functional divergence, genomic specialization, and metabolic changes across the microbiome of distinct ruminal sacs. Single-cell profiling reveals changes of immune responses and structural remodeling of the ruminal ventral epithelium. We demonstrate that vitamin B12 promotes epithelial growth and we identify genes enhancing stem cell differentiation. Our results highlight variation in microbial ecology and epithelial architecture among three ruminant species, offering insights to improve livestock productivity.}, }
@article {pmid41520281, year = {2026}, author = {Tang, TWH and Ullah, K and Lee, JJ and Chen, HC and Hsieh, PCH}, title = {Comparative insights into the gut-heart axis: cross-species and cross-population perspectives.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2611617}, pmid = {41520281}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Animals ; *Cardiovascular Diseases/microbiology ; *Heart/physiology ; Swine ; Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Host Microbial Interactions ; Species Specificity ; *Gastrointestinal Tract/microbiology ; Disease Models, Animal ; }, abstract = {Gut microbiota research has rapidly expanded our understanding of host-microbe interactions in cardiovascular diseases, yet translation of these insights remains challenged by species-specific differences and substantial population heterogeneity. In this review, we synthesize current evidence across rodents, swine, non-human primates, and multi-ethnic human cohorts to delineate conserved versus context-dependent features of the gut-heart axis. Rodent models remain indispensable for mechanistic discovery, enabling causal testing through germ-free, antibiotic-treated, and humanized microbiota platforms, whereas large-animal models better replicate human cardiac anatomy, physiology, and microbial ecology. Human studies provide essential clinical relevance, demonstrating that patients with myocardial infarction, coronary artery disease, atrial fibrillation, and heart failure harbor distinct microbial and metabolite signatures. However, these findings vary across populations due to differences in diet, lifestyle, host genetics, medication exposure, and environmental transitions. Despite taxonomic variability, several functional pathways, most notably short-chain fatty acid production, bile acid biotransformation, and aromatic amino acid metabolism generating molecules such as trimethylamine-N-oxide and phenylacetylglutamine, consistently associate with cardiovascular risk. At the same time, population-specific features, including glycan-microbe interactions shaped by ABO and FUT2 genotypes, diet-responsive metabolite profiles, and variable drug-microbiome interactions, highlight the importance of genetic and environmental context. By integrating cross-species and cross-population evidence, this review outlines a framework for identifying robust microbial pathways, clarifying their translational boundaries, and guiding the development of microbiota-informed diagnostics and interventions that account for biological, cultural, and environmental diversity.}, }
@article {pmid41519975, year = {2026}, author = {Christoffersen, SN and Østergaard, SK and de Jonge, N and Pertoldi, C and Sørensen, JG and Noer, NK and Kristensen, TN and Nielsen, JL and Bahrndorff, S}, title = {Arctic Insects Show a Highly Dynamic Microbiome Shaped by Abiotic and Biotic Variables.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02685-z}, pmid = {41519975}, issn = {1432-184X}, abstract = {Arctic regions are inhabited by terrestrial ectotherms that have adapted to an extreme environment where food resources are limited. The host associated microbiome may partly explain their ability to live under these conditions, but very little is known about the microbiome of Arctic ectotherms. We investigate how the bacterial community of the Greenlandic seed bug (Nysius groenlandicus) and damsel bug (Nabis flavomarginatus) is affected by different abiotic and biotic factors (time, acclimation temperature, humidity, and diet) under both field and laboratory conditions. We found large differences in the bacterial composition and diversity between the two species including species-specific presence of potentially symbiotic bacteria. The bacterial community of both species changed across the season, which may be explained by the changing climatic conditions, such as temperature and humidity. This was further supported by results from the laboratory experiments. We also found that diet changed the bacterial composition in both species and that bacteria could be transferred from prey to predator. Together, these results show that the bacterial community of some Arctic insects are highly dynamic and modulated by different abiotic and biotic factors, suggesting that the microbiome plays an important role for these organisms to persist in an extreme and resource-limited Arctic environment.}, }
@article {pmid41509481, year = {2026}, author = {Hallberg, ZF and Alvarez-Aponte, ZI and Gaudinier, AC and Taga, ME}, title = {Quenching corrinoid-based interactions in a model bacterial coculture.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41509481}, issn = {2692-8205}, abstract = {Microbial community structure is driven, in part, by the metabolic interdependencies of resident microbes. Thus, manipulating specific metabolic interactions represents one attractive way to both understand how microbial communities perform complex functions and alter them for therapeutic or environmental effects. However, it is not yet possible to control the availability of those metabolites produced by some members of the community that are required by others. Here, we report the development of a metabolite 'quenching' strategy that disrupts a specific metabolic interaction involving corrinoids, the vitamin B12 family of cofactors, by applying a high-affinity corrinoid-binding protein, BtuG, to bacteria engaged corrinoid cross-feeding. Using a model coculture composed of Sinorhizobium meliloti, a bacterium that produces a corrinoid (cobalamin), and an Escherichia coli strain engineered to be corrinoid-dependent, we demonstrate corrinoid quenching by sequestration of extracellular corrinoid and show that BtuG specifically blocks corrinoid-dependent growth. We use this tool to calculate the amount of cobalamin released by S. meliloti cells and find that the cobalamin release rate is dependent on the growth phase of the producer, increasing to a maximum of approximately 40 cobalamin molecules per minute per cell in late exponential phase. This work establishes a strategy to selectively block microbial interactions that may be more broadly applied to dissecting community structure and function. We expect that applying high-affinity 'molecular sponges' to quench nutrient sharing will allow for the identification of key nutrients that structure microbial communities and empower precision microbiome manipulation strategies.}, }
@article {pmid41292826, year = {2025}, author = {Backman, T and Cui, J and Caullireau, E and Bleak, E and Bezrukov, I and Girardi, P and Hawks, A and Lasky, JR and Latorre, SM and Erberich, JM and Lopez, L and Neumann, M and Perkins, AM and Symeonidi, E and Azadi, P and Horvath, MP and Muszyński, A and Lang, PLM and Karasov, TL and Burbano, HA}, title = {Persistent trade-offs balance competition and colonization across centuries.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41292826}, issn = {2692-8205}, support = {T32 GM007276/GM/NIGMS NIH HHS/United States ; T32 AI055434/AI/NIAID NIH HHS/United States ; R24 GM137782/GM/NIGMS NIH HHS/United States ; R35 GM138300/GM/NIGMS NIH HHS/United States ; R35 GM150722/GM/NIGMS NIH HHS/United States ; }, abstract = {Microbial competition drives rapid adaptation, often forcing organisms to specialize in new ecological niches. Adaptations that improve competitive ability can reduce performance in other environments creating trade-offs. Whether such trade-offs persist in nature-or are eroded as lineages adapt through compensatory changes-remains largely unknown. Here we show that a trade-off between competitive ability and host colonization has been stably maintained in natural Pseudomonas populations for centuries. Wild plant-pathogenic Pseudomonas compete using tailocins-phage-derived molecular weapons that bind to specific cell-surface receptors. Genomic surveys and functional assays reveal that the most broadly lethal tailocins remain rare-while the tailocin's production increases competitive killing, it also compromises plant colonization. We determine that the polymorphisms behind this trade-off are not transient - historical genomes spanning two centuries show that the trade-off has been maintained for at least 10[5]-10[6] generations. Our results demonstrate that, in natural populations, a trade-off between competition and pathogenicity is fundamental and not easily overcome.}, }
@article {pmid41518539, year = {2026}, author = {Kou, C and Li, D and Liu, Z and Gao, W and Zhang, W and Xiong, L and He, L and Li, M and Shu, A and Ma, J and Gao, Z}, title = {Rare Microbial Taxa Dominate the Microecological Landscape of Cadmium Exposure in Rice Rhizosphere.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02690-2}, pmid = {41518539}, issn = {1432-184X}, support = {2023YFD2301301, 2017YFD0301601//This study was supported by National Key R&amp;D Program of China/ ; 2023YFD2301301, 2017YFD0301601//This study was supported by National Key R&amp;D Program of China/ ; 2023YFD2301301, 2017YFD0301601//This study was supported by National Key R&amp;D Program of China/ ; 2023YFD2301301, 2017YFD0301601//This study was supported by National Key R&amp;D Program of China/ ; 2023YFD2301301, 2017YFD0301601//This study was supported by National Key R&amp;D Program of China/ ; 2023YFD2301301, 2017YFD0301601//This study was supported by National Key R&amp;D Program of China/ ; 2023YFD2301301, 2017YFD0301601//This study was supported by National Key R&amp;D Program of China/ ; 2023YFD2301301, 2017YFD0301601//This study was supported by National Key R&amp;D Program of China/ ; 2023YFD2301301, 2017YFD0301601//This study was supported by National Key R&amp;D Program of China/ ; 2023YFD2301301, 2017YFD0301601//This study was supported by National Key R&amp;D Program of China/ ; 2023YFD2301301, 2017YFD0301601//This study was supported by National Key R&amp;D Program of China/ ; 20232BAB215012//The Jiangxi Provincial Natural Science Foundation/ ; 20232BAB215012//The Jiangxi Provincial Natural Science Foundation/ ; 20232BAB215012//The Jiangxi Provincial Natural Science Foundation/ ; 20232BAB215012//The Jiangxi Provincial Natural Science Foundation/ ; 20232BAB215012//The Jiangxi Provincial Natural Science Foundation/ ; 20232BAB215012//The Jiangxi Provincial Natural Science Foundation/ ; 20232BAB215012//The Jiangxi Provincial Natural Science Foundation/ ; 20232BAB215012//The Jiangxi Provincial Natural Science Foundation/ ; 20232BAB215012//The Jiangxi Provincial Natural Science Foundation/ ; 20232BAB215012//The Jiangxi Provincial Natural Science Foundation/ ; 20232BAB215012//The Jiangxi Provincial Natural Science Foundation/ ; 42377309, 42407427//The National Natural Science Foundation of China/ ; 42377309, 42407427//The National Natural Science Foundation of China/ ; 42377309, 42407427//The National Natural Science Foundation of China/ ; 42377309, 42407427//The National Natural Science Foundation of China/ ; 42377309, 42407427//The National Natural Science Foundation of China/ ; 42377309, 42407427//The National Natural Science Foundation of China/ ; 42377309, 42407427//The National Natural Science Foundation of China/ ; 42377309, 42407427//The National Natural Science Foundation of China/ ; 42377309, 42407427//The National Natural Science Foundation of China/ ; 42377309, 42407427//The National Natural Science Foundation of China/ ; 42377309, 42407427//The National Natural Science Foundation of China/ ; SDAST2024QTA012//The Young Talent of Lifting engineering for Science and Technology in Shandong/ ; SDAST2024QTA012//The Young Talent of Lifting engineering for Science and Technology in Shandong/ ; SDAST2024QTA012//The Young Talent of Lifting engineering for Science and Technology in Shandong/ ; SDAST2024QTA012//The Young Talent of Lifting engineering for Science and Technology in Shandong/ ; SDAST2024QTA012//The Young Talent of Lifting engineering for Science and Technology in Shandong/ ; SDAST2024QTA012//The Young Talent of Lifting engineering for Science and Technology in Shandong/ ; SDAST2024QTA012//The Young Talent of Lifting engineering for Science and Technology in Shandong/ ; SDAST2024QTA012//The Young Talent of Lifting engineering for Science and Technology in Shandong/ ; SDAST2024QTA012//The Young Talent of Lifting engineering for Science and Technology in Shandong/ ; SDAST2024QTA012//The Young Talent of Lifting engineering for Science and Technology in Shandong/ ; SDAST2024QTA012//The Young Talent of Lifting engineering for Science and Technology in Shandong/ ; SKL81103//The Funding for the 'First Class Discipline' Construction Project of Shandong Agricultural University/ ; SKL81103//The Funding for the 'First Class Discipline' Construction Project of Shandong Agricultural University/ ; SKL81103//The Funding for the 'First Class Discipline' Construction Project of Shandong Agricultural University/ ; SKL81103//The Funding for the 'First Class Discipline' Construction Project of Shandong Agricultural University/ ; SKL81103//The Funding for the 'First Class Discipline' Construction Project of Shandong Agricultural University/ ; SKL81103//The Funding for the 'First Class Discipline' Construction Project of Shandong Agricultural University/ ; SKL81103//The Funding for the 'First Class Discipline' Construction Project of Shandong Agricultural University/ ; SKL81103//The Funding for the 'First Class Discipline' Construction Project of Shandong Agricultural University/ ; SKL81103//The Funding for the 'First Class Discipline' Construction Project of Shandong Agricultural University/ ; SKL81103//The Funding for the 'First Class Discipline' Construction Project of Shandong Agricultural University/ ; SKL81103//The Funding for the 'First Class Discipline' Construction Project of Shandong Agricultural University/ ; }, abstract = {Cadmium (Cd) contamination in soil is a growing problem, posing a significant threat to soil microorganisms and plant growth. Understanding how Cd exposure disrupts the evolution of soil microbial communities and the mechanisms underlying community remodeling requires further investigation. In this study, the rice rhizosphere treated with 0 (CK), 2.5 (LC), 5 (MC), and 15 (HC) mg kg[-1] Cd was used as a model and combined with 16S rRNA gene sequencing to systematically evaluate the response patterns of rice rhizosphere microbial communities under Cd gradient treatments. The study found that rice rhizosphere microbial communities responded to Cd exposure with a unimodal pattern of "low-promotion and high-suppression". LC treatment significantly increased the alpha diversity of rare fungal taxa and significantly enriched rare genera such as Candidatus Solibacter and Penicillium. Network analysis further confirmed that LC treatment significantly enhanced symbiotic relationships within and across rare taxa. The assembly of abundant bacterial and fungal taxa was consistently dominated by stochastic diffusional constraints, while rare taxa were primarily driven by deterministic homogeneous selection. In summary, rice rhizosphere microbial communities showed specific response patterns under Cd gradient treatment. Rare fungal taxa, as core members, actively responded to Cd exposure, made prominent contributions to shaping the community composition, and played a crucial role in maintaining the complexity and stability of the microbial network.}, }
@article {pmid41518434, year = {2026}, author = {Klammsteiner, T and Heussler, CD and Stonig, KT and Insam, H and Schlick-Steiner, BC and Steiner, FM}, title = {Stage-Specific Microbiota Transitions Throughout Black Soldier Fly Ontogeny.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02691-1}, pmid = {41518434}, issn = {1432-184X}, abstract = {The growing global population increases the demand for protein, while organic waste management has become more challenging. Alternative protein sources are essential to mitigate the environmental impact of food production. The black soldier fly (BSF; Hermetia illucens) has emerged as an alternative to traditional protein sources (e.g., soybean meal, fishmeal) due to its ability to convert diverse organic waste, addressing both issues simultaneously. This makes the BSF a promising candidate for industrial rearing, with its successful development closely tied to microbial influences on growth and behaviour, particularly bacterial influences on oviposition. In this study, we focus on the microbiota throughout insect development with a special focus on egg surface microbiota and their origin. We analysed the microbiota in the haemolymph and gut of larvae raised on sterilized and non-sterilized feed, pupal cell pulp, the wash of the ovipositor, eggs directly collected after oviposition, ovarian eggs, the empty female abdomen, eggs exposed to adult BSF, and surface-sterilized eggs. Our analysis revealed distinct bacterial community profiles across life stages, indicating a transition from larval dominance of Enterobacteriaceae to Burkholderiaceae on all analysed eggs. At the genus level, larval stages were characterized by Morganella, Escherichia, and Proteus, transitioning to less diverse communities in egg samples predominated by Burkholderia-Caballeronia-Paraburkholderia. Our study reveals that while predominant microbiota persist throughout all life stages, microbial community composition transforms progressively during maturation, particularly before oviposition. Understanding egg surface microbiota and the cues guiding oviposition has the potential to boost egg production and simplify mass harvesting of BSF larvae.}, }
@article {pmid41515900, year = {2025}, author = {Wu, J and Zhou, L and Qiu, D and Wei, T and Xie, C and Chen, E and Lin, M and Fan, Y}, title = {Integrating Bioinformatics and Experimental Validation Identifies SCD as a Ferroptosis-Related Immune Regulator and Therapeutic Target in Crohn's Disease.}, journal = {International journal of molecular sciences}, volume = {27}, number = {1}, pages = {}, doi = {10.3390/ijms27010019}, pmid = {41515900}, issn = {1422-0067}, support = {2025J011410//the Natural Science Foundation of Fujian Province/ ; 2025J08298//the Natural Science Foundation of Fujian Province/ ; }, mesh = {*Ferroptosis/genetics/immunology ; *Crohn Disease/genetics/immunology/metabolism/pathology/drug therapy ; *Computational Biology/methods ; Humans ; Animals ; Mice ; Disease Models, Animal ; Gene Expression Profiling ; Colitis/genetics/chemically induced/immunology ; }, abstract = {This study investigates the role of ferroptosis-related genes (FRGs) in the intestinal inflammation of Crohn's disease (CD). Through integrated bioinformatics and experimental validation, we identified differentially expressed genes from RNA-seq data and intersected them with known FRGs to obtain ferroptosis-related differentially expressed genes (FEDGs). Functional enrichment and immune infiltration analyses were performed, and seven hub FEDGs were selected using machine learning. A diagnostic model based on these genes showed strong predictive ability. Immune analysis revealed significant associations with macrophages, neutrophils, dendritic cells, and CD4+ T cells. Protein expression of key hub genes was validated in clinical CD samples and a DSS-induced colitis model. Importantly, localized inhibition of SCD alleviated disease severity in experimental colitis. These findings highlight the involvement of ferroptosis in CD immune dysregulation and propose SCD as a potential therapeutic target.}, }
@article {pmid41514812, year = {2026}, author = {Huang, Q and Chang, M and Sun, P}, title = {Early-Life Galacto-Oligosaccharide Supplementation Induces Persistent Immunoglobulin and Metabolic Alterations in Holstein Dairy Calves by Shaping Gut Microbiota.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {1}, pages = {}, doi = {10.3390/ani16010126}, pmid = {41514812}, issn = {2076-2615}, support = {2022YFD1301101//National Key Research and Development Program of China/ ; 2022YFD1300505//National Key Research and Development Program of China/ ; CARS-37//The earmarked fund for China Agriculture Research System/ ; Y2025YC52//Central Public-interest Scientific Institution Basal Research Fund/ ; ASTIP-IAS07//Agricultural Science and Technology Innovation Program/ ; }, abstract = {Early-life development of immune functions is crucial for calf health, growth, and future productivity. Galacto-oligosaccharides (GOSs) have been reported to facilitate ruminal microbial establishment and improve growth in Holstein dairy calves, but their prolonged influence on immunoglobulin levels, hindgut microbiota, and metabolic regulation remains insufficiently understood. This study evaluated the effects of early-life GOS supplementation on immune-related indicators, intestinal microbial ecology, and metabolic profiles in Holstein calves. Twenty-four newborn Holstein female dairy calves were randomly assigned to a control group (CON, n = 12) or a GOS group (GOS, n = 12; 10 g/day from birth to day 28). After supplementation ceased on day 28, calves previously receiving GOS were referred to as the GOSS group (n = 6). Immunoglobulin levels, gut microbiota, and fecal and serum metabolomes were evaluated during supplementation and six weeks after withdrawal. GOS supplementation significantly increased serum IgA and IgG levels during the treatment, with IgG levels remaining elevated for six weeks after discontinued supplementation. Although overall microbial diversity was not markedly altered, GOS selectively enriched bacterial taxa and function pathways linked to amino acid synthesis, unsaturated fatty acid production, and coenzyme-related metabolism. On day 70, GOSS group displayed distinct fecal and serum metabolomic profiles, with altered metabolites primarily associated with vitamin B6, folate, cobalamin metabolism, branched-chain amino acid biosynthesis, and purine and arginine pathways. These results demonstrate that early-life GOS supplementation promotes sustained immune and metabolic alterations following supplementation cessation, potentially mediated by modulation of gut microbial functions. These findings suggest that early dietary GOS supplementation may support physiological maturation in calves and could be useful as a nutritional strategy in calf-rearing systems.}, }
@article {pmid41514032, year = {2026}, author = {Roncero-Ramos, B and Romano-Rodríguez, E and Mateos-Naranjo, E and Valle-Romero, P and Redondo-Gómez, S}, title = {Hydro- and Xerohalophyte Species Drive Compositional and Functional Divergence in Bacterial Leaf Endosphere.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02679-x}, pmid = {41514032}, issn = {1432-184X}, support = {PAIDI-DOCTOR 21_00571//Junta de Andaluc&#xed;a/ ; FPU21/04133//Ministerio de Universidades/ ; FPU22/02078//Ministerio de Universidades/ ; PID2021-124750NB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; }, abstract = {Hydro- and xerohalophytes withstand stress thanks to the resistance traits they have, complemented with the functions of their associated microbiota. Besides, given a higher exposition of the phyllosphere to environmental conditions compared to roots, their endospheric bacteria should be more resistant to stress. In this study, we analysed the composition and functional traits of the bacterial leaf endosphere of six xero- and hydrohalophytes species in two seasons. We sequenced their endospheric metagenomes by shotgun and annotated genes related with Plant-Growth-Promoting (PGP) properties. We showed that the composition, structure and functions of the bacterial endosphere are mainly influenced by host plant species, followed by functional type. Moreover, plant species and functional type promoted a different relative abundance of, respectively, 62 and 6 PGP properties. This study shows that not only the composition but also the functionality of the bacterial leaf endosphere of halophytes is more influenced by host species than functional type. Moreover, the leaf endosphere of the different plant species and functional type could be an important source of bacteria with diverse PGP properties.}, }
@article {pmid41513996, year = {2026}, author = {Zhang, R and Mayer, L and Hikida, H and Shichino, Y and Mito, M and Willemsen, A and Iwasaki, S and Ogata, H}, title = {A giant virus forms a specialized subcellular environment within its amoeba host for efficient translation.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {41513996}, issn = {2058-5276}, support = {JP18H02279//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP22H00384//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP23KJ1258//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP24H02307//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JPMJFS2123//MEXT | Japan Science and Technology Agency (JST)/ ; }, abstract = {Many eukaryotic viruses, including amoeba-infecting mimiviruses, have codon usage that deviates from their hosts. However, codon usage patterns that align with the cellular tRNA pool enable efficient translation. How these viruses cope with the mismatch between tRNA supply and demand is unclear. Here we show that Acanthamoeba polyphaga mimivirus (APMV) generates a subcellular area to translate viral mRNAs. tRNA sequencing showed that the tRNA pool was not substantially altered during the infection, even though the virus encodes tRNA genes. Using in situ labelling, we found that viral mRNAs and newly synthesized proteins were localized in the periphery of the viral factory, suggesting that APMV creates a discrete subcellular environment to facilitate translation. Frequently used codons in viral mRNAs had higher tRNA accessibility than the same type of codons in amoeba mRNAs. Our data show how local translation assists the virus in overcoming the mismatch between tRNA supply and demand.}, }
@article {pmid41513647, year = {2026}, author = {Lu, Y and Eisenhauer, N and Patoine, G and Chen, Y and Heintz-Buschart, A and Küsel, K and Wegner, CE and Buscot, F and Liu, X and Araujo, ASF and Frey, B and Maestre, FT and Vadeboncoeur, M and van den Brink, L and Ponette, Q and Didion, M and Wohlfahrt, G and Gaxiola, A and Branquinho, C and Meesenburg, H and Fukuzawa, K and Adair, EC and Andrić, A and Barna, M and Bei, Q and Bruelheide, H and Caliman, A and Canessa, R and Carbognani, M and Cazzolla Gatti, R and Chen, C and Christiansen, CT and Danger, M and Davydov, EA and de Graaff, MA and Delire, C and Cecco, VD and Martino, LD and Djukic, I and Drollinger, S and Enoki, T and Fekete, I and Fransson, P and Freitag, M and Frenzel, M and Gavilán, RG and Glatzel, S and Glushkova, M and González, G and Gripp, ADR and Haase, P and Hamer, U and Hishi, T and Hiura, T and Hornung, E and Hoshizaki, K and Jäger, H and Jiménez, JJ and Kelly-Slatten, MJ and Kepfer-Rojas, S and Kotroczó, Z and Kriiska, K and Kurokawa, H and Lajtha, K and Loehr, J and Löfgren, S and Maire, V and Martins, RL and Maunoury-Danger, F and Melece, I and Ochoa, V and Ostonen, I and Paquette, A and Parker, WC and Peri, PL and Mast, R and Petraglia, A and Petřík, P and Pușcaș, M and Rebmann, C and Reich, PB and Rillig, MC and Schädler, M and Schaub, M and Schmidt, A and Seeber, J and Serrano, HC and Sousa, AI and Scheu, S and Stefanski, A and Tomaselli, M and Tóth, Z and Trevathan-Tackett, SM and Trogisch, S and Turtureanu, PD and Ursu, TM and Venn, SE and Verstraeten, A and Vijayanathan, J and Vujanović, D and Wagner, M and Weih, M and Zehetner, F and Guerra, CA}, title = {Landscape effects on global soil pathogenic fungal diversity across spatial scales.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-025-67929-5}, pmid = {41513647}, issn = {2041-1723}, support = {EI 862/29-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, abstract = {Growing evidence has shown that, apart from local environmental factors, changes in landscape-level factors by accelerated land-use change can also shape soil pathogenic fungal diversity. However, the global representativeness of such patterns remains unclear. Here, we assess how pathogenic fungal diversity in 511 soil samples worldwide responds to landscape factors, including landscape complexity index based on eight landscape metrics and quantity of different land cover types across six spatial scales (i.e., surrounding landscape, 250 m to 10,000 m radii from the sampling coordinate). We find that while soil variables explain over half of the variance, pathogenic fungal alpha diversity increases with landscape complexity and crop cover proportion, but decreases with grass and tree cover proportion, together explaining 23.4% of the total variance. Landscape factors have weaker impacts on beta diversity, explaining 13.0% of the variance. Across spatial scales, grassland ecosystems exhibit increasingly stronger responses to landscape variables compared to forest ecosystems. Landscape factors have a higher relative contribution to root-associated fungi than leaf/fruit/seed-associated fungi. Our results emphasize the importance of local factors and the complementary role of landscape patterns in shaping global soil pathogenic fungal distributions, highlighting scale-dependent effects across ecosystems and fungal functional groups.}, }
@article {pmid41511110, year = {2026}, author = {Gallardo Molina, P and Choi, BI and Vanek, M and Khan, MH and Tomasek, K and Kwant, AN and Dijkstra, P and de Vos, MGJ and Wolfe, AJ}, title = {SimUrine: a novel, fully defined artificial urinary medium for enhanced microbiological research of urinary bacteria.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0155925}, doi = {10.1128/aem.01559-25}, pmid = {41511110}, issn = {1098-5336}, abstract = {UNLABELLED: Urinary tract infections represent one of the most prevalent bacterial diseases, yet current diagnostic and research methodologies are hampered by inadequate culture media that fail to replicate the bladder biochemical environment. Conventional artificial urine formulations contain undefined components, lack essential nutrients, or inadequately support urinary microbiome (urobiome) growth. To address these limitations, we developed SimUrine, a fully defined synthetic urine medium that aims to replicate human bladder chemistry while supporting diverse microbial growth requirements. SimUrine was systematically developed through iterative optimization of multi-purpose artificial urine, incorporating defined concentrations of carbon sources, vitamins, trace elements, and amino acids within physiologically relevant ranges. The modular design enables component substitution without complete reformulation, facilitating customization for culturomics, antimicrobial susceptibility testing, and microbial ecology studies, while reducing batch-to-batch variability associated with authentic urine. Performance evaluation demonstrated SimUrine's capability to support the growth of fastidious urobiome members, including Lactobacillus species, Aerococcus urinae, and Corynebacterium riegelii, which fail to proliferate in conventional minimal media. Physicochemical characterization confirmed that SimUrine formulation exhibits properties within normal human urine ranges for density, conductivity, osmolarity, and viscosity, ensuring physiological relevance. Clinical applications revealed reduced antibiotic susceptibility compared to standard media, suggesting a more accurate representation of in vivo conditions. Co-culture experiments using Escherichia coli and Enterococcus faecalis demonstrated previously unobserved microbial interactions, highlighting SimUrine's utility for investigating urobiome dynamics. SimUrine represents a significant advancement in urobiome research methodology, providing a standardized, reproducible platform for investigating the urobiome under physiologically relevant conditions, potentially improving fundamental understanding and clinical diagnostic approaches.<br><br>IMPORTANCE: Urinary tract infections (UTIs) affect millions globally, yet current research and diagnostic methods rely on inadequate culture media that fail to replicate the bladder's unique biochemical environment. This fundamental limitation has hindered accurate UTI research and potentially compromised clinical treatment decisions. SimUrine addresses this critical gap as the first fully defined synthetic urine medium that mimics human bladder chemistry while supporting the growth of diverse urinary microbes. The breakthrough enables the cultivation of urobiome organisms in a minimal medium that resembles natural conditions, revealing novel microbial interactions that influence urinary health. Crucially, SimUrine demonstrates different antimicrobial susceptibility patterns compared to standard clinical media, suggesting current testing protocols may inaccurately predict treatment outcomes. This standardized, reproducible platform eliminates the variability of authentic urine samples while maintaining physiological relevance, potentially transforming urobiome research methodology and providing a new tool for the study of UTIs worldwide.}, }
@article {pmid41508507, year = {2026}, author = {Lee, G and Heo, S and Jeong, DW}, title = {Origin and prevalence of food-derived coagulase-negative staphylococci in fermentation: impact of protein, lipid, salt, and pH conditions.}, journal = {Food research international (Ottawa, Ont.)}, volume = {225}, number = {}, pages = {118096}, doi = {10.1016/j.foodres.2025.118096}, pmid = {41508507}, issn = {1873-7145}, mesh = {*Staphylococcus/isolation &amp; purification/classification/enzymology/metabolism ; Hydrogen-Ion Concentration ; *Fermentation ; *Food Microbiology ; *Fermented Foods/microbiology ; Coagulase/metabolism ; Sodium Chloride/analysis ; }, abstract = {Coagulase-negative staphylococci (CNS) are primarily detected in protein-rich and high-salt fermented foods, such as fermented meat and soybean products. This review investigates the relationship between CNS species and the nutritional and physicochemical properties of fermented foods, focusing on protein, fat, carbohydrate composition, salt concentration, and pH. Published studies over the past 20 years were systematically analyzed to identify CNS species and their distribution across food types and regions. Among the species, Staphylococcus saprophyticus, S. xylosus, S. equorum, and S. gallinarum were most frequently reported. S. saprophyticus was detected across a broad range of conditions, whereas S. xylosus was more common in acidic environments (pH 4-6). S. equorum dominated in higher pH (5-8) and high-salt (>20%) conditions, whereas S. gallinarum persisted even in salt concentrations exceeding 15%. These findings indicate that nutrient composition, pH, and salt concentration shape the dominant CNS species in fermented foods. Such correlations not only improve our understanding of microbial ecology in fermentation but also provide a basis for the selection and application of tailored starter cultures in the food industry.}, }
@article {pmid41506929, year = {2026}, author = {Rodríguez-Gijón, A and Laso-Pérez, R}, title = {Deep-learning dive into the antimicrobial potential of Archaea.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2025.12.004}, pmid = {41506929}, issn = {1878-4380}, abstract = {The global burden of antimicrobial resistance demands the urgent development of new antibiotics. To face this threat, Torres et al. leveraged deep-learning models to identify archaeal encrypted peptides (termed 'archaeasins') with potential antimicrobial activity. This work highlights Archaea as an underexplored but potentially rich source of antibiotics.}, }
@article {pmid41506577, year = {2026}, author = {Sagar, K and Priti, K and Chandra, H}, title = {Artificial intelligence in metagenome-assembled genome reconstruction: Tools, pipelines, and future directions.}, journal = {Journal of microbiological methods}, volume = {}, number = {}, pages = {107390}, doi = {10.1016/j.mimet.2026.107390}, pmid = {41506577}, issn = {1872-8359}, abstract = {Metagenomic sequencing has revolutionised the field of microbial ecology, as it has led to cultivation-independent exploration of complicated microbial communities. The assembly of metagenome-assembled genomes has provided genome-scale information about uncultivated microorganisms, but issues such as sequencing errors, fragmented assemblies, residual redundancy, uneven coverage, recovery of low-abundance taxa, and highly diversified taxa continue to impair the quality of these genomes. The latest achievements in artificial intelligence, particularly in machine learning and deep learning, have played a significant role in overcoming these limitations by enhancing quality control, error correction, assembly, binning, refinement, and annotation procedures. It is demonstrated that representation learning and graph-based binning methods have high strain-level resolution and can reduce contamination in complex microbial communities, whereas artificial intelligence-based assemblers and polishing tools improve base-level precision and assembly contiguity. This review synthesises traditional and artificial intelligence-based workflows involved in the reconstruction of metagenome-assembled genomes, encompassing quality control, assembly, binning, refinement, and annotation, as well as quantitative benchmarking of significant artificial intelligence-based pipelines. As future directions, the focus on emerging trends, such as explainable artificial intelligence, federated learning, cloud-native scalable pipelines, multimodal and multi-omics integration, and large language model-based annotation, is covered. In general, the incorporation of artificial intelligence represents a paradigm shift in the reconstruction of metagenome-assembled genomes, allowing for a more relevant, scalable, and biologically informative search of the microbial dark matter in various ecosystems.}, }
@article {pmid41504899, year = {2026}, author = {Cottorello-Fonsêca, M and Rezende, EGF and Freitas, FRS and Carneiro, RB and Sakamoto, IK and Ribeiro, R and Zaiat, M}, title = {Understanding the kinetics of antibiotic mixture biotransformation and microbial interactions in an anaerobic fixed-bed reactor for wastewater treatment.}, journal = {Bioprocess and biosystems engineering}, volume = {}, number = {}, pages = {}, pmid = {41504899}, issn = {1615-7605}, support = {2020/15087-8//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 22/04367-5//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2019/22532-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2020/15087-8//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; Financial Code 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; PCI2022-121990//EU and the State Research Agency (AEI)/ ; PCI2022-121990//EU and the State Research Agency (AEI)/ ; 869178//ERA-NET AquaticPollutants Joint Transnational Call/ ; 869178//ERA-NET AquaticPollutants Joint Transnational Call/ ; }, abstract = {The increase of antibiotics in aquatic environments, along with the emergence of antibiotic-resistant bacteria, highlights the improvement of wastewater treatment technologies. This study investigates a plug-flow structured anaerobic fixed-bed reactor (PF-AnFBR) for removal nine antibiotics representing different classes-an approach rarely explored in anaerobic systems. By integrating spatially resolved sampling along the reactor bed with advanced kinetic modeling, the study provides the first mechanistic evaluation of antibiotic mixture removal in a PF-AnFBR. COD removal remained high (COD > 97%) despite the presence of antibiotics, and significant removal was observed for trimethoprim (100%), sulfamethoxazole (83.3%), and enrofloxacin (81.3%). The first-order model accurately described COD removal, while the reversible biotransformation model (RevBio) successfully captured antibiotic fate (NRMSE < 3.5%), revealing class-specific mechanisms: fluoroquinolones dominated by adsorption (high KD and ksor), sulfonamides exhibiting reversible biotransformation, and trimethoprim characterized by highly irreversible biotransformation. Microbial community and KEGG-based functional analyses identified key taxa (e.g., Pseudomonas, Lactivibrio, Syntrophorhabdus, Methanothrix) and metabolic pathways (ABC transporters, cytochrome P450 enzymes) responsible for antibiotic transformation. By coupling reactor hydrodynamics, kinetic modeling, and microbial ecology, this study provides novel mechanistic insight into the removal of complex antibiotic mixtures in anaerobic fixed-bed reactors and supports PF-AnFBR as a robust technology for decentralized wastewater treatment.}, }
@article {pmid41504158, year = {2025}, author = {Chen, T and Guo, Y and Liang, D and Li, D and Xing, S and Li, D and Zhang, C and Wang, F}, title = {Discriminative Gut Microbial Signatures in Hyperuricemia and Overweight Populations Revealed by Metagenomic Sequencing.}, journal = {International journal for vitamin and nutrition research. Internationale Zeitschrift fur Vitamin- und Ernahrungsforschung. Journal international de vitaminologie et de nutrition}, volume = {95}, number = {6}, pages = {42590}, doi = {10.31083/IJVNR42590}, pmid = {41504158}, issn = {0300-9831}, support = {S2023KFKT-12//Ministry of Agriculture and Rural Affairs/ ; 2024YFF1107000//National Key Research and Development Program of China/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Hyperuricemia/microbiology ; Male ; Female ; *Overweight/microbiology ; Middle Aged ; Cross-Sectional Studies ; Feces/microbiology ; Adult ; Metagenomics ; Metagenome ; }, abstract = {BACKGROUND: This cross-sectional study aimed to investigate the relationships between gut microbiota compositional alterations and chronic metabolic disorders by analyzing taxonomic diversity, community structure, and species-level differences in individuals with hyperuricemia (HUA) and a history of being overweight. Our findings offer novel insights into microbiota-targeted therapeutic strategies for managing metabolic diseases. A total of 144 participants were recruited and divided into three diagnostic categories: healthy controls (HL, n = 29), hyperuricemia group (HU, n = 24), and overweight (OW, n = 91).<br><br>METHODS: Comprehensive phenotypic profiles and metagenomes were analyzed for fecal samples from the three groups.<br><br>RESULTS: Significant differences were observed in psychological states and microbial ecology between the metabolic disorder groups (HU and OW) and the control group (HL) (p < 0.05). Both the overweight individuals and those with HUA presented significant changes in gut microbial composition, with reduced &#x3b1;-diversity indices (Shannon index: HU vs HL Mann-Whitney U = 306; p = 0.462; OW vs HL Mann-Whitney U = 1008; p = 0.040; richness index: HU vs HL Mann-Whitney U = 307; p = 0.469; OW vs HL Mann-Whitney U = 1072; p = 0.092) compared to healthy individuals. Moreover, analysis of the linear discriminant analysis effect size (LEfSe) identified four discriminatory species in the HU group (Alistipes putredinis, Mediterraneibacter faecis, Streptococcus oralis, and Gemella sanguinis), and five in the OW group (Pantoea endophytica, Pantoea vagans, Phocaeicola coprophilus, Ruminococcus SGB4421, and Klebsiella oxytoca), representing potential biomarkers for the progression of chronic metabolic diseases.<br><br>CONCLUSION: This study elucidates the characteristics of overweight individuals and those with HUA in terms of phenotypic features and gut microbiota, providing a theoretical reference for gut microbiota-targeted therapies and lifestyle interventions in chronic metabolic diseases.}, }
@article {pmid41502987, year = {2026}, author = {Mohan, R and Johnson, SD and Dean, PN and Acharya, A and Byrareddy, SN}, title = {Methods to characterize the vaginal microbiome in a rhesus macaque model of simian human immunodeficiency virus (SHIV) transmission uncover epithelium-associated enrichment of Prevotella.}, journal = {Current research in microbial sciences}, volume = {10}, number = {}, pages = {100526}, pmid = {41502987}, issn = {2666-5174}, abstract = {The vaginal microbiome plays a crucial role in maintaining mucosal integrity and mitigating pathogen transmission, yet its comprehensive characterization remains challenging due to limited sampling and analysis methods. In this study, we aimed to characterize bacterial and fungal taxa diversities in the vaginal microbiomes of Simian Human Immunodeficiency (SHIV)-infected rhesus macaques, as well as their metabolic activities, using three sampling methods. The cervicovaginal lavage (CVL), vaginal swab, and vaginal mucosal tissue methods offer novel insights into microbial diversity and their potential impacts on HIV transmission. Using 16S rRNA and Internal Transcribed Spacer (ITS) sequencing, we assessed bacterial and fungal community composition and abundances, respectively, across all sampling methods. PICRUSt2 was used for functional predictions, and a modified glycosidase assay to further characterize glycan-degrading enzymatic activity in CVL samples. Our findings reveal that tissue samples were uniquely enriched for microbial taxa such as Prevotella spp. and Helicobacter spp., showing notable abundance differences compared to CVL and swab samples. Tissue samples exhibited higher alpha diversity and distinct metabolic prediction profiles, particularly elevated sialidase activity. While fewer differences were found in fungal microbiome composition and diversity, marked correlations were observed between bacterial and fungal taxa, emphasizing complex interkingdom interactions. These results highlight the significance of sampling methods in microbial ecology studies, which should be carefully considered due to their potential influence on pathogen transmission risk.}, }
@article {pmid41502854, year = {2025}, author = {Su, JW and Qin, SY and Liu, J and Lei, CC and Zhang, XT and Shi, WH and Xie, LH and Liu, Y and Ni, HB and Yu, MY and Liang, HR and Qin, Y and Jiang, J and Sun, HT and Ma, H and Li, ZY and Zhang, XX}, title = {Blastocystis presence alters gut archaeal communities and metabolic functions in Tibetan antelopes (Pantholops hodgsonii).}, journal = {Frontiers in veterinary science}, volume = {12}, number = {}, pages = {1744013}, pmid = {41502854}, issn = {2297-1769}, abstract = {BACKGROUND: Archaea are vital members of the gut microbiota, yet their diversity and functions in high-altitude wildlife remain poorly understood. Understanding their ecological roles can provide insights into host health and microbial community dynamics.<br><br>METHODS: We applied metagenome-assembled genome (MAG)-based approaches to investigate gut archaea in Tibetan antelopes (Pantholops hodgsonii) and assess their shifts in the presence of Blastocystis. A total of 463 non-redundant archaeal MAGs were reconstructed and analyzed for taxonomic diversity and functional potential.<br><br>RESULTS: The MAGs encompassed 16,189 protein clusters, with over 70% representing potentially novel species, highlighting substantial unexplored archaeal diversity. Alpha diversity showed no significant differences between healthy and Blastocystis-present groups, but beta diversity analysis revealed marked community restructuring, including decreased Methanobacteriota and increased Halobacteriota and Thermoplasmatota in the Blastocystis-present group. Functional annotation indicated changes in energy and nucleotide metabolism and alterations in carbohydrate-active enzyme composition. Additionally, putative viral sequences were detected within archaeal MAGs, suggesting potential virus-microbe interactions.<br><br>CONCLUSION: Our findings provide novel insights into the diversity and ecological functions of gut archaea in Tibetan antelopes, offering a foundation for future research on their contributions to host health and microbial ecology.}, }
@article {pmid41501262, year = {2026}, author = {Carofano, I and Martinez-Sañudo, I and Riegler, M and Hancock, DL and Morrow, JL and Mazzon, L}, title = {Detection of a Conserved Bacterial Symbiosis in non-frugivorous Australian Fruit Flies (Diptera, Tephritidae, Tephritinae) Supports its Widespread Association.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02686-y}, pmid = {41501262}, issn = {1432-184X}, support = {DOR2271053/22//Universit&#xe0; degli Studi di Padova/ ; }, abstract = {Several insect lineages, including some fruit flies, have evolved mutualistic associations with primary symbiotic bacteria. Some species of Tephritinae, the most specialized subfamily of fruit flies (Diptera, Tephritidae) harbour co-evolved, vertically transmitted and non-culturable bacterial symbionts in their midgut, known as Candidatus Stammerula spp. (Enterobacteriaceae). While such associations have previously been reported in the Palearctic and Hawaiian Archipelago, their occurrence in Australasia had not been investigated. In this study we assessed the genetic diversity of eight Australian fruit fly's species from six genera belonging to the Tephritini tribe using mitochondrial markers (16 S rRNA and COI-tRNALeu-COII genes) and compared their bacterial diversity using the 16 S rRNA gene. We detected the presence of specific symbiotic bacteria in all sampled species. Analysis of bacterial 16 S rRNA showed that, with one exception, all Australian symbionts clustered in a well-supported monophyletic clade with Ca. Stammerula detected in Palearctic and Hawaiian Tephritini. Distinct Stammerula lineages were identified in several taxa, while two species, Trupanea prolata and Spathulina acroleuca shared identical symbiont sequences and the same host plant. Notably, Australian and Palearctic Sphenella spp. harboured closely related symbionts. The cophylogenetic analysis revealed a substantial congruence between host and symbiont tree, supporting a history of cospeciation and suggesting biogeographic links between Australasian and Palearctic taxa. Overall, the results expand the geographic knowledge of Tephritini-Ca. Stammerula association and highlight a global pattern of co-diversification.}, }
@article {pmid41499160, year = {2026}, author = {Hai, Q and Li, D and Huang, T and Dang, X and Xu, J and Ma, Z and Zhou, Z}, title = {The Honeybee Gut Microbiome: A Novel Multidimensional Model of Antimicrobial Resistance Transmission and Immune Homeostasis from Environmental Interactions to Health Regulation.}, journal = {FEMS microbiology reviews}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsre/fuag001}, pmid = {41499160}, issn = {1574-6976}, abstract = {The honeybee gut microbiome has emerged as a model system in microbial ecology, valued for its structural stability and host specificity, and has garnered significant attention for elucidating universal principles of host-microbe interactions. This review advocates for the honeybee as a multidisciplinary model organism, highlighting the unique role of its gut microbiota in maintaining colony immune homeostasis, driving host co-evolution, unraveling the transmission mechanisms of antibiotic resistance genes (ARGs), and enhancing host adaptability to environmental stressors. By integrating multidimensional factors, including environmental gradients and apicultural practices, we construct an "Environment-Microbiota-Host Health" interaction framework to transcend the limitations of single-factor analyses. This framework provides a novel paradigm for the ecological containment of antimicrobial resistance, the conservation of pollinator resources, and microbiome-based engineering interventions. The review underscores the unique value of the honeybee model in unraveling social insect-microbe coevolution and resistance transmission dynamics, while also prospecting its application potential in developing novel antimicrobial peptides, designing probiotic formulations, and monitoring environmental resistance.}, }
@article {pmid41499039, year = {2026}, author = {Madjirebaye, P and Penga, Z and Mueeda, A and Huang, T and Peng, F and Muyan, X and Liua, Z and Mahamat, B and Allasra, Y and Xu, Y and Xiong, T and Xie, M}, title = {Unraveling Streptococcus Thermophilus NCU074001-Based Anti-Diarrheal Actions Via Integrated Immune-Gut Microbiota and Tryptophan Metabolic Pathway Identification.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {41499039}, issn = {1867-1314}, support = {Project No. 20243BCC31004; Project No. S20251709//Key Research and Development Projects of Jiangxi Province/ ; Project No. 20232BCD44005//National Key Laboratory Project/ ; Project No. 2022-PYXM-04//), Jiangxi Medicine Academy of Nutrition and Health Management 2022 Cultivation project/ ; Project No. JXNK202303-05//Agricultural key core technology research project of Jiangxi Province/ ; Project No. JXARS-06//Vegetable Industry Technology System Post Expert Project of Jiangxi Province/ ; Project No. ZDYF2024XDNY277//the Hainan Provincial Key Research and Development Project/ ; }, abstract = {Diarrhea, a common gastrointestinal disorder, is often exacerbated by conventional antibiotic treatments that disrupt gut microbiota, necessitating the exploration of Lactic acid bacteria (LAB) alternatives. This study investigates the therapeutic potential and mechanisms of Streptococcus thermophilus NCU074001 (ST) in a rat model of PEG3350-induced osmotic diarrhea. ST treatment mitigated diarrheal symptoms and improved key markers of intestinal health by acting as a key modulator of the gut ecosystem. Its efficacy was driven by balancing immune responses via elevated IL-10 and suppressed pro-inflammatory cytokines (IL-6, IL-1β, TNF-α, IFN-γ). Furthermore, ST reinforced the intestinal barrier by upregulating MUC2 expression and reshaping gut microbial ecology by suppressing certain genera (Bacteroides and Anaerofilum) while enriching others (Lactobacillus, Akkermansia, Phascolarctobacterium, and Parabacteroides). This taxonomic restoration was accompanied by a functional metabolic shift, characterized by increased production of short-chain fatty acids (acetate and butyrate) and a targeted modulation of tryptophan metabolism that enhanced the production of anti-inflammatory indole derivatives. Correlation analyses suggested potential links between ST-mediated microbiota remodeling and barrier strengthening and immunomodulation. Collectively, these results indicate that ST functions as a promising probiotic integrating immunomodulation, microbiota restoration, and metabolic reprogramming to alleviate diarrhea, and thus presents a promising therapeutic alternative to conventional antibiotics.}, }
@article {pmid41495312, year = {2026}, author = {Kiran, R and Sharma, M and Subramanian, S and Patil, SA}, title = {Halophilic Anaerobic Cultures Enriched with CO2:H2 from Different Saline Environments Reveal Unknown Autotrophic Bacterial Diversity and Modular Carbon Fixation Pathways.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02654-6}, pmid = {41495312}, issn = {1432-184X}, abstract = {The subsurface sediments of saline-aquatic systems host diverse microbes, with unclear ecological roles and challenging lab cultivability. Chemolithotrophic anaerobes involved in CO2-fixation are one of the poorly studied groups. This study focused on understanding these bacteria from subsurface sediments of four representative saline environments, two marine (i.e., Coastal Arabian and Bay of Bengal seas) and two lake (Sambhar and Lonar) systems through enrichment and metagenomics. Enrichment cultures with bicarbonate/CO2 and hydrogen as the carbon and energy sources, respectively, showed CO2 fixation, producing acetic and formic acids as the major organic products. Enriched culture with Sambhar Lake sediment produced more formic acid (391 ± 8 mg/L) than acetic acid (92 ± 20 mg/L); however, other enriched cultures produced considerably higher acetic acid (up to 966 ± 24 mg/L) than formic acid (up to 367 ± 30 mg/L). The organics production was accompanied by unique thread-like (up to 500 μm long) aggregates, harbouring chains of rod and oval-shaped microbes in all cultures. Metagenome sequencing revealed dominance of Vibrio spp. (relative sequence abundance of 91% to 97%) across all cultures, while canonical CO2-fixing taxa were nearly absent (< 0.01%). KEGG analysis revealed partial genes for various CO2 fixation pathways, including Wood-Ljungdahl, reverse-TCA, dicarboxylate-hydroxybutyrate, hydroxypropionate bicycle, hydroxypropionate-hydroxybutyrate, and the reductive-glycine pathway. The presence of a near-complete serine variant of the reductive glycine pathway, which has been demonstrated in engineered systems, suggests that this pathway may play an operational role in natural systems. The consistent production of organic acids and incomplete pathway representation suggests modular CO2 fixation within the Vibrio-dominated enriched mixed cultures.}, }
@article {pmid41493483, year = {2026}, author = {Sharma, N and Pal, J and Mahajan, R and Chandel, S and Sud, D and Sanspal, A}, title = {Pathogens without borders: a review on cross-kingdom transmission strategies and pathogenicity of plant and human pathogens.}, journal = {Archives of microbiology}, volume = {208}, number = {2}, pages = {98}, pmid = {41493483}, issn = {1432-072X}, }
@article {pmid41493101, year = {2026}, author = {Hoffert, M and Gorman, E and Lladser, ME and Fierer, N}, title = {Constructing a "periodic table" of bacteria to map diversity in trait space.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf289}, pmid = {41493101}, issn = {1751-7370}, abstract = {Despite an ever-expanding number of bacterial taxa being discovered, many of these taxa remain uncharacterized with unknown traits and environmental preferences. This diversity makes it challenging to interpret ecological patterns in microbiomes and understand why individual taxa, or assemblages, may vary across space and time. Although we can use information from the rapidly growing databases of bacterial genomes to infer traits, we still need an approach to organize what we know, or think we know, about bacterial taxa to match taxonomic and phylogenetic information to trait inferences. Inspired by the periodic table of the elements, we have constructed a "periodic table" of bacterial taxa to organize and visualize monophyletic groups of bacteria based on the distributions of key traits predicted from genomic data. By analyzing 50 745 genomes across 31 bacterial phyla, we used the Haar-like wavelet transformation, a model-free transformation of trait data, to identify clades of bacteria which are nearly uniform with respect to six selected traits - oxygen tolerance, autotrophy, chlorophototrophy, maximum potential growth rate, GC content, and genome size. The identified functionally uniform clades of bacteria are presented in a concise periodic table-like format to facilitate identification and exploration of bacterial lineages in trait space. While our approach could be improved and expanded in the future, we demonstrate its utility for integrating phylogenetic information with genome-derived trait values to improve our understanding of the bacterial diversity found in environmental and host-associated microbiomes.}, }
@article {pmid41492298, year = {2025}, author = {Jones, MK and Morris, D and Zhu, H and Marty, AM}, title = {One Health turns 10: A decade at the intersection of human, animal, and environmental health.}, journal = {One health (Amsterdam, Netherlands)}, volume = {21}, number = {}, pages = {101218}, pmid = {41492298}, issn = {2352-7714}, }
@article {pmid41492005, year = {2026}, author = {Miyamoto, K and Sujino, T}, title = {Microbiota-derived D-amino acids in intestinal homeostasis and inflammatory bowel disease.}, journal = {Inflammation and regeneration}, volume = {}, number = {}, pages = {}, doi = {10.1186/s41232-025-00403-3}, pmid = {41492005}, issn = {1880-9693}, abstract = {Inflammatory bowel disease (IBD) encompasses chronic, relapsing inflammatory disorders of the gastrointestinal tract, which are driven by intricate interactions between the host immune system and intestinal microbiota. Recent studies have revealed that microbiota-derived D-amino acids (D-AAs), once considered biologically inert, play critical roles in maintaining mucosal homeostasis and modulating immune responses. These metabolites, which are increasingly classified as postbiotics, directly influence epithelial barrier integrity, immune cell activity, and microbial ecology. In this review, we summarize the current insights into the biosynthesis, bacterial functions, and immunological implications of D-AAs in the gut, with a particular focus on their involvement in IBD pathogenesis. Specific D-AAs, such as D-alanine, contribute to bacterial cell wall integrity and quorum sensing and interact with host immune cells, alter microbial communities, and regulate mucosal barrier function. Evidence from both human studies and murine models highlights how disrupted D-AAs' metabolism through dysbiosis or impaired host sensing via enzymes such as D-amino acid oxidase (DAO) exacerbates inflammation. Finally, we discuss the translational potential of D-AAs as non-invasive biomarkers and therapeutic targets in IBD, emphasizing the need for integrative multi-omics approaches that connect microbial metabolism with host immune regulation and disease outcomes.}, }
@article {pmid41490489, year = {2026}, author = {Pontrelli, S and Guessous, G and Trouillon, J and Krishna, A and Hwa, T and Sauer, U}, title = {Hypersensitivity of chitin degradation to initial species densities due to monomer diffusion.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {123}, number = {2}, pages = {e2512676123}, doi = {10.1073/pnas.2512676123}, pmid = {41490489}, issn = {1091-6490}, support = {542395//Simons Foundation (SF)/ ; }, mesh = {*Chitin/metabolism ; Acetylglucosamine/metabolism ; Diffusion ; *Bacteria/metabolism ; Chitinases/metabolism ; }, abstract = {Resource competition strongly shapes microbial community dynamics and functionality. In polysaccharide-degrading communities, primary degraders release hydrolytic enzymes, whereas exploiters consume released products without producing enzyme themselves. We investigate the competitive strategies employed by marine chitin degraders and N-acetylglucosamine (GlcNAc) exploiters, revealing various mechanisms that impact community viability and growth dynamics. In addition to direct competition strategies such as antibiotic secretion or cell aggregation on chitin particles (which helps monopolize enzyme access), exploiters also inhibit degraders by diverting limiting GlcNAc flux during the early stages of particle degradation. This critical phase requires degraders to overcome the diffusive loss of GlcNAc to sustain their chitinase production. Through quantitative measurements and modeling, we demonstrate that nutrient competition among species and nutrient loss through diffusion during the initial stages of community dynamics strongly influence the long-term success of the community. The initial community composition dictates the former mechanisms, while the latter is closely related to particle size, both of which have profound implications for environmental carbon cycling. The resulting hypersensitivity of the community is analogous to the Allee effect observed in population biology, where the outcomes-in our case polymer degradation-are heavily dependent on starting conditions. This study sheds light on how metabolic competition in the early phases of particle degradation governs species interactions, resource partitioning, and overall community viability, even under identical environmental and genetic conditions.}, }
@article {pmid41485602, year = {2026}, author = {Adejumo, S and Lewis, G and Das, P and Lim, CKY and Malas, J and Oli, AN and Allen, JM and Hampton-Marcell, J}, title = {Dietary Protein Source Shapes Gut Microbial Structure and Predicted Functional Potential: A Systematic Integrative Re-analysis Using Machine Learning.}, journal = {Advances in nutrition (Bethesda, Md.)}, volume = {}, number = {}, pages = {100582}, doi = {10.1016/j.advnut.2025.100582}, pmid = {41485602}, issn = {2156-5376}, abstract = {BACKGROUND: Dietary proteins shape gut microbial ecology, yet the taxonomic and functional consequences of plant- versus animal-based proteins remain poorly defined. Although digestibility and fermentation profiles differ by protein type, a systematic evaluation of how these differences influence microbial diversity, community structure, and metabolic capacity is lacking. This study represents a systematic integrative re-analysis of raw 16S rRNA sequencing datasets derived from independent controlled animal feeding studies.<br><br>METHODS: Following PRISMA guidelines, we analyzed 16S rRNA sequencing data from 10 murine studies (n = 187) comparing plant- and animal-protein diets. Alpha diversity was assessed using Shannon, Inverse Simpson, and Chao1 indices, and beta diversity with Aitchison distances. Differentially abundant taxa were identified using LEfSe and class-weighted Random Forest models. Functional potential was inferred with PICRUSt2, and taxon-pathway relationships were explored using correlation and network analyses.<br><br>RESULTS: Plant-protein diets increased gut microbial diversity across all alpha diversity metrics and were associated with higher representation of saccharolytic and nitrogen-recycling genera such as Bacteroides, Muribaculaceae, and Allobaculum. Animal-protein diets favored proteolytic taxa, including Clostridium sensu stricto 1 and Colidextribacter. Microbial community structure differed significantly between diets (ANOSIM R = 0.663, p < 0.001). Random Forest models achieved >88% accuracy (AUC = 0.995) in predicting dietary groups, and LEfSe identified consistent discriminating taxa. Functional profiling showed that plant-based diets enriched pathways linked to short-chain fatty acid and aromatic amino acid metabolism, whereas animal-based diets favored sulfur- and branched-chain amino acid-associated pathways. Network analysis identified Muribaculaceae as a plant-associated hub and Lactobacillus as an animal-associated hub.<br><br>CONCLUSION: Dietary protein source significantly influences gut microbiota composition and functional potential in mice. Plant- and animal-based proteins generate distinct metabolic signatures with implications for nitrogen cycling, sulfur metabolism, and microbial ecology. Future controlled dietary studies that harmonize protein source with other macronutrient variables are needed to isolate protein-specific effects.<br><br>STATEMENT OF SIGNIFICANCE: This study presents the first standardized systematic integrative re-analysis of murine protein-intervention microbiome datasets, integrating taxonomic, machine learning, and predicted functional profiling to identify robust microbial and metabolic signatures that differentiate plant- from animal-based protein diets. By harmonizing raw sequencing data across diverse experimental contexts, this work clarifies foundational ecological responses to protein source and provides mechanistic hypotheses to guide future controlled nutrition and microbiome research.}, }
@article {pmid41485298, year = {2026}, author = {Chopra, C and Kukkar, D and Kaur, H}, title = {A 16S rRNA-based meta-analysis of gut microbiota in diabetic nephropathy using QIIME2 and publicly available NGS datasets.}, journal = {Computational biology and chemistry}, volume = {121}, number = {}, pages = {108876}, doi = {10.1016/j.compbiolchem.2026.108876}, pmid = {41485298}, issn = {1476-928X}, abstract = {Gut microbial profiles can differ significantly between diabetic nephropathy (DN), diabetic patients, and healthy controls (HCs). The exact microbial taxa involved in DN progression is yet to be fully characterized. Therefore, this study aims to compare the gut microbiota od DN patients with diabetic and healthy individuals. Accordingly, this study executes a pioneering metanalytical view using the publicly available datasets (National centre for biotechnology information) to evaluate DN associated variation in gut-microbiota diversity. We hypothesize that the DN patients should have a smaller number of beneficial microbes along with a greater fraction of pathogenic microbial composition relative to the other two groups. Specifically, this report utilizes quantitative insights into microbial ecology 2 (QIIME2) platform to identify an association between gut microbiota composition and DN advancement. This novelty provides distinctive nature to our work in comparison to the broader diabetes microbiome studies. Our study enables comprehensive taxonomic profiling, differential abundance testing, and alpha and beta diversity analyses across multiple studies. A total of six studies were included, comprising 684 samples from both DN patients and HCs. Post quality control check, these samples were processed using QIIME2 platform for taxonomic profiling and diversity analysis to characterize microbial dysbiosis in DN patients in relation to other two groups. Alpha diversity indicates insignificant trend towards reduction of microbial diversity as observed using the Kruskal-Wallis test, Shannon index, Observed features (richness), and Faith's PD analysis (p > 0.05). Additionally, beta diversity analyses revealed a trend toward microbial richness in DN compared to diabetic individuals and HCs, though differences were statically insignificant (P > 0.05). Taxonomic profiling showed a depletion of beneficial genera (e.g., Faecalibacterium, Roseburia, and Bifidobacterium) with false discovery rate (FDR)-adjusted p < 0.05. Contrarily, pathogenic and pro-inflammatory taxa including Escherichia-Shigella, Enterococcus, and Klebsiella showed higher abundance in the DN group (FDR-adjusted p < 0.05). These compositional shifts highlight pronounced gut dysbiosis during the transition from diabetes to DN, suggesting a potential association between gut-kidney axis.}, }
@article {pmid41485297, year = {2025}, author = {Chen, Y and Li, Y and Niu, L and Grossart, HP and Wang, Y and Ma, X and Lin, L}, title = {Hydrodynamics regulates microbial degradation of microplastics by modulating bottom-up and top-down effects in a river-lake confluence zone.}, journal = {Water research}, volume = {292}, number = {}, pages = {125311}, doi = {10.1016/j.watres.2025.125311}, pmid = {41485297}, issn = {1879-2448}, abstract = {River-lake confluence zones, characterized by unique hydrodynamic conditions, are critical areas for pollutant transformation. Nevertheless, degradation of microplastics (MP) mediated by multi-trophic microbial communities remains poorly understood under such complex hydrodynamic disturbances. This study investigated the characteristics of multi-trophic microbiota of the microplastome and explored their roles in MP degradation across four distinct hydrodynamic zones, i.e., maximum velocity zone (Z1), flow buffer zone (Z2), flow deflection zone (Z3), and flow reestablishment zone (Z4), in a river-lake confluence. A pronounced spatial heterogeneity in MP abundance and available nutrients was revealed among the four flow zones, with Z3 exhibiting the most intense MP degradation. Additional microcosm experiments demonstrated that microbial MP degradation was primarily driven by the enriched degrading bacteria and fungi, facilitated by multi-trophic microbial interactions. Furthermore, in situ analysis revealed that both bottom-up and top-down effects occurred across all flow zones, with their intensity being positively correlated with the degree of MP degradation. Thereby, nutrient availability driven by hydrodynamics stimulated the growth of MP degrading bacteria and fungi through a bottom-up effect. The increase in the relative abundance of MP degrading bacteria, concurrent with enhanced protozoan predation on bacteria, suggested that this top-down control operated through the selective predation of protozoa on non-MP degrading bacteria. Across the entire river-lake confluence zone, directional flow fluctuations were identified as the paramount environmental factor through the causal effect model, explaining >50% of the variance in bottom-up and top-down effects. Our study demonstrates how hydrodynamics governs MP degradation via multi-trophic microbial interactions, advancing our fundamental understanding of MP fate in aquatic ecosystems.}, }
@article {pmid41446066, year = {2025}, author = {Link, AC and Moser, KA and Wang, J and Woodruff, GC}, title = {A novel, fig-associated microbe promotes reproductive success via variable life history mechanisms in C. elegans and C. inopinata.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41446066}, issn = {2692-8205}, support = {P40 OD010440/OD/NIH HHS/United States ; }, abstract = {Variation in life history strategies is among the most striking features of animal diversity. Simultaneously, the microbes an animal interacts with are a critical and dynamic aspect of the host environment that can have profound impacts on their life history traits. As microbial environments diverge across animal lineages, life histories and their responses to such microbial contexts are expected to evolve as a consequence. Caenorhabditis nematodes are bacterivores that exhibit a diversity of life history strategies and fill diverse ecological niches. C. elegans thrives on rotting plants and grows rapidly with high fecundity; C. inopinata thrives in fresh figs and grows more slowly with lower fecundity. To understand how hosts with divergent life histories and ecologies respond to the microbes they interact with, we isolated over forty bacterial species from the natural fig environment of C. inopinata. This microbial survey revealed an isolate, Klebsiella sp. WOUb2, that doubles the population growth rate of C. inopinata. While this isolate also increases the population growth rate of C. elegans, Klebsiella sp. WOUb2 increases individual fecundity and developmental rate in C. elegans, whereas it only increases developmental rate of C. inopinata. Thus, fitness is modulated by variable life history mechanisms in the two species. Comparisons with nucleotide databases reveal Klebsiella sp. WOUb2 is closely related to other Klebsiella isolates known to influence Caenorhabditis nematode fitness. Additionally, the similarity of Klebsiella sp. WOUb2 to microbes associated with fig wasps and figs suggests C. inopinata frequently encounters this microbe in its natural context. Taken together, this shows that different physiological responses can underlie conserved, beneficial interspecific interactions.}, }
@article {pmid41484934, year = {2026}, author = {Gouka, L and Serra I Melendez, C and Vardazaryan, N and Nor Nielsen, K and Riber, L and Hestbjerg Hansen, L and Raaijmakers, JM and Seidl, MF and Melkonian, C and Cordovez, V}, title = {Genomic insights into adaptative traits of phyllosphere yeasts.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-025-00839-7}, pmid = {41484934}, issn = {2524-6372}, support = {Grant NNF19SA0059348//Novo Nordisk Fonden/ ; Grant OCENW.XS23.3.113//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; Grant NWO/OCW 024.004.014//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 24AA-IF0651//higher education and science committee MESCS RA PhD Support Program/ ; }, abstract = {BACKGROUND: Yeasts are ubiquitous microorganisms thriving in diverse environments. They are prevalent members of the phyllosphere microbiome, but genomic studies of plant-associated yeasts remain limited.<br><br>RESULTS: We established a taxonomically diverse yeast culture collection from flag leaves of field-grown wheat. This collection captured between 48-56% of the genus-level diversity detected by ITS amplicon sequencing conducted over two consecutive years, including the core members Aureobasidium, Dioszegia, Filobasidium, Papiliotrema, Sporobolomyces, and Vishniacozyma. De novo sequencing of 96 high-quality genomes from this collection, representing 14 yeast genera, and comparative genomics revealed specific signatures associated with life in the phyllosphere, the aboveground part of the plant. These adaptive traits encompass enriched carbohydrate metabolism, secondary metabolite biosynthetic pathways, and pectin degradation. The substantially smaller genomes of the phyllosphere yeast genera Candida and Metschnikowia suggest niche specialization via prioritizing metabolic pathways that are essential for survival in the nutrient-limited phyllosphere.<br><br>CONCLUSIONS: This study represents a significant advancement in our understanding of the diverse and largely unknown genomic traits of environmental yeasts and their adaptation to life in the phyllosphere environment. Our findings highlight their untapped functional potential for biotechnological applications in sustainable crop production.}, }
@article {pmid41483762, year = {2026}, author = {Ortiz-Rivero, J and Gultemirian, ML and Oliva, F and Sànchez-Melsió, A and Freixa, A and Sabater, S}, title = {Pesticide exposure sequence and duration modify the effects of heatwaves and water level reduction on river biofilms.}, journal = {Journal of environmental management}, volume = {398}, number = {}, pages = {128482}, doi = {10.1016/j.jenvman.2025.128482}, pmid = {41483762}, issn = {1095-8630}, abstract = {Fluvial ecosystems are increasingly affected by stressors from anthropogenic activities and climate change-related pressures. Here we examined the potential relevance of stressor interaction, sequence and timing of exposure through a controlled laboratory experiment. We selected both chemical (mixture of pesticides) and physical (temperature heatwave and decreased water level) stressors and we performed two 96 h microcosm experiments designed to assess the effects on the structure and function of epilithic biofilms. Biofilms respond rapidly to these stressors, making them valuable indicators of global change. Our results showed that pesticides negatively impacted photosynthetic activity, while heatwaves increased both structural (chlorophyll concentration) and functional (glucosidase activity) biofilm descriptors. In contrast, water level reduction had comparatively mild effects. The impacts of pesticides were more pronounced when exposure was continuous or occurred during the final 48 h of the experiment, whereas early exposure combined (first 48 h) with a water level reduction resulted in weaker effects, accompanied by an increase and partial recovery of microbial abundance. Furthermore, adverse pesticide effects were more pronounced at 8 °C than at 15 °C. Overall, our results highlight that the sequence, timing and duration of stressor exposure play a critical role in the biofilm structure and function, with likely effects on the whole river ecosystem.}, }
@article {pmid41483182, year = {2026}, author = {Caviedes-Triana, K and Vivero-Gómez, R and Duque-Granda, D and Junca, H and Cadavid-Restrepo, G and Moreno-Herrera, CX}, title = {Structure and Diversity of the Microbiome in Amazonian Sand Flies: Insights into Vector-Microbe Interactions.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02663-5}, pmid = {41483182}, issn = {1432-184X}, support = {Scholarship Program of Ministerio de Ciencia, Tecnolog&#xed;a e Innovaci&#xf3;n, Call 15, for Human Capital Development in the context of the Bicentennial and the 2021-2022 Biennial Plan.//Ministerio de Ciencia, Tecnolog&#xed;a e Innovaci&#xf3;n/ ; Hermes 57545//Universidad Nacional de Colombia/ ; }, abstract = {This study uses high-throughput sequencing of the 16 S rRNA gene and specific PCR to analyze the microbiome and identify secondary endosymbionts in sand flies from the Amazon region, important vectors of parasitic and viral diseases. Specimens of Psychodopygus, Trichophoromyia, Nyssomyia, Trichopygomyia and Brumptomyia were collected and analyzed. The results revealed that the richness, diversity, and composition of the microbiome are influenced by several factors, such as insect species specific composition, and insect sex. The core microbiome community was represented by 18 genera, with Novosphingobium, Cutibacterium, Methylobacterium and Staphylococcus being the most prevalent. The highest diversity at the genus level was observed in sand flies of epidemiological relevance as Psychodopygus and Nyssomyia, dominated by Novosphingobium (66.5%), Cutibacterium (29.4%) and Methylobacterium (20.4%), while in non-vectors such as Trichophoromyia, Delftia predominated (59.9%). Endosymbiont analysis showed a high prevalence of Cardinium (20%) and Wolbachia (33%), as well as the presence of Spiroplasma, Arsenophonus and Rickettsia. In addition, some bacterial genera related to the inhibition of parasite development, which have entomopathogenic activity and are involved in the degradation of insecticides were identified. Our results are relevant and contribute to the knowledge of the characterization of the microbiome and the endosymbionts in leishmaniasis vectors in the Amazon region and show promise for improving vector management, highlighting the importance of investigating their interaction with pathogens and their impact on vector biology.}, }
@article {pmid41482669, year = {2026}, author = {Islam, W and Zhihao, Z and Khan, KA and Zeng, F}, title = {Resilience and Adaptation in Desert Ecosystems: Unveiling Microbial Legacies and Plant Functional Trait Coordination Under Climate Change.}, journal = {Global change biology}, volume = {32}, number = {1}, pages = {e70678}, doi = {10.1111/gcb.70678}, pmid = {41482669}, issn = {1365-2486}, support = {2023TSYCLJ0046//Tianshen Talent Training Program/ ; 42271071//National Natural Science Foundation of China/ ; 42571075//National Natural Science Foundation of China/ ; }, mesh = {*Climate Change ; *Desert Climate ; *Ecosystem ; *Soil Microbiology ; *Microbiota ; *Plant Physiological Phenomena ; *Adaptation, Physiological ; *Plants ; }, abstract = {Desert ecosystems, which cover more than one-third of Earth's land surface, are experiencing intensifying pressures from land-use disturbances and climate change that threaten their stability and biodiversity. Yet despite their global extent and ecological importance, deserts remain among the least studied biomes, particularly with respect to the belowground processes that sustain productivity, biogeochemical cycling, and long-term ecosystem resilience. Most prior work has focused on vegetation, leaving the roles of soil microbiomes and plant functional trait coordination comparatively underexplored. This knowledge gap is significant because growing evidence shows that microbial dynamics and plant trait syndromes jointly regulate nutrient cycling, carbon stabilization, and drought recovery, potentially determining whether desert ecosystems cross critical thresholds under future climate scenarios. This review synthesizes recent advances in understanding the influence of microbial legacies (persistent effects of past environmental conditions) on ecosystem processes, and how desert plants adapt via coordinated traits that optimize water and nutrient use under extreme conditions. We propose a novel framework that integrates belowground microbial responses and aboveground plant trait strategies, highlighting their interactions and feedback loops in shaping desert ecosystem resilience. By explicitly linking these two domains, the review addresses a major knowledge gap in predicting dryland responses to intensifying climate extremes, offering a mechanistic foundation for improving ecological models and management strategies. This integrated perspective provides new insights into the mechanisms that underlie adaptation to climate stress and offers actionable pathways for conservation, restoration, and climate adaptation in desert landscapes. By bridging microbial ecology and trait-based plant science, this review contributes to a more comprehensive understanding of how desert ecosystems can persist and function in a rapidly changing world.}, }
@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 &amp; 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.}, }
@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.<br><br>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 &#x3b1;- and &#x3b2;-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.<br><br>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.<br><br>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.<br><br>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).<br><br>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 &#x3b1;-glucosidase (AG), &#x3b2;-glucosidase (BG), cellobiohyrolase (CBH), and &#x3b2;-xylosidase (XYL), were consistently elevated under N-amended treatments during mid- to late-stage decomposition. Similarly, activities of N-acquiring enzymes (&#x3b2;-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&#xa0;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 &amp; 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.}, }
@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.}, }
@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.<br><br>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.<br><br>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/&#x3bc;L) 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.<br><br>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&#xff1b;246Z6604G&#xff1b;HBCT2024270204&#xff1b;CARS-41-13&#xff1b;KY2024006//This research was funded by the special project of introducing talents for scientific research in Hebei Agricultural University&#xff1b;Central government guided local science and technology development fund projects&#xff1b;Hebei Agriculture Research System&#xff1b;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&amp;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, &#xc1; 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. &amp; 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.<br><br>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.<br><br>RESULTS: The extracts (100&#xa0;&#xb5;g/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&#x2009;&#xb1;&#x2009;3.7% for leaves methanol extract and 42.6&#x2009;&#xb1;&#x2009;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.<br><br>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.}, }
@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.}, }
@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&amp;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.<br><br>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.<br><br>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.}, }
@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.}, }
@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.<br><br>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.<br><br>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.<br><br>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 &amp; 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.}, }
@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.<br><br>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.<br><br>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&amp;E and Masson's trichrome staining), immunohistochemistry (&#x3b1;-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.<br><br>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.<br><br>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.<br><br>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.<br><br>METHODS: This paper introduces the Constrained Disorder Principle (CDP) as a new framework for understanding microbial diversity.<br><br>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.<br><br>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 \&amp; prediction, microbe-X interactions, microbial ecology, metabolic modeling, precision nutrition, clinical microbiology, to prevention \&amp; 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 &amp; 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.<br><br>METHOD: This study examined changes in gut microbiota and SCFA across three groups; Cognitively unimpaired individuals with low amyloid-beta ((CU) A&#x3b2; Low (n&#xa0;=&#xa0; 71)), CU A&#x3b2; High (n&#xa0;=&#xa0; 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.<br><br>RESULT: Firmicutes, Proteobacteria, and Bacteroidetes exhibited significant correlations with SCFAs across all groups. In the CU A&#x3b2; 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 A&#x3b2; Low group, and a positive correlations between Proteobacteria and Actinobacteria with butyric acid in the CU A&#x3b2; 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.<br><br>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.}, }
@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).<br><br>MATERIALS AND METHODS: Rumen inoculum from three cannulated Holstein Friesian cows was incubated across 16 vessels (four treatments &#xd7; 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 &#xb5;L/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.<br><br>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.<br><br>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 &amp; 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 Investigaci&#xf3;n/ ; }, 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.}, }
@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 &amp; purification ; *Fungi/genetics/metabolism/classification/isolation &amp; 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.}, }
@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-S&#xe4;&#xe4;ti&#xf6;/ ; 3825//Maj ja Tor Nesslingin S&#xe4;&#xe4;ti&#xf6;/ ; 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 &amp; pharmacotherapy = Biomedecine &amp; 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 &amp; 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, &#xc1; 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.}, }
@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.}, }
@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//R&#xe9;gion Auvergne-Rh&#xf4;ne-Alpes/ ; Pack Ambition Recherche 2021 MICROMETiv//R&#xe9;gion Auvergne-Rh&#xf4;ne-Alpes/ ; Pack Ambition Recherche 2021 MICROMETiv//R&#xe9;gion Auvergne-Rh&#xf4;ne-Alpes/ ; Pack Ambition Recherche 2021 MICROMETiv//R&#xe9;gion Auvergne-Rh&#xf4;ne-Alpes/ ; Pack Ambition Recherche 2021 MICROMETiv//R&#xe9;gion Auvergne-Rh&#xf4;ne-Alpes/ ; Pack Ambition Recherche 2021 MICROMETiv//R&#xe9;gion Auvergne-Rh&#xf4;ne-Alpes/ ; Pack Ambition Recherche 2021 MICROMETiv//R&#xe9;gion Auvergne-Rh&#xf4;ne-Alpes/ ; Pack Ambition Recherche 2021 MICROMETiv//R&#xe9;gion Auvergne-Rh&#xf4;ne-Alpes/ ; Pack Ambition Recherche 2021 MICROMETiv//R&#xe9;gion Auvergne-Rh&#xf4;ne-Alpes/ ; Pack Ambition Recherche 2021 MICROMETiv//R&#xe9;gion Auvergne-Rh&#xf4;ne-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 Ayd&#x131;n 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.<br><br>METHODS: Ninety-eight patients underwent endoscopic evaluation and were divided into two groups according to the presence or absence of ulcers. Group 1 (n&#x2009;=&#x2009;52) included individuals with NUD, while Group 2 (n&#x2009;=&#x2009;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.<br><br>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&#x2009;=&#x2009;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&#x2009;<&#x2009;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&#x2009;<&#x2009;0.05). These genera, typically associated with the oral cavity, appeared to expand opportunistically when H. pylori was absent.<br><br>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 T&#xfc;rkiye 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.}, }
@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 &amp; 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 &amp; 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.<br><br>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.<br><br>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.<br><br>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.}, }
@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//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 22-03662S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 22-33245S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 20-12496X//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 21-21990S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; 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 f&#xfc;r Gew&#xe4;sser&#xf6;kologie 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 Cercet&#x103;rii &#x15f;i Inov&#x103;rii/ ; }, 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.<br><br>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&#xa0;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.<br><br>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.<br><br>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.<br><br>RESULTS: We found that RF models could predict AD status using both skin and nasal microbiomes (AUCs: skin&#x2009;=&#x2009;0.69-0.79; nasal&#x2009;=&#x2009;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&#x2009;=&#x2009;0.45 to AD r&#x2009;=&#x2009;0.67) compared to urban CT (healthy r&#x2009;=&#x2009;0.27 to AD r&#x2009;=&#x2009;0.65). The skin microbiome diversity was higher in children from rural UM with healthy skin than in those from urban CT (p&#x2009;=&#x2009;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&#x2009;=&#x2009;0.001-0.002) than their urban CT counterparts (p&#x2009;=&#x2009;0.002-0.349).<br><br>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.<br><br>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.<br><br>RESULTS: Twenty-four patients were analyzed: 15 (62.5%) were male and 12 (50%) were White. Children with lower cognitive (Chao1 P&#x2009;=&#x2009;0.024) and language scores (Chao1 P&#x2009;=&#x2009;0.018) had lower alpha diversity; beta diversity showed marginally significant dissimilarities (Jaccard P&#x2009;=&#x2009;0.102 and P&#x2009;=&#x2009;0.051, respectively). Lower cognitive scores were associated with less Parabacteroides (P&#x2009;=&#x2009;0.031), Bacteroides (P&#x2009;=&#x2009;0.041), and Bifidobacterium (P&#x2009;=&#x2009;0.047), and lower language scores were associated with less Bifidobacterium (P&#x2009;=&#x2009;0.044) and Enterococcus (P&#x2009;=&#x2009;0.024). Lower motor scores were associated with less Rothia (P&#x2009;=&#x2009;0.017) but a higher abundance of Serratia (P&#x2009;<&#x2009;0.001), Acinetobacter (P&#x2009;=&#x2009;0.016), and Proteus (P&#x2009;=&#x2009;0.013).<br><br>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 {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 &amp; biotechnology}, volume = {23}, number = {4}, pages = {100623}, doi = {10.1016/j.jgeb.2025.100623}, pmid = {41386888}, issn = {2090-5920}, abstract = {Pseudomonas stutzeri is a type of microorganism widely present in nature, particularly in petroleum-contaminated environments, where it exhibits a high capacity for biodegradation. In this study, two strains of Pseudomonas stutzeri 1W1-1A and DW2-1A, were isolated from oil-water samples from Dagang Oilfield and their whole genomes were sequenced. The whole genome of 1W1-1A is 4,454,378 bp in size, with a GC content of 64.23 % in its single circular chromosome; the whole genome of DW2-1A is 3,967,155 bp in size, with a GC content of 62.98 % in its single circular chromosome. Comparing these two strains with Pseudomonas sp. in the NCBI database, we counted the strains with genes related to hydrocarbon oxidation, nitrate, sulfite, and oxygen reduction in the genome and their global distribution. Genes related to hydrocarbon oxidation, nitrate, sulfite, and oxygen reduction were found in the genome, revealing the survival strategies and adaptation mechanisms of Pseudomonas in extreme oil reservoir environments, including its genomic characteristics, functional gene distribution, and tolerance to different environmental conditions. These findings enrich our understanding of the ecological adaptability and functional evolution of Pseudomonas, providing a new perspective for research in microbial ecology and environmental microbiology. The results of this study offer new strain resources and a scientific basis for microbial enhanced oil recovery (MEOR). Utilizing the hydrocarbon degradation capabilities and biosurfactant production characteristics of these strains is of great significance for microbial industrial applications such as MEOR and the remediation of petroleum-contaminated environments.}, }
@article {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 {pmid41385904, year = {2025}, author = {Pan, X and Elsayed, SS and van Wezel, GP and Raaijmakers, JM and Carrión, VJ}, title = {Disentangling the molecular mechanisms of disease suppression by endophytic Flavobacterium sp. 98.}, journal = {Microbiological research}, volume = {304}, number = {}, pages = {128415}, doi = {10.1016/j.micres.2025.128415}, pmid = {41385904}, issn = {1618-0623}, abstract = {Endophytic microorganisms colonize internal plant tissues and enhance host resistance to pathogens. We previously showed that endophytic Flavobacterium sp. 98 (Fl98) protects sugar beet against the fungal root pathogen Rhizoctonia solani via biosynthetic gene cluster 298 (BGC298). However, the molecular mechanisms underlying this protection remained poorly understood. Here, comparative metabolomic analyses revealed that knockout of BGC298 led to reduced production of the antifungal compound 5,6-dimethylbenzimidazole (DMB) in Fl98. We hypothesized that BGC298 is involved in regulating DMB biosynthesis and therefore contributes to Fl98's disease suppression as a novel protective mechanism. Subsequent site-directed mutagenesis of the DMB-synthase gene bluB abolished DMB production by Fl98, and both ΔBGC298 and ΔbluB mutants were compromised in protecting sugar beet seedlings in greenhouse bioassays. Bioinformatic analyses further indicated that bluB is widespread across Flavobacterium, while BGC298 is limited to a small subset of plant-associated strains. Together, our findings highlight the pivotal role of BGC298 and DMB biosynthesis in plant protection by endophytic Flavobacterium sp. 98.}, }
@article {pmid41384736, year = {2025}, author = {Madrid-Restrepo, MA and León-Inga, AM and Peñuela-Martínez, AE and Cala, MP and Reyes, A}, title = {Metagenomic, metabolomic, and sensorial characteristics of fermented Coffea arabica L. var. Castillo beans inoculated with microbial starter cultures.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0136425}, doi = {10.1128/msystems.01364-25}, pmid = {41384736}, issn = {2379-5077}, abstract = {UNLABELLED: Coffee is one of the most important and widely consumed drinks around the world, and fermentation plays a pivotal role in shaping its quality. This research explores the impact of co-fermentation with "starter cultures" on the sensory and metabolic profiles, as well as on the dynamics of microbial communities involved in coffee processing. Freshly harvested Arabica coffee beans were subjected to two wet-fermentation processes, one inoculated with a microbial starter culture and the other undergoing spontaneous fermentation. Quantitative descriptive analysis revealed that the inoculated coffee outperformed the spontaneous fermentation in all sensory attributes, boasting higher sweetness, reduced acidity and bitterness, and the presence of consumer-preferred notes. Untargeted metabolomic analysis identified over a hundred differential metabolites distinguishing both fermentation processes in green and roasted beans. Inoculated coffee displayed elevated levels of compounds such as sucrose, mannitol, methyl phenylacetate, and organic acids like malic, citric, and quinic acid, compounds likely associated with improved sensory perception. The inoculated process was characterized by shifts in the abundance of lactic acid bacteria and Kazachstania yeasts, groups linked to desirable metabolites such as lactic, acetic, isobutyric, and hexanoic acids. Our results strongly suggest that the use of starter cultures can enhance coffee beverage quality, as reflected by standardized cupping, metabolic profiles, and microbial community dynamics. Future studies should focus on disentangling microbial contributions and metabolite pathways to inform the design of commercially viable starter cultures for coffee fermentation.<br><br>IMPORTANCE: Our study demonstrates that inoculating coffee fermentation alters the sensory qualities of coffee and reshapes the dynamics of bacterial and fungal communities during this process. We identified distinct changes in microbial diversity and metabolite composition associated with inoculation, which correlated with improved sensory attributes. In addition, we detected aminophenol and phenol at higher levels in spontaneously fermented coffees, compounds that are likely responsible for phenolic defects. To our knowledge, this is the first report directly linking these compounds to defective flavor notes in coffee. Together, these findings show that inoculation not only enhances desirable flavor profiles but may also serve as a strategy to reduce the risk of cup defects by modulating the fermentation microbiota. Our work advances the understanding of community-level microbial processes in coffee fermentation and opens opportunities for developing techniques to produce coffee with unique, high-quality, and reproducible sensory characteristics.}, }
@article {pmid41383741, year = {2025}, author = {Song, J and He, Q and Cao, K and Song, X and Zeng, Q}, title = {Effects of continuous cropping on soil metabolomics and rhizosphere bacterial communities in Panax quinquefolius L.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1698779}, pmid = {41383741}, issn = {1664-302X}, abstract = {INTRODUCTION: Continuous cropping obstacles (CCOs) due to long-term monoculture have emerged as a pervasive challenge in contemporary agriculture worldwide. The practices of CCOs are the primary causes of restraining the Panax quinquefolius L. (P. quinquefolius) growth, whereas its underlying microbial mechanisms have not been fully elucidated.<br><br>METHODS: We investigated the effects of CCOs on soil physicochemical properties, enzyme activities, microbial community composition, and metabolite profiles in the rhizosphere of P. quinquefolius cultivated continuously for one, two, three, and four consecutive years (designated as CC1, CC2, CC3, and CC4, respectively) without crop rotation. Rhizosphere soil samples were collected from fields with different years of CCOs and analyzed for physicochemical properties and enzyme activities. Microbial community composition was assessed using Illumina high-throughput sequencing, and metabolite profiles were analyzed using non-targeted metabolomics (UPLC-MS/MS).<br><br>RESULTS: Significant decreases were observed in soil pH (12.2-28.0%), cation exchange capacity (42.6-65.5%), organic matter (8.7-27.3%), total nitrogen (7.6-27.8%), and ammonium (NH4 [+]) content (16.9-56.6%) with an increasing number of continuous cropping years. Enzymatic activities, including urease, invertase, alkaline phosphatase, catalase, protease, and polyphenol oxidase, were also reduced. The occurrence of CCOs decreased bacterial richness and number but increased bacterial diversity. Key microbial biomarkers were shifted from Gemmatimonadota, Actinobacteriota, and Proteobacteria to Acidobacteriota, Chloroflexi, and WPS-2 with P. quinquefolius CCOs. Consequently, the number of beneficial microorganisms decreased, whereas the number of pathogenic microorganisms increased. Non-targeted metabolomic profiling showed significant enantioselectivity in phenylpropanoid biosynthesis and pyrimidine metabolism. Time-series analysis revealed a decrease in metabolites classified as lipids and lipid-like molecules and an increase in organic acids, derivatives, phenylpropanoids, and polyketides with continuous cropping. Partial least squares-path modeling identified reduced soil enzymatic activity due to CCOs as the primary factor regulating soil bacterial communities and metabolites.<br><br>SIGNIFICANCE: These findings offer new insights into the microecological mechanisms of CCOs in P. quinquefolius, aiding in controlling pathogenic bacteria and maintaining soil health in agricultural systems.<br><br>CONCLUSION AND PROSPECTS: P. quinquefolius CCOs significantly alter soil physicochemical properties, microbial community structure, and metabolite profiles, leading to reduced soil fertility and increased prevalence of soil-borne diseases. Future research should focus on exploring sustainable agricultural practices, such as crop rotation and soil amendments, to mitigate these adverse effects and improve the long-term viability of P. quinquefolius cultivation.}, }
@article {pmid41383635, year = {2025}, author = {Zhu, W and Ni, R and Cai, B and Ma, S and Jiang, J and Wang, B}, title = {In-situ diet-microbiota associations across taxonomic scales in desert-dwelling amphibians and reptiles.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf213}, pmid = {41383635}, issn = {2730-6151}, abstract = {Understanding how host and environmental factors shape gut microbiota is central to microbial ecology and evolution. However, the extent to which gut microbes covary with diet and how such variation reflects host phylogeny, remains unclear under natural conditions. Here, we used DNA metabarcoding of gut contents to analyze the dietary arthropod composition and gut microbiota of four amphibian and three reptile species from the Tarim Desert, Xinjiang, China. These species showed pronounced differences in both diet and microbial profiles. Dominant dietary arthropod families exhibited generally low overlap among species, and dietary variation did not align with host phylogeny. Interestingly, Bufotes pewzowi (amphibian) and Teratoscincus przewalskii (reptile)-the most common species in their respective groups-both primarily consumed ants (Formicidae). Conversely, gut microbial composition more closely reflected host phylogeny than diet, with a clear separation between amphibians and reptiles, particularly in the relative abundances of Bacteroidetes and the genera Bacteroides and Blautia. These findings suggest that the previously reported phylosymbiosis in these species is not primarily driven by dietary overlap. Significant diet-microbiota correlations were observed across all species and within each taxonomic class but were largely absent within species. This highlights taxonomic-level differences in the diet-microbiota relationship, indicating that diet-microbiota covariation is more pronounced over evolutionary timescales than in response to real-time dietary variation. Taken together, our results show that gut microbiota and diet exhibit distinct phylogenetic patterns, with microbiota showing both associations with diet and resilience to short-term dietary changes, underscoring the importance of considering timescales in diet-microbiota studies.}, }
@article {pmid41381925, year = {2025}, author = {González-Villalobos, E and Aranda, A and de Almeida, ACM and Balcázar, JL}, title = {Global Transcriptomic Profiling Reveals Conserved and Phage-specific Responses to Phage Infection in Escherichia Coli.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02665-3}, pmid = {41381925}, issn = {1432-184X}, support = {792686//EU Horizon 2020 Programme (Marie Sk&#x142;odowska-Curie)/ ; }, abstract = {Although phages shape bacterial evolution and physiology, the specificity of host transcriptomic responses to phage infection remains incompletely understood. Here, we performed global transcriptomic profiling of Escherichia coli exposed to two lytic phages, ΦX174 and T4, and the temperate phage λ, to explore both conserved and phage-specific host responses. All infections induced stress-related genes, including SOS and general stress pathways, along with repression of anabolic processes such as purine and amino acid biosynthesis, suggesting a metabolic shift to conserve resources. Notably, ΦX174 strongly activated the phage shock protein operon, while both ΦX174 and λ selectively induced soxS, a regulator of oxidative stress. Despite infecting the same host, each phage triggered distinct transcriptional signatures. These findings highlight the complexity of bacterial responses and the value of transcriptomics in decoding host-phage interactions, offering insights into resistance, survival, and co-evolution.}, }
@article {pmid41381498, year = {2025}, author = {Dong, Z and Zhou, H and Cao, R and Zhang, O and Zhao, S and Lyu, P and Alcalde, R and Yang, C}, title = {Analytic Fourier ptychotomography for aberration-free and high-resolution volumetric refractive index imaging.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-025-67460-7}, pmid = {41381498}, issn = {2041-1723}, abstract = {Three-dimensional (3D) refractive index tomography offers label-free quantitative volumetric imaging. However, existing tomography approaches are limited by optical aberrations, limited resolution, and computational complexity. To overcome these issues, we propose Analytic Fourier Ptychotomography (AFP), a computational microscopy technique that analytically reconstructs aberration-free, complex-valued 3D refractive index distributions without iterative optimization or axial scanning. AFP employs a unique prior based on the finite sample thickness to recast the inverse scattering problem into analytically solvable linear equations. Unlike iterative methods, AFP does not require parameter tuning and computationally intensive optimizations, and can achieve efficient, robust, and generalizable image reconstructions across diverse samples and systems. We experimentally demonstrated that AFP greatly enhanced image quality and resolution under various aberration conditions across a range of applications. AFP corrected aberrations associated with 25 Zernike modes (with maximal phase difference of 2.3π and maximal Zernike coefficient value of 4), extended the synthetic numerical aperture from 0.41 to 0.99, and provided a two-fold resolution enhancement in all directions. With its simplicity, robustness, and broad applicability, AFP offers a user-friendly imaging platform for quantitative 3D analysis in biology, microbial ecology, and clinical science.}, }
@article {pmid41378987, year = {2025}, author = {Niu, S and Al, MA and Zhang, D and Ming, Y and Liu, H and Zhu, W and Li, M and Yu, X and Niu, M and Wu, K and Xie, W and He, Z and Yan, Q}, title = {Assembly and interactions of denitrifying and anammox communities in a typical eutrophic lake.}, journal = {FEMS microbiology letters}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsle/fnaf139}, pmid = {41378987}, issn = {1574-6968}, abstract = {Nitrogen removal is crucial for controlling nitrogen levels in eutrophic lakes and depends on the high transformation capacity of nitrogen-cycling microorganisms. However, the assembly mechanisms and interactions of nitrogen removal microbial communities in lake water remain unclear. This study aimed to clarify how nitrogen levels influence the diversity, interactions, and assembly of denitrifying and anaerobic ammonia oxidation (anammox) communities. We collected lake water from different areas in a typical eutrophic lake and investigated the nitrogen removal bacterial communities by high-throughput sequencing of two representative functional genes (nirS and hzsB). Our results indicated that the α-diversity of anammox bacteria was higher in sites with high concentration of nitrogen (> 1.5 mg/L) than in sites with low concentration of nitrogen (< 1.5 mg/L). Anammox bacteria in high-nitrogen sites were dominated by the potential keystone taxon Candidatus Brocadia. Co-occurrence network analysis revealed that low-nitrogen sites had more negative connections between denitrifying and anammox communities. Moreover, total nitrogen and electrical conductivity were key factors determining community structure. Microbial community assembly analysis indicated that both denitrifying and anammox communities were primarily governed by stochastic processes across different nitrogen levels. This study enhanced our understanding of microbial community dynamics in nitrogen removal processes in eutrophic lakes.}, }
@article {pmid41377758, year = {2026}, author = {Benjamin, K and Yuan, Q and Boyer, J}, title = {Increased gut Saccharomyces and decreased pathogenic fungi associated with food protein-induced enterocolitis syndrome resolution.}, journal = {The journal of allergy and clinical immunology. Global}, volume = {5}, number = {1}, pages = {100598}, pmid = {41377758}, issn = {2772-8293}, abstract = {BACKGROUND: Food protein-induced enterocolitis syndrome (FPIES) is a non-IgE-mediated allergy, primarily affecting infants and children, with potentially severe gastrointestinal impacts. As with other allergic diseases, the cause of FPIES is unknown. Preliminary research suggests that the gut microbiome may play a role in FPIES, as well as other allergy, yet data on the mycobiome are limited.<br><br>OBJECTIVE: We sought to examine the role of the gut mycobiome in FPIES by comparing the stool mycobiome of children with FPIES to that of children who have outgrown FPIES.<br><br>METHODS: Caregivers of children with FPIES and children who had outgrown FPIES completed a demographic and lifestyle survey. DNA was extracted and sequenced from stool samples of 23 children with FPIES and 17 children with resolved FPIES. Fungal diversity and composition between the 2 groups were compared using QIIME2 (Quantitative Insights Into Microbial Ecology 2).<br><br>RESULTS: Children with resolved FPIES had significantly more Saccharomyces than children with current FPIES. Children with current FPIES had significantly more diverse samples and included opportunistic pathogens, such as Candida spp. Children with resolved FPIES reported significantly less infant antibiotic usage and proton pump inhibitor usage.<br><br>DISCUSSION: This study identified distinct mycobiome profiles in children with current versus resolved FPIES. Resolved FPIES was associated with Saccharomyces enrichment, whereas children with current FPIES had more diverse, opportunistic pathogen-associated communities and greater infant antibiotic and proton pump inhibitor usage. Although these associations do not establish causality, they underscore the need for larger, longitudinal studies to determine whether the mycobiome and early-life exposures influence FPIES outcomes, because it could have implications for treatment and prevention.}, }
@article {pmid41376875, year = {2026}, author = {Yadav, BNS and Sharma, P and Maurya, S and Yadav, A and Tiwari, N and Reddy, MS and Yadav, RK}, title = {Spatial and seasonal variations of active micro-eukaryotic community structure in heavy metal-contaminated soils.}, journal = {3 Biotech}, volume = {16}, number = {1}, pages = {6}, pmid = {41376875}, issn = {2190-572X}, abstract = {UNLABELLED: Heavy metal contamination of soil poses a significant hazard to the environment. However, numerous eukaryotic microbes can sustain themselves and thrive in such polluted soils, playing a pivotal role in transforming heavy metal contaminants into more stable and less toxic forms. This study employed an amplicon-based metatranscriptomic approach to investigate the active micro-eukaryotic community structure in heavy metal-contaminated soils across two locations in India, KJ (Jajmau) and UZ (Zawar Mines), during two different seasons (spring and autumn). The diversity assessment targeted the V4 hypervariable region of the 18S rRNA gene, amplified from reverse-transcribed RNA. The supergroup Opisthokonta was found to be dominant across all soil samples, constituting a significant proportion of the eukaryotic community. The microbial communities exhibited clear seasonal variation. In UZ, the genera Aplanochytrium and Colpoda dominated in spring, whereas Hypocreales prevailed in autumn. In KJ, Chlorella, Acari, and Colpoda dominated in spring, while Acari remained dominant in autumn. Regardless of seasonal or spatial fluctuations, 44 genera were found to be common across all samples. Alpha and beta diversity measures, along with hierarchical clustering, network analysis, heatmap visualization, and Principal Component Analysis (PCA), provided strong support for the variations in biodiversity and community organization across the datasets. The ecological significance of these findings lies in demonstrating how micro-eukaryotic communities reorganize spatially and seasonally to maintain resilience in contaminated soils. Such adaptive associations highlight their potential role in natural attenuation and provide a foundation for developing targeted bioremediation strategies by leveraging stress-adapted micro-eukaryotes.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-025-04605-x.}, }
@article {pmid41373555, year = {2025}, author = {Zhang, J and Shen, J and Ji, L and Tan, P and Liu, C and Zhang, X and Ma, X}, title = {Lacticaseibacillus rhamnosus MS27 Potentially Prevents Ulcerative Colitis Through Modulation of Gut Microbiota.}, journal = {International journal of molecular sciences}, volume = {26}, number = {23}, pages = {}, doi = {10.3390/ijms262311397}, pmid = {41373555}, issn = {1422-0067}, mesh = {Animals ; *Colitis, Ulcerative/prevention &amp; control/microbiology/chemically induced ; *Gastrointestinal Microbiome/drug effects ; *Lacticaseibacillus rhamnosus/physiology/isolation &amp; purification ; *Probiotics/pharmacology/therapeutic use ; Mice ; RNA, Ribosomal, 16S/genetics ; Disease Models, Animal ; Dextran Sulfate ; Male ; }, abstract = {(1) This study explored Lacticaseibacillus rhamnosus MS27, a newly isolated strain, as a potential probiotic candidate for alleviating the onset and severity of ulcerative colitis (UC). (2) L. rhamnosus MS27 was isolated and subjected to biochemical identification, antibiotic sensitivity testing, and antibacterial activity assessment. Dextran sulfate sodium (DSS) colitis model mice were used to evaluate its alleviating effects. In this study, 16S rRNA microbiome and eukaryotes reference transcriptome analyses were conducted to investigate its impact on intestinal microbial ecology and potential molecular mechanisms. (3) L. rhamnosus MS27 exhibits high acid tolerance at pH 3.23 and maintains a high viable bacterial count for 24 h. It can utilize sucrose, lactose, maltose, inulin, esculin, salicin, and mannitol but not raffinose, and it is sensitive to carbenicillin, erythromycin, tetracycline, chloramphenicol, clindamycin, and penicillin. It effectively increases the abundance of beneficial microbes, particularly Akkermansia, Muribaculaceae, and Limosilactobacillus reuteri (p < 0.05), while significantly reducing microorganisms linked to human pathogens causing diarrhea and gastroenteritis (p < 0.05). Transcriptomic analysis demonstrated that the expression levels of Igkv16-104 and C1qtnf3 were significantly downregulated in the presence of L. rhamnosus MS27 treatment compared to DSS treatment alone (p < 0.05). Further analysis revealed significant differences in genes related to immune functions, antigen presentation, and immune cell markers, indicating potential protein-protein interaction networks, particularly among genes of the major histocompatibility complex (MHC). (4) L. rhamnosus MS27, as a novel strain, demonstrates a significant capacity to alleviate inflammatory phenotypes. L. rhamnosus MS27 exhibits distinctive metabolic characteristics in lactic acid utilization, acetic acid and oleic acid production. Furthermore, it contributes to systemic homeostasis regulation by modulating Turicibacter to link intestinal microbiota composition with host immune function.}, }
@article {pmid41373452, year = {2025}, author = {Mehelleb, D and Ghidouche, A and Baldi, S and Djoudi, F and Bertorello, S and Di Gloria, L and Ramazzotti, M and Niccolai, E and Madaoui, M and Takbou, I and Tliba, S and Amedei, A}, title = {Specific Intratumoral Microbiome Signatures in Human Glioblastoma and Meningioma: Evidence for a Gut-Brain Microbial Axis.}, journal = {International journal of molecular sciences}, volume = {26}, number = {23}, pages = {}, doi = {10.3390/ijms262311290}, pmid = {41373452}, issn = {1422-0067}, support = {THE-Tuscany Health Ecosystem-ECS00000017-CUP B83C22003920001; #NEXTGENERA-TIONEU (NGEU)//European Union/ ; National Recovery and Resilience Plan (NRRP), project MNESYS (PE0000006) - A Multiscale in-tegrated approach to the study of the nervous system in health and disease (DR. 1553 11.10.2022)//Ministero dell'universit&#xe0; e della ricerca/ ; }, mesh = {Humans ; *Meningioma/microbiology/pathology ; *Glioblastoma/microbiology/pathology ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; *Brain Neoplasms/microbiology/pathology ; *Meningeal Neoplasms/microbiology ; Aged ; Adult ; Bacteria/genetics/classification ; Case-Control Studies ; }, abstract = {Brain tumors (BTs), including glioblastoma (GBM) and meningioma (MGM), contribute significantly to the global cancer burden. The microbiome has been implicated in carcinogenesis, yet its role in BTs remains underexplored. We performed 16S rRNA gene sequencing of the gut microbiota (GM) and intratumoral microbiome (ItM) from fresh tissue samples of 9 patients with GBM and 18 with MGM. 12 age- and sex-matched healthy controls (HCs) were also enrolled. GM profiling revealed reduced alpha diversity and distinct microbial communities in BT patients versus HCs. Notably, Verrucomicrobiota and Synergistaceae were enriched, while Lachnospiraceae, Peptostreptococcaceae, and Muribacter spp. were depleted. GBM patients showed reductions in Peptostreptococcaceae and the Eubacterium hallii group, while MGM patients had increased Synergistia and Erysipelatoclostridium. Compared with MGM, GBM patients were enriched in Peptostreptococcales-Tissierellales, Coprobacillus, and Peptoniphilus but depleted in Weissella. Venn analysis revealed 176 genera shared across groups with unique taxa distinguishing tumor patients and HCs. ItM profiling revealed enrichment of Proteobacteria, Actinomycetota, and Campylobacterota in GBM, while MGM contained higher levels of Bacillota and Bacteroidota. GBM tissues harbored Burkholderia-Caballeronia-Paraburkholderia, Helicobacter, and Leifsonia, whereas MGM tissues were dominated by Bacteroides and Blautia. Notably, stool and tumor samples shared 91 genera in GBM and 105 in MGM. This study provides novel insights by (i) characterizing ItM from fresh samples, (ii) comparing ItM profiles of GBM and MGM, (iii) linking GM and ItM within the same patients, and (iv) suggesting potential clinical implications for BT management.}, }
@article {pmid41369196, year = {2025}, author = {Gundrum, J and Ramirez-Puebla, ST and Mark Welch, JL and Borisy, GG}, title = {Slicing overcomes the bacterial cell wall barrier to fluorescence in situ hybridization.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0200125}, doi = {10.1128/spectrum.02001-25}, pmid = {41369196}, issn = {2165-0497}, abstract = {UNLABELLED: Simultaneous visualization of all bacterial species in a polymicrobial biofilm by fluorescence in situ hybridization (FISH) remains a challenge because bacterial taxa respond differently to the hybridization procedure. This heterogeneity is due, in part, to the cell wall barrier of Gram-positive taxa. Enzymatic procedures required to permeabilize the cell walls of Gram-positive microbes can result in the disruption or loss of Gram-negative bacteria. Here, we demonstrate a procedure that enables the hybridization of difficult-to-hybridize bacteria while preserving the microarchitecture of all bacteria within a biofilm. The key feature of the procedure is to physically cut through the cell wall, thus allowing probe entry. We first embed the sample in a covalently crosslinked, glycol methacrylate resin to preserve the structure of the biofilm. Embedment is followed by sectioning and hybridization of material with the methacrylate still in place. We tested the procedure on common oral species, including difficult Gram-positive taxa, and found marked improvement in hybridization; both average signal intensity and homogeneity of hybridization were improved as compared to standard whole cell mount procedures. Our results confirm that the cell wall is the major barrier preventing efficient hybridization in whole mount samples. By physically overcoming the cell wall barrier, our protocol provides a universal procedure to visualize all bacteria in a polymicrobial community.<br><br>IMPORTANCE: It has long been recognized that the major barrier to efficient in situ hybridization of bacteria is the cell wall, with Gram-positive bacteria generally being the most problematic. Because enzymatic methods that facilitate hybridization of Gram-positive bacteria can result in the loss of Gram-negative bacteria, visualization of both kinds of bacteria simultaneously is often not feasible. In this study, we use embedding and sectioning to establish a universal approach for the simultaneous visualization of all bacteria within a microbial community while preserving its microarchitecture. We show that the mechanism underlying the approach is the physical slicing of the bacterial cell, thus obviating the barrier posed by the cell wall. These findings will benefit researchers within the microbiology community interested in complex microbial communities.}, }
@article {pmid41368505, year = {2025}, author = {Di Leo, D and Nilsson, E and Krinos, A and Pinhassi, J and Lundin, D}, title = {The Nextflow nf-core/metatdenovo pipeline for reproducible annotation of metatranscriptomes, and more.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e20328}, pmid = {41368505}, issn = {2167-8359}, mesh = {*Software ; Reproducibility of Results ; Workflow ; *Transcriptome ; *Computational Biology/methods ; *Molecular Sequence Annotation/methods ; *Metagenomics/methods ; }, abstract = {Metatranscriptomics-the sequencing of community RNA-has become a popular tool in microbial ecology, proving useful for both in situ surveys and experiments. However, annotating raw sequence data remains challenging for many research groups with limited computational experience. Standardized and reproducible analyses are important to enhance transparency, comparability across studies, and long-term reproducibility. To simplify metatranscriptome processing for biologists, and to promote reproducible analyses, we introduce nf-core/metatdenovo, a Nextflow-based workflow. Nextflow pipelines run on different computing platforms, from standalone systems to high-performance computing clusters and cloud platforms (e.g., AWS, Google Cloud, Azure) and use container technology such as Docker or Singularity to reproducibly provision software. Biologists can access the pipeline using either the command line or the Seqera platform, which provides a web browser-based interface to Nextflow pipelines. Collaborating with nf-core ensures high-quality, documented, reproducible workflows. Our nf-core/metatdenovo pipeline adheres to these established standards, enabling FAIR metatranscriptome de novo assembly, quantification, and annotation.}, }
@article {pmid41367422, year = {2025}, author = {Yu, H and Guo, Y and Li, J and Fu, R and Zhang, Y and Guo, W}, title = {Disruption of the gut bile acid-microbiota axis precedes severe bronchopulmonary dysplasia in preterm infants.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1705965}, pmid = {41367422}, issn = {1664-302X}, abstract = {BACKGROUND: Bronchopulmonary dysplasia (BPD) remains a major cause of morbidity in preterm infants, yet current diagnostic criteria are delayed and underlying mechanisms are incompletely defined. Evidence suggests that intestinal dysbiosis may influence pulmonary outcomes via the gut-lung axis, but the metabolic mediators of this interaction remain unclear.<br><br>METHODS: We conducted a prospective cohort study of 50 preterm infants (&#x2264; 32 weeks gestation), stratified by BPD severity at 36 weeks. Stool samples collected on postnatal day 7 underwent 16S rRNA sequencing and targeted bile acid metabolomics. Differential features were identified via multivariate statistics and LEfSe. Spearman correlation analysis explored bile acid-microbiota interactions. An interpretable machine learning model (XGBoost) incorporating bile acid and microbial features was developed and validated using five-fold cross-validation and an independent test set.<br><br>RESULTS: Infants with severe BPD showed significantly reduced levels of 16 bile acids-including primary, secondary, and sulfated species-compared to non-BPD controls. Gut microbiome &#x3b2;-diversity differed significantly among groups, with enrichment of opportunistic Proteobacteria (e.g., Brevundimonas) in severe BPD. Negative correlations were observed between depleted bile acids and enriched bacterial genera. The XGBoost model predicted BPD severity with 80% accuracy (AUC = 0.91), leveraging key features such as chenodeoxycholic acid (CDCA), hyocholic acid (HCA), and Brevundimonas.<br><br>CONCLUSIONS: Preterm infants who develop severe BPD exhibit early disruption of the bile acid-microbiota axis, characterized by reduced bile acid levels and enrichment of opportunistic taxa. Integrating these features within interpretable machine-learning models enables accurate early risk stratification and provides mechanistic insights beyond traditional inflammation-based frameworks. Validation in larger, multicenter cohorts is warranted to refine biomarker panels and explore targeted interventions that modulate bile acid signaling or microbial ecology to prevent or attenuate BPD.}, }
@article {pmid41366526, year = {2025}, author = {Zhang, Y and Zhou, J and Wu, M and Wang, Z and Zhang, N and Wang, W}, title = {Impact of Different Aquaculture Densities on the Growth Performance and Intestinal Health of Triploid Rainbow Trout (Oncorhynchus mykiss) Fry in High-altitude Environments.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02653-7}, pmid = {41366526}, issn = {1432-184X}, abstract = {The high-altitude regions of the Tibet Autonomous Region possess abundant cold-water resources, with annual average water temperatures suitable for culturing triploid rainbow trout. However, environmental challenges-including low atmospheric pressure, hypoxic water conditions, and significant diurnal temperature fluctuations-necessitate precise optimization of stocking density. Inadequate densities result in suboptimal resource utilization, whereas excessive densities induce chronic stress, leading to suppressed growth, reduced survival, and intestinal microbiota dysbiosis. Currently, research on appropriate stocking densities under these specific conditions remains limited. This study investigated the effects of stocking density on growth performance, intestinal microbiota, and tissue health of triploid rainbow trout, to identify the optimal density to support sustainable aquaculture in high-altitude plateau areas. Three stocking densities were tested over a 60-day culture period in 0.25 m[3] cylindrical tanks (radius 0.45 m, water depth 0.45 m, adjusted for internal volume): Low-Density (LD, 100 fish/barrel), Medium-Density (MD, 200 fish/barrel), and High-Density (HD, 300 fish/barrel). Results demonstrated that the final body weight (Wt) and specific growth rate (SGR) in the LD treatment were significantly higher than those in the HD group (Wt: P ≤ 0.009; SGR: P ≤ 0.019). Survival rate was also significantly greater in the LD treatment compared to HD (P < 0.036), with values of 84.67%, 80.83%, and 72.67% for LD, MD, and HD, respectively. Alpha diversity of both water and gut microbial communities varied with stocking density. Principal component analysis (PCA) revealed differentiated clustering of microbial communities in water and the intestine across density treatments (Water: P = 0.35; intestinal microbiota: P = 0.7). The dominant phyla in aquatic and intestinal microbiomes were Proteobacteria, Firmicutes, and Bacteroidetes. In intestinal samples, the genus Pseudomonas was significantly more abundant in the HD and MD treatments than in the LD treatment. Co-occurrence network analysis revealed a higher average degree in LD and MD treatments, suggesting enhanced stability of microbial ecosystems in both the intestine and water under these conditions. In conclusion, low and medium stocking densities are more suitable for cultivating triploid rainbow trout in high-altitude plateau environments. These findings provide a scientific basis for ecologically sound, efficient, and healthy aquaculture practices for this species in alpine regions.}, }
@article {pmid41365804, year = {2025}, author = {Thompson, AR and Adams, BJ and Hogg, ID and Yooseph, S}, title = {Evidence for Trace Gas Metabolism and Widespread Antibiotic Synthesis in an Abiotically Driven, Antarctic Soil Ecosystem.}, journal = {Environmental microbiology reports}, volume = {17}, number = {6}, pages = {e70249}, doi = {10.1111/1758-2229.70249}, pmid = {41365804}, issn = {1758-2229}, support = {ANT 2133685//National Science Foundation/ ; OPP-2224760//National Science Foundation/ ; DBI-2400009//National Science Foundation/ ; OAC-2408259//National Science Foundation/ ; OPP-1043681//National Science Foundation/ ; OPP-1559691//National Science Foundation/ ; OPP-2129685//National Science Foundation/ ; //Antarctica New Zealand (Event K024)/ ; //New Zealand Antarctic Research Institute (Event K024)/ ; //Monte L. Bean Life Science Museum, the Department of Biology, Brigham Young University/ ; //Kravis Department of Integrated Sciences, Claremont McKenna College/ ; }, mesh = {Antarctic Regions ; *Soil Microbiology ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; Metagenome ; *Anti-Bacterial Agents/biosynthesis ; Ecosystem ; Soil/chemistry ; *Gases/metabolism ; }, abstract = {The McMurdo Dry Valleys (MDVs) of Antarctica are a uniquely pristine, low-biodiversity model system for understanding fundamental ecological phenomena, the impact of a warming climate on ecosystem functioning, community structure and composition and the dynamics of adaptation. Despite the scientific value of this system, we still know little about the functional ecology of its biota, especially the bacteria. Here, we analysed the bacterial taxonomic and functional diversity of 18 shotgun metagenomes using the VEBA metagenome processing pipeline. We recovered 701 medium-to-high quality metagenome-assembled genomes (MAGs) (≥ 50% completeness and contamination < 10%) and 201 high-quality MAGs (≥ 80% completeness and < 10% contamination), almost 50% more than found in similar sites previously. We found that: (1) community composition shifts along environmental gradients correlated with soil moisture, elevation and distance to the coast; (2) many MDV bacteria are capable of performing trace gas metabolism; (3) genes associated with antibiotic-mediated competitive interactions (e.g., antibiotic biosynthesis and antibiotic resistance genes) are widespread; and (4) MDV bacteria employ survival strategies common to bacteria in similarly extreme environments. This study provides novel insight into microbial survival strategies in extreme environments and lays the groundwork for a more comprehensive understanding of the autecology of MDV bacteria.}, }
@article {pmid41364266, year = {2025}, author = {Carrasco, N and Miranda, MH and Aristimuño Ficoseco, C and Nader-Macías, MEF and LeBlanc, JG}, title = {Lactic acid bacteria: potentials in canine formulas for puppies.}, journal = {Veterinary research communications}, volume = {50}, number = {1}, pages = {70}, pmid = {41364266}, issn = {1573-7446}, support = {PICT 2018-00473//MINCYT-ANPCYT:/ ; 2019-00942 and 2021-00071//Mincyt-Anpcyt/ ; }, mesh = {Animals ; Dogs/microbiology ; *Probiotics ; *Animal Feed/microbiology/analysis ; *Lactobacillales/physiology ; }, abstract = {The use of probiotics and natural nutraceuticals with demonstrated therapeutic effects for companion animals is becoming increasingly popular in the veterinary community. Probiotics are alternative to antibiotics, which produce adverse effects, such as promoting bacterial resistance and altering the intestinal microbial ecology and in turn affecting the animal's health. In this study, the in vitro safety and technological characteristics of previously isolated beneficial canine strains were evaluated for the design of a probiotic formulation for dogs. The screening of inhibitory substances production was performed in 100 isolates by plate diffusion technique. 30 strains were pre-selected to evaluate their in vitro safety and innocuity by phenotypic and genotypic antibiotic resistance and expression of pathogenicity enzymes related to virulence factors. Finally, 10 were selected to assay their tolerance to gastrointestinal conditions and stress situations such as high temperatures and solute concentrations by microplate assays. Compatibility between the selected strains was also determined in order to include them in a probiotic multi-strain formulation for canines. According to the results obtained, some strains showed inhibitory activity against common pathogens, and 38% were able to produce H2O2. Antibiotic resistance genes were detected in only one of the selected strains, none evidenced gelatinase or lecithinase activity and most isolates showed alpha and gamma hemolysis. Resistance to gastrointestinal tract and stress conditions was strain dependent. The compatible strains with complementary beneficial characteristics were: Lactobacillus johnsonii 67, Lactiplantibacillus plantarum 74, Ligilactobacillus salivarius 84 and Pediococcus acidilactici 81 and are being included in the design of a probiotic formulas to be evaluated in small dogs.}, }
@article {pmid41364243, year = {2025}, author = {Xie, T and Lin, Y and Jia, P and Li, X}, title = {Warming Promotes Deterministic Assembly of Bacterial and Fungal Communities in Drylands.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02668-0}, pmid = {41364243}, issn = {1432-184X}, support = {32061123006//National Natural Science Foundation of China/ ; }, abstract = {Warming is altering the functioning of desert ecosystems in global drylands. Microbial communities are crucial for maintaining these ecosystems, yet how their co-occurrence networks and assembly mechanisms respond to warming remains unclear. Using 16 S and ITS rRNA amplicon sequencing, we examined bacterial and fungal community composition and structure. Further, we investigated cross-trophic bacterial-fungal interactions via inter-domain ecological network analysis. Warming significantly altered the diversity, composition, and structure of both bacterial and fungal communities. It increased bacterial network complexity but simplified the fungal network. Notably, warming enhanced cross-trophic interactions between bacteria and fungi, facilitating the maintenance of microbial hierarchical interactions, particularly bacterial network complexity. However, microbial keystone taxa declined dramatically under warming, 41.18% of these belonged to Ascomycota. Neutral community models and normalized stochastic ratio-based analyses revealed that deterministic processes dominated community assembly, with warming increasing their relative importance by 8-46%. This suggests a potential deterministic environmental filtering induced by warming. Collectively, these findings advance our understanding of the ecological mechanisms and microbial interactions underpinning rhizospheric communities in drylands under future climate change.}, }
@article {pmid41363836, year = {2025}, author = {Wang, B and Zhang, J and Zhu, X and Wang, Y and Teng, HH}, title = {Mineral substrates as evolutionary drivers of soil microbial diversity through the rare biosphere.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0201125}, doi = {10.1128/aem.02011-25}, pmid = {41363836}, issn = {1098-5336}, abstract = {UNLABELLED: Minerals are fundamental yet underappreciated drivers of microbial ecology. Traditionally viewed as passive nutrient sources or inert scaffolds, their broader ecological roles remain poorly defined. This study investigates the evolutionary influence of substrates (minerals and rocks) on soil bacterial communities through serial passage evolution experiments. Soil-derived microbial consortia from three distinct locations were exposed to nutritive (olivine, granite, diorite) and non-nutritive (quartz, kaolinite, montmorillonite) substrates under nutrient-rich conditions to isolate substrate-specific effects. Results revealed systemic variations of community structure across all treatments, characterized by elevated Firmicutes/Bacteroidetes ratio and taxonomic changes predominantly driven by rare taxa. These discoveries indicate that, under the influence of substrates, the communities shifted toward ones that preferentially utilize more labile carbon. Crucially, the acute responsiveness of rare taxa to mineral-induced environmental selection suggests that, although abundant taxa appeared to maintain core community functions, the rare biosphere facilitated niche specialization and functional diversification. These findings position minerals as dynamic drivers of microbial ecology and evolution, highlighting the mineralosphere as a critical microhabitat where abiotic properties govern biodiversity, functional redundancy, and evolutionary innovation in soil ecosystems.<br><br>IMPORTANCE: Even under nutrient-rich conditions, non-nutritive and chemically inert minerals, exemplified by quartz, actively reshape microbial community assembly. Through controlled serial-passage experiments, we show that distinct substrates selectively enrich rare biosphere members that expand functional potential and seed adaptation, while dominant taxa sustain core processes. These results reveal that mineral surface properties and physical interfaces, rather than nutrient supply, govern microbial diversification and evolutionary trajectories. Accordingly, the mineralosphere emerges as a dynamic microhabitat where abiotic complexity regulates biodiversity, metabolism, and long-term community succession. This reframes minerals and rocks as active ecological and evolutionary agents, bridging geomicrobiology and evolutionary ecology, with implications for soil health, biogeochemical cycling, and the origin and maintenance of microbial diversity.}, }
@article {pmid41363449, year = {2025}, author = {Meyer, KM and Lindow, SE}, title = {Microbial dispersal from surrounding vegetation influences phyllosphere microbiome assembly of corn and soybean.}, journal = {mBio}, volume = {}, number = {}, pages = {e0333525}, doi = {10.1128/mbio.03335-25}, pmid = {41363449}, issn = {2150-7511}, abstract = {Non-crop plants surrounding agricultural fields provide numerous ecological services to crops but have rarely been considered a source of microorganisms during the early stages of crop growth. In this study, we test whether crops in close proximity to surrounding woodland habitat fragments develop a denser microbiome that more closely resembles the microbiome composition of the surrounding vegetation than plants farther away. We sampled epiphytic bacteria from corn and soybean plants weekly for 4 (corn) and 3 (soybean) weeks during early development using a spatially explicit design, and on the final time point, we sampled additional cohorts of younger leaves. To contextualize the source strength of the surrounding vegetation, we also sampled soil at each sampling location. Both crop species exhibited a microbiome density gradient and a decay of microbiome similarity to the surrounding vegetation over a distance of 100 m from the vegetation at many time points. Phyllosphere microbiome similarity to the soil tended to increase into the field interior. The strength of host microbiome filtering also depended on the proximity to the surrounding vegetation, with intermediate to most distant locations exhibiting the highest values of host filtering. Last, the microbiomes of younger leaves tended to more closely resemble those of the older surrounding conspecific leaves than the soil or surrounding woodland vegetation. Overall, our study demonstrates that dispersal of bacteria from nearby leaves can shape the abundance and composition of developing crop phyllosphere microbiomes and highlights the diminishing role that soil plays when plant sources are closer or more abundant.IMPORTANCEA central concern in microbial ecology is understanding the sources of microbial colonists and how proximity to such sources impacts community assembly. This area of research is especially important for plants during early stages of development, where the arrival of leaf-specialized bacteria plays an influential role in priming plant immunity and consequently promoting disease resistance. In this study, we test the effect of dispersal from surrounding vegetation on the phyllosphere assembly of corn and soybean using a time series over the early stages of growth. Our work demonstrates that at these early developmental stages, non-crop vegetation surrounding croplands acts as a meaningful source of phyllosphere microorganisms. We further show that the influence of soil on the phyllosphere depends on host proximity to surrounding vegetation and that microbiomes of young leaves emerging on more mature plants tend to be more influenced by older surrounding crop leaves than soil or non-crop leaves.}, }
@article {pmid41359884, year = {2025}, author = {Zhang, Q and Zhou, Z and Cheung, YM and Yeung, HW and Li, M and He, C and Tian, XY and Li, C and Wong, WT}, title = {Hydroxylation-Driven Microbial and Metabolic Reshaping: Coumarin Derivatives as Novel Prebiotics for Aging Gut Health.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.5c10344}, pmid = {41359884}, issn = {1520-5118}, abstract = {This study aimed to investigate the therapeutic potential of three naturally occurring coumarin derivatives─coumarin, umbelliferone, and esculetin, which exhibit distinct hydroxylation patterns in mitigating age-related gut dysbiosis through in vitro colonic fermentation models. By integrating antioxidant profiling, short-chain fatty acid (SCFA) profiling, 16S rRNA sequencing, and metabolomics, we assessed their structural specificity in modulating microbial ecology and metabolic pathways. Results demonstrated a hydroxylation-dependent hierarchy in antioxidant capacity and differential regulation of SCFA production. Coumarin partially enriched g__Turicimonas but showed limited SCFA induction, whereas umbelliferone selectively enhanced butyrate synthesis and enriched g__Bacteroides. Esculetin exhibited the broadest impact, characterized by both increased acetate and propionate levels and the concurrent enrichment of g__Ileibacterium and g__Enterococcus. Metabolomic profiling further revealed that three coumarins released antioxidant metabolites, correlating with microbiota-driven detoxification. These findings highlight hydroxylated coumarins as promising prebiotics that counter age-related dysbiosis via multitarget microbiota-metabolite modulation, providing a mechanistic basis for antiaging strategies.}, }
@article {pmid41359033, year = {2025}, author = {ElKhouri-Vidarte, N and Useros, F and Lara, E}, title = {Beneath the Cedars: Exploring the Water-Energy Balance on Arcellinida Biodiversity in Lebanon's Cedar Forests.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02666-2}, pmid = {41359033}, issn = {1432-184X}, abstract = {The distribution of diversity in function of climate has been largely studied in plants and animals, leading to a large body of literature on macroecological rules applied to large geographic scales. However, the applicability of these rules to microbes has almost never been tested at local scales. Arcellinida are a diverse group of protists known to be narrow ecological specialists and constitute therefore an excellent group to test general rules validated on "macrobes", like the water-energy balance that stipulates that biodiversity peaks with humidity and temperature. In order to test that hypothesis, we collected 122 samples from four cedar forests situated along an elevation gradient in Lebanon, spanning different local climates. We evaluated their diversity using an Arcellinida-specific metabarcoding approach based on the cytochrome oxidase subunit I gene. Our study shows that Arcellinida richness and phylogenetic diversity follow a unimodal distribution, peaking at mid-elevations. β-diversity was chiefly the product of turnover, illustrating the high spatial heterogeneity of the forests. Precipitation and actual evapotranspiration were identified as key drivers of diversity, thus supporting the water-energy balance hypothesis. Communities situated at higher or lower elevation were, to a large extent, subsets of more diverse mid-elevation assemblages, which designates the latter as biodiversity sources. These results suggest that, under the increasing aridification of the Middle East due to climate change, Arcellinida communities will lose diversity and will undergo a process of homogenisation, with possible consequences on ecosystem functioning.}, }
@article {pmid41358850, year = {2025}, author = {Winther-Have, CS and Rasmussen, JA and Zhai, X and Nielsen, DS and Sicheritz-Pontén, T and Gopalakrishnan, S and Clokie, MRJ and Middelboe, M and Limborg, MT}, title = {Ecological strategies of bacteria shape inherent phage diversity in Atlantic salmon gut microbiomes.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf272}, pmid = {41358850}, issn = {1751-7370}, abstract = {Understanding host-specific phage diversity is essential for deciphering the complex dynamics shaping microbial ecology and evolution. However, the lack of inherent host associations between uncultivated bacteria and their viruses remains a major limitation to understanding the drivers of viral diversity and its role in bacterial ecology, particularly given the intricate specificity of phage-host interactions. The naturally low complexity of the gut microbiota within piscivorous fish, such as Atlantic salmon (Salmo salar), makes it a valuable model for unravelling ecological patterns of viral diversity in the context of a limited bacterial species composition, and to explore the impact of an invading pathogen on the "steady-state" viral community. The intestinal microbiota of the salmon studied here, was in some cases dominated by a salmon-associated Mycoplasma or increasing levels of an opportunistic Aliivibrio, the latter observed in response to a disease outbreak. The two bacteria are distinctively different in their ecological strategies and their overall genomic and functional properties. A pronounced difference was observed in the gut viral communities and diversity, depending on whether it was dominated by a commensal or an invading bacterial species. Samples dominated by Mycoplasma sp. had few to no viruses, whereas samples dominated by Aliivibrio sp. had viral communities comprising up to 22 viral taxonomic operational units. This study provides unique insights into the significance of bacterial ecological trade-offs linked to niche adaptation and how these affect the associated viral communities in a natural host-controlled environment.}, }
@article {pmid41358825, year = {2025}, author = {Kumar, C and Bertani, I and Chaouachi, M and Myers, MP and Garbeva, P and Bez, C and Venturi, V}, title = {AHL quorum sensing regulates T6SS and volatiles production in rice root-colonizing Enterobacter asburiae AG129.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaf120}, pmid = {41358825}, issn = {1574-6941}, abstract = {Pseudomonadota (formerly Proteobacteria) commonly use a contact independent cell-cell communication system known as quorum sensing (QS) mediated by N-acyl-homoserine lactone (AHL) signal molecules. The canonical AHL QS system involves a luxI-family gene which encodes an AHL synthase, and a luxR-family gene, which encodes a transcriptional regulator responsive to the cognate AHL(s). This study involves the AHL QS system of Enterobacter asburiae AG129, a root associated strain isolated from rice (Oryza sativa). E. asburiae AG129 produces the N-butanoyl homoserine lactone (C4-AHL) signal molecule. Genome sequencing of strain AG129 revealed the presence of a canonical AHL QS system, comprising genetically adjacent easI-like and easR-like genes. A genomic easI knockout mutant was no longer able to produce AHLs, but the in-trans complementation with a plasmid carrying the easI gene restored the AHL production. QS mediated by AHLs in AG129 was found to influence rice root colonization, and secretome analysis highlighted a significant regulatory role in the expression of Type VI secretion system (T6SS) proteins. GC-MS analysis identified sixteen volatile organic compounds (VOCs) that were more abundantly emitted by the wild-type strain compared to the easI mutant. Overall, our findings suggest that AHL-based QS in E. asburiae AG129 positively regulates T6SS expression and VOC production, while negatively affecting root colonization. This study is among the first to explore the role of QS signaling in a bacterial root-endophyte, providing evidence of a connection between QS activity and the ability of the bacterium to inhabit, compete and colonize the plant endosphere.}, }
@article {pmid41358465, year = {2025}, author = {Tang, X and Wang, R and Yang, S and Wang, G and Luo, J and Peng, S and Liang, K and Yang, J}, title = {Species-Specific Antibacterial Materials: From Design to Application.}, journal = {Small (Weinheim an der Bergstrasse, Germany)}, volume = {}, number = {}, pages = {e07114}, doi = {10.1002/smll.202507114}, pmid = {41358465}, issn = {1613-6829}, support = {SKLOD-2025RD002//State Key Laboratory of Oral Diseases/ ; 2023YFSY0048//Sichuan Science and Technology Program/ ; 82170949//National Natural Science Foundation of China/ ; 82270970//National Natural Science Foundation of China/ ; 82470967//National Natural Science Foundation of China/ ; 51903169//National Natural Science Foundation of China/ ; }, abstract = {Traditional broad-spectrum antibacterial strategies are known to contribute to the increase in drug-resistant microorganisms and the disruption of microbial ecological balance. To break this stalemate, researchers have begun to explore selective antibacterial strategies that minimize the impact on normal flora and maintain microbial ecological balance. Species-specific antibacterial materials, which can target particular bacterial species or even specific strains, offer innovative perspectives and methodologies for the prevention and treatment of infectious diseases. This review first explores the selective mechanisms that underpin species-specific antibacterial strategies, summarizes the main classifications of species-specific antibacterial strategies, investigates the engineering techniques employed in the development of such materials, and emphasizes the importance of structure-activity relationships in the design of species-specific antibacterial materials. It explores techniques like peptide modification, nanoparticle engineering, and genetic manipulation, highlighting that a thorough understanding of the structure and function of antibacterial materials is essential for improving their efficacy and specificity. Ultimately, it anticipates the potential applications of species-specific antibacterial materials in disease diagnosis and treatment, while addressing the challenges associated with clinical translation. It is expected that this comprehensive review will offer novel perspectives for the development of species-specific antibacterial materials.}, }
@article {pmid41358355, year = {2025}, author = {Shen, S and Xu, Y and Liu, Z and Luo, Y and Wang, R and Li, G and Liu, Y}, title = {Combined application of biochar and halophyte intercropping enhances cucumber yield and quality by ameliorating soil properties in a continuous cropping system.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1711099}, pmid = {41358355}, issn = {1664-462X}, abstract = {Biochar amendment and halophyte intercropping are viable strategies for alleviating soil degradation in greenhouse systems, specifically the secondary salinization and autotoxicity induced by continuous cropping. Nevertheless, the potential synergistic effects of combining these practices remain poorly understood. This study investigated their synergistic effects on soil properties, microbial communities, and cucumber performance. A pot experiment was conducted with the following treatments: soil without amendment (CK), biochar (B), Paspalum vaginatum intercropping (S), and biochar combined with Paspalum vaginatum intercropping. The results showed that BS treatment led to the highest increases in soil organic carbon content, pH, total nitrogen content, available phosphorus content, and available potassium content compared to CK (p<0.05). Concurrently, BS significantly reduced available nitrogen, electrical conductivity, Na[+], SO4 [2-], and Cl[-] levels, while total phosphorus remained unaffected. Cucumber yield increased significantly by 11.50% and 27.12% under B and BS treatments, respectively, whereas S showed no significant effect. BS also achieved the highest fruit quality enhancement, followed by B and S. Notably, B and S treatments displayed the highest and lowest K[+], Ca[2+]and Mg[2+] accumulation, respectively, whereas the BS treatment led to K[+] and Ca[2+] concentrations that were significantly lower than those in the B treatment. Soil bacterial diversity was significantly enhanced under BS. The PLS-PM identified the alleviation of soil salinity and acidity, along with improved nutrient availability, as the primary drivers for enhanced crop performance, with soil bacterial diversity playing a secondary yet significant role. These findings suggest that biochar combined with intercropping (BS) effectively mitigates continuous cropping obstacles in greenhouse systems by synergistically improving soil health and microbial ecology.}, }
@article {pmid41358162, year = {2025}, author = {Nicolas-Asselineau, L and Speth, DR and Zeller, LM and Woodcroft, BJ and Singleton, CM and Liu, L and Dueholm, MKD and Milucka, J}, title = {Occurrence and temporal dynamics of denitrifying protist endosymbionts in the wastewater microbiome.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf209}, pmid = {41358162}, issn = {2730-6151}, abstract = {Effective wastewater treatment is of critical importance for preserving public health and protecting natural environments. Key processes in wastewater treatment, such as denitrification, are performed by a diverse community of prokaryotic and eukaryotic microbes. However, the diversity of the microbiome and the potential role of the different microbial taxa in some wastewater treatment plant setups is not fully understood. We aimed to investigate the presence and diversity of denitrifying bacteria of the candidate family Azoamicaceae that form obligate symbioses with protists in wastewater treatment plants. Our analyses showed that denitrifying endosymbionts belonging to the Ca. Azoamicus genus are present in 20%-50% of wastewater treatment plants worldwide. Time-resolved amplicon data from four Danish WWTPs showed high temporal fluctuations in the abundance and composition of the denitrifying endosymbiont community. Twelve high-quality metagenome-assembled genomes of denitrifying endosymbionts, four of which were circular, were recovered. Genome annotation showed that a newly described, globally widespread species, Ca. Azoamicus parvus, lacked a nitrous oxide reductase, suggesting that its denitrification pathway is incomplete. This observation further expands the diversity of metabolic potentials found in denitrifying endosymbionts and indicates a possible involvement of microbial eukaryote holobionts in wastewater ecosystem dynamics of nitrogen removal and greenhouse gas production.}, }
@article {pmid41357478, year = {2025}, author = {Ni, J and Tang, Y and Zhou, F and Hu, Y and Liu, L and Huang, M and Ouyang, H and Xie, C}, title = {Association between serum total cholesterol levels and Crohn's clinical disease severity: a retrospective cross-sectional study.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1708838}, pmid = {41357478}, issn = {2296-858X}, abstract = {BACKGROUND: This retrospective cross-sectional study aimed to investigate the relationship between serum total cholesterol (TC) levels and the clinical activity of Crohn's disease (CD).<br><br>METHODS: One hundred and four patients with Crohn's disease (CD) and twenty healthy volunteers were included in the analysis. Serum uric acid (SUA) levels and indicators related to lipid metabolism were measured within 1 week before undergoing endoscopic and CT enterography (CTE) examinations. Patients were divided into groups based on their Crohn's Disease Activity Index (CDAI) scores.<br><br>RESULTS: Patients were categorized into mild and moderate groups, with no patients meeting the criteria for severe CD. The serum uric acid (SUA) and triglyceride (TG) levels were similar between CD patients and the control group (p > 0.05). However, the levels of total cholesterol (TC), apolipoprotein A1 (apo A1), apolipoprotein B (apo B), high-density lipoprotein cholesterol (HDL-C), and low-density lipoprotein cholesterol (LDL-C) were higher in the control group (p < 0.05). The TC and LDL-C levels were lower in the moderate patients compared to those in mild group (p < 0.05). TC &#x2264; 3.5 mmol/L was identified as an independent risk factor for more severe disease (OR = 4.50, 95%CI 1.612-12.561, p = 0.004). TC levels were correlated to both CRP and CDAI scores negatively (p < 0.05).<br><br>CONCLUSION: TC may serve as a potential supplementary marker for clinical disease activity in CD, but further research, including longitudinal studies, is needed to confirm its reliability.}, }
@article {pmid41356477, year = {2025}, author = {Chakraborty, A and Roy, A and He, S and Castellano-Hinojosa, A and Asiegbu, FO and Coutinho, TA}, title = {Editorial: Forest microbiome: dynamics and interactions in the anthropocene era.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1729625}, pmid = {41356477}, issn = {1664-302X}, }
@article {pmid41356467, year = {2025}, author = {Castelli, L and García-Amado, MA and Rudolf, CA and Contreras, M and Espinosa-Blanco, AS and Godoy-Vitorino, F}, title = {Microbial diversity in the critically endangered Orinoco crocodile (Crocodylus intermedius): influence of body site and Helicobacter spp. on microbiota composition.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1697111}, pmid = {41356467}, issn = {1664-302X}, abstract = {INTRODUCTION: The Orinoco crocodile (Crocodylus intermedius), a critically endangered species from Colombia and Venezuela Llanos, continues to face significant threats despite existing legal protections. Understanding the microbial diversity associated with this species, particularly in captive populations, can offer valuable insights into its health status and inform conservation strategies. In this study, we characterized the bacterial microbiota of C. intermedius, focusing on the influence of body site and the presence of Helicobacter spp. on microbial diversity.<br><br>METHODS: We collected oral and cloacal samples from five captive C. intermedius individuals and analyzed their bacterial microbiota using high-throughput sequencing techniques. The study specifically investigated how microbial diversity varies by body site and how the presence of Helicobacter spp. influences community structure and composition.<br><br>RESULTS: Oral samples exhibited higher microbial diversity compared to cloacal samples. This difference is likely attributable to greater environmental exposure and dietary variation affecting the oral cavity. The presence of Helicobacter spp. was associated with a marked reduction in bacterial richness and significant shifts in community composition. Samples positive for Helicobacter spp. were notably enriched in potentially pathogenic genera, including Campylobacter and Escherichia, suggesting a dysbiotic effect on the microbiota.<br><br>DISCUSSION: Our findings indicate that both body site and Helicobacter spp. presence play significant roles in shaping the microbial communities of C. intermedius. These results have important implications for reptile health management and zoonotic disease surveillance, as dysbiosis could compromise host health and facilitate pathogen transmission. Furthermore, this study underscores the role of reptiles as potential reservoirs for Campylobacter spp. and Helicobacter spp., highlighting the need for continued research into the microbial ecology of endangered species to guide conservation strategies and inform public health policies.}, }
@article {pmid41356191, year = {2026}, author = {Xiao, Y and Li, X and Fang, Y and Guo, M and Shui, M and Zhong, G and Zhou, H and Lin, C and Sun, B and Wang, S}, title = {Berberine suppresses colon inflammation via integrated modulation of host metabolism, microbial ecology, and innate immune signaling.}, journal = {Theranostics}, volume = {16}, number = {4}, pages = {2019-2036}, pmid = {41356191}, issn = {1838-7640}, mesh = {*Berberine/pharmacology ; Animals ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Immunity, Innate/drug effects ; *Colitis/drug therapy/chemically induced/microbiology ; RNA, Ribosomal, 16S/genetics ; Mice, Inbred C57BL ; Signal Transduction/drug effects ; Metabolomics ; *Anti-Inflammatory Agents/pharmacology ; Fatty Acids, Volatile/metabolism ; Male ; Inflammation/drug therapy ; Colon/drug effects/pathology ; Single-Cell Analysis ; Disease Models, Animal ; Dextran Sulfate ; Energy Metabolism/drug effects ; Interleukin-1beta/metabolism ; }, abstract = {Background: Berberine, a natural compound with unique bioactivity, has been widely used in the treatment of gastrointestinal inflammatory diseases. Despite its well-documented anti-inflammatory properties, the system-level regulatory network underlying its multifaceted mechanisms remains poorly understood. Methods: In this study, we employed a multi-level analytical approach, integrating single-cell RNA sequencing, targeted metabolomics, 16S rRNA gene sequencing, and drug-target analysis, to elucidate the integrative effects of berberine on gut microbiota-metabolism-immune interactions. Results: Single-cell RNA sequencing revealed that berberine enhances energy metabolism in intestinal cells of DSS-induced mice, thereby maintaining normal physiological functions. Targeted metabolomics analysis of short-chain fatty acids, combined with 16S rRNA gene sequencing, demonstrated that berberine supplementation significantly increases short-chain fatty acid (SCFA) levels in the intestinal environment and selectively enriches the abundance of Akkermansia. Furthermore, single-cell RNA sequencing data indicated that berberine inhibits fibroblast-to-lymphatic transformation and suppresses the expression of interleukin-1β, leading to reduced immune activation in innate immune cells. Drug-target analysis identified shared molecular targets between berberine and various immunotherapeutic agents. Conclusion: This study provides a comprehensive understanding of berberine's multi-target mechanisms and highlights its potential as a therapeutic agent for inflammatory diseases through the modulation of gut microbiota, host metabolism, and immune responses.}, }
@article {pmid41356074, year = {2025}, author = {Tsuji, K and Yoshida, H and Saba, M and Terauchi, Y and Kawauchi, M and Honda, Y and Tanaka, C and Yoshimi, A}, title = {Hydrophobins in Bipolaris maydis do not contribute to colony hydrophobicity, but their heterologous expressions alter colony hydrophobicity in Aspergillus nidulans.}, journal = {Frontiers in fungal biology}, volume = {6}, number = {}, pages = {1604903}, pmid = {41356074}, issn = {2673-6128}, abstract = {Hydrophobins are small amphiphilic proteins secreted by filamentous fungi. These proteins confer hydrophobic properties to the hyphae and conidia. Bipolaris maydis is the causal agent of southern corn leaf blight; the biological function of its hydrophobins is not clear. In the present study, we focused on the broad function of hydrophobins in the life cycle of this fungus. We found that the B. maydis genome encodes four hydrophobins-Hyp1 of class I, and Hyp2, Hyp3 and Hyp4 of class II-and all of them are expressed. We generated single disruptants of each gene, as well as triple and quadruple disruptants. No differences were detected between the wild type and any of disruptants in mycelial growth, conidiation, stress tolerance, virulence, or sexual reproduction. The colony hydrophobicity of all disruptant strains was similar to that of the wild-type strain. Complementation of a null Aspergillus nidulans mutant of dewA, which showed a significantly reduced colony hydrophobicity, with each of the four B. maydis hydrophobin genes restored the hydrophobic phenotype, although the degree of hydrophobicity varied among them. Despite the absence of any significant phenotypic changes in the B. maydis mutants generated, results strongly suggest that all four hydrophobins have retained their function in hydrophobicity. Furthermore, the results of this study suggest that the role of hydrophobins might change depending on the fungal species.}, }
@article {pmid41355978, year = {2025}, author = {Oporto-Llerena, R and Huerto-Huánuco, R and Quispe-Hualpa, Y and Palomino-Kobayashi, LA and Soza, G and Rojas-Jaimes, J and Gonzales, P and Pollack, L and Gomez, AC and Salvador-Luján, G and Cuaresma, E and Luque, N and Casapia, M and Arteaga-Livias, K and Sáenz, Y and Pons, MJ and Ruiz, J}, title = {bla OXA-51-Negative Acinetobacter calcoaceticus-baumannii Complex as a Cause of Human Infection in Peru.}, journal = {Journal of tropical medicine}, volume = {2025}, number = {}, pages = {8851906}, pmid = {41355978}, issn = {1687-9686}, abstract = {BACKGROUND: Common identification techniques do not differentiate among members of the Acinetobacter calcoaceticus-baumannii (ACB) complex, and the presence of non-baumannii Acinetobacter is often misinterpreted. The bla OXA-51 gene is located within the chromosome of Acinetobacter baumannii. Despite its plasmid dissemination to other members of the genus, it may be considered in initial species screening. Thus, this study aimed to determine the presence of bla OXA-51-negative Acinetobacter spp. as a cause of infection in Peru.<br><br>METHODS: Two hundred ninety-eight ACB complex isolates from different regions of Peru were isolated between January 2018 and March 2024. Of these, 272 and 25 were confirmed as hospital-acquired and community infections, respectively. The presence of bla OXA-51 was determined by polymerase chain reaction, and the susceptibility levels to 12 antimicrobial agents were determined.<br><br>RESULTS: The results showed that 38 (12.7%) isolates were bla OXA-51-negative. These isolates were frequent among community infections (13/25, p < 0.0001), often causing urine infections. They showed significantly lower levels of resistance to almost all antimicrobial agents tested, and most of them were recovered from regions outside metropolitan Lima.<br><br>CONCLUSION: A relevant number of infections by non-baumannii Acinetobacter species in Peru is suggested, highlighting the need for systematic identification of these species in the country.}, }
@article {pmid41355197, year = {2025}, author = {Yi, F and Shao, L and Wu, S and Cheng, K and Zhang, Z and Li, Y and Hu, S and Wan, J and Liu, Q and Guo, L and Zhang, X and Shang, B and Yu, J and Zheng, H and Liu, J and Cai, Y and Zhang, X}, title = {Cotton gland formation genes GbCGF2/3 positively regulate Verticillium wilt resistance through modulating suberin biosynthesis.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.70809}, pmid = {41355197}, issn = {1469-8137}, support = {2022YFD1200303//National Key Research and Development Program of China/ ; 251111113800//Key Research and Development Project of Henan Province/ ; 32070262//National Natural Science Foundation of China/ ; 32401779//National Natural Science Foundation of China/ ; CB2024A16//State Key Laboratory of Cotton Bio-breeding and Integrated Utilization Open Fund/ ; CB2024A23//State Key Laboratory of Cotton Bio-breeding and Integrated Utilization Open Fund/ ; CB2023A14//State Key Laboratory of Cotton Bio-breeding and Integrated Utilization Open Fund/ ; CB2023A11//State Key Laboratory of Cotton Bio-breeding and Integrated Utilization Open Fund/ ; CB2025A26//State Key Laboratory of Cotton Bio-breeding and Integrated Utilization Open Fund/ ; 2024M760773//China Postdoctoral Science Foundation/ ; 234400510004//Project of Zhongyuan Scholars Workstation/ ; }, abstract = {Verticillium wilt, caused by Verticillium dahliae, is a serious vascular wilt disease in cotton (Gossypium spp.). However, the roles and mechanisms of cotton gland formation (CGF) genes in regulating cotton V. dahliae resistance remain elusive. Virus-induced gene silencing or CRISPR-/Cas9-mediated knockdown or knockout of GbCGF2/3 decreases cotton resistance to Verticillium wilt. RNA-sequencing (RNA-seq) shows lower transcript levels of the suberin biosynthetic gene fatty acyl-coenzyme A reductase 3.1 (FAR3.1) in GbCGF2/3-silenced cotton plants. Silencing or knocking out GbFAR3.1 impairs cotton resistance to V. dahliae and decreases suberin compositional monomer fatty acids (C16-C24) contents. GbCGF2/3 positively regulates GbFAR3.1 expression by binding to its promoter. Suberin deposition in the lamellae layer of the root cell wall decreases significantly in GbCGF2/3 Cas9-mediated knockout and GbFAR3.1-silenced cotton plants. Additionally, the expression of gossypol biosynthetic genes and defense-related genes PDF1.2 and PR4 in the phytohormone jasmonic acid (JA) pathway is also downregulated in GbCGF2/3-silenced or Cas9-mediated knockout plants. In conclusion, GbCGF2/3 positively regulates Verticillium wilt resistance through promoting suberin biosynthesis, gossypol accumulation and expression of JA signaling defense-related genes, providing a novel insight and strategy for breeding cotton cultivars resistant to Verticillium wilt.}, }
@article {pmid41353943, year = {2025}, author = {Zheng, Y and Zhou, X and Deng, S and Zhao, H}, title = {Spatial pattern of spring dissolved organic matter and microbial communities under dual anthropogenic-natural forcing in a tropical semi-enclosed bay.}, journal = {Marine environmental research}, volume = {214}, number = {}, pages = {107739}, doi = {10.1016/j.marenvres.2025.107739}, pmid = {41353943}, issn = {1879-0291}, abstract = {Coastal zones serve as vital interfaces between continental and oceanic ecosystems, where anthropogenic inputs strongly influence dissolved organic matter (DOM) and associated microbial processes. However, the response of DOM-microbe interactions to various human activities remains inadequately understood. In this study, we examined physicochemical parameters, DOM optical properties, and microbial community structures in surface waters of Zhanjiang Bay, which is influenced by agricultural runoff, sewage, and industrial effluent. This pattern could be attributed to the impact of agricultural runoff and sewage input. Nutrient-rich terrestrial inputs were associated with enhanced humic-like and protein-like fluorescent DOM (FDOM) and high-molecular-weight, aromatic chromophoric DOM (CDOM), accompanied by the enrichment of Cyanobacteria and Thermoplasmatota. In contrast, in the lower bay, industrial activities, particularly effluent from a steel plant, resulted in an increased humic-like and protein-like FDOM alongside low-aromatic CDOM. Additionally, an increase in Verrucomicrobiota and humification index indicated that DOM may undergo decomposition processes in addition to in situ production. Multivariate analyses (PCA, RDA) confirmed strong correlations between physicochemical parameters, DOM properties, and microbial community composition. Collectively, these findings demonstrate that anthropogenic activities primarily shape DOM characteristics, which in turn structure microbial communities, highlighting the cascading effects of anthropogenic activities in regulating coastal biogeochemistry. This study elucidates the mechanistic pathway through which anthropogenically altered DOM composition shapes microbial community assembly, providing insights into the coupling between DOM dynamics and microbial ecology in anthropogenically impacted coastal ecosystems.}, }
@article {pmid41353355, year = {2025}, author = {Todorović, I and Abrouk, D and Kyselková, M and Rey, M and López-Mondéjar, R and Raičević, V and Jovičić-Petrović, J and Moënne-Loccoz, Y and Muller, D}, title = {Fluorescent Pseudomonas spp. from suppressive and conducive soils share genomic and functional traits relevant to Fusarium graminearum disease suppression.}, journal = {BMC genomics}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12864-025-12374-3}, pmid = {41353355}, issn = {1471-2164}, support = {grant numbers 670-00-573/1/372/2019-04, 670-00-2590/1/304/2020-04, 670-00-2551/1/298/2021-04 and 670-00-1/1/317/2022-01//Ministry of Youth and Sports, Belgrade, Serbia/ ; grant numbers 964308G, 972203C and 103939T//Campus France/ ; PHC DANUBE 2020: 45296XM//Programme for Multilateral Scientific and Technological Cooperation in the Danube Region/ ; Ministry of Education, Youth and Sports of the Czech Republic, project number 8X20052//Programme for Multilateral Scientific and Technological Cooperation in the Danube Region/ ; Ministry of Education, Youth and Sports of the Czech Republic, project number 8X20052//Programme for Multilateral Scientific and Technological Cooperation in the Danube Region/ ; The Ministry of Education, Science, and Technological Development of the Republic of Serbia, project number: 451-03-01086/2020-09/07//Programme for Multilateral Scientific and Technological Cooperation in the Danube Region/ ; PHC DANUBE 2020: 45296XM//Programme for Multilateral Scientific and Technological Cooperation in the Danube Region/ ; PHC DANUBE 2020: 45296XM//Programme for Multilateral Scientific and Technological Cooperation in the Danube Region/ ; SuppressSOIL ANR-19-EBI3-0007//BiodivERsA3 ERA-Net COFUND programme/ ; SuppressSOIL ANR-19-EBI3-0007//BiodivERsA3 ERA-Net COFUND programme/ ; SuppressSOIL ANR-19-EBI3-0007//BiodivERsA3 ERA-Net COFUND programme/ ; SuppressSOIL ANR-19-EBI3-0007//BiodivERsA3 ERA-Net COFUND programme/ ; project number CZ.02.01.01/00/22_008/0004635//the Ministry of Education, Youth and Sports of the Czech Republic/ ; The Ministry of Education, Science, and Technological Development of the Republic of Serbia, project number: 451-03-01086/2020-09/07//Programme for Multilateral Scientific and Technological Cooperation in the Danube Region, The Ministry of Education/ ; grant number 451-03-137/2025-03/200116//The Ministry of Education, Science, and Technological Development of the Republic of Serbia/ ; }, abstract = {BACKGROUND: Soils suppressive to fungal pathogens harbor microbiomes that can inhibit disease development despite the presence of virulent pathogens and susceptible hosts. Fluorescent Pseudomonas are often implicated in such suppressiveness, but their genomic determinants and distribution in suppressive vs. non-suppressive (i.e., conducive) soils remain unclear.<br><br>RESULTS: We investigated the taxonomic and functional diversity of Pseudomonas populations from wheat rhizospheres in four agricultural soils with contrasting suppressiveness to Fusarium graminearum-induced seedling disease. rpoD-based metabarcoding and culture-dependent isolation revealed distinct Pseudomonas community structures linked to soil suppressiveness. However, major phylogenetic groups were shared across soils. From 406 isolates, 29 representative strains spanning seven subgroups of the P. fluorescens group were selected for whole-genome sequencing. Comparative genomics revealed 14 putative novel Pseudomonas genomospecies (dDDH&#x2009;<&#x2009;70% with closest described type strains). Genomic screening revealed wide distribution of genes linked to biocontrol and plant-growth promotion, including siderophore biosynthesis, hormone modulation, phosphate solubilization, and production of antimicrobial compounds. Biosynthetic genes for phenazine and pyrrolnitrin were detected exclusively in P. chlororaphis strains isolated from suppressive soils, and rpoD alleles corresponding to these strains were not found in conducive soils within our metabarcoding dataset. Other traits such as hydrogen cyanide, ACC deaminase, and auxin biosynthesis were broadly distributed across isolates from all soils. Functional assays demonstrated variable expression of predicted traits, indicating regulatory or environmental influence. Several strains inhibited F. graminearum mycelial growth via volatile organic compounds, while two strains also reduced conidia germination, including isolates from both suppressive and conducive soils.<br><br>CONCLUSIONS: This study demonstrates that Pseudomonas genomic traits important for biocontrol are not restricted to suppressive soils, and that functional redundancy and context-dependent expression may shape the contribution of Pseudomonas to disease suppression. Our results highlight the need for integrative analyses combining community profiling, genome-based prediction, and phenotyping to better understand microbiome-mediated plant protection. The identification of novel genomospecies and lineage-specific biosynthetic traits advances our knowledge of Pseudomonas diversity in agricultural soils and supports future development of targeted microbial consortia.}, }
@article {pmid41353279, year = {2025}, author = {Stuehrenberg, J and Kitzinger, K and von Arx, JN and Graf, JS and Lavik, G and Littmann, S and Milucka, J and Orsi, WD and Schorn, S and Speth, DR and Vuillemin, A and Wu, S and Marchant, HK and Kuypers, MMM}, title = {Urea use drives niche separation between dominant marine ammonia oxidizing archaea.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-025-67048-1}, pmid = {41353279}, issn = {2041-1723}, support = {EXC-2077-390741603//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, abstract = {Ammonia-oxidizing archaea (AOA) are among the most abundant microorganisms in the ocean and play a critical role in marine nitrogen cycling. Recently, urea has been shown to serve as an additional substrate for marine AOA, with substantial urea use in the ammonium-depleted open-ocean. Yet, the mechanisms that control urea use and potentially maintain high AOA abundances remain unclear. Here, we investigate urea and ammonia use by AOA in three contrasting marine environments, from coastal, ammonium-rich to open-ocean, ammonium-poor waters. Our combined results indicate that distinct substrate utilization strategies of Nitrosopumilus and Nitrosopelagicus control their environmental distribution. The more coastal AOA genus, Nitrosopumilus, primarily uses ammonium. In contrast, enhanced urea utilization in ammonium-limited waters is linked to the activity and growth of Nitrosopelagicus. Thus, the use of urea, and potentially other organic-N compounds by Nitrosopelagicus plays a major role in fueling open-ocean nitrification and sustaining primary productivity in these vast regions.}, }
@article {pmid41352799, year = {2026}, author = {Cheng, W and Jiang, C and Pan, T and Zhu, Q and Liu, G and Li, N and Wu, Z and Li, X}, title = {Effects of quinoa addition on physicochemical properties, microbiome profiles, and volatile organic compounds in medium-temperature Daqu.}, journal = {Food research international (Ottawa, Ont.)}, volume = {223}, number = {Pt 1}, pages = {117868}, doi = {10.1016/j.foodres.2025.117868}, pmid = {41352799}, issn = {1873-7145}, mesh = {*Volatile Organic Compounds/analysis ; *Chenopodium quinoa/chemistry ; *Microbiota ; Fermentation ; Food Microbiology ; Food Handling/methods ; Temperature ; }, abstract = {The selection of raw materials plays a pivotal role in shaping the microbial ecology and metabolic functions of Daqu, a fermentation starter widely used in Baijiu production. Quinoa (Chenopodium quinoa Willd.), a pseudocereal rich in proteins, polyphenols, and bioactive compounds, has recently gained attention as a functional food ingredient. In this study, Quinoa was used to replace a certain proportion of wheat and incorporated into the making process of medium-temperature Daqu (MTD), and its effects on the physicochemical properties, microbial community dynamics, and volatile organic compound (VOC) were investigated. Compared with traditional MTD, quinoa-supplemented Daqu (L-MTD) exhibited significantly higher starch (increased by 8.4 %), reducing sugar (increased by 12.7 %), and acidity (increased by 15.3 %) levels (p < 0.05), along with enhanced esterification and fermentation power of its central part (increased by 10.2 % and 9.5 %, respectively, p < 0.05). High-throughput sequencing revealed that quinoa addition reshaped the microbial community by enriching beneficial lactic acid bacteria (e.g., Lactobacillus and Weissella) and reducing potential spoilage fungi (e.g., Aspergillus and Rhizopus). In addition, Lactobacillus and Saccharomycopsis showed strong correlations with the accumulation of esters and aromatic compounds, including ethyl lactate, phenethyl acetate, DL-(-)-pantoyl lactone, and benzyl alcohol. Redundancy analysis (RDA) indicated strong correlations between Lactobacillus and Saccharomycopsis with the accumulation of esters (such as ethyl acetate and ethyl lactate) and aromatic compounds (such as benzyl alcohol and phenethyl acetate), providing a research basis for identifying functional microbial strains in MTD and conducting subsequent micro-fermentation experiments. These findings highlight the potential of quinoa as a functional additive that modulates the microbial ecology and enhances the aroma complexity of Daqu, thereby offering a novel strategy for improving the quality and potential health value of traditional fermented products.}, }
@article {pmid41352467, year = {2025}, author = {Nalladiyil, A and Khuntia, HK and Chanakya, HN and Babu, GLS}, title = {Treatment of ultra-high-strength compost leachate using an anaerobic biomass biofilm reactor.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {133774}, doi = {10.1016/j.biortech.2025.133774}, pmid = {41352467}, issn = {1873-2976}, abstract = {Leachate produced during the composting of the organic fraction of municipal solid waste (OFMSW) is highly concentrated and acidic (chemical oxygen demand (COD) -125 g/L, pH 3-5). Its recalcitrant nature necessitates long hydraulic retention times for effective digestion, which, in turn, leads to high organic loads and, consequently, large reactor footprints. This study evaluated the treatment performance, bioenergy potential, and microbial ecology of the Anaerobic Biomass Biofilm Reactor (ABBR) for ultra-high strength leachate treatment. The reactor employed lignocellulosic wastes such as coir, ridge gourd, and dried acacia leaves as natural biofilm supports. Operated over 180 days with a gradually increasing organic loading rate from 1.1 to 11.2 kg COD/m[3]/d, the reactor achieved 92.9 % COD removal and a methane yield of 0.357 NL/g COD removed at the maximum loading rate. Moreover, the reactor also exhibited exceptionally high space utilization efficiency (3.5-4 L CH4/L/d), highlighting its enhanced volumetric productivity and effectiveness in treating high-strength leachate. Metagenomic analysis revealed a diverse microbial community, with Methanospirillum (3 %) and Methanosaeta (2.6 %) identified as dominant archaea contributing to methanogenesis. The high moisture content of OFMSW, coupled with tropical climatic conditions, leads to rapid fermentation and the generation of large volumes of leachate. Therefore, the ABBR represents a sustainable and high-rate alternative to conventional anaerobic systems, enabling efficient leachate treatment and enhanced bioenergy recovery in windrow composting facilities.}, }
@article {pmid41351873, year = {2025}, author = {Pan, X and Hageman, JJ and Weits, DA and Caldas, L and Elsayed, SS and Bayona, LM and van Wezel, GP and Berendsen, RL and Carrión, VJ and Raaijmakers, JM}, title = {Hypoxia Induces Phenotypic and Metabolic Shifts in Endophytic Flavobacterium sp. 98.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf269}, pmid = {41351873}, issn = {1751-7370}, abstract = {Oxygen plays a crucial role in shaping microbial physiology, functions, and behavior. Endophytic bacteria, residing within plant tissues, inhabit microenvironments where oxygen availability can be limited. However, the magnitude of hypoxic conditions in the endosphere and how these affect functional microbial traits is largely unknown. Here, we showed with a microsensor that oxygen levels in roots of sugar beet seedlings drop drastically to variable, low oxygen levels when going from epidermal to endodermal root tissue into the vasculature. Subsequently, we investigated phenotypic and metabolic responses of endophytic Flavobacterium sp. 98 at oxygen levels of 100 ppm. Under these oxygen conditions, Flavobacterium sp. 98 showed reduced growth, enhanced motility, and an altered extracellular metabolite profile. Flavobacterium sp. 98 colonies spread out in response to oxygen limitation and more effectively restricted hyphal growth of the sugar beet root pathogen Rhizoctonia solani than Flavobacterium sp. 98 grown at ambient oxygen conditions. Exometabolome analysis revealed enhanced accumulation of lysophosphatidylethanolamine (lysoPE) and N-acetyl-phenylalanine under low-oxygen conditions, along with a reduced level of the antifungal compound 5,6-dimethylbenzimidazole. These responses reflect physiological and metabolic plasticity of Flavobacterium sp. 98, highlighting significant changes in the expression of specific traits under hypoxic conditions. Our findings provide insights into niche-adaptive strategies of endophytic bacteria and pinpoint functional traits in microbe-plant interactions operating inside plant tissue.}, }
@article {pmid41351708, year = {2025}, author = {Campbell, KL and Armitage, AR and Labonté, JM}, title = {Microbial Communities Display Key Functional Differences between Reference and Restored Salt Marshes.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02661-7}, pmid = {41351708}, issn = {1432-184X}, abstract = {Salt marshes, despite their ecological importance (i.e., carbon sequestration) and rapid decline due to climate change and sea-level rise. Salt marsh ecosystems provide essential services such as removal of pollutants, carbon sequestration, and protection of coastal lands from storm surges. These services are strongly influenced by plant productivity, which is closely linked to microbial processes such as biogeochemical cycling of carbon, nitrogen, and sulfur. To retain carbon sequestration and other ecological functions, substantial efforts are currently directed towards coastal marsh restoration. Restoration efforts often lack comprehensive assessments of ecosystem functioning. Here, in an effort to assess ecosystem functions, we compared the microbial and viral community composition, as well as the genetic potential between reference and 10-year-old restored marshes in Galveston Bay, TX, USA. Duplicate bulk surface sediment in stands of Spartina alterniflora were sampled for metagenomic analysis. Metagenome assembled genomes analysis showed that while the microbial community composition was largely similar among sites, the overall metabolic potential was dissimilar. Restored sites displayed a higher abundance of carbon and nitrogen cycling functions compared to reference sites, which mainly consisted of sulfur cycling. Although the restored sites developed sediment microbial communities that approached reference microbial composition, the differences in the metabolic functions suggest that even after 10 years, the restored sites were still in a transitional stage of development. The differences between the reference and restored sites were even more differentiated in the viral community's predicted host composition. Additionally, viruses potentially play a variety of roles within the sediment community, including population control and biogeochemical cycles participation through auxiliary metabolic genes. These results highlight the prolonged timeline of functional development in restored salt marshes and highlight the need to develop approaches to boost the development of soil microbial communities in newly created habitats.}, }
@article {pmid41350753, year = {2025}, author = {Kim, K and Park, S and Jinno, C and Ji, P and Liu, Y}, title = {Impact of dietary supplementation of Bacillus subtilis on the metabolic profiles and microbial ecology of weanling pigs experimentally infected with a pathogenic Escherichia coli.}, journal = {Journal of animal science and biotechnology}, volume = {16}, number = {1}, pages = {167}, pmid = {41350753}, issn = {1674-9782}, abstract = {BACKGROUND: Our previous study demonstrated that dietary supplementation of Bacillus subtilis enhanced growth performance and intestinal integrity in weaned pigs challenged with enterotoxigenic Escherichia coli (ETEC). Therefore, this study aimed to explore the impact of Bacillus subtilis on gut health and its role in modulating host-microbe interactions in post-weaning pigs.<br><br>RESULTS: ETEC infection disrupted key metabolic pathways in distal colon, including glutathione, beta-alanine, and pyrimidine metabolism, indicating increased oxidative stress, impaired nucleotide balance, and amino acid catabolic stress. Bacillus subtilis supplementation induced distinct metabolomic and microbiome profiles in colon digesta of weaned pigs challenged with ETEC. Bacillus subtilis-treated pigs under ETEC challenge exhibited significant enrichment in amino acid- and energy-related pathways such as arginine biosynthesis, phenylalanine metabolism, pantothenate and CoA biosynthesis. ETEC infection induced microbial dysbiosis in the distal colon, resulting in decrease (P < 0.05) in abundance of Streptococcaceae and Enterobacteriaceae compared to healthy controls. Bacillus subtilis supplementation mitigated the ETEC-induced disruptions by increasing the relative abundance of beneficial bacterial families, including Lachnospiraceae and Bacteroidaceae.<br><br>CONCLUSION: Supplementation of Bacillus subtilis improves intestinal health and resilience against ETEC challenge by mitigating infection-induced metabolic disruptions and gut dysbiosis in weaned pigs.}, }
@article {pmid41350118, year = {2025}, author = {Fukase, S and Kouketsu, A and Tamahara, T and Saito, T and Ito, A and Higashi, Y and Kajita, T and Kurobane, T and Miyakoshi, M and Iikubo, M and Shimizu, R and Takahashi, T and Yamauchi, K and Sugiura, T}, title = {Differences in the Oral Microbiome Between Patients With and Without Oral Squamous Cell Carcinoma.}, journal = {Journal of oral pathology &amp; medicine : official publication of the International Association of Oral Pathologists and the American Academy of Oral Pathology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jop.70099}, pmid = {41350118}, issn = {1600-0714}, abstract = {BACKGROUND: Although studies have demonstrated a relationship between pathogenic microorganisms and oral cancer, no study has demonstrated a relationship between changes in bacterial flora and oral squamous cell carcinoma (OSCC). Therefore, we investigated the association between oral microbiota and oral squamous cell carcinoma using metagenomic analysis.<br><br>METHODS: Saliva samples from 64 patients with OSCC and 50 healthy controls who visited the Department of Oral Surgery, Tohoku University Hospital, were collected, and bacterial genomic DNA was extracted using polymerase chain reaction amplification. Single-end sequencing was performed using the Illumina MiSeq platform, and sequence data were analyzed using the Quantitative Insights Into Microbial Ecology 2 platform. The Steel-Dwass test was used for between-group comparisons, and Analysis of Compositions of Microbiomes with Bias Correction was used to detect significant differences in microbiome composition.<br><br>RESULTS: Significant differences were observed in alpha-diversity indices of bacterial flora (richness, Faith- phylogenetic diversity, Shannon index) in the OSCC group compared to those in the control group. Among the OSCC group, patients with larger tumor diameters and lymph node metastases (T3/T4, N1 or greater) formed independent clusters in the beta diversity analysis of the bacterial flora. Bacteria of the Actinomycetia phylum, such as Actinomyces and Rothia, were significantly reduced in patients with higher stage and pathological grade. Conversely, bacteria of the phylum Spirochaetia and Proteobacteria, particularly those of the genus Treponema, were significantly elevated in advanced cancer cases.<br><br>CONCLUSIONS: Our results suggest that changes in the oral microbiota may play a role in OSCC development and progression.}, }
@article {pmid41348832, year = {2025}, author = {Cervantes-Echeverría, M and Jimenez-Rico, MA and Manzo, R and Hernández-Reyna, A and Cornejo-Granados, F and Bikel, S and González, V and Hurtado Ramírez, JM and Sánchez-López, F and Salazar-León, J and Pedraza-Alva, G and Perez-Martinez, L and Ochoa-Leyva, A}, title = {Human-derived fecal virome transplantation (FVT) reshapes the murine gut microbiota and virome, enhancing glucose regulation.}, journal = {PloS one}, volume = {20}, number = {12}, pages = {e0337760}, doi = {10.1371/journal.pone.0337760}, pmid = {41348832}, issn = {1932-6203}, mesh = {Animals ; *Gastrointestinal Microbiome ; Humans ; Mice ; *Fecal Microbiota Transplantation/methods ; *Virome ; Male ; Diet, High-Fat/adverse effects ; Obesity/therapy/microbiology ; *Feces/virology ; Mice, Inbred C57BL ; *Glucose/metabolism ; Metabolic Syndrome/therapy/microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; }, abstract = {The gut microbiome, comprising bacteria, viruses, archaea, fungi, and protists, plays a crucial role in regulating host metabolism and health. This study explored the effects of fecal virome transplantation (FVT) from healthy human donors on metabolic syndrome (MetS) in a diet-induced obesity (DIO) mouse model, without diet change. Mice received a single oral dose of human-derived virus-like particles (VLPs) and continued on a high-fat diet (HFD) for 17 weeks. Despite persistent dietary stress, FVT significantly improved glucose tolerance. Longitudinal profiling by virome shotgun metagenomics and bacterial 16S rRNA sequencing revealed marked, durable shifts in both viral and bacterial community composition. Notable bacterial changes included a decrease in Akkermansia muciniphila and Peptococcaceae and increases in Allobaculum and Coprococcus; A. muciniphila positively correlated with glucose levels and negatively correlated with body weight. Together, these results suggests that human-derived virome can durably reshape gut microbial ecology and improve glucose metabolism in mice with obesity, even without dietary modification, offering a novel avenue for developing phage-based therapies. This proof-of-concept study provides foundational observations for using human-derived VLPs for FVT in standard laboratory mouse models, and provides a foundation for elucidating bacteria-phage interactions and their role in host metabolic health.}, }
@article {pmid41348222, year = {2025}, author = {Soto-Pozos, &#xc1;F and Rebollar, EA and Rovito, SM and Parra-Olea, G}, title = {Imprints of Land Use History on the Cutaneous Microbiota of Mexican Cloud Forest Salamanders.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02671-5}, pmid = {41348222}, issn = {1432-184X}, support = {CF-2019/373914//Secretar&#xed;a de Ciencia, Tecnolog&#xed;a e Innovaci&#xf3;n del Distrito Federal/ ; IN208024//Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; }, abstract = {The cloud forest harbors the highest amphibian diversity in Mexico, particularly among plethodontid salamanders. However, the expansion of agricultural and cattle ranching activities has significantly impacted this ecosystem and their native species. Beyond direct effects on cloud forest-dwelling species, effects of land-use change on free-living and salamander skin associated bacterial assemblages are underexplored in the cloud forest and in plethodontid salamanders specifically. This study examines how historical land-use changes may influence environmental and salamander skin bacterial communities, focusing on two types of previous land-use and six sympatric plethodontid salamanders from the cloud forest. Furthermore, we explored the presence of the pathogenic fungus Batrachochytrium dendrobatidis (Bd), due to its potential interaction with salamander skin bacterial communities. We found that skin bacterial communities varied with land-use history: in habitats formerly used for agriculture salamanders exhibited higher bacterial diversity, and communities' dispersion varied depending on the previous land-use. We found a very low Bd prevalence throughout the study area. Our findings suggest that bacterial communities associated with the skin of plethodontid salamanders may be influenced by land-use history in cloud forest fragments.}, }
@article {pmid41345535, year = {2025}, author = {Guijosa-Ortega, JL and Romaní, AM and Grau, O and Pla-Rabés, S and Margalef, O and Salminci, JG and Zarroca, M and Pastor, A}, title = {Effects of Acid Rock Drainage on Microbial Communities in Alpine Streams of the Pyrenees.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02667-1}, pmid = {41345535}, issn = {1432-184X}, abstract = {Weathering of sulphur-bearing rocks leads to acid rock drainage (ARD), which decreases water pH, mobilizes heavy metals, and forms coloured coatings of metal precipitates on riverbeds. This study assessed the effects of ARD on microbial biofilm biodiversity and community structure in alpine streams across two Pyrenean regions (Núria and Chistau). Biofilms were sampled from acidic (pH < 5.5) and non-acidic (pH > 6.5) streams, and at their confluence, where metal precipitates occur (white-coated streams). We characterised bacterial and eukaryote communities by molecular tools and specifically analysed the diatom communities by morphology approach. Their respective community composition varied with stream category for both bacteria and eukaryotes, but only bacteria exhibited a loss in diversity in acidic and white-coated streams. Diatom communities and diversity differences were driven mainly by region. In acidic and white-coated streams, bacteria which can use metals and sulphurs in their metabolic processes increased, together with fungi and some photosynthetic groups (Chlorophyta, Streptophyta) among eukaryotes. Amplicon Sequence Variants (ASVs) assigned to acidophilic and psychrotolerant bacteria were highly associated with acidic streams, and Cyanophyceae ASVs were highly associated with white-coated ones. As for eukaryotes, ASVs of Chrysophyceae were associated with both acidic and white-coated streams. Nonetheless, the regional factor remained consistently significant across microbial communities. This study indicates that ARD-affected streams can support microbial communities adapted to their extreme conditions, with the communities in white-coated rivers differing markedly from those in acidic rivers.}, }
@article {pmid41345364, year = {2025}, author = {Zhai, L and Yang, J and Lu, M and Sun, T and Wang, Y and Tang, G and Wu, D and Xu, L}, title = {Effects of Leaf Structure, Physiological Characteristics, and Chemical Properties on Phyllosphere Microorganisms Associated with Four Forage Crops in Fallow Land.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02638-6}, pmid = {41345364}, issn = {1432-184X}, support = {2023//Xingzhao Talent Support Program/ ; QKHJCQN[2025]265//Guizhou Provincial Basic Research Program (Natural Sciences) Youth Guidance Project/ ; 52020-2024-PT-02//Liupanshui Municipal-Level Science and Technology Innovation Platform Construction Project/ ; LPSSYKYJJ202306//High-Level Talents Introduction Project of Liupanshui Normal University/ ; }, abstract = {Phyllosphere microorganisms promote plant health, facilitate plant growth, and support ecosystem function. In this study, we compared the effects of leaf anatomy, physiological properties, and chemical composition on the diversity and abundance of epiphytic microorganisms across four forage species: wheat (Triticum aestivum), rye (Secale cereale), barley (Hordeum vulgare), and Italian ryegrass (Lolium multiflorum). The results showed that crop type significantly influenced microbial abundances on leaf surfaces and in whole leaves (P < 0.05). Specifically, wheat exhibited higher abundances of aerobic bacteria, lactic acid bacteria, molds, and yeasts in whole leaves and on leaf surfaces than those of the other three forage species. Microbial abundance on leaf surfaces was lower than that in whole leaves among the four crops. The stomatal density on the abaxial leaf surface was significantly higher than that on the adaxial surface (P < 0.0001) among the four crops. The main drivers of whole-leaf microbial abundance included soluble sugars, stomatal density, intercellular CO2 concentration, and total water vapor conductance. Conversely, the key factors influencing surface microbial abundance were reducing sugars (affecting lactic acid bacteria and molds) and stomatal density on the adaxial surface (affecting yeasts). In conclusion, the morphology, physiology, and chemical composition of forage leaves collectively shape the colonization patterns and abundance of epiphytic microorganisms. Wheat exhibited larger microbial numbers than those of the other three forages. Soluble sugars and stomatal density emerged as key determinants of microbial community structure, whereas epidermal structure influenced the formation of specific functional microbial communities through a dual mechanism of physical selection and microenvironmental regulation.}, }
@article {pmid41345336, year = {2025}, author = {Antoł, W and Surmacz, B and Ostap-Chec, M and Stec, D and Miler, K}, title = {Do Shifts in Honeybee Crop Microbiota Enable Ethanol Accumulation? A Comparative Analysis of Caged and Foraging Bees.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02627-9}, pmid = {41345336}, issn = {1432-184X}, support = {Sonata 17 grant 2021/43/D/NZ8/01044//National Science Center in Poland/ ; }, abstract = {Honeybees encounter low environmental doses of ethanol, primarily through fermenting nectar, which can have both beneficial and detrimental effects on their functioning. Yet, ethanol traces can also be detected in the crop of caged bees with no access to environmental food sources. This raises the possibility that endogenous ethanol accumulation could occur under restricted conditions, with microbial contributions as a potential mechanism. The crop microbiota, although less diverse than that in other gut segments, plays important roles in food fermentation and pathogen defense. We hypothesized that captivity-induced shifts in crop microbiota may facilitate fermentation, resulting in measurable ethanol. To test this, we compared the crop contents of naturally foraging hive bees and caged bees reared without access to the natural environment. Ethanol levels were low in both groups and did not differ significantly, but non-zero measurements were more frequently observed in caged bees. Microbial community structure differed strongly in α- and β-diversity. Caged bees showed reduced abundance of nectar-associated genera (e.g., Apilactobacillus) and an increase in genera that include known ethanol-producing strains, such as Gilliamella and Bifidobacterium. While we did not directly assess metabolic activity, our results suggest that captivity alters microbial communities in ways that may influence ethanol levels. This raises broader questions about how microbe-host interactions modulate host phenotypes under different environmental conditions.}, }
@article {pmid41345266, year = {2025}, author = {Zhao, Z and Klawonn, I and Baltar, F and Grossart, HP}, title = {Size-fractionated fungal communities in the sunlit ocean.}, journal = {Communications biology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s42003-025-09314-y}, pmid = {41345266}, issn = {2399-3642}, abstract = {Marine fungi play key roles in organic matter cycling, yet their distribution across particle size fractions remains understudied. We analyze 18S rDNA data from four size fractions (0.8-5, 5-20, 20-180, and 180-2000 μm) collected across the global sunlit ocean. Here, we show fungal diversity and relative abundance decline with increasing particle size. Fungal community structure is influenced by eukaryotic diversity and chlorophyll levels. Fungi co-occur with other eukaryotes, especially zooplankton, hinting at potential predator-prey interactions. Generalist fungi dominate smaller fractions, while specialists dominate larger fractions, likely due to stronger microenvironmental selection. Co-occurrence networks are dominated by positive interactions and driven by fungal specialists. Dispersal limitation emerges as the main ecological process shaping community assembly. Our findings reveal strong niche differentiation among marine fungi along the particle continuum and emphasize the role of particle size and biological interactions in structuring fungal diversity and biogeography.}, }
@article {pmid41345123, year = {2025}, author = {Tucker, SJ and Füssel, J and Freel, KC and Kiefl, E and Freel, EB and Ramfelt, O and Sullivan, CES and Gajigan, AP and Mochimaru, H and de Souza, MR and Quinn, M and Ratum, C and Tran, LL and Sobczyk, M and Miller, SE and Trigodet, F and Lolans, K and Morrison, HG and Fallon, B and Huettel, B and Pan, T and Rappé, MS and Eren, AM}, title = {A high-resolution diel survey of surface ocean metagenomes, metatranscriptomes, and transfer RNA transcripts.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1913}, pmid = {41345123}, issn = {2052-4463}, support = {687269//Simons Foundation/ ; 989028//Simons Foundation/ ; 989028//Simons Foundation/ ; 2019589//NSF | GEO | Division of Ocean Sciences (OCE)/ ; }, mesh = {*Metagenome ; Pacific Ocean ; *Transcriptome ; *RNA, Transfer/genetics ; *Seawater/microbiology ; Ecosystem ; Microbiota ; }, abstract = {The roles of marine microbes in ecosystem processes are inherently linked to their ability to sense, respond, and ultimately adapt to environmental change. Capturing the nuances of this perpetual dialogue and its long-term implications requires insight into the subtle drivers of microbial responses to environmental change that are most accessible at the shortest scales of time. Here, we present a multi-omics dataset comprising surface ocean metagenomes, metatranscriptomes, tRNA transcripts, and biogeochemical measurements, collected every 1.5 hours for 48 hours at two stations within coastal and adjacent offshore waters of the tropical Pacific Ocean. We expect that this integrated dataset of multiple sequence types and environmental parameters will facilitate novel insights into microbial ecology, microbial physiology, and ocean biogeochemistry and help investigate the different mechanisms of adaptation that drive microbial responses to environmental change.}, }
@article {pmid41344775, year = {2026}, author = {Zhu, J and Liao, Y and Zhao, Y and Liu, J and Li, Z and Kong, X and Zhang, S and Song, C and Fu, Q and Wang, X and Xue, R and Shi, X and Tian, Y and Cao, R and You, J and Li, L}, title = {Functional division of labor within defined yeast consortia drives flavor formation during early solid-state fermentation of sichuan shai vinegar.}, journal = {Food microbiology}, volume = {135}, number = {}, pages = {104983}, doi = {10.1016/j.fm.2025.104983}, pmid = {41344775}, issn = {1095-9998}, mesh = {*Acetic Acid/metabolism/analysis ; Fermentation ; *Flavoring Agents/metabolism ; Saccharomyces cerevisiae/metabolism ; Taste ; *Microbial Consortia ; Pichia/metabolism ; Saccharomycetales/metabolism ; *Yeasts/metabolism/classification ; Ethanol/metabolism ; Fermented Foods/microbiology/analysis ; Food Microbiology ; Brettanomyces ; }, abstract = {Sichuan Shai vinegar (SSV) is a traditional fermented product with complex microbial ecology. This study elucidated the functional division of labor within the yeast microbiota during the early stage (days 1-5) of solid-state fermentation in SSV. Investigating of four key yeast strains (Saccharomyces cerevisiae, Pichia kudriavzevii, Kazachstania humilis, and Brettanomyces bruxellensis) via co-culturing, metabolomics, and simulated fermentation revealed distinct roles: Pichia kudriavzevii dominated ester synthesis, Brettanomyces bruxellensis primarily produced characteristic flavor compounds (e.g., acetaldehyde, 4-ethylguaiacol), Kazachstania humilis efficiently produced acids accelerating acidification, and Saccharomyces cerevisiae produced ethanol, which served as a precursor for ester synthesis by other yeasts. The triple-strain combination of Pichia kudriavzevii, Kazachstania humilis, and Brettanomyces bruxellensis exhibited optimal synergy, achieving peak total acid (10.96 g/100 g DW) and acetic acid (3.54 g/100 g DW) content while significantly enhancing characteristic flavor profiles. Untargeted metabolomics indicated that this combination efficiently regulated multiple flavor biosynthesis pathways through pyruvate-mediated metabolic hubs. This systematic clarification of functional roles within the yeast community provides an experimental foundation for designing synthetic microbial starters to modulate flavor profiles and advance the standardization of fermented food production.}, }
@article {pmid41344333, year = {2025}, author = {Cao, Y and Bowker, MA and Feng, Y and Delgado-Baquerizo, M and Xiao, B}, title = {The Great Wall of China harbors a diverse and protective biocrust microbiome.}, journal = {Current biology : CB}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cub.2025.10.087}, pmid = {41344333}, issn = {1879-0445}, abstract = {The Great Wall of China, one of the most emblematic human heritage sites ever built, is largely covered by a living skin that has a potentially distinct microbiome compared with bare wall surfaces. However, the structure and function of this microbiome remain virtually unknown, which hampers any effort to understand the impacts of this microbiome on the long-term conservation of the Great Wall. Here, we investigated the microbiome of the Great Wall at six sampling sites along a 600-km section, which stretches across arid and semiarid climates and is covered by a mosaic of biological soil crusts (biocrusts) and exposed wall surfaces. We hypothesized that these biocrusts could establish a unique microhabitat and support a microbiome with a community structure and function potentially distinct from those on bare walls, thereby modulating the biodeterioration processes affecting the Great Wall. Our findings revealed that biocrust-covered sections exhibited a 12%-62% increase in abundance, diversity, and co-occurrence network complexity for bacterial and fungal communities compared with bare walls. Further metagenomic analyses indicated that the biocrust cover enhanced the abundance of overall functional genes and stress-resistance pathways within the microbiome by 4%-15%, while decreasing the metabolic pathways linked to heritage biodeterioration. Aridity was an additional determinant of the microbiome. Our work serves as a critical step toward understanding the microbiome of the Great Wall, which contributes to conserving this unparalleled human monument for future generations.}, }
@article {pmid41344264, year = {2025}, author = {Li, C and Li, S and Ma, L and Wang, H and Li, X and Li, M and Yang, Q}, title = {Allantoin enhances growth and nutrient accumulation in Dioscorea opposita under saline-alkali stress through regulation of ion homeostasis and antioxidant capacity.}, journal = {Plant physiology and biochemistry : PPB}, volume = {229}, number = {Pt E}, pages = {110819}, doi = {10.1016/j.plaphy.2025.110819}, pmid = {41344264}, issn = {1873-2690}, abstract = {Saline-alkali stress (SAS) significantly impairs crop growth, yield and quality, while allantoin plays a crucial role in enhancing plant tolerance to this stress. Yam (Dioscorea opposita Thunb.) has substantial nutritional and medicinal value. However, the regulatory mechanism of allantoin in regulating yam growth and nutritional quality under SAS remains largely unclear. In this study, we found that SAS severely inhibited the growth and root development of yam bulbil seedlings. Specifically, in leaves, the contents of osmotic regulators (e.g., proline, soluble sugar) and malondialdehyde (MDA), along with the activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), were significantly increased. Additionally, leaf Na[+] content was increased, K[+] content was decreased, and the Na[+]/K[+] ratio was significantly elevated. Meanwhile, the contents of allantoin, diosgenin, and polysaccharides in tubers were significantly increased. Overexpression of the allantoin synthase gene DoAS in Arabidopsis thaliana further enhanced its tolerance to SAS. Furthermore, compared with the SAS-only group, allantoin treatment significantly improved yam seedling growth, reduced leaf proline and MDA contents, enhanced SOD and POD activities, decreased the Na[+]/K[+] ratio, increased tuber yield and contents of major active components, and lowered tuber Na[+] content. Taken together, allantoin significantly improves ionic balance and antioxidant capacity in yam bulbil seedlings under SAS, thereby promoting seedling growth and nutrient accumulation in tubers. This study thus highlights the critical role of allantoin in regulating the growth and nutrient accumulation in tuber crops under SAS.}, }
@article {pmid41342921, year = {2025}, author = {Taurozzi, D and Scalici, M}, title = {Regional γ Diversity of Diatoms in Mediterranean and Alpine Temporary Ponds.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02670-6}, pmid = {41342921}, issn = {1432-184X}, abstract = {Temporary ponds, characterized by periodic or intermittent hydroperiods, are globally widespread in all the biogeographical regions and host peculiar biotic communities. Here we investigated shifts in diatom community assemblages across two contrasting biogeographical regions in Italy, the Mediterranean and the Alpine. The study focused on 24 temporary ponds, with 12 ponds sampled at Castelporziano (CP) and 12 at Campo Imperatore (GS). Our results highlighted that γ diversity varied significantly between the two study sites, indicating a notably greater species richness in GS compared to CP. In GS, functional richness values were generally higher, whereas no significant differences were detected for functional distance and functional divergence. Species composition differed significantly between CP and GS indicating that the two sites host distinct communities, with species turnover (0.904) which contributed most to total beta diversity (0.926), while nestedness (0.021) was negligible. CP communities were characterized by pronounced functional clustering in specific sites while GS exhibited both clustering and slight overdispersion. However, although GS communities occupy slightly larger trait space, both regions shared most functional strategies, reflecting substantial redundancy in functional traits across the two environments. Overall, diatom communities in the GS were characterized by higher frequencies of small, mobile, low-profile, and mucilaginous-tube taxa, whereas CP ponds displayed relatively higher representation of larger or motile forms. Although our study is a starting point, large-scale analyses of diatom communities are crucial, as climate change may rapidly and irreversibly alter taxonomic and functional diversity, profoundly affecting the ecology of these temporary habitats and surrounding landscapes.}, }
@article {pmid41342600, year = {2025}, author = {Bauchinger, F and Berry, D}, title = {Metatranscriptomic-driven insights into mucosal glycan degradation by the human gut microbiota.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaf118}, pmid = {41342600}, issn = {1574-6941}, abstract = {The secreted mucus layer in the human gastrointestinal tract constitutes both a protective boundary between gut lumen and epithelium as well as an important nutrient source for members of the gut microbiota. While many gut microbes possess the genetic potential to degrade mucin it is still unclear which species transcribe the respective genes. Here, we systematically analyzed publicly available metagenome and metatranscriptome datasets to characterize the gut microbial community involved in mucosal glycan degradation. We utilized co-occurrence network analysis and linear regression to elucidate the ecological strategies of, and relationship between, mucus degraders. We found that although approximately 60% of species carrying genes encoding for mucosal-glycan-degrading enzymes have detectable transcription of these genes, only 21 species prevalently transcribe more than 1 gene. Furthermore, the transcription of individual genes was frequently dominated by single species in individual samples. Transcription patterns suggested the presence of competitive mucosal glycan degraders characterized by abundance-driven transcription that were negative predictors for the transcription of other degraders as well as opportunistic species with decoupled abundance and transcription profiles. These findings provide insights into the ecology of the mucosal glycan degradation niche in the human gut microbiota.}, }
@article {pmid41341498, year = {2025}, author = {Sun, D and Šmilauer, P and Pjevac, P and Rozmoš, M and Forczek, ST and Kotianová, M and Hršelová, H and Bukovská, P and Jansa, J}, title = {Arbuscular mycorrhiza suppresses microbial abundance, and particularly that of ammonia oxidizing bacteria, in agricultural soils.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1671859}, pmid = {41341498}, issn = {1664-302X}, abstract = {Interactions between arbuscular mycorrhizal (AM) fungi and ammonia-oxidizing (AO) microorganisms, two important microbial guilds contributing to soil-plant mineral nutrient cycling, are complex, given the high variability of soil biological, physical, and chemical properties. In addition, AO microorganisms are generally slow growing and require ample time to establish. Their communities are thus difficult to reconstruct under laboratory conditions, for example after soil sterilization. Therefore, in this study, we investigated quantitative and compositional responses of indigenous microorganisms occurring in 50 different field soils (collected from grasslands and arable fields) to actively growing mycelium of the AM fungus Rhizophagus irregularis. To this end, we quantified the abundance of various microbial guilds including AO bacteria (AOB), AO archaea (AOA), and comammox Nitrospira in pot-incubated soils exposed or not to actively growing AM fungus. Across the variety of soils, we observed systematic suppression by the AM fungus of different microbial groups including bacteria, protists, and fungi. The strongest suppression was noted for AOB and comammox Nitrospira, whereas the abundance and community structure of AOA remained unaffected by the AM fungal activity. Mycorrhizal suppression of AOB abundance was accompanied by changes in AOB community structure and correlated with soil pH. Contrary to the expected competition between AM fungus and AO microorganisms for available ammonium (NH4 [+]) in the soil solution, the presence of the actively growing AM fungus significantly increased soil NH4 [+] levels as compared to the non-mycorrhizal control, at least upon the final destructive harvest. Thus, the interaction between the AM fungi and AO microorganisms likely goes beyond the simple competition for the free ammonium ions and might involve microorganisms active in other pathways of soil nitrogen cycle (e.g., mineralization) or temporarily different trajectories of nutrient use in mycorrhizal vs. non-mycorrhizal systems. Alternatively, elusive biological nitrification inhibitors may have contributed to the observed effect, produced by the AM fungus or its host plant, and subsequently transported to the root-free soil via the AM fungal hyphae.}, }
@article {pmid41339548, year = {2025}, author = {Singleton, CM and Jensen, TBN and Delogu, F and Knudsen, KS and Sørensen, EA and Jørgensen, VR and Karst, SM and Yang, Y and Sereika, M and Petriglieri, F and Knutsson, S and Dall, SM and Kirkegaard, RH and Kristensen, JM and Overgaard, CK and Woodcroft, BJ and Speth, DR and Aroney, STN and ,  and Wagner, M and Dueholm, MKD and Nielsen, PH and Albertsen, M}, title = {The Microflora Danica atlas of Danish environmental microbiomes.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {41339548}, issn = {1476-4687}, abstract = {Over the past 20 years, there have been considerable advances in revealing the microbiomes that underpin processes in natural and human-associated environments. Recent large-scale metagenome surveys have recorded the variety of microbial life in the oceans[1], in the human gut[2] and on Earth[3], with compilations encompassing thousands of public datasets[4,5]. However, despite their broad scope, these studies often lack functional information, and their sample locations are frequently sparsely distributed, limited in resolution or lacking metadata. Here we present Microflora Danica-an atlas of Danish environmental microbiomes encompassing 10,683 shotgun metagenomes and 450 nearly full-length 16S and 18S rRNA datasets, linked to a five-level habitat classification scheme. We show that although human-disturbed habitats have high alpha diversity, species reoccur, revealing hidden homogeneity. This underlines the role of natural systems in maintaining total species (gamma) diversity and emphasizes the need for national baselines for tracking microbial responses to land-use and climate change. Consequently, we focused our dataset exploration on nitrifiers, a functional group closely linked to climate change and of major importance for Denmark's primary land use: agriculture. We identify several lineages encoding nitrifier key genes and reveal the effects of land disturbance on the abundance of well-studied, as well as uncharacterized, nitrifier groups, with potential implications for N2O emissions. Microflora Danica offers an unparalleled resource for addressing fundamental questions in microbial ecology about what drives microbial diversity, distribution and function.}, }
@article {pmid41338824, year = {2025}, author = {Guo, M and Chen, C and Wang, W and Zhang, C and Ma, J and Sadike, M and Niyazi, M and Feng, X and Zhu, K}, title = {Research on the relationship between HPV infection and alterations in vaginal microbial ecology.}, journal = {Enfermedades infecciosas y microbiologia clinica (English ed.)}, volume = {43}, number = {10}, pages = {688-697}, doi = {10.1016/j.eimce.2025.07.006}, pmid = {41338824}, issn = {2529-993X}, mesh = {Female ; Humans ; *Vagina/microbiology/virology ; Adult ; *Papillomavirus Infections/microbiology ; *Microbiota ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Young Adult ; }, abstract = {OBJECTIVE: To investigate the changes in vaginal microbiota under different HPV infection statuses and explore the correlation between vaginal microbiota alterations and HPV infection.<br><br>METHODS: 151 cervical samples from gynecological outpatients were grouped into HPV-negative (HN, N=51), transient infection (HTI, N=42), and persistent infection (HPI, N=58). Vaginal secretions were collected to assess microecology (pH, vaginal cleanliness, hydrogen peroxide, leukocyte esterase) via genital secretion analyzer. 16S ribosomal RNA (rRNA) sequencing analyzed vaginal microbiota characteristics, community state types (CST), richness, diversity, and biomarkers.<br><br>RESULTS: 16S rRNA sequencing identified 5 CST II, 52 CST III, and 94 mixed CST IV samples, showing diverse microbiota. Compared with HN, HTI and HPI had lower vaginal cleanliness, higher sialidase activity, elevated pH, and fewer Lactobacilli (P<0.05). Lactobacillus iners dominated all groups, while Sneathia amnii was significantly higher in HPI (P<0.05). HPV infection increased vaginal microbiota richness (HPI>HTI/HN, P<0.05), with distinct group compositions (P<0.05). Linear Discriminant Analysis Effect Size identified Lactobacillus gasseri, Atopobium vaginae, and Lactobacillus jensenii as biomarkers.<br><br>CONCLUSION: This study found significant differences in microbial community characteristics under different HPV infection statuses. The identification of biomarkers in vaginal microbiota under different infection statuses could provide new targets for clinical screening and prevention of cervical cancer.}, }
@article {pmid41335295, year = {2025}, author = {Jayanandan, M and Veeraraghavan, VP and Govindarajan, S and Mariyappa Subramani, S}, title = {Development of oral dysbiosis following use of antimicrobial mouthwashes: a systematic review.}, journal = {Odontology}, volume = {}, number = {}, pages = {}, pmid = {41335295}, issn = {1618-1255}, abstract = {The oral microbiome maintains the oral and systemic health. The extensive use of antimicrobial mouthwashes to control biofilm-related diseases has increased the concerns about their effect on microbial ecology. Specific formulations may cause microbial shifts which influences both the oral and systemic physiology in an individual. This systematic review evaluates the oral dysbiosis development after antimicrobial mouthwash use and correlates the microbial changes with clinical and systemic outcomes. A comprehensive search in various databases like PubMed, Scopus, etc. (till March 2025) was done. It identified 14 relevant studies from a total of 681 screened records. Risk of bias was assessed using ROB2, ROBINS-I, CRIS, and NOS tools, with data extracted on microbial diversity, taxonomic changes, nitrate reduction capacity, and antibiotic resistance. The findings showed that chlorhexidine caused the greatest dysbiosis and reduces the microbial diversity by 40-60%, with increasing Streptococcus spp. two-to-threefold, and elevating antibiotic resistance gene prevalence. Cetylpyridinium chloride and polyhexamethylene biguanide showed milder effects, thus preserving 70-80% of commensals, while herbal and plant-based rinses (o-cymen-5-ol, StellaLife®, Rosella) reduced pathogens by 25-40% without disrupting the balance. Fluoride-arginine formulations promote beneficial bacteria by 30-50% but marginally upregulated resistance genes, whereas mechanical hygiene methods maintained over 90% microbial diversity. Suppression of nitrate-reducing bacteria was associated with reduced nitric oxide bioavailability, potentially increasing vascular and cognitive risks. Hence, antimicrobial mouthwashes especially chlorhexidine induces significant dysbiotic shifts, while herbal, postbiotic, and mechanical alternatives demonstrate safer, microbiome thereby preserving the effects which is suitable for long-term oral health maintenance.}, }
@article {pmid41333479, year = {2025}, author = {Ni, Z and Zhou, W and Gao, Y}, title = {A social-architecture perspective on gut microbiota dynamics and host physiology.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1642080}, pmid = {41333479}, issn = {1664-3224}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology/immunology ; Animals ; *Host Microbial Interactions ; Homeostasis ; }, abstract = {The human gut microbiota, a dynamic consortium of trillions of microorganisms, is increasingly recognized not merely as a metabolic entity but as a structured "microbial society" exhibiting hierarchical organization, cooperative networks, and competitive exclusion. This hypothesis posits that gut microbiota communities operate under principles analogous to social structures, with emergent behaviors that directly impact host health. By integrating recent advances in microbial ecology, spatial omics, and neurogastroenterology, this paper proposes those microbial social dynamics-such as division of labor, territorial specialization, and collective decision-making-mediate critical host functions, including immune regulation, metabolic homeostasis, and cognitive processes. In research or therapy targeting the gut microbiota, safeguard the stability of the microbial society and eschew simplistic, blunt approaches. In short, the gut microbiota behaves like a collective mind, showing tight unity and rapid, fine-tuned adaptation to external cues. Its imbalance breeds disease; its vigor enhances human life.}, }
@article {pmid41330424, year = {2025}, author = {Zöhrer, J and Ascher-Jenull, J and Prem, EM and Wagner, AO}, title = {State-Specific Extraction of Environmental DNA: Spike-and-Recovery Controls to Validate and Optimise Extraction Protocols.}, journal = {Environmental microbiology}, volume = {27}, number = {12}, pages = {e70209}, doi = {10.1111/1462-2920.70209}, pmid = {41330424}, issn = {1462-2920}, support = {P36711//Austrian Science Fund/ ; }, mesh = {*DNA, Environmental/isolation &amp; purification ; *DNA, Bacterial/isolation &amp; purification ; *Bacteria/genetics/isolation &amp; purification/classification ; Polymerase Chain Reaction ; *Environmental Microbiology ; }, abstract = {Getting insights into the quantitative and qualitative contribution of different DNA states, i.e., extracellular (exDNA) and intracellular DNA (iDNA), to the total environmental DNA (eDNA) pool requires reliable methods for their separation. Even though a multitude of respective extraction protocols has been published, their validation is often missing. Here, we selected four protocols for the state-specific extraction of eDNA and traced the separation of exDNA and iDNA within natural environments using previously designed spike-and-recovery controls. Besides accounting for the different eDNA states, the spike-ins also distinguished different bacterial origins (gram-positive, gram-negative). Following their quantification by digital PCR, the recovery of exDNA and iDNA spike-ins in both the target as well as nontarget eDNA states differed among the selected extraction protocols and environmental matrices, albeit the effect of the former was far more decisive. While the recovery of exDNA spike-ins was mainly affected by the chemical composition of the washing buffer and the duration of each washing step, the lysis method determined the recovery of spiked iDNA. These aspects were further combined within an optimised protocol, providing a valuable step towards a more concise understanding of factors governing the state-specific extraction of eDNA and hence their relevance in molecular microbial ecology.}, }
@article {pmid41325059, year = {2025}, author = {Zhang, Y and Walker, RW and Kaplan, RC and Qi, Q}, title = {Added sugars, gut microbiota, and host health.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2592431}, doi = {10.1080/19490976.2025.2592431}, pmid = {41325059}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Animals ; Bacteria/classification/metabolism/genetics/isolation &amp; purification ; *Dietary Sugars/adverse effects/metabolism ; Fatty Acids, Volatile/metabolism ; Obesity/microbiology ; }, abstract = {Excessive intake of added sugars is a global public health concern, given its established links with cardiometabolic disease and other chronic conditions. Emerging evidence suggests that the gut microbiota might mediate the harms of high sugar intake. In this review, we summarize evidence from animal and human studies regarding the impact of added sugar intake on gut microbiota diversity and composition, and discuss potential mechanisms linking sugar-induced microbial changes to health outcomes. Added sugars, including glucose, fructose, and sucrose, can alter gut microbial diversity, enrich sugar-utilizing taxa, and deplete short-chain fatty acid-producing bacteria. These microbial changes may impair gut barrier integrity, increase luminal oxygen and alternative electron acceptors under inflammatory conditions, reduce short-chain fatty acid production, alter bile acid and amino acid metabolism, and promote translocation of endotoxin across the gut barrier into the bloodstream. Collectively, these pathways may link added sugar intake to irritable bowel syndrome, obesity, liver steatosis, diabetes, and cardiovascular diseases. However, inconsistent results on alterations in the gut microbiota related to added sugar intake were observed across studies, which may be due to differences in sugar dose and form (liquid vs. solid), as well as population variation in background diet, host genetics, and gut microbial ecology. Future research should focus on mechanistic investigations, characterization of inter-individual variability in response to added sugar intake, and clinical studies to assess whether dietary or therapeutic interventions can reverse sugar-induced gut microbial changes and improve host health outcomes.}, }
@article {pmid41321823, year = {2025}, author = {Zheng, Z and Xie, D and Han, Y and Li, G and Wang, S and Zhang, X and Huang, T and Xu, W and Wu, G}, title = {Deciphering the urinary microbiome and urological cancers: from correlation to mechanisms and treatment.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1699308}, pmid = {41321823}, issn = {1664-302X}, abstract = {Given that the sterility of urine and the urinary tract has been questioned by research, urinary microbiome dysbiosis has been recognized as one of the potential cancer-promoting factors. The composition of the urinary microbial community in healthy individuals has a relatively high similarity at the phylum level, with factors like age and gender influencing the expression and distribution. In contrast, the urinary microbiome of patients with urologic cancers shows significant variability and diversity depending on the type of cancer. Most of the early studies focused on the distribution, aggregation, and expression of microbiota in urologic cancers, warranting advanced studies on the causal relationship between microbes and urologic cancers. Bladder and prostate cancer tumorigenesis and progression can be influenced by microbes through chronic inflammatory or immunomodulatory pathways making them cancer models strongly associated with the urinary microbiome. Here, we summarize the expression characteristics of the microbiomes associated with these cancers and analyze the pathophysiological mechanisms and signaling pathways of the microbiome in the tumor promotion or suppression. By examining the role played by the urinary microbiome in the pathogenesis of urologic cancers, we assess the potential of specific microbial groups as biomarkers for diagnosis and surveillance. Additionally, involving the microbiome or using adjunctive participation in tumor therapy is becoming an emerging cancer treatment option. Improving urinary microbial homeostasis in urinary cancers by direct treatment with microbial products, microbial co-immunotherapy, probiotic-assisted therapy, and fecal microbial transplantation may broaden the scope of therapy and enhance the efficacy of conventional medicines.}, }
@article {pmid41321415, year = {2025}, author = {Horstmann, L and Lipus, D and Bartholomäus, A and Oses, R and Kitte, A and Friedl, T and Wagner, D}, title = {Microbial ecology of subsurface granitic bedrock: a humid-arid site comparison in Chile.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf199}, pmid = {41321415}, issn = {2730-6151}, abstract = {Subsurface microorganisms face extreme challenges such as anoxic, xeric, and oligotrophic conditions. In igneous systems, nutrient limitation is critical, as biomass input relies on surface-derived fluids via tectonic fractures. Despite growing interest in subsurface habitats, little is known about ecosystems beneath arid landscapes, where surface water input is limited by the low annual precipitation. This study compares granitic subsurface environments beneath arid and humid surface ecosystems, highlighting the link between surface climate and subsurface biodiversity. DNA was extracted from granitic subsurface rocks recovered from two endmember sites along a north-south climate gradient in Chile's Coastal Cordillera. Microbial communities inhabiting down to 55 m deep subsurface rocks were characterized using 16S rRNA amplicon and shotgun metagenomic sequencing. We identified an abundant and potentially active subsurface community below both climates dominated by heterotrophic bacteria, including Pseudarthrobacter, Janthinobacterium, and Pseudomonas. However, rare taxa affiliated with common chemolithoautrophs, e.g. Thiobacillus, Sulfuriferula, and Sulfuricurvum, were only observed in the arid subsurface, indicating increased oligotrophic conditions and reliance on inorganic electron donors in the deeper subsurface of the desert. Functional analysis revealed sulphur, hydrogen, and carbon monoxide as potential inorganic electron donors. These findings expand the current understanding of microbial life in the subsurface of granite rocks showing the influence of surface climate on nutrient conditions in the deeper subsurface, providing new insights into the extent and functional capacity of terrestrial subsurface habitats and their role in global biogeochemical processes.}, }
@article {pmid41320393, year = {2026}, author = {Wang, S and De Paepe, K and Onyango, SO and Zhang, B and Huang, Q and Wang, S and Van de Wiele, T}, title = {Starch-entrapped microspheres selectively promote propionate or butyrate production through individual-specific modulation of the human fecal microbiome.}, journal = {Carbohydrate polymers}, volume = {373}, number = {}, pages = {124614}, doi = {10.1016/j.carbpol.2025.124614}, pmid = {41320393}, issn = {1879-1344}, mesh = {Humans ; *Starch/chemistry/pharmacology ; *Feces/microbiology ; *Microspheres ; Prebiotics ; *Butyrates/metabolism ; *Propionates/metabolism ; *Gastrointestinal Microbiome/drug effects ; Adult ; Male ; Zea mays/chemistry ; Female ; Inulin/chemistry ; Fermentation ; Young Adult ; }, abstract = {Starch microspheres encapsulated with chitosan synergistically and beneficially modulate the microbiota composition and metabolic activity of a pooled fecal slurry compared to starch, suggesting a superior prebiotic potential. Interindividual differences in prebiotic potential are, however, unexplored. Therefore, we incubated starch-entrapped microspheres (MS), high amylose maize starch (HAMS) and the reference prebiotic inulin with the separate fecal microbiota derived from six healthy individuals. The variation in microbial community composition was largely driven by inter-individual variability (effect size of 71.7 %). Despite the inter-individual variability, the different prebiotic substrates significantly affected the microbiota composition (effect size of 9.5 %) and metabolic activity over the course of fermentation. MS delayed the fermentation and reduced the gas production and acidification in all donors compared to HAMS and inulin. Furthermore, compared to HAMS, MS more effectively promoted propionate or butyrate production in a donor-dependent manner. MS increased butyrate levels with 0.1 ± 0.72 mM per unit of starch across all donors. Additional, MS increased the propionate production with 0.52 ± 0.71 mM per unit of starch in donors 1, 2, 4, 6. The donor-specific propiogenic and butyrogenic effects of MS were linked to the enrichment of Bacteroides and Agathobacter species. Our findings confirm the superior prebiotic effect of MS and provide directions for the design and manufacture of starch-based functional foods to enhance gut health.}, }
@article {pmid41318730, year = {2025}, author = {González-Pimentel, JL and Cuecas, A and Álvarez, C and Mariscal, V}, title = {Soil Bacteriome Shifts along a Cultivation Gradient in Southwestern Spanish Wetlands.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02660-8}, pmid = {41318730}, issn = {1432-184X}, abstract = {Understanding how long-term agricultural practices affect soil bacteriome is essential for sustainable land management. In the Guadalquivir Marshes of southwestern Spain, which encompass both Doñana National Park and one of Europe's most productive rice cultivation areas, decades of rice farming have transformed natural wetlands into artificial agroecosystems. Although bacterial degradation in cultivated soils has been previously suggested, comparative analyses between rice paddies and adjacent natural wetlands remain scarce.Here, we characterized the soil bacteriome across a cultivation gradient by comparing undisturbed natural marshes, within Doñana National Park, with rice fields cultivated for 25 years (Cantarita) and 80 years (Mínima 2). Using full 16S rRNA gene via long-read metabarcoding and standardized soil physicochemical assays, we analysed taxonomic composition, environmental associations, and predicted functional profiles.Our results reveal a progressive restructuring of bacterial communities with increased cultivation time, notably a significant enrichment of Chloroflexota (especially Anaerolineae) and a decline in Actinomycetota and Planctomycetota in paddy soils. Functional predictions indicated a higher potential for denitrification in cultivated soils-likely involving Chloroflexota taxa-compared to more diverse nitrogen pathways in natural sites. These shifts were strongly associated with changes in pH, electrical conductivity, calcium carbonate, and nitrate levels. Remarkably, most bacterial differences were already evident within the first 25 years of cultivation, underscoring the rapid ecological impact of intensive rice cultivation.Notably, we identified specific bacterial groups (Anaerolineae and Nocardioides in paddy soils; Euzebya, Rubrobacter, and Planctomycetota in natural wetlands), whose enrichment was associated with soil type. This approach highlights the value of integrating bacterial-based assessments into sustainable wetland management strategies.}, }
@article {pmid41318612, year = {2025}, author = {Rivera, DS and Beltrán, V and Hoepfner, C and Del Pilar Fernández, M and Oliva, CA and Vera, MJ and Farías, C and Valenzuela, R and Pérez, I and Correa, LA and Urbina, F}, title = {Nutritional modulation of host physiology, behavior, and gut microbiome in the captive rodent Octodon degus.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-025-26991-1}, pmid = {41318612}, issn = {2045-2322}, support = {11190603//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; }, abstract = {Diet is a key determinant of health by affecting nutrient metabolism, energy balance, body weight regulation, and mental health. The gut-brain axis is a critical pathway through which dietary factors influence cognitive function and behavior via microbial metabolites. While this relationship has been extensively studied in traditional laboratory models, diet-microbiome-cognition interactions remain largely unexplored in Octodon degus, an emerging model for aging, neurodegeneration, and cognitive research. Here, we compared two widely used rodent diets-LabDiet and Champion-to evaluate their effects on digestive efficiency, behavior, and gut microbiome composition. We also examined the relationships between these variables using piecewise structural equation modeling (pSEM). Our results indicated that LabDiet-fed degus exhibited enhanced nutrient absorption, higher fecal acetic acid levels, and a higher abundance of Actinobacteria (particularly Bifidobacterium), likely driven by its vitamin C supplementation. These animals also showed improved working memory and social motivation, but they displayed increased anxiety-like behavior. In contrast, Champion-fed degus, which consumed a more fiber-diverse, plant-based diet, showed lower anxiety traits and significantly greater gut microbial richness, with higher abundance of Bacteroidota and Tenericutes. Innate behaviors, such as burrowing and nesting, remained unaffected by the diet. SEM analysis revealed that diet explained most of the variance in microbial activity and identified a positive association between acetic acid levels and cognitive performance. This emphasizes a strong relationship among diet, microbiome, and brain function. Overall, our results suggest that dietary composition is a key factor influencing experimental outcomes in degus, with important implications for physiology, cognition, and microbial ecology. Standardizing dietary inputs is essential to ensure reproducibility in behavioral and biomedical studies using this model. Additionally, our results reinforce the microbiome's role as a mediator of diet-driven brain function via SCFAs, underscoring degus as a powerful system for investigating diet-microbiome-neurobehavioral interactions relevant to aging and mental health.}, }
@article {pmid41317466, year = {2025}, author = {Belarbi, H and Kebede, F and De Leyn, I and Van Bockstaele, F and Van De Wiele, T and Lambrecht, F and Cakmak, I and Du Laing, G}, title = {Enhancing iodine delivery through sourdough wheat bread: influence of biofortified flour and iodized salt on iodine concentration and bioaccessibility.}, journal = {Food chemistry}, volume = {498}, number = {Pt 2}, pages = {147232}, doi = {10.1016/j.foodchem.2025.147232}, pmid = {41317466}, issn = {1873-7072}, abstract = {Iodine deficiency remains a critical health concern, particularly in populations with limited access to iodized salt or shifting dietary patterns. This study assessed the impact of iodine-biofortified wheat flour (IBF), alone or combined with iodized salt (IS), on iodine content and bioaccessibility in sourdough bread. In vitro digestion showed that IBF increased iodine content to 158 μg/kg, and to 340 μg/kg with IS, compared to 1.63 μg/kg in control bread. This corresponds to an estimated intake of 68 μg/day. The IBF + IS formulation demonstrated the highest iodine bioaccessibility (224 μg/kg; 65 %). Interestingly, while iodine-fortified breads showed reduced values for selenium, potassium, and calcium, breads made with plain salt exhibited higher bioaccessibility for these minerals. These findings confirm the efficacy of IBF in enhancing iodine intake and its potential as an alternative or complement to salt iodization. They also indicate the importance of fortification approaches, considering the broader nutritional matrix over individual nutrients.}, }
@article {pmid41315866, year = {2025}, author = {Engelberts, JP and Tyson, GW}, title = {Understanding microbial ecology and evolution with single-cell genomics.}, journal = {Nature reviews. Genetics}, volume = {}, number = {}, pages = {}, pmid = {41315866}, issn = {1471-0064}, }
@article {pmid41315055, year = {2025}, author = {Gallardo-Becerra, L and Cornejo-Granados, F and Bikel, S and Arenas, I and López-Leal, G and Alvarado-Gonzalez, C and Sánchez-López, F and Manzo, R and Corzo, G and Espino-Solis, GP and Canizales-Quinteros, S and Ochoa-Leyva, A}, title = {Bioactive Plasmid- and Phage-Encoded Antimicrobial Peptides (AMPs) in the Human Gut: A Metatranscriptome-Virome Profiling Reveals Exploratory Links to Metabolic Human Diseases.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02620-2}, pmid = {41315055}, issn = {1432-184X}, abstract = {Microbe-derived antimicrobial peptides (AMPs) can shape gut community structure; however, their contribution to disease-associated dysbiosis remains poorly understood. We assembled fecal metatranscriptomes from individuals with normal weight (NW), obesity (O), and obesity with metabolic syndrome (OMS), yielding 51,087 non-human transcripts. We screened 1,095 small open reading frames (smORFs) using AMP-prediction algorithms combined with stringent post-hoc bioinformatics filters identifying 51 high-confidence AMP candidates. Most matched bacterial homologs, predominantly Faecalibacterium prausnitzii, while eight mapped to plasmids or bacteriophages. Differential expression identified two and four AMPs overexpressed in O and OMS, respectively. Two of them were originated from chromosomes, three from phages, and one from plasmid. Notably, the over-expression of these AMPs was negatively correlated with healthy-associated bacteria and positively correlated with obesity-enriched taxa. Furthermore, these AMPs were broadly detectable across 372 external gut metatranscriptomes (prevalence up to 94% of the samples) indicating conservation within the human gut microbiome and highlighting mobile elements as an overlooked reservoir of transcriptionally active AMPs. Using DNA virome sequencing and prophage analyses, we suggested phage origin of the transcribed AMPs. We further synthesized a phage-encoded AMP (AMP-3020), demonstrating broad-spectrum activity against Gram-positive and Gram-negative bacteria, without detectable cytotoxicity toward human immune T cells. This supports the idea that phages could encode functional AMPs capable of shaping gut community structure by suppressing diverse bacteria without harming host immune cells. Our gut metatranscriptome-virome profiling revealed a conservative core of actively transcribed, plasmid- and phage-encoded AMPs with exploratory associations to obesity/MetS. These findings support mobile-element AMPs as candidate ecological regulators and motivate validation in larger cohorts and mechanistic models.}, }
@article {pmid41314076, year = {2025}, author = {Md Ali, SA and Saito, S and Nishiyama, M and Phung, LD and Watanabe, T}, title = {Composted sewage sludge reshapes soil resistome connectivity and enhances antibiotic resistance gene dissemination in paddy fields.}, journal = {The Science of the total environment}, volume = {1009}, number = {}, pages = {181049}, doi = {10.1016/j.scitotenv.2025.181049}, pmid = {41314076}, issn = {1879-1026}, abstract = {The reuse of organic waste streams, such as composted sewage sludge (CSS), provides agronomic benefits, but also represents a critical pathway for the environmental dissemination of antibiotic resistance genes (ARGs). The consequences of CSS application for soil resistome dynamics and microbial ecology remain insufficiently understood. Here, we investigated paddy soils in Tsuruoka, Japan, under three fertilization treatments: CSS, chemical fertilizer (CF), and their combination (CSS + CF). Quantitative PCR targeted total bacterial (16S rRNA), fecal indicators (E. coli, Enterococcus spp.), mobile genetic element (MGE) (inlt1), and five ARGs (sul1, blaTEM, blaCTX-M Groups 1, 2, and 9). CSS amended soils showed elevated levels of intI1, sul1, and blaTEM in 2023, with blaTEM persisting into 2024. Although both E. coli and Enterococcus spp. showed weak correlations with ARGs, only Enterococcus spp. (ρ = 0.37, p < 0.05) showed statistically significant associations with intI1. Network analysis demonstrated that CSS fostered a highly interconnected resistome with sul1 emerging as a central hub linking multiple bacterial families. In contrast, CF maintained a sparse modular structure while CSS + CF generated an intermediate network. Collectively, these results demonstrate that CSS amplifies the potential for ARG dissemination by fostering a highly connected resistome, whereas co-application with chemical fertilizers partially disrupts this connectivity, thereby reducing dissemination risk in the soil environment. Our findings provide field-based evidence of the environmental impacts of waste-derived fertilization and underscore the need for integrated fertilization strategies and ARG surveillance to promote sustainable soil management and safeguard environmental health.}, }
@article {pmid41313007, year = {2025}, author = {Fletcher, JR and Hansen, LA and Hoyser, JR and Hanna, AE and Martinez, R and Freeman, CD and Thorns, NT and Penningroth, MR and Villarreal, AR and Vogt, GA and Tyler, MA and Hines, KM and Hunter, RC}, title = {Commensal-derived short-chain fatty acids disrupt lipid membrane homeostasis in Staphylococcus aureus.}, journal = {mBio}, volume = {}, number = {}, pages = {e0139225}, doi = {10.1128/mbio.01392-25}, pmid = {41313007}, issn = {2150-7511}, abstract = {The role of commensal anaerobic bacteria in chronic respiratory infections is unclear, yet they can exist in abundances comparable to canonical pathogens in vivo. Their contributions to the metabolic landscape of the host environment may influence pathogen behavior by competing for nutrients and creating inhospitable conditions via toxic metabolites. Here, we show that the anaerobe-derived short-chain fatty acids (SCFAs) propionate and butyrate negatively affect Staphylococcus aureus physiology by disrupting branched-chain fatty acid (BCFA) metabolism. In turn, alterations to BCFA abundance impair S. aureus growth, compromise membrane integrity, diminish expression of the accessory gene regulator quorum-sensing system, and increase sensitivity to membrane-targeting antimicrobials. Disrupted BCFA metabolism also reduced S. aureus fitness in competition with Pseudomonas aeruginosa, suggesting that airway microbiome composition and the metabolites they exchange can directly impact pathogen succession over time. The pleiotropic effects of SCFAs on S. aureus fitness and their ubiquity as metabolites in the human host also suggest that they may be effective as adjuvants to traditional antimicrobial agents when used in combination.IMPORTANCEStaphylococcus aureus is a primary pathogen of chronic airway disease yet is also found in the upper airways of 30%-50% of the population to no obvious detriment. Thus, identifying the host and/or microbial factors that tip the balance between its commensal and pathogenic states may be key to its control. Here, we reveal that short-chain fatty acids produced by commensal microbiota promote a marked remodeling of the S. aureus lipid membrane that, in turn, sensitizes the pathogen to antimicrobials, disrupts accessory gene regulator quorum signaling, and reduces its competitive fitness. Altogether, these data suggest that co-colonizing microbiota and the metabolites they exchange with S. aureus may be key players in the microbial ecology of airway disease.}, }
@article {pmid41311479, year = {2025}, author = {Gao, Y and Zhang, L and Zhang, Y and Huang, J and Wu, C and Zhou, R}, title = {Synthetic microbial community SMC-L1 optimizes flavor chemistry in reduced salt soy sauce via targeted metabolic reprogramming.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1701479}, pmid = {41311479}, issn = {1664-302X}, abstract = {The high sodium content in traditional soy sauce presents significant public health concerns, particularly related to hypertension and cardiovascular diseases. However, reducing salt content often disrupts microbial ecology and impairs flavor formation during fermentation. To overcome this challenge, we developed synthetic microbial communities (SynMCs) for reduced-salt (13% NaCl) moromi fermentation under traditional sun-brewing conditions. Using integrated multi-omics analyses, we identified an optimal consortium (SMC-L1) incorporating Tetragenococcus halophilus T10 as a key lactic acid bacterium alongside functional yeast strains. This defined community maintained fermentation stability while significantly enhancing flavor-relevant biochemical profiles. SMC-L1 inoculation markedly improved key quality parameters, increasing total nitrogen by 40.8% and amino acid nitrogen by 56.7%. Furthermore, it elevated critical metabolites including organic acids, particularly succinate, free amino acids, and short-chain esters. Network analysis revealed robust ecology-metabolite relationships: Tetragenococcus abundance correlated with succinate production and ester synthesis, while Aspergillus dynamics corresponded with free amino acid accumulation. These findings highlight how targeted microbial consortia can reprogram metabolic networks under salt-reduced conditions. From a food microbiology perspective, this study demonstrates that rational design of microbial communities can effectively decouple salt reduction from flavor deterioration in fermented foods. The metabolic pathways observed, particularly the anaerobic TCA cycle activity connecting Tetragenococcus to succinate accumulation, provides mechanistic insights into microbial adaptation to reduced-salt environments. This approach offers a viable strategy for developing healthier fermented products without compromising their sensory characteristics, advancing both fundamental knowledge and practical applications in food biotechnology.}, }
@article {pmid41307726, year = {2025}, author = {Ferreira, CM and de Affonseca, DB and Barbosa, FAS and Campos, AB and Menezes, R and Brait, L and Viana, PAB and Trindade-Silva, AE and Loiola, M and Azevedo, AR and Coutinho, FH and Assis, APA and Bruce, T and Ramos, PIP and Ara, A and Brouns, R and Andrade, RFS and Guimarães, PR and Meirelles, PM}, title = {Rare Phyla, Such as CPR and DPANN, Shape Ecosystem-Level Microbial Community Structure Dissimilarities.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {135}, pmid = {41307726}, issn = {1432-184X}, support = {88887-468244-2019-00//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 114693/2022-6//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; RYC2022-037094-I//Ministerio de Ciencia e Innovaci&#xf3;n/ ; Serra-1709-17818//Instituto Serrapilheira/ ; }, mesh = {*Bacteria/classification/genetics/isolation &amp; purification ; *Archaea/classification/genetics/isolation &amp; purification ; *Microbiota ; *Ecosystem ; Metagenome ; Biodiversity ; Phylogeny ; Soil Microbiology ; }, abstract = {Rare microbial lineages, such as members of the candidate phyla radiation (CPR) bacteria and Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) archaea, are increasingly recognized as key components of microbial communities in natural systems. Yet, their global distribution, biogeographic patterns, and broader role in shaping microbial community structure across diverse ecosystems remain poorly characterized. Here, we analyzed 2860 metagenomes spanning nine ecosystems using a curated reference database and a bias-aware taxonomic filtering approach to quantify the richness, relative abundance, and structural influence of low-abundance microbial taxa on community structure across a wide range of ecosystems. Our findings reveal that rare taxa, primarily CPR and DPANN, disproportionately shape microbial community dissimilarities across global ecosystems. We observed that the richness of these two groups, that drives community structure variation, increases with latitude, peaking in temperate regions, thereby contrasting classical latitudinal diversity patterns and suggesting unique biogeographic drivers. CPR and DPANN were predominantly enriched in free-living environments, particularly groundwater and soil, then in host-associated habitats, consistent with niche specialization shaped by environmental filtering and dispersal constraints. These findings challenge abundance-centric assumptions in microbial ecology and highlight the need to integrate low-abundance taxa into macroecological frameworks. Fully resolving their ecological functions, however, will require targeted experimental and multi-omics investigations.}, }
@article {pmid41304320, year = {2025}, author = {Tawidian, P and Tucker, BJ and Zembsch, TE and Ip, HS and Bartholomay, LC}, title = {Infection-Mediated Shifts in the Microbial Communities of Deer-Fed Ixodes scapularis Ticks.}, journal = {Microorganisms}, volume = {13}, number = {11}, pages = {}, pmid = {41304320}, issn = {2076-2607}, support = {cooperative agreement U01CK000505/CC/CDC HHS/United States ; G21AC10134//United States Department of Agriculture/ ; }, abstract = {The holobiont of the blacklegged tick (Ixodes scapularis) includes maternally inherited rickettsial endosymbionts and environmentally acquired microbes that may influence tick fitness and vector competence. While previous studies have focused on characterizing the microbiota of I. scapularis ticks, less is known about the influence of tick infection status on microbial assemblages. Here, we collected engorged female I. scapularis ticks from hunter-harvested white-tailed deer (Odocoileus virginianus) across 11 counties in Wisconsin during fall 2022. The ticks were maintained in laboratory conditions for oviposition and then frozen for nucleic acid extraction. The infection status of each tick was determined using qPCR, targeting Borrelia spp., Babesia spp., and Powassan virus. Bacterial and fungal communities were characterized through amplicon-based sequencing targeting the 16S rRNA gene and ITS2 region, respectively. Our targeted pathogen testing revealed that 14.1% of the collected ticks were infected with Babesia odocoilei and 23.3% with Borrelia burgdorferi. The microbial community composition of ticks was significantly influenced by infection status and pathogen identity. Notably, Borrelia-infected ticks exhibited distinct microbiota profiles and increased microbial network connectivity. These findings provide new insights into the microbial ecology of deer-fed I. scapularis ticks and highlight the role of infection in shaping both microbiota and mycobiota communities.}, }
@article {pmid41304309, year = {2025}, author = {Paoli, JE and Thongthum, T and Bassett, M and Beardsley, J and Tagliamonte, MS and Cash, MN and Spertus Newman, J and Smith, LM and Anderson, BD and Salemi, M and Subramaniam, K and von Fricken, ME and Braun de Torrez, E and Mathis, V and Mavian, CN}, title = {Virome and Microbiome of Florida Bats Illuminate Viral Co-Infections, Dietary Viral Signals, and Gut Microbiome Shifts.}, journal = {Microorganisms}, volume = {13}, number = {11}, pages = {}, doi = {10.3390/microorganisms13112625}, pmid = {41304309}, issn = {2076-2607}, support = {Department of Pathology EPIG RAS 2021-2022//University of Florida/ ; Florida Informatics Institute SEED 2022-2023//University of Florida/ ; Biodiversity Institute SEED 2022-2023//University of Florida/ ; }, abstract = {Florida's bat virome remains poorly characterized despite the state's high bat species diversity and conservation importance. We characterized viral metagenomes from rectal tissues, anal swabs, and feces of Myotis austroriparius and Tadarida brasiliensis sampled across north Florida. We recovered a near-complete Hubei virga-like virus 2 (HVLV2) genome from T. brasiliensis feces, a finding consistent with an arthropod-derived dietary signal rather than active bat infection. An Alphacoronavirus (AlphaCoV) was detected in two M. austroriparius specimens, including one with a putative co-infection involving an Astrovirus (AstV), the first detection of AstV in Florida bats to date. Parallel profiling of the M. austroriparius gut microbiome highlighted compositional differences in the co-infected individual relative to AlphaCoV-only and virus-negative bats, suggestive of potential associations between viral detection and gut microbial shifts. Our study expands the known viral diversity in Florida bat populations, and demonstrates how metagenomics can simultaneously illuminate host diet, viral exposure, and gut microbial ecology. This approach provides a scalable framework for monitoring how diet, microbiome composition, and environmental pressures shape the bat virome, and inform conservation and zoonotic risk assessments.}, }
@article {pmid41304257, year = {2025}, author = {Ma, R and Chen, Y and Chen, X and Zhang, J and Liu, C and Yang, L and Song, Y and Sun, Z and Lin, X and Ai, T and Ren, D and Chen, S}, title = {The Dominant Role of Dietary Differences in Shaping the Intestinal Microbial Communities of Grass Carp, Carp, and Crucian Carp in a Saline-Alkali Lake in Xinjiang During Winter.}, journal = {Microorganisms}, volume = {13}, number = {11}, pages = {}, doi = {10.3390/microorganisms13112572}, pmid = {41304257}, issn = {2076-2607}, support = {Grant No. 2023YFD2401000;Grant No.2023TSYCCX0128;2024AB019;Grant No. XJARS-08-14//The Key R &amp; D plan of Ministry of Science and Technology;The Tianshan Talent Training Project of Xinjiang;The Key Scientific and Technological Research Projects of Xinjiang Production and Construction Corps;Xinjiang Agriculture Research System/ ; }, abstract = {In this study, gut microorganisms of herbivorous grass carp, omnivorous carp, crucian carp, and aquatic microorganisms were collected from natural salt-alkali lakes and ponds in Xinjiang in winter to analyze their community structures. We sequenced 16S rRNA amplicons to investigate the composition and function of the microorganisms in the gut. PCoA analysis revealed that the gut microbiota of herbivorous and omnivorous fish formed two distinct clusters. Proteobacteria, Actinobacteria, Desulfobacterota, Firmicutes, and Chloroflexia are the dominant bacteria in the gut of fish. Proteobacteria, Bacteroidetes, Actinobacteria, Cyanobacteria, and Gram-negative bacteria are the dominant bacteria in the water. Carbohydrate- and protein-degrading bacteria, such as Desulfofustis, Lactiplantibacillus, and Vibrio, were predominant in omnivorous fish (CC and GRC), while cold-resistant bacteria, such as Shewanella and Psychromonas, were colonized in grass carp. This suggests that the same environment does not lead to similar gut bacteria, and that specific endogenous factors play a far more important role in shaping the microbiota composition than environmental factors.}, }
@article {pmid41304168, year = {2025}, author = {Ouyang, H and Grześkowiak, &#x141; and Vahjen, W and Zentek, J and Martínez-Vallespín, B}, title = {Effects of Fibrous By-Products on Growth Performance, Ileal Nutrient Digestibility, Intestinal Morphology, and Microbiota Composition in Weaned Piglets.}, journal = {Microorganisms}, volume = {13}, number = {11}, pages = {}, doi = {10.3390/microorganisms13112482}, pmid = {41304168}, issn = {2076-2607}, abstract = {Three fibrous by-products were evaluated over a 35-day feeding period in 64 weaned piglets, randomly assigned to four groups: a control without by-products (CON) and three others with diets containing 8% carrot pomace (CRT), 8% brewers' spent grain (BSG), or 8% carob pods (CRB). The growth performance, feed intake, feed conversion ratio, and apparent ileal digestibility of protein and amino acids were not affected. The jejunal and colonic morphology showed no statistical differences, although small numerical increases in the villus height and villus height-to-crypt ratio were noted with the by-products. Total short-chain fatty acid concentrations were stable, but their profile shifted: acetate increased in CRT and CRB (p < 0.001) mainly at the expense of propionate (p = 0.005). The microbiota composition in the proximal colon showed modest changes, with the highest Bifidobacterium spp. abundance in CRT and lowest in CRB (p = 0.042), reduced Ruminococcaceae UCG 005 with all the by-products (p = 0.008), and greater microbial richness in CRB (p = 0.009). These results suggest that a moderate inclusion of fibrous by-products may influence intestinal microbial ecology and fermentation patterns without negatively affecting performance or nutrient digestibility in weaned piglets, with no source appearing superior, thereby highlighting their potential as sustainable feed ingredients.}, }
@article {pmid41304165, year = {2025}, author = {Tong, F and Feng, X and Yuan, H and Chen, Y and Chen, P}, title = {Oyster Aquaculture Impacts on Environment and Microbial Taxa in Dapeng Cove.}, journal = {Microorganisms}, volume = {13}, number = {11}, pages = {}, doi = {10.3390/microorganisms13112480}, pmid = {41304165}, issn = {2076-2607}, support = {SML2023SP237//Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai)/ ; 2023TD06//Central Public-interest Scientific Institution Basal, Research Fund, CAFS/ ; 2024YFD2401405; 2024YFB4206600//National Key Research and Development Program of China/ ; }, abstract = {Environmental physicochemical factors and microorganisms play critical roles in the health of oysters. However, the impact of high-density oyster farming-a highly efficient filter-feeding bivalve system-on environmental conditions and microbial community structure and function remains poorly understood. This study conducted four-season monitoring of the water and sediment parameters in a semi-enclosed bay commercial oyster aquaculture (OA) system and a control area (CT), coupled with 16S rRNA amplicon sequencing of the environmental microbiota. Oyster aquaculture caused negligible disruption to water column parameters but significantly increased the concentrations of total organic carbon (TOC, annual mean OA vs. CT:1.15% vs. 0.56%), sulfides (annual mean OA vs. CT:67.72 vs. 24.99 mg·kg[-1]), and heavy metals (Cd, Pb, Cu, Zn, and Cr) in the sediment. α-diversity (Shannon and Chao indices) exhibited minimal overall perturbation, with significant inter-regional differences observed only in winter for both water and sediment. The bacterial community structure of the water column was significantly altered only in winter, whereas sediment communities showed structural shifts in spring, summer, and autumn. Water microbiota were primarily influenced by turbidity, dissolved oxygen, salinity, the Si/N ratio, and silicates. Sediment microbiota were correlated with Pb, Cu, Zn, TOC, Cr, and sediment particle size. Water bacterial functions displayed only four significantly divergent biogeochemical processes annually (sulfur compound respiration; OA vs. CT). In contrast, sediment bacteria exhibited 29 significantly disrupted functions annually, with the greatest seasonal divergence in winter (11/67 functions). Spring, summer, and autumn sediment functions showed distinct patterns. Understanding these environmental-microbial interactions is essential for sustainable oyster aquaculture and ecological optimization.}, }
@article {pmid41304129, year = {2025}, author = {Zhong, Y and Wu, C and E, J and Gu, Y and Chi, H and Du, X}, title = {Bioavailability, Ecological Risk, and Microbial Response of Rare Earth Elements in Sediments of the Remediated Yitong River: An Integrated DGT and Multi-Parameter Assessment.}, journal = {Microorganisms}, volume = {13}, number = {11}, pages = {}, doi = {10.3390/microorganisms13112443}, pmid = {41304129}, issn = {2076-2607}, abstract = {The expanding use of rare earth elements (REEs) in high-tech industrials has increased their environmental release, raising concerns about their ecological risks. This study employed the Diffusive Gradients in Thin Films (DGT) technique to assess REE bioavailability, spatial distribution, and ecological risks of REEs in sediments of the Yitong River, a historically polluted urban river in Changchun, China. Sediment characteristics (organic matter, pH, salinity), nutrient dynamics (N, P), and metal concentrations (Fe, Mn, As, etc.) were analyzed alongside REEs to evaluate their interactions and environmental drivers. Results revealed that REE concentrations (0.453-1.687 μg L[-1]) were dominated by light REEs (50.1%), with levels an order of magnitude lower than heavily industrialized regions. Ecological risk quotients (RQ) for individual REEs were below thresholds (RQ < 1), indicating negligible immediate risks, though spatial trends suggested urban runoff influences. Probabilistic risk assessment integrating DGT data and species sensitivity distributions (SSD) estimated a low combined toxic probability (2.26%) for REEs and nutrients. Microbial community analysis revealed correlations between specific bacterial (e.g., Clostridium, Dechloromonas) and fungal genera (e.g., Pseudeurotium) with metals and REEs, highlighting microbial sensitivity to pollutant shifts. This study provides a multidimensional framework linking REE bioavailability, sediment geochemistry, and microbial ecology, offering insights for managing REE contamination in urban riverine systems.}, }
@article {pmid41304117, year = {2025}, author = {Guo, M and Liu, D and Xia, Z and Xie, T and Su, L and Pérez-Moreno, J and Yu, F}, title = {Geographic Provenances Outweigh Tissue Compartments in Bacteriome Assembly of the Ectomycorrhizal, Edible, and Hallucinogenic if Undercooked, Lanmoa asiatica (Boletaceae, Boletales) Mushroom from Yunnan China.}, journal = {Microorganisms}, volume = {13}, number = {11}, pages = {}, doi = {10.3390/microorganisms13112431}, pmid = {41304117}, issn = {2076-2607}, support = {KCXFZJ-DDBF-202403//Designated Support Project of Chinese Academy of Sciences/ ; Guike AB22080097//the Key Research and Development Program of GuangXi/ ; 202205AD160036//the Yunnan Technology Innovation Program/ ; }, abstract = {Ectomycorrhizal fungal sporomes represent complex microuniverses harboring structurally and functionally eclectic microbiomes with significant ecological roles and potential anthropogenic applications. Nevertheless, the factors governing the assembly of these microbial communities remain poorly understood, and numerous fungal taxa, including many ectomycorrhizal species, remain uninvestigated. This study characterizes the bacteriome of the socioculturally and economically important yet hallucinogenic-if-raw ectomycorrhizal bolete Lanmoa asiatica. We analyzed 36 basidiomata from four geographic locations within China, partitioning each into pileus, stipe, and hymenophore tissues, and sequenced the V5-V7 region of the bacterial 16S rRNA gene. Proteobacteria dominated (>85%), with Pantoea, Sphingomonas, and the Burkholderia complex identified as core genera. Contrary to expectations, α-diversity was highest in the stipe (Chao1 index up to 1934) rather than the exposed hymenophore. PERMANOVA indicated that geographic origin (R[2] = 0.46, p < 0.001) was a stronger structuring force than tissue type (R[2] = 0.28, p < 0.01). Functional prediction via PICRUSt2 revealed enrichments in lipid metabolism, antimicrobial resistance, and apoptosis pathways across sites, while tissue-specific functions involved carbohydrate and nitrogen metabolism. These findings support a hierarchical model of bacteriome assembly where broad-scale environmental filters override micro-niche differentiation, providing a biogeographic framework for the conservation of this highly valued edible mushroom.}, }
@article {pmid41301533, year = {2025}, author = {Sabharwal, A and Haase, EM and Scannapieco, FA}, title = {Amylase Binding to Oral Streptococci: A Key Interaction for Human Oral Microbial Ecology, Adaptation and Fitness.}, journal = {Biomolecules}, volume = {15}, number = {11}, pages = {}, doi = {10.3390/biom15111616}, pmid = {41301533}, issn = {2218-273X}, support = {1R01DE022673-01/NH/NIH HHS/United States ; 1C06DC022673-18/NH/NIH HHS/United States ; }, mesh = {Humans ; *Mouth/microbiology ; *Streptococcus/metabolism/enzymology ; Biofilms/growth &amp; development ; *Amylases/metabolism ; Bacterial Adhesion ; Adaptation, Physiological ; Microbiota ; }, abstract = {The interaction between human salivary alpha-amylase (HSAmy) and amylase-binding oral streptococci (ABS) helps determine the bacteria that colonize the oral cavity by establishing dental biofilms. Streptococci are important pioneer species of the oral cavity and influence oral health as well as common diseases such as dental caries. Various oral streptococcal species express distinct amylase-binding proteins, among which amylase-binding protein A (AbpA), encoded by the abpA gene in Streptococcus gordonii and several other species, which is the most extensively studied. Amylase binding facilitates microbial adhesion to host surfaces and biofilm formation and enables bacteria to harness the host's amylase enzymatic activity at their cell surface, enhancing their capacity to metabolize dietary starch for nutritional gain. Additionally, amylase binding may also influence bacterial cell division and stress tolerance by engaging novel bacterial signaling pathways. From an evolutionary perspective, both Neanderthals and modern humans exhibit functional adaptations in nutrient metabolism, including selection for salivary amylase-binding oral streptococci, highlighting the importance of microbial co-adaptation in response to host diet. Further research is warranted to elucidate the broader roles of amylase binding to bacteria in host-bacterial signaling, bacterial cell division and fitness and the evolutionary trajectory of the oral microbiome.}, }
@article {pmid41301495, year = {2025}, author = {Teslya, AV and Stepanov, AA and Poshvina, DV and Petrushin, IS and Vasilchenko, AS}, title = {From Lab to Field: Context-Dependent Impacts of Pseudomonas-Produced 2,4-Diacetylphloroglucinol on Soil Microbial Ecology.}, journal = {Biomolecules}, volume = {15}, number = {11}, pages = {}, doi = {10.3390/biom15111578}, pmid = {41301495}, issn = {2218-273X}, support = {19-76-30005//Russian Science Foundation/ ; FEVZ-2024-0005//The Ministry of Science and Higher Education of the Russian Federation/ ; }, mesh = {*Soil Microbiology ; *Phloroglucinol/analogs &amp; derivatives/pharmacology/metabolism ; *Pseudomonas/metabolism ; Fungi/drug effects/genetics ; Bacteria/drug effects/genetics ; Microbiota/drug effects ; }, abstract = {The secondary metabolite 2,4-diacetylphloroglucinol (2,4-DAPG), which is produced by Pseudomonas bacteria, is a potent antimicrobial agent with well-documented properties that suppress phytopathogens. However, its broader ecological impact on soil microbial communities is not understood. Through a combination of controlled microcosm and field trials, we have demonstrated that the effects of 2,4-DAPG are highly context-dependent. Laboratory exposure (10 mg kg[-1]) altered the abundance of 8.53% of bacterial and 6.91% of fungal amplicon sequence variants, and simplified the bacterial co-occurrence networks (reduced number of nodes and links). In contrast, field conditions amplified bacterial sensitivity (the Shannon index decreased from 4.77 to 4.17, p < 0.05) but maintained fungal stability (Shannon index varied from 3.93 to 3.97, p > 0.05); these conditions affected a smaller proportion of fungal ASVs (4.23%). Taxonomic analysis revealed consistent suppression of fungi of the Mucoromycota (e.g., Mortierella) and context-dependent shifts in bacteria, with an enrichment of Bacillota (e.g., Bacillus, Paenibacillus) in the laboratory but not in the field. Enzymatic responses revealed a dose-dependent activation of the C-cycle, with up to 7.4-fold increases in the laboratory and up to a 10.5-fold increase in the field. P- and N- cycles showed more complex dynamics, with acid phosphatase activity increasing 3.8-fold in laboratory conditions and recovering from initial suppression to an increase of 144% in field conditions, while N-acetylglucosaminidase activity increased and L-leucine aminopeptidase decreased under laboratory conditions. Our results suggest that the response of microorganisms to 2,4-DAPG in natural soils is reduced, probably due to functional redundancy and pre-adaptation to abiotic stresses. This difference between laboratory and field studies warns against extrapolating data from controlled experiments to predict outcomes in agricultural ecosystems, and emphasizes the need for a context-specific evaluation of biocontrol agents.}, }
@article {pmid41301464, year = {2025}, author = {Cai, Y and Zhao, F and Cheng, X}, title = {Gut Microbiota and Ferroptosis in Colorectal Cancer: A Comprehensive Review of Mechanisms and Therapeutic Strategies to Overcome Immune Checkpoint Resistance.}, journal = {Biomolecules}, volume = {15}, number = {11}, pages = {}, doi = {10.3390/biom15111546}, pmid = {41301464}, issn = {2218-273X}, mesh = {Humans ; *Ferroptosis/drug effects ; *Gastrointestinal Microbiome/drug effects ; *Colorectal Neoplasms/microbiology/immunology/therapy/drug therapy/pathology/metabolism ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; Animals ; *Drug Resistance, Neoplasm ; }, abstract = {Colorectal cancer (CRC) remains a leading cause of cancer-related mortality worldwide. Although immune checkpoint inhibitors (ICIs) have achieved striking clinical efficacy in the subset of CRCs with mismatch repair deficiency/high microsatellite instability (dMMR/MSI-H), the vast majority of patients-those with proficient mismatch repair/microsatellite-stable (pMMR/MSS) tumors-derive little benefit from current immunotherapies. Ferroptosis, an iron-dependent form of regulated cell death driven by lethal accumulation of lipid peroxides, has emerged as a promising antitumor mechanism that can interact with and modulate antitumor immunity. Concurrently, the gut microbiota exerts powerful control over host metabolism and immune tone through microbial community structure and metabolite production; accumulating evidence indicates that microbiota-derived factors can either sensitize tumors to ferroptosis (for example, via short-chain fatty acids) or confer resistance (for example, indole-3-acrylic acid produced by Peptostreptococcus anaerobius acting through the AHR→ALDH1A3→FSP1/CoQ axis). In this review we synthesize mechanistic data linking microbial ecology, iron and lipid metabolism, and immune regulation to ferroptotic vulnerability in CRC. We discuss translational strategies to exploit this "microbiota-ferroptosis" axis-including precision microbiome modulation, dietary interventions, pharmacologic ferroptosis inducers, and tumor-targeted delivery systems-and we outline biomarker frameworks and trial designs to evaluate combinations with ICIs. We also highlight major challenges, such as interindividual microbiome variability, potential collateral harm to ferroptosis-sensitive immune cells, adaptive antioxidant compensation (e.g., NRF2/FSP1 activation), and safety/regulatory issues for live biotherapeutics. In summary, this review highlights that targeting the microbiota-ferroptosis axis may represent a rational and potentially transformative approach to reprogramming the tumor microenvironment and overcoming immune checkpoint resistance in pMMR/MSS colorectal cancer; however, further research is essential to validate this concept and address existing challenges.}, }
@article {pmid41300079, year = {2025}, author = {Guo, X and Lin, M and Le, TN and Zhou, Z and Zhao, M and Cai, H}, title = {Impact of Aspergillus Species on Microbial Community Dynamics and Their Associations with Fermentation Properties in Fermented Walnut-Based Soy Sauce.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {22}, pages = {}, doi = {10.3390/foods14223921}, pmid = {41300079}, issn = {2304-8158}, support = {32172214, 31972079//National Natural Science Foundation of China/ ; }, abstract = {This study investigated microbial community dynamics and their links to fermentation traits in solid-state fermentation of walnut -based soy sauce (WSS) using walnut meal-soybean meal mixtures. Via 16S rRNA sequencing and molecular docking, it analyzed the effects of three distinct starter culture treatments-Aspergillus oryzae (AO), Aspergillus niger (AN), and mixed starter culture (A. oryzae + A. niger, ON)-as well as fermentation duration on microbial diversity and physicochemical properties, aiming to clarify microbial-driven quality mechanisms. Physicochemical analysis demonstrated superior fermentation performance in the AO group, showing significantly higher amino nitrogen (NH3-N) accumulation (0.23 g/100 mL) and protease activity (30.5 U/mL) compared to the AN group, with the mixed inoculation group (ON) exhibiting intermediate results, indicating A. oryzae's dominant role in mixed fermentation. Via PCA and Shannon index, microbial diversity analyses revealed starter cultures shaped microbial community structure: Enterococcus and Staphylococcaceae were enriched by AO starter, and Klebsiella dominated in AN group. Additionally, temporal succession of the microbiota occurred during post-fermentation of WSS, with Lactobacillales, Staphylococcus, and special flavor-producing functional flora dominating early, middle, and later stages, respectively. Staphylococcus positively correlated with protease activity and amino nitrogen, critical for quality. Molecular docking showed major walnut polyphenols significantly affected protease activity, aiding process optimization. This research provides theoretical foundations for improving WSS production and enriches understanding of solid-state fermentation microbial ecology.}, }
@article {pmid41299791, year = {2025}, author = {Cheng, Q and Ma, J and Yang, Y and Ma, J and Grossart, HP and Xu, L and Lin, H}, title = {Enrichment of vitamin B12-producing Porphyrobacter in the phycosphere microbiome promotes microalgal stress adaptation to antibiotic exposure.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {240}, pmid = {41299791}, issn = {2049-2618}, support = {42207285//National Natural Science Foundation of China/ ; 42177002//National Natural Science Foundation of China/ ; LMS25C150001//Natural Science Foundation of Zhejiang Province/ ; 2021R52045//Leading talents in scientific and technological innovation, high-level Talents of Zhejiang Special Support Program/ ; 202204T14//Key Scientific Research and Development Program of Hangzhou/ ; }, mesh = {*Vitamin B 12/biosynthesis/metabolism ; *Microalgae/drug effects/microbiology/growth &amp; development/physiology ; *Anti-Bacterial Agents/pharmacology ; *Microbiota ; Stress, Physiological ; Adaptation, Physiological ; }, abstract = {BACKGROUND: Planktonic microalgae deploy multifaceted responsive and adaptive strategies against anthropogenic pollutants; however, current understanding of antibiotic resistance mechanisms remains predominantly focused on intrinsic physiological adaptations. While microalgae maintain intimate relationships with the phycosphere microbiome, the ecological roles of these associated microbes in mediating host adaptation to polluted environments are inadequately characterized.<br><br>RESULTS: We identified a phycosphere microbiome-involved antibiotic resistance mechanism in Dictyosphaerium sp., a pollution-tolerant Chlorophyta microalgae exhibiting remarkable enrofloxacin (ENR) tolerance. Microalgal growth displayed initial inhibition followed by significant promotion under 5&#xa0;mg/L ENR exposure. This resilience was associated with the restructuring of phycosphere microbiome, characterized by Porphyrobacter enrichment and functional enhancement of algal fitness-promoting pathways, including upregulation of cobalamin biosynthesis genes (log2FC&#x2009;=&#x2009;7.76) and a 33.3-fold increase in extracellular B12 accumulation. Consequently, we isolated the ENR-selected microbial taxa to elucidate their roles in microalgal stress adaptation. Co-culturing axenic Dictyosphaerium sp. with Porphyrobacter enhanced microalgal growth by 36.5% after 8-day ENR exposure, whereas non-dominant bacteria exhibited negligible effects. Based on the transcriptomic and metabolomic analyses of the algal system when Porphyrobacter was dominant, we subsequently compared the growth of axenic microalgae with and without B vitamin (B1, B6, B7, B12) supplementation. Experimental validation demonstrated the pivotal role of B12-producing Porphyrobacter in enhancing microalgal ENR adaptation through (i) stimulating extracellular polymeric substances production and subsequently enhancing ENR removal via EPS-mediated adsorption and (ii) alleviating intracellular oxidative stress via elevating superoxide dismutase and peroxidase activities and reducing malondialdehyde levels. Additionally, this B12-producing bacteria/B12-mediated adaptability exhibited cross-species conservation, improving ENR resistance in Chlorella vulgaris and Scenedesmus quadricauda, with analogous protection observed under ciprofloxacin and norfloxacin exposures.<br><br>CONCLUSION: Collectively, our findings establish stress-induced enrichment of B12-producing Porphyrobacter within the phycosphere microbiome as a pivotal mechanism underlying microalgal antibiotic adaptation. This insight facilitates the rational development of microalgae-microbiome systems for enhanced wastewater treatment and sustainable bioproduction, with applications in aquatic feed supplementation, biofuel production, and biofertilizer development. Video Abstract.}, }
@article {pmid41299662, year = {2025}, author = {Jiménez, DJ and Jamil, T and Miliotis, G and Schultz, J and Patel, N and Aldakheel, L and Kontis, N and García, FC and Villela, HDM and Duarte, GAS and Barno, AR and Farran, A and Alsaggaf, A and Santoro, &#xc9;P and Tumeo, A and Page, A and Wong, S and Kabza, A and Putra, A and Park, C and Angelov, A and Driguez, P and Peixoto, RS and Green, SJ and Tighe, S and Rosado, AS and Venkateswaran, K}, title = {Microbial community characterization in Red Sea-derived samples using a field-deployable DNA extraction system and nanopore sequencing.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-025-00819-x}, pmid = {41299662}, issn = {2524-6372}, support = {BAS/1/1096-01-0//King Abdullah University of Science and Technology/ ; }, abstract = {BACKGROUND: In this study, xTitan, a field-deployable, automated, and versatile nucleic acid extraction system was employed to characterize microbial communities in Red Sea-derived samples, including coral colonies, mangrove sediments, and seawater. The use of the xTitan in the field was intended to minimize sample transport bias, obtaining data that may be closer to "ground truth" for microbial diversity. The observed microbial communities from DNA extracted in the field using the xTitan system were compared to DNA extractions performed in a laboratory setting using both xTitan and a standard commercial kit (Qiagen) after approximately 24 h of sample transfer and storage.<br><br>RESULTS: Microbial community analyses conducted on DNA extracted using the xTitan system and the Qiagen kit yielded similar alpha diversity metric values, with a trend toward higher diversity observed in most samples extracted with the xTitan. The microbial community structure in samples from a Pocillopora verrucosa colony, mangrove sediments, and seawater was affected by the DNA extraction system. In the P. verrucosa colony, 16S rRNA gene sequences affiliated to Endozoicomonas acroporae were preferentially abundant when DNA was extracted in the field with the xTitan system rather than in the lab. In mangrove sediments, significant differences (P-value&#x2009;<&#x2009;0.05) in beta diversity and functional gene profiles were observed when comparing in-field to in-lab xTitan DNA extracts. In seawater, a pronounced decrease in the relative abundance of cyanobacterial populations was observed when DNA was extracted with both methods after samples were transported to the lab on ice. In addition, hundreds of species in mangrove-associated samples were differentially abundant when DNA was extracted on-site with the xTitan system compared to in-lab extractions. Balneolaceae was one of the most abundant taxa in mangrove sediments and several genera from this family were detected in all replicates across all DNA extraction systems.<br><br>CONCLUSIONS: The usability of different field-deployable instruments for microbial community characterization in marine-derived samples was demonstrated. Moreover, differences in beta diversity were observed when DNA was extracted in-field versus in-lab using the xTitan system, particularly for mangrove-associated samples. These results highlight the value of on-site nucleic acid extraction for enhancing the detection of microbial taxa that can be sensitive to cold storage. This study enabled the testing of the xTitan on Red Sea-derived samples, generating comprehensive information on the effects of DNA extraction systems and transportation of samples on coral and mangrove-associated microbiomes.}, }
@article {pmid41299176, year = {2025}, author = {Wirbel, J and Hickey, AS and Chang, D and Enright, NJ and Dvorak, M and Chanin, RB and Schmidtke, DT and Bhatt, AS}, title = {Long-read metagenomics reveals phage dynamics in the human gut microbiome.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {41299176}, issn = {1476-4687}, abstract = {Gut bacteriophages profoundly impact microbial ecology and health[1-3]; yet, they are understudied. Using deep long-read bulk metagenomic sequencing, we tracked prophage integration dynamics in stool samples from six healthy individuals, spanning a 2-year timescale. Although most prophages remained stably integrated into their hosts, approximately 5% of phages were dynamically gained or lost from persistent bacterial hosts. Within a sample, we found that bacterial hosts with and without a given prophage coexisted simultaneously. Furthermore, phage induction, when detected, occurred predominantly at low levels (1-3× coverage compared to the host region), in line with theoretical expectations[4]. We identified multiple instances of integration of the same phage into bacteria of different taxonomic families, challenging the dogma that phages are specific to a host of a given species or strain[5]. Finally, we describe a new class of 'IScream phages', which co-opt bacterial IS30 transposases to mediate their mobilization, representing a previously unrecognized form of phage domestication of selfish bacterial elements. Taken together, these findings illuminate fundamental aspects of phage-bacterial dynamics in the human gut microbiome and expand our understanding of the evolutionary mechanisms that drive horizontal gene transfer and microbial genome plasticity.}, }
@article {pmid41299132, year = {2025}, author = {Zhang, J and Zhou, X and Rong, X and Salem, H and Zhang, J and Yin, B and Guo, X and Zhang, Y}, title = {Effects of Plant Phylogeny and Traits on the Composition of Phyllosphere Microbial Communities in a Typical Temperate Desert in Central Asia.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02635-9}, pmid = {41299132}, issn = {1432-184X}, support = {2022D01A351//The Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; Non//The Tianchi Talent Introduction Project of Xinjiang Uygur Autonomous Region/ ; 2022D01D083//The Key Project of Xinjiang Uygur Autonomous Region Natural Science Foundation/ ; 2022TSYCLJ0058//The Leading Talents in Sci-Technological Innovation Project of "Tianshan Talent" Training Plan of Xinjiang Uygur Autonomous Region/ ; }, abstract = {Phyllosphere microorganisms play a vital role in supporting host plant health and adaptability. Although previous research on the effects of host performance and their phylogenetic associations on phyllosphere microbial communities has predominantly focused on tropical, subtropical, and temperate forestry ecosystems, the responses of these microbial communities to plant phylogeny and functional traits in temperate desert environments remains poorly understood. In this study, we conducted a quantitative analysis of bacterial and fungal community structures in the phyllosphere of 39 plant species from the Gurbantunggut Desert, a typical temperate desert in Central Asia. Variation partitioning analysis revealed that plant phylogeny, leaf physicochemical properties, and leaf morphological characteristics collectively explained the variation in phyllosphere microbial communities. Specifically, these factors accounted for 19.26%, 14.53%, and 2.32% of the variance in bacterial communities, and 11.55%, 8.36%, and 2.19% of the variance in fungal communities, respectively. A significant hierarchical pattern emerged: plant phylogeny > leaf physicochemical properties > leaf morphological characteristics, highlighting the dominant role of plant filtering effects in community assembly. Linear mixed-effects model analysis further confirmed the significant influence of multiple plant attributes, including phylogeny and functional traits, on microbial community structure. Plant-microbe interaction analysis revealed distinct host preferences of microbial taxa across different plant taxonomic levels. Co-evolutionary analysis also indicated a significant phylogenetic association between host plants and their phyllosphere amplicon sequence variants (ASVs). Overall, our findings demonstrate that plant attributes, particularly plant phylogeny and functional traits, are key factors driving the assembly of phyllosphere microbial communities in deserts. This study provides new insights into species coexistence mechanisms in fragile habitats and enhances our understanding of plant-microbe interactions in global desert ecosystem.}, }
@article {pmid41297120, year = {2025}, author = {Rajbhandari, RM and Shrestha, S and Manandhar, P and Napit, R and Sadaula, A and Chaudhary, A and Raut, R and Gortázar, C and Alves, PC and de la Fuente, J and Queirós, J and Forcina, G and Karmacharya, D}, title = {Comparing the respiratory tract microbiome in captive elephants and humans in Chitwan National Park: Implications for conservation medicine.}, journal = {Comparative immunology, microbiology and infectious diseases}, volume = {125}, number = {}, pages = {102422}, doi = {10.1016/j.cimid.2025.102422}, pmid = {41297120}, issn = {1878-1667}, abstract = {The study of gut microbiome in both animals and humans living in proximity has proven crucial in understanding their coevolution, the potential for microbial transfer and the dynamics behind various diseases. Similarly, the investigation of respiratory microbiomes has been gaining popularity due to its significance and impact on respiratory health. Here, we use 16S rRNA metabarcoding to explore the respiratory microbiome of captive Asian elephants (Elephas maximus) and their mahouts (i.e., trainers and handlers) in Chitwan National Park (Nepal), with local villagers residing out of the protected area acting as control. Sputum samples were collected to characterize their bacterial composition, while its functional profile was inferred with PICRUSt2. Additionally, the occurrence of genera hosting potentially pathogenic ESKAPE-E species was evaluated. Our findings revealed high similarity in the bacterial and functional composition of the respiratory microbiome of elephants and mahouts, with Bacillota and Pseudomonadota emerging as the most abundant phyla across all host categories and the controls displaying the highest diversity. A striking difference was observed in relation to the family Bacillaceae that dominated the microbial composition of both mahouts and elephants but not controls. Genera hosting potentially pathogenic ESKAPE-E bacteria were found in all host categories, which underscores the need for in-depth analyses to identify the species involved. Our study delivers valuable insights in the respiratory microbial community of both Asian elephants and humans, thus laying the basis for further investigations on their diversity and function, unveiling their role in respiratory health of both host species.}, }
@article {pmid41296916, year = {2025}, author = {Rettura, F and Lambiase, C and Bottari, A and Filippini, F and Giacomelli, L and Pistello, M and Bellini, M}, title = {Gut Virome: What's the Role in Irritable Bowel Syndrome?.}, journal = {Reviews in medical virology}, volume = {35}, number = {6}, pages = {e70080}, doi = {10.1002/rmv.70080}, pmid = {41296916}, issn = {1099-1654}, support = {2022FRE3RH//Italian Ministry of University and Research/ ; CUP I53D23000480006//National Recovery and Resilience Plan/ ; }, mesh = {Humans ; *Irritable Bowel Syndrome/virology/microbiology/therapy ; *Virome ; *Gastrointestinal Microbiome ; Bacteriophages/physiology ; Dysbiosis/virology ; Animals ; }, abstract = {The gut virome, an integral but still poorly understood component of the gut microbiota, is emerging as an important player in the pathophysiology of irritable bowel syndrome (IBS). Recent evidence suggests that alterations in virome diversity and phage-bacteria interactions contribute to gut dysbiosis, immune modulation and gut barrier dysfunction in IBS. This review summarises current knowledge on virome alterations in IBS and emphasises the role of bacteriophages in shaping microbial ecology and host responses. Different virome signatures in the different subtypes of IBS highlight the potential of the virome for disease stratification and personalised therapeutic strategies. In addition, we discuss the analytical challenges in virome research and explore novel virome-targeted interventions, including phage therapy and dietary modulation. A deeper understanding of virome dynamics in the gut could open new avenues for precision medicine approaches to treat IBS.}, }
@article {pmid41296063, year = {2025}, author = {Guo, M and Zhou, Z and Zheng, Y and Fu, D and Hou, L and Zhu, R}, title = {Ubiquity and Dominance of Comammox Over AOB and AOA and their Links To ARGs in Antarctic Lake Sediments.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02664-4}, pmid = {41296063}, issn = {1432-184X}, support = {2022YFF0801101//National Key Research and Development Program of China/ ; 42576267//National Natural Science Foundation of China/ ; }, abstract = {Complete ammonia oxidizers (comammox), oxidizing ammonia to nitrate directly, have been found to exist widely in multiple environments, but their distribution patterns are still under-explored in Antarctic environments. For the first time, the sediments were collected from West Antarctic lakes to investigate distribution patterns and community structure for comammox, ammonia oxidizing archaea (AOA) and bacteria (AOB), and nitrite-oxidizing bacteria (NOB), as well as the associations between ammonia oxidizers and antibiotic resistance genes (ARGs). Comammox clade B and AOB were dominant ammonia oxidizers, with the abundances of (1.62 ± 0.10) × 10[2] - (5.21 ± 0.74) × 10[6] and (0.17 ± 0.05) × 10[5] - (4.79 ± 0.65) × 10[5] copies g[- 1] sediment, respectively. Comammox clade B, instead of clade A, occurred in all sediments, exhibiting higher abundances than AOB and AOA in most of the sediments. The abundances for comammox clade B demonstrated significant positive correlation (p < 0.01) with NH4[+]-N levels, but negative correlation (p < 0.05) with C: N ratios. The coexistence of ammonia oxidizers in lake sediments was jointly structured by niche differentiation and environmental variables, and pH, modulated by penguin guano input, was found to be the most crucial factor in shaping their community structure. Co-occurrence network analyses revealed strong synergistic interactions between comammox and AOB, AOA, NOB, which played a critical role in nitrification processes. Our results further confirmed that comammox could act as important hosts for ARGs, hence stimulated their transmission and proliferation in the sediments. This study presented novel insights into the distribution patterns for ammonia oxidizers, their niche differentiation and the associations with ARGs in natural lake sediments of West Antarctica.}, }
@article {pmid41295040, year = {2025}, author = {Abdul Rahiman, S and Qiblawey, H}, title = {Anammox-MBR Technology: Breakthroughs and Challenges in Sustainable Nitrogen Removal from Wastewater.}, journal = {Membranes}, volume = {15}, number = {11}, pages = {}, doi = {10.3390/membranes15110337}, pmid = {41295040}, issn = {2077-0375}, support = {QUHI-CENG-25/26-747//Qatar University/ ; }, abstract = {Wastewater nitrogen pollution is a serious environmental problem, and traditional treatment techniques are frequently constrained by their high energy requirements and operational complexity. The anaerobic ammonium oxidation (anammox) process combined with membrane bioreactor (MBR) technology (anammox-MBR) offers a practical and energy-efficient solution for the sustainable removal of nitrogen, further enhanced by its potential to minimize emissions of nitrous oxide (N2O), a potent greenhouse gas with a global warming potential nearly 300 times that of carbon dioxide. This review outlines the most recent advancements in anammox-MBR systems, highlighting their ability to achieve nitrogen removal efficiencies of more than 70-90% and, in integrated systems with reverse osmosis, to recover up to 75% of the inflow as high-quality reusable water. Significant advancements such as high-rate activated sludge coupling, reverse osmosis integration, microaeration methods, and membrane surface modifications have decreased membrane fouling, accelerated startup times, and enhanced system stability. Despite these achievements, there are still issues that hinder widespread use, such as membrane fouling exacerbated by hydrophobic anammox metabolites, sensitivity to low temperatures (≤10 °C), and the persistent challenge of suppressing nitrite-oxidizing bacteria (NOB), which compete for the essential nitrite substrate. To enable cost-effective, energy-efficient, and environmentally sustainable large-scale applications, future research directions will focus on creating cold-tolerant anammox strains, advanced anti-fouling membranes, and AI-driven process optimization.}, }
@article {pmid41294522, year = {2025}, author = {Špiljak, B and Andabak Rogulj, A and Lončar Brzak, B and Brailo, V and Škrinjar, I and Ozretić, P and Vidović Juras, D}, title = {Desquamative Gingivitis and the Oral Microbiome: Insights into Immune-Microbial Interactions in Mucosal Inflammation.}, journal = {Dentistry journal}, volume = {13}, number = {11}, pages = {}, doi = {10.3390/dj13110541}, pmid = {41294522}, issn = {2304-6767}, abstract = {Desquamative gingivitis (DG) is a clinical presentation characterized by erythema, epithelial desquamation, and mucosal fragility, commonly associated with immune-mediated diseases such as oral lichen planus (OLP), mucous membrane pemphigoid (MMP), and pemphigus vulgaris (PV). While traditionally viewed as a manifestation of immune dysregulation, growing evidence suggests that the oral microbiome may modulate disease onset, persistence, and severity. This review summarizes current knowledge on the oral microbiota in DG and its underlying diseases, explores mechanistic links between dysbiosis and immune activation, and discusses clinical and research implications. A narrative literature review was conducted using PubMed and Scopus, focusing on studies analyzing the oral microbiome in OLP, MMP, and PV. Emphasis was placed on molecular microbiology techniques, immune profiling, and functional or longitudinal approaches. In OLP, microbial dysbiosis is consistently reported, including reduced diversity and increased abundance of pro-inflammatory genera such as Fusobacterium, Prevotella, and Capnocytophaga. These shifts correlate with epithelial barrier disruption and inflammatory cytokine production. Although data on MMP and PV are limited, early findings suggest microbial involvement in sustaining inflammation, delaying healing, and possibly amplifying autoimmune responses. Dysbiosis may activate Toll-like receptors, skew T cell responses, and contribute to the breakdown of immune tolerance. DG may reflect a dynamic interplay between immune mechanisms and microbial ecology. While evidence is strongest for OLP, preliminary data suggest broader microbial contributions across DG-associated diseases. Microbiome-informed approaches could enhance diagnostic accuracy and support the development of adjunctive therapies.}, }
@article {pmid41293856, year = {2025}, author = {Schäfer, RB and Baikova, D and Bayat, HS and Beermann, AJ and Berger, SA and Boenigk, J and Brauns, M and Burfeid-Castellanos, A and Cardinale, BJ and David, GM and Feckler, A and Feld, CK and Fink, P and Gessner, MO and Hadziomerovic, U and Hering, D and Le, TTY and Macaulay, SJ and Madariaga, GM and Serge Mayombo, NA and Pimentel, IM and Orr, JA and Osakpolor, S and Schlenker, A and Sures, B and Vermiert, AM and Vos, M and Weitere, M and Schürings, C}, title = {Effects of Biodiversity Loss on Freshwater Ecosystem Functions Increase With the Number of Stressors.}, journal = {Global change biology}, volume = {31}, number = {11}, pages = {e70617}, doi = {10.1111/gcb.70617}, pmid = {41293856}, issn = {1365-2486}, support = {426547801//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Biodiversity ; *Fresh Water ; *Ecosystem ; *Stress, Physiological ; Biomass ; }, abstract = {A multitude of anthropogenic stressors drive biodiversity loss and alter ecosystem functioning. Freshwaters, which contribute disproportionally to global biodiversity and biogeochemical cycles, are particularly threatened. Although the relationship between biodiversity and ecosystem functions (BEF) is generally well-established, especially in terrestrial ecosystems, the role of multiple, co-occurring stressors in modulating the relationship remains unclear. We conducted a meta-analysis to address this knowledge gap by assessing the effect of multiple stressors on the relationship between taxon richness and four measures of ecosystem function. The relationship was generally positive, with the slope becoming steeper as the number of stressors increased, suggesting that exposure to multiple stressors exacerbates impacts of biodiversity loss on ecosystem function. Multiple stressor effects on both taxon richness and ecosystem functions were largely predictable from individual stressor effects, although antagonistic effects on ecosystem functions emerged in 14% of the considered cases. The type of stressor and ecosystem function, along with taxonomic group, exerted no influence on the BEF relationship, contrary to our expectations. Microbial production and biomass declined most strongly in response to stressors, despite notable variability. Overall, our findings imply that functional consequences of freshwater biodiversity loss are more severe under multifaceted environmental change than previously assumed.}, }
@article {pmid41292685, year = {2025}, author = {O'Brien, JM and Blais, ND and Holland-Moritz, H and Shek, KL and Douglas, TA and Barbato, RA and Ernakovich, JG}, title = {Consistent microbial responses during the aerobic thaw of Alaskan permafrost soils.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1654065}, pmid = {41292685}, issn = {1664-302X}, abstract = {Arctic systems are warming at four times the global average, causing permafrost-permanently frozen soil, ice, organic matter, and bedrock-to thaw. Permafrost thaw exposes previously unavailable soil carbon and nutrients to decomposition-a process mediated by microbes-which releases greenhouse gases such as carbon dioxide and methane into the atmosphere. While it is well established that thaw alters the composition and function of the permafrost microbiome, patterns revealing common responses to thaw across different permafrost soil types have not yet emerged. In this study, we address how permafrost thaw impacts microbiome diversity, alters species abundance, and contributes to carbon flux in the Arctic. We sampled peat-like, mineral, and organic-mineral permafrost from three locations in central and northern Alaska. We assessed their abiotic soil properties and microbiome characteristics before and after a 3-month laboratory microcosm incubation. Across all sites, prokaryotic biomass increased following thaw, measured as 16S rRNA gene copy number. This change in biomass was positively correlated with cumulative respiration, indicating an increase in microbial activity post-thaw. We evaluated the thaw response of microbial taxa across three sites, identifying taxa that significantly increased in abundance post-thaw. Common responders shared across all sites belonged to the families Beijerinckiaceae, Burkholderiaceae, Clostridiaceae, Oxalobacteraceae, Pseudomonadaceae, and Sporichthyaceae, indicating a common set of taxa that consistently respond to thaw regardless of site-specific conditions. Alpha diversity decreased with thaw across all sites, likely reflecting the increased dominance of specific thaw-responsive taxa that may be driving post-thaw biogeochemistry and increased respiration. Taken together, we deepen the understanding of different permafrost microbiomes and their response to thaw, which has implications for the permafrost-climate feedback and enables more accurate predictions of how Arctic ecosystem structure and function respond to change.}, }
@article {pmid41291355, year = {2025}, author = {Han, H and Luo, Z and Pei, X and Xie, Y and Zhu, Y and Li, J and Zou, T and Wang, Z and Su, C}, title = {Microbial-Plant Interaction: Bacillus subtilis-Driven Gravel Soil Improvement and Growth Promotion of Festuca arundinacea.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02634-w}, pmid = {41291355}, issn = {1432-184X}, abstract = {The rapid expansion of tunnel engineering in China has led to extensive excavation of gravelly soils, resulting in significant land occupation that threatens the ecological environment and surrounding biota. As a result, there is an increasing need for effective ecological restoration of nutrient-poor gravelly soils, where challenges in vegetation establishment and sustainable soil management persist. This study evaluates the potential of Bacillus subtilis to promote the growth of Festuca arundinacea in engineered gravel soils through a controlled greenhouse experiment, examining its effects on plant growth, soil nutrient dynamics, and microbial community structure. The results showed that, compared to the control group (CK), neither the Bacillus subtilis treatment group (Bs) nor the nutrient application treatment group (LB) significantly altered the soil bacterial species composition at the phylum level. However, at the genus level, Azotobacter dominated the LB group, while Sphingomonas was the predominant genus in both the CK and Bs groups. Additionally, Bacillus subtilis significantly increased bacterial diversity relative to the nutrient application treatment, leading to substantial changes in microbial community composition. Furthermore, Bacillus subtilis notably enhanced both aboveground and belowground biomass, improved nutrient uptake, and increased the availability of phosphorus and potassium. It also stimulated soil enzymatic activities involved in carbon, nitrogen, and phosphorus cycling, emphasizing its critical role in nutrient cycling. Thus, Bacillus subtilis-driven soil enhancement offers a promising solution for ecological restoration in nutrient-poor gravelly soils, where conventional amendments are often ineffective. These findings underscore the potential of microbial-plant synergies to improve soil fertility and support sustainable vegetation restoration.}, }
@article {pmid41291216, year = {2025}, author = {Jurado, J and Garcia-Vega, A and Vasquez, Y and Villegas-Plazas, M and Roldan, F}, title = {Field-Scale AMD Remediation: Microbial Community Dynamics and Functional Insights in Biochemical Passive Reactors.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02628-8}, pmid = {41291216}, issn = {1432-184X}, abstract = {Acid mine drainage (AMD) generated during coal mining activities is characterized by low pH, high concentrations of dissolved metals and metalloids, and elevated sulfate levels, all of which significantly impact surrounding ecosystems. Scaling up biochemical passive reactor (BPR) systems represents a promising approach for the in situ bioremediation of AMD. While numerous laboratory-scale studies have described the taxonomic and functional composition of microbial communities in BPRs, typically dominated by (ligno)cellulolytic organisms and sulfate-reducing bacteria (SRB), it remains unclear whether this composition is maintained at the field-pilot scale under environmental conditions. To address this gap, 16S rRNA gene metabarcoding and shotgun metagenomics analyses were performed to characterize the taxonomic and functional diversity of microbial communities in the BPRs within a multi-unit field-pilot system. The results revealed that bioremediation effectiveness was driven by syntrophic interactions among hydrolytic, fermentative, and sulfate-reducing bacteria, aligning with laboratory-scale observations. While community composition shifts altered specific taxa, core operational dynamics remained preserved.}, }
@article {pmid41291200, year = {2025}, author = {Zha, Y and Fan, L and Shen, T and Zhang, Y and Ren, H}, title = {Triptolide ameliorates LPS-induced acute lung injury in Balb/c mice through gut-lung axis-mediated regulation of bile acid metabolism and gut microbiota.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-025-29758-w}, pmid = {41291200}, issn = {2045-2322}, support = {PW2022A-21//the Scientific Research Program of Shanghai Pudong New Area Health Commission/ ; }, abstract = {Acute lung injury (ALI) associated with pulmonary edema is a severe clinical condition characterized by acute inflammation, disrupted lung barrier function, and high mortality. Current therapeutic strategies remain limited, highlighting the need for exploring novel agents and their underlying mechanisms. Triptolide (TP), an active component derived from Tripterygium wilfordii, has shown anti-inflammatory and tissue-protective properties[1,2], but its specific role in alleviating ALI and the involvement of the lung-gut axis in metabolic regulation remain poorly understood. This study aims to investigate the therapeutic effects of TP on LPS-induced ALI, focusing on its impact on pulmonary edema and inflammatory injury. By analyzing the lung-gut axis using multi-omics approaches, we seek to clarify the metabolic network regulatory mechanisms through which TP exerts its effects. LPS-induced ALI model was established in Balb/c mice, with TP administered as the therapeutic intervention. Histopathological examination of lung tissues and detection of pro-inflammatory cytokines were performed to assess lung injury. Untargeted metabolomics via LC-MS/MS was used to identify differential metabolites in lung tissues and serum, while metagenomic sequencing analyzed changes in gut microbiota composition. Integrated multi-omics analysis was applied to explore associations between gut microbiota alterations, serum metabolites, and pulmonary bile acid levels. TP administration significantly reduced histopathological damage in lung tissues of ALI mice and decreased pro-inflammatory cytokine levels. Metabolomics profiling revealed distinct changes in key metabolites, including bile acids, amino acid derivatives, and energy metabolism intermediates, in both lung tissues and serum after TP treatment. Metagenomic analysis showed that TP restructured gut microbiota composition, with functional enrichment in glycolysis and thiamine metabolism pathways. Integrated analysis confirmed strong correlations between dynamic microbiota changes, serum metabolite profiles, and pulmonary bile acid levels, indicating a regulatory role of the lung-gut axis. This study demonstrates that TP alleviates pulmonary edema and inflammatory injury in ALI by modulating gut microbial ecology and function, which drives bile acid metabolic reprogramming and regulates metabolite interactions within the lung-gut axis. These findings provide novel insights into TP's therapeutic mechanism and support its potential application in ALI treatment.}, }
@article {pmid41291153, year = {2025}, author = {Joshi, H and Caprio, M and Reon, L and Fan, P}, title = {Rumen Microbiota-Based Machine Learning Approach for Predicting Heat Stress and Identifying Associated Microbes.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02656-4}, pmid = {41291153}, issn = {1432-184X}, abstract = {Heat stress poses a significant global challenge to sustainable livestock production, leading to detrimental impacts on animal production and welfare. Reduced appetite and increased body temperature further disrupt the gastrointestinal microbial ecosystem of heat-stressed animals, altering nutrient digestion and affecting host production. However, reported heat-stress-associated microbes have varied across studies, partly due to inconsistencies in microbiota analysis pipelines and taxonomic levels reported. In this study, to identify consistent rumen microbial taxa influenced by heat stress and evaluate potential of rumen microbiota in heat stress prediction, we collected publicly available raw 16S rRNA gene amplicon sequencing data of rumen fluid samples from lactating Holstein cattle housed in thermoneutral or heat stress condition from eight studies, analyzed their microbial composition using a consistent bioinformatic pipeline, and built machine learning models with the rumen microbiota profile to predict heat stress. Important rumen microbial taxa were selected using Boruta (a feature selection algorithm to identify important features) as potential biomarkers to predict heat stress, such as lactate-producing bacteria Lactobacillales, fiber-degrading bacteria Ruminococcaceae UCG-001, and methanogenic archaea Methanomicrobium. Additionally, the random forest model using the available animal factors and relative abundance of rumen microbial taxa showed a much higher performance for heat stress prediction, compared to the model without rumen microbiota profile (Area Under the Curve: 0.851 vs. 0.440). This study confirmed a distinct rumen microbiota signature in heat-stressed lactating Holstein cattle and identified specific rumen microbial taxa as potential biomarkers that could be targeted to mitigate heat-stress responses in dairy cows.}, }
@article {pmid41291109, year = {2025}, author = {Cohen, DD and Faigenboim, A and Elingold, I and Sher, Y and Galpaz, N and Minz, D}, title = {Dynamics in Microbial Communities Associated with the Development of Soil Fatigue in Banana.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02637-7}, pmid = {41291109}, issn = {1432-184X}, abstract = {Soil fatigue, well documented in various crops, presents a significant challenge to banana production by causing fast and then gradual declines in plant growth and yield over years of cultivation. Despite its impact on profitability, the underlying mechanisms driving soil fatigue remain poorly understood; however, a strong link to shifts in the soil microbiome has been suggested. We investigated the dynamics of microbial communities in relation to soil fatigue, using a novel semi-controlled outdoor experimental system. Soil at different stages of fatigue (0 to 42 months of banana cultivation) was generated in large containers filled with initially healthy soil. Banana plants grown in these soils were replaced with new plants which showed soil age-dependent growth. Three months postplanting, soil and root samples were collected for analyses of soil parameters and microbial community composition using bacterial (16S) and fungal (ITS) amplicon sequencing. We identified minor age-related shifts in mainly pH, potassium, and organic matter in the soil. While alpha diversity remained unchanged, significant shifts in bacterial and fungal community composition were observed in fatigued soils. Notably, the relative abundance of bacterial families such as Flavobacteriaceae, Pseudomonaceae, and Acidibacter increased, as did some fungal taxa (many from groups with known pathogens)-Ceratobasidiaceae (including Rhizoctonia), Dothideomycetes, and Stachybotryaceae. Simultaneously, the relative abundance of bacterial families with known beneficial members, including Gemmatimonadaceae, Moraxellaceae, Sphingomonadaceae, and Azospirillaceae, as well as symbiotic fungal taxa such as Glomeraceae and Lasiosphaeriaceae, declined. Thus, soil fatigue may be correlated to the proliferation of pathogenic populations and a loss of beneficial microorganisms.}, }
@article {pmid41291103, year = {2025}, author = {Katanić, Z and Ćurković-Perica, M and Idžojtić, M and Boljevac, K and Krstin, L}, title = {Status of Dutch Elm Disease Fungus Ophiostoma novo-ulmi and Assessment of Its Temporal Variability in Croatia.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02601-5}, pmid = {41291103}, issn = {1432-184X}, abstract = {Dutch elm disease (DED) was originally caused by the ascomycete Ophiostoma ulmi, which has been replaced by a more virulent species, O. novo-ulmi, divided into subsp. novo-ulmi and subsp. americana. Permeable reproductive barriers, a period of co-occurrence of O. ulmi and O. novo-ulmi, and the current overlap of O. novo-ulmi subspecies have been important in shaping the present O. novo-ulmi populations in Europe, which were initially clonal, predominantly of the MAT-2 type. This study confirmed the persistence of O. novo-ulmi in Croatia over the years, although at some forest sites, the diseased elms were not detected. The methodology used to assess changes in O. novo-ulmi populations was based on the col1 and cu genes, which have subspecies-specific nucleotide differences, analysis of MAT idiomorphs, and temperature-growth responses. The col1 and cu gene sequencing did not reveal a change in the number of isolates with the recombinant col1/cu genotype over 10 years (2012-2022). At both sampling times, approximately one-fourth of all analyzed isolates had recombinant col1/cu genotypes. However, the frequency of MAT-1 isolates, which all have MAT-1 genes originating from O. ulmi, increased during this period. Differences in growth rate at 20, 26, and 30 °C revealed variations in the temperature response of isolates, which were affected by sampling time and mating type. The MAT-1 isolates were shown to grow more slowly than MAT-2 at the three temperatures tested. The advantage of MAT-2 was reflected in temporal differences in growth rate at resampled sites, particularly at lower temperatures. These results suggest that changes in the frequency of mating types in Croatia occurred between 2012 and 2022, accompanied by modifications in the pathogen's response to temperature at the population level.}, }
@article {pmid41291089, year = {2025}, author = {Calbet, A}, title = {Pelagic Shuttles of Antibiotic Resistance Genes: Zooplankton as Overlooked Vectors Across Space and Food Webs.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02669-z}, pmid = {41291089}, issn = {1432-184X}, abstract = {Antibiotic resistance genes (ARGs) accumulate in aquatic environments, where they create reservoirs and transmission pathways that can undermine antimicrobial treatments and alter the microbial community structure in ways that ultimately affect human and animal health. However, the contribution of zooplankton in these pathways remains critically overlooked. Emerging evidence shows that compared with surrounding water, copepods and cladocerans accumulate ARG loads that are one to two orders of magnitude greater, acting as microbial hotspots that disperse resistant bacteria across seasons and depths. Inside protistan vacuoles, densely packed prey cells undergo conjugation, rapidly accelerating horizontal ARG transfer. Long-term archives reveal persistent ocean-wide dissemination of the class-1 integron integrase (intI1) and sul2 genes since at least the 1970s. Here, I synthesize mechanistic and field evidence, pinpoint knowledge gaps, and recommend priorities: integrate zooplankton into routine ARG surveillance, quantify biofilm-mediated exchanges, and mitigate contamination from coselective pollutants to curb zooplankton-driven ARG propagation. By framing zooplankton-associated ARG dynamics within the broader community ecology of antimicrobial resistance, this mini-review highlights how aquatic food-web processes feed back into the emergence, evolution, and transmission of resistance that concerns for One Health outcomes beyond the clinic.}, }
@article {pmid41290433, year = {2025}, author = {Ishibashi, S and Susukida, S and Muto, K and Miyazawa, K and Zhang, S and Yoshimi, A and Tabata, E and Abe, K}, title = {Using pure oxygen aeration to increase recombinant protein production by an Aspergillus oryzae hyphal dispersion strain.}, journal = {Journal of bioscience and bioengineering}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jbiosc.2025.10.011}, pmid = {41290433}, issn = {1347-4421}, abstract = {A high growth rate is essential for increasing protein production efficiency in liquid fermentation of filamentous fungi, such as Aspergillus oryzae. However, the increase in culture viscosity due to fungal growth constrains the overall yield. We have demonstrated that culture viscosity is lower in A. oryzae AGΔ-GAGΔ strains, which are deficient in the cell surface polysaccharides α-1,3-glucan (AG) and galactosaminogalactan (GAG), than in the wild-type (WT) strains. Nevertheless, even in aerated fermentation, an increase in AGΔ-GAGΔ viscosity results in oxygen depletion, which limits fungal growth and enzyme production. In this study, we investigated viscosity dynamics and protein production during high-cell-density fermentation of AGΔ-GAGΔ under pure oxygen aeration. Fed-batch cultivation of the WT and AGΔ-GAGΔ strains, expressing recombinant xylanase (XynF1), was used to compare the effects of air and pure oxygen aeration at the same flow rate. At 60 h, AGΔ-GAGΔ under pure oxygen aeration showed higher cell density (1.2× WT under pure oxygen aeration, 2.1× AGΔ-GAGΔ under air aeration) and XynF1 activity (1.8× WT under pure oxygen aeration, 2.3× AGΔ-GAGΔ under air aeration). Under pure oxygen aeration, AGΔ-GAGΔ showed lower viscosity (0.32×) and mixing time (0.50×) than WT. At 60 h, fine mycelial pellets (micropellets; 200-700 μm) were clearly observed in AGΔ-GAGΔ under pure oxygen but not under air aeration. These findings suggest that oxygen enrichment during AGΔ-GAGΔ cultivation mitigated the increase in viscosity, thereby promoting higher cell density and protein production. The formation of micropellets in AGΔ-GAGΔ likely contributed to a reduction in culture viscosity.}, }
@article {pmid41289323, year = {2025}, author = {Li, C and Urem, M and Kotsogianni, I and Lau, J and Du, C and Elsayed, SS and Martin, NI and McNae, IW and Voskamp, P and Mayer, C and Rigali, S and Pannu, N and Abrahams, JP and Schada von Borzyskowski, L and van Wezel, GP}, title = {The novel GlcNAc 6-phosphate dehydratase NagS governs a metabolic checkpoint that controls nutrient signaling in Streptomyces.}, journal = {PLoS biology}, volume = {23}, number = {11}, pages = {e3003514}, doi = {10.1371/journal.pbio.3003514}, pmid = {41289323}, issn = {1545-7885}, abstract = {Streptomyces bacteria are renowned for their multicellular lifestyle and as Nature's medicine makers, producing the majority of the clinical antibiotics. A landmark event during early development is the lytic dismantling of the substrate mycelium. Degradation of the hyphal cell-wall leads to the accumulation of N-acetylglucosamine (GlcNAc) in the colonies, which is a metabolic checkpoint during the onset of development and antibiotic production. Here, we show that GlcNAc sensing requires a toxicity pathway dependent on the enzyme GlcNAc-6P dehydratase (NagS). Dehydration of GlcNAc-6P by NagS to 6P-chromogen I is an unprecedented reaction in central metabolism that is highly conserved in - and limited to - the Streptomycetaceae. 6P-chromogen I is metabolized into a structural analogue of ribose by a promiscuous activity of GlcNAc-6P deacetylase NagA. Toxicity is relieved by supplementing the growth media with ribose. Structure-function analysis of NagS not only highlighted key residues in the active site of the enzyme in interaction with its substrate GlcNAc-6P, but also revealed 6-phosphogluconate as its catalytic inhibitor. Our work uncovers a conserved metabolic toxicity pathway in Streptomyces that revolves around a novel enzyme that plays a key role in nutrient signaling.}, }
@article {pmid41288749, year = {2025}, author = {Ndabankulu, KP and Zama, N and Suinyuy, TN and Magadlela, A}, title = {Soil Microbe Interaction and Extracellular Enzyme Activity Mediated by Encephalartos villosus in KwaZulu-Natal Scarp Forest Ecosystems.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {132}, pmid = {41288749}, issn = {1432-184X}, support = {129403//National Research Foundation, South Africa/ ; 138091//National Research Foundation/ ; }, mesh = {*Soil Microbiology ; South Africa ; Soil/chemistry ; Forests ; *Bacteria/classification/enzymology/genetics/isolation &amp; purification/metabolism ; Rhizosphere ; Symbiosis ; Ecosystem ; Microbiota ; }, abstract = {Cycads are ancient gymnosperms that play a crucial role in the soil health of scarp forests through their symbiotic associations with nutrient-cycling bacteria. However, the abundance of cycads in scarp forests has been decreasing at an alarming rate, highlighting the importance of determining the role of these species in nutrient cycling, microbial dynamics, and soil health. This study examined soil nutrient and microbial dynamics associated with Encephalartos villosus across four scarp forest sites in KwaZulu-Natal, South Africa. Soil samples were collected from the rhizosphere and non-rhizosphere zones (3-5 m away from the canopy) of mature plants. Results show that collection point did not influence soil nutrient and properties statistically; however, site-level variation was evident, with Hlathikhulu showing higher pH and nutrient concentrations, while Vernon Crookes exhibited lower pH and nutrient availability. Rhizosphere soils supported a greater diversity of nutrient-cycling bacteria, particularly taxa from the genera Bacillus, Burkholderia, Enterobacter, Luteibacter, and Pseudomonas with N-fixing, P-solubilizing, and N-cycling functions. Non-metric multidimensional scaling (NMDS) revealed that site differences, mainly driven by Mg, Ca, K, Zn, pH, and total cations, were stronger predictors of soil nutrient and microbial community variation than collection point alone. Enzyme assays showed that glucosaminidase and acid phosphatase were associated with community differences. These findings indicate that E. villosus enhances soil nutrient enrichment and microbial functional diversity in scarp forests, although the strength of these effects depends on local site conditions. Conservation of E. villosus is therefore critical, not only for species survival but also for sustaining soil fertility and ecosystem functioning in nutrient-limited scarp forest habitats.}, }
@article {pmid41288747, year = {2025}, author = {Kim, J and Cui, Y and Nam, KH and Lee, JW and Kim, JG and Chun, SJ}, title = {Effects of CP4-EPSPS-Containing Brassica juncea Hybrids on the Gut and Fecal Microbiota of the Terrestrial Decomposer Armadillidium vulgare.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {131}, pmid = {41288747}, issn = {1432-184X}, support = {NIE-A-2025-04; NIE-A-2025-06//Ministry of Environment (MOE) of the South Korea/ ; }, mesh = {*Mustard Plant/genetics ; *Feces/microbiology ; *Gastrointestinal Microbiome ; *Plants, Genetically Modified/genetics ; Animals ; Bacteria/classification/genetics/isolation &amp; purification ; Fungi/classification/genetics/isolation &amp; purification ; Republic of Korea ; Plant Leaves ; }, abstract = {The unintended spread of genetically modified (GM) crops and introgression into wild relatives raises concerns about ecological impacts. In South Korea, CP4-EPSPS-containing Brassica juncea hybrids (GM-hybrid B. juncea) have been detected in natural ecosystems. However, the impact of these GM crops on ecology remains unclear. In this study, we aimed to investigate the potential effects of GM-hybrid B. juncea on the gut and fecal microbiomes of Armadillidium vulgare, a dominant decomposer in natural habitats and an ideal model organism for assessing the ecological impact of GM plant material. Leaf litter from wild-type and GM-hybrid B. juncea was collected from the field, and feeding experiments were conducted using A. vulgare under controlled conditions. Although no significant differences in survival rates or growth were observed between groups, microbiome analysis revealed significant changes in both bacterial and fungal community composition and functional profiles in the gut and feces of the GM-hybrid-fed group. Specifically, in the GM-hybrid-fed group, the proportion of intestinal Plectosphaerella (Glomerellales) increased. Additionally, the bacterial Shannon index decreased, whereas the fungal Shannon index increased. Microbial network analysis revealed distinct interaction patterns and GM-hybrid-specific modules. GM-hybrids may influence decomposer-associated microbiomes through indirect pathways. Such influences could affect ecosystem-level processes such as decomposition and nutrient cycling. This experimental framework can be extended to other crop-derived hybrids or applied to different ecological contexts, providing a valuable basis for future assessments of transgene impacts on ecosystem functions.}, }
@article {pmid41288715, year = {2025}, author = {Yang, W and Deng, Z and Blair, D and Hu, W and Yin, M}, title = {Heavy-metal Pollution Affects Daphnia Fitness by Altering Diversity of the Gut Microbiota.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {130}, pmid = {41288715}, issn = {1432-184X}, support = {32271690//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Daphnia/drug effects/microbiology/genetics/physiology ; *Gastrointestinal Microbiome/drug effects ; *Nickel/toxicity ; *Metals, Heavy/toxicity ; *Water Pollutants, Chemical/toxicity ; Bacteria/classification/genetics/drug effects ; Germ-Free Life ; *Genetic Fitness/drug effects ; }, abstract = {The role of gut microbiota in shaping host fitness is already well established. However, it remains unclear to what extent the gut microbiota influences host fitness in the presence of environmental stressors. Here, we tested the hypothesis that responses of water flea Daphnia to the heavy metal nickel are mediated by gut microbiota. Germ-free D. magna exhibited somewhat lower fitness than did those with gut microbiota transplant. Among germ-free Daphnia, those that were exposed to heavy metals did not differ in fitness from unexposed Daphnia. In contrast, when incubated with their donors' gut microbiota, initially germ-free D. magna continuously exposed to nickel for 21 days showed a significantly lower survival rate than those not exposed to nickel. We detected a reduced set of microbes in the formerly germ-free Daphnia in the presence of nickel. Transcriptomic analysis of Daphnia showed that expression/regulation of genes related to oxygen transport, chitin metabolism, and detoxification changed in response to the reduced gut microbiomes acquired in the presence of nickel. Our findings show that the toxic effects of heavy metal led to a reduced diversity of gut microbiota in Daphnia and can thus affect host fitness.}, }
@article {pmid41288688, year = {2025}, author = {Wardhani, R and Shin, J and Lee, S and Lee, J and Nam, YH and Lee, MH and Han, KL and Ahn, H}, title = {Evaluation of Aquamicrobium lusatiense NLF 2-7 as a Biocontrol Agent in Manure Composting: Effects on Odorous Compounds and Microbial Community Under Mesophilic Conditions.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {129}, pmid = {41288688}, issn = {1432-184X}, support = {NNIBR20253108//Nakdonggang National Institute of Biological Resources/ ; RS-2021-IP321088//Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry/ ; }, mesh = {*Composting/methods ; *Manure/microbiology ; *Odorants/prevention &amp; control/analysis ; Hydrogen Sulfide/metabolism/analysis ; *Soil Microbiology ; *Bacteria/classification/metabolism/genetics ; Biodegradation, Environmental ; Sulfides/metabolism/analysis ; Soil/chemistry ; *Biological Control Agents ; Microbiota ; }, abstract = {Microbial inoculation is a commonly applied approach in composting to enhance organic matter biodegradation and reduce odor emissions. However, the different characteristics of bacteria in terms of temperature can be considered to optimize their effect during different phases of composting. A mesophilic bacterium, namely Aquamicrobium lusatiense NLF 2-7, was evaluated to mitigate odor emissions and enhance the bacterial community under mesophilic composting. Two different treatments were designed: treatment 1 with a single inoculation on the initial day and treatment 2 with split inoculation at the initial and after 2 weeks. Results show that the treatments improve organic matter decomposition by 17.7-28.6% and significantly reduce volatile sulfur compound emissions, especially dimethyl sulfide (DMS) and hydrogen sulfide (H2S) during the initial phase of composting. DMS emissions were mostly emitted in the first week, with reduction rates of 60.3% and 61.5% in both treatments, respectively. Additionally, mean phenol emissions were reduced by 7.9% in treatment 1 and 11.7% in treatment 2. The dominant bacterial phyla during composting were Bacillota, Pseudomonadota, Bacteroidota, and Actinomycetota, comprising 74 to 95% of the total population. This experiment suggests that A. lusatiense NLF 2-7, which is known for reducing sulfur emissions, can also enhance organic matter decomposition. Split inoculation appears more beneficial, with an initial inoculation managing sulfur emissions early on, followed by a second inoculation after the thermophilic phase to control phenol emissions throughout the composting process.}, }
@article {pmid41288389, year = {2025}, author = {Taheri, S and Schwarzkopf, E and Berman, HL and Brandt, N and McNeill, J and Sevier, N and Ruffieux, M and Dunn, RR and Smukowski Heil, C}, title = {The role of flour type and feeding schedule on the sourdough microbiome.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0238025}, doi = {10.1128/spectrum.02380-25}, pmid = {41288389}, issn = {2165-0497}, abstract = {Sourdough starters are fermentations of various grains by bacteria and yeast and are of worldwide economic and cultural importance. Sourdoughs are sometimes spontaneously inoculated, and their resident microbial communities are in part shaped by environmental factors, potentially including flour, water, air, human microbiota, equipment, geography, and temperature. The number of different genera of bacteria and yeast found in sourdoughs is large; however, only a handful of species typically dominate an individual sourdough starter. Understanding how and why certain species form a mature climax community in a particular environment is a key question in microbial ecology. To investigate this question, we used a meta-barcoding approach and tested whether different baking flours (all-purpose, bread, and whole wheat) and frequency of feeding, also known as backslopping, shape the sourdough starter microbial community over the course of one month. We found that the yeast genus Kazachstania rapidly rose in frequency and became the most abundant yeast in all starters, regardless of flour type or feeding schedule. In contrast, flour type did affect the bacterial community. Mature sourdoughs all contained the bacterial genera Companilactobacillus, Levilactobacillus, Lactiplantibacillus, Furfurilactobacillus, and Acetobacter, with Companilactobacillus detected at higher relative abundance in whole wheat flour and Levilactobacillus detected at higher relative abundance in bread flour. We conclude that flour can shape the microbial community of sourdough and has potential implications for functional traits.IMPORTANCEHow organisms disperse and colonize new environments is central to our understanding of biodiversity. Sourdough, the often spontaneously inoculated fermentation of grains by bacteria and yeast, represents a great system to test and observe how microorganisms come to inhabit a particular niche. In our study, we investigate how environmental parameters such as flour type and feeding frequency influence the microbial community. We find that the common sourdough yeast genus Kazachstania is most abundant in all starters regardless of treatment, but we also find a significant effect of flour type on the lactic acid bacteria composition of the sourdough starters. This work shows how the environment can impact the presence and abundance of particular microorganisms and prompts future studies to test how particular lactic acid bacteria species can specialize on certain resources.}, }
@article {pmid41286473, year = {2025}, author = {Wang, H and Yang, Y and Zhang, H and Chen, X and Zhang, R and Hou, W and Zhang, G}, title = {Symbiotic N-Fixing Bacteria in the Root and Leaf of Typical Alpine Grassland Plants.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {127}, pmid = {41286473}, issn = {1432-184X}, mesh = {Grassland ; *Plant Roots/microbiology ; *Symbiosis ; *Plant Leaves/microbiology ; RNA, Ribosomal, 16S/genetics ; Tibet ; *Nitrogen-Fixing Bacteria/classification/genetics/isolation &amp; purification/physiology ; Nitrogen Fixation ; Phylogeny ; DNA, Bacterial/genetics ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Soil Microbiology ; }, abstract = {Alpine plants in nitrogen-deficient environments can acquire nitrogen by associating with endophytic nitrogen-fixing microorganisms that inhabit their roots and leaves to form symbiotic relationships. However, research is limited on nitrogen-fixing bacterial communities in the roots and leaves of alpine grassland plants, especially regarding the differences between various plant parts. In this study, we compared the root and leaf bacterial communities of four alpine plant families (Asteraceae, Leguminosae, Poaceae, and Rosaceae) in the alpine meadow ecosystem of Naqu, Tibet, using culture-based methods, 16S rRNA, and nifH gene pyrosequencing. The results showed greater bacterial diversity in the root compared to the leaf, and Fabaceae plants harbored a higher abundance of nitrogen-fixing bacteria. Interestingly, the roots and leaves of non-Fabaceae plants (Kobresia, Festuca ovina, and Leontopodium) also harbored abundant nitrogen-fixing communities such as Microbacterium, Curtobacterium, and Rhodococcus. Compared with subtropical environments, Cyanobacteria are important symbiotic nitrogen-fixing bacteria in plants of alpine ecosystems. These findings indicate that plant species and plant parts strongly influence the selection of bacterial populations. Understanding these microbial ecological functions in alpine grasslands provides scientific insights for optimizing agricultural practices and ecosystem management.}, }
@article {pmid41286374, year = {2025}, author = {Jones, AK and Jordan, HR and Wolff, CL and Lashley, MA and Barton, BT}, title = {Lasting Effects of Different Scaled Mass Mortality Events on Soil Microbial Communities.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02625-x}, pmid = {41286374}, issn = {1432-184X}, abstract = {Death is a natural process present in all ecosystems; however, mass mortality events are instances of larger than average numbers of animals dying in a relatively short period of time. These events are increasing in frequency and magnitude, and the effects of mass mortalities - especially their long-term effects - are understudied. To better understand the long-term effects of mass mortalities in terrestrial ecosystems, we conducted experimental mass mortality events to determine if key ecosystem properties remained affected after 4 years. The experiment crossed three types of input treatments (control, carrion, and nutrient additive) with scavenger access (open plots versus fenced plots). To evaluate how increasing carrion biomass affected the ecosystem, sites were randomly assigned biomass (25, 59, 182, 363, 726 kg total (20m[2] plots)). Biomasses consisted of feral swine carcasses or the equivalent amount of N, phosphorus, and K nutrients. After 4 years, we found that while soil N did not differ among treatments, soil K and Ca significantly increased with biomass. Microbial communities significantly differed at the 182 kg biomass treatments compared to others and indicated significant effects between carrion and nutrient additive treatments. These results demonstrate that large die-offs, such as mass mortality events, can have long-lasting effects on soil composition through increased soil nutrients and alter soil microbial community (i.e., reduced Bacilliaceae, etc.). These long-lasting impacts can permanently alter the soil community, which can lead to cascading bottom-up effects that can alter the entire ecosystem structure.}, }
@article {pmid41286365, year = {2025}, author = {Bondarenko, S and Obiol, A and Casamayor, EO and Massana, R}, title = {Non-Dikarya Fungal Clades Are Everywhere: What 18S rRNA Gene Metabarcoding Reveals About Cross-System Distribution of Fungi.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02642-w}, pmid = {41286365}, issn = {1432-184X}, support = {2020 BP 00293//Ag&#xe8;ncia de Gesti&#xf3; d'Ajuts Universitaris i de Recerca (AGAUR), Generalitat de Catalunya/ ; PID2021-127701NB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2019-108457RB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; }, abstract = {Non-Dikarya fungi remain poorly characterized due to their cryptic morphology, cultivation difficulties, and limited representation in reference databases. To investigate their diversity and environmental distribution at a global scale, we reanalyzed over 6000 environmental samples using metabarcoding targeting the V4 region of the 18S rRNA gene, encompassing marine, freshwater, soil, hypersaline, polar, and other habitats. We constructed reference phylogenetic trees based on near full-length 18S rRNA gene sequences to enable accurate placement of short-read amplicon sequence variants (ASVs). This approach yielded robust classification at the phylum level and provided finer-scale clade resolution within major non-Dikarya groups. We delineated precise clades within Chytridiomycota, Microsporidia, Rozellida, and Aphelidea, and unveiled several novel ones. Our results show strong ecological structuring of fungal communities across habitats, with inland systems harboring greater fungal abundance and broader phylogenetic diversity than marine systems. Non-Dikarya fungi were consistently detected across diverse environments, including extreme habitats such as hypersaline lakes, deep sediments, and polar regions, where they were often the dominant fungal taxa. Although most ASVs tended to occur in a limited number of ecologically related habitats, phylogenetically related ASVs within the same clade were often adapted to different environments, indicating ecological diversity within clades. Our findings underscore both the ecological relevance and the cryptic diversity of non-Dikarya fungi in globally distributed environments, including extreme ones. Improved taxonomic resolution and broader reference dataset coverage are required to fully integrate these newly characterized lineages into fungal systematics and environmental surveys.}, }
@article {pmid41286193, year = {2025}, author = {García-Gutiérrez, L and Mellado, E and Martin-Sanchez, PM}, title = {Contribution of DNA Metabarcoding to the Environmental Fungal Assessments in Hospitals.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02626-w}, pmid = {41286193}, issn = {1432-184X}, support = {PID2021-123184OA-I00//Agencia Estatal de Investigaci&#xf3;n/ ; }, abstract = {Hospitals are particularly sensitive environments where immunosuppressed patients might acquire invasive fungal infections. Therefore, it is necessary to carry out periodical environmental microbiological assessments that evaluate the fungal bioburden in air and surfaces from different hospital zones. Current microbiological monitoring protocols at healthcare settings are mostly based on cultivation, while environmental DNA (eDNA) assessments are still scarce and should be further evaluated. To fill this gap, this study combines a large sampling scheme, comprising > 200 samples (air, surface, dust and soil) collected from four zones at three Spanish hospitals in two campaigns (winter and autumn), with two eDNA approaches (DNA metabarcoding and quantitative PCR) to characterize the hospital mycobiomes (diversity, community composition and airborne load), compared to a parallel culture-dependent study. DNA metabarcoding revealed a much more comprehensive inventory of hospital fungi compared to culturing; however, both approaches found similar dominant taxa including a variety of potentially opportunistic human pathogens. Hospital mycobiomes were affiliated to 4 phyla (mostly Ascomycota and Basidiomycota), 35 classes, 114 orders, 305 families, 643 genera and 535 species. The dominant genera, in both air and surfaces from the three hospitals, were Cladosporium, Alternaria, Aureobasidium, Penicillium, Neodidymelliopsis, Aspergillus, Pseudopithomyces and Stemphylium. The yeasts Candida and Clavispora were particularly abundant on high-touch surfaces indoors. The most important explanatory factors for the variance in community composition were the hospital and zone where samples were collected, the type of sample and the sampling campaign. DNA metabarcoding can assist hospital managers by providing an in-depth characterization of the baseline hospital mycobiome during normal operating conditions, as well as identifying and controlling community imbalances and associated health risks under demanding situations such as construction works or reported clinical outbreaks.}, }
@article {pmid41286179, year = {2025}, author = {Sultanova, Z and Dönertaş, HM and Hita, A and Aguilar, P and Dag, B and Lucas-Lledo, JI and Latorre, A and Carazo, P}, title = {Age-Dependent Gut Microbiota Dynamics and Their Association with Male Life-History Traits in Drosophila melanogaster.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02640-y}, pmid = {41286179}, issn = {1432-184X}, support = {ECF-2022-214//Leverhulme Trust/ ; P2021-00-007//Carl-Zeiss-Stiftung/ ; CGL2014-58722-P//Spanish Ministry of Economy and Competitivity/ ; PGC2018-099344-B-I00//Spanish Ministry of Economy and Competitivity/ ; }, abstract = {Growing evidence suggests that the gut microbiota is closely intertwined with life-history evolution in a wide range of species, including well-studied model organisms like Drosophila melanogaster. Although recent studies have explored the relationship between gut microbiota and female life-history, the link between gut microbiota and male life-history remains relatively unexplored. In this study, we investigated how gut microbiota changes with male age as well as the associations between gut microbiota composition and male life-history traits in D. melanogaster. Using 22 isolines from the Drosophila melanogaster Genetic Reference Panel (DGRP), we measured lifespan, early/late-life reproduction, and early/late-life physiological performance. We characterized the gut microbiota composition in young (5 days old) and old (26 days old) flies using 16S rDNA sequencing. We observed substantial variation in both male life-history traits and gut microbiota composition across isolines and age groups. Using machine learning, we show that gut microbiota composition could predict the chronological age of the organisms with high accuracy. The most important species contributing to machine learning prediction belonged to the Acetobacter and Ralstonia genera. Associations between gut microbiota and life-history traits were also notable, particularly involving different species from the Acetobacter genus. Our findings suggest that taxa such as Acetobacter may be relevant to the evolutionary ecology of host-microbe interactions in male fruit flies.}, }
@article {pmid41286138, year = {2025}, author = {Liu, XQ and An, XP and He, WX and Xu, XH and Hashem, A and Abd-Allah, EF and Wu, QS}, title = {Hairy Vetch Intercropping Attenuates Mycorrhizal Benefits to Walnut Growth and Soil Organic Carbon Sequestration via Glomalin.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {128}, pmid = {41286138}, issn = {1432-184X}, support = {SCXX-XZCG-22016//Hubei Province '14th Five-Year' Major Science and Technology Aid Tibet Project/ ; ORF-2025-356//Ongoing Research Funding program, King Saud University, Riyadh, Saudi Arabia/ ; }, mesh = {*Juglans/growth &amp; development/microbiology ; *Mycorrhizae/physiology/growth &amp; development ; *Soil/chemistry ; Soil Microbiology ; *Carbon Sequestration ; Plant Roots/microbiology/growth &amp; development ; Carbon/metabolism/analysis ; Biomass ; *Agriculture/methods ; *Fungal Proteins/metabolism ; *Glycoproteins/metabolism ; }, abstract = {Intercropping is a prevalent soil management strategy within walnut orchards, while its impacts on the functionality of arbuscular mycorrhizal fungi (AMF) in walnuts (Juglans regia) remain unclear, especially concerning soil carbon (C) sequestration via glomalin-related soil protein (GRSP). This study aimed to explore the effects of inoculation with the AMF species Diversispora spurca and intercropping with hairy vetch (Vicia villosa) on walnut biomass accumulation, soil water-stable aggregate (WSA) stability, leaf and root C (Cleaf and Croot) content, soil organic carbon (SOC), GRSP, and GRSP-contained C (CGRSP), in addition to the contribution rate of CGRSP to SOC. The intercropping treatment significantly inhibited root mycorrhizal colonization rate, soil hyphal length, and spore density in AMF-inoculated walnut plants. Individual AMF inoculation, rather than individual intercropping, significantly promoted shoot and root biomass accumulation, WSA stability, SOC, Cleaf and Croot, the levels of purified easily extractable (EEG), difficultly extractable (DEG), and total GRSP (TG), as well as their C contents. The combination treatment (AMF inoculation + intercropping) displayed limited benefits, improving just WSA stability without yielding synergistic advantages over individual treatments. Arbuscular mycorrhizal fungal inoculation significantly increased CGRSP, especially CDEG, while individual intercropping resulted in a reduction of CDEG. The combination treatment elevated both CDEG and CTG, albeit to a lesser extent than AMF alone. The contribution rates of CEEG, CDEG, and CTG to SOC were 0.33% - 0.53%, 1.16% - 1.78%, and 1.49% - 2.31%, respectively. Although AMF inoculation significantly increased the contribution rates of CDEG and CTG to SOC, this effect was diminished when combined with intercropping. Notably, CDEG, rather than CEEG, exhibited a significantly positive correlation with SOC and WSA stability. The findings provide new insights into the mechanisms of SOC sequestration in walnuts grown in controlled environments and offer a theoretical basis for the application of AMF in walnut cultivation.}, }
@article {pmid41284260, year = {2025}, author = {Song, H and Dowdell, K and Delafont, V and Skerlos, S and Raskin, L}, title = {The Neglected Role of Heterotrophic Protists in Engineered Water Systems.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c04958}, pmid = {41284260}, issn = {1520-5851}, abstract = {Heterotrophic protists can be considered the dark matter of microbial communities in engineered water systems. They are ubiquitous and ecologically significant yet remain largely overlooked. Although a growing body of research demonstrates their pivotal roles (e.g., predation, symbiosis, and nutrient cycling) in microbial communities in natural ecosystems, their functions in engineered water systems are poorly characterized, and heterotrophic protists are frequently excluded from microbial analyses. This is largely due to methodological constraints that have only recently been overcome. Recent advances in imaging, high-throughput sequencing, and meta-omics approaches, combined with expanding reference databases, have revolutionized studies of protist diversity and functions in a wide range of natural environments. Drawing on research from the fields of protistology, microbial ecology, and environmental microbiology, this review explores how the well-documented ecological roles of heterotrophic protists in natural environments translate to engineered ecosystems, offering insights into their functions in water treatment. We critically evaluate recent literature to synthesize both beneficial roles and potential risks of heterotrophic protists in various water treatment systems, while identifying key knowledge gaps and proposing directions for future research. We advocate for a shift in perspective that recognizes heterotrophic protists as important players and call for their integration into microbial community characterization and ecological frameworks in microbial ecology studies of engineered water systems. This integration will transform our understanding of microbial communities in engineered water systems, ultimately enabling novel, mechanistic, and ecologically informed management strategies.}, }
@article {pmid41280504, year = {2025}, author = {Ganguly, D and Roy, R and Mondal, P and Chakraborty, P and Paul, P and Das, S and Mallik, M and Maity, A and Trivedi, S and Tribedi, P and Sarkar, S}, title = {Nisin, a promising antimicrobial peptide, forestalls the methicillin-resistant Staphylococcus aureus biofilm network via reactive oxygen species generation.}, journal = {3 Biotech}, volume = {15}, number = {12}, pages = {428}, pmid = {41280504}, issn = {2190-572X}, abstract = {UNLABELLED: Staphylococcal infections have been reported to be a significant global threat to the effective management of public healthcare due to their drug resistance property. This attribute has further been complicated by their robust biofilm-forming potential. This escalating threat of biofilm-associated infections necessitates innovative and promising therapeutic strategies. Hence, in the present study, the biofilm threat of methicillin-resistant Staphylococcus aureus (MRSA) has been challenged by Nisin, a natural lantibiotic produced by Lactococcus lactis. This compound showed a promising antibacterial effect with minimum inhibitory concentrations (MICs) of 150 µg/ml against MRSA. Furthermore, a series of experiments has been conducted to confirm the antibiofilm potential of Nisin against MRSA. Towards this direction, the sub-MIC dose of Nisin (40 µg/mL) was found to inhibit biofilm formation by ~ 51% for MRSA. To support this finding, extracellular polymeric substance (EPS) was measured under the Nisin-treated and untreated conditions of MRSA. It was observed that Nisin could destabilise the MRSA biofilm by reducing the EPS production to an extent of ~ 55%. Mechanistic studies further demonstrated that Nisin was found to increase the intracellular accumulation of reactive oxygen species (ROS), which could lead to the alteration of cell membrane permeability. Additionally, Nisin attenuated staphyloxanthin production (~ 54%), hemolytic ability (~ 26%), and fibrinogen clumping ability (~ 27%) of MRSA, suggesting its interference in the virulence profile of MRSA. Collectively, these findings suggest Nisin's dual role as a promising Staphylococcal biofilm inhibitor and virulence factor suppressor, making it a viable option for the treatment of MRSA-linked infections.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-025-04597-8.}, }
@article {pmid41278148, year = {2025}, author = {Dely, A and Racicot, R and Samples, R and Giddings, LA}, title = {Draft genome sequence and metabolomics data for Streptomyces sp. ADLamb9 isolated from the rhizosphere of Lavandula dentata.}, journal = {Data in brief}, volume = {63}, number = {}, pages = {112199}, pmid = {41278148}, issn = {2352-3409}, abstract = {Iron-chelating molecules or siderophores play pivotal roles in soil ecosystems, particularly in facilitating plant iron uptake as well as the phytoremediation of metal-polluted environments. Lavandula dentata, commonly referred to as French Lavender, is a valuable species for siderophore production due to its ability to thrive in iron-deficient Mediterranean soils by forming symbiotic relationships with siderophore-producing rhizosphere microbes. Here, we used a Chrome Azurol S (CAS) overlay assay to isolate a yellow-pigmented L. dentata rhizosphere siderophore-producing bacterium. This isolate also demonstrated antibacterial and antifungal activities against Bacillus subtilis and Aspergillus flavus, respectively. Genomic sequencing revealed that the isolate was Streptomyces sp. ADLamb9 with a genome size of 8.2 Mb and 71.77% GC content. antiSMASH analysis of the Streptomyces sp. ADLamb9 genome identified four putative siderophore biosynthetic gene clusters as well as the catecholate siderophore mirubactin. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) masses consistent with desferrioxamine B (561.3604 m/z), IC202C (517.3342 m/z), mirubactin (605.2207 m/z), as well as previously unreported desferrioxamine A1C. Notably, the presence of the rare earth element cerium differentially affected the accumulation of catecholate and hydroxamate siderophores, highlighting our incomplete understanding of the complex regulation and relationship between siderophore biosynthesis genes. These datasets, deposited at NCBI under the BioProject accession number PRJNA1224804, contribute to the broader scientific understanding of metabolite diversity and genomic features of Streptomyces sp. ADLamb9, providing insight into its use in bioremediation, especially in the presence of rare earth elements.}, }
@article {pmid41277839, year = {2025}, author = {Qian, M and Zhu, D and Yao, K-y and Liu, S-y and Li, M-k and Ye, M and Zhu, Y-g}, title = {Coexistence of virome-encoded health-associated genes and pathogenic genes in global habitats.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0150125}, doi = {10.1128/aem.01501-25}, pmid = {41277839}, issn = {1098-5336}, abstract = {UNLABELLED: Viral remnants constitute approximately 8% of the human genome, reflecting extensive historical gene exchange between viruses and their hosts. Some viral genomes harbor genes acquired through horizontal gene transfer that are associated with potential benefits to human health, alongside genes associated with pathogenicity. However, their global distribution, functional characteristics, and coexistence patterns remain poorly understood. Here, using the Integrated Microbial Genomes and Virome (IMG/VR v4) database, we identified 4,556 viruses carrying gene segments associated with human health across eight habitat types spanning 13 regions and 76 countries worldwide. Among viruses with identifiable hosts, those distributed in humans (478) accounted for the highest proportion. The viral genes associated with human health included BCO1 (beta-carotene oxygenase 1), bioB (biotin synthase), COQ2 (4-hydroxybenzoate polyprenyltransferase), GPX1 (glutathione peroxidase 1), GSTs (glutathione transferases), GSTT1 (glutathione S-transferase theta 1), GULO (L-gulonolactone oxidase), and menA (1,4-dihydroxy-2-naphthoate polyprenyltransferase). These genes not only associate with human health but also function as auxiliary metabolic genes in viral genomes. Notably, four pathogenic genes were found in viral sequences carrying health-associated genes, with potential for transcription and expression, indicating functional interactions. Experimental transduction of the viral bioB gene into Escherichia coli altered the expression of host pathogenic genes GCH1 (GTP cyclohydrolase IA) and UGDH (UDP-glucose 6-dehydrogenase), supporting potential cross-regulatory interactions. Overall, this study incorporates health-associated genes into viral genomics, highlighting their coexistence with pathogenic genes, and provides new insights into virus-host coevolution and potential biotechnological applications.<br><br>IMPORTANCE: Viruses are the most abundant biological entities on Earth and key drivers of microbial evolution through horizontal gene transfer. While often studied for their pathogenic effects, viruses can also carry genes that influence host metabolism and health. Genes associated with human health have been identified in viral genomes, yet their global distribution, functions, and coexistence with pathogenic genes remain largely unexplored. This study integrates datasets of health-associated genes into viral genomic analyses, revealing for the first time the coexistence of viral health-associated genes with those linked to pathogenicity. This dual genetic potential is observed across diverse habitats, highlighting viruses as multifaceted reservoirs of both beneficial and harmful genes. The study findings advance understanding of viral functional diversity and open new avenues for exploring viral roles in microbial ecology, biotechnology, and human health.}, }
@article {pmid41277251, year = {2025}, author = {Bron, A and Beltramo, C and Durif, C and Arora, T and Deschamps, C and Couturier, I and Domingo-Almenara, X and Otero, YF and Denis, S and Van de Wiele, T and Blanquet-Diot, S}, title = {Small intestine is not colon: a new in vitro model of the human ileum microbiome integrating the mucosal microenvironment and feeding status.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2579353}, doi = {10.1080/19490976.2025.2579353}, pmid = {41277251}, issn = {1949-0984}, mesh = {Humans ; *Ileum/microbiology ; *Gastrointestinal Microbiome/physiology ; *Colon/microbiology ; Adult ; *Intestinal Mucosa/microbiology ; Fatty Acids, Volatile/metabolism ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Fermentation ; Male ; Feces/microbiology ; Models, Biological ; Female ; Bile Acids and Salts/metabolism ; }, abstract = {The small intestinal microbiota plays a key role in human health but is understudied due to the invasiveness of sampling. There is no available model of the human ileal microbiome simulating the key nutritional and physicochemical parameters shaping this ecosystem, which has been fully validated based on in vivo data. Here, the Mucosal Artificial Ileum (M-ARILE) was set up to reproduce the pH, transit time, anoxic conditions, dynamics of feeding and microenvironments (luminal versus mucosal) found in a healthy human mid-ileum. To validate the newly developed in vitro system, nine-day fermentations were performed under either ileal or colonic conditions using the same fecal inoculum (n = 3 adult volunteers). The gut microbiota composition and metabolic activities were monitored daily. Distinct microbial signatures and metabolite profiles were obtained between in vitro ileum and colon conditions. In accordance with in vivo data, Peptostreptococcaceae, Clostridiaceae and Enterococcaceae were enriched in the ileum and associated with lower short-chain fatty acid production but higher O2 percentages. Interestingly, the abundances of key populations, such as Akkermansiaceae, and bile acid profiles were dependent on the feeding status of the M-ARILE. This new model provides a powerful platform for mechanistic studies on the role of ileal microbes in human nutrition and health considering inter-individual variabilities.}, }
@article {pmid41275375, year = {2025}, author = {Su, Z and Zhang, X and Wang, Q and Tang, Q and Yang, D and Liu, Y}, title = {amplysis: an R package for microbial composition and diversity analysis using 16S rRNA amplicon data.}, journal = {Briefings in functional genomics}, volume = {24}, number = {}, pages = {}, pmid = {41275375}, issn = {2041-2657}, support = {//Guangxi Education Agency/ ; //Guangxi Province Talent Project/ ; 42377012//National Natural Science Foundation of China/ ; }, mesh = {*RNA, Ribosomal, 16S/genetics ; *Software ; *Microbiota/genetics ; *Computational Biology/methods ; Biodiversity ; Bacteria/genetics/classification ; }, abstract = {The downstream analysis of 16S rRNA sequencing data remains a significant challenge for researchers lacking extensive bioinformatics expertise, often requiring proficiency in diverse tools and methodologies. To address this, we present amplysis, an R package designed to streamline the analysis and visualization of 16S rRNA amplicon sequencing data through an intuitive, code-light workflow. amplysis integrates data importing, processing, statistical analysis, and visualization into a unified framework. Key features include data normalization, microbial composition profiling, alpha/beta diversity analysis, ordination methods (e.g. Principal Component Analysis), and publication-ready visualization tools. The package's utility was demonstrated through three case studies, one of which analyzed microbial community responses to hexachlorocyclohexane (HCH) degradation in groundwater environments. Using amplysis, we efficiently generated phylum/genus-level abundance plots, alpha-diversity indices, and Principal Coordinates Analysis ordination, revealing significant shifts in community structure and diversity under HCH stress. The other case studies utilized publicly available data from published studies by other researchers. These results underscore the package's ability to simplify complex analyses while ensuring reproducibility and high-quality output. By integrating modular, user-friendly functions, amplysis lowers the barrier to robust microbiome data exploration. The package is available on GitHub (https://github.com/min-perilla/amplysis), offering a valuable resource for researchers in microbial ecology and environmental genomics.}, }
@article {pmid41275050, year = {2025}, author = {Naziębło, A and Pytlak, A and Furtak, A and Dobrzyński, J}, title = {Advances and Hotspots in Research on Verrucomicrobiota: Focus on Agroecosystems.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02657-3}, pmid = {41275050}, issn = {1432-184X}, support = {2021/41/B/NZ9/03130//Narodowe Centrum Nauki/ ; 2021/41/B/NZ9/03130//Narodowe Centrum Nauki/ ; }, abstract = {Members of the phylum Verrucomicrobiota are abundant yet relatively understudied soil bacteria that play key roles in biogeochemical cycling and plant-microbe interactions. They participate in the carbon (C) and nitrogen (N) cycles through the degradation of complex organic polymers such as cellulose, pectin, and starch - via the production of hydrolytic enzymes (e.g., cellulases, xylanases, chitinases), and through nitrogen transformations including denitrification, ammonification, and nitrogen fixation. Methanotrophic representatives (Methylacidiphilum, Methylacidimicrobium) oxidise methane under acidic or thermophilic conditions, thereby contributing to greenhouse gas mitigation. The ecological distribution and activity of Verrucomicrobiota are strongly influenced by nutrient availability, particularly of C, N, phosphorus (P), and potassium (K). Their variable responses to these elements reflect diverse life-history strategies, encompassing both copiotrophic (r-strategist) and oligotrophic (K-strategist) taxa. While Spartobacteria (e.g., Ca. Udaeobacter) are typically oligotrophic, classes such as Opitutia and Verrucomicrobiae exhibit mixed strategies. Beyond nutrient cycling, several members of the phylum function as plant growth-promoting and stress mitigating bacteria. They produce phytohormones (e.g., indole-3-acetic acid) and siderophores, increase the availability of nitrogen and solubilise phosphate. Some taxa exhibit antioxidant activity and can suppress phytopathogens such as Fusarium oxysporum through secondary metabolite production. These traits suggest a significant potential in soil health improvement. Overall, Verrucomicrobiota represent a functionally diverse and ecologically significant bacterial phylum whose metabolic versatility, adaptive life strategies, and plant-associated traits underscore their central role in sustainable agricultural ecosystems.}, }
@article {pmid41274594, year = {2025}, author = {Zou, H and Ying, W and Mafla Endara, PM and Klinghammer, F and Bai, J and Kang, H and Hammer, EC}, title = {Deep learning-driven investigation of nanoplastic impacts on soil protist behavior in soil chips.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {127414}, doi = {10.1016/j.envpol.2025.127414}, pmid = {41274594}, issn = {1873-6424}, abstract = {Nanoplastics are emerging environmental contaminants that increasingly threaten soil ecosystems, yet their effects on microbial behavior remain poorly understood. This is mainly due to the lack of experimental tools capable of directly observing microbial dynamics in situ under realistic soil-like conditions. Here, we present a proof-of-concept system that enables real-time, high-throughput monitoring of soil protists within microfluidic soil chips under nanoplastic exposure. Using microscopy video analysis integrated with a deep learning-based detection model and a transformer-based trajectory reconstruction algorithm, we quantitatively measured the movement of morpho-/locomotion type groups flagellates, ciliates, and amoebae across a gradient of nanoplastic concentrations (0, 2, and 10 mg/L). Our results showed reduced movement velocities for the groups of flagellates and ciliates under high nanoplastic conditions with a 24%-30% reduction in speed, while affect on amoebae was not detected. The trajectory data also provides novel insights into how protists navigate soil-like structures. Beyond these specific findings, our approach establishes a transformative framework for observing microbial life directly in its microenvironment, comparable to how animal behavior is monitored in ecological studies. By bridging real-time imaging and artificial intelligence, this method offers a new angle to study protist-environment interactions without the need for culture extraction. It opens the door to rethinking how microbial ecology, soil contamination, and biotic responses to environmental stressors are investigated, advancing opportunities from static, population-level measurements to dynamic, behavioral-level understanding within realistic habitats.}, }
@article {pmid41273983, year = {2025}, author = {Wu, YX and Wang, HY and Chu, WC and Gao, YY and Xia, MQ and Liu, FF}, title = {Ecological implications of biodegradable and conventional microplastics: Dissolved organic matter bioavailability and microbial response in marine systems.}, journal = {Journal of hazardous materials}, volume = {500}, number = {}, pages = {140526}, doi = {10.1016/j.jhazmat.2025.140526}, pmid = {41273983}, issn = {1873-3336}, abstract = {The increasing accumulation of microplastics (MPs) in marine environments raises concerns about their ecological impacts, particularly through the release of dissolved organic matter (DOM). However, the bioavailability and ecological effects of MPs-derived DOM (MPs-DOM) remain poorly understood. In this study, we systematically investigated the leaching characteristics and microbial bioavailability of DOM derived from three biodegradable MPs (BMPs) including polylactic acid (PLA), polycaprolactone (PCL), polybutylene adipate terephthalate (PBAT) and two conventional MPs (CMPs, PE: polyethylene, PET: polyethylene terephthalate) under simulated photoaging. Our results demonstrated that BMPs released significantly more dissolved organic carbon (DOC) than CMPs, with PBAT showing the highest yield (40.77 vs. PE: 11.63 mg-DOC g-C[-1]). Optical analyses revealed that BMPs-DOM contained more protein-like fluorescent components, with higher fluorescence index and biological index, indicating greater lability. BMPs-DOM stimulated microbial growth more efficiently, with PBAT supporting the highest bacterial concentrations (∼52 ×10[3] cells mL[-1]) and DOC utilization (76.39 %). 16S rRNA sequencing revealed that MPs-DOM exposure reduced community richness, reshaped microbial communities through selective enrichment of copiotrophic and plastic-degrading taxa (e.g., Pseudomonas, Bacteroidota), and promoted stochastically driven assembly with specialized functional modules. Our study highlights that while BMPs may alleviate particulate plastic accumulation, their labile DOM release warrants careful evaluation for potential impacts on marine microbial ecology.}, }
@article {pmid41273632, year = {2025}, author = {Bi, J and Li, J and Rahman, SU and Long, Y and Hui, N and Romantschuk, M and Zheng, J and Zhang, X and Hou, D and Tan, J and Bi, Q and Xia, H and Yu, X and Luo, L and Liu, X}, title = {Balancing water efficiency and crop productivity: rhizosphere microbiome shifts in drought-resistant rice.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {41}, number = {12}, pages = {469}, pmid = {41273632}, issn = {1573-0972}, }
@article {pmid41272024, year = {2025}, author = {Khatbane, M and Mangavel, C and Borges, F and Aridhi, S and Toussaint, Y}, title = {Knowledge graph embedding for predicting and analyzing microbial interactions.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-025-27591-9}, pmid = {41272024}, issn = {2045-2322}, support = {R31PNCVX//ML4Community Project/ ; R31PNCVX//ML4Community Project/ ; R31PNCVX//ML4Community Project/ ; R31PNCVX//ML4Community Project/ ; R31PNCVX//ML4Community Project/ ; }, abstract = {Interactions between microorganisms play a major role in shaping the structure and function of microbial communities, yet their prediction remains a challenge in microbial ecology. While currently available machine learning methods have shown promising performance, they often rely on extensive input features that are obtained from labor-intensive experiments. Here, we propose a new framework to predict pairwise interactions that minimizes the need for in vitro experimentation. Our approach is based on knowledge graph embedding, which learns the representation of microorganisms and their interactions in an embedding space. Using a dataset of interactions between 20 soil bacterial strains cocultured in 40 different carbon source environments, we demonstrate the effectiveness of our framework in accurately predicting pairwise interactions. Notably, we show that our model can predict interactions involving strains with missing culture data. We additionally show that the obtained embeddings can reveal similarities between carbon source environments, enabling the prediction of interactions in one environment based on the outcomes in a similar environment between the same pair of microorganisms. Furthermore, our approach allows the design of a recommendation system that can be used to guide microbial community engineering. These findings demonstrate that knowledge graph embedding is a promising modeling strategy in microbial ecology.}, }
@article {pmid41271578, year = {2025}, author = {Man, M and Castañeda-Gómez, L and Moisan, MA and Gagné, P and Martineau, C and Ghosh Biswas, R and Knorr, MA and Frey, SD and Cadotte, MW and Nadelhoffer, KJ and Lajtha, K and Simpson, AJ and Simpson, MJ}, title = {Deciphering the Complex Interactions between Litter Inputs and Microbial Responses in Modulating Long-Term Soil Organic Matter Dynamics.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c08706}, pmid = {41271578}, issn = {1520-5851}, abstract = {Natural climate solutions that focus on increasing carbon in forests rely on the potential for additional carbon that may be incorporated into soil organic matter (SOM). The fate of soil carbon in temperate forests remains uncertain due to the complex role of microbes and their regulation of carbon flows in soils, especially with the addition of extra litter. We identified comprehensive molecular-level evidence that revealed shifts in SOM composition and microbial communities after 30 years of added litter in a temperate deciduous forest. Chronic litter addition failed to add new soil carbon after 30 years and correlated with reorganization in microbial community composition and altered carbon use. Excluding detrital inputs decreased soil carbon content, resulting in enhanced SOM decomposition and shifts toward specific bacterial groups (such as oligotrophs) that can utilize less energetically favorable carbon substrates that are typically more recalcitrant. Collectively, we found that microbial communities shifted in composition and altered carbon use strategies and traits, which aligned with changes to the molecular composition of SOM. Finally, this work demonstrates that in mesic temperate forests, decadal increases in litterfall, resulting from increased ecosystem productivity or management, may not offset soil carbon losses from climate change nor enhance carbon sequestration.}, }
@article {pmid41270014, year = {2025}, author = {Madsusan, A and Krainara, S and Suksong, W and Sudchoo, K and Tohmoh, N and Jonggrijug, P and Maipunklang, C and Chadaram, C and Samaeng, K and Kurdthongmee, P and Noosab, U and Nakapong, A and Udomsri, Y and Kanaso, S and Sakorn, N and Guan, NY and Sangkhano, S}, title = {Impact of a tropical monsoon climate on formaldehyde exposure and microbial contamination in anatomy dissection hall.}, journal = {PloS one}, volume = {20}, number = {11}, pages = {e0337238}, doi = {10.1371/journal.pone.0337238}, pmid = {41270014}, issn = {1932-6203}, mesh = {*Formaldehyde/analysis/adverse effects ; Humans ; *Occupational Exposure/analysis ; *Tropical Climate ; *Dissection ; Thailand ; *Air Pollution, Indoor/analysis ; *Anatomy/education ; Microbiota ; }, abstract = {Gross anatomy dissection is an essential component of medical and health science education, yet it presents notable occupational hazards, particularly from formaldehyde (FA) exposure and microbial contamination. These risks may be intensified in anatomy dissection halls located in tropical monsoon (Am) climates, where elevated humidity and temperature promote both chemical volatility and microbial persistence. This study assessed the combined effects of such climatic conditions on FA concentrations and microbial ecology within a naturally ventilated dissection hall in southern Thailand. FA levels were measured through personal and area air sampling across seven anatomical regions, while microbial contamination on cadaver-contact surfaces was evaluated using culture-based methods and high-throughput sequencing. Functional prediction of microbial communities was performed using PICRUSt2 to assess their metabolic adaptation to environmental stressors. The results revealed that both personal and indoor FA concentrations (mean 1.17 ± 0.39 ppm and 1.09 ± 0.45 ppm, respectively) exceeded several international occupational exposure limits, with the highest levels observed during dissections involving deep or adipose-rich anatomical regions. Microbial analyses identified stress-tolerant and potentially pathogenic genera, including Bdellovibrio, Aequorivita, and Aspergillus spp., along with enriched pathways involved in aromatic compound degradation and environmental resilience. These findings highlight the limitations of natural ventilation in controlling occupational exposures and microbial contamination in Am climate anatomy laboratories. The study supports the implementation of climate-responsive engineering controls and laboratory management strategies that address chemical safety, thermal regulation, and biosafety to promote healthier and more sustainable dissection environments in similar high-risk settings.}, }
@article {pmid41269303, year = {2025}, author = {Xin, H and He, L and Zhu, B}, title = {Ecological Insights into Gut Microbiota Networks Across Cognitive States in Alzheimer's Disease.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02662-6}, pmid = {41269303}, issn = {1432-184X}, support = {No. 202212691//Jiangxi Provincial Health Commission/ ; }, abstract = {The ecological mechanisms governing gut microbial community stability during Alzheimer's disease (AD) progression remain poorly understood. This study employed an ecological network to investigate microbial interactions and stability across cognitively normal controls (CK), individuals with mild cognitive impairment (MCI), and AD patients. We observed a stepwise decline in network complexity across groups, characterized by reduced clustering coefficients and average degree, from CK to AD. While the MCI group exhibited intermediate structural complexity, it displayed the highest vulnerability and lowest robustness, indicating a critical transitional state. Keystone taxa analysis revealed a significant shift in microbial community, with the CK network was enriched with diverse, potentially beneficial keystone taxa, whereas the AD network retained only connector species, and the MCI network showed a complete absence of keystone taxa. Cohesion analysis revealed a non-linear trajectory of microbial interactions, with negative cohesion peaking in MCI. Our findings demonstrate that cognitive decline is associated with a fundamental reorganization of the gut microbial ecosystem. This reorganization pattern reveals a resilient state in health, a vulnerable phase in MCI, and a stable yet dysbiotic configuration in AD, with keystone taxa serving as pivotal regulators of community stability. Community assembly analysis showed a shift from deterministic to stochastic processes during cognitive decline, with weakened host regulatory mechanisms. These findings advance our understanding of the gut microbial ecology in neurodegenerative disease and reveal the mechanism by which microbial communities reorganize network to maintain stability in different cognitive states.}, }
@article {pmid41268901, year = {2025}, author = {Zhao, Y and Zhao, Y and Dong, Y and Sun, X and Zhang, W and Zhao, L and Grégori, G}, title = {Biogeography of Virioplankton Abundance and Subcluster Patterns in the Northwest Pacific: A Large-Scale Perspective.}, journal = {MicrobiologyOpen}, volume = {14}, number = {6}, pages = {e70161}, doi = {10.1002/mbo3.70161}, pmid = {41268901}, issn = {2045-8827}, support = {//This study was financially supported by the National Natural Science Foundation of China (No. 42076139), National Key Research and Development Program of China (No. 2024YFE0114300), and the Sino-French International Research Project (CNRS-CAS) Dynamics and Function of Marine Microorganisms (IRP-DYF2M): insight from physics and remote sensing./ ; }, mesh = {Pacific Ocean ; *Seawater/virology ; *Plankton/virology/classification ; *Viruses/classification/isolation &amp; purification/genetics ; Flow Cytometry ; Phylogeography ; Biodiversity ; }, abstract = {Marine virioplankton, the most abundant biological entities in the ocean, play essential roles in microbial ecology and biogeochemical cycling. This study investigates their biogeography in the Northwest Pacific using enhanced-resolution flow cytometry and phenotypic diversity analyses. By resolving four consistent viral subclusters across oceanic and coastal waters and detecting a fifth subcluster in the Yellow Sea, we revealed previously unrecognized patterns of viral community structures. Viral abundances ranged from 3.69 × 10[6] to 17.09 × 10[6] particles/mL, showing clear coastal-oceanic differentiation. Environmental gradients, particularly temperature, chlorophyll, and picoplankton abundance, emerged as the primary drivers of virioplankton community structure. These findings underscored the tight coupling between viral populations and their microbial hosts across contrasting marine environments. Phenotypic diversity analysis revealed distinct viral communities in the Luzon Strait, despite comparable abundance patterns to adjacent regions, demonstrating the method's sensitivity in detecting subtle community shifts. This study advances understanding of marine viral biogeography and introduces a robust framework for investigating viral community dynamics. The approach enables high-throughput screening across large spatial scales while maintaining sensitivity to fine-scale community variations, offering new possibilities for monitoring viral responses to environmental change in marine ecosystems.}, }
@article {pmid41268888, year = {2025}, author = {Trivedi, S and Roy, R and Naskar, A and Das, B and Chakraborty, P and Paul, P and Das, S and Malik, M and Tribedi, P}, title = {Cuminaldehyde Potentiates the Antimicrobial and Antibiofilm Activity of Vancomycin: A Biochemical Study to Manage the Threats of Methicillin Resistant Staphylococcus aureus (MRSA).}, journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica}, volume = {133}, number = {11}, pages = {e70087}, doi = {10.1111/apm.70087}, pmid = {41268888}, issn = {1600-0463}, support = {TNU/R&amp;D/MG/24/02//The Neotia University/ ; TNU/R&amp;D/MG/24/04//The Neotia University/ ; }, mesh = {*Methicillin-Resistant Staphylococcus aureus/drug effects/physiology ; *Vancomycin/pharmacology ; *Biofilms/drug effects ; *Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; Drug Synergism ; Humans ; Oxidative Stress/drug effects ; Bacterial Adhesion/drug effects ; Reactive Oxygen Species/metabolism ; *Benzaldehydes/pharmacology ; Staphylococcal Infections/microbiology/drug therapy ; Virulence Factors/metabolism ; }, abstract = {Methicillin-resistant Staphylococcus aureus (MRSA) is reported to cause serious health issues in humans by exploiting its biofilm network. To combat this global concern, the combined efficacy of cuminaldehyde (a bioactive phytochemical) and vancomycin (an antibiotic) was tested against MRSA strains. While both compounds exhibited independent antibacterial activity, their combination revealed improved efficacy against MRSA through additive interactions. Response surface methodology (RSM)-generated quadratic models optimized the combinatorial doses, revealing significant microbial growth inhibition of the MRSA strains (p < 0.05). Furthermore, the combined application of cuminaldehyde and vancomycin at sub-MIC doses could inhibit biofilm formation by lowering bacterial adhesion, extracellular polysaccharide (EP) synthesis and the extent of biofilm-associated proteins. Additionally, the mechanistic studies revealed that the said combination (cuminaldehyde and vancomycin) was found to accumulate oxidative stress with a ~2.5-fold increase in intracellular reactive oxygen species (ROS) and a ~2.3-fold reduction in membrane integrity. In view of the same, this combination attenuated key virulence factors (protease, hemolysin, and coagulase) and metabolic activity of MRSA. Hence, the combinations involving cuminaldehyde and vancomycin could potentially enhance the antimicrobial and antibiofilm efficacy, presenting a promising approach to combat the escalating crisis linked with MRSA-associated threats.}, }
@article {pmid41268502, year = {2025}, author = {Fu, Y and Dou, Q and Wang, F and Virta, M and Zhang, T and Elsner, M and Amelung, W and Jiang, X and Tiedje, JM}, title = {A flowing database: Harnessing sewage-based surveillance for antimicrobial resistance.}, journal = {Innovation (Cambridge (Mass.))}, volume = {6}, number = {11}, pages = {100977}, pmid = {41268502}, issn = {2666-6758}, }
@article {pmid41267490, year = {2025}, author = {Sharma, P and Dagariya, S and Sharma, S and Singh, M}, title = {Uncovering the nexus of human health hazards of nanoplastics, gut-dysbiosis and antibiotic-resistance.}, journal = {Journal of environmental science and health. Part C, Toxicology and carcinogenesis}, volume = {}, number = {}, pages = {1-60}, doi = {10.1080/26896583.2025.2578871}, pmid = {41267490}, issn = {2689-6591}, abstract = {Nanoplastics (1-1000 nm) (NPs) represent a novel and insidious class of emerging contaminants with the potential to profoundly disrupt gut microbial ecology and accelerate the spread of antibiotic resistance two critical and converging threats to global health. While prior studies have examined the toxicokinetics of NPs and their general microbial interactions, this review provides the first comprehensive synthesis specifically focused on the nexus between NPs, gut dysbiosis, and the propagation of antibiotic resistance genes (ARGs). This review highlights how NPs alter gut microbiota composition, suppressing beneficial microbes while fostering opportunistic pathogens and how such imbalances may contribute to human health issues. Importantly, emerging evidence also suggests that NPs may serve as unrecognized vectors for horizontal gene transfer (HGT), enabling the rapid dissemination of ARGs via conjugation, transformation, transduction, and extracellular vesicles within the gastrointestinal tract. In addition, this review also identifies urgent methodological gaps in detecting NPs in biological matrices and the environment, as well as assessing their mechanistic impacts, calling for innovation in analytical approaches. By presenting an interdisciplinary perspective that bridges nanotoxicology, microbiome science, and antimicrobial resistance, this article sheds light on an underexplored yet urgent frontier in environmental health, offering novel insights to guide future research, risk assessment, and policy development.}, }
@article {pmid41266882, year = {2025}, author = {Hu, H and Zhang, Y and Liu, Z and Han, Y and Luo, Y and Zhang, C and Yu, Y and Wang, J and Li, B and Su, S}, title = {Microbial Diversity Affects the Cold Tolerance of Red Swamp Crayfish (Procambarus clarkii) by Regulating Histamine Metabolism.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02659-1}, pmid = {41266882}, issn = {1432-184X}, support = {No. 2025JBFR03//Central Public-interest Scientific Institution Basal Research Fund, Freshwater Fisheries Research Center, CAFS/ ; No. 2025JBFR03//Central Public-interest Scientific Institution Basal Research Fund, Freshwater Fisheries Research Center, CAFS/ ; No. 2025JBFR03//Central Public-interest Scientific Institution Basal Research Fund, Freshwater Fisheries Research Center, CAFS/ ; No. 2025JBFR03//Central Public-interest Scientific Institution Basal Research Fund, Freshwater Fisheries Research Center, CAFS/ ; No. 2025JBFR03//Central Public-interest Scientific Institution Basal Research Fund, Freshwater Fisheries Research Center, CAFS/ ; DTYZ2024003//"Soil Transplantation" Team Project of Panjin Talent Program/ ; DTYZ2024003//"Soil Transplantation" Team Project of Panjin Talent Program/ ; DTYZ2024003//"Soil Transplantation" Team Project of Panjin Talent Program/ ; DTYZ2024003//"Soil Transplantation" Team Project of Panjin Talent Program/ ; DTYZ2024003//"Soil Transplantation" Team Project of Panjin Talent Program/ ; DTYZ2024003//"Soil Transplantation" Team Project of Panjin Talent Program/ ; JBGS [2021]123//"JBGS" Project of Seed Industry Revitalization in Jiangsu Province/ ; JBGS [2021]123//"JBGS" Project of Seed Industry Revitalization in Jiangsu Province/ ; JBGS [2021]123//"JBGS" Project of Seed Industry Revitalization in Jiangsu Province/ ; 2023TD39//Central Public-Interest Scientific Institution Basal Research Fund, CAFS/ ; 2023TD39//Central Public-Interest Scientific Institution Basal Research Fund, CAFS/ ; }, abstract = {The red swamp crayfish (Procambarus clarkii) is one of the important freshwater aquaculture species in China, but its growth and development are greatly affected by temperature, which makes it difficult to expand its aquaculture range to the northern regions of China. The composition of gut microbes plays a vital role in resisting environmental pressure, and is also an important driving factor for amino acid metabolism in the body. However, little is known about the relationship between microorganisms, metabolism, and cold-resistance ability of P. clarkii. In this study, we performed the cold-resistance and antioxidant ability test, gut microbiota diversity analysis, quantitative analysis of histamine, and bioinformatics analysis of histamine receptor (HR) family on P. clarkii. The results showed that the cold-resistance crayfish exhibited high antioxidant ability and low gut microbiota diversity after acute cold stress. Next, we also found that there was significant correlation between the Lactobacilli genus and histamine abundance, indicating that the excellent cold tolerance ability of crayfish may stem from the degradation of histamine by Lactobacilli. Finally, it was revealed that HR genes had considerable quantity of gene copies, conservative evolution in crustacean lineages and expression differences in low-temperature tolerant populations. These results suggested that the diversity of Lactobacillus mediated changes in histamine metabolism affect antioxidant capacity, which is one of the reasons why P. clarkii exhibits cold resistance ability. This finding provided a theoretical basis for understanding the microorganism-histamine regulation mechanism of red swamp crayfish under cold stress, promoting the breeding and healthy culture of cold-resistance strain.}, }
@article {pmid41266660, year = {2025}, author = {Caroppo, C and Caruso, G and Bergamasco, A and Decembrini, F}, title = {Phytoplankton diversity and size structure in the Central-Southern Tyrrhenian Sea: implications for microbial functioning.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02650-w}, pmid = {41266660}, issn = {1432-184X}, abstract = {Microbial community dynamics in relation to mesoscale hydrographical features are almost unknown particularly in the pelagic Central-Southern Tyrrhenian Sea. To get a more comprehensive view of phytoplankton community structure and microbial community functioning, datasets of phytoplankton abundance, composition and some microbial enzyme activities (leucine aminopeptidase, LAP, beta-glucosidase, GLU and alkaline phosphatase, AP) from six cruises carried out twenty years ago were analyzed. Hydrographic characteristics identified the presence of both Atlantic Waters (AW) and Tyrrhenian Intermediate Waters (TIW). Size structure of phytoplankton biomass showed an unexpected high contribution of the pico-phytoplankton to the total primary production (> 60%) determining a predominant microbial food web. Phytoplankton distribution patterns varied more significantly on a seasonal rather than spatial scale. Autumn assemblages were characterized by the highest abundance and carbon content, with species mainly belonging to dinoflagellates whose growth was supported by intense microbial activities. In contrast, in the summer diatoms developed in unstable TIW where microbial activity was declining. Enzymatic activities varied in the different water masses and seasons, with high LAP activity in summer AW (s-AW) as well as in deep TIW (d-TIW), while AP and GLU reached their maximum in autumn AW (a-AW), suggesting quick organic matter recycling. Coupled primary production and hydrolysis in mixed AW (m-AW) and in a-AW indicated synchronized autotrophic and heterotrophic processes, while in TIW organic matter was only partially recycled. Overall, microbial metabolism was closely shaped by hydrographic and seasonal dynamics, confirming its key role in biogeochemical cycles. Our data could provide a baseline study for future research dealing with the microbial functioning in this Mediterranean region.}, }
@article {pmid41074769, year = {2025}, author = {Tucker, SJ and Freel, KC and Eren, AM and Rappé, MS}, title = {Habitat-specificity in SAR11 is associated with a few genes under high selection.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, doi = {10.1093/ismejo/wraf216}, pmid = {41074769}, issn = {1751-7370}, support = {#989028//Simons Postdoctoral Fellowship in Marine Microbial Ecology/ ; NA20NOS4200123//National Science Foundation Graduate Research/ ; 1842402//National Science Foundation Graduate Research/ ; #687269//Simons Foundation/ ; }, mesh = {*Ecosystem ; Phylogeny ; *Selection, Genetic ; *Seawater/microbiology ; Metagenome ; *Alphaproteobacteria/genetics/classification/isolation &amp; purification ; Metagenomics ; Genome, Bacterial ; Pacific Ocean ; Genetic Variation ; }, abstract = {The order Pelagibacterales (SAR11) is the most abundant group of heterotrophic bacteria in the global surface ocean, where individual sublineages likely play distinct roles in oceanic biogeochemical cycles. Yet, understanding the determinants of niche-partitioning within SAR11 has been a formidable challenge due to the high genetic diversity within individual SAR11 sublineages and the limited availability of high-quality genomes from both cultivation and metagenomic reconstruction. Through an integrated metapangenomic analysis of 71 new SAR11 isolate genomes and a time-series of metagenomes from the prominent source of isolation, we reveal an ecological and phylogenetic partitioning of metabolic traits across SAR11 genera. We resolve distinct habitat-preferences among genera for coastal or offshore environments of the tropical Pacific and identify a handful of genes involved in carbon and nitrogen metabolisms that appear to contribute to these contrasting lifestyles. Furthermore, we find that some habitat-specific genes experience high selective pressures, indicating that they are critical determinants of SAR11 fitness and niche differentiation. Together, these insights reveal the underlying evolutionary processes shaping niche-partitioning within sympatric and parapatric populations of SAR11 and demonstrate that the immense genomic diversity of SAR11 bacteria naturally segregates into ecologically and genetically cohesive units, or ecotypes, that vary in spatial distributions in the tropical Pacific.}, }
@article {pmid41265332, year = {2025}, author = {Mol, Z and Segers, L and Van Langenhove, H and Vandermarliere, T and De Gusseme, B and Walgraeve, C and Demeestere, K}, title = {Pressure-induced taste and odour deviations within the high-pressure drinking water distribution system.}, journal = {Water research}, volume = {289}, number = {Pt B}, pages = {124965}, doi = {10.1016/j.watres.2025.124965}, pmid = {41265332}, issn = {1879-2448}, abstract = {Taste and odour (T&amp;O) issues in tap water decrease the willingness of consumers to drink it. Production and/or release of odour compounds during drinking water distribution should be avoided as the water is directly delivered to consumers without further treatment. Odours can be caused by leaching of compounds from pipe materials, microbial metabolism, disinfection reactions, or diffusion of odour compounds or precursors from external sources. Increasing knowledge of T&amp;O origins is needed to better solve future problems. Therefore, this research focuses on odour linked to changes in pressure because of maintenance work at the high-pressure (HP) drinking water distribution system. A trace analytical method targeting 45 T&amp;O compounds is further optimized by including derivatisation to improve halophenol detection. Next, in a field section of a real HP pipe (± 3 km), three scenarios were systematically investigated. Lowering the overpressure in the HP pipe from 10 to 5 bar resulted in an observed bitumen/asphalt odour, that further increased in intensity after a subsequent sudden pressure drop to 2 bar. Based on the odour threshold and profile, two halophenols were detected that may have contributed to this odour observation. When the section was partially emptied, 6 halophenols and 5 other T&amp;O compounds were identified. Our results indicate that pressure changes induce the leaching of T&amp;O compounds from sealing materials connecting the 6m-pipe sections. This is further supported by the detection of similar T&amp;O compounds in a water extract of the sealing materials and in an odorous household sample collected after maintenance work in the HP-network.}, }
@article {pmid41264968, year = {2025}, author = {Yang, C and Bao, L and Shi, Z and Xv, X and Li, J and Jiang, D and You, L}, title = {Jingning formula alleviates ADHD by restoring gut microbiota dysbiosis and tryptophan metabolic dysfunction.}, journal = {Journal of pharmaceutical and biomedical analysis}, volume = {269}, number = {}, pages = {117256}, doi = {10.1016/j.jpba.2025.117256}, pmid = {41264968}, issn = {1873-264X}, abstract = {Jingning Fang (JNF), a clinically used herbal medicine for attention deficit hyperactivity disorder (ADHD), demonstrates significant efficacy in alleviating core symptoms such as hyperactivity and impulsivity in pediatric patients. To systematically investigate its therapeutic mechanisms, we implemented an integrated approach encompassing UPLC-Q-TOF/MS-based untargeted metabolomics profiling of brain, serum, and fecal specimens, targeted quantification of tryptophan pathway metabolites across these biological compartments, and gut microbiome characterization via 16S rRNA sequencing. Our analysis revealed a prominently dysregulated metabolic pathway in ADHD, characterized by perturbations in tryptophan metabolism that were particularly pronounced in feces (P < 0.05). Notably, the kynurenic acid (KYNA)/quinolinic acid (QUINA) ratio, a pivotal indicator of kynurenine pathway homeostasis, exhibited robust correlations with both behavioral manifestations and gut microbial ecology. These findings provide a mechanistic basis for JNF's clinical efficacy in ADHD management by highlighting its role in restoring gut microbiome balance and tryptophan metabolic homeostasis.}, }
@article {pmid41264852, year = {2025}, author = {Kosmopoulos, JC and Anantharaman, K}, title = {Viral Dark Matter: Illuminating Protein Function, Ecology, and Biotechnological Promises.}, journal = {Biochemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.biochem.5c00349}, pmid = {41264852}, issn = {1520-4995}, abstract = {Viruses are the most abundant biological entities on Earth and play central roles in shaping microbiomes and influencing ecosystem functions. Yet, most viral genes remain uncharacterized, comprising what is commonly referred to as "viral dark matter." Metagenomic studies across diverse environments consistently show that 40-90% of viral genes lack known homologues or annotated functions. This persistent knowledge gap limits our ability to interpret viral sequence data, understand virus-host interactions, and assess the ecological or applied significance of viral genes. Among the most intriguing components of viral dark matter are auxiliary viral genes (AVGs), including auxiliary metabolic genes (AMGs), regulatory genes (AReGs), and host-physiology-modifying genes (APGs), which may alter host function during infection and contribute to microbial metabolism, stress tolerance, or resistance. In this Review, we explore recent advances in the discovery and functional characterization of viral dark matter. We highlight representative examples of novel viral proteins across diverse ecosystems, including human microbiomes, soil, oceans, and extreme environments, and discuss what is known and still unknown about their roles. We then examine the bioinformatic and experimental challenges that hinder functional characterization and present emerging strategies to overcome these barriers. Finally, we highlight both the fundamental and applied benefits that multidisciplinary efforts to characterize viral proteins can bring. By integrating computational predictions with experimental validation and fostering collaboration across disciplines, we emphasize that illuminating viral dark matter is both feasible and essential for advancing microbial ecology and unlocking new tools for biotechnology.}, }
@article {pmid41264018, year = {2025}, author = {Villalón, A and Rodríguez Alonso, &#xc1; and Carballo, J and Rodríguez López, LA and Pérez, MJ}, title = {Diversity of Bacteria and Yeasts Present in an Automobile Treatment System.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02651-9}, pmid = {41264018}, issn = {1432-184X}, abstract = {The formation of biofilms in industrial environments poses a significant challenge because of their ability to degrade materials, contaminate products, and harbour pathogenic microorganisms. In the automotive industry, surface treatment systems (STS) used to prepare car bodies can provide a favourable environment for microbial development, driven by the presence of water, organic matter, and variable physicochemical conditions. In this context, the microbial diversity present in the different STS baths of an automotive plant, as well as in the process water, was analysed. Through culture-based methods and molecular analysis, 33 bacterial and 6 yeast species were identified. The results revealed a constant presence of bacteria at all sampling points, whereas yeasts were detected less frequently and in more localized areas (Industrial and Dechromatized Water, E2, Conversion stage, E4 and Passivation stage). This study underscores the importance to enhance cleaning and disinfection protocols in STS, as high bacterial counts persisted even after rinsing stages, in order to prevent economic losses, product degradation and health risks. Furthermore, it highlights the potential use of certain microorganisms in biotechnology and bioremediation applications.}, }
@article {pmid41263569, year = {2025}, author = {Ding, W and Ling, Z and Liu, X and Zhang, J and Cheng, Y and Zhu, Z and Wu, L and Xu, X and Gao, Y and Hu, X}, title = {Impact of carbapenem-resistant Klebsiella pneumoniae infection on gut microbiota and host immunity: a case-control study.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0297525}, doi = {10.1128/spectrum.02975-25}, pmid = {41263569}, issn = {2165-0497}, abstract = {Carbapenem-resistant Klebsiella pneumoniae (CRKP) represents a critical global health threat with limited treatment options. While the gut microbiota is a reservoir for opportunistic pathogens and a regulator of host immunity, the reciprocal impact of systemic CRKP infection on gut microbial ecology and immune responses remains poorly defined. In a prospective case-control study, 38 patients with confirmed CRKP infection and 38 matched hospitalized controls without CRKP were enrolled. Fecal samples underwent 16S rRNA gene sequencing to characterize microbial profiles, and serum cytokine levels were quantified using multiplex immunoassays. CRKP infection was associated with significantly reduced microbial diversity and a distinct shift in community structure, characterized by depletion of beneficial commensals (Bacteroides, Faecalibacterium, Roseburia) and enrichment of pathobionts (Klebsiella, Enterococcus). Enterotype analysis revealed a predominance of a Klebsiella/Enterococcus-dominated enterotype in CRKP patients. Functional predictions indicated impaired carbohydrate and butyrate metabolism alongside increased virulence- and resistance-associated pathways. Systemically, patients exhibited elevated pro-inflammatory cytokines (IL-6, TNF-α, IFN-γ) and chemokines (IP-10, MCP-1, RANTES). Correlation analyses linked opportunistic taxa with heightened inflammatory markers, while beneficial short-chain fatty acid producers showed inverse associations. Systemic CRKP infection is associated with profound gut dysbiosis and a hyper-inflammatory immune response. The strong microbiota-immune correlations suggest that the gut microbiota may serve as a biomarker and a potential therapeutic target for mitigating CRKP-associated immune dysfunction, though the directional relationship (cause vs. consequence) between dysbiosis and CRKP infection remains to be elucidated.IMPORTANCECarbapenem-resistant Klebsiella pneumoniae (CRKP) is a critical global threat with limited therapeutic options. This study reveals that systemic CRKP infection is associated with profound gut dysbiosis-characterized by loss of beneficial commensals (e.g., Faecalibacterium) and expansion of pathobionts (e.g., Klebsiella, Enterococcus)-as well as a hyperinflammatory immune response. We demonstrate strong correlations between specific microbial taxa and host cytokines, suggesting that the gut microbiome may hold potential as a biomarker and therapeutic target. These findings enhance our understanding of host-microbe interactions in CRKP infection and support the exploration of microbiota-based therapies. However, further studies, including longitudinal and animal models, are needed to clarify whether gut dysbiosis directly influences CRKP outcomes or is a secondary consequence.}, }
@article {pmid41263391, year = {2025}, author = {Gilbert, JA and Scholz, AH and Dominguez Bello, MG and Korsten, L and Berg, G and Singh, BK and Boetius, A and Wang, F and Greening, C and Wrighton, K and Bordenstein, SR and Jansson, J and Lennon, JT and Souza, V and Allard, SM and Thomas, T and Cowan, D and Crowther, TW and Nguyen, N and Harper, L and Haraoui, LP and Ishaq, SL and McFall-Ngai, M and Redford, KH and Peixoto, R}, title = {Safeguarding microbial biodiversity: microbial conservation specialist group within the species survival commission of the International Union for Conservation of Nature.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, doi = {10.1093/ismejo/wraf239}, pmid = {41263391}, issn = {1751-7370}, }
@article {pmid41263344, year = {2025}, author = {Gilbert, JA and Scholz, AH and Dominguez Bello, MG and Korsten, L and Berg, G and Singh, BK and Boetius, A and Wang, F and Greening, C and Wrighton, K and Bordenstein, SR and Jansson, J and Lennon, JT and Souza, V and Allard, SM and Thomas, T and Cowan, D and Crowther, TW and Nguyen, N and Harper, L and Haraoui, LP and Ishaq, SL and McFall-Ngai, M and Redford, KH and Peixoto, R}, title = {Safeguarding microbial biodiversity: microbial conservation specialist group within the species survival commission of the International Union for Conservation of Nature.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {12}, pages = {}, doi = {10.1093/femsec/fiaf107}, pmid = {41263344}, issn = {1574-6941}, support = {//Gordon and Betty Moore Foundation/ ; }, }
@article {pmid41263324, year = {2025}, author = {Gilbert, JA and Scholz, AH and Dominguez Bello, MG and Korsten, L and Berg, G and Singh, BK and Boetius, A and Wang, F and Greening, C and Wrighton, K and Bordenstein, SR and Jansson, J and Lennon, JT and Souza, V and Allard, SM and Thomas, T and Cowan, D and Crowther, TW and Nguyen, N and Harper, L and Haraoui, L-P and Ishaq, SL and McFall-Ngai, M and Redford, KH and Peixoto, R}, title = {Safeguarding microbial biodiversity: microbial conservation specialist group within the species survival commission of the International Union for Conservation of Nature.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0150525}, doi = {10.1128/msystems.01505-25}, pmid = {41263324}, issn = {2379-5077}, }
@article {pmid41262936, year = {2025}, author = {Postec, A and Yumoto, I and Morales-Barrera, L and Gessesse, A and McMillan, DGG}, title = {Editorial: Microbial ecology and biotechnological potential of alkaline environments.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1726999}, pmid = {41262936}, issn = {1664-302X}, }
@article {pmid41262263, year = {2025}, author = {Bautista, J and López-Cortés, A}, title = {Chronobiome medicine: circadian regulation of host-microbiota crosstalk in systemic physiology.}, journal = {Frontiers in endocrinology}, volume = {16}, number = {}, pages = {1691172}, pmid = {41262263}, issn = {1664-2392}, mesh = {Humans ; *Circadian Rhythm/physiology ; *Gastrointestinal Microbiome/physiology ; Animals ; }, abstract = {Circadian rhythms, governed by central and peripheral clocks, orchestrate nearly all aspects of human physiology, including metabolism, endocrine function, neuroimmune activity, and behavior. Emerging evidence reveals that these oscillations are closely intertwined with the gut microbiota, which itself displays diurnal fluctuations in composition and metabolite production. This bidirectional regulation establishes a dynamic circadian-microbiota axis that synchronizes nutrient processing, hormonal secretion, immune surveillance, and neural signaling. Disruption of this temporal alignment, through genetic, environmental, or lifestyle factors, precipitates systemic dysregulation, fostering metabolic syndrome, endocrine imbalance, immune dysfunction, neuropsychiatric vulnerability, cardiovascular alterations, and carcinogenesis. Mechanistic studies highlight that microbial-derived metabolites such as short-chain fatty acids, bile acids, and indoles act as circadian cues, while host clock genes modulate microbial ecology and intestinal barrier integrity. These insights underscore the translational potential of circadian precision medicine, in which time-restricted feeding, probiotics, prebiotics, and chronotherapy restore synchrony between microbial and host clocks. This review synthesizes current knowledge on circadian modulation of microbiota-mediated crosstalk across metabolic, neural, immune, and endocrine pathways, emphasizing its implications for health, disease, and novel therapeutic strategies.}, }
@article {pmid41260033, year = {2025}, author = {Zhang, Q and Zhang, S and Cao, X and Zhi, Y and Guo, Y}, title = {The gut microbiota in post-stroke depression: A systematic review of microbial mechanisms and therapeutic targeting of neuroinflammation.}, journal = {Microbiological research}, volume = {303}, number = {}, pages = {128391}, doi = {10.1016/j.micres.2025.128391}, pmid = {41260033}, issn = {1618-0623}, abstract = {Post-stroke depression (PSD), a frequent and debilitating complication after stroke, severely hinders rehabilitation. Emerging evidence underscores the role of neuroinflammation and the gut microbiota in PSD pathogenesis. This review systematically elaborates the mechanisms by which gut dysbiosis contributes to PSD-related neuroinflammation via immune cell regulation (e.g., Treg/Th17 balance), microbial metabolites (e.g., SCFAs, tryptophan derivatives), and neural pathways (vagus nerve, HPA axis). A key focus is the comparative analysis of the gut microbiota in PSD against major depressive disorder (MDD) and Alzheimer's disease (AD), revealing a unique, stroke-induced microbial signature characterized by a loss of protective symbionts and a bloom of pro-inflammatory taxa. We further discuss the translational potential of microbiota-targeted interventions (e.g., probiotics, prebiotics) for PSD. By integrating clinical microbial ecology with mechanistic insights, this review synthesizes evidence suggesting that the gut microbiome may represent a promising diagnostic and therapeutic target for PSD, offering a distinct perspective from previous literature.}, }
@article {pmid41259914, year = {2025}, author = {Yang, W and Wang, X}, title = {Transmission mechanisms and risk tracing of antibiotic resistance genes in rivers driven by wastewater inputs.}, journal = {Journal of hazardous materials}, volume = {500}, number = {}, pages = {140523}, doi = {10.1016/j.jhazmat.2025.140523}, pmid = {41259914}, issn = {1873-3336}, abstract = {Aquatic environments are critical for ARG dissemination, yet contributions from different wastewater sources, dominant HGT mechanisms, and residual risks in natural waters remain unclear. Based on 863 metagenomic samples across China, we systematically analyzed wastewater inputs, HGT mechanisms, and risks of riverine ARGs. Wastewater treatment plants were the primary source, contributing about 50 % of riverine ARGs. Conjugation dominated ARG transfer, primarily via F-type type IV secretion systems. High-transmission plasmids were widespread. Although phage-mediated transduction represented only 3 % of HGT, it facilitated cross-environmental spread of clinically significant blaGES-18. Metagenome-assembled genomes revealed 78 % of resistant bacteria belonged to Pseudomonadota; 42 % co-harbored virulence factors. Phylogenetic analysis showed high inter-generic mobility of sul1/sul2, explaining their environmental persistence. Overall risk in rivers decreased by 44 % - 93 % compared to wastewaters. However, Acinetobacter carrying blaOXA and Cellvibrio sp002483145 carrying blaKHM-1 were phylogenetically close to Acinetobacter baumannii and Pseudomonas aeruginosa, indicating potential pathways toward key pathogens. Our study identifies wastewater as the main source of riverine ARGs, reveals conjugation as the primary transmission mechanism with transduction playing a secondary role, and demonstrates that high-risk ARGs can still spread to pathogenic bacteria in rivers. These findings are crucial for developing effective strategies to mitigate ARG risks.}, }
@article {pmid41259520, year = {2025}, author = {Usman, H and Molaei, M and House, SD and Haase, MF and Dennis, CL and Niepa, THR}, title = {Magnetically responsive nanocultures for direct microbial assessment in soil environments.}, journal = {Science advances}, volume = {11}, number = {47}, pages = {eady2654}, doi = {10.1126/sciadv.ady2654}, pmid = {41259520}, issn = {2375-2548}, mesh = {*Soil Microbiology ; *Soil/chemistry ; Bioreactors ; Magnetic Iron Oxide Nanoparticles/chemistry ; }, abstract = {Cultivating microorganisms in native-like conditions is vital for bioprospecting and accessing now unculturable species. However, there remains a gap in scalable tools that can both mimic native microenvironments and enable targeted recovery of microbes from complex settings. Such approaches are essential to advance our understanding of microbial ecology, predict community functions, and discover previously unidentified biotherapeutics. We present magnetic nanocultures-a high-throughput microsystem for isolating and growing environmental microbes under near-native conditions. These nanoliter-scale bioreactors are encapsulated in semipermeable membranes that form magnetic polymeric microcapsules using iron oxide nanoparticles within polydimethylsiloxane-based shells. This design offers mechanical stability and magnetic actuation, enabling efficient retrieval from soil-like environments. The nanocultures are optimized for optical and biological properties to support microbial encapsulation, growth, and sorting. Our study demonstrates the feasibility of using magnetically responsive microenvironments to cultivate elusive microbes, offering a promising platform for bioprospecting previously uncultured or unknown microbial species.}, }
@article {pmid41258716, year = {2025}, author = {Marsh, CC and Nel Van Zyl, K and Babalola, OO and Böhmer, R and Cowan, DA and Moganedi, KLM and Moroenyane, I and Naidoo, J and Nieves Delgado, A and Posma, JM and Segal, LN and Setati, ME}, title = {From description to implementation: key takeaways from the 3rd African Microbiome Symposium.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0068325}, doi = {10.1128/msphere.00683-25}, pmid = {41258716}, issn = {2379-5042}, abstract = {The 3rd African Microbiome Symposium was held in Cape Town, South Africa, from 20 to 22 November 2024. The symposium featured a diverse range of local and international microbiome research and provided a platform for 79 researchers, students, and industry members to engage in discussions on the microbiome within an African context and focusing on translational research. This meeting review shares highlights, findings, and recommendations derived from the event. Insights from two panel discussions revealed key barriers to microbiome research in Africa, including limited funding, infrastructure gaps, and a shortage of trained local scientists. Recommendations centered on increased investment, institutional training, adherence to ethical guidelines, and the fostering of equitable global partnerships.}, }
@article {pmid41258518, year = {2025}, author = {Cong, D and Liu, J and Yu, S and Wu, P and Qin, M}, title = {Assessment of Anthropogenic Impacts on Water Quality and Microbial Communities in the Heilongjiang Maolan Gou National Nature Reserve.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02645-7}, pmid = {41258518}, issn = {1432-184X}, abstract = {Freshwater ecosystems within protected areas play a vital role in maintaining biodiversity and ecological stability, yet they are increasingly threatened by anthropogenic disturbances such as agriculture and tourism. Understanding the impacts of human activities on water quality and microbial community dynamics is essential for the effective conservation and management. This study investigates the spatial variability of water quality and microbial communities across the core, buffer, and experimental zones of the Heilongjiang Maolan Gou National Nature Reserve. Twelve water samples were collected and analyzed for key physicochemical parameters (turbidity, electrical conductivity (EC), chemical oxygen demand (COD), biochemical oxygen demand (BOD), NH4[+], PO4[3-] and heavy metals). The core zone exhibited excellent water quality with low turbidity (0.4-0.5 NTU), EC (45-130 µS/cm), COD (8-10 mg/L), BOD (1.5-2.2 mg/L). In contrast, the experimental zone showed significant contamination due to agriculture and tourism, with high COD (up to 35 mg/L), BOD (up to 6.5 mg/L), NH4[+] (0.18-0.35 mg/L), and PO4[3-] (0.008-0.035 mg/L). Heavy metal concentrations, particularly Cd (up to 0.24 µg/L), were elevated in the experimental zone, correlating with higher Pollution and Water Quality Indices (HPI up to 96.4, WQI up to 61.28). According to standard classifications, HPI values > 100 indicated heavy pollution and WQI scores between 50 and 100 denoted moderate to poor water quality, highlighting degraded conditions in the experimental zone. Microbial analysis revealed distinct community structures across zones, with enhanced pollutant-degrading taxa such as Pseudomonas (noted for aromatic hydrocarbon degradation) and members of Bacteroidota (associated with organic matter breakdown) in the experimental zone. These findings highlight the need for sustainable management to mitigate human impacts and preserve ecological health within the reserve.}, }
@article {pmid41258495, year = {2025}, author = {Gutiérrez-Sarmiento, W and Fosado-Mendoza, M and Lozano-Flores, C and Varela-Echavarría, A}, title = {The Body Wall Microbiome of the Terrestrial Slug Deroceras laeve Reveals Potential Endosymbionts and Shares Core Organisms with Other Mollusks.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02652-8}, pmid = {41258495}, issn = {1432-184X}, support = {CBF2023-2024-834//SECIHTI/ ; IN211322//DGAPA-UNAM PAPIIT/ ; }, abstract = {The marsh slug Deroceras laeve is an invasive mollusk found in gardens, field crops, and wetlands. It lacks a protective shell, suggesting that microbial communities are associated with its adaptability to the environment. Here, we used a whole shotgun metagenomic approach to analyse the complex microbiome of D. laeve and compared it to that of other mollusks. This demonstrated the presence in D. laeve of bacteriophages such as Erwinia phage, Certrevirus, and Machinavirus, which target plant pathogen bacteria. In the Archaea domain the halophilics Halovivax and Halobaculum predominated, but also present were the methanogens Methanobacterium, Methanobrevibacter, Methanocaldococcus, Methanococcus, and Methanosarcina, involved in phosphate solubilization and methanogenesis during decomposition of organic matter. The Bacteria domain was dominated by γ-Pseudomonadota such as Buttiauxella, Citrobacter, Enterobacter, Klebsiella, Kluyvera, Leclercia, and Pseudomonas which are producers of enzymes that degrade biomass and complex carbohydrates. Regarding the fungal community, filamentous or yeast ascomycetes predominated such as Debaryomyces, Puccina, and Pyricularia known as plant pathogens or associated with decaying organic matter. Consistent with these findings, functional analysis revealed enrichment in genes involved in fermentation and carbohydrate metabolism. Remarkably, regardless of species, ecosystem, and tissue type, we found that the core microbiome of the mollusks in this study is mainly structured by the Phyla Uroviricota, Euryarchaeaota, Pseudomonadota, and Ascomycota, with diversity at the genus level. This suggests ancient symbiotic interactions of these mollusks with specific types of microbes which may have been critical for adaptability to their environment.}, }
@article {pmid41258437, year = {2025}, author = {Romaní, AM and Núria, P and Marta, P and Giulia, G}, title = {Drought Drives Extracellular Polymeric Substances Accumulation and Functional Shifts in Streambed Biofilm Communities.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02649-3}, pmid = {41258437}, issn = {1432-184X}, abstract = {This study investigates the adaptive response of streambed microbial biofilms to water scarcity, focusing on the role of extracellular polymeric substances (EPS) production across a gradient of hydrological conditions. Sediment samples from 37 streams in the north-eastern Iberian Peninsula, encompassing both permanent and intermittent flow regimes, were analysed for EPS-polysaccharide content, microbial biomass, chlorophyll-a, and biofilm function (carbon substrate utilization profiles). Drought conditions were characterized based on the number of dry days over the eight months preceding sampling. Results revealed that EPS production increased significantly in intermittent streams, particularly under long-term drought, reaffirming that EPS synthesis is a key microbial strategy to mitigate desiccation stress. Notably, when normalized to prokaryotic density, EPS content exhibited a significant positive correlation with drought duration, emphasizing the dominant role of heterotrophic bacteria over algae in EPS secretion. However, EPS content alone was not a universal indicator of water scarcity, which showed a large variability in permanently flowing streams. Functional profiling showed clear shifts in carbon substrate utilization associated with stream hydrology. Intermittent streams exhibited a broader metabolic range, and particularly a capacity to use phenolic compounds, suggesting an adaptation to terrestrial organic matter inputs. Contrary to expectations, functional diversity increased in drier conditions, challenging assumptions derived from controlled experiments and underscoring the resilience of Mediterranean microbial biofilm communities to drought. These findings provide empirical support for EPS-mediated drought adaptation in natural biofilms and highlight functional diversity as a potential mechanism maintaining ecosystem processes under increasing aridity due to climate change.}, }
@article {pmid41258129, year = {2025}, author = {Cabrerizo, MJ and González-Olalla, JM and Medina-Sánchez, JM and Vila-Duplá, M and Carrillo, P}, title = {Warming Fluctuations Strengthen the Photo-Phagotrophic Coupling in Mixoplanktonic Protists.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02658-2}, pmid = {41258129}, issn = {1432-184X}, support = {PID2022-136280NA-I00//MICIN/AEI/10.13039/501100011033 and the European Regional Development Fund/ ; RYC2023-042504-I//MICIU/AEI/10.13039/501100011033 and the European Social Fund plus (ESF+)/ ; DGP-POST-2024-00283//Junta de Andaluc&#xed;a/ ; TED2021-131262B-I00//MCIN/AEI/10.13039/501100011033 and by the European Union NextGeneration EU/PRTR/ ; FPU19/05924//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2020-118872RB-I00//MICIN/AEI/10.13039/501100011033 and the European Regional Development Fund (ERDF)/ ; }, abstract = {Mixoplankton, a major trophic group in aquatic ecosystems, are being affected by global warming. However, most studies on temperature effects use constant mean conditions, overlooking how short-term thermal fluctuations could deviate from climate projections and impact this group. We experimentally quantified how increasing amplitudes of warming fluctuation (± 1, 3, and 5 °C) alter carbon-specific electron transport (ETR[c]), net photosynthesis (P[c]), respiration (R[c]), phagotrophy (Ph[c]), carbon use efficiency (CUE), and growth (µ) in four protist species (three mixoplanktonic and one strict phototroph). We observed a consistent positive link between photosynthetic efficiency (P[c]:ETR[c] ratio) and Ph[c], and a shift towards a strengthening of the Ph[c] (P[c]:ETR[c] / Ph[c] ratio) with greater thermal fluctuation. A potential explanation is a selective behavior aimed to increase phagotrophy to obtain inorganic nutrients through ingested prey internal re-cycling rather than relying on the environment, to support an enhanced photosynthetic efficiency and growth. An enhanced, coupled photo-phagotrophy activity could boost mixoplankton competitiveness compared to phytoplankton. Our findings underscore the need to incorporate trophic flexibility and its interaction with environmental variability into trait-based models to better predict community dynamics, biogeochemical cycling, and food web structure in aquatic ecosystems.}, }
@article {pmid41254852, year = {2025}, author = {Alster, CJ and Schipper, LA and Bååth, E}, title = {Thermal Adaptation of Bacterial and Fungal Growth in a Geothermally Influenced Soil Transect.}, journal = {Global change biology}, volume = {31}, number = {11}, pages = {e70605}, doi = {10.1111/gcb.70605}, pmid = {41254852}, issn = {1365-2486}, support = {MFP-UOW1904//Marsden Fund/ ; }, mesh = {*Soil Microbiology ; New Zealand ; *Fungi/growth &amp; development ; *Bacteria/growth &amp; development ; Temperature ; *Soil/chemistry ; }, abstract = {Numerous studies have investigated microbial adaptation to increasing soil temperature, but limitations in experimental design hinder comprehensive understanding. These include short-term laboratory studies with constant environmental conditions and field studies with few distinct temperature treatments. Here, we utilized a long-term natural soil geothermal gradient in Aotearoa, New Zealand, ranging in mean annual soil temperature (MAT) from 17°C to 42°C to explore thermal adaptation of microbial growth rates. We collected soil from 28 locations along the gradient and measured bacterial growth rate (via leucine incorporation) at eight temperatures (4°C-45°C) and fungal growth rate (via Ac-in-ergosterol) at two temperatures (16°C and 39°C). We then fit Macromolecular Rate Theory and the Ratkowsky equation to estimate the temperature minimum (T min $$ {T}_{min} $$), optimum (T opt $$ {T}_{opt} $$), and inflection point (T inf $$ {T}_{inf} $$) for bacterial growth, and a temperature sensitivity index to compare relative fungal and bacterial growth rates. We found predictable changes in thermal adaptation of bacterial growth along the geothermal gradient with temperature response curves shifting 0.22°C-0.27°C per 1°C increase in MAT regardless of the temperature metric (i.e., T min $$ {T}_{min} $$ , T opt $$ {T}_{opt} $$ , and T inf $$ {T}_{inf} $$) used. Thermal adaptation of bacterial and fungal growth increased roughly in parallel. We also compared the bacterial growth results to published temperature response data of microbial respiration (with added glucose) from this geothermal gradient. Rates of thermal adaptation for bacterial growth and microbial respiration were similar, suggesting synchronicity across microbial processes. The less than 1°C change in all measured temperatures metrics per degree increase in MAT resulted in microbial growth and activity closer to in situ temperatures at high soil temperatures and lower than in situ temperatures under non-elevated soil temperatures. Overall, our results highlight the use of geothermal gradients and appropriate temperature models in studying thermal adaptation of soil microbial processes; the predictability of results also underscores potential for incorporating microbial thermal adaptation into soil carbon modeling efforts.}, }
@article {pmid41254344, year = {2025}, author = {Distante, A and Garino, D and Cerrato, C and Perez-Ardavin, J and Flores, FQ and Lopetuso, L and Mir, MC}, title = {The role of the human microbiome in prostate cancer: a systematic review from diagnosis to treatment.}, journal = {Prostate cancer and prostatic diseases}, volume = {}, number = {}, pages = {}, pmid = {41254344}, issn = {1476-5608}, abstract = {BACKGROUND: Prostate cancer (PC) heterogeneity and treatment resistance remain major clinical challenges, with emerging evidence implicating the microbiome as a key modulator of disease pathogenesis. While microbial dysbiosis has been linked to PC diagnosis, progression, and therapeutic outcomes, the mechanisms underlying these associations are poorly understood. This review synthesizes current evidence on the diagnostic, prognostic, and therapeutic potential of the microbiome in PC.<br><br>METHODS: A systematic search of PubMed, Embase, and Cochrane Central Register of Controlled Trials (through April 2024) was conducted following PRISMA guidelines (PROSPERO: CRD42024534899). Controlled and observational studies investigating microbial roles in PC diagnosis (e.g., ISUP grading group), prognosis, or treatment response were included. Data extraction and quality assessment used the QUIPS tool. From 810 screened records, 42 studies met inclusion criteria.<br><br>RESULTS: Distinct microbial profiles differentiated PC from controls, with Mycoplasma genitalium and Staphylococcus spp. enriched in prostate tumors (3.1- and 2.7-fold, respectively) and correlated with inflammation (IL-6: r&#x2009;=&#x2009;0.38, p&#x2009;=&#x2009;0.002). Urinary microbiota showed diagnostic potential (sensitivity: 58-82%), though sampling methods influenced variability. Prognostically, Betaproteobacteria gut enrichment predicted earlier castration-resistant progression (5.2 months; HR 1.8, 95% CI 1.3-2.5), while ADT-induced dysbiosis (e.g., Klebsiella overgrowth) accelerated resistance (2.1-fold risk). Therapies altered microbial ecology: radiotherapy depleted Bacteroides (linked to proctitis; OR 3.1), and immunotherapy responders harbored higher Akkermansia muciniphila. Microbial androgen synthesis and endotoxin production emerged as resistance mechanisms.<br><br>CONCLUSIONS: The microbiome influences PC detection, aggressiveness, and treatment efficacy through direct (tissue-resident) and indirect (gut-derived) mechanisms. Standardized profiling and microbiome-modulating strategies (e.g., probiotics during ADT) may personalize management. Prospective trials are needed to validate causality and translate microbial biomarkers into clinical practice.}, }
@article {pmid41252854, year = {2025}, author = {Chen, X and Huang, Y and Zhu, X and Gan, C and An, W and Liu, Y and Zhou, S and Xu, M}, title = {Global biogeographic patterns and assembly processes of landfill leachate microbiomes.}, journal = {Water research}, volume = {289}, number = {Pt B}, pages = {124922}, doi = {10.1016/j.watres.2025.124922}, pmid = {41252854}, issn = {1879-2448}, abstract = {Approximately 95 % of municipal solid waste is disposed of in landfill globally, generating leachate that is known as a complex mixture of biodegradable and persistent toxic compounds. Microbes are main forces for tackling the toxic leachate but the patterns of microbial assembly in such treatments are largely unknown, limiting the proper optimization of leachate treatment efficiency. This study, for the first time, presents a global-scale analysis involving 151 landfill leachate treatment samples for uncovering mechanisms of microbial assembly from an ecological perspective. The information of microbiome from 97 treatments in Asia, 41 treatments in Europe, and 13 treatments in North America were collected. The results revealed pronounced biogeographic divergence, with Asian samples (particularly those from India) exhibiting lower microbial diversity and richness compared to Europe and North America counterparts. Geographical-climatic and socio-economic factors significantly influenced microbial composition, with elevation and per capita GDP being primary drivers. Further, the community assembly was predominantly governed by deterministic processes. Co-occurrence network analyses demonstrated distinct microbial interaction patterns across continents, with Asian networks being more vulnerable to collapse under external disturbances. This study provides critical insights into the global microbial ecology of landfill leachate treatment, offering a foundation for developing targeted bioremediation strategies.}, }
@article {pmid41251823, year = {2025}, author = {Della Mónica, IF and Godeas, AM and Scervino, JM}, title = {Hyphosphere interactions: P-solubilizing fungi modulate AMF phosphatase activity and mycorrhizal symbiosis via exudate-mediated communication.}, journal = {Mycorrhiza}, volume = {35}, number = {6}, pages = {66}, pmid = {41251823}, issn = {1432-1890}, support = {UBACyT 20020220400300BA//Secretar&#xed;a de Ciencia y T&#xe9;cnica, Universidad de Buenos Aires/ ; PIBAA 28720210100694CO//Consejo Nacional de Investigaciones Cient&#xed;ficas y T&#xe9;cnicas/ ; PICT 01283-2021//Agencia Nacional de Promoci&#xf3;n de la Investigaci&#xf3;n, el Desarrollo Tecnol&#xf3;gico y la Innovaci&#xf3;n/ ; PINI 04/B253//Fundaci&#xf3;n de la Universidad Nacional del Comahue para el Desarrollo Regional/ ; }, mesh = {*Mycorrhizae/physiology/enzymology ; *Symbiosis ; Plant Roots/microbiology ; *Phosphorus/metabolism ; Acid Phosphatase/metabolism ; *Phosphoric Monoester Hydrolases/metabolism ; Daucus carota/microbiology ; *Glomeromycota/physiology/enzymology ; *Phosphates/metabolism ; }, abstract = {Arbuscular mycorrhizal fungi (AMF) form symbiotic associations with plant roots, enhancing water and nutrient absorption. Phosphate-solubilizing fungi (PSF) can solubilize and mineralize phosphorus, an essential nutrient with low bioavailability, and eventually interact with AMF. However, the understanding of how they interact in the hyphosphere, where root influence is absent, remains limited. Furthermore, the effect of PSF on the phosphatase activity of AMF, related to the P efficiency in acquisition and utilization, within the hyphosphere and mycorrhizosphere zones, remains unclear. Therefore, this study aimed to assess the effect of three different PSF (Talaromyces flavus, T. helicus, and T. diversus) exudates on extracellular acid phosphatases and alkaline phosphatases associated with intra- and extraradical AMF structures in the hyphosphere and mycorrhizosphere, in vitro. To achieve this aim, the AMF Rhizophagus intraradices was cultured with Ri T-DNA transformed carrot roots in a system using Petri dishes that mimicked the hyphosphere (with 2 sections: (a) with roots and AMF, and (b) with only AMF) and the mycorrhizosphere (with roots and AMF in the same place). Different concentrations of PSF exudates were placed in either the hyphosphere or the mycorrhizosphere, and at the end of the experiment (8 weeks), the phosphatase activity of the AMF was measured. This research highlights that the enzymatic activity of AMF is modulated by PSF exudates, depending on whether these exudates are present in the hyphosphere or the mycorrhizosphere. Exudates in the hyphosphere, where PSF are directly associated with AMF hyphae, have a more pronounced effect on AMF extraradical alkaline phosphatases than acid phosphatases, and promote symbiosis efficiency. In contrast, PSF exudates in the mycorrhizosphere had a neutral or negative effect on symbiosis efficiency, improving the extraradical alkaline phosphatases of AMF and the acid phosphatases of the roots. Also, the effect depends on the fungal identity. AMF act as mediators in this context, improving communication between the roots and the hyphosphere microbiome. When exploring the soil, the hyphae encounter compounds produced by microorganisms, thus establishing a complex network of interactions. These interactions enhance the symbiotic efficiency of AMF, modulating the host plant without direct contact. These results show that microbial interactions not only influence the efficiency of phosphorus transfer to plants but also have broader implications for soil health and fertility management.}, }
@article {pmid41251489, year = {2025}, author = {Ye, H and Šlipogor, V and Hanson, BT and Séneca, J and Hausmann, B and Herbold, CW and Pjevac, P and Bugnyar, T and Loy, A}, title = {Associations between gut microbiota and personality traits: insights from a captive common marmoset (Callithrix jacchus) colony.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0044325}, doi = {10.1128/spectrum.00443-25}, pmid = {41251489}, issn = {2165-0497}, abstract = {Recent studies have suggested associations between consistent inter-individual behavioral variation (i.e., animal personality) and gut microbiota. Non-human primates living under controlled conditions are valuable models to investigate diet-independent microbiome-host interactions. In this study, we investigated associations between specific gut microbiota members and personality traits, as well as group membership, sex, age class, breeding status, and relatedness of 26 captive common marmosets (Callithrix jacchus), maintained under the same diet and housing conditions. Personality was assessed using an established testing battery in repeated tests. Then, we collected a total of 225 fecal samples during the summers of 2017 and 2019 from five marmoset social groups for 16S rRNA gene amplicon sequencing. Within-individual microbiota variance was smaller than that between group members. Group members also exhibited more similar gut microbiota than individuals from different groups in each sampling year. Beta diversity of the gut microbiota was linked with personality traits, age class, sex, and breeding status, but not with genetic relatedness. We identified specific bacterial taxa associated with personality traits. In particular, members of the sulfite-reducing genus Desulfovibrio were enriched in more avoidant marmosets. Amplicon sequencing of the dissimilatory sulfite reductase gene dsrB confirmed this pattern, yet additionally revealed an unknown uncultured bacterium that was the predominant sulfite-reducing bacterium in the fecal samples and was linked to more explorative individuals. These findings highlight specific association patterns between identified microbial taxa and personality traits in captive common marmosets.IMPORTANCEThis study provides valuable insights into the intricate relationship between gut microbiota and host personality traits, using captive common marmosets as a model. By controlling for diet and housing conditions, it probes key host factors such as personality, age, sex, and social group membership, offering a robust framework for understanding microbiome-host interactions. The discovery of specific microbial taxa associated with personality traits, particularly the enrichment of sulfite-reducing genera in more avoidant individuals, underscores the potential of the gut microbiome to reflect or be associated with personality differences. These findings advance our understanding of microbiome-host dynamics and pave the way for future research on the mechanistic links between behavior and gut microbiota in other animal models and across broader ecological contexts.}, }
@article {pmid41251323, year = {2025}, author = {Ferreira, J and Lievens, B and Rediers, H}, title = {Development of a spore-based confrontation assay to screen for biocontrol organisms with antagonistic activity against oomycete and fungal pathogens.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxaf286}, pmid = {41251323}, issn = {1365-2672}, abstract = {AIMS: Screenings for biocontrol organisms against fungal and oomycete pathogens are typically performed on mycelium. While this allows for high-throughput screenings, it omits a major actor in pathogenicity, i.e. the spores. This study aims to improve the screening strategy using a spore-based confrontation assay (SBCA), as well as comparing its performance to the traditional mycelium-based confrontation assay (MBCA) and microscopy analyses of spore germination.<br><br>METHODS AND RESULTS: The SBCA was used to screen for 38 candidate biocontrol bacteria against two relevant broad-spectrum phytopathogens, Botrytis cinerea and Phytophthora cactorum. The performance of the SBCA was benchmarked to the traditional mycelium-based confrontation assay and microscopy observations for spore germination inhibition. The SBCA demonstrated a higher hit rate and reproducibility than its counterparts. The bacteria tested exhibited diverse traits in vitro such as production of lytic enzymes, biosurfactant, bioactive volatile organic compounds, and cell-free extracts. These characteristics suggest potential biocontrol modes of action, such as antibiosis (via diffusible metabolites and enzymes) or competition for nutrients and space. For two Pseudomonas strains, the biocontrol activity against P. cactorum was confirmed in planta in a detached leaf assay.<br><br>CONCLUSIONS: This study showcases a versatile and robust spore-based screening that outperforms conventional screening methods. Through the use of the SBCA, two promising biocontrol strains with antagonistic activity against P. cactorum in strawberry were identified.}, }
@article {pmid41250675, year = {2025}, author = {Gao, Y and Bai, J and Zhou, F and He, Y and Wang, Y and Huang, X}, title = {ICCTax: a hierarchical taxonomic classifier for metagenomic sequences on a large language model.}, journal = {Bioinformatics advances}, volume = {5}, number = {1}, pages = {vbaf257}, pmid = {41250675}, issn = {2635-0041}, abstract = {MOTIVATION: Metagenomic data increasingly reflect the coexistence of species from Archaea, Bacteria, Eukaryotes, and Viruses in complex environments. Taxonomic classification across the four superkingdoms is essential for understanding microbial communities, exploring genomic evolutionary relationships, and identifying novel species. This task is inherently imbalanced, uneven, and hierarchical. Genomic sequences provide crucial information for taxonomy classification, but many existing methods relying on sequence similarity to reference genomes often leave sequences misclassified due to incomplete or absent reference databases. Large language models offer a novel approach to extract intrinsic characteristics from sequences.<br><br>RESULTS: We present ICCTax, a classifier integrating the large language model HyenaDNA with complementary-view-based hierarchical metric learning and hierarchical-level compactness loss to identify taxonomic genomic sequences. ICCTax accurately classifies sequences to 155 genera and 43 phyla across the four superkingdoms, including unseen taxa. Across three datasets built with different strategies, ICCTax outperforms baseline methods, particularly on Out-of-Distribution data. On Simulated Marine Metagenomic Communities datasets from three oceanic sites, DairyDB-16S rRNA, Tara Oceans, and wastewater metagenomic datasets, it demonstrates strong performance, showcasing real-world applicability. ICCTax can further support identification of novel species and functional genes across diverse environments, enhancing understanding of microbial ecology.<br><br>Code is available at https://github.com/Ying-Lab/ICCTax.}, }
@article {pmid41249638, year = {2025}, author = {Tinning, Z and Kaestli, M and Nowland, SJ and Siboni, N and Seymour, JR and Gibb, KS and Padovan, AC}, title = {Dynamics of Bacterial and Vibrio Communities in Blacklip Rock Oysters in the Seasonal Tropics.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {125}, pmid = {41249638}, issn = {1432-184X}, support = {2020-043//Fisheries Research and Development Corporation/ ; Discovery Project DP240100370//Australian Research Council/ ; }, mesh = {Animals ; *Vibrio/isolation &amp; purification/genetics/classification ; *Ostreidae/microbiology ; Seasons ; Aquaculture ; Seawater/microbiology ; *Microbiota ; Australia ; Tropical Climate ; Shellfish/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Humans ; }, abstract = {Cultivation of the tropical Blacklip Rock Oyster (BRO) (Saccostrea spathulata) is an emerging Indigenous-led aquaculture industry in the seasonal tropics of northern Australia. However, little is currently known about the potential for pathogen outbreaks in this species. We conducted a year-long study to establish a microbial baseline to identify potential oyster and human health risks to inform future food safety decision making in this nascent industry. In healthy oysters, we identified both the core microbiome of this oyster species and the presence of potential oyster and human pathogens. The core bacteriome comprised nine bacterial families, while the core vibriome comprised the animal pathogens Vibrio harveyi and V. owensii. The potential human pathogen V. parahaemolyticus was detected in some oysters during the wet season, during periods of increased rainfall, turbidity and total nitrogen. The bacteriome and vibriome of oysters were significantly different to the adjacent seawater and therefore we concluded that seawater is not an appropriate surrogate for pathogen risk surveillance in this developing industry. These results provide new knowledge on the microbiology of a previously understudied oyster species and will inform monitoring methods, harvesting and shellfish quality compliance in this emerging Indigenous-led industry.}, }
@article {pmid41249586, year = {2025}, author = {Zhou, S and Bi, J and Zhou, S and Luo, L and Yan, X and Zou, J and Ji, Y and Zhao, S and Qiu, J and Liu, Z and Jiang, J and Wang, B and Liu, X}, title = {Community Assembly Mechanisms Underlying Divergent Responses of Indica and Japonica Rice Rhizosphere Microbiota to Drought Stress.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {126}, pmid = {41249586}, issn = {1432-184X}, support = {2022YFD2300302//National Key Research and Development Program of China/ ; 42277304//National Natural Science Foundation of China/ ; 42407399//National Natural Science Foundation of China/ ; XUEKEN2022003//Fundamental Research Funds for the Central Universities/ ; BX20240168//National Postdoctoral Program for Innovative Talents/ ; BK20241558//Natural Science Foundation of Jiangsu Province/ ; 2024ZB624//Jiangsu Funding Program for Excellent Postdoctoral Talent/ ; }, mesh = {*Oryza/microbiology/growth &amp; development/physiology/genetics/classification ; *Rhizosphere ; *Droughts ; *Microbiota ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; RNA, Ribosomal, 16S/genetics ; Stress, Physiological ; Agricultural Irrigation ; }, abstract = {Drought stress markedly reduces rice yield, with notable genotypic variation in drought tolerance. While the rhizosphere microbiome is regarded as the second genome of plants, how the indica and japonica rice rhizosphere microbial communities respond to deficit irrigation and their relationship with yield remain to be elucidated. Here, we conducted field experiments using 12 indica and 12 japonica rice varieties under full and deficit irrigation regimes. Yield-related traits, including filled grain number, seed setting rate, two-plant yield, and thousand grain weight, were measured, and the rhizosphere microbial communities were characterized by 16S rRNA gene sequencing. In line with previous studies, japonica varieties showed superior drought resistance in terms of yield performance. Both rice genotype and irrigation regime significantly influenced the composition and functional potential of the rhizosphere microbiome. Compared to indica rice, the japonica rice rhizosphere was enriched with more beneficial microorganisms. Enrichment of nitrogen‑metabolism‑related groups, such as Microvirga and Nitrososphaeraceae, may contribute to rhizosphere nitrogen cycling and support nitrogen availability for the rice. Similarly, higher abundance of Streptomyces in japonica varieties under drought conditions may be associated with improved drought tolerance. These microbial genera were closely associated with rice yield. Moreover, the japonica rhizosphere microbiome was less disturbed by water limitation, showing higher stability. Overall, the rhizosphere microbiome of japonica rice exhibited functional optimization under drought stress by promoting the enrichment of beneficial and nitrogen-cycling microbes, thereby enhancing drought resistance and yield stability. This study demonstrated a significant correlation between rhizosphere microbial communities and rice yield, providing fundamental insights that may contribute to future strategies for optimizing crop productivity through microbiome management in sustainable agriculture.}, }
@article {pmid41248576, year = {2025}, author = {Zhou, Y and Chang, L and Sun, H and Li, W and Ao, T and Lin, J}, title = {Evaluation of reclaimed treated wastewater on soil quality, microbial community and function in urban greening irrigation.}, journal = {Journal of environmental management}, volume = {395}, number = {}, pages = {127958}, doi = {10.1016/j.jenvman.2025.127958}, pmid = {41248576}, issn = {1095-8630}, abstract = {Reclaimed treated wastewater (TWW) offers a sustainable irrigation alternative for urban greening amid freshwater scarcity. However, its impact on soil quality and microbial ecology in urban landscapes remains underexplored. This study assessed the effects of three TWW types and one TWW-purified water mixture on soil properties, heavy metal accumulation, enzyme activity and microbial community dynamics in Common Nandina (Nandina domestica Thunb.) systems over three- and five-month in Nanjing, China, using a metagenomic approach. The results showed that TWW irrigation significantly increased soil nitrogen, phosphorus content and pH (P < 0.05), with stronger effects observed at three-month (P < 0.05). Soil heavy metal content varied, with Cr and As exhibiting potential accumulation. Enzyme activity (N-acetyl-glucosaminidase and phosphatase) was positively influenced by TWW irrigation at three-month. Metagenomic analysis revealed significant shifts in microbial community composition, particularly fungi, with Mucoromycota increasing and Ascomycota decreasing under TWW. The Normalized Stochasticity Ratio indicated increased stochasticity in microbial assembly under TWW irrigation (P < 0.05). Functionally, TWW increased abundance of functional genes related to amino acid metabolism and peroxisomes (P < 0.05), but decreased degradation genes for aromatic compounds. TWW also increased the abundance of antibiotic resistance genes (ARGs), particularly those related to triclosan and glycopeptide, and plant pathogenic genera like Aspergillus and Fusarium. The findings suggest that while TWW irrigation improves certain soil properties and microbial functions in the short term, it may pose ecological risks from heavy metal and microbial contamination, offering key insights for sustainable urban irrigation strategies.}, }
@article {pmid41247962, year = {2025}, author = {Wei, D and Hu, S and Tang, T and Yang, Y and Meng, F and Peng, Y}, title = {Confinement Reduces Surface Accumulation of Swimming Bacteria.}, journal = {Physical review letters}, volume = {135}, number = {18}, pages = {188401}, doi = {10.1103/dvc8-tlh1}, pmid = {41247962}, issn = {1079-7114}, mesh = {*Models, Biological ; Hydrodynamics ; *Bacterial Physiological Phenomena ; Movement ; *Escherichia coli/physiology ; }, abstract = {Many swimming bacteria naturally inhabit confined environments, yet how confinement influences their swimming behaviors remains unclear. Here, we combine experiments, continuum modeling, and particle-based simulations to investigate near-surface bacterial swimming in dilute suspensions under varying confinement. Confinement reduces near-surface accumulation and facilitates bacterial escape. These effects are quantitatively captured by models incorporating the force quadrupole, a higher-order hydrodynamic singularity, that generates a rotational flow reorienting bacteria away from surfaces. Under strong confinement, bacterial trajectories straighten due to the balancing torques exerted by opposing surfaces. These findings highlight the role of hydrodynamic quadrupole interactions in near-surface bacterial motility, with implications for microbial ecology, infection control, and industrial applications.}, }
@article {pmid41247508, year = {2025}, author = {Wenten, IG}, title = {Rethinking Biofilm Engineering and Fouling Resistance in Membrane Bioreactors.}, journal = {Langmuir : the ACS journal of surfaces and colloids}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.langmuir.5c03864}, pmid = {41247508}, issn = {1520-5827}, abstract = {Membrane bioreactors (MBRs) are increasingly recognized as a key technology in sustainable wastewater treatment, offering a high effluent quality through the integration of biological degradation and membrane filtration. Among the critical factors influencing their performance are biofilm dynamics and membrane fouling. This article critically examines recent advances in biofilm engineering and antifouling strategies for MBRs, with an emphasis on microbial community modulation, quorum quenching, and hydrodynamic control to improve biofilm stability. In parallel, the review examines material-based and biological methods to mitigate membrane fouling, emphasizing multifunctional surfaces and emerging biocontrol strategies. Key operational challenges, such as energy consumption, cleaning frequency, and membrane aging, are evaluated alongside future research directions in materials design, microbial ecology, and real-time system optimization. The integration of these innovations is essential for advancing MBR technologies that are robust, resource-efficient, and aligned with circular economy principles.}, }
@article {pmid41247324, year = {2025}, author = {Weagley, JS and Cárdenas, LAC and Romani, A and Sullender, ME and Aggarwal, S and Makimaa, H and Hogarty, MP and Rodgers, R and Kennedy, EA and Foster, L and Schriefer, LA and Baldridge, MT}, title = {Differential Microbial Community Assembly Following Co-housing versus Microbiota Transplant.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf256}, pmid = {41247324}, issn = {1751-7370}, abstract = {Mouse models are vital tools for discerning the relative contributions of host and microbial genetics to disease, often requiring the transfer of microbiota between different mouse strains. Transfer methods include antibiotic treatment of recipients and colonization using either co-housing with donors or the transplantation of faecal or caecal donor material. However, the efficiency and dynamics of these methods in reconstituting recipients with donor microbes is not well understood. We thus directly compared co-housing, faecal transplantation, and caecal transplantation methods. Donor mice from Taconic Biosciences, possessing distinct microbial communities, served as the microbial source for recipient mice from Jackson Laboratories, which were treated with antibiotics to disrupt their native microbiota. We monitored bacterial and viral populations longitudinally over the course of antibiotics treatment and reconstitution using 16S rRNA gene sequencing, quantitative PCR, and shotgun sequencing of viral-like particles. As expected, antibiotic treatment rapidly depleted microbial biomass and diversity, with slow and incomplete natural recovery of the microbiota in non-transfer-recipient control mice. Although all transfer methods reconstituted recipient mice with donor microbiota, co-housing achieved this more rapidly for both bacterial and viral communities. Overall, faecal and caecal transplant resulted in highly similar colonization processes with some minor variation in enrichment for two specific bacterial families. This study provides valuable insights into microbial ecology, as well as the dynamics underlying experimental microbial transfer methods, enhancing reproducibility and informing best practices for microbiota transfer in mouse models.}, }
@article {pmid41247030, year = {2025}, author = {Van Beek, JM and Robles, G and Mewalal, R and Blaby, I and Hatzenpichler, R}, title = {A collection of archaeal 16S rRNA Clone-FISH cultures for probe validation in fluorescence in situ hybridization experiments.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0113125}, doi = {10.1128/mra.01131-25}, pmid = {41247030}, issn = {2576-098X}, abstract = {We present a collection of 30 Escherichia coli cultures (Clone-FISH cultures), each carrying a plasmid for the heterologous expression of a (near) full-length 16S rRNA gene from 1 of 30 lineages of archaea, including 17 yet uncultured ones. We make these clones available for use as controls in fluorescence in situ hybridization experiments.}, }
@article {pmid41247018, year = {2025}, author = {Xiong, M and Kuang, W and Liu, Z and Tong, R and Deng, X and Wang, N and Wan, X and Feng, M and Luo, Y and Zhang, B and Zhang, Z and Zheng, F}, title = {Quercetin alleviates ulcerative colitis via regulating gut microbiota and tryptophan metabolism.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0070325}, doi = {10.1128/msystems.00703-25}, pmid = {41247018}, issn = {2379-5077}, abstract = {UNLABELLED: Quercetin, a natural flavonoid in traditional Chinese medicinal plants, has shown promise in alleviating ulcerative colitis symptoms despite uncertainties about its exact mode of action. This study explored how quercetin influences tryptophan breakdown and gut bacterial populations in mice with chemically induced colitis. The treatment demonstrated measurable improvements-normalizing body weight, reducing spleen enlargement, lowering clinical severity scores, preserving colon structure, and healing tissue damage. Through advanced microbiome profiling and metabolic analysis, researchers observed increased populations of helpful gut microbes alongside higher concentrations of tryptophan byproducts. These biochemical shifts stimulated the aryl hydrocarbon receptor system, which plays a key role in restoring gut lining integrity. The collective evidence points to quercetin's therapeutic potential through its dual action on microbial ecology and tryptophan-derived signaling pathways.<br><br>IMPORTANCE: Ulcerative colitis is a chronic inflammatory disease with limited effective therapeutic options. In this study, quercetin-a flavonoid commonly found in traditional Chinese medicinal herbs-was shown to relieve colitis symptoms by reshaping gut microbiota and restoring tryptophan metabolism. Notably, the increase in indolelactic acid, a key microbial metabolite, led to activation of the aryl hydrocarbon receptor, which supports intestinal barrier integrity and dampens inflammation. These findings reveal a gut microbiota-derived metabolite-host signaling axis as a central mechanism of action, highlighting the potential of quercetin as a microbiota-targeted therapeutic approach for UC.}, }
@article {pmid41246320, year = {2025}, author = {Dey, P}, title = {Genes, guts, and microbes: decoding host-driven microbial regulation using intestine-specific conditional knockouts.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1674913}, doi = {10.3389/fimmu.2025.1674913}, pmid = {41246320}, issn = {1664-3224}, mesh = {Animals ; *Gastrointestinal Microbiome/immunology/genetics ; Humans ; Dysbiosis ; Mice, Knockout ; *Intestines/microbiology/immunology ; *Intestinal Mucosa/metabolism/microbiology/immunology ; *Host Microbial Interactions/genetics ; Mice ; }, abstract = {This narrative review underscores the influence of host genetics in actively regulating gut microbiota composition and function, highlighting the distinctive advantages of intestine-specific conditional knockout (cKO) models in gut microbiome research. In contrast to whole-body knockouts or germ-free animals, these precision models, enabled by Cre-loxP technology, eliminate confounding systemic effects to elucidate how localized host genes within intestinal cells regulate the gut microbial ecology. The review identifies three fundamental host-driven regulatory mechanisms through the analysis of specific gene deletions: (1) barrier integrity (e.g., mucus and junction proteins), (2) immune defenses (e.g., antimicrobial peptides and glycan synthesis), and (3) metabolic signaling (e.g., bile acid receptors and glucose transporter). These pathways jointly impose microbial symbiosis, and their disruption leads to dysbiosis characterized by increased abundance of pathobionts (e.g., Escherichia, Proteobacteria), directly connecting host genetics to inflammatory and metabolic disorders. This host-centric viewpoint emphasizes the gut as an active regulator, rather than a passive microenvironment for the microbiota, providing significant insights for creating tailored therapeutics that focus on host pathways to restore microbial balance in disorders such as inflammatory bowel diseases.}, }
@article {pmid41246283, year = {2025}, author = {Phoo, MTP and Dechathai, T and Singkhamanan, K and Chusri, S and Pomwised, R and Wonglapsuwan, M and Morikawa, K and Surachat, K}, title = {Pseudomonas aeruginosa affects Acinetobacter baumannii's growth, gene expression and antibiotic resistance in in vitro co-culture system.}, journal = {Current research in microbial sciences}, volume = {9}, number = {}, pages = {100499}, doi = {10.1016/j.crmicr.2025.100499}, pmid = {41246283}, issn = {2666-5174}, abstract = {Pseudomonas aeruginosa and Acinetobacter baumannii are opportunistic pathogens co-isolated frequently in the same infection sites. In this study, we aimed to elucidate the interaction between P. aeruginosa and A. baumannii in in vitro co-culture system. Growth analysis showed that P. aeruginosa PA01 unilaterally exerts a negative effect on the growth of A. baumannii SK005. A. baumannii alone exhibited an altered transcriptome pattern, especially in the genes for metabolic pathways. Strong upregulation of genes in iron acquisition systems (acinetobactin, baumannoferrin, 2,3-dihydroxybenzoic acid synthesis cluster, and Feo iron transport system) and downregulation of iron-storage genes (bacterioferritin) were the most prominent changes. In terms of antibiotic resistance, we observed the downregulation of the fosfomycin resistance gene fosB. Strikingly, the phenotypic analysis demonstrated that A. baumannii in co-culture is more vulnerable to fosfomycin than in monoculture conditions, while it is more resistant to cefoxitin and imipenem. This study broadens our understanding of microbial ecology in co-infection settings by highlighting the fact that mixed pathogens do not always undergo interaction to a mutually equivalent extent.}, }
@article {pmid41244671, year = {2025}, author = {Zhang, Z and Jia, L and Liu, B and Liu, Y and Zhao, J and Wang, Y and Zhang, M and Qiao, W and Yang, B and Luo, L and Chen, L}, title = {Maternal gut microbiota and placenta-derived tissues microbes are important for initial gut microbial colonization in infants.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1631590}, doi = {10.3389/fmicb.2025.1631590}, pmid = {41244671}, issn = {1664-302X}, abstract = {BACKGROUND: Early infant gut microbiota colonization, influenced by various factors, significantly affects future growth and development. However, results related to how the initial microbial ecology is established in the infant gut remain inconsistent.<br><br>RESULTS: In this study, we collected maternal and infant feces, vaginal secretions, placental tissues, breast milk, amniotic membrane tissues, umbilical cord blood, and breast skin for homology comparisons and for exploring the main sources of infant intestinal microbiota. Our results revealed that early infant gut microbiota originated mainly from the vertical transmission of maternal microbiota, and that vaginal microbiota did not affect infant gut microbiota colonization. Microbiota was detected in the placenta, supporting the idea that the uterus is not sterile. Moreover, we verified microbial composition-related similarities in the amniotic tissues and umbilical cord blood, further validating our hypothesis that gut microbiota in the early stages of infancy are mainly vertically transmitted from the mother and placenta-derived tissues also play a significant role in the formation of the infant's initial gut microbiota. Notably, none of the hereby-mentioned influences (i.e., gender, delivery mode, feeding mode, and Hepatitis B virus) affected significantly infant gut microbiota colonization.<br><br>CONCLUSION: This study demonstrated that infant intestinal microbiota resulted from microbiotic co-provision from multiple maternal sites. In addition to the maternal gut microbiota, the placenta-derived tissues is the relevant contributor to initial infant gut microbiota, providing strong evidence for the source colonization of the infant gut microbiota.}, }
@article {pmid41244624, year = {2025}, author = {Addo, SO and Addo, M and DeWitt, ME and Tawiah-Mensah, CNL and Amoah, S and Obuam, PK and Unicorn, NM and Kyeremateng, ET and Desewu, G and Larbi, JA}, title = {Knowledge, Attitude and Practices of Abattoir Workers in Kumasi Towards Ticks and Tick-Borne Pathogens.}, journal = {Public health challenges}, volume = {4}, number = {4}, pages = {e70167}, doi = {10.1002/puh2.70167}, pmid = {41244624}, issn = {2769-2450}, abstract = {The high dependence on livestock in Ghana comes with the risk of zoonotic tick-borne pathogen infection. Abattoir workers are especially at risk due to their frequent contact with livestock that are infested with ticks and tick-borne pathogens. This study sought to assess the knowledge, attitude and practices of abattoir workers in Kumasi towards ticks and tick-borne pathogens. A total of 130 workers were recruited from the Kumasi abattoir (92), Suame abattoir (24) and Akwatia Line slaughter slab (14). The respondents were males, mostly aged between 46 and 55 years (36.2%), had no form of education (43.8%) and had >10 years (68.5%) of working experience. Given that a significant number of the workers handled live animals (95.4%) or dead animals or animal parts (87.7%), were involved in slaughtering (69.2%) and had experienced tick bites (81.5%), there was a risk of tick-borne pathogen infection. However, only 35.4% thought humans can get diseases from tick bites, and 58.5% of the respondents believed tick bites lead to the development of a tick-borne disease. It was observed that education (p = 0.008) had a significant influence on the risk of zoonotic tick-borne pathogen infection, with 52% of the respondents with no education believing humans cannot get infections from ticks. The findings of this study indicate that the abattoir workers are at risk of zoonotic tick-borne infections, and there is a need for frequent education as well as the adoption of effective tick control and preventive measures.}, }
@article {pmid41242981, year = {2025}, author = {Andonotopo, W and Bachnas, MA and Dewantiningrum, J and Adi Pramono, MB and Bernolian, N and Yeni, CM and Putra Wiradnyana, AAG and Hariyasa Sanjaya, IN and Akbar, MIA and Darmawan, E and Sulistyowati, S and Stanojevic, M and Kurjak, A}, title = {The fetal exposome and Preterm Birth: a systematic synthesis of environmental exposures and multi-omics evidence.}, journal = {Journal of perinatal medicine}, volume = {}, number = {}, pages = {}, pmid = {41242981}, issn = {1619-3997}, abstract = {OBJECTIVES: Preterm birth (PTB), defined as delivery before 37 weeks of gestation, is a leading cause of neonatal mortality and long-term developmental impairment. Its complex etiology, spanning environmental, genetic, psychosocial, and socio-economic domains, limits effective prediction and prevention. We systematically synthesized evidence on how environmental exposures influence PTB risk through multi-omic disruptions within a fetal exposome framework.<br><br>METHODS: A comprehensive literature search was conducted in major biomedical databases, following PRISMA guidelines. Ninety-five human studies published through May 2025 were included, encompassing exposures such as ambient air pollution, endocrine-disrupting chemicals, maternal stress, nutrition, occupational hazards, climate variability, and microbiome alterations. Two reviewers independently extracted data (exposure type, omics platform, biospecimen, PTB subtype) with inter-rater reliability assessment, and study quality was evaluated using the Newcastle-Ottawa Scale. Findings were narratively stratified by exposure category, study design, and spontaneous vs. indicated PTB.<br><br>RESULTS: Environmental exposures were consistently associated with disruptions in oxidative stress, inflammation, immune regulation, hormonal signaling, placental aging, and microbial ecology, mediated by multi-omic signatures in maternal, placental, and fetal tissues. Candidate biomarkers show promise for early risk stratification but lack validation and population-level predictive performance due to heterogeneous exposure assessment and study design.<br><br>CONCLUSIONS: Integrating fetal exposome concepts with multi-omics enhances mechanistic insight into PTB risk and may support biomarker discovery and precision-guided prenatal interventions. Clinical translation requires standardized exposure measurement, biomarker validation, and equity-focused implementation.}, }
@article {pmid41242561, year = {2025}, author = {Gloria, LD and Lotti, T and van Loosdrecht, MC and Ramazzotti, M}, title = {Who calls granules "home"? Domain-spanning meta-analysis charting microbial ecosystems underlying aerobic granular sludge reactors.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {133657}, doi = {10.1016/j.biortech.2025.133657}, pmid = {41242561}, issn = {1873-2976}, abstract = {The theatre of activity of complex microbial communities underpins the Aerobic Granular Sludge (AGS) systems, resulting in efficient wastewater treatment. Here, we present the first meta-analysis of DNA sequencing data from both published and newly generated AGS samples, aiming to define the "core microbiota" of AGS reactors, consisting of bacteria, archaea, eukaryotes and DNA viruses consistently featured and shared across different scales and operational settings. Briefly, the results indicated that a sequencing depth of at least 10 GB is required to profile the majority of the AGS community, revealed the core taxa, detected the recurrent presence of the uncultured genus ADurb.Bin028 in full-scale reactors and identified Rotaria and Diploscapter, as well as the sessile ciliates Stentor and Thuricola, as the most abundant eukaryotes in AGS. In conclusion, this work provided a taxonomic overview of AGS' common microbes and addressed potential technical caveats, aiming to establish a reference for future studies.}, }
@article {pmid41240073, year = {2025}, author = {Berkhout, MD and de Ram, C and Boeren, S and Plugge, CM and Belzer, C}, title = {Probiotic Engraftment of Akkermansia muciniphila in an In Vitro Synthetic Microbial Community.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {123}, pmid = {41240073}, issn = {1432-184X}, support = {0.24.002.002//Ministerie van Onderwijs, Cultuur en Wetenschap/ ; }, mesh = {*Probiotics ; *Gastrointestinal Microbiome ; Humans ; Mucins/metabolism ; *Verrucomicrobia/physiology ; Akkermansia ; Polysaccharides/metabolism ; Bacteroides thetaiotaomicron ; }, abstract = {Akkermansia muciniphila is a specialist mucin glycan-degrader that is common in the human gut. A. muciniphila is associated with host health and therefore proposed as a next-generation probiotic. However, it is unknown if consumption of live and active A. muciniphila will be effective in terms of survival and engraftment in the gut microbiome. Furthermore, it is of interest whether introduction of A. muciniphila would influence the resident mucosal microbiota. To this end, we investigate the addition of live A. muciniphila to a stable in vitro microbial mucin glycan-degrading synthetic community. A. muciniphila engrafted in this synthetic community and actively degraded mucin using essential mucin glycan-degrading enzymes. Addition of A. muciniphila did not induce major compositional changes, except that Bacteroides thetaiotaomicron increased in relative abundance at the expense of Bacteroides caccae. At the metaproteomic level, community function was not significantly affected, as peptidase, fucosidase, galactosidase and sulfatase expression remained stable. However, sialidase was significantly enriched after A. muciniphila addition, which can be explained by the relative increase of generalist glycan-degrader B. thetaiotaomicron. Overall, we show that a community without A. muciniphila still harbours a niche for this bacterium, but that A. muciniphila did not induce major changes in the in vitro mucosal synthetic community. This suggests that A. muciniphila applied as a probiotic can engraft and exert its beneficial effects on the host, without major impact on the human gut mucosal microbiota composition and function and warrants further research into A. muciniphila engraftment in vivo.}, }
@article {pmid41240069, year = {2025}, author = {Cambronero-Heinrichs, JC and Pepori, AL and Pecori, F and Santoiemma, G and Cavaletto, G and Santini, A and Rassati, D}, title = {Microbial Interactions Support the Role of Ambrosia Beetles as Potential Vectors of Dutch Elm Disease.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {124}, pmid = {41240069}, issn = {1432-184X}, support = {National Recovery and Resilience Plan (NRRP), Mission 4, Component 2, project: "Ulmus glabra protection in Italian peninsula - MONTANA", CUP:C53D23003510006//European Union - NextGenerationEU/ ; }, mesh = {Animals ; *Plant Diseases/microbiology ; *Ulmus/microbiology/parasitology ; Symbiosis ; *Coleoptera/microbiology ; *Microbial Interactions ; Female ; *Insect Vectors/microbiology ; Ophiostoma/physiology ; *Weevils/microbiology ; }, abstract = {Dutch elm disease (DED) has caused devastating pandemics in natural elm populations across Europe, North America, and Asia. The primary vectors of DED are native elm-associated bark beetles of the genus Scolytus. However, there is evidence suggesting that ambrosia beetles may also carry Ophiostoma novo-ulmi and potentially transmit it to elm trees. In this study, we explored microbial interactions and host selection mechanisms that could support the role of ambrosia beetles as vectors of O. novo-ulmi. Our study showed that females of Anisandrus dispar, Xyleborinus saxesenii, Xylosandrus crassiusculus, and Xylosandrus germanus emerging from both DED-infected and healthy elm logs carried O. novo-ulmi DNA. Furthermore, we showed that none of the tested ambrosia beetle fungal symbionts was adversely affected by O. novo-ulmi, while Dryadomyces spp. and the bacterial symbiont Erwinia sp. 1C4 partially restricted or inhibited O. novo-ulmi growth without fully suppressing it. Overall, these findings provide additional evidence supporting the potential role of ambrosia beetles as vectors of DED and emphasize the need for further research on this understudied insect-pathogen relationship.}, }
@article {pmid41239036, year = {2025}, author = {Casanova-Hernández, D and Pinacho-Pinacho, CD and Calixto-Rojas, M and Rubio-Godoy, M and Hernández-Velázquez, IM and Guevara-Avendaño, E and Méndez, O and Velázquez-Velázquez, E and Zamora-Briseño, JA}, title = {Challenging the paradigm: the Asian fish tapeworm (Schyzocotyle acheilognathi, Yamaguti 1934) lacks an intrinsic symbiotic bacterial community.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {41239036}, issn = {1618-1905}, abstract = {Schyzocotyle acheilognathi is an invasive generalist cestode with a high capacity for adaptation to multiple hosts and freshwater environments. Recent reports suggest that this parasite possesses an intrinsic symbiotic microbiota distinct from that of its fish hosts, and its presence induces gut dysbiosis in the host. In this study, we reassessed these ideas. For this, we collected naturally parasitized fish specimens from different locations in Mexico, encompassing different host species, including Cyprinus carpio, Pseudoxiphophorus bimaculatus, Tlaloc hildebrandi, and Vieja hartwegi. We also tested whether this parasite induces a dysbiotic process in the gut bacterial community of Tlaloc hildebrandi. Parasites were identified based on morphological and molecular criteria, and their bacterial communities were characterized using metataxonomy. Our results revealed that S. acheilognathi does not harbor a consistent microbial community among the different host species surveyed. We also did not detect any dysbiotic effect on the gut microbiota of Tlaloc hildebrandi. These findings contradict previous data and provide evidence of the loose relationship between this parasite and bacteria, which we propose could be a part of its successful generalist strategy. The results presented herein offer a novel perspective on the quest for understanding the microbial ecology in generalist cestodes of freshwater fish.}, }
@article {pmid41239026, year = {2025}, author = {Cao, D and Huang, W and Pang, M and Li, J and Huang, H and Ma, H and Li, D and Qin, Y and Peng, X and Fan, H}, title = {Investigation of the Alterations in the Gut Microbiota and Intestinal Mucosa in Mice Infected with Echinococcus multilocularis.}, journal = {Acta parasitologica}, volume = {70}, number = {6}, pages = {211}, pmid = {41239026}, issn = {1896-1851}, support = {No. 2020-ZJ-Y01//Key Laboratory Project of the Science and Technology Department of Qinghai Province/ ; Qinghai[2023]-125//The National Clinical Key Specialty Construction Project of Hepatobiliary Surgery (Hydatidosis) at Qinghai University Affiliated Hospital/ ; Qinghai Research Key Laboratory for Echinococcosis//The 2022 Science and Technology Plan Project of Qinghai Department of Science and Technology/ ; }, mesh = {Animals ; *Echinococcus multilocularis/physiology ; *Gastrointestinal Microbiome ; Mice ; *Intestinal Mucosa/pathology/microbiology/parasitology ; RNA, Ribosomal, 16S/genetics ; *Echinococcosis/parasitology/pathology ; Disease Models, Animal ; Feces/microbiology/parasitology ; Female ; Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {PURPOSE: Alveolar echinococcosis (AE), a zoonotic parasitic disease caused by the larval metacestode of Echinococcus multilocularis (E. multilocularis), primarily affects the liver and can invide other organs. Given its extremely poor prognsis, witha 10-year mortality rate exceeding 90% in untreated cases, this study aimed to investigate the characteristics and compositional alterations of the intestinal microbiota in AE-infected hosts and evaluate associated intestinal mucosal damage.<br><br>METHODS: We established a mouse model of AE for analysis. Fecal samples were collected from 12 AE-infected mice and 12 age-matched healthy controls at 3 and 6 months post-infection. Gut microbiota composition was assessed by 16S rRNA gene sequencing. Intestinal tissues were subjected to histopathological exnamination using hematoxylin-eosin staining (H&amp;E staining), Alcian blue-glucogen staining (AB-PAS staining), and Lendrum's fluorescent peach red staining, to evaluate mucosal structural integrity and quantify the Paneth and goblet cells.<br><br>RESULTS: The analysis revealed significant alterations in intestinal microbiota diversity and composition in AE-infected mice compared with controls, with changes becoming more pronounced as the infection progressed. Minimal disruption in microbial ecology was observed at 3&#xa0;months, whereas substantial reductions in alpha diversity and distinct shifts in beta diversity emerged after 6&#xa0;months of chronic infection. Phylum-level analysis showed an early increase in Verrucomicrobiota, Bacteroidota, and Campylobacterota at 3&#xa0;months, followed by a marked enrichment of Verrucomicrobiota and Actinobacteriota at 6&#xa0;months when compared with controls. At the genus level, AE infection led to a rapid depletion of Ligilactobacillus and Lactobacillus between 3 and 6&#xa0;months, while Akkermansia abundance significantly increased. Histopathological examination of intestinal tissue further demonstrated severe mucosal damage, including villous atrophy, reduced crypt depth, a pronounced decrease in Paneth cell density (P&#x2009;<&#x2009;0.01), and reduced goblet cell counts (P&#x2009;<&#x2009;0.05), collectively indicating compromised intestinal barrier integrity.<br><br>CONCLUSION: AE infection induces progressive gut microbiota dysbiosis and compromises intestinal barrier integrity. The specific microbial shifts, particularly the depletion of Ligilactobacillus and enrichment of Akkermansia, represent promising diagnostic biomarkers and potential targets for probiotic supplementation or microbial modulation. To further clarify their roles, future research should incorporate multi-omics strategies, including metagenomics and metabolomics, within larger cohorts to better characterize microbiota-host metabolic interactions and to validate stage-specific microbial biomarkers in AE.}, }
@article {pmid41237939, year = {2025}, author = {Devarajan, B and Sharma, S and Mills, B and Prajna, L and Venkatesh, PN and Dharmalingam, K}, title = {Dysbiosis of Bacterial and Fungal Microbiomes Affects the Disease Process and Treatment Outcome in Fungal Keratitis.}, journal = {Experimental eye research}, volume = {}, number = {}, pages = {110745}, doi = {10.1016/j.exer.2025.110745}, pmid = {41237939}, issn = {1096-0007}, abstract = {Fungal keratitis (FK) is a severe eye infection mainly caused by Aspergillus flavus and Fusarium solani. We examined the changes in bacterial and fungal microbiome profiles over a week of disease progression, treatment, and clinical status using targeted next-generation sequencing (NGS). Samples were collected from infected and healthy contralateral eyes of 25 FK patients and one eye of 10 healthy, non-infected cataract controls. QIIME (Quantitative Insights into Microbial Ecology) and MicrobiomeAnalyst were utilised for the data analysis. There was a reduction in beneficial bacteria like Prevotella, Lactobacillus, and Leuconostoc in FK patients compared to the control samples. On the other hand, opportunistic bacteria including Clostridium, Bifidobacterium, and Pseudomonas increased in FK patients. Aspergillus, Colletotrichum, and Basidiobolus were more abundant in keratitis patients, whereas Malassezia and Trichoderma were less abundant. This dysbiosis was also evident in the uninfected contralateral eyes of FK patients. Treatment resulted in significant changes in bacterial genera like Dolosigranulum, Sutterella, and Akkermansia, and fungal genera such as Myrothecium, Corynespora, and Penicillium. Further, treatment returned them to the control group levels, except for Akkermansia and Corynespora. Among the treated patients, a large subset remains nonresponsive to treatment. This treatment outcome, responder versus non-responder, was reflected in the abundance of bacterial genera such as Tannerella, Sutterella, Odoribacter, and fungal genera such as Coprinellus and Volutella. This study highlights the clinical relevance of microbiome signatures in FK, demonstrating bilateral dysbiosis, integrated bacterial-fungal profiling, and correlations with treatment outcomes. These findings suggest potential for microbiome-informed diagnostics, prognostic biomarkers, and risk stratification.}, }
@article {pmid41236361, year = {2025}, author = {Markfeld, M and Titcomb, G and Randriamoria, TM and Sehgal, G and Baksh, N and Kerrigan, A and Soarimalala, V and Nunn, CL and Pilosof, S}, title = {Differential Assembly of Core and Non-Core Host-Microbe Network Structures Along a Land-Use Change Gradient.}, journal = {Ecology letters}, volume = {28}, number = {11}, pages = {e70255}, doi = {10.1111/ele.70255}, pmid = {41236361}, issn = {1461-0248}, support = {1281/20//Israel Science Foundation/ ; 2308460//National Science Foundation/ ; R01-TW011493//NIH-NSF-NIFA Ecology and Evolution of Infectious Diseases program/ ; 2022721//United States-Israel Binational Science Foundation/ ; Provost's Collaboratory Award//Duke University/ ; RGY0064/2022//Human Frontier Science Program/ ; //Duke Lemur Center/ ; }, mesh = {Animals ; Rats/microbiology ; Madagascar ; *Microbiota ; *Host Microbial Interactions ; }, abstract = {Microbial communities are fundamental to host health, yet their assembly dynamics under environmental change remain poorly understood. We analysed individual-level host-microbe networks in the non-native wild black rats (Rattus rattus) across a land-use gradient in Madagascar. By applying a moving prevalence threshold, we distinguished between core and non-core microbes and compared the assembly drivers shaping their network structures. Non-core microbes formed fragmented, modular networks shaped mainly by heterogeneous selection, reflecting environmental filtering. In contrast, core microbes exhibited stable, less modular networks driven primarily by stochastic ecological drift. These distinct assembly processes persisted across thresholds, highlighting fundamental differences in microbial structuring. Land-use change significantly influenced the modular structure of non-core microbes but had minimal effects on core microbes, demonstrating the differential sensitivity of microbial groups to environmental variation. This study advances our understanding of host-microbe interactions and provides a framework for assessing microbiome assembly under anthropogenic change.}, }
@article {pmid41236145, year = {2025}, author = {Maillard, F and Klinghammer, F and Beatty, BH and Zou, H and Lara, E and Hammer, EC and Tunlid, A and Kennedy, PG}, title = {Keystone protist suppression triggers mesopredator release and biotic homogenization in complex soil microbial communities.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf253}, pmid = {41236145}, issn = {1751-7370}, abstract = {The keystone species concept holds that certain members of an ecological community, despite their low abundance, exert disproportionately large effects on species diversity and composition. In microbial ecology, experimental validation of this concept has been limited because targeted removal of individual species remains technically challenging. Here, we developed a procedure to test the keystone species concept within a soil microbial food web by selectively suppressing a protist predator at the microscale via UV-induced phototoxicity in a microfluidic soil chip system. We targeted a hypotrich ciliate (subclass Hypotrichia), and combined microscopy with high-throughput amplicon sequencing of microbial taxonomic markers to assess, across multiple trophic levels, how its suppression affected microbial community abundance, diversity, and composition. Over the 20-day incubation, the chip system supported complex communities of bacteria, fungi, and protists. Following Hypotrichia suppression, two distinct ecological responses were observed: first, an increase in the relative abundance of flagellates, consistent with mesopredator release, accompanied by a significant rise in overall protist diversity; second, a convergence in protist community composition, indicative of biotic homogenization. Bacterial community abundance, richness, and composition remained unchanged, likely due to compensatory predation from a relative increase in bacterivorous flagellates. In contrast, fungal diversity decreased, presumably because the altered protist community favored facultative fungal consumers. Collectively, these findings provide direct experimental evidence that low abundance microbial predators can function as keystone species, modulating predator community composition and diversity, and exerting cascading effects on lower trophic levels within microbial brown food webs.}, }
@article {pmid41234770, year = {2025}, author = {Wang, IC and Swanson, JL and Waters, JL and Kochukov, MY and Buffington, SA and Dooling, SW and Arenkiel, BR and Costa-Mattioli, M}, title = {Alteration of gut microbial ecology by the direct activation of the brain: Inverse gut-microbiome-brain dynamics.}, journal = {iScience}, volume = {28}, number = {11}, pages = {113709}, pmid = {41234770}, issn = {2589-0042}, abstract = {The gut-microbiome-brain axis is a bidirectional communication system influencing host physiology and overall fitness. While "bottom-up" effects-where gut microbes influence brain function and behavior-are well established, direct evidence for "top-down" modulation-where the brain shapes the gut microbial ecology-remains elusive. Here, we show that the selective expression of the bacterial ion channel mNaChBac in glutamatergic lateral habenula (LHb) neurons increases their bursting activity and leads to endophentypes associated with depression. Importantly, this chronic activation leads to changes in the gut microbiome composition over time, as reflected by shifts in alpha-diversity and alterations in specific microbial taxa. These findings provide direct evidence that the persistent activation of the brain acts as a selective pressure that affects the stability and diversity of the gut microbiome, providing a new dimension by which gut-microbiome-brain interactions may cooperate to modulate host physiology and health.}, }
@article {pmid41233937, year = {2025}, author = {Zhang, P and Roque, B and Romero, P and Shapiro, N and Eloe-Fadrosh, E and Kebreab, E and Diamond, S and Hess, M}, title = {Red seaweed supplementation suppresses methanogenesis in the rumen, revealing potentially advantageous traits among hydrogenotrophic bacteria.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {231}, pmid = {41233937}, issn = {2049-2618}, mesh = {Animals ; *Rumen/microbiology/metabolism ; *Methane/metabolism/biosynthesis ; Cattle ; *Seaweed ; *Dietary Supplements ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; Animal Feed/analysis ; *Gastrointestinal Microbiome ; Fermentation ; Metagenome ; Metagenomics ; Hydrogen/metabolism ; }, abstract = {BACKGROUND: Macroalgae belonging to the genus Asparagopsis have shown to reduce methane (CH4) production during rumen fermentation, while increasing feed efficiency when added to the feed of cattle. However, little is known about how the rumen microbiome responds to Asparagopsis supplementation, and how changes in the microbiome may contribute to changes in rumen function and host phenotype. Here, we generated and analyzed metagenomic and metatranscriptomic data from the rumen microbiome from cows receiving (treatment) and not receiving (control) an Asparagopsis armata supplemented diet.<br><br>RESULTS: Using a combination of metatranscriptome and metagenome analysis, we found that reduction of CH4 emission from animals receiving A. armata was coupled to a significant reduction in the transcription of methanogenesis pathways. Additionally, a significant decrease in the transcription of genes for carbon catabolism and a reorganization of carbon catabolic gene expression occurred at the species level within the rumen microbiome of animals that received red seaweed with their diet. Increased H2 production, a consequence of methanogenesis suppression, was coupled to a significant increase in the transcription of hydrogenases that mediate hydrogenotrophic metabolism in the treatment group. Metatranscriptome analysis identified a single metagenome assembled genome (MAG) of a Duodenibacillus sp., a hitherto uncultured hydrogenotrophic bacterial species, as the dominant driver of this transcriptional change.<br><br>CONCLUSIONS: Comparative genomic analysis between the Duodenibacillus sp. and other hydrogenotrophic rumen organisms revealed metabolic traits that may provide Duodenibacillus sp. with a competitive advantage in H2 scavenging. Our findings provide an initial understanding of how the rumen microbiome responds to a promising CH4 reducing feed additive and serve as a model for alternative stable rumen microbiome states that produce less methane and increase animal productivity. Ultimately, insights from the work presented here might enable the development of advanced microbiome-based strategies to reduce enteric methane production.}, }
@article {pmid41233936, year = {2025}, author = {Modolon, F and N Garritano, A and J Hill, L and Duarte, G and Bendia, A and de Moura, R and Pellizari, V and Thomas, T and Peixoto, RS}, title = {Putative promiscuous symbionts in deep-sea corals and crinoids may contribute to nitrogen cycling.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {234}, pmid = {41233936}, issn = {2049-2618}, support = {141954/2019-1//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; ANP 21005-4//Shell, Brazil/ ; BAS/1/1095-01-01 and FCC/1/1976-40-01//KAUST/ ; }, mesh = {*Anthozoa/microbiology ; Animals ; *Symbiosis ; *Nitrogen Cycle ; Metagenomics/methods ; Microbiota ; Brazil ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; In Situ Hybridization, Fluorescence ; }, abstract = {BACKGROUND: Crinoids (feather stars) are frequently found in association with corals, yet the physiological and microbial interactions between these organisms remain poorly understood. Both corals and crinoids host symbiotic microorganisms, but the functional roles of these symbionts, particularly in deep-sea environments, are largely unexplored. This study characterizes the microbiomes of the deep-sea corals Desmophyllum pertusum and Solenosmilia variabilis and their associated crinoid Koehlermetra sp. (Thalassometridae) from the Campos Basin, Brazil, to investigate potential cross-host microbial interactions and their ecological implications. We used multiple approaches for this investigation, including amplicon sequencing surveys, genome-resolved metagenomics, and fluorescence in situ hybridization.<br><br>RESULTS: We found that the same endosymbiotic members of the families Endozoicomonadaceae and Nitrosopumilaceae inhabit both corals and the crinoids, suggesting promiscuity in host-symbiont relationships. Metagenomic analysis revealed a novel and dominant Endozoicomonas species (E. promiscua sp. nov.), whose genome encodes pathways for dissimilatory nitrate reduction to ammonia (DNRA). This metabolic capability could provide a substrate for ammonia-oxidizing archaea (Nitrosopumilaceae), indicating a potential cross-host nitrogen-cycling network. Shared microbial taxa between corals and crinoids further support the hypothesis of symbiont promiscuity, where metabolic redundancy may facilitate colonization across species.<br><br>CONCLUSIONS: Our findings suggest that nitrogen cycling plays a key role in structuring microbial symbioses in deep-sea coral-crinoid holobionts. The promiscuous distribution of symbionts across hosts implies that metabolic interactions, such as DNRA-driven ammonia provisioning, could underpin resilience in nutrient-limited environments. This study highlights the importance of microbial versatility in deep-sea ecosystems and provides new insights into how cross-host symbiosis may contribute to biogeochemical cycling in the ocean. Video Abstract.}, }
@article {pmid41233829, year = {2025}, author = {Sieders, M and Candry, P and El Aidy, S}, title = {Hydrogel-based experimental models of the gastrointestinal tract.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {233}, pmid = {41233829}, issn = {2049-2618}, abstract = {The gut microbiome plays a pivotal role in human health, yet its complexity has long eluded detailed study under physiologically relevant conditions. Hydrogel-based models are revolutionizing microbiome research by bridging the gap between traditional in vitro systems and the complexity of in vivo environments. These advanced systems replicate key physical and biochemical features of the gastrointestinal tract, offering unprecedented opportunities to study microbial behavior, adaptation, and interactions within three-dimensional, tunable architectures. Unlike suspension cultures, hydrogels provide porous, mucosa-like environments that enable the cultivation of mucosa-associated microbes, co-culturing with human cells, and mimicking healthy and disease-related states. This review explores the transformative potential of hydrogel matrices in unveiling the spatial organization, nutrient gradients, and community communication that define microbial ecosystems. By integrating the benefits of in vitro and in vivo models, hydrogel-based platforms promise to accelerate discoveries in microbiome science, with far-reaching implications for understanding human health and developing targeted therapeutics. Video Abstract.}, }
@article {pmid41231796, year = {2025}, author = {Baral, T and Maile, A and Adimurthy, NH and Saravu, K and Kudru, CU and Singh, J and Mukhopadhyay, C and Rao, M and Manu, MK and Sekhar Miraj, S}, title = {Exploring gut microbiota and its predicted functions in pulmonary tuberculosis: A multi-regional study using public 16S datasets.}, journal = {PloS one}, volume = {20}, number = {11}, pages = {e0336337}, doi = {10.1371/journal.pone.0336337}, pmid = {41231796}, issn = {1932-6203}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics/drug effects ; *Tuberculosis, Pulmonary/microbiology/drug therapy ; Phylogeny ; *RNA, Ribosomal, 16S/genetics ; Antitubercular Agents/therapeutic use ; Male ; Female ; Mycobacterium tuberculosis/genetics ; Middle Aged ; Adult ; }, abstract = {BACKGROUND: Pulmonary tuberculosis, caused by the bacillus Mycobacterium tuberculosis, remains a major global health challenge, particularly in developing countries. In this study, we analyzed publicly available 16S amplicon sequencing datasets from four geographical locations using a single workflow.<br><br>METHODS: We employed Quantitative Insights Into Microbial Ecology v.2 for microbial diversity analysis and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States v.2 for functional pathway predictions of the gut microbiota in patients with PTB and antitubercular therapy.<br><br>RESULTS: Our analysis revealed statistically significant alpha diversity differences in West Africa with decreased microbial diversity in pulmonary tuberculosis patients after two months of antitubercular therapy. Additionally, there were no statistically significant differences observed in pairwise comparisons within the same location or in the aggregate beta diversity of the datasets. The predicted microbial metabolic pathways related to vitamin biosynthesis, amino acid synthesis, and energy production were depleted in pulmonary tuberculosis patients following antitubercular therapy.<br><br>CONCLUSIONS: The observed alterations of gut microbial diversity and predicted functional profile underscores the influence of antitubercular therapy on gut health, suggesting that longer treatment durations may aggravate these alterations in gut microbial function. Moreover, geographical location exerts a more significant impact on microbial diversity than the disease state in a specific location, highlighting the potential for precision medicine to tailor interventions based on individual or regional microbiome characteristics.}, }
@article {pmid41230548, year = {2025}, author = {Mukherjee, A and Tan, BH and Swarup, S}, title = {In Silico Prediction and In Vitro Validation of Bacterial Interactions in the Plant Rhizosphere Using a Synthetic Bacterial Community.}, journal = {Bio-protocol}, volume = {15}, number = {21}, pages = {e5496}, pmid = {41230548}, issn = {2331-8325}, abstract = {The rhizosphere, a 2-10 mm region surrounding the root surface, is colonized by numerous microorganisms, known as the rhizosphere microbiome. These microorganisms interact with each other, leading to emergent properties that affect plant fitness. Mapping these interactions is crucial to understanding microbial ecology in the rhizosphere and predicting and manipulating plant health. However, current methods do not capture the chemistry of the rhizosphere environment, and common plant-microbe interaction study setups do not map bacterial interactions in this niche. Additionally, studying bacterial interactions may require the creation of transgenic bacterial lines with markers for antibiotic resistance/fluorescent probes and even isotope labeling. Here, we describe a protocol for both in silico prediction and in vitro validation of bacterial interactions that closely recapitulate the major chemical constituents of the rhizosphere environment using a widely used Murashige &amp; Skoog (MS)-based gnotobiotic plant growth system. We use the auto-fluorescent Pseudomonas, abundantly found in the rhizosphere, to estimate their interactions with other strains, thereby avoiding the need for the creation of transgenic bacterial strains. By combining artificial root exudate medium, plant cultivation medium, and a synthetic bacterial community (SynCom), we first simulate their interactions using genome-scale metabolic models (GSMMs) and then validate these interactions in vitro, using growth assays. We show that the GSMM-predicted interaction scores correlate moderately, yet significantly, with their in vitro validation. Given the complexity of interactions among rhizosphere microbiome members, this reproducible and efficient protocol will allow confident mapping of interactions of fluorescent Pseudomonas with other bacterial strains within the rhizosphere microbiome. Key features • This method builds upon the widely used MS-based gnotobiotic system for growing plants and a synthetic bacterial community (SynCom) for plant-microbe interaction studies. • It considers the chemical composition of plant growth media (MS) and root exudates to map bacterial interactions. • It provides a method to both predict and validate interactions of fluorescent Pseudomonas with other strains within a SynCom. • This method is scalable for any bacterial pair with distinguishing markers (e.g., fluorescence, antibiotic resistance).}, }
@article {pmid41229186, year = {2025}, author = {Park, JW and Park, JS and Kook, PR and Cho, YH and Park, SK and Lee, JH and Kang, SK and Kim, SW and Kim, SR}, title = {Impact of Artificial Diet Versus Mulberry Leaves on Silkworm Growth, Nutrient Composition, and Gut Microbiota.}, journal = {Archives of insect biochemistry and physiology}, volume = {120}, number = {3}, pages = {e70113}, doi = {10.1002/arch.70113}, pmid = {41229186}, issn = {1520-6327}, support = {PJ01721401.//This study was supported by the 2025 RDA Fellowship Program of the National Institute of Agricultural Science./ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Morus/chemistry ; *Bombyx/growth &amp; development/microbiology/metabolism ; Plant Leaves/chemistry ; Larva/growth &amp; development/microbiology ; *Diet ; *Animal Feed/analysis ; Nutrients/analysis ; RNA, Ribosomal, 16S ; }, abstract = {Silkworms (Bombyx Mori) are traditionally reared on mulberry leaves; however, artificial diets have been developed to enable year-round rearing and automation. The physiological performance and cocoon yield of silkworms fed artificial diets remain inferior to those reared on mulberry leaves. We compared growth and nutrient composition in larvae reared on mulberry leaves (ML) and antibiotic-free artificial diet (ADS), and profiled gut microbiota in ML, ADS, and antibiotic-supplemented artificial diet (ADSA) to assess dietary effects on host physiology and microbial ecology. Proximate analysis revealed that protein accumulation was greater in ML-fed larvae, while ADS-fed larvae showed relatively higher fat content at the late fifth instar. Amino acid profiling showed consistently higher silk-related residues (Gly, Ala, Ser) and the derived Silk Amino Acid Index in ML-fed larvae, indicating enhanced fibroin synthesis potential. Microbiome analysis using 16S rRNA amplicon sequencing demonstrated dominance of Enterococcus mundtii in ADS groups, resulting in reduced alpha diversity and uneven community structure. In contrast, ML-fed larvae harbored diverse taxa, including Methylorubrum and Methylobacterium, while ADSA groups exhibited intermediate profiles with occasional dominance of Bacillus cereus. These findings highlight that artificial diet alters host nutrient metabolism and drives dysbiosis of gut microbiota, underscoring the need for optimized formulations and microbiome-stabilizing strategies, such as probiotics or prebiotics.}, }
@article {pmid41228488, year = {2025}, author = {Yin, C and Liu, X and Fang, W and Meng, Q and Feng, X and Zhang, W and Dang, G and Zhong, R and Chen, L and Wang, Z and Zhang, H}, title = {Hyocholic Acid Species as the Key Modulator for Cecal Epithelial Homeostasis in Low-Birth-Weight Piglets.}, journal = {Nutrients}, volume = {17}, number = {21}, pages = {}, doi = {10.3390/nu17213415}, pmid = {41228488}, issn = {2072-6643}, support = {32202709//National Natural Science Foundation of China/ ; U22A20515//National Natural Science Foundation of China/ ; Y2023QC09//Youth Innovation of Chinese Academy of Agricultural Sciences/ ; }, mesh = {Animals ; *Cecum/microbiology/drug effects/metabolism ; Swine ; *Homeostasis/drug effects ; Gastrointestinal Microbiome/drug effects ; *Intestinal Mucosa/metabolism/drug effects ; Bile Acids and Salts ; Animals, Newborn ; Birth Weight ; Dietary Supplements ; *Cholic Acids/pharmacology ; Dysbiosis ; }, abstract = {Background: Low birth weight (LBW) is correlated with gut microbiota dysbiosis and intestinal barrier function disruption, increasing susceptibility to enteric diseases. These alterations underscore the critical need to identify key regulators of gut homeostasis, among which bile acids are increasingly recognized as pivotal for barrier integrity, microbial ecology, and host metabolism. Methods: Eight pairs of LBW (the initial BW was 0.850 ± 0.053 kg) and normal-birth-weight (NBW; 1.488 ± 0.083 kg) piglets were compared to evaluate cecal morphology and bile acid profiles. Subsequently, sixteen LBW piglets and eight NBW piglets were allocated into three groups: NBW (1.563 ± 0.052 kg), LBW control (LBW-CON; 0.950 ± 0.120 kg), and LBW with bile acid supplementation (LBW-bile powder; 0.925 ± 0.116 kg). Piglets in the LBW-bile powder group received 25 mg/kg BW of bile powder (hyodeoxycholic acid-enriched) by daily oral gavage for 14 days. Results: LBW piglets exhibited retarded cecal development and lower abundance of hyocholic acid species (p = 0.006). Importantly, bile powder supplementation significantly improved cecal length (p = 0.009) and mucosal thickness (p = 0.020) compared with LBW-CON piglets. Microbial analysis showed that the microbial dysbiosis index was restored to near-normal levels. Transcriptomic analysis revealed impaired extracellular matrix structure and mucus secretion in LBW piglets. Notably, bile powder supplementation markedly upregulated the protein expression of WNT8B (p < 0.001) and the bile acid receptors (i.e., GPBAR1 and FXR), alongside enhanced tight junctions and the goblet cell marker mucin-2 expression (p < 0.05). Conclusions: These findings suggest that specific bile acid supplementation improves gut barrier function and partially supports cecal development in LBW piglets.}, }
@article {pmid41227744, year = {2025}, author = {Fu, Y and Wang, Y and Zhang, J and Ren, J and Fang, B}, title = {Prebiotic Structural Diversity Shapes Gut Microbial Diversity, Community Composition, and Metabolic Activity In Vitro.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {21}, pages = {}, pmid = {41227744}, issn = {2304-8158}, support = {81770558//National Natural Science Foundation of China/ ; 3502Z20149031//Xiamen Joint Projects for Major Diseases/ ; 22278343//National Natural Science Foundation of China/ ; }, abstract = {Prebiotics are selectively utilized substrates that modulate gut microbiota and host health, yet different prebiotic structures may elicit distinct ecological and metabolic responses. In this study, we investigated the effects of five structurally diverse prebiotics-isomaltooligosaccharides (IMO), arabinogalactans (AG), pectin, inulin, and stachyose-on human gut microbiota via a 24 h in vitro anaerobic culture with healthy donors' gut microbiota. Microbial community dynamics were profiled by 16S rRNA gene sequencing, and short-chain fatty acids (SCFAs) production was analyzed. All treatments resulted in decreased α-diversity compared with baseline, with pectin most effectively preserving microbial richness and evenness, whereas stachyose led to the greatest reduction. Community composition and functional profiles shifted in a substrate-specific manner, with AG promoting Bacteroidaceae, IMO stimulating Lachnospiraceae and Faecalibacterium, and pectin supporting balanced microbial structures and SCFA production. Pectin, IMO, and inulin enhanced butyrate levels, whereas AG and pectin promoted propionate formation. These findings demonstrate that prebiotic structural differences strongly shape gut microbial ecology and metabolism, providing a mechanistic basis for rationally selecting and combining prebiotics to beneficially modulate the gut microbiota.}, }
@article {pmid41227660, year = {2025}, author = {Alfonzo, A and Gaglio, R and Alongi, D and Franciosi, E and Perricone, G and Garofalo, G and Prestianni, R and Naselli, V and Pirrone, A and Francesca, N and Moschetti, G and Settanni, L}, title = {Polyphasic Characterisation of Microbiota Associated with Sant'Agostino Table Olives Flavoured with Foeniculum vulgare.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {21}, pages = {}, pmid = {41227660}, issn = {2304-8158}, support = {B7521002300001//Ministry of University and Research in Italy/ ; B73C23000060001//European Union/ ; }, abstract = {Sant'Agostino green table olives, traditionally processed in Apulia and flavoured with Foeniculum vulgare, represent a niche product whose microbial ecology remains largely unexplored. This study aimed to characterise the microbiota of the final product (both brine and fruit) after six months of storage with wild fennel. Four production batches were analysed using a combined culture-dependent and culture-independent approach. Microbiological counts revealed variable levels of aerobic mesophilic microorganisms, yeasts, lactic acid bacteria (LAB), and staphylococci, with yeasts and LAB being predominant. Ten LAB strains were identified, including Enterococcus faecium, Leuconostoc mesenteroides subsp. jonggajibkimchii, Leuconostoc mesenteroides subsp. cremoris, Leuconostoc pseudomesenteroides, Lactiplantibacillus plantarum, and Lactiplantibacillus pentosus. Yeast isolates belonged to Candida tropicalis, Torulaspora delbrueckii, and Saccharomyces cerevisiae. Amplicon sequencing (MiSeq Illumina) revealed distinct bacterial profiles between fruit and brine samples, with taxa from Actinobacteria, Bacteroidetes, Enterococcus, Lactobacillus, Leuconostoc, Alphaproteobacteria, Enterobacteriaceae, and other Gammaproteobacteria. Enterococcus and Leuconostoc were consistently detected, while Lactobacillus sensu lato appeared only in one fruit and one brine sample. These findings provide new insights into the microbial diversity of Sant'Agostino olives and contribute to the understanding of their fermentation ecology and potential for quality and safety enhancement.}, }
@article {pmid41227479, year = {2025}, author = {Chessari, G and Tumino, S and Castiglioni, B and Biscarini, F and Bordonaro, S and Avondo, M and Marletta, D and Cremonesi, P}, title = {Girgentana's Goat Milk Microbiota Investigated in an Organic Farm During Dry Season.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {21}, pages = {}, pmid = {41227479}, issn = {2076-2615}, support = {Agritech National Research Center and received funding from the European Union Next-GenerationEU (National Recovery and Resilience Plan (NRRP), Mission 4, Component 2, Investment 1.4-D.D. 1032 17/06/2022, CN00000022//Agritech National Research/ ; }, abstract = {Milk microbiota is a complex microbial ecosystem with implications for product quality, safety, and animal health. However, limited data exist on goat milk microbiota, particularly in local breeds. This study provides the first detailed characterization of the milk microbiota of Girgentana goats, a resilient Sicilian breed valued for high-quality dairy products. Illumina NovaSeq sequencing was used to analyze the 16S rRNA V3-V4 regions of 44 individual and 3 bulk milk samples. Briefly, 16S rRNA-gene sequencing produced a total of 8,135,944 high-quality reads, identifying 1134 operational taxonomic units (OTUs) across all individual samples. On average, each sample showed 864 OTUs with counts > 0. Alpha diversity metrics, based on richness estimators (Chao1: 948.1; ACE: 936.3) and diversity indices (Shannon: 4.06; Simpson: 0.95; Fisher: 118.5), indicated a heterogeneous community with both common and low-abundance taxa. Firmicutes (51%) and Proteobacteria (27%) were the predominant phyla, with Lactobacillaceae (54%) and Bifidobacteriaceae (22%) dominating at the family level. Notably, farm bulk milk profiles closely mirrored individual samples. These results establish a milk microbiota baseline for the Girgentana breed and offer valuable insights into microbial ecology in traditional dairy systems, supporting future comparisons across breeds and farming practices.}, }
@article {pmid41222858, year = {2025}, author = {Dvořák, P and Skoupý, S and Stanojković, A and Johansen, JR and Villanueva, C and Jung, P and Briegel-Williams, L and Laughinghouse, HD and Lefler, FW and Berthold, DE and Kaštovský, J and Hurley, AC and Casamatta, DA}, title = {A hitchhiker's guide to modern, practical cyanobacterial taxonomy.}, journal = {Journal of phycology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jpy.70102}, pmid = {41222858}, issn = {1529-8817}, support = {23-06507S//Grant Agency of the Czech Republic/ ; }, abstract = {There has been an explosion of new Cyanobacterial taxa described within the last two decades. Cyanobacteria exhibit incredible ecological versatility and morphological variability, and thousands of species have already been described using "traditional" approaches (e.g., morphological features). However, DNA sequencing and other molecular tools have provided extensive evidence that the diversity of cyanobacteria is not necessarily congruent with morphology, as many morphological genera (e.g., Phormidium, Leptolyngbya, and Nostoc) are polyphyletic, and species within the genera are often morphologically indistinguishable, thus cryptic. Further confounding systematic assessments, newly erected taxa are often based on a single strain with one or two 16S rRNA gene sequences, may have incomplete formal descriptions, and lack indication of the employed species concepts. Here we have proposed a set of guidelines for cyanobacterial taxonomists. We have focused on the whole process of erecting new taxa: sampling, sequencing (including genomes), phylogenetic inference, phenotype characterization, species concepts, formal descriptions, and codes of nomenclature. Our hope is that these guidelines will help with the laborious but ever-rewarding task of identifying and describing the taxa within the world of cyanobacteria.}, }
@article {pmid41221507, year = {2025}, author = {Clinton, CK and Jackson, FLC}, title = {Persistent human-associated microbial signatures in burial soils from the 17th and 18th century New York African burial ground.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf181}, pmid = {41221507}, issn = {2730-6151}, abstract = {Understanding the long-term persistence of human-associated microbial signatures in burial soils offers a untapped insights into historical human health, decomposition, and ecological transformation. This study investigates whether centuries-old burial soils retain distinguishable microbial evidence of human decomposition using 16S rRNA gene sequencing on 81 samples from the New York African Burial Ground (NYABG), a 17th and 18th century cemetery for free and enslaved Africans. Comparative analyses against six control soils from nearby urban parks were conducted using QIIME2, ALDEx2, and ANCOM. Burial soils exhibited significantly greater alpha diversity (Faith's PD, Shannon, observed ASVs; P < .01) and distinct beta diversity patterns (Bray-Curtis, UniFrac; PERMANOVA P = .001). Enrichment of Firmicutes, Actinobacteriota, and gut-associated genera such as Bacillus and Ruminococcus characterized burial soils, whereas oligotrophic taxa dominated controls. Tentative identifications of human-associated pathogenic genera (e.g. Fusobacterium periodonticum, Prevotella pleuritidis) were observed exclusively in burial soils, suggesting their origin from the interred individuals but requiring further validation. These findings demonstrate that soil microbiomes reflect host-associated microbial communities long after decomposition, providing a scalable, nondestructive approach for reconstructing ancient microbial communities and host-associated health signatures. This work establishes the NYABG burial soil microbiome as a valuable model for microbial archaeology and introduces a replicable framework for integrating environmental microbiology, bioarchaeology, and historical epidemiology through the lens of postmortem microbial ecology.}, }
@article {pmid41220415, year = {2025}, author = {Moseeb, HM and Aizaz, MM and Aiza, K and Hafsa, TH and Sania, M and Kamran, Z and Shamama, ZT and Usama, AM and Maroof, QP and Feroze, F and Ahmed, R and Ammara, N and Mahima, G}, title = {From obesity to cancer: Gut microbiome mechanisms, biomarkers, and U.S. public health strategies.}, journal = {Oncoscience}, volume = {12}, number = {}, pages = {175-188}, pmid = {41220415}, issn = {2331-4737}, abstract = {BACKGROUND: Obesity, metabolic syndrome, and colorectal cancer (CRC) remain major public health challenges in the United States, collectively driving substantial morbidity, mortality, and economic burden. Beyond diet and genetics, the gut microbiome has emerged as a pivotal determinant of host metabolism, immunity, and carcinogenesis, influenced by both environmental and behavioral factors.<br><br>OBJECTIVE: This review synthesizes current evidence linking gut microbial dysbiosis to obesity, metabolic syndrome, and CRC, emphasizing mechanistic pathways, environmental modifiers, and translational opportunities relevant to U.S. public health and precision medicine.<br><br>METHODS: Comprehensive searches of PubMed and Scopus (2000-2025) identified large epidemiologic studies, mechanistic experiments, and clinical trials, prioritizing research from U.S. populations and nationally representative databases including NHANES, SEER, and the Nurses' Health Study.<br><br>RESULTS: Microbial alterations such as enrichment of Fusobacterium nucleatum, enterotoxigenic Bacteroides fragilis, and colibactin-producing Escherichia coli contribute to CRC initiation and progression. In obesity and metabolic syndrome, shifts in Firmicutes-to-Bacteroidetes ratios, altered short-chain fatty acid metabolism, and endotoxin-mediated inflammation disrupt metabolic homeostasis. Environmental and lifestyle exposures, including air pollutants, smoking, and Westernized diets, modulate microbial ecology across the aerodigestive tract, affecting disease susceptibility. The emerging discipline of Molecular Pathological Epidemiology (MPE) integrates lifestyle, microbiome, and biomarker data to elucidate exposure-outcome relationships, enabling personalized prevention and therapeutic strategies.<br><br>CONCLUSIONS: The gut microbiome functions as both a biomarker and therapeutic target across metabolic and neoplastic diseases. Integrating microbiome science with environmental epidemiology and MPE frameworks offers transformative potential for precision prevention and equitable public health strategies in the U.S.}, }
@article {pmid41219483, year = {2025}, author = {Han, J and Fang, Q and Hao, Y and Huang, X and Kong, F and Chen, H and Liu, Y}, title = {Diversity of Yeast and Drosophila Species Associated with Grape Sour Rot in China.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {121}, pmid = {41219483}, issn = {1432-184X}, support = {2022E02073//Special Regional Collaborative Innovation Project of Xinjiang Uygur Autonomous Region (Science and Technology Aid Xinjiang Program)/ ; 32272550//National Natural Science Foundation of China/ ; CARS-29-bc-5//Agriculture Research System of China/ ; 202305AF150129//Expert Workstation Project in Yunnan Province/ ; }, abstract = {Sour rot is a complex disease of grapes, primarily caused by the synergistic effects of yeast and Drosophila species, leading to fruit decay, poor quality, and significant economic losses. The lack of information on species distribution and diversity of these organisms in China limits the efficacy of control strategies. In this study, we sequenced the 26S rRNA D1/D2 region in yeasts and the COI region in Drosophila. Nine yeast genera were identified. Hanseniaspora spp. (45.76% of total) were the most abundant, followed by Starmerella spp. (23.62%) and Saccharomyces spp. (17.34%). At the species level, 14 yeast species were identified. Starmerella bacillaris (23.62%), Saccharomyces cerevisiae (17.34%), H. opuntiae (17.34%), and H. uvarum (15.13%) predominated. Of the five species of Drosophila present, Drosophila melanogaster (63.16%) was the dominant species. This study is the first to characterize the diversity of yeasts and Drosophila across major grape-producing regions in China. The findings provide a scientific foundation for elucidating the key drivers of sour rot and designing targeted control strategies.}, }
@article {pmid41219454, year = {2025}, author = {Zhang, C and Zhang, X and Wang, F and Li, G and Ding, J and Cao, Y and Wang, H and Wu, S and Shang, X and Wei, K and Yang, L}, title = {Integrated Multi-Omics Analysis Reveals Microbial Community Restructuring and its Role in Key Carbohydrate Metabolic Pathways During Tobacco Leaf Curing.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {122}, pmid = {41219454}, issn = {1432-184X}, support = {1102022202016 / 110202201019 (LS-03)//Science and Technology Project of China Tobacco General Corporation/ ; QKHJC-ZK [2022] YB288//Science and Technology Project of Guizhou Provincial Department of Science and Technology/ ; 2022XM17//Science and Technology Project of Guizhou Tobacco Industry Technology Center/ ; 202111/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Plant Leaves/microbiology/metabolism/chemistry ; *Nicotiana/microbiology/metabolism/chemistry ; *Microbiota ; *Fungi/metabolism/genetics/classification/isolation &amp; purification ; *Carbohydrate Metabolism ; *Bacteria/metabolism/classification/genetics/isolation &amp; purification ; Metabolic Networks and Pathways ; Temperature ; Metabolomics ; Multiomics ; }, abstract = {Microorganisms play a significant role in improving the flavor and quality of plant products. Analyzing how tobacco processing affects the microbial community structure is essential. Understanding the synergistic mechanisms of microorganisms during this process can help optimize the flavor and quality of plant products. In this study, samples were collected from four processing stages (T1: fresh leaves, T2: 42 °C, T3: 54 °C, T4: 68 °C), and metabolite and Phylloplane microbial data of tobacco leaves were generated. A comprehensive multi-omics analysis was conducted. The study shows that the increase in temperature and the decrease in humidity during the processing lead to the reorganization of the microbial community. Brevibacterium, Staphylococcus, Aspergillus, and Ganoderma were identified as core biomarkers. Bacteria dominate in the initial degradation of starch, while fungi promote the accumulation of soluble sugars through the transformation of intermediate products. This study deepens our understanding of the role of microorganisms and their carbohydrate metabolism in the tobacco leaf processing process and proposes a new strategy for constructing regulatory models by integrating multi-omics.}, }
@article {pmid41218435, year = {2025}, author = {Ren, J and Wang, J and Dong, Y and Xiao, L and Wang, L and Ji, J and Liu, Y}, title = {Microbial community dynamics and its relationship with biogeochemical processes under geochemical perturbations.}, journal = {Water research}, volume = {289}, number = {Pt B}, pages = {124889}, doi = {10.1016/j.watres.2025.124889}, pmid = {41218435}, issn = {1879-2448}, abstract = {Environmental microbial communities are crucial in regulating ecosystem functions and are increasingly affected by human-induced geochemical perturbations. While microbial communities are known to shift under such perturbations, the explicit link between these shifts and corresponding biogeochemical processes remains unclear. Here, we conducted time-series sediment incubation experiments under elevated nitrate conditions, combining 16S rRNA gene sequencing, qPCR, and metagenomics to track microbial taxonomic and functional dynamics. We further developed a gene-centric, process-based biogeochemical model to quantitatively connect microbial community structure to geochemical reaction kinetics. Our results revealed that functional metagenomics provided a broader view of functional diversity than qPCR and enabled detailed analysis of gene co-occurrence. Through modeling, we uncover a quantitative coupling between functional gene abundance and reaction rates under geochemical perturbations. However, this relationship can be obscured by redox-driven abiotic processes affected by perturbations and the nonlinear nature of enzyme-mediated reactions, making it difficult to resolve using standard statistical approaches. Together, these findings improve our understanding of the linkage between microbial function and biogeochemical processes, and underscore the value of gene-centric, process-based models for predicting ecosystem behavior under geochemical stress.}, }
@article {pmid41217184, year = {2025}, author = {Creagh, JW and Rolfsmeier, M and Evans, KJ and Bizarria, R and Reetz, DC and Badigian, TJ and Fredericks, LR and Hasenoehrl, AM and Brown, AP and Graves, BM and Alexander, CK and Rodrigues, A and Stoffregen, EP and Patel, JS and Ytreberg, FM and Rowley, PA}, title = {The Saccharomyces killer toxin K62 is a protein of the aerolysin family.}, journal = {mBio}, volume = {}, number = {}, pages = {e0142525}, doi = {10.1128/mbio.01425-25}, pmid = {41217184}, issn = {2150-7511}, abstract = {UNLABELLED: K62 is an antifungal killer toxin produced by Saccharomyces paradoxus, encoded by a double-stranded RNA satellite. The toxin exhibits a unique antifungal activity but lacks sequence homology to other killer toxins, and its antifungal mechanism of action remains unknown. To understand the function of K62, its tertiary structure was predicted using AlphaFold, followed by molecular dynamics simulations to create high-confidence molecular models. These analyses revealed that K62 monomers closely resemble the five-beta-strand domain found in pore-forming aerolysin toxins. Models of K62 oligomers yielded a circular complex and beta-barrel with structural and biochemical similarities to aerolysin-family pre-pores and pores. Consistent with the formation of aerolysin-like pores, recombinant K62 assembled into membrane-associated high molecular weight oligomers (>250 kDa) that were heat- and detergent-resistant. K62 has more than 1,000 uncharacterized sequence homologs, which were mostly found in fungi of the Ascomycota, as well as in the Chytridiomycota, Basidiomycota, plants, and bacteria, with evidence of extensive horizontal gene transfer. Homologs were also identified in pathogenic fungal species, including human and plant pathogens from the Candida and Fusarium genera, but unlike aerolysins, K62 appeared to be non-toxic to higher eukaryotes. K62 is the first aerolysin family protein discovered in yeasts, revealing a likely role in fungal niche competition and establishing an entirely new, expansive family of aerolysin-like proteins.<br><br>IMPORTANCE: Pore-forming toxins are potent biological weapons used across nature, from virulence factors to immune defense proteins. This study identifies K62, a little-known antifungal toxin produced by a wild yeast, as a structural and functional relative of the aerolysin family, which is well-known for forming damaging pores in cell membranes. Using structure prediction, molecular simulations, and biochemical analysis, we show that K62 assembles into large, stable pore-like complexes. Remarkably, K62 is just one member of a large and previously unrecognized family of similar toxin-like proteins found in fungi, plants, and bacteria, including pathogens that affect humans and crops. These findings uncover an unexpected evolutionary link across kingdoms, suggesting that pore-forming toxins may play a widespread role in fungal pathogenesis and microbial warfare. This work lays the foundation for understanding a new group of antifungal molecules and their potential impacts on health, agriculture, and microbial ecology.}, }
@article {pmid41216320, year = {2025}, author = {González-Rosales, C and Rezaei Somee, M and Buck, M and Bertilsson, S and Mehrshad, M and Dopson, M}, title = {A global deep terrestrial biosphere core microbiome.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf176}, pmid = {41216320}, issn = {2730-6151}, abstract = {The deep biosphere encompasses life beneath the Earth's surface and constitutes a substantial portion of the planet's microbial biomass. This study analyzed nucleic acid datasets from low-carbon and low-energy deep terrestrial subsurface groundwaters across four continents and revealed four core global populations. These populations exhibited metabolic strategies and adaptations reflecting depth and environmental constraints. Erythrobacter featured heterotrophic metabolism; Thiobacillus demonstrated sulfur oxidation coupled to denitrification along with carbon and nitrogen fixation; Methanobacteriaceae were methanogenic autotrophs using the Wood-Ljungdahl pathway (WL); and Candidatus Desulforudis audaxviator functioned as a sulfate-reducer also encoding the WL pathway. Depth-related adaptations suggested heterotrophic dominance at shallower depths with increasing contributions from autotrophy with depth. Finally, comparative genomics revealed minimal evolutionary changes among these populations, suggesting functional conservation since diverging from their ancestral lineages. These findings underscore a global deep biosphere core community.}, }
@article {pmid41215682, year = {2025}, author = {Alonso, C and Zanetti, J and Griffero, L and Pereira-Flores, E and González, B and Lescano, C and Pérez-Parada, A and Crisci, C and Amann, R}, title = {Marine Bacterioplankton Composition Predicts Oxygen Consumption During Dissolved Organic Matter Degradation Experiments.}, journal = {Environmental microbiology}, volume = {27}, number = {11}, pages = {e70197}, doi = {10.1111/1462-2920.70197}, pmid = {41215682}, issn = {1462-2920}, support = {ANII_MPI_ID_2017_1_1007663//Agencia Nacional de Investigaci&#xf3;n e Innovaci&#xf3;n/ ; Grupos I+D 2022//Comisi&#xf3;n Sectorial de Investigaci&#xf3;n Cient&#xed;fica/ ; }, abstract = {Microbial communities play pivotal roles in ocean biogeochemistry, yet linking their composition to ecosystem functions remains a significant challenge. In this study, we demonstrate the predictive power of bacterioplankton taxonomic composition in explaining oxygen consumption during dissolved organic matter (DOM) degradation. Using 4 years of experimental data, we integrated 'omics with statistical modeling, applying feature selection and dimensionality reduction to develop high-performance linear regression models with strong predictive accuracy. Our framework also identifies key microbial groups driving oxygen consumption, including taxa known for their differential capabilities in DOM processing and recently shown to exhibit distinct respiration rates. Flavobacteriales emerge as central contributors to oxygen consumption, underscoring their ecological importance in nutrient-rich, highly productive coastal systems often referred to as 'green seas'. Their consistent dominance across varying oxygen consumption categories highlights their pivotal role in sustaining ecosystem functions in these environments. Beyond oxygen consumption, this framework provides a versatile tool for investigating microbially driven biogeochemical processes. By linking community composition with ecosystem functions, our study advances predictive microbial ecology. These findings deepen our understanding of microbial contributions to the ocean's carbon and oxygen cycles, improving our ability to anticipate their responses to environmental change.}, }
@article {pmid41215000, year = {2025}, author = {Graça, JS and Sachinelli, LDS and Tobar, N and Guadagnini, D and Cabral, L and Noronha, MF and Coutinho, LL and Cazarin, CBB and Bogusz-Junior, S and Belangero, WD and Brunetto, SQ and Pimentel, TC and Saad, MJA and Sant'Ana, AS}, title = {Fermented probiotic dairy products with buriti and orange byproducts enhance gut and bone health.}, journal = {Food research international (Ottawa, Ont.)}, volume = {221}, number = {Pt 3}, pages = {117364}, doi = {10.1016/j.foodres.2025.117364}, pmid = {41215000}, issn = {1873-7145}, abstract = {The integration of functional ingredients and probiotics in dairy matrices is a promising strategy to nehance bone and intestinal health and preventing the onset of diseases. This study aimed to evaluate the impact of fortification of fermented dairy products (yogurt and fermented milk) with buriti pulp or orange bagasse added, added or not of a probiotic strain L. acidophilus DSM 13241 (Nu-trish® LA-5®) (Chr. Hansen, Hoersholm, Denmark) (yogurt and fermented milk) on bone and intestinal health of Wistar rats. The experimental design consisted of male Wistar rats (n = 6/group) that received supplementation daily for 60 days. The parameters assessed included the quantification of minerals (Ca, P, and Mg) in the products and femurs, the biomechanical and densitometric parameters, the fecal microbiota composition through the sequencing analysis of the 16S rRNA gene, the short-chain fatty acid (SCFA) content, and the permeability of the intestinal barrier. It was observed that the consumption of buriti pulp was responsible for the bone strength and stiffness of the femurs. The consumption of buriti pulp increased the bone strength and stiffness of the femurs and the relative abundance of the Lachnospiraceae NK4A136 group. The fortification of probiotic yogurt with buriti pulp led to an increase in the production of SCFA (acetic acid) and the daily intake of Ca, Mg, and P. The consumption of orange bagasse increased the magnesium mineral content in the femur and serum calcium values. The consumption of orange bagasse increased the Mg content in the femur and serum values of Ca, improved the permeability of the intestinal barrier (reducing serum levels of lipopolysaccharide), and positively impacted the fecal composition (increases in the relative abundance of Lactobacillus and Muribaculaceae). The concentration of acetic and propionic acid increased after consumption of the two fermented milk formulations containing orange bagasse (LA OB and LA OX OB). The groups that consumed yogurt containing buriti pulp (Y BP) and yogurt containing L. acidophilus DSM 13241 (Nu-trish® LA-5®) and buriti pulp (Y LA BP) presented higher concentrations of acetic acid in the feces compared to the group that consumed only yogurt (Y). The consumption of all fermented products containing the probiotic L. acidophilus DSM 13241 (Nu-trish® LA-5®) (fermented milk or natural yogurts and yogurts fortified with buriti pulp and orange pulp: LA, LA OB, LA OX OB, Y LA, and Y LA BP) increased the abundance of the Lachnospiraceae family NK4A136 group. The findings of this study indicate that fruit byproducts and probiotic fermented dairy products exert synergistic effects on bone and gut microbial ecology health in growing rats. These results support the use of sustainable functional ingredients in food innovation to promote systemic health benefits.}, }
@article {pmid41212898, year = {2025}, author = {Mihajlovic, L and Hofacker, LM and Lindner, F and Jayakumar, P and Diepold, A and Huwiler, SG}, title = {A molecular toolbox to modulate gene expression and protein secretion in the bacterial predator Bdellovibrio bacteriovorus.}, journal = {PLoS genetics}, volume = {21}, number = {11}, pages = {e1011935}, doi = {10.1371/journal.pgen.1011935}, pmid = {41212898}, issn = {1553-7404}, abstract = {The predatory bacterium Bdellovibrio bacteriovorus kills and consumes other bacteria, thrives in diverse environments and holds great potential to address major challenges in medicine, agriculture, and biotechnology. As a bacterial predator it represents an alternative to traditional antimicrobial strategies to combat multidrug-resistant bacterial pathogens and prevent food waste, while the multitude of predatory enzymes it produces have potential for biotechnological applications. However, while a limited set of genetic tools exist, the lack of secretion assays and fine-tuning of secretion constrain both fundamental studies and bioengineering of B. bacteriovorus. Here, we present a molecular toolbox for B. bacteriovorus by systematically tuning gene expression and secretion of a reporter protein. Building on functional native and synthetic promoters from the Anderson library with varying expression levels of fluorescent reporter protein mScarletI3, we evaluated different ribosomal binding sites (RBS) to fine-tune gene expression. To examine secretion, we established a novel protocol to quantify extracellular release of a Nanoluc luciferase reporter protein in B. bacteriovorus using different native Sec-dependent signal sequences. We anticipate that the newly developed genetic toolkit and techniques will advance research on this fundamental predator-prey system, laying the foundation for its broader application and future bioengineering efforts. This work will pave the way for tailored applications of B. bacteriovorus in microbial ecology, agriculture, biotechnology, and medicine.}, }
@article {pmid41212266, year = {2025}, author = {Malassigné, S and Valiente Moro, C and Luis, P}, title = {Microbial Volatiles from Human Skin and Floral Nectar: Insufficiently Understood Adult Feeding Cues To Improve Odor-Based Traps for Aedes Vector Control.}, journal = {Journal of chemical ecology}, volume = {51}, number = {6}, pages = {108}, pmid = {41212266}, issn = {1573-1561}, abstract = {Mosquitoes of the genus Aedes, including the invasive Aedes albopictus, are responsible for the transmission of arboviruses such as dengue, chikungunya, and Zika. Their global expansion has intensified public health concerns, while the efficacy of insecticide-based control is declining due to resistance and environmental risks. These limitations have increased interest in odor-baited traps as complementary tools for surveillance and population reduction. Yet, their performance in the field remains inconsistent, largely because lures rely on a restricted set of human skin microbial volatiles and capture mainly host-seeking females. This review highlights the contribution of microorganisms inhabiting human skin and floral nectar to mosquito feeding ecology. Skin microbiota shape odor profiles by producing volatile organic compounds that mediate host attractiveness and species-specific mosquito responses. Likewise, nectar-dwelling yeasts and bacteria alter nectar chemistry and floral scent, generating volatiles that influence insect foraging, although their role in Aedes attraction remains poorly studied. By integrating data from Aedes and other insect models, we highlight microbial semiochemicals with demonstrated or potential roles in guiding blood- and sugar-feeding behaviors. We further discuss how microbial ecology, compound concentration, and chemical interactions drive variability in mosquito responses, raising both opportunities and challenges for trap design. Expanding research to nectar-associated microbial cues, while considering ecological specificity and possible non-target effects, could help create more versatile lures that attract both sexes and multiple feeding stages. This review advances our understanding of microbial-associated cues as critical drivers of mosquito behavior and outlines future directions to improve odor-based surveillance and control of Aedes vectors.}, }
@article {pmid41211947, year = {2025}, author = {Calvez, E and Quétel, I and Saint-Alban, L and Gutiérrez-Bugallo, G and Dollin, C and Ramdini, C and Vega-Rúa, A}, title = {Contrasted impacts of commercial diets and rearing water on Aedes aegypti fitness and microbiota.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0054325}, doi = {10.1128/msphere.00543-25}, pmid = {41211947}, issn = {2379-5042}, abstract = {Mosquito rearing optimization in laboratory conditions is crucial for both vector research and control. Although the addition of nutrients is important for Aedes aegypti development from immature stages to adult mosquitoes, little is known about the nutrient composition of commercial diets used for mosquito rearing and their influence on Ae. aegypti life traits. Here, we evaluated the influence of four commercial diets commonly used to rear Ae. aegypti in the laboratory on its fitness, lifespan, and microbiota. We also compared the effect of these diets on this mosquito when combined with two different rearing waters (laboratory versus field-collected waters). Our investigations demonstrated that higher levels of protein and lipid in commercial diets promote better Ae. aegypti development, lifespan, and size in both water. Metagenomic analysis revealed specific modulations of adult microbiota composition according to both diet and rearing water. Chryseobacterium dominated the microbiota of female mosquitoes reared in laboratory water, except for yeast condition, where a more diverse microbiota was observed. When reared in larval site water, the microbiota diversity was overall higher despite diet addition, except for fish food, which promoted Sphingobacterium dominance. Given the pivotal influence of diet addition during the larval stage on Ae. aegypti microbiota and life traits, rearing conditions should be carefully chosen according to the goals of the research (i.e., vectorial capacity estimations) or vector control intervention.IMPORTANCEAedes aegypti is the main vector of arbovirus, such as dengue, yellow fever, and chikungunya viruses. Vector research and control are primarily carried out in laboratories, with larval stage rearing conducted using commercial diet. If many nutrients are essential for Ae. aegypti development, gaining insight into the influence of these diets and their nutrient levels is important to promote optimized rearing worldwide. In this study, our results indicated a significant impact of commercial diet on Ae. aegypti development, lifespan, size, and microbiota related to contrasted protein, lipid, and carbohydrate levels in these diets. This study will help people working with Ae. aegypti raise awareness in staff working with Ae. aegypti to select optimized diets for their specific purpose.}, }
@article {pmid41210076, year = {2025}, author = {Bayer, B and Kitzinger, K and Paul, NL and Albers, JB and Saito, MA and Wagner, M and Carlson, CA and Santoro, AE}, title = {Minor contribution of ammonia oxidizers to inorganic carbon fixation in the ocean.}, journal = {Nature geoscience}, volume = {18}, number = {11}, pages = {1144-1151}, pmid = {41210076}, issn = {1752-0894}, abstract = {Ammonia-oxidizing archaea are the most abundant chemolithoautotrophs in the ocean and are assumed to dominate carbon fixation below the sunlit surface layer. However, the supply of reduced nitrogen delivered from the surface in sinking particulate organic matter is insufficient to support the amount of nitrification required to sustain measured carbon fixation rates in the dark ocean. Here we attempt to reconcile this observed discrepancy by quantifying the contribution of ammonia oxidizers to dark carbon fixation in the eastern tropical and subtropical Pacific Ocean. We used phenylacetylene-a specific inhibitor of the ammonia monooxygenase enzyme-to selectively inhibit ammonia oxidizers in samples collected throughout the water column (60-600 m depth). We show that, despite their high abundances, ammonia oxidizers contribute only a small fraction to dark carbon fixation, accounting for 4-25% of the total depth-integrated rates in the eastern tropical Pacific. The highest contributions were observed within the upper mesopelagic zone (120-175 m depth), where ammonia oxidation could account for ~50% of dark carbon fixation at some stations. Our results challenge the current view that carbon fixation in the dark ocean is primarily sustained by nitrification and suggest that other microbial metabolisms, including heterotrophy, might play a larger role than previously assumed.}, }
@article {pmid41209725, year = {2025}, author = {Wang, F and Li, S and Li, P and Feng, C and Zhao, Z and Yang, Y and Han, F and Xue, A and Li, Z and Han, P}, title = {The assembly processes and network characteristics of bacterial, fungal and archaeal communities in the middle Yangtze River and river-connected lakes.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1701799}, pmid = {41209725}, issn = {1664-302X}, abstract = {Despite the crucial ecological roles of bacterial, fungal and archaeal communities in rivers and lakes, their interactions and dynamic changes in large, hydrologically-connected river-lake systems remain poorly understood. This study investigated the biogeographic patterns, assembly processes and co-occurrence network characteristics of bacterial, fungal and archaeal communities in the middle reaches of Yangtze River (MYR) and its two largest connected lakes, Dongting Lake (DTL) and Poyang Lake (PYL). Our results revealed significant spatial heterogeneity in microbial diversity and composition, with higher sedimentary microbial diversity in lakes than in the river. Stochastic processes, particularly dispersal limitation, dominated community assembly across all habitats. β-NRI analysis showed that deterministic processes were more influential for planktonic bacterial and archaeal communities in the lakes. Co-occurrence network analysis demonstrated that inter-domain cooperation was prevalent in PYL, whereas intra-domain interactions were more common in MYR and DTL, reflecting distinct hydrological connectivity. Keystone taxa differed between rivers and lakes, with rare taxa prevailing in MYR and both rare and abundant taxa contributing in lakes. Our findings highlight how connectivity and flow dynamics fundamentally shape microbial ecology, providing insights into for the management and conservation of large river-lake ecosystems.}, }
@article {pmid41207985, year = {2025}, author = {Mei, J and Li, L and Ma, ZS}, title = {Unraveling the Ecological Mechanisms Influencing the Structure and Composition of Lung Cancer Microbiomes.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {119}, pmid = {41207985}, issn = {1432-184X}, abstract = {This study investigates the ecological mechanisms governing the structure and composition of lung microbiome communities within tumor tissue from lung cancer patients. While this field has attracted increasing research attention, the ecological and etiological mechanisms driving microbial community assembly in this environment remain poorly characterized. To address this gap, we applied Sloan's near neutral model, Ning et al.'s normalized stochasticity ratio framework and Harris et al.'s multi-site neutral model to evaluate the influences of stochastic and deterministic factors at species, community and metacommunity levels, respectively. Our findings include: (i) Stochastic drift exhibited predominant influence at both species and community levels in normal adjacent tissue (NT), exceeding its effects in LUAD (lung adenocarcinoma) and LUSC (lung squamous cell carcinoma). (ii) At the metacommunity level, neutrality was not rejected at the metacommunity or local community levels, which is consistent with the previous finding (i). (iii) Elevated metacommunity biodiversity (θ) and immigration rates (m) in LUAD/LUSC compared to NT (observed in ∼50% of cases) suggest that tumor occurrence/progression may actively promote microbial recruitment to tumor microenvironments. We propose three non-exclusive mechanistic interpretations: (i) Tumor-mediated immune modulation creates permissive ecological niches; (ii) structural remodeling of tissue enhances microbial colonization potential; (iii) selective enrichment of opportunistic taxa (e.g., Streptococcus) through tumor-specific microenvironmental changes. Our results demonstrate that LUAD and LUSC microbiomes are shaped by deterministic tumor-driven selection, in contrast to the predominantly stochastic assembly observed in NT microbiomes. These findings reveal substantial reorganization of tumor-associated microbial communities, warranting further biomedical investigation and clinical validation.}, }
@article {pmid41207977, year = {2025}, author = {Oliveira-Pinto, PR and Oliveira-Fernandes, J and Gramaje, D and Santos, C}, title = {Metabarcoding Profiling Reveals Microbiome Structure and Predicts Functional Shifts in Grapevines Challenged by Phyllosticta ampelicida.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {120}, pmid = {41207977}, issn = {1432-184X}, abstract = {Black rot disease (BRD), caused by the still understudied Phyllosticta ampelicida, is spreading across several grape producing countries, posing a growing threat to the agroindustry. The role of the grapevine microbiome in defending against this pathogen, particularly in terms of microbiota structure and community homeostasis, remains unclear. In this study, we aimed to characterize the epiphytic phyllosphere microbiota of grapevines and identify shifts in microbial genetic structure associated with BRD symptoms. We sampled three vineyards of the cultivar "Touriga Nacional" in the Douro region (Portugal), collecting 20 leaves from (a) five healthy and (b) five BRD-symptomatic grapevines. The presence of P. ampelicida was confirmed in all symptomatic samples. Epiphytic bacterial DNA was extracted and sequenced using next-generation sequencing (NGS). Results indicate that although overall the diversity and richness indexes were not different in diseased plants compared to healthy ones, there was a reduction in OTU richness in black rot-affected grapevines. Diseased plants exhibited significant shifts in microbial network assemblages and showed an increased relative abundance of certain taxa, such as Acinetobacter, suggesting a possible recruitment of beneficial bacteria in response to biotic stress. Additionally, we observed a higher abundance of antibiotic resistance-related KEGG Orthologues (KOS) in symptomatic plants, raising potential concerns for human health. This study presents the first characterization of the grapevine phyllosphere epiphytic bacterial microbiota and its structural shifts in response to BRD.}, }
@article {pmid41206559, year = {2025}, author = {Fournier, P and Pellan, L and Aubert, J and This, P and Vacher, C}, title = {A new scenario of pathogen-microbiota interactions involving the oomycete Plasmopara viticola.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaf111}, pmid = {41206559}, issn = {1574-6941}, abstract = {A key question in microbial ecology is how the microbiota regulates host invasion by pathogens. Several ecological theories link the diversity, abundance and assembly processes of the microbiota with its resistance to invasion, but the specific properties of microbial communities that confer protection to the host are poorly understood. We addressed this question for the oomycete Plasmopara viticola, the causal agent of grapevine downy mildew. Using state-of-the-art microbial ecology methods, we compared microbial communities associated with asymptomatic and symptomatic leaf tissues to elucidate pathogen-microbiota interactions. Despite visible symptoms, P. viticola infection induced only subtle changes in microbial community composition. Symptomatic tissues showed enrichment in basidiomycete yeasts and Bacillus species, both known for their biocontrol activity, and exhibited a higher degree of determinism in community assembly processes. Asymptomatic tissues hosted more diverse microbiota, but lacked consistent associations with known biocontrol agents. Instead, they were often associated with other airborne grapevine pathogens. These findings suggest a novel interaction scenario: upon infection, P. viticola reshapes locally the leaf microbiota, excluding other pathogens and selecting for beneficial microbes. Although further studies are needed to uncover the underlying mechanisms, these findings underscore the relevance of targeting disease lesions in the search for protective microbial consortia.}, }
@article {pmid41204663, year = {2025}, author = {Budziak, M and Ilicic, D and Grossart, HP and Krztoń, W and Walusiak, E and Fyda, J and Wilk-Woźniak, E}, title = {Phytoplankton Under Pressure: Temperature, Precipitation and Cyanobacterial Blooms as Drivers of Chytrid Infections.}, journal = {Environmental microbiology reports}, volume = {17}, number = {6}, pages = {e70224}, doi = {10.1111/1758-2229.70224}, pmid = {41204663}, issn = {1758-2229}, support = {Statutory funds//Institute of Nature Conservation Polish Academy of Sciences/ ; GR 1540/48-1//German Research Foundation (DFG)/ ; COST Action ParAqua CA20125//European Cooperation in Science and Technology/ ; life17 env/lt/000407//European Union (EU) Life programme/ ; }, mesh = {Temperature ; *Cyanobacteria/growth &amp; development ; *Phytoplankton/microbiology/growth &amp; development ; Seasons ; Fresh Water/microbiology ; Ecosystem ; Rain ; Diatoms/microbiology ; *Chytridiomycota/isolation &amp; purification ; Chlorophyta/microbiology ; Eutrophication ; }, abstract = {The area of fungal parasitism is attracting growing attention because of its great importance for aquatic organisms and their community dynamics. Despite increasing interest in this area, few studies have addressed baseline data on occurrence and environmental factors associated with chytrid parasite infections in natural ecosystems. This work provides insights into occurrence, prevalence, and dynamics of parasitic infections by studying three freshwater reservoirs over a period of 6 years. Chytrid infections were detected in each of the studied water bodies, infecting species of cyanobacteria, green algae and diatoms. However, recurring and prevalent infections were observed in only one water body, which is classified as a natural aquatic ecosystem. The recorded infection prevalence (IPC) ranged between 0% and 20%, while the mean infection severity remained low. Infection rates were highest in summer and most prominent during cyanobacterial blooms. Yet, the most infected group of phytoplankton consisted of green algae. GLM revealed a significantly positive correlation between IPC and water temperature and precipitation. Overall, these results demonstrate the dynamic nature of chytrid infections, which are shaped by multiple environmental factors across space and time.}, }
@article {pmid41204024, year = {2025}, author = {Mileng, K and Mani, S and Bezuidenhout, JJ and Mokgokong, PS and Ramatla, TA and Thekisoe, OMM and Lekota, KE}, title = {Bacterial Communities Harboured by Amblyomma Hebraeum Infesting Small Stock in Mahikeng city, South Africa.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {118}, pmid = {41204024}, issn = {1432-184X}, support = {GUN: CSUR23030681021//National Research Foundation/ ; }, mesh = {Animals ; South Africa ; *Bacteria/classification/genetics/isolation &amp; purification ; Goats/parasitology/microbiology ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Sheep/parasitology ; *Amblyomma/microbiology ; *Tick Infestations/veterinary/parasitology/epidemiology ; *Goat Diseases/parasitology/microbiology/epidemiology ; Phylogeny ; *Sheep Diseases/parasitology/microbiology/epidemiology ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing ; }, abstract = {Ticks are important vectors of pathogens affecting livestock productivity and public health, yet their bacterial communities remain poorly characterized in many parts of South Africa. This study investigated the bacterial diversity and potential pathogenic bacterial etiology associated with Amblyomma hebraeum ticks collected from sheep and goats in Mahikeng, North West province. A total of 168 adult ticks were sampled across four villages. Microbiome profiling was performed using high-throughput sequencing of the V3-V4 hypervariable regions of the 16S rRNA gene on the Illumina MiSeq platform. High-throughput 16S rRNA sequencing revealed 16,193 ASVs in goat-derived ticks and 16,510 ASVs in those from sheep. Proteobacteria emerged as the dominant phylum across all samples, with ticks collected from goats showing a particularly high dominance of Rickettsia spp. (51.64% relative abundance), suggesting potential zoonotic risks. In contrast, ticks from sheep harboured significantly more diverse and evenly distributed bacterial communities, as indicated by Shannon (p = 0.0138) and Simpson (p = 0.0233) diversity indices, despite comparable species richness. A core microbiome comprising 1,374 ASVs (32.3%) was shared across all ticks, alongside 1,504 and 1,372 unique ASVs in goat- and sheep-derived ticks, respectively. Notably, several medically and veterinary-relevant genera, including Coxiella, Ehrlichia, Staphylococcus, Bacillus, Acinetobacter, Corynebacterium, and Streptococcus, were detected across both host groups. While total species richness was comparable between hosts, alpha diversity indices that account for evenness revealed host-based differences, and beta diversity patterns further showed clear separation of bacterial communities by host species. This study indicates that the host plays a crucial role as an ecological driver affecting the diversity of microbial communities associated with ticks. This study improves our understanding of the diversity, composition, and abundance of tick-associated microbiomes and pathogens in South African small ruminants. These insights support the development of microbiome-targeted strategies for detecting and controlling tick-borne diseases.}, }
@article {pmid41203821, year = {2025}, author = {Young, JD and Pinnell, LJ and Wolfe, CA and Scott, MA and Lawrence, TE and Cavasin, JP and Ellis, JA and Langsten, KL and Richeson, JT and Morley, PS}, title = {Microbial communities and tight junction protein expression in the gastrointestinal tract of feedlot cattle.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {39055}, pmid = {41203821}, issn = {2045-2322}, mesh = {Animals ; Cattle ; *Tight Junction Proteins/metabolism/genetics ; *Gastrointestinal Microbiome ; *Gastrointestinal Tract/microbiology/metabolism ; RNA, Ribosomal, 16S/genetics ; Rumen/microbiology/metabolism ; Male ; Tight Junctions/metabolism ; Bacteria/genetics/classification ; }, abstract = {The gastrointestinal tract (GIT) of cattle plays a vital role in nutrient absorption, immune function, and microbial homeostasis. While the importance of the GIT microbiome and epithelial barrier integrity has been increasingly recognized, the typical composition of microbial communities and the expression of tight junction proteins (TJPs) in feedlot cattle remains poorly characterized. We investigated microbial community structure and TJP expression at three GIT sites: the rumen (RU), small intestine (SI), and large intestine (LI) in 21 finish-fed feedlot steers sourced from 21 commercial feedyards in the Texas Panhandle. Samples of luminal contents and GIT tissue were collected from each region, as well as feces and liver abscess material. Microbial communities were characterized using 16S rRNA gene sequencing. TJP gene expression was quantified by RT-qPCR using synthetic standards, and protein expression was evaluated by immunohistochemistry (IHC) with both computer-generated and pathologist-generated scoring. Microbial community structures varied primarily by GIT region rather than by individual animals raised at different locations. Nine bacterial families were identified as core microbiome members, with Lachnospiraceae being the most abundant across the GIT. TJP gene expression varied considerably by site, with RU having significantly lower Claudin 1, Claudin 2, and E-Cadherin expression than the SI and LI. IHC results paralleled qPCR findings, with region-specific patterns of protein localization and intensity. Computerized and pathologist-generated H-scores showed moderate agreement but differed notably between epithelial and lamina propria regions. This study provides a comprehensive baseline of microbial and host factors associated with gut health in a uniquely diverse population of feedlot cattle. The identification of regional microbial communities and distinct TJP expression patterns offers foundational insights into gastrointestinal physiology and barrier function. This work establishes baseline data to support future investigations into the relationships among microbial ecology, epithelial barrier function, and cattle health and productivity.}, }
@article {pmid41202998, year = {2025}, author = {Kuang, B and Yang, W and Li, C and Lee, CW and Liu, BY and Bong, CW and Wang, W and Chen, S}, title = {Long-Term Oral Administration of Inactivated Vibrio harveyi Vaccine Triggers Immunosuppression in Penaeus vannamei.}, journal = {Fish &amp; shellfish immunology}, volume = {}, number = {}, pages = {110983}, doi = {10.1016/j.fsi.2025.110983}, pmid = {41202998}, issn = {1095-9947}, abstract = {This study investigated optimal oral vaccination strategies to enhance Vibrio resistance in Penaeus vannamei by comparing two feeding regimens: continuous administration of inactivated Vibrio harveyi (IVH) (CF group) and intermittent IVH feeding (7-day IVH followed by 7-day commercial feed, IF group). Results demonstrated that 7-day IVH feeding effectively induced anti-Vibrio immunity. The IF group maintained >60% relative percent survival (RPS) during challenge tests at 14, 21 and 28 days post-immunization, whereas the CF group exhibited a sharp RPS decline to -22.73% at day 14, with persistently low values thereafter. Specific growth rates were significantly reduced in the CF group compared to controls. Immune enzymatic activity analysis at day 14 revealed sustained high levels in the IF group but marked declines in the CF group. Histopathological examination confirmed severe cellular necrosis in intestinal and hepatopancreatic tissues of the CF group at day 14. Gut microbiota analysis indicated comparable dominant taxa between groups at day 14, while the IF group exhibited higher proportions of Ruegeria genera. Proteomic profiling identified distinct expression patterns between groups, with the CF group displaying significant downregulation of proteins associated with energy metabolism, immune responses, metabolic pathways, and cell/tissue maintenance. These data demonstrated that continuous IVH feeding elicited substantial physiological stress, leading to cellular and tissue damage and consequent immunosuppression in P. vannamei, whereas intermittent feeding mitigated immune impairment and conferred V. harveyi resistance. This study highlights the critical need for temporally optimized vaccination protocols in shrimp aquaculture.}, }
@article {pmid41202458, year = {2025}, author = {Biswas, A and Saini, N and Chivukula, N and Samal, A and Jansari, MR and Bhadury, P and Darbha, GK}, title = {The dawn of a new air pollutant: inhalable microplastics as emerging vectors of hazardous contaminants and their implications for human health.}, journal = {Environment international}, volume = {205}, number = {}, pages = {109897}, doi = {10.1016/j.envint.2025.109897}, pmid = {41202458}, issn = {1873-6750}, abstract = {This study presents the first comprehensive research on inhalable microplastics (iMPs, <10 μm), a notorious subset of airborne microplastics (AMPs). To identify human health risk, ambient iMPs concentrations were assessed at human breathing height across the markets of four major Indian cities. With winter evening being the highest iMPs concentration, in Kolkata (14.23 µg/m[3]), followed by Delhi (14.18 µg/m[3]), linked to the highest footfalls, use of synthetic clothing, and poor waste management. Coastal cities (Chennai: 4 µg/m[3], and Mumbai: 2.65 µg/m[3]) showed lower levels, likely due to improved air circulation, less winter, and reduced apparel, confirmed by Principal Component Analysis. Py-GC-MS quantified 11 polymers, with PET (Polyester) from textiles as the most abundant, followed by PE and SBR from single-use plastics, packaging, vehicles, and footwear. Urban areas in India show an average iMPs concentration of 8.8 µg/m[3], translating to a lifetime lung load of ∼2.9 g/person. Furthermore, this investigation highlights the risks of iMPs-associated tracers such as diethyl phthalates and lead. This pioneering research is the first-ever study to explore AMPs carrier capabilities for ultrafine particulate matter, PTEs, POPs, PPCPs, and microbes. During peak exposure periods like autumn festivals, AMPs harbored diverse microbial communities, including pathogenic (Aspergillus fumigatus) and new strains of bacteria/fungi with antibiotic resistance and virulence factor genes. This suggests that microbes carried by iMPs possess enhanced pathogenicity and resistance against broad-spectrum drugs like tetracycline and are more likely to be multidrug-resistant. Cross-referencing toxicological databases revealed that exposure to AMPs-linked modern-day contaminants elevates the risk of cancer, gastrointestinal, endocrine, breast, and respiratory diseases.}, }
@article {pmid41201519, year = {2025}, author = {López-Sandoval, DC and Fernández-González, C and González-García, C and Marañón, E}, title = {Warming Accelerates Phytoplankton Bloom Dynamics and Differentially Affects the Fluxes of Carbon, Nitrogen, and Oxygen Through a Coastal Microbial Community.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {117}, pmid = {41201519}, issn = {1432-184X}, support = {Project POLARIS (PGC2018-094553-B-I00)//Spanish Ministry of Science and Innovation/ ; }, mesh = {*Nitrogen/metabolism ; *Carbon/metabolism ; *Phytoplankton/growth &amp; development/metabolism ; *Oxygen/metabolism ; *Microbiota/physiology ; Seawater/microbiology/chemistry ; Biomass ; *Eutrophication ; Carbon Cycle ; Ecosystem ; Global Warming ; Hot Temperature ; }, abstract = {Marine heatwaves affect the abundance and community structure of microbial plankton, with implications for food web and ecosystem processes, but their impact on microbially mediated elemental cycling remains poorly constrained. To determine the biogeochemical effects of increased temperature, we conducted an experiment in September 2023 in which a plankton community from a coastal, productive ecosystem (Ría de Vigo, NW Iberia) was exposed to a warming of + 2 °C and + 4 °C under unamended and nutrient-enriched conditions. The response of microbial plankton was characterized in terms of organic matter production, carbon fixation, nitrogen uptake, and oxygen net production. We found that warming caused increased nutrient consumption and biomass production, as well as faster bloom dynamics, both in unamended and nutrient-enriched treatments, indicating that the community was robust to thermal perturbation. Accelerated nutrient depletion under warming gave way to an earlier decrease in carbon fixation and nitrate uptake rates, together with a shift towards a negative or less positive metabolic balance. Carbon fixation was less sensitive than nitrate uptake to the different temperature and nutrient scenarios, leading to wide changes in the carbon-to-nitrogen uptake ratio, while respiration increased non-linearly with temperature. Overall, the investigated microbial fluxes were more responsive to nutrient availability than to temperature. Our results show that microbially driven ecosystem services in coastal waters have the potential to be enhanced during short-term warming events.}, }
@article {pmid41199522, year = {2025}, author = {Chen, HJ and Liu, Y and Zhong, YS and Li, MZ and Lai, JJ and Luo, YY and Huang, SL and Liu, SQ and Yu, GH and Sun, YH and Shao, MW}, title = {Modulating Surfactin Biosynthesis in Bacillus subtilis R31 Enhances Behavioural Traits and Biocontrol Efficacy Against Banana Fusarium Wilt.}, journal = {Microbial biotechnology}, volume = {18}, number = {11}, pages = {e70261}, doi = {10.1111/1751-7915.70261}, pmid = {41199522}, issn = {1751-7915}, support = {202206010083//Guangzhou Municipal Science and Technology Project/ ; 2021ZDJS002//Guangdong Province Key Discipline Research Capacity Enhancement Project/ ; 32302450//National Natural Science Foundation of China/ ; 22-035-31-23KF03//Guangxi Key Laboratory of Crop Pest Biology Foundation/ ; 2023B0202010012//Guangdong Province Key Area Research and Development Program/ ; }, mesh = {*Fusarium/growth &amp; development/drug effects/physiology ; *Bacillus subtilis/genetics/metabolism/physiology ; *Plant Diseases/microbiology/prevention &amp; control ; *Musa/microbiology ; *Lipopeptides/biosynthesis/pharmacology ; *Peptides, Cyclic/biosynthesis ; RNA, Ribosomal, 16S/genetics ; Metabolic Engineering ; Quorum Sensing ; Rhizosphere ; Biofilms/growth &amp; development ; Bacterial Proteins/genetics/metabolism ; DNA, Ribosomal/chemistry/genetics ; }, abstract = {Surfactin, a lipopeptide antibiotic and quorum-sensing (QS) mediator from Bacillus subtilis, has dual functions in microbial ecology and plant disease suppression. This study engineered B. subtilis R31 to overproduce comK and phrC, key regulators of surfactin biosynthesis, increasing surfactin yield by 45% compared to the WT strain. While elevated surfactin enhanced antimicrobial potential, comK-mediated overproduction impaired biofilm formation and swarming motility, but rhizosphere colonisation was mostly unaffected. 16S rRNA sequencing of banana rhizospheres showed that surfactin selectively shaped the microbial community by enriching beneficial Bacillus species. Mechanistic studies confirmed surfactin's dual role as an antimicrobial and an intercellular signalling molecule for coordinated development in Bacillus populations. These results reveal the molecular mechanisms of R31-mediated suppression of banana Fusarium wilt and offer a strategy for engineering synthetic microbial consortia by manipulating metabolic signalling pathways.}, }
@article {pmid41197919, year = {2025}, author = {Mohit,  and Verma, S and Venkatesh, V and Nityanand, S}, title = {Immuno-Microbial Crosstalk in Aplastic Anemia: Role of Gut and Viral Triggers.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {108158}, doi = {10.1016/j.micpath.2025.108158}, pmid = {41197919}, issn = {1096-1208}, abstract = {Aplastic anemia (AA) is a rare but life-threatening hematological disorder, manifested in bone marrow failure and pancytopenia, which occurs worldwide due to the preferential immune mediated destruction of hematopoietic stem and progenitor cells. Despite the autoimmune etiology of AA, recent findings emphasize the key role of microbial and viral factors in the pathogenesis of AA by driving the host immune dysregulation. We delve into the immune-microbial crosstalk that is relevant in AA pathogenesis to provide novel insights related to gut microbial ecology, microbial metabolites, viral infections mediated inflammation and cytotoxicity against bone marrow components. Additionally, providing the roadmap of current knowledge for immune-mediated bone marrow failure focusing on activated cytotoxic T cells, altered regulatory T cells and proinflammatory cytokines. Imbalanced immune activation via defects in gut barrier function which promotes pathogen-associated molecular patterns (PAMPs) signaling through Toll-like receptors (TLRs) and other innate sensors. Considering the role of viral trigger such as Parvovirus B19, Epstein-Barr and Hepatitis as inducers of dysregulated immunity and their ability to affect antigen presentation, T cell receptor repertoires, and interferon pathways. We also delineate the potential of targeting the gut-immune axis for personalized AA therapy, including potential microbiome-directed interventions, antiviral and anti-cytokine approaches, as promising complement lines for standard immunosuppression therapy in AA. This cited approach will provide the advanced and novel clinical paradigm for the interconnected immune-microbial signals in pathogenesis of AA which promotes the host immune surveillance and also lead to precision medicine in AA treatment.}, }
@article {pmid41197741, year = {2025}, author = {Chen, Y and Chen, Y and Hu, C and Xing, X and Zhang, S and Zeng, K and Yin, Z and Meng, C and Situ, F and Li, J and Chen, C and Ma, K and Chen, J and Li, F}, title = {Simultaneous control of disinfection by-products, opportunistic pathogens, and antibiotic resistance genes in drinking water based on a novel advanced treatment process consisting of Fenton-like reaction and biological activated carbon.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {133602}, doi = {10.1016/j.biortech.2025.133602}, pmid = {41197741}, issn = {1873-2976}, abstract = {Disinfection by-products (DBPs), opportunistic pathogens (OPs), and antibiotic resistance genes (ARGs) are typical drinking water quality risks today, and the synchronous control of these factors has always been an important challenge. Herein, a novel drinking water treatment process (Fe3C-NC/PMS-BAC) consisting of Fe3C-NC Fenton-like reaction and biological activated carbon (BAC) was established in this study. Fe3C-NC/PMS caused the decomposition of high molecular weight organic matter into low molecular weight organic matter, which was efficiently biodegraded in the subsequent BAC biofilter (PBAC). In addition, the suspended extracellular polymeric substances (EPS) in the effluent of PBAC contained only a small amount of polysaccharides, markedly weakening the biofilm stability and its protective effect against OPs. The changes in organic matter and EPS ultimately led to the reduction of DBPs precursors. More importantly, the Fe3C-NC/PMS treatment remarkably changed the microbial ecology in subsequent PBAC, including shaping the microbial community, regulating EPS characteristics, weakening quorum sensing, and even inhibiting microbial activities, contributing to the inhibition of horizontal gene transfer of ARGs. Therefore, the Fe3C-NC/PMS-BAC is a promising alternative to BAC treatment for future applications, providing new ideas for the collaborative removal of chemical and microbial water quality risks in drinking water.}, }
@article {pmid41194431, year = {2025}, author = {Truant, A and Giacometti, F and Losasso, C and Peruzzo, A and Petrin, S and Zancato, I and Di Leva, V and Giaccone, V}, title = {First Metataxonomic Characterisation of Gut Microbiota of Swordfish (Xiphias gladius).}, journal = {Environmental microbiology reports}, volume = {17}, number = {6}, pages = {e70199}, doi = {10.1111/1758-2229.70199}, pmid = {41194431}, issn = {1758-2229}, mesh = {Animals ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; *Perciformes/microbiology ; Phylogeny ; *Fishes/microbiology ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; Biodiversity ; }, abstract = {Swordfish (Xiphias gladius) is a large, migratory apex predator with a carnivorous diet, occupying a top position in the marine food chain. Although it is a valuable teleost pelagic fish with a significant commercial value, its gut microbiota has never been studied. The gut microbiota of 100 individuals was characterised by sequencing the V3-V4 region of the bacterial 16S rRNA gene. Gut microbiota findings were classified with consideration to diversity, taking into account their weight (10-20; 21-30; over 31 kg) and the FAO fishing areas in which they were caught (FAO 27, 34, 37.1.1 areas). Significant differences in the alpha diversity were observed among the weight categories for all metrics examined (except for the evenness index) and only by Shannon's index among the FAO fishing areas. Beta-diversity analysis revealed no significant differences. The phylum Pseudomonadota dominated the swordfish gut microbiota, followed by Fusobacteriota. Photobacterium was the most abundant genus across all weight categories and FAO fishing areas. Smaller fishes showed a less rich and diverse gut microbiota, dominated almost exclusively by Photobacterium. Conversely, Pseudoalteromonas, Psychrobacter, Psychrilyobacter, and Cetobacterium appeared to increase in abundance with fish weight. Although Photobacterium was dominant across the different FAO fishing areas, distinctive microbial community compositions were observed: Cetobacterium was more prevalent in FAO 27, while Pseudoalteromonas was more prevalent in the other areas. Unlike the gut microbiota of other marine fish species, Vibrio and Lactobacillus were largely absent. This study represents the first metataxonomic characterisation of the gut microbiota of swordfish using next-generation sequencing.}, }
@article {pmid41193960, year = {2025}, author = {Van Goethem, MW and Vikram, S and Cowan, DA and Makhalanyane, TP}, title = {Comparative genomics reveals adaptive traits in novel Antarctic lithic cyanobacteria.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {994}, pmid = {41193960}, issn = {1471-2164}, }
@article {pmid41193926, year = {2025}, author = {Wei, N and Nakaji-Conley, M and Tan, J}, title = {Contrasting Diversity and Network Dynamics of Soil Fungal Functional Groups in the Plant Rhizosphere.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {116}, pmid = {41193926}, issn = {1432-184X}, support = {2300058//Directorate for Biological Sciences/ ; 2300057//Directorate for Biological Sciences/ ; E455990101//Wuhan Botanical Garden, Chinese Academy of Sciences/ ; }, mesh = {*Rhizosphere ; *Soil Microbiology ; *Fungi/classification/genetics/isolation &amp; purification/physiology ; Mycorrhizae/genetics/classification/isolation &amp; purification ; *Biodiversity ; *Plants/microbiology ; Microbiota ; Soil/chemistry ; Plant Roots/microbiology ; }, abstract = {Soil microbiomes, critical for plant productivity and ecosystem functioning, mediate essential functions such as pathogenesis, mutualism, and decomposition through different fungal functional groups. Yet, our understanding of the dynamics of co-existing soil fungal functional groups in the rhizosphere remains limited. By leveraging urban farming-featuring fields of different ages and multiple genotypes-we tracked the relative abundance, richness, and microbial networks of putative plant pathogenic fungi, mycorrhizal fungi, and saprotrophic fungi across fields over two years. We observed an increase in the relative abundance of putative plant pathogenic fungi in the rhizosphere in older fields relative to younger fields, supporting the prediction of pathogen accumulation over time. In contrast, there was a decrease in the relative abundance of mycorrhizal fungi in older fields. The relative abundance of saprotrophic fungi remained similar between younger and older fields. While the richness of putative plant pathogenic fungi and saprotrophic fungi was similar across the examined fields, the community structure of both groups differed between younger and older fields. For mycorrhizal fungi, the richness declined in older fields and over the two years. These dynamics led to distinct microbial networks, with decreased network links for mycorrhizal fungi and increased links for saprotrophic fungi in older fields, whereas the links for plant pathogenic fungi remained similar across fields. Our study reveals contrasting dynamics of essential soil fungal functional groups in the rhizosphere and provides predictive insight into the potential shifts in soil function and their impact on plant productivity.}, }
@article {pmid41193719, year = {2025}, author = {Sugden, S and Davis, CL and Quinn, MW and Whyte, LG}, title = {Current and projected effects of climate change in cryosphere microbial ecosystems.}, journal = {Nature reviews. Microbiology}, volume = {}, number = {}, pages = {}, pmid = {41193719}, issn = {1740-1534}, abstract = {Cold environments, including glaciers, ice sheets, permafrost soils and sea ice, are common across the surface of the Earth. Despite the challenges of life at subzero temperatures, the global cryosphere hosts diverse microbial communities that support biogeochemical cycling and ecosystem functioning in areas where few other organisms can survive. However, the composition and function of cryosphere microbial communities, and the continued existence of cryosphere habitats, are threatened by ongoing climate change, which has disproportionate impacts in polar regions. In this Review, we survey the breadth of cryosphere habitats and the composition, function and unique adaptations of the microbial communities that inhabit them. We outline how climate change can affect these communities and the ecosystem services they provide through short-term changes in substrate availability, enzyme activity and redox potentials as well as longer-term changes in community composition. We also explore the wide-ranging consequences these changes may have for local ecosystems, human communities and the global climate. Finally, we outline the knowledge gaps in cryosphere microbial ecology that contribute to uncertainties about the future of these ecosystems in a warming world.}, }
@article {pmid41192073, year = {2025}, author = {McDonagh, F and Kovarova, A and Tumeo, A and O'Connor, A and McEvoy, N and Lonappan, AM and Venkateswaran, K and Murray, EK and Hallahan, B and Miliotis, G}, title = {Complete genome and comparative genomic analysis of cefpodoxime resistant Pantoea septica strain GABEPS69 isolated from saliva of a patient diagnosed with treatment resistant schizophrenia.}, journal = {International journal of medical microbiology : IJMM}, volume = {321}, number = {}, pages = {151681}, doi = {10.1016/j.ijmm.2025.151681}, pmid = {41192073}, issn = {1618-0607}, abstract = {OBJECTIVES: This study aims to generate the first complete genome of Pantoea septica and provide a thorough genomic characterisation of this under-documented species. The study seeks to enhance understanding of P. septica, clarifying features relevant to opportunistic infection in vulnerable cohorts.<br><br>METHODS: P. septica GABEPS69 was an opportunistic coloniser isolated from the saliva of a patient prescribed the antipsychotic clozapine, leading to a dysbiotic oral microbiome. A hybrid sequencing approach yielded a closed genome comprising a 4.1&#x202f;Mb chromosome and six plasmids. Phenotypic susceptibility was determined by disk-diffusion and minimum inhibitory concentration (MIC) assays. Its chromosomal and plasmidic content was bioinformatically analysed alongside all canonical GenBank available P. septica genomes and the type strains of taxonomic neighbours Pantoea piersonii and "Pantoea latae", with focus on virulence-factors (VFs), antimicrobial-resistance-genes (ARGs), metal-resistance-genes (MRGs) and biosynthetic gene clusters.<br><br>RESULTS: GABEPS69 exhibited a narrow resistance spectrum, displaying resistance to the third-generation cephalosporin cefpodoxime. Plasmid pGABEPS69_1 harboured an aerobactin pathogenicity island homologue; a locus implicated in enhanced virulence, that was also identified across most other P. septica genomes and in the closely related human-pathogen Pantoea piersonii. A conserved chromosomal class-A &#x3b2;-lactamase homologue was also identified. Additionally, a universal presence of bioactive thiopeptide biosynthetic-gene-clusters was observed in P. septica genomes, suggesting a potential role in microbiome modulation.<br><br>CONCLUSION: This study presents a first complete genome of P. septica, revealing its genomic architecture, resistance, and virulence potential. Detailed plasmid analysis and comparative genomics enhance our understanding of the species clinical relevance and microbiome-modulating capacity. These findings motivate surveillance of transient oral microbiota in at-risk populations, including patients receiving clozapine.}, }
@article {pmid41191617, year = {2025}, author = {Rivas-Santisteban, J and Fernández-González, N and Laso-Pérez, R and Tamames, J and Pedrós-Alió, C}, title = {Picoplankton nitrogen guilds in the tropical and subtropical oceans: From the surface to the deep.}, journal = {PloS one}, volume = {20}, number = {11}, pages = {e0335222}, doi = {10.1371/journal.pone.0335222}, pmid = {41191617}, issn = {1932-6203}, mesh = {*Nitrogen/metabolism ; Oceans and Seas ; Ecosystem ; *Nitrogen Cycle ; Tropical Climate ; *Plankton/metabolism ; Seawater/microbiology ; *Phytoplankton/metabolism ; }, abstract = {Ecological guilds quantify the incidence and extent of resource transformation functions, irrespective of the species involved. Therefore, tackling the microbial nitrogen guilds is key to our understanding of the oceanic nitrogen cycle, but quantitative estimates of guild contribution across varying depths and under specific environmental conditions have yet to be accomplished. In this study, we examine the main picoplankton guilds participating in nitrogen cycling within the low and mid-latitude ocean ecosystems, from the surface down to 4000 m, using data obtained from 75 samples belonging to 11 stations in the Malaspina dataset. In particular, we used a quantitative approach to investigate the stability of nitrogen acquisition and nitrogen-redox guilds separately. Our results showed that nitrogen acquisition guilds are more stable and redundant than nitrogen-redox guilds across depths and site specific conditions. For example, differential conditions such as nitrogen depletion and oxygen availability affected the two groups of guilds in different ways. These findings have implications for the understanding of global nitrogen fluxes and the biosphere's functional diversification.}, }
@article {pmid41188621, year = {2025}, author = {Kwon, SL and Seo, CW and Kwon, H and Cho, M and Yoo, Y and Lee, SH and Kwon, DY and Lee, YM and Heo, YM and Kim, GH and Lim, YW and Lee, D and Choi, YS and Lee, H and Kim, JJ}, title = {Exploring Multifaceted Roles of Bambusicolous Apiospora in Phyllostachys bambusoides.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {115}, pmid = {41188621}, issn = {1432-184X}, support = {2021R1A2C1011894//National Research Foundation of Korea/ ; PN24120//Korea Polar Research Institute/ ; }, mesh = {*Endophytes/genetics/physiology/classification/isolation &amp; purification ; Symbiosis ; *Ascomycota/genetics/physiology/classification/isolation &amp; purification ; Plant Diseases/microbiology ; Mycobiome ; Soil Microbiology ; Phylogeny ; *Cyperaceae/microbiology ; Plant Roots/microbiology ; }, abstract = {Bamboo plays a crucial role in mitigating climate change. Among various microorganisms inhabiting bamboo, Apiospora is a common bambusicolous fungus that induces black spots, functioning either as a saprobe or as a plant pathogen. However, the diversity and ecological roles of Apiospora as an endophyte in bamboo remain poorly understood. This study explored the diversity and ecological functions of bambusicolous Apiospora in Phyllostachys bambusoides forests. Bamboo samples representing different stages-young (1-year-old, without black spots), mature (aged 3 years, few black spots), and dead (with many black spots)-were collected. Mycobiome analyses across different tissues (culm, leaf, root) and environmental samples (forest soil) revealed diverse Apiospora species throughout the bamboo lifecycle. Notably, Apiospora hysterina emerged as a prevalent endophyte, inhabiting not only mature but also younger, healthier bamboo stages. Biological activity assays, including antioxidant, antifungal, and plant hormone tests, indicated that A. hysterina exhibits potential mutualistic interactions beneficial to bamboo. Conversely, genomic analyses of carbohydrate-active enzyme profiles, effector/virulence factors, and putative biosynthetic gene clusters suggested potential pathogenic capabilities that may involve secondary metabolites, though functional validation is required. These findings reveal the widespread presence of Apiospora species as endophytes from the early to senescent bamboo stages, highlighting A. hysterina's dual capacity as a symbiont and pathogen. Our study underscores the complexity of bambusicolous Apiospora's ecological roles, emphasizing the need for further investigation into its interactions with bamboo ecosystems.}, }
@article {pmid41188517, year = {2025}, author = {Hettiarachchi, A and Tuerlings, T and Weekers, T and Marshall, L and Leclercq, N and Wood, TJ and Cejas, D and Gerard, M and Vereecken, NJ and Michez, D and Smagghe, G and Joossens, M and Vandamme, P}, title = {The Gut Microbial Community of Solitary Bees is Acquired through Host and Location Filtering.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {114}, pmid = {41188517}, issn = {1432-184X}, support = {3094785//Fonds Wetenschappelijk Onderzoek/ ; 3094785//Fonds De La Recherche Scientifique - FNRS/ ; }, mesh = {Animals ; Bees/microbiology/physiology ; *Gastrointestinal Microbiome ; *Fungi/classification/isolation &amp; purification/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; Europe ; Biodiversity ; }, abstract = {Species traits and environmental conditions are among the many factors that shape bee communities. Their effective conservation is currently challenged due to global changes. The gut microbiome likely contributes to bee plasticity and resilience but is largely understudied in solitary bees. A stable core microbiome in social bees has been identified to be important for health and survival in changing environmental conditions, but knowledge on a host-specific core microbiome in solitary bees is very scarce. In the present study, we analyzed the gut bacterial and fungal communities of eight solitary bee species commonly found in apple orchards along a latitudinal gradient throughout Europe. We aimed to understand the intra- and interspecific variations in the gut microbial communities and the extent to which host species and local environment shape the solitary bee gut microbiota. The bacterial community showed strong host effects, with each bee species having a distinct core bacterial community that was mostly stable across locations. The fungal community was most strongly influenced by the local environment, while different environmental variables were responsible for the variation in bacterial and fungal communities. Our study demonstrated that the examined solitary bee species harbor a distinct microbial diversity and composition, which undergoes host- and location-specific filtering.}, }
@article {pmid41059692, year = {2025}, author = {Bedi de Silva, A and Polson, SW and Schvarcz, CR and Steward, GF and Edwards, KF}, title = {Genomic diversity and global distribution of four new prasinoviruses from the tropical north Pacific.}, journal = {Microbiology spectrum}, volume = {13}, number = {11}, pages = {e0258324}, pmid = {41059692}, issn = {2165-0497}, support = {1559356, 2129697, 1736030//National Science Foundation/ ; Investigator Award in Marine Microbial Ecology and Evolution//Simons Foundation/ ; }, mesh = {*Genome, Viral/genetics ; Phylogeny ; Pacific Ocean ; *Genetic Variation ; Phytoplankton/virology ; Seawater/virology ; *Chlorophyta/virology ; *Phycodnaviridae/genetics/classification/isolation &amp; purification ; *DNA Viruses/genetics/classification/isolation &amp; purification ; }, abstract = {Viruses that infect phytoplankton are an integral part of marine ecosystems, but the vast majority of viral diversity remains uncultivated. Here, we introduce four near-complete genomic assemblies of viruses that infect the widespread marine picoeukaryote Micromonas commoda, doubling the number of reported genomes of Micromonas dsDNA viruses. All host and virus isolates were obtained from tropical waters of the North Pacific, a first for viruses infecting green algae in the order Mamiellales. Genome length of the new isolates ranges from 205 to 212 kb, and phylogenetic analysis shows that all four are members of the genus Prasinovirus. Three of the viruses form a clade that is adjacent to previously sequenced Micromonas viruses, while the fourth virus is relatively divergent from previously sequenced prasinoviruses. We identified 61 putative genes not previously found in prasinovirus isolates, including a phosphate transporter and a potential apoptosis inhibitor novel to marine viruses. Forty-eight genes in the new viruses are also found in host genome(s) and may have been acquired through horizontal gene transfer. By analyzing the coding sequences of all published prasinoviruses, we found that ~25% of prasinovirus gene content is significantly correlated with host genus identity (i.e., Micromonas, Ostreococcus, or Bathycoccus), and the functions of these genes suggest that much of the viral life cycle is differentially adapted to the three host genera. Mapping of metagenomic reads from global survey data indicates that one of the new isolates, McV-SA1, is relatively common in multiple ocean basins.IMPORTANCEThe genomes analyzed here represent the first viruses from the tropical North Pacific that infect the abundant phytoplankton order Mamiellales. Comparing isolates from the same location demonstrates high genomic diversity among viruses that co-occur and presumably compete for hosts. Comparing all published prasinovirus genomes highlights gene functions that are likely associated with adaptation to different host genera. Metagenomic data indicate these viruses are globally distributed, and one of the novel isolates may be among the most abundant marine viruses.}, }
@article {pmid41187907, year = {2025}, author = {Marrec, L and Bank, C}, title = {Drivers of diversity within and between microbial communities during stochastic assembly.}, journal = {Journal of the Royal Society, Interface}, volume = {22}, number = {232}, pages = {20250329}, doi = {10.1098/rsif.2025.0329}, pmid = {41187907}, issn = {1742-5662}, support = {//HORIZON EUROPE European Innovation Council/ ; //Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; }, mesh = {*Microbiota/physiology ; *Models, Biological ; Stochastic Processes ; *Biodiversity ; }, abstract = {No two microbial communities share the same species richness and abundance profiles. Experiments have shown that the assembly of new microbial communities from the same environmental pool is sufficient to generate diversity within and between communities: when microbial dispersal is slower than division, communities exhibit low richness but high between-community dissimilarity; when dispersal is faster, richness increases while dissimilarity decreases. Here, we study a minimal stochastic model that recovers these empirically observed assembly regimes. Our mathematical framework yields explicit expressions for the abundance fluctuation distributions across low-, intermediate- and high-dispersal regimes, providing a quantitative lens on microbiome assembly. We derive analytical predictions for the bimodality coefficient that quantifies the transition between assembly regimes, which appears as a robust metric to predict community richness and dissimilarity. Additionally, we highlight the mean relative abundance as a complementary metric sensitive to differences in microbial traits (e.g. dispersal or division rates). Applying these metrics to experimental data indicates their practical value for the rapid identification of assembly regimes and trait asymmetries. Overall, our study provides general predictions about how stochasticity, timescales and microbial traits influence both within-community diversity (richness) and between-community diversity (dissimilarity) during the assembly of new microbial communities. Our work thus contributes to a better understanding of the factors driving variation in microbiome formation.}, }
@article {pmid41185310, year = {2025}, author = {Wu, S and Li, Y and Zhang, H and Pan, Y and Yang, H and Tan, Y}, title = {Microbial community reshaping: Calcium chloride-heat treatment synergy in fresh-cut jackfruit preservation via antagonistic yeast enrichment.}, journal = {Food research international (Ottawa, Ont.)}, volume = {221}, number = {Pt 4}, pages = {117558}, doi = {10.1016/j.foodres.2025.117558}, pmid = {41185310}, issn = {1873-7145}, mesh = {*Calcium Chloride/pharmacology ; *Food Preservation/methods ; *Hot Temperature ; *Food Microbiology/methods ; *Fruit/microbiology ; *Artocarpus/microbiology ; Penicillium/drug effects/growth &amp; development ; *Yeasts/drug effects/growth &amp; development ; Antibiosis ; }, abstract = {Fresh-cut jackfruit is highly susceptible to microbial contamination and rapid spoilage due to mechanical damage and its nutrient-rich substrate. We evaluated calcium chloride combined with heat treatment (CH, 2 % CaCl2 - 55 °C) for controlling spoilage and preservation of fresh-cut jackfruit. The results identified Gilbertella hainanensis, Penicillium kongii, and P. citrinum as the dominant spoilage fungi in fresh-cut jackfruit. CH inhibited these fungi with in vitro inhibition rates of 80.14 %, 43.75 %, and 52.94 %, and corresponding in vivo rates of 83.1 %, 77.9 %, and 83.7 %, respectively. In vitro assays indicated CH compromises fungal membrane integrity, causing leakage of cellular contents. Further analysis revealed that CH markedly increased the relative abundance of the antagonistic yeast Meyerozyma guilliermondii (42.82 %, 8.13-fold vs. control) and was associated with reduced relative abundance of plant pathogenic and saprotrophic fungi. Correlation analysis linked dominant yeast genera to higher total phenolic content and reduced weight loss and other quality deterioration. Overall, CH treatment effectively delayed spoilage and preserved fruit physicochemical and nutritional quality, likely via direct antifungal effects and beneficial reshaping of the surface microbiome. These findings advance understanding of jackfruit postharvest microbial ecology and CH as a promising preservation strategy for fresh-cut jackfruit fruit.}, }
@article {pmid41184333, year = {2025}, author = {Ghosh, A and Maile, A and Nagarajaram, HA}, title = {Prokaryotic co-occurrence patterns in diverse Indian mangrove ecosystems.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {38283}, pmid = {41184333}, issn = {2045-2322}, mesh = {India ; *Wetlands ; Biodiversity ; *Bacteria/genetics/classification/isolation &amp; purification ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Ecosystem ; Phylogeny ; Soil Microbiology ; }, abstract = {Mangrove ecosystems are unique coastal zones known to harbour a rich biodiversity of flora and fauna, including microbial communities. These microorganisms play a crucial role in nutrient cycling and sustain the primary productivity driven by plants within this ecosystem. Recent advancements in microbial ecology research emphasise that microbial community structure and composition are critical for an ecosystem to thrive. Studies have focused on the microbial diversity within Indian mangrove forests; however, there is a limited understanding of the co-occurrence patterns and functional roles of microbial communities in these ecosystems. This study explores prokaryotic diversity, primarily focusing on community interactions across three major Indian mangrove forests: the Bhitarkanika mangrove forest in Odisha, the Goan mangroves, and the Sundarbans in West Bengal. By analysing the publicly available 16 S rRNA amplicon datasets of the Indian mangrove microbiomes and performing co-occurrence network analysis on these datasets, we identified positively correlated genera and their predicted functional roles. Furthermore, the findings revealed the co-occurrence of several pathogenic bacteria in two of the mangrove ecosystems. Overall, our study highlights the shared functional roles adopted by co-occurring microbes in three major Indian mangrove ecosystems and suggests the need for large-scale studies in these understudied Indian ecosystems.}, }
@article {pmid41183683, year = {2025}, author = {Ali, S and Burke, LP and Fitzpatrick, F and Fitzgerald-Hughes, D}, title = {A Scoping Review of Disinfection Strategies for Carbapenemase-Producing Enterobacterales (CPE) in Hospital Water Systems.}, journal = {The Journal of hospital infection}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jhin.2025.10.021}, pmid = {41183683}, issn = {1532-2939}, abstract = {BACKGROUND: Carbapenemase-producing Enterobacterales (CPE) pose a global health crisis. Their resistance to conventional antimicrobials and many disinfectants, increases the healthcare costs of treatment and risk mitigation. Hospital water systems are reservoirs for CPE, necessitating targeted infection prevention and control (IPC) strategies.<br><br>OBJECTIVE: To review and consolidate current evidence of disinfection strategies for CPE in hospital water systems, focusing on practical application, challenges and IPC integration.<br><br>METHODOLOGY: A scoping review was conducted following PRISMA guidelines, encompassing studies from 1[st] December 2014 to 31[st] December 2024. Of 1,188 records screened, 22 met inclusion criteria. Thematic analysis categorised findings into chemical, physical and integrative strategies.<br><br>KEY FINDINGS: Sodium hypochlorite and hydrogen peroxide reduced contamination temporarily but were poorly effective against biofilms, while acetic acid showed consistent efficacy with regular use. Quaternary ammonium compounds proved effective but required standardised protocols. Physical interventions, such as steam cleaning and drain covers, reduced contamination; and plumbing modifications minimised biofilm formation. Resource-intensive measures, like removing contaminated sinks or adopting water-free environments were also effective. Integrative approaches combining chemical disinfection, infrastructural upgrades and enhanced sink protocols demonstrated the most sustained outcomes, with novel technologies like UV light and biofilm-targeting foams showing great promise.<br><br>CONCLUSION: Effective CPE control in hospital water systems requires multidisciplinary action addressing biofilm-protected reservoirs. Regular application of proven disinfectants, tailored to specific contexts, coupled with infrastructural upgrades and comprehensively implemented IPC strategies, offers the most promising outcomes. Novel technologies and updated guidelines are essential to standardising practices and mitigating the broader threat of antimicrobial resistance.}, }
@article {pmid41180493, year = {2025}, author = {Choi, JM and Wu, X and Zhang, L}, title = {FastST: an efficient tool for inferring decomposition and directionality of microbial communities.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e20161}, pmid = {41180493}, issn = {2167-8359}, mesh = {*Microbiota ; Humans ; Bayes Theorem ; Computer Simulation ; *Software ; *Computational Biology/methods ; }, abstract = {Microbiomes play crucial roles in human health, disease development, and global ecosystem functioning. Understanding the origins, movements, and compositions of microbial communities is essential for unraveling the principles governing microbial ecology. Microbial source tracking (MST) approaches have emerged as valuable tools for quantifying the proportions of different microbial sources within target communities, enabling researchers to track transmissions between hosts and environments, identify similarities between microbiome samples, and determine sources of contamination in various settings. Current MST methods like SourceTracker2 and FEAST have advanced the field by employing Bayesian and expectation-maximization approaches, respectively, but are limited by computational inefficiency with high-dimensional data and inability to infer directionality in source-sink relationships. This study presents a novel computational framework for microbial source tracking called FastST. FastST infers the relative contributions of source environments to sink microbiomes while also determining directionality when source-sink relationships are not predefined. Through extensive simulation studies with varying numbers of sources and complexity, FastST demonstrates superior performance in both accuracy and computational efficiency compared to FEAST and SourceTracker2, maintaining consistent execution times even as the number of source environments increases. Furthermore, the proposed method achieved over 90% accuracy in directionality inference across all tested scenarios, even when multiple major sources are present, broadening its applicability in practical microbiome research and environmental monitoring. FastST and data simulation codes are publicly available at https://github.com/joungmin-choi/FastST.}, }
@article {pmid41178963, year = {2025}, author = {Whitehead, K and Eppinger, J and Srinivasan, V and Ugalde, JA}, title = {Microbial cross contamination in household laundering and microbial ecology of household washing machines.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1667606}, pmid = {41178963}, issn = {1664-302X}, abstract = {Household washing machines host diverse microbial communities that may include opportunistic pathogens, potentially impacting laundry hygiene and human health. However, our understanding of these communities and their transfer abilities remains limited. We examined microbial communities from 10 household washing machines (five front-load and five top-load) using surface swabs from specific hotspots and sterile sentinel washcloths. Samples were analyzed using culture-based methods and 16S rRNA/ITS metabarcoding. We tested microbial transfer during washing cycles with and without clothing and evaluated the effects of machine drying on this transfer. Front-load machines had significantly higher microbial loads than top-load machines (average bacterial counts: 6.50 ± 2.46 Log10/swab vs. 3.79 ± 1.73 Log10/swab). The microbial community composition was mainly shaped by the machine user rather than the machine type or sampling location. The dominant bacterial genera included Pseudomonas, Micrococcus, and Sphingomonas, while Aspergillus, Cladosporium, and Penicillium dominated the fungal communities. Opportunistic microorganisms were identified, but no highly pathogenic species (pathogenicity score 3) were found. Machine drying did not significantly decrease microbial loads, whereas the presence of soiled clothing impacted community composition. Household washing machines host user-specific microbial communities, including potential opportunistic pathogens. Current laundry practices may be inadequate for the complete elimination of pathogens, especially in immunocompromised individuals. These results support the need for additional household laundry sanitization strategies.}, }
@article {pmid41177050, year = {2025}, author = {Su, F and Li, Y and Zhu, C and Gurmesa, GA and Fang, Y}, title = {Impact of freeze-thaw cycle on metagenomics in subsurface wastewater infiltration systems: Ecological implications for greenhouse gas emissions.}, journal = {Journal of environmental management}, volume = {395}, number = {}, pages = {127839}, doi = {10.1016/j.jenvman.2025.127839}, pmid = {41177050}, issn = {1095-8630}, abstract = {Nitrous oxide (N2O) is a potent greenhouse gas, with a global warming potential 273 times that of carbon dioxide (CO2) and is a significant byproduct of wastewater treatment. Subsurface wastewater infiltration systems (SWIS) effectively treat nitrate-rich wastewater but can also contribute to N2O emissions, particularly during freeze-thaw cycles. This study used metagenomics and [15]N isotope tracing to investigate the impacts of freeze-thaw on microbial ecology and nitrogen transformation in SWIS. Results show that freeze-thaw significantly increased abundances of denitrifying bacteria (Bradyrhizobium, Streptomyces and Nocardioides), on average, by 16-63 %. Denitrification genes (nirK and norB) were also increased by 40 ± 16 % and 22 ± 5 %, while the N2O reductase gene (nosZ) decreased by 19 ± 0.46 %. These impacts collectively increased N2O emissions by more than 20 %. During freezing, about one-third of the added [15]NO3[-]-N was recovered as gas (25 % as N2O and 13 % as N2), increasing to 43 % during thawing (29 % N2O and 15 % N2). This study underscores the need for targeted strategies N2O emission in SWIS, particularly under freeze-thaw conditions, to maximize their sustainability in wastewater treatment.}, }
@article {pmid41175425, year = {2025}, author = {Awasthi, A and Sandal, A and Mahajan, R and Kaundal, R and Sharma, N and Sharma, S}, title = {Fermentation induced changes in physicochemical properties, antioxidant activity, total sugars, and comprehensive polyphenolic profiles of the Rhododendron-infused wine blends.}, journal = {Food chemistry}, volume = {496}, number = {Pt 2}, pages = {146743}, doi = {10.1016/j.foodchem.2025.146743}, pmid = {41175425}, issn = {1873-7072}, abstract = {This study evaluated the sensory, physicochemical, and functional attributes of seven experimental wine formulations incorporating apple juice, ginger, honey or sucrose, and varying levels of Rhododendron arboreum flower juice. Sensory scores revealed significant improvements in color, aroma and sweetness in rhododendron-enriched blends, with Treatment T7 (apple + honey + ginger + R. arboreum) achieving the highest overall acceptability. Physicochemical analyses showed variations in titratable acidity (0.19-0.51 %), alcohol (9.50-11.97 %), and ascorbic acid (4.76-8.53 mg/100 mL), influenced by substrate composition and sweetener type. Inclusion of R. arboreum substantially enhanced total phenolic (up to 19.78 mg GAE/mL) and flavonoid levels (25.84 mg QE/mL) alongside targeted compounds such as quercetin and caffeic acid. Antioxidant assays also confirmed superior radical scavenging activity. Multivariate analyses highlighted strong correlations between polyphenolic content and antioxidant performance. Overall, R. arboreum addition improved both sensory appeal and functional properties, supporting its potential in functional wine development.}, }
@article {pmid41174663, year = {2025}, author = {Waclawiková, B and Schwalbe, M and Ilyaskina, D and Toptas, S and Thome, NU and Du, C and Elsayed, SS and de Jong, A and van Wezel, GP and El Aidy, S}, title = {Serotonin modulation of metabolism and stress response in Pseudomonas fluorescens.}, journal = {BMC biology}, volume = {23}, number = {1}, pages = {330}, pmid = {41174663}, issn = {1741-7007}, mesh = {*Pseudomonas fluorescens/metabolism/physiology/genetics ; *Serotonin/metabolism/analogs &amp; derivatives ; Oxidative Stress ; *Stress, Physiological ; }, abstract = {BACKGROUND: Pseudomonas fluorescens is a Gram-negative bacterium with a remarkable metabolic and physiological versatility that enables it to adapt and colonize diverse ecological niches, including the human small intestine. While serotonin is primarily found in high concentrations in gut tissue, its levels in the lumen can be elevated in conditions such as celiac disease, where P. fluorescens is also found in increased abundance. The potential effects of serotonin on P. fluorescens in such contexts remain unclear.<br><br>RESULTS: We demonstrate that P. fluorescens metabolizes serotonin primarily into 5-hydroxyindole-3-acetic acid (5-HIAA) and, to a lesser extent, into 5-hydroxytryptophol and N-acetylserotonin. Gene expression analysis revealed significant changes in oxidative stress-related pathways over time, and proteomic analysis confirmed the shifts seen particularly in amino acid catabolic pathways. Serotonin metabolism also enhanced bacterial resistance to oxidative stress, suggesting a protective role.<br><br>CONCLUSIONS: The findings reveal a novel mechanism by which serotonin modulates the metabolism and stress responses of P. fluorescens. This study provides insight into how P. fluorescens adapts to serotonin-rich environments, such as in celiac disease, and may inform future research on microbial interactions with host-derived metabolites in disease contexts.}, }
@article {pmid41174295, year = {2025}, author = {Afonso, AC and Simões, M and Saavedra, MJ and Simões, L and Lema, JM and Trueba-Santiso, A}, title = {Physicochemical, Structural, and Proteomic Insights into Drinking Water-Isolated Acinetobacter calcoaceticus Aggregation and Biofilm Dynamics.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {113}, pmid = {41174295}, issn = {1432-184X}, mesh = {*Biofilms/growth &amp; development ; Proteomics ; Bacterial Proteins/metabolism/genetics ; *Acinetobacter calcoaceticus/physiology/isolation &amp; purification/genetics ; *Drinking Water/microbiology ; *Bacterial Adhesion ; Proteome ; }, abstract = {Acinetobacter calcoaceticus, a ubiquitous Gram-negative bacterium, exhibits remarkable adaptability across diverse environments, including drinking water distribution systems (DWDS), where its biofilm-forming and coaggregation capabilities pose significant public health challenges. This study integrates physicochemical, structural, and proteomic analyses to elucidate the mechanisms underlying A. calcoaceticus aggregation and biofilm dynamics. Surface characterization through contact angle measurements, zeta potential, and co-adhesion energy assessments revealed a predominantly hydrophilic surface with strong electron donor properties and a highly negative charge, promoting intercellular adhesion. Transmission electron microscopy unveiled dense cellular aggregates with extracellular filamentous structures, indicative of enhanced cell-to-cell interactions and potential extracellular polymeric substance involvement. Proteomic profiling identified 2593 differentially expressed proteins between aggregation stages, highlighting metabolic shifts, stress response activation, and upregulation of biofilm-associated proteins, including chaperones and quorum-sensing regulators. Our multidisciplinary approach emphasizes the importance of surface characterization in understanding bacterial community and underscores the critical role of physicochemical properties and proteomic flexibility in A. calcoaceticus biofilm and aggregation ability.}, }
@article {pmid41174268, year = {2025}, author = {Almansour, A and Akkaya, SN and Akbulut, S and Adiguzel, G and Yilmaz, B and Adiguzel, A}, title = {Biogenic Amine Degradation by Lactic Acid Bacteria Isolated from Home-Made White Cheese: Molecular and HPLC-Based Assessment.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {41174268}, issn = {1867-1314}, abstract = {Due to the potential health risks to humans associated with biogenic amines (BAs) accumulation in cheeses and other foods, this study is the first of its kind on Erzurum home-made white cheese to investigate the presence of BA-degrading lactic acid bacteria (LAB). Polymerase chain reaction (PCR) was applied for all putative LAB strains to detect the presence of (hdcA, cadA, tdcA, and odc) genes responsible for BA formation (histamine, cadaverine, tyramine, and putrescine, respectively). Only 72% of all strains showed amplicons for hdcA and tdcA, and no strains were found to have cadA, ldc, and odc genes. High-performance liquid chromatography (HPLC) analysis confirmed these findings. Furthermore, 12% of BA-nonproducing LAB have the sufI gene responsible for Multicopper Oxidases (MCOs) production. HPLC analysis was then applied to these strains to investigate their ability to degrade BAs. Nine strains were found to have degradation abilities with optimal conditions at pH 4.5-5.5 and 32-37 °C. Importantly, analysis of twenty home-made white cheeses revealed that the levels of BAs were within safe limits. This research provides valuable insights into the microbial ecology of these cheeses and highlights the potential of utilizing indigenous LAB for controlling BA formation and improving cheese quality.}, }
@article {pmid41171124, year = {2025}, author = {Lv, J and Ma, S and Ma, C and Liu, F and Duan, X and Huang, X and Geng, Q and Liu, F and Li, G and Li, Y and Wang, J and Li, C and Zheng, H and Zhang, Y and Sun, Z and Wang, J and Fan, G and Huang, S and Zhang, L and Bao, Z and Wang, S}, title = {Ocean-M: an integrated global-scale multi-omics database for marine microbial diversity, function and ecological interactions.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkaf1098}, pmid = {41171124}, issn = {1362-4962}, support = {2024YFC2816000//National Key Research and Development Program of China/ ; LSKJ202202804//Marine S&amp;T Fund of Shandong Province for Laoshan Laboratory/ ; 2025B1111180001//Guangdong Provincial Key Areas R&amp;D Program Project/ ; SOLZSKY2025013//Hainan Province Science and Technology Special Fund/ ; 32573498//Natural Science Foundation of China/ ; 32222085//Natural Science Foundation of China/ ; QDLYY-2024011//Blue Seed Industry Science and Technology Innovation Project/ ; GZB20250215//Postdoctoral Fellowship Program of CPSF/ ; }, abstract = {Multi-omics analyses have significantly advanced the understanding of complex marine microbial communities and their interactions. Despite notable progress from recent large-scale ocean meta-analysis efforts, the effective integration and accessibility of these diverse datasets remain challenging. To address this, we introduce Ocean-M (http://om.qnlm.ac), a comprehensive and publicly accessible platform for marine microbial multi-omics data integration, analysis, and visualization. Ocean-M provides a systematic view of 54 083 high-quality metagenome-assembled genomes, including genome assembly statistics, genome clustering, gene annotation, and interactive tools for global-scale taxonomic profiling. The platform also incorporates microbial community networks, host-microbiome interactions, and environmental DNA datasets to support an integrated ecological framework for studying microbial interactions and ecosystem functions. Additionally, Ocean-M enables large-scale mining of ecologically and biotechnologically important genes, with curated catalogs of 151 798 biosynthetic gene clusters, 52 699 antibiotic resistance genes, and millions of carbohydrate-active enzymes and plastic-active enzymes. By combining multi-omics data with environmental metadata, Ocean-M serves as a valuable resource for advancing marine microbial ecology, global biogeography, and functional gene discovery.}, }
@article {pmid41169038, year = {2025}, author = {Buccola, MJ and Satheesh Babu, AK and Paz, HA and Porter, ND and Srinivasan, H and Ricks, RL and Rosquist, K and Torres, JL and Zhong, Y and Jalili, T and Wankhade, UD and Anandh Babu, PV}, title = {Dietary Prebiotics Modulate Omeprazole-Induced Alterations in the Gut Microbial Signature.}, journal = {Molecular nutrition &amp; food research}, volume = {}, number = {}, pages = {e70307}, doi = {10.1002/mnfr.70307}, pmid = {41169038}, issn = {1613-4133}, abstract = {Proton pump inhibitors (PPIs) are commonly used to treat heartburn and acid-related disorders. However, their misuse and prolonged use contribute to gut dysbiosis. This study investigated whether well-known prebiotic dietary sources, blueberries or strawberries, can reverse PPI (omeprazole) induced dysbiosis and gut inflammation by modulating gut microbes. Male C57BL/6J mice (7 weeks old) were fed a diet with or without omeprazole (40 mg/kg diet), blueberry (3.7% in the diet; ∼1.5 human servings) or strawberry (2.35% in the diet; ∼2 human servings) for 12 weeks. Metabolic parameters, gut microbes (in the cecum and colon), and inflammatory markers were assessed. In this study, no changes were observed in metabolic parameters in mice fed a diet supplemented with omeprazole or berries. Second, blueberry or strawberry supplementation at nutritional dosages improved alterations in gut microbial ecology induced by omeprazole, with effects varying between the cecum and colon. Third, strawberry supplementation reduced omeprazole-induced gut inflammation. Fourth, selected genera were either positively or negatively associated with markers of gut inflammation, suggesting that dietary berries can ameliorate inflammatory signaling through modifications in the gut microbiome. Dietary berries represent a potential nutritional strategy for improving PPI-induced gut dysbiosis and inflammation.}, }
@article {pmid41168937, year = {2025}, author = {Brangarí, AC and Knorr, MA and Frey, SD and Rousk, J}, title = {Shifts in Microbial Thermal Traits Mitigate Heat-Induced Carbon Losses in Soils.}, journal = {Global change biology}, volume = {31}, number = {11}, pages = {e70579}, doi = {10.1111/gcb.70579}, pmid = {41168937}, issn = {1365-2486}, support = {2022-01478//Svenska Forskningsr&#xe5;det Formas/ ; CTS 22: 2131//Carl Tryggers Stiftelse f&#xf6;r Vetenskaplig Forskning/ ; KAW 2022.0175//Knut och Alice Wallenbergs Stiftelse/ ; KAW 2023.0384//Knut och Alice Wallenbergs Stiftelse/ ; DEB-1832110//National Science Foundation/ ; DEB-1456610//National Science Foundation/ ; }, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Hot Temperature ; *Carbon/metabolism/analysis ; *Global Warming ; *Carbon Cycle ; Carbon Dioxide/metabolism ; Forests ; }, abstract = {Global warming is expected to transfer carbon from soil organic matter to atmospheric CO2, with microbial communities playing a crucial role in regulating this exchange. While the immediate impact of temperature on microbial functions is well understood and causes soil carbon losses, the long-term response remains unclear, with losses stabilising over time, reducing the overall effect of chronic warming on soil organic carbon (SOC) stocks. Here, we examined the temperature dependence of microbial respiration and growth after 9 years of +5°C warming in a temperate forest. Using these temperature dependences and field temperature data, we modelled in situ carbon fluxes and changes in SOC stocks. Results showed that the direct effect of temperature initially increased respiration and growth, projecting a potential 31% SOC stock loss if the trend had persisted. However, the gradual optimisation of microbial traits to warming balanced the direct temperature effects, enhanced carbon use efficiency and offset CO2 emissions. Together, these microbial trait shifts limited the heat-induced SOC loss to 15%, closely aligning with empirical observations. These findings suggest that microbial trait optimisation can moderate carbon emissions, providing a parsimonious mechanistic explanation for observations worldwide and underscoring the need to integrate microbial dynamics into models.}, }
@article {pmid41168882, year = {2025}, author = {Bowers, RM and Bennett, S and Riley, R and Villada, JC and Da Silva, IR and Woyke, T and Frank, AC}, title = {Host species and geographic location shape microbial diversity and functional potential in the conifer needle microbiome.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {222}, pmid = {41168882}, issn = {2049-2618}, support = {10.46936/10.25585/60000936//U.S. Department of Energy/ ; DEB-1442348//Directorate for Biological Sciences/ ; }, mesh = {*Microbiota/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; Metagenomics/methods ; *Tracheophyta/microbiology ; Metagenome ; Phylogeny ; *Plant Leaves/microbiology ; Pinus/microbiology ; }, abstract = {BACKGROUND: The aerial surface of plants, known as the phyllosphere, hosts a complex and dynamic microbiome that plays essential roles in plant health and environmental processes. While research has focused on root-associated microbiomes, the phyllosphere remains comparatively understudied, especially in forest ecosystems. Despite the global ecological dominance and importance of conifers, no previous study has applied shotgun metagenomics to their phyllosphere microbiomes.<br><br>RESULTS: This study uses metagenomic sequencing to explore the microbial phyllosphere communities of subalpine Western conifer needle surfaces from 67 trees at six sites spanning the Rocky Mountains, including 31 limber pine, 18 Douglas fir, and 18 Engelmann spruce. Sites span&#x2009;~&#x2009;1,075&#xa0;km and nearly 10&#xb0; latitude, from Glacier National Park to Rocky Mountain Biological Laboratory, capturing broad environmental variation. Metagenomes were generated for each of the 67 samples, for which we produced individual assemblies, along with three large coassemblies specific to each conifer host. From these datasets, we reconstructed 447 metagenome-assembled genomes (MAGs), 417 of which are non-redundant at the species level. Beyond increasing the total number of extracted MAGs from 153 to 294, the three coassemblies yielded three large MAGs, representing partial sequences of host genomes. Phylogenomics of all microbial MAGs revealed communities predominantly composed of bacteria (n&#x2009;=&#x2009;327) and fungi (n&#x2009;=&#x2009;117). We show that both microbial community composition and metabolic potential differ significantly across host tree species and geographic sites, with site exerting a stronger influence than host.<br><br>CONCLUSIONS: This dataset offers new insights into the microbial communities inhabiting the conifer needle surface, laying the foundation for future research on needle microbiomes across temporal and spatial scales. Variation in functional capabilities, such as volatile organic compound (VOC) degradation and polysaccharide metabolism, closely tracks shifts in taxonomic composition, indicating that host-specific chemistry, local environmental factors, and regional microbial source pools jointly shape ecological roles. Moreover, the observed patterns of mobile genetic elements and horizontal gene transfer suggest that gene exchange predominantly occurs within microbial lineages, with occasional broader transfers dispersing key functional genes (e.g., those involved in polysaccharide metabolism), which may facilitate microbiome adaptation.}, }
@article {pmid41168506, year = {2025}, author = {Martinez-Urtaza, J}, title = {From clonality to complexity: a journey through microbial ecology and evolution.}, journal = {Nature reviews. Genetics}, volume = {}, number = {}, pages = {}, pmid = {41168506}, issn = {1471-0064}, }
@article {pmid41165314, year = {2025}, author = {Nauwynck, W and Sakarika, M and Faust, K and Boon, N}, title = {Differential recovery of chain-elongating bacteria: comparing droplet, plating, and dilution-to-extinction methods.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0135625}, doi = {10.1128/msystems.01356-25}, pmid = {41165314}, issn = {2379-5077}, abstract = {Microbial chain elongation via reverse β-oxidation offers a more sustainable route to produce medium-chain fatty acids like caproate, commodity chemicals typically produced via (petro)chemical processes. Thermophilic anaerobic microbiomes allow production at a high rate and selectivity but remain poorly understood due to the limited cultivability of their members. To better access functional taxa from a thermophilic chain-elongating reactor community, we applied multiple isolation strategies: conventional anaerobic plating, dilution-to-extinction (DTE), droplet-based microfluidics, and fluorescence-activated cell sorting (FACS). We evaluated the taxonomic range and cultivation success of each method using 16S rRNA gene sequencing. Each method yielded a distinct subset of microbial taxa. While Clostridium acetireducens-related strains were consistently isolated across all strategies, key thermophilic chain elongators (e.g., Thermocaproicibacter melissae-like organisms) only appeared in DTE. Droplet microfluidics enriched the most unique taxa in total, mostly rare taxa, including Caproicibacter and Thermoanaerobacterium spp. Plating yielded the lowest diversity, recovering only dominant taxa. FACS-based approaches failed to yield isolates, likely due to stress during processing. Comparing droplet-based isolation to DTE revealed critical insights: although droplets offer higher throughput, which intrinsically increases the chance of capturing rare taxa, not all DTE-cultivated organisms grew in droplets. This suggests additional contributing factors (apart from an increased throughput), such as encapsulation stress and droplet-specific microenvironments. These findings clarify the advantages and limitations of droplet cultivation strategies, allowing a more informed application of these techniques to access the so-called "microbial dark matter."IMPORTANCEMany environmentally and industrially relevant microbes remain uncultured, limiting our ability to understand and use them. This is especially true in thermophilic anaerobic microbiomes, which are promising systems for producing sustainable chemicals from organic waste streams. In this study, we explored how different cultivation strategies influence which microbes can be isolated from a thermophilic chain-elongating reactor. By comparing traditional and novel methods, including droplet microfluidics, we showed that each method recovers a unique set of microbes. While droplet-based methods enable high sampling depth with minimal effort and excel at isolating rare microbes, we found that they also introduce clear biases, as certain organisms recovered by other methods did not grow in droplets. Our work highlights the importance of the cultivation method in isolation success and helps shine a light on the selective forces at play in droplet-based microbial isolation.}, }
@article {pmid41165014, year = {2025}, author = {Freudenthal, J and Schlegel, M and Bonkowski, M and Dumack, K}, title = {A Novel Protistan Trait Database Reveals Functional Redundancy and Complementarity in Terrestrial Protists (Amoebozoa and Rhizaria).}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e70064}, doi = {10.1111/1755-0998.70064}, pmid = {41165014}, issn = {1755-0998}, support = {221301018//Deutsche Forschungsgemeinschaft/ ; 447013012//Deutsche Forschungsgemeinschaft/ ; SPP 1991//Deutsche Forschungsgemeinschaft/ ; }, abstract = {The inclusion of functional traits of protists in environmental sequencing surveys, in addition to the traditional taxonomic framework, is essential for a better understanding of their roles and impacts on ecosystem processes. We provide a database of functional traits for a widespread and important clade of protists-the Amoebozoa-based on extensive literature research in eight trait categories: Habitat, locomotion, nutrition, morphology, morphotype, size, spore formation, and disease-relatedness. The comparison of community traits of the Amoebozoa with sympatric but highly divergent Cercozoa (Rhizaria) revealed both convergent evolution of morphology or locomotion and distinct differences in habitat preference and feeding selectivity. Amoebozoa seem to be rather unselective in their prey choice compared to Cercozoa. Indeed, the feeding preferences of Amoebozoa appeared to be related to cell size, whereas Cercozoa selectively feed on prey. Applications to metatranscriptomic data from soil, litter, and bark surfaces revealed differences in the average community trait compositions and ecosystem functioning, such as an increased proportion of disease-related Amoebozoa in soil or different proportions of nutrition types of Amoebozoa and Cercozoa on bark. This database will facilitate ecological analyses of sequencing data and improve our understanding of the diversity of adaptations of Amoebozoa to the environment and their functional roles in ecosystems.}, }
@article {pmid41164406, year = {2025}, author = {Sierra, AM and Escolástico-Ortiz, DA and Zartman, CE and Derome, N and Lovejoy, C and Villarreal A, JC}, title = {Assembly and co-occurrence networks of nitrogen-fixing bacteria associated with epiphyllous liverworts in fragmented tropical forests.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf173}, pmid = {41164406}, issn = {2730-6151}, abstract = {Understanding the spatial dynamics of plant-associated microbial communities is increasingly urgent in the context of habitat loss and the biodiversity crisis. However, the influence of reduced habitat size and connectivity on the assembly mechanisms underlying microbial associations is fundamental to advancing microbial ecology and conservation. In the Brazilian Amazon, we investigated nitrogen-fixing (diazotrophic) bacterial communities associated with two epiphyllous liverworts, Cololejeunea surinamensis and Radula flaccida, across 11 forest sites within the Biological Dynamics of Forest Fragments Project landscape. Using amplicon sequencing targeting the nitrogenase gene (nifH), we characterized diazotroph community diversity, inferred assembly mechanisms through null models, and analyzed co-occurrence network structure. Host-specific associations were evident: C. surinamensis predominantly hosted Hassallia, while R. flaccida was primarily associated with Fischerella. Despite habitat fragmentation, diazotrophic richness and composition remained similar across habitats of different sizes, consistent with strong homogenizing dispersal. Network analyses revealed that smaller fragments harbored more modular communities with fewer module hubs, pronounced shifts in key species relative abundance, and reduced network robustness. Our findings underscore the influence of habitat size on the stability of liverwort-associated diazotrophs, with smaller fragments exhibiting lower key species specificity and disruption of microbe-microbe interactions. Our results emphasize the importance of conserving large, connected forest habitats to maintain the functional integrity of phyllosphere N-fixing microbiota.}, }
@article {pmid41164176, year = {2025}, author = {Cai, S and Lin, L and Cai, Y and Wang, C and Lin, Y and Zhou, J and Zhou, F and Chen, M}, title = {Correction: Phase angle associates with severity and mortality in acute-on-chronic liver failure.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1695643}, doi = {10.3389/fmed.2025.1695643}, pmid = {41164176}, issn = {2296-858X}, abstract = {[This corrects the article DOI: 10.3389/fmed.2025.1541795.].}, }
@article {pmid41164007, year = {2025}, author = {Lerner, H and Eck, M and Link, C and Witt, T and Battagliarin, G and Mecking, S and Schleheck, D}, title = {Thermomonospora spp. are implicated in the biodegradation of long-chain aliphatic polyester bioplastics during thermophilic composting.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1671731}, pmid = {41164007}, issn = {1664-302X}, abstract = {Biodegradable plastics are an important component for achieving a circular polymer economy. To be considered biodegradable at the regulatory level, plastics must pass standardized tests, for example under industrial composting conditions at 58 °C (ISO 14855-1). Although such tests are frequently applied, little is known about the microorganisms catalyzing these degradation processes. Recently, bioplastics with properties similar to polyethylene, Long-Chain Aliphatic Polyesters (LCAP), for example polyester 1,18-octadecanediol-alt-1,18-octadecanedioic acid (abbreviated PE-18,18), were shown to biodegrade under industrial composting conditions. In this work, we analyzed the microbial communities that had developed in the compost treatments at the end of the biodegradation test for three different LCAPs (PE-18,18, PE-12,12 and PE-2,18) relative to the untreated controls, via amplicon-sequencing of bacterial 16S and fungal ITS2 rDNA. This revealed significant treatment-induced shifts in the bacterial communities (p < 0.05), with Pseudonocardia and Thermomonospora ASVs enriched in all LCAP-treated samples compared to the controls (p ≤ 0.0001), while no pronounced shifts were observed for the fungal community. Thermomonospora sequences showed high similarity to T. curvata DSM43183, which encodes the known polyester hydrolase Tcur1278, and the presence of gene tcur1278 was confirmed in LCAP-treated samples via PCR. Enzyme assays with heterologously expressed and partially purified Tcur1278 demonstrated its activity on PE-2,18 LCAP, releasing up to 230 μmol of soluble monomers over 48 h at 50 °C. Hence, our study implicated Thermomonospora species in LCAP degradation during thermophilic composting, based on taxonomic enrichment, and provided evidence linking the detected phylotypes to Tcur1278, the first bacterial enzyme demonstrated to depolymerize LCAP. It thereby is the first evidence for an ecological relevance of Tcur1278-encoding Thermomonospora phylotypes for bioplastic degradation in situ.}, }
@article {pmid41162221, year = {2025}, author = {Hodžić, A}, title = {The contribution of the Midichloria mitochondrii endosymbiont to Borrelia infection dynamics.}, journal = {Trends in parasitology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.pt.2025.10.003}, pmid = {41162221}, issn = {1471-5007}, abstract = {Recent studies have revealed a positive correlation between the presence of the Midichloria mitochondrii endosymbiont and Borrelia species in the tick vector, suggesting potential interactions that may influence pathogen infection and the transmission dynamics of Lyme borreliosis. This article discusses the possible mechanistic pathways underlying these interactions.}, }
@article {pmid41160321, year = {2025}, author = {de Azevedo, CS and Schork, IG and Passos, LF and Goodhead, I and Young, RJ}, title = {The domestic cat microbiome: mapping knowledge gaps through scientometric analysis in feline microbial research.}, journal = {Veterinary research communications}, volume = {50}, number = {1}, pages = {6}, pmid = {41160321}, issn = {1573-7446}, mesh = {Animals ; Cats/microbiology ; *Microbiota ; *Gastrointestinal Microbiome ; }, abstract = {In this study, we present the first comprehensive scientometric analysis of research on the domestic cat microbiome, providing a transparent and data-driven overview of the field. We examined 282 publications on the microbiome of domestic cats (Felis catus) to uncover dominant research themes, methodological patterns, microbial niches, and knowledge gaps. Our results reveal a sharp rise in publications since 2012, with a peak in 2024, where most work is concentrated in high-income countries and driven by a small number of academic institutions. Current efforts are heavily focused on the bacterial gut microbiome, typically using genomic tools for taxonomic profiling in comparative designs. In contrast, research on other microbial communities (e.g., oral or skin), non-bacterial taxa, functional analyses, and behavioural outcomes remains scarce, with behavioural studies virtually absent. Although some studies report health-related effects, mainly positive or neutral, the functional roles of the microbiota and their possible influence on feline behaviour remain largely unexplored. By mapping these trends and gaps, our study provides a strategic framework for advancing microbiome research in domestic cats. These findings highlight priority areas and methodological opportunities that can guide future investigations, foster interdisciplinary collaboration, and ultimately deepen our understanding of the intricate links between microbial ecology, feline health, and behaviour. Studies connecting the microbiome with feline diseases, behaviour, and diet are strongly encouraged, given their high applicability to everyday animal care and management. Such research has the potential to improve both feline health and welfare, while also strengthening the human-cat bond.}, }
@article {pmid41159880, year = {2025}, author = {,  and Cuthbertson, BH and Billot, L and Campbell, MK and Daneman, N and Davis, JS and Delaney, A and Devaux, A and Ferguson, ND and Finfer, SR and Fowler, R and Gordon, AC and Hammond, NE and Klein, G and Li, Q and Marshall, J and Micallef, S and Murthy, S and Mysore, J and Naik, C and Patel, C and Pinto, R and Rose, L and Seppelt, IM and Venkatesh, B and Young, PJ and Myburgh, JA}, title = {Selective Decontamination of the Digestive Tract during Ventilation in the ICU.}, journal = {The New England journal of medicine}, volume = {}, number = {}, pages = {}, doi = {10.1056/NEJMoa2506398}, pmid = {41159880}, issn = {1533-4406}, support = {1084244//National Health and Medical Research Council/ ; MYG-151210/CAPMC/CIHR/Canada ; PJT-153367/CAPMC/CIHR/Canada ; }, abstract = {BACKGROUND: Whether selective decontamination of the digestive tract (SDD) reduces mortality among patients undergoing mechanical ventilation and whether it adversely affects microbial ecology in the intensive care unit (ICU) remain unclear. In an earlier analysis of data from Australia, SDD did not result in a lower incidence of in-hospital death than standard care, but data from the full international trial are needed.<br><br>METHODS: We randomly assigned ICUs in Australia and Canada to use SDD or to continue standard care for two 12-month periods in patients undergoing mechanical ventilation. Patients in the SDD group received specific oral and gastric antimicrobial interventions for the duration of ventilation and an intravenous antibiotic agent for the first 4 days after enrollment. All other patients in the ICU were included in an observational ecologic assessment. Previously reported data from Australia are now combined with data from Canada. The primary outcome was in-hospital death from any cause at 90 days. The secondary clinical outcomes, assessed at 90 days, were death in the ICU and the number of days alive and free of mechanical ventilation, ICU admission, and hospitalization. Microbiologic secondary outcomes included new positive cultures for bloodstream infections and antibiotic-resistant organisms. For the ecologic assessment, the microbiologic outcomes were tested for noninferiority (noninferiority margin, 2 percentage points).<br><br>RESULTS: In this trial involving 20,000 patients in 26 ICUs, 9289 patients were enrolled in the randomized trial and 10,711 were included in the ecologic assessment. At 90 days, 1175 of 4215 patients (27.9%) in the SDD group and 1494 of 5065 (29.5%) in the standard-care group had died before hospital discharge (odds ratio, 0.93; 95% confidence interval [CI], 0.84 to 1.05; P&#x2009;=&#x2009;0.27). New bloodstream infections occurred in 4.9% of the patients in the SDD group and in 6.8% of those in the standard-care group (adjusted mean difference, -1.30 percentage points; 95% CI, -2.55 to -0.05); antibiotic-resistant organisms were cultured in 16.8% and 26.8%, respectively (adjusted mean difference, -9.60 percentage points; 95% CI, -12.40 to -6.80). In the ecologic assessment, noninferiority of SDD was not confirmed for the development of new antibiotic-resistant organisms. Adverse events considered to be related to SDD or standard care were reported in 12 patients (0.3%) in the SDD group and in no patients in the standard-care group. Serious adverse events occurred in 47 patients (1.1%) and 59 patients (1.2%), respectively.<br><br>CONCLUSIONS: Among critically ill patients undergoing mechanical ventilation, SDD did not result in a lower incidence of in-hospital death than standard care. (Funded by the National Health and Medical Research Council of Australia and the Canadian Institutes of Health Research; ClinicalTrials.gov number, NCT02389036.).}, }
@article {pmid41159723, year = {2025}, author = {Duan, Z and Yang, R and Lai, T and Jiang, W and Zhang, J and Chen, B and Liao, L}, title = {Development of a CRISPR/Cas9-induced gene editing system for Pseudoalteromonas fuliginea and its applications in functional genomics.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0177125}, doi = {10.1128/aem.01771-25}, pmid = {41159723}, issn = {1098-5336}, abstract = {Pseudoalteromonas has been used as a model system to study cold adaptation and is of widespread interest in biotechnology and ecology. To explore its physiological responses to extreme cold, uncover functional genes, and clarify their ecological roles, efficient genetic tools are essential. However, existing genetic manipulation methods in Pseudoalteromonas rely on traditional homology-based recombination, which is laborious and time-consuming in this bacterial system. Consequently, improving editing efficiency is crucial for advancing both basic research and applied potential. Here, we established a CRISPR/Cas9 system in Pseudoalteromonas and carried out an extensive investigation of the Type II CRISPR/Cas9 platform for gene editing in Pseudoalteromonas fuliginea, a representative species thriving in the frigid polar oceans. To validate the feasibility of the CRISPR/Cas system in P. fuliginea, multiple genes were selected as targets, and the gene editing effects were confirmed through phenotypic changes or gene expression. We have successfully achieved both gene knockouts and insertions in P. fuliginea, encompassing the deletion of genes such as fliJ, indA, and genes encoding Pf sRNAs, as well as the in vivo insertion of 3×FLAG and the gfp gene. The average CRISPR/Cas9 gene editing efficiency in P. fuliginea exceeded 70%. In summary, we developed an efficient CRISPR/Cas9-based editing system in P. fuliginea, which can be utilized to accelerate the development of Pseudoalteromonas as a model system for addressing fundamental questions related to extreme environmental adaptation and to fulfill its potential biotechnological applications.IMPORTANCEPseudoalteromonas fuliginea is a marine bacterium with great potential for ecological and biotechnological research, yet its genetic manipulation has long been a technical challenge. In this study, we developed a gene editing system based on CRISPR technology that enables efficient and precise genome modification in this organism. Using this system, we successfully deleted, inserted, and tagged multiple genes, including regulatory and non-coding elements, with high success rates. Notably, several of these genes are linked to key traits such as motility and stress response, which contribute to microbial adaptation in polar environments. This tool allows researchers to directly test gene function and study microbial adaptation in cold marine environments. The ability to perform reliable genetic edits in P. fuliginea opens new possibilities for its use as a model organism and will support future advances in microbial ecology, environmental microbiology, and marine biotechnology.}, }
@article {pmid41159286, year = {2025}, author = {Shirani, K and Mottaghi, A and Shabani, M}, title = {Honey as a Functional Food: Evaluating Its Antimicrobial Properties and Bacterial Safety Concerns.}, journal = {Foodborne pathogens and disease}, volume = {}, number = {}, pages = {}, doi = {10.1177/15353141251392181}, pmid = {41159286}, issn = {1556-7125}, abstract = {Honey is increasingly recognized as a functional food with intrinsic antimicrobial properties. Its complex chemical makeup, high sugar content, low water activity, acidic pH, hydrogen peroxide generation, and a spectrum of bioactive phytochemicals create a multifaceted defense against microbial growth, yet honey also harbors diverse microorganisms, including potential pathogens, underscoring the need for robust quality control and safety considerations across production, processing, and storage. This study synthesizes current evidence on the antimicrobial mechanisms of honey and evaluates bacterial safety concerns, with emphasis on probiotic potential and risks associated with pathogens such as Clostridium botulinum, to inform safe use and innovative functional food applications. A comprehensive review of existing literature and honey-specific data was conducted to collate chemical, microbiological, and safety-related parameters. Key antimicrobial mechanisms (osmotic pressure, acidic environment, hydrogen peroxide production, and bioactive compounds such as methylglyoxal in certain varieties) were mapped to their effects on diverse microbes. Safety considerations, contamination pathways, and regulatory frameworks were qualitatively assessed to identify critical control points. Honey's antimicrobial activity arises from synergistic interactions among sugars, pH, hydrogen peroxide, enzymes, and phytochemicals, yielding broad-spectrum inhibition. Beneficial lactic acid bacteria from honey and bees contribute probiotic potential, while the risk of contamination by pathogens necessitates stringent hygiene, processing controls, and adherence to quality standards. Processors can leverage nonthermal and thermal reduction methods to balance safety with the preservation of bioactive components. Honey remains a robust functional food with antimicrobial advantages and probiotic opportunities, provided that meticulous quality control and regulatory compliance are maintained to mitigate safety risks for vulnerable populations. Future work should optimize honey-based probiotic formulations and establish standardized safety protocols across the supply chain.}, }
@article {pmid41158777, year = {2025}, author = {Skoog, EJ and Cutts, E and Bosak, T}, title = {Linking microbial ecology to the cycling of neutral and acidic polysaccharides in pustular mats from Shark Bay, Western Australia.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1684648}, pmid = {41158777}, issn = {1664-302X}, abstract = {Cyanobacteria and other microbes in peritidal microbial mats have produced extracellular polymeric substances (EPS) for more than two billion years. The production and degradation of EPS contributes to the biogeochemical cycling of carbon and carbonate precipitation within modern microbial mats, but key microbes involved in the cycling of EPS remain unidentified. Here, we investigate the cycling of EPS in the peritidal pustular mats of Shark Bay, Western Australia. We characterize the chemical composition of EPS produced by cyanobacterial enrichment cultures under natural and UV-stress conditions and link these findings to the metabolic potential for EPS production and degradation encoded in 84 metagenome-assembled genomes (MAGs) from the mat community. We further identify the key microbial degraders of specific acidic and neutral polysaccharides in this community by cultivating enrichment cultures on seven commercially available polysaccharides representative of those present in the mats and assessing the dominant taxa. All sequenced Cyanobacteria MAGs have the potential to synthesize mannose, fucose, glucose, arabinose, rhamnose, galactose, xylose, N-acetylglucosamine, galacturonic acid and glucuronic acid. Biochemical analyses confirm the presence of nearly all these monosaccharides in the hydrolysates of EPS extracted from UV- and non-UV exposed cyanobacterial enrichments. Ultraviolet radiation influences the structure and composition of EPS by reducing the hydration, potentially due to cross-linking among polymers in EPS and increasing the relative abundances of uronic acids and xylose in polysaccharides. Analyses of carbohydrate-active enzymes (CAZymes) in the MAGs and of 16S rRNA sequences from experimental polysaccharide enrichments point to major roles for Bacteroidetes, Planctomycetes, and Verrucomicrobia in the cycling of acidic EPS. These experiments reveal a complex interplay among microbial community composition, CAZyme diversity, environmental stressors, and EPS cycling, which together shape carbon flow and biomineralization in pustular mats in Shark Bay.}, }
@article {pmid41156863, year = {2025}, author = {Rajput, AP and Sun, D and Zhou, S and Meegaskumbura, M}, title = {Distinct Gut and Skin Microbiomes of a Carnivorous Caecilian Larva (Ichthyophis bannanicus) Show Ecological and Phylogenetic Divergence from Anuran Tadpoles.}, journal = {Microorganisms}, volume = {13}, number = {10}, pages = {}, doi = {10.3390/microorganisms13102405}, pmid = {41156863}, issn = {2076-2607}, support = {Guangxi University's startup-funding to Madhava Meegaskumbura;Postdoctoral Project funding to Amrapali Prithvisingh Rajput//Guangxi University/ ; }, abstract = {The amphibian microbiome plays a vital role in host health, yet the bacterial communities of caecilians (Order: Gymnophiona) remain largely uncharacterised. We investigated this by providing the first characterisation of the gut and skin microbiome of larval Ichthyophis bannanicus, a carnivorous caecilian, using 16S rRNA gene metabarcoding. Our analyses show distinct communities between the faecal samples and skin, with significant enrichment of Laribacter in faeces and Flavobacterium on skin. Despite significant variation in their community structures, the core genera Escherichia-Shigella were shared between both regions, suggesting similar microbial exchange in the aquatic environments. Skin bacterial diversity exhibited relatively higher richness, but lower evenness than that of faeces. Further, the skin bacterial community exhibited more complex interactions, suggesting stronger resilience to changes. The relationships and interactions of skin and faecal bacterial communities suggest their interactive effects on the host's overall health. Compared with anuran tadpoles, the I. bannanicus larval microbiome showed taxonomic overlap, but possessed certain unique core bacteria. This work on an understudied amphibian lineage is foundational, highlighting how diet, phylogeny, and aquatic environment shape microbial communities and informing future research into amphibian health and disease.}, }
@article {pmid41156709, year = {2025}, author = {Liu, X and Zhao, G and Bai, J and Qu, X and Chai, J and Lin, D}, title = {Pediococcus pentosaceus OL77 Enhances Oat (Avena sativa) Silage Fermentation Under Cold Conditions.}, journal = {Microorganisms}, volume = {13}, number = {10}, pages = {}, doi = {10.3390/microorganisms13102248}, pmid = {41156709}, issn = {2076-2607}, support = {32160810//National Natural Science Foundation of China/ ; }, abstract = {Ensiling forage under low-temperature conditions often leads to poor fermentation and nutrient losses. This study evaluated the effects of a cold-tolerant Pediococcus pentosaceus OL77 strain on oat silage. Silages were prepared with or without Pediococcus pentosaceus inoculation (1 × 10[5] cfu/g FM). After 90 days, OL77-treated silage showed markedly higher lactic acid (45.83 vs. 30.51 g/kg DM), lower pH (3.88 vs. 4.443), and better preservation of WSC (64.68 vs. 47.60 g/kg DM) and crude protein (89.26 vs. 65.52 g/kg DM) than the control. Microbial analysis revealed accelerated colonization by Pediococcus, reduced bacterial diversity, and faster stabilization of the fermentation process. Functional predictions indicated enhanced carbohydrate and energy metabolism. These findings demonstrate that OL77 can effectively improve fermentation quality and nutrient preservation of oat silage under low-temperature conditions, offering a practical inoculant option for cold regions.}, }
@article {pmid41151518, year = {2025}, author = {Ouyang, S and Zhao, HP and Lai, CY}, title = {Propane-driven efficient BPA degradation in groundwater: Transformation pathways, microbial ecology and enzymatic mechanisms in a membrane biofilm reactor.}, journal = {Journal of hazardous materials}, volume = {499}, number = {}, pages = {140214}, doi = {10.1016/j.jhazmat.2025.140214}, pmid = {41151518}, issn = {1873-3336}, abstract = {The widespread occurrence of bisphenol A (BPA) in groundwater has raised growing concern due to its endocrine-disrupting effects. This study demonstrates for the first time that a propane-fed membrane biofilm reactor (C3H8-MBfR) achieved efficient BPA degradation, with rates up to 1157.8 ± 42.7 μg·L[-1]·d[-1]. In-situ withdrawal experiments confirmed that propane is essential for maintaining degradation performance. Transformation products (TPs) analysis revealed hydroxylation, oxidative skeletal rearrangement, ipso substitution, and ring-cleavage steps consistent with stepwise detoxification. ECOSAR-based toxicity predictions indicated that BPA degradation potentially leads to a reduced overall ecological risk, although minor toxic TPs might still pose residual risks. Multi-omic profiling identified a metabolically diverse microbial consortium dominated by J033 sp., Methyloversatilis discipulorum (M. discipulorum), Macondimonas, and Gemmobacter sp., which expressed key oxidative enzymes including cytochrome P450 (CYP450), particulate methane monooxygenase (pMMO), and propane monooxygenase (PrMO). Enzymatic inhibition assays supported their crucial roles in BPA transformation. The generated intermediates were subsequently transformed by these upstream oxidizers together with downstream degraders, such as M. discipulorum. These findings reveal a previously unrecognized, enzyme-driven network for BPA degradation in the C3H8-fed biofilm, offering a sustainable strategy for mitigating endocrine disrupting compounds from groundwater.}, }
@article {pmid41151427, year = {2025}, author = {Hernández-Villamor, D and Jeaidi, A and Boydens, R and Rabaey, K and Van de Wiele, T and Prévoteau, A}, title = {Mediated electron transfer in five prevalent human oral microbial species.}, journal = {Bioelectrochemistry (Amsterdam, Netherlands)}, volume = {168}, number = {}, pages = {109149}, doi = {10.1016/j.bioelechem.2025.109149}, pmid = {41151427}, issn = {1878-562X}, abstract = {An increasing number of microbial species within the human body, many of which are pathogenic, are being reported as "electroactive". However, the mechanisms and kinetics of extracellular electron transfer (EET) and its putative ecological relevance remain understudied. We utilized rotating disk electrodes (RDEs) to assess mediated electron transfer (MET) in five oral species via their ability to reduce riboflavin and ferricyanide. The use of both mediators was confirmed in Streptococcus mutans, Fusobacterium nucleatum, Aggregatibacter actinomycetemcomitans and Porphyromonas gingivalis, while A. viscosus only reduced riboflavin. Kinetics of EET (turnover rate per cell) were slow with riboflavin (kcat, RF< 10[4] s[-1]) in all species but F. nucleatum, whereas ferricyanide resulted in fast kinetics (kcat, Ferri(app)> 10[4] s[-1]) in all but S. mutans. Due to its central role in oral biofilms and association to systemic diseases, MET was further characterized in F. nucleatum. Apparent Michaelis-Menten kinetics showed Km values of (0.57 ± 0.16 and 10.43 ± 0.91) μM for ferricyanide and riboflavin. The presence of mediators enhanced acetate production compared to mediator-free controls; when ferricyanide was used, butyrate and formate production was triggered only after its depletion. Finally, the putative molecular mechanisms enabling MET in F. nucleatum are discussed.}, }
@article {pmid41146339, year = {2025}, author = {Barker, EM and Small, CM and Bassham, S and Beck, EA and Currey, MC and Healey, HM and Johnson, BD and Cresko, WA and Jones, AG}, title = {Signatures and likely sources of the male pregnancy microbiome in wild bay pipefish (Syngnathus leptorhynchus).}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {112}, pmid = {41146339}, issn = {2524-4671}, abstract = {BACKGROUND: Understanding the origin and structure of microbiomes and their associations with ecologically significant host traits is essential for understanding the evolution of host-microbe interactions. These interactions support a wide range of physiological processes important for development, survival, and reproduction. Syngnathid fishes (seahorses, pipefish, and seadragons) represent a compelling system for investigating host-microbiome interactions due to their unique evolution of male pregnancy. Males harbor a fitness-critical brood pouch that provides embryos with protection, osmoregulation, and nutrient exchange through a placenta-like structure, all while requiring the male to modulate his immune system to accommodate developing offspring. These features create a tightly regulated internal environment where microbial interactions could be especially influential to supporting a successful pregnancy. While we have some understanding of the physiological and genetic factors underlying brood pouch development and maintenance, the role of the microbiome and host-microbe interactions in male pregnancy has remained underexplored across the broader diversity of Syngnathidae species and geographic regions. To investigate this relationship further, and for the first time sampling microbiota from a wild syngnathid population, we characterized microbiomes of the bay pipefish (Syngnathus leptorhynchus) using high-throughput 16S rRNA gene sequencing. We quantified microbial community diversity and composition across the brood pouch, embryos, ovaries, gills, intestines, and outer skin body tissues, focusing on sex-specific (brood pouch, embryo, ovary) and sex-shared (gill, intestine, skin) tissues, and variation in pregnancy stage (non-pregnant, early, mid, and late pregnancy).<br><br>RESULTS: We found that the male brood pouch microbiome was distinct from all other body sites (ovaries, embryos, gills, intestines, and outer skin) in community composition, and in that it exhibited the highest richness and phylogenetic diversity of microbes of any site on average, possibly supporting a specialized environment for embryonic development. Moreover, we found that microbial diversity was lower in non-pregnant brood pouches compared to each pregnancy stage (non-pregnant, early, mid, and late pregnancy) but found no significant differences among the pregnancy stages. Female ovaries had the lowest microbial richness and phylogenetic diversity compared to nonpregnant brood pouches, pregnant brood pouches, and embryos. Source tracking analysis using fast expectation-maximization for microbial source tracking (FEAST) indicated that the male outer skin serves as a significant microbial source for both the pregnant brood pouch and developing embryos, establishing a strong paternal influence on the offsprings&#x2019; microbial communities. Overall, we identified Proteobacteria, Bacteroidota, Cyanobacteria, Planctomycetota, and Actinobacteriota as the dominant phyla spanning all surveyed bay pipefish tissue sites, consistent with previous teleost fish microbiome studies. Analysis of core microbiome and indicator species further revealed that sequences classified as Methylotenera_A_557637 (two species), GCA-2862085 sp., Yoonia_491068 sp., Pla163 sp007750655, and Roseibacillus_B sp. show relatively high abundance and specificity with respect to the male brood pouch, suggesting that these taxa may have functional connections to the biology of male pregnancy.<br><br>CONCLUSIONS: These findings reveal insights into the microbial ecology of a unique reproductive system in its natural environment, highlighting the paternal microbiome&#x2019;s potential functional role in shaping the developing offspring. Our results also indicate a likely influence of both environmental and host-specific factors in shaping the bay pipefish microbiome, but there is need for future research on the functional implications of these microbial communities, especially in the brood pouch during pregnancy, and with respect to offspring viability and fitness.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-025-00476-y.}, }
@article {pmid41149922, year = {2025}, author = {Blanchette, RA and Held, BW and Chemello, C and Mardikian, P}, title = {Evaluation of Wood Decay and Identification of Fungi Found in the USS Cairo, a Historic American Civil War Ironclad Gunboat.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {11}, number = {10}, pages = {}, doi = {10.3390/jof11100732}, pmid = {41149922}, issn = {2309-608X}, support = {no number//US National Park Service/ ; Hatch project MIN22-089//USDA/ ; }, abstract = {Studies of microbial degradation of historic woods are essential to help protect and preserve these important cultural properties. The USS Cairo is a historic Civil War gunboat and one of the first steam-powered and ironclad ships used in the American Civil War. Built in 1861, the ship sank in the Yazoo River of Mississippi in 1862 after a mine detonated and tore a hole in the port bow. The ship remained on the river bottom and was gradually buried with sediments for over 98 years. After recovery of the ship, it remained exposed to the environment before the first roofed structure was completed in 1980, and it has been displayed under a tensile fabric canopy with open sides at the Vicksburg National Military Park in Vicksburg, Mississippi. Concerns over the long-term preservation of the ship initiated this investigation to document the current condition of the wooden timbers, identify the fungi that may be present, and determine the elemental composition resulting from past wood-preservative treatments. Micromorphological characteristics observed using scanning electron microscopy showed that many of the timbers were in advanced stages of degradation. Eroded secondary cell walls leaving a weak framework of middle lamella were commonly observed. Soft rot attack was prevalent, and evidence of white and brown rot degradation was found in some wood. DNA extraction and sequencing of the ITS region led to the identification of a large group of diverse fungi that were isolated from ship timbers. Soft rot fungi, including Alternaria, Chaetomium, Cladosporium, Curvularia, Xylaria and others, and white rot fungi, including Bjerkandera, Odontoefibula, Phanerodontia, Phlebiopsis, Trametes and others, were found. No brown rot fungi were isolated. Elemental analyses using induced coupled plasma spectroscopy revealed elevated levels of all elements as compared to sound modern types of wood. High concentrations of boron, copper, iron, lead, zinc and other elements were found, and viable fungi were isolated from this wood. Biodegradation issues are discussed to help long-term conservation efforts to preserve the historic ship for future generations.}, }
@article {pmid41148908, year = {2025}, author = {Zhang, X and Wang, Z and Feng, G and Xiao, Q and Tang, M}, title = {Temporal Dynamics of Bacterial Communities in Ectropis grisescens Following Cryogenic Mortality.}, journal = {Insects}, volume = {16}, number = {10}, pages = {}, doi = {10.3390/insects16101040}, pmid = {41148908}, issn = {2075-4450}, support = {31700613 and CAAS-ASTIP-TRICAAS//the National Natural Science Foundation of China and the Innovative Program of the Chinese Academy of Agricultural Sciences/ ; }, abstract = {Ectropis grisescens (Lepidoptera: Geometridae) is a destructive pest in tea plantations, leading to significant economic losses through defoliation. Existing control strategies, including chemical insecticides and biological agents, are often limited by environmental concerns, resistance, and variable efficacy. Recent evidence suggests that bacteria influence insect physiology and could be leveraged for pest management, but the postmortem microbial ecology of E. grisescens remains uncharacterized. In this study, we employed 16S rRNA sequencing to investigate temporal changes in the bacterial communities of E. grisescens cadavers at 0, 7, and 21 days following cryogenic mortality. Our results indicate a time-dependent decline in microbial diversity, while species richness initially increased before subsequent reduction. The dominant endosymbiont Wolbachia gradually diminished after host death, whereas Enterobacter remained abundant. Notably, non-dominant genera including Lysinibacillus and Sporosarcina exhibited a transient increase in abundance at day 7 before reverting to control levels by day 21. This study presents the first comprehensive analysis of postmortem microbial succession in a lepidopteran system, highlighting dynamic shifts in bacterial composition and offering potential avenues for microbiome-based pest management strategies.}, }
@article {pmid41147699, year = {2025}, author = {Bick, B and Lumpi, T and Lindström, ES and Langenheder, S}, title = {Linking nutrient availability and community size to stochasticity in microbial community assembly.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaf110}, pmid = {41147699}, issn = {1574-6941}, abstract = {Both deterministic (e.g. species-environment interactions) and stochastic processes (e.g. random birth and death events) shape communities, but it remains poorly understood which environmental conditions promote stochasticity. Here we investigated interactive effects of nutrient availability and community size on stochasticity in order to predict how eutrophication and biomass loss shift the balance between predictable and random community dynamics. For this, we used freshwater bacterial communities in a microcosm experiment where communities were diluted to varying sizes and exposed to low, intermediate and high nutrient concentrations. Stochasticity was estimated with null modelling and as beta-diversity among replicate communities. At low nutrient concentrations, deterministic processes dominated, especially in smaller communities, which had the lowest diversity and abundance. In contrast, higher nutrient concentrations increased stochasticity. In contrast to theoretical predictions, this was particularly the case in larger communities with the highest diversity and abundance, likely due to stochastic initial growth. The findings underline how nutrient availability and community size jointly influence stochastic assembly processes, with important consequences for bacterial diversity and ecosystem functioning under environmental change.}, }
@article {pmid41144669, year = {2025}, author = {Tao, A and Fu, S and Zhang, R and Yuan, J}, title = {Flagellar location determines the stability of bacterial surface entrapment.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {44}, pages = {e2506380122}, doi = {10.1073/pnas.2506380122}, pmid = {41144669}, issn = {1091-6490}, support = {12090053//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {*Flagella/physiology ; *Pseudomonas aeruginosa/physiology ; Escherichia coli/physiology ; }, abstract = {Surface interactions play a crucial role in shaping the motility patterns and ecological adaptations of swimming bacteria. Previous studies have primarily focused on peritrichous bacteria like Escherichia coli, whose multiple flagella form a bundle during swimming, allowing them to remain trapped at surfaces for extended periods. However, this surface entrapment phenomenon varies significantly among different bacterial species, despite all fitting into the simplified theoretical models of pusher-type bacteria, suggesting that key factors remain unidentified. Here, we demonstrate that flagellar location is a critical determinant of surface entrapment stability in pusher-type bacteria. Using fluorescently labeled Pseudomonas aeruginosa, we show that cells with a single lateral flagellum exhibit substantially longer surface residence times compared to those with a single polar flagellum, despite similar cell morphology and swimming speeds. Through direct visualization of bacterial orientation angles relative to surfaces, we reveal that this difference results from the distinct bending directions of the flagellar hook-the flexible joint connecting the rigid filament to the cell body. The hook-generated torque resists reorientation differently depending on flagellar location, facilitating surface escape for polar-flagellated bacteria while enhancing entrapment for lateral-flagellated bacteria. Our findings highlight the previously overlooked importance of flagellar placement in bacterial surface interactions, providing insights for understanding microbial ecology and designing biomimetic microswimmers.}, }
@article {pmid41140797, year = {2025}, author = {Zöchling, A and Séneca, J and Pjevac, P and Auñon-Lopez, A and Zebeli, Q and Pignitter, M and Duszka, K}, title = {Comparative analysis of dietary fiber impact on bile acid metabolism and gut microbiota composition in mice.}, journal = {Npj gut and liver}, volume = {2}, number = {1}, pages = {26}, pmid = {41140797}, issn = {3004-9806}, abstract = {Dietary fiber is essential for health but remains under-consumed in Western diets. Fiber types differ in their physicochemical properties, which influence gastrointestinal function, bile acid (BA) metabolism, and gut microbiota composition. C57Bl/6 mice were fed control or 10% (w/w) fiber diets containing cellulose, chitin, resistant starch, pectin, inulin, β-glucan, psyllium, dextrin, or raffinose. All fibers reduced bacterial diversity, while most increased Akkermansia muciniphila abundance. Cellulose/chitin and inulin/β-glucan/raffinose formed distinct microbiome clusters. Rikenellaceae correlated positively with taurine-conjugated BAs levels. BA concentrations were reduced across tissues. Taurine conjugates showed inverse liver-intestine distribution. Inulin and β-glucan resulted in the highest taurine conjugate levels and reduced intestinal taurine-conjugated BAs concentrations, suggesting enhanced bile salt hydrolase (BSH) activity. Resistant starch had a minimal effect. Psyllium most strongly impacted BA- and taurine-related gene expression, cecum size and weight loss. Dietary fibers distinctly modulate BA metabolism and gut microbiota, with implications for metabolic health and targeted therapies.}, }
@article {pmid41140306, year = {2025}, author = {Merges, AK and Manning, P and Baulechner, D and John, K and Zaitsev, A and Wolters, V and Baranski, D and Grossart, HP and Woodhouse, J and Schneider, C and Bálint, M}, title = {StrataSeq: A Workflow for Rapid Development of Molecular Databases for Hard-To-Identify Species.}, journal = {Ecology and evolution}, volume = {15}, number = {10}, pages = {e72375}, pmid = {41140306}, issn = {2045-7758}, abstract = {Biodiversity loss necessitates improved monitoring of small, species-rich taxa, such as protists, phyto- and zooplankton and terrestrial invertebrates. Traditional biomonitoring is often infeasible for these taxa due to complex morphology and few taxonomists. DNA-based approaches offer promising solutions by enabling rapid species identification. However, the effectiveness of these methods depends on the completeness of molecular reference databases, which remain incomplete, particularly for remote and biodiverse regions. To address this, we propose the StrataSeq workflow, a systematic approach to optimise the generation of DNA reference databases for hard-to-identify taxa. Reference sequences allow us to connect molecular operational taxonomic units to a wealth of information available for many described taxa. StrataSeq consists of four key steps: (1) Habitat-stratified sample subsetting selects a minimal but ecologically representative sample set by stratifying along key environmental gradients. (2) Prioritising morphospecies involves sorting specimens into morphospecies and ranking them based on their occurrence across samples, prioritising common taxa for detailed identification. (3) Detailed morphological identification focuses on common morphospecies to maximise taxonomic coverage while minimising effort. (4) Reference DNA sequence generation targets taxa lacking molecular references, with sequenced specimens deposited as museum vouchers. We benchmarked the StrataSeq workflow using two datasets of Collembola from grassland soils in Germany. In comparison with a species list generated by a more labour-intensive traditional approach (identification of randomly selected individuals from all samples), the StrataSeq workflow captured 69% of species but required only 22% of the effort. StrataSeq is adaptable to various organism groups and environmental settings, including both spatial and temporal gradients. The workflow enhances the cost-effectiveness of generating reference DNA databases, supporting improved biodiversity monitoring and ecological research. StrataSeq offers a scalable solution to accelerate the completion of molecular databases, thereby improving biomonitoring and ecosystem assessments under global change pressures.}, }
@article {pmid41139509, year = {2025}, author = {Roy, R and Gogoi, UR and Das, M and Paul, P and Chakraborty, P and Das, S and Sarkar, S and Gupta, AD and Malik, M and Sarker, RK and Tribedi, P}, title = {Optimization of Doses of Antibiotics and Cuminaldehyde to Combat Methicillin-Resistant Staphylococcus aureus (MRSA): A Study With Machine Learning.}, journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica}, volume = {133}, number = {10}, pages = {e70076}, doi = {10.1111/apm.70076}, pmid = {41139509}, issn = {1600-0463}, support = {TNU/R&amp;D/M P/2021/008//The Neotia University/ ; TNU/R&amp;D/M/12//The Neotia University/ ; }, mesh = {*Methicillin-Resistant Staphylococcus aureus/drug effects/physiology ; *Anti-Bacterial Agents/pharmacology/administration &amp; dosage ; Biofilms/drug effects ; *Machine Learning ; Tobramycin/pharmacology/administration &amp; dosage ; Humans ; Microbial Sensitivity Tests ; Gentamicins/pharmacology/administration &amp; dosage ; Staphylococcal Infections/drug therapy/microbiology ; *Benzaldehydes/pharmacology/administration &amp; dosage ; }, abstract = {Methicillin-resistant Staphylococcus aureus (MRSA), a drug-resistant organism, can cause a spectrum of infections in the human host involving biofilm. Therefore, novel therapeutic approaches need to be explored to mitigate this persistent infection. This study investigated a combinatorial approach that incorporates cuminaldehyde (a phytochemical) alongside aminoglycoside antibiotics (gentamicin and tobramycin) to improve antibiofilm efficacy by addressing multiple targets. In this regard, to achieve precise dosing of the chosen compounds for effective biofilm management, different machine learning models, namely multiple linear regression (MLR), polynomial regression (PR), artificial neural network regression (ANNR), and support vector regression (SVR), were employed. The results suggested that ANNR exhibited a strong association between the predicted and experimental observations (R[2] = 98.07). Furthermore, the ANNR model, followed by genetic algorithm (GA), recommended that the combinatorial doses of the selected compounds [cuminaldehyde (40 μg/mL); gentamicin (0.5 μg/mL); and tobramycin (0.035 μg/mL)] could show the highest antibiofilm activity against MRSA. Additionally, this study revealed that the combination of the mentioned compounds at their recommended doses not only accumulated intracellular reactive oxygen species (ROS) but also increased the cell membrane permeability of MRSA. Thus, this study provides a promising foundation for developing novel therapeutic strategies against MRSA biofilm through an AI-driven approach.}, }
@article {pmid41135758, year = {2025}, author = {Declerck, L and Bouchon, F and Demeester, W and Guidi, C and De Mey, M}, title = {Accelerated adaptive laboratory evolution: A tool for evolutionary biotechnology.}, journal = {Biotechnology advances}, volume = {}, number = {}, pages = {108741}, doi = {10.1016/j.biotechadv.2025.108741}, pmid = {41135758}, issn = {1873-1899}, abstract = {Adaptive laboratory evolution (ALE) is a powerful strategy for enhancing microbial traits by harnessing the principles of natural selection in controlled environments. It has enabled significant advances in microbial growth, stress tolerance, and product yield across a variety of organisms, while also providing insight into evolutionary mechanisms. However, the traditional ALE workflow is time- and resource-intensive, relying on prolonged cultivation to allow beneficial mutations to emerge and be maintained in the population. To improve this, a range of evolutionary engineering tools have been developed to accelerate ALE by increasing mutation rates and genetic diversity in evolving strains. In this review, we explore the core parameters that shape ALE, such as selection pressure, transfer method, and passage size, and provide a comprehensive overview of both established and emerging acceleration methods. These techniques are categorized based on portability (applicability across different microorganisms), genomic targetability (specificity of mutagenesis), and reliability (minimal off-target mutations and mutational reproducibility), with the resulting framework for selecting the most suitable approach summarized in Table 3 at the end of the review. We highlight the growing potential of accelerated ALE and outline future directions, including the integration of genome-wide and targeted mutagenesis, computational modeling, laboratory automation, and broader application beyond model organisms. This review aims to streamline the use of accelerated ALE, unlocking its true potential for advancing microbial strain engineering.}, }
@article {pmid41135394, year = {2025}, author = {Khalil, S and Ugolini, V and Forsbacka, J and Karlsson, M and Vetukuri, RR and Lai, FY}, title = {Could extracts from spent mushroom materials transform reclaimed water quality? - A pilot study on pathogen suppression, antimicrobial chemical removal, and plant growth enhancement.}, journal = {Journal of environmental management}, volume = {395}, number = {}, pages = {127688}, doi = {10.1016/j.jenvman.2025.127688}, pmid = {41135394}, issn = {1095-8630}, }
@article {pmid41135049, year = {2025}, author = {Zhang, X and Guo, Y and Shi, J and Zang, Q and Li, Y}, title = {Exclusive Effects of Moxibustion on Gut Microbiota: Protocol for a Focused Systematic Review and Meta-Analysis.}, journal = {JMIR research protocols}, volume = {14}, number = {}, pages = {e73317}, doi = {10.2196/73317}, pmid = {41135049}, issn = {1929-0748}, mesh = {*Moxibustion/methods ; *Gastrointestinal Microbiome/physiology ; Humans ; Meta-Analysis as Topic ; Systematic Reviews as Topic ; Animals ; Research Design ; }, abstract = {BACKGROUND: The gut microbiota (GM) plays a critical role in systemic health, influencing immune, metabolic, and neurological functions. There is emerging evidence suggesting that moxibustion, a traditional thermal therapy, may modulate the GM to restore microbial homeostasis, yet its exclusive effects remain undifferentiated from those of combined therapies such as acupuncture. Previous meta-analyses lack mechanistic specificity, necessitating a focused evaluation of moxibustion's impact on microbial ecology.<br><br>OBJECTIVE: This systematic review and meta-analysis aims to quantify moxibustion-induced changes in GM diversity, taxonomic composition, and functional metabolites (eg, short-chain fatty acids).<br><br>METHODS: We will systematically search the PubMed, Web of Science, Cochrane Library, China National Knowledge Infrastructure, Wanfang, and VIP databases from inception to December 31, 2024, using keywords such as "moxibustion," "gut microbiota," and "intestinal flora." Eligible preclinical (animal) and clinical (human) studies evaluating stand-alone moxibustion interventions on the GM will be included. Primary outcomes include microbial &#x3b1; diversity indexes (Shannon and Simpson) and relative abundance of key taxa (eg, Firmicutes and Bacteroidetes). Risk of bias will be assessed using the Systematic Review Center for Laboratory Animal Experimentation risk-of-bias tool for animal studies and the modified Collaborative Approach to Meta-Analysis and Review of Animal Data from Experimental Studies criteria for human trials. Pooled effect estimates for continuous outcomes (eg, diversity indexes and taxa ratios) will be calculated using the ratio of means with 95% CIs. Statistical analyses will be conducted in RevMan (version 5.4) and R (metafor package), with data archived on Figshare for reproducibility.<br><br>RESULTS: As of March 2025, the literature search and screening have been completed, and 31 studies meeting the inclusion criteria have been identified. The comprehensive analysis is scheduled to be completed by October 2025, with results anticipated to be published in late 2025. On the basis of previous work, an anticipated result is that moxibustion may reduce pathogenic genera such as Ruminococcus while enhancing beneficial genera, effects that are expected to be associated with improved intestinal barrier integrity and anti-inflammatory responses.<br><br>CONCLUSIONS: This protocol provides a rigorous framework to evaluate moxibustion's unique role in GM modulation, bridging traditional medicine with microbiome science. The results will inform optimized, nonpharmacological strategies for managing microbiome-associated chronic diseases and guide future research priorities.}, }
@article {pmid41131424, year = {2025}, author = {Aidarova, A and Carels, M and Haegman, M and Driege, Y and Timmermans, S and Van Damme, E and Aguilera-Lizarraga, J and Viola, MF and de Cássia Collaço, R and Manils, J and Ley, SC and Bosmans, F and Van de Wiele, T and Boeckxstaens, G and Libert, C and Beyaert, R and Afonina, IS}, title = {CARD14 signaling in intestinal epithelial cells induces intestinal inflammation and intestinal transit delay.}, journal = {EMBO molecular medicine}, volume = {}, number = {}, pages = {}, pmid = {41131424}, issn = {1757-4684}, support = {G035517N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; 3G0I1422//Fonds Wetenschappelijk Onderzoek (FWO)/ ; G000220N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; 12Z3922N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; G0A7T24N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; 3G086521//Fonds Wetenschappelijk Onderzoek (FWO)/ ; 3S003122//Strategic Basic Research grants from FWO/ ; 3179K5620//Strategic Basic Research grants from FWO/ ; 01G00419//Ghent University grant GOA/ ; 01M00121//Methusalem/ ; 2024/01/511//Universiteit Gent (UGent)/ ; 365C06721//Stichting Tegen Kanker (Fondation Contre le Cancer)/ ; 222487/Z/21/Z//Wellcome Trust Investigator/ ; }, abstract = {CARD14 is an intracellular NF-κB signaling mediator in the skin, and rare CARD14 variants have been associated with psoriasis and atopic dermatitis. CARD14 is also expressed in intestinal epithelial cells (IEC). However, its function in the intestine remains unknown. We demonstrate here that transgenic mice expressing the psoriasis-associated gain-of-function human CARD14(E138A) mutant specifically in IEC show mild intestinal inflammation, without epithelial damage. Moreover, CARD14(E138A)[IEC] mice show a drastic reduction in intestinal motility, often associated with rectal prolapse. Enteric neuronal survival and functionality are unaffected in CARD14(E138A)[IEC] mice. Transcriptome analysis of IEC from CARD14(E138A)[IEC] mice reveals decreased expression of antimicrobial peptides by Paneth cells, accompanied by microbial dysbiosis and increased susceptibility to enteric bacterial infection. Our findings suggest that gain-of-function CARD14 mutations may not only predispose patients to psoriasis but also mild intestinal inflammation, reduced intestinal motility, and increased sensitivity to intestinal infection. CARD14(E138A)[IEC] mice are also a valuable tool for further investigation of IEC-intrinsic molecular processes involved in intestinal inflammation and motility disorders.}, }
@article {pmid41131131, year = {2025}, author = {Corduneanu, A and Bendjeddou, ML and Sándor, AD and Mihalca, AD and Hornok, S and Péter, &#xc1; and Khelfaoui, F and Aželytè, J and Obregon, D and Mateos-Hernández, L and Maitre, A and Abuin-Denis, L and Wu-Chuang, A and Kratou, M and Ben Said, M and Cabezas-Cruz, A}, title = {Microbial network assembly in bat flies with differing host specificity from North Africa.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {41131131}, issn = {1618-1905}, support = {14/2022-2024//Ministerul Cercet&#x103;rii &#x15f;i Inov&#x103;rii/ ; 1500107//Hungarian Research Network/ ; NTP-NFT&#xd6;-20-B-0094//Hungarian Ministry of Human Resources, Hungary/ ; SGCE - RAPPORT No 0300//Collectivit&#xe9; de Corse/ ; ANR-10-LABX-62-IBEID//Agence Nationale de la Recherche/ ; }, abstract = {The study investigates the microbial composition of bat flies (Diptera: Nycteribiidae) collected from Myotis punicus in Algeria, focusing on the diversity and dynamics of their microbiota through network analysis. The analysis targets two genera, Nycteribia and Penicillidia, comparing oioxenous and stenoxenous species to understand host specificity's influence on microbial communities. Utilizing 16S rRNA sequencing, alpha and beta diversity metrics, and co-occurrence networks, the study assesses microbial diversity, community composition, and the impact of specific bacteria (endosymbionts, commensals, and pathogens) on network stability. Results reveal significant microbial community variations between genera and species, with N. latreillii exhibiting the most complex network. We showed that host specificity and feeding strategies significantly influence microbial diversity and interactions within bat flies. Robustness analysis through node removal simulations identifies the roles of key bacteria, such as Wolbachia, Arsenophonus, and Bartonella, in maintaining network stability. Findings highlight the complex interplay between these microorganisms and their hosts, offering insights into microbial ecology and vector-pathogen dynamics. The research underscores the importance of bat flies in shaping pathogen transmission networks, contributing valuable knowledge to wildlife ecology, disease control, and conservation strategies.}, }
@article {pmid41129402, year = {2025}, author = {Kovács, E and Szűcs, C and Juhász-Erdélyi, A and Bagi, Z and Kovács, KL}, title = {Anaerobic fungi - effective warriors in lignocellulosic biomass degradation and fermentation.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaf108}, pmid = {41129402}, issn = {1574-6941}, abstract = {The significant advancements in understanding the roles of anaerobic fungi within microbial ecology have opened numerous avenues for biotechnological exploitation, particularly in enhancing the productivity of livestock. The efficient, unique, and complex enzyme systems of anaerobic fungi play a determining role in the metabolic conversion of lignocellulosic plant matter into animal products such as milk and meat by mammalian herbivores. Mitigation of methane emissions through microbial or dietary strategies in ruminants is a major environmental climate change issue. In turn, controlled management of the inter-kingdom syntrophic interactions among the eukaryotic anaerobic fungi, prokaryotic bacteria and archaea can lead to the production of valuable biofuels, (biomethane, biohydrogen, bioethanol), and organic acids. These products can also serve as building blocks in numerous processes to generate high value chemicals in circular bioeconomy.}, }
@article {pmid41128906, year = {2025}, author = {Ma, Z and Wang, J and Huang, C and Cao, Y and Sun, Y and Hu, Y and Basit, MF and Huang, J}, title = {Effects of Facility Cultivation Shaping Soil Microbial Community Structure in Jujube Orchard.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {112}, pmid = {41128906}, issn = {1432-184X}, support = {2019YFD1001605//National Key Research and Development Program of China/ ; 2019YFD1001605//National Key Research and Development Program of China/ ; 2019YFD1001605//National Key Research and Development Program of China/ ; 2019YFD1001605//National Key Research and Development Program of China/ ; 2019YFD1001605//National Key Research and Development Program of China/ ; 2019YFD1001605//National Key Research and Development Program of China/ ; 2019YFD1001605//National Key Research and Development Program of China/ ; 2019YFD1001605//National Key Research and Development Program of China/ ; 31870584//National Natural Science Foundation of China/ ; 31870584//National Natural Science Foundation of China/ ; 31870584//National Natural Science Foundation of China/ ; 31870584//National Natural Science Foundation of China/ ; 31870584//National Natural Science Foundation of China/ ; 31870584//National Natural Science Foundation of China/ ; 31870584//National Natural Science Foundation of China/ ; 31870584//National Natural Science Foundation of China/ ; XJCYTX-01//Xinjiang Jujube Industrial Technology System/ ; XJCYTX-01//Xinjiang Jujube Industrial Technology System/ ; XJCYTX-01//Xinjiang Jujube Industrial Technology System/ ; XJCYTX-01//Xinjiang Jujube Industrial Technology System/ ; XJCYTX-01//Xinjiang Jujube Industrial Technology System/ ; }, mesh = {*Soil Microbiology ; *Ziziphus/microbiology/growth &amp; development ; *Bacteria/classification/genetics/isolation &amp; purification ; Soil/chemistry ; *Mycorrhizae/classification/genetics/isolation &amp; purification ; *Microbiota ; Nitrogen/analysis ; *Agriculture/methods ; Carbon/analysis ; Hydrogen-Ion Concentration ; Biodiversity ; }, abstract = {Facility cultivation systems provide protection for jujube (Ziziphus jujuba) against rain-induced fruit cracking during the maturation and regulate the fruit ripening process. Prolonged cultivation within these controlled environments may alter the soil microbial community structure, potentially detrimentally affecting plant growth and fruit quality. There is a lack of information regarding the arbuscular mycorrhizal fungi (AMF) and bacterial communities in orchards under facility conditions. This study compared the soil bacterial and AMF communities in jujube orchards under greenhouse and rain shelter conditions. Greenhouse cultivation significantly increased soil organic carbon (SOC), total nitrogen (TN), and electrical conductivity, while it decreased soil pH compared to rain shelters. These changes were associated with reduced α-diversity indices in both bacterial and AMF communities. Non-metric multidimensional scaling analysis demonstrated distinct differences between bacteria and AMF communities under the two cultivation types. The phyla Actinobacteria, Gemmatimonadetes, and Rokubacteria were identified as key contributors to the observed alterations in the bacterial community, while variations in the genus Glomus and Paraglomus were responsible for changes in the AMF communities between the two cultivation types. Redundancy analysis revealed that pH was the primary factor shaping microbial community structure across the two cultivation types. Using a Zi-Pi plot, we identified several keystone ASVs, which showed a positive correlation with pH, SOC, and TN. The findings highlight the significant impact of cultivation type on soil microbial community structure and function, which has important implications for optimizing cultivation practices and ensuring sustainable jujube production.}, }
@article {pmid41127647, year = {2025}, author = {von Friesen, LW and Farnelid, H and von Appen, WJ and Benavides, M and Grosso, O and Laber, CP and Schüttler, J and Sundbom, M and Torres-Valdés, S and Bertilsson, S and Peeken, I and Snoeijs-Leijonmalm, P and Riemann, L}, title = {Nitrogen fixation under declining Arctic sea ice.}, journal = {Communications earth &amp; environment}, volume = {6}, number = {1}, pages = {811}, pmid = {41127647}, issn = {2662-4435}, abstract = {With climate change-induced sea ice decline in the Arctic Ocean, nitrogen is expected to become an increasingly important determinant of primary productivity. Nitrogen fixation is the conversion of molecular nitrogen to bioavailable ammonium by microorganisms called diazotrophs. Here, we report nitrogen fixation rates, diazotroph composition, and expression under different stages of declining sea ice in the Central Arctic Ocean (multiyear ice, five stations) and the Eurasian Arctic (marginal ice zone, seven stations). Nitrogen fixation in the Central Arctic Ocean was positively correlated with primary production, ranging from 0.4 ± 0.1 to 2.5 ± 0.87 nmol N L[-1] d[-1]. Along two transects across the marginal ice zone, nitrogen fixation varied between days and ice regime from below detection up to 5.3 ± 3.65 nmol N L[-1] d[-1] associated with an ice-edge phytoplankton bloom. We show nitrogen fixation in sea ice-covered waters of the Arctic Ocean and provide insight into present and active non-cyanobacterial diazotrophs in the region.}, }
@article {pmid41127399, year = {2025}, author = {Guo, Y and Ouyang, H and Su, J and Zhong, M and Huang, W and Huang, M and Xie, C}, title = {Developing and validating a nomogram for predicting endoscopic hemostasis failure in cirrhotic patients with esophageal variceal bleeding.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1670759}, pmid = {41127399}, issn = {2296-858X}, abstract = {BACKGROUND AND AIMS: This study aimed to create and validate a model to predict the failure of endoscopic hemostasis in Chinese cirrhosis patients with acute esophagogastric variceal bleeding (EGVB), enabling early identification of high-risk individuals.<br><br>METHODS: A retrospective study analyzed 296 cirrhotic patients with EGVB who received emergency endoscopic therapy from January 2020 to February 2025. Patients were divided into success (n = 273) and failure (n = 23, defined as bleeding recurrence within 5 days) groups. LASSO regression optimized variable selection, and multivariate logistic regression identified independent predictors to create a nomogram. Internal validation used Bootstrap resampling (500 iterations). Model performance was assessed using ROC curves, calibration plots, and decision curve analysis (DCA), and compared with CTP (Child-Turcotte-Pugh), MELD (Model for End-Stage Liver Disease), and Rockall scores.<br><br>RESULTS: The cumulative incidence of endoscopic failure was observed to be 7.8%. Independent predictors identified included a shock index (SI) > 1.2 (OR = 5.447), the presence of a red color (RC) sign (OR = 10.005), active bleeding observed during endoscopy (OR = 5.962), and the CTP (OR = 1.584). The nomogram exhibited superior discriminatory power with an AUC of 0.890 (95% CI: 0.820-0.960), outperforming the CTP (AUC = 0.771, 95% CI: 0.656-0.886; P < 0.001), MELD (AUC = 0.733, 95% CI: 0.616-0.849; P < 0.001), and Rockall (AUC = 0.656, 95% CI: 0.545-0.768; P < 0.001). Calibration was satisfactory as indicated by the Hosmer-Lemeshow test (&#x3c7;[2] = 10.021, P = 0.263). DCA demonstrated a clinical net benefit across a broad range of thresholds.<br><br>CONCLUSION: A validated nomogram that integrates the SI, RC sign, active bleeding, and CTP provides an effective prediction of the risk of endoscopic hemostasis failure in patients with cirrhotic EGVB, thereby facilitating timely intervention.}, }
@article {pmid41126179, year = {2025}, author = {Heuberger, M and Wehrkamp, CM and Pfammatter, A and Poretti, M and Graf, JP and Herger, A and Isaksson, J and Schlagenhauf, E and Honegger, R and Wicker, T and Sotiropoulos, AG}, title = {A reference metagenome sequence of the lichen Cladonia rangiformis.}, journal = {BMC biology}, volume = {23}, number = {1}, pages = {319}, pmid = {41126179}, issn = {1741-7007}, support = {310030_212428//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; }, mesh = {*Lichens/genetics/microbiology ; *Metagenome ; Symbiosis/genetics ; *Genome, Fungal ; *Ascomycota/genetics ; Chlorophyta/genetics ; }, abstract = {BACKGROUND: Lichens are an ancient symbiosis comprising the thalli of lichen-forming fungi, their photoautotrophic partners, and their microbiome. So far, they were poorly studied at the genome sequence level. Here, we present a reference metagenome for the holobiont of Cladonia rangiformis, aiming to illuminate the genomic complexity and evolutionary interactions within lichen symbioses.<br><br>RESULTS: Using long-read sequences from an entire symbiotic complex, plus short-read libraries from 28 additional diverse European lichen samples, we were able to separate genome sequences of 20 individual species. We constructed chromosome-scale assemblies of the C. rangiformis fungus and its trebouxioid green algal photobiont Asterochloris mediterranea. The genome of the fungus comprises&#x2009;~&#x2009;22% transposable elements and is highly compartmentalized into genic regions and large TE-derived segments which show extensive signatures of repeat-induced point mutations (RIP). We found that A. mediterranea centromeres are predominantly derived from two interacting retrotransposon families. We also identified strong candidates for genes that were horizontally transferred from bacteria to both alga and fungus. Furthermore, we isolated 18 near-complete bacterial genomes, of which 13 are enriched in the lichen compared to surrounding soil. Analysis of gene content in fungus, algae, and bacteria identified 22 distinct biosynthetic gene cluster categories for known secondary metabolites.<br><br>CONCLUSIONS: Our findings revealed that the thalli of C. rangiformis have a highly complex microbiome, comprising a mix of species that may include opportunists, ecologically obligate symbionts and possibly even lichen-beneficial bacteria. This study provides the first chromosome-scale genomic framework for a lichen holobiont, offering a foundational resource for future research into metagenomics, symbiosis, and microbial ecology in lichens.}, }
@article {pmid41124090, year = {2025}, author = {Ahumada, D and Schwob, G and Osorio, M and Astorga, MS and Lavergne, C and Olgun, N and Thalasso, F and Poulin, E and Orlando, J and Cabrol, L}, title = {Higher variability of bacterial communities across space than over time in Antarctic lakes, and contrasting assembly processes.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0107925}, doi = {10.1128/aem.01079-25}, pmid = {41124090}, issn = {1098-5336}, abstract = {As sentinels of environmental changes, Antarctic lakes are ideal systems for studying the temporal and spatial dynamics of microbial communities. However, the relative magnitude and underlying mechanisms driving these variations remain poorly understood. Studying the spatiotemporal variation of microbial communities is crucial to provide a robust baseline for predicting ecosystem responses to global changes. Here, we investigated the spatial and inter-annual variation of bacterial community structure and their underlying assembly processes across sediment and water habitats in 11 lakes on the Fildes Peninsula, Maritime Antarctica, sampled during austral summers from 2017 to 2023, using 16S rRNA gene sequencing. The communities primarily clustered by habitat, with higher diversity in sediment (characterized by Rhodoferax, Intraporangiaceae, and Vicinamibacterales) compared to water (characterized by Polaromonas, Flavovacterium, and Sporichthyaceae). Spatial turnover of communities dominated over inter-annual variation in both habitats. Accordingly, the temporal core microbiome showed greater stability than the spatial core. The conserved bacterial communities (core communities) over time and across space exhibited a strikingly similar taxonomic composition. Community assembly processes differed between habitats, with a stronger contribution of dispersal limitation in sediment, versus ecological drift in water, as expected from the differences in connectivity within each habitat. Spatial and temporal variations in sediment were driven by globally similar assembly processes. In contrast, in water communities, different assembly processes explained the spatial and temporal variation. These insights emphasize the need to consider both spatial and temporal scales and various habitat types when predicting future bacterial dynamics in Antarctic lakes in a changing environment.IMPORTANCEUnderstanding the inherent baseline microbial dynamics in Antarctic lakes is crucial for predicting their responses to environmental changes. Our findings underscore the predominance of spatial (rather than inter-annual) factors in shaping bacterial communities and highlight the slightly higher contribution of stochastic processes in sediment compared to water habitats. The stochastic processes differed considerably among habitats. The greater stability of the temporal core microbiome suggests a certain degree of resilience toward possible seasonal fluctuations between the inter-annual sampling dates. In water, dispersal limitation and homogeneous selection played a greater role in the spatial than in the temporal turnover of communities, whereas environmental filtering exerted a stronger influence over time. Future studies should integrate both spatial and temporal dimensions in evaluating microbial community variability to improve forecasting of ecosystem shifts in response to global change and thus provide a better baseline for Antarctic biodiversity conservation and management.}, }
@article {pmid41124050, year = {2025}, author = {Zhu, J and Chen, C and Zhang, Y and Li, C}, title = {Impact of ecological restoration on the soil microbial communities during the restoration of damaged Mountain Slope in China's Heilong River Basin.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxaf262}, pmid = {41124050}, issn = {1365-2672}, abstract = {AIMS: This study aimed to elucidate the dynamics of soil microbial communities during ecological restoration on degraded mountain slopes, specifically comparing the impacts of two common strategies: aggregate spray-seeding and planted forest establishment, against undisturbed natural slopes, and assessing key drivers of microbial recovery.<br><br>METHODS AND RESULTS: Soil microbial community composition (bacteria and fungi), diversity, and co-occurrence network structure were analyzed seven years after restoration initiation. Both restoration approaches facilitated microbial community recovery, with restored slope compositions converging towards natural slope baselines. Fungal communities exhibited greater OTU diversity than bacteria, attributed to engineered substrates and rapid vegetation stabilization from spray-seeding. Crucially, restoration successfully increased microbial network complexity. Spray-seeding specifically achieved network stability comparable to natural ecosystems. Significant environmental relationships were identified: soil water content (SWC) showed negative correlations with fungal richness and composition, while below-ground biomass (BGB) positively correlated with bacterial composition.<br><br>CONCLUSIONS: Restoration effectively promotes soil microbial community recovery towards natural ecosystem states, albeit with distinct dynamics for bacteria and fungi. Fungal communities are particularly responsive to restoration techniques like spray-seeding. Soil properties (SWC) and plant development (BGB) are pivotal drivers shaping microbial assemblage during restoration.}, }
@article {pmid41123377, year = {2025}, author = {Piccolo, BD and Chen, M-H and Lan, RS and Moody, B and Yao, T and Huang, T-Y and Pack, L and Adams, SH and Lindemann, SR}, title = {Xenometabolomics reveals metabolic functional guilds unique to specific inulin subtypes in human gut microbiota cultures.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0103125}, doi = {10.1128/msystems.01031-25}, pmid = {41123377}, issn = {2379-5077}, abstract = {UNLABELLED: Dietary fibers promote positive health outcomes that are generally attributed to large bowel bacterial fermentation and associated bioactive metabolites. Historically, studies of the latter have focused on short-chain fatty acids such as butyrate. The gastrointestinal microbiota generate thousands of xenometabolites (microbe-derived, "non-host" metabolites). Most remain uncharacterized for composition and potential bioactivity, and little is known about the impact of fiber structure on the xenometabolome. Using LC/MS, we characterized culture supernatant metabolite profiles in human stool lineages derived from three healthy adult donors and six inulins covering a range of degrees of polymerization (DPs): chicory-derived Frutalose L90 (L90; DP ~ 3), Alfa Aesar (AA; DP ~ 5), Frutafit CLR (CLR; DP ~ 8), Frutafit IQ (IQ; DP ~ 12), Frutafit TEX (TEX; DP > 23), and the highly branched Frutafit agave inulin (AGA). Of the 1,219 LC/MS detected metabolites included in the final data analysis, concentrations of 704 were statistically significant (FDR < 0.1; Kruskal-Wallis test). Of these, 15 metabolites had a structural annotation, highlighting the large number of "unknown" xenometabolites associated with inulin substrates. Each fiber type led to distinct metabolite signatures, despite lineages displaying highly disparate microbial community structures within and across donors. This illustrates that fiber-specific metabolic functional guilds manifest despite highly diverse human gut bacteria communities. While speculative, these metabolic functional guilds could help explain why health effects of dietary fibers are prevalent across the population despite highly disparate gut microbiota patterns. The results also reinforce that fiber structures have a profound effect on the xenometabolome.<br><br>IMPORTANCE: Dietary fibers can convey positive health effects, but the full suite of mechanisms and fiber type differences remains to be elaborated. Historically, most discussions have focused on the impact of fibers in promoting lower gut bacterial fermentation, leading to the generation of short-chain fatty acids (especially butyrate) and promoting growth of specific microbes. That said, health effects associated with dietary fiber are generally shared across diverse individuals harboring disparate gut microbial species, and it is increasingly appreciated that xenometabolites derived from microbial metabolism number in the thousands. In the current report, we applied metabolomics characterization to human stool cultures incubated with six structurally distinct inulin fibers. The results indicate that distinct, fiber-specific metabolite signatures manifest despite quite diverse bacterial community structures across donors. Such outcomes point to the existence of metabolic functional guilds that shape the metabolite landscape-and likely the unique bioactive characteristics-across dietary fiber types.}, }
@article {pmid41123360, year = {2025}, author = {Campbell, KD and Bohannan, BJM and Adair, KL}, title = {Assembly of skin microbiomes is more neutral than gut microbiomes in multiple animal species.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0222325}, doi = {10.1128/spectrum.02223-25}, pmid = {41123360}, issn = {2165-0497}, abstract = {The gut and external tissues of most animals are colonized by communities of microorganisms that can influence the health, development, and fitness of the host. The composition of these communities can vary greatly between individuals within a host species, and both selective factors (e.g., host immune response) and neutral processes (e.g., random loss of microbial cells) have been shown to contribute to this variation. Although it is known that microbiome composition differs between tissues within an individual host, less is known about the ecological processes that underlie these differences. To address this, we investigated whether the contribution of neutral ecological processes to microbiome assembly differs between external (skin and scale) and internal (gut) host tissues for a diverse panel of animal hosts. To do this, we fit a neutral ecological model to microbial communities from external and internal tissues across a variety of animal hosts. Strikingly, we discovered that the neutral model was equally or a better fit to skin or scale microbial communities across all hosts, suggesting that neutral processes play a larger role in the assembly of skin or scale microbiomes compared with gut microbiomes. Furthermore, we observed that this trend is robust to different definitions of the metacommunity (i.e., the microbial taxa available to colonize a host). Finally, we leveraged a simulation framework to compare the model fits of empirical versus simulated microbial communities. We found that neutral model fits to empirical communities can differ from simulated communities, emphasizing the importance of temporal sampling in profiling animal microbiomes.IMPORTANCEAnimal microbiomes are complex assemblages of microorganisms that influence a wide variety of host phenotypes. Despite their importance, we lack a thorough understanding of the processes that guide the formation of microbiomes (i.e., microbiome assembly). Understanding how microbiomes assemble is essential to managing microbiomes for host health, conservation, and other goals. Our work highlights the relatively underappreciated role of neutral ecological processes (the random loss or gain of microbial cells) in the assembly of animal microbiomes. We document a potentially general trend: the microbiomes of external tissues (i.e., skin or scales) tend to be more neutrally assembled than those of internal tissues (i.e., guts). This observation suggests that the commonly reported differences in microbiome composition of external and internal animal tissues may be due in part to different assembly processes. Our work also highlights the dynamic nature of microbiomes and the importance of longitudinal sampling when studying animal microbiomes.}, }
@article {pmid41123190, year = {2025}, author = {Dieter, C and Lemos, NE and Girardi, E and Massignam, ET and Kowalski, TW and Recamonde-Mendoza, M and Puñales, M and Assmann, TS and Crispim, D}, title = {Expression of long noncoding RNAs in peripheral blood mononuclear cells of patients with type 1 diabetes mellitus: potential biomarkers for disease onset.}, journal = {Archives of endocrinology and metabolism}, volume = {69}, number = {6}, pages = {e240496}, doi = {10.20945/2359-4292-2024-0496}, pmid = {41123190}, issn = {2359-4292}, mesh = {Humans ; *Diabetes Mellitus, Type 1/genetics/blood/diagnosis ; *RNA, Long Noncoding/genetics/blood/metabolism ; *Leukocytes, Mononuclear/metabolism ; Female ; Male ; Biomarkers/blood ; Adult ; Case-Control Studies ; Young Adult ; Up-Regulation ; Adolescent ; Glycated Hemoglobin/analysis ; }, abstract = {OBJECTIVE: Long non-coding RNAs (lncRNAs) do not encode proteins and are transcripts longer than 200 nucleotides. The precise involvement of lncRNAs in type 1 diabetes mellitus (T1DM) pathogenesis remains unclear. Therefore, this study aimed to analyze the expressions of five lncRNAs in peripheral blood mononuclear cells of individuals with T1DM and without DM.<br><br>MATERIALS AND METHODS: This study comprised 27 patients with T1DM (cases) and 13 individuals without DM (controls). The case group was divided into two subgroups based on T1DM duration: < 5 years of diagnosis group and long-term diabetes group (&#x2265;5 years). LncRNA expression was evaluated by qPCR.<br><br>RESULTS: MALAT1 and TUG1 were upregulated in patients within the first five years of diagnosis of T1DM compared to the other groups. MEG3 was upregulated in the case group of < 5 years of diagnosis compared to controls. TUG1 and MALAT1 levels were negatively correlated with the duration of T1DM, while TUG1 and MEG3 were positively correlated with glycated hemoglobin levels. Bioinformatics analysis revealed that MALAT1, MEG3, and TUG1 regulate and interact with protein-codifying genes and microRNAs involved in T1DM-related pathways.<br><br>CONCLUSION: Our study revealed MALAT1, MEG3, and TUG1 upregulation in patients within the first five years of diagnosis of T1DM.}, }
@article {pmid41118732, year = {2025}, author = {Zahn, G and Amend, A and Gladfelter, A}, title = {Mycology: The rising tide of marine fungal research.}, journal = {Current biology : CB}, volume = {35}, number = {20}, pages = {R946-R948}, doi = {10.1016/j.cub.2025.09.024}, pmid = {41118732}, issn = {1879-0445}, mesh = {*Fungi/physiology ; *Seawater/microbiology ; *Carbon Cycle ; Biomass ; Oceans and Seas ; }, abstract = {A new study provides a robust global estimate of pelagic fungal biomass. Their findings reveal fungi as ecologically significant components of the ocean carbon cycle, marking a turning point for integrating fungi into marine microbial ecology.}, }
@article {pmid41118316, year = {2025}, author = {Liang, B and Pu, M and Xu, YN and Li, Y and Sun, JN and Zhu, Y and Doraiswamy, C and Dadd, T and Chu, CC}, title = {Dandruff scalp microbiome exhibits flake severity and sex-related differences.}, journal = {The British journal of dermatology}, volume = {193}, number = {Supplement_2}, pages = {ii32-ii39}, doi = {10.1093/bjd/ljaf099}, pmid = {41118316}, issn = {1365-2133}, support = {//Unilever Global R&amp;D/ ; }, mesh = {Humans ; Female ; Male ; *Microbiota/genetics ; *Dandruff/microbiology/pathology ; *Scalp/microbiology ; Adult ; Severity of Illness Index ; Sex Factors ; Middle Aged ; *Dysbiosis/microbiology ; RNA, Ribosomal, 16S ; Young Adult ; }, abstract = {BACKGROUND: Dandruff is a prevalent scalp condition characterized by flakiness and itchiness. Its severity can be assessed clinically based on the grade of flakes and coverage area of flakes adhering to the scalp. Dysbiosis of the scalp microbiome is a key factor associated with dandruff, as revealed by studies comparing healthy individuals with those with dandruff.<br><br>OBJECTIVES: This study further investigated the interplay between microbiome alterations and dandruff severity, and whether these changes are consistent across different sexes.<br><br>METHODS: Dandruff condition was assessed using the Total Weighted Head Score for Adherent Flakes (TWHS AF). Male and female participants with lower dandruff severity (TWHS AF = 32-40 inclusive) and higher dandruff severity (TWHS AF &#x2265; 44) were recruited following ethical clearance of the study and obtaining informed consent. Scalp bacterial composition was investigated by 16S rRNA amplicon sequencing. The absolute abundance of key scalp microbes was quantified by quantitative polymerase chain reaction.<br><br>RESULTS: Notable microbiome compositional differences were observed between scalps with lower and higher dandruff severity. More severe dandruff exhibited a significantly reduced abundance of Cutibacterium acnes and elevated levels of Staphylococcus capitis and Corynebacterium spp. The absolute numbers of Malassezia restricta significantly increased with increased dandruff severity, while M. globosa remained similar. Additionally, distinctive scalp microbial profiles were observed between female and male participants with dandruff, even with the same levels of severity. Interestingly, beta diversity analysis revealed that the microbiomes from male participants with less severe dandruff clustered closely with those of male and female participants with more severe dandruff. Similarly, microbiome metabolic pathway profiles indicated that metabolic alteration in male participants with less severe dandruff was more similar to male and female participants with more severe dandruff.<br><br>CONCLUSIONS: Our findings underscored significant severity-associated variations in microbial ecology. For the first time, we unveiled sex-related differences in microbiome profiles among individuals with dandruff, with male profiles resembling a severe dandruff dysbiosis state. These results highlight a progressive development of microbiome dysbiosis with dandruff severity and suggest potential mechanistic differences between male and female dandruff conditions, which may require different intervention strategies.}, }
@article {pmid41117697, year = {2025}, author = {Li, Z and Kuang, X and Ling, J and Shen, T and Shan, G and Wu, J}, title = {Mouse chymase mast cell protease-4 facilitates blood feeding of Aedes aegypti (Diptera: Culicidae) mosquitoes.}, journal = {Journal of medical entomology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jme/tjaf137}, pmid = {41117697}, issn = {1938-2928}, support = {24 3505 Pj//Swedish Cancer Society/ ; //Guizhou High-level Innovative Talents Training Program (Qiankehe Platform Talents-GCC[2022]033-1)/ ; //Science and Technology Innovation Talent Team of Guizhou Province (Qian Ke He Platform Talent-CXTD [2022]004)/ ; ZK[2021]430]//Guizhou Provincial Basic Research Program (Natural Science)/ ; 21NSFCP29//Incubation Funding of Guizhou Medical University National Natural Science Foundation/ ; }, abstract = {Aedes aegypti (Linnaeus) are rapidly spreading across the globe. Evidence suggests that a Type I hypersensitivity reaction, characterized by IgE-mediated mast cell degranulation, may enhance the blood-feeding behavior of Ae. aegypti. Chymases, the mast cell-specific proteases, may play a critical role in this process. To investigate the role of mouse chymase mast cell protease-4 (mMCP-4) on mosquito blood feeding, we incubated bone marrow-derived mast cells with serum from mice sensitized by female Ae. aegypti bites and subsequently challenged the cells with salivary gland proteins (SGPs) from female mosquito. And the degradation of SGPs by mMCP-4 was assessed. Then, the MCP-4 deficient mice were sensitized twice by Ae. aegypti, the first bite on day 0 and the second on day 3. Throughout these experiments, we recorded the total blood meal duration, probing time, and blood feeding of the mosquitoes and analyzed the cutaneous microbiota. We discovered that serum from sensitized mice enhanced mast cell degranulation and chymase release. And mMCP-4 degraded some SGPs, in particular, potentially cleaving the blood-feeding-related salivary protein D7. Mcpt-4 deficiency resulted in prolonged blood-feeding duration during the second exposure, without affecting initial probing behavior. Moreover, Mcpt-4-deficient mice exhibited a reduced proportion of mosquitoes achieving rapid engorgement. Skin microbiome profiling revealed that Mcpt-4 deficiency attenuated the bite-induced expansion of potentially harmful bacterial taxa, including the dominant genus Corynebacterium (Mycobacteriales: Corynebacteriaceae). These findings identify mMCP-4 as a critical mediator of mosquito blood-feeding behavior and a modulator of skin microbial ecology in response to Ae. aegypti bites.}, }
@article {pmid41117590, year = {2025}, author = {Guo, X and Yang, C and Fu, Q and Li, H and Fang, J and Zheng, R}, title = {Impact of yak excreta on soil bacterial community in alpine marsh under warming conditions.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0149325}, doi = {10.1128/aem.01493-25}, pmid = {41117590}, issn = {1098-5336}, abstract = {Livestock excreta and climate warming are two main disturbances of wetlands embedded in grazing lands, resulting in long-lasting changes in soil microorganisms. However, the impact of livestock excreta on the soil bacteria community in wetlands with climate warming has not been elucidated. In the current study, a laboratory culture experiment was designed to investigate how yak excreta, temperature, and their interaction regulate the soil bacterial community in an alpine marsh. The results show that yak dung increased soil moisture, pH, total organic carbon (TOC), and available phosphorus (AP), but decreased NO3[-]-N (P < 0.05). Yak urine increased soil moisture, NH4[+]-N, and NO3[-]-N (P < 0.05). Warming decreased soil moisture and pH of marsh soil (P < 0.05). Warming increased the alpha-diversity of the bacterial community in marsh soil; yak dung had an opposite effect, while yak urine exerted almost a negligible effect. In comparison with warming, yak excreta was the main cause of changing the bacterial community in marsh soil. Yak dung altered more bacterial genera of marsh soil than yak urine. Moreover, yak dung obviously strengthened the bacterial association interaction in marsh soil, while yak urine had the opposite trend. Yak excreta and temperature altered the bacterial community by regulating NO3[-]-N, AP, pH, TOC, and moisture of marsh soil. This study confirms the different influences of yak dung and urine on the bacterial community of marsh soil under warming conditions and highlights that the impacts of yak excreta on the bacterial community are sensitive to climate warming.IMPORTANCEInvestigating the response of the bacterial community in marsh soil to external disturbances is an important but poorly elucidated topic in microbial ecology. In this study, we evaluated the impacts of yak excreta, temperature, and their interaction on the bacterial community in alpine marsh soil. Our results showed that yak excreta exhibited a stronger influence on the bacterial community of marsh soil than temperature. The response of the bacterial community of marsh soil to yak dung is more sensitive than to yak urine. Yak excreta and temperature significantly altered the bacterial community by regulating NO3[-]-N, AP, pH, TOC, and moisture of marsh soil. Understanding the impact of yak excreta on soil bacterial community under warming conditions is extremely significant for managing grazing and maintaining a healthy alpine marsh ecosystem.}, }
@article {pmid41117558, year = {2025}, author = {Maltz, MR and Topacio, TM and Lo, DD and Zaza, M and Freund, L and Botthoff, J and Swenson, M and Cocker, D and Biddle, T and Yisrael, K and Del Castillo, D and Drover, RW and Aronson, E}, title = {Lung microbiomes' variable responses to dust exposure in mouse models of asthma.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0020925}, doi = {10.1128/msphere.00209-25}, pmid = {41117558}, issn = {2379-5042}, abstract = {UNLABELLED: Inhalation of dust is significant and relevant to health effects. As pollution and climate change worsen in dryland regions, wind currents entrain loose sediment and dust. This potentially disperses toxic geochemical and microbial burdens throughout the region. When inhaled environmental dust and host-associated microbiomes mingle, they pose exposure risks to host respiratory health. The Salton Sea, California's largest lake, is shrinking, thus exposing nearby communities to playa dust. Therefore, we analyze the effect of Salton Sea dust exposure in murine models to relate lung microbial communities and respiratory health. We used an environmental chamber to expose mice to dust filtrate or ambient air and examined the effects of those exposures on lung microbiomes. We found that lung microbial composition varied by dust exposure. Furthermore, dust elicited neutrophil recruitment and immune responses more than mice exposed to ambient air. Sources of dust differentially affected the composition of the lung core microbiome. Lung microbial diversity correlated with neutrophil recruitment as lungs associated with inflammatory responses harbored more diverse microbiomes. Although Salton Sea dust influences dust microbiomes and prevalent taxa, these responses are variable. The composition of lungs exposed to dust collected further from the Salton Sea was more similar to lungs from ambient air exposures; in contrast, dust collected near the Salton Sea yielded lung microbiomes that clustered further from lungs exposed to ambient air. As lakes continue to dry out, we expect greater public health risks in proximal dryland regions, which may correlate with dust microbial dispersal-related changes to lung microbiomes.<br><br>IMPORTANCE: Dust inhalation can lead to health effects, especially when toxic chemicals and microbes mix in with the dust particles. As California's Salton Sea dries up, it exposes lake bottom sediments to wind, which disperses the dried sediments. To mimic the effect of inhaling Salton Sea dust, we collected and filtered airborne dust to use in exposure experiments with mice in environmental chambers. We predicted that inhaling small dust particles, chemicals, and microbial residues found in this dust would affect mouse respiratory health or change the microbes found inside their lungs. We found that inhaling dust led to lung inflammation, and the dust source influenced the type of microbes found inside mouse lungs. As lakes continue to dry out, we expect greater health risks and changes to lung microbiomes.}, }
@article {pmid41117325, year = {2025}, author = {Kaundal, R and Parkash, V and Paul, S and Thapa, M}, title = {Heavy metal stress alters soil microbial structure and diversity in the BBN industrial corridor, Himachal Pradesh, India.}, journal = {International journal of phytoremediation}, volume = {}, number = {}, pages = {1-13}, doi = {10.1080/15226514.2025.2572305}, pmid = {41117325}, issn = {1549-7879}, abstract = {Soil microorganisms are essential to ecosystem functioning, yet their communities are highly susceptible to environmental disturbances such as heavy metal contamination from industrial activities. This study investigates the impact of heavy metal pollution on soil bacterial and fungal communities in the Baddi-Barotiwala-Nalagarh (BBN) Industrial Corridor, Himachal Pradesh, India. Soil samples were analyzed for physicochemical properties and heavy metal content, i.e., cadmium (Cd), iron (Fe), copper (Cu), arsenic (As), lead (Pb), chromium (Cr), zinc (Zn), and manganese (Mn), followed by the isolation and characterization of culturable bacterial and fungal communities. Microbial profiling indicated significant variations in community composition, diversity, and abundance across industrial sites. Firmicutes (Bacillota) and Proteobacteria emerged as dominant bacterial phyla, while the fungal communities were predominantly composed of Ascomycota. Although overall microbial richness and diversity declined with increasing heavy metal concentrations, several isolates exhibited key plant growth-promoting (PGP) traits, including phosphate solubilization, siderophore production, indole-3-acetic acid (IAA) synthesis, ammonia production, and nitrate reduction. Pearson correlation analysis demonstrated a relation between microbial community structure and multiple environmental variables, including heavy metals and key soil physicochemical properties. The findings highlight the dual role of soil microbes as indicators of environmental stress and as potential agents for microbe-assisted bioremediation.}, }
@article {pmid41114872, year = {2025}, author = {Dyczko, D and Hałupka, L and Czyż, B and Czułowska, A and Kiewra, D}, title = {Ticks on migrating birds in southwestern Poland: occurrence of Ixodes ricinus and the first Polish record of Haemaphysalis concinna on birds.}, journal = {Experimental &amp; applied acarology}, volume = {95}, number = {4}, pages = {46}, pmid = {41114872}, issn = {1572-9702}, mesh = {Animals ; Poland/epidemiology ; *Bird Diseases/parasitology/epidemiology ; Nymph/physiology/growth &amp; development/genetics ; *Tick Infestations/veterinary/parasitology/epidemiology ; Larva/growth &amp; development/physiology/genetics/classification ; *Ixodidae/physiology/growth &amp; development/genetics/classification/anatomy &amp; histology ; Animal Migration ; Ixodes/physiology/growth &amp; development ; *Songbirds ; Female ; Male ; Animal Distribution ; }, abstract = {During ornithological research conducted at the Milicz Fishponds Nature Reserve (Barycz Valley Landscape Park, southwestern Poland) from May to July 2024, a total of 245 birds were captured. Four ticks were collected: two Ixodes ricinus larvae and two Haemaphysalis concinna nymphs. We present the first confirmed record of H. concinna parasitising a great reed warbler (Acrocephalus arundinaceus) in Poland. Identification of H. concinna was based on both morphological identification keys and molecular analysis of the COI gene. This finding expands current knowledge on the biodiversity of ticks parasitising birds in Poland and highlights the need for further research on the role of migratory birds in the dispersal of ticks across Central Europe.}, }
@article {pmid41114853, year = {2025}, author = {de Scally, SZ and McDonald, MJ}, title = {Evolution of One Species Increases Resistance to Invasion in a Simple Synthetic Community.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {110}, pmid = {41114853}, issn = {1432-184X}, support = {CE230100001//Australian Research Council/ ; }, mesh = {*Escherichia coli/genetics/growth &amp; development/physiology ; *Saccharomyces cerevisiae/genetics/growth &amp; development/physiology ; *Biological Evolution ; Models, Biological ; Ecosystem ; Introduced Species ; }, abstract = {The species that make up a microbial community determine its potential function. A major goal of microbial ecology is to make assemblages of microbes - synthetic communities - with targeted applications. Replacing a dysfunctional community with a synthetic microbial community can have transformative impacts upon a host or ecosystem, yet the introduced community may be outcompeted by local species or communities, resulting in transient effects. Here, we study a simple synthetic community comprised of two species - E. coli and S. cerevisiae - that have coevolved for either 0, 1000 or 4000 generations, and evaluate the potential for 12 bacterial strains, from five species, to invade. We find that the dominant species (E. coli) in the community protects the less dominant species from being outcompeted during an invasion, and that this effect is strengthened by longer periods of coevolution. Using a mathematical model, we show how prolonged co-evolution leads to protective effects for a community member sensitive to displacement.}, }
@article {pmid41114740, year = {2025}, author = {Hopton, CM and Cockell, CS}, title = {Spatiotemporal Impacts of Enceladus- and Earth-relevant Ammonia Gas On Cultivation of Extremophile Halomonas meridiana.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {111}, pmid = {41114740}, issn = {1432-184X}, support = {NE/S007407/1//Natural Environment Research Council/ ; ST/V000586/1//Science and Technology Facilities Council/ ; }, mesh = {*Ammonia/metabolism ; *Halomonas/growth &amp; development/metabolism/drug effects ; Volatilization ; }, abstract = {One underexplored aspect of microbial growth is the impact of toxic gases transported through the atmosphere. Ammonia is a gas that can supply essential nitrogen but also exert cellular toxicity. Ammonia volatilized from a concentrated source into surrounding environments is therefore a crucial consideration when assessing the capacity of environments to support life, such as within terrestrial environments polluted with ammonia, or the ice crusts above ammonia-water oceans of icy moons. We cultivate Halomonas meridiana proximal to an ammonia source and examine the impact of ammonia volatilization on growth. Lower cell densities (OD600 = 0-1) occurred nearest the ammonia source. At 24 h, wells exhibiting an OD600 = 0-0.5 were evident when ammonia concentrations were ≥ 0.5 M. H. meridiana in proximity to 0 M, 0.1 M, 0.25 M, 0.5 M, and 1 M ammonia exhibited OD600 > 2 in 89.86%, 57.97%, 37.32%, 30.07%, and 18.48% of culture wells at 48 h, respectively. Alteration to growth kinetics and viability of H. meridiana cultivated adjacently to an ammonia source ("adjacently exposed") were not as severe compared to direct culture in ammonia ("directly exposed"). Compared to control, adjacent exposure to 0.1 M ammonia exerted no significant detrimental effect on growth kinetics and enhanced cell density, but adjacent exposure to ≥ 0.5 M ammonia greatly extended lag time, doubling time, reduced cell density, and reduced viability. Ammonia volatilized from 0.1 M sources may thus minimally affect, if not improve, habitability, whereas environments exposed to ammonia volatilized from sources at ≥ 0.5 M could constrain habitability.}, }
@article {pmid41114647, year = {2025}, author = {Basso, TO and Venturini, AM and Ceccato-Antonini, SR and Gombert, AK}, title = {Microbial Ecology Applied to Fuel Ethanol Production from Sugarcane.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaf100}, pmid = {41114647}, issn = {1574-6941}, abstract = {The production of fuel ethanol in sugarcane biorefineries is a non-aseptic industrial operation, which employs cell recycling and the use of adapted Saccharomyces cerevisiae strains. Microbial contaminants are present and, depending on the conditions, may lead to process performance deterioration. Past studies have identified the main microbial species present in this environment, using culture-dependent techniques. A few recent studies started to deploy culture-independent techniques to better understand this microbiota and its dynamics. In both cases, lactic acid bacteria have been identified as the main contaminating microorganisms. Less than a handful of reports are available on the interactions between yeast and contaminating bacteria, using synthetic microbial communities, proposing that interactions are not necessarily always detrimental. The present mini-review aims at systematizing the current knowledge on the microbiota present in the alcoholic fermentation environment in sugarcane biorefineries and setting the ground and claiming the need for a microbial ecology perspective to be applied to this system, which in turn might lead to future process improvements.}, }
@article {pmid41114112, year = {2025}, author = {Yang, YQ and Li, N and Liu, S and Yu, YW}, title = {Uridine diphosphate-glucose 6-dehydrogenase-mediated glucuronidation and its emerging role in gut-liver immune regulation.}, journal = {World journal of gastrointestinal oncology}, volume = {17}, number = {10}, pages = {110464}, pmid = {41114112}, issn = {1948-5204}, abstract = {This editorial builds on a recent study by Cao et al, which identified uridine diphosphate-glucose 6-dehydrogenase (UGDH) as a pro-tumorigenic enzyme in hepatocellular carcinoma (HCC). UGDH, a key catalyst in glucuronidation, promotes tumor growth and correlates with immunosuppressive features in the HCC microenvironment. Expanding on these findings, we explore broader implications of UGDH within the gut-liver axis. We propose that UGDH regulates immune tone not only through detoxification of bile acids and microbial products, but also by maintaining intestinal barrier integrity. Its dysregulation may impair glucuronidation, leading to bile acid accumulation, increased gut permeability, and microbial translocation, collectively promoting hepatic immune tolerance. Additionally, emerging evidence suggests that gut microbiota-derived metabolites can modulate hepatic UGDH expression, forming a bidirectional feedback loop between microbial ecology and liver metabolism. In this context, UGDH may act as a metabolic immune checkpoint, linking metabolic dysfunction with immune escape mechanisms such as programmed cell death ligand 1 upregulation and cyclic guanosine monophosphate-adenosine monophosphate synthase-stimulator of interferon genes pathway activation. Targeting UGDH could therefore help restore gut-liver immune balance and delay gastrointestinal cancer progression, especially in metabolic HCC. This editorial integrates metabolic, microbial, and immunological perspectives to support a novel translational framework.}, }
@article {pmid41114005, year = {2025}, author = {Sun, R and Xu, W and Xu, Y and Xu, Z and Tan, Y and Li, J and Liu, H and Yung, CCM}, title = {Environmental gradients shape viral-host dynamics in the Pearl River estuary.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf164}, pmid = {41114005}, issn = {2730-6151}, abstract = {Marine viruses play critical roles in shaping microbial communities and driving biogeochemical cycles, yet their dynamics in estuarine systems are not well characterized. Here, we conducted a comprehensive metagenomic analysis of viral communities and virus-host interactions across the Pearl River estuary, a dynamic subtropical estuary in southern China. Using 24 metagenomic libraries from eight sampling sites, we identified 29,952 viral populations, with Uroviricota and potential Uroviricota accounted for 80.48% of taxa, underscoring their ecological importance. A key finding of our integrated analysis is the unexpectedly high abundance of nucleocytoplasmic large DNA viruses in offshore waters, which suggests a more significant role for eukaryotic viruses in coastal ecosystems than previously acknowledged and correlates with elevated levels of their eukaryotic hosts. Environmental variables, particularly salinity and nutrient availability, emerged as key drivers of viral and host distribution patterns. By linking environmental gradients to distinct community "envirotypes" and their underlying genomic features, we revealed novel virus-host interactions and highlighted the impact of environmental gradients on microbial ecology. Additionally, viral auxiliary metabolic genes linked to phosphorus and nitrogen metabolism suggest critical roles in modulating host metabolic pathways and influencing nutrient cycling. Our findings demonstrate how spatial heterogeneity and environmental gradients shape viral and microbial ecology in estuarine ecosystems. Our findings provide a holistic, multi-domain view of microbial and viral ecology, demonstrating how integrating prokaryotic, eukaryotic, and viral community analyses offers a more complete understanding of ecosystem function in these critical transition zones.}, }
@article {pmid41113651, year = {2025}, author = {Lan, R and De Paula Ramos, L and Chen, Z and Carrouel, F}, title = {Editorial: Exploring the oral-gut microbiome interactions: pathways to therapeutic strategies and implications for systemic health.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1691238}, pmid = {41113651}, issn = {1664-302X}, }
@article {pmid41112761, year = {2025}, author = {Lestin, L and Villemur, R}, title = {Modulation of carbon-to-nitrogen ratio shapes the microbial ecology in a methanol-fed recirculating marine denitrifying reactor.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e20129}, pmid = {41112761}, issn = {2167-8359}, mesh = {*Denitrification ; *Methanol/metabolism ; *Bioreactors/microbiology ; *Nitrogen/metabolism/analysis ; Biofilms/growth &amp; development ; *Carbon/metabolism/analysis ; Piscirickettsiaceae/metabolism/genetics ; Nitrates/metabolism ; Water Purification/methods ; }, abstract = {BACKGROUND: Nitrate (NO3 [-]) can accumulate in closed-circuit ecosystems to a toxic level. Adding heterotrophic denitrification process to the water treatment is a strategy to reduce this level. This type of process usually requires the addition of a carbon source. Carbon-to-nitrogen ratio (C/N) is a key parameter known to influence both the function and the activity of microbial communities in bioprocesses. Few studies have examined the influence of C/N on denitrification systems operated under methylotrophic and marine conditions. Here we assessed the influence of C/N (methanol and NO3 [-]) on the performance of a laboratory-scale, recirculating denitrifying reactor operated under marine conditions. We monitored the evolution of the bacterial community in the biofilm to assess its stability during the operating conditions. Finally, the relative gene expression profiles of Methylophaga nitratireducenticrescens strain GP59, the main denitrifier in the denitrifying biofilm, were determined during the operating conditions and compared with those of GP59 planktonic pure cultures.<br><br>METHODOLOGY: A 500-mL methanol-fed recirculating denitrification reactor operated under marine conditions and colonized by a naturally occurring multispecies denitrifying biofilm was subjected to eight different C/N. We monitored several physico-chemical parameters (denitrifying activities, methanol consumption, CO2 production) throughout the operating conditions. The evolution of the bacterial community in the biofilm during these conditions was determined by 16S rRNA gene amplicon sequencing. Metatranscriptomes were derived from the biofilm to determine (1) the relative gene expression profiles of strain GP59, and (2) the functional diversity of the active microorganisms in the biofilm.<br><br>RESULTS: Changes in C/N did not correlate with the denitrification dynamics (NO3 [-] and NO2 [-] reduction rates, NO2 [-] and N2O dynamics), but did correlate with the methanol consumption rates, and the CO2 production rates. Throughout the operating conditions, nitrite and N2O appeared transiently, and ammonium was not observed. The bacterial community in the reactor increased in diversity with biofilm aging, especially among heterotrophic bacteria, at the expense of methylotrophic bacteria. The relative expression profiles of strain GP59 in the biofilm are distinct from those of planktonic pure cultures of strain GP59, and that the expression of several riboswitches and xoxF would be involved in these differences.<br><br>CONCLUSIONS: When the biofilm community is well established in the reactor, it can withstand changes in C/N with limited impact on the denitrification performance. The increase in the proportion of heterotrophs would allow the reactor to be more flexible regarding carbon sources. This knowledge can be useful for improving the efficiency of denitrification system treating close circuit systems such as marine recirculating aquaculture wastewater or seawater aquarium.}, }
@article {pmid41112022, year = {2025}, author = {Gao, J and Zhang, J and Wang, J and Chang, Y and Qin, Z and Sun, L and Li, M and Yang, Q}, title = {Intraspecific Genetic Diversity Analyses of Yam (Dioscorea polystachya Turcz.) Based on DUS Traits and SSR Molecular Markers.}, journal = {Ecology and evolution}, volume = {15}, number = {10}, pages = {e72295}, pmid = {41112022}, issn = {2045-7758}, abstract = {Yam (Dioscorea polystachya Turcz.) is an asexually reproduced food and traditional Chinese medicinal crop with extensive genomic variability. However, the detailed characterization of genetic diversity among different yam germplasm samples is still insufficient. This study evaluated the genetic divergence and genetic structure of 113 D. polystachya accessions collected from 17 provinces in China based on 50 distinctness, uniformity, and stability (DUS) traits and 19 simple sequence repeat (SSR) markers. All the selected varieties were categorized into three groups based on morphological characteristics and further validated by principal component analysis. Furthermore, 14 core traits, including 6 leaf traits, 4 tuber traits, 3 bulbil traits, and 1 stem trait, were selected to increase field inspection efficiency. SSR fingerprinting, utilizing 19 highly polymorphic markers, successfully distinguished all 113 yam varieties, revealing relatively high levels of genetic variation. Interestingly, the optimal genetic structure defined three groups, whereas a finer-scale model consistently classified the varieties into five groups, corroborating the genotypic cluster analysis. Furthermore, this study preliminarily identified 10 groups of potential heterotypic synonyms and 13 groups of potential homonyms among the yam accessions. These results demonstrate that the 19 selected SSR markers, in conjunction with DUS traits, can effectively discriminate the 113 D. polystachya varieties. Our findings provide critical insights for the conservation of pure breeds and the utilization of Dioscorea germplasm resources.}, }
@article {pmid41109620, year = {2025}, author = {Rojas Oñate, D and Opazo Capurro, A and González Rocha, G and Zornoza, R and Torres Bustos, C and Hasbún, R and Bucarey, B and Osman, JR and Schoebitz, M}, title = {Plastisphere and the occurrence of antibiotic resistance in a 40-year-old abandoned coastal landfill site in Chile.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {127280}, doi = {10.1016/j.envpol.2025.127280}, pmid = {41109620}, issn = {1873-6424}, abstract = {Plastispheres are microbial communities that inhabit plastic surfaces and have been extensively studied in aquatic environments. However, little is known about their occurrence in landfills. We investigated plastisphere communities in a 40-year-old coastal abandoned landfill in Rocuant-Andalién, Chile, and aimed to characterize landfill plastisphere communities and assess their potential role as reservoirs of antibiotic resistance genes (ARGs). High-density polyethylene was the predominant plastic type (56 %). Microscopy revealed diverse bacterial morphotypes, including bacilli, cocci, and filamentous forms, forming clusters on plastic surfaces. 16S rRNA gene sequencing revealed that Actinobacteria, Firmicutes, and Proteobacteria dominated most samples, with high overall diversity and richness. Beta diversity analysis indicated significant variation in bacterial communities among sites but not among polymer types. Notably, the intI1 gene, associated with the spread of antibiotic resistance, was detected at 67 % of the sampled sites. These findings reveal that landfills act as reservoirs for a wide range of bacteria, some of which may have clinical significance, highlighting their ecological and public health impact. Furthermore, plastics are likely to transport resistance genes originating from human activities, spreading them into nearby ecosystems, such as wetlands and oceans, where they interact with wildlife.}, }
@article {pmid41107717, year = {2025}, author = {Khan, MSI and Wu, J and Hou, S and Ji, S and Li, H and Chang, Y and Sui, B and Tan, D and Yin, J}, title = {Bile modulates phage-host interactions in multidrug-resistant Pseudomonas aeruginosa.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {666}, pmid = {41107717}, issn = {1471-2180}, support = {2021-243//People's Government of Dalian Municipality/ ; 2021-243//People's Government of Dalian Municipality/ ; 2021-243//People's Government of Dalian Municipality/ ; 2021-243//People's Government of Dalian Municipality/ ; 2021-243//People's Government of Dalian Municipality/ ; 2021-243//People's Government of Dalian Municipality/ ; 2021-243//People's Government of Dalian Municipality/ ; }, mesh = {*Pseudomonas aeruginosa/virology/drug effects/genetics/physiology ; *Bile/metabolism ; *Drug Resistance, Multiple, Bacterial ; Biofilms/growth &amp; development/drug effects ; *Pseudomonas Phages/physiology ; Lipopolysaccharides/biosynthesis ; Pseudomonas Infections/microbiology ; *Host-Pathogen Interactions ; }, abstract = {Biliary tract infections (BTIs) arise within a bile-rich environment that profoundly shapes microbial ecology and pathogen adaptation. Pseudomonas aeruginosa, a major opportunistic pathogen in nosocomial settings, exhibits remarkable physiological plasticity, that enable persistence in such challenging niches. However, the influence of bile on P. aeruginosa's adaptive responses and phage-host interactions remains largely unexplored. Here, we demonstrate that ox-bile imposes concentration-dependent stress on P. aeruginosa strain ZS-PA-35, indicative of host-derived selective pressure. Notably, ox-bile enhances biofilm formation and promotes swarming and twitching motilities while concurrently suppressing swimming motility. Moreover, ox-bile modulates phage susceptibility, likely through altered receptor expression: exposure to ox-bile sensitizes P. aeruginosa to the type IV pili (T4P)-dependent phage phipa2, whereas susceptibility to the lipopolysaccharide (LPS)-targeting phage phipa10 remains unchanged. Genome-wide mutagenesis identified resistance-conferring mutations affecting T4P structures, LPS biosynthesis, and associated regulatory pathways. Among these, phage-resistant mutants ΔpilT and ΔgalU retained high fitness under ox-bile stress, accompanied by enhanced swarming and swimming motilities. Furthermore, in a lysogenic context, ox-bile markedly suppressed prophage accumulation in the T4P-dependent strain ZS-PA-05. These findings reveal that bile acts as a critical environmental cue shaping both adaptive physiology and phage susceptibility in P. aeruginosa, with broad implications for microbiome dynamics and the development of phage-based therapies targeting bile-impacted infections.}, }
@article {pmid41107300, year = {2025}, author = {Urrutia-Angulo, L and Ocejo, M and Yergaliyev, T and Oporto, B and Aduriz, G and Camarinha-Silva, A and Hurtado, A}, title = {Exploring colostrum microbiota and its influence on early calf gut microbiota development using full-length 16S rRNA gene metabarcoding.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {36350}, pmid = {41107300}, issn = {2045-2322}, support = {PRE2020-096275//MICIU/AEI/10.13039/501100011033 and ESF Investing in your future/ ; }, mesh = {*Colostrum/microbiology ; Animals ; Cattle ; *RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; Feces/microbiology ; DNA Barcoding, Taxonomic/methods ; Female ; Phylogeny ; }, abstract = {The early gut microbiota of calves is seeded by colostrum and shaped by diet, environment, disease, and antibiotic treatments. This study analyzed the colostrum microbiota of 42 cows and tracked their calves' gut microbiota during early life (days d1, d16, and d57), assessing the impact of antimicrobial dry cow therapy and infection treatments. The full-length 16S rRNA gene was sequenced using Oxford Nanopore, enabling taxonomic classification down to species level. Microbial richness and diversity were lowest at d1 and increased afterwards. Beta diversity analysis showed that d16 samples had microbial profiles intermediate to those of d1 and d57. The most abundant phyla (Pseudomonadota, Bacillota, and Bacteroidota) were common to all sample categories, while genus-level composition showed greater variability. Colostrum was dominated by Paraclostridium, Romboutsia, and Staphylococcus, while Escherichia/Shigella and Clostridium were more abundant in d1 feces, later replaced by Succinivibrio and Faecalibacterium at d16 and d57. Notably, 56.2% of species in d1 feces were also present in colostrum, and 37.4% of colostrum species persisted in feces at d57, highlighting colostrum´s role in bacterial gut colonization. Interindividual variability in gut microbiota decreased over time as richness and diversity increased. Antimicrobial treatments did not significantly alter microbiota diversity or composition, suggesting a limited long-term impact.}, }
@article {pmid41106786, year = {2025}, author = {Guo, M and Zhao, H and Song, N and Huang, P and Li, M and Han, L and Zeng, KW and Lu, Z}, title = {Shenmai injection attenuates sepsis-associated acute lung injury by remodeling gut microbiota and restoring steroid hormone biosynthesis.}, journal = {Fitoterapia}, volume = {}, number = {}, pages = {106935}, doi = {10.1016/j.fitote.2025.106935}, pmid = {41106786}, issn = {1873-6971}, abstract = {Sepsis-associated acute lung injury (SA-ALI), a critical complication of sepsis, is characterized by immune dysregulation-induced pulmonary dysfunction. Shenmai Injection (SMI) is a standardized herbal preparation consisting of Panax ginseng C.A.Mey (Hongshen) and Ophiopogon japonicus (Thunb.) Ker Gawl (Maidong), traditionally used for qi-replenishing, collapse-stabilizing, and lung-moistening therapy. Although clinically utilized in the management of SA-ALI, the specific mechanisms by which it acts against SA-ALI necessitate further investigation. The present study endeavors to comprehensively determine the therapeutic efficacy of SMI against SA-ALI through an integrated approach combining network pharmacology, metabolomics, metagenomic sequencing, and experimental validation. In this study, murine SA-ALI was established using lipopolysaccharide (LPS) and Poly(I:C). Results indicated that SMI administration significantly attenuated pulmonary inflammation, restored blood-gas barrier integrity, reduced serum pro-inflammatory cytokines and suppressed NF-κB pathway activation in SA-ALI mice. Network pharmacology elucidated the multi-targeted mechanism of SMI in modulating steroid hormone biosynthesis. Integrated metabolomics and target analysis revealed that ophiopogonin A/B and luteolin in SMI alleviates metabolic dysregulation by targeting key enzymes, including AKR1C3, HSD17B1/2, and SULT1E1. Metagenomic profiling demonstrated SMI-mediated gut microbiota remodeling, marked by suppression of pathogenic Chlamydiaceae (particularly Chlamydia abortus) and enrichment of commensal Lactobacillaceae. Correlation analysis showed that intestinal androstenedione and androsterone levels during SMI treatment recovery were negatively correlated with Chlamydia abortus abundance. In conclusion, SMI enhances the recovery from sepsis-associated SA-ALI by dual modulation of gut microbial ecology and host metabolic homeostasis, thereby establishing its potential as a multi-mechanistic therapeutic candidate for sepsis-related organ injury.}, }
@article {pmid41106598, year = {2025}, author = {Khan, KS and Alam, T and Fiaz, S and Azim, R and Qadeer, A and Iqbal, R and Li, L}, title = {Hyphosphere Fungi-Bacteria-Plant Interactions Regulate Phosphorus Tradeoffs in the Soil Plant System.}, journal = {Plant science : an international journal of experimental plant biology}, volume = {}, number = {}, pages = {112819}, doi = {10.1016/j.plantsci.2025.112819}, pmid = {41106598}, issn = {1873-2259}, abstract = {Tripartite interactions among arbuscular mycorrhizal fungi (AMF), phosphorus-solubilizing bacteria (PSB), and terrestrial plants are pivotal in plant stress resistance, nutritional cycling, and soil-microbe ecological functions. The convoluted association between AMF and PSB may play a significant role in the decomposition and absorption of soil organic phosphorus (P), because AMF dynamically secretes carbon-containing compounds from extraradical hyphae (ERH) to stimulate PSB growth rate and activities. PSB are the main contributors of plant nutrition and could play a pivotal role in making soluble P available to plants. In this context, this comprehensive review critically examined the AMF-PSB interactions in soil P mobilization, with a focus on soil biochemical dynamics, microbial ecology, physiological mechanisms, biochemical pathways, and gene expression. While the explored studies emphasize the role of AMF-PSB interactions in P mobilization, it is important to consider that many experiments used root-free compartments, potentially overestimating mycorrhizal contributions relative to root pathways. Future research should integrate root-inclusive systems to provide a more comprehensive understanding of P acquisition dynamics by regulating indigenous AMF in terrestrial ecosystems.}, }
@article {pmid41106329, year = {2025}, author = {Hill, RC and Pieńkowska, A and Merbach, I and Reitz, T and Muehe, EM and Vengosh, A}, title = {Impacts of fertilization on metal(loid) transfer from soil to wheat in a long-term fertilization experiment - using [87]Sr/[86]Sr isotopes as metal(loid) tracer.}, journal = {Environment international}, volume = {205}, number = {}, pages = {109851}, doi = {10.1016/j.envint.2025.109851}, pmid = {41106329}, issn = {1873-6750}, abstract = {Fertilizers are widely used to sustain food production but can alter soil chemistry and potentially contribute toxic metal(loid)s to agricultural systems. For the first time, this study examined the occurrence of select metal(loid)s (Zn, Sr, V, As, Cd, Pb, and U) alongside the [87]Sr/[86]Sr isotope ratio in agricultural soil- both total and mobile pools- and wheat grain. Samples were collected from one of four fertilization treatments- mineral (NPK), organic (manure), combined mineral+organic, and unfertilized controls- within the 120-year Static Fertilization Experiment in Bad Lauchstädt, Germany. Fertilization treatments altered soil pH and organic carbon resulting in mineral fertilization lowering pH and increasing cation mobility (Cd, Zn, Sr), whereas organic fertilization increased pH and enhanced the mobility of non-cationic elements (V, As). These effects translated into higher Cd in mineral-fertilized wheat grain and higher As in mineral+organic wheat grain. Fertilization shifted the [87]Sr/[86]Sr ratios in soils and wheat grains toward that of the applied fertilizers, with mineral and mineral+organic wheat grains inheriting the triple super phosphate signature (0.70778) and organic wheat grains matching manure (0.70883). The [87]Sr/[86]Sr ratio in the mobile soil pool was correlated with mobile As, V, and P, demonstrating that the [87]Sr/[86]Sr ratio reflects both fertilizer source and the mobility of select co-occurring metal(loid)s. Overall, this study demonstrates metal(loid) enrichment in soil and wheat from fertilization and establishes [87]Sr/[86]Sr ratio as a robust tracer of fertilizer impacts. These findings underscore the need for targeted fertilization strategies to reduce contaminant accumulation in agroecosystems.}, }
@article {pmid41106081, year = {2025}, author = {Krimech, A and Sbahi, S and Cherifi, O and Hejjaj, A and Mugani, R and Ouazzani, N and Kerner, M and Oudra, B and Mandi, L}, title = {Seasonal effects on Chlorella sorokiniana UCAM 001 growth and physiology in flat-plate photobioreactors in Morocco's arid climate.}, journal = {European journal of protistology}, volume = {101}, number = {}, pages = {126171}, doi = {10.1016/j.ejop.2025.126171}, pmid = {41106081}, issn = {1618-0429}, abstract = {This study aims to investigate the seasonal variation in growth and physiology of Chlorella sorokiniana UCAM 001 strain using annual optimization monitoring with a groundwater medium in two outdoor flat-plate photobioreactors (PBRs), which were first scaled up at the Faculty of Sciences Semlalia (Marrakech, Morocco). The culture medium was adjusted to ensure non-limiting nutrient concentrations (10 mg·L[-1] and 100 mg·L[-1] of additional phosphorus and nitrate, respectively). Temperature, light, and algal growth were monitored daily. Proline, glycine betaine, and catalase levels were measured every four days to assess the degree of algal stress. Biomass productivity increased during spring, reaching 30 mg·L[-1]·day[-1] with a specific growth rate of 0.73 day[-1]. However, no growth was observed during the summer. Physiological analysis revealed increased proline and glycine betaine levels during autumn and winter due to temperatures as low as 13 °C. In contrast, catalase concentration peaked in spring. Pearson correlation analysis indicated that nutrient limitation, together with temperature and light intensity, induced stress in C. sorokiniana, stimulating catalase production. Algal growth efficiently removed nutrients from the medium, achieving removal rates of 97 % for total phosphorus and 87 % for total nitrogen. Optimized cooling systems will improve PBR efficiency and support algal growth under extreme summer conditions.}, }
@article {pmid41105271, year = {2025}, author = {Castellano-Hinojosa, A and Llodrà-Llabrés, J and Ramos-Rodríguez, E and Smol, JP and Meyer-Jacob, C and Sigro, J and Pérez-Martínez, C}, title = {Temporal succession of bacterial and archaeal communities in a Mediterranean high-mountain lake over the last 430 years using sedimentary DNA.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {107}, pmid = {41105271}, issn = {1432-184X}, support = {LACEN (OAPN 2403-S/2017)//Ministry of Ecological transition in their National Park Autonomous Agency/ ; LifeWatch-2019-10-UGR-01//Ministry of Science and Innovation through the FEDER funds from the Spanish Pluriregional Operational Program 2014-2020 (POPE), LifeWatch-ERIC action line/ ; BIOD22_001//Consejer&#xed;a de Universidad, Investigaci&#xf3;n e Innovaci&#xf3;n and Gobierno de Espa&#xf1;a and Uni&#xf3;n Europea - NextGenerationEU/ ; }, mesh = {*Lakes/microbiology/chemistry ; *Archaea/classification/genetics/isolation &amp; purification ; *Geologic Sediments/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Climate Change ; Spain ; Microbiota ; DNA, Archaeal/genetics ; Biodiversity ; Ecosystem ; DNA, Bacterial/genetics ; Nitrogen/analysis ; DNA, Ancient/analysis ; Temperature ; }, abstract = {Despite the known influence of climate change on high-altitude ecosystems, the long-term response of prokaryotic communities in Mediterranean high-mountain lakes remains poorly understood. Here, we investigate the temporal dynamics of prokaryotic communities over the past ~ 430 years in a Mediterranean high-mountain lake, utilizing sedimentary ancient DNA (sedDNA). By examining a sediment core from Borreguil Lake in the Sierra Nevada (Spain), we evaluated bacterial and archaeal abundance, diversity, and community composition (β-diversity) in relation to paleoenvironmental and climate data. Our findings revealed a significant restructuring of prokaryotic communities, particularly since ca. 1960. A Random Forest model identified dissolved organic carbon, organic nitrogen, Saharan atmospheric dust inputs, and temperature as key drivers of the abundance, diversity, and composition of prokaryotic communities, particularly in the modern era. Notably, the abundance and diversity of bacterial communities increased in response to increased dissolved organic carbon, elevated temperatures, and dust deposition, while archaea demonstrated a more nuanced response linked to organic nitrogen availability and dust inputs. The temporal shifts in microbial community composition point to broader ecological changes within the lake, shaped by climate-driven environmental variations. For example, the increased relative abundance of Cyanobacteria and other taxa linked to higher nutrient availability indicates ongoing eutrophication processes, likely intensified by climate warming. This study highlights the importance of high-mountain lakes as indicators of climate change, contributing valuable insights into microbial ecology's response to long-term environmental change. Our findings offer a foundational understanding for predicting microbial responses in sensitive ecosystems under future climate scenarios.}, }
@article {pmid41105270, year = {2025}, author = {Gamoń, F and Ćwiertniewicz-Wojciechowska, M and Muszyński-Huhajło, M and Miodoński, S and Ziembińska-Buczyńska, A and Cema, G and Tomaszewski, M}, title = {Low-Temperature Anammox Supported by Zero-Valent Iron (ZVI): Microbial and Physicochemical Changes during Treatment of Synthetic and Municipal Wastewater.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {108}, pmid = {41105270}, issn = {1432-184X}, support = {UMO-2017/25/N/NZ9/01159//Narodowe Centrum Nauki/ ; }, mesh = {*Iron/metabolism/chemistry ; *Wastewater/microbiology/chemistry ; Oxidation-Reduction ; Bioreactors/microbiology ; Anaerobiosis ; *Ammonium Compounds/metabolism ; *Bacteria/metabolism/classification/genetics ; *Waste Disposal, Fluid/methods ; Cold Temperature ; }, abstract = {The anaerobic ammonium oxidation (anammox) process offers a sustainable and energy-efficient alternative for nitrogen removal in wastewater treatment, but its performance at low temperatures remains a major challenge. This study investigated the role of zero-valent iron (ZVI) in enhancing anammox activity across a temperature range of 10-30 °C using both synthetic and municipal wastewater (MWW). Short-term batch tests demonstrated that low-dose ZVI (5-10 mg/L) stimulated specific anammox activity (SAA) particularly at 13-20 °C, while ZVI increasing concentration (1-10 mg/L) enhanced the enzymatic activity of HDH and decreased NIR activity, as well as modulated oxidative stress (ROS and GSH balance). In contrast, the long-term operation of the anammox process in sequencing batch reactors (SBR) showed that while ZVI (5 mg/L) improved SAA and microbial stability under synthetic conditions at 13 °C in compared to control (without ZVI), these benefits diminished once real municipal wastewater was introduced, most likely due to biomass stress and organic load. Metataxonomic analysis confirmed that ZVI selectively promoted genera such as Candidatus Brocadia, Denitratisoma, Micavibrionales_unclassified, while reducing overall microbial diversity. These results indicate that low-dose ZVI can temporarily enhance anammox resilience at suboptimal temperatures. However, its long-term application in MWW requires further optimization to mitigate potential inhibitory effects and iron passivation.}, }
@article {pmid41105260, year = {2025}, author = {Phauk, S and Assentato, L and Sin, S and Uk, O and Hap, S and Terenius, O}, title = {Symbiont Diversity of Rice-Associated Leafhoppers (Cicadellidae) in the Tropical Floodplains of the Tonle Sap Lake, Cambodia.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {109}, pmid = {41105260}, issn = {1432-184X}, mesh = {Animals ; *Hemiptera/microbiology/physiology/classification ; *Symbiosis ; *Oryza/parasitology ; Cambodia ; Female ; Lakes/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Male ; Biodiversity ; Microbiota ; Phylogeny ; }, abstract = {Rice-associated leafhoppers (Cicadellidae) play a significant role in rice agroecosystems, contributing not only to direct crop damage but also to the transmission of plant pathogens. This study investigates the symbiont diversity of seventeen leafhopper species from the tropical floodplains of Tonle Sap Lake (TSL), Cambodia. The dominant symbiont across most species was Candidatus (Ca.) Karelsulcia muelleri, an obligate primary endosymbiont essential for nutrient synthesis. The co-obligate symbiont Ca. Nasuia deltocephalinicola was also consistently detected, particularly in Deltocephalinae hosts. In addition, several secondary symbionts, including Sodalis, Arsenophonus, Diplorickettsia, Rickettsia, Wolbachia, and Ca. Lariskella, were identified, showing species-specific associations and potential roles in host fitness and pathogen transmission. Variations in symbiont diversity were observed across cicadellid species, geographic origins, and between sex-associated symbionts, with notable differences in the bacterial composition of Nephotettix virescens. While geographical differences (Battambang vs. Kampong Thom) did not strongly affect microbial composition, sex-associated variations were evident in N. virescens. Females exhibited a higher abundance of Karelsulcia and Nasuia, suggesting possible microbial adaptation related to reproduction. This study highlights the complex and dynamic nature of cicadellid hosts-symbiont interactions and suggests that microbial communities are primarily structured by host species. While geographic distance can influence these communities, this effect is not the same for every species. These findings provide critical insights into the microbial diversity of rice-associated leafhoppers and their potential for ecological roles in rice farming systems. Further studies, including functional analysis and host-symbiont interactions, are crucial to understanding the ecological roles and evolutionary dynamics of these microbial communities.}, }
@article {pmid41105100, year = {2025}, author = {Arellano, AA and Prack, JL and Coon, KL}, title = {Host-mediated niche construction of bacterial communities in an aquatic microecosystem.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf233}, pmid = {41105100}, issn = {1751-7370}, abstract = {Microbes coordinate homeostasis in host-associated and environmental ecosystems alike, but the connectivity of these biomes is seldom considered. Hosts exert controls on the composition and function of their internally associated symbionts, but an underappreciated modality of microbiome curation is external to the host through changes to the environmental species pool from which they recruit microbial symbionts. Niche construction theory describes how organisms alter their environment and the selective landscape of their offspring and conspecifics. We hypothesize that host-driven manipulation of environmental microbial communities is an underexplored form of this concept. Using the pitcher plant mosquito (Wyeomyia smithii) as a model, we tested how hosts shape microbial communities across developmental stages and gradients of pre-existing community complexity. We report three lines of evidence supporting host-mediated niche construction, leveraging amplicon sequencing and microbiota manipulation experiments with germ-free (axenic) and selectively recolonized (gnotobiotic) mosquitoes. First, single female egg-laying assays showed repeatable adult inoculation of sterile water with beneficial bacteria capable of sustaining robust larval development. Second, increasing larval density in assays inoculated with complex, field-derived microbial communities selected for environmental and host-associated bacteria that correlated with increased larval fitness. Finally, exposing axenic larvae to mixtures of parentally and environmentally derived microbiota demonstrated that prior conditioning by conspecifics enhanced offspring fitness. Although the bacterial taxa associated with mosquito structuring varied, members of the Actinobacteriota and Acetobacteraceae were consistently associated with increased fitness. Overall, our results provide an example of host-mediated niche construction to favor environmental microbial communities that positively impact host fitness.}, }
@article {pmid41104934, year = {2025}, author = {Ryan, D}, title = {Gene regulation in Bacteroides fragilis: adaptive control in a dynamic host environment.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {}, number = {}, pages = {e0022525}, doi = {10.1128/mmbr.00225-25}, pmid = {41104934}, issn = {1098-5557}, abstract = {SUMMARYBacteroides fragilis occupies a dynamic position within the human gut. Though it comprises a relatively minor fraction of the gut microbiota, it is disproportionately enriched at extraintestinal sites of infection. This ability to survive in contrasting host environments pivots on a regulatory framework that is both modular and highly plastic. Rather than deploying a suite of hierarchical global regulators, B. fragilis employs numerous operon-embedded transcriptional switches, including site-specific DNA inversions, phase-variable epigenetic systems, extracytoplasmic function sigma/anti-sigma factor pairs, and hybrid two-component systems. These networks are further complemented by cis-regulatory elongation checkpoints and post-transcriptional control by small RNAs. This review explores the full spectrum of these regulatory mechanisms, highlighting how they facilitate niche adaptation, surface variation, immune evasion, and metabolic prioritization. It also explores intraspecies variation focusing on glycan metabolism, antibiotic resistance, and virulence. Additionally, it outlines recombination-driven regulation, alongside extracytoplasmic function sigma factor diversification, flexible promoter architecture, and elongation checkpoints, each contributing to the evolution of transcriptional control in B. fragilis. Finally, it outlines unanswered questions, including the largely unexplored sRNA regulon, the coordination of DNA inversions, elongation control, and phase-variable methylation, and proposes experimental strategies to investigate the integration of these regulatory systems during environmental transitions. Taken together, B. fragilis emerges as a model bacterium for studying decentralized gene regulation in complex microbial ecosystems, with implications for both microbial ecology and therapeutic targeting of the gut microbiota.}, }
@article {pmid41104481, year = {2025}, author = {}, title = {Laila P. Partida-Martínez.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.70665}, pmid = {41104481}, issn = {1469-8137}, abstract = {Laila P. Partida-Martínez, Cinvestav-Irapuato (Mexico).}, }
@article {pmid41104383, year = {2025}, author = {Kumar, P and Chitara, D and Sengupta, S and Banerjee, P and Rai, SN}, title = {Microbial consortia in biotechnology: applications and challenges in industrial processes.}, journal = {3 Biotech}, volume = {15}, number = {11}, pages = {386}, pmid = {41104383}, issn = {2190-572X}, abstract = {Microbial consortia, dynamic communities of interacting microorganisms, outperform single-species cultures in industrial biotechnology by overcoming metabolic bottlenecks and degrading complex compounds. These consortia are vital in bioremediation, bioenergy, bioproduction, agriculture, and wastewater treatment. In bioremediation, they efficiently break down persistent pollutants like polycyclic aromatic hydrocarbons. For bioenergy, they convert organic waste into biofuels such as methane and ethanol through multi-step metabolic processes unachievable by single microbes. They also enable sustainable synthesis of bioplastics, antibiotics, and other high-value compounds while enhancing agricultural productivity through improved nutrient availability and biocontrol of plant pathogens. Consortia degrade complex organic contaminants in wastewater treatment, ensuring cleaner effluents and environmental protection. The industrial application faces challenges, including ensuring microbial community stability, optimising performance, and scaling processes from laboratory to industrial scale. The intricate interactions within consortia complicate control, predictability, and real-time monitoring, while intellectual property and regulatory frameworks pose additional barriers. Limitations include gaps in understanding long-term ecological impacts and scalability in diverse environments. Advancements in microbial ecology, systems biology, and bioprocess engineering are crucial to address these issues. Prospects involve using CRISPR and AI to design robust consortia, improve predictive modelling, and foster interdisciplinary collaborations for sustainable applications. Overcoming these challenges will unlock the full potential of microbial consortia, revolutionise industrial processes, and advance sustainable biotechnology.}, }
@article {pmid41104112, year = {2025}, author = {Hayes, A and Zhang, L and Snape, J and Feil, E and Kasprzyk-Hordern, B and Gaze, WH and Murray, AK}, title = {Common non-antibiotic drugs enhance selection for antimicrobial resistance in mixture with ciprofloxacin.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf169}, pmid = {41104112}, issn = {2730-6151}, abstract = {Antimicrobial resistance (AMR) is a major health concern, and a range of antibiotic and non-antibiotic agents can select for AMR across a range of concentrations. Selection for AMR is often investigated using single compounds, however, in the natural environment and the human body, pharmaceuticals will be present as mixtures, including both non-antibiotic drugs (NADs), and antibiotics. Here, we assessed the effects of one of three NADs in combination with ciprofloxacin, a commonly used antibiotic that is often found at concentrations in global freshwaters sufficiently high to select for AMR. We used a combination of growth assays and qPCR to determine selective concentrations of mixtures and used metagenome sequencing to identify changes to the resistome and community composition. The addition of the three NADs to ciprofloxacin altered the selection dynamics for intI1 compared to the ciprofloxacin alone treatments, and sequencing indicated that mixtures showed a stronger selection for some AMR genes such as qnrB. The communities exposed to the mixtures also showed changed community compositions. These results demonstrate that NADs and ciprofloxacin are more selective than ciprofloxacin alone, and these mixtures can cause distinct changes to the community composition. This indicates that future work should consider combinations of antibiotics and NADs as drivers of AMR when considering its maintenance and acquisition.}, }
@article {pmid41103765, year = {2025}, author = {Li, M and Bi, J and Wang, X and Li, H}, title = {The hidden nitrogen nexus: stochastic assembly and linear gene synergies drive urban park microbial networks.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1652652}, pmid = {41103765}, issn = {1664-302X}, abstract = {Urban parks play a significant role in environmental greening, cultural heritage, and recreational activities. The diversity and distribution of park environmental microbiota have become a hot focus of microbial ecology. However, there has been limited attention on the functional attributes of microbial communities, highlighting the importance of studying the distribution and diversity of functional genes in urban parks. Here, we employed metagenomic sequencing and binning to explore the diversity, assembly, and functional synergy of nitrogen cycling genes from the grassland soil and water in urban parks. Our results showed that glutamate metabolism and assimilatory nitrate reduction are the predominant nitrogen cycling pathways in both the soil and water. The diversity of nitrogen cycling genes in water was more abundant than in soil. The assembly of nitrogen cycling genes in both the soil and water was primarily driven by stochastic processes. Nutrient factors (such as total sulfur) were the most significant influencers of nitrogen cycling genes in park soil, while bacterial communities were the most critical determinants in water. The gene narH, involved in multiple nitrogen cycling metabolic pathways, was identified as an important marker of nitrogen storage in both soil and water. Through metagenomic binning, we discovered linear arrangements of multiple nitrogen cycling genes, such as narG-narH-narJ-narI, which collectively participate in the reduction of nitrate to nitrite, demonstrating the synergy, functional redundancy, and complementarity among nitrogen cycling genes. Our study holds significant implications for the biochemical cycling and the management of nitrogen pollution in urban parks.}, }
@article {pmid41100058, year = {2025}, author = {Duncan, AH and Armenta, N and Garcia-Ledezma, F and Heck, CA and Hafner, S and Planer-Friedrich, B and Fendorf, S}, title = {Alternate Wetting and Drying Limits Arsenic in Porewater and Rice Grain under Severe Future Climate Conditions.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c03552}, pmid = {41100058}, issn = {1520-5851}, abstract = {Climate change, coupled with widespread soil arsenic (As) contamination, is expected to decrease rice yields and increase grain As, threatening food security. One promising mitigation strategy is alternate wetting and drying (AWD) irrigation. However, AWD has not previously been tested under potential future climate conditions. Using rhizoboxes to visualize the rhizosphere, we evaluated the efficacy of AWD for limiting porewater and grain As under both current (daily high of 33 °C and 420 ppmv CO2) and severe warming conditions (daily high of 38 °C and 850 ppmv CO2). Compared to continuous flooding, AWD decreased cumulative As exposure 10 cm below the surface by 8.2× under a 33 °C climate and by 15.9× under a 38 °C climate. Grain total As concentrations decreased by 1.5× with AWD under a 33 °C climate and by 1.3× under a 38 °C climate. Porewater cadmium (Cd) concentrations often increased following drainage but never exceeded 1 μg L[-1], and grain Cd concentrations were 14.7× to 119.7× lower than grain As concentrations. Both AWD and the 38 °C and 850 ppmv CO2 climate conditions enhanced root growth. Our findings indicate that AWD may still be an effective As mitigation strategy under severe future climate conditions.}, }
@article {pmid41099815, year = {2025}, author = {Price, A and Mog, SYA and Dubach, J and Billington, C and Larsen, P}, title = {Microbiomes of 2024's Periodical Cicada Brood XIII Vary By Species and Location.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {105}, pmid = {41099815}, issn = {1432-184X}, support = {2216567 &amp; 1912104//National Science Foundation (NSF)/ ; }, mesh = {Animals ; *Microbiota ; *Hemiptera/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; Illinois ; Male ; Female ; }, abstract = {The 17-year Periodical cicadas (Magicicada spp.) are long-lived insects that emerge in mass synchronized events after 17 years underground. Their survival and ecological success depend heavily on their microbiomes, which include obligate bacterial symbionts essential for nutrient acquisition, as well as occasional pathogens such as the behavior-altering fungus Massospora cicadina. While the periodical cicada lifecycle is well studied, little is known about how cicada microbiomes vary across species and environments during a single emergence event. During the 2024 emergence of Brood XIII in northern Illinois, 17-year cicadas were sampled from four ecologically distinct forest preserves. Cicadas were identified by species and sex; their microbiomes were assayed using 16S rRNA gene sequencing and tested for the presence of the fungal pathogen M. cicadina DNA in asymptomatic individuals. Sampling sites were characterized by plant community composition, historical disturbance, and potential presence of the antifungal compound juglone. Microbiome composition differed significantly by cicada species and site, but not by sex. The obligate symbionts Hodgkinia cicadicola and Sulcia muelleri dominated microbiome profiles, though other bacteria-including Pantoea agglomerans, a potential pheromone producer-were variably abundant. Cicada species distributions were non-random across sites and correlated with local plant diversity. M. cicadina DNA was detected in 23% of otherwise asymptomatic cicadas, with infection rates varying by location and negatively correlated with microbiome diversity. This study highlights complex interactions between cicada species, their microbial communities, and environmental variables such as plant diversity, soil chemistry, and land use history.}, }
@article {pmid41099800, year = {2025}, author = {Zhang, W and Yang, C and Zhao, K and Jin, M and Han, K and Wang, Y and Jiang, Z}, title = {Endophytic bacterial diversity of Vicatia thibetica collected from Xizang and the association with flavonoid accumulation.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {106}, pmid = {41099800}, issn = {1432-184X}, support = {82260759//National Natural Science Foundation of China/ ; }, mesh = {*Flavonoids/metabolism/analysis ; Plant Roots/microbiology/chemistry ; Rhizosphere ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Endophytes/classification/genetics/isolation &amp; purification/metabolism ; *Soil Microbiology ; China ; Biodiversity ; }, abstract = {Vicatia thibetica de Boiss is a unique medicinal and edible plant endemic to Xizang, China. It is one of the five primary root medicines in Tibetan medicine due to its high content of flavonoids. However, the community composition of endophytic bacteria in its various tissues and their potential role in flavonoid accumulation remain unclear. We employed high-throughput sequencing to compare the diversity of endophytic bacteria in the rhizosphere soil and various tissues of V. thibetica collected from three sampling sites in Nyingchi, Xizang. Concurrently, we assessed the types and concentrations of flavonoids present in the roots. Finally, we investigated the relationship between root endophytic bacteria and flavonoid accumulation through correlation analysis. The results indicated that the diversity and abundance of bacterial communities in the rhizosphere soil exceeded those of the endophytic bacterial communities of V. thibetica. Proteobacteria is the dominant phylum, and Sphingomonas is the dominant genus. Each tissue of a plant exhibits its dominant genus. PICRUSt predictive analysis revealed that RNA processing and modification were the predominant functions among related species. Targeted metabolomics analysis has revealed that the roots of the plants contain 14 flavonoid compounds. Correlation analysis revealed that the concentrations of flavonoids in the roots, including apigenin, rutin, astragalin, quercetin 3-glucoside, L-epicatechin, kaempferol, and luteolin, are associated with the distribution and abundance of specific bacterial genera, such as Lactobacillus, Kurthia, Bradyrhizobium, Phenylobacterium, Novosphingobium, and Mycobacterium, among others. This finding suggests that these bacterial genera may directly influence the production and accumulation of flavonoids in the plant. Our findings will enhance the understanding of plant-microbe interactions and provide crucial insights into the role of endophytes in the production of V. thibetica and its significant secondary metabolites.}, }
@article {pmid41099526, year = {2025}, author = {Lami, R}, title = {From biocides to biology: multispecies biofilms as a sustainable, self-regenerating, and effective antifouling strategy.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0160925}, doi = {10.1128/aem.01609-25}, pmid = {41099526}, issn = {1098-5336}, abstract = {Finding antifouling strategies that are effective and environmentally safe remains a central challenge for maritime operations and ecosystem protection. Amador et al.'s article in Applied and Environmental Microbiology (91:e01392-25, 2025, https://doi.org/10.1128/aem.01392-25) proposes a bioinspired, applied-microbial-ecology solution: deliberately shaping pioneer biofilm communities, so they form a physical barrier against macrofouler settlement, avoiding biocides and low-adhesion inert coatings. Though focused on the ocean, this paradigm could inform broader anti-biofilm interventions across microbiology, reframing control as ecological steering rather than chemical suppression or materials-based design.}, }
@article {pmid41096495, year = {2025}, author = {Phutthaphol, R and Bunchasak, C and Loongyai, W and Rakangthong, C}, title = {Effects of Vitamin D3 and 25(OH)D3 Supplementation on Growth Performance, Bone Parameters and Gut Microbiota of Broiler Chickens.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {19}, pages = {}, doi = {10.3390/ani15192900}, pmid = {41096495}, issn = {2076-2615}, support = {//Huvepharma (Thailand) Co., Ltd./ ; }, abstract = {Broiler chickens are commonly reared in closed housing systems with limited exposure to sunlight, thereby relying entirely on dietary sources of vitamin D. The hydroxylated metabolite 25-hydroxycholecalciferol [25(OH)D3] has been proposed as a more potent form than native vitamin D3 (cholecalciferol). This study evaluated the effects of dietary supplementation with vitamin D3 alone or in combination with 25(OH)D3 on growth performance, bone characteristics, and cecal microbiota in Ross 308 broilers. A total of 952 one-day-old male chicks were allocated to four treatments: a negative control (no vitamin D3), a positive control (vitamin D3 according to Ross 308 specifications), and a positive control supplemented with 25(OH)D3 at 1394 or 2788 IU/kg, in a randomized design with 17 replicates per treatment and 14 birds per replicate. Over a 40-day feeding trial, diets containing vitamin D3 (positive control) or supplemented with 25(OH)D3 significantly improved final body weight, weight gain, average daily gain, and feed conversion ratio compared with the negative control (p < 0.01), with no significant differences among the positive control and 25(OH)D3-supplemented groups, with a clear linear dose-dependent response. Although tibia ash and bone-breaking strength were not significantly affected, linear responses indicated a slight numerical trend toward improved skeletal mineralization with increasing 25(OH)D3. Microbiota analysis indicated that 25(OH)D3 affected cecal microbial ecology: low-dose inclusion showed reduced species richness and evenness, whereas high-dose inclusion restored richness to levels comparable to the positive control and enriched taxa associated with fiber fermentation and bile acid metabolism while reducing Lactobacillus dominance. In conclusion, supplementation with 25(OH)D3 in addition to vitamin D3 enhanced growth performance and selectively shaped the cecal microbiota of broilers, with suggestive benefits for bone mineralization. These findings highlight 25(OH)D3 as a more potent source of vitamin D than cholecalciferol alone and support its practical use in modern broiler nutrition to improve efficiency, skeletal health, and microbial balance.}, }
@article {pmid41092097, year = {2025}, author = {Almeida-Silva, F and Van de Peer, Y}, title = {Gene expression divergence following gene and genome duplications in spatially resolved plant transcriptomes.}, journal = {The Plant cell}, volume = {}, number = {}, pages = {}, doi = {10.1093/plcell/koaf243}, pmid = {41092097}, issn = {1532-298X}, abstract = {Gene and genome duplications expand genetic repertoires and facilitate functional innovation. Segmental or whole-genome duplications generate duplicates with similar and somewhat redundant expression profiles across multiple tissues, while other modes of duplication create genes that show increased divergence, leading to functional innovations. How duplicates diverge in expression across cell types in a single tissue remains elusive. Here, we used high-resolution spatial transcriptomic data from Arabidopsis thaliana, Glycine max, Phalaenopsis aphrodite, Zea mays, and Hordeum vulgare to investigate the evolution of gene expression following gene duplication. We found that genes originating from segmental or whole-genome duplications display increased expression levels, expression breadths, spatial variability, and number of coexpression partners. Duplication mechanisms that preserve cis-regulatory landscapes typically generate paralogs with more preserved expression profiles, but such differences generated by mode of duplication fade or disappear over time. Paralogs originating from large-scale (including whole-genome) duplications display redundant or overlapping expression profiles, indicating functional redundancy or subfunctionalization, while most small-scale duplicates diverge asymmetrically, consistent with neofunctionalization. Expression divergence also depends on gene functions, with dosage-sensitive genes displaying highly preserved expression profiles, and genes involved in more specialized processes diverging more rapidly. Our findings offer a spatially resolved view of expression divergence following duplication, elucidating the tempo and mode of gene expression evolution, and helping understand how gene and genome duplications shape cell identities.}, }
@article {pmid41089691, year = {2025}, author = {Li, W and Lu, K and Tang, J and Chen, Y and Lu, Y and Hu, X and Zhu, H and Feng, Y}, title = {The alterations of airway and intestine microbiota in asthma: a systematic review and meta-analysis.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1675124}, pmid = {41089691}, issn = {1664-3224}, mesh = {Humans ; *Asthma/microbiology/immunology ; *Gastrointestinal Microbiome/immunology ; *Respiratory System/microbiology/immunology ; }, abstract = {BACKGROUND: Emerging evidence highlights notable differences in microbial ecology between individuals with asthma and healthy controls (HC). This meta-analysis aims to compile data on microbial diversity indices in the airway and intestinal microbiota of both groups for comparative analysis.<br><br>METHODS: We conducted a thorough systematic search of literature in PubMed, Embase, the Web of Science, and the Cochrane Library to find English-language studies focused on airway and intestinal microbiota in asthma, published from May 16, 2020 to May 16, 2025. We extracted data regarding microbial diversity indices to facilitate comparisons between the asthma group and HC.<br><br>RESULTS: 26 studies were included in this systematic review. Our analysis revealed no significant differences in alpha diversity between the two participant groups; however, beta diversity exhibited significant differences in 9 of the studies reviewed.<br><br>CONCLUSION: Our meta-analysis did not confirm the hypothesis that asthma shows lower alpha diversity than HC. To enhance understanding and inform future diagnostic and therapeutic approaches, further studies should be conducted with larger sample sizes and more robust methodologies.<br><br>https://www.crd.york.ac.uk/prospero/, identifier CRD420251113790.}, }
@article {pmid41088478, year = {2025}, author = {Chen, X and Ma, X and Liu, Z and Gu, H and Fang, H and Shen, Z and Zhang, H and Wan, S and Li, W and Hao, X and Clarke, NJ and Liu, J}, title = {Organic fertilizers increase microbial community diversity and stability slowing down the transformation process of nutrient cycling.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {130}, pmid = {41088478}, issn = {2524-6372}, support = {07//the Straw Returning Project/ ; 07//the Straw Returning Project/ ; 07//the Straw Returning Project/ ; 07//the Straw Returning Project/ ; CHN-2152, 22/0013 SINOGRAIN III//Norwegian Ministry of Foreign Affairs/ ; CHN-2152, 22/0013 SINOGRAIN III//Norwegian Ministry of Foreign Affairs/ ; CX25PT02-01-04//Agricultural Science and Technology Innovation Project of Heilongjiang Province/ ; CX25PT02-01-04//Agricultural Science and Technology Innovation Project of Heilongjiang Province/ ; CX25PT02-01-04//Agricultural Science and Technology Innovation Project of Heilongjiang Province/ ; CX25PT02-01-04//Agricultural Science and Technology Innovation Project of Heilongjiang Province/ ; }, abstract = {BACKGROUND: Soil microbes play a central role in nutrient recycling in soils: however, the genetic mechanisms governing their responses to long-term fertilization remain poorly understood. While the agronomic benefits of long-term fertilization are well-documented, the genetic mechanisms and ecological processes underlying microbial community responses to different fertilization regimes remain poorly understood, particularly in unique soil systems such as black soils (Mollisols), which are critical for global food security. A deeper insight into how organic and inorganic fertilizers influence microbial assembly, functional potential, and community stability is essential for developing sustainable soil management practices.<br><br>RESULTS: This study deciphers microbial assembly mechanisms, functional gene dynamics, and community restructuring in black soils subjected to&#xa0;44&#xa0;years of chemical fertilizer (CF), manure amendment (M), and integrated chemical fertilizer with manure (CFM) treatments. Results revealed that CF significantly enhances functional gene abundance related to carbon (C) degradation (e.g., starch, cellulose, chitin and lignin) and nitrification, accelerating the conversion of recalcitrant C to labile C pools and ammonium to nitrate. Conversely, M and CFM treatments promote microbial diversity and stability while decelerating nutrient transformation processes. In addition, microbial assembly mechanisms shift from stochastic to deterministic processes with long-term fertilizer application in CF. The structural equation modeling (SEM) indicated that soil chemical properties shape both the diversity and composition of taxonomic and functional gene communities which subsequently regulate microbial -mediated nutrient cycling processes and crop yield.<br><br>CONCLUSIONS: Our findings highlight the trade-offs between microbial functional potential and community stability under contrasting fertilization strategies, emphasizing the need to integrate microbial metrics into sustainable land management frameworks.}, }
@article {pmid41086300, year = {2025}, author = {Peterson, BD and Poulin, BA}, title = {Illuminating the Black Box: Trace Element Biogeochemistry from a Microbial Perspective.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c06816}, pmid = {41086300}, issn = {1520-5851}, abstract = {Microbial processes are central to the transformation and fate of trace elements in the environment (e.g., mercury (Hg), arsenic (As)), but the complexities underlying microbial transformation rates and the influence of human impacts present considerable hurdles to developing conceptual and quantitative models of these processes. This perspective highlights processes that govern microbial activity in the environment as it pertains to trace elements, including redox, energy generation, resource limitation, and ecology and evolution. In this context, we compare and contrast the microbial-driven processes of Hg and As cycling, two elements with a genetic basis for microbial transformations (e.g., hgcAB, mer, arsH) that are used for microbial (i) metabolism (e.g., conversion of arsenate to arsenite), (ii) detoxification (e.g., reduction of divalent Hg(II) to volatile Hg(0)), (iii) warfare (e.g., conversion of arsenite to highly toxic trivalent methylated As(III)), or (iv) reasons not yet known (e.g., methylation of Hg(II) to toxic methylmercury). We argue for experimental approaches that quantify contaminant transformation(s) of interest in parallel with relevant metrics of microbial community activity. This microbe-centric framework may catalyze advancement that facilitates microbial integration into conceptual and quantitative models used to forecast environmental and human exposure to contaminants.}, }
@article {pmid41085588, year = {2025}, author = {Purohit, HV and Chakraborty, J}, title = {Metagenomic approaches for studying ubiquitous yet diverse nucleoid associated proteins in microbial communities: challenges and advances.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {41}, number = {10}, pages = {383}, pmid = {41085588}, issn = {1573-0972}, }
@article {pmid41085259, year = {2025}, author = {Li, S and Ye, X and Luo, K and Yu, L and Shen, Z and Yi, T and Wang, M and Gu, Q}, title = {High-Throughput Absolute Quantification Sequencing Advances Characterisation of Microbial Community Ecology.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {e70139}, doi = {10.1111/mec.70139}, pmid = {41085259}, issn = {1365-294X}, support = {2023YFD2400902//National Key Research and Development Program of China/ ; 31800388//National Natural Science Foundation of China/ ; 41601203//National Natural Science Foundation of China/ ; 2019JJ50314//Natural Science Foundation of Hunan Province, China/ ; kq2208163//Natural Science Foundation of Changsha, China/ ; 23B0073//Scientific Research Foundation of Hunan Provincial Education Department/ ; 2108085ME186//Anhui Provincial Natural Science Foundation/ ; }, abstract = {High-throughput sequencing has been extensively used in microbial ecology research, but this technology typically generates semi-quantitative relative abundance data. The discrepancies of community dynamics delivered by relative and absolute abundances have long been recognised by microbial ecologists. However, few studies have considered the discrepancies and their potential effects on related ecological interpretations. Here, the absolute copy numbers (absolute abundances) of taxa were quantified using a 'spike-in' based 16S absolute quantification sequencing to investigate the dynamics, co-occurrence patterns, and ecological assembly processes of microbial community in the river-connected Lake Dongting, Hunan province, China. Routine sequencing data analysis based on relative abundance was also obtained for comparison. The results indicated that outcomes based on relative and absolute abundances were comparable at the community level but differed significantly at the population level when dynamics and interactions of specific taxa were of interest. Specifically, at the population level, the dynamics of individual taxa were usually masked by their relative abundances, particularly for abundant taxa. The correlation-based co-occurrence network constructed from relative abundance largely underestimated the importance of rare taxa, consisted of massive false negative connections, and was less stable than the one constructed using absolute abundance. At the community level, the diversity and composition of microbial communities in Lake Dongting exhibited significant temporal rather than spatial variations, and temperature was determined to be the most important factor shaping microbial community composition and assembly processes, regardless of which abundance data were used. Nonetheless, relative abundance data yielded stronger environmental and deterministic effects on microbial assembly than absolute abundance. In summary, our study highlights the importance of incorporating absolute quantification to unveil the underlying microbial ecological patterns masked by relative abundance.}, }
@article {pmid41082055, year = {2025}, author = {Aderolu, AZ and Salam, LB and Lawal, MO and Kabiawu-Mutiu, LF and Bassey, ME and Shobande, MA}, title = {Microbial ecology and functional landscape of black soldier fly larval bioconversion of orange waste: A metataxonomic perspective.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {41}, number = {10}, pages = {377}, pmid = {41082055}, issn = {1573-0972}, mesh = {Animals ; Larva/microbiology/metabolism ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Gastrointestinal Microbiome/genetics ; *Simuliidae/microbiology ; *Citrus sinensis/metabolism ; *Diptera/microbiology ; Nigeria ; Metagenome ; Metagenomics ; Phylogeny ; }, abstract = {The accumulation of citrus waste, particularly orange waste (OW), presents significant environmental and economic challenges in Nigeria and worldwide. This study presents the first high-resolution, species-level metataxonomic analysis of OW bioconversion mediated by black soldier fly larvae (BSFL) in a West African context, addressing a critical gap in region-specific microbial ecology. Using long-read PacBio 16S rRNA sequencing and PICRUSt2-based functional prediction, microbial communities were profiled across three ecologically distinct substrates: untreated OW, BSFL gut microbiota (OW-BSFL), and post-digestion frass (OWF). Results revealed a dramatic microbial shift driven by host filtering: the OW-BSFL metagenome was overwhelmingly dominated (> 96%) by Lysinibacillus and Cytobacillus, while OWF exhibited markedly higher diversity (263 species), including Mycolatisynbacter and Sphingobacterium. Functional analysis revealed a significant enrichment of genes associated with carbohydrate (e.g., COG2814, COG0726) and amino acid metabolism (e.g., COG1173, COG0444) in the BSFL gut, indicating an elevated enzymatic processing capacity during waste digestion. In contrast, OWF displayed unique enrichment in genes associated with residual carbohydrate turnover and environmental colonization. This microbial succession highlights the selective enrichment and functional specialization that occur across the substrate-gut-frass continuum. By elucidating keystone taxa and metabolic signatures, the study not only advances understanding of insect-microbiome symbiosis but also provides a microbial blueprint for optimizing waste-to-value strategies. The findings support the deployment of BSFL bioconversion as a scalable, sustainable solution for organic waste valorization and biofertilizer production in sub-Saharan Africa's circular bioeconomy.}, }
@article {pmid41081862, year = {2025}, author = {Bandyopadhyay, A and Sarkar, D and Das, A and Das, A}, title = {Intersections of ABO blood group, secretor status, and the gut microbiome: implications for disease susceptibility and therapeutics.}, journal = {Archives of microbiology}, volume = {207}, number = {11}, pages = {296}, pmid = {41081862}, issn = {1432-072X}, mesh = {Humans ; *ABO Blood-Group System/genetics/metabolism ; *Gastrointestinal Microbiome ; Disease Susceptibility ; Galactoside 2-alpha-L-fucosyltransferase ; Bacteria/classification/genetics/isolation &amp; purification ; Probiotics ; }, abstract = {The human gut microbiome is a dynamic ecosystem. It is shaped by host factors, including genetic traits such as ABO blood type and associated secretor status (FUT2 gene). In secretor individuals (~ 80% of the population), ABO antigens are expressed on the gut mucosal surfaces. These antigens serve as adhesion sites and nutrient substrates for select microorganisms. Evidence links blood groups to gut microbial ecology, with taxa such as Bacteroidessp., Eubacteriumsp., and Faecalibacterium sp. exhibiting preferential colonization patterns influenced by mechanisms including mucin glycan foraging, pathogen adhesion, and competitive exclusion. ABO blood type further modulates susceptibility to infectious, metabolic, and autoimmune diseases by affecting microbiome composition. Secretor status impacts microbiota diversity and probiotic colonization Non-secretors exhibit altered Bifidobacterium sp. profiles and reduced norovirus adhesion. These insights suggest possible avenues for tailoring microbiome-based interventions; however, current evidence remains preliminary and requires validation through controlled clinical studies. We outline a conceptual model linking host genetics, microbial ecology, and health outcomes, recognizing that these associations are still being mapped. The idea of incorporating blood type and secretor status into precision microbiome approaches remains exploratory and requires rigorous validation.}, }
@article {pmid41081374, year = {2025}, author = {Hoshyaripour, S and Mauri, M and Hobbs, JK and Foster, SJ and Allen, RJ}, title = {Cell wall mechanical stress could coordinate septal synthesis and scission in Staphylococcus aureus.}, journal = {mBio}, volume = {}, number = {}, pages = {e0172825}, doi = {10.1128/mbio.01728-25}, pmid = {41081374}, issn = {2150-7511}, abstract = {Staphylococcus aureus divides by building a septum and then splitting into two daughter cells. Scission should be coordinated with septum completion to avoid cell lysis; however, it is not known how this is achieved, or what the relative roles of mechanical forces and the activity of peptidoglycan hydrolase enzymes are. Here, we show using thin-shell mechanics that septum formation causes a localized decrease in mechanical stress at the cell's equator. We propose that this local decrease in stress could act as a mechanical trigger for hydrolase activity, leading eventually to splitting. This mechanical trigger model can explain observed cell division defects, including premature splitting and failure to initiate splitting. The model also shows how cell size, turgor pressure, cell wall thickness and stiffness, and the relative rates of synthesis and hydrolysis combine to determine cell cycle timing and the outcome of antibiotic exposure. Bacterial cell division requires dynamic orchestration of molecular players, in concert with cell wall mechanics. Our work suggests how mechanical forces could coordinate with enzyme activity in the control of this complex process.IMPORTANCEStaphylococcus aureus is a major threat due to its ability to generate antibiotic-resistant strains. Understanding S. aureus division is therefore of great importance, but we do not know how septum formation is coordinated with cell scission. Previous works have shown that both mechanical stress and autolysin activity play key roles in scission, but it is unclear how mechanical and biochemical cues work together. Here, we propose a "mechanical trigger" model for the interplay between mechanical stress and autolysin activation. We use mathematical modeling to show that stress decreases in the S. aureus cell wall close to the division site as the septum is formed, and we propose that this could trigger autolysin activity. Our model explains reports of diverse division outcomes in the presence of mutations and antibiotics and points to a general link between cell geometry and antibiotic resistance.}, }
@article {pmid41080577, year = {2025}, author = {Wang, Z and Yu, J and Liu, Y and Gong, J and Hu, Z and Liu, Z}, title = {Role of the microbiota-gut-lung axis in the pathogenesis of pulmonary disease in children and novel therapeutic strategies.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1636876}, pmid = {41080577}, issn = {1664-3224}, mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; Child ; *Lung/immunology/microbiology/metabolism ; *Lung Diseases/therapy/microbiology/immunology/etiology/metabolism ; Dysbiosis ; Animals ; Fatty Acids, Volatile/metabolism ; }, abstract = {Emerging evidence highlights the microbiota-gut-lung axis (MGLA) as a pivotal regulator of pediatric respiratory health, yet mechanistic insights are lacking and therapeutic applications remain unclear. This review synthesizes cutting-edge findings to delineate how gut microbiota-derived metabolites, particularly short-chain fatty acids (SCFAs), orchestrate pulmonary immunity and disease pathogenesis in children. Leveraging multi-omics integration (metagenomics, metabolomics, transcriptomics), emerging studies have uncovered novel microbe-host interactions driving immune dysregulation in asthma, pneumonia, and cystic fibrosis. A comprehensive map of gut-lung crosstalk has been established across these conditions. Current studies suggest that early-life gut dysbiosis, shaped by delivery mode, antibiotics, and diet, disrupts SCFA-mediated immune homeostasis, amplifying T-helper 2 cell inflammation and impairing alveolar macrophage function. Crucially, we identified disease-specific microbial signatures (e.g., depletion of Lachnospira and Faecalibacterium in asthma) and demonstrated that fecal microbiota transplantation and probiotic interventions restore microbial balance, attenuating airway inflammation in preclinical models. This work pioneers the translation of MGLA insights into precision medicine strategies, highlighting dietary modulation and microbial therapeutics as viable alternatives to conventional treatments. By bridging microbial ecology and immune dynamics, our findings provide actionable biomarkers for early diagnosis and personalized interventions, addressing critical gaps in pediatric respiratory disease management. The integration of multi-omics frameworks not only advances mechanistic understanding but also positions the MGLA as a transformative target in reducing global childhood morbidity. Future research must prioritize longitudinal studies and clinical trials to validate these innovations, ultimately redefining therapeutic paradigms for GLA-driven pathologies.}, }
@article {pmid41079626, year = {2025}, author = {Papadopoulou, K&#x39a; and Chatzinotas, A and Diaz-Otero, BG and Brader, G and Karpouzas, DG and Garces Ruiz, M and Alonso Prados, JL and Declerck, S and Kellari, LM and Sessitsch, A}, title = {Benefits and challenges of upcoming microbial plant protection applications sustaining planetary health.}, journal = {iScience}, volume = {28}, number = {10}, pages = {113557}, pmid = {41079626}, issn = {2589-0042}, abstract = {Plant disease outbreaks pose severe risks to global food security. Due to climate change, new diseases are expected to emerge, and the current use of chemical pesticides poses risks to environmental and human health. In the last decade, alternative plant protection agents of microbial origin have been developed, which also raise great expectations in the industry. Current products primarily represent individual microbial strains, either fungi or bacteria, which occasionally fail under field conditions due to various factors while their regulatory status differs globally. Recently, more diverse applications have started to emerge, ranging from microbial consortia, phages and protists to microbiome modulation or soil translocation. Integrated solutions, incorporating artificial intelligence are also proposed. In this review, we discuss the opportunities and challenges of these solutions, providing specific examples and discuss the regulatory needs for their market entry as well as their relevance for improving food security and planetary health.}, }
@article {pmid41078603, year = {2025}, author = {Otto, JFM and Pohnert, G and Wichard, T and Bauer, M and Busch, A and Ueberschaar, N}, title = {Global DNA-methylation in quantitative epigenetics: orbitrap mass spectrometry.}, journal = {Frontiers in molecular biosciences}, volume = {12}, number = {}, pages = {1681568}, pmid = {41078603}, issn = {2296-889X}, abstract = {DNA methylation is the most common epigenetic modification in both prokaryotic and eukaryotic genomes. Here we present a method based on highly efficient acid-hydrolysis of DNA, liquid chromatography, and detection by mass spectrometry to accurately quantify cytosine methylation in highly methylated DNA samples. This approach enables direct, rapid, cost-efficient, and sensitive quantification of the methyl-modified nucleobase 5-methylcytosine and 6-methyl adenine, along with their unmodified nucleobases. In contrast to standard sequencing techniques, our method only gives quantitative information on the overall degree of methylation, but it requires only small amounts of DNA and is not dependent on lengthy bioinformatic analyses. Our method allows rapid, global methylome analysis and quantifies a central epigenetic marker. In a proof-of-principle study, we show that it can also be extended to the monitoring of other DNA modifications, such as methylated adenine. Uncomplicated data analysis facilitates a quick and straightforward comparison of DNA methylation across biological contexts. In a case study, we also successfully identified changes in methylation signatures in the marine macroalga Ulva mutabilis "slender". The advantage of global methylation analysis compared to sequencing allows for generating fast prior knowledge on which sample sequencing is senseful. The great benefit of the presented method is the speed and accuracy of the global methylation analysis, which is independent of the total methylation rate and gives accurate results, whereas competitive based on enzymatic digestion might fail.}, }
@article {pmid41078307, year = {2025}, author = {He, H and Xiao, M and Song, L and Tian, Y and Jia, Y}, title = {Lipidome-microbiome crosstalk as an outer niche in the skin: regulatory networks in health and disease.}, journal = {The British journal of dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1093/bjd/ljaf353}, pmid = {41078307}, issn = {1365-2133}, support = {//Beijing Technology and Business University/ ; //Beijing Municipal Education Commission/ ; 32100254//National Science Foundation of China/ ; }, abstract = {The skin is the outermost barrier to organisms from the external environment. This natural role, endowed by evolution, results in a nutrient-poor skin surface that enables microbial nutrition-dependent lipids to shape microbial ecology by survival pressure and nutrient preference. In turn, the skin microbiota produce microorganism-metabolized bioactive molecules (MBMs) to increase molecular diversity. This crosstalk functions as a crucial component of niche-regulating skin properties via multiple mechanisms. Furthermore, the local and remote effects of different barrier sites provide a more comprehensive explanation for the crosstalk from a global perspective. The variable function and mechanism of crosstalk may represent an evolutionary means by which the skin uses fluctuating commensal signals - the highly dynamic MBMs - to calibrate skin status and provide heterologous protection against invasive pathogens. Elucidating the reasons for the differing selectivity and catalytic efficiency of lipid-metabolizing enzymes in microorganisms and revealing the biologic processes and regulatory mechanisms of the 'co-metabolic systems' on the skin will advance diagnostic and therapeutic strategies for local cutaneous disorders and comorbid diseases of distant organs.}, }
@article {pmid41069707, year = {2025}, author = {Rubio-Portillo, E and Arias-Real, R and Rodríguez-Pérez, E and Bañeras, L and Antón, J and de Los Ríos, A}, title = {Short-term virus-host interactions and functional dynamics in recently deglaciated Antarctic tundra soils.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf157}, pmid = {41069707}, issn = {2730-6151}, abstract = {Long-term chronosequence studies have shown that, as glaciers retreat, newly exposed soils become colonized through primary succession. To determine the key drivers of this process and their vulnerability to climate change, the short-term responses of these pioneering microbial communities also need to be elucidated. Here, we investigated how the taxonomic and functional structure of microbial communities, including viruses, changed over a 7-year period in an Antarctic glacier forefield. Using metagenomics and metatranscriptomics we assessed the influence of both abiotic and biotic factors on these communities. Our results revealed a highly heterogeneous bacteria-dominated microbial community, with Pseudomonas as the most abundant genus, followed by Lysobacter, Devosia, Cellulomonas, and Brevundimonas. This community exhibited the capacity for aerobic anoxygenic phototrophy, carbon and nitrogen fixation, and sulfur cycling, processes vital for survival in nutrient-poor environments. 52 high-quality metagenome-assembled genomes (MAGs) were recovered, representing both transient and cosmopolitan taxa, some of which were able to rapidly respond to environmental changes. A diverse and highly dynamic collection of lytic and temperate viruses was identified across all samples, with high clonal viral genomes typically detected in only one of the eight samples analyzed. Metatranscriptomic analyses confirmed the activity of lytic viruses, while prophage genomes featured much lower expression levels. Prophages appeared to influence host fitness through the expression of genes encoding membrane transporters. Additionally, the abundance of genes linked to antimicrobial compound synthesis and resistance, along with antiphage defense systems, highlights the importance of biotic interactions in driving microbial community succession and shaping short-term responses to environmental fluctuations.}, }
@article {pmid41069527, year = {2025}, author = {Jiang, W and Gu, S}, title = {Editorial: The oral microbiome and its impact on systemic health: from disease development to biomaterials development.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1697069}, pmid = {41069527}, issn = {2235-2988}, }
@article {pmid41066956, year = {2025}, author = {Huang, P and Zhou, R and Huang, Z and Wu, C}, title = {Deciphering the environmental response and assembly of rare and abundant taxa in zaopei employing daqu produced by different pressing patterns.}, journal = {International journal of food microbiology}, volume = {445}, number = {}, pages = {111471}, doi = {10.1016/j.ijfoodmicro.2025.111471}, pmid = {41066956}, issn = {1879-3460}, abstract = {Baijiu fermentation relies on complex microbial communities within zaopei, which are significantly shaped by the microbial starter daqu. This study investigated the rare and abundant taxa composition, and flavor characteristics of zaopei (fermented grains) employing Nongxiangxing daqu produced by different pressing patterns (mechanically pressed, artificially pressed) from microbial ecology perspective. Then, the origin, environmental response, assembly patterns and driving factors of rare and abundant taxa were revealed. The results indicated that both Lactobacillus and Acetobacter consistently dominated in rare bacteria and abundant bacteria of zaopei, the dominant abundant fungi were Thermoascus and Issatchenkia, while the dominant rare fungi were Aspergillus and Pichia. The microbial community of zaopei was significantly influenced by fungi originating from daqu, according to Fast expectation-maximization microbial source tracking (FEAST) analysis. Moreover, daqu significantly influenced the assembly process of abundant fungi taxa in zaopei, with the mechanically pressed daqu (MDQ) increased the proportion of heterogeneous selection. Moreover, water, starch and ethanol contents were important factors driving the rare bacteria assembly. Co-occurrence network analysis indicated that artificially pressed daqu (ADQ) enhanced microbial interactions in zaopei, which were closely related to rare bacteria. Meanwhile, Spearman's correlation between microorganisms and differential flavor compounds showed that fungal taxa (abundant Clavispora, rare Pichia and rare Issatchenkia) played a dominant role in flavor synthesis. These results contributed to a better understanding of the functional contributions of rare and abundant taxa in baijiu fermentation and provided theoretical support and technical guidance for regulating baijiu quality.}, }
@article {pmid41065083, year = {2025}, author = {Cantoran, A and Maillard, F and Bermudez, R and Stefanski, A and Reich, PB and Kennedy, PG}, title = {Warming and Reduced Rainfall Alter Fungal Necromass Decomposition Rates and Associated Microbial Community Composition and Functioning at a Temperate-Boreal Forest Ecotone.}, journal = {Global change biology}, volume = {31}, number = {10}, pages = {e70536}, doi = {10.1111/gcb.70536}, pmid = {41065083}, issn = {1365-2486}, support = {DE-FG02-07ER64456//Biological and Environmental Research/ ; NSF-DBI-2021898//Division of Biological Infrastructure/ ; }, mesh = {*Rain ; *Soil Microbiology ; *Climate Change ; Minnesota ; *Microbiota ; Soil/chemistry ; *Fungi/metabolism ; Taiga ; *Global Warming ; }, abstract = {Changes in temperature and rainfall associated with altered climatic conditions are likely to significantly alter rates of soil organic matter decomposition. To determine how the combined effects of warming and drought impact the decomposition of fungal necromass, a large and fast-cycling portion of the global soil organic carbon (C) pool, we incubated Hyaloscypha bicolor necromass under both ambient and altered conditions (+3.3°C air and soil warming and ~40% reduced rainfall) at the B4Warmed experiment in Minnesota, USA. We conducted two multi-week incubations, one assessing mass loss and microbial community composition on decaying necromass after 1, 2, 7, and 14 weeks and the second characterizing the substrate utilization capacities of necromass-associated microbial communities after Weeks 1 and 7. Warming and reduced rainfall accelerated the initial rate of necromass decay by ~20%, yet slowed overall mass loss by ~6% at the end of the 14-week incubation. These different rates of decay over time paralleled shifting abiotic conditions, with altered plots experiencing warmer and relatively moist conditions early, but hotter and drier conditions later. The microbial community composition also varied by treatment and time, with warming and reduced rainfall stimulating fast-growing fungi as well as fungal relative to bacterial growth overall. Additionally, the functional capacity of the microbial community also changed over time, having a higher metabolic capability to utilize C and N substrates in the altered plots early in decomposition but a lower capability later in decay. Collectively, our findings highlight a dynamic, stage-dependent response of fungal necromass decomposition to altered climate regimes. By linking these decay dynamics to shifts in environmental conditions as well as microbial community composition and function, our study highlights the critical roles of both abiotic and biotic changes in mediating decomposition responses to climate change.}, }
@article {pmid41064756, year = {2025}, author = {Lofgren, L and Maillard, F and Michaud, T and Gredeby, A and Tunlid, A and Kennedy, PG}, title = {Diverse nitrogen acquisition strategies of conifer-associated ectomycorrhizal fungi shape unique responses to changing nitrogen regimes.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1666003}, pmid = {41064756}, issn = {1664-462X}, abstract = {Ectomycorrhizal fungi are critical mediators of nitrogen acquisition in forest ecosystems, exhibiting variation in both host association and metabolic traits that mediate differential responses to forest nitrogen availability. However, how nitrogen acquisition strategies vary among closely related fungal species, how these patterns manifest in conifer-associated ECM fungi, and whether they persist over changing nitrogen regimes, remains poorly understood. Using an integrative approach combining in silico genomic analysis, in vitro growth assays, and isotopic analysis of in situ specimens spanning six decades, we provide the first comprehensive examination of nitrogen assimilation in congeneric conifer-associated ectomycorrhizal fungi using six Suillus species. We found highly conserved genes for inorganic nitrogen assimilation across species, but striking interspecific variation in the genetic capacity for organic nitrogen metabolism. Interspecific differences were also observed in fungal growth on varying nitrogen substrates in the growth assays, as well as in the isotopic signatures of historical specimens. For the latter, carbon isotopic patterns showed divergent temporal trends among Suillus species, suggestive of differential N use over time. Collectively, these genomic, physiological, and isotopic findings support the presence of notable interspecific diversity in ectomycorrhizal fungal nitrogen acquisition and suggest that coniferous forests and their fungal symbionts exhibit distinct responses to shifts in nitrogen availability compared to broadleaf forests. The ability of even closely related ectomycorrhizal fungi to employ diverse nitrogen acquisition strategies has important implications for forest ecosystem resilience, as different species may provide complementary services to host trees under varying environmental conditions, potentially reducing competition, and influencing forest responses to altered nutrient availability.}, }
@article {pmid41064004, year = {2025}, author = {Pérez-Ramos, DW and Caragata, EP}, title = {Fungal communities in Florida salt marsh mosquito midguts vary between species and over time but have low structure.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1648091}, pmid = {41064004}, issn = {1664-3224}, mesh = {Animals ; *Fungi/genetics/classification ; *Mycobiome ; *Culicidae/microbiology ; Florida ; Wetlands ; *Aedes/microbiology ; Species Specificity ; *Culex/microbiology ; *Gastrointestinal Microbiome ; }, abstract = {INTRODUCTION: Microorganisms are intrinsically tied to the developmental and reproductive success of mosquitoes, can influence their ability to resist insecticides, and can strongly influence their ability to harbor and transmit pathogens of medical importance. Although mosquito-associated fungi have oben been overlooked at the expense of bacteria, several different fungal taxa are known to modulate interactions between mosquitoes and pathogens, while others have potential applications as biopesticides due to their entomopathogenic activity. Accordingly, understanding how and why different fungi associate with mosquito tissues is an important step toward elucidaUng the impact the diverse kingdom of microorganisms has on mosquito biology and mosquito- borne disease.<br><br>METHODS: In this study, we used Illumina Mi-Seq profiling of the internal transcribed spacer gene to characterize the midgut mycobiota of field collected adult mosquitoes from three species: Aedes taeniorhynchus, Anopheles atropos, and Culex nigripalpus, at two different collection times.<br><br>RESULTS: We observed that all mosquito specimens carried high loads of Rhodotorula lamellibrachiae, a common environmental yeast that is known to be involved in nitrogen fixation, although its role in mosquito biology is not clear. We also find that the mycobiome is strongly influenced by mosquito species, that few fungi have both high abundance and prevalence, and that few fungi consistently co- associate across time and host species.<br><br>DISCUSSION: These findings suggest that there is limited structure to mosquito associated fungal communities, implying that their assembly may be more driven by stochastic than deterministic processes. Our findings highlight the influence of key variables on mosquito fungal diversity and help facilitate understanding of how and when mosquitoes acquire fungi and the roles that fungi play in mosquito biology.}, }
@article {pmid41063836, year = {2025}, author = {Chen, X and Ye, L and Zou, X and Zhou, Y and Peng, C and Huang, R}, title = {The role of gut microbiota in myocardial ischemia-reperfusion injury.}, journal = {Frontiers in cardiovascular medicine}, volume = {12}, number = {}, pages = {1625299}, pmid = {41063836}, issn = {2297-055X}, abstract = {Myocardial ischemia-reperfusion injury denotes the pathological damage resulting from the restoration of blood flow and oxygen supply following acute coronary artery occlusion. Myocardial ischemia-reperfusion injury is commonly seen in acute coronary syndromes and is an important factor in the development of ischemic cardiomyopathy, which severely affects the prognosis of coronary heart disease. The gut microbiota, a complex ecosystem with multifaceted functions, plays a crucial role in host health. Dysregulation of the gut microbiota exerts substantial effects on the onset and progression of cardiovascular diseases, including myocardial ischemia-reperfusion injury. This review elucidates the mechanisms underlying myocardial ischemia-reperfusion injury and the involvement of the gut microbiota in this process, encompassing aspects such as intestinal barrier integrity, microbial dysbiosis, inflammatory responses, oxidative stress, mitochondrial dysfunction, and metabolic alterations. Additionally, we investigate various interventions that modulate myocardial ischemia-reperfusion injury by influencing the gut microbiota. Maintaining a healthy intestinal barrier and a stable microbial ecology is paramount in preventing myocardial ischemia-reperfusion injury. High-fiber diets, probiotic consumption, short-chain fatty acids supplementation, and Traditional Chinese Medicine, can safeguard the heart against myocardial ischemia-reperfusion injury by regulating gut microbiota through diverse mechanisms. As the role of gut microbiota in myocardial ischemia-reperfusion injury continues to be investigated, it provides important therapeutic targets and drug development opportunities for the prevention and treatment of myocardial ischemia-reperfusion injury. However, further in-depth and comprehensive studies are required to fully realize these potentials.}, }
@article {pmid41063423, year = {2025}, author = {Bartz, PM and Grullón-Penkova, IF and Cavaleri, MA and Reed, SC and Shahid, S and Wood, TE and Bachelot, B}, title = {Experimental warming alters free-living nitrogen fixation in a humid tropical forest.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.70592}, pmid = {41063423}, issn = {1469-8137}, support = {1754713//Division of Environmental Biology/ ; 2120085//Division of Environmental Biology/ ; 89243018S-SC-000014//Basic Energy Sciences/ ; 89243018S-SC-000017//Basic Energy Sciences/ ; 89243021S-SC-000076//Basic Energy Sciences/ ; DE-SC-0011806//Basic Energy Sciences/ ; DE-SC-0018942//Basic Energy Sciences/ ; DE-SC0012000//Basic Energy Sciences/ ; DE-SC0022095//Basic Energy Sciences/ ; }, abstract = {Microbial nitrogen (N) fixation accounts for c. 97% of natural N inputs to terrestrial ecosystems. These microbes can be free-living in the soil and leaf litter (asymbiotic) or in symbiosis with plants. Warming is expected to increase N-fixation rates because warmer temperatures favor the growth and activity of N-fixing microbes. We investigated the effects of warming on asymbiotic components of N fixation at a field warming experiment in Puerto Rico. We analyzed the function and composition of bacterial communities from surface soil and leaf litter samples. Warming significantly increased asymbiotic N-fixation rates in soil by 55% (to 0.002 kg ha[-1] yr[-1]) and by 525% in leaf litter (to 14.518 kg ha[-1] yr[-1]). This increase in N fixation was associated with changes in the N-fixing bacterial community composition and soil nutrients. Our findings suggest that warming increases the natural N inputs from the atmosphere into this tropical forest due to changes in microbial function and composition, especially in the leaf litter. Given the importance of leaf litter in nutrient cycling, future research should investigate other aspects of N cycles in the leaf litter under warming conditions.}, }
@article {pmid41062579, year = {2025}, author = {Wang, Y and Wang, Y and Hou, L and Zhong, L and Yang, H and Kang, X and Zhou, Y and Pan, J}, title = {Assessment of airborne and surface microbes on leather cultural relics in museums of arid regions represented by xinjiang, China.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {35107}, pmid = {41062579}, issn = {2045-2322}, support = {2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; }, mesh = {China ; *Museums ; *Air Microbiology ; *Bacteria/genetics/classification/isolation &amp; purification/drug effects ; Microbiota ; }, abstract = {This study investigates the airborne microbial contamination in three museums located in the dry region of Xinjiang region, China-Bayingolin, Hami, and Turpan. Airborne microbial concentrations in these museums were found to be relatively low, ranging from 7.5 to 38.3 CFU/m[3], which is advantageous for the preservation of cultural relics, especially in comparison to humid regions where higher microbial concentrations have been reported. The microbial communities were dominated by bacteria, with Firmicutes being the most abundant phylum, followed by Proteobacteria and Bacteroidetes. Notably, Pseudomonas sp., Bacillus sp., and Staphylococcus hominis were identified as potential threats to the degradation of leather cultural relics. Additionally, Mycobacterium sp., Pantoea sp., and Priestia aryabhattai were first identified in the context of cultural heritage conservation. Metagenomic sequencing revealed a significant presence of salt-tolerant, spore-forming bacteria, which are characteristic of dry environments. Antibacterial tests showed that 0.5% K100 exhibited the best antimicrobial effect. This study provides valuable insights into the microbial ecology of museums in rid climates and suggests the need for targeted preservation strategies to mitigate microbial-induced biodeterioration, particularly through the use of antimicrobial agents and environmental management.}, }
@article {pmid40981661, year = {2025}, author = {Pearl Mizrahi, S and Lee, H and Goyal, A and Owen, E and Gore, J}, title = {Structured interactions explain the absence of keystone species in synthetic microcosms.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, doi = {10.1093/ismejo/wraf211}, pmid = {40981661}, issn = {1751-7370}, support = {//Schmidt Science Polymath award/ ; 542385//Simons Foundation Principles of Microbial Ecology Collaboration/ ; LT000378/2018//HSFP Long-term fellowships/ ; GBMF4513//Gordon and Betty Moore Foundation/ ; T32GM087237//NIH Training/ ; /GM/NIGMS NIH HHS/United States ; }, mesh = {*Ecosystem ; *Bacteria/growth &amp; development/classification ; *Microbial Interactions ; *Extinction, Biological ; }, abstract = {In complex ecosystems, the loss of certain species can trigger a cascade of secondary extinctions and invasions. However, our understanding of the prevalence of these critical "keystone" species and the factors influencing their emergence remains limited. To address these questions, we experimentally assembled microcosms from 16 marine bacterial species and found that multiple extinctions and invasions were exceedingly rare upon removal of a species from the initial inoculation. This was true across eight different environments with either simple carbon sources (e.g. glucose) and more complex ones (e.g. glycogen). By employing a generalized Lotka-Volterra model, we could reproduce these results when interspecies interactions followed a hierarchical pattern, wherein species impacted strongly by one species were also more likely to experience strong impacts from others. Such a pattern naturally emerges due to observed variation in carrying capacities and growth rates. Furthermore, using both statistical inference and spent media experiments, we inferred interspecies interaction strengths and found them consistent with structured interactions. Our results suggest that the natural emergence of structured interactions may provide community resilience to extinctions.}, }
@article {pmid41061000, year = {2025}, author = {Cummings, CL and Landreville, KD and Kuzma, J}, title = {Public perceptions and support for introduced microbes to combat hospital-acquired infections and antimicrobial resistance.}, journal = {PloS one}, volume = {20}, number = {10}, pages = {e0332578}, doi = {10.1371/journal.pone.0332578}, pmid = {41061000}, issn = {1932-6203}, mesh = {Humans ; *Cross Infection/prevention &amp; control/microbiology ; Female ; Adult ; Male ; Middle Aged ; *Microbiota ; *Public Opinion ; Surveys and Questionnaires ; Aged ; Young Adult ; *Drug Resistance, Microbial ; Adolescent ; United States ; }, abstract = {Hospital-acquired infections and antimicrobial resistance (AMR) remain major global health threats, prompting interest in microbiome-based interventions that introduce beneficial microbes or genetic interventions to control pathogens and reduce AMR genes in hospital environments. Microbiome engineering, which can use advanced biotechnology, genetics, and microbial ecology principles to restructure microbial communities, is a rapidly growing field with applications in infection control. As researchers explore deploying beneficial microbes and other genetic interventions in clinical settings like hospital sinks, public perception becomes critical to responsible implementation. This study addresses how U.S. adults perceive microbiome evaluation, and education. Drawing on a nationally representative survey (N = 1,000), we conducted hierarchical ordinary least squares regression modeling to assess predictors of support across three domains: implementation of introduced microbiomes (IM), rigorous testing, and education for healthcare stakeholders. Results demonstrate that support for IM in hospital sinks is shaped less by demographic traits and more by emotional responses, trust in institutional efficacy, belief in intervention benefits, and a desire to learn about microbiome science. These findings advance previous knowledge by distinguishing cognitive, affective, and contextual predictors across distinct types of support. Contrary to expectations, prior familiarity and information-seeking were negatively associated with IM support, suggesting that some engagement or exposure to risk-framing may drive skepticism. Meanwhile, emotional reactions and perceived efficacy consistently predicted support for IM, testing, and education (i.e., across all dependent variables), underscoring the need to address affective and trust-based components of public engagement. This research contributes to an emerging empirical foundation for responsible microbiome innovation by grounding the analysis in the Responsible Research and Innovation (RRI) framework. With the technology still in early development, these insights provide critical guidance for biotechnology developers, policymakers, and hospital leaders seeking to align microbiome engineering with societal values through transparent communication, rigorous oversight, and inclusive education.}, }
@article {pmid41057344, year = {2025}, author = {Sun, X and Frey, C and McCoy, D and Spieler, MBA and Kelly, CL and Maloney, AE and Garcia-Robledo, E and Lehmann, MF and Ward, BB and Zakem, EJ}, title = {Mechanistic understanding of nitrate reduction as the dominant production pathway of nitrous oxide in marine oxygen minimum zones.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {8916}, pmid = {41057344}, issn = {2041-1723}, mesh = {*Nitrous Oxide/metabolism ; *Nitrates/metabolism ; *Oxygen/metabolism ; Oxidation-Reduction ; *Seawater/microbiology/chemistry ; Ecosystem ; Denitrification ; Nitrites/metabolism ; Bacteria/metabolism ; }, abstract = {Nitrous oxide (N2O), a potent greenhouse gas and ozone-depleting agent, is produced intensely in oxygen minimum zones (OMZs) predominantly through nitrate reduction NO 3 - → N 2 O . However, mechanisms and controls of this pathway remain unclear. Here, we investigate the microbial ecology governing this pathway using experiments and an ecosystem model. We experimentally confirm a critical hypothesis: most NO 3 - → N 2 O denitrifiers do not utilize extracellular nitrite, an intermediate of the pathway. Model results demonstrate that the NO 3 - → N 2 O pathway is compatible with oxygen, and that its response to oxygen is heterogeneous because it is governed by niche partitioning of distinct microbial types and thus may not follow a smooth curve. Lastly, experiments demonstrate that this pathway is sensitive to the type of organic matter, its electron acceptor, in addition to organic matter availability. These findings advance our mechanistic understanding of the primary N2O production pathway, necessary for predictions of marine N2O emissions.}, }
@article {pmid41057270, year = {2025}, author = {Hallett, EN and Comte, J}, title = {Identification and Global Distribution of a Core Microbiome From High-Arctic Lakes.}, journal = {Environmental microbiology}, volume = {27}, number = {10}, pages = {e70182}, doi = {10.1111/1462-2920.70182}, pmid = {41057270}, issn = {1462-2920}, support = {RGPIN-2020-06874//Natural Sciences and Engineering Research Council of Canada/ ; RGPNS-2020-06874//Natural Sciences and Engineering Research Council of Canada/ ; //Natural Resources Canada/ ; }, mesh = {*Lakes/microbiology ; Arctic Regions ; *Microbiota/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; DNA, Bacterial/genetics ; Biodiversity ; High-Throughput Nucleotide Sequencing ; }, abstract = {Arctic lakes are sentinels of climate change, yet their microbial community structure and functioning remain poorly understood. This study analysed the genetic content of clear-water Arctic lakes and their surroundings using high-throughput amplicon sequencing of the 16S rRNA gene to identify their core microbiome and its contribution to the overall taxonomy pool. To assess geographical constraints and oligotrophic conditions, these results were compared with a latitudinally diverse multi-basin oligotrophic lake in a temperate climate. Arctic and temperate lakes exhibited different assemblages, but both showed similar transitional gradients of microbial community composition from upstream soils/inlets through the lake system to the outlet, driven mainly by the dissolved organic matter (DOM) characteristics. Distinct core microbiomes were identified for temperate and Arctic lakes, with Arctic lakes appearing more diverse. A limited shared core microbiome was observed between the two regions, composed mostly of typical freshwater bacteria. While core taxa identities differed between regions, most exhibited characteristics of generalist bacteria with a strong global presence. These results provide key insights into the structure of remote high Arctic lakes, contributing to our understanding of aquatic microbial ecology in a transitioning Arctic and identifying microbial communities and individual taxa of interest for further study on oligotrophy.}, }
@article {pmid41056783, year = {2025}, author = {Guo, H and Lu, Y and Bulok, Y and Huang, W and Liu, Y}, title = {Advances and challenges of anammox-based PN/A and PD/A coupled processes in treating diverse wastewater qualities: A review.}, journal = {Journal of environmental management}, volume = {394}, number = {}, pages = {127484}, doi = {10.1016/j.jenvman.2025.127484}, pmid = {41056783}, issn = {1095-8630}, abstract = {The anammox process is critical for sustainable nitrogen removal, yet widespread use faces operational, environmental and microbial challenges. This review evaluates recent advances in anammox-based coupled processes, particularly PN/A and PD/A, highlighting their adaptation to varied wastewater types. PN/A has been extensively validated at full scale for high-ammonia wastewaters, including sludge digestion liquor, landfill leachate, and industrial effluents, and is now being extended to mainstream municipal applications. However, persistent barriers such as NOB suppression, sensitivity to low temperature, and heterotrophic competition under high C/N conditions continue to limit its performance. In contrast, successful PD/A deployment in mainstream wastewater depends on innovative solutions to temperature-related constraints, including biofilm buffering, metabolic adaptation, and kinetic optimization. The performance of both PN/A and PD/A systems is closely tied to wastewater composition (e.g. such as salinity, organic load, and the presence of toxic compounds) and its influence on microbial kinetics. Emerging innovations, including EPS-enriched biofilms, granular sludge, quorum sensing microbial regulation, and AI-driven controls have enhanced system resilience. Furthermore, integrated approaches enabling simultaneous nitrogen and phosphorus removal and novel reactor configurations are expanding the practical applicability of anammox processes, supporting resource recovery goals. This review synthesizes mechanistic insights, highlights full-scale implementation cases, and outlines emerging frontiers such as nanotechnology-enhanced biofilms and digital twin modelling for process optimization. By bridging microbial ecology with advanced process engineering, this work provides strategic direction for scaling up anammox-based systems in pursuit of energy-neutral and sustainable wastewater treatment under tightening environmental regulations.}, }
@article {pmid41054273, year = {2025}, author = {Wang, S and Bao, Z and Li, Z and Zhao, M and Wang, X and Liu, F}, title = {The impact of very-low-calorie ketogenic diets on gut microbiota in individuals with obesity: a systematic review and meta-analysis.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2566305}, doi = {10.1080/19490976.2025.2566305}, pmid = {41054273}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Diet, Ketogenic ; *Obesity/microbiology/diet therapy ; Bacteria/classification/genetics/isolation &amp; purification ; Body Mass Index ; *Caloric Restriction ; }, abstract = {OBJECTIVE: This study aimed to systematically review and meta-analyze the effects of very-low-calorie ketogenic diets (VLCKD) on gut microbiota in individuals with obesity.<br><br>METHODS: A comprehensive literature search was conducted across four electronic databases-PubMed, EBSCOhost, Cochrane Library, and Web of Science-up to June 2025. Outcomes included changes in gut microbial diversity and the relative abundance of key taxa. Subgroup analyses were performed based on body mass index (BMI), age, and intervention duration.<br><br>RESULTS: A total of 14 studies were included. Random-effects meta-analysis revealed that VLCKD interventions significantly improved gut microbial &#x3b1;-diversity, as indicated by increased Shannon index (SMD: 0.54, 95% CI: 0.03 to 1.04, P&#x2009;=&#x2009;0.0378) and Faith's Phylogenetic Diversity (PD) index (SMD: 0.77, 95% CI: 0.36 to 1.18, P&#x2009;=&#x2009;0.0002). In addition, VLCKD significantly increased the abundance of Akkermansia (SMD: 1.76, 95% CI: 0.48 to 3.03, P&#x2009;=&#x2009;0.0069) and the Firmicutes-to-Bacteroidetes (F/B) ratio (SMD: 1.01, 95% CI: 0.67 to 1.34, P < 0.0001), while significantly reducing the probiotic genus Bifidobacterium (SMD: -1.23, 95% CI: -1.81 to -0.64, P < 0.0001). Subgroup analyses indicated that the increase in Shannon index was more pronounced in participants with BMI&#x2009;&#x2264;&#x2009;30 kg/m&#xb2; and age >30 years. Akkermansia showed a greater increase in those with BMI 30-35 kg/m&#xb2;, age >40 years, and intervention duration &#x2264;6 weeks. Conversely, Bifidobacterium abundance declined significantly in individuals with BMI 30-35 kg/m&#xb2;, age >40 years, and within an intervention period &#x2264;12 weeks.<br><br>CONCLUSION: VLCKD appears to be a promising dietary intervention for modulating gut microbiota in individuals with obesity. However, its bidirectional effects on microbial ecology warrant caution. Future studies should further investigate its long-term safety and explore personalized strategies for microbiota-targeted interventions.}, }
@article {pmid41053793, year = {2025}, author = {Ou, HX and Chen, Y and Zheng, DL and Lu, YG and Gan, RH}, title = {Evaluating microbial regulation as a preventive strategy for radiation-related caries: A review.}, journal = {Head &amp; face medicine}, volume = {21}, number = {1}, pages = {67}, pmid = {41053793}, issn = {1746-160X}, support = {2022J01270//Fujian provincial Natural Science Foundation of China/ ; 2021GGA055//Fujian Provincial Health Technology Project/ ; }, mesh = {Humans ; *Dental Caries/prevention &amp; control/microbiology/etiology ; *Microbiota/radiation effects ; *Head and Neck Neoplasms/radiotherapy ; Probiotics/therapeutic use ; *Radiation Injuries/prevention &amp; control/microbiology ; Squamous Cell Carcinoma of Head and Neck/radiotherapy ; }, abstract = {Radiotherapy is a crucial treatment for head and neck squamous cell carcinoma but is associated with several complications, particularly the onset of radiation-related caries (RRC), which severely compromises patients' oral health and quality of life. Most studies have focused on the direct effects of radiation on host organs. Such as radiotherapy/Concurrent Chemoradiotherapy (CCRT) contributing to RRC primarily by inducing salivary gland hypofunction and directly damaging tooth structure. However, emerging evidence implicates additional mechanisms including dietary modifications and oral microbial dysbiosis in driving pathogenic microbial shifts characterized by cariogenic bacterial/fungal proliferation, thereby exacerbating RRC progression. In particular, changes in common cariogenic bacteria/fungi after radiotherapy remain poorly understood. Furthermore, clinical translation of microbial ecology principles into effective RRC prevention strategies remains underexplored. This review centers on radiation-induced oral microbiota alterations, critically analyzing documented microbial shifts characterized by marked proliferation of cariogenic taxa including Streptococcus mutans, Lactobacillus, Prevotella melaninogenica, Veillonella, and Actinomyces, alongside fungal overgrowth of Candida albicans. We propose a dual-focused intervention protocol: initiating probiotic supplementation at radiotherapy commencement to stabilize microbial ecology and preserve salivary function, combined with standardized oral care encompassing mechanical plaque removal, fluoride therapy, and natural anticariogenic agents. While mechanistically plausible, this paradigm requires rigorous validation through multicenter randomized controlled trials assessing ecological stability maintenance and caries incidence reduction.}, }
@article {pmid41051094, year = {2025}, author = {Cheng, Z and Xia, W and McKelvey, S and He, Q and Chen, Y and Yuan, H}, title = {Building Predictive Understanding of the Activated Sludge Microbiome by Bridging Microbial Growth Kinetics and Microbial Population Dynamics.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c05925}, pmid = {41051094}, issn = {1520-5851}, abstract = {Modeling microbiomes can provide predictive insights into microbial ecology, but current modeling approaches suffer from inherent limitations. In this study, a novel modeling approach was developed based on the intrinsic connection between the growth kinetics of guilds and the dynamics of microbial populations. To implement this approach, 466 samples from four full-scale activated sludge systems were retrieved. The raw samples were processed using a data transformation method that tripled the data set size and enabled quantification of population dynamics. Of the 42 family level core populations, 36 showed overall dynamics statistically close to zero (within ± 0.05 d[-1]). Bayesian networks were built to classify the core populations into heterotrophic and autotrophic guilds. Topological data analysis was applied to identify keystone populations and time-dependent microbial interactions. The data-driven inferences were validated directly using the Microbial Database for Activated Sludge (MiDAS) and indirectly by predicting community structure using artificial neural networks. The Bray-Curtis similarity between predicted and observed communities was higher with microbial kinetic parameters than without these parameters (0.70 vs 0.66, t test, p < 0.05). Owing to the flexibility of the modeling framework, this proposed hybrid approach might potentially be adapted to time-dependent data from natural systems for predictive understanding of the involved microbiomes.}, }
@article {pmid41049421, year = {2025}, author = {Yan, J and Zhao, J and Naizemuding, P and Zhao, W and Sun, J and Wang, Y and Yang, J and Li, D and Zhang, F and Cao, H}, title = {Unraveling the Anti-Obesity Potential of White Kidney Bean α-Amylase Inhibitors: Mechanistic Insights From Enzyme Kinetics to Gut Microbiota Modulation.}, journal = {Food science &amp; nutrition}, volume = {13}, number = {10}, pages = {e71043}, pmid = {41049421}, issn = {2048-7177}, abstract = {The global rise in obesity, driven largely by excessive carbohydrate consumption, highlights the demand for innovative dietary interventions targeting starch digestion. This study investigates the anti-obesity effects of α-amylase inhibitors (α-AI) extracted from white kidney beans, employing a multidisciplinary strategy encompassing botanical screening, enzyme kinetics, clinical trials, and gut microbiota profiling. Among 10 varieties evaluated, the A10 strain from Jilin Province demonstrated the highest α-AI activity, characterized by noncompetitive inhibition that remains effective across varying starch concentrations. In an 8-week randomized controlled trial, α-AI supplementation significantly reduced body weight, BMI, waist circumference, and hip circumference compared to placebo. Further, 16S rRNA sequencing revealed dual mechanisms: enrichment of SCFA-producing bacteria (e.g., Bifidobacterium and Bacteroides ovatus) and modulation of microbial lipid metabolic pathways. These results highlight α-AI as a dual-action anti-obesity agent, combining direct enzymatic inhibition with microbiome-mediated metabolic effects. By bridging phytochemical characterization with clinical outcomes, this work proposes a novel therapeutic approach that simultaneously targets carbohydrate absorption and gut microbial ecology, supporting the development of standardized α-AI formulations as potential nutraceuticals for metabolic syndrome.}, }
@article {pmid41048979, year = {2025}, author = {Nurhazli, NAA and Tan, JH and Kamaroddin, MF and Shamsir, MS and Yaakop, AS and Goh, KM}, title = {Microbial Community Profiles of Biofilms from Hot Springs: 16S and 18S rRNA Amplicon Sequencing Data.}, journal = {Data in brief}, volume = {62}, number = {}, pages = {112093}, pmid = {41048979}, issn = {2352-3409}, abstract = {This article presents microbial diversity data from biofilms collected from the sides or outflows of several Malaysian hot springs, with temperatures ranging from 38 to 56 °C and pH values between 7.1 and 8.7. Genomic DNA was extracted from the biofilms and subjected to 16S V3-V4 and 18S V4 amplicon sequencing using the Illumina NovaSeq 6000 platform. Reads were processed with various bioinformatic tools including QIIME2, and eventually, amplicon sequence variants (ASVs) were identified. In almost all analyzed biofilms, approximately 50% of the total ASVs belonged to Cyanobacteriota and Chloroflexota, except for one biofilm, labeled DTO, which was dominated by Pseudomonadata and Cyanobacteriota. Besides bacteria, the data also suggest the presence of various eukaryotic organisms, including small animals such as nematodes, rotifers, and arthropods; fungi and fungus-like organisms such as Ascomycota, Zoopagomycota, Oomycota, and Cryptomycota; as well as photosynthetic eukaryotes from the Viridiplantae group. This dataset serves as a valuable resource for microbial ecology studies in hot spring biofilms and is openly available for reuse, providing a foundation for future research on microbial diversity and functional roles in geothermal ecosystems.}, }
@article {pmid41048492, year = {2025}, author = {Chen, X and Yu, D and Yan, Y and Yuan, C and He, J}, title = {Soil viruses drive carbon turnover during subtropical secondary forest succession.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1633379}, pmid = {41048492}, issn = {1664-302X}, abstract = {INTRODUCTION: Soil viruses are increasingly recognized as key regulators of microbial ecology and ecosystem function, yet their roles in forest ecosystems, particularly during natural secondary succession, remain largely unexplored.<br><br>METHODS: We examined soil viral communities across five successional stages of secondary forests to investigate their taxonomic dynamics and functional potential. Using high-throughput viral metagenomics, we characterized viral community structure, abundance, and auxiliary metabolic gene content.<br><br>RESULTS: Our results demonstrate that soil viral abundance and community composition shift significantly with forest stand age. Viral richness increased during succession, with compositional transitions observed across stages; however, tailed bacteriophages consistently dominated. Structural equation modeling and linear mixed-effects analysis identified soil pH and bacterial diversity as primary environmental determinants of viral diversity. Functionally, soil viruses harbored auxiliary metabolic genes related to carbohydrate metabolism, indicating their potential involvement in modulating host metabolic processes. Successional trends in viral functional profiles revealed a transition from carbon assimilation to carbon release pathways, suggesting viral mediation of carbon turnover. Notably, the enrichment of glycoside hydrolase and glycosyl transferase genes across forest ages implies a role for viruses in shaping microbial carbon processing capacities through carbohydrate-active enzyme contributions.<br><br>DISCUSSION: These findings provide novel evidence that soil viruses actively participate in ecosystem succession by influencing microbial functional potential and biogeochemical cycling. This study underscores the ecological importance of soil viral communities in regulating carbon dynamics during secondary forest development.}, }
@article {pmid41048389, year = {2025}, author = {Kong, S and Abrams, E and Binik, Y and Cappelli, C and Chu, M and Cornett, T and Culbertson, I and Garcia, E and Henry, J and Lam, K and Lampman, DB and Morenko, G and Rivera, I and Swift, T and Torres, I and Velez, R and Waxman, E and Wessely, S and Yuen, A and Lardner, CK and Weissman, JL}, title = {Metagenomes and metagenome-assembled genomes from tidal lagoons at a New York City waterfront park.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e20081}, pmid = {41048389}, issn = {2167-8359}, mesh = {New York City ; *Metagenome ; *Parks, Recreational ; Metagenomics ; Humans ; *Seawater/microbiology ; Microbiota/genetics ; *Water Microbiology ; }, abstract = {New York City parks serve as potential sites of both social and physical climate resilience, but relatively little is known about how microbial organisms and processes contribute to the functioning of these deeply human-impacted ecosystems. We report the sequencing and analysis of 15 shotgun metagenomes, including the reconstruction of 129 high-quality metagenome-assembled genomes, from tidal lagoons and bay water at Bush Terminal Piers Park in Brooklyn, NY sampled from July to September 2024. Our metagenomic database for this site provides an important baseline for ongoing studies of the microbial communities of public parks and waterfront areas in NYC. In particular, we provide rich functional and taxonomic annotations that enable the use of these metagenomes and metagenome-assembled genomes for a wide variety of downstream applications.}, }
@article {pmid41047820, year = {2025}, author = {Lu, Q and Feng, Y and Wang, H and Zhu, K and Teng, L and Yue, M and Li, Y}, title = {Gut microbiota as a regulator of vaccine efficacy: implications for personalized vaccination.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2563709}, doi = {10.1080/19490976.2025.2563709}, pmid = {41047820}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Vaccine Efficacy ; *Precision Medicine ; Vaccination ; Immunity, Innate ; *Vaccines/immunology ; Animals ; Adaptive Immunity ; }, abstract = {Vaccines are one of the most significant achievements in global health, as they have substantially reduced morbidity and mortality from infectious diseases. However, the vaccine efficacy varies markedly across different populations, particularly among infants, older adults, and people living in low- and middle-income countries. Host-intrinsic factors, such as sex, age, and genetic predisposition, contribute to these heterogeneities. However, accumulating data indicate that the gut microbiota also plays a pivotal role in modulating vaccine efficacy. This review summarizes current knowledge, demonstrating that vaccine efficacy is shaped not only by host biology but also by a dynamic, bidirectional interplay between the gut microbiota and immune system. We discuss how the microbiota influences vaccine outcomes through several mechanisms, including priming the innate immune response, regulating adaptive responses through metabolites, and facilitating antigen cross-reactivity. Furthermore, we examine the potential for microbiota-informed precision vaccinology, which integrates multiomics profiling and artificial intelligence to predict and improve vaccine performance. These advancements establish a framework for personalized vaccine development based on microbial ecology.}, }
@article {pmid41046701, year = {2025}, author = {Yao, H and Yu, J and Yang, X and Xu, J}, title = {Mechanisms of disruption of the gut-brain axis by environmental endocrine disruptors.}, journal = {Ecotoxicology and environmental safety}, volume = {304}, number = {}, pages = {119124}, doi = {10.1016/j.ecoenv.2025.119124}, pmid = {41046701}, issn = {1090-2414}, abstract = {Environmental endocrine disruptors (EEDs) are exogenous chemicals that impair physiological health by disrupting endocrine function. The gut-brain axis represents a complex bidirectional communication network integrating the gut microbiome, immune system, neural signaling, and endocrine pathways to maintain systemic homeostasis. Within this interconnected system, gut microbiota influence mood regulation, immune activity modulates neural processes, and neural signaling governs circadian and sleep cycles. This review explores the multi-system impacts of EEDs across four key physiological domains: (1) gut microbial ecology, (2) immune function, (3) neuroendocrine regulation, and (4) developmental processes. Evidence indicates that EED exposure disrupts intestinal microbial composition, leading to dysbiosis marked by the depletion of beneficial taxa and the expansion of pathogenic species. Concurrently, EEDs impair gut-associated immune cell populations (T cells, B cells, and macrophages), undermining mucosal immunity and increasing susceptibility to inflammatory bowel disease, autoimmune conditions, and gastrointestinal malignancies. At the endocrine level, EEDs interfere with the hypothalamic-pituitary-adrenal and hypothalamic-pituitary-gonadal axes, contributing to hormonal imbalances and impaired reproductive development. Neurochemically, they disrupt the synthesis, release, and degradation of key neurotransmitters, including norepinephrine, dopamine, and serotonin, while exerting direct neurotoxic effects such as cerebrovascular abnormalities and delayed cerebellar myelination. In summary, this review delineates the mechanistic pathways through which EEDs perturb gut-brain axis homeostasis. These insights provide a scientific basis for designing targeted therapeutic interventions and shaping evidence-based public health policies.}, }
@article {pmid41044018, year = {2025}, author = {Araujo, ASF and Pereira, APA and de Medeiros, EV and Mendes, LW}, title = {Soil microbes: below-ground defenders against desertification.}, journal = {Trends in ecology &amp; evolution}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tree.2025.09.014}, pmid = {41044018}, issn = {1872-8383}, abstract = {Soil microbes act as below-ground defenders against desertification by several mechanisms, such as rhizosheath formation, necromass accumulation, biological soil crusts, exopolysaccharide (EPS) production, hyphal networks, and calcium carbonate precipitation. Here, we discuss how soil microbes drive ecosystem recovery in drylands, offering promising, nature-based strategies for restoring soils in the face of desertification.}, }
@article {pmid41041139, year = {2025}, author = {Berlanga, M and Martín-García, A and Guerrero, R and Riu-Aumatell, M and López-Tamames, E}, title = {Changes in healthy Wistar rat gut microbiome by short-term dietary cava lees intervention.}, journal = {Frontiers in nutrition}, volume = {12}, number = {}, pages = {1641612}, pmid = {41041139}, issn = {2296-861X}, abstract = {INTRODUCTION: The gut microbiome plays a crucial role in host health through complex host-microbe interactions. Beta-glucans, structural polysaccharides found in yeast cell walls, have emerged as promising modulators of immune function and microbial ecology. Cava lees, a by-product of sparkling wine production composed of Saccharomyces cerevisiae cell walls, represent a rich source of beta-glucans that could be upcycled for nutritional and therapeutic applications.<br><br>METHODS: Twenty-four Wistar rats (12 males, 12 females) were randomly divided into control and treatment groups. The treatment group received daily doses of 2,000&#x202f;mg lees/kg body weight for 14&#x202f;days. Shotgun metagenomic analysis was performed to assess microbial composition and functional changes.<br><br>RESULTS: A 14-day cava lees supplementation study revealed significant shifts in gut microbiota composition and function. Baseline microbiota was dominated by Bacillota (64-72%) and Bacteroidota (23-32%) with sex-specific differences at the family level. Post-supplementation analysis showed increased Shannon diversity across both sexes, with beneficial enrichment of Bifidobacteriaceae and Rikenellaceae families and reduction of Eubacteriaceae. While global metabolic profiles remained stable, targeted functional pathways were significantly changed, including butyrate production genes. Females exhibited particularly elevated secondary bile acid modification genes (Mann-Whitney-Wilcoxon test p&#x202f;=&#x202f;0.032), and male oxidative stress response pathways (Mann-Whitney-Wilcoxon test p&#x202f;=&#x202f;0.016) showing both a potentially sex-dependent responses to dietary intervention.<br><br>CONCLUSION: Working with healthy individuals provides a clear understanding of the normal, baseline microbiota composition and function before any intervention. These findings suggest a degree of plasticity of the gut microbiome and its responsiveness to dietary modifications. Beta-glucans from cava lees appear to create a favorable environment for beneficial bacteria, with sex-specific changes of certain bacterial families and functions. These findings provide a foundation for future translational research in humans. Nonetheless, to establish their true impact on human health, these observations in rodent models must be validated through appropriately designed human clinical studies.}, }
@article {pmid41039213, year = {2025}, author = {IJdema, F and Arias-Giraldo, LM and Vervoort, E and Struyf, T and Van den Ende, W and Raaijmakers, JM and Lievens, B and De Smet, J}, title = {Metagenome-based identification of functional traits of the black soldier fly gut microbiome associated with larval performance.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {612}, pmid = {41039213}, issn = {1471-2180}, support = {S008519N//ENTOBIOTA/ ; IMP20028//KU Leuven Impuls grant/ ; C3/22/041//KU Leuven CHITINERY grant/ ; G0C4622N//Fonds Wetenschappelijk Onderzoek/ ; }, mesh = {Animals ; Larva/microbiology/growth &amp; development ; *Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism ; *Metagenome ; *Diptera/microbiology/growth &amp; development ; Animal Feed/analysis ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Diet ; Phylogeny ; Chickens ; }, abstract = {BACKGROUND: The relationship between microbiomes and their hosts has been the subject of intensive study in recent years. For black soldier fly larvae (BSFL) (Hermetia illucens L., Diptera: Stratiomyidae), correlations between shifts in its microbial gut community composition and its health and performance suggest that the BSFL gut microbiome encodes important functions that complement the insect's own immune system and metabolism. To date, most BSFL microbiome studies have been based on 16S rRNA sequencing data. Because this approach derives a lot of information from very short sequencing reads, it was hypothesized that more insight into bacterial functionality could be generated using more extensive sequencing technologies. Here, whole genome shotgun (WGS) metagenomic sequencing was employed to investigate which microbiome-associated taxa and functions were associated with increased performance of larvae reared on a chicken feed (CF) or artificial supermarket food waste (SFW) based diet.<br><br>RESULTS: Taxonomic and functional profiling of the BSFL gut microbiome revealed a significant shift in response to diet, where bacterial genes encoding specific metabolic functions, such as the metabolism of sorbitol, were significantly enriched in the microbiome of larvae reared on SFW-diet. This indicates that the nutritional composition of the substrate alters the gut bacterial composition by providing competitive benefits or new niches for specific bacteria that can utilise these compounds. Moreover, specific microbial functions, such as cobalamin synthesis, appear to be correlated with larval performance. Aside from metabolic functions, biosynthetic gene cluster analysis revealed potential antimicrobial competition and protective functions among bacterial species. Improved taxonomic resolution provided by WGS led to the identification of several metagenome assembled genomes (MAGs), including a potentially novel BSFL-associated Scrofimicrobium species. Furthermore, there were differences in larval performance between rearing diets, and larval growth was correlated with high abundance of several MAGs.<br><br>CONCLUSIONS: Variation in the nutritional and bacterial load of a diet can result in functional shifts in the gut microbiome of the larvae. Analysis of the BSFL metagenome identified several bacteria that are positively correlated with larval performance, which could potentially provide beneficial metabolic functions for the host that should be further explored.}, }
@article {pmid41037135, year = {2025}, author = {Cárdenas, P and Carpio-Arias, V and Chávez, M and Benítez, AD and Baldeón, AD and Suárez-Jaramillo, A and Fornasini, M and Robles, J and Loza, G and Baldeón, ME}, title = {Nutritional Status and Fecal Microbiota in School Children from the Galapagos and the Andean Region.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {103}, pmid = {41037135}, issn = {1432-184X}, support = {I+D+I-XVII-2022-03//This work was supported by the Ecuadorian Consortium for the Development of Advanced Internet (CEDIA) and Universidad Internacional del Ecuador, Universidad San Francisco de Quito, and Escuela Superior Politecnica del Chimborazo./ ; }, mesh = {Humans ; Ecuador/epidemiology ; *Feces/microbiology ; *Nutritional Status ; Child ; Male ; Female ; *Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome ; Intestinal Diseases, Parasitic/epidemiology/microbiology ; }, abstract = {Schoolchildren from the Galapagos and the Andean region present the worst indices of malnutrition in Ecuador and are exposed to distinctive food and water insecurity. We compared the nutritional status, the fecal microbiota composition of schoolchildren from the Galapagos (n = 51; 8.88 ± 2.15 years) and the Andean region (n = 114; 8.69 ± 1.83 years). Children had a nutritional evaluation and provided fecal samples for microbiota analysis by 16S rRNA gene sequencing. Excess weight was more prevalent in Galapagos (41.18%) than in the Andes (24.5%). Additionally, intestinal parasitosis was more prevalent in children from the Andes (76.4%) than in Galapagos (13.0%). Species richness was lower in fecal samples of children from the Galapagos than those from the Andes (Chao1 index p = 0.001). Beta-diversity metrics also showed significant differences between these samples. Bacteroidota and Proteobacteria were enriched in the microbiota of Galapagos children, whereas Firmicutes A and Cyanobacteria were enriched in the Andean children. At the genus level, the top 3 genera present in schoolchildren from the Galapagos were Bacteroides, Phocaeicola, and Escherichia, while in children from the Andes were Cryptobacteroides, Prevotella, and Clostridium. Cyanobacteria were inversely associated with BMI z-score in the Galapagos region (q = 0.009), while, Firmicutes D had a direct relationship with BMI z-score in children from the Andes (q = 0.05). At the genus level, only Butyrivibrio was inversely associated with BMI z-score in children of the Galapagos (q = 0.04). We conclude that schoolchildren with different degrees of malnutrition from two distinct geographical areas have dissimilar fecal microbiota characteristics.}, }
@article {pmid41037127, year = {2025}, author = {Arunrat, N and Mhuantong, W and Sereenonchai, S}, title = {Land-use legacies shape soil microbial communities and nutrient cycling functions in rotational shifting cultivation fields of Northern Thailand.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {102}, pmid = {41037127}, issn = {1432-184X}, support = {MU-SRF-RS-21 B/67//Mahidol University (Strategic Research Fund: 2024)/ ; }, mesh = {*Soil Microbiology ; Thailand ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Soil/chemistry ; *Microbiota ; Nitrogen/metabolism ; Nitrification ; *Agriculture/methods ; Nitrogen Fixation ; Nitrogen Cycle ; }, abstract = {How land-use history-particularly in contrasting systems such as rotational shifting cultivation (RSC) and continuously fallow (CF) fields-influences soil microbial communities and their biogeochemical functions remains insufficiently understood. In this study, shotgun metagenomic sequencing was used to compare the taxonomic composition and functional gene profiles of soils under RSC and CF systems in Northern Thailand. The results revealed distinct microbial assemblages and metabolic potentials shaped by land-use legacy. RSC soils were characterized by a higher abundance of nitrifiers and nitrogen-fixing taxa, including Nitrosocosmicus and Streptomyces, along with enriched genes involved in nitrification (e.g., amoC_B, nxrB) and nitrogen fixation (nifD, nifK), reflecting an enhanced potential for nitrogen acquisition and retention. In contrast, CF soils showed enrichment in Bradyrhizobium, Halobaculum, and Russula, and exhibited higher expression of denitrification-related genes (norB, narJ), suggesting increased nitrogen loss via gaseous emissions. Functional genes related to phosphate metabolism (phoX, glpQ) and nutrient signal transduction were more abundant in RSC soils, indicating active nutrient cycling in response to recent disturbance. Conversely, CF soils demonstrated broader metabolic capabilities, including genes for sulfur oxidation and redox regulation, suggesting microbial adaptation to more stable but nutrient-limited conditions. These findings demonstrate that land-use legacies strongly influence microbial composition and function, with important implications for nutrient cycling and soil fertility restoration in shifting cultivation landscapes.}, }
@article {pmid41037066, year = {2025}, author = {Scott, CM and Holman, DB and Gzyl, KE and Ibe, A and Taheri, AE}, title = {Production Systems and Age Influence Fecal Mycobiota Diversity and Composition in Swine.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {104}, pmid = {41037066}, issn = {1432-184X}, mesh = {Animals ; *Feces/microbiology ; Swine/microbiology ; *Fungi/classification/genetics/isolation &amp; purification ; *Animal Husbandry/methods ; *Gastrointestinal Microbiome ; *Mycobiome ; Biodiversity ; DNA, Fungal/genetics ; Age Factors ; Female ; }, abstract = {The gut microbiome is an important factor in animal health and can be influenced by factors such as age, diet, stress, environmental conditions, and farming practices. Bacterial communities of the gut microbiome in many species have been extensively studied, but research on the fungal microbiota remains limited and underrepresented in the literature. The objective of this study was to characterize the fecal mycobiota of swine raised under two different production systems: outdoor pasture-based or conventional indoor systems. Fecal samples from nursery, growing-finishing, and sow pigs from both farming systems were collected, and the mycobiota was profiled using PCR amplification and sequencing of the universal fungal internal transcribed spacer 1 (ITS1) region. A significant difference in fungal community structure was observed between the conventionally raised and pasture-raised pigs, as well as among all three production phases. Four species, Arthrographis kalrae, Enterocarpus grenotii, Pseudallescheria angusta, and Sagenomella oligospora, were differentially abundant between the two farms, all of which had higher relative abundance in the pasture-raised pigs. Additionally, pasture-raised pigs hosted a more diverse fungal community with higher species richness in their gastrointestinal tract. In summary, farming practices and pig age influenced the pig fecal mycobiota.}, }
@article {pmid41036845, year = {2025}, author = {Du Plessis, I and Snyder, H and Calder, R and Rolando, JL and Kostka, JE and Weitz, JS and Dominguez-Mirazo, M}, title = {Viral community diversity in the rhizosphere of the foundation salt marsh plant Spartina alterniflora.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0023425}, doi = {10.1128/msphere.00234-25}, pmid = {41036845}, issn = {2379-5042}, abstract = {Viruses of microorganisms impact microbial population dynamics, community structure, nutrient cycling, gene transfer, and genomic innovation. In wetlands, root-associated microbial communities mediate key biogeochemical processes important for plants involved in ecosystem maintenance. Nonetheless, the presence and role of microbial viruses in salt marshes remain poorly understood. In this study, we analyzed 24 metagenomes retrieved from the root zone of Spartina alterniflora, a foundation plant in salt marshes of the eastern and Gulf coasts of the U.S. The samples span three plant compartments-bulk sediment, rhizosphere, and root-and two cordgrass plant phenotypes: short and tall. We observed differentiation between phenotypes and increased similarity in viral communities between the root and rhizosphere, indicating that plant compartment and phenotype shape viral community composition. The majority of viral populations characterized are novel at the genus level, with a subset predicted to target microorganisms known to carry out key biogeochemical functions. The findings contribute to ongoing efforts to understand plant-associated viral diversity and community composition and to identify potential targets for exploring viral modulation of microbially mediated ecosystem functioning in intertidal wetlands.IMPORTANCESalt marshes are vital coastal ecosystems. Microbes in these environments drive nutrient cycling and support plant health, with Spartina alterniflora serving as a foundation species. This study explores viral communities associated with S. alterniflora, revealing how plant compartments and phenotypes shape viral composition. The discovery of numerous novel viruses, some potentially influencing microbes involved in key biogeochemical processes, highlights their ecological significance. Given the increasing pressures on coastal ecosystems, understanding virus-microbe-plant interactions is essential for predicting and managing ecosystem responses to environmental change.}, }
@article {pmid41033533, year = {2025}, author = {Kim, YJ and Jung, DH and Jung, JH and Seo, DH and Kim, JS and Park, CS}, title = {Genomic and functional characterization of carbohydrate-active enzymes from Ruminococcoides bili FMB-CY1 reveals modular strategy for resistant starch degradation in the human gut.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {147957}, doi = {10.1016/j.ijbiomac.2025.147957}, pmid = {41033533}, issn = {1879-0003}, abstract = {Ruminococcoides bili FMB-CY1, a human gut bacterium, exhibits strong resistant starch (RS)-degrading ability. To elucidate its RS-degradation strategy, we performed comprehensive genomic annotation and biochemical characterization of 19 encoded carbohydrate-active enzymes (CAZymes). Genome analysis revealed glycoside hydrolases (GH13, GH31, GH77), glycosyltransferase (GT35), carbohydrate-binding modules (CBMs), and domains associated with amylosome-like multienzyme complexes, including dockerin and cohesin motifs. All 19 CAZyme genes were heterologously expressed in Escherichia coli, and their enzymatic properties were systematically characterized. Most α-amylases exhibited extracellular activity against raw RS granules, particularly those harboring CBMs. Hydrolysis profiling revealed distinct substrate preferences, leading to functional reannotation of four enzymes. Domain analyses further suggested that select CAZymes form a surface-associated complex analogous to the amylosome. Together, these enzymes suggest a putative RS-degradation system, in which extracellular α-amylases initiate starch breakdown and are followed by pullulanases, glucosidases, and transferases that complete RS degradation. The released sugars support microbial cross-feeding and potentially contribute to host energy metabolism. The study provides molecular insight into RS utilization by Rc. bili FMB-CY1 and identifies enzymatic features relevant to gut microbial ecology and functional food applications targeting RS metabolism.}, }
@article {pmid41031660, year = {2025}, author = {Wick, LY}, title = {Rebuttal to Correspondence on "DC Electric Fields Promote Biodegradation of Waterborne Naphthalene in Biofilter Systems".}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c12499}, pmid = {41031660}, issn = {1520-5851}, }
@article {pmid41029470, year = {2025}, author = {Cutajar, S and Braglia, C and Alberoni, D and Mifsud, M and Baffoni, L and Spiteri, J and Di Gioia, D and Mifsud, D}, title = {Gut microbiome of Vespa orientalis: functional insights and potential honey bee pathogen dynamics.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {95}, pmid = {41029470}, issn = {2524-4671}, support = {TESS 2022//Tertiary Education Scholarships Scheme by the Ministry for Education, Sport, Youth, Research and Innovation in Malta (TESS 2022)./ ; CN00000022//European Union Next-GenerationEU, PIANO NAZIONALE DI RIPRESA E RESILIENZA (PNRR) - MISSIONE 4 COMPONENTE 2, INVESTIMENTO 1.4 - D.D. 1032 17/06/2022/ ; CN00000022//European Union Next-GenerationEU, PIANO NAZIONALE DI RIPRESA E RESILIENZA (PNRR) - MISSIONE 4 COMPONENTE 2, INVESTIMENTO 1.4 - D.D. 1032 17/06/2022/ ; }, abstract = {Vespa orientalis, the oriental hornet, is an emerging predator of honey bees whose ecological impact and microbial ecology remain poorly understood. Here, we present the first detailed characterisation of its gut microbiota by integrating 16S rRNA gene sequencing, predicted microbial function, pathogen screening, and a three-year beekeeper survey across urban and rural sites in Malta. Hornets were sampled from four locations and classified by observed foraging behaviour, either predation on honey bees or scavenging on cat food.Survey data confirmed consistent V. orientalis sightings and seasonal colony losses, particularly during peak foraging months. Microbiome analysis revealed a conserved core community dominated by Spiroplasma, Arsenophonus, and Rosenbergiella, with overall diversity stable across sites and diets. However, specific taxa varied with foraging behaviour. For example, Arsenophonus was enriched in bee-predating hornets, while Enterobacter and Serratia were more common in scavenging individuals, suggesting environmental and dietary influences on microbiota composition. Predicted functional profiles remained broadly conserved, reflecting robust nutrient metabolism and potential detoxification capabilities, with some variations related to the diet behaviour.Pathogen screening detected Nosema ceranae and Crithidia bombi in a substantial proportion of hornets, including those not observed feeding on bees. Although our findings do not demonstrate pathogen transmission, they support the hypothesis that V. orientalis may act as a transient carrier, potentially contributing to pathogen persistence via environmental exposure.Together, these results reveal the dietary flexibility and microbial flexibility within the gut microbiome of V. orientalis, and highlight its potential involvement in pollinator pathogen dynamics.}, }
@article {pmid41028416, year = {2025}, author = {Sidharthan, VK and Patel, R and Thiyaharajan, M and Krishnappa, C and Pattanaik, S and Kumar, A}, title = {Metabarcoding reveals unique rhizospheric microbiomes of Rhizophora in Indian Mangroves.}, journal = {Folia microbiologica}, volume = {}, number = {}, pages = {}, pmid = {41028416}, issn = {1874-9356}, support = {IFB/T-1/WME/23-1//Indian Council of Forestry Research and Education/ ; }, abstract = {Rhizophora species are ecologically significant true mangroves with a broad tropical distribution. We examined the rhizospheric microbiomes of dominant Rhizophora species from two contrasting Indian mangrove ecosystems-Coringa and Pichavaram-using high-throughput metabarcoding. Soil properties differed significantly between sites: Pichavaram exhibited higher electrical conductivity (24.53 dS/m), organic carbon (1.70%), sodium (8811.86 ppm), sodium adsorption ratio (220.15), and exchangeable sodium percentage (64.27%), while Coringa soils showed higher pH (8.01). Sequencing generated 1.31, 1.24, and 1.22 million high-quality reads for archaea, bacteria, and fungi, respectively. Taxonomic profiling revealed Nitrososphaeria (62.3-91.9%), Gammaproteobacteria (16.8-25.1%), and Sordariomycetes (18.6-27.8%) as dominant classes. Core taxa across both sites included Candidatus Nitrosopumilus, Woeseia, and Aspergillus. Alpha diversity indices (Chao1, Shannon, Simpson) indicated significantly higher bacterial richness and evenness in R. apiculata at Coringa (P < 0.001), while archaeal and fungal diversity showed no marked differences. Beta diversity analysis (PCoA, PERMANOVA) revealed distinct community compositions between Coringa and Pichavaram, with stronger segregation in archaeal and bacterial assemblages than in fungi. Differential abundance analysis identified nine archaeal, fifty-nine bacterial, and three fungal genera enriched between sites, with methanogens (Methanosarcina, Methanocella) predominant in Coringa and halophiles (Halococcus, Haloferax) in Pichavaram. Redundancy analysis showed sodium adsorption ratio as the key determinant of microbial assemblages, while electrical conductivity significantly shaped archaeal and fungal communities. These findings provide the first baseline dataset of the Coringa rhizospheric microbiome and new insights into the microbial ecology of Indian mangroves, with implications for ecosystem functioning, methane emissions, and conservation strategies.}, }
@article {pmid41026240, year = {2025}, author = {Abdelali, SK and Aissaoui, L and Cano-Argüelles, AL and Piloto-Sardiñas, E and Abuin-Denis, L and Maitre, A and Foucault-Simonin, A and Mateos-Hernández, L and Kratou, M and Wu-Chuang, A and Obregon, D and Cabezas-Cruz, A}, title = {Seasonal Variations in the Microbiome of Hyalomma excavatum Ticks in Algeria.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {96}, pmid = {41026240}, issn = {1432-184X}, mesh = {Animals ; *Seasons ; Algeria ; *Microbiota ; *Ixodidae/microbiology ; Female ; *Bacteria/classification/genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; RNA, Ribosomal, 16S/genetics ; Rickettsia/isolation &amp; purification/genetics ; Biodiversity ; }, abstract = {Ticks are key vectors of zoonotic diseases, with their microbiomes playing a critical role in tick physiology, survival, and vector competence. This study presents the first investigation of the microbiome in Hyalomma excavatum ticks from Algeria, focusing on seasonal variations in bacterial diversity, community composition, and pathogen interactions. Using next-generation sequencing (NGS), the microbiome of 21 female ticks collected during spring, summer, and autumn was analyzed. Beta diversity analysis revealed significant seasonal shifts in microbial community structure, while alpha diversity metrics showed no significant differences in richness and evenness. Co-occurrence network analysis demonstrated seasonal shifts in microbial interactions, particularly between symbionts and pathogens, highlighting Francisella as a key taxon in tick survival and pathogen dynamics. Rickettsia presence varied by season, influencing microbial network stability. These findings underscore the ecological determinants shaping the microbiome and its potential role in pathogen transmission. Understanding seasonal microbiome shifts provides valuable insights for managing tick-borne diseases and could inform the development of targeted, season-specific vector control strategies.}, }
@article {pmid41026216, year = {2025}, author = {Martin-Pozas, T and Fernandez-Cortes, A and Calaforra, JM and Sanchez-Moral, S and Saiz-Jimenez, C and Jurado, V}, title = {Aerobiology and Environmental Zonation in Gypsum Caves: A Comparative Study of Culturing and NGS Approaches.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {95}, pmid = {41026216}, issn = {1432-184X}, support = {PID2020-114978GB-I00 and PDI2023-146299OB-C22//Ministerio de Ciencia e Innovaci&#xf3;n/ ; }, mesh = {*Caves/microbiology ; *Calcium Sulfate/analysis ; *Bacteria/genetics/classification/isolation &amp; purification/growth &amp; development ; High-Throughput Nucleotide Sequencing/methods ; *Air Microbiology ; *Microbiota ; Spain ; *Fungi/isolation &amp; purification/genetics/classification ; Geologic Sediments/microbiology ; Phylogeny ; Biodiversity ; }, abstract = {Classical aerobiological studies commonly use high-volume air samplers to quantify and identify cultivable airborne bacteria and fungi. However, this approach introduces a significant bias, as it overlooks the non-cultivable fraction, which likely constitutes a major component of the airborne microbiome. The advent of next-generation sequencing (NGS) has addressed this limitation, enabling a more comprehensive characterization of the cave aerobiome. This study analyzes both cultivable and non-cultivable airborne bacteria from Covadura and C3 caves, located in the Gypsum Karst of Sorbas (SE Spain). A total of 24 bacterial genera were identified using culture-based methods, whereas NGS revealed 749 genera. Culture-based methods using the surface air system (SAS) predominantly recovered Gram-positive spore-forming bacteria from the phyla Bacillota and Actinomycetota, which were largely absent or present in low relative abundances in the NGS datasets. In contrast, NGS revealed a broader diversity, including numerous Gram-negative and rare airborne bacteria not detected by culture. The NGS results from airborne samples showed greater similarity to the microbial communities found in cave biofilms and sediments, suggesting that a portion of airborne bacteria originates from within the cave and is influenced by microclimatic conditions such as ventilation and air stagnation. Although the short-read sequencing approach used in this study has limitations, such as reduced taxonomic resolution compared to the culture-based approach, it remains the most effective tool for capturing the diversity and ecological patterns of airborne microorganisms. The integration of gas tracers and other environmental data allowed the identification of zones within the cave with different ventilation patterns and degrees of isolation, which corresponded to different spatial distributions of airborne bacteria. Our findings underscore that reliable aerobiological studies in caves require the combination of non-culture dependent-based sequencing approaches and environmental monitoring to fully understand the origin, diversity, and ecological dynamics of airborne microbial communities.}, }
@article {pmid41026209, year = {2025}, author = {Gutiérrez-Pavón, AJ and Pereyra, MM and Chacón, FI and Monroy-Morales, E and Rebollar, EA and Dib, JR and Serrano, M and Romero-Contreras, YJ}, title = {Bacteria from the Amphibian Skin Inhibit the Growth of Phytopathogenic Fungi and Control Postharvest Rots.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {101}, pmid = {41026209}, issn = {1432-184X}, support = {PICT-2021-GRF-TII-0020//Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; N203023//Programa de Apoyo a Proyectos de Investigaci&#xf3;n e Innovaci&#xf3;n Tecnol&#xf3;gica/ ; }, mesh = {Animals ; *Plant Diseases/microbiology/prevention &amp; control ; Botrytis/growth &amp; development ; *Skin/microbiology ; Penicillium/growth &amp; development ; *Antibiosis ; *Bacteria/isolation &amp; purification/metabolism ; Fruit/microbiology ; *Biological Control Agents ; Solanum lycopersicum/microbiology ; Alternaria/growth &amp; development ; *Anura/microbiology ; Citrus/microbiology ; *Fungi/growth &amp; development ; Volatile Organic Compounds/pharmacology ; Aspergillus niger/growth &amp; development ; Pest Control, Biological ; }, abstract = {Postharvest diseases caused by phytopathogenic fungi represent one of the main challenges in the agricultural industry, leading to significant losses in fruit production. Although chemical treatments have been widely used for the control of these pathogens, the emergence of resistant strains and concerns regarding food safety and environmental impact have driven the search for novel effective and eco-friendly alternatives, such as the use of biological control agents (BCAs). Previously, we demonstrated that bacteria isolated from frog skin inhibit the growth of the phytopathogenic fungus Botrytis cinerea. Based on these findings, in this study we aimed to investigate the biocontrol potential of three bacterial isolates obtained from the skin of the frog Craugastor fitzingeri. Dual culture assays showed that these bacteria strongly inhibited the mycelial growth of several postharvest fungal phytopathogens, including Penicillium digitatum, P. italicum, Alternaria alternata, Aspergillus niger, and Alternaria solani. This antagonistic activity was further confirmed through assays using bacterial filtrates (BFs) and volatile organic compounds (VOCs), effectively delaying or suppressing fungal development under in vitro conditions. Additionally, in vivo experiments on citrus fruits, tomato, and blueberry demonstrated that treatments with bacterial cell suspensions or BFs significantly reduced disease incidence caused by P. digitatum, A. alternata, and B. cinerea. However, no inhibitory effects were observed against Geotrichum citri-aurantii, Fusarium sp., Fusarium oxysporum, and Phytophthora capsici, suggesting a degree of specificity. Our findings highlight the potential of frog skin-associated bacteria as a novel source of BCAs for the sustainable management of postharvest diseases in fruits.}, }
@article {pmid41026187, year = {2025}, author = {Cheng, P and Liu, F and Li, L and Wu, S and Xiao, W and Zong, Q and Liu, T and Peng, Y}, title = {Impact of Tebuconazole On the Development and Symbiotic Microbial Communities of Pardosa Pseudoannulata.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {97}, pmid = {41026187}, issn = {1432-184X}, mesh = {*Triazoles/toxicity ; *Symbiosis/drug effects ; Animals ; *Microbiota/drug effects ; Bacteria/drug effects/classification/genetics/isolation &amp; purification ; *Fungi/drug effects/classification/genetics ; *Fungicides, Industrial/toxicity ; *Spiders/microbiology/drug effects/growth &amp; development/physiology ; RNA, Ribosomal, 16S/genetics ; Animals, Poisonous ; }, abstract = {Tebuconazole is a widely used triazole fungicide to control fungal diseases. While there have been reported side effects on non-target arthropods, its ecological risks to natural enemies remain poorly understood. In this study, we evaluated the developmental toxicity and symbiotic microorganism responses of the wolf spider Pardosa pseudoannulata, an important predator in rice ecosystems, following exposure to tebuconazole. The results indicated that tebuconazole did not significantly increase the mortality rate of spiderlings; however, it did lead to a significant decrease in spiderling body weight, as well as the length and width of the carapace. High-throughput sequencing of the 16S rRNA gene V3-V4 regions and the ITS region revealed that tebuconazole significantly reduced bacterial diversity indices in the short term, with a gradual recovery over time. In contrast, the impact on the fungal community was continuous and irreversible, with a significant decrease in the Shannon index observed after 15 days. At the genus level, the relative abundances of Cupriavidus and Staphylococcus in the bacterial community decreased significantly after tebuconazole exposure, while Stenotrophomonas increased. In the fungal community, Fungi_gen_Incertae_sedis decreased significantly, and Simplicillium increased. Our findings highlight the ecological risks of fungicide exposure to beneficial predators and underscore the importance of considering symbiotic microbiota in pesticide risk assessments.}, }
@article {pmid41026185, year = {2025}, author = {Borja-Martínez, G and de León-Lorenzana, A and Yanez-Montalvo, A and Hernández-Canchola, G and Falcón, LI and Vázquez-Domínguez, E}, title = {Evolutionary and Ecological Drivers of Gut Microbiota in Wild Rodent Species from the Yucatán Peninsula.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {100}, pmid = {41026185}, issn = {1432-184X}, support = {887756//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as (CONAHCyT)/ ; IV200421//Programa de Apoyo a Proyectos de Investigaci&#xf3;n e Innovaci&#xf3;n Tecnol&#xf3;gica-DGAPA/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Mexico ; *Rodentia/microbiology/classification ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; *Biological Evolution ; Biodiversity ; Symbiosis ; }, abstract = {The host-microbiome association is considered a coevolutionary process, in which the microbiome provides important functions for host development, physiology and health. However, the ecological and evolutionary forces shaping the diversity and structure of the bacterial communities that form the microbiome are still being elucidated. We assessed the composition of gut microbiota in six rodent species from three geographic regions across the Yucatán peninsula, Mexico. We evaluated the contribution of host species identity, phylogenetic relationships, and geography to the rodents' gut microbiota, using 16S rRNA V4 sequences. We performed a comprehensive set of analytical approaches, including Hill numbers, machine learning, and phylogenetic comparative frameworks. Our results show that phylosymbiosis is one of the main mechanisms driving microbiota dissimilitude across species and specific microbiota diversity traits. Additionally, the microbial pool in each region was geographically differentiated, shaped by the rodent community ensemble, while ecological filtering rendered a microbial pool characteristic of each species. The environment also played a significant role for some species like Heteromys gaumeri, while dietary habits showed a stronger signal for Oryzomys couesi. Rodents with more specialized habits like Ototylomys phyllotis (semi-arboreal, folivorous) had higher bacterial diversity. The abundance of eight bacterial families determined key differences of the gut microbiota which, in addition to phylogeny and geography, are associated with distinct diet and metabolic functions among rodents. Distinct metabolic functions were related, among others, to toxins metabolism and digestion of complex food components. Overall findings show that both evolutionary and ecological drivers influence these rodents gut microbial structure and composition.}, }
@article {pmid41026172, year = {2025}, author = {Gao, H and Ma, X and Lu, M and Wang, Y and Liu, H and Hu, X and Nie, Y}, title = {Population and Spatial Features Impact the Gut Phageome-Bacteriome Structure and Interactions in a Mammal Species Living in Fragmented Habitats.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {98}, pmid = {41026172}, issn = {1432-184X}, support = {32225033//National Natural Science Foundation of China/ ; 2022YFF1301500//Ministry of Science and Technology of China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Bacteriophages/genetics/classification/physiology/isolation &amp; purification ; *Bacteria/classification/genetics/isolation &amp; purification/virology ; *Ecosystem ; RNA, Ribosomal, 16S/genetics ; *Antelopes/microbiology/virology ; Metagenome ; Feces/microbiology ; }, abstract = {The mammalian gut microbiome composition has been shown to promote host adaptation to ecological environments. However, the variation in the gut phageome and bacteriome composition at both the population level and spatial scale in wild animals has not been well investigated. Here, we used viral metagenomes and 16S rRNA gene sequencing to explore how these characteristics affect the gut microbiome of Przewalski's gazelle, an endangered group-living ungulate that lives in several fragmented habitats due to anthropogenic activities. The results revealed that population and habitat geographic characteristics collectively explained much more of the variation in phageome and bacteriome compositions than did host-associated factors. Both gut phage and bacterial diversity were positively associated with population size, and differentiation in gut microbiome diversity increased with geographic distance among populations. Additionally, the gut phage and the bacterial hosts displayed similar patterns in composition across habitats, indicating that the microbiome may exhibit complex interactions in response to the environment. For the first time, our study reveals the important roles of population and habitat geographic characteristics in driving spatial patterns of gut microbiome structures in wild animals and highlights the interactions between gut phages and the bacteriome in adaptation to living environments under the influence of human disturbances.}, }
@article {pmid41026164, year = {2025}, author = {Yeo, IC and Shim, KY and Min, JO and Kim, JH and Ha, SY and Jeong, CB}, title = {Vertical Structure and Functional Diversity of Microbial Communities in the Ross Sea, Antarctica.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {99}, pmid = {41026164}, issn = {1432-184X}, support = {KIMST RS-2022-KS221661//Korea Institute of Marine Science and Technology promotion/ ; NRF-2022R1C1C1010575//National Research Foundation of Korea/ ; }, mesh = {Antarctic Regions ; *Seawater/microbiology/chemistry ; *Microbiota ; *Biodiversity ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Ecosystem ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; }, abstract = {The Ross Sea, Antarctica, encompasses distinct water masses, each characterized by unique physicochemical conditions influencing microbial community composition and functional diversity. This study examined microbial communities across five stations covering various water masses, including Antarctic Surface Water (AASW), Circumpolar Deep Water (CDW), and Shelf Water (SW). Despite limited horizontal variability, significant vertical structuring was observed, potentially driven by vertical microbial dispersal from surface waters. Surface communities exhibited lower alpha diversity due to abundant labile organic matter favoring fast-growing heterotrophic taxa, whereas deeper communities displayed increased microbial richness, reflecting adaptation to more refractory organic matter. Functional diversity revealed distinct depth-related patterns, with metabolic pathways associated with organic matter predominantly enriched in surface layers. Concurrently, rare taxa became more abundant with depth, emphasizing their potential role as keystone organisms in deep-ocean nutrient cycling. These findings highlight the critical role of vertical microbial connectivity and organic matter composition in shaping microbial community structure and functional specialization, contributing significantly to our understanding of microbial-mediated biogeochemical processes in polar marine ecosystems.}, }
@article {pmid41025798, year = {2025}, author = {Damashek, J and Sheik, CS and Petro, C and Reeder, CF and Chowdhury, S and Kramer, BJ and DeVilbiss, SE and Pierella Karlusich, JJ and Marks, JC and Valdespino-Castillo, PM and Furey, PC and Berberich, ME and Marcarelli, AM and Scott, JT and Fulweiler, RW}, title = {DiazoTIME: a metabolically-resolved reference database of nitrogen-fixing microbial genomes.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0089725}, doi = {10.1128/mra.00897-25}, pmid = {41025798}, issn = {2576-098X}, abstract = {Microbial nitrogen fixation (diazotrophy) is a critical ecological process. We curated DiazoTIME (Diazotroph Taxonomic Identity and MEtabolism), a comprehensive database of diazotroph genomes including taxonomic annotation and metabolic prediction. DiazoTIME is unique among databases for classifying diazotrophs because it resolves both taxonomy and metabolic functionality.}, }
@article {pmid41025789, year = {2025}, author = {Hodgskiss, LH and Kerou, M and Luo, Z-H and Bayer, B and Maier, A and Weckwerth, W and Nägele, T and Schleper, C}, title = {Metabolic response of a chemolithoautotrophic archaeon to carbon limitation.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0073225}, doi = {10.1128/msystems.00732-25}, pmid = {41025789}, issn = {2379-5077}, abstract = {The ubiquitously distributed ammonia-oxidizing archaea generate energy from ammonia and build cell mass from inorganic carbon sources, thereby contributing to both the global nitrogen and carbon cycles. However, little is known about the regulation of their predicted core carbon metabolism. A thermodynamic model for Nitrososphaera viennensis was developed to estimate the consumption of inorganic carbon in relation to ammonia consumed for energy and was tested experimentally by growing cells in carbon-limited and excess conditions. A combined proteomic and metabolomic approach to the experimental conditions revealed distinct metabolic adaptation depending on the amount of carbon supplied, either in a catalase or pyruvate background as a reactive oxygen species scavenger. Integration of protein and metabolite dynamics revealed a cellular strategy under carbon limitation to maintain a pool of amino acids and an upregulation of proteins necessary for translation initiation to stay primed for protein synthesis. The combination of modeling and functional genomics fills gaps in the understanding of the central metabolism and its regulation in a chemolithoautotrophic, ammonia-oxidizing archaeon, even in the absence of available genetic tools.IMPORTANCELittle is known about the regulation of carbon metabolism within ammonia-oxidizing archaea (AOA), a widespread clade that plays a critical role in the global nitrogen cycle while also fixing inorganic carbon. To address this missing knowledge, the soil AOA Nitrososphaera viennensis was subjected to various levels of inorganic carbon and analyzed via a systems biology approach to better understand how its core metabolism is regulated. The results demonstrate a strong dependence on the carbon fixation cycle and highlight key connection points between the core metabolic pathways. The analysis additionally revealed tight control on translational processes and elucidated unique cellular responses when the organism was exposed to either exogenous catalase or pyruvate to relieve oxidative stress from reactive oxygen species. The presented data highlight metabolic responses of N. viennensis and provide a better understanding of how the organism, and likely other AOA, respond to various environmental conditions.}, }
@article {pmid41024334, year = {2025}, author = {Zhan, J and Zhang, L and Lai, S and Guo, J and Lin, T and Liu, G and Rensing, C and Liu, X and Zhou, S}, title = {Fe(III)-dependent Nrf activity determines nitrate reduction partitioning in nitrate-reducing communities.}, journal = {mBio}, volume = {}, number = {}, pages = {e0222025}, doi = {10.1128/mbio.02220-25}, pmid = {41024334}, issn = {2150-7511}, abstract = {Identifying the factors that affect the nitrate reduction partitioning between dissimilatory nitrate reduction to ammonium (DNRA) and denitrification is crucial for mitigating nitrogen loss in ecosystems. Conventionally, the nutrient status of the environment (e.g., the carbon-to-nitrogen ratio) is recognized as the key determinant of nitrogen conversion pathways. Here, we report that the availability of Fe(III) regulates the nitrate reduction partitioning in Geobacter metallireducens and Alcaligenes faecalis co-culture. We controlled the availability of Fe(III) in the coculture medium and tracked nitrogen conversion dynamics and community composition. The results demonstrated that the coculture performed DNRA, contributed mainly by G. metallireducens under Fe(III)-replete conditions, while performing interspecies synergistic denitrification between both species under Fe(III)-depleted conditions. Nitrate/nitrite reductase activity calculations and mutation analyses indicated that nitrate reduction partitioning in the coculture was governed by the nitrite reductase (Nrf) activity of G. metallireducens, which was Fe(III)-dependent. Further validation in urban river water confirmed that Fe(III) supplementation significantly enhances DNRA activity. Our findings establish Fe(III) as a previously unrecognized regulator of microbial nitrogen retention, showing insights into strategies for managing nitrogen fluxes in agricultural and aquatic systems.IMPORTANCENitrogen is essential for life, but its loss from ecosystems through microbial processes like denitrification harms agricultural productivity and contributes to greenhouse gas emissions. Retaining nitrogen as ammonium via microbial dissimilatory nitrate reduction to ammonium (DNRA) could mitigate these issues, but the factors governing microbial prioritization of DNRA over denitrification remain unclear. Our study reveals that Fe(III) plays a critical, previously unrecognized role in steering this process. We show that Fe(III) availability determines whether the nitrate-reducing community conserves nitrogen as ammonium or releases it as gas, with implications for managing nitrogen in soils and waterways. By demonstrating Fe(III)'s ability to enhance nitrogen retention in environmental systems like urban rivers, our findings offer a new lever for sustainable agriculture and pollution control. This work bridges microbial ecology and environmental management, highlighting how trace metals shape nutrient cycles in ways that can be harnessed to protect ecosystem health.}, }
@article {pmid41023320, year = {2025}, author = {Musiałowski, M and Mierzwa-Hersztek, M and Gondek, K and Dębiec-Andrzejewska, K}, title = {A novel two-step metabarcoding approach improves soil microbiome biodiversity assessment.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {33697}, pmid = {41023320}, issn = {2045-2322}, support = {LIDER/13/0051/L-11/NCBR/2020//Narodowe Centrum Bada&#x144; i Rozwoju,Poland/ ; LIDER/13/0051/L-11/NCBR/2020//Narodowe Centrum Bada&#x144; i Rozwoju,Poland/ ; }, mesh = {*Soil Microbiology ; *Biodiversity ; *DNA Barcoding, Taxonomic/methods ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; High-Throughput Nucleotide Sequencing ; *Bacteria/genetics/classification ; Phylogeny ; }, abstract = {The foundation of microbial ecology research is Next-Generation Sequencing (NGS), which allows for reconstruction of the soil microbiome taxonomical structure and the calculation of biodiversity metrics. However, obtaining reliable data on soil biodiversity poses several challenges, with accurate primer selection being one of the most critical. While 16S rDNA primers are widely used for their ability to broadly target bacterial communities, they can introduce biases. These primers may preferentially amplify certain bacterial groups, leading to a skewed representation of the microbial diversity in soil samples. To overcome the bias, we developed a novel, Two-Step Metabarcoding (TSM) approach to obtain more accurate and detailed data on soil microbiome structure and biodiversity. The first step involved sequencing of amplicons generated using universal 16S rDNA primers, provided an initial overview of the microbial community, and allowed the identification of key taxonomical groups. In the second step, we employed sequencing of amplicons generated with taxa-specific primers designed for the most abundant phyla in the community. We used the obtained data for a more reliable reconstruction of microbiome taxonomic structure and biodiversity. This two-step approach ensures a thorough exploration of the soil microbiome and promises to enhance our understanding of soil microbial dynamics and ecology.}, }
@article {pmid41018004, year = {2025}, author = {Neilson, R and King, D and Giles, ME}, title = {The microbiome associated with Trichodorus primitivus is enriched with Janthinobacterium compared to soil.}, journal = {Journal of nematology}, volume = {57}, number = {1}, pages = {20250043}, pmid = {41018004}, issn = {0022-300X}, abstract = {Although soil biota mediates many key processes that deliver multiple environmental benefits, interactions between soil biota are not well characterized. In an ecological context, studies to date on the associations between nematodes and bacteria have mostly focused on either intracellular bacteria or bacteria that have a potential role in crop pathogenesis by endoparasitic nematode species, that is, those species that have a component of their life cycle within the plant host. Moreover, evolutionary studies have utilized the model nematode species, Caenorhabditis elegans, for studies on survival, behavior, and fecundity. In this study, we characterize the bacterial communities associated with an ectoparasitic nematode species, Trichodorus primitivus, whose complete life cycle is external to the plant host. Compared to the soil from which the nematodes were extracted, the diversity of bacterial communities associated with T. primitivus was reduced. By contrast, the nematode-associated bacterial community was significantly enriched with Janthinobacterium, a known antagonist of soilborne pathogens. This study advances knowledge on the interactions between bacteria and ectoparasitic nematodes, which could help inform the future development of novel strategies for nematode control.}, }
@article {pmid41017558, year = {2025}, author = {Han, P and Liu, C and Abdal-Hay, A and Reed, S and Liaw, A and Wang, J and Ning, Y and Ivanovski, S}, title = {Proteome and microbiome profiles of polymicrobial salivary biofilms on 3D MEW fibrous scaffolds: biomimetic ECM-inspired structures.}, journal = {Journal of materials chemistry. B}, volume = {}, number = {}, pages = {}, doi = {10.1039/d5tb01410g}, pmid = {41017558}, issn = {2050-7518}, abstract = {Replicating the structural complexity of polymicrobial oral biofilms in vitro remains a significant challenge in biomaterials research. Nevertheless, developing clinically relevant biofilm models is crucial for advancing our understanding of biofilm-host interactions and elucidating how biomaterials influence microbial composition, behaviour, and overall biofilm dynamics. In this work, 3D biomimetic fibrous scaffolds made from medical-grade polycaprolactone (mPCL) were fabricated using the melt electrowriting (MEW) technique. The effects on biofilm viability, activity, microbiome, and proteome profiles were assessed on 3D fibrous scaffolds and conventional 2D tissue culture plates (TCP). Human saliva was cultured on MEW mPCL (3D BF) and TCP (2D BF) for 4 days, followed by microbiome profiling via 16S rRNA sequencing and proteomic analysis using LC-MS/MS, SWATH with GO and KEGG pathway enrichment. The results demonstrated that 3D MEW mPCL scaffolds enhanced biofilm biomass, thickness, and viability. Microbiome analysis revealed that 3D BF was enriched with both commensals and pathogens, including Veillonella, Peptostreptococcus, Porphyromonas gingivalis, and Treponema denticola, alongside probiotic species like Lactobacillus acidophilus. Pooled proteomic data from three technical repeats, along with GO and KEGG analyses, revealed a functionally dynamic biofilm ecosystem characterised by elevated expression of proteins involved in glycolysis, the TCA cycle, and nucleotide metabolism, highlighting pathways essential for biofilm survival, stress adaptation, and host interaction. These 'proof-of-concept' findings highlight the potential of 3D MEW fibrous mPCL scaffolds as a biomimetic 3D platform capable of accurately recapitulating the dynamic spatial and metabolic complexity of oral biofilms, thereby facilitating innovative investigations into microbial ecology, host-pathogen interactions, and the accelerated development of targeted antimicrobial therapies.}, }
@article {pmid41016925, year = {2025}, author = {Li, C and Wu, M and Tang, W and Yu, B and Saiz-Lopez, A and Poulain, A and Bank, MS and Zhou, Q and Bodelier, PLE and Yan, Z and Frey, B and Hu, H and Chen, J and Jiang, Y and Zhong, H}, title = {Aligning global mercury mitigation with climate action.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {7826}, pmid = {41016925}, issn = {2041-1723}, support = {42107223//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41673075//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Mercury/analysis/toxicity ; *Climate Change ; Greenhouse Gases/metabolism/analysis ; Humans ; *Environmental Pollution/prevention &amp; control ; Microbiota/drug effects ; *Environmental Pollutants/analysis ; }, abstract = {Environmental mercury (Hg) pollution affects microbial community structure and functions. Yet, whether and how this influence cascades through microbe-mediated cycling of major greenhouse gases (GHGs) remains poorly understood. This Perspective synthesizes emerging evidence on the Hg-microbe-GHG nexus, exploring the possibility that global Hg emission reductions, while critical for human and planetary health, may cause alterations to microbe-mediated GHG fluxes. Significant knowledge gaps persist, however, regarding the Hg-microbe-GHG nexus, particularly concerning the magnitude and direction of the nexus's net impact on climate and global environmental change. To bridge these gaps, we propose a three-step roadmap aimed at disentangling the potential impacts of global Hg emission mitigation strategies on microbial communities, associated GHG emissions, and subsequent climate change. Collectively, these joint efforts from scientists, industry, community stakeholders, and policymakers are critical to harmonizing global Hg mitigation efforts with climate action and to ensuring a sustainable future for Earth systems and their inhabitants.}, }
@article {pmid41016813, year = {2025}, author = {Lee, HH}, title = {Iodine Biogeochemical Cycle and Microbial Bioremediation of Radioactive Iodine-129.}, journal = {Journal of microbiology and biotechnology}, volume = {35}, number = {}, pages = {e2508018}, doi = {10.4014/jmb.2508.08018}, pmid = {41016813}, issn = {1738-8872}, mesh = {*Biodegradation, Environmental ; *Iodine Radioisotopes/metabolism ; *Bacteria/metabolism ; *Iodine/metabolism ; Oxidation-Reduction ; Humans ; Hydrocarbons, Iodinated ; }, abstract = {Iodine is an essential biophilic element that plays pivotal roles in both environmental systems and human physiology, particularly as a key constituent of thyroid hormones and a regulator of atmospheric ozone. In contrast, its radioactive isotope, iodine-129 (I-129), predominantly generated through anthropogenic nuclear activities, represents a persistent environmental and public health concern. With an exceptionally long half-life of approximately 15.7 million years and high environmental mobility, especially in groundwater, combined with a strong tendency to bioaccumulate in the human thyroid, I-129 poses a disproportionate and long-term radiological hazard in contaminated sites. The biogeochemical cycling of iodine involves intricate interconversions among multiple oxidation states and phases across the lithosphere, hydrosphere, atmosphere, and biosphere. Microorganisms are central to these processes, mediating oxidation, reduction, methylation, accumulation, and sorption. While microbial methylation can increase I-129 mobility via the production of volatile methyl iodide, other microbial pathways, notably biosorption and binding to organic matter, provide promising mechanisms for immobilization and natural attenuation. Microbial bioremediation offers a sustainable and cost-effective alternative or complement to conventional physicochemical methods for managing radioactive contaminants. Strategies such as bioreduction, biosorption, bioaccumulation, and biomineralization exploit the metabolic versatility of microorganisms to alter radionuclide speciation, solubility, and mobility. However, practical application to I-129 remains challenging due to its extreme persistence, environmental variability, and uncertainties in predicting its long-term geochemical fate. Effective management of I-129 contamination will require an integrated, multidisciplinary approach that combines advanced microbial ecology insights, optimized biotechnological processes, and long-term monitoring frameworks.}, }
@article {pmid41016251, year = {2025}, author = {Schubert, K and Shosanya, T and García-Bayona, L}, title = {The role of mobile genetic elements in adaptation of the microbiota to the dynamic human gut ecosystem.}, journal = {Current opinion in microbiology}, volume = {88}, number = {}, pages = {102675}, doi = {10.1016/j.mib.2025.102675}, pmid = {41016251}, issn = {1879-0364}, abstract = {The human intestinal microbiota is a dynamic ecosystem shaped by extensive horizontal gene transfer, particularly in individuals from industrialized populations. In this review, we discuss recent advances in our understanding of how mobile genetic elements (MGEs) contribute to microbial ecology and evolution in this diverse community, focusing on MGEs carrying fitness-conferring genes. Bacteroidales species can colonize individuals for decades and serve as major hubs for MGE exchange. Most MGEs are highly variable across individuals and geographies. Occasionally, conserved MGEs can spread across geography and lifestyles. Functional characterizations of MGEs reveal their roles in antibiotic resistance, interbacterial antagonism, biofilm formation, immune evasion, and nutrient acquisition, among others. Substantive progress in our understanding of MGEs in the gut microbiome offers promising avenues for therapeutic microbiome interventions. However, major challenges remain in functional prediction, host-MGE linkage, and experimental characterization.}, }
@article {pmid41013679, year = {2025}, author = {Ramljak, A and Jurburg, S and Chatzinotas, A and Lučić, M and Žižek, M and Babić, I and Udiković-Kolić, N and Petrić, I}, title = {Identifying the drivers of microbial community changes and interactions in polluted coastal sediments.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {117}, pmid = {41013679}, issn = {2524-6372}, support = {IP-2020-02-6510//Hrvatska Zaklada za Znanost/ ; IP-2020-02-6510//Hrvatska Zaklada za Znanost/ ; IP-2020-02-6510//Hrvatska Zaklada za Znanost/ ; IP-2020-02-6510//Hrvatska Zaklada za Znanost/ ; }, abstract = {Despite over three decades of research into the composition and distribution of microbial communities, gaps remain in our mechanistic understanding of microbial community assembly processes, especially in benthic communities in coastal zones continuously exposed to anthropogenic pressures. We analyzed the microbial communities (prokaryotes, fungi, and protists) in sediment samples from ports and bays located along the Adriatic coast chronically exposed to chemical and nutrient pollution, and explored how selective pressures (pollutants, nutrients, and environmental conditions) and dispersal shape these communities. We found that biogeographic factors (i.e. location) play a key role in structuring microbial communities, with benthic fungi also being shaped by the presence of pollutants and nutrients. Strong correlations between nutrient loads and pollutants were observed, along with weakened interactions between microbial communities, particularly between prokaryotes and protists, in the presence of specific pollutants (bismuth, cadmium, copper, zinc, mercury). These results are an important step in disentangling the complex interactions between pollutants and microbial community dynamics in aquatic ecosystems. Further research is needed to assess how these shifts in microbial community dynamics may affect ecosystem services in vulnerable coastal zones.}, }
@article {pmid41012703, year = {2025}, author = {Johnson, ML and Boezen, D and Grum-Grzhimaylo, AA and van der Vlugt, RAA and de Visser, JAGM and Zwart, MP}, title = {Living Together Apart: Quantitative Perspectives on the Costs and Benefits of a Multipartite Genome Organization in Viruses.}, journal = {Viruses}, volume = {17}, number = {9}, pages = {}, doi = {10.3390/v17091275}, pmid = {41012703}, issn = {1999-4915}, support = {016.VIDI.171.061/NWO_/Dutch Research Council/Netherlands ; }, mesh = {*Genome, Viral ; *Plant Viruses/genetics/physiology ; Host Specificity ; Metagenomics ; Plant Diseases/virology ; Plants/virology ; }, abstract = {BACKGROUND: Multipartite viruses individually package their multiple genome segments into virus particles, necessitating the transmission of multiple virus particles for effective viral spread. This dependence poses a cost in the form of reduced transmission compared to monopartite viruses, which only have a single genome segment. The notable cost of a multipartite genome organization has spurred debate on why multipartite viruses are so common among plant viruses, including a search for benefits associated with this organizational form.<br><br>METHODS: We investigated the costs and benefits of multipartite viruses with three approaches. First, we reanalyzed dose-response data to measure the cost of multipartition to between-host transmission for multipartite viruses. Second, we developed a simulation model to explore when the sharing of viral gene products between cells is beneficial. Third, we tested whether multipartite viruses have a broad host range by estimating the host range for plant viruses using metagenomics data.<br><br>RESULTS: We find that the observed cost to transmission exceeds theoretical predictions. We predict that a virus gene-product-sharing strategy only confers benefits under limited conditions, suggesting that this strategy may not be common. Our results suggest that multipartite and segmented viruses have broader host ranges than monopartite viruses.<br><br>CONCLUSIONS: Our analyses also suggest there is limited evidence for the costs and benefits of a multipartite organization, and we argue that the diversity of multipartite virus-host systems demands pluralistic explanatory frameworks.}, }
@article {pmid41011533, year = {2025}, author = {Dai, X and He, Y and Su, Y and Mo, H and Li, W and Li, W and Zi, S and Liu, L and Di, Y}, title = {Pathogen Identification, Antagonistic Microbe Screening, and Biocontrol Strategies for Aconitum carmichaelii Root Rot.}, journal = {Microorganisms}, volume = {13}, number = {9}, pages = {}, doi = {10.3390/microorganisms13092202}, pmid = {41011533}, issn = {2076-2607}, support = {202403AP140013//The Sino-Vietnamese International Joint Laboratory for Characteristic &amp; Cash Crops Green De-velopment of Yunnan Province/ ; Yunnan Academic Degrees Committee Document [2024] No. 19//The Construction Project for Postgraduate Tutor Team of Yunnan Province in 2024/ ; 2024J0486//Scientific Research Fund of the Educational Department of Yunnan Province/ ; }, abstract = {The undefined microbial ecology of Aconitum carmichaelii root rot in western Yunnan constrains the advancement of eco-friendly control strategies. The identification of potential pathogenic determinants affecting A. carmichaelii growth is imperative for sustainable cultivation and ecosystem integrity. High-throughput sequencing was employed to profile microbial communities across four critical niches, namely rhizosphere soil, tuberous root epidermis, root endosphere, and fibrous roots of healthy and diseased A. carmichaelii. The physicochemical properties of corresponding rhizosphere soils were concurrently analyzed. Putative pathogens were isolated from diseased rhizospheres and tubers through culturing with Koch's postulates validation, while beneficial microorganisms exhibiting antagonism against pathogens and plant growth-promoting (PGP) traits were isolated from healthy rhizospheres. Highly virulent strains (2F14, FZ1, L23) and their consortia were targeted for suppression. Strain DX3, demonstrating optimal PGP and antagonistic capacity in vitro, was selected for pot trials evaluating growth enhancement and disease control efficacy. Significant disparities in rhizosphere soil properties and bacterial/fungal community structures were evident between healthy and diseased cohorts. Fifteen putative pathogens spanning eight species across four genera were isolated: Fusarium solani, F. avenaceum, Clonostachys rosea, Mucor racemosus, M. irregularis, M. hiemalis, Serratia liquefaciens, and S. marcescens. Concurrently, eight PGP biocontrol strains were identified: Bacillus amyloliquefaciens, B. velezensis, B. subtilis, B. pumilus, and Paenibacillus polymyxa. Pot trials revealed that Bacillus spp. enhanced soil physiochemical properties through nitrogen fixation, phosphate solubilization, potassium mobilization, siderophore production, and cellulose degradation, significantly promoting plant growth. Critically, DX3 inoculation elevated defense-related enzyme activities in A. carmichaelii, enhanced host resistance to root rot, and achieved >50% disease suppression efficacy. This work delineates key pathogenic determinants of Yunnan A. carmichaelii root rot and identifies promising multifunctional microbial resources with dual PGP and biocontrol attributes. Our findings provide novel insights into rhizosphere microbiome-mediated plant health and establish a paradigm for sustainable disease management.}, }
@article {pmid41011501, year = {2025}, author = {Dai, L and Hao, X and Niu, T and Liu, Z and Wang, Y and Geng, X and Cai, Q and Wang, J and Ren, Y and Liu, F and Liu, H and Li, Z}, title = {Analysis of Microbial Community Structure and Diversity in Different Soil Use Types in the Luo River Basin.}, journal = {Microorganisms}, volume = {13}, number = {9}, pages = {}, doi = {10.3390/microorganisms13092173}, pmid = {41011501}, issn = {2076-2607}, support = {30803302//Henan Provincial Finance Forest and Grass Science and Technology (Intermediate Trial) Promo-tion Demonstration Project "Introduction and Cultivation of desia polycarpa Maxim. 'Yulu/ ; 2025-2627//Henan Province Science and Technology Research Project "Innovative Utilization of Germplasm Resources and Breeding of Excellent New Varieties of desia polycarpa Maxim."/ ; }, abstract = {The Luohe River boasts a profound historical heritage. Due to long-term impacts of human activities along its banks, significant variations in soil environmental conditions may exist across different land use types within the region. This study focused on four land use types (farmland, bamboo forest, grassland, and abandoned land) in Luoning County of the Luohe River Basin and employed high-throughput sequencing technology to analyze the characteristics of soil microbial communities and differences in soil nutrients. The results showed the following: There were significant differences in soil nutrients and microbial diversity among different land use types. Specifically, the organic matter content in farmland was significantly higher than that in bamboo forests (p < 0.05), and the available phosphorus content in farmland was significantly higher than that in abandoned land (p < 0.05); the abandoned land had a significant advantage in alkali-hydrolyzable nitrogen and available potassium contents (p < 0.05) but the lowest soil water content (p < 0.05). Microbial diversity indices indicated that Pielou's evenness index (Pieloue) in farmland was significantly higher than that in grassland. The bacterial community was dominated by Acidobacteria, Proteobacteria, and Actinobacteria. At the genus level, available potassium was the key factor affecting the top 20 dominant bacterial genera. Redundancy Analysis (RDA) showed that pH was the core environmental variable driving the variation of bacterial community structure. Metabolic pathway analysis revealed that biosynthetic metabolism was the main pathway, and grassland exhibited outstanding performance in the secondary metabolite synthesis pathway. The results of this study fill the gap in soil microbial ecology research in this region and provide a theoretical basis for the sustainable utilization of land resources and agricultural ecological management in the Luohe River Basin.}, }
@article {pmid41011387, year = {2025}, author = {Wang, Y and Deng, C and Sui, M and Wei, P and Duan, B and Li, Z and Zou, F}, title = {Acute Toxoplasma gondii Infection Drives Gut Microbiome Dysbiosis and Functional Disruption in Mice as Revealed by Metagenomic Sequencing.}, journal = {Microorganisms}, volume = {13}, number = {9}, pages = {}, doi = {10.3390/microorganisms13092056}, pmid = {41011387}, issn = {2076-2607}, support = {202449CE340019//the Yunnan Key Laboratory of Veterinary Etiological Biology/ ; U2202201//the NSFC-Yunnan Joint Fund/ ; 202401AT070440//the Yunnan Fundamental Research Projects/ ; 2024Y339//the Scientific Research Fund of Education Department of Yunnan Province/ ; No.XXX//the Yunnan Provincial University Key Industry Service Science and Technology Program/ ; }, abstract = {Toxoplasma gondii is a widely distributed intracellular parasite that disrupts host immune and metabolic homeostasis. Although accumulating evidence highlights the role of gut microbiota in parasitic infections, the effects of acute T. gondii infection on host gut microbial ecology remain poorly understood. In this study, metagenomic sequencing technology was used to systematically analyze the composition and functional alterations of the ileal microbiota in BALB/c mice on day 10 post-infection. Compared to uninfected controls, T. gondii infected mice exhibited a significant reduction in microbial diversity and a pronounced shift in community structure. Notably, there was an expansion of Proteobacteria, particularly the Enterobacteriaceae family, alongside a marked decline in beneficial taxa such as Actinobacteria and Bacillota. Functional annotation using the KEGG and CAZy databases revealed enrichment of metabolic pathways related to glycolysis/gluconeogenesis, O-antigen nucleotide sugar biosynthesis, bacterial secretion systems, and biofilm formation-Escherichia coli in the infected microbiota. These findings provide novel insights into the dysbiosis of gut microbiota and host-microbe interactions during acute T. gondii infection.}, }
@article {pmid41010480, year = {2025}, author = {Duysburgh, C and Fiore, W and Marzorati, M}, title = {Survival and Impact on Microbial Diversity of Lacticaseibacillus paracasei DG in a Simulation of Human Intestinal Microbial Ecosystem.}, journal = {Nutrients}, volume = {17}, number = {18}, pages = {}, doi = {10.3390/nu17182952}, pmid = {41010480}, issn = {2072-6643}, support = {N/A//Alfasigma S.p.A./ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Probiotics ; *Lacticaseibacillus paracasei/physiology/growth &amp; development/metabolism ; Microbial Viability ; Hydrogen-Ion Concentration ; Fatty Acids, Volatile/metabolism ; Colon/microbiology ; Lactic Acid/metabolism ; Feces/microbiology ; }, abstract = {Background/Objectives: The probiotic Lacticaseibacillus paracasei DG (LpDG) has shown promising results for various gastrointestinal diseases. This study evaluated the survival, metabolic activity, and impact on colonic microbiota of LpDG in an in vitro gastrointestinal tract simulation. Methods: Encapsulated LpDG was tested under simulated fed, fasted, and shortened fasted conditions compared with a blank control in a modified Simulator of the Human Intestinal Microbial Ecosystem (SHIME[®]) reactor. Capsule integrity, and cell culturability and viability were assessed at the end of each digestion phase. Metabolic activity (pH, total gas production, and concentrations of short-chain fatty acids, lactate, and ammonium) was assessed after a 24 h colonic incubation with a faecal inoculum. The impact of LpDG on the colonic microbial community was analysed by quantitative polymerase chain reaction and shallow shotgun sequencing. Results: The capsule was completely degraded at the end of the jejunum under all conditions. A low pH had a minimal impact on LpDG culturability and viability. Compared with blank control, LpDG remained metabolically active in the microbial community following a 24 h colonic incubation (LpDG [0-24 h] vs. blank control [0-24 h]: ΔpH, decreased [0.29-0.38 vs. 0.12-0.34]; Δlactic acid, decreased [1.52-1.69 mM vs. 0.13-0.21 mM]; and Δbutyrate, increased [7.49-10.52 mM vs. 5.19-7.76 mM]). Under fed conditions, treatment with LpDG compared with blank control significantly decreased levels of Escherichia coli and Blautia wexlerae and increased Clostridiaceae, Eubacteriaceae, and Lachnospiraceae. Conclusions: LpDG remains viable and metabolically active in the gastrointestinal tract, positively affecting intestinal microbiota and metabolite production.}, }
@article {pmid41009926, year = {2025}, author = {Dealis Gomes, ML and Afonso, L and Basso, KR and Alves, LC and Macías, EJN and Yamada-Ogatta, SF and Guidi, AC and de Mello, JCP and Andrade, FG and Cabeça, LF and Cely, MVT and Andrade, G}, title = {Liposomal Fluopsin C: Physicochemical Properties, Cytotoxicity, and Antibacterial Activity In Vitro and over In Vivo MDR Klebsiella pneumoniae Bacteremia Model.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {14}, number = {9}, pages = {}, doi = {10.3390/antibiotics14090948}, pmid = {41009926}, issn = {2079-6382}, support = {439754/2018-6 (AMR MCTIC)//Brazilian National Council for Scientific and Technological Development (CNPq)/ ; 406016/2022-4, PPSUS-Aracauria Foundation-PR//Brazilian National Council for Scientific and Technological Development (CNPq)/ ; }, abstract = {Introduction: Antimicrobial resistance has become a global concern, and few new antimicrobials are currently being developed. Fluopsin C has proven broad-spectrum activity, being a promising candidate for new antimicrobial development. To optimize antimicrobial activity, this research aimed at fluopsin C (Flp) encapsulation in liposomes to achieve controlled release and reduce cytotoxicity. Methods: Liposomal formulations were prepared by extruding formulations based on soy phosphatidylcholine (SPC) or poly (ethylene glycol)-distearoylphosphatidylethanolamine (DSPE-PEG) plus cholesterol, and were characterized by their size, polydispersity index, zeta potential, encapsulation efficiency, shelf-life stability, in vitro release profile, cytotoxicity, and antimicrobial activity against Klebsiella pneumoniae in vitro and in vivo. Results: The results indicated that the DSPE-PEG DMSO+Flp formulation presented superior physicochemical stability and unaltered antimicrobial activity. In vitro, CC50 decreased by 54%. No lethal dose was obtained in mice within the concentration range tested. The most effective doses in vivo were 2 × 2 mg/kg for free fluopsin C and 1 × 2 mg/kg for DSPE-PEG DMSO+Flp, resulting in a 40% reduction in mortality from bacteremia. Only discrete inflammatory infiltration was detected in the liver, while kidney necrosis ranged from discrete to moderate. Encapsulation of fluopsin C in liposomes showed promising features supporting to use against infections by MDR K. pneumoniae.}, }
@article {pmid41009119, year = {2025}, author = {Kiewra, D and Ojrzyńska, H and Czułowska, A and Dyczko, D and Jawień, P and Plewa-Tutaj, K}, title = {Dermacentor reticulatus (Fabricius, 1794) in Southwestern Poland: Changes in Range and Local Scale Updates.}, journal = {Insects}, volume = {16}, number = {9}, pages = {}, doi = {10.3390/insects16090935}, pmid = {41009119}, issn = {2075-4450}, abstract = {The ornate dog tick Dermacentor reticulatus is a key vector of several pathogens and has been expanding its range across Europe, raising concerns about the associated veterinary and public health risks. This study aimed to assess the current distribution and local-scale expansion of D. reticulatus in southwestern Poland, particularly in and around the city of Wrocław. In 2024, host-seeking ticks were collected using the flagging method at 80 sites, including 30 previously monitored locations and 50 newly designated ones, selected based on land cover analysis and field verification. Spatial statistics and kriging method were applied to evaluate changes in the tick's range compared to data from 2014-2019. The presence of D. reticulatus was confirmed at 68 sites, including 13 located beyond the previously estimated range. A shift in the mean center of tick occurrence toward the southeast was observed, along with an increase in the compact area of occurrence. The results indicate a continued expansion of D. reticulatus in the region, with urbanization and landscape structure likely influencing its spread. These findings underscore the importance of local-scale surveillance and spatial modeling in assessing the risk of tick-borne diseases.}, }
@article {pmid41006295, year = {2025}, author = {van Galen, LG and Smith, GR and Margenot, AJ and Waldrop, MP and Crowther, TW and Peay, KG and Jackson, RB and Yu, K and Abrahão, A and Ahmed, TA and Alatalo, JM and Anslan, S and Anthony, MA and Araujo, ASF and Ascher-Jenull, J and Bach, EM and Bahram, M and Baker, CCM and Baldrian, P and Bardgett, RD and Barrios-Garcia, MN and Bastida, F and Beggi, F and Benning, LG and Bragazza, L and Broadbent, AAD and Cano-Díaz, C and Cates, AM and Cerri, CEP and Cesarz, S and Chen, B and Classen, AT and Dahl, MB and Delgado-Baquerizo, M and Eisenhauer, N and Evgrafova, SY and Fanin, N and Fornasier, F and Francisco, R and Franco, ALC and Frey, SD and Fritze, H and García, C and García-Palacios, P and Gómez-Brandón, M and Gonzalez-Polo, M and Gozalo, B and Griffiths, R and Guerra, C and Hallama, M and Hiiesalu, I and Hossain, MZ and Hu, Y and Insam, H and Jassey, VEJ and Jiang, L and Kandeler, E and Kohout, P and Kõljalg, U and Krashevska, V and Li, X and Lu, JZ and Lu, X and Luo, S and Lutz, S and Mackie-Haas, KA and Maestre, FT and Malmivaara-Lämsä, M and Mangelsdorf, K and Manjarrez, M and Marhan, S and Martin, A and Mason, KE and Mayor, J and McCulley, RL and Moora, M and Morais, PV and Muñoz-Rojas, M and Murugan, R and Nottingham, AT and Ochoa, V and Ochoa-Hueso, R and Oja, J and Olsson, PA and Öpik, M and Ostle, N and Peltoniemi, K and Pennanen, T and Pescador, DS and Png, GK and Poll, C and Põlme, S and Potapov, AM and Priemé, A and Pritchard, W and Puissant, J and Rocha, SMB and Rosinger, C and Ruess, L and Sayer, EJ and Scheu, S and Sinsabaugh, RL and Slaughter, LC and Soudzilovskaia, NA and Sousa, JP and Stanish, L and Sugiyama, SI and Tedersoo, L and Trivedi, P and Vahter, T and Voriskova, J and Wagner, D and Wang, C and Wardle, DA and Whitaker, J and Yang, Y and Zhong, Z and Zhu, K and Ziolkowski, LA and Zobel, M and van den Hoogen, J}, title = {A global database of soil microbial phospholipid fatty acids and enzyme activities.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1568}, pmid = {41006295}, issn = {2052-4463}, support = {DEB-1845544//National Science Foundation (NSF)/ ; DEB-1926335//National Science Foundation (NSF)/ ; DGE 1450271//National Science Foundation (NSF)/ ; QUEX-CAS-QP-RD-18/19//Qatar Petroleum (QP)/ ; QUEX-CAS-QP-RD-18/19//Qatar Petroleum (QP)/ ; 305069/2018-7//Ministry of Science, Technology and Innovation | Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (National Council for Scientific and Technological Development)/ ; I989-B16//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; I989-B16//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; I989-B16//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; CZ.02.01.01/00/22_008/0004635//Ministerstvo &#x160;kolstv&#xed;, Ml&#xe1;de&#x17e;e a T&#x11b;lov&#xfd;chovy (Ministry of Education, Youth and Sports)/ ; NE/N009452/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/N009452/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/I027037/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/I027037/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/N009452/1//RCUK | Natural Environment Research Council (NERC)/ ; PICT 2014-2838//Ministry of Science, Technology and Productive Innovation, Argentina | Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica (National Agency for Science and Technology, Argentina)/ ; 315260_149807//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; BIPD_01_2021_FCT-PTDC/BIA-CBI/2340/2020, UIDB/05937/2020, UIDP/05937/2020//NOVA | Faculdade de Ci&#xea;ncias e Tecnologia, Universidade Nova de Lisboa (FCT/UNL)/ ; UID/EMS/00285/2020//NOVA | Faculdade de Ci&#xea;ncias e Tecnologia, Universidade Nova de Lisboa (FCT/UNL)/ ; UID/EMS/00285/2020//NOVA | Faculdade de Ci&#xea;ncias e Tecnologia, Universidade Nova de Lisboa (FCT/UNL)/ ; DFG- FZT 118, 202548816//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DFG- FZT 118, 202548816, Ei 862/29-1 and Ei 862/31-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DFG- FZT 118, 202548816//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 192626868-SFB 990//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 316045089//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 192626868-SFB 990//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 315415//Academy of Finland (Suomen Akatemia)/ ; PTDC/BIA-CBI/2340/2020//Ministry of Education and Science | Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia (Portuguese Science and Technology Foundation)/ ; ANR; MIXOPEAT; ANR-17-CE01-0007//Agence Nationale de la Recherche (French National Research Agency)/ ; 31872994//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41922056//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32101286//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32061143027//National Natural Science Foundation of China (National Science Foundation of China)/ ; CIDEGENT/2018/041//Generalitat Valenciana (Regional Government of Valencia)/ ; PRG1065, PRG1789, PSG784//Eesti Teadusagentuur (Estonian Research Council)/ ; PRG1065, PRG1789, PSG784//Eesti Teadusagentuur (Estonian Research Council)/ ; PRG1065, PRG1789, PSG784//Eesti Teadusagentuur (Estonian Research Council)/ ; PRG1065, PRG1789, PSG784//Eesti Teadusagentuur (Estonian Research Council)/ ; PRG1065, PRG1789, PSG784//Eesti Teadusagentuur (Estonian Research Council)/ ; NE/T012226//National Eye Research Centre (NERC)/ ; PRG1065, PRG1789, PSG784//Ministry of Education and Research | Estonian Research Competency Council (Research Competency Council)/ ; 2021M693360//China Postdoctoral Science Foundation/ ; }, mesh = {*Soil Microbiology ; *Phospholipids ; *Fatty Acids ; *Databases, Factual ; *Enzymes ; Soil/chemistry ; Ecosystem ; }, abstract = {Soil microbes drive ecosystem function and play a critical role in how ecosystems respond to global change. Research surrounding soil microbial communities has rapidly increased in recent decades, and substantial data relating to phospholipid fatty acids (PLFAs) and potential enzyme activity have been collected and analysed. However, studies have mostly been restricted to local and regional scales, and their accuracy and usefulness are limited by the extent of accessible data. Here we aim to improve data availability by collating a global database of soil PLFA and potential enzyme activity measurements from 12,258 georeferenced samples located across all continents, 5.1% of which have not previously been published. The database contains data relating to 113 PLFAs and 26 enzyme activities, and includes metadata such as sampling date, sample depth, and soil pH, total carbon, and total nitrogen. This database will help researchers in conducting both global- and local-scale studies to better understand soil microbial biomass and function.}, }
@article {pmid41005096, year = {2025}, author = {Wang, J and Hao, J and Jing, W and Gao, Y and Qiu, S}, title = {Effects of polyethylene terephthalate microplastics on performance of sequencing-batch membrane bioreactor for simulated municipal wastewater treatment.}, journal = {Journal of hazardous materials}, volume = {498}, number = {}, pages = {139956}, doi = {10.1016/j.jhazmat.2025.139956}, pmid = {41005096}, issn = {1873-3336}, abstract = {Municipal wastewater treatment plants (WWTPs) are recognized as key recipients of microplastics (MPs), with polyethylene terephthalate (PET) being among the most prevalent types in sewage. However, the systemic impact of PET MPs on integrated biological-membrane systems-especially their role in microbial ecology and membrane fouling-remains poorly understood. Therefore, the influence of PET MPs on the performance, microbial community and membrane fouling in a sequencing-batch membrane bioreactor (SMBR) was evaluated in this study. Based on the results, adding PET MPs decreased the MLSS from around 5000 mg/L to 4500 mg/L whereas the MLVSS/MLSS remain basically consistent. The SV30 and SVI increased rapidly to 76 % and 173.2 mL/g on the 3rd day (from 64 % and 128.3 mL/g on the 1st day) of adding PET MPs, however, they could be restored in the following days. For pollutants removal, the COD and NH4[+]-N removal were initially negatively affected but gradually recovered after several days of operation. The addition of PET MPs enhanced denitrification, resulting in a decrease in the effluent TN concentration from 15.1 ± 4.9 mg/L to 10.4 ± 4.4 mg/L. PET MPs changed microbial community structure and decreased the abundance of dominant bacteria and species diversity in activated sludge. Arenimonas and Sphingopyxis had strong relationships with PET MPs addition. PET MPs addition exacerbated membrane biofouling, and the microbial diversity on membrane at was basically consistent with activated sludge whereas the abundance changed significantly. This research provides a comprehensive understanding of how PET MPs affect the performance of integrated biological-membrane systems.}, }
@article {pmid41000638, year = {2025}, author = {Flores, C and Seekatz, AM}, title = {Reduced carbohydrate complexity alters gut microbial structure independent of total carbohydrate intake.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.09.20.677466}, pmid = {41000638}, issn = {2692-8205}, abstract = {Dietary habits have dramatically altered over recent decades, yet the impact of simplified carbohydrate intake on the gut microbiome's complexity and function remains poorly understood. This study investigates how the variety of dietary carbohydrates - not just their amount - shapes gut microbial diversity and resilience in C57BL/6 mice. Over eight weeks, mice consumed diets varying in carbohydrate complexity but matched for total carbohydrate content. Using 16S rRNA sequencing, we found that reduced carbohydrate diversity led to significant declines in microbial diversity and taxonomic redundancy among important bacterial groups, such as unclassified Lachnospiraceae, Ruminococcaceae, and Muribaculaceae, despite no immediate changes in host physiology. Concurrently, Akkermansia increased under low-complexity diets, suggesting a shift toward mucin degradation when complex polysaccharides are scarce. These changes indicate that loss of carbohydrate complexity narrows microbial niches, potentially disrupting metabolic interactions and functional stability of the gut ecosystem. Given the widespread adoption of processed, low-fiber diets in modern societies, these findings emphasize the importance of macronutrient complexity in maintaining gut microbial health. While short-term host effects were minimal, the microbial shifts observed could presage long-term consequences for gut resilience and disease susceptibility. This study underscores the need to consider carbohydrate diversity in dietary recommendations and microbial ecology research to safeguard gut health in the face of global dietary simplification.}, }
@article {pmid41000006, year = {2025}, author = {Hodgson, RJ and Cando-Dumancela, C and Davies, T and Dinsdale, EA and Doane, MP and Edwards, RA and Liddicoat, C and Peddle, SD and Ramesh, SA and Robinson, JM and Breed, MF}, title = {Contrasting Microbial Taxonomic and Functional Colonisation Patterns in Wild Populations of the Pan-Palaeotropical C4 Grass, Themeda triandra.}, journal = {Plant, cell &amp; environment}, volume = {}, number = {}, pages = {}, doi = {10.1111/pce.70205}, pmid = {41000006}, issn = {1365-3040}, support = {//This metagenomics sequencing for this project was supported by the Flinders University Accelerator for Microbiome Exploration. We also received funding from the Holsworth Wildlife Research Endowment with the Ecological Society of Australia, the Conservation Biology Grant 2022 with the Biological Society of South Australia and Nature Conservation Society of South Australia and the Lirabenda Wildlife Research Fund from the Field Naturalists Society of South Australia. We also received support from the Australian Research Council (grant numbers LP190100051 and LP190100484) and the New Zealand Ministry of Business Innovation and Employment (grant UOWX2101)./ ; }, abstract = {The interactions between native plants and soil microbiota are not well characterised, despite growing recognition of their importance for host plant fitness and ecological functioning. We used shotgun metagenomics to examine microbial taxonomic and functional colonisation patterns in wild populations of the pan-palaeotropical C4 grass, Themeda triandra, across a globally representative aridity gradient (aridity index 0.318-0.903). We investigated these patterns through the two-step selection process whereby microbes are recruited from bulk soils into rhizospheres (soil on the root surface), and root interiors (endospheres). We provide clear evidence of this process through decreasing microbial taxonomic diversity from bulk soil to T. triandra roots. Surprisingly, microbial functional potential showed the opposite trend: the diversity of potential functions (exponent of Shannon's diversity) increased from bulk soil to the rhizosphere and endosphere, but functional richness did not. Finally, we found that increasing aridity was associated with rhizospheres that were more compositionally similar, yet remained highly diverse in functional potential. Overall, aridity is strongly associated with the root-associated microbiome of T. triandra, selecting for microbiota that likely support plant resilience under dry conditions. Furthermore, microbial functional potential closely tracks taxonomic composition and aridity trends, highlighting how native plants can shape their microbial communities.}, }
@article {pmid40999741, year = {2025}, author = {Sun, J and Huang, H and Li, J and Xu, J and Jia, J and Li, W and Cheng, J and Zhu, D and Liu, M and Yuan, M and Xiao, S and Xue, C}, title = {Mitochondrial iron transporter ClMrs3/4 regulates iron homeostasis to modulate nitric oxide balance facilitating appressorial development in Curvularia lunata.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.70594}, pmid = {40999741}, issn = {1469-8137}, support = {2024YFD1400304//National Key Research &amp; Development Program of China/ ; 2023JH101300163/2022JH2/101300168//Liaoning Provincial Applied Basic Research Program/ ; 2024JH1/11700007-3//Liaoning Provincial Key Projects of Science and Technology/ ; JYTYB2024053//Basic Research Project of the Department of Education of Liaoning Province/ ; }, abstract = {Iron is indispensable for the vast majority of organisms, and iron homeostasis plays a pivotal role in both the physiology and pathogenesis of fungal pathogens. However, the underlying mechanisms by which iron homeostasis modulates fungal pathogenesis remain to be fully elucidated. We therefore focused on investigating the functions of mitochondrial iron transporter ClMrs3/4 in virulence. We conducted targeted gene deletions, expression analyses, biochemistry, and pathogenicity assays, demonstrating that ClMrs3/4 regulates appressorial development via maintenance of cellular iron balance in Curvularia lunata. ClMrs3/4 modulates virulence by influencing appressorial development in C. lunata, which is dependent on iron homeostasis. ClMrs3/4 controls nitric oxide (NO) balance via the nitrate (NO3 [-]) assimilation pathway by modulating cytoplasmic iron levels, a process crucial for turgor pressure accumulation within the appressoria independent of mitochondrial and cytoplasmic Fe-S cluster biosynthesis. Our findings underscore the conserved role of Mrs3/4 in iron homeostasis among pathogenic fungi and propose a novel mechanism by which iron homeostasis regulates virulence, particularly through the NO3 [-] assimilation pathway mediated by cytoplasmic iron levels to regulate appressorial development.}, }
@article {pmid40998779, year = {2025}, author = {Li, Y and Sun, M and Raaijmakers, JM and Mommer, L and Zhang, F and Song, C and Medema, MH}, title = {Predicting rhizosphere-competence-related catabolic gene clusters in plant-associated bacteria with rhizoSMASH.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {8400}, pmid = {40998779}, issn = {2041-1723}, support = {24.004.014//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; }, mesh = {*Rhizosphere ; *Bacteria/genetics/metabolism/classification ; *Plant Roots/microbiology ; Soil Microbiology ; Microbiota/genetics ; *Multigene Family ; *Plants/microbiology ; Machine Learning ; Algorithms ; }, abstract = {Plants release a substantial fraction of their photosynthesized carbon into the rhizosphere as root exudates that drive microbiome assembly. Deciphering how plants modulate the composition and activities of rhizosphere microbiota through root exudates is challenging, as no dedicated computational methods exist to systematically identify microbial root exudate catabolic pathways. Here, we integrate published information on catabolic genes in bacteria that contribute to their rhizosphere competence and develop the rhizoSMASH algorithm for genome-synteny-based annotation of rhizosphere-competence-related catabolic gene clusters (rCGCs) in bacteria with 58 curated detection rules. Our analysis reveals heterogeneity in rCGC prevalence both across and within plant-associated bacterial taxa, indicating extensive niche specialization. Furthermore, we demonstrate the predictive value of the presence or absence of rCGCs for rhizosphere competence in machine learning with two case studies. rhizoSMASH provides an extensible framework for studying rhizosphere bacterial catabolism, facilitating microbiome-assisted breeding approaches for sustainable agriculture.}, }
@article {pmid40997605, year = {2025}, author = {Wu, G and Ding, Z and Wang, J and Xie, J}, title = {Frontier research on the risk of spoilage microorganisms in refrigerated marine fish: From regional to global perspectives.}, journal = {International journal of food microbiology}, volume = {444}, number = {}, pages = {111465}, doi = {10.1016/j.ijfoodmicro.2025.111465}, pmid = {40997605}, issn = {1879-3460}, abstract = {Microbial spoilage is creating safety risks and significant wastage of refrigerated marine fish. Spoilage microorganisms possess distinct physiological adaptations that enable them to contribute to the spoilage of refrigerated marine fish, thereby complicating the accuracy of microbial risk predictions and the efficacy of control strategies. This review integrates research findings from diverse geographical regions to elucidate mechanisms of microbial spoilage and underscores the ongoing challenges in cross-regional collaborative studies. Omics serve as guiding tools for elucidating the molecular mechanisms by which metabolite mediate spoilage microorganisms-induced deterioration of flavor, texture, and safety. Quantitative Microbial Risk Assessment (QMRA) provides a critical framework for risk prediction, with its future development being intrinsically linked to the integration of omics data, rapid fluorescence sensing, and artificial intelligence (AI) for enhanced prediction and modeling. In conclusion, this review underscores the critical role of spoilage microorganisms in the deterioration of refrigerated marine fish, highlights the complex interplay between microbial ecology, cold adaptation, and spoilage potential, and emphasizes the necessity for collaborative global efforts. Advancing research on native microbial communities, molecular spoilage mechanisms, and AI-powered QMRA frameworks is paramount for reducing food waste, enhancing food safety risk assessment, and the sustainable development of preservation technology.}, }
@article {pmid40996662, year = {2025}, author = {Rév, A and Parádi, I and Füzy, A and Juhász, P and Kocsis, K and Cseresnyés, I and Takács, T}, title = {Improvement of soil fertility and enzymatic activity by wastewater sludge compost and arbuscular mycorrhizal fungi in giant reed's rhizosphere.}, journal = {Biologia futura}, volume = {}, number = {}, pages = {}, pmid = {40996662}, issn = {2676-8607}, support = {SA-26/2021//E&#xf6;tv&#xf6;s Lor&#xe1;nd Research Network/ ; }, abstract = {The effect of low-dose, commercially available wastewater sludge compost (WSC; 15 t ha[-1]) treatment was examined with or without arbuscular mycorrhizal fungal (AMF) inoculation on the nutritional status, heavy metal (HM) concentration and the rhizosphere activity of giant reed (Arundo donax L. var. BL clone (Blossom)) plants. Funneliformis mosseae (BEG12; AMF1), F. geosporum (BEG11; AMF2) or their combination (AMFmix) were applied as AMF treatments in a short-term pot experiment. The physiological and growth parameters of the host plants, the AMF root colonization and the microbiological enzyme activity of the mycorrhizosphere were examined. We assumed that the combined treatment (WSC + AMF) enhances the fertility of low-fertility acidic sandy soil. Neither the WSC treatment nor the AMF inoculations changed the extent of root colonization. Based on the results of root electrical capacitance and the phosphorous uptake, plant nutritional status was improved by WSC addition, without any negative impacts among the measured parameters. AMF treatments increased the enzyme activity in the soil and decreased the concentrations of the potentially toxic HMs (Cu, Mn, Pb, Zn) in roots, but that mitigation of Cu and Zn was compensated in shoots. According to the results of MicroResp™ measurements, the catabolic activity profile of the soil microbial community was changed in case of the AMF2 treatment. The efficient regulatory mechanism of giant reed might be able to adjust optimal/maximal colonization rate, and to select the preferential AMF partners, this supposed mechanism might be responsible for its invasiveness and tolerance to a wide range of environmental conditions.}, }
@article {pmid40996559, year = {2025}, author = {Han, SI and Kim, JO and Lee, YR and Ekpeghere, KI and Koh, SC and Whang, KS}, title = {Correction: Denitratimonas tolerans gen. nov., sp. nov., a denitrifying bacterium isolated from a bioreactor for tannery wastewater treatment.}, journal = {Antonie van Leeuwenhoek}, volume = {118}, number = {10}, pages = {157}, doi = {10.1007/s10482-025-02169-7}, pmid = {40996559}, issn = {1572-9699}, }
@article {pmid40995846, year = {2025}, author = {Stephenson, T and Crowder, DW and Osburn, E and Strickland, M and Jones, M and Bartel, S and Kittipalawattanapol, K and Cunningham, CX and Hudiburg, T and Storfer, A and Piaskowski, J and Lynch, L}, title = {Apex Scavenger Declines Have Cascading Effects on Soil Biogeochemistry and Ecosystem Processes.}, journal = {Global change biology}, volume = {31}, number = {9}, pages = {e70520}, doi = {10.1111/gcb.70520}, pmid = {40995846}, issn = {1365-2486}, support = {DEB-2054716//National Science Foundation/ ; }, mesh = {Animals ; *Soil/chemistry ; *Soil Microbiology ; *Food Chain ; *Marsupialia/physiology ; *Ecosystem ; Seasons ; Microbiota ; }, abstract = {Global apex scavenger declines strongly alter food web dynamics, but studies rarely test whether trophic downgrading impacts ecosystem functions. Here, we leverage a unique, disease-induced gradient in Tasmanian devil (Sarcophilus harrisii) population densities to assess feedbacks between carcass persistence, subordinate scavenger guilds, and biogeochemical cycling. We further explored interkingdom and seasonal interactions by manipulating carcass access and replicating experiments in warmer, drier summer versus cooler, wetter winter periods. We show Tasmanian devil declines significantly extend carcass persistence and increase the flux of carcass-derived nutrients belowground (e.g., by 18-134-fold for ammonium). Greater nutrient availability reduces soil microbiome diversity by up to 26%, increasing the relative abundance of putative zoonotic pathogens. Nutrient subsidies also shift microbial communities toward faster-growing taxa that invest less energy in resource acquisition, with implications for soil carbon sequestration. Rates of carcass decomposition were reduced in the winter, dampening soil biogeochemical responses and interkingdom competition. Notably, while less efficient scavenger guilds clearly facilitate carcass consumption, they were not able to fill the functional role of apex scavengers. Our study illustrates how trophic downgrading effects can ripple across all levels of ecological organization.}, }
@article {pmid40993772, year = {2025}, author = {Dubey, JP and Alić, A and Hodžić, A and Lopez-Flores, J and Baneth, G}, title = {Hepatozoon infections in domestic and wild Carnivora: etiology, prevalence, clinical disease, diagnosis and treatment, and redescription of Hepatozoon silvestris, H. martis, and H. ursi.}, journal = {Parasites &amp; vectors}, volume = {18}, number = {1}, pages = {391}, pmid = {40993772}, issn = {1756-3305}, mesh = {Animals ; Prevalence ; *Coccidiosis/veterinary/diagnosis/epidemiology/parasitology/drug therapy/therapy ; *Eucoccidiida/classification/isolation &amp; purification ; *Carnivora/parasitology ; Animals, Wild/parasitology ; Animals, Domestic/parasitology ; Life Cycle Stages ; }, abstract = {Hepatozoon spp. are common pathogens in dogs and other Carnivora in many parts of the world, especially in the tropics. There is considerable taxonomic debate concerning the Hepatozoon species infecting Carnivora. Morphological descriptions of several Hepatozoon species are inadequate and their validity is questionable. Additionally, different terminology has been used for the description of life cycle stages. Here, we provide a comprehensive review of the Hepatozoon species in the Carnivora, using a uniform terminology. Worldwide prevalence of clinical and subclinical Hepatozoon infections for the past century is tabulated and critically evaluated. We also review the epizootiology, clinical signs, diagnosis, and treatment of hepatozoonosis in the Carnivora. The morphology and life cycles of seven valid species with known merogonic stages (Hepatozoon americanum, H. canis, H. felis, H. martis, H. rufi, H. silvestris, H. ursi) are summarized in a table using standard terminology. Additional information on H. apri, H. martis, and H. silvestris life cycle stages is provided. Information lacking for H. procyonis, H. luiperdjie and H. ingwe is discussed. The relevance of H. mustelis, H. banethi and H. ewingi is discussed and they are considered as invalid species. For the benefit of future researchers, worldwide reports of prevalence, clinical disease, diagnosis, and treatment of Hepatozoon infections in domestic and wild Carnivora for the past century are summarized in tables alphabetically and chronologically for each country. Co-infections of H. canis, H. americanum, H. felis, and H. silvestris are summarized and discussed. The role of Hepatozoon infections causing clinical illness in wild Carnivora is discussed, particularly for red foxes, coyotes, and mustelids.}, }
@article {pmid40993491, year = {2025}, author = {Sun, S and Qiao, Z and Tikhonenkov, DV and Gong, Y and Li, H and Li, R and Sun, K and Huo, D}, title = {Temporal Dynamics and Adaptive Mechanisms of Microbial Communities: Divergent Responses and Network Interactions.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {94}, pmid = {40993491}, issn = {1432-184X}, support = {24-44-00093//Russian Science Foundation/ ; 32361133561//National Natural Science Foundation of China/ ; 2021M703430//China Postdoctoral Science Foundation/ ; }, mesh = {*Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; Biodiversity ; Ecosystem ; *Rivers/microbiology ; *Eukaryota/genetics/classification/physiology ; Water Microbiology ; High-Throughput Nucleotide Sequencing ; }, abstract = {Microbial communities are vital to aquatic ecosystems, driving biogeochemical cycles, nutrient recycling, and overall ecosystem functioning. However, their instant feedback, particularly in response to environmental fluctuations, remain insufficiently understood. In this study, we investigated the interaction of prokaryotic and eukaryotic microbial communities in riverine ecosystems under temporal dynamics using high-throughput sequencing and co-occurrence network analysis. We observed distinct patterns, with eukaryotic communities showing a consistent increase in alpha diversity, while prokaryotic communities exhibited more variable and directional shifts over time. Two key phases were identified: a dynamic phase characterized by rapid changes in both alpha and beta diversity and a stabilization phase where community composition became more stable, with increased evenness. Co-occurrence network analysis revealed a transition from a modular structure in the dynamic phase to a more centralized and highly connected network in the stabilization phase. While modularity can enhance stability by localizing perturbations within distinct subnetworks, increased centralization and connectivity may weaken this stabilizing effect, potentially making the network less resilient to environmental fluctuations. Our findings provide new insights into the adaptive mechanisms that sustain microbial community stability and resilience in dynamic aquatic ecosystems, emphasizing the importance of diversity and network structure in maintaining ecological stability.}, }
@article {pmid40991823, year = {2025}, author = {Lennon, JT and Bittleston, LS and Chen, Q and Cooper, VS and Fernández, J and Gilbert, JA and Häggblom, MM and Harper, LV and Jansson, JK and Jiao, N and Kuurstra, EM and Peixoto, RS and Rappuoli, R and Schembri, MA and Ventosa, A and Vullo, DL and Zhang, C and Nguyen, NK}, title = {Microbes without borders: uniting societies for climate action.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, doi = {10.1093/ismejo/wraf199}, pmid = {40991823}, issn = {1751-7370}, }
@article {pmid40991432, year = {2025}, author = {van Gestel, J and Koo, BM and Stürmer, VS and Garriga-Canut, M and Wagner, J and Zanon, A and Gross, CA}, title = {Bacillus subtilis in defense mode: Switch-like adaptations to protistan predation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {39}, pages = {e2518989122}, doi = {10.1073/pnas.2518989122}, pmid = {40991432}, issn = {1091-6490}, support = {101116560//EC | ERC | HORIZON EUROPE European Research Council (ERC)/ ; P400PB_186789//Swiss National Science Foundation (Postdoc.Mobility)/ ; R35GM118061//HHS | National Institutes of Health (NIH)/ ; }, mesh = {*Bacillus subtilis/genetics/physiology/growth &amp; development ; *Dictyostelium/physiology ; *Adaptation, Physiological ; Bacterial Proteins/metabolism/genetics ; Phenotype ; }, abstract = {Single-cell eukaryotic predators in the soil are a primary cause of bacterial cell death. Yet, most functional genomic studies on soil bacteria have been performed without predation, thereby selecting for phenotypes impacting growth rather than survival and biasing our view on the ecological factors driving genomic evolution. Here, we study how predation by the ubiquitous amoebal predator Dictyostelium discoideum affects Bacillus subtilis' growth and survival using both a genome-scale mutant screen and de novo evolution of resistance. We show that predation-related genes (many not previously identified) promote survival by enabling filament or aggregate formation, thereby outsizing D. discoideum and slowing or preventing ingestion. Importantly, we find that predation resistance is costly, causing a trade-off between growth and survival. B. subtilis navigates this trade-off through switch-like adaptations, where cells switch back-and-forth between a slow-growing resistant state and a fast-growing susceptible state. These behaviors are controlled through both genotypic and phenotypic switches, with a central role for the Spo0A phosphorylation cascade, whose ancestral function may have been to evade or slow predation. Taken together, we uncover how the antagonist selection pressure imposed by predation is an important ecological driver of phenotypic heterogeneity in B. subtilis.}, }
@article {pmid40990948, year = {2025}, author = {Basu, A and Mondal, S and Roy, A and Tewari, S and Chattopadhyay, S and Ghosh, A and Sil, AK}, title = {Paraclostridium sp. AKS46 vesicles facilitate extracellular electron transport.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxaf239}, pmid = {40990948}, issn = {1365-2672}, abstract = {AIMS: Paraclostridium sp. AKS46 was shown to have high exoelectrogenic activity. The current study investigated whether membrane vesicles (MVs) contribute to this electrogenic activity of this organism.<br><br>METHODS AND RESULTS: To examine the contribution of MVs to electrogenic activity, formation of MVs was first investigated by microscopic analyses of AKS46 cells at different time points of growth. The results showed increasing MV formation with time, especially in electrode-attached cells. To test electrogenic activity, the redox property and the electrochemical activity of the vesicles were examined. To this end, purified AKS46 vesicles demonstrated robust redox activities, and cyclic voltammetry and electrochemical impedance spectroscopy revealed high electrochemical properties of purified vesicles. Furthermore, proteomic analysis of the vesicles identified the presence of redox-active proteins, particularly flavoproteins, which might significantly contribute to electron carrier properties. AKS46 MVs also harbour enzymes involved in CO2 and nitrogen fixation, suggesting their roles in nutrient cycling and maintaining microbial ecology.<br><br>CONCLUSION: The exoelectrogenic gram-positive bacteria Paraclostridium sp. AKS46 produces extracellular vesicles packed with electron-rich molecules and thus, these vesicles act as electron transporters. The work highlights a vesicle-mediated mechanism for energy harvesting from waste degradation in microbial fuel cells.}, }
@article {pmid40990516, year = {2025}, author = {Wang, Y and Xu, J and Liu, Y and Liu, L and Xiao, S and Wang, X and Zhang, J and Huang, S and Zheng, Q}, title = {Ocean currents and environmental gradients shape prokaryotic community structure and function in the South China Sea.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0102025}, doi = {10.1128/spectrum.01020-25}, pmid = {40990516}, issn = {2165-0497}, abstract = {UNLABELLED: The South China Sea (SCS) is characterized by complex hydrodynamic conditions that influence the structure and function of prokaryotic microbial communities. This study conducted a comprehensive analysis of prokaryotic diversity, community assembly, and functional potential across various water masses within the SCS. Using 16S rRNA gene sequencing and co-occurrence network analyses, we found that geographic distance and environmental gradients, particularly temperature and nutrient levels, significantly impacted community composition. Our findings indicate that ecological drift is the primary mechanism governing community assembly, with spatial turnover primarily driven by the dispersal of microorganisms facilitated by ocean currents. Distinct modules in co-occurrence networks were associated with specific environmental factors, reflecting potential environmental selection processes along the SCS current. Keystone species and biomarkers identified through network analysis and random forest modeling exhibited varying associations with environmental variables, highlighting their adaptability to changing conditions. This work underscores the importance of ocean currents and environmental factors in shaping prokaryotic community dynamics and provides insights into microbial biogeography and ecosystem function in the SCS.<br><br>IMPORTANCE: Microorganisms, especially prokaryotes, are fundamental in sustaining marine ecosystems through nutrient cycling and organic matter decomposition. However, understanding what shapes their diversity and distribution remains challenging. Our study highlights the significant role ocean currents and environmental conditions play in influencing prokaryotic communities in the South China Sea-a critical marine environment due to its dynamic currents and ecological complexity. We found that currents facilitate microbial dispersal, shaping community composition over vast areas, while temperature gradients act as key selective pressures, determining which species thrive. Additionally, we reveal that both predictable environmental selection and random ecological drift significantly contribute to community structuring. By identifying keystone microbes and biomarkers sensitive to environmental change, our work offers essential insights into marine microbial ecology. These findings are crucial for predicting how microbial communities, and thus ocean health and productivity, respond to ongoing environmental changes.}, }
@article {pmid40989908, year = {2025}, author = {Lopez-Alforja, X and Sà, EL and Quiroga, MV and Pernice, MC and Cardelús, C and Balagué, V and Gasol, JM and Coutinho, FH and Massana, R and Vaqué, D}, title = {Long-term decline of marine viruses associated with warming and oligotrophication at a NW Mediterranean coastal site.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf150}, pmid = {40989908}, issn = {2730-6151}, abstract = {Viruses play key roles in controlling microbial abundance and community composition, nutrient cycling, and productivity in marine systems. Rising ocean temperatures, alongside increasing oligotrophy, are expected to alter the availability of inorganic nutrients and oxygen-key environmental factors that shape microbial community structure and virus-host interactions. While many studies have investigated viral abundances and community structure across spatial gradients, less is known about their long-term temporal variations, which is particularly relevant in the current context of global change. To address this gap, we analyzed two decades of surface water data from the Blanes Bay Microbial Observatory, located at the North-Western Mediterranean, to describe how biotic and abiotic variables influence temporal dynamics of viral abundances and community composition. Statistical tools for time series, including GAMMs, anomaly analysis, and neural networks, allowed us to demonstrate that viral abundance follows strong seasonality and a clear decrease starting midway (ca. 2011) through the sampled period (2005-2022). Fingerprint analysis evidenced that viral community composition was significantly influenced by seasonality and some environmental and biotic factors, with strong differences in viral communities between summer and winter months. Our analyses revealed that over the last 18 years, the abundance of most microbial groups, including viruses and their potential hosts, has declined, coinciding with an increase in seawater temperature and transparency, as well as a notable decrease in nutrient concentrations and phytoplankton biomass. We identified the ongoing shift toward more oligotrophic conditions as a potential driver of the observed decline in viral abundance, particularly in the last decade.}, }
@article {pmid40989192, year = {2025}, author = {Alfahl, Z and O'Connor, L and Morris, D and Smith, TJ and O'Dwyer, J and Hynds, PD and Cormican, M and Burke, LP}, title = {A novel enrichment-free, low-volume filtration and rapid lysis (ELR) method in combination with real-time PCR for detection of Shiga toxin-producing Escherichia coli (STEC) in water.}, journal = {Access microbiology}, volume = {7}, number = {7}, pages = {}, pmid = {40989192}, issn = {2516-8290}, abstract = {Consequences of Shiga toxin-producing Escherichia coli (STEC) infection can range in severity from asymptomatic infection to haemolytic uraemic syndrome, renal failure and death. Groundwater-derived drinking water is an important route for STEC transmission. Detection of STEC in water is crucial for timely response and public health interventions; however, currently used culture-based methods are time-consuming and laborious. Therefore, there is a need for rapid methods that maintain high sensitivity and specificity [1]. We describe a novel, sensitive, enrichment-free water filtration method using a convenient sample volume (100 ml) to detect DNA markers of STEC serogroups and virulence factors within 6 h. Quantitative real-time PCR (qPCR) was used to detect and quantify the most common STEC infection-associated serogroups globally, O157 and O26. Real-time PCR was used to detect genetic determinants of STEC virulence (stx1, stx2 and eae genes) and specific marker genes for the clinically relevant serogroups O111, O103, O145 and O104. Results showed that the novel method can detect as low as 5 c.f.u. ml[-1] of STEC in water. The limit of detection for O157 and O26 qPCR assays was two and six copies, respectively. Groundwater and surface water samples (n=28) were collected and processed using the novel method. STEC O157 and O26 serogroups were detected in 23 out of 28 (82.1%) samples (mean 5.2×10[4] copies/reaction) and 19 out of 28 (67.9%) samples (mean 7.83×10[4] copies/reaction), respectively. Shiga toxin genes stx1 or stx2 were detected in 15 out of 28 (53.6%) and 9 out of 28 (32.1%) samples, respectively. The virulence factor intimin gene eae was detected in 24 out of 28 (85.7%) samples. STEC serogroups O111, O103, O145 and O104 were detected in 15 out of 28 (53.6%), 10 out of 28 (35.7%), 11 out of 28 (39.3%) and 15 out of 28 (53.6%) samples, respectively. This novel method reproducibly detects low copies of STEC in low-volume fresh water and has the potential to be used for the detection and quantification of waterborne bacterial pathogens.}, }
@article {pmid40987850, year = {2025}, author = {Laso-Pérez, R}, title = {Deep-mining the archaeal proteome for antibiotics.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {40987850}, issn = {2058-5276}, }
@article {pmid40987416, year = {2025}, author = {Liaqat, F and Khazi, MI and Ismail, W}, title = {Microbial transport systems of organic sulfur compounds: Diversity and implications for biocatalysis, healthcare, and environmental biotechnology.}, journal = {Biotechnology advances}, volume = {}, number = {}, pages = {108718}, doi = {10.1016/j.biotechadv.2025.108718}, pmid = {40987416}, issn = {1873-1899}, abstract = {The global sulfur cycle plays a vital role in human health, global warming and biogeochemistry. Organic sulfur compounds constitute a substantial sulfur reservoir and serve as an energy and/or carbon source for prokaryotes. In addition, microbial interactions with organic sulfur compounds are pivotal for several biotechnological applications in petroleum biorefining, industrial biocatalysis, bioremediation, healthcare, and plant growth promotion. Microbial degradation of organic sulfur compounds is hindered by slow degradation rates, substrate specificity, toxicity of by-products, and challenges in scalability and efficiency. While degradation pathways of some organic sulfur compounds have been elucidated, transport systems involved in their uptake and efflux remain less explored. Regulating the uptake and efflux of organic sulfur compounds in microorganisms can help overcome several of the limitations associated with their transformation. Membrane transporters are not only crucial for uptake and efflux of organic sulfur compounds but also play a key role in stress tolerance by facilitating the excretion of toxic metabolites. Understanding the intricacies of these transporters provides valuable insights into microbial ecology and the development of strategies for harnessing microbial sulfur metabolism for important biotechnological applications. This review systematically presents the diversity, mechanisms, and potential evolution pathways of microbial membrane transporters involved in organic sulfur compounds acquisition. Furthermore, it highlights and discusses advances in the characterization of transporter systems and current limitations in using transporter systems for fuel biodesulfurization and organic sulfur compound degradation. Eventually, we explore the implications of organic sulfur compounds transporters in biotechnology and identify future research directions toward leveraging the biotechnological potential of microbial sulfur metabolism, fueled by advanced techniques of systems microbiology, metabolic engineering, as well as artificial intelligence.}, }
@article {pmid40986398, year = {2025}, author = {Lennon, JT and Bittleston, LS and Chen, Q and Cooper, VS and Fernández, J and Gilbert, JA and Häggblom, MM and Harper, LV and Jansson, JK and Jiao, N and Kuurstra, EM and Peixoto, RS and Rappuoli, R and Schembri, MA and Ventosa, A and Vullo, DL and Zhang, C and Nguyen, NK}, title = {Microbes without borders: uniting societies for climate action.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {10}, pages = {}, doi = {10.1093/femsec/fiaf084}, pmid = {40986398}, issn = {1574-6941}, }
@article {pmid40985999, year = {2025}, author = {Lennon, JT and Bittleston, LS and Chen, Q and Cooper, VS and Fernández, J and Gilbert, JA and Häggblom, MM and Harper, LV and Jansson, JK and Jiao, N and Kuurstra, EM and Peixoto, RS and Rappuoli, R and Schembri, MA and Ventosa, A and Vullo, DL and Zhang, C and Nguyen, NK}, title = {Microbes without borders: uniting societies for climate action.}, journal = {mBio}, volume = {}, number = {}, pages = {e0213625}, doi = {10.1128/mbio.02136-25}, pmid = {40985999}, issn = {2150-7511}, abstract = {The climate crisis is one of the greatest challenges of our time, yet the role of microorganisms remains underrecognized in climate science and policy. Microbes are highly sensitive to environmental change and regulate essential biogeochemical processes, while also offering solutions for reducing emissions, restoring ecosystems, and enhancing resilience. Microbiology societies from five continents recently convened in Washington, DC, for the inaugural Global Strategy Meeting on Microbes and Climate Change. The gathering launched a global alliance to position microbial science as a pillar of climate action and identified four priorities: building a coalition, embedding microbes in climate frameworks, transforming communication, and advancing real-world demonstration projects. This initiative marks the beginning of coordinated global action to harness microbial life for climate solutions.}, }
@article {pmid40985636, year = {2025}, author = {Grosso Giordano, F and Mariën, Q and De Belie, N and Rodriguez-Navarro, C and Boon, N}, title = {Characterization of isolates used in bacterial-based strategies for accelerated carbonation of lime mortars.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0068325}, doi = {10.1128/aem.00683-25}, pmid = {40985636}, issn = {1098-5336}, abstract = {Portland cement largely replaced hydraulic lime over the past century because of its rapid hardening. Achieving earlier hardening in lime through faster carbonation is thus essential to help overcome one of lime's limiting qualities. Here, we isolated two alkaliphilic bacteria, Shouchella clausii and Shouchella patagoniensis, from a lime mortar wall. S. clausii was then further grown in high pH (>11) by adaptive laboratory evolution to acclimate a third isolate. Bacterial suspensions of all three isolates were followed for 14 days in serum bottles at pH 11, and gas composition of the headspace, intact/damaged cell populations, and pH were measured. In parallel, lime mortar samples were incubated in a closed environment with bacterial suspension of the isolates and analyzed with thermogravimetric analysis after 7 and 14 days to quantify carbonation. S. patagoniensis produced more CO2, close to the estimated maximum CO2 uptake rate of lime, and carbonated the lime mortars to a larger extent than the other isolates. Finally, the bacterial suspensions were directly mixed with lime. A linear and homogeneous carbonation of the paste samples was measured compared to water-based pastes, and the development of Liesegang patterns was observed upon phenolphthalein spreading. All this indicated that the organic addition altered the carbonation dynamics of the material, although bacteria did not accelerate carbonation relative to media alone and inhibited it relative to water-based paste. Still, a relationship between bacterial activity, CO2 emission, and carbonation rate was established, but practical aspects of bacterial delivery into lime must be addressed.IMPORTANCEPortland cement is the dominant binder used in most construction today, but until last century, lime was the ubiquitous construction material. The increase in use of cement has sprung from its higher strength and faster hardening; yet, lime still remains a relevant material, particularly in masonry structures and the built heritage. As such, novel lime materials are necessary to tackle some of the current limitations of lime, such as earlier hardening, which would not only make lime easier to work with but would also limit failure due to environmental conditions. As existing strategies to speed up lime hardening have had limited uptake due to their reliance on expensive and often toxic chemicals, the need for novel solutions is in place. We show that bacterial-based strategies could be a viable option to go beyond the limitations of current strategies, but limitations are in place.}, }
@article {pmid40985445, year = {2025}, author = {Shen, K and Tang, Y and Shi, J and Hu, Z and He, M and Li, J and Wang, Y and Shao, M and Liu, H}, title = {Relationship Between Aquatic Fungal Diversity in Surface Water and Environmental Factors in Yunnan Dashanbao Black-Necked Crane National Nature Reserve, China.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {11}, number = {7}, pages = {}, doi = {10.3390/jof11070526}, pmid = {40985445}, issn = {2309-608X}, support = {2024//Yunnan Provincial Department of Education Scientific and Technological Innovation Team for Development and Utilization of Gastrodia Resources/ ; 202110BA070001-059//Special Basic Cooperative Research Programs of Yunnan Provincial Undergraduate Universities' Association/ ; 2023-3//Zhaotong "Xingzhao Talent Support Program" Team Project/ ; }, abstract = {Aquatic fungi serve as core ecological engines in freshwater ecosystems, driving organic matter decomposition and energy flow to sustain environmental balance. Wetlands, with their distinct hydrological dynamics and nutrient-rich matrices, serve as critical habitats for these microorganisms. As an internationally designated Ramsar Site, Yunnan Dashanbao Black-Necked Crane National Nature Reserve in China not only sustains endangered black-necked cranes but also harbors a cryptic reservoir of aquatic fungi within its peat marshes and alpine lakes. This study employed high-throughput sequencing to characterize fungal diversity and community structure across 12 understudied wetland sites in the reserve, while analyzing key environmental parameters (dissolved oxygen, pH, total nitrogen, and total phosphorus). A total of 5829 fungal operational taxonomic units (OTUs) spanning 649 genera and 15 phyla were identified, with Tausonia (4.17%) and Cladosporium (1.89%) as dominant genera. Environmental correlations revealed 19 genera significantly linked to abiotic factors. FUNGuild functional profiling highlighted saprotrophs (organic decomposers) and pathogens as predominant trophic guilds. Saprotrophs exhibited strong associations with pH, total nitrogen, and phosphorus, whereas pathogens correlated primarily with pH. These findings unveil the hidden diversity and ecological roles of aquatic fungi in alpine wetlands, emphasizing their sensitivity to environmental gradients. By establishing baseline data on fungal community dynamics, this work advances the understanding of wetland microbial ecology and informs conservation strategies for Ramsar sites.}, }
@article {pmid40983756, year = {2025}, author = {Dong, S and Wang, S and Li, L and Yu, J and Zhang, Y and Xue, JY and Chen, H and Ma, J and Zeng, Y and Cai, Y and Huang, W and Zhou, X and Wu, J and Li, J and Yao, Y and Hu, R and Zhao, T and Villarreal A, JC and Dirick, L and Liu, L and Ignatov, M and Jin, M and Ruan, J and He, Y and Wang, H and Xu, B and Rozzi, R and Wegrzyn, J and Stevenson, DW and Renzaglia, KS and Chen, H and Zhang, L and Zhang, S and Mackenzie, R and Moreno, JE and Melkonian, M and Wei, T and Gu, Y and Xu, X and Rensing, SA and Huang, J and Long, M and Goffinet, B and Bowman, JL and Van de Peer, Y and Liu, H and Liu, Y}, title = {Bryophytes hold a larger gene family space than vascular plants.}, journal = {Nature genetics}, volume = {}, number = {}, pages = {}, pmid = {40983756}, issn = {1546-1718}, abstract = {After 500 million years of evolution, extant land plants compose the following two sister groups: the bryophytes and the vascular plants. Despite their small size and simple structure, bryophytes thrive in a wide variety of habitats, including extreme conditions. However, the genetic basis for their ecological adaptability and long-term survival is not well understood. A comprehensive super-pangenome analysis, incorporating 123 newly sequenced bryophyte genomes, reveals that bryophytes possess a substantially greater diversity of gene families than vascular plants. This includes a higher number of unique and lineage-specific gene families, originating from extensive new gene formation and continuous horizontal transfer of microbial genes over their long evolutionary history. The evolution of bryophytes' rich and diverse genetic toolkit, which includes new physiological innovations like unique immune receptors, likely facilitated their spread across different biomes. These newly sequenced bryophyte genomes offer a valuable resource for exploring alternative evolutionary strategies for terrestrial success.}, }
@article {pmid40981669, year = {2025}, author = {Riisgaard-Jensen, M and Valença, RM and Peces, M and Nielsen, PH}, title = {Sewer microbiomes shape microbial community composition and dynamics of wastewater treatment plants.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf213}, pmid = {40981669}, issn = {1751-7370}, abstract = {The link between the sewer microbiome and microbial communities in activated sludge wastewater treatment plants is currently poorly understood despite the systems being directly interconnected. Microbial immigration from wastewater has been identified as a key factor determining activated sludge community assembly. Here, we present the first comprehensive study of the sewer microbiome and hypothesize that it harbors a process-critical activated sludge microbes, thus critical for activated sludge community assembly and performance. We integrated species-level microbial analyses of biofilm, sediment, and sewer wastewater in domestic gravity and pressure sewers in Aalborg, Denmark, with samples from influent wastewater and activated sludge from two downstream wastewater treatment plants. By tracing the sources of incoming bacteria and determining their growth fate in the activated sludge, we confirmed the hypothesis that most activated sludge process-critical bacteria were part of the sewer microbiome. Within the sewer system, a gradient was observed, from dominance of gut-bacteria in the wastewater upstream to prevalence of biofilm and sediment bacteria downstream at the wastewater treatment plants inlet, with the relative ratio strongly affected by rain events. A holistic understanding of the sewer system and activated sludge is essential, as the sewers hold massive amounts of active biomass serving as a major microbial source for community composition and dynamics in wastewater treatment plants. Sewer systems should be recognized as a crucial environmental filtration step, and the sewer microbiome as an important source community for activated sludge, helping to explain the observed regional and global differences in activated sludge community structure.}, }
@article {pmid40981467, year = {2025}, author = {Qiao, Y and Wang, L and Wang, S and Li, S and Wang, F and Wang, B and Lin, S and Liu, Y}, title = {Bacterial generalists and fungal specialists play important roles in maintaining community stability and regulating microbial diversity of the algae-associated microbiome throughout the growth cycle of Alexandrium pacificum.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0135925}, doi = {10.1128/aem.01359-25}, pmid = {40981467}, issn = {1098-5336}, abstract = {The algae-associated microbiome represents a consortium that has been chronically domesticated by specific algae, maintaining a close relationship with the host population. Although the microbes associated with dinoflagellates have garnered significant attention in recent years, the interactions and contributions of microbial generalists and specialists through the growth cycle of a bloom-forming dinoflagellate remain largely unexplored. Herein, the ecological and evolutionary characteristics of free-living generalists and specialists within bacterial and fungal communities were investigated during the growth process of Alexandrium pacificum cultured in the laboratory for years without antibiotic treatment. From an ecological perspective, bacterial generalists and fungal specialists dominated the community, indicating different microbial niche patterns between the bacterial and fungal consortia. Furthermore, microbial specialists were more susceptible to disturbance from algal proliferation, as evidenced by greater community dissimilarity and determinacy-dominated assembly processes. Compared with their counterparts, the molecular networks of bacterial generalists and fungal specialists were more complex and robust, suggesting that they significantly contributed to resistance to environmental stress and functional maintenance. Evolutionarily speaking, bacterial generalists and fungal specialists showed much higher diversification potential, and others featured higher extinction rates. Despite these differences, a continuous transition from the former two to their counterparts was observed, alleviating the "Matthew effect" in the biological world for ecological trade-offs. Collectively, these findings emphasize that bacterial generalists and fungal specialists play important roles in maintaining community stability and regulating microbial diversity during the growth process, which expands the current understanding of the maintenance mechanisms of the diversity and community of phytoplankton-associated microbes in the face of disturbance from bloom-forming dinoflagellates.IMPORTANCELike the microbes residing in the rhizosphere and human gut, bacteria that coexist chronically with microalgae exemplify a relationship, forming potentially intimate partnerships with the host. However, studies on the ecological significance of algae-associated microbiomes with different niches under the interference of bloom-forming species are still lacking. This work investigated the ecological interactions and contributions of generalists and specialists within algae-associated bacterial and fungal communities across the growth cycle of Alexandrium pacificum for the first time. These results increase the understanding of the microbial ecology of algae-associated microbes in the context of interference from the proliferation of harmful algal bloom species.}, }
@article {pmid40981420, year = {2025}, author = {Wing, AJ and Hegarty, B and Bastien, GE and Denef, VJ and Evans, J and Dick, GJ and Duhaime, MB}, title = {Tracking putative Microcystis viruses and virus-host associations across distinct phases of a Microcystis-dominated bloom.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0057525}, doi = {10.1128/msystems.00575-25}, pmid = {40981420}, issn = {2379-5077}, abstract = {Viruses significantly impact microbial community composition and function. Yet their role in the fate of freshwater cyanobacterial harmful algal blooms (cHABs), an increasing threat to freshwater systems, remains poorly understood. Here, we address this with a metagenomic analysis of viruses of bloom-forming Microcystis aeruginosa through a seasonal cHAB in the western basin of Lake Erie. We identified globally distributed Microcystis viruses in Lake Erie based on sequence homology to well-studied isolates. A machine-learning model was then used to predict associations between uncharacterized viral populations and the Microcystis and non-Microcystis hosts of the cHAB. Size fractionation of water samples allowed us to identify significant fraction-specific trends in Microcystis viral diversity that corresponded with Microcystis genetic diversity. Viral diversity was highest in the non-colony-associated fraction and lowest in the colony-associated fraction, suggesting that colony formation may lead to bottlenecks in viral diversity in cHABs. Significant turnover of predicted Microcystis virus populations was observed through time, but not between stations miles apart. The virus-host networks revealed extensive interconnectivity and the potential for virus-mediated cross-species genetic exchange. The networks predicted that Lake Erie Microcystis viruses infect hosts spanning phyla, in agreement with lab studies in other systems but challenging previous notions of "narrow" host-virus associations in this genus. Abundant Microcystis virus genes revealed a potential role in key metabolic pathways and host adaptation. These findings advance our understanding of Microcystis viruses and their potential influence on host metabolism, species interactions, and coevolution in Microcystis-dominated cHABs.IMPORTANCEUnderstanding associations between viruses, their hosts, and environmental factors is key for identifying the mechanisms behind the rise and fall of cyanobacterial harmful algal blooms. This study explores the diversity and host ranges of viruses predicted to infect Microcystis, reporting how these properties vary over time, across sample stations in western Lake Erie, and among different filter size fractions. We found that Microcystis virus diversity is highest in non-colony-associated fractions and the lowest in colony-associated fractions, suggesting a link between Microcystis colony formation and reduced viral diversity. We identify abundant genes belonging to predicted Microcystis viruses and their potential roles in key metabolic pathways and adaptation to environmental changes. These findings enhance our understanding of the interplay among viruses, Microcystis, and co-occurring bacteria in cHABs, offering insights into the mechanisms driving bloom dynamics, species interactions, and coevolutionary processes.}, }
@article {pmid40980873, year = {2025}, author = {Lai, W and Alberdi, A and Leu, A and de Leon, AVP and Kobel, CM and Aho, VTE and Roehe, R and Pope, PB and Hvidsten, TR}, title = {Metabolic capabilities of key rumen microbiota drive methane emissions in cattle.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0060125}, doi = {10.1128/msystems.00601-25}, pmid = {40980873}, issn = {2379-5077}, abstract = {UNLABELLED: The rumen microbiome plays a critical role in determining feed conversion and methane emissions in cattle, with significant implications for both agricultural productivity and environmental sustainability. In this study, we applied a hierarchical joint species distribution model to predict directional associations between biotic factors and abundances of microbial populations determined via metagenome-assembled genomes (MAGs). Our analysis revealed distinct microbial differences, including 191 MAGs significantly more abundant in animals with a higher methane yield (above 24 g/kg dry matter intake [DMI]; high-emission cattle), and 220 MAGs more abundant in low-emission cattle. Interestingly, the microbiome community of the low-methane-emission rumen exhibited higher metabolic capacity but with lower functional redundancy compared to that of high-methane-emission cattle. Our findings also suggest that microbiomes associated with low methane yields are prevalent in specific functionalities such as active fiber hydrolysis and succinate production, which may enhance their contributions to feed conversion in the host animal. This study provides an alternate genome-centric means to investigate the microbial ecology of the rumen and identify microbial and metabolic intervention targets that aim to reduce greenhouse gas emissions in livestock production systems.<br><br>IMPORTANCE: Ruminant livestock are major contributors to global methane emissions, largely through microbial fermentation in the rumen. Understanding how microbial communities vary between high- and low-methane-emitting animals is critical for identifying mitigation strategies. This study leverages a genome-centric approach to link microbial metabolic traits to methane output in cattle. By reconstructing and functionally characterizing hundreds of microbial genomes, we observe that a low-methane-emission rumen harbors well-balanced, "streamlined" microbial communities characterized by high metabolic capacity and minimal metabolic overlap across populations (low functional redundancy). Our results demonstrate the utility of genome-level functional profiling in uncovering microbial community traits tied to climate-relevant phenotypes.}, }
@article {pmid40980756, year = {2025}, author = {Kosmopoulos, JC and Anantharaman, K}, title = {Viral Dark Matter: Illuminating Protein Function, Ecology, and Biotechnological Promises.}, journal = {ArXiv}, volume = {}, number = {}, pages = {}, pmid = {40980756}, issn = {2331-8422}, abstract = {Viruses are the most abundant biological entities on Earth and play central roles in shaping microbiomes and influencing ecosystem functions. Yet, most viral genes remain uncharacterized, comprising what is commonly referred to as "viral dark matter." Metagenomic studies across diverse environments consistently show that 40-90% of viral genes lack known homologs or annotated functions. This persistent knowledge gap limits our ability to interpret viral sequence data, understand virus-host interactions, and assess the ecological or applied significance of viral genes. Among the most intriguing components of viral dark matter are auxiliary viral genes (AVGs), including auxiliary metabolic genes (AMGs), regulatory genes (AReGs), and host physiology-modifying genes (APGs), which may alter host function during infection and contribute to microbial metabolism, stress tolerance, or resistance. In this review, we explore recent advances in the discovery and functional characterization of viral dark matter. We highlight representative examples of novel viral proteins across diverse ecosystems including human microbiomes, soil, oceans, and extreme environments, and discuss what is known, and still unknown, about their roles. We then examine the bioinformatic and experimental challenges that hinder functional characterization, and present emerging strategies to overcome these barriers. Finally, we highlight both the fundamental and applied benefits that multidisciplinary efforts to characterize viral proteins can bring. By integrating computational predictions with experimental validation, and fostering collaboration across disciplines, we emphasize that illuminating viral dark matter is both feasible and essential for advancing microbial ecology and unlocking new tools for biotechnology.}, }
@article {pmid40980429, year = {2025}, author = {Rahman, MS and Chlingaryan, A and Thomson, PC and Islam, MR and Lees, AM and Gregorini, P and Pereira, FC and Clark, CEF}, title = {In vitro simulation of drinking events in cattle.}, journal = {MethodsX}, volume = {15}, number = {}, pages = {103593}, pmid = {40980429}, issn = {2215-0161}, abstract = {Drinking causes a rapid decline in reticulorumen temperature (RT) followed by an exponential recovery, which may potentially impact the reticulorumen ecosystem. However, the nexus between drinking events and their effects on ruminal fermentation and microbial diversity has not yet been studied, either in vitro or in vivo. Although artificial (in vitro) rumen systems are widely used in ruminant research to simulate the reticulorumen environment, no such simulation has been described to consider the impact of drinking events on the reticulorumen environment. Therefore, we have developed a method for the in vitro simulation of drinking events in the fermentation jar where the jar temperature was considered a proxy for RT is reduced by adding a measured amount of cold water to the water bath, and the subsequent recovery period is achieved following a temperature profile regulated by a heating immersion circulator. This method enables the replication of RT fluctuations from drinking events, allowing for the monitoring of their impact on fermentation characteristics and microbial ecology in future research. The features of this method are: Creation of a hypothetical drinking event Estimation of volume and temperature of cold water for a drinking event Establishing a temperature profile to regulate the recovery period.}, }
@article {pmid40978322, year = {2025}, author = {Phonlamai, A and Khetkorn, W and Thongpool, V and Panyachanakul, T and Suriyachadkun, C and Kitpreechavanich, V and Sakdapetsiri, C and Lomthong, T}, title = {Profiling of the bacterial community and the degradative capability of newly isolated poly(lactic acid) (PLA)- and poly(butylene succinate) (PBS)-degrading bacteria from coastal samples.}, journal = {3 Biotech}, volume = {15}, number = {10}, pages = {352}, pmid = {40978322}, issn = {2190-572X}, abstract = {UNLABELLED: The coastal area of Thailand is a tropical marine environment with high microbial diversity, providing favorable conditions for microorganisms capable of degrading bioplastics. The current study aimed to investigate the bacterial community profiling of four samples collected from a coastal area in Thailand and to isolate the potential thermophilic bacteria with the ability to produce bioplastic-degrading enzymes. Our analysis revealed site-specific predominant genera: Brevibacillus in seawater (64.34 ± 0.27%), Pseudomonas in plastic waste (39.69 ± 3.77%), Pseudoalteromonas in soil (54.83 ± 2.40%), and Psychrobacter in moss rock (41.01 ± 1.67%). The thermophilic bacteria, including 6 poly(lactic acid) (PLA)- and 3 poly(butylene succinate) (PBS)-degrading bacteria, were isolated using a two-step technique in an emulsified polymer medium. These nine isolates were classified into five species across four genera: Brevibacillus gelatini, Microbispora rosea, Actinomadura keratinilytica, Paenibacillus thermoaerophilus, and P. ginsengihumi. Among these, Actinomadura keratinilytica LDF1 and M. rosea BS2-4 exhibited the highest enzymatic activities for PLA and PBS degradation (0.87 ± 0.11 U/mL and 0.31 ± 0.03 U/mL, respectively). Scanning electron microscopy confirmed the degradation capabilities of these strains in culture medium. Crude enzyme from the LDF1 strain demonstrated versatility in degrading various types of PLA, including PLA film, PLA powder, commercial cup, and commercial cutlery, while the strain BS2-4 enzyme effectively degraded PBS in film, powder, commercial cup, and commercial drinking straw. These findings advance our understanding of coastal microbial ecology and also highlight the potential of indigenous bacteria for bioplastic waste management, contributing to sustainable environmental solutions.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-025-04521-0.}, }
@article {pmid40976393, year = {2025}, author = {Cui, J and Dörmann, P}, title = {Microbial degradation of hydrocarbons from petroleum assisted by biosurfactants: pathways and bioremediation potential.}, journal = {Biochimie}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.biochi.2025.09.011}, pmid = {40976393}, issn = {1638-6183}, abstract = {Petroleum pollution from oil extraction, transportation, and industrial activities poses significant threats to marine ecosystems and socioeconomic stability due to the high toxicity of alkanes and polycyclic aromatic hydrocarbons (PAHs) to many organisms. Traditional remediation methods, including physical removal and chemical oxidation, are often costly and ecologically disruptive. Microbial degradation, facilitated by hydrocarbonoclastic bacteria like Pseudomonas aeruginosa and Alcanivorax borkumensis, offers a sustainable alternative by converting hydrocarbons into non-toxic CO2 and water. This review examines the degradation pathways of aliphatic and aromatic hydrocarbons by these bacteria, highlighting key enzymatic mechanisms and the pivotal role of biosurfactants-specifically rhamnolipids, and glycine-glucolipid-in enhancing hydrocarbon bioavailability. It also delves into the biosynthesis of these biosurfactants, along with the involvement of non-ribosomal peptide synthetases (NRPS) in producing lipopeptide biosurfactants such as surfactin. Additionally, the review addresses the challenges associated with scaling up biosurfactant production for bioremediation applications. Through a synopsis of recent research, this work proposes strategies to optimize biosurfactant efficacy, contributing to environmental sustainability and advancing the field of microbial ecology.}, }
@article {pmid40976174, year = {2025}, author = {Allouche, M and Bouzidi, I and Lassoued, A and Sellami, B and Derguini, A and Idres, T and Badraoui, R and Ben Hamadi, N and Chaudhary, AA and Bendif, H and Pacioglu, O and Abd-Elkader, OH and Boufahja, F and Plavan, G}, title = {How do polyethylene microplastics, ibuprofen, and sediment mud levels influence meiobenthic features and their interactions with CeO2-doped ZnO nanoparticles? Answers through nematode taxon/functional traits, allometry of Metoncholaimus pristiurus, and computational analyses.}, journal = {Marine environmental research}, volume = {212}, number = {}, pages = {107564}, doi = {10.1016/j.marenvres.2025.107564}, pmid = {40976174}, issn = {1879-0291}, abstract = {Microplastic pollution and pharmaceutical contaminants represent growing environmental threats, particularly in aquatic ecosystems. This research examines the individual and combined effects of polyethylene microplastics, sediment particles, and ibuprofen on meiobenthic species, specifically free-living nematodes. Abundance changes, species diversity, and functional characteristics were monitored during a 30-day microcosm experiment. The binding affinities and molecular interactions of both contaminants with germ-line development protein 3 (GLD-3) and sex-determining protein (SDP) have been assessed using computational modeling assays. The results indicate that contamination significantly alters nematode communities, with pronounced declines in sensitive species such as Dorylaimopsis timmi and Halalaimus longicaudatus. At the same time, opportunistic taxa like Paramonhystera pellucida and Parodontophora beviseta exhibited increased abundance, resulting in a worldwide reduction of nematofauna (432 individuals in controls compared to 233-322 individuals in treated communities). The experimental results and computational assays supported each other. Furthermore, the strongest negative effects were observed in combined polyethylene-ibuprofen treatments, suggesting a synergistic interaction that enhances toxicity. Polyethylene microplastics appear to modulate the bioavailability and toxicity of ibuprofen, potentially exacerbating its impact on benthic communities. According to regressions linking body dimensions, the combination of polyethylene microplastics and ibuprofen with ZnO-CeO2 (slopes: 0.53629 and 0.31718, respectively) nanoparticles enhanced the growth rate of the nematode Metoncholaimus pristiurus, compared to the control group (slopes: 0.05775).}, }
@article {pmid40976099, year = {2025}, author = {Saci, S and Nabti, EH and Sebbane, H and Issad, HA and Boufahja, F and De Martino, L and Nocera, FP and Bendif, H and Derguini, A and Hamadi, NB and Chaudhary, AA and Rebai, A and Cruz, C and Idres, T and Houali, K}, title = {Exploring Thymus vulgaris Extract as a Phytotherapeutic Agent: A Multifaceted Approach to tackle Avian Colibacillosis and Drug Resistance.}, journal = {Poultry science}, volume = {104}, number = {11}, pages = {105794}, doi = {10.1016/j.psj.2025.105794}, pmid = {40976099}, issn = {1525-3171}, abstract = {Avian colibacillosis remains a major threat to poultry production and food security, whereas its antibiotic-based control accelerates antimicrobial resistance. This study investigated the antibacterial potential of the hydroethanolic extract of Thymus vulgaris, alone and in combination with antibiotics, against avian pathogenic Escherichia coli (APEC). The phytochemical composition of the extract was analyzed by HPLC, while its antibacterial activity was assessed using agar diffusion and minimum inhibitory concentration (MIC) assays. Antibiotic-extract interactions were evaluated by the checkerboard method, and mechanisms of action were explored through assays targeting membrane permeability, proton pump inhibition, catalase inhibition, oxidative stress, and biofilm formation. Its antioxidant, anti-inflammatory, and cytotoxic activities were also evaluated. HPLC analysis revealed 16 phenolic compounds, including rosmarinic, ferulic, and salicylic acids, as well as flavonoids such as quercetin and luteolin, with an extraction yield of 15% ± 0.55. The extract displayed significant antibacterial activity (MIC: 5.46-10.93 mg/ml, p < 0.05). In synergy tests, the extract enhanced ampicillin efficacy 4-8-fold and showed additive effects with ciprofloxacin and tetracycline (2-4-fold). Mechanistic assays demonstrated disruption of bacterial membranes (32.66% electrolyte leakage, p < 0.05), inhibition of H[+]-ATPase proton pumps (p < 0.05), catalase activity reduction by 79.2% (p < 0.05), >50% decrease in cell hydrophobicity, and inhibition of biofilm formation (49.07-72.47%), alongside eradication of mature biofilms (41.89-64.67%) (p < 0.05). Beyond antimicrobial effects, the extract exhibited notable antioxidant capacity. In DPPH radical scavenging, the extract showed an IC50 of 9.76 ± 0.228 μg/ml (p < 0.05), while in the TAC assay, it reached 467.25 ± 1.889 μg/ml (p < 0.05), and it reduced ampicillin-induced lipid peroxidation by 42.85% (p < 0.05). Anti-inflammatory testing revealed inhibition of protein denaturation (4.95-52.48% at 15-2000 µg/ml, p < 0.05), although weaker than aspirin. Hemolysis assays confirmed the extract was non-hemolytic at concentrations up to 11 mg/ml (p < 0.05). In conclusion, Thymus vulgaris extract demonstrated safe, multi-target bioactivity, supporting its potential as a promising alternative to combat avian colibacillosis and antimicrobial resistance.}, }
@article {pmid40975416, year = {2025}, author = {Bi, Z and Wang, X and Fu, H and Huang, Y}, title = {Carbon source shaped microbial ecology, metabolism and performance in biofilm system for simultaneous phosphorus recovery and nitrogen removal.}, journal = {Environmental research}, volume = {}, number = {}, pages = {122800}, doi = {10.1016/j.envres.2025.122800}, pmid = {40975416}, issn = {1096-0953}, abstract = {The application of biofilm-based phosphorus enrichment technology has been hampered by the limited information on the performance, microbial interactions and metabolic patterns of dominant functional bacteria, especially those fed with complex carbon sources conditions. In this study, three representative carbon sources contained in real sewage, i.e., volatile fatty acids (VFAs), glucose, and amino acids were selected as the complex carbon sources. The comparison in phosphorus removal/enrichment performance, carbon utilization, and metabolic characteristics were performed during the biofilm system changed the sole carbon source (acetate sodium) feeding to complex carbon source feeding gradually. The performance reduction and instability were observed in initial stage of complex carbon source feeding, while the phosphorus removal/enrichment efficiency improved significantly after long-term acclimation by extending the anaerobic HRT. The concentration of phosphorus enrichment solution exceeded 50 mg/L, meanwhile the total nitrogen and total phosphorus removal efficiencies over 82% and 97%, respectively. Intriguing, intracellular organic phosphorus (OP) contents fluctuated with phosphorus uptake and release, which may be a hint of the important role of OP in PAOs energy conversion. Complex carbon sources induced the succession of biofilm community, especially the enrichment of hydrolytic fermentation bacteria, and a more intricate microbial interaction network among functional microbiota. The co-occurrence of the EMP and ED pathways during glycolysis implied more extensive carbon utilization pathways, and amino acids was speculated to complement intracellular energy metabolism via the tricarboxylic acid cycle (TCA). This study demonstrated that the biofilm systems have great potential to simultaneously achieve phosphorus removal and enrichment by using complex carbon sources in sewage wastewater.}, }
@article {pmid40972460, year = {2025}, author = {Arulananthan, A and Scholz, B and Karsten, U and Grossart, HP and Sigurbjörnsdóttir, A and Rolfsson, &#xd3; and Joerss, H and Duarte, B and Vilhelmsson, O&#xde;}, title = {Arctic and sub-Arctic marine diatom responses to PFAS exposure: Understanding physiological changes and resilience.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {289}, number = {}, pages = {107562}, doi = {10.1016/j.aquatox.2025.107562}, pmid = {40972460}, issn = {1879-1514}, abstract = {Per- and polyfluoroalkyl substances (PFAS) are persistent organic pollutants widely detected across diverse ecosystems. Despite regulatory bans on several PFAS compounds, PFAS remain prevalent in remote areas like the Arctic, raising significant ecological health concerns. This study addresses a critical knowledge gap regarding the effects of PFAS on unicellular primary producers, with a focus on diatom physiology and fitness. Two ecologically important Arctic and sub-Arctic diatom species, Cylindrotheca closterium and Thalassiosira pseudonana, as well as legacy long-chain PFAS, and two emerging PFAS replacements were investigated. Exposures were conducted for 10 days at three concentrations (100 mg/L, 1 mg/L, and 0.9 ng/L). Following the 10 d (short-term) toxicity assessment, one PFAS mixture was exposed for 28 days (long-term) at an environmentally relevant concentration of 0.9 ng/L. Physiological and biochemical responses, including growth, photosynthetic capacity, stress biomarkers, and metabolic changes, were assessed. Results revealed distinct impacts of PFAS on individual PFAS and their mixtures. Perfluorooctane sulfonic acid (PFOS), perfluorooctanoic acid (PFOA), perfluorononanoic acid (PFNA), perfluorododecanoic acid (PFDoA), perfluorotridecanoic acid (PFTrDA), and perfluorotetradecanoic acid (PFTeDA) often exhibited the most detrimental effects on both species relative to controls. PFAS mixtures exhibited synergistic impacts, with increasing effects as the number of PFAS compounds increased. Both diatoms exhibited significant reductions in growth and photochemical efficiency of photosystem II, along with elevated proline and total antioxidant activity, during short-term exposure to PFAS. During the long-term experiment, after the exponential growth phase (after 14 d), growth rates were not significantly different from those of the controls, suggesting potential compensatory responses over time. Despite the mild growth inhibition, enhanced biochemical activity relative to controls indicates sustained metabolic adjustment under prolonged PFAS exposure. These findings emphasize the potential impacts of PFAS, specially in mixtures, on disrupting primary producers in cold marine ecosystems, highlighting the need to assess the cumulative effects of pollutants on foundational Arctic biota.}, }
@article {pmid40972045, year = {2025}, author = {Feliu-Paradeda, L and Puig, S and Bañeras, L}, title = {Electron conductive compounds alter fermentative pathways and cooperation in Clostridium carboxidivorans and Clostridium acetobutylicum in co-culture.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaf090}, pmid = {40972045}, issn = {1574-6941}, abstract = {The addition of conductive materials promotes interactions between bacteria as they facilitate the exchange of reducing equivalents among cells. In this work, the impact of electron conductive compounds (magnetite, activated carbon or iron salts) was investigated on a Clostridium acetobutylicum/Clostridium carboxidivorans co-culture. Co-culturing both species with soluble iron salts or magnetite significantly improved carbon recovery in liquid end-products (75-85% of added carbon) compared to control and activated carbon supplementation (50-55% of added carbon). The addition of magnetite enhanced the production of longer-chain acids and alcohols (C4 and C6) when compared to all other treatments and reached the highest production after 44 h of fermentation. This effect was not observed in C. carboxidivorans nor in C. acetobutylicum pure cultures, advocating for a cooperation between the two species. Among comparisons to the behaviour observed in pure cultures, we suggest magnetite was first used as a sink of reduced equivalents produced by C. carboxidivorans and later as a source of energy for C. acetobutylicum for the production of elongated short-chain fatty acids and alcohols. We propose that adding magnetite (iron) could be an effective strategy to enhance alcohol production in synthetic clostridia consortia.}, }
@article {pmid40970936, year = {2025}, author = {Uddin, MR and Saifullah, S}, title = {Type II toxin-antitoxin systems as stress-responsive survival circuits in archaea and bacteria.}, journal = {Archives of microbiology}, volume = {207}, number = {11}, pages = {269}, pmid = {40970936}, issn = {1432-072X}, support = {23-FoBST-02//Research Cell, JUST/ ; }, mesh = {*Toxin-Antitoxin Systems/genetics ; *Archaea/genetics/physiology/metabolism ; *Bacteria/genetics/metabolism ; *Stress, Physiological ; Bacterial Proteins/genetics/metabolism ; DNA Repair ; Phylogeny ; *Antitoxins/genetics/metabolism ; Bacterial Toxins/genetics/metabolism ; Biofilms/growth &amp; development ; }, abstract = {Simple early lifeforms with relatively small genomes were evolved with certain genetic circuitry to better their stress-response mechanism which significantly enhances their survival during stress, hypothetically. In this review, we conducted a comprehensive investigation to identify survival-focused genetic circuitry in microorganisms, focusing on type II toxin-antitoxin (TA) systems, particularly sought after due to their ubiquitousness in nature, composed of two functionally coordinated genes: one that transiently inhibits reproduction during stress and another that represses this inhibition under normal conditions, while simultaneously promoting DNA repair under stress. Our comprehensive analysis of 22 type II TA systems reveals diverse roles, including dormancy induction, biofilm formation, pathogenicity and DNA repair. While canonical modules such as HigAB and RelBE are well-characterized, others like ParDE, Kid-Kis, and YafO-YafN remain understudied in the context of dormancy or biofilm involvement. Additionally, systems such as DarT-DarG, YafQ-DinJ and CcdB-CcdA have been implicated in DNA repair pathways, suggesting broader functional repertoires beyond growth inhibition. Phylogenetic analyses further reveal that TA systems such as VapC-VapB and MazF-MazE are widely distributed among bacteria, archaea, and cyanobacteria, including lineages thriving in extreme environments like deep-sea hydrothermal vents, which are considered potential sites for the emergence of early life. The presence of TA loci in ancient microorganisms like Methanocaldococcus jannaschii and Microcystis aeruginosa hints at their ancient origin and possible role in microbial survival on early Earth. This review synthesizes current knowledge on type II TA systems as stress-responsive survival circuits and highlights their significance in microbial ecology, evolution, and adaptation.}, }
@article {pmid40970741, year = {2025}, author = {Lee, W and Kim, G and Park, T}, title = {Refining microbial biomarker identification in rumen microbiome studies: a viability PCR-based approach.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0142925}, doi = {10.1128/aem.01429-25}, pmid = {40970741}, issn = {1098-5336}, abstract = {The rumen microbiome significantly affects host performance, influencing feed efficiency, nitrogen utilization, and methane emission. However, conventional DNA-based marker gene sequencing cannot distinguish between viable and non-viable microbes, leading to inaccurate microbiota analyses. Viability PCR (v-PCR) with propidium monoazide (PMA) can inhibit DNA amplification from membrane-compromised cells, allowing the detection of viable microbes in rumen cultures. Therefore, this study aims to identify conditions for applying PMA in rumen culture experiments using qPCR and to examine its effect on the rumen microbial community using 16S rRNA gene sequencing in standard in vitro experiments. PMA treatment conditions were applied using a fivefold inoculum dilution, 100 µM PMA concentration, 30 min dark incubation, and 20 min light exposure, validated by a decrease in absolute abundance in heat-treated samples. When applied to in vitro rumen experiments, PMA treatment reduced bacterial evenness and induced shifts in key bacterial and archaeal taxa. Additionally, it affected major functional profiles of the microbiota. PMA treatment increased the relative abundance of Ruminobacter [log fold change (LFC) = 0.52] and Succinivibrio (LFC = 0.68) at 0 h (no incubation), along with Ruminobacter (LFC = 0.83) after 24 h of incubation, while decreasing that of Xylanibacter (LFC = -0.39) at 24 h. These shifts align with those of RNA-based studies showing higher Succinivibrionaceae abundance than Prevotellaceae, supporting the effectiveness of PMA in capturing active microbial dynamics. PMA-based v-PCR offers a reliable alternative to RNA-based methods, improving microbial community assessments and facilitating the identification of viability-associated microbial biomarkers in rumen studies.IMPORTANCEThis study identifies the optimal conditions for applying propidium monoazide (PMA) in in vitro rumen experiments to selectively amplify DNA from viable microorganisms while suppressing amplification from nonviable ones. PMA-based viability PCR (v-PCR) improves the accuracy of microbial community analysis by selectively detecting viable microorganisms, addressing the limitations of conventional DNA-based methods. Additionally, this approach provides a potential cost-effective alternative to RNA-based analyses, offering a practical tool for studying rumen microbial ecology.}, }
@article {pmid40970700, year = {2025}, author = {Havlena, ZE and Lucero, K and Graham, HV and Stern, JC and Wankel, SD and Mainiero, M and Jones, DS}, title = {Microbial ecology of acidic, biogenic gypsum: community structure and distribution of extremophiles on freshly formed and relict sulfate deposits in a hydrogen sulfide-rich cave.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0139725}, doi = {10.1128/aem.01397-25}, pmid = {40970700}, issn = {1098-5336}, abstract = {UNLABELLED: Sulfate minerals are abundant on the Martian surface, and many of these evaporite deposits are thought to have precipitated from acidic fluids. On Earth, gypsum (CaSO4•2H2O) and other sulfates sometimes form under acidic conditions, so exploring the extremophilic life that occurs in these mineral environments can help evaluate the astrobiological potential of acid sulfate depositional settings. Here, we characterized the microbial communities associated with acidic gypsum deposits in a sulfuric acid cave, where sulfate precipitation is driven by sulfide-oxidizing bacteria and archaea. We used 16S rRNA gene sequencing and cell counts to characterize gypsum-associated microorganisms in freshly formed and relict deposits throughout the cave, to test how microbial community composition and abundance would vary with distance from the sulfidic water table and with the concentration of H2S(g) and other gases in the cave atmosphere. We found that actively forming gypsum in the lower cave levels was colonized by low-diversity communities that have few cells compared to other environments in the cave. The most abundant taxa were Acidithiobacillus, Metallibacterium, Mycobacteria, and three different Thermoplasmatales-group archaea, which occupied distinct niches based on proximity to sulfidic streams and the concentration of gases in the cave air. By contrast, deposits in older cave levels had more diverse communities that were distinct from those associated with freshly formed gypsum and likely represent a community reliant on different energy resources. These findings show that acidic sulfate deposits serve as habitats for extremophilic microorganisms and broaden our knowledge of the life associated with terrestrial sulfates.<br><br>IMPORTANCE: Gypsum and other sulfate salts are common on Mars, and many of these deposits are thought to have formed from acidic fluids early in the planet's history. Understanding the life that survives and thrives in similar environments on Earth is therefore crucial for evaluating whether these Martian sulfates are or ever were habitable. One such environment where acidic gypsum occurs is in sulfuric acid caves, where extremophilic microorganisms drive the precipitation of sulfate minerals by oxidizing hydrogen sulfide gas from the cave atmosphere. Here, we characterized the communities of microorganisms on freshly formed and ancient gypsum in the Frasassi Caves and found that the gypsum deposits hosted microbial communities that changed based on chemical energy availability and the age of the gypsum. Our findings underscore the importance of chemical and microbiological interactions in shaping habitable niches and provide context for searching for past or present life in acidic Martian sulfates.}, }
@article {pmid40969862, year = {2025}, author = {Wang, H and Lindemann, E and Liebmann, P and Varsadiya, M and Svenning, MM and Waqas, M and Petters, S and Richter, A and Guggenberger, G and Barta, J and Urich, T}, title = {Methane-cycling microbiomes in soils of the pan-Arctic and their response to permafrost degradation.}, journal = {Communications earth &amp; environment}, volume = {6}, number = {1}, pages = {748}, pmid = {40969862}, issn = {2662-4435}, abstract = {The methane-cycling microbiomes play crucial roles in methane dynamics. However, little is known about their distributions on a pan-Arctic scale as well as their responses to the widespread permafrost degradation. Based on 621 datasets of 16S rRNA gene amplicons from intact permafrost soils across the pan-Arctic, we identified only 22 methanogen and 26 methanotroph phylotypes. Their relative abundances varied significantly between sites and soil horizons. Only four methanogen phylotypes were detected at all locations. Remarkably, the permafrost soil methane filter was almost exclusively dominated by some obligate methanotroph (Methylobacter-like) phylotypes. However, a case study in Alaska suggests that atmospheric methane oxidizing bacteria (Methylocapsa-like phylotypes) dominated methanotrophs in a drier condition after permafrost degradation. These findings point towards a few key microbes particularly relevant for future studies on Arctic methane dynamics in a warming climate and that under future dry conditions, increased atmospheric methane uptake in Arctic upland soils may occur.}, }
@article {pmid40968530, year = {2025}, author = {Popov, IV and Chikindas, ML and Venema, K and Ermakov, AM and Popov, IV}, title = {KEGGaNOG: A Lightweight Tool for KEGG Module Profiling From Orthology-Based Annotations.}, journal = {Molecular nutrition &amp; food research}, volume = {}, number = {}, pages = {e70269}, doi = {10.1002/mnfr.70269}, pmid = {40968530}, issn = {1613-4133}, support = {23-14-00316//Russian Science Foundation/ ; }, abstract = {Functional interpretation of bacterial genomes and metagenomes is essential for applications ranging from microbial ecology to probiotic development. KEGGaNOG is a lightweight and scalable Python tool that enables pathway-level profiling by translating orthology-based annotations into KEGG module completeness scores. KEGGaNOG accepts input from eggNOG-mapper annotations and supports both individual genome and multi-sample analyses. It calculates completeness scores for KEGG modules using internally integrated KEGG-Decoder logic and offers a suite of visualization options, including heatmaps, grouped summaries, barplots, radar plots, and correlation networks. We demonstrate its use on 11 well-characterized bacterial genomes, including several probiotic strains. KEGGaNOG accurately captured core biosynthetic capabilities and highlighted functionally informative differences across samples, such as vitamin biosynthesis, stress-response pathways, and transport systems. KEGGaNOG provides a practical framework for high-throughput functional annotation and comparative metabolic profiling in bacterial genomics and microbiome research. It is particularly well suited for preliminary analysis of novel or uncharacterized strains and is applicable to both isolate and metagenome-derived data. In the context of probiotic research, KEGGaNOG supports mechanistic exploration and strain selection by linking genomic content to functional capacity in a reproducible and interpretable manner.}, }
@article {pmid40968492, year = {2025}, author = {Dong, X and Chu, Y and Tong, Z and Yi, X and Sun, M and Meng, D and Gao, T and Wang, M and Duan, J}, title = {The adsorption mechanism of tembotrione on modified biochar and its impact on soil microbial communities.}, journal = {Pest management science}, volume = {}, number = {}, pages = {}, doi = {10.1002/ps.70225}, pmid = {40968492}, issn = {1526-4998}, support = {2023YFD1400900//National Key Research and Development Program of China/ ; 32372609//National Natural Science Foundation of China/ ; 32302414//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Tembotrione, a triketone herbicide with high mobility and persistence, poses significant environmental risks by disrupting soil microbial ecology and threatening crop rotation systems. This study investigates the adsorption mechanism and ecological benefits of hydrogen peroxide-modified biochar (HPBC-700) for mitigating tembotrione contamination in soil environments.<br><br>RESULTS: The oxidative modification introduces abundant oxygen-containing functional groups, including hydroxyl, carboxyl, and carbonyl, which substantially enhance the biochar's adsorption capacity and surface reactivity. Density Functional Theory (DFT) calculations and non-covalent interaction analyses reveal that hydrogen bonding and &#x3c0;-&#x3c0; stacking are the dominant adsorption mechanisms. Among the functional groups, carboxyl contributes the strongest binding due to its ability to form dual hydrogen-bond interactions. In addition to physically immobilizing the herbicide, HPBC-700 improves soil microbial diversity and enriches degradation-related functional taxa, particularly Proteobacteria and Acinetobacter, thereby alleviating pesticide-induced ecological stress.<br><br>CONCLUSION: These findings highlight the dual function of HPBC-700 as both an efficient adsorbent and a regulator of soil microbiomes, providing a sustainable strategy for pesticide remediation and agroecosystem restoration. This work advances the understanding of biochar-pesticide interactions and offers new insights into integrating chemical immobilization with ecological recovery for effective soil pollution control. &#xa9; 2025 Society of Chemical Industry.}, }
@article {pmid40968405, year = {2025}, author = {Trubl, G and Probst, AJ}, title = {Clarifying Terminology in Microbial Ecology: A Call for Precision in Scientific Communication.}, journal = {Environmental microbiology}, volume = {27}, number = {9}, pages = {e70177}, doi = {10.1111/1462-2920.70177}, pmid = {40968405}, issn = {1462-2920}, support = {SCW1632//U.S. Department of Energy Office of Biological and Environmental Research through the Genomic Science Program and the Lawrence Livermore National Laboratory/ ; CRC 1439/1//Deutsche Forschungsgemeinschaft/ ; CRC 1439/2//Deutsche Forschungsgemeinschaft/ ; 426547801//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Terminology as Topic ; *Ecology ; *Microbiota ; *Microbiology ; Communication ; }, abstract = {The rapid evolution of microbiology as a field of research has led to the introduction of new terminology and the adaptation of existing terms. However, inconsistencies in the use of these terms, including variations across different scientific disciplines, can lead to confusion and miscommunication within the scientific community. This article discusses the importance of precise terminology in microbiome research, highlighting examples where terms have been misused or redefined without clear justification. We also present a list of frequently used terms in microbial ecology along with their specific definitions. We argue that the misuse of terminology can hinder scientific progress by creating ambiguity and misunderstanding. To address this, we propose a set of guidelines for the consistent use of key terms and provide clear definitions for some of the most commonly misused or newly introduced terms in the field. The definitions provided herein will also function as a guide for young researchers new to the field of microbial ecology. Accurate and consistent use of terminology is crucial for effective communication and collaboration in microbiology research. By adhering to standardised definitions, researchers can ensure that their work is clearly communicated and contributes meaningfully to the progress of science.}, }
@article {pmid40967376, year = {2025}, author = {Huang, M and Lian, Y and Xie, C}, title = {A rare case of recurrent abdominal pain with facial edema.}, journal = {Gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1053/j.gastro.2025.09.019}, pmid = {40967376}, issn = {1528-0012}, }
@article {pmid40969174, year = {2024}, author = {Matz, LM and Shah, NS and Porterfield, L and Stuyck, OM and Jochum, MD and Kayed, R and Taglialatela, G and Urban, RJ and Buffington, SA}, title = {Gut pathobiont enrichment observed in a population predisposed to dementia, type 2 diabetics of Mexican descent living in South Texas.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {}, pmid = {40969174}, issn = {2813-4338}, abstract = {Type 2 diabetes (T2D) is a common forerunner of neurodegeneration and accompanying dementia, including Alzheimer's Disease (AD), yet the mechanisms underlying this comorbidity remain unresolved. Individuals of Mexican descent living in South Texas have increased prevalence of comorbid T2D and early onset AD, despite low incidence of the APOE-ε4 risk variant among the population and an absence of a similar predisposition among relatives residing in Mexico - suggesting a role for environmental factors in coincident T2D and AD susceptibility. We therefore sought to test if differences in gut community structure could be observed in this population prior to any AD diagnosis. Here, in a small clinical trial (ClinicalTrials.gov Identifier NCT04602650), we report evidence for altered gut microbial ecology among subjects of Mexican descent living in South Texas with T2D (sT2D) compared to healthy controls without T2D (HC), despite no differences in expressed dietary preferences. We performed metataxonomic 16S rRNA gene amplicon sequencing of study participant stool samples. Although no significant decrease in microbial alpha diversity was observed between sT2D gut communities versus those of HC, body mass index was identified as a driver of gut community structure. Intriguingly, we observed a significant negative association of Faecalibacterium with T2D and an increase in the abundance of pathobionts Escherichia-Shigella, Enterobacter, and the erysipelotrichial species Clostridia innocuum among sT2D gut microbiota, as well as differentially abundant gene and metabolic pathways. Future large-scale, longitudinal sequencing efforts of the gut microbiome of individuals with T2D who go onto develop AD might identify key actors among "disease state" microbiota that contribute to increased susceptibility to comorbid dementia among type 2 diabetics. Finally, we identified candidate microbiome-targeted approaches for the treatment of T2D.}, }
@article {pmid40966281, year = {2025}, author = {Dai, J and Chen, C and Zhai, ZQ and Gao, AX and Johnson, DR and Kopittke, PM and Zhao, FJ and Wang, P}, title = {The balance between microbial arsenic methylation and demethylation in paddy soils underpins global arsenic risk and straighthead disease in rice.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {38}, pages = {e2508311122}, doi = {10.1073/pnas.2508311122}, pmid = {40966281}, issn = {1091-6490}, support = {42325701 W2411035//National natural science foundation of china/ ; }, mesh = {*Oryza/microbiology/metabolism ; *Arsenic/metabolism/toxicity ; *Soil Microbiology ; Methylation ; Soil/chemistry ; *Plant Diseases/microbiology ; *Soil Pollutants/metabolism ; Bacteria/metabolism/genetics ; Cacodylic Acid/metabolism ; Food Contamination/analysis ; }, abstract = {Arsenic contamination in rice poses a global challenge to food safety and agricultural productivity, as toxic methylated arsenic species-dimethylarsinic acid (DMA) and its highly toxic derivative, methylated monothioarsenate (DMMTA)-accumulate in rice grains. These arsenic species endanger human health and trigger rice straighthead disease, a crop disorder that drastically reduces yields. However, the microbial ecological processes driving arsenic speciation in paddy soils, and their link to striking geographic disparities in rice arsenic speciation profiles and disease prevalence, remain poorly understood. Here, we integrate soil chronosequences spanning 1 to 2,000 y of rice cultivation, a global metagenomic survey of 801 paddy soils, controlled incubations, and field surveys to demonstrate that the balance between arsenic-methylating and arsenic-demethylating microbes is the key determinant of rice grain arsenic speciation and straighthead disease susceptibility. We show that young and moderate-age paddy soils (<700 y), common in regions such as the Americas and Europe, are enriched in arsenic-methylating bacteria, leading to elevated DMA and DMMTA in soils and rice grains. In contrast, ancient paddies in Southeast Asia harbor robust populations of DMA-demethylating methanogenic archaea that effectively mitigate the buildup of these toxic arsenic species. We identify core microbial taxa whose abundances serve as predictive biomarkers and construct a global risk map linking a high methylator-to-demethylator ratio in soils with increased straighthead disease incidence. These findings advance our understanding of arsenic biogeochemistry in agroecosystems and establish a predictive framework for identifying regions at elevated risk of arsenic-induced crop disorders and food contamination.}, }
@article {pmid40965595, year = {2025}, author = {Nieto, EE and Ghanem, N and Cammarata, RV and Borim Corrêa, F and Coppotelli, BM and Chatzinotas, A}, title = {Effects of a novel Paraburkholderia phage IPK on the phenanthrene degradation efficiency of the PAH-degrading strain Paraburkholderia caledonica Bk.}, journal = {Biodegradation}, volume = {36}, number = {5}, pages = {86}, pmid = {40965595}, issn = {1572-9729}, mesh = {*Phenanthrenes/metabolism ; Biodegradation, Environmental ; *Polycyclic Aromatic Hydrocarbons/metabolism ; *Bacteriophages/genetics/isolation &amp; purification/physiology/metabolism ; Soil Pollutants/metabolism ; *Burkholderiaceae/virology/metabolism ; Genome, Viral ; Soil Microbiology ; }, abstract = {Phages are a major cause of bacterial mortality, affecting bacterial diversity and ecosystem functioning. However, the impact of phage-host interactions in contaminated environments and their role in pollutant biodegradation have largely been overlooked. We isolated and characterized a novel phage that infects the PAH-degrading bacterium Paraburkholderia caledonica Bk from a polycyclic aromatic hydrocarbon (PAH)-contaminated soil and investigated the effect of different multiplicity of infection (MOI) ratios on the degradation efficiency of phenanthrene. The phage IPK is a temperate phage with a wide pH and temperature tolerance and a burst size of 80 PFU ml[-][1]. The phage was classified as a member of the Caudoviricetes and is related to Pseudomonas and Burkholderia phages. However, its low intergenomic similarity indicates that it is a new species. Three auxiliary metabolic genes (AMGs) related to amino acid metabolism and to bacterial growth regulation were identified in the phage genome. The highest multiplicity of infection (MOI 10) showed a rapid recovery of the host density and greater phenanthrene degradation than MOIs ranging from 0.01 to 1. This work highlights the important role of phage-host interactions in modulating the efficiency of pollutant degradation, which could be a key for improving the establishment of inoculants in bioremediation processes.}, }
@article {pmid40965271, year = {2025}, author = {Dell'Acqua, AN and Scicchitano, D and Simoncini, N and Mercanti, I and Leuzzi, D and Turroni, S and Corlatti, L and Rampelli, S and Colonna, M and Corinaldesi, C and Candela, M and Palladino, G}, title = {Ski Tourism Shapes the Snow Microbiome on Ski Slopes in the Italian Central Alps.}, journal = {Environmental microbiology reports}, volume = {17}, number = {5}, pages = {e70195}, doi = {10.1111/1758-2229.70195}, pmid = {40965271}, issn = {1758-2229}, mesh = {Italy ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; *Skiing ; *Snow/microbiology/virology ; RNA, Ribosomal, 16S/genetics ; *Tourism ; Humans ; Viruses/classification/genetics/isolation &amp; purification ; Metagenomics ; Seasons ; }, abstract = {Winter sports exert significant anthropogenic pressures on the snow microbiome, affecting the entire alpine ecosystem. The massive usage of artificial snow, human occupation, and the release of xenobiotics like microplastics or ski wax components on ski tracks can profoundly alter snow microbial ecology. Here, we reconstructed the temporal dynamics of the snow microbiome at three sites in the Italian Alps: inside and outside a ski track at the impacted site of Santa Caterina Valfurva and near Cancano lake as an unimpacted control. Using epifluorescence microscopy, 16S rRNA amplicon sequencing, and inferred metagenomics, we found that the snow microbiome inside the track presented a higher load of prokaryotes and viruses. Notably, N2-fixing microorganisms from cryospheric environments and host-associated taxa, like Terrisporobacter, Clostridium sensu stricto, Enterococcus, and Muribaculaceae, and the opportunistic pathogen Citrobacter characterised the impacted site. These microorganisms could originate from the river water used to produce artificial snow during winter. Our findings highlight the complexity and multifunctionality of the snow microbiome, where microorganisms with different ecological propensities can coexist, and the detectable impact of ski tourism, which enriches host-associated and xenobiotic-degrading microorganisms. This underscores the need for systematic monitoring and protection of the snow microbiome in the Alpine environment from anthropogenic threats.}, }
@article {pmid40965193, year = {2025}, author = {Armin, G and Boros, G and Kis, M and Burányi, M and Horváth, H and Krassován, K and Masuda, T and Bernát, G and Inomura, K}, title = {The effect of temperature on phytoplankton physiology: a mesocosm and modeling study.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0045725}, doi = {10.1128/spectrum.00457-25}, pmid = {40965193}, issn = {2165-0497}, abstract = {Strategies that focus on reducing nutrient loading to freshwater lakes have historically been successful in improving water quality by curbing large phytoplankton blooms. However, as waters warm, little is known about the resultant phytoplankton physiology and ensuing perturbations in the food web that may occur. Here, we designed a mesocosm experiment to investigate the impact of warming water on phytoplankton physiology and further validate a previously developed, coarse-grained model that predicts the key aspects of phytoplankton physiology, including elemental stoichiometry and macromolecular allocation, across varying temperatures. We found that higher temperatures double the maximum cellular density (cells L[-1]) of phytoplankton, suggesting that high temperature stimulates cell division over maximizing carbon storage. Also, the cells in warmer waters dedicate fewer resources to proteins and RNA production, leading to higher fractions of carbon allocated to storage. This work illustrates the potential impact warming waters may have on the ecosystem, as higher fractions of carbohydrates are often associated with less nutritious food for higher trophic levels.IMPORTANCEWe take a novel approach to investigating the impact of warming on phytoplankton physiology by utilizing mesocosms and a coarse-grained cellular model. Previous work in this field tends to use idealized laboratory experiments, mesocosms, or models alone. By synthesizing model and mesocosm results, we test the model's ability to capture physiology in semi-natural environments. We conducted this experiment under phosphorus limitation and saw high cell densities in the heated, treatment tanks. Thus, warming waters may negate some successful management practices that curb eutrophication. With increased temperatures, we also observed increased N:P values in both the experimental and model results, which may be due to the combined effects of a lack of P storage, fewer enzymes required, and a corresponding decrease in RNA production. Our model predictions closely aligned to mesocosm observations, suggesting the capability of our model to represent lower trophic organisms in ecosystem models.}, }
@article {pmid40965139, year = {2025}, author = {Kim, M and Kamagata, Y and Park, S-J}, title = {Genomics and physiological characterizations of an acidotolerant nitrite-oxidizing Nitrospira enriched from freshwater pond.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0152225}, doi = {10.1128/aem.01522-25}, pmid = {40965139}, issn = {1098-5336}, abstract = {Nitrite-oxidizing bacteria (NOB) play a crucial role in global nitrogen cycling, yet their presence and adaptations in acidic environments remain poorly understood. This study unveils the cultivation and characterization of a novel acid-tolerant NOB, NS4 culture, affiliated with lineage II (Nitrospira_D) within the genus Nitrospira. Enriched and isolated from a freshwater pond sediment, NS4 culture exhibits remarkable physiological and genomic traits that shed light on NOB survival strategies in low pH conditions. NS4 culture demonstrates the optimal growth at pH 6 and 0.5 mM nitrite concentration, with a maximum growth rate of 0.62 day[-1]. Kinetic analyses reveal a high affinity for nitrite (Km(app) = 4.02 µM), suggesting adaptation to oligotrophic environments. Phylogenomic and genomic-relatedness analyses position NS4 culture as a novel member within the genus Nitrospira, for which we propose as "Candidatus Nitrospira acidotolerans." Genomic investigations indicate the presence of a complete reductive tricarboxylic acid cycle and genes for nitrite oxidation, confirming its chemolithoautotrophic lifestyle. Intriguingly, NS4 genome lacks complete pathways for cobalamin biosynthesis, implying a potential dependence on symbiotic partners for this essential cofactor. The NS4 genome harbors genes associated with acid resistance, including chaperones, transporters, and amino acid metabolism, suggesting a genetic potential for adaptation or resistance to low pH conditions. This discovery expands our understanding of NOB diversity and adaptability, offering insights into nitrogen cycling in acid-impacted ecosystems. The physiological and genomic traits of this acid-tolerant NOB open new insights for exploring the ecological significance of NOB in previously overlooked acidic habitats.IMPORTANCENitrite-oxidizing bacteria (NOB) are integral to the global nitrogen cycle, yet their adaptations to acidic environments remain poorly understood. This study introduces Candidatus Nitrospira acidotolerans, an acid-tolerant NOB highly enriched from freshwater pond sediment. By combining physiological and genomic analyses, this work reveals unique adaptations that enable survival and nitrite oxidation under low pH conditions. Notably, the NS4 culture demonstrates high nitrite affinity and resistance to acidic stress, suggesting its ecological significance in acid-impacted ecosystems. Additionally, NS4 genomic traits reveal genetic potential of metabolic dependencies, including reliance on symbiotic partners for cobalamin synthesis. These findings expand our understanding of NOB diversity and their role in nitrogen cycling under extreme conditions, offering novel insights into microbial ecology and potential applications in managing nitrogen processes in acidic environments.}, }
@article {pmid40961788, year = {2025}, author = {Kotowska, D and Báldi, A and Dobosy, P and Felföldi, T and Garamszegi, LZ and Horváth, Z and Kröel-Dulay, G and Ódor, P and Valkó, O and Batáry, P}, title = {Aligning land use with sustainability: Context-sensitive pathways forward.}, journal = {Journal of environmental management}, volume = {394}, number = {}, pages = {127252}, doi = {10.1016/j.jenvman.2025.127252}, pmid = {40961788}, issn = {1095-8630}, abstract = {The concept of sustainable development states that economic, social, and technological progress needs to be harmonised with nature. However, with the rate of global environmental deterioration now higher than at any time in human history and an ever-increasing human population, sustainability slips out of reach. One of the central processes and key issues in attaining sustainability is human use of and interaction with land resources. These can be described by two main processes that often go hand in hand: land conversion and land-use intensification. As these two phenomena accelerate, the level of disturbance in the environment increases, transforming natural ecosystems into altered, novel ecosystems or intensively used ecosystems. Depending on the degree of human-induced land alterations, different actions are needed to achieve and maintain sustainability. Conservation and prevention are necessary in natural areas with a low level of anthropogenic pressures. In areas that have already been disturbed by humans, sustainable management allows for a harmonious coexistence between humans and nature. Restoration and mitigation can help address the negative impacts of the most altered habitats. Sustainability, however, is not a fixed target but a dynamic condition shaped by evolving local contexts and global drivers. We advocate for transformative change grounded in flexible, context-sensitive land-use strategies that integrate ecological resilience, participatory governance, and institutional adaptability. With such systemic shifts, land systems can become catalysts for long-term sustainability.}, }
@article {pmid40832858, year = {2025}, author = {Gregor, R and Vercelli, GT and Szabo, RE and Gralka, M and Reynolds, RC and Qu, EB and Levine, NM and Cordero, OX}, title = {Vitamin auxotrophies shape microbial community assembly on model marine particles.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, doi = {10.1093/ismejo/wraf184}, pmid = {40832858}, issn = {1751-7370}, support = {542395//Simons Collaboration on Principles of Microbial Ecosystems/ ; 653410//Simons Postdoctoral Fellowship in Marine Microbial Ecology/ ; OCE-2019589//Center for Chemical Currencies of a Microbial Planet Postdoctoral Fellowship/ ; #031//NSF Center for Chemical Currencies of a Microbial Planet/ ; }, mesh = {*Seawater/microbiology/chemistry ; *Bacteria/metabolism/classification/isolation &amp; purification/genetics ; *Vitamins/metabolism ; Polysaccharides/metabolism ; *Microbiota ; }, abstract = {Microbial community assembly is governed by the flow of carbon sources and other primary metabolites between species. However, central metabolism represents only a small fraction of the biosynthetic repertoire of microbes: metabolites such as antimicrobial compounds, signaling molecules, and co-factors are underexplored in their potential to shape microbial communities. Here, we focus on B vitamin exchange in marine bacterial communities that degrade polysaccharides, a key component of particulate organic matter. We found that in a screen of 150 natural isolates, almost a third were auxotrophs for one or more B vitamins. By measuring physiological parameters such as uptake affinities and comparing those to ambient seawater concentrations, we showed that marine bacteria live at the edge of vitamin limitation in the environment. To understand how auxotrophs survive in the open oceans, we used our experimental data to model vitamin cross-feeding on particles through both secretion and lysis. Our results highlight the importance of vitamin auxotrophies in shaping microbial community assembly and succession, adding another layer of complexity to the trophic structure of particle-associated communities.}, }
@article {pmid40959279, year = {2025}, author = {Liu, X and Chen, Z and Lin, J and Lian, Y and Gan, W and Liu, H and Huang, X and Mei, J and Ma, T and Lu, Z and Zeng, W and Gong, Y and Chen, S and He, W}, title = {DLGAP5 Promotes Acute Liver Injury via Hepatocyte Pyroptosis-Driven Macrophage Metabolic Reprogramming and M1 Polarization.}, journal = {International journal of biological sciences}, volume = {21}, number = {12}, pages = {5563-5585}, pmid = {40959279}, issn = {1449-2288}, mesh = {Animals ; *Pyroptosis/physiology/genetics ; *Hepatocytes/metabolism ; Mice ; *Macrophages/metabolism ; Methyltransferases/metabolism/genetics ; Mice, Inbred C57BL ; Mice, Knockout ; Male ; NLR Family, Pyrin Domain-Containing 3 Protein/metabolism/genetics ; Inflammasomes/metabolism ; Metabolic Reprogramming ; }, abstract = {Pyroptosis is a novel programmed cell death that exists in inflammatory diseases and methyltransferase-like 3 (METTL3) is a core N6-methyladenosine (m6A) modified methyltransferase that has been shown to regulate cell fate. However, the role of pyroptosis in acute liver injury (ALI) is still unknown and whether it is regulated by m6A modification needs to be elucidated. Here, Mettl3 mutant and Nlrp3 knockout mouse were constructed, CCl4- and TAA-induced ALI models were established and primary cells were isolated, and cell pyroptosis and m6A modification were evaluated. We found that hepatocyte pyroptosis is a key characteristic of ALI, and METTL3-mediated m6A modification was upregulated in hepatocytes during ALI. Inhibition of METTL3-mediated m6A modification alleviated hepatocyte pyroptosis and ALI. Through MeRIP-seq analysis and verification, Dlgap5 was determined as the target of METTL3-mediated m6A modification, which was regulated in an IGF2BP2-dependent manner. Mechanistically, METTL3 can bind to DLGAP5, and then DLGAP5 promoted pyroptosis through NF-κB-dependent NLRP3 inflammasome activation and direct potentiation of inflammasome structure formation and assembly. Mettl3 mutation or AT9283-mediated DLGAP5 inhibition alleviated pyroptosis and ALI. The effects of hepatocyte pyroptosis on cell interaction were then explored and we revealed that NLRP3 inflammasome and interleukin releasing by the GSDMD-N-dependent membrane pores from pyroptotic hepatocytes activated macrophage metabolic reprogramming and M1 polarization, further exacerbating ALI. Nlrp3 deficiency alleviated ALI by suppressing hepatocyte pyroptosis and blocking communication between macrophages and hepatocytes. Our findings indicate the potential mechanisms of ALI from an intercellular communication perspective, and targeted-inhibition of DLGAP5 and -blockade of hepatocyte-macrophage interaction provide promising strategies for ALI treatment.}, }
@article {pmid40958166, year = {2025}, author = {Ghaly, TM and Rajabal, V and Russell, D and Colombi, E and Tetu, SG}, title = {EcoFoldDB: Protein Structure-Guided Functional Profiling of Ecologically Relevant Microbial Traits at the Metagenome Scale.}, journal = {Environmental microbiology}, volume = {27}, number = {9}, pages = {e70178}, doi = {10.1111/1462-2920.70178}, pmid = {40958166}, issn = {1462-2920}, support = {CE200100029//ARC Centre of Excellence in Synthetic Biology/ ; //Macquarie University Research Fellowship/ ; }, mesh = {*Metagenome ; *Metagenomics/methods ; *Bacteria/genetics/classification/metabolism ; Soil Microbiology ; Phylogeny ; *Microbiota/genetics ; Computational Biology/methods ; *Bacterial Proteins/genetics/chemistry ; *Databases, Protein ; Protein Conformation ; }, abstract = {Microbial communities are fundamental to planetary health and ecosystem processes. High-throughput metagenomic sequencing has provided unprecedented insights into the structure and function of these communities. However, functionally profiling metagenomes remains constrained due to the limited sensitivity of existing sequence homology-based methods to annotate evolutionarily divergent genes. Protein structure, more conserved than sequence and intrinsically tied to molecular function, offers a solution. Capitalising on recent breakthroughs in structural bioinformatics, we present EcoFoldDB, a database of protein structures curated for ecologically relevant microbial traits, and its companion pipeline, EcoFoldDB-annotate, which leverages Foldseek with the ProstT5 protein language model for rapid structural homology searching directly from sequence data. EcoFoldDB-annotate outperforms state-of-the-art sequence-based methods in annotating metagenomic proteins, in terms of sensitivity and precision. To demonstrate its utility and scalability, we performed structure-guided functional profiling of 32 million proteins encoded by 8000 high-quality metagenome-assembled genomes from the global soil microbiome. EcoFoldDB-annotate could resolve the phylogenetic partitioning of important nitrogen cycling pathways, from taxonomically restricted nitrifiers to more widespread denitrifiers, as well as identifying novel, uncultivated bacterial taxa enriched in plant growth-promoting traits. We anticipate that EcoFoldDB will enable researchers to extract ecological insights from environmental genomes and metagenomes and accelerate discoveries in microbial ecology.}, }
@article {pmid40957333, year = {2025}, author = {Sánchez, N and Merbach, I and Drabesch, S and Blagodatskaya, E and Jamoteau, F and Keiluweit, M and Bachelder, J and Tarkka, M and Muehe, EM}, title = {Bioavailability and phyto-extractability of metals in a peat-amended agricultural soil under climate stress.}, journal = {Journal of environmental management}, volume = {394}, number = {}, pages = {127167}, doi = {10.1016/j.jenvman.2025.127167}, pmid = {40957333}, issn = {1095-8630}, abstract = {Climate-induced mobilization of harmful metals in soils with a pH below 7 threatens food safety through plant uptake. While organic amendments like peat are known to immobilize metals, it remains unclear how their immobilization effectiveness changes under future climate scenarios and whether there is an optimal amendment threshold before immobilization turns into re-mobilization. This study assessed how varying peat input levels (3, 5 and 8 %) and projected climatic conditions (+4 °C, +320 ppmv CO2) affect metal fractionation, bioavailability, and uptake by a metal-tolerant plant in historically contaminated soils. Intermediate 5 % peat levels enhanced metal immobilization via organic matter complexation, reducing exchangeable Zn and Cd ∼2-fold compared to 3 % peat, despite acidification. At high 8 % peat input, a 0.65-unit pH decline and increased dissolved organic matter reversed this trend, increasing exchangeable Zn and Cd > 2-fold relative to 5 % peat. Chemical equilibrium modeling (WHAM VII) confirmed greater metal complexation with dissolved organic matter at higher 5-8 % peat levels. Under future climatic conditions-elevated temperature and CO2-metal immobilization improved at low 3 % peat input, likely due to stable organic matter and functional group buffering. Nevertheless, metal re-mobilization occurred at higher peat inputs, likely due to enhanced peat decomposition. Despite these variations, plant Cd uptake remained low across peat and climate treatments. This emphasizes peat's protective role against Cd while maintaining the plant's nutritional status for Zn. This study highlights the dual effects of peat amendments: intermediate levels optimize metal immobilization, but excessive amendments may destabilize harmful metals, especially under future conditions.}, }
@article {pmid40954372, year = {2025}, author = {Jauri, PV and Silva, C and Massa, AM}, title = {Early shifts in soil microbial community structure and functions upon application of a biofertilizer in a kaki (Diospyros kaki) orchard.}, journal = {Folia microbiologica}, volume = {}, number = {}, pages = {}, pmid = {40954372}, issn = {1874-9356}, abstract = {Biofertilizers are key tools for sustainable agriculture and soil health Maintenance, yet their specific effects on soil functions and microbiota remain unclear. In order to address this, we aimed to evaluate how a biofertilizer alters soil microbial communities, physicochemical properties, and functions after 18 months of periodical use in a kaki monoculture. We found that the biofertilizer indirectly reshaped microbial community structure-especially bacterial diversity-likely through interactions with the native microbiome. Functional changes included increased microbial biomass, nitrogen mineralization, and dehydrogenase activity, with reduced acid phosphatase activity. The composition of bacterial and fungal communities exhibited significant differences between biofertilizer-treated soils and control soils across most evaluated taxonomic levels. Biodiversity was altered with biofertilizer application in bacterial communities, while fungal communities were less affected. Microbial co-occurrence networks differed between the two soil treatments, although a few patterns were consistent among treated and control soils. A novel contribution of this work is the integration of co-occurrence network analysis with microbial functional traits, revealing that core microbial networks linked to nitrogen and phosphate cycling persist despite disturbance. These findings highlight the role of microbial biodiversity and community assembly in sustaining soil functions under biofertilizer application.}, }
@article {pmid40952163, year = {2025}, author = {Nir, I and Armoza-Zvuloni, R and Barak, H and De Los Ríos, A and McKay, CP and Kushmaro, A}, title = {The Biology, Microclimate, and Geology of a Distinctive Ecosystem Within the Sandstone of Hyper-Arid Timna Valley, Israel.}, journal = {Environmental microbiology reports}, volume = {17}, number = {5}, pages = {e70188}, doi = {10.1111/1758-2229.70188}, pmid = {40952163}, issn = {1758-2229}, support = {PID2023-147027NB-I00B//Agencia Estatal de Investigaci&#xf3;n. Write: Agencia Estatal de Investigacion (AEI), MICINN/ ; EXO-92-4//NASA AMES/ ; 3-17370//Minstry of Science and Technology (MOST), Israel/ ; }, abstract = {Microbial endolithic communities in the sandstone rocks of the southern Negev Desert, particularly in Timna Park, were initially discovered by Imre Friedmann and Roseli Ocampo-Friedmann in their pioneering study about 50 years ago. Nonetheless, this harsh microecosystem, dominated by cyanobacterial taxa, raises questions about the adaptive mechanisms that enable the survival of these microorganisms. The present study provides comprehensive data, including extensive precipitation records for the Timna Valley, and multi-year microclimatic data from a colonised site. It includes examinations of rock structure, as well as microscopic and metagenomic analysis. Our findings point to a distinct bacterial endolithic population dominated by the cyanobacterial genus Chroococcidiopsis. Although the taxa are well known, we show here how their exclusive persistence is driven by the sandstone's fine porosity and thermal properties, combined with rare, low-volume precipitation. This highly selective microenvironment highlights how specific rock and climate interactions can filter microbial diversity in hyper-arid deserts. Additionally, it demonstrates an adaptation strategy based on both short-term and decadal-scale dormancy. Thus, it offers new insights for the survival of these unique ecosystems and provides valuable perspectives for astrobiology and the search for evidence of microbial life on Mars.}, }
@article {pmid40951970, year = {2025}, author = {Guan, Y and Berne, E and Hennessy, RC and Garbeva, P and Nicolaisen, MH and Bak, F}, title = {NRPS gene dynamics in the wheat rhizoplane show increased proportion of viscosin NRPS genes of importance for root colonization during drought.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0085224}, doi = {10.1128/msphere.00852-24}, pmid = {40951970}, issn = {2379-5042}, abstract = {Secondary metabolites are bioactive compounds, diverse in structure, with versatile ecological functions, including key roles in mediating interactions between microorganisms and plants. Importantly, these compounds can promote the colonization of plant surfaces, such as roots, or modulate root exudates to enhance microbial recruitment and establishment. However, owing to the vast diversity of secondary metabolites, their importance in plant root colonization-particularly under stress conditions, such as drought-remains unclear. To determine the involvement of some of these secondary metabolites in root colonization, we used amplicon sequencing targeting the adenylation domain of the non-ribosomal peptide synthases (NRPSs) and the 16S rRNA gene from the rhizoplane of wheat grown in soil under normal and drought stress conditions. Results showed that drought transiently affected the bacterial community composition and the NRPS composition in the rhizoplane. We observed that drought selected for distinct groups of siderophores from different taxonomical groups, enriching for Streptomyces and depleting Pseudomonas siderophores. In addition, drought enriched Pseudomonas-derived NRPS genes encoding viscosin, a cyclic lipopeptide with biosurfactant properties, indicating that compounds linked to motility and colonization provide a competitive advantage during rhizoplane colonization under drought stress conditions. This observation was experimentally confirmed using the viscosin-producing P. fluorescens SBW25 and its viscosin-deficient mutant. A higher abundance of SBW25 colonized the roots under drought stress conditions compared to the viscosin-deficient mutant. In summary, our work demonstrates the potential for amplicon sequencing of NRPS genes, coupled with in planta experiments, to elucidate the importance of secondary metabolites in root colonization.IMPORTANCETo harness beneficial plant-microbe interactions for improved plant resilience, we need to advance our understanding of key factors required for successful root colonization. Bacterial-produced secondary metabolites are important in plant-microbe interactions; thus, targeting these genes generates new knowledge that is essential for leveraging bacteria for sustainable agriculture. We used amplicon sequencing of the NRPS A domain on the rhizoplane of wheat exposed to drought stress to identify important secondary metabolites in plant-microbe interactions during drought. We show that the siderophores respond differently to drought stress depending on taxonomic affiliation and that the potential to synthesize viscosin increases root colonization. Importantly, this study demonstrates the potential of amplicon sequencing of NRPS genes to reveal specific secondary metabolites involved in root colonization, particularly in relation to drought stress, and highlights how the resolution provided by this approach can link specific compounds to a specific stress condition in a soil system.}, }
@article {pmid40951136, year = {2025}, author = {Al Harrasi, RJ and Al Balushi, AY and Al Kindi, FI and Al Kindi, NA and Kamel, AH}, title = {Potential Role of Oral Microbiota in Medication-Related Osteonecrosis of the Jaw in Cancer Patients: A Narrative Review.}, journal = {Cureus}, volume = {17}, number = {8}, pages = {e89943}, pmid = {40951136}, issn = {2168-8184}, abstract = {Medication-related osteonecrosis of the jaw (MRONJ) is a severe complication frequently observed in cancer patients undergoing antiresorptive therapies, such as bisphosphonates and denosumab. Emerging evidence suggests that dysbiosis of the oral microbiota plays a pivotal role in the pathogenesis of MRONJ. The complex interplay between microbial communities, host immune responses, and the effects of cancer treatments creates an environment conducive to pathogenic colonization, chronic inflammation, and impaired bone healing, which are the key hallmarks of MRONJ. Chemotherapy, radiotherapy, and antiresorptive agents significantly disrupt oral microbiota homeostasis, reducing microbial diversity and the overgrowth of opportunistic pathogens. These alterations exacerbate the inflammatory responses, accelerate bone resorption, and impede tissue repair. The identification of specific microbial biomarkers associated with MRONJ could facilitate early detection and targeted interventions, such as antimicrobial and probiotic therapies, to restore the microbial balance and mitigate the risk of MRONJ. Furthermore, the implementation of personalized preventive protocols, including rigorous oral hygiene and multidisciplinary collaboration among oncologists, dentists, and microbiologists, is critical for reducing the incidence and severity of MRONJ in high-risk populations. Future research should focus on elucidating the mechanisms by which microbial dysbiosis contributes to MRONJ, validating microbiome-based diagnostic tools, and optimizing therapeutic strategies to preserve oral and systemic health in patients with cancer. Integrating microbial ecology into the MRONJ management framework offers a promising avenue for addressing this challenging condition and improving the outcomes for vulnerable individuals.}, }
@article {pmid40950580, year = {2025}, author = {Panteleev, V and Kulbachinskiy, A and Gelfenbein, D}, title = {Evaluating phage lytic activity: from plaque assays to single-cell technologies.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1659093}, pmid = {40950580}, issn = {1664-302X}, abstract = {Bacteriophages are the most abundant biological entities on Earth, playing critical roles in microbial ecology, evolution, and horizontal gene transfer. Since the discovery of bacteriophages in the early 20th century, a wide range of techniques has been developed to study their lytic activity. This review provides a perspective on the wide range of methods for studying phage-bacteria interactions, spanning classical bulk-culture techniques and modern single-cell and high-throughput approaches. The first section covers solid culture methods relying on plaque formation phenomenon, which allow for quantification of infectious viruses, phage host-range establishment, and analysis of certain phage traits, now augmented by robotic high-throughput screening. The second section focuses on liquid culture approaches, utilizing optical density measurements, quantitative PCR, metabolic assays and cell damage assays to measure the infection dynamics. The third section details single-cell techniques, which help to dissect the heterogeneity of infection within cell populations, using microscopy, microfluidics, next-generation sequencing, and Hi-C methods. The integration of these diverse methods has greatly advanced our understanding of the molecular mechanisms of phage infection, bacterial immunity, and facilitated phage therapy development. This review is dedicated to the 110th anniversary of phage discovery and is aimed to guide researchers in selecting optimal techniques in the fast-growing field of phage biology, phage-host interactions, bacterial immunity, and phage therapy.}, }
@article {pmid40950160, year = {2025}, author = {Pratyush, MR and Prentice, JA and Eutsey, RA and Mikheyeva, I and Hiller, NL and Bridges, AA}, title = {Label-free microscopy enables high-throughput identification of genes controlling biofilm development.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.09.02.673883}, pmid = {40950160}, issn = {2692-8205}, abstract = {The biofilm mode of growth plays a critical role in microbial ecology and in the persistence of human pathogens. Yet, much remains unknown regarding the molecular determinants of biofilms in human pathogens. In this study, we present label-free analysis of biofilms (LFAB), an imaging approach that combines time-lapse, low-magnification brightfield microscopy with regional optical density measurements to quantify biofilm biomass. Unlike other approaches to biofilm biomass quantification, LFAB enables real-time, non-perturbative, and high-throughput monitoring of biofilms. We validated LFAB in diverse microbes and found that our measurements strongly correlate with traditional biofilm assays. We then used LFAB to identify and characterize critical factors mediating biofilm formation in Streptococcus pneumoniae , a major human pathogen whose biofilm lifecycle is known to be intimately related to colonization and infection. Initial characterization revealed that S. pneumoniae microcolonies form by radial expansion of attached cells, displaying reproducible morphology and growth dynamics. Screening of a transposon mutant library revealed that genes spanning carbohydrate metabolism, signaling, surface binding, cell wall synthesis, and adhesion impinge on the biofilm lifecycle of S. pneumoniae . We performed follow-up investigations of choline binding protein A (CbpA) and its adjacently encoded two-component system regulator, which we find are critical for the dynamics of microcolony biofilms in S. pneumoniae . Overall, this work establishes LFAB as a powerful approach for identifying and characterizing biofilm determinants across bacteria and uncovers key regulators of the biofilm lifecycle in a major human pathogen.}, }
@article {pmid40949998, year = {2025}, author = {Garabello, E and Yoon, H and Reid, MC and Giometto, A}, title = {Tunable Low-Rate Genomic Recombination with Cre-lox in Escherichia coli : A Versatile Tool for Environmental Biosensing and Synthetic Biology.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.10.02.616356}, pmid = {40949998}, issn = {2692-8205}, abstract = {UNLABELLED: The ability to induce heritable genomic changes in response to environmental cues is valuable for environmental biosensing, for experimentally probing microbial ecology and evolution, and for synthetic biology applications. Site-specific recombinases provide a route to genetic memory via targeted DNA modifications, but their high specificity and efficiency are offset by leaky expression and limited tunability in prokaryotes. We developed a tightly regulated, titratable Cre recombinase system for Escherichia coli that achieves low recombination rates and minimal basal activity. Implemented on both plasmids and the chromosome, the latter showed superior retention of genetic memory across generations. These features make the system broadly useful for environmental biosensing and other applications. To demonstrate applicability to environmental biosensing, we developed a whole-cell recombination-based biosensor for arsenite, a toxic and ubiquitous pollutant that is primarily mobilized in anoxic environments such as flooded soils, sediments, and aquifers. However, existing arsenite whole-cell biosensors face limitations in sensitivity and workflow in anaerobic settings. Our biosensor reliably recorded anoxic arsenite exposure as a stable genetic memory for delayed fluorescence readout in aerobic conditions, with detection sensitivity comparable to conventional wet chemical methods. By decoupling exposure from measurement, this approach offers a foundation for arsenite biosensing under field-relevant conditions, including redox variability and other physicochemical gradients, without the constraints of anoxic measurement. More broadly, the ability to induce low-rate, heritable genetic changes expands the genetic toolkit for environmentally responsive systems, with applications in environmental monitoring, bioproduction, bioengineering, as well as experimental studies of microbial ecology, evolution, and host-microbe interactions.<br><br>IMPORTANCE: Arsenic is a toxic and globally prevalent pollutant, mobilized primarily under anoxic conditions where detection is challenging. Whole-cell biosensors offer a promising route for monitoring bioavailable arsenic in situ , but their development has largely focused on aerobic conditions, with anoxic assays limited by sensitivity and workflow constraints. Genetic tools that enable heritable, low-frequency genomic changes in bacteria can expand biosensor capabilities by recording transient exposures and supporting applications in environmental monitoring, synthetic biology, and quantitative microbial population dynamics research. Here, we developed a tightly regulated, chemically inducible Cre- lox system in Escherichia coli that enables recombination at low, tunable rates. We demonstrate its utility by constructing an arsenite biosensor that reliably detects low concentrations and records exposures under both aerobic and anoxic conditions. This approach is broadly applicable for biosensors designed for field deployment and for experiments investigating microbial ecology and evolution, where controllable genetic diversification may be desirable.}, }
@article {pmid40945448, year = {2025}, author = {Pei, T and Liu, X and Xu, G and Xin, T and Wu, G and Ma, B and Liu, X and Zhang, H}, title = {Hydraulic regimes-driven microbial community assembly and network stability in drinking water distribution systems: Mechanistic linkages with transport distance and stagnation effects.}, journal = {Journal of hazardous materials}, volume = {498}, number = {}, pages = {139825}, doi = {10.1016/j.jhazmat.2025.139825}, pmid = {40945448}, issn = {1873-3336}, abstract = {Hydraulic regimes within drinking water distribution system (DWDS) critically alter water quality and microbial communities, posing significant public health risks. However, how hydraulic regimes modify microbial (bacteria and fungi) assembly and network stability in DWDS remains poorly understood. This study investigated spatiotemporal dynamics of water quality and microbial succession across a full-scale DWDS, focusing on hydraulic regimes (transport distance (1-5 km) and stagnation) effects. Results indicated that increasing transport distance and hydraulic stagnation led to water quality deterioration, while concurrently amplifying microbial diversity and triggering community structural reorganization. Transport distance predominantly influenced microbial diversity during summer, whereas stagnation dominated community succession in winter. Besides, microbial species richness was greater in the 5 km tap water in summer, while higher species evenness was observed in winter. Integrated neutral community modeling and null model analysis (βNTI and RCbray metrics) demonstrated that a deterministic to stochastic transition in microbial assembly mechanisms - from niche-based selection at treatment plants to increasing stochastic dominance along distribution networks (|βNTI| < 2). Hydraulic regimes enhanced microbial stability and complexity, evidenced by elevated graph density and natural connectivity, conferring rapid resilience to bacterial and fungal communities. These findings establish a hydraulic-microbial ecology coupling framework within DWDS, proposing operational strategies for hydraulic regime optimization management in drinking water management.}, }
@article {pmid40945439, year = {2025}, author = {Wang, W and Yang, W and Jiang, L and Yao, C and Zhang, Z and Xu, M and Yan, X and Qian, X}, title = {Applications of Oxford Nanopore Technology in the analysis of antibiotic resistance genes: A review.}, journal = {Journal of hazardous materials}, volume = {498}, number = {}, pages = {139824}, doi = {10.1016/j.jhazmat.2025.139824}, pmid = {40945439}, issn = {1873-3336}, abstract = {Antibiotic misuse has led to the rapid expansion of the antibiotic resistance gene (ARGs) pool, making antimicrobial resistance (AMR) a major global health threat. The efficient identification of ARGs and the development of strategies to control AMR have become research hotspots. However, the Next-generation sequencing (NGS) has many limitations in ARGs identification, hindering our understanding of their genetic context. This review uses Oxford Nanopore Technology (ONT) as an example to summarize the advantages and application prospects of the third-generation sequencing technologies in the migration and transmission of ARGs. By analyzing 12 sets of NGS - ONT datasets, this review demonstrates the strengths and limitations of ONT from multiple perspectives, including the identification of ARGs, key pathogens, plasmids, viruses, and horizontal gene transfer events, and provides detailed analytical workflows. It offers comprehensive analytical approaches and application insights for ARGs research based on ONT, highlighting the importance and necessity of the third-generation sequencing technologies in studying the prevalence and transmission of ARGs in complex environments.}, }
@article {pmid40945060, year = {2025}, author = {Zhang, M and Zhao, C and Zhang, W and Guo, Y and Han, F and Li, Y and Zhou, W}, title = {Stable ammonium assimilation mediates the metabolic adaptation of halophilic microbiome to hypo-osmotic stress in wastewater treatment.}, journal = {Water research}, volume = {288}, number = {Pt A}, pages = {124572}, doi = {10.1016/j.watres.2025.124572}, pmid = {40945060}, issn = {1879-2448}, abstract = {Salinity barrier shapes distinct microbial ecology on earth, and applications of microbiomes are frequently hindered by trans-osmotic challenges. As a central nutrient metabolism, nitrogen transformations may contribute to conquering osmotic perturbations in microbiomes, and thus understanding the nitrogen metabolic responses to non-isosmotic exposure is crucial. Here we uncover that ammonium assimilation mediates the maintenance of physicochemical properties in a marine-derived halophilic microbiome when adapting to hypo-osmotic stress from salinity of 3 % to 0.5 %. An adaptive threshold at salinity approximately around 1 % is observed that reducing osmotic gradients disrupt ammonium assimilation and microbial community stability with decreasing specific ammonium assimilation rates from 2.34 to 0.62 mg-N/(g MLSS h). Multi-omics analysis demonstrates that enhancing ammonium-assimilating function prevents nitrogen metabolic differentiation and promotes production of amino acids and their derivatives recognized as osmoprotectants. Genes coding for transporter systems and mechanosensitive channels are also up-regulated. The results of this study suggest that maintaining stable ammonium assimilation could enhance the amino acid metabolism and subsequent osmoprotectant production, thus improving the metabolic adaptation of the halophilic microbiome to hypotonic conditions. Our findings provide insights into the adaptation of microbiomes to osmotic alterations, and highlight the importance of enhancing ammonium assimilation in engineering microbiomes under environmental stress.}, }
@article {pmid40941211, year = {2025}, author = {Yu, Z and Zhao, H and Ma, T and Zhang, X and Yan, Y and Zhu, Y and Yu, Y}, title = {Insights into the Composition and Function of Virus Communities During Acetic Acid Fermentation of Shanxi Aged Vinegar.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {17}, pages = {}, doi = {10.3390/foods14173095}, pmid = {40941211}, issn = {2304-8158}, support = {2023M741438//China Postdoctoral Science Foundation/ ; 20220401931002//Open Project Program of Shanxi Provincial Key Laboratory for Vinegar Fermentation Science and Engineering/ ; }, abstract = {Viruses play a regulatory role in microbial ecology. Traditional fermented foods have complex fermentation environments with abundant viral participation, yet current research on viral communities in fermented foods remains insufficient. Traditional, manually produced solid-state fermented vinegar serves as an excellent model for studying the role of viral communities in fermented foods. Using metagenomic approaches, this study investigates the structure and dynamics of viral communities during the acetic acid fermentation process of Shanxi aged vinegar. All identified viruses were bacteriophages, and the dominant families were identified as Herelleviridae, Autographiviridae, and Stanwilliamsviridae. The richness and diversity of viral communities exhibited significant variations during acetic acid fermentation. Furthermore, correlation analysis revealed a strong association (p < 0.01) between core bacteria and core viruses. Functional annotation revealed the presence of viral genes associated with amino acid and carbohydrate metabolism. Notably, abundant auxiliary carbohydrate-active enzyme (CAZyme) genes were identified in viruses, with glycoside hydrolases (GHs), glycosyltransferases (GTs), and carbohydrate-binding modules (CBMs) demonstrating particularly high abundance. Additionally, several antibiotic resistance genes were detected in viruses. This study elucidates the impact of viral communities on microbial dynamics during food fermentation, advancing our understanding of viral roles in traditional fermented food ecosystems.}, }
@article {pmid40940565, year = {2025}, author = {Gilbert, JA and Peixoto, RS and Scholz, AH and Dominguez Bello, MG and Korsten, L and Berg, G and Singh, B and Boetius, A and Wang, F and Greening, C and Wrighton, K and Bordenstein, S and Jansson, JK and Lennon, JT and Souza, V and Thomas, T and Cowan, D and Crowther, TW and Nguyen, N and Harper, L and Haraoui, LP and Ishaq, SL and Redford, K}, title = {Launching the IUCN Microbial Conservation Specialist Group as a global safeguard for microbial biodiversity.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {40940565}, issn = {2058-5276}, }
@article {pmid40935756, year = {2025}, author = {Ledford, SM and Geffre, P and Marschmann, GL and Karaoz, U and Brodie, EL and Meredith, LK}, title = {Volatile traits expand the microbial playbook.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2025.08.001}, pmid = {40935756}, issn = {1878-4380}, abstract = {Microbial metabolic functions are increasingly conceptualized as fitness-regulating traits. However, volatile compounds (the volatilome), despite their key roles in metabolism and ecology, are often overlooked in trait-based frameworks. We propose that volatile traits not only reflect ecological strategies but also shape them by mediating responses to selection pressures. Their volatility affects diffusion, substrate access, and interactions across space, conferring selective advantages as resources or waste products. We outline approaches to incorporate volatile traits into predictive models to improve understanding of microbial selection and community dynamics. This integration enables a more holistic view of microbial life by accounting for the ecological and evolutionary consequences of volatile-mediated processes.}, }
@article {pmid40934885, year = {2025}, author = {Kujawska, M and Seki, D and Chalklen, L and Malsom, J and Kiu, R and Goatcher, S and Christoforou, I and Mitra, S and Crouch, L and Hall, LJ}, title = {Host-specific microbiome and genomic signatures in Bifidobacterium reveal co-evolutionary and functional adaptations across diverse animal hosts.}, journal = {Cell host &amp; microbe}, volume = {33}, number = {9}, pages = {1502-1517.e13}, doi = {10.1016/j.chom.2025.08.008}, pmid = {40934885}, issn = {1934-6069}, abstract = {Animals harbor divergent microbiota, including various Bifidobacterium species, yet their evolutionary relationships and functional adaptations remain understudied. Using samples from insects, reptiles, birds, and mammals, we integrated taxonomic, genomic, and predicted functional annotations to uncover how Bifidobacterium adapts to host-specific environments. Host phylogeny is a major determinant of gut microbial composition. Distinct microbiota in mammalian and avian hosts reflect evolutionary adaptations to dietary niches, such as carnivory, and ecological pressures. At a strain-resolved level, Bifidobacterium and their hosts exhibit strong co-phylogenetic associations, driven by vertical transmission and dietary selection. Functional analyses highlight striking host-specific adaptations in Bifidobacterium, particularly in carbohydrate metabolism and oxidative stress responses. In mammals, Bifidobacterium strains are enriched in glycoside hydrolases tailored to complex carbohydrate-rich diets, including multi-domain GH13_28 α-amylases associated with degradation of resistant starch. Together, these findings deepen our understanding of host-microbe co-evolution and the critical role of microbiota in shaping animal health and adaptation.}, }
@article {pmid40931664, year = {2025}, author = {Krespach, MKC and Rosin, M and Scherlach, K and Stroe, MC and Hertweck, C and Brakhage, A}, title = {The Linear Arginoketides Neotetrafibricin A, B, and C have Algicidal and Signal Function in Microbial Interactions.}, journal = {Chembiochem : a European journal of chemical biology}, volume = {}, number = {}, pages = {e202500479}, doi = {10.1002/cbic.202500479}, pmid = {40931664}, issn = {1439-7633}, support = {239748522-CRC 1127//Deutsche Forschungsgemeinschaft/ ; }, abstract = {Soils harbor some of the most diverse microbiomes on Earth. Interactions within these microbial communities are often mediated by natural products, many functioning as chemical signals. Specialized metabolites known as arginoketides, or arginine-derived polyketides, have been linked to mediate these interactions. However, the effect of linear arginoketides on soil microalgae has not yet been investigated. Here, we report that Streptomyces mashuensis DSM40221 produces the linear arginoketide neotetrafibricin A, and show that it exhibits algicidal activity against the green alga Chlamydomonas reinhardtii and induces production of orsellinic acid and derivatives encoded by the silent ors biosynthetic gene cluster (BGC) in the fungus Aspergillus nidulans. Thus, neotetrafibricin serves as an inter-kingdom signaling molecule. Genome mining identified the neotetrafibricin BGC in S. mashuensis. Disrupting the first polyketide synthase gene abolished neotetrafibricin production. Further mutational studies identified two neotetrafibricin congeners, including the novel neotetrafibricin C, which contains a terminal guanidino group. Structure-activity relationship analyses revealed that neither the terminal amino group nor the sugar moiety is essential for its algicidal activity or the induction of the ors BGC in the fungus. These findings expand the understanding of linear arginoketides in microbial ecology and highlight their potential as multifunctional signaling compounds in soil environments.}, }
@article {pmid40931662, year = {2025}, author = {Bains, JS and Baggaley, AW and Croze, OA}, title = {Drift velocity of bacterial chemotaxis in dynamic chemical environments.}, journal = {Philosophical transactions. Series A, Mathematical, physical, and engineering sciences}, volume = {383}, number = {2304}, pages = {20240261}, pmid = {40931662}, issn = {1471-2962}, support = {//EPSRC/ ; }, mesh = {*Chemotaxis/physiology ; *Models, Biological ; Computer Simulation ; *Bacterial Physiological Phenomena ; Monte Carlo Method ; Chemotactic Factors ; Bacteria ; }, abstract = {Chemotaxis allows swimming bacteria to navigate through chemical landscapes. To date, continuum models of chemotactic populations (e.g. Patlak-Keller-Segel models) have considered bacteria responding only to spatial chemical gradients. In these models, chemotactic advection is modelled through a drift velocity proportional to the spatial chemical gradient. In nature and industry, however, bacterial populations experience dynamic, spatio-temporally varying chemical environments, such as the neighbourhood of lysing phytoplankton cells. Recent analyses have shown how temporal gradients can 'confuse' individual bacteria, impacting the precision of their gradient estimation. However, very few studies have considered how temporal gradients influence the chemotactic drift velocity of whole populations. Here, we use Monte Carlo simulations to infer the drift velocity of a population when both spatial and temporal gradients are present. We propose an ansatz for the drift velocity, which fits the simulations well. This ansatz allows us to account for how temporal gradients can significantly impact chemotaxis of bacterial populations up a spatial gradient. We explore the consequences of this new effect through a Patlak-Keller-Segel type model applied to single decaying and oscillating pulses of chemoattractant. Finally, we discuss possible biological consequences of our results and extensions of our modelling framework.This article is part of the theme issue 'Biological fluid dynamics: emerging directions'.}, }
@article {pmid40930771, year = {2025}, author = {Feng, L and Loi, JX and Séneca, J and Pjevac, P and Adnan, FH and Ngoh, GC and Khor, BC and Aris, AM and Oshiki, M and Daims, H and Chua, ASM}, title = {Nitrifying Communities in Biological Nitrogen Removal Processes at Tropical Municipal Wastewater Treatment Plants.}, journal = {Microbes and environments}, volume = {40}, number = {3}, pages = {}, doi = {10.1264/jsme2.ME25036}, pmid = {40930771}, issn = {1347-4405}, mesh = {*Nitrification ; *Wastewater/microbiology/chemistry ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Nitrogen/metabolism ; RNA, Ribosomal, 16S/genetics ; Ammonia/metabolism ; *Archaea/classification/genetics/metabolism/isolation &amp; purification ; Malaysia ; Sewage/microbiology ; Phylogeny ; Tropical Climate ; Water Purification ; Oxidoreductases/genetics ; Oxidation-Reduction ; In Situ Hybridization, Fluorescence ; }, abstract = {Nitrifying communities in activated sludge play a crucial role in biological nitrogen removal processes in municipal wastewater treatment plants. While extensive research has been conducted in temperate regions, limited information is available on nitrifiers in tropical regions. The present study investigated all currently known nitrifying communities in two full-scale municipal wastewater treatment plants in Malaysia operated under low-dissolved oxygen (DO) (0.2-0.7‍ ‍mg‍ ‍DO‍ ‍L[-1]) or high-DO (2.0-5.5‍ ‍mg‍ ‍DO‍ ‍L[-1]) conditions at 30°C. The core nitrifiers in the municipal wastewater treatment plants were Nitrosomonas (ammonia-oxidizing bacteria, AOB), Nitrospira (nitrite-oxidizing or complete ammonia-oxidizing, comammox, bacteria), and ammonia-oxidizing archaea (AOA) as identified by a 16S rRNA gene amplicon sequencing ana-lysis and corroborated by 16S rRNA-targeted fluorescence in situ hybridization. A quantitative polymerase chain reaction (qPCR) targeting ammonia monooxygenase subunit A (amoA) genes revealed stable populations of comammox Nitrospira and AOB in both wastewater treatment plants. AOA were detected in only one of the plants and their population sizes fluctuated, with higher temporary abundance under high-DO conditions. These results provide important insights into the composition and dynamics of nitrifying communities in tropical municipal wastewater treatment plants.}, }
@article {pmid40928120, year = {2025}, author = {Lauwens, K and Saghi, M and Germonpré, PJ and Zayed, N and Boon, N and Bernaerts, K and Teughels, W and Van Holm, W}, title = {Can We Combine Mouthrinses With Probiotics? An Evaluation of Their Compatibility and Combined Therapy on Oral Biofilms.}, journal = {Journal of periodontal research}, volume = {}, number = {}, pages = {}, doi = {10.1111/jre.70033}, pmid = {40928120}, issn = {1600-0765}, abstract = {AIM: Multiple oral pathologies requiring antiseptic mouthrinses for prevention or treatment. However, nonselective elimination of the microbes may also harm beneficial commensal, healthy bacteria. Promicrobial strategies, such as probiotics, aim to rebalance the oral microbiome rather than eradicate it; however, we hypothesised that their incorporation might be challenged due to the microbiome's inherent resistance to outsiders. In this study, their combined effect on an in vitro oral biofilm model was assessed. Instead of comparing mouthrinses to probiotics, could they be combined to obtain the best of both worlds?<br><br>METHODS: The compatibility of two commonly used Limosilactobacillus reuteri strains with 13 commercially available mouthrinses was tested by evaluating probiotic survival in the mouthrinses and their combined effect on a multispecies in&#xa0;vitro biofilm model.<br><br>RESULTS: Differences in compatibility were observed. Several mouthrinses showed moderate compatibility and improved the probiotics incorporation into biofilms. One mouthrinse (O7 Active Oxygen) demonstrated the most favourable compatibility, enabling abundant probiotic incorporation and beneficial biofilm composition changes.<br><br>CONCLUSION: The combination of mouthrinses and probiotics has the potential to improve the treatment of oral pathologies and promote a healthier oral microbiome, although compatibility varies.}, }
@article {pmid40927988, year = {2025}, author = {Veresoglou, SD}, title = {Mycorrhizal ecology: In the land of the one-eyed king.}, journal = {Journal of experimental botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/jxb/eraf399}, pmid = {40927988}, issn = {1460-2431}, abstract = {Unlike most of the other disciplines in microbial ecology, a substantial fraction of the theory on mycorrhizal ecology originates from times when assaying microbes was laborious and inefficient. Most of those hypotheses target, as a result, the plant partner of the symbiosis, or at best treat the two mycorrhizal partners as a unified organism, a holobiont. I here address the legacy of this era of mycorrhizal ecology, as a means of systematizing our understanding of the discipline, but also identifying gaps of knowledge. First, I pair and review hypotheses that align with the holobiont concept with complementary hypotheses that explicitly consider the fitness of the mycorrhizal fungus. Second, I generate a hierarchy of hypotheses in mycorrhizal ecology to showcase the high potential for classifying theory that the distinction between hypotheses considering mycorrhiza as either a holobiont or an association of two individual partners maintains. Third, I identify settings that might dictate when to better abstract mycorrhizas into holobionts and when to consider all their partners individually to foster research progress. I conclude the review with suggestions on how to further unify expectations in mycorrhizal ecology.}, }
@article {pmid40926344, year = {2025}, author = {Sarango Flores, S and Cordovez, V and Oyserman, BO and Arias Giraldo, LM and Stopnisek, N and Raaijmakers, JM and van 't Hof, P}, title = {Microbiome-Mediated Resistance of Wild Tomato to the Invasive Insect Prodiplosis longifila.}, journal = {Environmental microbiology reports}, volume = {17}, number = {5}, pages = {e70190}, doi = {10.1111/1758-2229.70190}, pmid = {40926344}, issn = {1758-2229}, support = {024.004.014/NWO_/Dutch Research Council/Netherlands ; CZ07-000440-2018//SENESCYT scholarship/ ; 10093//Chancellor Research Grant/ ; }, mesh = {*Solanum lycopersicum/microbiology/parasitology/immunology ; Animals ; *Microbiota ; *Soil Microbiology ; *Diptera/physiology ; Ecuador ; Plant Roots/microbiology/parasitology ; Introduced Species ; Bacteria/classification/genetics/isolation &amp; purification ; Plant Leaves/parasitology ; }, abstract = {Plant roots are colonised by diverse communities of microorganisms that can affect plant growth and enhance plant resistance to (a) biotic stresses. We investigated the role of the indigenous soil microbiome in the resistance of tomato to the invasive sap-sucking insect Prodiplosis longifila (Diptera: Cecidomyiidae). Native and agricultural soils were sampled from the Andes in Southern Ecuador and tested, in greenhouse bioassays, for leaf tissue damage caused by P. longifila on domesticated Solanum lycopersicum cv. Moneymaker and wild tomato S. pimpinellifolium. We observed no significant differences in insect damage between domesticated and wild tomatoes grown in live native or agricultural soils. However, when grown in sterilised native and agricultural soils, wild tomato was more severely affected by the insect than the domesticated tomato. Microbiome analyses revealed that soil sterilisation impacted overall rhizobacterial diversity and abundance in wild tomato. Particularly, Actinoplanes abundance was reduced upon sterilisation, which significantly correlated with loss of insect resistance. Metagenome analyses and genome assembly of Micromonosporaceae (Actinoplanes family) suggested a putative association between motility, chemotaxis, membrane transport, chorismate, and lanthipeptide biosynthesis and insect resistance. This indicates that wild S. pimpinellifolium, in contrast to domesticated S. lycopersicum, relies on specific members of the root-associated microbiome for P. longifila protection.}, }
@article {pmid40925292, year = {2025}, author = {Sumana, SL and Tarawallie, S and Osei, SA and Kamara, AM and Xiaofei, Y and Mansaray, A and Zhang, J}, title = {Chemical interactions between filter-feeding mussels and Ulvaprolifera: The role of dissolved organic matter and secondary metabolites in growth promotion and competition inhibition of algal species.}, journal = {Marine environmental research}, volume = {212}, number = {}, pages = {107529}, doi = {10.1016/j.marenvres.2025.107529}, pmid = {40925292}, issn = {1879-0291}, abstract = {This review examines the chemical and ecological interactions between filter-feeding mussels and the green macroalga Ulva prolifera in integrated multi-trophic aquaculture (IMTA) systems. Mussels are crucial for nutrient recycling, as they filter water and release bioavailable compounds such as ammonium (NH4[+]), urea (CO(NH2)2), and dissolved organic matter (DOM). These compounds promote Ulva growth and enhance microbial activity. In turn, U. prolifera produces sulfated polysaccharides, phenolics, and halogenated metabolites that can influence microbial communities, suppress competitors, and potentially affect mussel physiology at high concentrations. The review emphasizes the interconnectedness of nutrient exchange, DOM cycling, and microbial genes such as pmoA and mcrA, highlighting the novelty of integrating microbial ecology with biogeochemical cycles and ecosystem outcomes, illustrating both the synergies and risks present in co-culture systems. While moderate production of metabolites helps control biofouling and maintain ecosystem stability, excessive DOM or allelochemical accumulation can hinder mussel filtration and lead to hypoxia. Maintaining specific thresholds, such as DOM concentrations below 5 mg C/L and labile-to-refractory DOM ratios above 1:1, is essential for balance. This synthesis integrates microbial ecology, metabolite feedbacks, and biogeochemical processes to provide a framework for resilient IMTA design. It also emphasizes practical strategies like adjusting stocking densities, optimizing water exchange, and employing microbial monitoring tools to promote sustainable IMTA practices. By linking molecular interactions to ecosystem-scale outcomes, the review offers guidance for sustainable aquaculture systems that enhance productivity, minimize environmental risks, and improve resilience in the face of climate stress.}, }
@article {pmid40923842, year = {2025}, author = {Alteio, LV and Spiegel, F and Rychli, K and Wagner, M}, title = {Nevertheless, they persist: addressing the stalemate of persistence in food-associated Listeria monocytogenes research.}, journal = {Critical reviews in microbiology}, volume = {}, number = {}, pages = {1-21}, doi = {10.1080/1040841X.2025.2555938}, pmid = {40923842}, issn = {1549-7828}, abstract = {Foodborne illness is a critical food safety and public health concern, often resulting from contamination events by resident pathogens in food processing environments (FPEs). Listeria monocytogenes, the causative agent of listeriosis, can persist in FPEs over long time periods. Despite rigorous research on the phenotypic and genotypic traits of L. monocytogenes, no clear pattern has arisen to explain why some strains are able to persist. Researchers face definitional and methodological challenges, which influence identification and comparison of persistent and non-persistent strains. Moreover, only weak associations between persistence and gene-level patterns have been detected, necessitating new perspectives. In this review, we synthesize years of research based on whole genome sequencing, highlighting sequence-type and gene-level patterns linked to persistence. As these patterns do not robustly explain persistence, we critically assess how applied definitions and methodological approaches have shaped, and potentially biased, our current understanding. We evaluate existing hypotheses on persistence and suggest future research directions, integrating insights from ecology, evolution, and predictive modeling to disentangle factors and mechanisms that enable L. monocytogenes to persist in food processing environments.}, }
@article {pmid40923499, year = {2025}, author = {Van Hecke, T and Jakobsen, LMA and Tian, X and Van Pee, J and Elias Masiques, N and Vermeersch, AS and Deforce, D and Van Nieuwerburgh, F and Van Royen, G and De Vrieze, J and Bertram, HC and De Smet, S}, title = {Metabolic consequences and gut microbiome alterations in rats consuming pork or a plant-based meat analogue.}, journal = {Food &amp; function}, volume = {}, number = {}, pages = {}, doi = {10.1039/d5fo02197a}, pmid = {40923499}, issn = {2042-650X}, abstract = {It is unknown how human health is affected by the current increased consumption of ultra-processed plant-based meat analogues (PBMA). In the present study, rats were fed an experimental diet based on pork or a commercial PBMA, matched for protein, fat, and carbohydrate content for three weeks. Rats on the PBMA diet exhibited metabolic changes indicative of lower protein digestibility and/or dietary amino acid imbalance, alongside increased mesenteric (+38%) and retroperitoneal (+20%) fat depositions despite lower food and energy intake. In contrast, rats on the pork diet demonstrated signs of a disturbed gut-liver axis with increased liver weight (+15%) and blood low-density lipoprotein (+86%), which may have been facilitated by gut microbial changes. The colon of rats on the PBMA diet was characterized by an outgrowth of bacterial groups including Muribaculaceae, Roseburia and various Eubacterium spp. known to improve cholesterol metabolism, whereas a remarkable outgrowth of Akkermansia, Oscillospiraceae and Desulfovibrionaceae in rats on the pork diet may be conducive to colon mucin degradation. Effects on oxidative stress parameters were equivocal, with increased lipid oxidation (+27%) in the colon mucosa of PBMA-fed rats, whereas lower blood levels of the endogenous antioxidant glutathione (-30%) were found in pork-fed. Overall, the present rat study reveals major differences in the physiological and microbiota-related responses to diets containing either conventional pork or PBMA, which could have implications for human health.}, }
@article {pmid40919941, year = {2025}, author = {Bodelier, PL}, title = {Expansion of aerobic methanotrophy to the phylum of Actinomycetota and its environmental implications.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0133425}, doi = {10.1128/aem.01334-25}, pmid = {40919941}, issn = {1098-5336}, abstract = {For over a century, taxonomically validated pure cultures of aerobic methanotrophs belonged to Pseudomonadota, or since 2007, Verrucomicrobiota. A recent article published in Applied and Environmental Microbiology by H. Kambara, T. Kawamoto, S. Matsushita, T. Kindaichi, et al. (91:e00796-25, 2025, https://doi.org/10.1128/aem.00796-25) expands the phylogenetic radiation of aerobic methanotrophs to the Actinomycetota with the description of Ca. Mycobacterium methanica MM1. This isolate confirms and strengthens the position of the genus Mycobacterium as methanotrophs displaying a wide pH and ammonia tolerance and expanding the habitat range for methane capture.}, }
@article {pmid40919204, year = {2025}, author = {Shukla, A and Goswami, D and Jha, CK}, title = {Editorial: Navigating challenges and innovations in antimicrobial resistance, environmental microbiology, and industrial solutions (ARTEMIS).}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1677866}, doi = {10.3389/fmicb.2025.1677866}, pmid = {40919204}, issn = {1664-302X}, }
@article {pmid40916293, year = {2025}, author = {Ma, J and Yin, Z and Zhang, K and Zhang, X and Ye, L}, title = {Concentration-specific effects of micropollutants on microbial communities and antibiotic resistance genes in activated sludge systems.}, journal = {Journal of hazardous materials}, volume = {497}, number = {}, pages = {139720}, doi = {10.1016/j.jhazmat.2025.139720}, pmid = {40916293}, issn = {1873-3336}, abstract = {Micropollutants are widespread in wastewater systems and can impact microbial communities and the transfer of antibiotic resistance genes (ARGs). Nevertheless, the specific concentration thresholds for these effects under environmental conditions remain largely unknown. This study evaluated six micropollutants at five environmentally relevant concentrations (0.1-500 μg/L) to clarify the concentration-dependent effects on microbial ecology and ARG dynamics. The results showed micropollutant exposure generally reduced microbial diversity. Most micropollutants, except triclosan (TCS), influenced microbial community structure and ARG profiles at even 0.1-1 μg/L, indicating a close association between taxonomic shifts and resistome changes. In contrast, low concentration TCS (0.1-1 μg/L) affected ARG dynamics without altering community composition. Moreover, ARG abundance generally increased with micropollutant concentration. Nevertheless, the acetaminophen and naproxen posed lower horizontal transfer risks despite ARG elevation. In contrast, diclofenac and TCS markedly enhanced ARG transfer at ≥ 10 and 1 μg/L, respectively. Network analysis identified high-risk ARG hosts (e.g., Burkholderiales, Rhodocyclaceae) and highlighted mobile genetic elements involved in replication/recombination/repair. These findings demonstrate that micropollutant-induced resistance dissemination is both concentration-specific and compound-specific, guiding ARG management in wastewater.}, }
@article {pmid40915198, year = {2025}, author = {Zhai, Y and Chen, G and Xiao, Y and Tian, H and Liu, G and Li, X and Bai, J and Cui, B}, title = {Urbanization cast a shadow over bacterial community in river sediment: Insights from community diversity, assembly processes and network interactions.}, journal = {Journal of environmental management}, volume = {393}, number = {}, pages = {127190}, doi = {10.1016/j.jenvman.2025.127190}, pmid = {40915198}, issn = {1095-8630}, abstract = {Rivers reflect natural-anthropogenic interactions, yet how urbanization affects riverine bacterial communities along rural-urban gradients is poorly understood. This study examined bacterial diversity and assembly mechanisms along such a gradient of river sediments. Results showed that bacterial diversity significantly decreased with increasing urban influence. Community assembly shifted from stochastic processes dominating in rural zones to environmental selection prevailing in urban zones. The rural-urban transition caused bacterial network instability, potentially reducing resilience. The participation of prevalent taxa decreased but the rare taxa related to chitinolysis and nitrate/nitrite denitrification were selectively enriched along with rural-urban gradient, suggesting rapid functional recruitment to exploit dissolved organic nitrogen and nitrate pulses typical of urban runoff. Our findings underscore that urbanization's influence on bacterial communities is more pronounced than the river's inherent natural characteristics. These insights highlight the profound ecological consequences of urbanization on river microbiomes, informing protection and restoration strategies.}, }
@article {pmid40914221, year = {2025}, author = {Geng, J and Zhang, W and Christie-Oleza, JA and Abdolahpur Monikh, F and Yang, Q and Yang, Y}, title = {Succession-driven potential functional shifts in microbial communities in the Tire-plastisphere:Comparison of pristine and scrap tire.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {127074}, doi = {10.1016/j.envpol.2025.127074}, pmid = {40914221}, issn = {1873-6424}, abstract = {Tire microplastics (TMPs) represent a major contributor to microplastic pollution, posing threats to aquatic ecosystems. As carbon-rich substrates, TMPs influence microbial colonization and ecological functions. This study investigates the impacts of pristine (P-TMPs) and scrap (S-TMPs) TMPs from the same brand on microbial communities within the tire-plastisphere. We incubated wood particles, P-TMPs, and S-TMPs in situ in a lake environment for 60 days. Utilizing amplicon and metagenome sequencing, we analyzed structural and potential functional changes in microbial communities across five colonization time points. Our findings reveal that TMPs establish distinct ecological niches, functioning as hotspots of microbial activity in aquatic environments. Both niche specificity and colonization time significantly shape microbial community structure. During the early adaptation stage, we observed clustering patterns in both microbial composition and functional genes associated with the particles. Over time, divergent succession in community composition and potential function emerged, primarily driven by differences in substrate availability between niches. Notably, the substrate availability of S-TMPs promoted microbial community shifts, whereas the P-TMPs posed challenges to microbial adaptation. This study elucidates the long-term adaptive processes exhibited by microbial communities when colonizing the contrasting ecological niches represented by these two TMP states (pristine vs. scrap), documenting the progression from community structural change to functional adaptation. The results underscore the complexity of TMP impacts on microbial ecology and highlight the critical need for long-term monitoring to fully understand their environmental implications.}, }
@article {pmid40914115, 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 = {Interplay between temperature and redox conditions regulates wetland biogeochemistry and greenhouse gas emissions.}, journal = {The Science of the total environment}, volume = {1000}, number = {}, pages = {180413}, doi = {10.1016/j.scitotenv.2025.180413}, pmid = {40914115}, issn = {1879-1026}, abstract = {Wetlands play a crucial role in global greenhouse gas (GHG) dynamics, yet their response to climate change is not yet fully understood. Here, we investigate how increasing temperature and oxygen availability interact to regulate wetland GHG emissions through combined analysis of biogeochemical and functional gene measurements. We found distinct temperature-dependent shifts in carbon emission pathways, with CO2 emissions unexpectedly declining as temperature rose from 15 to 25 °C, while increasing consistently at higher temperatures (25-35 °C), reflecting a transition to more thermally-driven processes. Conversely, CH4 production exhibited exceptionally high temperature sensitivity in the lower range (Q10 = 32.3 ± 2.4 in oxic conditions) before normalizing at higher temperatures (Q10 = 4.1 ± 2.2), suggesting a fundamental shift from aerobic respiration to methanogenesis dominance when temperature increases. Similarly, N2O production pathways transitioned from nitrification-dominated at lower temperatures to denitrification-dominated at higher temperatures, supported by substantial changes in ammonia-oxidizing (amoA AOA and amoA AOB) and denitrifying (nirK, nirS, and nosZ) gene expression. We observed unexpectedly high CH4 production and denitrification activity under oxic conditions, particularly at elevated temperatures, suggesting that anoxic microsites play a crucial role in wetland GHG dynamics. These findings reveal the complex interactions between temperature, oxygen availability and microbial processes in the wetland ecosystem, which underscores the need for incorporating pathway-specific temperature sensitivities into climate models to better predict wetland responses to global change.}, }
@article {pmid40913309, year = {2025}, author = {Harris, KJ and Bennett, AE}, title = {Exploring Bacterial Interactions Under the Stress Gradient Hypothesis in Response to Selenium Stress.}, journal = {Environmental microbiology reports}, volume = {17}, number = {5}, pages = {e70191}, doi = {10.1111/1758-2229.70191}, pmid = {40913309}, issn = {1758-2229}, support = {//Ohio State University/ ; }, mesh = {*Selenium/metabolism/toxicity ; *Bacteria/metabolism/drug effects/growth &amp; development ; *Stress, Physiological ; *Microbial Interactions ; Oxidative Stress ; Metals, Heavy/metabolism/toxicity ; *Bacterial Physiological Phenomena ; }, abstract = {The Stress Gradient Hypothesis (SGH) predicts that interspecific interactions shift from competition under low stress to facilitation under high stress. Historically, this framework has been extensively studied in plants, but its application to microbial communities remains underexplored. Here, we review literature to examine bacterial interactions under heavy metal stress, using selenium (Se) stress as a model for heavy metal-induced environmental pressures. Se, a naturally occurring and anthropogenic metalloid contaminant, provides oxidative stress on bacteria, which will modify competitive and facilitative behaviours under the SGH framework. At low Se concentrations, bacterial interactions are predominantly competitive, driven by resource competition and antimicrobial strategies. However, as Se stress increases, we predict facilitative interactions to increase, including detoxification mechanisms that reduce toxicity for Se intolerant species. We discuss methodologies to measure bacterial competition and facilitation, propose experimental approaches to identify the transition between these interaction modes, and explore the implications of species richness in microbial stress resilience. Understanding these interactions provides insights into microbial ecology, biogeochemical cycling and potential applications in bioremediation.}, }
@article {pmid40913044, year = {2025}, author = {Müller, MC and Wissink, M and Mukherjee, P and Von Possel, N and Laso-Pérez, R and Engilberge, S and Carpentier, P and Kahnt, J and Wegener, G and Welte, CU and Wagner, T}, title = {Atomic resolution structures of the methane-activating enzyme in anaerobic methanotrophy reveal extensive post-translational modifications.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {8229}, pmid = {40913044}, issn = {2041-1723}, support = {101125699//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; WA 4053/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; VI.Vidi.223.012//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; }, mesh = {*Methane/metabolism ; Anaerobiosis ; *Protein Processing, Post-Translational ; *Oxidoreductases/metabolism/chemistry/genetics ; *Archaeal Proteins/metabolism/chemistry/genetics ; Oxidation-Reduction ; *Archaea/enzymology/metabolism ; Phylogeny ; Methanosarcinales/enzymology/metabolism ; Models, Molecular ; Catalytic Domain ; }, abstract = {Anaerobic methanotrophic archaea (ANME) are crucial to planetary carbon cycling. They oxidise methane in anoxic niches by transferring electrons to nitrate, metal oxides, or sulfate-reducing bacteria. No ANMEs have been isolated, hampering the biochemical investigation of anaerobic methane oxidation. Here, we obtained the true atomic resolution structure of their methane-capturing system (Methyl-Coenzyme M Reductase, MCR), circumventing the isolation barrier by exploiting microbial enrichments of freshwater nitrate-reducing ANME-2d grown in bioreactors, and marine ANME-2c in syntrophy with bacterial partners. Despite their physiological differences, these ANMEs have extremely conserved MCR structures, similar to homologs from methanogenic Methanosarcinales, rather than the phylogenetically distant MCR of ANME-1 isolated from Black Sea mats. The three studied enzymes have seven post-translational modifications, among them was a novel 3(S)-methylhistidine on the γ-chain of both ANME-2d MCRs. Labelling with gaseous krypton did not reveal any internal channels that would facilitate alkane diffusion to the active site, as observed in the ethane-specialised enzyme. Based on our data, the methanotrophic MCRs should follow the same radical reaction mechanism proposed for the methane-generating homologues. The described pattern of post-translational modifications underscores the importance of native purification as a powerful approach to discovering intrinsic enzymatic features in non-isolated microorganisms existing in nature.}, }
@article {pmid40911620, year = {2025}, author = {Yuen, ELH and Savage, Z and Pražák, V and Liu, Z and Adamkova, V and King, F and Vuolo, C and Ibrahim, T and Wang, Y and Jenkins, S and Zhou, Y and Tumtas, Y and Erickson, JL and Prautsch, J and Balmez, AI and Stuttmann, J and Duggan, C and Rivetti, F and Molinari, C and Gaboriau, DCA and Carella, P and Zhuang, X and Schattat, M and Bozkurt, TO}, title = {Membrane contact sites between chloroplasts and the pathogen interface underpin plant focal immune responses.}, journal = {The Plant cell}, volume = {}, number = {}, pages = {}, doi = {10.1093/plcell/koaf214}, pmid = {40911620}, issn = {1532-298X}, abstract = {Communication between cellular organelles is essential for mounting effective innate immune responses. The transport of organelles to pathogen penetration sites and their assembly around the host membrane, which delineates the plant-pathogen interface, are well-documented. However, whether organelles associate with these specialized interfaces, and the extent to which this process contributes to immunity, remain unknown. Here, we discovered defense-related membrane contact sites (MCS) comprising a membrane tethering complex between chloroplasts and the extrahaustorial membrane (EHM) surrounding the haustorium of the pathogen Phytophthora infestans in Nicotiana benthamiana. The assembly of this complex involves association between the chloroplast outer envelope protein CHLOROPLAST UNUSUAL POSITIONING 1 (CHUP1) and its plasma membrane-associated partner KINESIN-LIKE PROTEIN FOR ACTIN-BASED CHLOROPLAST MOVEMENT 1 (KAC1). Our biochemical assays revealed that CHUP1 and KAC1 interact, and infection cell biology assays demonstrated their co-accumulation in foci where chloroplasts contact the EHM. Genetic depletion of CHUP1 or KAC1 reduces the focal deposition of callose around the haustorium without affecting other core immune processes. Our findings suggest that the chloroplast-EHM attachment complex promotes plant focal immunity, revealing key components and their potential roles in the deposition of defense materials at the pathogen interface. These results advance our understanding of organelle-mediated immunity and highlight the significance of MCS in plant-pathogen interactions.}, }
@article {pmid40911039, year = {2025}, author = {Dagenais Roy, M and Déziel, E}, title = {Microbial Primer: Biosurfactants - the ABCs of microbial surface-active metabolites.}, journal = {Microbiology (Reading, England)}, volume = {171}, number = {9}, pages = {}, doi = {10.1099/mic.0.001604}, pmid = {40911039}, issn = {1465-2080}, mesh = {*Surface-Active Agents/metabolism/chemistry ; *Fungi/metabolism/genetics ; *Bacteria/metabolism/genetics ; Biosynthetic Pathways ; Yeasts/metabolism ; Biosurfactants ; }, abstract = {Microbial surfactants (biosurfactants) are low-molecular-weight amphiphilic secondary metabolites synthesized by a wide range of micro-organisms, including bacteria, yeasts and fungi. These compounds reduce surface and interfacial tension, promote emulsification and self-assemble into supramolecular structures such as micelles. Their remarkable structural diversity reflects the metabolic complexity of their microbial producers. In this primer, we outline shared features across biosurfactant-producing organisms, focusing on biosynthetic pathways, biological functions and regulatory mechanisms. The study of biosurfactants lies at the intersection of ecological, biotechnological and medical research, offering valuable insights into microbial ecology and promising avenues for sustainable innovation.}, }
@article {pmid40908830, year = {2025}, author = {Yamlahi, YE and Remmal, I and Maurady, A and Britel, MR and Bakali, AH and Mokhtar, NB and Galiatsatos, I and Stathopoulou, P and Tsiamis, G}, title = {Characterization of the olive fly (Bactrocera oleae) microbiome across diverse geographic regions of Morocco.}, journal = {Insect science}, volume = {}, number = {}, pages = {}, doi = {10.1111/1744-7917.70126}, pmid = {40908830}, issn = {1744-7917}, support = {22662//International Atomic Energy Agency/ ; }, abstract = {The olive fruit fly (Bactrocera oleae) is a significant pest threatening olive production worldwide. Bactrocera oleae relies on symbiotic bacteria for nutrition, development, and adaptation to its environment. Among these, Candidatus Erwinia dacicola is the most dominant symbiont and plays a key role in the fly's physiology and ecological adaptation. Understanding the dynamics between B. oleae, Ca. E. dacicola, and other components of the B. oleae microbiome is essential for developing effective targeted area-wide pest management strategies. This study aims to leverage full 16S rRNA gene sequencing to enhance the characterization of microbiome diversity in wild B. oleae populations from different regions in Morocco: Ouezzane, Rabat, Tanger, Errachidia, and Beni-Mellal. The results revealed distinct microbiome compositions influenced by geographic locations, with Candidatus Erwinia dacicola as the dominant symbiont, followed by Erwinia persicina as a secondary contributor. Other bacterial taxa, including Asaia bogorensis, were also identified, highlighting the functional diversity within the olive fly microbiome. These findings provide insights into the microbial ecology of B. oleae, contributing to the development and enhancement of sustainable pest control strategies.}, }
@article {pmid40908508, year = {2025}, author = {Boden, L and Bludau, D and Sieber, G and Deep, A and Baikova, D and David, GM and Hadžiomerović, U and Stach, TL and Buchner, D and Boenigk, J}, title = {Varying Responses to Heat Stress and Salinization Between Benthic and Pelagic Riverine Microbial Communities.}, journal = {Environmental microbiology}, volume = {27}, number = {9}, pages = {e70173}, doi = {10.1111/1462-2920.70173}, pmid = {40908508}, issn = {1462-2920}, support = {CRC 1439/1//Deutsche Forschungsgemeinschaft/ ; //Open Access Publication Fund of the University of Duisburg-Essen/ ; }, abstract = {Microbial communities play a crucial role in the functioning of freshwater ecosystems but are continuously threatened by climate change and anthropogenic activities. Elevated temperatures and salinisation are particularly challenging for freshwater habitats, but little is known about how microbial communities respond to the simultaneous exposure to these stressors. Here, we use mesocosm experiments and amplicon sequencing data to investigate the responses of pelagic and benthic microbial communities to temperature and salinity increases, both individually and in combination. Our results highlight the varying responses of freshwater microbial communities, with sediment communities exhibiting greater stability in response to environmental changes compared to water column communities, and salinisation having a more pronounced impact on microeukaryotes compared to prokaryotes. Simultaneous exposure to elevated temperature and salinity reduced the impact of salinisation on prokaryotes, while microeukaryotes were similarly affected by the combined treatments and salinisation alone. These findings emphasise the complexity of microbial responses to single and multiple stressors, underscoring the need to consider both individual and interactive effects when predicting ecosystem responses to environmental changes.}, }
@article {pmid40907150, year = {2025}, author = {Prósperi de Oliveira Paula, M and Wurdig Roesch, LF and Coutinho Ramos, A and Tótola, MR and Satler Pylro, V}, title = {Bacterial consortia enhance glyphosate breakdown and drive soil microbial dynamics.}, journal = {Chemosphere}, volume = {387}, number = {}, pages = {144677}, doi = {10.1016/j.chemosphere.2025.144677}, pmid = {40907150}, issn = {1879-1298}, abstract = {This study assessed the bioremediation potential of four microbial consortia in soil microcosms contaminated with glyphosate, focusing on their metabolic activity and impact on microbial diversity. Among the tested consortia, Con_CC-G-isolated from Conilon Coffee soil that had remained glyphosate-free for three years-demonstrated the most pronounced effects. Microbial metabolic activity was quantified using respirometry, which tracked CO2 production over 140 h in both inoculated and control soils. Changes in microbial community composition were analyzed using 16S rRNA gene metataxonomics. The results revealed that glyphosate exposure stimulated respiratory activity, particularly in inoculated treatments. Differential abundance analysis revealed significant increases in Achromobacter and Serratia in inoculated microcosms, as well as in other key herbicide-degrading genera. Complementary HPLC-DAD analyses confirmed glyphosate degradation, with Con_CC and Con_CC-G achieving the highest removal efficiencies under both carbon- and phosphorus-limited conditions. These findings provide direct evidence of glyphosate biodegradation and highlight the strong bioremediation potential of Con_CC-G for soils contaminated with this herbicide. Further research must assess its environmental impact and safety before field-scale application.}, }
@article {pmid40906125, year = {2025}, author = {Basit, A and Haq, IU and Hyder, M and Humza, M and Younas, M and Akhtar, MR and Ghafar, MA and Liu, TX and Hou, Y}, title = {Microbial Symbiosis in Lepidoptera: Analyzing the Gut Microbiota for Sustainable Pest Management.}, journal = {Biology}, volume = {14}, number = {8}, pages = {}, doi = {10.3390/biology14080937}, pmid = {40906125}, issn = {2079-7737}, support = {National Natural Science Foundation of China (U22A20489; 32361143791).//National Natural Science Foundation of China (U22A20489; 32361143791)./ ; }, abstract = {Recent advances in microbiome studies have deepened our understanding of endosymbionts and gut-associated microbiota in host biology. Of those, lepidopteran systems in particular harbor a complex and diverse microbiome with various microbial taxa that are stable and transmitted between larval and adult stages, and others that are transient and context-dependent. We highlight key microorganisms-including Bacillus, Lactobacillus, Escherichia coli, Pseudomonas, Rhizobium, Fusarium, Aspergillus, Saccharomyces, Bifidobacterium, and Wolbachia-that play critical roles in microbial ecology, biotechnology, and microbiome studies. The fitness implications of these microbial communities can be variable; some microbes improve host performance, while others neither positively nor negatively impact host fitness, or their impact is undetectable. This review examines the central position played by the gut microbiota in interactions of insects with plants, highlighting the functions of the microbiota in the manipulation of the behavior of herbivorous pests, modulating plant physiology, and regulating higher trophic levels in natural food webs. It also bridges microbiome ecology and applied pest management, emphasizing S. frugiperda as a model for symbiont-based intervention. As gut microbiota are central to the life history of herbivorous pests, we consider how these interactions can be exploited to drive the development of new, environmentally sound biocontrol strategies. Novel biotechnological strategies, including symbiont-based RNA interference (RNAi) and paratransgenesis, represent promising but still immature technologies with major obstacles to overcome in their practical application. However, microbiota-mediated pest control is an attractive strategy to move towards sustainable agriculture. Significantly, the gut microbiota of S. frugiperda is essential for S. frugiperda to adapt to a wide spectrum of host plants and different ecological niches. Studies have revealed that the microbiome of S. frugiperda has a close positive relationship with the fitness and susceptibility to entomopathogenic fungi; therefore, targeting the S. frugiperda microbiome may have good potential for innovative biocontrol strategies in the future.}, }
@article {pmid40906100, year = {2025}, author = {Li, W and Yang, L and Cong, X and Mao, Z and Zhou, Y}, title = {Distribution Patterns and Assembly Mechanisms of Rhizosphere Soil Microbial Communities in Schisandra sphenanthera Across Altitudinal Gradients.}, journal = {Biology}, volume = {14}, number = {8}, pages = {}, doi = {10.3390/biology14080944}, pmid = {40906100}, issn = {2079-7737}, support = {2025NC-YBXM-059//the Shaanxi Provincial Department of Science and Technology Key Research and Development Program-General Project/ ; }, abstract = {To investigate the characteristics of rhizosphere soil microbial communities associated with Schisandra sphenanthera across different altitudinal gradients and to reveal the driving factors of microbial community dynamics, this study collected rhizosphere soil samples at four elevations: 900 m (HB1), 1100 m (HB2), 1300 m (HB3), and 1500 m (HB4). High-throughput sequencing and molecular ecological network analysis were employed to analyze the microbial community composition and species interactions. A null model was applied to elucidate community assembly mechanisms. The results demonstrated that bacterial communities were dominated by Proteobacteria, Acidobacteriota, Actinobacteriota, and Chloroflexi. The relative abundance of Proteobacteria increased with elevation, while that of Acidobacteriota and Actinobacteriota declined. Fungal communities were primarily composed of Ascomycota and Basidiomycota, with both showing elevated relative abundances at higher altitudes. Diversity indices revealed that HB2 exhibited the highest bacterial Chao, Ace, and Shannon indices but the lowest Simpson index. For fungi, HB3 displayed the highest Chao and Ace indices, whereas HB4 showed the highest Shannon index and the lowest Simpson index. Ecological network analysis indicated stronger bacterial competition at lower elevations and enhanced cooperation at higher elevations, contrasting with fungal communities that exhibited increased competition at higher altitudes. Altitude and soil nutrients were negatively correlated with soil carbon content, while plant nutrients and fungal diversity positively correlated with soil carbon. Null model analysis suggested that deterministic processes dominated bacterial community assembly, whereas stochastic processes governed fungal assembly. These findings highlight significant altitudinal shifts in the microbial community structure and assembly mechanisms in S. sphenanthera rhizosphere soils, driven by the synergistic effects of soil nutrients, plant growth, and fungal diversity. This study provides critical insights into microbial ecology and carbon cycling in alpine ecosystems, offering a scientific basis for ecosystem management and conservation.}, }
@article {pmid40905693, year = {2025}, author = {González-Marín, C and García-Botero, C and Metaute-Molina, E and Caraballo-Rodríguez, AM and Dorrestein, PC and Villegas-Escobar, V}, title = {Bacillus spp. Antibacterial Activity Induced by Triphenyl Tetrazolium Chloride against Ralstonia solanacearum: Oxidative Stress Response and Metabolome Changes.}, journal = {ACS chemical biology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acschembio.5c00171}, pmid = {40905693}, issn = {1554-8937}, abstract = {High salt concentrations affect the electron transport chain of bacterial cells, leading to an oxidative stress response that encompasses the formation of reactive oxygen species (ROS). The salt 2,3,5-triphenyltetrazolium chloride (TTC) triggers antibacterial activity against the phytopathogen Ralstonia solanacearum in Bacillus species; however, the underlying mechanisms remain unknown. Here, we tested the hypothesis that TTC-inducible activity is related to the formation of ROS and its metabolites. We found that l-ascorbic acid, superoxide dismutase, and catalase counteracted TTC-inducible activity in various Bacillus species. Furthermore, R. solanacearum exhibited a higher susceptibility to H2O2 than Bacillus spp. Genomic analysis showed differences in stress-related genes, with Bacillus strains containing the ROS scavengers bacillithiol and bacillibactin, while glutathione inR. solanacearum. Multivariate analysis indicated that the Bacillus species and TTC influence Bacillus metabolome, resulting in higher levels of quinazoline alkaloids, with potential antibacterial activity against R. solanacearum. Results suggest that TTC induces the production of O2[•-] and H2O2 and metabolites that arrest R. solanacearum growth.}, }
@article {pmid40904889, year = {2025}, author = {Lv, J and Zhao, HP and Yu, Y and Wang, JH and Zhang, XJ and Guo, ZQ and Jiang, WY and Wang, K and Guo, L}, title = {From gut microbial ecology to lipid homeostasis: Decoding the role of gut microbiota in dyslipidemia pathogenesis and intervention.}, journal = {World journal of gastroenterology}, volume = {31}, number = {30}, pages = {108680}, pmid = {40904889}, issn = {2219-2840}, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Dyslipidemias/microbiology/therapy/metabolism/etiology ; Homeostasis ; *Lipid Metabolism ; Animals ; Fecal Microbiota Transplantation ; Probiotics/therapeutic use ; Prebiotics/administration &amp; dosage ; Dysbiosis/microbiology/therapy ; }, abstract = {Dyslipidemia, a complex disorder characterized by systemic lipid profile abnormalities, affects more than half of adults globally and constitutes a major modifiable risk factor for atherosclerotic cardiovascular disease. Mounting evidence has established the gut microbiota (GM) as a pivotal metabolic modulator that is correlated with atherogenic lipid profiles through dietary biotransformation, immunometabolic regulation, and bioactive metabolite signaling. However, the host-microbe interactions that drive dyslipidemia pathogenesis involve complex gene-environment crosstalk spanning epigenetic modifications to circadian entrainment. Mechanistically, GM perturbations disrupt lipid homeostasis via lipopolysaccharide-triggered hepatic very low-density lipoprotein overproduction, short-chain fatty acid-G protein-coupled receptor 43/41-mediated adipocyte lipolysis, bile acid-farnesoid X receptor/Takeda G protein-coupled receptor 5 axis dysfunction altering cholesterol flux, microbial β-oxidation intermediates impairing mitochondrial energetics, and host-microbiota non-coding RNA crosstalk regulating lipogenic genes. This comprehensive review systematically examines three critical dimensions, including bidirectional GM-lipid axis interactions, molecular cascades bridging microbial ecology to metabolic dysfunction, and translational applications of GM modulation through precision probiotics, structure-specific prebiotics, and a metabolically optimized fecal microbiota transplantation protocol. Notwithstanding these advances, critical gaps persist in establishing causal microbial taxa-pathway relationships and optimal intervention timing. Future directions require longitudinal multi-omic studies, gnotobiotic models for mechanistic validation, and machine learning-driven personalized microbiota profiling. This synthesis provides a framework for developing microbiota-centric strategies targeting dyslipidemia pathophysiology, with implications for precision dyslipidemia management and next-generation cardiovascular disease prevention.}, }
@article {pmid40904105, year = {2025}, author = {Elliott, JFK and Cozens, K and Cai, Y and Waugh, G and Watson, BN and Westra, E and Taylor, TB}, title = {Phage susceptibility to a minimal, modular synthetic CRISPR-Cas system in Pseudomonas aeruginosa is nutrient dependent.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {380}, number = {1934}, pages = {20240473}, pmid = {40904105}, issn = {1471-2970}, support = {//UK Government's Horizon Europe funding guarantee/ ; //Royal Society/ ; //Philip Leverhulme Prize/ ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Pseudomonas aeruginosa/virology/genetics ; *CRISPR-Cas Systems ; *Pseudomonas Phages/physiology/genetics ; *Nutrients/metabolism ; *Bacteriophages/physiology ; }, abstract = {CRISPR-Cas systems can provide adaptive, heritable immunity to their prokaryotic hosts against invading genetic material such as phages. It is clear that the importance of acquiring CRISPR-Cas immunity to anti-phage defence varies across environments, but it is less clear if and how this varies across different phages. To explore this, we created a synthetic, modular version of the type I-F CRISPR-Cas system of Pseudomonas aeruginosa. We used this synthetic system to test CRISPR-Cas interference against a panel of 13 diverse phages using engineered phage-targeting spacers. We observed complete protection against eight of these phages, both lytic and lysogenic and with a range of infectivity profiles. However, for two phages, CRISPR-Cas interference was only partially protective in high-nutrient conditions, yet completely protective in low-nutrient conditions. This work demonstrates that nutrient conditions modulate the strength of CRISPR-Cas immunity and highlights the importance of environmental conditions when screening defence systems for their efficacy against various phages.This article is part of the discussion meeting issue 'The ecology and evolution of bacterial immune systems'.}, }
@article {pmid40904103, year = {2025}, author = {Le Roux, F}, title = {The ecology and evolution of microbial immune systems: a look on the wild vibrio side.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {380}, number = {1934}, pages = {20240078}, pmid = {40904103}, issn = {1471-2970}, support = {/ERC_/European Research Council/International ; //Canada Excellence Research Chairs Program/ ; //Agence Nationale de la Recherche/ ; }, mesh = {*Bacteriophages/physiology/genetics ; *Vibrio/virology/immunology/genetics ; *Biological Evolution ; Host Specificity ; Interspersed Repetitive Sequences ; Animals ; }, abstract = {Natural populations of vibrio beyond the well-studied pandemic strains of Vibrio cholerae, provide a powerful model for investigating the eco-evolutionary dynamics of microbial immune systems. Their genetic diversity, ecological versatility, ease of culturability and the availability of time-series data enable detailed studies of phage-host interactions in natural contexts. This review synthesizes recent advances in vibriophage research, highlighting key findings and emerging tools. High-throughput assays and genomic tools have offered new perspectives on phage specificity, host range and the evolutionary pressures shaping these interactions. Theoretical frameworks, such as arms race and fluctuating selection dynamics, are informed by empirical data from vibrio-phage systems, with time-series sampling providing crucial insights into their temporal and spatial dynamics. A major finding is the role of mobile genetic elements (MGEs) in encoding bacterial defence systems, which shape phage-host coevolution. Discoveries like the phage satellite PICMI illustrate how MGEs facilitate the transfer of antiviral systems, influencing ecological and evolutionary dynamics. The paradox of generalist vibriophages, rare despite their broad host ranges, is also explored. By integrating experimental approaches with field observations, vibriophage research advances microbial ecology and informs sustainable applications in aquaculture and phage therapy, reinforcing vibrios as a versatile model system.This article is part of the discussion meeting issue 'The ecology and evolution of bacterial immune systems'.}, }
@article {pmid40904102, year = {2025}, author = {Pons, BJ and Łapińska, U and Lopes-Domingues, I and Chisnall, MAW and Westra, ER and Pagliara, S and van Houte, S}, title = {Phage provoke growth delays and SOS response induction despite CRISPR-Cas protection.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {380}, number = {1934}, pages = {20240474}, pmid = {40904102}, issn = {1471-2970}, support = {/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; /MRC_/Medical Research Council/United Kingdom ; //UK Government's Horizon Europe funding guarantee/ ; //Leverhulme Trust/ ; }, mesh = {*Pseudomonas aeruginosa/virology/growth &amp; development/genetics ; *CRISPR-Cas Systems ; *Pseudomonas Phages/physiology ; *SOS Response, Genetics ; *Bacteriophages/physiology ; }, abstract = {Bacteria evolve resistance against their phage foes with a wide range of resistance strategies whose costs and benefits depend on the level of protection they confer and on the costs for maintainance. Pseudomonas aeruginosa can evolve resistance against its phage DMS3vir either by surface mutations that prevent phage binding or through CRISPR-Cas immunity. CRISPR immunity carries an inducible cost whose exact origin is still unknown, and previous work suggested it stems from the inability of the CRISPR-Cas system to completely prevent phage DNA injection and subsequent gene expression before clearing the phage infection. However, the bacterial processes involved are still unknown, and we hypothesize that CRISPR-immunity-associated costs could come from increased mortality rate or reduced growth ability compared with surface-resistant bacteria. To tease apart these two mechanisms with divergent ecological consequences, we use a novel microfluidics-based single-cell approach combined with flow cytometry methods to monitor the effects of phage exposure on the survival and growth of its host. We observed that while CRISPR immunity protects from phage-induced lysis, it cannot prevent phage-induced division lag, filamentation and SOS response activation in a subpopulation of the host bacteria. These results suggest that the costs associated with CRISPR immunity at the population level are caused by heterogeneity in phage-induced growth defects.This article is part of the discussion meeting issue 'The ecology and evolution of bacterial immune systems'.}, }
@article {pmid40902774, year = {2025}, author = {Azeem, M and Han, R and Liu, S and Jacques, KJ and Abdelrahman, H and Kazmi, SSH and Kareem, A and Khan, ZH and Rafiq, N and Li, H and Kuzyakov, Y and Qin, K}, title = {Biochar-derived dissolved organic matter induced changes in the bacterial communities structure and metabolic functions in As and Cd contaminated soil.}, journal = {Environmental research}, volume = {}, number = {}, pages = {122749}, doi = {10.1016/j.envres.2025.122749}, pmid = {40902774}, issn = {1096-0953}, abstract = {This study investigates the effects of pyrolytic temperature and feedstock type on the release of biochar-derived dissolved organic matter (BDOM) and its impact on the soil bacterial community and the composition of soil dissolved organic matter (SDOM). The BDOM was extracted from biochars produced from sheep bones, rice husk, and rabbit manure, prepared at low (400 °C, LPT) or high (700 °C, HPT) pyrolytic temperatures. The BDOM was then applied at a concentration of 2.5% (w/w). LPT-BDOM produced higher contents of BDOM (up to 1440±43 mg kg[-1]), resulting in higher SDOM (up to 78%, compared with control soil) after application and higher availability of nutrients (Ca, Mg, and P) and toxic metalloids (TMs; As and Cd) in soil. The addition of BDOM altered the bacterial community composition, with increased bacterial richness and diversity observed in the HPT-BDOM compared to the control. The community shift was linked with higher levels of volatile organic compounds and increased nutrient availability compared with HPT. The increase in fluorescence (up to 54%), freshness (up to 29%), biological (up to 112%), and humification (up to 52%) indices was associated with LPT-derived BDOM, particularly with sheep bone-BDOM. Manure-LPT and sheep bone-HPT enhanced hydrocarbon degradation, while rice husk-LPT enriched taxa related to nitrogen fixation and nitrate reduction. LPT treatments favored cellulolysis and fermentation, whereas HPT treatments promoted methylotrophy, aligning with their contrasting carbon lability. These findings highlight the dual role of biochar's labile fraction in shaping carbon availability, influencing SDOM dynamics, nutrient and total metals (TMs) bioavailability, and microbial ecology, underscoring the need for feedstock- and temperature-specific selection in environmental applications.}, }
@article {pmid40901853, year = {2025}, author = {Gómez-Palacio, A and Junca, H and Vivero-Gomez, RJ and Suaza, J and Moreno-Herrera, CX and Cadavid-Restrepo, G and Pieper, DH and Uribe, S}, title = {Metagenomic profiling of the insect-specific virome in non-urban mosquitoes (Culicidae: Culicinae) from Colombia's Northern inter-Andean valleys.}, journal = {PloS one}, volume = {20}, number = {9}, pages = {e0331552}, doi = {10.1371/journal.pone.0331552}, pmid = {40901853}, issn = {1932-6203}, mesh = {Animals ; Colombia ; *Virome/genetics ; *Culicidae/virology ; *Metagenomics/methods ; *Metagenome ; Phylogeny ; *Insect Viruses/genetics/classification ; }, abstract = {Hematophagous mosquitoes are major vectors of diverse pathogens and serve as bioindicators in tropical ecosystems, yet their virome in non-urban Neotropical regions remains poorly characterized. We analyzed the virome of 147 mosquitoes from two natural ecosystems in Colombia using a hybrid viral identification approach, combining high-confidence and less stringent methods. Most high-confidence viral contigs remained unclassified or unknown, as expected for metagenomic surveys in novel ecosystems. However, members for the Magrovirales and Ortervirales, and other six orders were detected at lower abundance. Using a complementary, less stringent approach, we identified 168 viral species from 68 genera and 22 families across four mosquito tribes (Aedini, Culicini, Orthopodomyiini, Sabethini), with dominance of Metaviridae, Retroviridae, Iridoviridae, and Poxviridae, though many sequences could not be taxonomically assigned. Insect-specific viruses predominated, while no medically relevant arboviruses were detected. Both methods consistently identified Trichoplusia ni TED virus, Cladosporium fulvum T-1 virus, Lymphocystis disease viruses, and Oryctes rhinoceros nudivirus among the most abundant and frequently detected taxa across samples. Alpha diversity indices revealed the highest virome diversity in Sabethini, followed by Orthopodmyiini, and substantially lower richness and diversity in Aedini and Culicini. These results provide a baseline for virome characterization in sylvatic mosquitoes from Colombia and highlight the need for further research on the ecological roles of the mosquito virome in pathogen transmission and microbiome evolution.}, }
@article {pmid40901273, year = {2025}, author = {Worsley, SF and Lee, CZ and Versteegh, MA and Burke, T and Komdeur, J and Dugdale, HL and Richardson, DS}, title = {Gut microbiome communities demonstrate fine-scale spatial variation in a closed, island bird population.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf138}, doi = {10.1093/ismeco/ycaf138}, pmid = {40901273}, issn = {2730-6151}, abstract = {Environmental variation is a key factor shaping microbial communities in wild animals. However, most studies have focussed on separate populations distributed over large spatial scales. How ecological factors shape inter-individual microbiome variation within a single landscape and host population remains poorly understood. Here, we use dense sampling of individuals in a natural, closed population of Seychelles warblers (Acrocephalus sechellensis) on Cousin Island (<0.7 km diameter, 0.34 km[2] total area) to determine whether gut microbiome communities exhibit high-resolution spatial variation over fine scales (average territory area is 0.0023 km[2]). We identified a small but highly significant quadratic relationship between geographic distance and gut microbiome beta diversity across the island. Microbiome composition initially diverged with increasing geographic distance between territories. However, after ca. >300 m, microbiome composition became increasingly similar amongst individuals situated on different sides of the island. This relationship was robust to the effects of host relatedness, age, and sex. Further analysis showed that microbiome composition differed between individuals inhabiting coastal and inland territories. Warblers in coastal territories harboured greater abundances of marine bacteria and lower abundances of anaerobic taxa commonly linked to host metabolic health, suggesting that exposure to different environmental microbes and variation in host condition (which is lower in coastal territories) could drive spatial patterns of gut microbiome variation across the island. This work demonstrates that host-microbe interactions can be labile even at very fine spatial scales. Such variability may have implications for how species respond to anthropogenic disturbance in wild habitats.}, }
@article {pmid40900750, year = {2025}, author = {Li, Y and Zhang, S and Guo, Y and Xu, K and Zhang, X and Pan, M and Sun, Q and Zhang, Y and Fan, Y}, title = {Analysis of microbial diversity and functions in sediments and overlying water of the Shiliu River.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19979}, pmid = {40900750}, issn = {2167-8359}, mesh = {*Rivers/microbiology ; *Geologic Sediments/microbiology ; *Bacteria/genetics/classification/isolation &amp; purification ; *Fungi/genetics/classification/isolation &amp; purification ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; *Water Microbiology ; *Microbiota ; }, abstract = {BACKGROUND: With the acceleration of urbanization, urban rivers have become a significant component of the urban ecosystem, attracting considerable attention regarding their ecological status and biodiversity. This study focuses on the Shiliu River, aiming to analyze the microbial diversity and functions present in the overlying water and sediments of severely polluted areas.<br><br>METHODS: This study investigated the Shiliu River. In August 2024, sediment and overlying water samples were collected from its severely polluted reaches. The NextSeq 2000 PE300 platform was employed for sequencing to detect bacterial and fungal taxa abundances. PICRUSt and FUNGuild predicted sample functional abundances using bacterial 16S rRNA and fungal internal transcribed spacer (ITS) gene sequences, respectively.<br><br>RESULTS: The findings demonstrate that sediments exhibit higher bacterial and fungal richness than overlying water, with significant discrepancies in bacterial and fungal community compositions. Dominant taxa differ at both phylum and genus levels: in sediments, the predominant bacterial phylum is Proteobacteria and genus norank_Anaerolineaceae, while the dominant fungal phylum is Rozellomycota and genus unclassified_Rozellomycota. In overlying water, the bacterial phylum remains Proteobacteria but the dominant genus shifts to Acinetobacter, whereas fungal phyla and genera (Rozellomycota and unclassified_Rozellomycota) are consistent with sediments. Kyoto Encyclopedia of Genes and Genomes (KEGG) functional annotation identifies 25 metabolic pathways, with amino acid metabolism-related genes showing the highest abundance in both environments. Clusters of Orthologous Genes (COG) annotation reveals the highest abundance of [R] General function prediction in both sample groups, and FUNGuild analysis indicates that Animal Endosymbiont-Animal Pathogen-Plant Pathogen-Undefined Saprotroph is the most prevalent functional category in both sediments and overlying water. This study provides a microbiological foundation by clarifying microbial community structures (dominant phyla, functional taxa), decoding pollutant-degrading metabolic potentials (N/C cycling pathways), and identifying river health ecological indicators. This enables targeted bioremediation strategies (e.g., sediment microbial consortia for nutrient removal) and integrates microbial ecological data into urban river restoration.<br><br>CONCLUSIONS: This study reveals the microbial community structures in the sediments and overlying water of the polluted Shiliu River, finding diverse patterns with higher richness in sediments, Proteobacteria and Ascomycota as dominants. Shared taxa have different abundances, indicating niche differentiation. Sediments have enriched nitrogen/carbon cycling pathways for pollutant degradation. These results offer a microbiological basis for urban river restoration, identify bioremediation-target taxa, and stress the integration of microbial ecology into pollution management.}, }
@article {pmid40388809, year = {2025}, author = {Mijatović Scouten, J and Hsieh, SC and Sung, LK and Wen, YV and Kuo, CH and Lai, EM and Chang, JH}, title = {Function, Evolution, and Ecology of Type VI Secretion Systems of Plant-Associated Bacteria.}, journal = {Annual review of phytopathology}, volume = {63}, number = {1}, pages = {333-356}, doi = {10.1146/annurev-phyto-121423-084620}, pmid = {40388809}, issn = {1545-2107}, mesh = {*Type VI Secretion Systems/genetics/metabolism/physiology ; *Plants/microbiology ; *Bacteria/genetics/metabolism/pathogenicity ; Biological Evolution ; *Plant Diseases/microbiology ; Virulence ; Bacterial Proteins/metabolism/genetics ; }, abstract = {Intense competition for resources among microorganisms imposes strong selective pressure for traits that provide a competitive advantage, including traits that harm others. The type VI secretion system (T6SS) is a versatile contractile injection apparatus encoded by many Gram-negative bacteria. This system is best known for its lethal use in deploying effectors toxic to neighboring bacteria. However, T6SSs can also be used to secrete effectors into the environment to influence nutrient acquisition. Additionally, for some bacteria, T6SSs deploy effectors toxic to eukaryotic hosts and are involved in virulence, which, however, has not been demonstrated for plant-associated bacteria. Here, we review the diverse functions and evolutionary basis of T6SSs. We discuss the potential ecological impacts of T6SSs in plant-associated communities. Understanding outcomes is important for finding the best approaches for using bacteria in sustainable management of plant agricultural systems.}, }
@article {pmid40896518, year = {2025}, author = {Elias Masiques, N and Vermeiren, S and De Vrieze, J and Gansemans, Y and Deforce, D and Van Nieuwerburgh, F and De Smet, S and Van Hecke, T}, title = {Food hydrocolloids κ-carrageenan and xanthan gum in processed red meat modify gut health in rats.}, journal = {Current research in food science}, volume = {11}, number = {}, pages = {101162}, doi = {10.1016/j.crfs.2025.101162}, pmid = {40896518}, issn = {2665-9271}, abstract = {The food hydrocolloids κ-carrageenan and xanthan gum, used in processed foods including meat products, have unclear effects on gut health. This study investigated the effects of incorporating 1 % κ-carrageenan or xanthan gum into pork on protein digestibility, gut microbiota, oxidative stress, and gene expression using both in vitro gastrointestinal digestion/fermentation and an in vivo rodent model. In vitro, xanthan gum reduced protein digestibility (-11 %) in the simulated small intestine, thus elevating protein fermentation metabolites (up to 4-fold), but this was not observed in vivo. Consumption of a low-fiber pork diet without hydrocolloids promoted Akkermansia (29.5 % median abundance) and Tannerellaceae (24.7 %) growth in the colon, whereas κ-carrageenan increased Desulfovibrio (7.95 %) and Alistipes (6.14 %), and xanthan gum enhanced unclassified Muribaculaceae (14.8 %) and Bacteroides (12.1 %). Unexpectedly, transcriptomic analysis revealed a down-regulation of gut inflammatory pathways, accompanied by lower fecal calprotectin levels, in rats consuming pork with hydrocolloids. While κ-carrageenan notably reduced lipid oxidation in stomach contents, only xanthan gum lowered plasma and colonic oxidative stress. These findings highlight the potential of hydrocolloids to modulate dietary responses, suggesting a role in influencing gut health following high processed meat consumption.}, }
@article {pmid40894307, year = {2025}, author = {van den Bergh, SG and Chardon, I and Meima-Franke, M and Pérez, G and Rocha, GS and Brenzinger, K and Korthals, GW and Mayer, J and Cougnon, M and Reheul, D and de Boer, W and Bodelier, PLE}, title = {Improved methane mitigation potential and modulated methane cycling microbial communities in arable soil by compost addition.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf139}, doi = {10.1093/ismeco/ycaf139}, pmid = {40894307}, issn = {2730-6151}, abstract = {The global atmospheric concentration of the potent greenhouse gas methane (CH4) is rising rapidly, and agriculture is responsible for 30%-50% of the yearly CH4 emissions. To limit its global warming effects, strong and sustained reductions are needed. Sustainable agricultural management strategies, as the use of organic amendments like compost, have previously proven to have a potent CH4 mitigation effect in laboratory experiments. Here we investigated, using an extensive field study, the effect of organic amendments on the CH4 mitigation potential and CH4 cycling microbial communities of arable soils. Organic-amended soils had higher potential CH4 uptake rates and an improved potential to oxidize CH4 to sub-atmospheric concentrations. Also, we showed for the first time that the methanotrophic and methanogenic microbial communities of arable soils were unequivocally altered after organic amendment application by increasing in size while getting less diverse. Compost-amended soils became dominated by the compost-originating methanotroph Methylocaldum szegediense and methanogen Methanosarcina horonobensis, replacing the indigenous methane cycling community members. However, multivariate analyses didn't point out type Ib methanotrophs like M. szegediense as significant driving factors for the observed improved soil CH4 uptake potential. Conventional type IIa methanotrophs like Methylocystis sp. also had higher differential abundances in organic-amended soils and are speculated to contribute to the improved CH4 uptake potential. Altogether, the results showed that compost serves as a vector for the introduction of CH4 cycling microbes and improves the soil's CH4 uptake potential, which emphasizes the potential of organic fertilization with compost to contribute to CH4 mitigation in agricultural soils.}, }
@article {pmid40892732, year = {2025}, author = {Yssel, J and Everaerts, V and Van Hemelrijk, W and Bylemans, D and Setati, ME and Lievens, B and Blancquaert, E and Crauwels, S}, title = {Assessing the potential of seaweed extracts to improve vegetative, physiological and berry quality parameters in Vitis vinifera cv. Chardonnay under cool climatic conditions.}, journal = {PloS one}, volume = {20}, number = {9}, pages = {e0331039}, pmid = {40892732}, issn = {1932-6203}, mesh = {*Vitis/drug effects/growth &amp; development/physiology ; *Seaweed/chemistry ; *Fruit/drug effects/growth &amp; development/physiology ; Ascophyllum/chemistry ; Plant Leaves/drug effects/growth &amp; development ; Climate ; }, abstract = {Seaweed extracts are promising plant biostimulants for viticulture, but their effects on white winegrape cultivars grown under cool climates remain fairly undocumented. Furthermore, information is limited on the biostimulant potential of some brown seaweed species like Ecklonia maxima. This study evaluated the impact of two commercial extracts (derived from Ascophyllum nodosum and Ecklonia maxima) on Vitis vinifera cv. Chardonnay in Belgium during the 2021 and 2022 growing seasons. The extracts, alongside a water‑control and an NPK‑reference (NPK‑Ref) treatment (with nitrogen, phosphorus, and potassium levels comparable to the extracts), were applied as foliar sprays five times at regular intervals, from flowering to ripening. In 2021 and 2022, A. nodosum significantly increased individual leaf area (+12% and +15%), while in 2021 A. nodosum‑treated vines had an increased chlorophyll content index (+12% CCI) and photosystem II (PSII) reaction centre density (+6%) relative to control vines. This corresponded with a small, but significant, improvement (+1.5%) in PSII maximum quantum yield (Fv∕Fm), whereas PSII electron transport efficiency (ΦE0) remained unchanged. Furthermore, increased berry size, mass, and sugar content were observed in A. nodosum‑treated vines during ripening in 2022, comparable to NPK‑Ref vines. Conversely, the E. maxima extract had limited effects on vegetative growth, physiology, and subsequent berry development. Yield increase from 2021 to 2022 varied by treatment, with a significant increase observed for E. maxima (+60%) and NPK‑Ref vines (+80%), relative to control vines. Our results indicate that seaweed extracts, specifically A. nodosum‑based, can enhance grapevine leaf area, CCI, and Fv∕Fm under cool climatic conditions. A. nodosum treatment was also associated with increased berry size and sugar content, while E. maxima treatment was associated with increased yield in the subsequent, warmer season. Altogether, our study highlights that the differential effects of seaweed extracts on grapevine development are modulated by species and environmental conditions.}, }
@article {pmid40892071, year = {2025}, author = {Gordon, DAR and Burke, DJ and Carrino-Kyker, SR and Bashian-Victoroff, C and Mabrouk, AI and Van Stan, JT}, title = {Community Composition of Microbial Eukaryotes Transported by Stemflow from Fagus grandifolia Ehrh. (American Beech) Trees in Northeastern Ohio (USA).}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {93}, pmid = {40892071}, issn = {1432-184X}, support = {DEB-2213623//Division of Environmental Biology/ ; }, mesh = {Ohio ; *Fagus/microbiology ; Fungi/genetics/classification/isolation &amp; purification ; *Eukaryota/classification/genetics/isolation &amp; purification ; *Rain ; RNA, Ribosomal, 18S/genetics ; Seasons ; Trees/microbiology ; Biodiversity ; Forests ; *Microbiota ; }, abstract = {Stemflow, the concentrated fraction of rainfall that drains down tree trunks, can translocate canopy biota to the forest floor, but its eukaryotic composition remains uncharacterized via eDNA methods. We collected stemflow from 18 Fagus grandifolia (American beech) trees during ten storms in northeastern Ohio (USA) and analyzed 18S rRNA eDNA to resolve transported microbial-eukaryote communities. Over 12 million reads (83 samples) revealed 920 zero-radius OTUs spanning fungi, algae, protists, and metazoans. Community composition differed significantly among storm events (PERMANOVA F = 3.6, r[2] = 0.31, p < 0.001) and among NOAA HYSPLIT modeled air-mass back-trajectories (F = 8.9, r[2] = 0.36, p < 0.001). Summer storms were dominated by fungal taxa (Entomophthoromycota, Basidiomycota, and Ascomycota comprised up to 90% of reads), whereas late-autumn and winter storms carried mainly algal stramenopiles (Ochrophyta). Large storms (> 60 mm event[-1]) mobilized conspicuously higher relative abundances of larger metazoans (tardigrades and arthropods). We infer from stemflow eDNA that (i) seasonal resource shifts in tree canopies favor parasitic fungi in summer and saprotrophic fungi in autumn; (ii) northerly winter storms entrain Great Lakes aerosol algae that deposit onto canopies; (iii) rainfall intensity and duration jointly control the detachment of well-attached canopy eukaryotes. Together, our results establish stemflow eDNA as a non-invasive window into storm-mediated linkages between above- and below-ground biodiversity, offering new scope for monitoring canopy microbiomes under intensifying hydro-climatic regimes.}, }
@article {pmid40886609, year = {2025}, author = {Wen, C and Dai, Z and Cheng, F and Cheng, H and Zha, X and Dai, H and Lu, X}, title = {Partially water-level-fluctuating strategy enhances rural greywater treatment in vertical flow constructed wetlands.}, journal = {Water research}, volume = {287}, number = {Pt B}, pages = {124484}, doi = {10.1016/j.watres.2025.124484}, pmid = {40886609}, issn = {1879-2448}, abstract = {Vertical flow constructed wetlands (VFCWs) represent a cost-effective and eco-friendly solution for sustainable wastewater management in rural areas. However, their limited capacity to tolerate influent fluctuations constrains their reliability in practical applications. This study aims to enhance the efficiency and reliability of rural greywater treatment by developing a new partially water-level-fluctuating strategy (PFCW) in VFCWs. The performance of PFCW was systematically evaluated and compared with conventional unsaturated (USCW) and partially saturated (PSCW) strategies under field conditions with varying hydraulic and pollutant loads. Results showed that PFCW significantly improved oxygen transfer and utilization, consistently achieving high removal efficiencies for COD (> 93 %) and NH4[+]-N (> 92 %). Weibull reliability analysis confirmed that PFCW maintained 100 % treatment reliability with discharge standards under all tested conditions, whereas others did not. Microbial analysis revealed that the dynamic water-level fluctuations in PFCW balanced anaerobic and aerobic conditions, promoting a stable and interconnected microbial community, which significantly enhanced key metabolic pathways associated with organic and nitrogen removal, thereby supporting high performance and contributing to long-term stability. Overall, this study demonstrates how water level management strategies shape microbial ecology and functional metabolism in VFCWs, offering a reliable, simple, and cost-efficient solution for greywater treatment in resource-constrained rural areas.}, }
@article {pmid40885026, year = {2025}, author = {Bajić, D and van Oort, M and Gabriëls, M and Gojković, U}, title = {Structuring complexity by mapping the possible in microbial ecosystems.}, journal = {Current opinion in microbiology}, volume = {88}, number = {}, pages = {102658}, doi = {10.1016/j.mib.2025.102658}, pmid = {40885026}, issn = {1879-0364}, abstract = {Microbial ecosystems consist of many interacting components that integrate through stochastic and highly dynamic processes across multiple scales. Yet, despite this complexity, microbial communities exhibit remarkably robust patterns and reproducible functions. This apparent paradox reflects the role of constraints, whether physical, physiological, or evolutionary, that channel stochasticity into structured outcomes. Due to the limited knowledge of the nature of these constraints, models in ecology have traditionally relied on stochastic exploration under minimal mechanistic assumptions. Now, advances in data availability and computational methods increasingly allow us to construct models that incorporate explicit mechanistic constraints. In this review, we synthesize emerging modeling approaches that explore the space of ecological possibility in microbial ecosystems under realistic constraints, such as those imposed by metabolic stoichiometry, thermodynamics, or the structure of ecological interaction networks. We argue that integrating such constraints can significantly improve the predictive resolution of models, helping us build a much needed bridge between theory and data. We further discuss how novel statistical approaches are revealing simple, low-dimensional patterns in microbial communities, offering empirical clues for identifying the underlying constraints. Together, these developments suggest a path toward a data-driven and mechanistically informed theory in microbial ecology.}, }
@article {pmid40884577, year = {2025}, author = {Kumar, V and Sandil, S and Verma, P and Ameen, F}, title = {Decoding microbial ecology and functions: metagenomic profiling of activated sludge contaminated with chlorolignin compounds in a pulp-paper mill treatment system.}, journal = {Archives of microbiology}, volume = {207}, number = {10}, pages = {247}, pmid = {40884577}, issn = {1432-072X}, support = {ORF-2025-364//The authors extend their appreciation to the ongoing research funding program, (ORF-2025-364), King Saud University, Riyadh, Saudi Arabia./ ; }, mesh = {*Sewage/microbiology/chemistry ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism ; Metagenomics ; *Water Pollutants, Chemical/analysis ; Microbiota ; Metals, Heavy/analysis ; Industrial Waste/analysis ; }, abstract = {This study aimed to profile the dynamics of indigenous bacterial communities in activated sludge, assess the pollutant load, and unlock the functional genes involved during the activated sludge treatment process. The physicochemical analyses of activated sludge revealed high amounts of phosphate, sulfate, chloride, and lignin, along with heavy metals like Fe, Zn, Cu, Ni, and Pb. Simultaneously, the GC-MS/MS technique identified decane, 1 bromo-2-methyl, pentadecanoic acid, methyl ester, benzene dicarboxylic acid, stigmasterol, borinic acid, diethyl, 2-hydroxymethyl cyclopropane, 2-methoxy-4-ethyl-phenol, 3,4,5-trichlorophenol, octadecanoic acid, and tetracosanic acid as major compounds. Furthermore, taxonomic classification of operational taxonomic unit (OTU) data revealed that Proteobacteria was the most abundant phylum, comprising 44.54% of the microbial community. In addition, other phyla, such as Bacteriodetes, Acidobacteria, Planctomycetes, Chlorolfexi, Actinobacteria, and Verrucomicrobia were also recorded within a range between 13.27 and 4.1% in the sludge. At the genus and species levels, the dominant organisms were unclassified (3.62%) and belonged to the family Rhodospirillacea. Further, PICRUSt2-based KEGG Orthology (KO) analysis showed enriched energy metabolism as the most abundant category, driven by oxidative phosphorylation and the TCA cycle. Furthermore, the MetaCyc analysis revealed a robust and adaptable microbial community with the dominant pathways of aerobic respiration I (cytochrome c) and fatty acid biosynthesis pathways, such as cis-vaccenate biosynthesis. The EC assignments highlighted a broad range of enzymatic functions, with a strong emphasis on oxidoreductases and transferases involved in energy production and biosynthesis. This research offers valuable insights into microbial community dynamics in wastewater treatment processes and identifies their functional role in a chlorolignin waste-polluted environment.}, }
@article {pmid40883892, year = {2025}, author = {Kanaan, G and Deming, JW}, title = {Multiple roles of DNA methylation in sea-ice bacterial communities and associated viruses.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf198}, pmid = {40883892}, issn = {1751-7370}, abstract = {Despite growing evidence for the role of DNA methylation in bacterial acclimation to environmental stress, this epigenetic mechanism remains unexplored in sea-ice microbial communities known to tolerate multiple stressors. This study presents a first analysis of DNA methylation patterns in bacterial communities and associated viruses across the vertical thickness of sea ice. Using a novel stepped-sackhole method, we collected sea-ice brines from distinct horizons of an Arctic ice floe, capturing microbial communities that had been exposed to different environmental conditions. Through Oxford Nanopore sequencing, we characterized methylation patterns in bacterial and associated viral DNA, analysing for methylation motifs and differences between ice horizons. We identified 22 unique bacterial methylation motifs and 27 viral motifs across three nucleotide methylation types (5mC, 6mA, and 4mC), with evidence of differential methylation between upper and lower ice. Analysis of metagenome-assembled genomes revealed the regulatory potential of methylation in both ice-adapted (Psychromonas and Polaribacter) and non-adapted bacteria (Pelagibacter); e.g., in Pelagibacter, differential methylation of the GANTC motif between upper and lower ice affected genes involved in core cellular processes. Viral methylation patterns showed evidence of recent infection. We also identified orphan methyltransferases in sea-ice phages, suggesting a mechanism for bypassing host restriction-modification systems and regulating host genes. Our findings reveal that DNA methylation serves functions in sea ice beyond traditional restriction-modification systems that protect against foreign DNA, opening new avenues for research on the role of epigenetic mechanisms not only in acclimation to the cryosphere but also more generally in microbial ecology and evolution.}, }
@article {pmid40883737, year = {2025}, author = {Feng, C and Shou, Y and Wu, S and Mo, H and Mao, X and Huang, H and Lu, Q and Xia, L and Lu, L and Su, Z and Guo, H and Huang, Z}, title = {Sea cucumber polypeptide ameliorates aging properties via the brain-gut axis in naturally aging mice.}, journal = {Chinese medicine}, volume = {20}, number = {1}, pages = {136}, pmid = {40883737}, issn = {1749-8546}, support = {GUIKE AB22080063//Guangxi Key Research and Development Program/ ; }, abstract = {BACKGROUND: Sea cucumber has been recognized as a traditional nutraceutical in Chinese medicine for millennia, with its derived polypeptide (SCP) demonstrating diverse bioactive properties. Nevertheless, the molecular mechanisms underlying SCP's potential geroprotective effects remain insufficiently characterized.<br><br>METHODS: We systematically evaluated SCP's impact on neuromotor function and cognitive performance in physiologically aged C57BL/6&#xa0;J mice models using a behavioral test battery comprising open field, Y-maze, and Barnes maze paradigms. Complementary multi-omics approaches were employed to interrogate age-related perturbations in gut microbial ecology (16S rRNA sequencing) and systemic metabolism (untargeted LC-MS).H&amp;E and immumohistochemical staining was used to evaluate the pathological features of mice brain tissues and intestinal tissue. Bulk RNA-sequencing was used to detect gene expression profiles in mice brain tissue.<br><br>RESULTS: Behavioral assessments (open field, Y-maze, Barnes maze) demonstrated that SCP intervention effectively delayed the decline in exercise, learning and memory abilities in aging mice. SCP administration enhanced cerebral organosomatic indices and hepatic functional markers while reducing neuronal senescence biomarkers. Furthermore, SCP improved intestinal mucosal barrier function in aging mice restored gut microbial diversity metrics, effectively counteracting age-associated dysbiosis. Mechanistically, SCP induced taxonomic restructuring characterized by increased abundance of neuroprotective Eubacterium_brachy_group and Prevotellaceae genera, concomitant with suppression of dementia-linked Dubosiella. Metabolomic integration revealed SCP-mediated upregulation of steroidogenic pathways correlating with cognitive enhancement. Multi-omics validation through integrated transcriptomic profiling and immunohistochemical quantification corroborated these physiological improvements.<br><br>CONCLUSION: Our findings propose a mechanism whereby SCP might exert geroprotective effects through multimodal regulation of the gut-brain axis and systemic metabolic homeostasis, establishing mechanistic foundations for its translational potential in healthy longevity promotion.}, }
@article {pmid40881287, year = {2025}, author = {Pluym, T and Waegenaar, F and Dejaeger, K and Dhoore, M and Mestdagh, E and Cornelissen, E and Boon, N and De Gusseme, B}, title = {Membrane filtration reduces nutrient availability and invasion potential in drinking water systems, without affecting mature biofilms.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1622038}, doi = {10.3389/fmicb.2025.1622038}, pmid = {40881287}, issn = {1664-302X}, abstract = {Ensuring biostable drinking water is a growing priority for drinking water utilities, especially in non- or minimally chlorinated distribution systems where microbial regrowth is controlled through nutrient limitation. In this study, we evaluated the efficacy of ultrafiltration (UF) and nanofiltration (NF) in reducing total organic carbon (TOC) and their impact on the microbiology in a pilot-scale drinking water distribution system over 7 weeks. NF achieved significantly higher TOC removal (75.4%) compared to UF (25.4%), with high performance size exclusion chromatography revealing almost complete removal of all molecular weight fractions in NF-treated water. When introduced into the pilot system, NF-, UF-treated water, and untreated tap water supported similar increasing bulk cell concentrations, but exhibited distinct bacterial community compositions, with NF-treated water showing the most divergent microbiome. Despite these differences in the bulk water, the mature biofilm community (~2 years old) remained stable, underscoring it resilience to changes in nutrient conditions. An invasion assay demonstrated that decay rates of unwanted microorganisms increased with decreasing organic carbon content. For example, decay rates for the introduced microorganism Pseudomonas putida in NF-, UF- treated water, and untreated tap water were respectively, -0.18 h[-1], -0.143 h[-1], and -0.089 h[-1], indicating enhanced biostability in membrane-treated systems.}, }
@article {pmid40879794, year = {2025}, author = {Sun, X and Xia, R and Xie, J and Duan, K and Xun, W and Zhang, N and Huang, G and Zhang, R and Shen, Q and Wu, K and Xu, Z}, title = {Cooperative Interactions Between Bacillus and Lysobacter Enhance Consortium Stability and Fusarium Wilt Suppression in Cucumber.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {92}, pmid = {40879794}, issn = {1432-184X}, support = {42307173//National Natural Science Foundation of China/ ; 2023M747140//China Postdoctoral Science Foundation/ ; GZB20230309//Postdoctoral Fellowship Program of CPSF/ ; 2023ZB250//Excellent Postdoctoral Program of Jiangsu Province/ ; 2024YFD1701002//National Key Research and Development Program of China/ ; 2023WPY00002//Rural Revitalization Strategy Project Seed Industry Vitalization Action Project of Guangdong Province/ ; }, mesh = {*Cucumis sativus/microbiology ; *Fusarium/physiology ; *Bacillus/physiology ; *Plant Diseases/microbiology/prevention &amp; control ; Rhizosphere ; Soil Microbiology ; *Lysobacter/physiology ; *Microbial Consortia/physiology ; Microbial Interactions ; Biofilms/growth &amp; development ; }, abstract = {The rhizosphere microbiome plays a pivotal role in plant health by mediating interactions between hosts, beneficial microbes, and pathogens. However, the ecological mechanisms underlying microbial consortia that suppress soil-borne diseases remain largely unexplored. In this study, we investigated how the biocontrol bacterium Bacillus velezensis SQR9 influences the assembly of the cucumber rhizosphere bacterial community in the presence of the pathogenic fungus Fusarium oxysporum f. sp. cucumerinum (FOC). Inoculation with B. velezensis SQR9 significantly enriched the genus Lysobacter, a known biocontrol taxon. Meta-analysis revealed a positive correlation between Bacillus and Lysobacter abundances in healthy plant rhizospheres-a relationship absent in Fusarium wilt-diseased soils-suggesting a conserved ecological association linked to disease suppression. Mechanistic assays demonstrated that Lysobacter enzymogenes XL8, an antifungal bacterium isolated from the cucumber rhizosphere, formed synergistic biofilms with B. velezensis SQR9. Spent medium growth assays indicated that strain SQR9 facilitated the growth of L. enzymogenes XL8 through metabolic interactions. Targeted RT-qPCR and UHPLC-MS/MS analyses confirmed that treatment with spent medium of the partner strain enhanced the expression and production of antifungal metabolites bacillomycin D and heat-stable antifungal factor (HSAF), both antagonistic to F. oxysporum. Greenhouse trials confirmed that this dual-species consortium more effectively suppressed Fusarium wilt than single-species inoculations, as evidenced by reduced pathogen abundance and enhanced plant growth. Together, our findings underscore the importance of microbial metabolic cooperation and biofilm-mediated coexistence in shaping rhizosphere community assembly and function, providing ecological insights for the development of synthetic microbial consortia aimed at sustainable plant disease management.}, }
@article {pmid40879396, year = {2025}, author = {Li, D and Li, Y and Xu, H and Wu, J}, title = {Nonlinear response of soil microfauna network complexity and stability to multilevel warming in an old-growth subtropical forest.}, journal = {mBio}, volume = {}, number = {}, pages = {e0015625}, doi = {10.1128/mbio.00156-25}, pmid = {40879396}, issn = {2150-7511}, abstract = {The influence of climate warming on soil microbes and the mechanisms underlying these effects have become the subject of intense focus in microbial ecology and climate change research. However, it is largely unknown how warming affects soil microfauna network complexity and stability or how warming-induced changes may affect ecosystem functioning in old-growth forests. Here, we conducted a 3-year multilevel warming experiment in an old-growth subtropical forest using infrared heating with five treatments: ambient soil temperature and 0.8°C, 1.5°C, 3.0°C, and 4.2°C above ambient soil temperature. We found that soil microfauna network complexity and stability and multinutrient cycling were significantly higher under warming and showed similar hump-shaped trends across rising temperatures. The nonlinear responses of soil microfauna network complexity and stability were primarily linked to soil temperature, moisture, organic carbon, and microbial biomass. Importantly, we found that soil multinutrient cycling was positively influenced by microfauna network complexity and stability. Consequently, our findings provide insights into the key role of soil microfauna network structure in regulating soil multinutrient cycling, highlighting the need to consider soil organisms' potential interactions and that it is crucial to preserve soil microfauna "interactions" for ecosystem management in forests under global change.IMPORTANCEIt is largely unknown how warming affects soil microfauna network complexity and stability or how warming-induced changes may affect ecosystem functioning in old-growth forests. We conducted a 3-year multilevel warming experiment in an old-growth subtropical forest using infrared heating. We found that soil microfauna network complexity and stability were significantly higher under warming treatments and displayed nonlinear responses to different warming levels. Soil multinutrient cycling was positively and significantly influenced by microfauna network complexity and stability. Given that complex interconnections between soil microfauna are critical for sustaining ecosystem functioning, protecting microfauna "interactions" may be critical to mitigating the adverse impacts of warming-induced biodiversity reduction on ecosystem functioning.}, }
@article {pmid40875436, year = {2025}, author = {Maguire, M and Serna, C and Delgado-Blas, JF and Clarke, C and DeLappe, N and Cormican, M and Coughlan, SC and Miliotis, G and Gonzalez-Zorn, B and Burke, LP}, title = {Healthcare-related transmission of mobile genetic elements co-carrying bla NDM and 16S rRNA methyltransferase genes in multiple Enterobacterales.}, journal = {Microbial genomics}, volume = {11}, number = {8}, pages = {}, doi = {10.1099/mgen.0.001473}, pmid = {40875436}, issn = {2057-5858}, mesh = {*beta-Lactamases/genetics ; *Methyltransferases/genetics ; *Interspersed Repetitive Sequences ; *Enterobacteriaceae/genetics/drug effects/isolation &amp; purification ; Humans ; Ireland ; Plasmids/genetics ; RNA, Ribosomal, 16S/genetics ; Anti-Bacterial Agents/pharmacology ; *Enterobacteriaceae Infections/microbiology/transmission ; Bacterial Proteins/genetics ; Drug Resistance, Multiple, Bacterial/genetics ; }, abstract = {Aminoglycosides are used in the treatment of serious infections with Gram-negative bacteria, especially those resistant to beta-lactams and carbapenems. 16S rRNA methyltransferases (16S-RMTase) are capable of conferring resistance to nearly all aminoglycosides. They are sometimes detected in combination with bla NDM. This study describes the mobile genetic elements associated with bla NDM and 16S-RMTase (co-)carriage in Enterobacterales from Ireland in the period 2019-2023. All isolates (n=58) carrying both bla NDM and a 16S-RMTase gene between 2019 and 2023 were obtained from the CPE National Reference Laboratory Service. Short-read sequences were generated for all isolates, and long-read sequences were generated for a subset of isolates (n=27). MOB-recon was used to distinguish plasmid-derived contigs from draft assemblies. The containment distance and DCJ-indel distance were used to find clusters of related plasmids. Isolates carrying bla NDM-1 were associated with armA (n=31) but also rmtC (n=6) carriage. These genes were co-localized most frequently on IncFIB/HI1B (n=12), IncM2 (n=10) and IncC (n=8) plasmids. Closely related plasmids were identified in multiple species (range: 2-5) and at different sites around Ireland; however, the IncM2 plasmids were largely associated with a single hospital. Isolates carrying bla NDM-5 were associated with rmtB1 (n=28) carriage. The majority (n=15) were carried on a diverse range of mosaic IncF-type plasmids. Two discrete clusters of IncM1 (n=3) and IncFII (n=4) type plasmids were also detected. The study highlights the diverse plasmids co-carrying carbapenem and aminoglycoside resistance genes in Ireland. Detection of plasmids across multiple species and hospitals suggests dissemination driven by antimicrobial selective pressure and environmental reservoirs within healthcare networks. The co-dissemination of these genes on highly mobile plasmids poses a significant public health concern and emphasizes the need for greater awareness that chains of transmission of antimicrobial resistance in the healthcare setting may involve multiple species.}, }
@article {pmid40875044, year = {2025}, author = {Shao, Q and Yang, Q and Xu, Y and Zhang, L and Ding, M and Li, F and He, C}, title = {The Impact of Artificial Water Diversion-induced Algal Blooms on Carbon Balance in a Semi-enclosed Bay.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {91}, pmid = {40875044}, issn = {1432-184X}, support = {2022J195//Ningbo Natural Science Foundation/ ; 2022S116//Ningbo Public Welfare Science and Technology Project/ ; SS//K.C. Wong Magna Fund in Ningbo University/ ; }, mesh = {*Phytoplankton/growth &amp; development/metabolism/classification ; *Eutrophication ; *Bays/microbiology/chemistry ; *Carbon/metabolism ; Diatoms/growth &amp; development/metabolism ; Ecosystem ; Seasons ; *Carbon Cycle ; Dinoflagellida/growth &amp; development ; Seawater/chemistry ; }, abstract = {Artificial water diversion is widely used to address water security; yet, its impacts on phytoplankton communities and coastal carbon balance remain poorly understood. Using a seasonal diversion project in a semi-enclosed bay as a case study, we analyzed phytoplankton composition via morphological methods and assessed carbon balance through simultaneous measurements of primary production (P), ecosystem respiration rate (R), and production-to-respiration (PP/R) ratio. Our results showed that artificial water diversion activities during the wet month enhanced hydrological connectivity and phytoplankton homogeneity, triggering a mixed diatom-dinoflagellate bloom. Phytoplankton abundance during the wet month increased by sevenfold (surface layer) and 26.5-fold (bottom layer) compared to dry month values. This simultaneously resulted in the PP value of the wet month being more than twice that of the dry month. Although R rose with increasing phytoplankton abundance, no significant correlation was observed between them. Instead, dry-month R was primarily driven by pH and dissolved organic carbon, whereas wet-month R showed minimal environmental linkages. PP/R ratios of surface and bottom layers were always less than 1, implying Meishan bay was a net heterotrophic ecosystem, despite significant changes in phytoplankton community structure induced by artificial water diversion and associated algal bloom. Furthermore, our results strongly suggest that changes in PP, but not in R, control the PP/R ratio of Meishan bay. This study offers valuable guidance for the ecological management of artificial water diversions and can serve as a reference for similar water diversion projects in other semi-enclosed bays.}, }
@article {pmid40871342, year = {2025}, author = {Touati, A and Ibrahim, NA and Tighilt, L and Idres, T}, title = {Anti-QS Strategies Against Pseudomonas aeruginosa Infections.}, journal = {Microorganisms}, volume = {13}, number = {8}, pages = {}, doi = {10.3390/microorganisms13081838}, pmid = {40871342}, issn = {2076-2607}, support = {IMSIU-DDRSP2501//Deanship of Scientific Research at Imam Mohammad Ibn Saud Islamic University (IMSIU)./ ; }, abstract = {Pseudomonas aeruginosa poses significant health threats due to its multidrug-resistant profile, particularly affecting immunocompromised individuals. The pathogen's ability to produce virulence factors and antibiotic-resistant biofilms, orchestrated through quorum-sensing (QS) mechanisms, complicates conventional therapeutic interventions. This review aims to critically assess the potential of anti-QS strategies as alternatives to antibiotics against P. aeruginosa infections. Comprehensive literature searches were conducted using databases such as PubMed, Scopus, and Web of Science, focusing on studies addressing QS inhibition strategies published recently. Anti-QS strategies significantly attenuate bacterial virulence by disrupting QS-regulated genes involved in biofilm formation, motility, toxin secretion, and immune evasion. These interventions reduce the selective pressure for resistance and enhance antibiotic efficacy when used in combination therapies. Despite promising outcomes, practical application faces challenges, including specificity of inhibitors, pharmacokinetic limitations, potential cytotoxicity, and bacterial adaptability leading to resistance. Future perspectives should focus on multi-target QS inhibitors, advanced delivery systems, rigorous preclinical validations, and clinical translation frameworks. Addressing current limitations through multidisciplinary research can lead to clinically viable QS-targeted therapies, offering sustainable alternatives to traditional antibiotics and effectively managing antibiotic resistance.}, }
@article {pmid40871329, year = {2025}, author = {McKay, S and Churchill, H and Hayward, MR and Klein, BA and Van Meulebroek, L and Ghyselinck, J and Marzorati, M}, title = {Effects of cRG-I Prebiotic Treatment on Gut Microbiota Composition and Metabolic Activity in Dogs In Vitro.}, journal = {Microorganisms}, volume = {13}, number = {8}, pages = {}, doi = {10.3390/microorganisms13081825}, pmid = {40871329}, issn = {2076-2607}, abstract = {Low-dose carrot rhamnogalacturonan-I (cRG-I) has shown consistent modulatory effects on the gut microbiota and immune function in humans. In this study we investigated its effects on the microbial composition and metabolite production of the gut microbiota of small (5-10 kg), medium-sized (10-27 kg), and large (27-45 kg) dogs, using inulin and xanthan as comparators. Fecal samples from six dogs of each size group were evaluated. Overall microbiome composition, assessed using metagenomic sequencing, was shown to be driven mostly by dog size and not treatment. There was a clear segregation in the metabolic profile of the gut microbiota of small dogs versus medium-sized and large dogs. The fermentation of cRG-I specifically increased the levels of acetate/propionate-producing Phocaeicola vulgatus. cRG-I and inulin were fermented by all donors, while xanthan fermentation was donor-dependent. cRG-I and inulin increased acetate and propionate levels. The responses of the gut microbiota of different sized dogs to cRG-I were generally consistent across donors, and interindividual differences were reduced. This, together with the significant increase in P. vulgatus during fermentation in both this study and an earlier human ex vivo study, suggests that this abundant and prevalent commensal species has a core capacity to selectively utilize cRG-I.}, }
@article {pmid40870599, year = {2025}, author = {Guo, H and Wang, Y and Guo, Y and Liu, X and Gui, T and Ling, M and Qian, H}, title = {Correlation of Midgut Microbiota and Metabolic Syndrome-Related Lipids in Hemolymph Between Obese and Lean Silkworm Strains.}, journal = {Insects}, volume = {16}, number = {8}, pages = {}, doi = {10.3390/insects16080798}, pmid = {40870599}, issn = {2075-4450}, support = {No. CARS-18//The present study was supported by the China Agriculture Research System (Sericulture industry, No. CARS-18)/ ; }, abstract = {Metabolic syndrome is a global health crisis. However, there are no effective therapeutic strategies for metabolic syndrome. Therefore, this study was conducted to find out a novel silkworm-based metabolic syndrome model that bridges microbial ecology and metabolic dysregulation by integrating hemolymph lipids and midgut microbiota. Our results showed that the levels of HDL-C in the hemolymph of the lean silkworm strain were significantly higher than that in the obese silkworm strain. Furthermore, correlation analysis revealed that Lactococcus and Oceanobacillus were positively related to HDL-C levels, while SM1A02 and Pseudonocardia were negatively associated with HDL-C levels. These relationships between the identified bacteria in the midgut and HDL-C, known as the "good" lipid, in the hemolymph could help guide the development of new treatments for obesity and metabolic problems like high cholesterol in humans. Overall, our results not only established a framework for understanding microbiota-driven lipid dysregulation in silkworms but also offered potential probiotic targets and a bacterial biomarker for obesity and metabolic dysfunction intervention in humans.}, }
@article {pmid40869967, year = {2025}, author = {Fu, Y and Bonifacio-Mundaca, J and Desterke, C and Casafont, &#xcd; and Mata-Garrido, J}, title = {Genomic Alterations and Microbiota Crosstalk in Hepatic Cancers: The Gut-Liver Axis in Tumorigenesis and Therapy.}, journal = {Genes}, volume = {16}, number = {8}, pages = {}, doi = {10.3390/genes16080920}, pmid = {40869967}, issn = {2073-4425}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Liver Neoplasms/genetics/microbiology/therapy/pathology ; *Carcinoma, Hepatocellular/genetics/microbiology/therapy/pathology ; *Carcinogenesis/genetics ; Liver/pathology/metabolism/microbiology ; *Cholangiocarcinoma/genetics/microbiology/therapy ; Mutation ; Epigenesis, Genetic ; Animals ; }, abstract = {Background/Objectives: Hepatic cancers, including hepatocellular carcinoma (HCC) and cholangiocarcinoma (CCA), are major global health concerns due to rising incidence and limited therapeutic success. While traditional risk factors include chronic liver disease and environmental exposures, recent evidence underscores the significance of genetic alterations and gut microbiota in liver cancer development and progression. This review aims to integrate emerging knowledge on the interplay between host genomic changes and gut microbial dynamics in the pathogenesis and treatment of hepatic cancers. Methods: We conducted a comprehensive review of current literature on genetic and epigenetic drivers of HCC and CCA, focusing on commonly mutated genes such as TP53, CTNNB1, TERT, IDH1/2, and FGFR2. In parallel, we evaluated studies addressing the gut-liver axis, including the roles of dysbiosis, microbial metabolites, and immune modulation. Key clinical and preclinical findings were synthesized to explore how host-microbe interactions influence tumorigenesis and therapeutic response. Results: HCC and CCA exhibit distinct but overlapping genomic landscapes marked by recurrent mutations and epigenetic reprogramming. Alterations in the gut microbiota contribute to hepatic inflammation, genomic instability, and immune evasion, potentially enhancing oncogenic signaling pathways. Furthermore, microbiota composition appears to affect responses to immune checkpoint inhibitors. Emerging therapeutic strategies such as probiotics, fecal microbiota transplantation, and precision oncology based on mutational profiling demonstrate potential for personalized interventions. Conclusions: The integration of host genomics with microbial ecology provides a promising paradigm for advancing diagnostics and therapies in liver cancer. Targeting the gut-liver axis may complement genome-informed strategies to improve outcomes for patients with HCC and CCA.}, }
@article {pmid40868890, year = {2025}, author = {Zhang, M and Zhang, Y and Zhao, Z and Deng, F and Jiang, H and Liu, C and Li, Y and Chai, J}, title = {Bacterial-Fungal Interactions: Mutualism, Antagonism, and Competition.}, journal = {Life (Basel, Switzerland)}, volume = {15}, number = {8}, pages = {}, doi = {10.3390/life15081242}, pmid = {40868890}, issn = {2075-1729}, abstract = {The interaction between bacteria and fungi is one of the key interactions of microbial ecology, including mutualism, antagonism, and competition, which profoundly affects the balance and functions of animal microbial ecosystems. This article reviews the interactive dynamics of bacteria and fungi in more concerned microenvironments in animals, such as gut, rumen, and skin. Moreover, we summarize the molecular mechanisms and ecological functions of the interaction between bacteria and fungi. Three major bacterial-fungal interactions (mutualism, antagonism, and competition) are deeply discussed. Understanding of the interactions between bacteria and fungi allows us to understand, modulate, and maintain the community structure and functions. Furthermore, this summarization will provide a comprehensive perspective on animal production and veterinary medicine, as well as guide future research directions.}, }
@article {pmid40866705, year = {2025}, author = {Chen, SC and Li, XM and Battisti, N and Guan, G and Montoya, MA and Osvatic, J and Pjevac, P and Pollak, S and Richter, A and Schintlmeister, A and Wanek, W and Mussmann, M and Loy, A}, title = {Microbial iron oxide respiration coupled to sulfide oxidation.}, journal = {Nature}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41586-025-09467-0}, pmid = {40866705}, issn = {1476-4687}, abstract = {Microorganisms have driven Earth's sulfur cycle since the emergence of life[1-6], yet the sulfur-cycling capacities of microorganisms and their integration with other element cycles remain incompletely understood. One such uncharacterized metabolism is the coupling of sulfide oxidation with iron(III) oxide reduction, a ubiquitous environmental process hitherto considered to be strictly abiotic[7,8]. Here we present a comprehensive genomic analysis of sulfur metabolism across prokaryotes, and reveal bacteria that are capable of oxidizing sulfide using extracellular solid phase iron(III). Based on a phylogenetic framework of over hundred genes involved in dissimilatory transformation of sulfur compounds, we recorded sulfur-cycling capacity in most bacterial and archaeal phyla. Metabolic reconstructions predicted co-occurrence of sulfur compound oxidation and iron(III) oxide respiration in diverse members of 37 prokaryotic phyla. Physiological and transcriptomic evidence demonstrated that a cultivated representative, Desulfurivibrio alkaliphilus, grows autotrophically by oxidizing dissolved sulfide or iron monosulfide (FeS) to sulfate with ferrihydrite as an extracellular iron(III) electron acceptor. The biological process outpaced the abiotic process at environmentally relevant sulfide concentrations. These findings expand the known diversity of sulfur-cycling microorganisms and unveil a biological mechanism that links sulfur and iron cycling in anoxic environments, thus highlighting the fundamental role of microorganisms in global element cycles.}, }
@article {pmid40864652, year = {2025}, author = {Rigou, S and Schmitt, A and Moreno, AB and Lartigue, A and Danner, L and Mayer, L and Giry, C and Trabelsi, F and Belmudes, L and Olivero-Deibe, N and Le Guenno, H and Couté, Y and Berois, M and Legendre, M and Jeudy, S and Abergel, C and Bisio, H}, title = {Evolutionarily conserved grammar rules viral factories of amoeba-infecting members of the hyperdiverse Nucleocytoviricota phylum.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {35}, pages = {e2515074122}, doi = {10.1073/pnas.2515074122}, pmid = {40864652}, issn = {1091-6490}, support = {101160452//EC | European Research Council (ERC)/ ; 832601//EC | European Research Council (ERC)/ ; ANR-10-INBS-08//Agence Nationale de la Recherche grant ProFI/ ; ANR-17-EURE-0003//Chemistry Biology Health (CBH) Graduate School of University Grenoble Alpes grant/ ; }, abstract = {Despite sharing fewer than 10 core genes, the hyperdiverse Nucleocytoviricota phylum (ranging from poxviruses to giant viruses) universally assembles viral factories (VFs) resembling biomolecular condensates. Regardless, it is unclear how these viruses achieve such a level of functional conservation without clear conserved genetic information. We demonstrate that the VFs produced by amoeba-infecting viruses have liquid-like properties and identify a conserved molecular grammar governing viral factory scaffold protein: charge-patterned intrinsically disordered regions that drive phase separation independently of sequence homology. This grammar predicts functional scaffold proteins across the 15 viral families, revealing evolutionary constraints invisible to sequence or structural analysis. Strikingly, VFs exhibit subcompartmentalization analogous to nuclei, segregating transcription and mRNA processing (inner condensates) from replication (interphase zones) and translation (host cytoplasm). Our work establishes phase separation as a fundamental organizational principle bridging extreme genomic diversity, explaining how biological complexity emerges without gene conservation. This grammar is likely also conserved in non-amoeba-infecting members of the phylum and thus may represent a primordial solution for organelle-like organization, with broad implications for antiviral targeting.}, }
@article {pmid40863168, year = {2025}, author = {Buckley, AM and Zaidan, S and Sweet, MG and Ewin, DJ and Ratliff, JG and Alkazemi, A and Davis Birch, W and McAmis, AM and Neilson, AP}, title = {Choline Metabolism to the Proatherogenic Metabolite Trimethylamine Occurs Primarily in the Distal Colon Microbiome In Vitro.}, journal = {Metabolites}, volume = {15}, number = {8}, pages = {}, pmid = {40863168}, issn = {2218-1989}, support = {N/A/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; N/A//OIRC INFORM hub/ ; N/A/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; N/A//North Carolina Agricultural Research Service/ ; N/A//Applied Microbiology International/ ; N/A//Hatch program, USDA/ ; }, abstract = {BACKGROUND/OBJECTIVES: Gut microbial metabolism of choline and related quaternary amines to trimethylamine (TMA) is the first step in the production of trimethylamine N-oxide (TMAO), a circulating metabolite that contributes to the development of atherosclerosis and other forms of cardiovascular disease (CVD). No data exist on regional differences in TMA production within the colon due to difficulties studying gut regions in vivo. A better understanding of TMA production by gut microbiota is needed to develop strategies to limit TMA production in the gut and TMAO levels in circulation with the goal of reducing CVD risk.<br><br>METHODS: We employed our novel three-compartment MiGut in vitro model, which establishes three distinct microbial ecologies mimicking the proximal, mid, and distal colon, to study conversion of choline to TMA by human gut microbiota using isotopically labelled substrate.<br><br>RESULTS: Choline-d9 was almost completely converted to TMA-d9 in vessels 2-3 (mimicking the mid and distal colon) within 6-8 h, but little conversion occurred in vessel 1 (mimicking the proximal colon). Abundance of cutC, part of the cutC/D gene cluster responsible for choline conversion to TMA, was highest in vessel 1 vs. 2-3, suggesting that its expression or activity may be suppressed in the proximal colon. Another possibility is that the viability/activity of bacteria expressing cutC could be suppressed in the same region.<br><br>CONCLUSIONS: This novel finding suggests that while bacteria capable of converting choline to TMA exist throughout the colon, their activity may be different in distinct colon regions. The regional specificity of TMA production, if confirmed in vivo, has implications for both basic microbial ecology related to CVD and the development of strategies to control TMA and TMAO production, with the goal of lowering CVD risk. These findings warrant further study in vitro and in vivo.}, }
@article {pmid40862636, year = {2025}, author = {Modin, O}, title = {From ecology to engineering: the role of myxobacteria in recirculating aquaculture systems.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0137625}, doi = {10.1128/aem.01376-25}, pmid = {40862636}, issn = {1098-5336}, abstract = {Open microbial communities play vital roles in many engineered systems, providing essential ecosystem services but also posing operational challenges. In recirculating aquaculture systems (RASs), microbial activity is crucial for water purification, yet it can also lead to the accumulation of taste-and-odor compounds that compromise fish quality. In a recent study, Södergren et al. (Appl Environ Microbiol 91:e00757-25, 2025, https://doi.org/10.1128/aem.00757-25) report the first successful isolation of myxobacteria from RAS and demonstrate their ability to produce geosmin and other volatile organic compounds under various nutrient conditions, including in real RAS water. This work provides foundational insights into the ecological roles of myxobacteria and their contributions to off-flavor formation in aquaculture environments. In this commentary, I reflect on the broader significance of microbial ecology in environmental biotechnology and discuss how the findings of Södergren et al. may inform future strategies for managing microbial communities in RAS to improve system performance and product quality.}, }
@article {pmid40862349, year = {2025}, author = {Benot, AO and Waldschmidt, G and Tiyapun, C and Okyere, IJ and Goff, JL}, title = {Metagenomic characterization of fire-adapted soil microbiomes in the Albany Pine Bush Preserve.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0066425}, doi = {10.1128/mra.00664-25}, pmid = {40862349}, issn = {2576-098X}, abstract = {The Albany Pine Bush Preserve's documented fire history enables a unique study of fire-dependent ecosystems. We identified 94 unique bacterial and archaeal metagenome-assembled genomes spanning 27 classes, providing genomic insights into microbial nutrient cycling in these systems.}, }
@article {pmid40862159, year = {2025}, author = {Wang, Y and Jiang, L and Zhou, F and Zhang, Y and Fine, RD and Li, M}, title = {The hidden dancers in water: the symbiotic mystery of Legionella pneumophila and free-living amoebae.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1634806}, pmid = {40862159}, issn = {1664-302X}, abstract = {Legionella pneumophila, a Gram-negative bacillus, is the primary etiological agent of Legionnaires' disease, a severe respiratory infection. The symbiotic relationship between L. pneumophila and free-living amoebae (FLAs), particularly Acanthamoeba spp., represents a critical intersection of microbial ecology and human pathogenesis. This symbiosis provides Legionella with a protective intracellular niche, enhancing its resistance to biocides, increasing its pathogenicity, and facilitating horizontal gene transfer. These interactions not only boost the environmental persistence and dissemination of L. pneumophila but also elevate the risk of human exposure through contaminated drinking water systems. This review delves into the sophisticated survival strategies employed by L. pneumophila within host cells, including evasion of endocytic pathways, inhibition of phagosome maturation and acidification, and prevention of phagosome-lysosome fusion. By elucidating these mechanisms, we underscore the critical need for in-depth research into the Legionella-amoebae symbiosis and its broader implications for public health. Additionally, we address the challenges and strategies for mitigating environmental risks, emphasizing the importance of innovative approaches to ensure water system safety and prevent pathogen transmission.}, }
@article {pmid40860928, year = {2025}, author = {Šikić, A and Gagović, E and Rojas, A and Sindičić, M and Žilić, DJ and Naletlić, &#x160; and Balić, D and Hodžić, A and Beck, R}, title = {First molecular identification of Spirometra mansoni in the golden jackal (Canis aureus) in Croatia.}, journal = {Frontiers in veterinary science}, volume = {12}, number = {}, pages = {1629099}, pmid = {40860928}, issn = {2297-1769}, abstract = {This study presents the first molecularly confirmed identification of the cestode Spirometra mansoni in the golden jackals (Canis aureus) in Croatia, and possibly the first such report in Europe. Of 198 jackals examined between 2020 and 2025, adult Spirometra worms were recovered from three individuals. The morphological characteristics of these specimens were consistent with S. mansoni, and their identity was confirmed by PCR and sequencing of the mitochondrial cox1 and nad1 genes. Phylogenetic analysis grouped the obtained sequences within the S. mansoni clade, with strong posterior probability support. This finding expands the known host range and geographic distribution of S. mansoni and underscores the importance of integrating molecular diagnostics in parasitological surveys. Further research is needed to assess the role of golden jackals and other wildlife in the epidemiology of Spirometra spp. in Europe.}, }
@article {pmid40860758, year = {2025}, author = {Tuoliu, D and Cheng, J and Xia, L and Wen, Z and Wang, M and Yang, W and Yang, Q}, title = {Bacterial microbiome and their assembly processing in two sympatric desert rodents (Dipus sagitta and Meriones meridianus) from different geographic sources.}, journal = {Current zoology}, volume = {71}, number = {4}, pages = {440-448}, pmid = {40860758}, issn = {1674-5507}, abstract = {The microbiome of mammals has profound effects on host fitness, but the process, which drives the assembly and shift of mammalian microbiome remains poorly understood. To explore the patterns of small mammal microbial communities across host species and geographical sites and measure the relative contributions of different processes in driving assembly patterns, 2 sympatric desert rodent species (Dipus sagitta and Meriones meridianus) were sampled from 2 geographically distant regions, which differed in the environment, followed by 16S rRNA gene sequencing. The microbiomes differed significantly between D. sagitta and M. meridianus, and linear mixed modeling (LMM) analysis revealed that microbial diversity was mostly affected by species rather than the environment. For each rodent species, the microbiome diversity and structure differed across geographical regions, with individuals from lower rainfall environments exhibiting greater diversity. The null modeling results suggested dispersal limitation and ecological drift rather than differential selective pressures acting on the microbiome. In addition, each group had a different core genus, suggesting that the taxonomic composition of the microbiome was shaped most strongly by stochastic processes. Our results suggest that variation in the microbiome between hosts, both within and among geographic rodent populations, is driven by bacterial dispersal and ecological drift rather than by differential selective pressures. These results elucidated the diversity patterns and assembly processes of bacterial microbiomes in small desert mammals. Deciphering the processes shaping the assembly of the microbial community is a premise for better understanding how the environment-host-microbe interactions of mammals are established and maintained, particularly in the context of increased environmental disturbances and global changes.}, }
@article {pmid40860567, year = {2025}, author = {Gavriilidou, A and Murace, M and Portoghese, M and Schouten, S and Hamidjaja, R and Escobar Doncel, &#xc1; and Boeren, S and Giesbers, M and Capoulade, J and Vignolini, S and Smidt, H and Ingham, CJ}, title = {Pseudosulfitobacter pseudonitzschiae hitchhikes on gliding colonies of Cellulophaga lytica.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf118}, pmid = {40860567}, issn = {2730-6151}, abstract = {Interspecies interactions shape microbial communities; this is central for microbial ecology. Cellulophaga lytica PlyA2 is a marine flavobacterium, which glides over surfaces and forms ordered, structurally coloured colonies, which display angle-dependent reflection of light. Pseudosulfitobacter pseudonitzschiae SW is an apparently nonmotile, nonstructurally coloured marine bacterium. Here, we aim to understand the interaction of both strains at cellular, genomic, optical, and proteomic levels. Cocultivation on agar showed that P. pseudonitzschiae uses gliding C. lytica to spread by microbial hitchhiking in which Pseudosulfitobacter appears to "surf" on basal layers of motile Cellulophaga. This dispersal mechanism was found to be often beneficial for P. pseudonitzschiae, which could maximally expand its population up to 350-fold relative to monoculture. Coculture was often of limited benefit for C. lytica, only in extended cultivation on rich medium was the presence of P. pseudonitzschiae detrimental to its viability. The proteome of P. pseudonitzschiae was strongly impacted by the association with C. lytica. Quorum-sensing signalling, potential exchange of amino acids, vitamins, and other metabolites are likely mediating this hitchhiking interaction. In contrast, C. lytica made minimal adjustments to its proteome composition in coculture. Supported by optical analysis, P. pseudonitzschiae patterned C. lytica by changing how groups of the latter organised to reflect light. Our results underscore the unusual, dynamic interplay between two bacterial species and provide insights on the mechanisms underlying this relationship.}, }
@article {pmid40860566, year = {2025}, author = {Arnau, V and Ortiz-Maiques, A and Valero-Tebar, J and Mora-Quilis, L and Kurmauskaite, V and Campos Dopazo, L and Domingo-Calap, P and Džunková, M}, title = {CleanBar: a versatile demultiplexing tool for split-and-pool barcoding in single-cell omics.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf134}, pmid = {40860566}, issn = {2730-6151}, abstract = {Split-and-pool barcoding generates thousands of unique barcode strings through sequential ligations in 96-well plates, making single-cell omics more accessible, thus advancing microbial ecology, particularly in studies of bacterial interactions with plasmids and bacteriophages. While the wet-lab aspects of the split-and-pool barcoding are well-documented, no universally applicable bioinformatic tool exists for demultiplexing single cells barcoded with this approach. We present CleanBar (https://github.com/tbcgit/cleanbar), a flexible tool for demultiplexing reads tagged with sequentially ligated barcodes, accommodating variations in barcode positions and linker lengths while preventing misclassification of natural barcode-like sequences and handling diverse ligation errors. It also provides statistics useful for optimizing laboratory procedures. We demonstrate CleanBar's performance with the Atrandi platform for microbial single-cell genomics, coupled with PacBio sequencing, to reach a cell throughput comparable with traditional bulk metagenomics, but overcoming its limitations in studying phage-bacteria interactions. In four Klebsiella strains infected with their corresponding phages and a control phage, the single-cell genomics revealed infection heterogeneity and enabled phage copy number estimation per cell. By combining efficiency, adaptability, and precision, CleanBar, when applied to the Atrandi split-and-pool barcoding platform and PacBio sequencing, serves as a powerful high-throughput tool for advancing microbial single-cell genomics and understanding microbial ecology and evolution.}, }
@article {pmid40858791, year = {2025}, author = {Tocino-Márquez, I and Zehl, M and Séneca, J and Pjevac, P and Felkl, M and Becker, CFW and Loy, A and Rattei, T and Ostrovsky, AN and Zotchev, SB}, title = {The bacterial community of the freshwater bryozoan Cristatella Mucedo and its secondary metabolites production potential.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {31456}, pmid = {40858791}, issn = {2045-2322}, support = {MetaBac Research Platform//Universit&#xe4;t Wien/ ; }, abstract = {While marine bryozoans were shown to be a promising source of bioactive compounds with the potential to be developed into drugs, their freshwater counterparts remain understudied. Considering that bioactive compounds isolated from bryozoans may originate from bacterial communities associated with the hosts, we explored the bacterial community of the freshwater bryozoan Cristatella mucedo using genomics and metabolomics. 16 S rRNA gene amplicon sequencing of the bacterial community associated with C. mucedo showed a considerable overlap with communities from surrounding water and sediment. Using different isolation approaches we retrieved a diverse collection of bacterial strains representing 26 genera, including a potentially new one. Genome sequencing and analyses of representative isolates of each genus revealed considerable potential for secondary metabolite biosynthesis. The secondary metabolomes of both mono- and co-cultures of selected isolates and enriched bryozoan-derived communities were investigated, allowing the identification of several known and potentially novel secondary metabolites. This work provides important information regarding the composition of the bacterial community associated with C. mucedo and sets the stage for its further exploration and exploitation for drug discovery.}, }
@article {pmid40858551, year = {2025}, author = {Salcher, MM and Layoun, P and Fernandes, C and Chiriac, MC and Bulzu, PA and Ghai, R and Shabarova, T and Lanta, V and Callieri, C and Sonntag, B and Posch, T and Lepori, F and Znachor, P and Haber, M}, title = {Bringing the uncultivated microbial majority of freshwater ecosystems into culture.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {7971}, pmid = {40858551}, issn = {2041-1723}, support = {19-23469S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky (Grant Agency of the Czech Republic)/ ; 22-03662S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky (Grant Agency of the Czech Republic)/ ; 25-15813S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky (Grant Agency of the Czech Republic)/ ; 20-12496X//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky (Grant Agency of the Czech Republic)/ ; 21-21990S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky (Grant Agency of the Czech Republic)/ ; 022/2019/P//Jiho&#x10d;esk&#xe1; Univerzita v &#x10c;esk&#xfd;ch Bud&#x11b;jovic&#xed;ch (University of South Bohemia in &#x10c;esk&#xe9; Bud&#x11b;jovice)/ ; 017/2022/P//Jiho&#x10d;esk&#xe1; Univerzita v &#x10c;esk&#xfd;ch Bud&#x11b;jovic&#xed;ch (University of South Bohemia in &#x10c;esk&#xe9; Bud&#x11b;jovice)/ ; }, abstract = {Axenic cultures are essential for studying microbial ecology, evolution, and genomics. Despite the importance of pure cultures, public culture collections are biased towards fast-growing copiotrophs, while many abundant aquatic prokaryotes remain uncultured due to uncharacterized growth requirements and oligotrophic lifestyles. Here, we applied high-throughput dilution-to-extinction cultivation using defined media that mimic natural conditions to samples from 14 Central European lakes, yielding 627 axenic strains. These cultures include 15 genera among the 30 most abundant freshwater bacteria identified via metagenomics, collectively representing up to 72% of genera detected in the original samples (average 40%) and are widespread in freshwater systems globally. Genome-sequenced strains are closely related to metagenome-assembled genomes (MAGs) from the same samples, many of which remain undescribed. We propose a classification of several novel families, genera, and species, including many slowly growing, genome-streamlined oligotrophs that are notoriously underrepresented in public repositories. Our large-scale initiative to cultivate the "uncultivated microbial majority" has yielded a valuable collection of abundant freshwater microbes, characterized by diverse metabolic pathways and lifestyles. This culture collection includes promising candidates for oligotrophic model organisms, suitable for a wide array of ecological studies aimed at advancing our ecological and functional understanding of dominant, yet previously uncultured, taxa.}, }
@article {pmid40858256, year = {2025}, author = {Bain, JA and Ogilvie, JE and Petry, WK and CaraDonna, PJ}, title = {Nutrient niche dynamics among wild pollinators.}, journal = {Proceedings. Biological sciences}, volume = {292}, number = {2053}, pages = {20250643}, doi = {10.1098/rspb.2025.0643}, pmid = {40858256}, issn = {1471-2954}, support = {//National Science Foundation/ ; //National Science Foundation Graduate Research Fellowship Program/ ; }, mesh = {Animals ; *Pollination ; Bees/physiology ; *Pollen/chemistry ; *Nutrients ; Feeding Behavior ; Seasons ; }, abstract = {Food underpins fitness and ecological interactions, yet how nutrient availability shapes species interactions in natural communities remains poorly understood. Most nutritional ecology research focuses on laboratory or single-species systems, limiting insight into how nutrient use and nutrient niche dynamics occur in complex, multispecies assemblages in the wild. We combined long-term plant-pollinator interaction data with pollen macronutrient analyses to examine how wild bumble bees exploit macronutrients and whether they occupy distinct nutrient niches. Pollen macronutrient composition varied across plant species and over the season, with protein-rich pollen peaking in spring and lipid- and carbohydrate-rich pollen increasing by late summer. Across this nutrient landscape, bumble bee species occupied two distinct macronutrient niches: one high in protein and low in lipid and carbohydrate, and the other lower in protein but moderate in lipid and carbohydrate. Nutrient niche partitioning was associated with differences in feeding morphology and colony life stage (but not phenology). We found little evidence that nutrient niche breadth differed among species or was explained by feeding morphology or colony life stage. Our results extend nutritional ecology to a multispecies context, provide evidence for nutrient niche partitioning among wild pollinators and highlight the need to consider species-specific nutritional requirements in pollinator conservation.}, }
@article {pmid40858018, year = {2025}, author = {Xu, J and Wen, X and Wang, S and Worrich, A and Ma, B and Zou, Y and Wang, Y and Wu, Y}, title = {Identification of key species and molecular mechanisms driving conjugative transfer of antibiotic resistance genes in swine manure-derived bacterial communities.}, journal = {Journal of hazardous materials}, volume = {497}, number = {}, pages = {139638}, doi = {10.1016/j.jhazmat.2025.139638}, pmid = {40858018}, issn = {1873-3336}, abstract = {The spread of antimicrobial resistance in livestock environments poses a major public health risk. Conjugative transfer plays a key role in antimicrobial resistance transmission, but the diversity of bacterial hosts involved and the molecular mechanisms driving conjugative transfer within complex microbial communities remain poorly understood. To address this, we investigated plasmid-mediated conjugation in both a swine manure-derived bacterial community and isolated strains from manure. Our study identified 53 OTUs as plasmid recipients, with 66 % belonging to Proteobacteria. Exposure to subinhibitory doxycycline levels decreased the diversity of transconjugants, but conjugation-related gene expression was significantly upregulated, which also became apparent in a marked increase in conjugation frequency. Increased conjugation frequency correlated with increased ATP, ROS and eLDH levels both in the complex bacterial community and in pairwise strains, pointing to the physiological shifts occurring in species that engage in conjugation. Among the identified recipients, Bacillus velezensis exhibited the highest conjugation frequency, likely due to the upregulation of its two-component system, quorum sensing pathways, and strong biofilm-forming ability. Our findings provide new insights into conjugative transfer in livestock manure, identifying potential key spreaders and highlighting opportunities for targeted intervention strategies to mitigate antimicrobial resistance transmission, thereby enhancing its sustainability as a fertilizer.}, }
@article {pmid40856799, year = {2025}, author = {Pushkareva, E and Keilholz, L and Böse, J and von Berg, KL}, title = {Genetic Diversity and Potential of Cyanobacteria and Fungi Living on Arctic Liverworts.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {90}, pmid = {40856799}, issn = {1432-184X}, support = {PU867/1-1//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Arctic Regions ; *Hepatophyta/microbiology ; *Cyanobacteria/genetics/classification/isolation &amp; purification/physiology ; *Fungi/genetics/classification/isolation &amp; purification ; *Genetic Variation ; Symbiosis ; Soil Microbiology ; Phylogeny ; Nitrogen Fixation ; }, abstract = {Liverworts often form symbiotic associations with fungi and cyanobacteria, yet the distribution and specificity of these relationships remain largely unexplored, particularly in Arctic environments. This study used metagenomic sequencing to investigate fungal and cyanobacterial communities associated with Arctic liverworts, analyzing photosynthetic parts of gametophytes and their rhizoids with attached soil separately. The results revealed that Ascomycota dominated the fungal community. The cyanobacterial community was primarily composed of heterocytous Nostoc and non-heterocytous filamentous Leptolyngbya, with Nostoc showing evidence of nitrogen fixation, especially in gametophytes, suggesting a potential role in enhancing nitrogen availability for the host. These findings underscore the ecological significance of liverwort-associated microorganisms in Arctic ecosystems, with microbial composition differing between upper and lower parts of plants, as well as between leafy and thalloid liverworts, indicating possible functional specialization.}, }
@article {pmid40855532, year = {2025}, author = {Babalola, OO and Ogundeji, FO and Akanmu, AO}, title = {Dataset of 16S rRNA and ITS gene amplicon sequencing of celery and parsley rhizosphere soils.}, journal = {BMC genomic data}, volume = {26}, number = {1}, pages = {60}, pmid = {40855532}, issn = {2730-6844}, support = {UID123634 and UID132595//National Research Foundation/ ; }, abstract = {OBJECTIVES: This amplicon metagenomic study examines the relative abundance, taxonomic profiles and community structure of bacterial and fungal communities associated with the roots of parsley (Petroselinum crispum) and celery (Apium graveolens) under monocropping and intercropping systems. The study aims to provide a baseline understanding of how intercropping influences rhizosphere microbial dynamics.<br><br>DATA DESCRIPTION: The dataset provides insight into the effects of parsley-celery intercropping system on soil microbial richness, diversity and community structure. Amplicon metagenomic sequencing was performed on the DNA samples, targeting the 16S rRNA gene (V3-V4 region) and the ITS region for bacterial and fungal communities, respectively. The quantified libraries were pooled and sequenced using Illumina platforms, and the raw sequences were analyzed using the Quantitative Insights Into Microbial Ecology (QIIME 2 version 2019.1.) pipeline. The resulting Amplicon Sequence Variant (ASV) profiles revealed Actinobacteria and Protobacteria as the most predominant bacteria phyla, followed by Bacteroidota, Gemmatimonadota and Acidobacteriaota. The most predominant taxonomic distribution of fungi at the phylum level includes Ascomycota and Mortierellomycota. The dataset includes raw sequence reads in FASTQ format (.fastq.gz), which have been deposited in the Sequence Read Archive (SRA) of the National Center for Biotechnology Information (NCBI) under the Bioproject Accession numbers; SRP540554 (16S rRNA) and SRP540675 (ITS).}, }
@article {pmid40854362, year = {2025}, author = {Mo, Y and Lin, J and Li, X and Grossart, HP and Lin, L and Sido, MY and Yang, J}, title = {Single brand tire wear particles promote toxin-producing of an invasive cyanobacterium.}, journal = {Environmental research}, volume = {}, number = {}, pages = {122679}, doi = {10.1016/j.envres.2025.122679}, pmid = {40854362}, issn = {1096-0953}, abstract = {Tire wear particles (TWPs), as newly emerging pollutants, frequently co-occur with potentially toxic cyanobacteria in eutrophic waters. However, it is unknown how these new pollutants affect ecology of mass bloom-forming cyanobacteria. Here, we compared single brand and mixed brand TWPs how to affect the invasive and toxic cyanobacterium Raphidiopsis raciborskii. Our results demonstrate that, in the short-term, single- and mixed-brand TWPs have no significant influence on cyanobacterial growth, whereas single-brand TWPs and large-sized mixed-brand TWPs at high doses significantly reduced photosynthetic pigments. In the long-term, mixed-brand TWPs inhibit cyanobacterial growth and photosynthetic pigments synthesis more strongly than single-brand TWPs, especially exposed to high doses of large-sized mixed-brand TWPs (growth inhibitory effect up to about 80%). In addition, prolonged exposure to high-dose single-brand TWPs resulted in a marked reduction of photosynthetic activity. Moreover, high doses of large-sized single-brand TWPs significantly promoted toxin production by R. raciborskii. In contrast, mixed-brand TWPs have no significant effect on cyanobacterial toxin production. Our findings provide novel insights into potential risks for environmental and human health via the interaction between toxigenic R. raciborskii and different types of TWPs.}, }
@article {pmid40847400, year = {2025}, author = {Wang, Y and Jiang, Y and Song, Z and Zhu, C and Tang, Y and Peng, J and Liu, P}, title = {MreB: unraveling the molecular mechanisms of bacterial shape, division, and environmental adaptation.}, journal = {Cell communication and signaling : CCS}, volume = {23}, number = {1}, pages = {377}, pmid = {40847400}, issn = {1478-811X}, support = {2424017529//Guidance Plan Project of Hengyang City, China/ ; 32370209//National Natural Science Foundation of China (NSFC)/ ; 2023JJ30503//Natural Science Foundation of Hunan Province, China/ ; 22A0297//The Scientific Research Foundation of Hunan Provincial Education Department, China/ ; }, abstract = {As a key bacterial actin-like protein, MreB plays crucial roles in maintaining cell shape, regulating peptidoglycan synthesis, and coordinating chromosome segregation, making it a promising target for novel antibiotics. This review comprehensively explores MreB’s molecular architecture, its assembly into antiparallel protofilaments, and its pivotal roles in bacterial cell morphology and division. We also delve into how MreB interacts with membrane-associated proteins such as RodZ and MreC/D to coordinate cell wall synthesis and respond to environmental signals like ion gradients and temperature changes. Furthermore, we highlight the cooperation and functional divergence between MreB and FtsZ, underscoring the evolutionary adaptability of bacterial cytoskeletal structures. The structural and functional parallels between MreB and eukaryotic cytoskeletal proteins are also examined, offering new insights into the evolution of cytoskeletal systems. By integrating insights from structural biology, synthetic biology, and microbial ecology, this review aims to provide a deeper understanding of MreB’s role in bacterial biology, its dynamic responses to environmental cues, and its implications for therapeutic innovation. This comprehensive analysis not only enhances our knowledge of bacterial self-organization mechanisms but also paves the way for the development of innovative antimicrobial strategies to address the growing challenge of antibiotic resistance.}, }
@article {pmid40850119, year = {2025}, author = {Ellwood, KM and Kramer, AE and Dutta, A}, title = {Age-driven changes in the layer hen reproductive microbiome are associated with lay performance.}, journal = {Poultry science}, volume = {104}, number = {11}, pages = {105703}, doi = {10.1016/j.psj.2025.105703}, pmid = {40850119}, issn = {1525-3171}, abstract = {Eggs are a globally important food source and integral to optimal poultry production. Understanding the microbial ecology of the hen reproductive tract is essential for improving both food safety and reproductive efficiency. While the oviduct has been shown to harbor a continuous microbial community, this study is the first to demonstrate the presence of microbiota on the hen ovary surface, suggesting that the ovary is an extension of the oviductal microbial continuum. In this study, the ovarian and oviductal microbiomes of white-leghorn hens from mid-lay (high laying) and post-lay (lower laying) cohorts were analyzed. Using 16S rRNA sequencing, we identified significant shifts in reproductive tract microbiota between 9- and 18-month-old hens, coinciding with changes in lay performance. Several differentially abundant genera, including Acinetobacter, Ligilactobacillus, Bacillus, and Akkermansia, are known to modulate steroid hormone metabolism, with age-related abundance changes suggesting potential effects on hormone-driven reproductive processes. Other genera such as Ruminococcus_torques_group, Mucispirillum, and Fusobacterium-not traditionally associated with reproductive hormone pathways-may influence laying efficiency through their roles in mucin degradation, immune modulation, and inflammation. Notably, Turicibacter, newly identified on the ovary, increased with age and negatively correlated with lay performance, raising questions about its role in bile acid metabolism and stress response within the hen reproductive tract. Collectively, these findings highlight the ovary as an active microbial niche influenced by age and suggest that both hormone-associated and mucosal-interactive microbes contribute to lay dynamics. This work opens new avenues for probiotic strategies targeting key genera to support hen fertility and egg production across the productive lifespan.}, }
@article {pmid40849283, year = {2025}, author = {Tharp, CL and Custer, GF and Castrillo, G and Dini-Andreote, F}, title = {Revisiting the cry-for-help hypothesis in plant-microbe interactions.}, journal = {Trends in plant science}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tplants.2025.07.015}, pmid = {40849283}, issn = {1878-4372}, abstract = {The 'cry-for-help hypothesis' (CHH) is broadly used to study how root exudate modulation under stress influences recruitment of beneficial microbes in the rhizosphere. Here, we explored common misconceptions and limitations of the CHH and advocate for the reassessment of this prevalent hypothesis to unfold the ecological complexities of plant-microbe interactions.}, }
@article {pmid40843988, year = {2025}, author = {Crocker, K and Skwara, A and Kannan, R and Murugan, A and Kuehn, S}, title = {Timescale of environmental change modulates metabolic guild cohesion in microbial communities.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf186}, pmid = {40843988}, issn = {1751-7370}, abstract = {Microbial communities experience environmental fluctuations across timescales from rapid changes in moisture, temperature, or light levels to long-term seasonal or climactic variations. Understanding how microbial populations respond to these changes is critical for predicting the impact of perturbations, interventions, and climate change on communities. Because communities typically harbor tens to hundreds of distinct taxa, the response of microbial abundances to perturbations is potentially complex. However, even though taxonomic diversity is high, in many communities taxa can be grouped into metabolic guilds of strains with similar metabolic traits. These guilds effectively reduce the complexity of the system by providing a physiologically motivated coarse-graining. Here, using a combination of simulations, theory, and experiments, we show that the response of guilds to nutrient fluctuations depends on the timescale of those fluctuations. Rapid changes in nutrient levels drive cohesive, positively correlated abundance dynamics within guilds. For slower timescales of environmental variation, members within a guild begin to compete due to similar resource preferences, driving negative correlations in abundances between members of the same guild. Our results provide a route to understanding the relationship between metabolic guilds and community response to changing environments, as well as an experimental approach to discovering metabolic guilds via designed nutrient perturbations to communities.}, }
@article {pmid40843346, year = {2025}, author = {Xia, K and Hu, Y and Cai, S and Lin, M and Lu, M and Lu, H and Ye, Y and Lin, F and Gao, L and Xia, Q and Tian, R and Lin, W and Xie, L and Tan, D and Lu, Y and Lin, X and Yang, X and Zhong, L and Xu, L and Zhang, Z and Wang, L and Ren, J and Xu, H}, title = {GastritisMIL: An interpretable deep learning model for the comprehensive histological assessment of chronic gastritis.}, journal = {Patterns (New York, N.Y.)}, volume = {6}, number = {8}, pages = {101286}, pmid = {40843346}, issn = {2666-3899}, abstract = {The comprehensive histological assessment of chronic gastritis is imperative for guiding endoscopic follow-up strategies and surveillance of early-stage gastric cancer, yet rapid and objective assessment remains challenging in clinical workflows. We propose a powerful deep learning model (GastritisMIL) to effectively identify pathological alterations on H&amp;E-stained biopsy slides, thereby expediting pathologists' evaluation and improving decision-making regarding follow-up intervals. We have trained and tested GastritisMIL by using retrospective data from 2,744 patients and evaluated discriminative performance across three medical centers (467 patients). GastritisMIL attained areas under the receiver operating curve greater than 0.971 in four tasks (inflammation, activity, atrophy, and intestinal metaplasia) and superior performance comparable to that of two senior pathologists. Specifically, interpretable attention heatmaps generated by GastritisMIL effectively assist junior pathologists in locating suspicious lesion regions across the entire field and minimizing missed diagnosis risk. Moreover, the high generalizability of this developed model across multiple external cohorts demonstrates its potential translational value.}, }
@article {pmid40842826, year = {2025}, author = {Ahadi, R and Alizadeh, A and Chenari Bouket, A and Masigol, H and Grossart, HP}, title = {Multigene phylogeny, morphology, and pathogenicity uncover two novel Globisporangium species (Oomycota) from freshwater habitats in northwestern Iran.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1615096}, pmid = {40842826}, issn = {1664-302X}, abstract = {During the study of oomycete biodiversity in aquatic environments of northwestern Iran (East Azarbaijan), four Globisporangium isolates were recovered from a river and irrigation canal. These isolates were identified based on multi-locus phylogenetic analyses (ITS, cox1, and cox2 genomic regions) and morphological features. As a result, two novel species were described, namely Globisporangium parvizense sp. nov. and G. sarabense sp. nov., both exhibiting unique sporangial structures and growth patterns. Pathogenicity assays on cucumber seedlings confirmed strains' high potential to cause root and crown rot. This research highlights the diversity of Globisporangium in Iranian freshwater habitats, providing insights into its taxonomy and phylogenetic relationships. Detailed morphological descriptions and illustrations are provided for these novel species.}, }
@article {pmid40841038, year = {2025}, author = {Tang, Z and Zhang, Y and Shangguan, H and Xie, A and Xu, X and Jiang, Y and Breed, MF and Sun, X}, title = {Urban organic manure application enhances antibiotic resistance gene diversity and potential human pathogen abundance in invasive giant African snails.}, journal = {Journal of environmental sciences (China)}, volume = {158}, number = {}, pages = {610-620}, doi = {10.1016/j.jes.2025.02.028}, pmid = {40841038}, issn = {1001-0742}, mesh = {Animals ; *Manure ; *Drug Resistance, Microbial/genetics ; *Snails/microbiology ; Humans ; Introduced Species ; Gastrointestinal Microbiome ; Soil Microbiology ; Environmental Monitoring ; RNA, Ribosomal, 16S ; Feces/microbiology ; }, abstract = {The giant African snail (Achatina fulica) is an invasive species served as potential vectors for antibiotic resistance genes (ARGs) and potential human bacterial pathogens. Currently, urban green spaces receive extensive organic manure additions as part of their management, may intensify the biological contamination potential of these snail vectors, thereby increasing the risk of biological pollution in green spaces. However, the specific impacts of this practice on the microbial ecology of these invasive species remain poorly understood. Here, we investigated the effects of organic manure application on the gut microbiome of giant African snails, focusing on ARGs, bacterial community structure, and potential human bacterial pathogens. Microcosm experiments compared snail gut microbiomes in different treatments (Soil: soil samples collected after manure amendment, before any snail exposure. Feces: fecal samples collected from snails that lived on manure-amended soil. Control: fecal samples collected from snails that lived on unamended soil) using 16S rRNA high-throughput sequencing and metagenomic analysis. Our results show that manure application significantly altered gut bacterial community structure and increased ARG diversity by enriching specific high-risk ARGs (such as sul1 and sul2 in the Feces group increased by 2.89 and 2.43 times, respectively, compared to the Control group), and the introduction of eight novel ARG subtypes, despite decreasing overall ARG abundance. Moreover, the relative abundance of potential human pathogens, particularly Pseudomonadaceae, was greatly increased by manure application. These findings reveal that organic manure application in urban green spaces can potentially enhances their role as reservoirs and vectors of ARGs and human pathogens.}, }
@article {pmid40840191, year = {2025}, author = {Vermeersch, M and Jacxsens, L and Baele, T and Van Damme, I and Verhaegen, B and Boon, N and Uyttendaele, M}, title = {Microbiological hygiene and food safety assessment of urban aquaponic farming.}, journal = {International journal of food microbiology}, volume = {442}, number = {}, pages = {111393}, doi = {10.1016/j.ijfoodmicro.2025.111393}, pmid = {40840191}, issn = {1879-3460}, abstract = {Aquaponic production presents a promising approach in developing sustainable (urban) food systems, through combined production of plants and aquatic organisms for food. A commercial aquaponic farm was subjected to a longitudinal microbiological assessment of hygiene and food safety. Foodborne pathogenic bacteria (Salmonella spp., and Listeria monocytogenes), indicator bacteria (generic E. coli, coliforms, and Enterobacteriaceae) and total plate counts were determined during two distinct two-month production periods, focused on basil production from seed to mature plant and all water streams composing the irrigation water. The results indicated no direct food safety concerns to consumers, with neither Salmonella spp., nor Listeria monocytogenes detected on the ready-to-market basil leaves. The soilless substrate and irrigation water were identified as major risk factors for introducing and spreading foodborne pathogenic bacteria within the aquaponic environment. Overall, E. coli was present (LOD 1 CFU/100 mL or 10 CFU/g) in 21.1 % of samples and Salmonella spp. was detected in 8 out of 94 analyses. Generic E. coli was not a suitable marker for Salmonella spp. presence in irrigation water within the aquaponic farm. Strong correlations were found between Enterobacteriaceae and coliforms in water samples, however, elevated levels were not linked to positive Salmonella spp. detection. To mitigate microbiological food safety risks in aquaponics, the use of fit-for-purpose water, establishing a water quality monitoring plan, implementing effective UV treatment and applying appropriate cleaning and disinfection protocols are recommended. The implementation of tailored good agricultural practices (GAP) is key to ensure safe food production within aquaponic farming.}, }
@article {pmid40840036, year = {2025}, author = {Zhu, M and Zhang, W and Zhang, F and Duan, X and Qiu, Z and Zhao, S and Gao, S and He, F}, title = {C28-aldehyde (n-octacosanal) modulates stage-specific temporal expression of effector genes in the wheat powdery mildew fungus.}, journal = {Microbiological research}, volume = {301}, number = {}, pages = {128311}, doi = {10.1016/j.micres.2025.128311}, pmid = {40840036}, issn = {1618-0623}, abstract = {The prepenetration processes of the wheat powdery mildew fungus, Blumeria graminis f. sp. tritici (Bgt), are triggered by C28 aldehyde (n-octacosanal), a component of cuticular waxes. Despite being the most severe crop disease worldwide, the underlying molecular mechanisms of the prepenetration processes remain obscure. Utilizing a Formvar®-based in vitro system, transcriptomes of Bgt conidia impacted by n-octacosanal were profiled without the effects from plant host. A total of 1354 differentially expressed genes were identified between n-octacosanal- and n-octacosane (non-chemical signal)-treated conidia. The expression of effectors, transcription factors, and HOG-MAPK pathways is specifically regulated by n-octacosanal in a developmental stage-dependent manner. Among them, 25 effectors and three transcription factors, including COD 1, VEA, and CreA, were highly expressed at all stages. While some genes of the HOG-MAPK pathway were significantly upregulated during conidial growth, other genes were downregulated. These results revealed that C28 aldehyde-triggered Bgt conidial prepenetration in the plant host might be achieved by activating specific transcription factors and differentially regulating the HOG-MAPK pathway. The genes detected by our gene expression analysis may be crucial for successful infection by Bgt and thus serve as candidates for future functional analysis of the molecular mechanisms of conidia development in powdery mildew. These findings provide new insights into the chemical-signal-orchestrated development of an important phytopathogenic fungus and will potentially support efforts for the control and management of fungal diseases in wheat.}, }
@article {pmid40838740, year = {2025}, author = {Wang, J and Hashem, I and Bhonsale, S and F M Van Impe, J}, title = {Individual-based modeling (IbM) unravels spatial and social interactions in bacterial communities.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf116}, pmid = {40838740}, issn = {1751-7370}, abstract = {Bacterial interactions are fundamental in shaping community structure and function, driving processes that range from plastic degradation in marine ecosystems to dynamics within the human gut microbiome. Yet, studying these interactions is challenging due to difficulties in resolving spatiotemporal scales, quantifying interaction strengths, and integrating intrinsic cellular behaviors with extrinsic environmental conditions. Individual-based modeling addresses these challenges through single-cell-level simulations that explicitly model growth, division, motility, and environmental responses. By capturing both the spatial organization and social interactions, individual-based modeling reveals how microbial interactions and environmental gradients collectively shape community architecture, species coexistence, and adaptive responses. In particular, individual-based modeling provides mechanistic insights into how social behaviors-such as competition, metabolic cooperation, and quorum sensing-are regulated by spatial structure, uncovering the interplay between localized interactions and emergent community properties. In this review, we synthesize recent applications of individual-based modeling in studying bacterial spatial and social interactions, highlighting how their interplay governs community stability, diversity, and resilience. By linking individual-scale interactions with the ecosystem-level organization, individual-based modeling offers a predictive framework for understanding microbial ecology and informing strategies for controlling and engineering bacterial consortia in both natural and applied settings.}, }
@article {pmid40440482, year = {2025}, author = {Zhao, L}, title = {Guild-Level Response of the Gut Microbiome to Nutritional Signals: Advancing Precision Nutrition for Metabolic Health.}, journal = {Annual review of nutrition}, volume = {45}, number = {1}, pages = {197-221}, doi = {10.1146/annurev-nutr-122424-022254}, pmid = {40440482}, issn = {1545-4312}, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Precision Medicine ; Diet ; Dietary Fiber ; Animals ; Metabolic Diseases/microbiology ; Inflammation ; }, abstract = {The gut microbiome functions as a hidden organ, providing essential ecosystem services to sustain human health. By identifying stably connected bacteria, we reveal two competing guilds (TCG) as the resilient core of the microbiome: the health-promoting foundation guild (FG) and the proinflammatory pathobiont guild (PG). FG members produce short-chain fatty acids (SCFAs), enhancing gut barrier integrity and systemic resilience, while PG members disrupt metabolism through endotoxins, indoles, and hydrogen sulfide. Together, the FG and PG mediate ∼85% of ecological interactions in a dynamic, seesaw-like relationship. As evolved nutrient sensors for coping with feast-famine cycles, these guilds align host metabolism with dietary patterns. Fiber-rich diets bolster FG activity, maintaining microbial balance and metabolic health, whereas fiber-deficient diets in modern-day society favor chronic PG dominance, driving inflammation and disease. Synthesizing clinical and experimental evidence, this review positions the TCG model as a transformative framework for precision nutrition, guiding strategies to restore microbial balance and address metabolic disorders.}, }
@article {pmid40835811, year = {2025}, author = {Luzics, S and Baka, E and Otto, M and Kosztik, J and Szalontai, H and Bata-Vidács, I and Nagy, I and Tóth, &#xc1; and Táncsics, A and Pápai, M and Nagy, I and Orsini, M and Kukolya, J}, title = {High-quality de novo genome assembly and functional genomic insights into Thermobifida alba DSM43795[T], a mesophilic actinobacterium isolated from garden soil.}, journal = {Biologia futura}, volume = {}, number = {}, pages = {}, pmid = {40835811}, issn = {2676-8607}, support = {K142686//National Research, Development and Innovation Office/ ; EK&#xd6;P- 24- VI/MATE-3//Ministry for Culture and Innovation from the source of the National Research, Development and Innovation Fund/ ; EK&#xd6;P-MATE/2024/25/D//Ministry for Culture and Innovation from the source of the National Research, Development and Innovation Fund/ ; }, abstract = {Thermobifida alba DSM43795[T], a mesophilic actinobacterium isolated from garden soil, plays a vital role in lignocellulose degradation and holds biotechnological and pharmaceutical potential. We present a high-quality, complete de novo genome assembly of T. alba DSM43795[T] using combined PacBio long-read and Illumina short-read sequencing, resulting in a single circular chromosome of 4.9 Mbp with 72.1% GC content. Comparative genomics with the thermophilic relative T. fusca YX revealed 83.39% average nucleotide identity and extensive genome synteny alongside niche-specific differences. Functional annotation identified 4345 genes, including a rich complement of carbohydrate-active enzymes (CAZymes) such as glycoside hydrolases (GHs), esterases, and polysaccharide lyases, supporting versatile plant biomass degradation. GH gene sets were largely conserved between the species in both gene number and distribution, but T. alba uniquely encodes a novel GH10 endo-xylanase near a characterised palindrome regulatory sequence, indicating species-specific regulation. We hypothesise that thermophilic adaptation in T. fusca requires more proteins for ribosome integrity and amino acid metabolism, with reduced emphasis on carbohydrate metabolism and defence compared to T. alba. Moreover, T. alba harbours a broader array of defence-related genes and mobile genetic elements, including integrases and transposases. Although lacking a complete CRISPR-Cas system, two CRISPR arrays were detected, suggesting alternative immune strategies. Virulence factor homologs shared by both species likely reflect environmental survival rather than pathogenicity. This genomic characterisation elucidates T. alba's metabolic versatility and ecological adaptations, laying the groundwork for its potential applications in biomass conversion, environmental biotechnology, and drug discovery.}, }
@article {pmid40835614, year = {2025}, author = {Ma, H and Cornadó, D and Raaijmakers, JM}, title = {The soil-plant-human gut microbiome axis into perspective.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {7748}, pmid = {40835614}, issn = {2041-1723}, support = {32201402//National Natural Science Foundation of China (National Science Foundation of China)/ ; 202206205006//China Scholarship Council (CSC)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Soil Microbiology ; *Plants/microbiology ; Soil/chemistry ; Ecosystem ; Animals ; }, abstract = {Microbiomes of soil, plants, and the animal gut are pivotal for key life processes such as nutrient cycling, stress resilience, and immunity. While studies have hinted at a shared microbial reservoir connecting these environments, compelling evidence of a soil-plant-gut microbiome axis is scarce. This perspective explores the potential continuum and diversification of microbes along this axis, highlighting specific microorganisms capable of moving from soil to plants to the human gut. A conceptual framework is proposed to better understand the mechanisms driving interactions among these microbiomes. We also examine how soil, plant, and gut microbiomes may co-evolve and influence one another through reciprocal effects. We consider external environmental factors that could strengthen their interconnections, potentially creating beneficial feedback loops that impact ecosystem and human health.}, }
@article {pmid40830705, year = {2025}, author = {Oulkhir, FE and Allaoui, A and Idbella, A and Danouche, M and Bargaz, A and Biskri, L and Idbella, M}, title = {Bacillus subtilis ED24 Controls Fusarium culmorum in Wheat Through Bioactive Metabolite Secretion and Modulation of Rhizosphere Microbiome.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {89}, pmid = {40830705}, issn = {1432-184X}, mesh = {*Triticum/microbiology/growth &amp; development ; *Fusarium/growth &amp; development/drug effects/physiology ; *Bacillus subtilis/physiology/metabolism ; *Rhizosphere ; *Plant Diseases/microbiology/prevention &amp; control ; *Microbiota ; Soil Microbiology ; Plant Roots/microbiology ; Endophytes/physiology ; Fungicides, Industrial/pharmacology ; }, abstract = {Fusarium culmorum is a soil-borne fungal pathogen causing root and stem rot, seedling blight, and significant yield losses in small grain cereals, including wheat. This study aimed to evaluate the antifungal potential of Bacillus subtilis ED24, an endophytic strain isolated from Ziziphus lotus (L.) roots, and its effects on wheat growth and yield under controlled conditions. In vitro assays demonstrated that B. subtilis ED24 inhibited F. culmorum mycelial growth by up to 87%, associated with the secretion of 37 distinct secondary metabolites, predominantly involved in carbon cycling. In pot experiments, B. subtilis ED24 significantly enhanced wheat germination (85%) and growth compared to infected plants treated with the chemical fungicide tebuconazole. Although nutrient analysis showed significantly higher shoot nitrogen (32.34 mg/pot) and phosphorus (2.41 mg/pot) contents in the B. subtilis ED24 treatment compared to tebuconazole (8.11 and 0.18 mg/pot, respectively), no significant differences were observed when compared to the infected control (C-). Similarly, B. subtilis ED24 led to improved thousand grain weight (40.4 g), protein content (19.98%), and ash content (1.95%) relative to tebuconazole (29.1 g, 18.31%, and 1.74%, respectively), yet these values did not differ significantly from the infected control (C-). Notably, the number of seeds per pot was significantly increased by B. subtilis ED24 compared to the infected control (C-) (113.8 seeds/pot vs. 54.2 seeds/pot). Additionally, B. subtilis ED24 modulated the wheat rhizosphere microbiome, enriching beneficial taxa such as Eurotiomycetes fungal class and the bacterial genus Paramesorhizobium. These findings suggest that the antifungal activity and growth-promoting effects of B. subtilis ED24 are likely mediated through the synthesis of unique bioactive metabolites and microbiome modulation, offering a promising sustainable alternative to chemical fungicides in wheat production.}, }
@article {pmid40828659, year = {2025}, author = {Wang, X and Chen, Z and Liu, C and Zhang, Z and Deng, Y and Tao, L and Tiedje, JM and Deng, J}, title = {Type I-F CRISPR-associated transposons contribute to genomic plasticity in Shewanella and mediate efficient programmable DNA integration.}, journal = {Microbial genomics}, volume = {11}, number = {8}, pages = {}, doi = {10.1099/mgen.0.001476}, pmid = {40828659}, issn = {2057-5858}, abstract = {The genome plasticity of species and strains in the genus Shewanella is closely associated with the diverse mobile genetic elements embedded in its genomes. One mobile element with potential for accurate and efficient DNA insertion in Shewanella is the type I-F3 CRISPR-associated transposon (I-F3 CAST). However, relatively little is known about the distribution and ecological significance of I-F3 CASTs and whether they could be suitable as a tool for targeted genetic manipulation in situ. To better understand the distribution of I-F3 CASTs in Shewanella, we analysed 602 Shewanella genomes. We found that I-F3 CASTs were present in 12% of all genomes, although differences in both gene arrangement and integration locus were observed. These Shewanella I-F3 CASTs carried up to 89 cargo genes, which were associated with diverse functions, including defence, resistance and electron transfer, demonstrating an important role in genomic diversification and ecological adaptation. We tested whether the I-F3 CAST present in Shewanella sp. ANA-3 enhanced gene insertion, both in situ and in a heterologous host. We observed I-F3 CAST-mediated crRNA-targeted integration of the supplied genes into the pyrF locus in Shewanella sp. ANA-3. Heterologous gene insertion with high integration efficiency in Escherichia coli was also demonstrated using a simplified version of ANA-3 I-F3 CAST. Altogether, this work highlights the important role of I-F3 CASTs in promoting genomic plasticity of the Shewanella genus and demonstrates the gene-editing capability of ANA-3-CAST both endogenously and heterologously.}, }
@article {pmid40824433, year = {2025}, author = {Schneider, T}, title = {Interactions at sea: on the microbiome life-cycle and biogeochemical processes.}, journal = {History and philosophy of the life sciences}, volume = {47}, number = {3}, pages = {41}, pmid = {40824433}, issn = {1742-6316}, abstract = {The marine phycosphere is a microscale mucosal region of microbiomes surrounding a phytoplankton cell. The phycosphere (analogous to the terrestrial rhizosphere) is where microbial interactions navigate the biochemistry of the sea. The study of this microsphere deals with the causal relation enigma between two spatiotemporal scales: the micro-communal interactions and the macro-level of the biogeochemical cycles (Stocker, Science, 338(6107), 628-633, 2012); Segev et al., eLife, 5, e17473, 2016; Seymour et al., Nature Microbiology 2, Article 17065, 2017). This study of communities and ecosystems looks at metabolic interactions and interdependence relations, not focusing on biodiversity as the object of study. Following marine microbial ecology, an epistemic view of interactions and inter-communal relations seems to take the bulk of consideration. In this paper, I ask what it is about the sea that promotes an interactionist epistemic framework that is different than other fields in microbial ecology. Using Helen Longino's interactionist ontology (2020, 2021), I ask whether the sea presents a unique epistemic framework focusing on understanding interactions and interdependence. I look into the insights marine environmental studies may provide to the methodological and conceptual challenges in understanding microbial ecological stability and life cycles. By paralleling marine and soil microbial ecology, I highlight the distinct features of the water column that offer a unique epistemic and methodological framework focused on interactions and interdependence. Exploring microbial ecology at sea, I detail its epistemic advantages in shaping an interactionist theoretical and conceptual framework.}, }
@article {pmid40824088, year = {2025}, author = {Baty, JJ and Drozdick, AK and Pfeiffer, JK}, title = {Pseudomonas aeruginosa rhamnolipids stabilize human rhinovirus 14 virions.}, journal = {Journal of virology}, volume = {}, number = {}, pages = {e0093125}, doi = {10.1128/jvi.00931-25}, pmid = {40824088}, issn = {1098-5514}, abstract = {Many mammalian viruses encounter bacteria and bacterial molecules over the course of infection. Previous work has shown that the microbial ecology of the gut plays an integral role in poliovirus and coxsackievirus infection, where bacterial glycans can facilitate virus-receptor interactions, enhance viral replication, and stabilize viral particles. However, how airway bacteria alter respiratory viral infection is less understood. Therefore, we investigated whether a panel of airway bacteria affects rhinovirus stability. We found that Pseudomonas aeruginosa, an opportunistic airway pathogen, protects human rhinovirus 14 (HRV14) from acid or heat inactivation. Further investigation revealed that P. aeruginosa rhamnolipids, glycolipids with surfactant properties, are necessary and sufficient for stabilization of rhinovirus virions. However, airway bacteria did not stabilize HRV16, a distantly related rhinovirus with higher capsid stability. Taken together, this work demonstrates that specific molecules produced by an opportunistic airway pathogen can influence a respiratory virus.IMPORTANCEBacteria can enhance viral stability and infection for enteric members of the Picornaviridae, such as poliovirus and coxsackievirus; however, whether bacteria influence respiratory picornaviruses is unknown. In this study, we examined the impacts of airway bacteria on rhinovirus, a major etiological agent of the common cold. We found that Pseudomonas aeruginosa protects human rhinovirus 14 from both acid and heat inactivation through rhamnolipids. Overall, this work demonstrates bacterial effects on respiratory viruses through specific bacterial molecules.}, }
@article {pmid40821451, year = {2025}, author = {Pignon, E and Schaerli, Y}, title = {Deciphering microbial spatial organization: insights from synthetic and engineered communities.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf107}, pmid = {40821451}, issn = {2730-6151}, abstract = {Microbial communities are frequently organized into complex spatial structures, shaped by intrinsic cellular traits, interactions between community members, initial growth condition or environmental factors. Understanding the mechanisms that drive these spatial patterns is essential for uncovering fundamental principles of microbial ecology and for developing applications. Using genetic engineering and synthetic microbial communities allows us to decipher how specific parameters influence spatial organization. In this review, we highlight recent studies that leverage synthetic microbial communities to deepen our understanding of microbial spatial ecology. We begin by exploring how initial conditions, such as cell density and relative species abundance, influence spatial organization. We then focus on studies that examine the role of individual microbial traits, such as cell shape and motility. Next, we discuss the impact of contact-dependent and long-range interactions, including metabolite exchange and toxin release. Furthermore, we highlight the influence of environmental factors on spatial dynamics. Finally, we address the current limitations of synthetic approaches and propose future directions to bridge the gap between engineered and natural systems.}, }
@article {pmid40816674, year = {2025}, author = {Hou, N and Yin, X and Wang, W and Huang, X and Fang, Y and Vancov, T and Sardans, J and Tariq, A and Zeng, F and Wiesmeier, M and Peñuelas, J}, title = {Soil carbon stabilization associated with iron-aluminum complexes and microbial communities in paddy.}, journal = {Environmental research}, volume = {}, number = {}, pages = {122601}, doi = {10.1016/j.envres.2025.122601}, pmid = {40816674}, issn = {1096-0953}, abstract = {Rice paddies play a pivotal role in global carbon cycling, offering significant potential for climate change mitigation and sustainable agriculture. This study investigates the synergistic effects of long-term fertilization, iron-aluminum-soil organic carbon (Fe(Al)-SOC) complexes, and microbial communities on soil organic carbon (SOC) stabilization across major rice-growing regions. Black soils exhibited the highest SOC content (43.9 g kg[-1]), surpassing other soils by 41.6-82.6%, suggesting distinct stabilization mechanisms. Key findings include: (1) Fe(Al)-SOC complexes and aromatic carbon (20.4% in black soils) jointly enhanced long-term SOC preservation; (2) CO2 emissions were controlled by nitrogen (N) and phosphorus (P) stoichiometry and physical protection within 0.25-0.5 mm aggregates; (3) Bacterial abundance negatively correlated with SOC and light fraction organic carbon (LFOC) levels, concomitant with reduced CO2 emissions; and (4) N/P fertilization boosted carbonyl-C (recalcitrant pool) while maintaining Alkyl-C (31.7% in brick-red soils), indicating balanced C stabilization. Critically, we demonstrate that Fe/Al-microbial interactions-where Fe/Al complexes modulate microbial composition and activity-are central to SOC storage. These results provide a mechanistic framework for optimizing rice cultivation practices to maximize soil carbon storage through the synergistic management of mineral-organic complexes, microbial ecology, and fertilization strategies.}, }
@article {pmid40815158, year = {2025}, author = {Berman, HL and McKenney, EA and Roche, CE and Michalski, S and Kwon, SH and Weichel, E and Matson, A and Nichols, LM and Alvarado, S and Horvath, JE and Dunn, RR}, title = {Cooking-class style fermentation as a context for co-created science and engagement.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0266024}, doi = {10.1128/spectrum.02660-24}, pmid = {40815158}, issn = {2165-0497}, abstract = {Fermented foods have been consumed for thousands of years and have been used as a model system to study community succession and other ecological questions. Additionally, cooking classes offer opportunities to learn about food preparation and history. In the present study, scientists and chefs delivered cooking-class style workshops in which participants learned the recipes of one of three fermented foods and the microbial ecology within these foods. Participants prepared jars of chow chow, kimchi, or kombucha to set up experiments to study microbial community succession and pH changes. The fermented foods were also used to test the following hypotheses: that increasing the number of substrates results in increased alpha diversity, and that phylogenetically diverse substrates will lead to greater beta diversity among microbial communities. Microbial communities contained lactic and acetic acid bacteria described previously in fermented foods, and indicator species were identified for cabbage and radish substrates in kimchi. Finally, we qualitatively comment on the experience of developing workshops with chefs and the use of participatory science in these experiments.IMPORTANCEThe present study demonstrates the utility of using fermented foods as an inexpensive and effective tool to investigate ecological phenomena and engage the public in microbiology and ecology through cooking-class style workshops. We also model a creative, interdisciplinary collaboration between scientists and chefs.}, }
@article {pmid40812185, year = {2025}, author = {Common, JE and Payne, RP}, title = {Microbial Makeover: Skin microbiome reset after stem cell transplantation.}, journal = {Cell host &amp; microbe}, volume = {33}, number = {8}, pages = {1318-1320}, doi = {10.1016/j.chom.2025.07.014}, pmid = {40812185}, issn = {1934-6069}, abstract = {Inborn errors of immunity disrupt host-microbe interactions. In this issue of Cell Host &amp; Microbe, Che et al.[1] examine DOCK8-deficient individuals undergoing stem cell transplantation and show that immune reconstitution rebalances the skin microbiome, underscoring the central role of immunity in shaping cutaneous microbial ecology.}, }
@article {pmid40809134, year = {2024}, author = {Casey, J and Bennion, B and D'haeseleer, P and Kimbrel, J and Marschmann, G and Navid, A}, title = {Transporter annotations are holding up progress in metabolic modeling.}, journal = {Frontiers in systems biology}, volume = {4}, number = {}, pages = {1394084}, pmid = {40809134}, issn = {2674-0702}, abstract = {Mechanistic, constraint-based models of microbial isolates or communities are a staple in the metabolic analysis toolbox, but predictions about microbe-microbe and microbe-environment interactions are only as good as the accuracy of transporter annotations. A number of hurdles stand in the way of comprehensive functional assignments for membrane transporters. These include general or non-specific substrate assignments, ambiguity in the localization, directionality and reversibility of a transporter, and the many-to-many mapping of substrates, transporters and genes. In this perspective, we summarize progress in both experimental and computational approaches used to determine the function of transporters and consider paths forward that integrate both. Investment in accurate, high-throughput functional characterization is needed to train the next-generation of predictive tools toward genome-scale metabolic network reconstructions that better predict phenotypes and interactions. More reliable predictions in this domain will benefit fields ranging from personalized medicine to metabolic engineering to microbial ecology.}, }
@article {pmid40804729, year = {2025}, author = {Rezaei, Z and Amoozegar, MA and Moghimi, H}, title = {Innovative approaches in bioremediation: the role of halophilic microorganisms in mitigating hydrocarbons, toxic metals, and microplastics in hypersaline environments.}, journal = {Microbial cell factories}, volume = {24}, number = {1}, pages = {184}, pmid = {40804729}, issn = {1475-2859}, abstract = {Hypersaline environments are ecologically, industrially, and scientifically important because they host unique extremophiles used in biotechnology, bioremediation, and enzyme production. These habitats are seriously threatened by three common contaminants: hydrocarbon pollutants, toxic metals, and microplastics. In particular, the remediation of hazardous substances under extreme conditions is challenging due to limited accessibility and bioavailability of pollutants, harsh physicochemical conditions, reduced microbial abundance and diversity, and instability of enzymes. Halophiles are extremophilic microorganisms that thrive in high-salt environments, exhibiting notable metabolic diversity and resilience, and play a critical role in overcoming these challenges. Their ability to degrade recalcitrant pollutants makes them valuable for bioremediation in contaminated hypersaline ecosystems. Advancements in engineering tools and synthetic biology have revolutionized halophile-based biotechnologies. Techniques like gene editing and recombinant DNA have facilitated the precise modification of halophiles, enabling them to efficiently target and degrade toxic compounds and significantly improve their bioremediation potential. Furthermore, with the rapid progress of omics approaches, identifying new halophilic microbes, their enzymes, and their metabolic pathways is now becoming possible. Despite these advances, challenges remain in optimizing genetically tractable strains, ensuring biosafety, and understanding microbial ecology for scalable, safe, and cost-effective applications. This review provides an overview of halophilic and halotolerant microorganisms, their habitat, and their unique adaptations to saline and hypersaline environments. Key pollutants threatening extreme environments, as well as the ability of halophiles to degrade them, are also discussed. Additionally, it highlights current challenges, including the introduction of engineered halophiles into natural ecosystems, scaling up bioprocesses, cost management, and regulatory concerns, and explains future perspectives to address these issues. Ultimately, it emphasizes the need for advanced research to fully harness the potential of halophiles in sustainable bioremediation.}, }
@article {pmid40804168, year = {2025}, author = {Sun, L and Wen, X and Li, L and Li, M and Xing, X and Zhang, Z and Dong, C}, title = {Formation and sustenance mechanism of bacterial diversity in nutrient-deficient environment of indoor stadium.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {29685}, pmid = {40804168}, issn = {2045-2322}, abstract = {Bacterial diversity has been found in indoor stadiums which can be considered as a specific nutrient-deficient environment (NDE), it remains a mystery and opens to new ideas why the bacterial diversity can be formed and maintained in NDE of indoor stadiums, since it is obvious to violate the famous competitive exclusion principle (CEP) in ecology. In the article, five most common genera, Pseudomonas, Acinetobacter, Exiguobacterium, Sphingobacterium, Chryseobacterium in indoor stadiums were selected and periodically sampled to supervise the dynamic characteristics of bacterial community. Based on quorum sensing (QS) and non-monotonic interspecific interaction (NMII) in combination with microbial ecology, clustering analysis and experimental observation, a new hypothesis was put forward to elucidate QS and NMII of substrate location information (SLI) mechanism driving bacterial community succession with high diversity in NDE of indoor stadium. A valid cellular automation (CA) model was derived from assumptions directly, and the CA simulation sufficiently proved that QS and NMII of SLI can effectively weaken interspecific competition to drive the spatiotemporal succession of bacterial community in NDE of indoor stadium towards a climax community with high richness and evenness, namely bacterial diversity. The succession mechanism confirmed by CA simulation can set up a theoretical framework for comprehensive apprehension about ecological effect of QS with NMII of SLI sharing on formation and sustenance of bacterial diversity in NDE of indoor stadium.}, }
@article {pmid40802392, year = {2025}, author = {Shaikenova, K and Issabekova, S and Sadenova, M and Omarova, K and Uskenov, R}, title = {Synergistic impact of integrated mechanical, physical, and chemical disinfection on microbial ecology and morphophysiological development in dairy calves.}, journal = {Brazilian journal of biology = Revista brasleira de biologia}, volume = {85}, number = {}, pages = {e295880}, doi = {10.1590/1519-6984.295880}, pmid = {40802392}, issn = {1678-4375}, abstract = {The article presents the results of studies of the influence of the complex process of cleaning and disinfection of the dispensary using mechanical, physical and chemical methods on the growth and development of calves of the dairy period. The dispensary for calves is divided into two rooms, where there were animals of the control and experimental groups selected by the method of pairs of analogues in the same feeding and maintenance conditions. Studies before the treatment of rooms for calves showed a massive growth of bacilli and bacteria - 100%, mold fungi - 80%, yeast - 20%, actinomycetes - 80%. After processing the room for calves of the experimental group, the number of microorganisms during mechanical treatment, microbial contamination decreased by 31%, during physical treatment by 62%, and during chemical treatment by 95%. Monitoring of live weight, exterior features of calves showed that the live weight of calves of the experimental group of monthly calves averaged 58.9 kg, and the control group 58.6 kg, respectively. In the second month, the live weight of the experimental was 7.5 kg or 9.1% more than the control. And also for all body measurements, the experimental group exceeded the control group by an average of 10%. The results of the study of hematological parameters showed that in the experimental group they are all within the normal range, whereas in the control group the content of leukocytes is 13.2 * 109 liters, lymphocytes are 7.7 * 109 liters higher than normal, which indicates inflammatory processes in the body of calves.}, }
@article {pmid40795028, year = {2025}, author = {Park, HS and Chavarria, X and Shatta, A and Kang, D and Oh, S and Choi, DY and Choi, JH and Kim, M and Cho, YH and Yi, MH and Kim, JY}, title = {Distinct microbial communities of drain flies (Clogmia albipunctata) across sites with differing human influence.}, journal = {FEMS microbiology letters}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsle/fnaf078}, pmid = {40795028}, issn = {1574-6968}, abstract = {Drain flies (Clogmia albipunctata) are insects that thrive in humid urban environments such as bathrooms drains and sewage systems. While their role in pathogen transmission has been suggested, little is known about their microbiome or ecology in non-clinical contexts. Using 16S rRNA gene metabarcoding, we characterized the bacterial communities of drain flies from three locations in South Korea, public bathrooms from a college in Seoul, a rural port in Ulleungdo island, and a highly frequented public park in Yeouido. In total, we obtained 221 families and 1 474 features. We found significant differences in microbiome composition and diversity as well as a small core microbiome shared among locations, with environmental bacteria such as Pseudomonas and Ralstonia being the dominant taxa across samples. The majority of the detected amplicon sequence variants (ASV) were not shared among locations. These findings suggest drain fly transport a location-specific environmental bacteria. Notably, we also identified ASVs of potential clinical relevance, including Mycobacterium, Acinetobacter baumanii, Providencia, and Nocardia. This is the first metagenomic insight into the microbiome of this species and adds to a renewed interest in the role that non-hematophagous insects play in urban microbial ecology and the spread of microbes.}, }
@article {pmid40793771, year = {2025}, author = {Bhandari, R and Wong, AC-N and Lee, JC and Boyd, A and Shelby, K and Ringbauer, J and Kang, DS}, title = {Microbiome composition and co-occurrence dynamics in wild Drosophila suzukii are influenced by host crop, fly sex, and sampling location.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0260824}, doi = {10.1128/spectrum.02608-24}, pmid = {40793771}, issn = {2165-0497}, abstract = {Microbial control of insect pests offers promising alternatives to traditional pesticides. However, the microbial communities and factors influencing these communities within insect hosts remain poorly understood. This study examined the whole-body bacterial communities in wild Drosophila suzukii, commonly known as spotted wing Drosophila (SWD). Fly samples were collected from two farms growing wild Himalayan blackberries near blueberry crops, one blackberry farm, and one elderberry farm across four locations in the United States. Our analyses showed significant differences in microbial communities in flies across various host crops and sampling locations. We identified co-occurring bacterial genera, dominated by Gluconobacter and Morganella, and the overall microbiome was distinct from those found in laboratory-grown flies. Our findings suggest that the host crop, sex of the fly, sampling location, and their interactions play a crucial role in shaping microbial communities in SWD, indicating the influence of various ecological interactions. While no significant differences in microbiome composition were observed between male and female flies, network analysis revealed distinct sex-specific microbial co-occurrence patterns. Female flies displayed a more stable and interconnected microbial network than male flies, suggesting that sex-specific factors might influence bacterial interactions. Interestingly, the most abundant microbial taxa were not necessarily the most connected in the networks, showing that less abundant taxa may also play a significant role in shaping the fly microbiome. This study underscores the complexity of microbial ecology in SWD and highlights the necessity of considering these dynamics when developing pest management strategies in agriculture.IMPORTANCEStudies on the microbiome of spotted wing Drosophila (SWD) have primarily focused on laboratory-reared flies in controlled environments and fed artificial diets. In contrast, we examined microbial communities in wild flies from various host crops across four locations in the United States. Our findings show that these communities are distinct from those of laboratory-grown flies and are influenced by the fly's sex, host crop, geographical location, and their interactions. Our study identifies several dominant bacterial genera across samples, suggesting that these may represent the core microbial communities in wild SWD. Given that microbial communities influence physiological activities in SWD, manipulating the microbiome may have either a positive or negative impact on insect fitness. This study enhances our understanding of microbial dynamics in understudied wild SWD populations, emphasizing the importance of these dynamics in effective integrated pest management strategies.}, }
@article {pmid40791242, year = {2025}, author = {Song, HC and Elsheikha, H and Yang, T and Cong, W}, title = {Global spillover of land-derived microbes to Ocean hosts: Sources, transmission pathways, and one health threats.}, journal = {Environmental science and ecotechnology}, volume = {27}, number = {}, pages = {100603}, pmid = {40791242}, issn = {2666-4984}, abstract = {Terrestrial pathogens are increasingly being detected in marine organisms, raising concerns about ecosystem sustainability, biodiversity loss, and threats to human health. Over the past two decades, reports of microbial contaminants crossing from land to sea have increased, suggesting shifts in pathogen ecology driven by environmental changes and human activities. Pathogens originating on land can spread, adapt, and persist in marine environments, infecting a wide range of hosts and potentially re-entering terrestrial environments. Despite growing recognition of this issue, a comprehensive understanding of the distribution, diversity, and transmission pathways of these pathogens in marine ecosystems remains limited. In this Review, we provide a global analysis of terrestrial pathogen contamination in marine animal populations. Drawing from pathogen detection data across 66 countries, we used phylogenetic methods to infer land-to-sea transmission routes. We identified 179 terrestrial pathogen species, including 38 bacterial, 39 viral, 80 parasitic, and 22 fungal species, in 20 marine host species. Terrestrial pathogens are not only widespread but also highly diverse in marine ecosystems, highlighting the frequency and ecological significance of cross-system microbial exchange. By revealing the scale and complexity of land-to-sea pathogen flow, we show that climate change, pollution, and other anthropogenic pressures may intensify pathogen spillover events, with potential feedback effects on terrestrial systems. This highlights the urgent need for integrated surveillance and policy frameworks acknowledging the interconnectedness of terrestrial and marine health. Our work advocates a One Health approach to microbial ecology, stressing the need to safeguard marine and human populations from emerging cross-system threats.}, }
@article {pmid40787310, year = {2025}, author = {S, S and Nayak, P and Pal, K}, title = {Exploring the Microbial Peptides Derived from the Human Gut Microbiota to Regulate Class B GPCRS Using an In Silico Approach.}, journal = {ACS omega}, volume = {10}, number = {30}, pages = {33270-33287}, pmid = {40787310}, issn = {2470-1343}, abstract = {Class B G-protein coupled receptors (GPCRs) are significant therapeutic recipients in cardiovascular, neurological, and metabolic diseases. The human gut microbiome is a complex microbial ecology recently identified as a possible source of bioactive peptides that control host physiological functions. Candidate peptides were found using advanced bioinformatics tools including sequence homology analysis, structure modeling, and molecular docking. These peptides were then evaluated for their binding affinity and potential functional regulation of the GPCR activity. Molecular dynamics simulations offered additional insights regarding the stability and interaction diversity of peptide-receptor complexes, highlighting receptor conformational state of G-protein interaction. The findings identify unique microbial peptides capable of influencing class B GPCR function, providing important insights into microbiome-host interactions and therapeutic potential. This study emphasizes the gut microbiome's previously untapped potential as a source of GPCR modulators, opening up new avenues for microbiome-driven therapy approaches for metabolic and endocrine disorders.}, }
@article {pmid40783766, year = {2025}, author = {Son, SJ and Wu, X and Roh, HW and Cho, YH and Hong, S and Nam, YJ and Hong, CH and Park, S}, title = {Distinct gut microbiota profiles and network properties in older Korean individuals with subjective cognitive decline, mild cognitive impairment, and Alzheimer's disease.}, journal = {Alzheimer's research &amp; therapy}, volume = {17}, number = {1}, pages = {187}, pmid = {40783766}, issn = {1758-9193}, support = {HR21C1003//the Ministry of Health and Welfare, Republic of Korea/ ; HR21C1003//the Ministry of Health and Welfare, Republic of Korea/ ; RS-2019-NR040055//National Research Foundation of Korea (NRF), funded by the Ministry of Science and ICT/ ; RS-2019-NR040055//National Research Foundation of Korea (NRF), funded by the Ministry of Science and ICT/ ; RS-2023-00208567//National Research Foundation of Korea (NRF), funded by the Ministry of Science and ICT/ ; }, abstract = {BACKGROUND: The gut microbiota may influence cognitive function via the gut-brain axis. This study aimed to investigate the gut microbiota profiles of 346 older Korean individuals with subjective cognitive decline but no symptoms (SCD), mild cognitive impairment (MCI), or Alzheimer’s disease (AD).<br><br>METHODS: Participants aged an average of 72.3 years underwent the profiling of cognitive function, amyloid-&#x3b2; (A&#x3b2;) deposition, apolipoprotein E (APOE) genetic variants, depression status, nutrition, and lifestyles. Human fecal bacterial FASTA/Q data (SCD, n&#x2009;=&#x2009;24; MCI, n&#x2009;=&#x2009;246; AD, n&#x2009;=&#x2009;76) were processed using Quantitative Insights Into Microbial Ecology 2 (QIIME2) tools. Operational taxonomic units (OTUs) and their counts were assigned with the National Center for Biotechnology Information Basic Local Alignment Search Tool (BLAST). Machine learning models (random forest and XGBoost) identified key bacterial taxa differentiating groups.<br><br>RESULTS: Redundancy analysis revealed associations between gut microbiota composition and cognitive function, age, gender, nutritional status, and body mass index. All three groups shared 71 common bacterial genera with distinct taxonomic profiles across cognitive states. The AD group uniquely harbored Hominisplanchenecus and Lentihominibacter, while the SCD group exclusively contained Anaerosacchariphilus and Anaerobutyricum. Phascolarctobacterium was shared between the AD and MCI groups, and Anaerostipes between the MCI and SCD groups. The SCD group showed significantly elevated Bifidobacterium catenulatum, Anaerobutyricum hallii, and Anaerostipes hadrus. Network analysis demonstrated greater microbial community complexity in the SCD group compared to the MCI and AD groups. Gut bacteria correlated with depression, A&#x3b2; deposition, APOE status, and cognitive scores.<br><br>CONCLUSIONS: This study identified distinct gut microbiota profiles associated with different stages of cognitive impairment in older Korean adults. The observed associations between gut bacterial composition and cognitive function, neurodegeneration biomarkers, and related clinical factors suggest potential relationships that warrant further investigation. These findings contribute to the growing understanding of gut-brain interactions in cognitive aging.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13195-025-01820-9.}, }
@article {pmid40781808, year = {2025}, author = {Jalili, M and Mazloomirad, F and Jalilian, FA}, title = {The effect of bacteriophage in oral health: developing microbial ecology and emerging potential therapeutic target.}, journal = {Future microbiology}, volume = {20}, number = {12}, pages = {807-816}, pmid = {40781808}, issn = {1746-0921}, mesh = {Humans ; *Bacteriophages/physiology ; *Phage Therapy/methods ; *Mouth/microbiology/virology ; *Oral Health ; Biofilms/growth &amp; development ; Microbiota ; *Bacteria/virology ; *Periodontal Diseases/therapy/microbiology ; }, abstract = {The human oral cavity provides a convenient entry point for viruses and bacteria from the environment. The role of these viral communities remains unclear; however, many of them are bacteriophages that may actively influence the ecology of bacterial communities within the oral cavity. Bacteriophages are abundant and influential components of the oral microbiome and play a crucial role in shaping microbial ecology in oral health. They dynamically interact with oral bacteria, influencing biofilm formation, bacterial population structure, antibiotic resistance, and metabolic functions, thereby affecting disease progression and microbial community dynamics. Recent advances in studies have increased our understanding of oral phages and their impact on the amelioration of oral diseases such as periodontal disease. Nowadays, phage therapy has been identified as a potential therapeutic approach for major oral pathogens. The advantages of phage therapy include low toxicity, high specificity, the ability to penetrate biofilm structures, and the ability to replicate continuously in pathogenic bacteria. Hence, the aim of this review is to provide a comprehensive study about the role of bacteriophages as potential therapeutic target in oral health. Additionally, further studies are necessary to evaluate the role of phages in oral health and to develop safe and effective clinical applications in dentistry.}, }
@article {pmid40780001, year = {2025}, author = {Grimard-Conea, M and Reyes, EV and Marchand-Senécal, X and Faucher, SP and Prévost, M}, title = {In situ dosing of monochloramine in a hospital hot water system results in drastic microbial communities changes.}, journal = {The Science of the total environment}, volume = {997}, number = {}, pages = {180204}, doi = {10.1016/j.scitotenv.2025.180204}, pmid = {40780001}, issn = {1879-1026}, abstract = {Understanding changes in microbial composition under selective pressures is crucial to assess the emergence of resistant taxa and the survival of drinking water-associated pathogens. This study evaluated the impact of in situ monochloramine disinfection in a hospital hot water system on bacterial (16S rRNA gene amplicon sequencing, 112 samples) and eukaryotic communities (18S rRNA gene amplicon sequencing, 103 samples), and on general microbial measurements (180 samples), including adenosine triphosphate (ATP) and flow cytometry counts. After the onset of treatment, ATP decreased by 1.2- and 3.5-fold, and total cell counts (TCC) dropped by 1- and 2-log at distal and system sites, respectively. During the dosage interruption (27-day), TCC rebounded to pre-treatment levels, but viability percentage decreased, indicating that cells were predominantly damaged. Low-use sites (e.g., showerheads) showed elevated ATP (>15 pg/mL) and TCC (10[5]-10[6] cells/L). Monochloramine drastically altered bacterial and eukaryotic communities. Alpha-diversity showed increased amplicon sequence variant richness during treatment, driven by new, low-abundant taxa, while Beta-diversity revealed distinct shifts in community composition over time, with tight or looser clusters corresponding to each treatment phase. Post-treatment, temporal and spatial heterogeneity was evident across distal sites, while elevated temperatures, consistent flow, and higher monochloramine concentrations in the hot water system resulted in more uniform communities at system sites. Additionally, the persistence of potential pathogenic strains belonging to Legionella and Mycobacterium genera highlights the value of comprehensive risk assessments. These findings emphasize the need to understand microbial shifts under disinfection stress and their public health implications, offering new insights into how treatment interventions shape microbial ecology and pathogen dynamics.}, }
@article {pmid40777436, year = {2025}, author = {Shrestha Gurung, BD and Rayamajhi, M and Maharjan, N and Do, T and Bhandari, D and Yadav, R and Aryal, S and Gnimpieba, EZ}, title = {Forecasting Urban Wastewater Microbiome Dynamics Using a Digital Twin Framework.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40777436}, issn = {2692-8205}, support = {P20 GM103443/GM/NIGMS NIH HHS/United States ; }, abstract = {Urban wastewater microbiomes are complex and temporally dynamic, offering valuable insight into community-scale microbial ecology and potential public health trends. However, existing wastewater-based studies often remain descriptive, lacking tools for predictive modeling. In this study, we introduce a digital twin framework that forecasts microbial abundance trajectories in urban wastewater using an interpretable generative model, Q-net. Trained on a 30-week longitudinal metagenomic dataset from seven wastewater treatment plants, the model captures temporal microbial dynamics with high fidelity (R 2 > 0.97 for key taxa; R 2 = 0.998 at the final timepoint). Beyond accurate forecasting, Q-net provides transparent model structure through conditional inference trees and enables simulation of realistic microbial trends under hypothetical scenarios. This work demonstrates the potential of digital twins to move wastewater microbiome studies from static snapshots to dynamic, predictive systems, with broad implications for environmental monitoring and microbial ecosystem modeling.}, }
@article {pmid40777262, 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 = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40777262}, issn = {2692-8205}, support = {R01 AI143638/AI/NIAID NIH HHS/United States ; R01 AI188648/AI/NIAID NIH HHS/United States ; }, 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 preferentially occurs with E. faecalis among the enterococci, as other enterococcal species do not show a similar effect, suggesting that the composition of the polymicrobial environment in the gut is likely critical to shaping 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.}, }
@article {pmid40771314, year = {2025}, author = {Wang, L and Wang, H and Wu, J and Ji, C and Wang, Y and Gu, M and Li, M and Yang, H}, title = {Gut microbiota and metabolomics in metabolic dysfunction-associated fatty liver disease: interaction, mechanism, and therapeutic value.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1635638}, pmid = {40771314}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Metabolomics ; Dysbiosis ; Liver/metabolism/pathology ; Animals ; *Fatty Liver/metabolism/therapy/microbiology ; *Non-alcoholic Fatty Liver Disease/metabolism/therapy/microbiology ; Biomarkers ; Precision Medicine ; }, abstract = {The global epidemic of Metabolic dysfunction-associated fatty liver disease (MAFLD) urgently demands breakthroughs in precision medicine strategies. Its pathogenesis centers on the cascade dysregulation of the gut microbiota-metabolite-liver axis: microbial dysbiosis drives hepatic lipid accumulation and fibrosis by suppressing short-chain fatty acid synthesis, activating the TLR4/NF-κB inflammatory pathway, and disrupting bile acid signaling. Metabolomics further reveals characteristic disturbances including free fatty acid accumulation, aberrantly elevated branched-chain amino acids (independently predictive of hepatic steatosis), and mitochondrial dysfunction, providing a molecular basis for disease stratification. The field of precision diagnosis is undergoing transformative innovation-multi-omics integration combined with AI-driven analysis of liver enzymes and metabolic biomarkers enables non-invasive, ultra-high-accuracy staging of fibrosis. Therapeutic strategies are shifting towards personalization: microbial interventions require matching to patient-specific microbial ecology, drug selection necessitates efficacy and safety prediction, and synthetically engineered "artificial microbial ecosystems" represent a cutting-edge direction. Future efforts must establish a "multi-omics profiling-AI-powered dynamic modeling-clinical validation" closed-loop framework to precisely halt MAFLD progression to cirrhosis and hepatocellular carcinoma by deciphering patient-specific mechanisms.}, }
@article {pmid40713799, year = {2025}, author = {Soleimani Samarkhazan, H and Nouri, S and Maleknia, M and Aghaei, M}, title = {"The microbiome in graft-versus-host disease: a tale of two ecosystems".}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {832}, pmid = {40713799}, issn = {1479-5876}, mesh = {*Graft vs Host Disease/microbiology/therapy ; Humans ; *Microbiota ; Hematopoietic Stem Cell Transplantation ; Animals ; *Ecosystem ; Fecal Microbiota Transplantation ; Dysbiosis ; }, abstract = {Graft-versus-host disease (GVHD), a life-threatening complication of allogeneic hematopoietic stem cell transplantation (HSCT), is shaped by a dynamic interplay between two microbial ecosystems: the recipient's disrupted microbiome and the donor's transplanted microbiota. This narrative review unravels the "tale of two ecosystems," exploring how pre-transplant chemotherapy, radiation, and antibiotics induce recipient dysbiosis-marked by loss of beneficial taxa (Clostridia, Faecalibacterium) and dominance of pathobionts (Enterococcus). These shifts impair barrier integrity, fuel systemic inflammation, and skew immune responses toward pro-inflammatory T-cell subsets, exacerbating GVHD. Conversely, emerging evidence implicates donor microbiota in modulating post-transplant immune reconstitution, though its role remains underexplored. Therapeutic strategies, including probiotics, prebiotics, and fecal microbiota transplantation (FMT), demonstrate promise in restoring microbial balance, enhancing short-chain fatty acid (SCFA)-driven immune regulation, and reducing GVHD severity. However, challenges such as strain-specific efficacy, safety in immunocompromised hosts, and protocol standardization persist. By bridging microbial ecology and immunology, this review underscores the microbiome's transformative potential in redefining GVHD management and advocates for personalized, microbiome-targeted interventions to improve HSCT outcomes.}, }
@article {pmid40704792, year = {2025}, author = {Zhang, M and Zhang, C and Ramos, A and Whitaker, RJ and Whiteley, M}, title = {Conserved cross-domain protein-to-mRNA ratios enable proteome prediction in microbes.}, journal = {mBio}, volume = {16}, number = {8}, pages = {e0141125}, pmid = {40704792}, issn = {2150-7511}, support = {GBMF9195//Gordon and Betty Moore Foundation/ ; R01 DE023193/DE/NIDCR NIH HHS/United States ; R01DE020100/DE/NIDCR NIH HHS/United States ; R01 DE020100/DE/NIDCR NIH HHS/United States ; R01DE023193/DE/NIDCR NIH HHS/United States ; }, abstract = {UNLABELLED: Microbial communities are often studied by measuring gene expression (mRNA levels), but translating these data into functional insights is challenging because mRNA abundance does not always predict protein levels. Here, we present a strategy to bridge this gap by deriving gene-specific RNA-to-protein conversion factors that improve the prediction of protein abundance from transcriptomic data. Using paired mRNA-protein data sets from seven bacteria and one archaeon, we identified orthologous genes where mRNA levels poorly predicted protein abundance, yet each gene's protein-to-RNA ratio was consistent across these diverse organisms. Applying the resulting conversion factors to mRNA levels dramatically improved protein abundance predictions, even when the conversion factors were obtained from distantly related species. Remarkably, conversion factors derived from bacteria also enhanced protein prediction in an archaeon, demonstrating the robustness of this approach. This cross-domain framework enables more accurate functional inference in microbiomes without requiring organism-specific proteomic data, offering a powerful new tool for microbial ecology, systems biology, and functional genomics.<br><br>IMPORTANCE: Deciphering the biology of natural microbial communities is limited by the lack of functional data. While transcriptomics enables gene expression profiling, mRNA levels often fail to predict protein abundance, the primary indicator of microbial function. Prior studies addressed this by calculating RNA-to-protein (RTP) conversion factors using conserved protein-to-RNA (ptr) ratios across bacterial strains, but their cross-species and cross-domain utility remained unknown. We generated comprehensive transcriptomic and proteomic data sets from seven bacteria and one archaeon spanning diverse metabolisms and ecological niches. We identified orthologous genes with conserved ptr ratios, enabling the discovery of RTP conversion factors that significantly improved protein prediction from mRNA, even between distant species and domains. This reveals previously unrecognized conservation in ptr ratios across domains and eliminates the need for paired proteomic data in many cases. Our approach offers a broadly applicable framework to enhance functional prediction in microbiomes using only transcriptomic data.}, }
@article {pmid40701356, year = {2025}, author = {Hu, L and Ye, Y and Li, Y and Tan, X and Liu, X and Zhang, T and Wang, J and Du, Z and Ye, M}, title = {Bacteria-algae synergy in carbon sequestration: Molecular mechanisms, ecological dynamics, and biotechnological innovations.}, journal = {Biotechnology advances}, volume = {83}, number = {}, pages = {108655}, doi = {10.1016/j.biotechadv.2025.108655}, pmid = {40701356}, issn = {1873-1899}, mesh = {*Biotechnology/methods ; *Microalgae/metabolism ; *Carbon Sequestration ; *Bacteria/metabolism ; Carbon Dioxide/metabolism ; Photosynthesis ; Carbon/metabolism ; }, abstract = {Rising atmospheric CO2 levels require innovative strategies to increase carbon sequestration. Bacteria-algae interactions, as pivotal yet underexplored drivers of marine and freshwater carbon sinks, involve multiple mechanisms that amplify CO2 fixation and long-term storage. This review systematically describes the synergistic effects of bacteria-algae consortia spanning both microalgae (e.g., Chlorella vulgaris and Phaeodactylum tricornutum) and macroalgae (e.g., Macrocystis and Laminaria) on carbon sequestration. These effects include (1) molecular-level regulation (e.g., signal transduction via N-acyl-homoserine lactones (AHLs), and horizontal gene transfer), (2) ecological facilitation of recalcitrant dissolved organic carbon (RDOC) formation, and (3) biotechnological applications in wastewater treatment and bioenergy production. We highlight that microbial crosstalk increases algal photosynthesis by 20-40 % and contributes to 18.9 % of kelp-derived RDOC storage. Furthermore, engineered systems integrating algal-bacterial symbiosis achieve greater than 80 % nutrient removal and a 22-35 % increase in CO2 fixation efficiency (compared with axenic algal systems), demonstrating their dual role in climate mitigation and a circular economy. This review is the first to integrate molecular mechanisms (e.g., quorum sensing), ecological carbon transformation processes (e.g., the formation of RDOC), and applications in synthetic biology (e.g., CRISPR-engineered consortia) into a unified framework. Moreover, the novel strategy "microbial interaction network optimization" for enhancing carbon sinks is proposed. However, scalability challenges persist, including light limitations in photobioreactors and the ecological risks of synthetic consortia. By bridging microbial ecology with synthetic biology, this work provides a roadmap for harnessing bacteria-algae synergy to achieve carbon neutrality.}, }
@article {pmid40695133, year = {2025}, author = {Shi, F and Fang, H and Cheng, S and Guo, Y and Wang, H and Chen, L and Pu, H and Liu, B}, title = {Cadmium accumulation suppresses rice nitrogen use efficiency by inhibiting rhizosphere nitrification and promoting nitrate reduction.}, journal = {Journal of hazardous materials}, volume = {496}, number = {}, pages = {139298}, doi = {10.1016/j.jhazmat.2025.139298}, pmid = {40695133}, issn = {1873-3336}, abstract = {Cadmium (Cd) pollution significantly disrupts paddy soil nitrogen (N) availability and impairs rice nitrogen use efficiency (NUE). However, most existing studies rely on microcosm or pot experiments, with limited field-based manipulative studies involving Cd addition. The regulatory mechanisms by which N transformation processes influence rice N utilization under Cd stress remain poorly understood. In this study, a field experiment incorporating multiple levels of Cd addition was conducted to address this gap. Plant traits, nutrient content, and microbial community characteristics in rhizosphere and bulk soils were examined through soil chemical analysis, metagenomic sequencing, and bioinformatics approaches. The results demonstrated that microbial communities, soil N transformation potential, and rice NUE responded to Cd addition in a dose-dependent manner, with rhizosphere soils exhibiting greater sensitivity than bulk soils. Cd addition reduced dissolved organic carbon (DOC), NH4[+]-N, and NO3[-]-N in rhizosphere soil, while increasing total and available phosphorus (P) contents in both rhizosphere and bulk soils. Although Cd addition enhanced aboveground biomass and total N uptake, it led to a decline in plant N concentration and NUE. Moreover, Cd accumulation markedly suppressed the abundance of nitrification genes while promoting genes involved in dissimilatory nitrate reduction to ammonium (DNRA) and denitrification. Overall, Cd stress altered microbial community structure and soil N and P availability, thereby impairing rice N uptake and NUE. These findings suggest that acute Cd exposure rapidly disrupts microbial ecology, decouples the soil N cycle, and reduces N supply potential of paddy soils and rice NUE, ultimately threatening agroecosystem stability in southern China. These impacts warrant greater consideration in future farmland management strategies.}, }
@article {pmid40603778, year = {2025}, author = {Brinck, JE and Sinha, AK and Laursen, MF and Dragsted, LO and Raes, J and Uribe, RV and Walter, J and Roager, HM and Licht, TR}, title = {Intestinal pH: a major driver of human gut microbiota composition and metabolism.}, journal = {Nature reviews. Gastroenterology &amp; hepatology}, volume = {}, number = {}, pages = {}, pmid = {40603778}, issn = {1759-5053}, abstract = {In the human gastrointestinal tract, pH is a key factor in shaping gut microbial composition and activity, while also being influenced by microbial metabolism. pH varies substantially along the gastrointestinal tract within an individual and between different individuals due to a combination of host, diet, microbial and external factors. The importance of pH on microbiota composition and metabolic response has been widely explored over the past century. Here, we review the literature to explore the major physiological and dietary factors that influence pH along the gastrointestinal tract. From a microbial ecology perspective, we discuss how gastrointestinal pH affects microbiota composition and metabolism. We explore mechanisms by which pH can influence bacterial acid response systems, gene expression and the production of microbial metabolites important for health. Finally, we review the literature regarding the potential role of gastrointestinal pH in human diseases. We propose that we can advance our understanding of the gut microbiota in health and disease by considering gastrointestinal pH. We argue that pH-mediated gut microbial metabolic variation is highly important for predicting and manipulating metabolic output relevant to human health.}, }
@article {pmid40600721, year = {2025}, author = {Peters, DI and Shin, IJ and Deever, AN and Kaspar, JR}, title = {Design, development, and validation of new fluorescent strains for studying oral streptococci.}, journal = {Microbiology spectrum}, volume = {13}, number = {8}, pages = {e0016825}, pmid = {40600721}, issn = {2165-0497}, support = {P30 CA016058/CA/NCI NIH HHS/United States ; R03 DE031766/DE/NIDCR NIH HHS/United States ; R03DE031766/DE/NIDCR NIH HHS/United States ; }, mesh = {Biofilms/growth &amp; development ; *Luminescent Proteins/genetics/metabolism ; Humans ; Streptococcus gordonii/genetics ; *Streptococcus/genetics/metabolism/physiology ; *Mouth/microbiology ; Streptococcus mutans/genetics/metabolism ; Green Fluorescent Proteins/genetics/metabolism ; Red Fluorescent Protein ; Streptococcus sanguis/genetics ; Microscopy, Confocal ; }, abstract = {Bacterial strains that are genetically engineered to constitutively produce fluorescent proteins have aided our study of bacterial physiology, biofilm formation, and interspecies interactions. Here, we report on the construction and utilization of new strains that produce the blue fluorescent protein mTagBFP2, the green fluorescent protein sfGFP, and the red fluorescent protein mScarlet-I3 in species Streptococcus gordonii, Streptococcus mutans, and Streptococcus sanguinis. Gene fragments, developed to contain the constitutive promoter Pveg, the fluorescent gene of interest, as well as aad9, providing resistance to the antibiotic spectinomycin, were inserted into selected open reading frames on the chromosome that were both transcriptionally silent and whose loss caused no measurable changes in fitness. All strains, except for sfGFP in S. sanguinis, were validated to produce a detectable and specific fluorescent signal. Individual stains, along with extracellular polymeric substances (EPS) within biofilms, were visualized and quantified through either widefield or super-resolution confocal microscopy approaches. Finally, to validate the ability to perform single-cell-level analysis using the strains, we imaged and analyzed a triculture mixed-species biofilm of S. gordonii, S. mutans, and S. sanguinis grown with and without the addition of human saliva. Quantification of the loss in membrane integrity using a SYTOX dye revealed that all strains had increased loss of membrane integrity with water or human saliva added to the growth media, but the proportion of the population stained by the SYTOX dye varied by species. In all, these fluorescent strains will be a valuable resource for the continued study of oral microbial ecology.IMPORTANCEStreptococci are among the earliest colonizers of the soft and hard tissues of the oral cavity and are contributors to the oral health status of the host, with involvement in dental caries, endodontic infections, periodontal disease, and the development of oral cancer. Strains genetically modified to produce fluorescent proteins that can be either visualized through microscopy imaging or quantified by their specific fluorescent intensity signal are critical tools toward the study of individual or mixed-species cultures. Our report here details the development and testing of several new strains of fluorescent oral streptococci that can be utilized in the study of microbial ecology, increasing both the availability of tools and documenting experimental approaches toward in vitro assay applications such as the study of intermicrobial interactions.}, }
@article {pmid40568985, year = {2025}, author = {Zhao, J and Brandt, G and Gronniger, JL and Wang, Z and Li, J and Hunt, DE and Rodriguez-R, LM and Hatt, JK and Konstantinidis, KT}, title = {Quantifying the contribution of the rare biosphere to natural disturbances.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {40568985}, issn = {1751-7370}, support = {OCE 1416673 and DEB 1831582//US National Science Foundation/ ; ICER 2033934, DEB 2224819//US National Science Foundation/ ; }, mesh = {Metagenome ; *Ecosystem ; *Microbiota ; }, abstract = {Understanding how populations respond to disturbances represents a major goal for microbial ecology. While several hypotheses have been advanced to explain microbial community compositional changes in response to disturbance, appropriate data to test these hypotheses is scarce, due to the challenges in delineating rare vs. abundant taxa and generalists vs. specialists, a prerequisite for testing the theories. Here, we operationally define these two key concepts by employing the patterns of coverage of a (target) genome by a metagenome to identify rare populations, and by borrowing the proportional similarity index from macroecology to identify generalists. We applied these concepts to time-series (field) metagenomes from the Piver's Island Coastal Observatory to establish that coastal microbial communities are resilient to major perturbations such as tropical cyclones and (uncommon) cold or warm temperature events, in part due to the response of rare populations. Therefore, these results provide support for the insurance hypothesis [i.e. the rare biosphere has the buffering capacity to mitigate the effects of disturbance]. Additionally, generalists appear to contribute proportionally more than specialists to community adaptation to perturbations like warming, supporting the disturbance-specialization hypothesis [i.e. disturbance favors generalists]. Several of these findings were also observed in replicated laboratory mesocosms that aimed to simulate disturbances such as a rain-driven washout of microbial cells and a labile organic matter release from a phytoplankton bloom. Taken together, our results advance understanding of the mechanisms governing microbial population dynamics under changing environmental conditions and have implications for ecosystem modeling.}, }
@article {pmid40556886, year = {2025}, author = {Klein, ML and Erikson, CB and McCabe, CJ and Huang, L and Rodrigues, JLM and Mitloehner, FM}, title = {Limited effects of tannin supplementation on the dairy cattle fecal microbiome with modulation of metabolites.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1570127}, pmid = {40556886}, issn = {1664-302X}, abstract = {Tannins are plant secondary metabolites that bind organic carbon (C) and nitrogen (N), potentially altering substrate bioavailability for enteric fermentation in ruminants. This interaction may reduce greenhouse gas (GHG) emissions and influence nitrogen partitioning. Given tannins' resistance to ruminal degradation and persistence through the gastrointestinal tract, this study investigated the effects of a tannin-based feed additive on fecal microbial diversity, fecal chemical composition, and GHG emissions. Twenty-four early- to mid-lactation dairy cows were randomized to receive either a tannin-based feed additive (TRT; containing condensed and hydrolyzable tannins from Schinopsis quebracho-colorado [Schltdl.]) or a control diet (CON) for 64 days. Cows were blocked by parity, dry matter intake, milk yield, body weight, and days in milk. Fecal samples were collected on days 0, 16, 32, and 64 and analyzed using 16S rRNA gene amplicon sequencing. Fecal C, N, and indole-3-lactate were measured, and GHG emissions (N2O, CH4, CO2) were assessed via 14-day laboratory incubation. A total of 1,538 amplicon sequence variants were identified, with Firmicutes as the dominant phylum. Fecal phylogenetic diversity showed a significant treatment × day interaction (p < 0.01), with TRT cows exhibiting reduced microbial diversity from day 16 to 64. Fecal C and N concentrations were significantly lower (p < 0.01) in TRT cows on day 16, while indole-3-lactate levels were higher on day 64 (p = 0.02). GHG emissions did not differ significantly between treatments. The tannin-based feed additive influenced fecal microbial community structure and select chemical parameters but did not significantly affect GHG emissions from feces. These findings suggest that dietary tannins may modulate gut microbial ecology with minimal impact on downstream manure-related emissions.}, }
@article {pmid40184706, year = {2025}, author = {He, L and Li, J and Tang, L and Wang, Y and Zhao, X and Ding, K and Xu, L and Gu, L and Cheng, S and Wei, YY}, title = {Applying side-stream gas recirculation to promote anaerobic digestion of food waste under ammonia stress: Overlooked impact of gaseous atmospheres on microorganisms.}, journal = {Water research}, volume = {281}, number = {}, pages = {123571}, doi = {10.1016/j.watres.2025.123571}, pmid = {40184706}, issn = {1879-2448}, mesh = {*Ammonia ; Anaerobiosis ; Bioreactors/microbiology ; Hydrogen ; Gases ; Food Loss and Waste ; }, abstract = {High ammonia concentrations can be toxic to microorganisms, leading to the accumulation of hydrogen (H2) and acids in anaerobic digestion (AD) system. In this study, a side gas recycling strategy (SGR), coupled with a primary reactor and a small side-stream reactor, which recirculates biogas between primary reactor and side reactor was employed to mitigate ammonia inhibition. This approach enabled the mesophilic side-stream gas recirculation system (SMGR) and the thermophilic side-stream gas recirculation system (STGR) to ultimately withstand ammonia stress levels of 2.5 g/L and 3.5 g/L, respectively, while maintaining lower hydrogen partial pressures. In contrast, the control group experienced system failure at an ammonia concentration of 2 g/L. Enzyme activity, microbial community, and metaproteomic analysis indicated that the side reactor enriched microorganisms with strong hydrogen-utilizing capacity, while the primary reactor was enriched with Methanosaeta. Furthermore, key pathways related to propionate metabolism, ABC transporters, and methane production were enhanced in the primary reactor, along with increased ATPase activity. The activity of key enzymes involved in AD was also significantly enhanced. This study enhances the understanding of the impact of gas atmosphere control on the microbial ecology and metabolic characteristics of AD system, providing valuable insights and practical guidance for the development of Engineering applications in this field.}, }
@article {pmid40179787, year = {2025}, author = {Wang, Z and Tu, S and Shehzad, K and Hou, J and Xiong, S and Cao, M}, title = {Comparative study of organosilicon and inorganic silicon in reducing cadmium accumulation in wheat: Insights into rhizosphere microbial communities and molecular regulation mechanisms.}, journal = {Journal of hazardous materials}, volume = {492}, number = {}, pages = {138061}, doi = {10.1016/j.jhazmat.2025.138061}, pmid = {40179787}, issn = {1873-3336}, mesh = {*Triticum/metabolism/growth &amp; development/drug effects ; *Cadmium/metabolism ; *Silicon/pharmacology/chemistry ; Rhizosphere ; *Soil Pollutants/metabolism ; Microbiota/drug effects ; Soil Microbiology ; }, abstract = {Silicon is widely used as a "quality element" and "stress resistance element" in crop production and the remediation of heavy metal-contamination soils. Compared to inorganic silicon, organosilicon has unique properties such as amphiphilicity, low surface energy and high biocompatibility. Our previous research has confirmed the effectiveness of organosilicon-modified fertilizers in inhibiting Cadmium (Cd) absorption in wheat. Therefore, it is of great importance to further explore the potential mechanisms and comprehensive benefits of organosilicon. In this study, the microbiological and molecular mechanisms by which organosilicon reduces Cd concentration in wheat compared to inorganic silicon were investigated in depth. The findings indicated that, in comparison with inorganic silicon, organosilicon exhibited a more remarkable efficacy. Specifically, it was more effective in reducing the Cd concentration in wheat grains, achieving a reduction range of 35-39 % as opposed to the 23-28 % reduction achieved by inorganic silicon. Moreover, it manifested a greater ability to mitigate health risks, with a reduction range of 33-42 % compared to the 25-30 % reduction of inorganic silicon. Furthermore, organosilicon contributed to a significant increase in wheat yield, with a growth range of 11-14 % in contrast to the 8-11 % increase from inorganic silicon. Additionally, it enhanced the quality of the grains, substantially improving the protein content and amino acid content. The comparative advantages of organosilicon over inorganic silicon would be firstly due to the reduction of the bioavailability of soil Cd by increasing the available silicon content in the soil and improving the soil microbial ecology (increasing the abundance of Bacillus, Pseudomonas, Massilia and Talaromyces and reducing the enrichment of Fusarium). Secondly, organosilicon achieved vacuolar compartmentalization of Cd by upregulating the expression of the ABC transporter gene (TaABCB7), thereby alleviating Cd toxicity and restricting Cd transport from leaves to grains. Meanwhile, organosilicon increased the wheat yield by optimizing the availability of soil nutrients and enhancing photosynthesis. These results demonstrate the immense potential of organosilicon in mitigating heavy metal contamination in crops.}, }
@article {pmid40041702, year = {2025}, author = {Xu, Z and Chen, J and Liang, W and Chen, ZL and Wu, W and Xia, X and Chen, B and He, D and Liu, H}, title = {Contrasting diversity patterns between microeukaryotic and prokaryotic communities in cold-seep sediments.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf002}, pmid = {40041702}, issn = {2730-6151}, abstract = {Cold seeps are hotspots of biodiversity. However, the quantification of the microbial diversity, particularly that of microeukaryotes, remains scarce and little is known about the active groups. In this study we investigated the diversity and activity of prokaryotes and microeukaryotes in the Haima cold seep sediments in the northern South China Sea using both DNA (whole community) and RNA (active community) signatures. We found that, in general, prokaryotes had lower diversity in the seep sediment than in non-seep regions while microeukaryotes showed the opposite pattern. This finding could be explained by the dominance of homogeneous selection in the prokaryotic community while microeukaryotic communities were less affected by environmental selection, harboring high richness of abundant groups in the seep regions. The compositional difference between DNA and RNA communities was much larger in microeukaryotes than prokaryotes, which could be reflected by the large number of inactive microeukaryotic taxa. Compared to the whole community, the seep-active groups, e.g. among microeukaryotes, Breviatea, Labyrinthulomycetes, and Apicomplexa were more sensitive to and directly influenced by environmental factors, suggesting their pivotal roles in ecosystem biodiversity and functions. This study provides insight into the distinct diversity patterns and regulating mechanisms that occur between prokaryotic and microeukaryotic communities in cold-seep sediments, deepening our understanding of microbial ecology in deep-sea extreme habitats.}, }
@article {pmid39752189, year = {2025}, author = {Bloomfield, SJ and Hildebrand, F and Zomer, AL and Palau, R and Mather, AE}, title = {Ecological insights into the microbiology of food using metagenomics and its potential surveillance applications.}, journal = {Microbial genomics}, volume = {11}, number = {1}, pages = {}, pmid = {39752189}, issn = {2057-5858}, mesh = {*Metagenomics/methods ; *Food Microbiology ; Metagenome ; Bacteria/genetics/classification/isolation &amp; purification ; Salmonella/genetics/isolation &amp; purification/classification ; Drug Resistance, Bacterial/genetics ; Escherichia coli/genetics/isolation &amp; purification/classification ; }, abstract = {A diverse array of micro-organisms can be found on food, including those that are pathogenic or resistant to antimicrobial drugs. Metagenomics involves extracting and sequencing the DNA of all micro-organisms on a sample, and here, we used a combination of culture and culture-independent approaches to investigate the microbial ecology of food to assess the potential application of metagenomics for the microbial surveillance of food. We cultured common foodborne pathogens and other organisms including Escherichia coli, Klebsiella/Raoultella spp., Salmonella spp. and Vibrio spp. from five different food commodities and compared their genomes to the microbial communities obtained by metagenomic sequencing following host (food) DNA depletion. The microbial populations of retail food were found to be predominated by psychrotrophic bacteria, driven by the cool temperatures in which the food products are stored. Pathogens accounted for a small percentage of the food metagenome compared to the psychrotrophic bacteria, and cultured pathogens were inconsistently identified in the metagenome data. The microbial composition of food varied amongst different commodities, and metagenomics was able to classify the taxonomic origin of 59% of antimicrobial resistance genes (ARGs) found on food to the genus level, but it was unclear what percentage of ARGs were associated with mobile genetic elements and thus transferable to other bacteria. Metagenomics may be used to survey the ARG burden, composition and carriage on foods to which consumers are exposed. However, food metagenomics, even after depleting host DNA, inconsistently identifies pathogens without enrichment or further bait capture.}, }
@article {pmid39651889, year = {2025}, author = {Wang, J and Schamp, CN and Hudson, LK and Chaggar, HK and Bryan, DW and Garman, KN and Radosevich, M and Denes, TG}, title = {Whole-genome sequencing and metagenomics reveal diversity and prevalence of Listeria spp. from soil in the Nantahala National Forest.}, journal = {Microbiology spectrum}, volume = {13}, number = {1}, pages = {e0171224}, pmid = {39651889}, issn = {2165-0497}, mesh = {*Soil Microbiology ; *Listeria/genetics/classification/isolation &amp; purification ; *Metagenomics ; *Whole Genome Sequencing ; North Carolina ; *Forests ; *Genome, Bacterial ; *Phylogeny ; Humans ; Listeriosis/microbiology/epidemiology/transmission ; Listeria monocytogenes/genetics/classification/isolation &amp; purification ; Metagenome ; Prevalence ; Soil/chemistry ; }, abstract = {UNLABELLED: Listeria spp. are widely distributed environmental bacteria associated with human foodborne illness. The ability to detect and characterize Listeria strains in the natural environment will contribute to improved understanding of transmission routes of contamination. The current standard for surveillance and outbreak source attribution is whole-genome sequencing (WGS) of Listeria monocytogenes clinical isolates. Recently, metagenomic sequencing has also been explored as a tool for the detection of Listeria spp. in environmental samples. This study evaluated soil samples from four locations across altitudes ranging from 1,500 to 4,500 ft in the Nantahala National Forest in North Carolina, USA. Forty-two Listeria isolates were cultured and sequenced, and 12 metagenomes of soil bacterial communities were generated. These isolates comprised 14 distinct strains from five species, including Listeria cossartiae subsp. cayugensis (n = 8; n represents the number of distinct strains), L. monocytogenes (n = 3), "Listeria swaminathanii" (Lsw) (n = 1), Listeria marthii (n = 1), and Listeria booriae (n = 1). Most strains (n = 13) were isolated from lower altitudes (1,500 or 2,500 ft), while the L. swaminathanii strain was isolated from both higher (4,500 ft) and lower (1,500 ft) altitudes. Metagenomic analysis of soil described a reduction in both bacterial community diversity and relative abundance of Listeria spp. as the altitude increased. Soil pH and cation exchange capacity were positively correlated (P < 0.05) with the abundance of Listeria spp. as detected by metagenomics. By integrating culture-independent metagenomics with culture-based WGS, this study advances current knowledge regarding distribution of Listeria spp. in the natural environment and suggests the potential for future use of culture-independent methods in tracking the transmission of foodborne pathogens.<br><br>IMPORTANCE: As a foodborne pathogen, Listeria continues to cause numerous illnesses in humans and animals. Studying the diversity and distribution of Listeria in soil is crucial for understanding potential sources of contamination and developing effective strategies to prevent foodborne outbreaks of listeriosis. Additionally, examining the ecological niches and survival mechanisms of Listeria in natural habitats provides insights into its persistence and adaptability, informing risk assessments and public health interventions. This research contributes to a broader understanding of microbial ecology and the factors influencing foodborne pathogen emergence, ultimately enhancing food safety and protecting public health. Moreover, using a metagenomic approach provides a detailed understanding of the soil microbial ecosystems, leading to more effective monitoring and control of foodborne pathogens. This study also highlights the potential for integrating metagenomics into routine surveillance systems for food safety in the near future.}, }
@article {pmid39545729, year = {2024}, author = {Beaudry, MS and Bhuiyan, MIU and Glenn, TC}, title = {Enriching the future of public health microbiology with hybridization bait capture.}, journal = {Clinical microbiology reviews}, volume = {37}, number = {4}, pages = {e0006822}, pmid = {39545729}, issn = {1098-6618}, support = {R01 AI148667/AI/NIAID NIH HHS/United States ; 75D30118C02889, 75D30120R67837//HHS | Centers for Disease Control and Prevention (CDC)/ ; 1R01AI148667-01A1//HHS | National Institutes of Health (NIH)/ ; }, mesh = {Humans ; Bacteria/genetics/classification/isolation &amp; purification ; Fungi/classification/genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; *Microbiological Techniques/methods/trends ; Nucleic Acid Hybridization/methods ; *Public Health ; }, abstract = {SUMMARYPublic health microbiology focuses on microorganisms and infectious agents that impact human health. For years, this field has relied on culture or molecular methods to investigate complex samples of public health importance. However, with the increase in accuracy and decrease in sequencing cost over the last decade, there has been a transition to the use of next-generation sequencing in public health microbiology. Nevertheless, many available sequencing methods (e.g., shotgun metagenomics and amplicon sequencing) do not work well in complex sample types, require deep sequencing, or have inherent biases associated with them. Hybridization bait capture, also known as target enrichment, brings in solutions for such limitations. It is an increasingly popular technique to simultaneously characterize many thousands of genetic elements while reducing the amount of sequencing needed (thereby reducing the sequencing costs). Here, we summarize the concept of hybridization bait capture for public health, reviewing a total of 35 bait sets designed in six key topic areas for public health microbiology [i.e., antimicrobial resistance (AMR), bacteria, fungi, parasites, vectors, and viruses], and compare hybridization bait capture to previously relied upon methods. Furthermore, we provide an in-depth comparison of the three most popular bait sets designed for AMR by evaluating each of them against three major AMR databases: Comprehensive Antibiotic Resistance Database, Microbial Ecology Group Antimicrobial Resistance Database, and Pathogenicity Island Database. Thus, this article provides a review of hybridization bait capture for public health microbiologists.}, }
@article {pmid39298326, year = {2024}, author = {Gordon, JI and Barratt, MJ and Hibberd, MC and Rahman, M and Ahmed, T}, title = {Establishing human microbial observatory programs in low- and middle-income countries.}, journal = {Annals of the New York Academy of Sciences}, volume = {1540}, number = {1}, pages = {13-20}, doi = {10.1111/nyas.15224}, pmid = {39298326}, issn = {1749-6632}, support = {//Fondazione Internazionale Premio Balzan/ ; //Bill and Melinda Gates Foundation/ ; /NH/NIH HHS/United States ; /NH/NIH HHS/United States ; }, mesh = {Humans ; *Developing Countries ; Global Health ; *Microbiota ; }, abstract = {Studies of the human microbiome are progressing rapidly but have largely focused on populations living in high-income countries. With increasing evidence that the microbiome contributes to the pathogenesis of diseases that affect infants, children, and adults in low- and middle-income countries (LMICs), and with profound and rapid ongoing changes occurring in our lifestyles and biosphere, understanding the origins of and developing microbiome-directed therapeutics for treating a number of global health challenges requires the development of programs for studying human microbial ecology in LMICs. Here, we discuss how the establishment of long-term human microbial observatory programs in selected LMICs could provide one timely approach.}, }
@article {pmid38965531, year = {2024}, author = {Babajanyan, SG and Garushyants, SK and Wolf, YI and Koonin, EV}, title = {Microbial diversity and ecological complexity emerging from environmental variation and horizontal gene transfer in a simple mathematical model.}, journal = {BMC biology}, volume = {22}, number = {1}, pages = {148}, pmid = {38965531}, issn = {1741-7007}, support = {Intramural Research Program//U.S. National Library of Medicine/ ; }, mesh = {*Gene Transfer, Horizontal ; *Microbiota/genetics ; Biodiversity ; Symbiosis/genetics ; Models, Theoretical ; Models, Biological ; }, abstract = {BACKGROUND: Microbiomes are generally characterized by high diversity of coexisting microbial species and strains, and microbiome composition typically remains stable across a broad range of conditions. However, under fixed conditions, microbial ecology conforms with the exclusion principle under which two populations competing for the same resource within the same niche cannot coexist because the less fit population inevitably goes extinct. Therefore, the long-term persistence of microbiome diversity calls for an explanation.<br><br>RESULTS: To explore the conditions for stabilization of microbial diversity, we developed a simple mathematical model consisting of two competing populations that could exchange a single gene allele via horizontal gene transfer (HGT). We found that, although in a fixed environment, with unbiased HGT, the system obeyed the exclusion principle, in an oscillating environment, within large regions of the phase space bounded by the rates of reproduction and HGT, the two populations coexist. Moreover, depending on the parameter combination, all three major types of symbiosis were obtained, namely, pure competition, host-parasite relationship, and mutualism. In each of these regimes, certain parameter combinations provided for synergy, that is, a greater total abundance of both populations compared to the abundance of the winning population in the fixed environment.<br><br>CONCLUSIONS: The results of this modeling study show that basic phenomena that are universal in microbial communities, namely, environmental variation and HGT, provide for stabilization and persistence of microbial diversity, and emergence of ecological complexity.}, }
@article {pmid38691424, year = {2024}, author = {Xiong, X and Othmer, HG and Harcombe, WR}, title = {Emergent antibiotic persistence in a spatially structured synthetic microbial mutualism.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38691424}, issn = {1751-7370}, support = {R01 GM121498/GM/NIGMS NIH HHS/United States ; R01-GM121498/NH/NIH HHS/United States ; }, mesh = {*Escherichia coli/drug effects/genetics/growth &amp; development ; *Anti-Bacterial Agents/pharmacology ; *Symbiosis ; *Salmonella enterica/drug effects/genetics ; Coculture Techniques ; Microbial Interactions ; Ampicillin/pharmacology ; Drug Resistance, Bacterial ; }, abstract = {Antibiotic persistence (heterotolerance) allows a subpopulation of bacteria to survive antibiotic-induced killing and contributes to the evolution of antibiotic resistance. Although bacteria typically live in microbial communities with complex ecological interactions, little is known about how microbial ecology affects antibiotic persistence. Here, we demonstrated within a synthetic two-species microbial mutualism of Escherichia coli and Salmonella enterica that the combination of cross-feeding and community spatial structure can emergently cause high antibiotic persistence in bacteria by increasing the cell-to-cell heterogeneity. Tracking ampicillin-induced death for bacteria on agar surfaces, we found that E. coli forms up to 55 times more antibiotic persisters in the cross-feeding coculture than in monoculture. This high persistence could not be explained solely by the presence of S. enterica, the presence of cross-feeding, average nutrient starvation, or spontaneous resistant mutations. Time-series fluorescent microscopy revealed increased cell-to-cell variation in E. coli lag time in the mutualistic co-culture. Furthermore, we discovered that an E. coli cell can survive antibiotic killing if the nearby S. enterica cells on which it relies die first. In conclusion, we showed that the high antibiotic persistence phenotype can be an emergent phenomenon caused by a combination of cross-feeding and spatial structure. Our work highlights the importance of considering spatially structured interactions during antibiotic treatment and understanding microbial community resilience more broadly.}, }
@article {pmid37970497, year = {2023}, author = {Lee, JH and Kim, S and Kim, ES and Keum, GB and Doo, H and Kwak, J and Pandey, S and Cho, JH and Ryu, S and Song, M and Cho, JH and Kim, S and Kim, HB}, title = {Comparative analysis of the pig gut microbiome associated with the pig growth performance.}, journal = {Journal of animal science and technology}, volume = {65}, number = {4}, pages = {856-864}, pmid = {37970497}, issn = {2055-0391}, abstract = {There are a variety of microorganisms in the animal intestine, and it has been known that they play important roles in the host such as suppression of potentially pathogenic microorganisms, modulation of the gut immunity. In addition, the gut microbiota and the livestock growth performance have long been known to be related. Therefore, we evaluated the interrelation between the growth performance and the gut microbiome of the pigs from 3 different farms, with pigs of varied ages ready to be supplied to the market. When pigs reached average market weight of 118 kg, the average age of pigs in three different farms were < 180 days, about 190 days, and > 200 days, respectively. Fecal samples were collected from pigs of age of 70 days, 100 days, 130 days, and 160 days. The output data of the 16S rRNA gene sequencing by the Illumina Miseq platform was filtered and analyzed using Quantitative Insights into Microbial Ecology (QIIME)2, and the statistical analysis was performed using Statistical Analysis of Metagenomic Profiles (STAMP). The results of this study showed that the gut microbial communities shifted as pigs aged along with significant difference in the relative abundance of different phyla and genera in different age groups of pigs from each farm. Even though, there was no statistical differences among groups in terms of Chao1, the number of observed operational taxonomic units (OTUs), and the Shannon index, our results showed higher abundances of Bifidobacterium, Clostridium and Lactobacillus in the feces of pigs with rapid growth rate. These results will help us to elucidate important gut microbiota that can affect the growth performance of pigs.}, }
@article {pmid37354976, year = {2023}, author = {Kable, ME and Chin, EL and Huang, L and Stephensen, CB and Lemay, DG}, title = {Association of Estimated Daily Lactose Consumption, Lactase Persistence Genotype (rs4988235), and Gut Microbiota in Healthy Adults in the United States.}, journal = {The Journal of nutrition}, volume = {153}, number = {8}, pages = {2163-2173}, doi = {10.1016/j.tjnut.2023.06.025}, pmid = {37354976}, issn = {1541-6100}, mesh = {Male ; Female ; Humans ; Adult ; United States ; Lactose ; *Lactose Intolerance/genetics ; *Gastrointestinal Microbiome/genetics ; Cross-Sectional Studies ; RNA, Ribosomal, 16S/genetics ; Dairy Products ; Lactase/genetics ; Genotype ; }, abstract = {BACKGROUND: Lactase persistence (LP) is a heritable trait in which lactose can be digested throughout adulthood. Lactase nonpersistent (LNP) individuals who consume lactose may experience microbial adaptations in response to undigested lactose.<br><br>OBJECTIVES: The objective of the study was to estimate lactose from foods reported in the Automated Self-Administered 24-Hour Dietary Assessment Tool (ASA24) and determine the interaction between lactose consumption, LP genotype, and gut microbiome in an observational cross-sectional study of healthy adults in the United States (US).<br><br>METHODS: Average daily lactose consumption was estimated for 279 healthy US adults, genotyped for the lactase gene -13910G>A polymorphism (rs4988235) by matching ASA24-reported foods to foods in the Nutrition Coordinating Center Food and Nutrient Database. Analysis of covariance was used to identify whether the A genotype (LP) influenced lactose and total dairy consumption, with total energy intake and weight as covariates. The 16S rRNA V4/V5 region, amplified from bacterial DNA extracted from each frozen stool sample, was sequenced using Illumina MiSeq (300 bp paired-end) and analyzed using Quantitative Insights Into Microbial Ecology (QIIME)2 (version 2019.10). Differential abundances of bacterial taxa were analyzed using DESeq2 likelihood ratio tests.<br><br>RESULTS: Across a diverse set of ethnicities, LP subjects consumed more lactose than LNP subjects. Lactobacillaceae abundance was highest in LNP subjects who consumed more than 12.46 g/d (upper tercile). Within Caucasians and Hispanics, family Lachnospiraceae was significantly enriched in the gut microbiota of LNP individuals consuming the upper tercile of lactose across both sexes.<br><br>CONCLUSIONS: Elevated lactose consumption in individuals with the LNP genotype is associated with increased abundance of family Lactobacillaceae and Lachnospriaceae, taxa that contain multiple genera capable of utilizing lactose. This trial was registered on clinicaltrials.gov as NCT02367287.}, }
@article {pmid37338363, year = {2023}, author = {Ye, L and Yang, X and Zhang, B and Zhou, J and Tian, H and Zhang, X and Li, X}, title = {Seasonal Succession of Fungal Communities in Native Truffle (Tuber indicum) Ecosystems.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {7}, pages = {e0019523}, pmid = {37338363}, issn = {1098-5336}, mesh = {Ecosystem ; Seasons ; *Mycobiome ; *Ascomycota ; *Mycorrhizae ; Soil ; Soil Microbiology ; }, abstract = {Truffles are a rare underground fungus and one of the most expensive, and sought-after kitchen ingredients in the world. Microbial ecology plays an important role in the annual growth cycle of truffles, but fungal communities in native truffle ecosystems are still largely unknown, especially for Tuber indicum from China. In this study, the spatial and temporal dynamics of soil physicochemical properties and fungal communities were described associated with four T. indicum-producing plots (TPPs) and one non-truffle-producing plot in four successive growing seasons. A total of 160 biological samples were collected, 80 of which were used for the determination of 10 soil physicochemical indices and 80 for Illumina-based analysis of the fungal microbiome. Soil physicochemical properties and fungal communities exhibited considerable seasonal variation. Ascomycetes, Basidiomycetes, and Mucormycoides dominated. The core microbiome work on the microecological changes in TPPs, and the identified core members contribute to the seasonal succession of communities. The genus Tuber occupies a central position in healthy TPPs. There was a strong correlation between soil physicochemical properties and fungal communities. The genus Tuber showed a positive correlation with Ca, Mg, and total nitrogen, but a negative correlation with total phosphorus and available potassium. This study describes the complex ecological dynamics of soil physicochemical indices and fungal communities occurring during the annual cycle of Tuber indicum, and highlights the succession of core communities in truffle plots, which contribute to better protection of native truffle ecosystems and control of mycorrhizal fungal contamination in artificial truffle plantations in China. IMPORTANCE The spatial and temporal dynamics of soil physicochemical properties and fungal communities associated with four Tuber indicum-producing plots and one non truffle producing plot in four different growing seasons are described. Soil physicochemical properties and fungal communities exhibited considerable seasonal variation. This study examines the complex ecological dynamics of soil physicochemical indices and fungal communities occurring during the annual cycle of Tuber indicum and highlights the succession of core communities in truffle plots, which contributes to better protection of native truffle ecosystems and control of mycorrhizal fungal contamination in artificial truffle plantations in China.}, }
@article {pmid36061686, year = {2022}, author = {Liu, B and Chen, J and Li, Y}, title = {Keystone Microorganisms Regulate the Methanogenic Potential in Coals with Different Coal Ranks.}, journal = {ACS omega}, volume = {7}, number = {34}, pages = {29901-29908}, pmid = {36061686}, issn = {2470-1343}, abstract = {Microorganisms are the core drivers of coal biogeochemistry and are closely related to the formation of coalbed methane. However, it remains poorly understood about the network relationship and stability of microbial communities in coals with different ranks. In this study, a high-throughput sequencing data set was analyzed to understand the microbial co-occurrence network in coals with different ranks including anthracite, medium-volatile bituminous, and high-volatile bituminous. The results showed similar topological properties for the microbial networks among coals with different ranks, but a great difference was found in the microbial composition in different large modules among coals with different ranks, and these three networks had three, four, and four large modules with seven, nine, and nine phyla, respectively. Among these networks, a total of 46 keystone taxa were identified in large modules, and these keystone taxa were different in coals with different ranks. Bacteria dominated the keystone taxa in the microbial network, and these bacterial keystone taxa mainly belonged to phyla Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. Besides, the removal of the key microbial data could reduce the community stability of microbial communities in bituminous coals. A partial least-squares path model further showed that these bacterial keystone taxa indirectly affected methanogenic potential by maintaining the microbial community stability and bacterial diversity. In summary, these results showed that keystone taxa played an important role in determining the community diversity, maintaining the microbial community stability, and controlling the methanogenic potential, which is of great significance for understanding the microbial ecology and the geochemical cycle of coal seams.}, }
@article {pmid35938717, year = {2022}, author = {Okazaki, Y and Nakano, SI and Toyoda, A and Tamaki, H}, title = {Long-Read-Resolved, Ecosystem-Wide Exploration of Nucleotide and Structural Microdiversity of Lake Bacterioplankton Genomes.}, journal = {mSystems}, volume = {7}, number = {4}, pages = {e0043322}, pmid = {35938717}, issn = {2379-5077}, mesh = {*Lakes/microbiology ; Ecosystem ; Nucleotides ; Metagenome ; Bacteria/genetics ; *Bacteriophages/genetics ; }, abstract = {Reconstruction of metagenome-assembled genomes (MAGs) has become a fundamental approach in microbial ecology. However, a MAG is hardly complete and overlooks genomic microdiversity because metagenomic assembly fails to resolve microvariants among closely related genotypes. Aiming at understanding the universal factors that drive or constrain prokaryotic genome diversification, we performed an ecosystem-wide high-resolution metagenomic exploration of microdiversity by combining spatiotemporal (2 depths × 12 months) sampling from a pelagic freshwater system, high-quality MAG reconstruction using long- and short-read metagenomic sequences, and profiling of single nucleotide variants (SNVs) and structural variants (SVs) through mapping of short and long reads to the MAGs, respectively. We reconstructed 575 MAGs, including 29 circular assemblies, providing high-quality reference genomes of freshwater bacterioplankton. Read mapping against these MAGs identified 100 to 101,781 SNVs/Mb and 0 to 305 insertions, 0 to 467 deletions, 0 to 41 duplications, and 0 to 6 inversions for each MAG. Nonsynonymous SNVs were accumulated in genes potentially involved in cell surface structural modification to evade phage recognition. Most (80.2%) deletions overlapped with a gene coding region, and genes of prokaryotic defense systems were most frequently (>8% of the genes) overlapped with a deletion. Some such deletions exhibited a monthly shift in their allele frequency, suggesting a rapid turnover of genotypes in response to phage predation. MAGs with extremely low microdiversity were either rare or opportunistic bloomers, suggesting that population persistency is key to their genomic diversification. The results concluded that prokaryotic genomic diversification is driven primarily by viral load and constrained by a population bottleneck. IMPORTANCE Identifying intraspecies genomic diversity (microdiversity) is crucial to understanding microbial ecology and evolution. However, microdiversity among environmental assemblages is not well investigated, because most microbes are difficult to culture. In this study, we performed cultivation-independent exploration of bacterial genomic microdiversity in a lake ecosystem using a combination of short- and long-read metagenomic analyses. The results revealed the broad spectrum of genomic microdiversity among the diverse bacterial species in the ecosystem, which has been overlooked by conventional approaches. Our ecosystem-wide exploration further allowed comparative analysis among the genomes and genes and revealed factors behind microbial genomic diversification, namely, that diversification is driven primarily by resistance against viral infection and constrained by the population size.}, }
@article {pmid35134909, year = {2022}, author = {Foster-Nyarko, E and Pallen, MJ}, title = {The microbial ecology of Escherichia coli in the vertebrate gut.}, journal = {FEMS microbiology reviews}, volume = {46}, number = {3}, pages = {}, pmid = {35134909}, issn = {1574-6976}, mesh = {Animals ; Bacteria ; *Escherichia coli ; *Escherichia coli Infections/microbiology ; Symbiosis ; Vertebrates ; }, abstract = {Escherichia coli has a rich history as biology's 'rock star', driving advances across many fields. In the wild, E. coli resides innocuously in the gut of humans and animals but is also a versatile pathogen commonly associated with intestinal and extraintestinal infections and antimicrobial resistance-including large foodborne outbreaks such as the one that swept across Europe in 2011, killing 54 individuals and causing approximately 4000 infections and 900 cases of haemolytic uraemic syndrome. Given that most E. coli are harmless gut colonizers, an important ecological question plaguing microbiologists is what makes E. coli an occasionally devastating pathogen? To address this question requires an enhanced understanding of the ecology of the organism as a commensal. Here, we review how our knowledge of the ecology and within-host diversity of this organism in the vertebrate gut has progressed in the 137 years since E. coli was first described. We also review current approaches to the study of within-host bacterial diversity. In closing, we discuss some of the outstanding questions yet to be addressed and prospects for future research.}, }
@article {pmid34989745, year = {2022}, author = {Hua, Q and Han, Y and Zhao, H and Zhang, H and Yan, B and Pei, S and He, X and Li, Y and Meng, X and Chen, L and Zhong, F and Li, D}, title = {Punicalagin alleviates renal injury via the gut-kidney axis in high-fat diet-induced diabetic mice.}, journal = {Food &amp; function}, volume = {13}, number = {2}, pages = {867-879}, doi = {10.1039/d1fo03343c}, pmid = {34989745}, issn = {2042-650X}, mesh = {Animals ; Diabetes Mellitus, Experimental/*complications ; Diabetic Nephropathies/*drug therapy ; *Diet, High-Fat ; Fatty Acids, Volatile/metabolism ; Gastrointestinal Microbiome/*drug effects ; Gene Expression Regulation/drug effects ; Hydrolyzable Tannins/*pharmacology ; Inflammation/metabolism ; Kidney/*metabolism ; Mice ; Mice, Inbred C57BL ; Pomegranate/chemistry ; }, abstract = {Diabetic renal injury was associated with dysbiosis of the gut microbiota and intestinal barrier. Punicalagin (PU) from pomegranates potentially impacts the microbial ecosystem, intestinal barrier, and renal function. Therefore, we hypothesized that PU may improve diabetic renal injury by modulating the gut-kidney axis. The present study evaluated the effect of PU on the gut-kidney axis and kidney function in a diabetic renal injury mouse model induced by a high-fat diet (HFD). Mice were fed a HFD without PU or with at doses of 50 and 100 mg kg[-1] d[-1] for 8 weeks. Targeted metabolomics by GC-MS and 16S rRNA sequencing were implemented to determine short-chain fatty acids (SCFAs) and microbes. Further RNA sequencing analyses were performed to determine which differentially expressed genes were changed by PU. Compared with the DM model group, PU supplementation improved diabetic renal injury, ameliorated kidney architecture and function, and reshaped gut microbial ecology. Additionally, PU reversed HFD-induced gut barrier dysfunction, promoted cecal SCFA concentrations and inhibited serum lipopolysaccharide (LPS) and diamine oxidase (DAO) levels. Moreover, correlation analysis found that cecal SCFAs were significantly negatively correlated with inflammation-related genes in the kidney. The present results indicated that PU, a promising bioactive polyphenol, successfully improved diabetic renal injury, most likely through the gut-kidney axis.}, }
@article {pmid34958387, year = {2022}, author = {Kable, ME and Chin, EL and Storms, D and Lemay, DG and Stephensen, CB}, title = {Tree-Based Analysis of Dietary Diversity Captures Associations Between Fiber Intake and Gut Microbiota Composition in a Healthy US Adult Cohort.}, journal = {The Journal of nutrition}, volume = {152}, number = {3}, pages = {779-788}, doi = {10.1093/jn/nxab430}, pmid = {34958387}, issn = {1541-6100}, mesh = {Adolescent ; Adult ; Aged ; Cross-Sectional Studies ; Diet ; Dietary Fiber/analysis ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; Middle Aged ; RNA, Ribosomal, 16S/analysis/genetics ; Young Adult ; }, abstract = {BACKGROUND: Diet patterns are a significant and modifiable contributing factor to the composition of the human gut microbiota.<br><br>OBJECTIVES: We set out to identify reproducible relationships between diet and gut microbial community composition in a diverse, healthy US adult cohort.<br><br>METHODS: We collected 2 to 3 automated self-administered 24-hour dietary recalls over 10-14 days, together with a single stool sample, from 343 healthy adults in a cross-sectional phenotyping study. This study examined a multi-ethnic cohort balanced for age (18-65 years), sex, and BMI (18.5-45 kg/m2). Dietary data were edited to a tree format according to published methods. The tree structure was annotated with the average total grams of dry weight, fat, protein, carbohydrate, or fiber from each food item reported. The alpha and beta diversity measurements, calculated using the tree structure, were analyzed relative to the microbial community diversity, determined by a Quantitative Insights Into Microbial Ecology (QIIME) 2 analysis of the bacterial 16S ribosomal RNA V4 region, sequenced from stool samples. K-means clustering was used to form groups of individuals consuming similar diets, and gut microbial communities were compared among groups using differential expression analysis for sequence count data.<br><br>RESULTS: The alpha diversity of diet dry weight was significantly correlated with the gut microbial community alpha diversity (r&#xa0;=&#xa0;0.171). The correlation improved when diet was characterized using grams of carbohydrates (r&#xa0;=&#xa0;0.186) or fiber (r&#xa0;=&#xa0;0.213). Bifidobacterium was enriched with diets containing higher levels of total carbohydrate from cooked grains. Lachnospira, was enriched with diet patterns containing high consumption of fiber from fruits excluding berries.<br><br>CONCLUSIONS: The tree structure, annotated with grams of carbohydrate, is a robust analysis method for comparing self-reported diet to the gut microbial community composition. This method identified consumption of fiber from fruit robustly associated with an abundance of pectinolytic bacterial genus, Lachnospira, in the guts of healthy adults. This trial was registered at clinicaltrials.gov as NCT02367287.}, }
@article {pmid37938641, year = {2021}, author = {Röttjers, L and Vandeputte, D and Raes, J and Faust, K}, title = {Null-model-based network comparison reveals core associations.}, journal = {ISME communications}, volume = {1}, number = {1}, pages = {36}, pmid = {37938641}, issn = {2730-6151}, support = {STG/16/006//KU Leuven (Katholieke Universiteit Leuven)/ ; STG/16/006//KU Leuven (Katholieke Universiteit Leuven)/ ; 801747//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 801747//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 30770923//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; 30770923//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; }, abstract = {Microbial network construction and analysis is an important tool in microbial ecology. Such networks are often constructed from statistically inferred associations and may not represent ecological interactions. Hence, microbial association networks are error prone and do not necessarily reflect true community structure. We have developed anuran, a toolbox for investigation of noisy networks with null models. Such models allow researchers to generate data under the null hypothesis that all associations are random, supporting identification of nonrandom patterns in groups of association networks. This toolbox compares multiple networks to identify conserved subsets (core association networks, CANs) and other network properties that are shared across all networks. We apply anuran to a time series of fecal samples from 20 women to demonstrate the existence of CANs in a subset of the sampled individuals. Moreover, we use data from the Global Sponge Project to demonstrate that orders of sponges have a larger CAN than expected at random. In conclusion, this toolbox is a resource for investigators wanting to compare microbial networks across conditions, time series, gradients, or hosts.}, }
@article {pmid33952552, year = {2021}, author = {Tang, H and Bohannon, L and Lew, M and Jensen, D and Jung, SH and Zhao, A and Sung, AD and Wischmeyer, PE}, title = {Randomised, double-blind, placebo-controlled trial of Probiotics To Eliminate COVID-19 Transmission in Exposed Household Contacts (PROTECT-EHC): a clinical trial protocol.}, journal = {BMJ open}, volume = {11}, number = {5}, pages = {e047069}, pmid = {33952552}, issn = {2044-6055}, support = {R03 AG064260/AG/NIA NIH HHS/United States ; }, mesh = {*COVID-19 ; Double-Blind Method ; Humans ; Pandemics ; *Probiotics ; RNA, Ribosomal, 16S/genetics ; Randomized Controlled Trials as Topic ; SARS-CoV-2 ; Treatment Outcome ; }, abstract = {INTRODUCTION: The COVID-19 pandemic has proven to be an unprecedented challenge to worldwide health, and strategies to mitigate the spread and severity of COVID-19 infection are urgently needed. Emerging evidence suggests that the composition of the gut microbiome and modification of microbial ecology via probiotics can affect susceptibility to a wide range of infections, including respiratory tract infections. In this study, we aim to evaluate the effects of the probiotic Lactobacillus rhamnosus GG (LGG) versus placebo on COVID-19 infection status and the gut microbiome in subjects with a household contact who has tested positive for COVID-19.<br><br>METHODS AND ANALYSIS: In this double-blinded, randomised, placebo-controlled trial, we will randomise 1132 subjects having a household contact who has recently (&#x2264;7&#x2009;days) tested positive for COVID-19 to daily oral LGG or placebo for 28 days. We hypothesise that taking LGG as a probiotic will protect against COVID-19 infection and reduce the severity of disease in those who become infected (primary endpoint: decreased symptoms), and will be associated with beneficial changes in the composition of the gut microbiome. Stool samples and nasal swabs will be collected to evaluate the microbiome by 16S rRNA sequencing and the presence of SARS-CoV-2 by PCR, respectively. We will also conduct multivariate analysis of demographic, behavioural, temporal, and other variables that may predict development of symptoms and other outcomes.<br><br>ETHICS AND DISSEMINATION: This trial is conducted under a Food and Drug Administration Investigational New Drug for LGG, has received ethics approval by the institutional review board of Duke University and enrolment has begun. We plan to disseminate the results in peer-reviewed journals and at national and international conferences.<br><br>TRIAL REGISTRATION NUMBER: NCT04399252.}, }
@article {pmid33653941, year = {2021}, author = {Belk, AD and Duarte, T and Quinn, C and Coil, DA and Belk, KE and Eisen, JA and Quinn, JC and Martin, JN and Yang, X and Metcalf, JL}, title = {Air versus Water Chilling of Chicken: a Pilot Study of Quality, Shelf-Life, Microbial Ecology, and Economics.}, journal = {mSystems}, volume = {6}, number = {2}, pages = {}, pmid = {33653941}, issn = {2379-5077}, abstract = {The United States' large-scale poultry meat industry is energy and water intensive, and opportunities may exist to improve sustainability during the broiler chilling process. By USDA regulation, after harvest the internal temperature of the chicken must be reduced to 40°F or less within 16 h to inhibit bacterial growth that would otherwise compromise the safety of the product. This step is accomplished most commonly by water immersion chilling in the United States, while air chilling methods dominate other global markets. A comprehensive understanding of the differences between these chilling methods is lacking. Therefore, we assessed the meat quality, shelf-life, microbial ecology, and techno-economic impacts of chilling methods on chicken broilers in a university meat laboratory setting. We discovered that air chilling methods resulted in superior chicken odor and shelf-life, especially prior to 14 days of dark storage. Moreover, we demonstrated that air chilling resulted in a more diverse microbiome that we hypothesize may delay the dominance of the spoilage organism Pseudomonas Finally, a techno-economic analysis highlighted potential economic advantages to air chilling compared to water chilling in facility locations where water costs are a more significant factor than energy costs.IMPORTANCE As the poultry industry works to become more sustainable and to reduce the volume of food waste, it is critical to consider points in the processing system that can be altered to make the process more efficient. In this study, we demonstrate that the method used during chilling (air versus water chilling) influences the final product microbial community, quality, and physiochemistry. Notably, the use of air chilling appears to delay the bloom of Pseudomonas spp. that are the primary spoilers in packaged meat products. By using air chilling to reduce carcass temperatures instead of water chilling, producers may extend the time until spoilage of the products and, depending on the cost of water in the area, may have economic and sustainability advantages. As a next step, a similar experiment should be done in an industrial setting to confirm these results generated in a small-scale university lab facility.}, }
@article {pmid32546676, year = {2020}, author = {Gulino, K and Rahman, J and Badri, M and Morton, J and Bonneau, R and Ghedin, E}, title = {Initial Mapping of the New York City Wastewater Virome.}, journal = {mSystems}, volume = {5}, number = {3}, pages = {}, pmid = {32546676}, issn = {2379-5077}, abstract = {Bacteriophages are abundant members of all microbiomes studied to date, influencing microbial communities through interactions with their bacterial hosts. Despite their functional importance and ubiquity, phages have been underexplored in urban environments compared to their bacterial counterparts. We profiled the viral communities in New York City (NYC) wastewater using metagenomic data collected in November 2014 from 14 wastewater treatment plants. We show that phages accounted for the largest viral component of the sewage samples and that specific virus communities were associated with local environmental conditions within boroughs. The vast majority of the virus sequences had no homology matches in public databases, forming an average of 1,700 unique virus clusters (putative genera). These new clusters contribute to elucidating the overwhelming proportion of data that frequently goes unidentified in viral metagenomic studies. We assigned potential hosts to these phages, which appear to infect a wide range of bacterial genera, often outside their presumed host. We determined that infection networks form a modular-nested pattern, indicating that phages include a range of host specificities, from generalists to specialists, with most interactions organized into distinct groups. We identified genes in viral contigs involved in carbon and sulfur cycling, suggesting functional importance of viruses in circulating pathways and gene functions in the wastewater environment. In addition, we identified virophage genes as well as a nearly complete novel virophage genome. These findings provide an understanding of phage abundance and diversity in NYC wastewater, previously uncharacterized, and further examine geographic patterns of phage-host association in urban environments.IMPORTANCE Wastewater is a rich source of microbial life and contains bacteria, viruses, and other microbes found in human waste as well as environmental runoff sources. As part of an effort to characterize the New York City wastewater metagenome, we profiled the viral community of sewage samples across all five boroughs of NYC and found that local sampling sites have unique sets of viruses. We focused on bacteriophages, or viruses of bacteria, to understand how they may influence the microbial ecology of this system. We identified several new clusters of phages and successfully associated them with bacterial hosts, providing insight into virus-host interactions in urban wastewater. This study provides a first look into the viral communities present across the wastewater system in NYC and points to their functional importance in this environment.}, }
@article {pmid32031212, year = {2020}, author = {Fenske, GJ and Ghimire, S and Antony, L and Christopher-Hennings, J and Scaria, J}, title = {Integration of culture-dependent and independent methods provides a more coherent picture of the pig gut microbiome.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {3}, pages = {}, doi = {10.1093/femsec/fiaa022}, pmid = {32031212}, issn = {1574-6941}, mesh = {Animals ; Bacteroidetes/genetics ; *Gastrointestinal Microbiome ; Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Swine ; }, abstract = {Bacterial communities resident in the hindgut of pigs, have profound impacts on health and disease. Investigations into the pig microbiome have utilized either culture-dependent, or far more commonly, culture-independent techniques using next generation sequencing. We contend that a combination of both approaches generates a more coherent view of microbiome composition. In this study, we surveyed the microbiome of Tamworth breed and feral pigs through the integration high throughput culturing and shotgun metagenomics. A single culture medium was used for culturing. Selective screens were added to the media to increase culture diversity. In total, 46 distinct bacterial species were isolated from the Tamworth and feral samples. Selective screens successfully shifted the diversity of bacteria on agar plates. Tamworth pigs are highly dominated by Bacteroidetes primarily composed of the genus Prevotella whereas feral samples were more diverse with almost equal proportions of Firmicutes and Bacteroidetes. The combination of metagenomics and culture techniques facilitated a greater retrieval of annotated genes than either method alone. The single medium based pig microbiota library we report is a resource to better understand pig gut microbial ecology and function. It allows for assemblage of defined bacterial communities for studies in bioreactors or germfree animal models.}, }
@article {pmid31506516, year = {2019}, author = {Bridier, A and Le Grandois, P and Moreau, MH and Prénom, C and Le Roux, A and Feurer, C and Soumet, C}, title = {Impact of cleaning and disinfection procedures on microbial ecology and Salmonella antimicrobial resistance in a pig slaughterhouse.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {12947}, pmid = {31506516}, issn = {2045-2322}, mesh = {Abattoirs ; Animals ; Anti-Bacterial Agents/*pharmacology ; Disinfection/*methods ; *Drug Resistance, Bacterial ; Microbial Sensitivity Tests ; Salmonella/*drug effects ; Salmonella Infections, Animal/*drug therapy/epidemiology/microbiology ; Swine ; Swine Diseases/epidemiology/microbiology/*prevention &amp; control ; }, abstract = {To guarantee food safety, a better deciphering of ecology and adaptation strategies of bacterial pathogens such as Salmonella in food environments is crucial. The role of food processing conditions such as cleaning and disinfection procedures on antimicrobial resistance emergence should especially be investigated. In this work, the prevalence and antimicrobial resistance of Salmonella and the microbial ecology of associated surfaces communities were investigated in a pig slaughterhouse before and after cleaning and disinfection procedures. Salmonella were detected in 67% of samples and isolates characterization revealed the presence of 15 PFGE-patterns belonging to five serotypes: S.4,5,12:i:-, Rissen, Typhimurium, Infantis and Derby. Resistance to ampicillin, sulfamethoxazole, tetracycline and/or chloramphenicol was detected depending on serotypes. 16S rRNA-based bacterial diversity analyses showed that Salmonella surface associated communities were highly dominated by the Moraxellaceae family with a clear site-specific composition suggesting a persistent colonization of the pig slaughterhouse. Cleaning and disinfection procedures did not lead to a modification of Salmonella susceptibility to antimicrobials in this short-term study but they tended to significantly reduce bacterial diversity and favored some genera such as Rothia and Psychrobacter. Such data participate to the construction of a comprehensive view of Salmonella ecology and antimicrobial resistance emergence in food environments in relation with cleaning and disinfection procedures.}, }
@article {pmid29134738, year = {2018}, author = {Xiao, X and Liang, Y and Zhou, S and Zhuang, S and Sun, B}, title = {Fungal community reveals less dispersal limitation and potentially more connected network than that of bacteria in bamboo forest soils.}, journal = {Molecular ecology}, volume = {27}, number = {2}, pages = {550-563}, doi = {10.1111/mec.14428}, pmid = {29134738}, issn = {1365-294X}, mesh = {Biodiversity ; Carbon/metabolism ; China ; Forests ; Fungi/*growth &amp; development ; Microbiota/*genetics ; Plants/genetics/microbiology ; Sasa/genetics/*microbiology ; *Soil Microbiology ; }, abstract = {A central aim of this microbial ecology research was to investigate the mechanisms shaping the assembly of soil microbial communities. Despite the importance of bacterial and fungal mediation of carbon cycling in forest ecosystems, knowledge concerning their distribution patterns and underlying mechanisms remains insufficient. Here, soils were sampled from six bamboo forests across the main planting area of Moso bamboo in southern China. The bacterial and fungal diversities were assessed by sequencing 16S rRNA and ITS gene amplicons, respectively, with an Illumina MiSeq. Based on structural equation modelling, dispersal limitation had strongest impact on bacterial beta diversity, while the mean annual precipitation had a smaller impact by directly or indirectly mediating the soil organic carbon density. However, only the mean annual temperature and precipitation played direct roles in fungal beta diversity. Moreover, the co-occurrence network analyses revealed a possibly much higher network connectivity in the fungal network than in the bacteria. With less dispersal limitation, stronger environmental selection and a potentially more connected network, the fungal community had more important roles in the soil carbon metabolisms in bamboo forests. Fungal beta diversity and the clustering coefficient explained approximately 14.4% and 6.1% of the variation in the carbon metabolic profiles among sites, respectively, but that of bacteria only explained approximately 1.7% and 1.8%, respectively. This study explored soil microbial spatial patterns along with the underlying mechanisms of dispersal limitation, selection and connectivity of ecological networks, thus providing novel insights into the study of the distinct functional traits of different microbial taxa.}, }
@article {pmid28680053, year = {2017}, author = {Cheng, G and Sun, M and Lu, J and Ge, X and Zhang, H and Xu, X and Lou, L and Lin, Q}, title = {Role of biochar in biodegradation of nonylphenol in sediment: Increasing microbial activity versus decreasing bioavailability.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {4726}, pmid = {28680053}, issn = {2045-2322}, mesh = {Bacteria/drug effects ; Biodegradation, Environmental ; Biological Availability ; Charcoal/*chemistry ; Geologic Sediments/chemistry/*microbiology ; Oryza/chemistry ; Phenols/*chemistry/toxicity ; Soil Pollutants/chemistry ; }, abstract = {The observed strong sorption of hydrophobic organic contaminants (HOCs) to biochar presents potential implications for HOCs bioavailability and bioaccessibility in sediments, while biochar could impact sediment microbial ecology. However, the comprehensive study on the effects of biochar on HOC biodegradation coupled with bioavailability and microbial ecology are rarely documented. In this paper, the effects of biochar on the biodegradation of nonylphenol (NP) were investigated using 3 different NP concentrations (20, 50 and 500 mg/Kg) in sediments amended with different percentage of rice straw biochar (RC). Results showed that the influence of RC on NP biodegradation varied with different NP concentrations. At low NP concentrations, RC suppressed NP biodegradation by reducing NP bioavailability, while at high NP concentrations, moderate RC addition promoted biodegradation by reducing toxicity of NP to microbes. The effects of NP on microbial community structures were significant (P < 0.01), but those of RC were not significant (P > 0.05). The RC affected microorganisms through altering NP toxicity, microbial quantity and activity, but not microbial community structures. This study indicated that there could be an optimal biochar percentage in biochar-sediment systems at different HOC concentrations, which strengthened HOC biodegradation process and accelerated biodegradation rate, forming adsorption-biodegradation coupled bioremediation.}, }
@article {pmid27144092, year = {2016}, author = {Marques, C and Meireles, M and Norberto, S and Leite, J and Freitas, J and Pestana, D and Faria, A and Calhau, C}, title = {High-fat diet-induced obesity Rat model: a comparison between Wistar and Sprague-Dawley Rat.}, journal = {Adipocyte}, volume = {5}, number = {1}, pages = {11-21}, pmid = {27144092}, issn = {2162-3945}, abstract = {In the past decades, obesity and associated metabolic complications have reached epidemic proportions. For the study of these pathologies, a number of animal models have been developed. However, a direct comparison between Wistar and Sprague-Dawley (SD) Rat as models of high-fat (HF) diet-induced obesity has not been adequately evaluated so far. Wistar and SD rats were assigned for 2 experimental groups for 17 weeks: standard (St) and high-fat (HF) diet groups. To assess some of the features of the metabolic syndrome, oral glucose tolerance tests, systolic blood pressure measurements and blood biochemical analysis were performed throughout the study. The gut microbiota composition of the animals of each group was evaluated at the end of the study by real-time PCR. HF diet increased weight gain, body fat mass, mesenteric adipocyte's size, adiponectin and leptin plasma levels and decreased oral glucose tolerance in both Wistar and SD rats. However, the majority of these effects were more pronounced or earlier detected in Wistar rats. The gut microbiota of SD rats was less abundant in Bacteroides and Prevotella but richer in Bifidobacterium and Lactobacillus comparatively to the gut microbiota of Wistar rats. Nevertheless, the modulation of the gut microbiota by HF diet was similar in both strains, except for Clostridium leptum that was only reduced in Wistar rats fed with HF diet. In conclusion, both Wistar and SD Rat can be used as models of HF diet-induced obesity although the metabolic effects caused by HF diet seemed to be more pronounced in Wistar Rat. Differences in the gut microbial ecology may account for the worsened metabolic scenario observed in Wistar Rat.}, }
@article {pmid25567040, year = {2015}, author = {Huang, YJ and Boushey, HA}, title = {The microbiome in asthma.}, journal = {The Journal of allergy and clinical immunology}, volume = {135}, number = {1}, pages = {25-30}, pmid = {25567040}, issn = {1097-6825}, support = {K23 HL105572/HL/NHLBI NIH HHS/United States ; }, mesh = {Allergens ; Animals ; Asthma/*microbiology ; Environmental Exposure ; Gastrointestinal Tract/*microbiology ; Humans ; *Microbiota ; Respiratory System/microbiology ; Respiratory Tract Infections/microbiology ; Virus Diseases/microbiology ; }, abstract = {The application of recently developed sensitive, specific, culture-independent tools for identification of microbes is transforming concepts of microbial ecology, including concepts of the relationships between the vast complex populations of microbes associated with ourselves and with states of health and disease. Although most work initially focused on the community of microbes (microbiome) in the gastrointestinal tract and its relationship to gastrointestinal disease, interest has expanded to include study of the relationships of the airway microbiome to asthma and its phenotypes and to the relationships between the gastrointestinal microbiome, development of immune function, and predisposition to allergic sensitization and asthma. Here we provide our perspective on the findings of studies of differences in the airway microbiome between asthmatic patients and healthy subjects and of studies of relationships between environmental microbiota, gut microbiota, immune function, and asthma development. In addition, we provide our perspective on how these findings suggest the broad outline of a rationale for approaches involving directed manipulation of the gut and airway microbiome for the treatment and prevention of allergic asthma.}, }
@article {pmid25033448, year = {2014}, author = {Baron, JL and Vikram, A and Duda, S and Stout, JE and Bibby, K}, title = {Shift in the microbial ecology of a hospital hot water system following the introduction of an on-site monochloramine disinfection system.}, journal = {PloS one}, volume = {9}, number = {7}, pages = {e102679}, pmid = {25033448}, issn = {1932-6203}, mesh = {Actinobacteria/genetics/growth &amp; development ; Base Sequence ; Biofilms/drug effects/growth &amp; development ; Chloramines/*pharmacology ; Cyanobacteria/genetics/growth &amp; development ; DNA, Bacterial/genetics ; Disinfectants/pharmacology ; Disinfection/*methods ; Drinking Water/*microbiology ; *Hospital Distribution Systems ; Proteobacteria/genetics/growth &amp; development ; RNA, Ribosomal, 16S/genetics ; Sanitary Engineering ; Sequence Analysis, DNA ; Tertiary Care Centers ; Water Microbiology ; Water Purification/*methods ; Water Quality ; }, abstract = {Drinking water distribution systems, including premise plumbing, contain a diverse microbiological community that may include opportunistic pathogens. On-site supplemental disinfection systems have been proposed as a control method for opportunistic pathogens in premise plumbing. The majority of on-site disinfection systems to date have been installed in hospitals due to the high concentration of opportunistic pathogen susceptible occupants. The installation of on-site supplemental disinfection systems in hospitals allows for evaluation of the impact of on-site disinfection systems on drinking water system microbial ecology prior to widespread application. This study evaluated the impact of supplemental monochloramine on the microbial ecology of a hospital's hot water system. Samples were taken three months and immediately prior to monochloramine treatment and monthly for the first six months of treatment, and all samples were subjected to high throughput Illumina 16S rRNA region sequencing. The microbial community composition of monochloramine treated samples was dramatically different than the baseline months. There was an immediate shift towards decreased relative abundance of Betaproteobacteria, and increased relative abundance of Firmicutes, Alphaproteobacteria, Gammaproteobacteria, Cyanobacteria and Actinobacteria. Following treatment, microbial populations grouped by sampling location rather than sampling time. Over the course of treatment the relative abundance of certain genera containing opportunistic pathogens and genera containing denitrifying bacteria increased. The results demonstrate the driving influence of supplemental disinfection on premise plumbing microbial ecology and suggest the value of further investigation into the overall effects of premise plumbing disinfection strategies on microbial ecology and not solely specific target microorganisms.}, }
@article {pmid24704907, year = {2014}, author = {Brooks, JP and Adeli, A and McLaughlin, MR}, title = {Microbial ecology, bacterial pathogens, and antibiotic resistant genes in swine manure wastewater as influenced by three swine management systems.}, journal = {Water research}, volume = {57}, number = {}, pages = {96-103}, doi = {10.1016/j.watres.2014.03.017}, pmid = {24704907}, issn = {1879-2448}, mesh = {Animal Husbandry/*methods ; Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/*genetics/*isolation &amp; purification ; Bacterial Proteins/genetics/metabolism ; Drug Resistance, Bacterial/*genetics ; Manure/*microbiology ; Methicillin-Resistant Staphylococcus aureus/drug effects/genetics/isolation &amp; purification ; *Microbiota ; RNA, Ribosomal, 16S/genetics/metabolism ; Real-Time Polymerase Chain Reaction ; Southeastern United States ; Sus scrofa ; Wastewater/*microbiology ; }, abstract = {The environmental influence of farm management in concentrated animal feeding operations (CAFO) can yield vast changes to the microbial biota and ecological structure of both the pig and waste manure lagoon wastewater. While some of these changes may not be negative, it is possible that CAFOs can enrich antibiotic resistant bacteria or pathogens based on farm type, thereby influencing the impact imparted by the land application of its respective wastewater. The purpose of this study was to measure the microbial constituents of swine-sow, -nursery, and -finisher farm manure lagoon wastewater and determine the changes induced by farm management. A total of 37 farms were visited in the Mid-South USA and analyzed for the genes 16S rRNA, spaQ (Salmonella spp.), Camp-16S (Campylobacter spp.), tetA, tetB, ermF, ermA, mecA, and intI using quantitative PCR. Additionally, 16S rRNA sequence libraries were created. Overall, it appeared that finisher farms were significantly different from nursery and sow farms in nearly all genes measured and in 16S rRNA clone libraries. Nearly all antibiotic resistance genes were detected in all farms. Interestingly, the mecA resistance gene (e.g. methicillin resistant Staphylococcus aureus) was below detection limits on most farms, and decreased as the pigs aged. Finisher farms generally had fewer antibiotic resistance genes, which corroborated previous phenotypic data; additionally, finisher farms produced a less diverse 16S rRNA sequence library. Comparisons of Camp-16S and spaQ GU (genomic unit) values to previous culture data demonstrated ratios from 10 to 10,000:1 depending on farm type, indicating viable but not cultivatable bacteria were dominant. The current study indicated that swine farm management schemes positively and negatively affect microbial and antibiotic resistant populations in CAFO wastewater which has future "downstream" implications from both an environmental and public health perspective.}, }
@article {pmid24296350, year = {2013}, author = {Hannigan, GD and Grice, EA}, title = {Microbial ecology of the skin in the era of metagenomics and molecular microbiology.}, journal = {Cold Spring Harbor perspectives in medicine}, volume = {3}, number = {12}, pages = {a015362}, pmid = {24296350}, issn = {2157-1422}, support = {P30 AR057217/AR/NIAMS NIH HHS/United States ; R00 AR060873/AR/NIAMS NIH HHS/United States ; AR060873/AR/NIAMS NIH HHS/United States ; AR057217/AR/NIAMS NIH HHS/United States ; }, mesh = {Alphapapillomavirus/physiology ; Biodiversity ; Fungi/physiology ; Humans ; Malassezia/physiology ; Metagenomics/trends ; Microbiology/trends ; Microbiota/physiology ; Skin/*microbiology ; Skin Diseases, Infectious/diagnosis/*microbiology ; }, abstract = {The skin is the primary physical barrier between the body and the external environment and is also a substrate for the colonization of numerous microbes. Previously, dermatological microbiology research was dominated by culture-based techniques, but significant advances in genomic technologies have enabled the development of less-biased, culture-independent approaches to characterize skin microbial communities. These molecular microbiology approaches illustrate the great diversity of microbiota colonizing the skin and highlight unique features such as site specificity, temporal dynamics, and interpersonal variation. Disruptions in skin commensal microbiota are associated with the progression of many dermatological diseases. A greater understanding of how skin microbes interact with each other and with their host, and how we can therapeutically manipulate those interactions, will provide powerful tools for treating and preventing dermatological disease.}, }
@article {pmid23736549, year = {2013}, author = {Zhang, N and Liu, W and Yang, H and Yu, X and Gutknecht, JL and Zhang, Z and Wan, S and Ma, K}, title = {Soil microbial responses to warming and increased precipitation and their implications for ecosystem C cycling.}, journal = {Oecologia}, volume = {173}, number = {3}, pages = {1125-1142}, pmid = {23736549}, issn = {1432-1939}, mesh = {Acclimatization/*physiology ; Analysis of Variance ; Bacteria/metabolism ; Carbon Cycle/*physiology ; China ; *Ecosystem ; *Global Warming ; *Rain ; *Soil Microbiology ; }, abstract = {A better understanding of soil microbial ecology is critical to gaining an understanding of terrestrial carbon (C) cycle-climate change feedbacks. However, current knowledge limits our ability to predict microbial community dynamics in the face of multiple global change drivers and their implications for respiratory loss of soil carbon. Whether microorganisms will acclimate to climate warming and ameliorate predicted respiratory C losses is still debated. It also remains unclear how precipitation, another important climate change driver, will interact with warming to affect microorganisms and their regulation of respiratory C loss. We explore the dynamics of microorganisms and their contributions to respiratory C loss using a 4-year (2006-2009) field experiment in a semi-arid grassland with increased temperature and precipitation in a full factorial design. We found no response of mass-specific (per unit microbial biomass C) heterotrophic respiration to warming, suggesting that respiratory C loss is directly from microbial growth rather than total physiological respiratory responses to warming. Increased precipitation did stimulate both microbial biomass and mass-specific respiration, both of which make large contributions to respiratory loss of soil carbon. Taken together, these results suggest that, in semi-arid grasslands, soil moisture and related substrate availability may inhibit physiological respiratory responses to warming (where soil moisture was significantly lower), while they are not inhibited under elevated precipitation. Although we found no total physiological response to warming, warming increased bacterial C utilization (measured by BIOLOG EcoPlates) and increased bacterial oxidation of carbohydrates and phenols. Non-metric multidimensional scaling analysis as well as ANOVA testing showed that warming or increased precipitation did not change microbial community structure, which could suggest that microbial communities in semi-arid grasslands are already adapted to fluctuating climatic conditions. In summary, our results support the idea that microbial responses to climate change are multifaceted and, even with no large shifts in community structure, microbial mediation of soil carbon loss could still occur under future climate scenarios.}, }
@article {pmid1345176, year = {1992}, author = {Molin, S}, title = {Designing microbes for release into the environment.}, journal = {Science progress}, volume = {76}, number = {300 Pt 2}, pages = {139-148}, pmid = {1345176}, issn = {0036-8504}, mesh = {Bacteria/*genetics ; Containment of Biohazards ; Ecology ; *Genetic Engineering ; }, abstract = {After 20 years in which gene technology has become an important part of modern biotechnology we have seen very beneficial applications of the new techniques in the pharmaceutical industry. We are now entering a second phase involving the deliberate release of genetically engineered organisms into the environment. This next step causes concern because of a low level of predictability of their possible effects. While the risk assessment of microbial release is far from easy, the strain designers also face problems concerning optimization of performance of the organisms. The two groups of actors in this new development--the risk assessors and the strain designers--need the same platform of understanding from the field of microbial ecology, and a number of specific areas which may now be approached by modern technology deserve particular attention. An increased understanding of the activities of microbes in the environment will also allow construction of more predictable, and therefore safer, strains. Biological containment and molecular microbial ecology are two sides of the same coin in the context of release of genetically engineered microorganisms.}, }
@article {pmid40822855, year = {2025}, author = {Roman, FA and Byrne, T and Martin, RL and Mena-Aguilar, D and Smeltz, RE and Finkelstein, R and Pruden, A and Edwards, MA}, title = {Retrospective Analysis of Drinking Water Microcosm Microbiomes Reveals an Apparent Antagonistic Relationship between and.}, journal = {Environmental science &amp; technology letters}, volume = {12}, number = {8}, pages = {990-996}, doi = {10.1021/acs.estlett.5c00590}, pmid = {40822855}, issn = {2328-8930}, abstract = {(Lp) can sometimes establish in drinking water microbial communities and infect individuals inhaling contaminated aerosols. The premise plumbing portion of the drinking water distribution system is often especially vulnerable to Lp growth. Innovative approaches to intentionally manipulate the microbial ecology to control Lp have been proposed but remain elusive. Here, we retrospectively analyzed 16S rRNA gene amplicon sequences and droplet digital PCR data in samples derived from prior drinking water studies, wherein some inexplicable stochastic variations in the Lp occurrence were observed in replicate microcosms. We discovered an apparent antagonistic relationship between and . This relationship was noted across three water sources (Flint, Detroit, and Blacksburg) and was at least partially mediated by the presence of copper, through either copper pipes or a dosed range of 0-2000 μg/L total copper. The observations of this study, which was conducted under realistic drinking water conditions harboring mixed microbial communities, are consistent with recent pure culture studies reporting that amoebic uptake may be inhibited when are established as amoebal endosymbionts. The findings may help explain the apparent stochastic behavior of Lp in field and research settings and may open a door to new engineered ecological control strategies for Lp.}, }
@article {pmid40818553, year = {2025}, author = {Galinytė, D and Aroffu, M and Manconi, M and Žilius, M and Rysevaitė-Kyguolienė, K and Karosienė, J and Koreivienė, J and Briedis, V and Pauža, DH and Savickas, A and Ferrer, EE and Manca, ML and Savickienė, N}, title = {Cyano-phycocyanin loaded enriched transfersomes for enhanced topical skin delivery and antioxidant protection.}, journal = {International journal of pharmaceutics}, volume = {}, number = {}, pages = {126079}, doi = {10.1016/j.ijpharm.2025.126079}, pmid = {40818553}, issn = {1873-3476}, abstract = {This study aimed to develop and evaluate cyano-phycocyanin (C-PC)-loaded enriched transfersomes for topical application, improved skin delivery, and antioxidant protection. The main objective was to overcome the limitations associated with C-PC's instability and poor skin permeability due to its high molecular weight and hydrophilicity. Six formulations were prepared using an organic solvent-free two-step method: glycerol-enriched transfersomes (Gly-transfersomes),glycerol and cholesterol-enriched transfersomes (Gly-chol-transfersomes),hyaluronate-enriched transfersomes (Hyal-transfersomes),hyaluronate and cholesterol-enriched transfersomes (Hyal-chol-transfersomes),glycerol and hyaluronate-enriched transfersomes (Hyal-gly-transfersomes), anda combination of all three (Hyal-gly-chol-transfersomes). Empty vesicles were prepared via direct sonication, then C-PC was gently loaded using mild sonication in a temperature-controlled ultrasonic bath. All formulations demonstrated properties suitable for skin delivery, with mean diameters <115 nm, polydispersity indexes <0.2, and zeta potential below -30 mV. Cryo- transmission electron microscopy confirmed spherical, unilamellar or oligolamellar morphology. Gly- and Gly-chol-transfersomes exhibited the highest encapsulation efficiency (∼52 %) and remained stable for up to 8 months at 4 °C. Antioxidant activity of C-PC (∼23-27 μmol TE/g of dry C-PC) was confirmed via DPPH assay. Biological tests on HaCaT cells exposed to H2O2-induced oxidative stress showed ∼80 % cell viability after treatment with C-PC formulations, compared to ∼60 % in untreated cells, indicating cytoprotective activity. Ex vivo skin penetration studies revealed significantly higher C-PC accumulation in the epidermis especially for Gly- and Gly-chol-transfersomes versus aqueous C-PC. These findings confirm the potential of enriched transfersomes as effective carriers to improve the skin delivery and bioactivity of C-PC in antioxidant skin care formulations.}, }
@article {pmid40815942, year = {2025}, author = {McDonagh, F and Ryan, K and Kovářová, A and Tumeo, A and Clarke, C and Cormican, M and Miliotis, G}, title = {Identification of blaESBL- and blaCARBA- Positive Multi-Drug Resistant Mixta calida Isolates from Distinct Human Hosts.}, journal = {International journal of medical microbiology : IJMM}, volume = {320}, number = {}, pages = {151669}, doi = {10.1016/j.ijmm.2025.151669}, pmid = {40815942}, issn = {1618-0607}, abstract = {OBJECTIVE: This study aimed to investigate the identification of blaCARBA-positive multidrug-resistant Mixta calida isolates from human hosts and to elucidate their genomic determinants in a species-wide context.<br><br>METHODS: Two carbapenemase-producing M. calida isolates were received by the Galway Reference Laboratory Service in Ireland between June and July 2024. One isolate originated from a sputum sample, while the other was recovered from a routine screening rectal swab. Initial identification was performed using MALDI-ToF mass spectrometry, with genomic confirmation via 16S rRNA sequencing, digital DNA-DNA hybridization, and Average Nucleotide Identity analysis. Antimicrobial susceptibility testing was conducted using a MicroScan panel, following EUCAST and CLSI guidelines. Whole-genome sequencing, plasmid replicon typing, and antibiotic-resistance-gene and virulence-factor profiling were employed. Comparative analysis included all additional canonical M. calida genomes from NCBI database.<br><br>RESULTS: Both Irish isolates were taxonomically placed as M. calida and exhibited multidrug resistance against penicillins, cephalosporins, monobactams and ertapenem. The acquired genes blaKPC-3, blaOXA-9, and blaTEM-122 were detected on plasmid-borne contigs, indicating horizontal acquisition. Seven plasmid replicon types were shared between the two isolates. Both plasmid replicons and acquired antimicrobial-resistance-genes (ARGs) were seldomly identified across the species. Phylogenetic inference based on core genome analysis identified a monophyletic cluster, suggesting a single introductory event.<br><br>CONCLUSION: This study documents a dual occurrence of blaCARBA-positive M. calida in human colonisation and infection. The findings highlight the potential for horizontal-gene-transfer to drive the emergence of multidrug-resistant profiles in the species, underscoring the need for enhanced surveillance, diagnostic precision, and targeted infection control strategies to mitigate public health risks.<br><br>IMPACT STATEMENT: This study reports blaESBL and blaCARBA-positive multi-drug resistant Mixta calida isolates from distinct human hosts. Genomic analysis revealed the co-occurrence of plasmid-borne resistance genes blaKPC-3, blaOXA-9, and blaTEM-122. Species-wide phylogenetic analysis grouped the two isolates into a monophyletic cluster, suggesting a single introductory event.}, }
@article {pmid40815475, year = {2025}, author = {Kondrotaite, Z and Petersen, J and Singleton, C and Peces, M and Petriglieri, F and Jensen, TBN and Sereika, M and Daugberg, AOH and Wagner, M and Dueholm, MKD and Nielsen, PH}, title = {Ecophysiology and niche differentiation of three genera of polyphosphate-accumulating bacteria in a full-scale wastewater treatment plant.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0032225}, doi = {10.1128/msystems.00322-25}, pmid = {40815475}, issn = {2379-5077}, abstract = {Polyphosphate-accumulating organisms (PAOs) are the main bacteria responsible for phosphorus removal and recovery in full-scale wastewater treatment plants (WWTPs). They encompass members of the genera Candidatus Accumulibacter, Azonexus (formerly Dechloromonas), and Candidatus Phosphoribacter (formerly Tetrasphaera), with most studies focusing on Ca. Accumulibacter, primarily using lab-scale enrichment cultures. Although members from the three genera often co-exist in full-scale WWTPs, the metabolic capabilities and traits that determine the niche differentiation of the specific species are still unknown. We retrieved 214 high-quality metagenome-assembled genomes from a full-scale plant with phosphorus removal and examined the polyphosphate-related metabolic pathways using genome-resolved metatranscriptomics in the different process tanks in situ and by using short-term incubations ex situ. We observed the co-existence of nine uncultured PAO species from the three genera with clear niche differentiation in the utilization of different carbon sources and involvement in the denitrification process. Additionally, we observed several physiological differences among species of the same genus, indicating variations in niche specialization. This suggests that biological P removal and other processes in full-scale WWTPs are carried out by a complex and diverse PAO community that together ensures stable plant performance.IMPORTANCEThe current understanding of the ecology and physiology of polyphosphate-accumulating organisms (PAOs) is mostly based on Candidatus Accumulibacter, primarily studied in enriched lab-scale studies. Recent taxonomic reclassification revealed that the most studied Ca. Accumulibacter species are either not present or present in low abundance in full-scale wastewater treatment plants (WWTPs). This raises concerns that knowledge from lab-scale studies may not apply to species in full-scale plants. Additionally, the indication of a distinct PAO physiology in Candidatus Phosphoribacter compared to Ca. Accumulibacter and the other abundant PAO Ca. Azonexus poses further questions about the accuracy of the current PAO model. Here, we show that in full-scale plant species from Ca. Accumulibacter, Ca. Azonexus, and Ca. Phosphoribacter always co-exist, and they have distinct niche separations in terms of carbon source utilization and the use of electron acceptors. This co-existence and metabolic diversity indicate that a complex microbial community is crucial for efficient phosphorus removal in full-scale WWTPs.}, }
@article {pmid40812274, year = {2025}, author = {Bermúdez, JR and Metian, M and Swarzenski, PW and Bank, MS and Bjorøy, &#xd8; and Cajas, J and Bucheli, R and González-Muñoz, R and Lynch, J and Piguave, E and Vargas, N and Vilela, K and Calle, L and Borbor-Cordova, MJ and Gaibor, N}, title = {Marine microplastics on the rise in the Eastern Tropical Pacific: Abundance doubles in 11 years and a ten-fold increase is projected by 2100.}, journal = {Marine pollution bulletin}, volume = {221}, number = {}, pages = {118437}, doi = {10.1016/j.marpolbul.2025.118437}, pmid = {40812274}, issn = {1879-3363}, abstract = {Plastic abundance in the ocean has increased systematically since the mid-20th century. Here we present a time-series dataset of microplastic abundance collected at several stations located in the Eastern Tropical Pacific Ocean off Ecuador from 2008 to 2018. The data reveals a significant and sustained increase in the abundance of microplastics over time across all sampling sites; this implies a homogeneous and sustained input, which likely also occurs at other coastal and marine ecosystems. Fiber strands were the most common microplastic observed, while polyethylene and polypropylene were the principal polymers identified by μFTIR analysis. A forecast model of the time-series data predicted that microplastics will be 3.2, 5.1 and 9.7 times more abundant in 2030, 2050 and 2100, respectively, relative to 2008 observations. These results provide insights into the decade-plus trend in microplastic abundance observed in coastal waters, which have important implications for future marine plastic pollution projections and associated ecosystem impacts.}, }
@article {pmid40812176, year = {2025}, author = {Ramirez-Villacis, DX and Leon-Reyes, A and Pieterse, CMJ and Raaijmakers, JM}, title = {Born to rewild: Reconnecting beneficial plant-microbiome alliances for resilient future crops.}, journal = {Cell host &amp; microbe}, volume = {33}, number = {8}, pages = {1241-1255}, doi = {10.1016/j.chom.2025.06.017}, pmid = {40812176}, issn = {1934-6069}, abstract = {Plant domestication is a coevolutionary process shaped by human selection, favoring traits supporting modern-day agriculture. This process has reduced genetic diversity and fixed alleles for desirable traits, coinciding with changes in agricultural practices, particularly soil tilling, crop monocultures, and the (over)use of fertilizers and pesticides. The combined effects-collectively termed "domestication syndrome"-have contributed to the homogenization of soil and plant-associated microbial communities, reducing diversity and disrupting beneficial plant-microbiome alliances. Microbiome rewilding has uncovered ecological, genetic, and molecular principles underlying these depleted plant-microbiome partnerships. Studies have revealed ancestral microbial taxa enriched in wild crop relatives, plant genes, and metabolites critical for microbial recruitment, as well as the potential of reintroducing microbes to enhance nutrient uptake, pathogen resistance, and stress tolerance. These findings offer models for restoring such interactions in modern crops. We review the current state of crop microbiome rewilding and highlight how these discoveries are instrumental for designing resilient crop systems.}, }
@article {pmid40812095, year = {2025}, author = {Rodríguez-González, L and Santás-Miguel, V and Alexandropoulou, S and Rousk, J}, title = {Effects of salinisation on Cu-contaminated vineyard soils: Assessment of changes in microbial communities and resistance to salt, Cu, and antibiotics.}, journal = {Ecotoxicology and environmental safety}, volume = {303}, number = {}, pages = {118838}, doi = {10.1016/j.ecoenv.2025.118838}, pmid = {40812095}, issn = {1090-2414}, abstract = {Climate change increases the risk of soil salinisation in Southern European vineyards. In this study, six of those soils were experimentally salinised, half of which were contaminated with Cu, a widely used fungicide. Changes in soil microbiota were assessed, including bacterial and fungal growth, respiration, carbon use efficiency calculation, and microbial community phospholipid fatty acids composition. The study also investigated whether salinisation induced a shift in the bacterial community toward increased tolerance to salt, Cu, and the antibiotics tetracycline and vancomycin. Results showed that experimental salinisation decreased bacterial growth and respiration, increased fungal growth, and limited fungal, bacterial, and microbial biomass. These effects were strongest in soils with high initial Cu content. In such soils, tolerance to salt stress was more pronounced, and salt-induced tolerance to vancomycin was observed. In contrast, tolerances to Cu and tetracycline antibiotic were not significantly increased by either Cu or salt. Subsequently, the soils underwent leaching, and analyses were repeated. Most changes in microbial parameters and tolerances were reversed, with soil texture being a particularly influential factor. However, leaching caused Cu tolerance in soils that had been salinised and had high Cu content to be greater than in soils that had not been salinised, regardless of whether they had high or low Cu content. After leaching, vancomycin tolerance also became positively correlated with soil Cu content in soils with low Cu levels. This preliminary study explored salinisation effects on soils, revealing possible bacterial resistance linked to past conditions and microbial shifts. Further research is needed to broaden the dataset and explore the underlying mechanisms and microbial species involved.}, }
@article {pmid40811531, year = {2025}, author = {Guo, D and Liu, Z and Raaijmakers, JM and Xu, Y and Yang, J and Erb, M and Zhang, J and Zhu, YG and Xu, J and Hu, L}, title = {Linalool-triggered plant-soil feedback drives defense adaptation in dense maize plantings.}, journal = {Science (New York, N.Y.)}, volume = {389}, number = {6761}, pages = {eadv6675}, doi = {10.1126/science.adv6675}, pmid = {40811531}, issn = {1095-9203}, abstract = {High planting density boosts crop yields but also heightens pest and pathogen risks. How plants adapt their defenses under these conditions remains unclear. In this study, we reveal that maize enhances its defense in high-density conditions through a plant-soil feedback mechanism triggered by the leaf volatile linalool. Linalool activates jasmonate signaling in neighboring plants and promotes root exudation of benzoxazinoids, especially 2-(2-hydroxy-4,7-dimethoxy-1,4-benzoxazin-3-one)-β-d-glucopyranose (HDMBOA-Glc). These exudates in turn reshape the rhizosphere microbiome composition to favor growth of specific bacterial taxa that trigger broad-spectrum resistance, albeit at the cost of maize growth. This microbiome-driven feedback loop is governed by salicylic acid signaling. Our findings uncover intricate chemical signaling in high-density cropping, which is instrumental for improving soil health and designing sustainable strategies that balance the trade-off between plant growth and defense.}, }
@article {pmid40810014, year = {2025}, author = {Fischer, MH and Rzepczynska, A and Kjøller, R}, title = {Taxonomic diversity in the global wheat phyllosphere mycobiome - a meta analysis.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1597807}, pmid = {40810014}, issn = {1664-462X}, abstract = {Wheat (Triticum aestivum L.) is a major crop grown on all continents. Due to environmental concerns, it is desirable to reduce the inputs of both chemical pesticides and inorganic fertilizers. However, yield reduction must be expected when switching to low-input systems. To mitigate such losses, the use of natural or introduced microbiomes may provide the key to maintaining sustainable yield. Phyllosphere fungi, both endophytic and phylloplane-associated, colonize aboveground plant structures, some of which have the potential to mitigate biotic and abiotic stressors. A first step toward realizing the potential of the wheat microbiome is to map the current knowledge on wheat phyllosphere fungi. This meta-analysis aims to map the diversity and abundance of fungal taxa associated with the wheat phyllosphere across global wheat-producing areas. To this end, we searched previous published literature and retrieved fungal community data from relevant studies. Retrieved studies included both culturing-based and metabarcoding amplicon sequence-based studies. We retrieved and analyzed 33 studies from five regions across the world, which differed greatly in their taxonomic composition. Across all regions, we found that while the majority of identified genera were unique to individual studies, some genera occurred across all five wheat growing regions, specifically Alternaria, Aspergillus, Bipolaris, Candida, Chaetomium, Cladosporium, Epicoccum, Fusarium, Nigrospora, Penicillium, Pyrenophora, Stemphylium and Trichoderma. Furthermore, we identified that while community composition differed between wheat growing regions, the identification method used was the most significant factor determining the depiction of community composition. We also highlight a lack of research in important wheat growing regions that are important for global wheat production. These considerations and other knowledge gaps are used to pinpoint future research.}, }
@article {pmid40809124, year = {2024}, author = {Trego, A and Palmeiro-Sánchez, T and Graham, A and Ijaz, UZ and O'Flaherty, V}, title = {First evidence for temperature's influence on the enrichment, assembly, and activity of polyhydroxyalkanoate-synthesizing mixed microbial communities.}, journal = {Frontiers in systems biology}, volume = {4}, number = {}, pages = {1375472}, pmid = {40809124}, issn = {2674-0702}, abstract = {Polyhydroxyalkanoates (PHA) are popular biopolymers due to their potential use as biodegradable thermoplastics. In this study, three aerobic sequencing batch reactors were operated identically except for their temperatures, which were set at 15 °C, 35 °C, and 48 °C. The reactors were subjected to a feast-famine feeding regime, where carbon sources are supplied intermittently, to enrich PHA-accumulating microbial consortia. The biomass was sampled for 16S rRNA gene amplicon sequencing of both DNA (during the enrichment phase) and cDNA (during the enrichment and accumulation phases). All temperatures yielded highly enriched PHA-accumulating consortia. Thermophilic communities were significantly less diverse than those at low or mesophilic temperatures. In particular, Thauera was highly adaptable, abundant, and active at all temperatures. Low temperatures resulted in reduced PHA production rates and yields. Analysis of the microbial community revealed a collapse of community diversity during low-temperature PHA accumulation, suggesting that the substrate dosing strategy was unsuccessful at low temperatures. This points to future possibilities for optimizing low-temperature PHA accumulation.}, }
@article {pmid40804956, year = {2025}, author = {Idres, T and Ibrahim, NA and Lamara, A and Boudjellaba, S and Derguini, A and Basher, NS and Temim, S and Aleissa, MS and Chebloune, Y}, title = {Epidemiological Insights into Maedi-Visna Virus in Algeria: First National Seroprevalence Survey and Risk Factor Profiling in Sheep Herds.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {15}, pages = {}, pmid = {40804956}, issn = {2076-2615}, support = {IMSIU- DDRSP2502//Deanship of Scientific Research at Imam Mohammad Ibn Saud Islamic University (IMSIU)/ ; }, abstract = {Maedi-visna virus (MVV), a small ruminant lentivirus causing chronic multisystemic disease in sheep, poses significant economic burdens due to reduced productivity and a lack of effective treatments. Despite its worldwide prevalence, epidemiological data from Algeria remain absent. This first national seroprevalence study aimed to elucidate MVV distribution, risk factors, and transmission dynamics in Algerian sheep herds. A cross-sectional survey of 1400 sheep across four regions (East, Center, West, South) was conducted, with sera analyzed via indirect ELISA (IDvet). Risk factors (geography, age, sex, breed, farming system) were evaluated using chi-square tests and Cramer's V. Overall seroprevalence was 9.07% (95% CI: 7.57-10.57), with significant variation by sex (females: 20.44% vs. males: 3.68%; p < 0.05), age (1-5 years: 6.86% vs. <1 year: 0.29%; p = 0.01), and region (Central: 3.36% vs. Eastern: 0.86%; p < 0.05). Notably, no association was found with breed or farming system (p ≥ 0.08), contrasting prior studies and suggesting region-specific transmission dynamics. Females exhibited heightened seropositivity, implicating prolonged herd retention and vertical transmission risks. Geographic disparities highlighted industrialized farming in central Algeria as a potential transmission amplifier. Strikingly, seronegative animals in high-prevalence herds hinted at genetic resistance, warranting further investigation. This study provides foundational insights into MVV epidemiology in North Africa, underscoring the need for targeted surveillance, ewe-focused control measures, and genetic research to mitigate transmission. The absence of prior national data elevates its significance, offering actionable frameworks for resource-limited settings and enriching the global understanding of SRLV heterogeneity.}, }
@article {pmid40803134, year = {2025}, author = {Wu, F and Campbell, BC and Greenfield, P and Hose, GC and Midgley, DJ and George, SC}, title = {There and back again: Genomic insights into microbial life in a recirculating petroleum refinery wastewater biotreatment system.}, journal = {Microbiological research}, volume = {301}, number = {}, pages = {128299}, doi = {10.1016/j.micres.2025.128299}, pmid = {40803134}, issn = {1618-0623}, abstract = {Petroleum refinery wastewater biotreatment relies on microbes to remediate carbon, nitrogen, and sulfur compounds, yet their life strategies and ecological roles remain unclear. This study characterises the ecological functions of 20 metagenome-assembled genomes (MAGs) from a full-scale petroleum refinery wastewater treatment plant in southern China. The taxonomic identity, nutrient metabolism genes (including C/N/S cycling), carbohydrate-active enzymes, and CRISPR-Cas systems of these MAGs were analysed. The recovered MAGs represented bacteria primarily from the Pseudomonadota and Bacteroidota phyla. The major carbon sources for the represented organisms are likely aromatic and aliphatic compounds, as well as carbohydrates including peptidoglycan, chitin, and starch. Almost all MAGs contained genes for nitrate or nitrite reduction, while metabolic pathways for sulfur metabolism were generally less prevalent. Meiothermus sp. bin.89 was the most metabolically versatile MAG. This organism possessed genes that allowed it to recycle biomass, break down aliphatic and monoaromatic compounds, and perform anaerobic respiration using nitrate. However, it was likely the most susceptible to viral predation, as indicated by the high abundance of CRISPR spacers. Overall, the results revealed that stress-tolerant ecological traits were common among organisms in this microbiome, showcasing the ability of the microbes to obtain carbon from aromatic and aliphatic compounds. This study provides a substantial contribution towards future efforts in optimising microbiome stability for pollutant removal in petroleum refinery wastewater biotreatment systems.}, }
@article {pmid40800619, year = {2025}, author = {van Eijnatten, AL and van Zon, L and Manousou, E and Bikineeva, M and Wubs, ERJ and van der Putten, WH and Morriën, E and Dutilh, BE and Snoek, LB}, title = {SpeSpeNet: an interactive and user-friendly tool to create and explore microbial correlation networks.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf036}, pmid = {40800619}, issn = {2730-6151}, abstract = {Correlation networks are commonly used to explore microbiome data. In these networks, nodes are microbial taxa and edges represent correlations between their abundances. As clusters of correlating taxa (co-abundance clusters) often indicate a shared response to environmental drivers, network visualization contributes to the system understanding. Currently, most tools for creating and visualizing co-abundance networks from microbiome data either require the researcher to have coding skills or are not user-friendly, with high time expenditure and limited customizability. Furthermore, existing tools lack a focus on the association between environmental drivers and the structure of the microbiome, even though many edges in correlation networks can be understood through a shared association of two taxa with the environment. For these reasons, we developed SpeSpeNet (Species-Species Network, https://tbb.bio.uu.nl/SpeSpeNet), a practical and user-friendly R-shiny tool to construct and visualize correlation networks from taxonomic abundance tables. The details of data preprocessing, network construction, and visualization are automated, require no programming ability for the web version, and are highly customizable, including associations with user-provided environmental data. Here, we present the details of SpeSpeNet and demonstrate its utility using three case studies.}, }
@article {pmid40800617, year = {2025}, author = {Fuschi, A and Merlotti, A and Remondini, D}, title = {Microbiome data: tell me which metrics and I will tell you which communities.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf125}, pmid = {40800617}, issn = {2730-6151}, abstract = {In microbial community studies, analyzing diversity is crucial for uncovering ecological complexity. However, the intrinsic characteristics of Next-gen sequencing data challenge the use of Euclidean metrics for estimating proximity and correlation. Consequently, a variety of distance measures have been developed within ecological frameworks. In this study, we compare several of these metrics-including Bray-Curtis, Canberra, Jensen-Shannon, Hellinger, Euclidean, and Aitchison distances-demonstrating how the choice of metric can significantly influence the interpretation of microbial community structures. Among these, Aitchison distance specifically defined for compositional data shows markedly different behavior from the others, highlighting different features related to the data. We consider two real-world examples: the human gut microbiome sampled using 16S rRNA sequencing with multiple measurements for different patients (G-HMP2) and urban sewage environmental metagenomes collected over time at different sites through shotgun sequencing (E-WADES). We show that, for the same dataset-independently on the sequencing technique or on the sampling context-the community structure depends strongly on the choice of specific metrics. This can be explained by the mathematical properties of the chosen metrics and the specific characteristics of microbiome data, namely their high heterogeneity in species abundance. This provides clear insights into how distance metrics influence interpretation and assists in choosing the most appropriate one for the study objectives.}, }
@article {pmid40799503, year = {2025}, author = {Parret, L and Simoens, K and De Vrieze, J and Smets, I}, title = {BIO-SPEC: An open-source bench-top parallel bioreactor system.}, journal = {HardwareX}, volume = {23}, number = {}, pages = {e00670}, pmid = {40799503}, issn = {2468-0672}, abstract = {The BIO-SPEC is an open-source, cost-effective, and modular bench-top bioreactor system designed for batch, sequencing batch, and chemostat cultivation. Featuring thermoelectric condensers to eliminate the need for a chiller, it ensures stable long-term operation. Controlled by a Raspberry Pi, the BIO-SPEC offers flexibility in headplate design, gas supply, and feeding strategies, making it a versatile alternative to high-cost commercial systems. This paper details the design, construction, and validation of the BIO-SPEC system, demonstrating its potential to advance microbiology and bioprocessing research through accessible and reliable hardware at a fraction of the cost of commercial systems.}, }
@article {pmid40797302, year = {2025}, author = {Baborski, A and Barth, SA and Jung, EM and Bloos, F and Rödel, J and Löffler, B and Bauer, M and Busch, A}, title = {Surviving antibiotic treatment as a gut bacterium: genomic characterization of an Enterobacter cloacae.}, journal = {BMC genomic data}, volume = {26}, number = {1}, pages = {56}, pmid = {40797302}, issn = {2730-6844}, abstract = {Enterobacter cloacae complex is a group of common opportunistic pathogens on intensive care units. On intensive care units sepsis is treated with high doses of antibiotics. This treatment does not only eliminate pathogenic bacteria but parts of the microbiome community as well. This leads to an imbalance of the gut microbiome. However, some bacteria can survive such treatment due to certain survival and resistance mechanisms. Not only antibiotic resistance mechanisms but also forming strong communities via biofilm formation promotes cell survival. Here, we investigated the properties of the isolate AT70PIP076 from a sepsis patient treated with piperacillin and tazobactam. After biochemical analysis and MALDI-TOF analysis, the strain was found to be Enterobacter cloacae. In addition to in vitro, antimicrobial susceptibility testing the genome was further investigated in situ regarding antibiotic resistance. Further live/dead staining was performed, and the biofilm formation was investigated using confocal laser microscopy (cLSM). The genome shows the presence of biofilm-associated genes EU554560, bcsABZC_AP010953, ehaB, KF662843, and crl. The understanding of the underlying mechanism of survival of potential pathogens might contribute to elucidate potential treatment options.ObjectivesGenomic analysis of a bacterium that can survive antibiotic treatment within the gut of an antibiotictreated patient to elucidate survival and resistance mechanisms.Data descriptionThe isolate AT70PIP076 was isolated in 2021 from feces collected from a patient treated with Piperacillin and tazobactam. Whole genome DNA was isolated using the Nextera DNA Flex microbial colony extraction protocol and the Nextera Flex DNA preparation kit according to the manufacturer's instructions. Following paired-end sequencing was performed on the MiSeq platform (Illumina, Inc., San Diego, CA, USA) using a 300-cycle MiSeq reagent kit and a read length of 151 bp. Contamination check and identification of 16 S RNA sequences was done by using ContESt16S. The genomic sequence contained 4,988,237 bp and the G + C content is represented at 54.80%. This genome and its associated data set will serve as a useful resource for further analyses.}, }
@article {pmid40797046, year = {2025}, author = {Wei, L and Chen, S and Qin, Z and Pan, N and Lan, M and Zhang, T and He, R and Liang, H and Deng, W and Mo, C and Yu, K}, title = {Responses of the Coral Symbiont Cladocopium goreaui to Extreme Temperature Stress in Relatively High-Latitude Reefs, South China Sea.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {88}, pmid = {40797046}, issn = {1432-184X}, abstract = {Global climate change has led to frequent extreme temperature events in oceans. Corals are susceptible to extreme high-temperature stress in summer and extreme low-temperature stress in winter in the relatively high-latitude reef areas of the South China Sea (SCS). The most abundant symbiotic coral Symbiodiniaceae in the higher-latitude reefs of the SCS is Cladocopium goreaui, predominantly associating with dominant coral hosts such as Acropora and Porites. However, to date, relatively few studies have focused on the response and mechanism of C. goreaui to the extreme high- and low-temperature stress. In this study, the responses and regulatory mechanisms of the dominant C. goreaui to extreme high- and low-temperature stress were investigated based on physiological indexes, transmission electron microscopy (TEM), and transcriptome analysis. The results showed that (1) under 34 °C heat stress, the disintegration of thylakoids triggered photosynthetic collapse in C. goreaui; survival is enabled through metabolic reprogramming that upregulates five protective pathways and redirects energy via pentose/glucuronate shunting to sustain ATP homeostasis, revealing a trade-off between damage containment and precision energy governance under thermal extremes. (2) Low temperature exposure induced suppression of maximum quantum yield (Fv/Fm), compounded by glutathione pathway inhibition, crippling ROS scavenging. The transcriptome results revealed that C. goreaui prioritizes gene fidelity maintenance under low temperature stress. These findings reveal that energy allocation trade-offs constitute the core strategy of C. goreaui temperature response: prioritizing energy maintenance under high-temperature stress, while safeguarding genetic fidelity at the expense of antioxidant defense under low-temperature stress.}, }
@article {pmid40796291, year = {2025}, author = {Mohr, AE and Mach, N and Pugh, J and Grosicki, GJ and Allen, JM and Karl, JP and Whisner, CM}, title = {Mechanisms underlying alterations of the gut microbiota by exercise and their role in shaping ecological resilience.}, journal = {FEMS microbiology reviews}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsre/fuaf037}, pmid = {40796291}, issn = {1574-6976}, abstract = {The gut microbiota (GM) is a dynamic ecosystem intricately linked to human health, including metabolic, immune, endocrine, and gastrointestinal functions. Exercise is recognized as a significant modifier of this microbial ecosystem, yet the complexities of this relationship are underexplored. Here, we delve into the multifaceted interactions between structured physical activity and the GM, emphasizing the role of exercise-induced stressors in shaping microbial composition and function. Unique to our review, we discuss the acute effects of different forms of exercise-induced stress on the GM and explore how these responses may influence long-term adaptability, stability, and resilience. Furthermore, we address critical junctures in microbial dynamics leading to shifts between different stable states. Finally, we explore the implications of host-controlled factors such as diet, exercise training, and nutritional supplementation in modulating the microbial community in the gut to optimize athletic performance. We conclude that while the potential to harness the synergistic effects of exercise-induced stressors, dietary interventions, and microbial adaptations appears promising, current evidence remains preliminary, highlighting the need for additional targeted research to guide future strategies that manipulate the GM for optimal health and athletic performance.}, }
@article {pmid40795952, year = {2025}, author = {Pluer, BD and Travis, J}, title = {The Digestive Microbiome Diversity of the Least Killifish, Heterandria formosa, and Its Implications for Host Adaptability to Varying Trophic Levels.}, journal = {Environmental microbiology reports}, volume = {17}, number = {4}, pages = {e70164}, pmid = {40795952}, issn = {1758-2229}, support = {G2020031598770049//Sigma Xia/ ; //Florida State University/ ; }, abstract = {Symbiotic microbes, in associations with aquatic hosts, aid in the acquisition of nutrients, breakdown xenobiotics, and contribute to immune system function. If associations with microbial communities facilitate host adaptation to different ecosystems, understanding the important ecological factors that act as drivers of differences among conspecific populations' microbiomes can help conservation efforts to promote beneficial interactions between fish and their microbiome for freshwater fish species facing rapid environmental changes. Here we describe the microbial communities in the gut of a freshwater fish, Heterandria formosa, in spring habitats using 16S rRNA sequencing. We quantified microbiota composition and diversity among springs ranging from oligotrophic to near eutrophic to determine the extent to which the microbiota are associated with different environmental conditions. We found higher microbial richness at sites with lower nutrient load stress. At more eutrophic sites, we detected the potential for increased metabolic capacity for pollutant degradation in the associated microbiota. We noted greater phylogenetic similarity between more environmentally similar sites, supporting previous evidence that the microbiota of freshwater fish is influenced by site water chemistry. Our findings bring to light microbial taxa and pathways that might play critical roles in the bioremediation of stressful environmental conditions.}, }
@article {pmid40795673, year = {2025}, author = {Cano, NO and Borrego, CM and Radjenovic, J}, title = {Irreversible inactivation of multidrug-resistant Gram-positive bacteria using S-functionalized graphene sponge anode.}, journal = {Water research}, volume = {287}, number = {Pt A}, pages = {124300}, doi = {10.1016/j.watres.2025.124300}, pmid = {40795673}, issn = {1879-2448}, abstract = {Graphene sponges functionalized with sulfur were employed as anodes and coupled with N-doped graphene sponge cathodes for electrochemical inactivation of a Gram-positive multidrug-resistant bacterium Enterococcus gallinarum in drinking water. The application of 43.5 A m[-2] resulted in 2.3 log removal of E. gallinarum in one-pass, flow-through mode, at 2.7 kWh m[-3] of energy demand. In the case of non-functionalized graphene sponge electrode, 1.8 log removal of E. gallinarum required 3.8 kWh m[-3]. Moreover, no bacterial regrowth was measured in any of the experiments conducted during storage of the treated samples for 16 h. Indeed, the storage of samples led to an additional 1 log removal for the S-functionalized graphene sponge anode, somewhat higher compared with the 0.7 log removal observed for the non-functionalized electrode. To further decrease the energy consumption and exploit the capacitance of graphene, the flow-through system was operated with intermittent current. Application of 43.5 A m[-2] in an intermittent mode, led to a similar, 2.4 log removal of E. gallinarum but with a significantly reduced energy consumption, from 2.7 with continuous current to 1.8 kWh m[-3]. Scanning electron microscopy analyses of the inactivated bacteria confirmed the irreversible damage to the cell walls due to low-voltage electroporation that co-occurred with the presence of abundant cellular debris resulting from the leakage of intracellular material. Using two sequential reactors equipped with the S-doped graphene sponge anode and N-doped graphene sponge cathode operated at 43.5 A m[-2] of anodic current density resulted in an overall 5.8 log removal of E. gallinarum (including storage) from drinking water, and at the energy consumption of 5.4 kWh m[-3] (i.e., electric energy per order of 0.94 kWh m[-3]). Overall, this study demonstrated the feasibility of using an S-functionalized graphene sponge anode for chlorine-free electrochemical inactivation of a multidrug resistant Gram-positive bacterium from low conductivity drinking water.}, }
@article {pmid40795332, year = {2025}, author = {Aguilera-Campos, KI and Boisard, J and Törnblom, V and Jerlström-Hultqvist, J and Behncké-Serra, A and Cotillas, EA and Stairs, CW}, title = {Anaerobic breviate protist survival in microcosms depends on microbiome metabolic function.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf171}, pmid = {40795332}, issn = {1751-7370}, abstract = {Anoxic and hypoxic environments serve as habitats for diverse microorganisms, including unicellular eukaryotes (protists) and prokaryotes. To thrive in low-oxygen environments, protists and prokaryotes often establish specialized metabolic cross-feeding associations, such as syntrophy, with other microorganisms. Previous studies show that the breviate protist Lenisia limosa engages in a mutualistic association with a denitrifying Arcobacter bacterium based on hydrogen exchange. Here, we investigate if the ability to form metabolic interactions is conserved in other breviates by studying five diverse breviate microcosms and their associated bacteria. We show that five laboratory microcosms of marine breviates live with multiple hydrogen-consuming prokaryotes that are predicted to have different preferences for terminal electron acceptors using genome-resolved metagenomics. Protist growth rates vary in response to electron acceptors depending on the make-up of the prokaryotic community. We find that the metabolic capabilities of the bacteria and not their taxonomic affiliations determine protist growth and survival and present new potential protist-interacting bacteria from the Arcobacteraceae, Desulfovibrionaceae, and Terasakiella lineages. This investigation uncovers potential nitrogen and sulfur cycling pathways within these bacterial populations, hinting at their roles in syntrophic interactions with the protists via hydrogen exchange.}, }
@article {pmid40790855, year = {2025}, author = {Xie, R and Yu, H and Wang, Y and Leung, KY and Habimana, O}, title = {Synergistic effects of sodium acetate and calcium on structure and function in multispecies biofilms.}, journal = {Biofouling}, volume = {}, number = {}, pages = {1-16}, doi = {10.1080/08927014.2025.2545940}, pmid = {40790855}, issn = {1029-2454}, abstract = {This investigation scrutinizes the manner in which sodium acetate (SA) and calcium cations (Ca[2+]) independently and collaboratively affect biofilm development. Confocal microscopy revealed that SA (1 mM) increased biofilm biovolume (5.5-fold) and thickness by enhancing microbial growth, while Ca[2+] (1.5 mM) stabilized the matrix via EPS crosslinking. Combined, SA and Ca[2+] synergistically boosted biovolume (1.5-fold) and thickness (21.3 µm) compared to SA alone. 16S rRNA sequencing showed SA-enriched Actinobacteriota (11%) and exopolysaccharide-producing Brevifollis, whereas Ca[2+] improved surface coverage (22.3%). Functional predictions linked SA to purine degradation and Ca[2+] to fatty acid oxidation, aligning with EPS modifications. These findings highlight how carbon sources and divalent cations collaboratively shape biofilm resilience, offering insights for biofilm management in environmental, industrial, and medical settings where SA and Ca[2+] gradients exist.}, }
@article {pmid40789383, year = {2025}, author = {Rout, AK and Rout, SS and Panda, A and Tripathy, PS and Kumar, N and Parida, SN and Dey, S and Dash, SS and Behera, BK and Pandey, PK}, title = {Potential applications and future prospects of metagenomics in aquatic ecosystems.}, journal = {Gene}, volume = {}, number = {}, pages = {149720}, doi = {10.1016/j.gene.2025.149720}, pmid = {40789383}, issn = {1879-0038}, abstract = {Metagenomics plays a vital role in advancing our understanding of microbial communities and their functional contributions in various ecosystems. By directly sequencing DNA from environmental samples-such as soil, water, air, and the human body-metagenomics enables the identification of previously uncultivable or unknown microorganisms, offering key insights into their ecological functions. Beyond taxonomic classification, metagenomic analyses reveal functional genes and metabolic pathways, facilitating the discovery of enzymes, bioactive compounds, and other molecules with applications in agriculture, biotechnology, and medicine. This review discusses the wide-ranging applications of metagenomics in environmental monitoring, including sample collection, high-throughput sequencing, and data analysis and interpretation. We review different sequencing platforms, library preparation methods, and advanced bioinformatics tools used for quality control, sequence assembly, and both taxonomic and functional annotation. Special focus is given to the role of metagenomics in evaluating microbial responses to environmental stress, contaminant degradation, disease emergence, and climate change. The use of microbial bioindicators for aquatic ecosystem monitoring and toxicological assessments is also examined. A comprehensive evaluation of current bioinformatics pipelines is provided for their effectiveness in processing large-scale metagenomic datasets. As global environmental pressures intensify, integrative meta-omics approaches, including whole-genome metagenomics, will be crucial for understanding the complexity, functions, and dynamics of microbiomes in both natural and affected ecosystems.}, }
@article {pmid40788461, year = {2025}, author = {Torres, MC and Breyer, GM and da Silva, MERJ and de Itapema Cardoso, MR and Siqueira, FM}, title = {Metagenomic approaches for the quantification of antibiotic resistance genes in swine wastewater treatment system: a systematic review.}, journal = {Molecular biology reports}, volume = {52}, number = {1}, pages = {816}, pmid = {40788461}, issn = {1573-4978}, support = {408693/2022-3//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico,Brazil/ ; }, mesh = {Swine ; *Wastewater/microbiology ; Animals ; *Metagenomics/methods ; *Drug Resistance, Microbial/genetics ; Metagenome/genetics ; Bacteria/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; Water Purification/methods ; Computational Biology/methods ; Anti-Bacterial Agents/pharmacology ; }, abstract = {This systematic review aims to identify the metagenomic methodological approaches employed for the detection of antimicrobial resistance genes (ARGs) in swine wastewater treatment systems. The search terms used were metagenome AND bacteria AND ("antimicrobial resistance gene" OR resistome OR ARG) AND wastewater AND (swine OR pig), and the search was conducted across the following electronic databases: PubMed, Scopus, ScienceDirect, Web of Science, Embase, and Cochrane Library. The search was limited to studies published between 2020 and 2024. Of the 220 studies retrieved, eight met the eligibility criteria for full-text analysis. The number of publications in this research area has increased in recent years, with China contributing the highest number of studies. ARGs are typically identified using bioinformatics pipelines that include steps such as quality trimming, assembly, metagenome-assembled genome (MAG) reconstruction, open reading frame (ORF) prediction, and ARG annotation. However, comparing ARGs quantification across studies remains challenging due to methodological differences and variability in quantification approaches. Therefore, this systematic review highlights the need for methodological standardization to facilitate comparison and enhance our understanding of antimicrobial resistance in swine wastewater treatment systems through metagenomic approaches.}, }
@article {pmid40788124, year = {2025}, author = {Ferreira, J and Rediers, H}, title = {Draft genome sequences of 25 candidate biocontrol bacteria against Phytophthora cactorum.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0050225}, doi = {10.1128/mra.00502-25}, pmid = {40788124}, issn = {2576-098X}, abstract = {To provide a biocontrol solution for managing the phytopathogen Phytophthora cactorum, bacteria were tested for antagonistic activity in vitro and in planta. This paper presents the draft genomes of 25 candidate biocontrol organisms, providing a solid foundation to decipher the underlying mechanisms of their antagonistic activity.}, }
@article {pmid40781093, year = {2025}, author = {Kojima, CY and Henson, MW and Coelho, JT and Lanclos, VC and Bañuelas, D and Thrash, JC}, title = {Metagenomes and 1,313 metagenome-assembled genomes from a northern Gulf of Mexico coastal time series.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1388}, pmid = {40781093}, issn = {2052-4463}, support = {OCE-1931113//National Science Foundation (NSF)/ ; Simons Investigator in Aquatic Microbial Ecology Award//Simons Foundation/ ; Faculty Innovation Research Award//USC | Wrigley Institute for Environmental Studies, University of Southern California (USC Wrigley Institute for Environmental Studies)/ ; }, mesh = {Gulf of Mexico ; *Metagenome ; *Water Microbiology ; }, abstract = {Coastal and estuarine systems are hotspots of microbial diversity, activity, and biogeochemical cycling. Despite their importance, we have few comprehensive datasets of microbial populations across space and time from these ecosystems. To improve our understanding of these systems, we generated metagenomes averaging 46 M reads per sample (nearly 389 Gbp total) from four coastal/estuarine locations in the northern Gulf of Mexico across seven timepoints spanning nine months. Using standard methodology combined with a unique assembly and binning approach called subtractive iterative assembly (SIA), we generated 1,313 non-redundant metagenome-assembled genomes (MAGs) with 5% contamination or less and at least 75% completeness. We produced approximately a third of the MAGs through SIA. Actinobacteria and Proteobacteria were represented most. We recovered MAGs of great ecological significance including SAR11, Marine Group I (Thaumarcheaota), Marine Group II Euryarchaeota, SAR324, and Asgardarchaeota. We describe both our methodology using the SIA approach as well as the 28 metagenomes and 1,313 MAGs that provide a rich spatiotemporal dataset with which to study coastal and estuarine microbiology.}, }
@article {pmid40779244, year = {2025}, author = {Sung, J and Choi, DH and Lee, Y and Kim, JH and Shin, HH and Kim, YE and Choi, JH and Noh, JH and Gobler, CJ and Park, BS}, title = {Temperature-Driven Intraspecific Diversity in Paralytic Shellfish Toxin Profiles of the Dinoflagellate Alexandrium pacificum and Intragenic Variation in the Saxitoxin Biosynthetic Gene, sxtA4.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {87}, pmid = {40779244}, issn = {1432-184X}, support = {20163MFDS641//Ministry of Food and Drug Safety/ ; 20163MFDS641//Ministry of Food and Drug Safety/ ; 20163MFDS641//Ministry of Food and Drug Safety/ ; 20163MFDS641//Ministry of Food and Drug Safety/ ; 20163MFDS641//Ministry of Food and Drug Safety/ ; 20163MFDS641//Ministry of Food and Drug Safety/ ; 20163MFDS641//Ministry of Food and Drug Safety/ ; 20210469//Ministry of Oceans and Fisheries/ ; 20210469//Ministry of Oceans and Fisheries/ ; RS-2021-KS211530//Ministry of Oceans and Fisheries/ ; RS-2023-00209356//Ministry of Science and ICT, South Korea/ ; }, mesh = {*Dinoflagellida/genetics/metabolism/growth &amp; development ; *Saxitoxin/biosynthesis/genetics ; *Genetic Variation ; Temperature ; Harmful Algal Bloom ; Phylogeny ; }, abstract = {Alexandrium pacificum, a globally distributed dinoflagellate, is well-known for causing harmful algal blooms and producing Paralytic Shellfish Toxins (PSTs), a threat to marine life and human health. The frequency and intensity of Alexandrium blooms have increased in recent decades, driven, in some cases, by increasing temperatures. Here, we investigated the temperature-dependent (15 °C, 20 °C, 25 °C, and 30 °C) growth rates and paralytic shellfish toxin profiles of eight A. pacificum strains while concurrently examining differences in sequences of the saxitoxin biosynthetic gene, sxtA4. While maximum cell densities were lowest at 30 °C, toxin production per cell was highest at higher temperatures that inhibited growth, with greater diversity of toxin analogs peaking at 30 °C, as confirmed by the higher Shannon's diversity index obtained for the toxin profiles with the increasing temperatures. Furthermore, genetic analysis of the sxtA4 gene showed that greater genetic diversity-quantified by nucleotide diversity (π) ranging from 9.91 to 30.21 across strains-was positively correlated with this wider array of toxin analogs (Shannon's diversity index; p < 0.0001). Conserved regions within the gene were identified, suggesting that these regions may play important structural or functional roles in the saxitoxin biosynthetic pathway. These findings highlight the role of temperature, genetic diversity, and sxtA4 conserved regions in influencing toxin production and profiles in Alexandrium. Further research into the genetic mechanisms underlying saxitoxin biosynthesis will improve our understanding of Alexandrium's adaptability to changing temperatures. Such insights are essential for effective ecosystem management and safeguarding public health.}, }
@article {pmid40778431, year = {2025}, author = {Maillard, F and Beatty, BH and Geisen, S and Lara, E and Kennedy, PG}, title = {Secondary Decomposers Meet Their Predators: Decomposition Stage and Substrate Quality Jointly Structure Microbial Brown Food Webs During Fungal Necromass Decay.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {e70060}, doi = {10.1111/mec.70060}, pmid = {40778431}, issn = {1365-294X}, support = {DEB #2038293//National Science Foundation/ ; }, abstract = {Mycelial residues, also known as fungal necromass, represent a substantial fraction of soil organic matter (SOM) pools in terrestrial ecosystems worldwide. Although microbial decomposers are increasingly recognised as key drivers of fungal necromass carbon stock formation, the diversity and composition of their microbial predators-and the roles these predators play in mediating fungal necromass decomposition-have not been explored to date. To address this gap, we produced fungal necromass of varying biochemical quality from Hyaloscypha bicolor and decomposed it in forest topsoil in Minnesota, USA, to investigate how microbial decomposer (bacteria and fungi) and predator (protists and nematodes) communities differ between soil and necromass. We also examined whether microbial predators influence the abundance of fungal necromass decomposers and affect necromass decomposition rates. Over two sampling times (4 and 12 weeks), necromass exhibited rapid early mass loss followed by reduced decay, with a higher stabilised mass in high melanin necromass. Microbial abundances were higher in necromass than in surrounding soil, especially in low melanin necromass. Community composition of both decomposers and their predators differed between soil and necromass and shifted markedly with necromass quality and decomposition stage. Predator community composition was linked to bacterial and fungal abundances at both early and late stages of decay and was marginally associated with decomposition rates. We conclude that fungal necromass acts as a microbial 'hotspot' not only for decomposers but also for their predators. These findings highlight the importance of microbial predator-decomposer interactions to better understand the formation of fungal-derived SOM.}, }
@article {pmid40775374, year = {2025}, author = {Krasenbrink, J and Hanson, BT and Weiss, AS and Borusak, S and Tanabe, TS and Lang, M and Aichinger, G and Hausmann, B and Berry, D and Richter, A and Marko, D and Mussmann, M and Schleheck, D and Stecher, B and Loy, A}, title = {Sulfoquinovose is exclusively metabolized by the gut microbiota and degraded differently in mice and humans.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {184}, pmid = {40775374}, issn = {2049-2618}, support = {10.55776/DOC69//Austrian Science Fund/ ; 10.55776/COE7//Austrian Science Fund/ ; 10.55776/DOC69//Austrian Science Fund/ ; 10.55776/COE7//Austrian Science Fund/ ; 10.55776/DOC69//Austrian Science Fund/ ; 10.3030/101205556//HORIZON EUROPE Marie Sklodowska-Curie Actions/ ; 395357507 "SFB1371"//Deutsche Forschungsgemeinschaft/ ; EvoGutHealth, 865615/ERC_/European Research Council/International ; 503-5-7-06.712_00 and 503-5-7-06.709_00//Germany Centre for Infection Research/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Humans ; Mice ; Mice, Inbred C57BL ; Feces/microbiology ; *Bacteria/metabolism/classification/genetics/isolation &amp; purification ; Male ; Hydrogen Sulfide/metabolism ; Female ; }, abstract = {BACKGROUND: Sulfoquinovose (SQ) is a green-diet-derived sulfonated glucose and a selective substrate for a limited number of human gut bacteria. Complete anaerobic SQ degradation via interspecies metabolite transfer to sulfonate-respiring bacteria produces hydrogen sulfide, which has dose- and context-dependent health effects. Here, we studied potential SQ degradation by the mammalian host and the impact of SQ supplementation on human and murine gut microbiota diversity and metabolism.<br><br>RESULTS: [13]CO2 breath tests with germ-free C57BL/6 mice gavaged with [13]C-SQ were negative. Also, SQ was not degraded by human intestinal cells in vitro, indicating that SQ is not directly metabolized by mice and humans. Addition of increasing SQ concentrations to human fecal microcosms revealed dose-dependent responses of the microbiota and corroborated the relevance of Agathobacter rectalis and Bilophila wadsworthia in cooperative degradation of SQ to hydrogen sulfide via interspecies transfer of 2,3-dihydroxy-1-propanesulfonate (DHPS). Similar to the human gut microbiome, the genetic capacity for SQ or DHPS degradation is sparsely distributed among bacterial species in the gut of conventional laboratory mice. Escherichia coli and Enterocloster clostridioformis were identified as primary SQ degraders in the mouse gut. SQ and DHPS supplementation experiments with conventional laboratory mice and their intestinal contents showed that SQ was incompletely catabolized to DHPS. Although some E. clostridioformis genomes encode an extended sulfoglycolytic pathway for both SQ and DHPS fermentation, SQ was only degraded to DHPS by a mouse-derived E. clostridioformis strain.<br><br>CONCLUSIONS: Our findings suggest that SQ is solely a nutrient for the gut microbiota and not for mice and humans, emphasizing its potential as a prebiotic. SQ degradation by the microbiota of conventional laboratory mice differs from the human gut microbiota by absence of DHPS degradation activity. Hence, the microbiota of conventional laboratory mice does not fully represent the SQ metabolism in humans, indicating the need for alternative model systems to assess the impact of SQ on human health. This study advances our understanding of how individual dietary compounds shape the microbial community structure and metabolism in the gut and thereby potentially influence host health. Video Abstract.}, }
@article {pmid40774531, year = {2025}, author = {Morales, MLP and Capurro, L and Bordert, F and Chenia, H and Alonso, C and Bentos, FR and Boccardi, L and Brugnoli, E and They, NH and Agostini, VO and Leães Pinho, GL}, title = {Evaluating macrophyte extracts as eco-friendly antifouling additives for freshwater made-man structures: a field assessment.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {126952}, doi = {10.1016/j.envpol.2025.126952}, pmid = {40774531}, issn = {1873-6424}, abstract = {Biofouling on artificial aquatic surfaces yields substantial economic losses and operational challenges. Traditional antifouling strategies often rely on synthetic chemical coatings, which have harmful environmental impacts, thus environmentally sustainable solutions, such as natural antifouling compounds are increasingly being sought. Extracts derived from the aquatic macrophytes Pontederia crassipes and Typha domingensis have demonstrated potential antifouling properties in preliminary studies; however, their efficacy under natural field conditions remains unverified. This study is the first to evaluate the antifouling potential of these macrophyte extracts when incorporated with epoxy coatings in a natural freshwater environment (Salto Grande Reservoir, Uruguay River). Stainless steel substrates were treated with 2.5, 5, and 10 g L[-1] of lyophilized macrophyte extracts combined with epoxy and compared to uncoated and epoxy-coated controls. Over a 165-hour period, biofouling was assessed via chlorophyll levels, bacterial counts, macro-organism presence and attachment and taxonomic diversity. Analytical techniques, including gas and liquid chromatography, along with Fourier transform infrared spectroscopy, were employed to identify active compounds in extracts. The P. crassipes extract at 5 and 10 g L[-1] exhibited superior antifouling efficacy compared to T. domingensis. Coatings with P. crassipes significantly reduced bacterial colonization (37%), algae growth (for different photosynthetic pigments), fungal presence, and macro-organism attachment (not found), while promoting the occurrence of opportunistic taxa less conducive to fouling. The observed antifouling activity may be attributed to specific chemical compounds, including long-chain hydrocarbons and phenolic derivatives, identified in the extracts. The study findings demonstrate the field antifouling efficacy of macrophyte extracts incorporated with epoxy coatings, highlighting P. crassipes as a particularly promising, sustainable antifouling candidate. Its high biomass availability and ease of cultivation enhance its potential for industrial-scale development as natural antifouling agents. This work provides critical insights into developing eco-friendly antifouling coatings that minimize environmental impact while maintaining efficacy in biofouling control being the first study to prove in a natural environment the antifouling potential of these macrophytes.}, }
@article {pmid40770074, year = {2025}, author = {Myers, T and Song, SJ and Chen, Y and De Pessemier, B and Khatib, L and McDonald, D and Huang, S and Gallo, R and Callewaert, C and Havulinna, AS and Lahti, L and Roeselers, G and Laiola, M and Shetty, SA and Kelley, ST and Knight, R and Bartko, A}, title = {Chronological age estimation from human microbiomes with transformer-based Robust Principal Component Analysis.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {1159}, pmid = {40770074}, issn = {2399-3642}, mesh = {Humans ; *Aging ; *Biometry/methods ; *Deep Learning ; *Gastrointestinal Microbiome ; *Principal Component Analysis/methods ; *Skin Microbiome ; Software Validation ; }, abstract = {Deep learning for microbiome analysis has shown potential for understanding microbial communities and human phenotypes. Here, we propose an approach, Transformer-based Robust Principal Component Analysis(TRPCA), which leverages the strengths of transformer architectures and interpretability of Robust Principal Component Analysis. To investigate benefits of TRPCA over conventional machine learning models, we benchmarked performance on age prediction from three body sites(skin, oral, gut), with 16S rRNA gene amplicon(16S) and whole-genome sequencing(WGS) data. We demonstrated prediction of age from longitudinal samples and combined classification and regression tasks via multi-task learning(MTL). TRPCA improves age prediction accuracy from human microbiome samples, achieving the largest reduction in Mean Absolute Error for WGS skin (MAE: 8.03, 28% reduction) and 16S skin (MAE: 5.09, 14% reduction) samples, compared to conventional approaches. Additionally, TRPCA's MTL approach achieves an accuracy of 89% for birth country prediction across 5 countries, while improving age prediction from WGS stool samples. Notably, TRPCA uncovers a link between subject and error prediction through residual analysis for paired samples across sequencing method (16S/WGS) and body site(oral/gut). These findings highlight TRPCA's utility in improving age prediction while maintaining feature-level interpretability, and elucidating connections between individuals and microbiomes.}, }
@article {pmid40768991, year = {2025}, author = {Li, J and Sun, Q and Wang, S and Lei, K}, title = {Environmental gradients drive the ecological dynamics of bacterioplankton in the East China Sea based on eDNA metabarcoding.}, journal = {Marine pollution bulletin}, volume = {221}, number = {}, pages = {118539}, doi = {10.1016/j.marpolbul.2025.118539}, pmid = {40768991}, issn = {1879-3363}, abstract = {Understanding the interactions between environmental factors and ecological processes that shape bacterioplankton is a fundamental goal of microbial ecology. With increasing urbanization and environmental stress, marine coastal ecosystems necessitate careful evaluation of microbial dynamics. Environmental DNA was utilized to investigate bacterioplankton in the coastal waters of the East China Sea, revealing distinct environmental gradients that significantly shape bacterioplankton community composition. Distinct spatial differentiation of microbial assemblages was observed along these gradients, primarily driven by nitrogen-related nutrient dynamics. Furthermore, shifts in coastal habitats have driven a transition in community assembly processes from predominantly stochastic to deterministic mechanisms. Changes in environmental conditions also increase the vulnerability of offshore bacterioplankton networks, compromising their stability. These findings emphasize the critical role of environmental gradients in forming coastal microbial community composition, offering valuable insights for advancing marine ecosystem management, biodiversity conservation, and sustainable environmental policies.}, }
@article {pmid40767881, year = {2025}, author = {Fowler, AE and McFrederick, QS and Adler, LS}, title = {Correction to: Pollen Diet Diversity does not Affect Gut Bacterial Communities or Melanization in a Social and Solitary Bee Species.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {86}, doi = {10.1007/s00248-025-02573-6}, pmid = {40767881}, issn = {1432-184X}, }
@article {pmid40767488, year = {2025}, author = {Harris, JE and Bledsoe, RB and Guha, S and Omari, H and Crandall, SG and Burghardt, LT and Couradeau, E}, title = {The activity of soil microbial taxa in the rhizosphere predicts the success of root colonization.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0045825}, doi = {10.1128/msystems.00458-25}, pmid = {40767488}, issn = {2379-5077}, abstract = {UNLABELLED: Plant-beneficial microbes have great potential to improve sustainability in agriculture. Still, managing beneficial microbes is challenging because the impact of microbial dormancy on community assembly across the soil, rhizosphere, and endosphere is poorly understood. We address this gap with the first documented use of Biorthogonal Non-Canonical Amino Acid Tagging (BONCAT) to probe active microbes in the soil-to-root gradient. Using nodule-forming legume Trifolium incarnatum, we confirmed that BONCAT is suitable for labeling endospheric microbes with microscopy. Next, we coupled BONCAT to Flow Cytometer Activated Cell Sorting (FACS) and 16S rRNA amplicon sequencing to probe patterns of microbial activity and the structure of the active microbial community across the soil, rhizosphere, root, and nodule with a native soil microbial community. As expected, we found 10 times higher microbial activity in the endosphere than in the rhizosphere or bulk soil, likely due to increased plant resources. Finally, we revealed that microbial activity in the rhizosphere was significantly associated with successful endosphere colonization, more so than microbial abundance alone. This last finding has implications for the development of microbial inoculants, suggesting colonizing plant roots is linked to a microbe's ability to overcome dormancy once deployed in the soil.<br><br>IMPORTANCE: Most soil microbes are dormant, so they must exit dormancy to have the potential to carry out plant-beneficial functions. It is unclear if dormant microbes revive in proximity to plant-produced resources and if overcoming dormancy in the soil is important for successful plant colonization. We use a novel microbial activity probing technique for the first time on and in plant roots, and with it, we observe microbes increased in activity 10&#xd7; inside plant tissues compared to the soil, likely in response to plant-produced resources. In complex, native microbial communities, we observe that microbes that are active and abundant are more likely to colonize plant roots successfully than just abundant microbes. Our research shows that plants could be leveraged to promote a distinct active microbial community from the native soil, a discovery that has the potential to improve sustainability in agriculture.}, }
@article {pmid40766845, year = {2025}, author = {Zheng, N and Yu, HL and Zhang, BJ and Wang, D and Ji, YL and Dai, LL and Li, W and Li, SH and Hu, ZL and Zheng, YS}, title = {Metagenomic next-generation sequencing-based characterization of the viral spectrum in clinical pulmonary and peripheral blood samples of patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1562965}, pmid = {40766845}, issn = {2235-2988}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing ; *Metagenomics/methods ; *Bronchoalveolar Lavage Fluid/virology ; *Virome/genetics ; *Viruses/genetics/classification/isolation &amp; purification ; Female ; Male ; Middle Aged ; Adult ; Aged ; *Lung/virology ; *Blood/virology ; Bacteria/classification/genetics/isolation &amp; purification ; *Virus Diseases/virology ; }, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) enables comprehensive profiling of viral communities in clinical samples. However, comparative analyses of the virome across anatomical compartments and disease states remain limited. This study aims to characterize the virome in bronchoalveolar lavage fluid (BALF) and peripheral blood samples from patients with various clinical conditions using mNGS.<br><br>METHODS: A total of 338 clinical samples-including 240 BALF and 69 blood samples for DNA sequencing, and 18 BALF and 11 blood samples for RNA sequencing-underwent shotgun metagenomic sequencing. Following removal of host-derived reads, high-quality non-human sequences were aligned to a viral reference database. Virome composition was assessed through alpha and beta diversity metrics. Principal coordinates analysis was used to evaluate disease-related variation, and virus-bacteria associations in BALF were investigated via Spearman correlation.<br><br>RESULTS: Sequencing yielded an average of 51 million raw reads per sample, resulting in approximately 8 million non-human reads after host filtering. Distinct virome profiles were observed between BALF and blood samples. Bacteriophages dominated all groups, with Siphoviridae and Myoviridae as the most abundant families, although only 13.6% of viral abundance could be assigned to known families. Diversity analyses revealed significant differences between BALF and peripheral blood, and DNA-sequenced BALF samples showed disease-specific viral signatures in pulmonary infections. In contrast, tumor presence had no significant effect on virome composition in either BALF or blood. Network analysis identified complex virus-bacteria correlations in BALF, with genera such as Haemophilus, Megasphaera, and Treponema as key bacterial hosts.<br><br>CONCLUSIONS: This study reveals pronounced differences in virome composition between the respiratory and circulatory systems and highlights the specific influence of pulmonary disease-but not tumors-on the pulmonary virome. The observed virus-bacteria networks provide novel insights into pulmonary microbial ecology and underscore the importance of integrating host and disease context in virome studies.}, }
@article {pmid40766442, year = {2025}, author = {Rathod, D and Silverman, JD}, title = {PCR Bias Impacts Microbiome Ecological Analyses.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40766442}, issn = {2692-8205}, support = {R01 GM148972/GM/NIGMS NIH HHS/United States ; }, abstract = {Polymerase Chain Reaction (PCR) is a critical step in amplicon-based microbial community profiling, allowing the selective amplification of marker genes such as 16S rRNA from environmental or host-associated samples. Despite its widespread use, PCR is known to introduce amplification bias, where some DNA sequences are preferentially amplified over others due to factors such as primer-template mismatches, sequence GC content, and secondary structures. Although these biases are known to affect transcript abundance, their implications for ecological metrics remain poorly understood. In this study, we conduct a comprehensive evaluation of how PCR-bias influences both within-samples (α -diversity) and between-sample (β -diversity) analyses. We show that perturbation-invariant diversity measures remain unaffected by PCR bias, but widely used metrics such as Shannon diversity and Weighted-Unifrac are sensitive, with their values varying according to the true community composition. To address this, we provide theoretical and empirical insight into how PCR-induced bias varies across ecological analyses and community structures, and we offer practical guidance on when bias-correction methods should be applied. Our findings highlight the importance of selecting appropriate diversity metrics for PCR-based microbial ecology workflows and offer guidance for improving the reliability of diversity analyses.}, }
@article {pmid40765478, year = {2025}, author = {Stevens-Green, R and Chénard, C and Mordret, S and MacKinnon, J and Robicheau, BM and LaRoche, J}, title = {Organellar Genomes of Three Globally Important Nanoplanktonic Diatoms Refine Their Taxon-Specific Distribution and Succession Patterns in the Northwest Atlantic.}, journal = {The Journal of eukaryotic microbiology}, volume = {72}, number = {5}, pages = {e70033}, pmid = {40765478}, issn = {1550-7408}, support = {A1-019982//NRC-ACRD Internal Project/ ; OCN-500//NRC Ocean Program Grant and Contribution/ ; (RGPIN/04060-2021)//NSERC Discovery Grant awarded to JLR/ ; //CFREF (NWA BCP) awarded to JLR/ ; }, mesh = {*Diatoms/genetics/classification ; Atlantic Ocean ; *Genome, Mitochondrial ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Genome, Chloroplast ; *Phytoplankton/genetics/classification ; DNA Barcoding, Taxonomic ; }, abstract = {Nanoplanktonic diatoms (2-20 μm) are a significant yet historically understudied component of marine ecosystems. We investigated three recently isolated nanoplanktonic diatoms from the Northwest Atlantic Ocean (NWA): Minidiscus spinulatus, Mediolabrus comicus, and Minidiscus trioculatus. Using Oxford Nanopore sequencing, we assembled and annotated their complete chloroplast and mitochondrial genomes. Pangenome analyses revealed that Minidiscus species consistently clustered more closely with select Thalassiosira species, whereas M. comicus formed a sister clade with Skeletonema. Circularized chloroplast genomes allowed us to characterize the full-length 16S ribosomal RNAs for each isolate, thereby leading to higher resolution of these taxa in preexisting 16S metabarcoding data. During our study, M. spinulatus was primarily restricted to the Bedford Basin. In contrast, both M. trioculatus and M. comicus had larger geographic ranges extending to the Labrador Sea, and in the case of M. comicus, to the Canadian Arctic Gateway. Weekly metabarcoding from the coastal Bedford Basin, N.S., Canada (2014-2022), revealed a seasonal succession of nanoplanktonic taxa, with Minidiscus trioculatus dominating in the early months, followed by M. comicus and M. spinulatus. Our results highlight the critical value of phytoplankton isolations and organelle genomics for expanding our understanding of the diversity and biogeography of nanoplanktonic diatoms.}, }
@article {pmid40765283, year = {2025}, author = {Zhang, Y and Wu, H and Wu, X and Grossart, HP and Lorke, A}, title = {Revisiting Cyanobacteria-Temperature Dynamics: Intraspecific Competition and Trait Diversity as Keys to Predicting Harmful Algal Blooms under Climate Change.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c04849}, pmid = {40765283}, issn = {1520-5851}, abstract = {Cyanobacterial harmful algal blooms are expanding spatiotemporally, with an increasing occurrence of cold-water cyanobacterial blooms (CWCBs), intensifying ecological and water quality challenges. While abiotic drivers have been identified as contributors to CWCBs, the role of biotic factors─particularly the adaptation induced by the shifts in intraspecific trait distributions─in this process remains largely unexplored. Here, we tested the hypothesis that the thermal history of cyanobacteria affects their thermal adaptations by reshaping the distribution of optimum growth temperature (Topt). Using a trait-based phytoplankton model coupled with a one-dimensional lake model, we simulated cyanobacteria dynamics over 364 days in a large, eutrophic, shallow lake recently experiencing CWCBs. The model demonstrated that Topt diversification promotes cold-adapted strains, leading to CWCBs while mitigating summer blooms. This occurs because the thermal response of Topt-diverse populations depends on their Topt distribution, which is determined by past temperature sequence, allowing Topt-diverse populations to retain a 'memory' of temperatures preceding summer. Consequently, increased summer temperatures inhibit these cold-adapted populations, challenging the prevailing cyanobacteria-temperature paradigm, which suggests that high temperatures universally favor cyanobacteria. These findings reveal that models assuming fixed traits may misrepresent cyanobacterial dynamics under climate change, highlighting the necessity of incorporating trait diversity into predictive frameworks for improved forecasting and to support adaptive lake management strategies.}, }
@article {pmid40762371, year = {2025}, author = {Li, X and Chen, Y and Gao, Z and Liu, X and Song, Z and Gao, F and Wang, S and Yu, C and Sun, L and Huang, Y and Zheng, L and Wang, G and Sun, Y and Li, J and Yang, X and Bao, Y}, title = {TSP50 in Neural Stem Cells Regulates Aging-Related Cognitive Decline and Neuroinflammation by Altering the Gut Microbiota.}, journal = {Aging cell}, volume = {}, number = {}, pages = {e70188}, doi = {10.1111/acel.70188}, pmid = {40762371}, issn = {1474-9726}, support = {GZC20240236//Postdoctoral Fellowship Program of CPSF/ ; 20230204067YY//the Science and Technology Development Program of Jilin Province/ ; 135131002//Fundamental Research Funds for the Central Universities/ ; }, abstract = {Aging is a process of gradual decline in physical and cognitive function and is a major risk factor for mortality. Despite the increasing number of relevant studies, the mechanisms regulating the aging process have not been fully elucidated. Genetic factors have long been recognized as key factors in controlling the rate of aging. Testes-specific protease 50 (TSP50) has been shown to be involved in the regulation of embryonic development and intestinal homeostasis, but its role in the regulation of aging remains unclear. Here, we showed that TSP50 expression was reduced in the hippocampus of both aged humans and mice. TSP50 deficiency in neural stem cells (NSCs) drove accelerated aging in mice, characterized by exacerbated age-related cognitive impairments and significantly elevated neuroinflammation. Notably, aged mice with NSCs-specific knockout of TSP50 exhibited impaired intestinal mucosal barriers, dysbiosis of gut microbiota, and a marked reduction in the production of short-chain fatty acids (SCFAs). Restoring gut microbial ecology using fecal microbiota transplantation (FMT) and overexpressing TSP50 successfully alleviated aging-associated cognitive decline and neuroinflammation. Taken together, our study suggests that TSP50 plays a critical role in the aging process and identifies gut microbiota as a pivotal mediator of TSP50's influence on age-related cognitive decline and neuroinflammation. These findings highlight the potential therapeutic value of targeting TSP50 and gut microbiota for aging, offering insights into aging mechanisms and interventions for aging-related neurodegenerative diseases.}, }
@article {pmid40761850, year = {2025}, author = {Cai, S and Lin, L and Cai, Y and Wang, C and Lin, Y and Zhou, J and Zhou, F and Chen, M}, title = {Phase angle associates with severity and mortality in acute-on-chronic liver failure.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1541795}, pmid = {40761850}, issn = {2296-858X}, abstract = {BACKGROUND: Acute-on-chronic liver failure is characterized by acute hepatic decompensation and high short-term mortality, thereby necessitating prompt prognostic assessment. Although phase angle (PhA) has been established as a biomarker in chronic diseases, its prognostic significance in ACLF remains unclear.<br><br>METHODS: In this study, we evaluated PhA in 78 ACLF patients and compared the results with those of two control groups: 45 patients with chronic hepatitis B infection but normal liver function, and 51 patients with abnormal liver function who did not meet the ACLF criteria. Upon hospital admission, comprehensive laboratory parameters were obtained, and PhA measurements were conducted to explore the associations among PhA, organ dysfunction indices, and established prognostic scoring systems for predicting 90-days outcomes in ACLF patients.<br><br>RESULTS: Our analysis demonstrated that ACLF patients exhibited significantly lower PhA values compared with both control groups. Notably, non-survivors within 90 days had substantially lower PhA levels than survivors. Additionally, patients with complications, including hepatic encephalopathy, ascites, gastrointestinal bleeding, and infection, showed markedly lower PhA values than those without such complications. Moreover, the combination of PhA with the Chronic Liver Failure - Sequential Organ Failure Assessment (CLIF-SOFA) score enhanced the predictive accuracy of 90-days mortality in ACLF patients.<br><br>CONCLUSION: Phase angle serves as a valuable biomarker for evaluating ACLF severity and predicting short-term mortality, potentially offering a novel approach to risk stratification in ACLF management.}, }
@article {pmid40761338, year = {2025}, author = {Zhao, Y and Chen, J and Qin, Y and Yuan, J and Yu, Z and Ma, R and Liu, F and Zhao, J}, title = {Linking Short-Chain Fatty Acids to Systemic Homeostasis: Mechanisms, Therapeutic Potential, and Future Directions.}, journal = {Journal of nutrition and metabolism}, volume = {2025}, number = {}, pages = {8870958}, pmid = {40761338}, issn = {2090-0724}, abstract = {Short-chain fatty acids (SCFAs), pivotal metabolites derived from microbial fermentation of dietary fiber, serve as critical modulators of glucose and lipid metabolism. Dysregulation of SCFA levels, often stemming from inadequate fiber intake or dysbiosis of SCFA-producing microbiota, correlates with heightened susceptibility to diverse pathologies, including autoimmune disorders, metabolic syndromes, and malignancies. Emerging evidence underscores the pleiotropic roles of SCFAs in orchestrating gut and systemic homeostasis, positioning them as novel therapeutic candidates for immune dysregulation, inflammatory conditions, and transplant rejection. This review synthesizes current knowledge on SCFA biosynthesis, absorption dynamics, and their multifaceted regulatory mechanisms, spanning epigenetic modulation, G protein-coupled receptor (GPR) signaling, and immune cell crosstalk. We further elucidate their therapeutic potential in clinical contexts, emphasizing their capacity to recalibrate immune responses, suppress chronic inflammation, and mitigate oncogenesis. By integrating recent advances in microbiome research and translational applications, this work highlights the imperative for precision interventions targeting SCFA pathways to bridge the gap between microbial ecology and clinical innovation.}, }
@article {pmid40760940, year = {2025}, author = {Petrullo, L and Webber, Q and Raulo, A and Boutin, S and Lane, JE and McAdam, AG and Dantzer, B}, title = {Social Microbial Transmission in a Solitary Mammal.}, journal = {Ecology letters}, volume = {28}, number = {8}, pages = {e70186}, pmid = {40760940}, issn = {1461-0248}, support = {//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada/ ; 0515849//Division of Environmental Biology/ ; 2010726//Division of Environmental Biology/ ; 2338394//Division of Environmental Biology/ ; }, mesh = {Animals ; *Sciuridae/microbiology/physiology ; *Social Behavior ; *Gastrointestinal Microbiome ; Territoriality ; Population Density ; Behavior, Animal ; Male ; Female ; }, abstract = {Microbial transmission is hypothesised to be a major benefit of sociality, facilitated by affiliative behaviours such as grooming and communal nesting in group-living animals. Whether microbial transmission is also present in animals that do not form groups because territoriality limits interactions and prevents group formation remains unknown. Here, we investigate relationships among gut microbiota, population density and dynamic behavioural and spatial measures of territoriality in wild North American red squirrels (Tamiasciurus hudsonicus). Periods of high population density predicted population-level gut microbial homogeneity but individual-level diversification, alongside changes in obligately anaerobic, non-sporulating taxa indicative of social transmission. Microbial alpha-diversity increased with more frequent territorial intrusions, and pairs with stronger intrusion-based social associations had more similar gut microbiota. As some of the first evidence for social microbial transmission in a solitary system, our findings suggest that fluctuations in density and territorial behaviours can homogenise and diversify host microbiomes among otherwise non-interacting animals.}, }
@article {pmid40760525, year = {2025}, author = {Deng, M and Chen, W and Wang, X}, title = {Characteristics of gut microbiota in longevity populations in China and its relationship with healthy aging.}, journal = {Medicine}, volume = {104}, number = {31}, pages = {e43633}, pmid = {40760525}, issn = {1536-5964}, support = {He Technology 202217//Hezhou Science and Technology Bureau/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; China ; *Longevity/physiology ; Male ; Middle Aged ; Female ; Aged ; Adult ; *Healthy Aging/physiology ; Feces/microbiology ; Aged, 80 and over ; Child ; Young Adult ; RNA, Ribosomal, 16S/genetics ; Cohort Studies ; }, abstract = {This study aimed to investigate the differences in gut microbiota diversity and compositional characteristics between long-lived individuals (≥90 years) and individuals at different life stages (children, young and middle-aged adults, and elderly), in order to provide a foundational basis for microbial interventions in healthy aging. An observational cohort design was adopted, recruiting healthy participants divided into 4 age groups: children, young and middle-aged adults, elderly, and long-lived individuals. Fecal samples were collected and subjected to high-throughput 16S rRNA gene sequencing. The alpha diversity, beta diversity, and community structural differences of the gut microbiota were assessed, and representative microbial taxa were identified using LEfSe analysis. The long-lived group exhibited significantly higher species richness and diversity (Chao1 and Shannon indices, P < .05), with a more balanced and stable microbial structure. At the phylum level, the long-lived group had the highest relative abundance of Firmicutes and the lowest of Bacteroidetes. At the genus level, lactic acid bacteria such as Lactobacillus were significantly enriched. LEfSe analysis indicated that lactic acid bacteria-related taxa may serve as characteristic markers of this population. The gut microbiota of long-lived individuals exhibits higher ecological stability and a distinctive composition, which may be associated with healthy aging. These findings provide preliminary evidence for the relationship between longevity and gut microbial ecology and suggest that structural characteristics of these microbial communities may be involved in the process of healthy aging, offering a basis for future exploration of microbial intervention strategies.}, }
@article {pmid40759677, year = {2025}, author = {Huang, J and Wu, F and Xiao, Y and Ye, M and Wu, X and Chen, H and Xu, Q}, title = {Deciphering nitrogen-driven microbial succession in an anaerobic membrane bioreactor-coupled A[2]/O ecological system for the remediation of industrial swine wastewater.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {28422}, pmid = {40759677}, issn = {2045-2322}, support = {2024R1031001, 2024R1031003 and 2022R1032003//Basic Public Welfare Research Program of Fujian Province of China/ ; 2024R1031001, 2024R1031003 and 2022R1032003//Basic Public Welfare Research Program of Fujian Province of China/ ; 2024R1031001, 2024R1031003 and 2022R1032003//Basic Public Welfare Research Program of Fujian Province of China/ ; 2023S0003//Fuzhou Science and Technology Bureau spark project/ ; Q20194303//Scientific Research Items Foundation of Hubei Educational Committee/ ; YY202446//Jingchu University of Technology Ph.D. Startup Fund/ ; }, mesh = {*Bioreactors/microbiology ; Animals ; *Wastewater/microbiology/chemistry ; Swine ; *Nitrogen/metabolism ; Anaerobiosis ; *Waste Disposal, Fluid/methods ; Biological Oxygen Demand Analysis ; Water Purification/methods ; Membranes, Artificial ; Phosphorus ; Industrial Waste ; Biodegradation, Environmental ; }, abstract = {Rapid expansion of industrial pig farming has intensified existing challenges in the management of nutrient-rich wastewater, characterized by high organic loads (chemical oxygen demand (COD): 15,000-30,000 mg/L) and ammonium nitrogen (NH4[+]-N): 800-2,500 mg/L) concentrations. In this study, an integrated treatment system with a combination of a high-density polyethylene (HDPE) membrane-based anaerobic membrane bioreactor and an anoxic/aerobic/oxidation pond (A[2]/O) was developed for swine wastewater remediation. The system achieved exceptional remediation efficiency, removing 99.4, 99.5, 95.4, 92.8, and 97.9% of COD, biochemical oxygen demand (BOD), NH4[+]-N, total phosphorus (TP), and suspended solids (SS), respectively, with the anoxic and aerobic (A[2]) phases contributing to removal of 62.5, 60.9, 80.9, 94.6% of COD, BOD, TP, and SS, respectively. Microbial community analysis revealed process-specific dynamics, including Firmicutes enrichment (8.52 ± 3.33 to 10.81 ± 0.39%) in anaerobic stages and Nitrosomonas dominance (2.38 ± 0.21%) during nitrification. The HDPE membrane-based bioreactor performed effectively under high organic loading rates (5-8 kg COD·m[-3]·day[-1]), whereas the A[2]/O system optimized nutrient cycling through synchronized nitrification-denitrification (dissolved oxygen: 2.0-3.5 mg/L). In this study, we establish a scalable framework for the treatment of industrial swine wastewater by combining engineered infrastructure with the principles of microbial ecology to address conventional pollutants.}, }
@article {pmid40757865, year = {2025}, author = {Södergren, J and Noguera, PM and Petersen, MA and Jørgensen, NOG and Podduturi, R and Nicolaisen, MH}, title = {Myxobacteria isolated from recirculating aquaculture systems (RAS): ecology and significance as off-flavor producers.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0075725}, doi = {10.1128/aem.00757-25}, pmid = {40757865}, issn = {1098-5336}, abstract = {Despite advances in the operation of recirculating aquaculture systems (RAS), accumulation of earthy-muddy off-flavors in the fish remains a potential risk. Myxobacteria (Myxococcota) are reported to be among the most abundant geosmin synthase-harboring groups in RAS, but previous isolation attempts have been unsuccessful, limiting the knowledge of their role in off-flavor production. For the first time, we successfully isolated two geosmin-producing myxobacteria from RAS: Myxococcus virescens AT3 and Corallococcus exiguus AT4. Cell-specific geosmin production varied with the nutrient content in different media but was highest in a low-nutrient medium and when cultivated in water from RAS. Cultivation in RAS water also stimulated the production of other volatile organic compounds (VOCs). Newly identified potential off-flavor compounds included 4-methyl-2-heptanone ("forest" odor), 3-methyl-1-butanol ("medicinal" and "chemical"), and a presumptive sesquiterpenoid described as "musty," "earthy," and "flowery." The previously known off-flavor compound dimethyl sulfide was also detected. Myxobacteria have previously been proposed as keystone bacteria in the environment due to their predatory lifestyle. In predation assays using isolated bacteria from RAS, M. virescens AT3 and C. exiguus AT4 could successfully feed on 15 of 16 tested strains, suggesting a large influence on the biology of RAS microbiomes. The combination of predatory behavior and potent production of geosmin and other VOCs underscores the ecological and sensory impact of these bacteria in RAS. Understanding their behavior and metabolic outputs is critical to developing strategies for mitigating off-flavors in RAS.IMPORTANCEIssues with off-flavored fish in recirculating aquaculture systems (RAS) due to the presence of the earthy-musty smelling compounds geosmin and 2-MIB are considered as one of the industry's most economically significant challenges. Knowledge of conditions that affect off-flavor production is essential information in the development of viable solutions for its mitigation. Little is known about the function of these microbially produced compounds or the conditions that trigger their production, especially in the underexplored myxobacteria. Investigation of natural isolates is crucial to determine the function of the genes involved and their differential expression in response to environmental cues. While myxobacteria in RAS have been previously shown to harbor the geosmin synthase gene in molecular studies, the present study is the first attempt to isolate these bacteria from RAS and quantify their geosmin production under various nutrient conditions. Through cultivation-based methods, we demonstrate their production of both known and novel compounds with earthy attributes.}, }
@article {pmid40757859, year = {2025}, author = {Adekoya, AE and West, SR and Arriaga, SK and Ibberson, CB}, title = {Infections as ecosystems: community metabolic interactions in microbial pathogenesis.}, journal = {Infection and immunity}, volume = {}, number = {}, pages = {e0053024}, doi = {10.1128/iai.00530-24}, pmid = {40757859}, issn = {1098-5522}, abstract = {Microbes rarely exist alone; instead, they live in dynamic multi-species communities with a range of metabolic capacities. To establish within a polymicrobial community, an organism must compete with the other members of the community for space and nutrients. In addition, microbes form complex metabolic interdependencies in polymicrobial environments, and these nutrient exchanges are central to overall community function. Interactions between microbial community members dictate key processes, including nutrient cycling, tolerance to disturbances, and disease progression, and these interactions are known to depend on the environment in which they are measured. Therefore, understanding these ecological interactions is fundamental to our understanding of community composition, function, and impacts on disease. In this mini-review, we will describe the mechanisms microbes use to exchange nutrients in host-associated environments, with a focus on the oral and respiratory tracts. We will particularly emphasize the environmental factors that influence community composition and how interactions between organisms, ranging from cooperation to competition, impact nutrient bioavailability and overall community function during infection.}, }
@article {pmid40756216, year = {2025}, author = {Li, M and Liu, J and Cao, D and Chen, X and Shi, J and Hu, W and Xiao, C and Fang, Y}, title = {Heavy metal pollution simplifies microbial networks and enhances modularity during tailings primary succession: divergent assembly dynamics for bacterial and fungal communities.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1566627}, pmid = {40756216}, issn = {1664-302X}, abstract = {Microbial community play a fundamental role in primary succession of tailings ecosystems. However, the influence of heavy metal pollution on microbial interactions and assembly dynamics during this process remains poorly understood. In this study, we investigated bacterial and fungal communities in tailing soil and biological soil crusts (BSCs) undergoing primary succession under varying heavy metal pollution. By integrating microbial community profiling with measurements of soil nutrients and heavy metal concentrations, we aimed to elucidate how pollution levels shape microbial composition, co-occurrence networks, and assembly processes. Our results revealed clear differences in soil physicochemical properties, microbial diversity, community structure, and ecological interactions between low and high pollution conditions. Under high contamination, Burkholderiales dominated the bacterial communities, while Saccharomycetales and Pleosporales were representative among fungi. Microbial diversity decreased with increasing pollution, accompanied by simplified co-occurrence networks and increased modularity. In highly polluted environments, both bacterial and fungal communities exhibited stronger correlations with environmental factors. Interestingly, bacterial communities were more strongly associated with soil nutrient parameters, whereas fungal communities responded more closely to heavy metal concentrations. Community assembly analysis further showed a shift toward deterministic processes in bacterial communities under high pollution, while fungal assembly remained largely stochastic. These findings highlight the differential responses of bacterial and fungal communities to heavy metal stress and underscore the critical role of pollution in shaping microbial succession in tailing ecosystems. This study provides important insights into microbial ecology under environmental stress and may inform strategies for the bioremediation and management of contaminated mine lands.}, }
@article {pmid40756212, year = {2025}, author = {Cortez-Lázaro, AA and Vázquez-Medina, PJ and Caro-Degollar, EM and García Evangelista, JV and Cortez-Lázaro, RA and Rojas-Paz, JL and Legua-Cardenas, JA and Fernandez-Herrera, F and Pesantes-Rojas, CR and Ocrospoma-Dueñas, RW and Oliva-Cruz, SM and Manes-Cangana, GA and Romero Bozzetta, JL and Leiva Espinoza, ST}, title = {Global trends in Trichoderma secondary metabolites in sustainable agricultural bioprotection.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1595946}, pmid = {40756212}, issn = {1664-302X}, abstract = {The use of Trichoderma spp. constitutes a promising biotechnological strategy for sustainable agriculture, owing to its capacity to control phytopathogens and to produce bioactive secondary metabolites. This study, one of the first of its kind, addresses the absence of a comprehensive bibliometric assessment in this field. A systematic bibliometric analysis was conducted on 235 publications indexed in Scopus (2000-2025). Advanced tools such as VOSviewer and Bibliometrix were employed to track publication trends, identify key research themes, map collaborative networks, and assess the influence of leading authors and institutions. An exponential increase in scientific output was observed, peaking in 2023. Four principal research clusters were identified: antifungal activity, gene regulation, secondary metabolite production, and biosynthesis. India and China accounted for the highest publication volume, while Italy, represented by authors such as Francesco Vinale, accounted for the greatest scientific impact. International collaboration was extensive, particularly between Asia and Europe. The analysis indicates a progression from applied biocontrol studies to research focusing on molecular and genetic mechanisms, highlighting the need for multidisciplinary approaches that integrate biotechnology, agronomy, and microbial ecology. This bibliometric study provides an overview of Trichoderma secondary metabolites in agricultural biocontrol and outlines a research agenda emphasizing field validation, interdisciplinary collaboration, and the adoption of innovative technologies to bridge the gap between research and on-farm application in sustainable agriculture.}, }
@article {pmid40755785, year = {2025}, author = {Abuassaf, RA and Al-Jamal, FF and Abusara, OH and Zihlif, M and Deeb, AA and Al-Rshaidat, MMD}, title = {Evaluating the antibacterial properties of deep-sea sponges Dactylospongia elegants, Stelletta fibrosa, and Haliclona manglaris from the Jordanian Gulf of Aqaba.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19735}, pmid = {40755785}, issn = {2167-8359}, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; *Porifera/chemistry/genetics ; *Gram-Positive Bacteria/drug effects ; *Haliclona/chemistry ; *Gram-Negative Bacteria/drug effects ; Tandem Mass Spectrometry ; }, abstract = {Marine sponges are known for their rich variety of secondary metabolites, many of which show potential for pharmaceutical applications. In this study, three deep-sea sponge species-Stelletta fibrosa, Dactylospongia elegans, and Haliclona manglaris-were identified using DNA barcoding, and their ethanolic extracts were tested for antibacterial activity. The extracts were evaluated against Gram-positive (e.g., Bacillus pumilus, Staphylococcus aureus, Staphylococcus epidermidis, and methicillin-resistant Staphylococcus aureus, MRSA) and Gram-negative bacteria (e.g., Escherichia coli and Klebsiella aerogenes) using the agar well diffusion method. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) were also determined. Among the extracts, D. elegans exhibited the most potent antibacterial activity, with inhibition zones ranging from six to 21 mm against gram-positive bacteria and low MIC/MBC values from 0.25 to three mg/ml. Liquid chromatography-mass spectrometry (LC-MS/MS) analysis of D. elegans revealed the presence of bioactive compounds such as gallic acid, caffeic acid, bolinaquinone, dactyloquinone, and others, which are known for their antimicrobial properties. These findings suggest that D. elegans has promising antibacterial properties that could be valuable in combating antimicrobial resistance.}, }
@article {pmid40751837, year = {2025}, author = {Cruz-Cano, R and Bretón-Deval, L and Martínez-García, M and Díaz-Jaimes, P and Kolb, M}, title = {Changes in Microbial Community Assemblages Due To Urban Pollution, Detected via rRNA Gene Amplicon Sequencing in the Magdalena River, Mexico City.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {85}, pmid = {40751837}, issn = {1432-184X}, support = {516486//Secretaria de Ciencia, Humanidades, Tecnolog&#xed;a e Innovaci&#xf3;n/ ; IN211921//UNAM-PAPIIT/ ; IN211921//UNAM-PAPIIT/ ; IN211921//UNAM-PAPIIT/ ; }, mesh = {Mexico ; *Rivers/microbiology/chemistry ; *Bacteria/genetics/classification/isolation &amp; purification ; *Microbiota/genetics ; Cities ; Environmental Monitoring ; RNA, Ribosomal, 16S/genetics ; Water Quality ; *Water Pollution/analysis ; Water Microbiology ; Water Pollutants, Chemical/analysis ; }, abstract = {As freshwater sources become increasingly polluted and depleted, the delicate balance of aquatic environments is disrupted, leading to cascading effects throughout entire ecosystems. This disruption manifests in various ways, including changes in water chemistry, temperature fluctuations, and the introduction of contaminants, all of which contribute to alterations in microbial communities. We applied eDNA metabarcoding to characterize microbial communities along an anthropogenic pollution gradient in the Magdalena River, a tropical river in Mexico City. Sampling was conducted at four sites representing different levels of human influence. Results revealed differences in both bacterial and microeukaryotic community compositions between sites. In areas with low to moderate disturbance, bacterial genera associated with nitrogen cycling and plant-microbe interactions (e.g., Rhizobacter, Rhodoferax, and Flavobacterium) were predominant, whereas in more heavily impacted sites, genera linked to enteric, nosocomial, or fecal sources (e.g., Arcobacter, Acinetobacter, and Aeromonas) dominated. Peri-urban sites exhibited higher alpha diversity at the phylum level for bacteria, and microeukaryotic communities; two phyla account for over 75% of the relative abundance throughout the year (Ciliophora &amp; Chlorophyta). Statistical analysis showed that water quality influences microbial composition in the sites. These findings demonstrate that urban influence alter microbial community composition, showing similar patterns to other studies. Our study, however, also discovered certain taxa that had not been previously recorded in tropical urban rivers, thereby broadening the existing knowledge, which has primarily been based on temperate systems. This research offers one of the initial thorough evaluations of microbial communities in urban rivers in Mexico and highlights the potential of eDNA metabarcoding as a valuable tool for environmental monitoring.}, }
@article {pmid40750488, year = {2025}, author = {Lopes, ACA and Martins, LV and Ferreira, GNC and Trivedi, P and Araujo, ASF}, title = {Do plants remember their microbial partners?.}, journal = {Trends in plant science}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tplants.2025.07.005}, pmid = {40750488}, issn = {1878-4372}, abstract = {Plants host dynamic microbiomes that are critical for stress resilience and productivity. Emerging evidence suggests that 'microbiome memory' enables plants to retain beneficial microbes via epigenetic mechanisms and vertical transmission. Understanding how 'microbiome memory' forms, persists, and influences plant adaptation is crucial for advancing resilient crop systems and sustainable agriculture.}, }
@article {pmid40749586, year = {2025}, author = {Li, H and Hong, L and Wang, Y and Chai, S and Huang, P and Chen, H and Liu, W and Zhu, W and Marzorati, M and Wang, H and Tian, J and Zhang, X}, title = {Origin-dependent metabolic variations: How Atractylodes macrocephalae Rhizoma extract's chemical diversity leads to stage-specific changes in simulated digestion.}, journal = {Journal of pharmaceutical and biomedical analysis}, volume = {266}, number = {}, pages = {117082}, doi = {10.1016/j.jpba.2025.117082}, pmid = {40749586}, issn = {1873-264X}, abstract = {Atractylodes macrocephalae Rhizoma (AMR), a traditional Chinese medicine, is extensively utilized in clinical practice for its pharmacological properties, including anti-inflammatory, anti-tumor, and gastrointestinal regulatory effects. Nonetheless, the intricate nature of traditional Chinese medicine extracts has resulted in few studies into the effects of compositional variations in Atractylodes macrocephalae Rhizoma extracts (AMRE) from diverse sources on gastrointestinal metabolic processes. This study developed an integrated in vitro and in vivo compound analysis strategy utilizing Ultrahigh-performance liquid chromatography Quadrupole-Orbitrap tandem mass spectrometry (UHPLC-Q-Orbitrap-MS/MS) and the Simulator of Human Intestinal Microbial Ecosystem (SHIME) to examine the metabolic alterations caused by variations in the chemical constituents of AMRE from diverse sources. A total of 117 chemical constituents were found, primarily classified as terpenoids, organic acids, alkaloids, coumarins, and phenylpropanoids. 51 prototype components and 79 metabolites were identified. The metabolic processes were predominantly observed among terpenoids, with reaction types encompassing hydroxylation, oxidation, hydrogenation, methylation, glucuronidation, and sulfonation. Analysis of dynamic changes revealed that the majority of the prototype components underwent a considerable reduction in the colon, while the metabolites were markedly enriched in both the small intestine and colon. Differential analysis showed that AMRE3 contained the highest number of terpenoid compounds, AMRE1 exhibited the highest average content of chemical constituents, and AMRE2 had the lowest. These disparities were consistently observed in both prototype components and metabolic behaviors, thereby affirming the robust correlation between metabolite distribution and chemical constituents. This study elucidates, for the first time, the variations in the chemical constituents of AMRE from diverse sources and the metabolic characteristics and discrepancies they elicit in the human gastrointestinal tract (GI tract), offering a viable strategy for further clarifying the material basis of its pharmacological effects and clinical applications.}, }
@article {pmid40748243, year = {2025}, author = {Portal-Gonzalez, N and Wang, W and He, W and Santos-Bermudez, R}, title = {Engineering Plant Holobionts for Climate-Resilient Agriculture.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf158}, pmid = {40748243}, issn = {1751-7370}, abstract = {The plant holobiont-an integrated unit of the host and its microbiome-has co-evolved through ecological and genetic interactions. Microbiome engineering offers a promising route to enhance resilience in response to climate stress, soil degradation, and yield stagnation. This review presents an integrated framework combining microbial ecology, synthetic biology, and computational modeling to rationally design synthetic microbial communities (SynComs) for agriculture. We outline ecological principles-priority effects, keystone taxa, and functional redundancy-that shape microbiome assembly and guide SynCom design. Strategies like CRISPR interference, biosensor circuits, and quorum-sensing modules enable programmable microbial functions. We also highlight the predictive potential of in silico modeling-including genome-scale metabolic models, dynamic flux balance analysis, and machine learning-to simulate interactions, optimize SynCom composition, and enhance design accuracy. To bridge lab and field, we discuss native microbial chassis, encapsulation, and precision delivery as tools for scalable, ecosystem-integrated deployment. We introduce the concept of the programmable holobiont: an engineered plant-microbe partnership capable of dynamic feedback, interkingdom signaling, and ecological memory. This systems-level perspective reframes plants as designable ecosystems. By synthesizing cross-disciplinary advances, we offer a roadmap for climate-resilient agriculture, where engineered microbiomes improve sustainability, yield stability, and environmental adaptation.}, }
@article {pmid40743118, year = {2025}, author = {Ozturk, S and Ekmen, FG and Ekmen, H and Ünal, EM and Er, A and Keskin, E and Arbuckle, BS}, title = {Decoding past microbial life and antibiotic resistance in İnonü Cave's archaeological soil.}, journal = {PloS one}, volume = {20}, number = {7}, pages = {e0326358}, pmid = {40743118}, issn = {1932-6203}, mesh = {*Soil Microbiology ; *Archaeology ; *Bacteria/genetics/classification/drug effects ; *Caves/microbiology ; RNA, Ribosomal, 16S/genetics ; Humans ; *Drug Resistance, Microbial/genetics ; Microbiota/genetics ; Turkey ; }, abstract = {This study, which bridges the disciplines of archaeology and microbiology, examines the ancient bacterial communities and antibiotic-resistance genes in soil samples collected from İnönü Cave in Zonguldak, Turkiye. Our aim is to provide a comprehensive understanding of historical human activities and their influence on microbial communities. Soil samples were gathered from four distinct cultural levels from the Chalcolithic Age to the Early Iron Age. The microbial communities were characterized, and antibiotic-resistance genes were identified using high-throughput sequencing of 16S rRNA genes and metagenomic studies. This interdisciplinary approach not only enriches our understanding of ancient microbial communities but also opens up new avenues for research and collaboration. The results of our study showed a wide range of microorganisms, including prominent bacterial groups such as Acidobacteriota, Actinobacteriota, Bacteroidota, Chloroflexi, Cyanobacteria, Firmicutes, Myxococcota, and Proteobacteria. The study identified the presence of the tetracycline resistance gene tetA in Chalcolithic samples, the class 1 integron intl1 in Early Bronze Age samples, and the oxacillinase gene OXA58 in Late Bronze Age samples. These findings underscore the long-term impact of human activities on microbial communities, as antibiotic-resistance genes have been present and have remained over various historical periods, perhaps influenced by both human activities and environmental variables. This knowledge is crucial for understanding the resilience and adaptability of microbial communities in the face of human-induced changes. The coexistence of these resistance genes and alterations in the microbial population suggest substantial connections between human activities and soil microbiota. This study, which draws on the fields of archaeology, microbiology, and environmental science, offers valuable insights into the ancient microbial ecology and underscores the enduring presence of antibiotic resistance. It emphasizes the necessity of a comprehensive, interdisciplinary approach, spanning multiple fields, to comprehend microbial communities' evolution and resistance mechanisms in archaeological settings.}, }
@article {pmid40742751, year = {2025}, author = {Fischer, MT and Xue, KS and Costello, EK and Dvorak, M and Raboisson, G and Robaczewska, A and Caty, SN and Relman, DA and O'Connell, LA}, title = {Effects of parental care on skin microbial community composition in poison frogs.}, journal = {eLife}, volume = {14}, number = {}, pages = {}, pmid = {40742751}, issn = {2050-084X}, support = {DP2 HD102042/HD/NICHD NIH HHS/United States ; DP2HD102042/NH/NIH HHS/United States ; Erwin Schroedinger Stipend J-4526B//Austrian Science Fund/ ; }, mesh = {Animals ; *Skin/microbiology ; *Microbiota ; *Anura/microbiology/physiology ; Larva/microbiology ; Female ; Male ; *Bacteria/classification/isolation &amp; purification/genetics ; Poison Frogs ; }, abstract = {Parent-offspring interactions constitute the first contact of many newborns with their environment, priming community assembly of microbes through priority effects and shaping host health and disease. Microbe acquisition during parental care is well studied in humans and agriculturally relevant species but remains poorly understood in other vertebrate groups, such as amphibians. Here, we investigate vertical transmission of skin microbiota in poison frogs (Dendrobatidae), where fathers transport tadpoles piggyback-style from terrestrial clutches to aquatic nurseries. We found that substantial bacterial colonization of embryos begins after hatching, suggesting that the vitelline envelope acts as a microbial barrier. A cross-foster experiment demonstrated that poison frogs performing tadpole transport serve as a source of skin microbes for tadpoles on their back. To study how transport impacts skin communities of tadpoles in an ecologically relevant setting, we sampled sympatric species that do or do not exhibit tadpole transport in their natural habitat. We did not find a higher degree of similarity between microbial communities of tadpoles and adults in species that transport their offspring compared to those that do not. Similarly, communities of tadpoles were no more similar to their caregiver than to unrelated adults, indicating that most caregiver-associated microbes do not remain in tadpole communities long-term. Nonetheless, some taxa persisted on tadpoles over development. This study is the first to demonstrate that offspring transport facilitates transmission of parental skin microbes in anurans.}, }
@article {pmid40742667, year = {2025}, author = {Liang, M and Wu, WJ and Li, L and Qin, H and Li, SN and Zheng, GL and Hou, DM and Huang, Q and Cheng, L and Jie, HQ and Lu, JR and He, JC and Yang, J and Wei, W}, title = {Characteristics of the microbiota in the nasopharynx and nasal cavity of healthy children before and during the COVID-19 pandemic.}, journal = {World journal of pediatrics : WJP}, volume = {}, number = {}, pages = {}, doi = {10.1007/s12519-025-00953-z}, pmid = {40742667}, issn = {1867-0687}, support = {81800903//National Natural Science Foundation of China/ ; 82171135//National Natural Science Foundation of China/ ; 82371140//National Natural Science Foundation of China/ ; 81970881//National Natural Science Foundation of China/ ; 82271160//National Natural Science Foundation of China/ ; 21Y31900504//Science and Technology Innovation Plan Of Shanghai Science and Technology Commission/ ; 2024YFC2511100//National Key R&amp;D Program of China/ ; }, abstract = {BACKGROUND: Microbial colonization in the nasopharynx and nasal cavity plays a defensive role in children. The coronavirus disease 2019 (COVID-19) pandemic may have an influence on the nasopharynx and nasal cavity microbiota. This study aimed to identify and compare the microbiota in the nasopharynx and nasal cavity before and during the COVID-19 pandemic in a healthy pediatric population.<br><br>METHODS: Separate mucosal swabs were collected from the nasopharynx and nasal cavity of healthy children before and during the COVID-19 pandemic. A 16S ribosomal RNA-based metagenomic approach was employed to characterize and analyze alterations in the nasopharyngeal and nasal microbiota to determine whether isolation measures, such as mask wearing, influence microbial ecology.<br><br>RESULTS: The richness and diversity of the nasopharyngeal and nasal microbiota decreased during the COVID-19 pandemic compared with before the pandemic. Firmicutes and Proteobacteria were the most abundant phyla in the nasopharyngeal and nasal microbiota, respectively, both before and during the pandemic. Corynebacterium and Moraxella were the dominant genera in the nasopharyngeal and nasal microbiota during the COVID-19 pandemic, whereas Pseudomonas and Corynebacterium were dominant before the pandemic. Compared with pre-pandemic conditions, microbial colonization differed significantly for Cyanobacteria/Chloroplast and Bacteroidetes in the nasopharynx and for Planctomycetes in the nasal cavity during the COVID-19 pandemic.<br><br>CONCLUSIONS: This study revealed a lower microbiota diversity during COVID-19, possibly accompanied by microbiota dysbiosis, increased risk of respiratory infections and inflammatory responses in healthy children. This study underscores the importance of reestablishing microbiota balance and highlights the need for personalized treatment and prophylactic strategies in routine public health practice. Supplementary file3 (MP4 150533 KB).}, }
@article {pmid40742453, year = {2025}, author = {Lezcano, M&#xc1; and Carrizo, D and Lominchar, M&#xc1; and Sánchez-García, L and Quesada, A and Parro, V}, title = {Temperature-Sensitive Lipids Reveal Intraspecific Diversity in Bacteria Isolated from an Ancient Antarctic Microbial Mat.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {84}, pmid = {40742453}, issn = {1432-184X}, support = {FJC2018-037246-I//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2022-140180OB-C21//Ministerio de Ciencia e Innovaci&#xf3;n/ ; RYC2018-023943-I//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2021-126746NB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; }, mesh = {Antarctic Regions ; *Bacteria/genetics/classification/isolation &amp; purification/chemistry/metabolism ; RNA, Ribosomal, 16S/genetics ; Fatty Acids/analysis ; *Lipids/analysis/chemistry ; Temperature ; Phylogeny ; *Geologic Sediments/microbiology ; }, abstract = {Ancient Antarctic microbial mats harbour viable bacteria that have been exposed to extreme cold and arid conditions for hundreds of years. To delve into the molecular mechanisms underlaying their survival, we isolated 12 bacterial strains from a 1,000-year-old desiccated microbial mat from the McMurdo Ice Shelf and studied their lipid composition as a function of temperature. Six of the bacterial strains were classified as Paenisporosarcina macmurdoensis, and the other six as Arthrobacter sp., according to 16S rRNA gene analyses. Two strains of each taxon were incubated at their minimum and maximum growth temperatures, and the changes in their lipid profiles were analyzed. The proportion of major fatty acids (saturated, unsaturated, and iso- and anteiso-) remained relatively constant across temperature in the four strains, but the composition of hydrocarbons and alcohols differed between taxa (e.g., presence of unsaturated alkenes in Arthrobacter sp., or unidentified isoprenoid alcohols in P. macmurdoensis). This highlights the diagnostic value of non-fatty acid lipids and revealed a taxon-dependent lipid composition. Despite the taxon-associated lipid profile, incubation temperature also influenced lipid composition in both taxa, with higher temperature correlating with greater lipid richness. Interestingly, the two P. macmurdoensis strains showed distinct lipid profiles at 20°C, suggesting that intraspecific lipid diversity reflects within-species physiological variability with potential relevance for adaptation to temperature fluctuations in the mat. Therefore, assessing the influence of temperature on bacterial lipids is crucial for understanding their adaptation and survival in extreme environments, as well as for expanding species lipid inventories for biological interpretations of ancient samples.}, }
@article {pmid40742287, year = {2025}, author = {Zhang, Y and Sun, H and Huang, Q and Zhang, L and Zou, X and Liu, Y}, title = {Anaerobic Digestion Performance and Microbial Community Structures in a Pilot-Scale Up-Flow Anaerobic Sludge Blanket (UASB) Treating Distillery Wastewater.}, journal = {Water environment research : a research publication of the Water Environment Federation}, volume = {97}, number = {8}, pages = {e70153}, pmid = {40742287}, issn = {1554-7531}, support = {//Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Grant/ ; //NSERC Alliance/ ; //Alberta Distillers Limited/ ; //Alberta Innovates/ ; //City of Calgary/ ; //Canada Research Chair (CRC) in Future Water Services/ ; //China Scholarship Council (CSC) PhD Scholarship/ ; }, mesh = {Anaerobiosis ; *Waste Disposal, Fluid/methods ; *Bioreactors/microbiology ; Pilot Projects ; *Sewage/microbiology ; *Wastewater/microbiology ; *Industrial Waste ; Bacteria/metabolism ; Methane ; }, abstract = {Anaerobic digestion (AD) is a promising technology for treating high-strength industrial wastewater while recovering biogas as a renewable energy source. In this study, a pilot-scale up-flow anaerobic sludge blanket (UASB) reactor, with a working volume of 225 L, was operated for 130 days to treat raw distillery wastewater. Three different types of distillery wastewater, including centrate, spent caustic, and other low-strength process wastewater generated during operations (e.g., condensation water), were mixed to balance extreme pH levels and create conditions more suitable for AD. The UASB reactor demonstrated stable performance at an organic loading rate (OLR) of 10.0 kg COD/m[3]/day, achieving a COD removal efficiency of 86%. Average methane yield was more than 71% throughout the operation. Microbial community analysis revealed a significant increase in key syntrophic bacteria and methanogens, with Methanobacterium accounting for 55.8% of the archaeal population. Network and Mantel analyses indicated that syntrophic partnerships play a crucial role in enhancing AD of distillery wastewater under high OLR conditions. Overall, the UASB reactor exhibited high process stability, highlighting its potential for large-scale application in distillery wastewater treatment.}, }
@article {pmid40742109, year = {2025}, author = {Jones, KR and Song, Y and Rinaldi, SS and Moran, NA}, title = {Effects of priority on strain-level composition of the honey bee gut community.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0082825}, doi = {10.1128/aem.00828-25}, pmid = {40742109}, issn = {1098-5336}, abstract = {Host-associated microbiomes are complex communities shaped by interactions between members. The type VI secretion system (T6SS), among other bacterial weapons, allows gram-negative bacteria to deliver toxic effectors into competitors. In this study, we investigated the impact of differential colonization timing on the competitive advantage associated with T6SS possession using Snodgrassella alvi, a core symbiont of the honey bee gut microbiome. Following a timeline based on the natural establishment window of the gut microbiome, we sequentially inoculated newly emerged bees with fluorescently labeled strains that differed in presence of the T6SS-1. When inoculated simultaneously, the T6SS-1-possessing strain (wkB2) consistently excluded the T6SS-1-lacking strain (wkB332); however, when given a 5-day advantage, the second strain was consistently excluded regardless of strain identities. With a 1-day advantage, the effect of priority was weakened, but wkB332 was able to persist following introduction of wkB2. Utilizing a wkB2 T6SS-1 knockout strain, we repeated our 24 hour priority experiments and found that the T6SS-1 contributes to invasion outcomes along with other mechanisms of competition. Through fluorescent microscopy, we explored how coexisting strains in these experimental scenarios organize spatially within the bee ileum. Our results demonstrate that colonization timing can have lasting consequences for strain composition of the established microbiome. These findings illustrate the influence of stochastic processes in microbial community assembly and emphasize that differences in colonization timing may alter competitive outcomes between taxa, impacting taxon coexistence.IMPORTANCEThe bacterial gut communities of honey bees possess considerable strain-level diversity between hives, between individual bees, and within individual bees. However, the factors underlying strain coexistence are unclear. Here, we provide support for timing of colonization, or priority effects, as one factor driving this strain-level diversity. Our results show that priority inoculation can prevent colonization by subsequent competing bacterial strains and mitigate advantages conferred through bacterial weaponry. Further, a brief window of priority can facilitate the coexistence of strongly and weakly competitive strains within single bees. These results add to our understanding of the impacts of priority effects in host-associated microbial communities. Such an understanding can aid the development of future probiotic strategies aimed at improving honey bee health.}, }
@article {pmid40740319, year = {2025}, author = {Siceloff, AT and Waltman, D and Gunning, CE and Nolan, SP and Rohani, P and Shariat, NW}, title = {Longitudinal study highlights patterns of Salmonella serovar co-occurrence and exclusion in commercial poultry production.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1570593}, pmid = {40740319}, issn = {1664-302X}, abstract = {Recent advances in next-generation sequencing approaches have revealed that Salmonella often exists in multiserovar populations, with important implications for public health as time and resource constraints limit serovar characterization by colony-based isolation methods. It is important to characterize Salmonella population dynamics to then understand how the microbial ecology influences serovar evolution and thus, animal and human health outcomes. Chicken remains the leading source of foodborne Salmonella outbreaks in the U. S., despite reductions in contamination at the product level, underscoring the need for targeted control strategies. This study aimed to survey multiserovar Salmonella populations in broiler breeder flocks and monitor fluctuations throughout production. Deep serotyping was performed on environmental breeder samples collected over 2 years as part of a surveillance program. About 18% (104/568) of samples contained multiple serovars, with serovar Kentucky negatively associated with other serovars, often excluding them. Longitudinal sampling across two commercial complexes over 65 weeks included pullet and breeder farms. Environmental samples were collected via pre-moistened boot socks and rodent bait boxes, with on-farm rodents captured. Salmonella prevalence in pullet flocks was 17% (11/64), while 41% (135/330) of breeder samples were positive, peaking at 38 weeks of age. Rodents showed 35% (17/49) positivity in gastrointestinal samples and 9% (3/33) in bait station swabs, with six serovars identified, three of which were shared with flocks. Our cross-sectional and longitudinal Salmonella surveillance highlights the complexity of serovar interactions with further work required to elucidate the mechanisms of competitive exclusion.}, }
@article {pmid40739711, year = {2025}, author = {Xu, Y and Zhu, Y and Wu, X and Peng, W and Zhong, Y and Cai, Y and Chen, W and Liu, L and Tan, B and Chen, T}, title = {Gut Microbiota-Derived Acetate Ameliorates Endometriosis via JAK1/STAT3-Mediated M1 Macrophage Polarisation.}, journal = {Microbial biotechnology}, volume = {18}, number = {8}, pages = {e70202}, pmid = {40739711}, issn = {1751-7915}, support = {8216140922//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Female ; *Endometriosis/therapy/microbiology/metabolism ; Mice ; Humans ; Fecal Microbiota Transplantation ; *STAT3 Transcription Factor/metabolism ; *Janus Kinase 1/metabolism ; *Macrophages/metabolism/immunology ; Disease Models, Animal ; *Acetates/metabolism ; Signal Transduction ; Feces/microbiology/chemistry ; }, abstract = {Endometriosis (EMs) is a common inflammatory disorder in women of reproductive age, severely impacting patients' quality of life and fertility. Current hormonal therapies offer limited efficacy, and surgical interventions often fail to prevent recurrence. Recent studies suggest a close association between gut microbiota and the pathophysiology of EMs, though the precise mechanisms remain unclear. To investigate the influence of gut microbiota on EMs, this study established an EMs mouse model and performed faecal microbiota transplantation (FMT) using samples from healthy donors (AH group) and EMs patients (AE group) into the model mice. Results demonstrated that compared to the model group (M group), FMT from healthy donors (AH group) significantly reduced ectopic lesion volume (658.3 ± 116.1 vs. 167.2 ± 112.8 mm[3], p < 0.01) and weight (0.7420 ± 0.1233 vs. 0.1885 ± 0.1239 mg, p < 0.01). Conversely, FMT from EMs patients exacerbated disease progression. Mechanistic studies revealed that healthy donor FMT attenuated EMs by remodelling the gut microbial composition (enhancing α-diversity and Lactobacillus abundance while suppressing Bacteroidetes), significantly elevating acetate levels in faeces and ectopic lesions, activating the JAK1/STAT3 signalling pathway within lesions, and thereby driving macrophage polarisation toward the M1 phenotype (by increased iNOS/CD86 expression and decreased Arg1/CD206 expression). Simultaneously, healthy donor FMT enhanced intestinal barrier integrity by upregulating tight junction proteins (ZO-1, Occludin, Claudin-1/5) and reducing levels of intestinal permeability markers (DAO, IFABP). In contrast, AE group FMT disrupted gut microbial ecology, reduced acetate production, failed to activate the JAK1/STAT3 pathway, promoted M2 macrophage polarisation and impaired intestinal barrier function. Collectively, this study elucidates for the first time that acetate, as a key gut microbiota metabolite, exerts anti-EMs effects by activating the JAK1/STAT3 signalling pathway to drive macrophage reprogramming toward the M1 phenotype, thereby positioning gut microbiota reconstruction as a novel therapeutic strategy for endometriosis.}, }
@article {pmid40736560, year = {2025}, author = {Braglia, C and Cutajar, S and Magagnoli, S and Asciano, D and Burgio, G and Di Gioia, D and Baffoni, L and Alberoni, D}, title = {The Ground Beetle Poecilus (Carabidae) Gut Microbiome and Its Functionality.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {83}, pmid = {40736560}, issn = {1432-184X}, support = {ALMAIDEA-2018//University of Bologna/ ; ALMAIDEA-2018//University of Bologna/ ; ALMAIDEA-2018//University of Bologna/ ; ALMAIDEA-2018//University of Bologna/ ; ALMAIDEA-2018//University of Bologna/ ; }, mesh = {Animals ; *Coleoptera/microbiology ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Nosema/isolation &amp; purification/genetics ; High-Throughput Nucleotide Sequencing ; DNA, Bacterial/genetics ; Solanum lycopersicum ; }, abstract = {Ground beetles of the genus Poecilus (Carabidae) play key ecological roles in pest control and soil health. However, their gut microbiome remains largely unexplored despite increasing interest in insect-associated microbiota and its environmental implications. This study used next-generation sequencing and qPCR to characterise the gut microbiome of Poecilus beetles collected from organic and conventional tomato fields. Core microbiota were identified through prevalence-abundance filtering, revealing dominant genera including Gilliamella, Weissella, Enterobacter, and Enterococcus, alongside several low-abundance but consistently present taxa. Notably, Carnobacterium was detected for the first time in an insect host, and Nosema ceranae was identified for the first time in Carabidae, expanding the known host range of this microsporidian pathogen. Functional predictions based on 16S rRNA data and comparative genomic analysis showed enrichment in pathways related to amino acid synthesis, protein degradation, and monosaccharide metabolism. Significant inter-individual variation in microbial diversity and predicted functionality was observed, with lowest diversity and metabolic potential in beetles from conventionally managed fields, potentially indicating dysbiosis and environmental stress. The detection of Nosema and Serratia pathogens in some individuals adds new insights into pathogen dynamics within carabid beetles. Our findings reveal that the gut microbiome of Poecilus may be shaped by environmental factors and agricultural practices, influencing host health and ecological performance. These insights support the use of Poecilus as a bioindicator for soil ecosystem health and highlight the potential of microbiome-based metrics in agroecological monitoring.}, }
@article {pmid40732998, year = {2025}, author = {Herrera, M and Byerley, LO}, title = {Dietary Nitrogen and Its Role in the Gut Microbiome and Inflammatory Bowel Disease: A Narrative Review.}, journal = {Nutrients}, volume = {17}, number = {14}, pages = {}, pmid = {40732998}, issn = {2072-6643}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Inflammatory Bowel Diseases/microbiology/metabolism ; *Nitrogen/metabolism ; *Diet ; Dysbiosis ; Animals ; }, abstract = {In recent years, gut microbiota has emerged as a critical regulator of gastrointestinal health and disease, with its role in inflammatory bowel disease (IBD)-including Crohn's disease and ulcerative colitis-being particularly significant. Among the many factors influencing the gut microbiota, dietary components such as fibers, fats, and polyphenols have received substantial attention. However, nitrogen-containing compounds, such as amino acids, nitrates, urea, and even nucleic acids, such as purines, remain underexplored despite their integral role in shaping microbial ecology, host metabolism, and immune responses. Some of these compounds are metabolized by gut bacteria into bioactive molecules such as short-chain fatty acids, ammonia, and nitric oxide, which exert diverse effects on mucosal integrity and inflammation. IBD pathophysiology is characterized by chronic inflammation, microbial dysbiosis, and compromised epithelial barriers. Nitrogen metabolism contributes significantly to these processes by influencing microbial composition, metabolite production, and host immune pathways. The breakdown of various nitrogen-containing compounds in the body leads to the production of byproducts, such as ammonia and hydrogen sulfide, which have been implicated in mucosal damage and immune dysregulation. At the same time, nitrogen-derived molecules, such as short-chain fatty acids and nitric oxide, exhibit protective effects, underscoring the dual role of dietary nitrogen in health and disease. This narrative review highlights the complex interactions between dietary nitrogen sources, gut microbiota, and IBD pathogenesis. We summarize the mechanisms by which nitrogen compounds influence microbial dynamics, identify their contributions to inflammation and barrier dysfunction, and explore their therapeutic potential. Multidisciplinary approaches integrating clinical, metabolomic, and microbiome research are essential to unravel the full scope of nitrogen's role in gut health and identify novel therapeutic targets.}, }
@article {pmid40732683, year = {2025}, author = {Lin, H and Zeng, Z and Zhang, H and Jia, Y and Pang, J and Chen, J and Zhang, H}, title = {Gut-Vaginal Microbiome Crosstalk in Ovarian Cancer: Implications for Early Diagnosis.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {7}, pages = {}, pmid = {40732683}, issn = {2076-0817}, support = {2021YFH0189//Sichuan International Science and Technology Innovation Cooperation/HongKong/Macao/Taiwan Science and Technology Innovation Cooperation Project/ ; 2022NSFSC1363//the Sichuan International Science Foundation Project/ ; 2021HXFH065//the project for disciplines of excellence-Clinical Research Incubation Project, West China Hospital, Sichuan University/ ; }, mesh = {Humans ; Female ; *Ovarian Neoplasms/diagnosis/microbiology ; *Vagina/microbiology ; *Gastrointestinal Microbiome ; Early Detection of Cancer/methods ; Dysbiosis/microbiology ; }, abstract = {Ovarian cancer remains a formidable global health burden, characterized by frequent late-stage diagnosis and elevated mortality rates attributable to its elusive pathogenesis and the critical lack of reliable early-detection biomarkers. Emerging investigations into the gut-vaginal microbiome axis have unveiled novel pathogenic mechanisms and potential diagnostic targets in ovarian carcinogenesis. This comprehensive review systematically examines the compositional alterations in and functional interplay between vaginal and intestinal microbial communities in ovarian cancer patients. We elucidate three principal mechanistic pathways through which microbial dysbiosis may drive oncogenesis: (1) estrogen-mediated metabolic reprogramming via β-glucuronidase activity; (2) chronic activation of pro-inflammatory cascades (particularly NF-κB and STAT3 signaling); (3) epigenetic silencing of tumor suppressor genes through DNA methyltransferase modulation. We propose an integrative diagnostic framework synthesizing multi-omics data-incorporating microbial profiles, metabolic signatures, pathway-specific molecular alterations, established clinical biomarkers, and imaging findings-within a multifactorial etiological paradigm. This innovative approach aims to enhance early-detection accuracy through machine learning-enabled multidimensional pattern recognition. By bridging microbial ecology with tumor biology, this review provides novel perspectives for understanding ovarian cancer etiology and advancing precision oncology strategies through microbiome-targeted diagnostic innovations.}, }
@article {pmid40732215, year = {2025}, author = {Bodkhe, GA and Kumar, V and Li, X and Pei, S and Ma, L and Kim, M}, title = {Biosensors in Microbial Ecology: Revolutionizing Food Safety and Quality.}, journal = {Microorganisms}, volume = {13}, number = {7}, pages = {}, pmid = {40732215}, issn = {2076-2607}, support = {RS-2025-00515546//National Research Foundation (NRF) of Korea grant funded by the Korea Government (MIST)/ ; RS-2020-NR049591//National Research Foundation of Korea/ ; }, abstract = {Microorganisms play a crucial role in food processes, safety, and quality through their dynamic interactions with other organisms. In recent years, biosensors have become essential tools for monitoring these processes in the dairy, meat, and fresh produce industries. This review highlights how microbial diversity, starter cultures, and interactions, such as competition and quorum sensing, shape food ecosystems. Diverse biosensor platforms, including electrochemical, optical, piezoelectric, thermal, field-effect transistor-based, and lateral flow assays, offer distinct advantages tailored to specific food matrices and microbial targets, enabling rapid and sensitive detection. Biosensors have been developed for detecting pathogens in real-time monitoring of fermentation and tracking spoilage. Control strategies, including bacteriocins, probiotics, and biofilm management, support food safety, while decontamination methods provide an additional layer of protection. The integration of new techniques, such as nanotechnology, CRISPR, and artificial intelligence, into Internet of Things systems is enhancing precision, particularly in addressing regional food safety challenges. However, their adoption is still hindered by complex food matrices, high costs, and the growing challenge of antimicrobial resistance. Looking ahead, intelligent systems and wearable sensors may help overcome these barriers. Although gaps in standardization and accessibility remain, biosensors are well-positioned to revolutionize food microbiology, linking ecological insights to practical solutions and paving the way for safer, high-quality food worldwide.}, }
@article {pmid40731978, year = {2025}, author = {Garcia, M and Bruna, P and Duran, P and Abanto, M}, title = {Cyanobacteria and Soil Restoration: Bridging Molecular Insights with Practical Solutions.}, journal = {Microorganisms}, volume = {13}, number = {7}, pages = {}, pmid = {40731978}, issn = {2076-2607}, abstract = {Soil degradation has been accelerating globally due to climate change, which threatens food production, biodiversity, and ecosystem balance. Traditional soil restoration strategies are often expensive, slow, or unsustainable in the long term. In this context, cyanobacteria have emerged as promising biotechnological alternatives, being the only prokaryotes capable of performing oxygenic photosynthesis. Moreover, they can capture atmospheric carbon and nitrogen, release exopolysaccharides (EPSs) that stabilize the soil, and facilitate the development of biological soil crusts (biocrusts). In recent years, the convergence of multi-omics tools, such as metagenomics, metatranscriptomics, and metabolomics, has advanced our understanding of cyanobacterial dynamics, their metabolic potential, and symbiotic interactions with microbial consortia, as exemplified by the cyanosphere of Microcoleus vaginatus. In addition, recent advances in bioinformatics have enabled high-resolution taxonomic and functional profiling of environmental samples, facilitating the identification and prediction of resilient microorganisms suited to challenging degraded soils. These tools also allow for the prediction of biosynthetic gene clusters and the detection of prophages or cyanophages within microbiomes, offering a novel approach to enhance carbon sequestration in dry and nutrient-poor soils. This review synthesizes the latest findings and proposes a roadmap for the translation of molecular-level knowledge into scalable biotechnological strategies for soil restoration. We discuss approaches ranging from the use of native biocrust strains to the exploration of cyanophages with the potential to enhance cyanobacterial photosynthetic activity. By bridging ecological functions with cutting-edge omics technologies, this study highlights the critical role of cyanobacteria as a nature-based solution for climate-smart soil management in degraded and arid ecosystems.}, }
@article {pmid40731225, year = {2025}, author = {Sharma, P and Muehe, EM}, title = {Metal-tainted soils: a hidden threat to agriculture and health.}, journal = {Trends in plant science}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tplants.2025.07.004}, pmid = {40731225}, issn = {1878-4372}, abstract = {Hou et al. have revealed widespread metal contamination in agricultural soils, threatening food security, food quality, and human health. We propose climate-informed risk mapping of the mobile metal pool aligned with crop production mapping, followed by risk management strategies through engineered crops, metal-remediating plants, and targeted organic and microbial amendments.}, }
@article {pmid40730873, year = {2025}, author = {Roegiers, I and Gheysens, T and Minsart, M and De Clercq, P and Vanbeversluys, K and Rać, N and Stroka, G and de Croock, J and Van de Wiele, T and Dubruel, P and Arroyo, MC}, title = {Author Correction: GelMA as scaffold material for epithelial cells to emulate the small intestinal microenvironment.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {27634}, doi = {10.1038/s41598-025-13398-1}, pmid = {40730873}, issn = {2045-2322}, }
@article {pmid40728944, year = {2025}, author = {Lange-Enyedi, NT and Tóth, E and Abbaszade, G and Németh, P and Garvie, LAJ and Wolf, J and Neumann-Schaal, M and Khayer, B and Sipos, G and Makk, J}, title = {Pseudogemmobacter sonorensis sp. nov., a new alphaproteobacterium isolated from the slime flux of a tree (Populus fremontii) in the Sonoran Desert (Arizona, USA).}, journal = {International journal of systematic and evolutionary microbiology}, volume = {75}, number = {7}, pages = {}, doi = {10.1099/ijsem.0.006859}, pmid = {40728944}, issn = {1466-5034}, mesh = {RNA, Ribosomal, 16S/genetics ; *Phylogeny ; Bacterial Typing Techniques ; Fatty Acids/chemistry/analysis ; Base Composition ; DNA, Bacterial/genetics ; Desert Climate ; Sequence Analysis, DNA ; Ubiquinone/chemistry/analogs &amp; derivatives/analysis ; *Populus/microbiology ; Phospholipids/analysis ; Nucleic Acid Hybridization ; *Methylobacteriaceae/classification/isolation &amp; purification/genetics ; *Soil Microbiology ; Trees/microbiology ; }, abstract = {The bacterial strain PA1-206B[T] is a Gram-stain-negative, aerobic, non-motile and non-spore-forming bacterium with an irregular rod shape. It was isolated from a tree wound exudate of the Populus fremontii trunk in the Sonoran Desert (USA), and its taxonomic position was investigated by a polyphasic approach. Strain PA1-206B[T] grew optimally at 28-30 °C and from pH 6 to 10 without NaCl. Based on 16S rRNA gene sequence analysis, this isolate showed only 96.0% sequence similarity to the type strain of Pseudogemmobacter hezensis and similarity of 94.4-95.7% to other species of the genus. Phylogenetic analysis based on whole-proteome comparisons placed strain PA1-206B[T] within the genus Pseudogemmobacter but, on a distinct branch, clearly separated from its closest relatives. The major isoprenoid quinone of the strain was ubiquinone Q-10. The predominant fatty acids (>5%) were C18:1 ω7c, C16:0 and 11-methyl-C18:1 ω7c. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified aminolipid and two unidentified phospholipids were present. The assembled draft genome of strain PA1-206B[T] had 115 contigs with a total length of 4.5 Mb and a G+C content of 67.4 mol%. The overall genome-related indices (average nucleotide identity <80.4%, average amino acid identity <70.6%, digital DNA-DNA hybridization <21.6%) with respect to close relatives were below the corresponding threshold to demarcate bacterial species. Strain PA1-206B[T] (=DSM 115559[T]=NCAIM B.02680[T]) is suggested as the type strain of a novel Pseudogemmobacter species, for which the name Pseudogemmobacter sonorensis sp. nov. is proposed.}, }
@article {pmid40727685, year = {2025}, author = {Webb, H and Fuchs, M and Abbott, BW and Douglas, TA and Elder, CD and Ernakovich, JG and Euskirchen, ES and Göckede, M and Grosse, G and Hugelius, G and Jones, MC and Koven, C and Kropp, H and Lathrop, E and Li, W and Loranty, MM and Natali, SM and Olefeldt, D and Schädel, C and Schuur, EAG and Sonnentag, O and Strauss, J and Virkkala, AM and Turetsky, MR}, title = {A Review of Abrupt Permafrost Thaw: Definitions, Usage, and a Proposed Conceptual Framework.}, journal = {Current climate change reports}, volume = {11}, number = {1}, pages = {7}, pmid = {40727685}, issn = {2198-6061}, abstract = {PURPOSE OF REVIEW: We review how 'abrupt thaw' has been used in published studies, compare these definitions to abrupt processes in other Earth science disciplines, and provide a definitive framework for how abrupt thaw should be used in the context of permafrost science.<br><br>RECENT FINDINGS: We address several aspects of permafrost systems necessary for abrupt thaw to occur and propose a framework for classifying permafrost processes as abrupt thaw in the future. Based on a literature review and our collective expertise, we propose that abrupt thaw refers to thaw processes that lead to a substantial persistent environmental change within a few decades. Abrupt thaw typically occurs in ice-rich permafrost but may be initiated in ice-poor permafrost by external factors such as hydrologic change (i.e., increased streamflow, soil moisture fluctuations, altered groundwater recharge) or wildfire.<br><br>SUMMARY: Permafrost thaw alters greenhouse gas emissions, soil and vegetation properties, and hydrologic flow, threatening infrastructure and the cultures and livelihoods of northern communities. The term 'abrupt thaw' has emerged in scientific discourse over the past two decades to differentiate processes that rapidly impact large depths of permafrost, such as thermokarst, from more gradual, top-down thaw processes that impact centimeters of near-surface permafrost over years to decades. However, there has been no formal definition for abrupt thaw and its use in the scientific literature has varied considerably. Our standardized definition of abrupt thaw offers a path forward to better understand drivers and patterns of abrupt thaw and its consequences for global greenhouse gas budgets, impacts to infrastructure and land-use, and Arctic policy- and decision-making.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s40641-025-00204-3.}, }
@article {pmid40725499, year = {2025}, author = {Saint-Jean, M and Claisse, O and Marrec, CL and Samot, J}, title = {Structural and Genetic Diversity of Lysis Modules in Bacteriophages Infecting the Genus Streptococcus.}, journal = {Genes}, volume = {16}, number = {7}, pages = {}, pmid = {40725499}, issn = {2073-4425}, mesh = {*Streptococcus/virology/genetics ; *Genetic Variation ; *Genome, Viral ; *Streptococcus Phages/genetics ; *Bacteriophages/genetics ; Endopeptidases/genetics ; Phylogeny ; Viral Proteins/genetics ; *Bacteriolysis/genetics ; }, abstract = {Background/Objectives: Bacteriophages infecting the genus Streptococcus play a crucial role in microbial ecology and have potential applications in biotechnology and medicine. Despite their importance, significant gaps remain in our understanding of their lysis modules. This study aims to address these deficiencies by analyzing the genomic diversity and lysis module organization in Streptococcus phages. Methods: A search was conducted in the NCBI RefSeq database to identify phage genomes infecting Streptococcus. A representative panel was selected based on taxonomic diversity. Lysis modules were annotated and visualized, functional domains in endolysins were identified, and holins were characterized. Results: A total of 205 phage genomes were retrieved from the NCBI RefSeq database, of which 185 complete genomes were analyzed. A subset of 34 phages was selected for in-depth analysis, ensuring the representation of taxonomic diversity. The lysis modules were annotated and visualized, revealing five distinct organizations. Among the 256 identified endolysins, 25 distinct architectural organizations were observed, with amidase activity being the most prevalent. Holins were classified into 9 of the 74 families listed in the Transporter Classification Database, exhibiting one to three transmembrane domains. Conclusions: This study provides insights into the structural diversity of lysis modules in Streptococcus phages, paving the way for future research and potential biotechnological applications.}, }
@article {pmid40725462, year = {2025}, author = {Ait Zenati, F and Baldi, S and Di Gloria, L and Djoudi, F and Bertorello, S and Ramazzotti, M and Niccolai, E and Amedei, A}, title = {Compositional and Functional Disparities in the Breast Oncobiome Between Patients Living in Urban or Rural Areas.}, journal = {Genes}, volume = {16}, number = {7}, pages = {}, pmid = {40725462}, issn = {2073-4425}, support = {2020-WIDE SPREAD-05-2020-Twinning Grant Agreement, No. 952583//European Commission/ ; }, mesh = {Humans ; *Breast Neoplasms/microbiology/genetics/epidemiology/pathology ; Female ; *Microbiota/genetics ; Rural Population ; Middle Aged ; Urban Population ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; Adult ; Aged ; }, abstract = {Background/Objectives: Breast cancer (BC) is the leading cause of cancer incidence and mortality among women and the recent identification of a resident mammary microbiota has highlighted its potential role in breast carcinogenesis. Given that environmental and socioeconomic factors influence both BC prevalence and tumor-associated bacterial composition, this study aimed to evaluate the compositional and functional features of the mammary microbiota in cancerous (oncobiome) and adjacent healthy BC tissues from patients living in urban and rural areas. Methods: Microbiota composition in both the oncobiome and adjacent healthy BC tissues was analyzed using 16S rRNA sequencing. Results: Significant variations in breast oncobiome composition were observed among BC patients from urban and rural areas. A statistically significant β dispersion among breast oncobiome of patients from urban or rural areas was highlighted. Specifically, the genera Selenomonas, Centipeda, Leptotrichia, Neisseria and Porphyromonas were found exclusively in BC tissues of patients from rural areas. Additionally, bacteria from the Neisseriaceae, Porphyromonadaceae, and Selenomonadaceae families, as well as the Selenomonas genus, were significantly enriched in the oncobiome of rural BC patients. Furthermore, the results of the PICRUSt2 (phylogenetic investigation of communities by reconstruction of unobserved states) revealed a significant increase in phospholipid biosynthesis pathways in breast oncobiome of patients from rural areas compared to those from urban areas. Conclusions: This study provides evidence of distinct compositional and functional differences in the breast oncobiome between BC patients from rural and urban areas. These findings suggest that environmental factors influence local microbiome composition, potentially contributing to BC development and/or progression.}, }
@article {pmid40724585, year = {2025}, author = {Liu, W and Zhang, C and Kuang, X and Zeng, X and Zhang, J and Wang, Q and Yang, H}, title = {Effects of Dietary Calcium and Phosphorus Levels on Growth Performance, Calcium-Phosphorus Homeostasis, and Gut Microbiota in Ningxiang Pigs.}, journal = {Life (Basel, Switzerland)}, volume = {15}, number = {7}, pages = {}, pmid = {40724585}, issn = {2075-1729}, support = {2021YFD1300402//Key National Research and Development Program projects/ ; 24A0044//Hunan Provincial Department of Education key project/ ; }, abstract = {Optimal dietary calcium (Ca) and phosphorus (P) requirements remain undetermined for Ningxiang pigs, a valuable indigenous Chinese breed. This study conducted a continuous feeding trial with two growth phases (grower: 30-50 kg; finisher: 50-80 kg) using fixed Ca/P ratios to systematically evaluate the effects of Ca/P levels on growth performance and mineral metabolism. A total of 180 pigs per phase were allocated to four Ca/P levels. During the grower phase, a dietary regimen of 0.83% Ca/0.67% P significantly increased the average daily feed intake (ADFI), average daily gain (ADG), and apparent total tract digestibility (ATTD) of energy and P. In the finisher phase, 0.60/0.48% Ca/P showed optimal growth performance, upregulated jejunal mineral transporters (CaSR and SLC34A2), enhanced bone mineralization (metatarsal ash content), and improved intestinal morphology (duodenal and jejunal villus height, jejunal villus surface area). This regimen also selectively enriched Peptostreptococcaceae abundance, indicating improved host-microbe interactions. Based on these findings, stage-specific nutritional strategies were recommended: 0.83% Ca/0.67% P during the grower phase and 0.60% Ca/0.48% P during the finisher phase. These protocols synergistically improve microbial ecology, intestinal function, and bone metabolism, thereby maximizing the growth potential of Ningxiang pigs.}, }
@article {pmid40723916, year = {2025}, author = {Wei, M and Liu, H and Hu, Z and Wen, P and Ye, Y and Chamba, Y and Zhang, H and Shang, P}, title = {A Mechanistic Approach to Replacing Antibiotics with Natural Products in the Treatment of Bacterial Diarrhea.}, journal = {Biomolecules}, volume = {15}, number = {7}, pages = {}, pmid = {40723916}, issn = {2218-273X}, support = {533325001//Xizang agriculture and Aninal Husbandry University Doctoral Progran in forestry (Fhase I) funded by Grant/ ; XZ202501ZY0147//Sxpported by Science and Technology Projects of Xizang Axtonomoxs Region, China/ ; 2023YFD1801304//National Key Research and Development Program/ ; }, mesh = {*Biological Products/therapeutic use/pharmacology ; *Diarrhea/drug therapy/microbiology ; Humans ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Gastrointestinal Microbiome/drug effects ; Animals ; Bacteria/drug effects ; *Bacterial Infections/drug therapy/microbiology ; }, abstract = {Natural products have emerged as potential alternatives to antibiotics in the treatment of bacterial diarrhea, due to their multi-targeting effects, low potential for inducing resistance, and favorable safety profiles. Currently, the search for natural product-based therapies has become an emerging focus in medical research. This growing interest is driven by the increasing awareness that the widespread and irrational use of antibiotics has contributed to the alarming rise in antibiotic-resistant bacterial strains, which in turn diminishes the efficacy of conventional drugs. Among these concerns, the limitations of antibiotics in managing bacterial diarrhea and the potential mechanisms by which natural products exert therapeutic effects are the main focus of this paper. Natural products, containing a wide array of bioactive compounds, can not only directly inhibit the growth of pathogenic bacteria, disrupt bacterial membrane synthesis, and reduce toxin production, but also modulate inflammatory responses, enhance immune function, repair intestinal barriers, and restore gut microbial ecology-highlighting their systemic and multi-targeted therapeutic potential. Therefore, this paper will elaborate on how natural products combat bacterial diarrhea from three aspects: the pathogen and pathogenesis of bacterial diarrhea, natural product-based therapeutic studies, and the underlying mechanisms of action, thereby proposing natural products as viable alternatives to antibiotics.}, }
@article {pmid40723361, year = {2025}, author = {Jiang, J and Zhang, H and Hussain, M and Abdullah,  and Feng, F and Guan, R and Zhong, H}, title = {Novel Approaches in Glucose and Lipid Metabolism Disorder Therapy: Targeting the Gut Microbiota-Bile Acid Axis.}, journal = {Biology}, volume = {14}, number = {7}, pages = {}, pmid = {40723361}, issn = {2079-7737}, support = {32402088//National Natural Science Foundation of China/ ; 2024C04012//"Pioneer" and "Leading Goose" R&amp;D Program of Zhejiang Province/ ; LQ23C200011//Zhejiang Provincial Natural Science Foundation of China/ ; KYY-HX-20230084, KYY-HX-20240810//Zhejiang University of Technology - Company Crosswise Project/ ; }, abstract = {Metabolic dysregulation involving glucose and lipids is closely associated with chronic diseases such as type 2 diabetes mellitus. Emerging evidence highlights the regulatory role of bile acid (BA)-gut microbiota interactions in these metabolic disorders. The gut microbiota orchestrates the biotransformation of primary BAs into bioactive secondary BAs, which function as endocrine signaling molecules by activating the nuclear farnesoid X receptor (FXR) and G protein-coupled membrane receptor (TGR5), forming a communication network essential for metabolic homeostasis. BAs also reciprocally modulate gut microbiota composition. This BA-gut microbiota co-metabolism has emerged as a promising therapeutic target for lipid metabolism disorders. This comprehensive review examines the bidirectional interplay between gut microbiota and BA metabolism, focusing on microbial transformation of BAs, host-microbial co-regulatory pathways and mechanisms of BA metabolism, and the therapeutic implications of modulating the gut microbiota-BA axis in addressing glucose and lipid metabolism disorders. The synthesis of current evidence aims to elucidate the intricate crosstalk between microbial ecology and host metabolism mediated by BA signaling pathways, thereby exploring novel therapeutic intervention strategies.}, }
@article {pmid40722002, year = {2025}, author = {Jordan, S and Pothier, JF and de Maayer, P and Broders, K and Kvitko, BH and Coutinho, TA and Smits, THM}, title = {Design of genus-specific semi-nested primers for simple and accurate identification of Enterobacter strains.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {456}, pmid = {40722002}, issn = {1471-2180}, support = {310030L_204333//Swiss National Science Foundation (SNSF)- South-African National Research Foundation (NRF) Lead Agency project/ ; 2019-51181-30013//USDA NIFA SCRI/ ; }, mesh = {*Enterobacter/genetics/classification/isolation &amp; purification ; *Polymerase Chain Reaction/methods ; *DNA Primers/genetics ; DNA, Bacterial/genetics ; Phylogeny ; }, abstract = {BACKGROUND: The genus Enterobacter, in the family Enterobacteriaceae, is of both clinical and environmental importance. This genus has undergone frequent taxonomic changes, making it challenging to identify taxa even at genus level. This study aimed to design Enterobacter genus-specific primers that can be used for simple PCR identification of large sets of putative Enterobacter isolates.<br><br>RESULTS: Comparative genomic approaches were employed to identify genes that were universally present on Enterobacter genomes but absent from the genomes of other members of the family Enterobacteriaceae, based on an initial set of 89 genomes. The presence of these genes was further confirmed in 4,276 Enterobacter RefSeq genomes. While no strictly genus-specific genes were identified, the hpaB gene demonstrated a restricted distribution outside of the genus Enterobacter. Semi-nested primers were designed for hpaB and its flanking gene hpaC (hpaBC) and evaluated on 123 strains in single-tube PCR reactions. All taxa showing positive reactions belonged to the genus Enterobacter. For Enterobacter strains the PCR yielded two amplicons at 110&#xa0;bp and at 370&#xa0;bp, while strains only displaying the 110&#xa0;bp amplicon were classified as Leclercia pneumoniae. A blind-test on 120 strains accessioned as Enterobacter sp. from the USDA-ARS culture collection (NRRL), revealed that one third of the strains had an incorrect genus assignment. Comparison of gene trees of the hpaBC fragment sequences with marker genes frequently used for single-gene barcoding or multi-locus sequence analysis (MLSA) further demonstrated its potential for preliminary species identification.<br><br>CONCLUSIONS: The nested PCR assay represents a rapid and cost-effective approach for preliminary identification of Enterobacter species. As the primer design was based on large-scale genomic comparison, including currently undescribed species clades, it will remain valid even after taxonomic changes within the genus.}, }
@article {pmid40721486, year = {2025}, author = {de Aviz, RO and Campos, JR and Silva, DEO and Barbosa, LMP and Costa, RM and Borges, JF and Leite, MRL and Rocha, SMB and Morais, PGC and Dauala, GA and Pereira, APA and de Medeiros, EV and Araujo, ASF}, title = {Microbial biomass and enzymatic activity in the rhizosphere of prickly-pear cactus genotypes inoculated with Bacillus subtilis and Paenibacillus Sp.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {27415}, pmid = {40721486}, issn = {2045-2322}, mesh = {*Rhizosphere ; *Paenibacillus/physiology ; *Bacillus subtilis/physiology ; Biomass ; Genotype ; Soil Microbiology ; *Cactaceae/microbiology/genetics ; }, abstract = {Some bacterial taxa, such as Bacillus and Paenibacillus, are known to colonize the rhizosphere and promote plant growth. However, little is known about their effect on microbial biomass and enzymatic activity in the rhizosphere of plants under semi-arid conditions. This field study assessed the effects of B. subtilis and Paenibacillus sp. in the rhizosphere of two prickly-pear cactus genotypes on microbial biomass of C, N, and P, and on enzymatic activity during early and late growth stages. The analysis of variance showed that microbial biomass and enzymatic activity were significantly influenced by the interaction between PGPB taxa (B. subtilis and Paenibacillus sp.), prickly-pear cactus genotypes ('Baiana' and 'Doce'), and plant growth stage (90 and 270 days). Specifically, PGPB inoculation increased microbial biomass P, β-glucosidase, and acid phosphatase, while microbial biomass of C and N were primarily driven by differences between cactus genotypes 'Baiana' and 'Doce'. At the early growth stage (90 days), the highest values of microbial biomass C, P, and acid phosphatase were observed, whereas N biomass was higher at the later stage (270 days). B. subtilis increased microbial biomass P in the 'Doce' genotype and acid phosphatase in 'Baiana,' while Paenibacillus sp. increased β-glucosidase in 'Baiana.' The combination of the 'Doce' genotype with B. subtilis enhanced phosphorus availability, suggesting that specific plant-microbe interactions may benefit nutrient acquisition in arid, nutrient-poor soils; however, further research is needed to confirm whether this effect extends to other genotypes.}, }
@article {pmid40719475, year = {2025}, author = {Fan, X and Guo, X and Qi, Q and Gui, H and Li, Y and Yang, Y and He, J-S and Wu, L}, title = {Long-term elevated precipitation promotes an acid metabolic preference in soil microbial communities in a Tibetan alpine grassland.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0047025}, doi = {10.1128/msystems.00470-25}, pmid = {40719475}, issn = {2379-5077}, abstract = {Alpine ecosystems store vast amounts of soil organic carbon but are highly sensitive to climate change. Despite this, the response of in situ soil microbial metabolic processes, especially carbon substrate utilization, to climatic shifts remains underexplored. Here, we assessed microbial activity by metatranscriptomics in a Tibetan alpine grassland after a decade of experimental warming (+2°C) and altered precipitation (+50% and -50% of ambient precipitation). The experiment revealed that altered precipitation, rather than warming, shaped the active microbial community. Altered precipitation and warming had significant interactions: warming combined with increased precipitation generally suppressed microbial carbohydrate metabolism and methane oxidation, while warming with decreased precipitation enhanced these processes. Notably, increased precipitation induced a shift in microbial communities towards acid metabolism over sugar metabolism, predominantly driven by taxa such as Betaproteobacteria. This metabolic shift corresponded with an increased emission ratio of methane (CH4) to carbon dioxide (CO2), a change primarily driven by CH4, underscoring the critical role of microbial carbon metabolic preferences in regulating greenhouse gas emissions. Our findings highlight the necessity of integrating microbial carbon metabolic preferences and their interactions with climatic factors into models to accurately predict carbon-climate feedbacks.IMPORTANCEMicrobes have specific preferences for different carbon substrates, but their responses to climate change remain unclear. Our study, conducted through a long-term climate manipulation experiment in a Tibetan alpine grassland, reveals that increased precipitation leads soil microbial communities to favor acid metabolism over sugar metabolism. This shift significantly affects greenhouse gas emissions by increasing the CH4/CO2 ratio, which has important implications for global warming. These findings are crucial for accurately forecasting carbon-climate feedbacks and managing alpine ecosystems as climate change progresses.}, }
@article {pmid40715283, year = {2025}, author = {Tan, JH and Liew, KJ and Sani, RK and Samanta, D and Pointing, SB and Chan, KG and Goh, KM}, title = {Microbial diversity and metabolic predictions of high-temperature streamer biofilms using metagenome-assembled genomes.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {27297}, pmid = {40715283}, issn = {2045-2322}, mesh = {*Biofilms/growth &amp; development ; *Hot Springs/microbiology ; *Metagenome ; Hot Temperature ; *Bacteria/genetics/metabolism/classification ; Microbiota ; Phylogeny ; Biodiversity ; Genome, Bacterial ; Metagenomics/methods ; Malaysia ; }, abstract = {High-temperature streamer biofilm communities (SBCs) are often dominated by Aquificota, which can comprise over 90% of the microbial population in shallow water channels, such as those found at Mammoth hot springs of Yellowstone National Park and the Rehai hot springs in China. This study examines SBCs from the Dusun Tua (DT) hot spring in Malaysia (75 °C, pH 7.6), where Aquificota accounted for only ~ 35% of the total amplicon sequence variants. Amplicon and hybrid metagenomic sequencing revealed a more balanced microbial community, co-dominated by Aquificota, Chloroflexota, Desulfobacterota, Bacteroidota, Deinococcota, and Candidatus Hydrothermae, along with Thermoproteota and Micrarchaeota. To our knowledge, the co-dominance of Aquificota and Chloroflexota in SBCs has not been previously reported. The unexpected abundance of Chloroflexota may stem from dispersal from upstream Cyanobacteriota-Chloroflexota biofilms, contributing to community diversification. Genome-resolved analyses identified more than 60 medium- to high-quality metagenome-assembled genomes (MAGs), suggesting that biofilm formation was initially driven by chemoautotrophic sulfur oxidation and CO2 fixation, followed by the gradual integration of heterotrophic taxa. Nitrogen cycling and hydrogen oxidation are likely to contribute additional sources of energy. The presence of diverse CAZymes suggests that plant litter may serve as an additional carbon source. Genome-centric analyses across multiple phyla indicated that extracellular polymeric substances (EPS), curli fibers, and other matrix components contribute to the biofilm matrix, enhancing structural resilience and supporting persistence under harsh conditions. Overall, this study highlights the distinct microbial ecology of the DT SBC and broader metabolic roles beyond Aquificota dominance. The genes identified in this study may hold biotechnological potential and serve as a valuable resource for future enzyme discovery and functional screening.}, }
@article {pmid40711892, year = {2025}, author = {Turner, D and Adriaenssens, EM and Amann, RI and Bardy, P and Bartlau, N and Barylski, J and Błażejak, S and Bouzari, M and Briegel, A and Briers, Y and Carrillo, D and Chen, X and Claessen, D and Cook, R and Crisci, MA and Dechesne, A and Deptula, P and Dutilh, BE and Ely, B and Fieseler, L and Fogg, PCM and Fukudome, A and Ganjoor, MS and Gientka, I and Holmfeldt, K and Kalatzis, PG and Kauffman, KM and Kempff, A and Knezevic, P and Koonin, EV and Kropinski, AM and Krupovic, M and Kurtböke, I and Lambon, K and Lavigne, R and Lehman, SM and Liu, HT and Lood, C and Lurz, R and Mäntynen, S and Matrishin, CB and Middelboe, M and Millard, AD and Moraru, C and Nielsen, DS and Nobrega, FL and Nunoura, T and Oksanen, HM and Ongenae, V and Parra, B and Pas, C and Pogliano, J and Poranen, MM and Potipimpanon, S and Prichard, A and Pye, HV and Rothschild-Rodriguez, D and Rozen, DE and Santini, JM and Sha, Y and Shymialevich, D and Sokołowska, B and Soleimani-Delfan, A and Średnicka, P and Tavares, P and Telatin, A and Tolstoy, I and Urayama, SI and van Neer, V and Vogensen, FK and Wen, Q and Wichels, A and Wójcicki, M and Ictv Taxonomy Summary Consortium,  and , }, title = {Summary of taxonomy changes ratified by the International Committee on Taxonomy of Viruses (ICTV) from the Bacterial Viruses Subcommittee, 2025.}, journal = {The Journal of general virology}, volume = {106}, number = {7}, pages = {}, doi = {10.1099/jgv.0.002111}, pmid = {40711892}, issn = {1465-2099}, mesh = {*Viruses/classification/genetics ; *Bacteria/virology ; Phylogeny ; *Classification/methods ; }, abstract = {This article summarises the activities of the International Committee on Taxonomy of Viruses Bacterial Viruses Subcommittee, detailing developments in the classification of bacterial viruses. We provide here an overview of all new, abolished, moved and renamed taxa proposed in 2024, approved by the Executive Committee, and ratified by membership vote in 2025. Through the collective efforts of 74 international contributors of taxonomy proposals in this round, 43 ratified proposals have led to the creation of one new phylum, one class, four orders, 33 families, 14 subfamilies, 194 genera and 995 species. These proposals mark significant progress in refining the taxonomy of bacterial viruses. Key updates include the creation of new orders and families that include existing taxa to better reflect genomic and evolutionary relationships. As sequencing and bioinformatics approaches continue to advance, further expansion and refinements in viral taxonomy can be anticipated in the coming years.}, }
@article {pmid40711674, year = {2025}, author = {Xiong, Q and Wang, R and Lai, D and Cai, S and Wang, H and Zhou, N}, title = {Metagenomic Insights into the Root‒Soil Response Mechanisms of Indica and Japonica Rice Under Nitrogen Deficiency and High-Efficiency Nitrogen Compensation.}, journal = {Rice (New York, N.Y.)}, volume = {18}, number = {1}, pages = {72}, pmid = {40711674}, issn = {1939-8425}, support = {32101816//National Natural Science Foundation of China/ ; 2021M702768//China Postdoctoral Science Foundation/ ; 2021K292B//Jiangsu Province Postdoctoral Research Funding/ ; 2021KY47//Jiangxi Province Postdoctoral Scientific Research Funding/ ; 202425YBKT17//Jiangxi Provincial Water Resources Department Science and Technology Project/ ; 20242BAB20263//Natural Science Foundation of Jiangxi Province/ ; PAPD//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; }, abstract = {Nitrogen (N) dynamics critically regulate rice productivity through root-mediated absorption and assimilation processes. This study investigates the differential responses of japonica (Suxiu 867) and indica (Yangxianyou 918) rice to N deficiency and subsequent high-efficiency compensation, integrating metagenomic analysis with physiological assessments of N metabolism. Building on an established high-efficiency N compensation period (18 days after tillering for japonica and 12 days for indica), we demonstrate that optimized N compensation significantly enhances dry matter accumulation and yield in both subspecies through distinct biological mechanisms. Compensation treatment elevated key metabolic indicators including soluble protein content (Cpr), glutamine synthetase (GDH) activity, soil urease (S-UE) activity, glutamate synthase (GOGAT) activity, and glutamine synthetase (GS) activity, collectively enhancing N assimilation efficiency. Rhizosphere microbiome restructuring showed subspecies-specific patterns, with Chloroflexi and Betaproteobacteria abundance positively correlating with N metabolic enzymes in indica, versus Actinomycetia, Deltaproteobacteria associations in japonica. Functional microbial analysis revealed divergent keystone taxa, with Noviherbaspirillum (indica) and Bacillus (japonica) driving N conversion efficiencies through niche-specific community synergies. Notably, indica rice presented a relatively high N absorption capacity and conversion efficiency, while japonica rice presented relatively stable N absorption and distribution mechanisms, and relatively high N fertilizer application significantly increased the abundance of specific microbial communities in japonica rice. These findings elucidate how subspecies-specific root physiology coordinates with rhizosphere microbial ecology to optimize N utilization, providing actionable insights for precision N management strategies tailored to rice genetic types.}, }
@article {pmid40711470, year = {2025}, author = {Lera-Lozano, D and Ruiz-Toquica, JS and Kratman, SA and Holt, MW and McIntyre, CA and Jones, EK and Lopez-Victoria, M and Ritchie, KB and Medina, M and González-Pech, RA}, title = {Genomic potential of crustose coralline algae-associated bacteria for the biosynthesis of novel antimicrobials.}, journal = {Microbial genomics}, volume = {11}, number = {7}, pages = {}, doi = {10.1099/mgen.0.001456}, pmid = {40711470}, issn = {2057-5858}, mesh = {*Bacteria/genetics/metabolism/isolation &amp; purification/classification ; *Rhodophyta/microbiology ; Biosynthetic Pathways/genetics ; *Anti-Bacterial Agents/biosynthesis ; Multigene Family ; *Anti-Infective Agents/metabolism ; Genome, Bacterial ; Animals ; *Anthozoa/microbiology ; Genomics ; Microbiota/genetics ; Phylogeny ; }, abstract = {The global rise of antimicrobial resistance has intensified efforts in bioprospecting, with researchers increasingly exploring unique marine environments for novel antimicrobials. In line with this trend, our study focused on bacteria isolated from the unique microbiome of crustose coralline algae (CCA), which has yet to be investigated for antimicrobial discovery. In the present work, bacteria were isolated from a CCA collected from Varadero Reef located in Cartagena Bay, Colombia. After performing antimicrobial assays against antibiotic-resistant human and marine pathogens, three isolates were selected for genome sequencing using the Oxford Nanopore technology. Genome mining of the high-quality assemblies revealed 115 putative biosynthetic gene clusters (BGCs) and identified genes in relevant biosynthetic pathways across the three genomes. Nonetheless, we hypothesize that the biosynthesis of antimicrobial compounds results from the expression of undescribed BGCs. Further analysis revealed the absence of genes pertaining to the synthesis of coral larvae settling molecule tetrabromopyrrole, commonly produced by CCA-associated bacteria. We also discuss how differential representation of gene functions between the three isolates may be attributed to the distinct ecological niches they occupy within the CCA. This study provides valuable resources for future research aimed at the discovery of novel antimicrobials, particularly in the face of the antibiotic-resistance global crisis, and highlights the potential of specialized marine environments like CCA.}, }
@article {pmid40709922, year = {2025}, author = {Li, H and Li, W and Liu, X and Zhang, J and Lin, C and Ji, S and Jiang, H and Wang, T and Su, Z}, title = {The gut microbiota features and the application value in predicting recurrent risks for gallstone patients who underwent laparoscopic cholecystectomy.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0176024}, doi = {10.1128/msystems.01760-24}, pmid = {40709922}, issn = {2379-5077}, abstract = {Gut microbiota is associated with gallstone occurrence and recurrence. But whether they can predict post-cholecystectomy choledocholithiasis recurrence needs to be investigated. From September 2020 to June 2021, a total of 100 symptomatic gallstone patients scheduled for laparoscopic cholecystectomy were enrolled in the Disease group in the Department of Hepatobiliary Surgery at Quanzhou First Hospital. Meanwhile, a total of 50 age- and sex-matched healthy controls were included in the Control group. Fecal specimens were collected from both groups and subjected to 16S rDNA sequencing (V3V4 region) for microbiologic analysis. After laparoscopic cholecystectomy, patients were followed up, and recurrent cases were recorded. Finally, a nomogram for predicting recurrent risks was built. The gut microbial diversity in the Disease group was significantly lower than that of the Control group (all P < 0.05). The Chao1 index of the recurrent group was remarkably lower than the control group (P < 0.05). Linear discriminant analysis (LDA) effect size (LEfSe) analysis showed that Phocaeicola dorei (LDA score = 4.2, P < 0.05) was the feature microbiota in the recurrent group. Logistic regression analysis showed that the composition of stones, the high abundances of P. dorei and Fusobacterium necrogenes were potential risk factors for recurrent choledocholithiasis, and a nomogram based on these factors demonstrated high accuracy and excellent calibration. This study has identified potential risk factors for recurrent choledocholithiasis and built a nomogram that can well predict recurrent risks for patients who undergo cholecystectomy, which might serve as a useful tool for patients' stratification and post-surgery management.IMPORTANCEThis study identifies specific gut microbiome signatures of gallstone patients and indicates that reduced diversity and high abundances of Phocaeicola dorei and Fusobacterium necrogenes might be potential predictors for choledocholithiasis recurrence after cholecystectomy. By demonstrating a link between gut microbiota composition and post-surgical recurrence risk, it advances our understanding beyond simple association with predictive capability. The development of a nomogram incorporating these microbial markers provides a novel, clinically applicable tool for accurate risk stratification of patients undergoing cholecystectomy, therefore bridging the gap between microbial ecology and clinical practice. The significance of this study lies in that it aims to address a critical unmet need in gallstone disease management by offering a more cost-effective and non-invasive tool to improve long-term patient outcomes and pave the way for microbiome-targeted interventions.CLINICAL TRIALSThis study is registered with Chinese Clinical Trial Registry Center as ChiCTR2400090232.}, }
@article {pmid40708948, year = {2025}, author = {Zai, X and Zhu, F and Zhao, M and Diao, X and Zhang, F and Dini-Andreote, F and Melkonian, C and Medema, MH and Raaijmakers, JM and Cordovez, V and Song, C}, title = {Harnessing the phyllosphere microbiota of wild foxtail millet for designing beneficial cross-kingdom synthetic communities.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf066}, pmid = {40708948}, issn = {2730-6151}, abstract = {Understanding the interplay between mechanisms in plant microbiome assembly and functioning of wild ancestors has led to the proposal of a novel strategy to enhance resilience to the (a)biotic stresses of domesticated crops. The challenge is determining how to harness the diverse microbiota of wild crop ancestors in their natural habitats in order to design effective synthetic microbial communities (SynComs) that reconstitute specific microbiome-associated plant phenotypes. In this study, we profiled the phyllosphere microbiota of wild green foxtail collected from seven geographically diverse natural ecosystems and showed that variations in soil parameters and climatic conditions as well as plant genetic distance significantly correlated with bacterial and fungal community compositions. Environmental selection and dispersal limitation differently governed the assembly of bacterial and fungal communities with distinct habitat niche breadth. Specific bacterial and yeast genera were identified as core phyllosphere taxa of wild green foxtail millet on the basis of their abundance and prevalence across the seven sampling sites. Moreover, several genera of bacteria (Bacillus, Pantoea, Methylobacterium) and yeast (Vishniacozyma, Filobasidium, Sporobolomyces) displayed significant correlations with the abundances of one or more foliar pathogenic fungi, in particular fungi of the genus Alternaria. Subsequent isolation and characterization of these bacterial and yeast genera allowed the design of cross-kingdom SynComs that protected domesticated foxtail millet from leaf infections by Alternaria alternata. These results provide fundamental insight into the mechanisms governing the phyllosphere microbiota assembly of a wild crop ancestor across large geographic scales and a practical framework to leverage this fundamental knowledge for the design of SynComs that mitigate the biotic stress of the domesticated crop.}, }
@article {pmid40708946, year = {2025}, author = {Liu, ZQ and Yang, XY and Chen, JH and Ge, SC and Dai, SX and Zhu, SH and Xian, ZY}, title = {From dysbiosis to precision therapy: decoding the gut-bladder axis in bladder carcinogenesis.}, journal = {Frontiers in oncology}, volume = {15}, number = {}, pages = {1630726}, pmid = {40708946}, issn = {2234-943X}, abstract = {The gut-bladder axis (GBA), a bidirectional network connecting gastrointestinal and urinary systems, has recently emerged as a pivotal focus in bladder cancer research. Beyond conventional risk factors, gut dysbiosis, aberrant microbial metabolites, and neuro-immune pathway disruptions have been implicated in tumorigenesis and progression. Short-chain fatty acids (SCFAs), microbial-derived metabolites, are shown to indirectly modulate tumor behavior through immune microenvironment regulation and inflammatory response attenuation. Cross-organ crosstalk is further mediated by neural pathways (e.g., vagal signaling) and shared receptors, including the Farnesoid X Receptor (FXR) and Toll-like Receptor 4 (TLR4). Novel therapies leveraging microbial ecology principles demonstrate potential, including immune checkpoint inhibitors combined with microbiota modulation (e.g., Parabacteroides distasonis-enhanced PD-1 efficacy), probiotics to reverse chemoresistance, and microbiota reprogramming for SCFA-targeted strategies. However, molecular mechanisms underlying GBA-host interactions remain poorly characterized. Clinical translation is hindered by limited cohort sizes and interindividual heterogeneity. Current studies, while revealing partial pathways, face methodological inconsistencies, particularly in urinary microbiome profiling, and a lack of longitudinal human data. Future breakthroughs will require multi-omics integration, organoid-based models, and interdisciplinary collaboration to address these gaps.}, }
@article {pmid40708752, year = {2025}, author = {Zhang, Y}, title = {Fucoidan as a therapeutic agent for ulcerative colitis: mechanisms of action and modulation of the gut microbiota.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1626614}, pmid = {40708752}, issn = {2235-2988}, mesh = {*Polysaccharides/pharmacology/therapeutic use ; Humans ; *Gastrointestinal Microbiome/drug effects ; *Colitis, Ulcerative/drug therapy/microbiology ; Animals ; Cytokines/metabolism ; *Anti-Inflammatory Agents/pharmacology/therapeutic use ; NF-kappa B/metabolism ; Signal Transduction/drug effects ; }, abstract = {Ulcerative colitis (UC), a chronic inflammatory bowel disease driven by gut dysbiosis, immune dysregulation, and oxidative stress, lacks universally effective therapies. Fucoidan (FCD), a sulfated polysaccharide derived from brown algae, has emerged as a multifaceted therapeutic candidate due to its anti-inflammatory, antioxidant, and immunomodulatory properties. This review synthesizes FCD's mechanisms in UC pathogenesis, emphasizing its suppression of NF-κB and MAPK signaling pathways to reduce proinflammatory cytokines (e.g., IL-6, TNF-α) and regulate TLR-mediated macrophage polarization. FCD enhances intestinal barrier integrity via upregulation of tight junction proteins (Claudin-1, ZO-1) and mucin MUC2 expression, while remodeling gut microbial ecology through enrichment of SCFAs-producing bacteria (e.g., Ruminococcaceae) and suppression of pathogens (Escherichia coli, Candida albicans). Preclinical studies highlight LMWF as a superior candidate, demonstrating enhanced bioavailability and efficacy in mitigating DSS-induced colitis. Despite its promise, challenges persist in structural heterogeneity (source- and extraction-dependent), scalable production of LMWF, and insufficient pharmacokinetic data. Emerging strategies-including nanoparticle-based delivery systems and structural modifications (cross-linking, covalent bonding)-aim to overcome bioavailability limitations. This review underscores FCD's potential as a functional food or adjuvant therapy for UC, while advocating for rigorous clinical validation to bridge translational gaps, Enrichment of SCFAs-producing taxa and suppression of pathobionts (Escherichia coli, Candida albicans), mediated through prebiotic fermentation. Suppression of NF-κB activation via IκBα stabilization and inhibition of p65 nuclear translocation, and downregulation of MAPK phosphorylation (ERK1/2, JNK, p38), reducing proinflammatory cytokines (IL-6, TNF-α, IL-1β). FCD can be used as a potential treatment for UC.}, }
@article {pmid40708120, year = {2025}, author = {Perkins, AK and Grossart, HP and Rojas-Jimenez, K and Retter, A and Oakes, JM}, title = {The Functional Role of Fungi and Bacteria in Sulfur Cycling During Kelp (Ecklonia Radiata) Degradation: Unconventional Use of PiCrust2.}, journal = {Environmental microbiology reports}, volume = {17}, number = {4}, pages = {e70140}, pmid = {40708120}, issn = {1758-2229}, support = {RRF-2.3.1-21-2022-00008//National Laboratory for Water Science and Water Security, HUN-REN Balaton Limnological Research Institute/ ; DFG GR1540/47-1//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Sulfur/metabolism ; *Bacteria/metabolism/genetics/classification ; *Fungi/metabolism/genetics/classification ; *Kelp/microbiology/metabolism ; Metabolic Networks and Pathways ; Ecosystem ; High-Throughput Nucleotide Sequencing ; }, abstract = {Macroalgae is a major source of detritus in coastal ecosystems, contributing approximately 1521 ± 732 Tg C year[-1] to global net primary production. Fungal remineralisation of Ecklonia radiata detritus produces substantial amounts of dimethylsulfoniopropionate, total alkalinity, and dissolved inorganic carbon, supporting coastal biogeochemical cycles. To expand on the role of fungi during E. radiata degradation, we examined changes in fungal and bacterial communities at the start and after 21 days in a mesocosm, comparing microbial functional roles between blades and stipes. We employed next-generation sequencing to evaluate the potential contributions of fungi and bacteria, and additionally utilized FUNGuild, FungalTraits, and PiCrust2 databases. We cross-referenced the metabolic pathways predicted by PiCrust2 with the literature to determine whether these pathways have been documented in fungi. Of the 423 metabolic pathways identified, 342 have also been reported in fungi, including 281 redox-related pathways, 220 associated with nicotinamide adenine dinucleotide, and 194 linked to sulfur metabolism. These overlaps suggest that bacteria and fungi could play complementary roles in kelp degradation, contributing distinct yet interconnected functions. Our results highlight that these metabolic pathways cannot be attributed to bacteria alone and fungi are essential to kelp remineralisation.}, }
@article {pmid40707845, year = {2025}, author = {Jürisoo, L and Agan, A and Tedersoo, L and Witzell, J and Selikhovkin, A and Drenkhan, R}, title = {Fungal Assemblages in Northern Elms-Impacts of Host Identity and Health, Growth Environment, and Presence of Dutch Elm Disease.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {82}, pmid = {40707845}, issn = {1432-184X}, support = {PRG1615//Estonian Research Competency Council/ ; TEMTA22//the European Union and Ministry of Education and Research/ ; }, mesh = {*Plant Diseases/microbiology ; *Ulmus/microbiology/growth &amp; development/genetics ; Estonia ; Endophytes/genetics/classification/isolation &amp; purification ; *Mycobiome ; *Ophiostoma/genetics/isolation &amp; purification ; Russia ; *Fungi/classification/genetics/isolation &amp; purification ; }, abstract = {Dutch elm disease (DED), caused by the pathogenic ascomycete Ophiostoma novo-ulmi, has devastated natural elm (Ulmus spp.) populations in Europe and North America. Elm species vary in their susceptibility to this vascular disease, which may partly reflect differences in their associated mycobiomes. To investigate the diversity and composition of fungal endophyte communities in relation to host genotype, health status, and environment, we analyzed twig-associated fungi in symptomatic and asymptomatic individuals of highly susceptible U. glabra, less susceptible U. laevis, and hybrid elms growing in Estonia and Russia. Fungal communities were analyzed using PacBio long-read amplicon sequencing of the ITS1-5.8S-ITS2 gene region. Tree species exhibited distinct fungal community profiles. Ophiostoma novo-ulmi was detected exclusively in symptomatic trees and was dominant in U. glabra; it was absent in symptomatic hybrid elms. In contrast, the canker-associated pathogen Sphaeropsis ulmicola occurred in both symptomatic and asymptomatic trees, was dominant in symptomatic U. laevis, and common in symptomatic and healthy U. glabra, though less prevalent in symptomatic hybrid elms. Remarkably, S. ulmicola was associated with the highest level of damage in U. laevis while being present also in hybrid elms. While O. novo-ulmi's presence did not affect overall fungal richness, S. ulmicola was linked to higher fungal diversity. Additionally, fungal species richness was significantly greater in urban compared to rural environments. This was the first comparable analysis of fungal diversity and composition on three different Ulmus species shoots.}, }
@article {pmid40707215, year = {2025}, author = {Li-Hau, F and Nakagawa, M and Kakegawa, T and Ward, LM and Ueno, Y and McGlynn, SE}, title = {Metabolic Potential and Microbial Diversity of Late Archean to Early Proterozoic Ocean Analog Hot Springs of Japan.}, journal = {Microbes and environments}, volume = {40}, number = {3}, pages = {}, doi = {10.1264/jsme2.ME24067}, pmid = {40707215}, issn = {1347-4405}, mesh = {*Hot Springs/microbiology/chemistry ; Japan ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; *Archaea/classification/metabolism/genetics/isolation &amp; purification ; Oxidation-Reduction ; Phylogeny ; Nitrogen Fixation ; Oceans and Seas ; Iron/metabolism ; *Biodiversity ; Carbon Cycle ; RNA, Ribosomal, 16S/genetics ; Nitrogen Cycle ; Hydrogen/metabolism ; }, abstract = {Circumneutral iron-rich hot springs may represent analogues of Neoarchean to Paleoproterozoic oceans of early Earth, potentially providing windows into ancient microbial ecology. Here we sampled five Japanese hot springs to gain insights into functional processes and taxonomic diversity in these analog environments. Amplicon and metagenomic sequencing confirm a hypothesis where taxonomy is distinct between sites and linked to the geochemical setting. Metabolic functions shared among the springs include carbon fixation via the reductive pentose phosphate cycle, nitrogen fixation, and dissimilatory iron oxidation/reduction. Among the sites, Kowakubi was unique in that it was dominated by Hydrogenophilaceae, a group known for performing hydrogen oxidation, motivating a hypothesis that H2 as an electron donor may shape community composition even in the presence of abundant ferrous iron. Evidence for nitrogen cycling across the springs included N2 fixation, dissimilatory nitrate reduction to ammonia (DNRA), and denitrification. The low-salinity springs Furutobe and OHK lacked evidence for ammonium oxidation by ammonia monooxygenase, but evidence for complete nitrification existed at Kowakubi, Jinata, and Tsubakiyama. In most sites, the microaerophilic iron-oxidizing bacteria from the Zetaproteobacteria or Gammaproteobacteria classes had higher relative abundances than Cyanobacteria. Microaerophilic iron oxidizers may outcompete abiotic Fe oxidation, while being fueled by oxy-phototrophic Cyanobacteria. Our data provide a foundation for considering which factors may have controlled productivity and elemental cycling as Earth's oceans became oxygenated at the onset of the Great Oxidation Event.}, }
@article {pmid40705368, year = {2025}, author = {Duff, AM and Giles, M and Ganasamurthy, S and Santos, A and Morales, SE and Brennan, F}, title = {Counting soil microbial communities: the impact of qPCR platform and mastermix on accuracy and precision.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {8}, pages = {}, doi = {10.1093/femsec/fiaf073}, pmid = {40705368}, issn = {1574-6941}, support = {696356//European Union/ ; }, mesh = {*Soil Microbiology ; *Real-Time Polymerase Chain Reaction/methods/standards ; *Microbiota/genetics ; *Bacteria/genetics/isolation &amp; purification ; }, abstract = {Quantitative polymerase chain reaction (qPCR) is widely used in soil microbial ecology to quantify microbial communities, but its accuracy can be compromised by coextracted inhibitors. Furthermore, large-scale international studies involving multiple laboratories or meta-analyses studies can introduce variation in qPCR results when data generated from different sources are compared. This study evaluated the performance of four commercial mastermixes across different soil types, a mock community, and a positive template control against three targets on three widely used platforms. Sensitivity to inhibitors was tested, with one mastermix affected, although this was mitigated by adding 1 mg/ml bovine serum albumin. Amplification success varied by mastermix, platform, gene, and sample matrix. Most mastermix-platform combinations showed low accuracy emphasizing the need for careful pairing. Precision was primarily influenced by gene target, followed by platform, sample matrix, and mastermix, and was reduced at lower template concentrations. Only 64.67% of intraassay (within an assay) measurements meet accepted thresholds. Interassay (between platforms) quantification was unreliable due to significant variability, which increased the risk of inaccurate data interpretation. The study highlights the necessity of considering inter- and intraassay variation, assay accuracy, and inhibitors that may impact sample amplification when utilizing qPCR for quantification of microbial communities in environmental samples.}, }
@article {pmid40705167, year = {2025}, author = {Gdanetz, K and Noel, ZA and Saville, K and Marsh, T and Scribner, KT and Trail, F}, title = {Eukaryotic Microbiome of Lake Sturgeon Eggs, and Identification of Chemical Thresholds for Infection Control.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {80}, pmid = {40705167}, issn = {1432-184X}, mesh = {Animals ; *Fishes/microbiology ; *Microbiota/drug effects ; Lakes/microbiology ; *Fish Diseases/microbiology/prevention &amp; control/parasitology ; *Ovum/microbiology ; *Fungi/isolation &amp; purification/classification/drug effects/genetics ; Oomycetes/drug effects/isolation &amp; purification ; Aquaculture ; *Eukaryota/isolation &amp; purification/classification/drug effects/genetics ; }, abstract = {Eukaryotic microorganisms are an important, but understudied, component of freshwater aquatic ecosystems, and are significant sources of mortality in early life stages of fishes in natural and aquaculture systems. The eukaryotic microbiome colonizing egg surfaces of the lake sturgeon (Acipenser fulvescens) was characterized from eggs collected in natural stream habitats and a streamside hatchery in the Cheboygan River watershed in MI, USA. The taxonomic diversity of members of the Kingdoms Fungi and Stramenopile associated with infections of lake sturgeon eggs during spawning is contributing to lake sturgeon mortality in the hatchery. Characterization of the microbial communities from deposited eggs demonstrated heavy influence of spawning location on the diversity of Pythium, an Oomycete predominating in the microbiome. The Ascomycota also had a strong and distinguishing presence, with members of the Dothidiales found only on eggs from the streamside hatchery. Aureobasidium pullulans, a ubiquitous pigmented yeast, was present in the greatest numbers of egg samples, and Helotiales were found only on samples from the Black River. Independent isolates were collected from egg surfaces and tested for chemical sensitivity to the oomicides ethaboxam and mefenoxam, which are used for control of Oomycete agricultural pathogens. Ethaboxam inhibited mycelial growth almost completely for all Saprolegnia strains tested, while mefenoxam, at 20 × strength, was largely ineffective. Water prevents the natural inactivation of mefenoxam by light, thus is not advisable in aquatic systems, where it could accumulate. Alternatively, ethaboxam may be a nonpersistent, welcome control option for these fish pathogens.}, }
@article {pmid40705121, year = {2025}, author = {Martin-Pozas, T and Ghezzi, D and D'Angeli, IM and Madonia, G and Chiarini, V and Vattano, M and De Waele, J and Cappelletti, M and Saiz-Jimenez, C and Jurado, V}, title = {Microbial and Geochemical Variability in Sediments and Biofilms from Italian Gypsum Caves.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {81}, pmid = {40705121}, issn = {1432-184X}, support = {JDC2023-051909-I//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2020-114978GB-I00 and PDI2023-146299OB-C22//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2020-114978GB-I00 and PDI2023-146299OB-C22//Ministerio de Ciencia e Innovaci&#xf3;n/ ; Europlanet 2020 7-EPN3-021//European Commission/ ; }, mesh = {*Biofilms/growth &amp; development ; *Geologic Sediments/microbiology/chemistry ; *Calcium Sulfate/analysis ; *Caves/microbiology/chemistry ; *Bacteria/classification/genetics/isolation &amp; purification ; Italy ; *Archaea/classification/isolation &amp; purification/genetics ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; }, abstract = {In Europe, several gypsum karst regions occur among which the gypsum karsts located in Emilia-Romagna (UNESCO World Heritage Site since 2023) and Sicily are notable. The sediments, spring water microbial aggregates, and wall biofilms from three caves, Re Tiberio, Befana (Emilia-Romagna), and the Sicilian Santa Ninfa, have been studied from a microbiological and geochemical point of view. The samples of wall biofilms from gypsum caves were exclusively composed of Bacteria, while the sediments showed negligible abundances of Archaea. The two most abundant phyla in most sediments and biofilms were Actinomycetota and Pseudomonadota, whereas the microbial aggregates floating in the spring waters of Befana Cave showed a deviation from the typical abundance pattern as Campylobacterota replaced Actinomycetota, and the abundances of Bacteroidota and Desulfobacterota were high. The most abundant genus in the wall biofilms was Crossiella (Actinomycetota), but it was absent in the water aggregates collected in Befana Cave. The abundances of Crossiella in the cave sediments were very low. The dominant genera in Befana microbial aggregates showed different abundances and microbial composition when compared with the previously studied Frasassi and Fetida thermal sulfuric acid caves, located in Central and South Italy, respectively, suggesting that the community composition of the microbial aggregates is specific for each cave and related to the geochemistry of the sulfidic spring. Also, a different microbial community composition was found in Befana water aggregates with respect to the wall biofilms from Befana and Santa Ninfa caves. In the case of sediments, they significantly clustered together indicating that the microbial communities associated with sediments are similar, independently from the cave and possible other environmental parameters.}, }
@article {pmid40704825, year = {2025}, author = {Fang, J and Deng, Y and Liu, Z and Adams, JM}, title = {Is Everything Everywhere? Dispersal Limitation Impacts Methanotroph Community Functioning.}, journal = {Environmental microbiology}, volume = {27}, number = {7}, pages = {e70158}, doi = {10.1111/1462-2920.70158}, pmid = {40704825}, issn = {1462-2920}, support = {SBX2020010098//The Provincial Policy Guidance Program-Jiangsu "100 Foreign Experts Program"/ ; 42371135//The National Natural Science Foundation of China/ ; 41971077//The National Natural Science Foundation of China/ ; }, mesh = {*Methane/metabolism ; *Geologic Sediments/microbiology ; *Methylococcaceae/metabolism/genetics/classification/isolation &amp; purification ; Salinity ; Rivers/microbiology ; Ecosystem ; Lakes/microbiology ; China ; Oxidation-Reduction ; }, abstract = {The significance of dispersal limitation in microbial ecology and biogeography remains debated. We aimed to clarify the role of dispersal limitation in the adaptation of methanotroph communities to salt-stress, essentially testing the 'everything is everywhere' hypothesis in functional terms. Riparian sediments along the Yangtze River and lakeshore sediments at varying geographical distances inland from the river were collected. Microcosms were incubated with ~5% CH4 under three conditions: 50 g/L salinity, 50 g/L salinity plus a methanotroph community inoculum, and a control. We observed a significant delay in methane oxidation at increased salinity, but salt-tolerant methanotrophic activity persisted in riparian sediments. Using DNA-SIP, we identified halotolerant Methylobacter-taxa that possibly dispersed from the saline estuary. By contrast, in lakes/ponds inland away from the Yangtze, progressively fewer samples oxidised methane under high salinity without inoculation, until at 130 km distance, no samples could adapt. Methanotrophy was restored in every case by inoculation with propagules from the saline Yangtze Delta, confirming the impact of dispersal limitation of halotolerant Methylobacter-propagules in constraining ecosystem functional adaptation. By focusing on ecosystem functions rather than just taxonomic communities, this study uniquely tests a key paradigm in microbial ecology, suggesting that broad-scale microbial dispersal limitation can constrain ecosystem adaptation.}, }
@article {pmid40704813, year = {2025}, author = {Zeng, Q and Jian, L and Shi, S and Guo, Q and Quadri, SR and Long, L and Tian, X}, title = {Identified Neptunicella plasticusilytica sp. nov. and its novel PET-degrading enzyme derived from mangrove plastic debris.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0113625}, doi = {10.1128/aem.01136-25}, pmid = {40704813}, issn = {1098-5336}, abstract = {Mangrove ecosystems are critical for coastal protection and biodiversity but are increasingly threatened by plastic pollution, particularly polyethylene terephthalate (PET). In this study, a novel marine bacterium, strain SCSIO 80796[T], was isolated from PET debris collected from the mangrove in QiAo Island, Zhuhai, China. Using a polyphasic taxonomic approach, including 16S rRNA gene sequencing, genome-based comparisons (average nucleotide identity [ANI] 72.2%, digital DNA-DNA hybridization [dDDH] 19.0%, average amino acid identity [AAI] 70.6%), and phenotypic and chemotaxonomic analyses, the strain was classified as a novel species within the genus Neptunicella. It is proposed as Neptunicella plasticusilytica sp. nov. (type strain SCSIO 80796ᵀ = MCCC 1K08369[T] = KCTC 92826[T]). Genomic analysis revealed that strain SCSIO 80796ᵀ encodes a novel PET-degrading enzyme, NmCut, which degrades PET and yields 105-120 µM of degradation products [terephthalic acid (TPA), mono(2-hydroxyethyl) terephthalate (MHET), bis(2-hydroxyethyl) terephthalate (BHET)] within 48 h at 60°C. NmCut exhibits both structural and evolutionary novelty, featuring a unique PET-binding module (PBM) absent in known PETases. PBM is characterized by a long, positively charged α-helix enriched in aromatic residues, forming a distinct substrate-interacting surface with potential as a transferable domain to enhance the efficiency of other plastic-degrading enzymes. This study not only expands the known diversity within Neptunicella but also highlights the potential of marine-derived microbes in addressing plastic pollution through biotechnological applications.IMPORTANCEThe discovery of Neptunicella plasticusilytica sp. nov. advances marine microbial ecology by revealing a novel species in the scarcely studied genus Neptunicella, which previously contained only one cultured representative. Isolated from plastic-polluted mangroves, this bacterium exemplifies microbial adaptation to anthropogenic habitats. Its functional uniqueness is underscored by a phylogenetically distinct polyethylene terephthalate (PET)-degrading enzyme (NmCut), forming an evolutionary clade separate from all known plastic-degrading enzymes. By integrating taxonomic discovery with functional genomics, this study bridges the gap between microbial diversity and biotechnological potential. The dual novelty of N. plasticusilytica-as a taxonomic addition and a source of evolutionarily unique enzymes-highlights the importance of exploring understudied environments to address global challenges like plastic pollution.}, }
@article {pmid40704791, year = {2025}, author = {Reasoner, SA and Francis, J and Hadjifrangiskou, M}, title = {The urinary microbiome: the next frontier of bacterial ecology.}, journal = {Journal of bacteriology}, volume = {}, number = {}, pages = {e0010525}, doi = {10.1128/jb.00105-25}, pmid = {40704791}, issn = {1098-5530}, support = {F30 AI169748/AI/NIAID NIH HHS/United States ; P20 DK123967/DK/NIDDK NIH HHS/United States ; R01 AI168468/AI/NIAID NIH HHS/United States ; }, abstract = {The human urinary tract, once presumed to be sterile, has emerged as a new frontier of microbial ecology. Recent advancements in high-throughput sequencing technologies have revealed the complexity and diversity of microbial communities that reside within the urinary tract. This mini-review discusses the prominent bacteria identified in the urinary microbiome and their correlations with various urologic conditions. This review serves to summarize the current state of urobiome research and chart a path for ongoing discovery. Additionally, we address the methodological challenges in urinary microbiome research, emphasizing the need for standardization in study protocols and the refinement of bioinformatics tools. We highlight that although differences in urobiome composition have been described for various urologic diseases. Similarly, the pathophysiologic source and consequences of those differences remain uncertain. We outline the steps to move urobiome research from descriptive to mechanistic studies, emphasizing rigorous study design, integrating multi-omics approaches, and developing robust model systems for experimental investigation. Finally, we outline critical questions for future investigation aimed at elucidating the intricate connections between the urinary microbiome and host health.}, }
@article {pmid40704790, year = {2025}, author = {Best, MB and Kazemi Motlagh, Z and McLemore, VT and Jones, DS}, title = {Historic mine waste contains diverse microbial communities that reflect waste type and geochemistry.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0043425}, doi = {10.1128/aem.00434-25}, pmid = {40704790}, issn = {1098-5336}, abstract = {UNLABELLED: Waste rock and tailings left behind by historic mining operations can contain substantial critical mineral resources. However, over the decades and centuries, since these deposits were emplaced, microbial communities developed that can catalyze rock weathering and elemental cycling, which could have impacted the economic resources but also might be harnessed for future biomining or other metal recovery efforts. Here, we combined microbial cell counting, rRNA gene and transcript sequencing, and whole rock geochemistry to compare the composition and abundance of microbial communities from five inactive mine sites in south-central New Mexico that contain critical minerals. While acidic seeps and adits at the sites contained organisms commonly found in acid rock drainage and bioleaching operations, these organisms were only present at very low abundance in the waste rock and tailings, which were instead dominated by bacteria and archaea that are related to inorganic nitrogen- and organic carbon-oxidizing taxa. Generally, rRNA transcript libraries contain many of the same organisms as rRNA gene libraries, indicating that most of these populations are active. Differences among total and active microbial communities correspond to waste rock geochemistry, including concentrations of sulfur, iron, and other variables such as copper, lead, and rare earth elements. Nevertheless, many of the rRNA gene and transcript sequences in these deposits were from groups without cultured representatives, and these unknown microorganisms are likely important for biogeochemical cycling over the long lifetime of these waste deposits. We also discuss recommendations for microbiological assessment of similar large historic mine waste deposits.<br><br>IMPORTANCE: New Mexico has a long history of mining, with hundreds of mining districts across the state, many of which contain inactive operations with historic tailings and waste rock. Because metallurgical processing was in its infancy when most of these mines were active, they contain substantial metal resources in tailings and waste rock that could be used to support domestic demand for critical minerals. We found that microbial communities associated with these deposits do not represent typical bioleaching communities, and instead are dominated by taxa not typically associated with mine waste. However, the deposits did contain rare iron and sulfur-cycling taxa that could catalyze metal mobilization, as well as active populations of novel microorganisms that are likely important for biogeochemical cycling. These microbial communities could represent important resources for bioremediation and other biotechnological applications to recover valuable elements from these and other historic mine wastes.}, }
@article {pmid40703236, year = {2025}, author = {Žilić, DJ and Naletilić, &#x160; and Mihaljević, &#x17d; and Gagović, E and Špičić, S and Reil, I and Duvnjak, S and Tuk, MZ and Hodžić, A and Beck, R}, title = {Hemotropic pathogens in aborted fetuses of domestic ruminants: transplacental transmission and implications for reproductive loss.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1632135}, pmid = {40703236}, issn = {1664-302X}, abstract = {OBJECTIVE: Hemotropic pathogens of the genera Anaplasma, Babesia, Theileria, and hemotropic Mycoplasma are significant infectious agents in domestic ruminants, most commonly associated with vector-borne transmission. However, their potential for transplacental transmission and their contribution to reproductive disorders remains poorly understood. This study aimed to investigate the presence of hemopathogens in aborted fetuses of cattle, sheep, and goats in Croatia, and to evaluate their potential role in transplacental transmission.<br><br>METHODS: Molecular analyses were conducted on tissue samples from 651 aborted fetuses collected between 2016 and 2019 as part of national abortion surveillance programs. PCR screening followed by sequencing were used to detect Anaplasmataceae, Babesia, Theileria, and hemotropic Mycoplasma.<br><br>RESULTS: Thirteen hemopathogens were detected in 94 of 651 fetuses (14.44%), including Anaplasma marginale, Anaplasma ovis, Anaplasma phagocytophilum, Theileria orientalis, Theileria ovis, Theileria sp. OT3, Babesia ovis, Babesia canis, Babesia vulpes, Mycoplasma wenyonii, Mycoplasma haemobos, Mycoplasma ovis, and Mycoplasma haemominutum. The highest infection rates were observed in cattle (17.27%) and sheep (15.85%), while goats showed significantly lower prevalence (5.3%). A. marginale and A. ovis were the most frequently detected pathogens in bovine and ovine fetuses, respectively. Hemotropic mycoplasmas were reported for the first time in Croatia, with the first Western Balkan record of 'Candidatus M. haemobos'. Our study represents the first molecular documentation of a wide array of hemopathogens in aborted ruminant fetuses in Croatia, strongly indicating the possibility of transplacental transmission. The detection of species-specific patterns and the unexpected identification of protozoan species typically associated with canines highlight complex epidemiological dynamics.<br><br>CONCLUSION: Vertical transmission of the detected pathogens may play a role in abortion in endemic regions and should be integrated into differential diagnostic protocols for reproductive failure investigations.}, }
@article {pmid40699317, year = {2025}, author = {Mairi, A and Ibrahim, NA and Idres, T and Basher, NS and Smaili, A and Idres, T and Toutati, A}, title = {Emerging antimicrobial resistance and high prevalence of genital Mycoplasma hominis and Ureaplasma urealyticum infections among infertile women in Algeria : Implications for reproductive health.}, journal = {Wiener klinische Wochenschrift}, volume = {}, number = {}, pages = {}, pmid = {40699317}, issn = {1613-7671}, support = {IMSIU-DDRSP2501//Deanship of Scientific Research at Imam Mohammad Ibn Saud Islamic University (IMSIU)./ ; }, abstract = {BACKGROUND: Genital infections caused by Mycoplasma hominis and Ureaplasma urealyticum are increasingly linked to female infertility, yet their epidemiology and resistance patterns remain poorly characterized in low-resource settings.<br><br>OBJECTIVE: This study aimed to determine the prevalence, antimicrobial resistance (AMR) profiles, and risk factors of M.&#xa0;hominis and U.&#xa0;urealyticum infections among infertile women in Akbou, Algeria.<br><br>METHODS: In this cross-sectional analysis (February-July 2024), cervicovaginal swabs from 79 infertile women were tested using the MYCOFAST&#xae; RevolutioN&#xa0;2 system. Demographic, clinical, and reproductive data were collected via structured questionnaires. Statistical analyses included &#x3c7;[2]-testsand logistic regression.<br><br>RESULTS: The overall infection prevalence was 37.9% (n&#x202f;=&#x2009;30), with U.&#xa0;urealyticum (17.7%), M.&#xa0;hominis (13.9%), and co-infections (6.3%) predominating. Infections peaked in women aged 31-35&#xa0;years (63.3%). Resistance to tetracycline was high (U.&#xa0;urealyticum: 71.4%; M.&#xa0;hominis: 54.5%), while doxycycline and clindamycin retained full efficacy. Significant risk factors included prior abortion (adjusted odds ratio, OR&#x202f;=&#x2009;4.2, p&#x202f;<&#x2009;0.001), STI history (OR&#x202f;=&#x2009;3.8, p&#x202f;<&#x2009;0.001), and artificial insemination (OR&#x202f;=&#x2009;2.9, p&#x202f;=&#x2009;0.018).<br><br>CONCLUSION: The high prevalence of genital Mycoplasma infections and emerging AMR in Algeria underscores the need for routine screening, updated treatment guidelines, and targeted antimicrobial stewardship programs to safeguard reproductive health.}, }
@article {pmid40699244, year = {2025}, author = {Bei, Q and Zhang, J and Huang, Q and Yang, C and Li, Y and Mu, R and Shu, D and Dai, Y and Megharaj, M and He, W and Tian, H}, title = {Rhizosphere Microbiome-Root Exudate Synergy in Pteris vittata: Coordinated Arsenic Speciation and Multielement Metabolic Coupling Drive Hyperaccumulation Efficiency.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {79}, pmid = {40699244}, issn = {1432-184X}, support = {2023YFD1700102//the National Key R&amp;D Program of China/ ; 2024NC-ZDCYL-02-14//the Key R&amp;D Program of Shaanxi Province/ ; 2025JC-QYCX-034//Frontier Exploration Project (Innovative Exploration Category)/ ; }, mesh = {*Arsenic/metabolism ; *Rhizosphere ; *Pteris/microbiology/metabolism ; *Plant Roots/microbiology/metabolism ; *Microbiota ; Soil Microbiology ; Bacteria/metabolism/classification/genetics/isolation &amp; purification ; *Soil Pollutants/metabolism ; Biodegradation, Environmental ; Fungi/metabolism/classification/genetics/isolation &amp; purification ; *Plant Exudates/metabolism ; Soil/chemistry ; }, abstract = {Rhizosphere microorganisms play a pivotal role in enhancing the arsenic (As) remediation efficiency of Pteris vittata. However, the interactions among rhizosphere microorganisms, root exudates, and As, as well as their influence on As uptake by Pteris vittata at different As concentrations, remain poorly understood. This study systematically elucidates the molecular-ecological mechanisms through which Pteris vittata facilitates arsenic (As) remediation within a multidimensional interaction network. It was found that the rhizosphere microbial community was dominated by Proteobacteria, Acidobacteriota, and Ascomycota, with 44 bacterial and 10 fungal genera identified as genetically conserved core microorganisms. Microbial-mediated arsenic (As) methylation and reduction processes, coupled with metabolic pathways such as carbon fixation, sulfur oxidation, and phosphorus mineralization, contribute to the formation of an "As-multielement cycling" synergy. This synergy drives As speciation transformation and enhances plant uptake. Root exudates, such as L-phenylalanine and citric acid, enhance arsenic (As) activation and detoxification by selectively recruiting functional microbes, including Sphingomonas carrying arsC. The resulting metabolite profiles exhibit soil-specific response patterns. High As stress shifted microbial community assembly from stochastic to deterministic processes while maintaining remediation efficiency through enhanced fungal network stability (increased average connectivity). These findings reveal the dual "genetic conservation-environmental adaptation" regulatory strategy of Pteris vittata, providing both theoretical and practical foundations for designing targeted rhizosphere microecological technologies to enhance the phytoremediation of arsenic (As)-contaminated soils.}, }
@article {pmid40699006, year = {2025}, author = {Nauwynck, W and Faust, K and Boon, N}, title = {Droplet microfluidics for single-cell studies: a frontier in ecological understanding of microbiomes.}, journal = {FEMS microbiology reviews}, volume = {49}, number = {}, pages = {}, pmid = {40699006}, issn = {1574-6976}, support = {11E3422N//Research Foundation Flanders/ ; G020119N//Research Foundation Flanders/ ; }, abstract = {Recent advances in single-cell technologies have profoundly impacted our understanding of microbial communities-shedding light on cell-to-cell variability in gene expression, regulatory dynamics, and metabolic potential. These approaches have shown that microbial populations are more heterogeneous and functionally complex than previously thought. However, direct probing of single-cell physiology-arguably more ecologically relevant by focusing on functional traits such as growth, metabolic activity, and enzymatic activity-remains underexplored. Droplet microfluidics provides a practical and high-throughput approach to address this gap, allowing functional characterization of individual microbial cells within complex communities and offering new opportunities to study ecological processes at high resolution. In this review, we look at the state of droplet microfluidics for single-cell microbial ecology. We revisit the fundamentals of microbial droplet workflows, we overview the current capabilities of droplet microfluidics that exist for microbial ecology and we look at the phenomena these workflows have uncovered and understanding they have generated. Finally, we integrate these capabilities to envision future droplet workflows that could enhance our understanding of single-cell physiology and discuss the fundamental limitations that go together with the droplet format.}, }
@article {pmid40698177, year = {2025}, author = {Roy, A and Ghosh, A and Yash,  and Mehra, P and Roy, S and Bhadury, P}, title = {Insights into the genome of Azotobacter sp. strain CWF10, isolated from an agricultural field in Central India.}, journal = {Access microbiology}, volume = {7}, number = {1}, pages = {}, pmid = {40698177}, issn = {2516-8290}, abstract = {Azotobacter sp. strain CWF10, an aerobic gram-negative, oval-shaped and motile bacterium, was isolated from the lateritic agricultural soil of Madhya Pradesh, India. The draft genome of the isolate is 5.7 Mb in size, consisting of 14 contigs with 65.09% G+C content. Average nucleotide identity (94.66%) and digital DNA-DNA hybridization (62%) calculation with the closest reference strains underpin the bacterium as a potential novel species. The bacterium has a plethora of plant growth-promoting genes that point towards the potential ability to enhance available nitrogen and biosynthesis of folic acid, among others. Siderophores such as vibrioferrin and crochelin A are also present in the genome and are known to regulate iron uptake. Overall, mining the genome of Azotobacter sp. strain CWF10 has revealed the potential of this strain for application in regenerative agriculture and sustaining soil health.}, }
@article {pmid40696151, year = {2025}, author = {Laso-Pérez, R}, title = {Anaerobic oxidation of methane: it takes two to tango.}, journal = {Nature reviews. Microbiology}, volume = {}, number = {}, pages = {}, pmid = {40696151}, issn = {1740-1534}, }
@article {pmid40694412, year = {2025}, author = {Benz, BR and Lopez-Echartea, E and Whitaker, BK and Baldwin, T and Geddes, BA}, title = {Improved efficiency of two-step amplicon PCR using an acoustic liquid handler.}, journal = {Microbiology (Reading, England)}, volume = {171}, number = {7}, pages = {}, pmid = {40694412}, issn = {1465-2080}, mesh = {*Polymerase Chain Reaction/methods/instrumentation/economics ; *High-Throughput Nucleotide Sequencing/methods ; Humans ; *Bacteria/genetics/classification/isolation &amp; purification ; Microbiota/genetics ; Gene Library ; *Acoustics/instrumentation ; DNA, Bacterial/genetics ; }, abstract = {The improvement in next-generation sequencing technologies has reduced the costs of sequencing significantly. However, library preparation costs for amplicon sequencing have remained largely unchanged - which is ultimately the cost-limiting step in processing large numbers of microbiome samples. Acoustic liquid handlers can transfer volumes as low as 2.5 nl and have been used to miniaturize several different molecular and cellular assays, including single-step PCR amplicon library preparations. However, there are no current methods available for a two-step library preparation process using an acoustic liquid handler. In this study, we tested the efficiency of an acoustic liquid handler to automate the PCRs and library quantification while also incorporating automated library bead cleanup. We compared the material usage and costs for library preparation and sequencing results of this automated method to the standard, manual method. The automated protocol was able to reduce both PCR reaction volumes fivefold and increased efficiency for library preparation by ~32% without affecting bacterial community compositions. The associated increase in the efficiency of our automated method will allow for greater throughput in sequencing hundreds of microbiome samples without affecting the quality of those sequences.}, }
@article {pmid40694117, year = {2025}, author = {Adam, MAC and Cailleau, G and Junier, P and Benrey, B}, title = {Host Diet and Species Interact to Shape the Bacterial and Fungal Microbiome in the Regurgitant of Four Spodoptera Species.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {78}, pmid = {40694117}, issn = {1432-184X}, support = {162860/SNSF_/Swiss National Science Foundation/Switzerland ; 162860/SNSF_/Swiss National Science Foundation/Switzerland ; 162860/SNSF_/Swiss National Science Foundation/Switzerland ; 162860/SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {Animals ; *Spodoptera/microbiology/physiology/classification ; *Bacteria/classification/genetics/isolation &amp; purification ; *Fungi/classification/genetics/isolation &amp; purification ; *Diet ; *Gastrointestinal Microbiome ; Herbivory ; Phylogeny ; *Mycobiome ; Microbiota ; }, abstract = {The gut microbiome of Lepidopteran insects is highly dynamic, influenced by both host diet and phylogeny. While microbial communities are thought to facilitate host adaptation to diverse diets and environments, the existence of a core microbiome shared among closely related herbivores remains largely untested. In this study, we examined the microbial communities in the regurgitant of four Spodoptera species (S. exigua, S. frugiperda, S. latifascia, and S. littoralis) across different diets (artificial diet, cotton, maize, and squash). Using a high-throughput sequencing, we characterized bacterial and fungal community composition and diversity. Bacterial communities were shaped by both diet and host species, indicating species-specific bacterial selection. In contrast, fungal communities were exclusively structured by diet, with lower diversity and dominance of a few key taxa. Notably, no operational taxonomic units were consistently shared across all species or diets, challenging the concept of a conserved core microbiome in these generalist herbivores. Understanding how microbial communities shape generalist herbivores' ability to feed on diverse plants may offer potential strategies for microbiome-based pest management.}, }
@article {pmid40693737, year = {2025}, author = {Kop, LFM and Koch, H and Speth, D and Lüke, C and Spieck, E and Jetten, MSM and Daims, H and Lücker, S}, title = {Comparative genome analysis reveals broad phylogenetic and functional diversity within the order Nitrospirales.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {40693737}, issn = {1751-7370}, support = {DFG SP 667/11-2//Deutsche Forschungsgemeinschaft/ ; //Austrian Science Fund/ ; 016.Vidi.189.050//Netherlands Organization for Scientific Research/ ; VI.Veni.192.086//Netherlands Organization for Scientific Research/ ; 024.002.002//Gravitation Program of the Dutch Ministry of Education, Culture, and Science/ ; }, abstract = {Nitrification, a key process in the nitrogen cycle, involves the oxidation of ammonia to nitrite and nitrate by a diverse group of chemolithoautotrophic microorganisms. The order Nitrospirales (referred to in literature as the genus Nitrospira), which includes both nitrite-oxidizing and complete ammonia-oxidizing bacteria, plays a central role in this process. We sequenced the genomes of nine Nitrospirales members, incorporating genomes from previously unsequenced taxonomic Nitrospirales lineages. A comprehensive genomic analysis of these new Nitrospirales was conducted, which included an examination of their habitat distribution, phylogenetic diversity, and functional capabilities. This was complemented by the construction of and comparison to a database of 446 non-redundant, high-quality Nitrospirales genomes. Our phylogenomic analysis uncovered the presence of additional unclassified lineages and provided a comparison between genome-based and 16S rRNA gene-based taxonomies. Whereas some Nitrospirales lineages seem to exhibit habitat preferences, others are found across a wide variety of ecosystems, suggesting a broad niche spectrum. This capacity to adapt to different environmental conditions is also reflected in the high variability and modularity of the respiratory chain and nitrogen assimilation mechanisms. Additionally, we found evidence of quorum sensing systems in species beyond lineage II, implying a broader ecological role for this communication mechanism within the Nitrospirales. Finally, we identified a set of conserved genes unique to nitrite oxidoreductase-containing Nitrospirales, providing insights into the emergence of this functional group. In conclusion, our study emphasizes the adaptability of the various nitrifying classes of the order Nitrospirales to diverse environments and reveals the presence of new taxonomic lineages.}, }
@article {pmid40693139, year = {2025}, author = {Nankova, BB and Hu, F and LaGamma, EF}, title = {Early life microbiome disbalance impacts neuroendocrine outcomes in pre-pubertal mice in a sexually dimorphic manner.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1504513}, pmid = {40693139}, issn = {1664-302X}, abstract = {INTRODUCTION: Adverse exposures during perinatal development disrupt the emerging gut microbial ecology that in turn negatively influences long term health. How gut dysbiosis affects complex neurobehavioral functions or even simple reflex arcs (e.g. the amplitude of sympathoadrenal adaptive responses to hypoglycemia) in the extrauterine environment is not well understood.<br><br>METHODS: The C57Bl6 dams were given broad-spectrum antibiotics in the drinking water at parturition until weaning of their litter to perturb the normal seeding and maturation of the postnatal microbiome, control animals received sterile water. To evaluate the impact of altered postnatal flora the offspring were subjected to behavioral tests or sacrificed after exposure to insulin-induced hypoglycemia. Fecal samples were collected for microbial whole genome shotgun taxonomic profiling and predictive functionality. As an index of host sympathoadrenal capacity, individual adrenal medulla samples from each group were subjected to RNA sequencing to identify differentially expressed genes between the groups and gain insights into molecular pathways contributing to the observed outcomes. Given that several neurodevelopmental disorders in humans are biased by sex we also included it as variable in this report.<br><br>RESULTS: The offspring of control dams displayed sex-specific differences in microbiome composition, exploratory behavior, adrenal transcriptome profiles and basal urinary epinephrine levels. Maternal antibiotics during nursing caused: (1) microbial dysbiosis in the offspring as evident by markedly enlarged ceca, no detectable by-products of bacterial fermentation (sp. SCFA) and dramatic changes in microbial composition, diversity (reduced - alpha Chao1and beta Bray-Curtis, as compared to their respective controls) and predictive metabolic activity; (2) alteration in the transcriptional signature of the adrenal medullae and attenuated peripheral stress responses in male offspring, associated with gap junction signaling pathways; (3) increased anxiety-like testing metrics, and decreased locomotor activity; all in a sexually dimorphic manner.<br><br>DISCUSSION: We speculate that the observed sex differences in the gut microbiome may contribute to neurodevelopmental disorders known to have sex-related disparities and in the capacity for successful adaptation to stress. A better understanding of how microbial communities and their hosts interact during critical portions of postnatal neurobehavioral development may help personalize nutritional and therapeutic strategies to promote long term health.}, }
@article {pmid40691348, year = {2025}, author = {Almario, J}, title = {Blurred lines in the mycorrhiza world.}, journal = {Nature reviews. Microbiology}, volume = {}, number = {}, pages = {}, pmid = {40691348}, issn = {1740-1534}, }
@article {pmid40689185, year = {2025}, author = {Li, K and Xu, J and Chen, S and Du, A and Feng, S and Yuan, S and Wu, B}, title = {Dose-dependent effects of capsaicin on intestinal morphology and microbiota composition in mice: Structural, immunohistochemical, and microbial insights.}, journal = {Veterinary world}, volume = {18}, number = {6}, pages = {1703-1714}, pmid = {40689185}, issn = {0972-8988}, abstract = {BACKGROUND AND AIM: Capsaicin (CAP), the pungent component of chili peppers, possesses diverse bioactive properties, including antioxidant, anti-inflammatory, and antimicrobial effects. However, its impact on gastrointestinal integrity and microbial ecology remains dose-dependent and incompletely understood. This study aimed to investigate the effects of varying CAP doses on intestinal morphology, tight junction protein expression, goblet cell density, mucosal injury markers, and gut microbiota composition in mice.<br><br>MATERIALS AND METHODS: Seventy-five male Kunming mice were randomly assigned to five groups (n = 15/group): Normal control, vehicle control (dimethyl sulfoxide), low-dose CAP (5 mg/kg), medium-dose (15 mg/kg), and high-dose (20 mg/kg). Mice received oral gavage every other day for 14 days. Histological assessments (H&amp;E and Alcian Blue-Periodic Acid-Schiff staining), enzyme-linked immunosorbent assays for diamine oxidase, fatty acid-binding protein 2, and plasma endotoxin as well as immunohistochemistry for ZO-1, Claudin-1, and Occludin, and 16S rRNA sequencing were employed to evaluate structural and microbial changes.<br><br>RESULTS: Low-dose CAP significantly enhanced villus height, reduced crypt depth, and elevated the villus-to-crypt ratio across all intestinal segments (p < 0.05). Tight junction protein expression and goblet cell counts were highest in the low-dose group, suggesting mucosal protection. In contrast, medium and high-dose CAP induced epithelial damage, villus atrophy, and downregulation of junctional proteins. Microbiota analysis revealed the suppression of Proteobacteria and the expansion of Firmicutes in the medium- and high-dose groups. All CAP doses stimulated microbial biosynthesis of cofactors, vitamins, and electron carriers, with enhanced alpha diversity at higher doses.<br><br>CONCLUSION: CAP exhibits a biphasic effect on intestinal physiology. While low-dose administration supports mucosal integrity and promotes beneficial microbial functions, higher doses disrupt epithelial architecture and induce dysbiosis. These findings underscore the importance of dose consideration in CAP's dietary and therapeutic applications, providing mechanistic insights into its gut-mediated effects.}, }
@article {pmid40688383, year = {2025}, author = {Liu, S and Rodriguez, JS and Munteanu, V and Ronkowski, C and Sharma, NK and Alser, M and Andreace, F and Blekhman, R and Błaszczyk, D and Chikhi, R and Crandall, KA and Della Libera, K and Francis, D and Frolova, A and Gancz, AS and Huntley, NE and Jaiswal, P and Kosciolek, T and Łabaj, PP and Łabaj, W and Luan, T and Mason, C and Moustafa, AM and Muralidharan, HS and Mutlu, O and Mansouri Ghiasi, N and Rahnavard, A and Sun, F and Tian, S and Tierney, BT and Van Syoc, E and Vicedomini, R and Zackular, JP and Zelikovsky, A and Zielińska, K and Ganda, E and Davenport, ER and Pop, M and Koslicki, D and Mangul, S}, title = {Analysis of metagenomic data.}, journal = {Nature reviews. Methods primers}, volume = {5}, number = {}, pages = {}, pmid = {40688383}, issn = {2662-8449}, support = {U01 DA053941/DA/NIDA NIH HHS/United States ; R01 AI125416/AI/NIAID NIH HHS/United States ; U19 AI174998/AI/NIAID NIH HHS/United States ; U54 AG089334/AG/NIA NIH HHS/United States ; R35 GM146980/GM/NIGMS NIH HHS/United States ; R01 GM146462/GM/NIGMS NIH HHS/United States ; R01 AI173172/AI/NIAID NIH HHS/United States ; R01 AI100947/AI/NIAID NIH HHS/United States ; R21 EB031466/EB/NIBIB NIH HHS/United States ; R01 AI151059/AI/NIAID NIH HHS/United States ; R21 AI129851/AI/NIAID NIH HHS/United States ; R35 GM138369/GM/NIGMS NIH HHS/United States ; }, abstract = {Metagenomics has revolutionized our understanding of microbial communities, offering unprecedented insights into their genetic and functional diversity across Earth's diverse ecosystems. Beyond their roles as environmental constituents, microbiomes act as symbionts, profoundly influencing the health and function of their host organisms. Given the inherent complexity of these communities and the diverse environments where they reside, the components of a metagenomics study must be carefully tailored to yield accurate results that are representative of the populations of interest. This Primer article examines the methodological advancements and current practices that have shaped the field, from initial stages of sample collection and DNA extraction to the advanced bioinformatics tools employed for data analysis, with a particular focus on the profound impact of next-generation sequencing (NGS) on the scale and accuracy of metagenomics studies. We critically assess the challenges and limitations inherent in metagenomics experimentation, available technologies and computational analysis methods. Beyond technical methodologies, we explore the application of metagenomics across various domains, including human health, agriculture and environmental monitoring. Looking ahead, we advocate for the development of more robust computational frameworks and enhanced interdisciplinary collaborations. This Primer serves as a comprehensive guide for advancing the precision and applicability of metagenomic studies, positioning them to address the complexities of microbial ecology and their broader implications for human health and environmental sustainability.}, }
@article {pmid40685652, year = {2025}, author = {Hedjem, A and Kouchkar, A and Ladjeroud, A and Zerrouki, N and Benaissa, F and Ibrahim, NA and Aleissa, MS and Basher, NS and Derguini, A and Idres, T and Houali, K}, title = {Androgen receptor expression in triple negative breast cancer: an Algerian population study.}, journal = {The Libyan journal of medicine}, volume = {20}, number = {1}, pages = {2535778}, pmid = {40685652}, issn = {1819-6357}, mesh = {Humans ; *Receptors, Androgen/metabolism ; *Triple Negative Breast Neoplasms/pathology/mortality/metabolism/genetics ; Female ; Middle Aged ; Algeria/epidemiology ; Adult ; Aged ; Biomarkers, Tumor/metabolism ; Survival Rate ; Ki-67 Antigen/metabolism ; }, abstract = {Triple-negative breast cancer (TNBC) is a molecular subtype of breast cancer characterized by the absence of estrogen and progesterone receptors and the lack of HER2 overexpression. TNBC is highly heterogeneous, complicating the identification of new therapeutic targets. However, the expression of the androgen receptor (AR) in the luminal androgen receptor (LAR TNBC) subgroup has opened the door to alternative therapeutic approaches. This study aimed to assess AR expression and correlate it with clinicopathological factors in 160 early-stage TNBC patients treated from February 2015 to February 2017. Our findings reveal that AR expression is observed in 16.87% (27/160) of ≥1% AR positivity cases. Moreover, a significant 12.5% (20/160) was found in ≥10% AR positive cases. Positive AR expression was inversely correlated with a high Ki-67 proliferation index and with the basal immunophenotype. The five-year survival rate for our cohort was 83.12%, and no significant association between AR expression and overall survival was observed (p = 0.77). The study highlights the potential role of AR expression in TNBC and its implications for therapeutic strategies, although no significant association with overall survival was found.}, }
@article {pmid40681538, year = {2025}, author = {Sedláček, I and Holochová, P and Sedlář, K and Staňková, E and Šedo, O and Kralova, S and Umair, M and Koublová, V and Švec, P}, title = {Two new psychrotolerant Massilia species inhibit plant pathogens Clavibacter and Curtobacterium.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {26134}, pmid = {40681538}, issn = {2045-2322}, support = {LM2023069//MEYS CR/ ; LM2023042//MEYS CR/ ; 101020356//Horizon 2020/ ; }, mesh = {Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Clavibacter/pathogenicity ; Antarctic Regions ; *Plant Diseases/microbiology ; }, abstract = {Three bacterial strains producing blue-violet pigmented colonies on R2A agar were isolated from a wet rock wall and lakes in the deglaciated northern part of James Ross Island, Antarctica. The isolated strains inhibited phytopathogenic Gram-positive bacteria Clavibacter spp., Curtobacterium flacumfaciens, and Paenarthrobacter ilicis. Phylogenetic analysis based on the 16S rRNA gene indicated that the isolates belonged to the genus Massilia and the closest relatives were Massilia violaceinigra B2[T], Massilia rubra CCM 8692[T], Massilia frigida CCM 8695[T], Massilia antarctica CCM 8941[T], and Massilia aquatica CCM 8693[T]. A polyphasic taxonomic study based on lepA genes sequencing, automated ribotyping, MALDI-TOF MS, chemotaxonomy analyses, extensive biotyping, average nucleotide identity, and digital DNA-DNA hybridization calculations based on whole-genome sequences proved that the isolates represent a novel Massilia species for which the names Massilia pseudoviolaceinigra sp. nov. and Massilia scottii sp. nov. are suggested, with the type strains P3689[T] (= CCM 9206[T] = LMG 33568[T]) and P5043[T] (= CCM 9029[T] = LMG 32502[T]), respectively. These two bioactive metabolite-producing species may play an important role in shaping the composition of fresh-water Antarctic microbiomes due to the inhibition of various Gram-positive bacteria.}, }
@article {pmid40681451, year = {2025}, author = {Nichols, HL and Coon, KL}, title = {Leveraging microbial ecology for mosquito-borne disease control.}, journal = {Trends in parasitology}, volume = {41}, number = {8}, pages = {670-684}, pmid = {40681451}, issn = {1471-5007}, support = {U01 AI184909/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Vector Borne Diseases/prevention &amp; control/transmission ; *Mosquito Vectors/microbiology ; *Microbiota ; *Mosquito Control/methods ; *Culicidae/microbiology ; Humans ; Mosquito-Borne Diseases ; }, abstract = {Mosquitoes transmit pathogens causing 700 000 deaths annually. Microbe-based vector control, which reduces vector populations or blocks pathogen development within vectors, offers an innovative way to lower global morbidity and mortality due to vector-borne disease. This review addresses challenges hindering the widespread adoption of microbe-based vector control in mosquitoes. We consider understudied transmission routes of mosquito-associated microbiota, factors affecting colonization and persistence of candidate microbial control agents in mosquito hosts, and the need for robust tools and methodologies to validate that observations in laboratory populations can be reliably extended to field populations. We highlight how understanding the microbial ecology underlying interactions between mosquitoes and their native microbiota can guide successful vector control efforts in these and other arthropod disease vectors.}, }
@article {pmid40679638, year = {2025}, author = {Fulke, AB and Sharma, N and Nadekar, J}, title = {Darkness to Discovery: A Comprehensive Mini-Review on Culturable and Non-Culturable Microbial Diversity from Deep Sea.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {77}, pmid = {40679638}, issn = {1432-184X}, support = {OLP2009//National Institute of Oceanography, India/ ; OLP2009//National Institute of Oceanography, India/ ; OLP2009//National Institute of Oceanography, India/ ; }, mesh = {*Seawater/microbiology ; *Bacteria/genetics/classification/isolation &amp; purification/growth &amp; development ; *Microbiota ; *Biodiversity ; Metagenomics/methods ; Ecosystem ; Hydrothermal Vents/microbiology ; Oceans and Seas ; }, abstract = {Microorganisms are essential players in Earth's ecosystems, demonstrating remarkable adaptability to harsh conditions including arctic ice caps, deep-sea hydrothermal vents, and high-pressure oceanic zones. While the study of these extremophiles has long been constrained by challenges in culturing, recent advances in metagenomic techniques have enabled a deeper understanding of microbial diversity in these extreme habitats. This review explores both culturable and non-culturable microbial communities, focusing on the diverse strategies employed by microorganisms to thrive in harsh conditions, including high pressure, temperature, salinity, and nutrient limitations. Traditional cultivation methods often fail to capture the full spectrum of deep-sea microbiota due to the unique growth requirements of many organisms. In the omic era, however, microbial cultivation and the function of microbial resources are important. Non-culturable methods, like metagenomic studies and environmental DNA sequencing, have uncovered hitherto unknown microbial taxa and metabolic pathways, offering important new information on microbial ecology and biogeochemistry. The complex microbial interactions and adaptive methods that support these ecosystems are highlighted by case studies, including as studies on hydrothermal plumes and hadal deposits. The expanding significance of non-culturable techniques in microbial research is highlighted in this review, which also highlights how they might help us better understand microbial life in harsh conditions and how they may be used in biotechnology and environmental management.}, }
@article {pmid40678115, year = {2025}, author = {Tankova, H}, title = {Association between the severity of gingival inflammation and microbial findings in children.}, journal = {Frontiers in dental medicine}, volume = {6}, number = {}, pages = {1638435}, pmid = {40678115}, issn = {2673-4915}, abstract = {INTRODUCTION: The oral cavity is home to hundreds of distinct microbial species, and specific periodontal pathogens are isolated from different ecological niches. Present study aimed to investigate the relationship between the severity of gingival inflammation and the presence of subgingival microorganisms in children with dental biofilm induced gingivitis.<br><br>MATERIAL AND METHODS: The study included 30 children aged 12-14 years, divided into two groups based on the extent of gingival inflammation: Group I-16 children with BOP up to 30%; Group II-14 children with BOP over 30%. All children were interviewed to assess oral hygiene habits. Clinical examination was performed using an electronic periodontal probe, and the following were recorded: oral hygiene status (FMPS) and gingival status through BOP and SBI. For quantitative assessment of subgingival periodontopathogens, a genetic method - PCR-Real Time was used, and the following microorganisms were examined: Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Treponema denticola, Tannerella forsythia, Prevotella intermedia, Peptostreptococcus micros, Fusobacterim nucleatum, Eubacterium nodatum, Capnocytophaga gingivalis. The critical significance level for testing the null hypothesis was set at &#x3b1;&#x2009;=&#x2009;0.05, corresponding to a 95% confidence level.<br><br>RESULTS: The majority of children showed improper oral hygiene habits. Children with generalized gingival inflammation had significantly higher plaque accumulation index values compared to those with localized inflammation. In children with generalized gingival inflammation, the quantities of all isolated periodontopathogens were higher compared to those with localized inflammation, which was also confirmed regarding the overall microbial load. A. actinomycetemcomitans was not isolated in children with localized gingival inflammation, while T. denticola was isolated in significantly lower quantities compared to generalized inflammation. P. intermedia and P. micros were isolated in significantly higher quantities in more severe gingival inflammation. In children with localized gingival inflammation, combinations of an average of 2 microorganisms were found in microbial complexes, while in children with generalized inflammation, microorganisms were twice as many and in more complex combinations.<br><br>CONCLUSION: The microbial diversity within the subgingival biofilm significantly increases with disease severity, providing further evidence for the critical role of microbial ecology in the pathogenesis of gingival inflammation in children.}, }
@article {pmid40676356, year = {2025}, author = {Sibanyoni, NR and Piater, LA and Kerchev, P and Madala, NE and Mhlongo, MI}, title = {Metabolomic Insights into Cross-Feeding Interactions Between Priestia megaterium PM and Pseudomonas fluorescens NO4: Unveiling Microbial Communication in Plant Growth-Promoting Rhizobacteria.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {76}, pmid = {40676356}, issn = {1432-184X}, support = {TTK2404507217709//National Research Foundation/ ; }, mesh = {*Pseudomonas fluorescens/metabolism/physiology/growth &amp; development ; Metabolomics ; Rhizosphere ; *Microbial Interactions ; Soil Microbiology ; Quorum Sensing ; Plant Development ; Metabolome ; Volatile Organic Compounds/metabolism ; }, abstract = {Plant growth-promoting rhizobacteria (PGPR) engage in complex chemical exchange and signalling processes to enhance their survival, rhizosphere colonisation, and plant-beneficial roles. These microbial interactions are mediated by various chemical cues, including quorum sensing (QS) molecules, cyclic peptides, lipopeptides, nutrients, volatile organic compounds (VOC), and phytohormones. Cross-feeding, where one microorganism consumes metabolites produced by another, exemplifies direct chemical communication that shapes community dynamics and metabolic cooperation. However, the effects of cross-feeding among different PGPR strains remain insufficiently characterised. In this study, an LC-MS-based metabolomics approach, combined with multivariate statistical analysis, was employed to investigate metabolic perturbations induced by cross-feeding among PGPR strains. Growth curve analysis revealed that cross-fed PGPR exhibited growth patterns comparable to controls, with a slight reduction in biomass. Metabolic profiling indicated time-dependent shifts in the metabolic state of the cross-fed organisms, suggesting adaptive metabolic reprogramming in response to the donor-conditioned media. Multivariate analysis identified distinct metabolite alterations between cross-fed and control groups across different time points, highlighting the influence of nutrient availability on microbial growth dynamics. Notably, cross-fed groups showed decreased levels of primary metabolites such as amino acids and sugars alongside increased production of secondary metabolites, including surfactins, salicylic acid, and carboxylic acids. These secondary metabolites are implicated in plant growth promotion and defence, indicating their potential as natural biostimulants. The findings advance the understanding of PGPR interactions and chemical communication in the rhizosphere, supporting the development of sustainable agricultural practices by leveraging beneficial microbial interactions. Future research should explore these interactions within more complex microbial communities.}, }
@article {pmid40671255, year = {2025}, author = {Bartsch, S and Kreutz, C and Scholz, KJ and Kohnert, E and Hertel, J and Wolf, M and Jakubovics, N and Al-Ahmad, A and Cieplik, F}, title = {Culturomics: Deciphering the Microbial Dark Matter in the Oral Cavity.}, journal = {Journal of dental research}, volume = {}, number = {}, pages = {220345251346781}, doi = {10.1177/00220345251346781}, pmid = {40671255}, issn = {1544-0591}, abstract = {The idea of the tree of life originated in the 19th century and has steadily evolved since then. In the last 20 y, high-throughput sequencing methods have revolutionized microbial ecology and expanded our understanding of this tree of life tremendously. However, this has led to a sharp increase in what is known as microbial dark matter, consisting of bacterial and archaeal taxa that are only known by sequencing and have not yet been cultivated. The lack of ecologic information about these species poses a major challenge. This has led to the need for other approaches to supplement the DNA sequence-based findings. The term "culturomics"-which describes the large-scale isolation, culture, and identification of species from an environment-was introduced in 2012 with a focus on the human gut microbiota. The cultivation of new species, which had been neglected for many years, is now firmly back in the spotlight since strains are required for experimental studies to complement the knowledge obtained from microbial DNA sequences. Laboratory culture is essential to gain knowledge of microbial physiology, assign functions to novel genes and proteins, identify resistance profiles, and better understand the impact of different microorganisms on human health. While many culturomics studies have focused on gut microbiota, significant progress has been made in oral microbiology, with the enrichment of Candidatus Nanosynbacter lyticus representing one of the greatest achievements. This review gives a comprehensive overview of the oral microbial community regarding the microbial dark matter and summarizes the work carried out to date on the oral microbiota using culturomics. The capability and challenges of metagenomics and culturomics and the potential use of artificial intelligence are examined, with insights from extensive culturomics research on gut microbiota, which promises applicability to the field of oral microbiology.}, }
@article {pmid40670676, year = {2025}, author = {Su, J and Su, Y and Weng, Y and Ayub, G and She, C and Xiao, Y}, title = {Insights Into Proliferation Effects of Low-Dose Glyphosate on Phytoplankton Communities.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {75}, pmid = {40670676}, issn = {1432-184X}, support = {FJ2025MGCA019//Fujian Province Social Science Fund Project/ ; 2024R016//Fujian Environmental Protection Science and Technology Program/ ; DH1408//Enterprise and Public Institution Commissioned Science and Technology Project/ ; }, mesh = {Glyphosate ; *Glycine/analogs &amp; derivatives/pharmacology/toxicity ; *Phytoplankton/drug effects/growth &amp; development ; *Herbicides/pharmacology/toxicity ; Biomass ; Cyanobacteria/drug effects/growth &amp; development ; Phosphorus/metabolism ; Microcystis/drug effects/growth &amp; development ; Harmful Algal Bloom/drug effects ; Microalgae/drug effects/growth &amp; development ; *Water Pollutants, Chemical/toxicity ; Ecosystem ; }, abstract = {Glyphosate-based herbicides are among the most widely used agricultural chemicals globally, and their widespread application presents risks to environmental health and aquatic ecosystems. Continuous glyphosate inputs disrupt phytoplankton communities, potentially triggering harmful algal blooms. This study examines the proliferation of microalgal species exposed to low glyphosate concentrations (0.05 mg/L) and various phosphorus sources, with a particular focus on C-P and C-O-P bond phosphonates, which have been insufficiently studied in previous research. We hypothesized that cyanobacteria might exhibit a competitive growth advantage over other algal species when exposed to C-P bond glyphosate, especially under phosphorus-limited conditions. In monoculture experiments, Microcystis aeruginosa and Peridinium umbonatum var. inaequale significantly increased their biomass when cultured with C-P bond phosphonates, whereas Scenedesmus bijuga failed to thrive under similar conditions. Peridinium umbonatum var. inaequale also displayed increased soluble protein content in response to glyphosate stress, indicating an adaptive stress response. In co-culture experiments, M. aeruginosa demonstrated greater tolerance to glyphosate than P. umbonatum var. inaequale, though biomass increases were not significantly correlated with soluble protein or APA. Sediment-water interface experiments revealed that glyphosate exposure significantly promoted cyanobacterial biomass, which was approximately five times greater than that of the inorganic phosphorus group. Notably, when cyanobacterial biomass exceeded 20% of the total, Cyanophyta replaced Chlorophyta as the dominant group, suggesting a potential competitive advantage under low-dose glyphosate exposure. These findings highlight that glyphosate may promote cyanobacterial dominance by altering phytoplankton community composition, potentially contributing to the increased frequency of harmful algal blooms in nutrient-limited aquatic environments.}, }
@article {pmid40668425, year = {2025}, author = {Mnguni, FC and Shin, GY and du Toit, LJ and Derie, ML and Coutinho, TA}, title = {Ewingella allii sp. nov. isolated from a diseased onion plant in the Columbia Basin of Washington State, USA.}, journal = {Antonie van Leeuwenhoek}, volume = {118}, number = {8}, pages = {115}, pmid = {40668425}, issn = {1572-9699}, support = {2019-51181-3//USDA NIFA SCRI/ ; 2019-51181-3//USDA NIFA SCRI/ ; 2019-51181-3//USDA NIFA SCRI/ ; 2019-51181-3//USDA NIFA SCRI/ ; 2019-51181-3//USDA NIFA SCRI/ ; }, mesh = {Phylogeny ; Washington ; RNA, Ribosomal, 16S/genetics ; *Onions/microbiology ; *Plant Diseases/microbiology ; DNA, Bacterial/genetics ; Base Composition ; Genome, Bacterial ; Bacterial Typing Techniques ; }, abstract = {Isolation of strain 20WA0182[T] from a diseased onion plant grown in the Columbia Basin of Washington State, USA, led to preliminary identification as a member of the genus Ewingella. The strain was characterised as a Gram-stain-negative, facultative anaerobe that is rod-shaped, motile with polar flagella, catalase positive, and oxidase negative. The strain 20WA0182[T] isolated was pathogenic to yellow onion bulbs, weakly pathogenic on onion leaves of the cv. Ranchero, and caused a pathogenic response using the red onion bulb scale necrosis assay. Phylogenetic analyses using the 16S rRNA gene and four housekeeping genes, atpD, gyrB, infB, and rpoB, showed that strain 20WA0182[T] formed a branch that clustered with E. americana strains, but on a separate node, indicating it is a novel species of this genus. Whole-genome sequencing of strain 20WA0182[T] revealed a genome size of 4,604,541 nt, with 25 contigs and a G + C content of 53.8%, strain 20WA0182[T] was 99.2% complete. The average nucleotide identity of strain 20WA0182[T] compared with E. americana strains scores ranged from 92.85 to 93.96%, below the 95% threshold to classify strains as the same species. Similarly, dDDH scores were 56.0 to 56.2%, less than the 70% threshold required to delineate prokaryotes as the same species. Strain 20WA0182[T] and Ewingella sp. CoE-038-23 shared the ANI score above 97.59% and 81.0% dDDH score to be classified as a novel species of Ewingella. As the type strain 20WA0182[T] (= BD 3290[ T] = LMG 33618[ T]) was pathogenic to onion bulbs and leaves, the name Ewingella allii is proposed. GenBank accession number = JAWUDN000000000.}, }
@article {pmid40667995, year = {2025}, author = {Garin, T and Brault, A and Marais, C and Briand, M and Préveaux, A and Bonneau, S and Simonin, M and Barret, M and Sarniguet, A}, title = {T6SS-mediated competition by Stenotrophomonas rhizophila shapes seed-borne bacterial communities and seed-to-seedling transmission dynamics.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0045725}, doi = {10.1128/msystems.00457-25}, pmid = {40667995}, issn = {2379-5077}, abstract = {UNLABELLED: Seeds harbor diverse microbial communities important for plant growth and health. During germination, seed exudation triggers intense microbial competition, shaping the communities transmitted to seedlings. This study explores the role of the bacterial type VI secretion system (T6SS)-mediated interference competition in seed microbiota transmission to seedlings. The analysis of T6SS distribution within 180 genome sequences of seed-borne bacterial strains enabled the construction of synthetic communities (SynCom) with different levels of phylogenetic diversity and T6SS richness. These SynComs were inoculated with Stenotrophomonas rhizophila CFBP13503, a bacterial strain possessing an active T6SS in vitro and in planta. The impact of the T6SS on SynCom composition was assessed in vitro by comparing the CFBP13503 wild-type strain or its isogenic T6SS-deficient mutant co-inoculation. Additionally, the effects of the T6SS on bacterial community dynamics during seed-to-seedling transmission were examined following seed inoculation. The T6SS of S. rhizophila CFBP13503 targets a broad range of bacteria belonging to five different orders. The susceptibility of competing bacteria was partly explained by their phylogenetic proximity and metabolic overlap with CFBP13503. Furthermore, the T6SS modulates the relative abundance of specific bacterial taxa during seed-to-seedling transmission depending on the initial seed inoculum and plant developmental stage. Depending on the sensitivity of the co-inoculated competitors, the T6SS can provide a competitive advantage to CFBP13503, resulting in an increase in population size.<br><br>IMPORTANCE: The high prevalence of the type VI secretion system (T6SS) in seed-borne bacteria supports the importance of T6SS-mediated competition for seed microbiota assembly. In vitro, S. rhizophila CFBP13503 T6SS exerts a strong impact on bacterial community dynamics. The susceptibility to the T6SS increases with the phylogenetic and metabolic proximities of bacteria to CFBP13503, suggesting the influence of interspecies trophic patterns in T6SS-mediated competitions. In planta and in soil, CFBP13503 T6SS influences specific bacterial taxa, leading to shifts in bacterial interactions and distinct community dynamics. T6SS-mediated competition plays a pivotal role in shaping seed bacterial communities and the dynamics of seed-to-seedling transitions.}, }
@article {pmid40666882, year = {2025}, author = {Orkin, JD and Fournier, A and Young, D and Webb, SE and Cheves Hernandez, SE and Jack, KM and Campos, FA and Dufour, A and Melin, AD}, title = {Fecal proteomics of wild capuchins reveals impacts of season, diet, age, and, sex on gut physiology.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40666882}, issn = {2692-8205}, support = {R61 AG078529/AG/NIA NIH HHS/United States ; }, abstract = {Understanding how the physiology of free-ranging mammals is impacted by environmental stressors is a major focus of ecological research. However, the constraints of non-invasive sampling pose serious challenges to the acquisition of physiological data from most species of primates. As a result, little is known about how the gut responds to ecological stimuli at the cellular level in wild populations. Recent research has demonstrated that proteomics could fill this knowledge gap by sequencing and quantifying proteins directly from primate feces. In order to ascertain how the gut of free-ranging white-faced capuchin monkeys (C. imitator) is influenced by environmental heterogeneity, diet, age, and sex, we sequenced 45 fecal proteomes from 24 individuals from the Sector Santa Rosa population in Costa Rica, using liquid chromatography-tandem mass spectrometry with label-free quantification. Fecal proteins assigned to C. imitator were strongly localized to gut tissues and functionally enriched for digestive and immune functions. We identified 41 capuchin candidate proteins linked to seasonality, age, sex, and diet. We also quantified abundances of dietary fruit, dietary insects, helminth gut parasites, and gut microbes. Our results demonstrate the viability of using quantitative fecal proteomics in free-ranging populations of mammals to integrate host physiology, diet, and microbial ecology through non-invasive means.}, }
@article {pmid40662685, year = {2025}, author = {Verstraete, W and Strubbe, L and Pikaar, I and Vinestock, TW and Lee, PH and Matassa, S and Chong, J and Zhou, J and Daigger, GT and Guo, M}, title = {Escaping Historical Lock-in─Redesigning Wastewater Treatment Plants and Their Microbiomes for the 21st Century.}, journal = {Environmental science &amp; technology}, volume = {59}, number = {29}, pages = {14862-14869}, pmid = {40662685}, issn = {1520-5851}, mesh = {*Wastewater ; *Microbiota ; *Water Purification ; *Waste Disposal, Fluid ; }, abstract = {Wastewater treatment plants (WWTPs) have gradually, over the last hundred years, been designed and extended to deal with a sequence of problems, including a) odor, b) suspended solids, c) organics, d) ammonia, e) nitrate and phosphate, and f) recalcitrant pollutants. The line of historical developments was piecemeal rather than holistic and did not focus on sustainability, resource recovery, and water reuse. On the contrary, microbial processes that accelerated the removal of nitrogen were incorporated and heralded as a positive part of the "cleanup" agenda, despite their relatively large energy consumption and substantial production of nitrous oxide, a potent greenhouse gas. The time has come to examine the historical, technological, and microbiological lock-in present in today's WWTPs, so that a more coherent integrated system can be developed for future generations. Some disruptive strategies are outlined, and a categorization of processes in terms of their potential for the future is formulated.}, }
@article {pmid40660619, year = {2025}, author = {Armstrong, R}, title = {Microbes as Teachers: Rethinking Knowledge in the Anthropocene.}, journal = {Microbial biotechnology}, volume = {18}, number = {7}, pages = {e70195}, pmid = {40660619}, issn = {1751-7915}, support = {101114746//European Innovation Council (EIC), Pathfinder Challenges/ ; }, mesh = {Humans ; Ecosystem ; *Microbiology/education ; }, abstract = {This opinion piece proposes that the environmental crises of our time arise from a failure to recognise the vital role of microbes in sustaining life on Earth, where ecosystems have been shaped for billions of years by microbial processes, including oxygen production, nutrient cycling and climate regulation. Yet the idea that microbes can 'teach' us how to navigate complexity, adapt across scales, and sustain planetary systems is still marginalised in science, policy, and education. A paradigm shift is proposed: microbes must be reframed as active collaborators in solving global challenges. This perspective is grounded in microbial ecology, Indigenous knowledge, and ethical philosophy, advocating for 'learning' through and with microbial life. To institutionalise this transition, policy and educational reforms are urged, centring microbial literacy as a foundation for ecological understanding. By integrating microbial agency into human knowledge systems, societal actions could be realigned with the biochemical and evolutionary logics that have sustained life for millennia. Ultimately, a deeper engagement with microbial knowledge is called for-one that informs a more sustainable future.}, }
@article {pmid40657876, year = {2025}, author = {Strachan, CR and Bowers, CM and Kim, BC and Movsesijan, T and Neubauer, V and Mueller, AJ and Yu, XA and Pereira, FC and Nagl, V and Faas, J and Wagner, M and Zebeli, Q and Weimer, PJ and Candry, P and Polz, MF and Lawson, CE and Selberherr, E}, title = {Distinct lactate utilization strategies drive niche differentiation between two co-existing Megasphaera species in the rumen microbiome.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {40657876}, issn = {1751-7370}, support = {//Austrian Federal Ministry for Digital and Economic Affairs and the National Foundation for Research, Technology and Development, through the Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock/ ; //Austrian Federal Ministry for Climate Action, Environment, Energy, Mobility, Innovation and Technology (BMK), Austrian Federal Ministry for Digital and Economic Affairs (BMDW) and the provinces of Lower Austria and Vienna within the framework of COMET-Competence Centers for Excellent Technologies, which is handled by the Austrian Research Promotion Agency (FFG)/ ; //Sparkling Science 2.0 grant (project "Micro-Tramper") funded by the Austrian Federal Ministry of Science, Research and Economy (BMWFW)/ ; //Fellowship from the Natural Science and Engineering Council of Canada Postgraduate Scholarship-Doctoral (NSERC PGS-D)/ ; }, abstract = {Lactate utilization mitigates rumen acidosis and is associated with decreased methane production in the rumen. While several lactate utilization pathways exist across different microbial species in the rumen, how they are metabolically differentiated remains unclear. Here, we show that the key lactate-utilizing species Megasphaera hexanoica and Megasphaera elsdenii display distinct growth strategies based on their fermentative end products. This allows them to co-exist and play distinct metabolic roles, which appear particularly relevant in the early stages of rumen development, as both species are highly enriched in the calf. Specifically, M. hexanoica is more strongly associated with rumen microbiome states that involve increased lactate utilization and preferentially runs reverse beta-oxidation (termed chain elongation) to produce butyrate and medium-chain fatty acids from lactate. As M. elsdenii instead utilizes lactate via the acrylate pathway to produce propionate, we leverage Enzyme Cost Minimization to predict how this pathway relates to a distinct growth strategy. We find that M. elsdenii maximizes growth rate when lactate transiently accumulates, which contrasts M. hexanoica's invariably high-yield strategy. This trade-off, which is supported by the analysis of growth kinetics, metabolic flux, and bioreactors simulating the rumen microbiome, ultimately contributes to co-existence on lactate and may have driven niche differentiation. Lastly, we demonstrate how lactate utilization in the Megasphaera is threatened by toxins widespread in feed, which points to dietary interventions to support calf health.}, }
@article {pmid40657038, year = {2025}, author = {Ronin, D and Hansen, MF and Flaig, ML and Dahl Dueholm, MK and Hostrup Daugberg, AO and Nesme, J and Kot, W and Burmølle, M}, title = {Unfolding the collective functional potential of a synergistic multispecies community through genotypic and phenotypic analyses.}, journal = {Biofilm}, volume = {10}, number = {}, pages = {100290}, pmid = {40657038}, issn = {2590-2075}, abstract = {By studying model multispecies biofilm systems, we can further our knowledge regarding why some properties emerge solely in a multispecies setting. In this study, the model system under investigation is composed of four bacterial species: Paenibacillus amylolyticus, Microbacterium oxydans, Stenotrophomonas rhizophila and Stenotrophomonas maltophilia. This community was isolated from soil and has previously shown synergistic biofilm formation capabilities in vitro, along with other intrinsic properties, some of which could lead to potential industrial and agricultural applications. In this study, we conducted the first complete genome assemblies for these four strains and performed a manually curated annotation of the genomes to identify genomic features that could guide the selection of relevant phenotypic assays. In all four strains, we identified genes linked to interspecies communication, biofilm formation, secondary metabolite production, antibiotic resistance, enzymatic activity and metabolism of toxic xenobiotics. With metabolism being the largest gene function category identified, we then conducted growth assays on various carbon sources and relevant polysaccharides. This revealed interesting emergent behaviors - regarding growth and enzymatic activity - in the four-species community which were not seen in the monocultures. Overall, analysis of the complete genomes of this model community uncovered gene functions which could play a role in the previously observed community intrinsic properties, as well as provided insight to the positive social interactions observed in vitro.}, }
@article {pmid40655931, year = {2025}, author = {Redondo, MA and Jones, CM and Legendre, P and Guénard, G and Hallin, S}, title = {Predicting gene distribution in ammonia-oxidizing archaea using phylogenetic signals.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf087}, pmid = {40655931}, issn = {2730-6151}, abstract = {Phylogenetic conservatism of microbial traits has paved the way for phylogeny-based predictions, allowing us to move from descriptive to predictive functional microbial ecology. Here, we applied phylogenetic eigenvector mapping to predict the presence of genes indicating potential functions of ammonia-oxidizing archaea (AOA), which are important players in nitrogen cycling. Using 160 nearly complete AOA genomes and metagenome assembled genomes from public databases, we predicted the distribution of 18 ecologically relevant genes across an updated amoA gene phylogeny, including a novel variant of an ammonia transporter found in this study. All selected genes displayed a significant phylogenetic signal and gene presence was predicted with an average of >88% accuracy, >85% sensitivity, and >80% specificity. The phylogenetic eigenvector approach performed equally well as ancestral state reconstruction of gene presence. We implemented the predictive models on an amoA sequencing dataset of AOA soil communities and showed key ecological predictions, e.g. that AOA communities in nitrogen-rich soils were predicted to have capacity for ureolytic metabolism while those adapted to low-pH soils were predicted to have the high-affinity ammonia transporter (amt2). Predicting gene presence can shed light on the potential functions that microorganisms perform in the environment, further contributing to a better mechanistic understanding of their community assembly.}, }
@article {pmid40654884, year = {2025}, author = {Wirbel, J and Hickey, AS and Chang, D and Enright, NJ and Dvorak, M and Chanin, RB and Schmidtke, DT and Bhatt, AS}, title = {Discovering Broader Host Ranges and an IS-bound Prophage Class Through Long-Read Metagenomics.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40654884}, issn = {2692-8205}, support = {R01 AI143757/AI/NIAID NIH HHS/United States ; R01 AI148623/AI/NIAID NIH HHS/United States ; T32 GM007276/GM/NIGMS NIH HHS/United States ; }, abstract = {Gut bacteriophages profoundly impact microbial ecology and human health, yet they are greatly understudied. Using deep, long-read bulk metagenomic sequencing, a technique that overcomes fundamental limitations of short-read approaches, we tracked prophage integration dynamics in 12 longitudinal stool samples from six healthy individuals, spanning a two-year timescale. While most prophages remain stably integrated into their host over two years, we discover that ~5% of phages are dynamically gained or lost from persistent bacterial hosts. Within the same sample, we find evidence of population heterogeneity in which identical bacterial hosts with and without a given integrated prophage coexist simultaneously. Furthermore, we demonstrate that phage induction, when detected, occurs predominantly at low levels (1-3x coverage compared to the host region). Interestingly, we identify multiple instances of integration of the same phage into bacteria of different taxonomic families, challenging the dogma that phage are specific to a host of a given species or strain. Lastly, we describe a new class of phages, which we name "IScream phages". These phages co-opt bacterial IS30 transposases to mediate their integration, representing a previously unrecognized form of phage domestication of selfish bacterial elements. Taken together, these findings illuminate fundamental aspects of phage-bacterial dynamics in the human gut microbiome and expand our understanding of the evolutionary mechanisms that drive horizontal gene transfer and microbial genome plasticity in this ecosystem.}, }
@article {pmid40650753, year = {2025}, author = {Pascual, A and Calabresi, F and de la Fuente, D and Catalano, MI and Brentassi, ME}, title = {Transcriptome Analysis of the Fat Body of the Maize Pest Delphacodes kuscheli (Hemiptera: Delphacidae) Reveals Essential Roles of Fungal Endosymbionts.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {74}, pmid = {40650753}, issn = {1432-184X}, support = {PICT 2021- 00914//Comisi&#xf3;n de Investigaciones Cient&#xed;ficas de la Provincia de Buenos Aires (CICPBA), Consejo Nacional de Investigaciones Cient&#xed;ficas y T&#xe9;cnicas (CONICET), Universidad Nacional de La Plata (UNLP), and Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica (ANPCyT) (PICT 2021- 00914)./ ; PICT 2021- 00914//Comisi&#xf3;n de Investigaciones Cient&#xed;ficas de la Provincia de Buenos Aires (CICPBA), Consejo Nacional de Investigaciones Cient&#xed;ficas y T&#xe9;cnicas (CONICET), Universidad Nacional de La Plata (UNLP), and Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica (ANPCyT) (PICT 2021- 00914)./ ; PICT 2021- 00914//Comisi&#xf3;n de Investigaciones Cient&#xed;ficas de la Provincia de Buenos Aires (CICPBA), Consejo Nacional de Investigaciones Cient&#xed;ficas y T&#xe9;cnicas (CONICET), Universidad Nacional de La Plata (UNLP), and Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica (ANPCyT) (PICT 2021- 00914)./ ; PICT 2021- 00914//Comisi&#xf3;n de Investigaciones Cient&#xed;ficas de la Provincia de Buenos Aires (CICPBA), Consejo Nacional de Investigaciones Cient&#xed;ficas y T&#xe9;cnicas (CONICET), Universidad Nacional de La Plata (UNLP), and Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica (ANPCyT) (PICT 2021- 00914)./ ; PICT 2021- 00914//Comisi&#xf3;n de Investigaciones Cient&#xed;ficas de la Provincia de Buenos Aires (CICPBA), Consejo Nacional de Investigaciones Cient&#xed;ficas y T&#xe9;cnicas (CONICET), Universidad Nacional de La Plata (UNLP), and Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica (ANPCyT) (PICT 2021- 00914)./ ; }, mesh = {Animals ; *Symbiosis ; *Hemiptera/microbiology/genetics ; Gene Expression Profiling ; Zea mays/parasitology ; *Fat Body/microbiology/metabolism ; *Transcriptome ; *Hypocreales/genetics/physiology ; Phylogeny ; }, abstract = {The fat body of certain insects, in addition to performing essential biosynthetic and metabolic functions, harbors endosymbionts that play critical roles for their host. While knowledge of the diversity and functions of fungal endosymbionts harbored in the fat body of planthoppers is mostly limited to rice pests of Asia, our study presents a comprehensive transcriptomic analysis of the fat body of Delphacodes kuscheli (Hemiptera: Delphacidae), an important agricultural pest of maize in Argentina. The dominant fungal endosymbionts, identified as yeast-like symbionts (YLS), include members of the genera Ophiocordyceps, Cordyceps, Hirsutella, and Tolypocladium (Ascomycota: Hypocreales). Transcriptomic data reveal that the fungal endosymbionts encode genes involved in vital metabolic processes for the host, such as essential amino acid biosynthesis, nitrogen recycling, and steroid biosynthesis. The genetic contribution of these endosymbionts to nutrient provision and metabolism supports a mutualistic obligate relationship with D. kuscheli. The results presented here provide insights into the evolutionary dynamics of endosymbiosis in the Delphacidae. Furthermore, this study highlights the potential of YLS as promising targets for innovative pest control strategies.}, }
@article {pmid40650575, year = {2025}, author = {Guigard, L and Nazaret, F and Almario, J and Bertolla, F and Boubakri, H and Cantarel, AAM and Cournoyer, B and Favre-Bonté, S and Florio, A and Galia, W and Hazard, C and Henry, G and Belaroussi, AH and Chong, SKTF and Lavire, C and Lobreau, C and Luis, P and Maréchal, M and Meyer, T and Pozzi, ACM and Minard, G and Nazaret, S and Nicol, GW and Prigent-Combaret, C and Richaume, A and Rodriguez-Nava, V and Sanchez-Cid, C and Moro, CV and Vial, L and Vigneron, A and Wisniewski-Dyé, F and Shade, A}, title = {The connections of climate change with microbial ecology and their consequences for ecosystem, human, and plant health.}, journal = {Journal of applied microbiology}, volume = {136}, number = {7}, pages = {}, doi = {10.1093/jambio/lxaf168}, pmid = {40650575}, issn = {1365-2672}, support = {//Universit&#xe9; Claude Bernard Lyon 1/ ; }, mesh = {*Climate Change ; Humans ; *Ecosystem ; *Microbiota ; *Plants/microbiology ; }, abstract = {The climate crisis presents an urgent challenge for Earth's living creatures and the habitats in which they have been adapted to thrive. Climate-related stress presents risks to microorganisms, the stability of the functions they provide, and their maintenance of beneficial interactions with their hosts and ecosystems. Microbes move across the continuum of anthropogenic influence on Earth's ecosystems, from pristine to human-managed to fully urbanized environments. Because microbial feedback within and across this continuum exists at multiple, connected scales from molecules to ecosystem-level processes, predicting microbial responses to climate stress and their potentially wide-ranging consequences remains difficult. Here, we discuss the broad implications of microbial and microbiome responses to climate change as they interface with human, plant, and ecosystem health. For each section on human, plant and ecosystem health, we briefly discuss the state of knowledge for each and follow with proposed future research, including some directions that are promising but require more work to evaluate. We end by considering overarching microbial ecology research needs across these systems and microbial solutions under investigation as possible climate-resilient interventions to maintain human, plant, and ecosystem health. This work draws on diverse expertise to identify broad research directions across typically separated disciplines and builds a holistic framework for considering their interrelationships.}, }
@article {pmid40650408, year = {2025}, author = {Beau, A and Natividad, J and Benoit, B and Delerive, P and Duboux, S and Feng, Y and Jammes, M and Barnel, C and Sequino, G and Pinteur, C and Glorieux, G and Fouque, D and Vidal, H and Koppe, L}, title = {A specifically designed multi-biotic reduces uremic toxin generation and improves kidney function.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2531202}, pmid = {40650408}, issn = {1949-0984}, mesh = {Humans ; *Uremic Toxins/metabolism ; *Renal Insufficiency, Chronic/microbiology/therapy ; Animals ; *Probiotics/administration &amp; dosage ; Feces/microbiology/chemistry ; *Gastrointestinal Microbiome ; Male ; Cresols/metabolism ; *Kidney/physiology ; Prebiotics/administration &amp; dosage ; Female ; Middle Aged ; Lactobacillus/metabolism/growth &amp; development ; *Uremia ; Cellobiose/metabolism ; Rats ; Indican ; Bacteria/metabolism/genetics/classification ; Disease Models, Animal ; }, abstract = {Chronic kidney disease (CKD) is characterized by accumulation of uremic toxins (UTs), such as p-cresyl sulfate and indoxyl sulfate, generated through the transformation of tyrosine and tryptophan by the gut microbiota. Using an ex vivo Simulator of the Human Intestinal Microbial Ecosystem (SHIME) colonized with fecal samples from eight CKD patients or nine healthy volunteers, a higher bacterial generation of p-cresol and indoles post-amino acid enrichment, as well lower basal butyrate levels, in the feces of CKD patients were found. Through in silico data mining, we selected a probiotic strain lacking the capacity to produce UT, i.e. without genes for tryptophanase, tyrosinase and urease. In vitro, we confirmed the potential of cellobiose as a prebiotic supporting the growth of this strain. We further designed a novel specific multi-biotic for CKD (SynCKD) [containing a probiotic Lactobacillus johnsonii NCC533, a prebiotic (1% cellobiose), and a postbiotic (1% short and medium chain triglycerides C4-C8, a source of butyrate)]. SynCKD effectively curtailed UT precursor generation ex vivo. The in vivo efficacy of SynCKD (and the synergic effect) was established in two uremic rodent models, demonstrating lower plasma levels of UTs and enhancing kidney function after 6-8 weeks of treatment. These effects were linked to better gut microbial ecology. Metagenomic analysis revealed reduced microbial genes for tryptophan/tyrosine degradation. This study lays the foundation for SynCKD as a potential therapy to mitigate CKD progression.}, }
@article {pmid40649758, year = {2025}, author = {Hu, Q and Huang, T and Zhu, A and Anglés, A and Abdelghany, O and Ahmed, A and Fernández-Remolar, DC}, title = {Comparing Protein Stability in Modern and Ancient Sabkha Environments: Implications for Molecular Remnants on Ancient Mars.}, journal = {International journal of molecular sciences}, volume = {26}, number = {13}, pages = {}, pmid = {40649758}, issn = {1422-0067}, support = {2021YFA0716100//National Key Research and Development Program of China/ ; 2022YFF0504000//National Key Research and Development Program of China/ ; 2024YFF0807702//National Key Research and Development Program of China/ ; 0005/2020/A1//Fundo para o Desenvolvimento das Ci&#xea;ncias e da Tecnologia/ ; 0052/2024/RIA1//Fundo para o Desenvolvimento das Ci&#xea;ncias e da Tecnologia/ ; 42441801//National Natural Science Foundation of China/ ; }, mesh = {Mars ; *Proteins/chemistry ; United Arab Emirates ; Oceans and Seas ; Gas Chromatography-Mass Spectrometry ; Chromatography, High Pressure Liquid ; Proteomics ; Microbiota ; }, abstract = {Understanding the mechanisms of protein preservation in extreme environments is essential for identifying potential molecular biosignatures on Mars. In this study, we investigated five sabkha sedimentary samples from the Abu Dhabi coast, spanning from the present day to ~11,000 years before present (BP), to assess how mineralogy and environmental conditions influence long-term protein stability. Using LC-MS/MS and direct Data-independent Acquisition (DIA) proteomic analysis, we identified 722 protein groups and 1300 peptides, revealing a strong correlation between preservation and matrix composition. Carbonate- and silica-rich samples favored the retention of DNA-binding and metal-coordinating proteins via mineral-protein interactions, while halite- and gypsum-dominated facies showed lower recovery due to extreme salinity and reduced biomass input. Functional profiling revealed a shift from metabolic dominance in modern samples to genome maintenance strategies in ancient ones, indicating microbial adaptation to prolonged environmental stress. Contrary to expectations, some ancient samples preserved large, multi-domain proteins, suggesting that early mineral encapsulation can stabilize structurally complex biomolecules over millennial timescales. Taxonomic reconstruction based on preserved proteins showed broad archaeal diversity, including Thaumarchaeota and thermophilic lineages, expanding our understanding of microbial ecology in hypersaline systems. These findings highlight sabkhas as valuable analogs for Martian evaporitic environments and suggest that carbonate-silica matrices on Mars may offer optimal conditions for preserving ancient molecular traces of life.}, }
@article {pmid40649719, year = {2025}, author = {Popov, IV and Manakhov, AD and Gorobets, VE and Diakova, KB and Lukbanova, EA and Malinovkin, AV and Venema, K and Ermakov, AM and Popov, IV}, title = {Metagenomic Investigation of Intestinal Microbiota of Insectivorous Synanthropic Bats: Densoviruses, Antibiotic Resistance Genes, and Functional Profiling of Gut Microbial Communities.}, journal = {International journal of molecular sciences}, volume = {26}, number = {13}, pages = {}, pmid = {40649719}, issn = {1422-0067}, support = {23-14-00316//Russian Science Foundation/ ; 075-10-2025-017//Ministry of Science and Higher Education of the Russian Federation/ ; }, mesh = {Animals ; *Chiroptera/microbiology/virology ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Drug Resistance, Microbial/genetics ; Phylogeny ; *Metagenome ; }, abstract = {Bats serve as key ecological reservoirs of diverse microbial communities, including emerging viruses and antibiotic resistance genes. This study investigates the intestinal microbiota of two insectivorous bat species, Nyctalus noctula and Vespertilio murinus, at the Rostov Bat Rehabilitation Center in Southern Russia using whole metagenome shotgun sequencing. We analyzed taxonomic composition, functional pathways, antibiotic resistance genes, and virulence factors. Densoviruses, especially those closely related to Parus major densovirus, were the most dominant viral sequences identified. Metagenome-assembled densovirus genomes showed high sequence similarity with structural variations and clustered phylogenomically with viruses from mealworms and birds, reflecting both dietary origins and the potential for vertebrate infection. Functional profiling revealed microbial pathways associated with cell wall biosynthesis, energy metabolism, and biofilm formation. A total of 510 antibiotic resistance genes, representing 142 unique types, mainly efflux pumps and β-lactamases, were identified. Additionally, 870 virulence factor genes were detected, with a conserved set of iron acquisition systems and stress response regulators across all samples. These findings highlight the ecological complexity of bat-associated microbiota and viromes and suggest that synanthropic bats may contribute to the circulation of insect-associated viruses and antimicrobial resistance in urban settings.}, }
@article {pmid40647934, year = {2025}, author = {Gao, X and Qian, H and Huang, R and He, W and Jiang, H and Shen, A and Li, Z and Hu, Y}, title = {Rhizosphere and Non-Rhizosphere Soil Microbial Communities in Alpine Desertified Grassland Affected by Vegetation Restoration.}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {13}, pages = {}, pmid = {40647934}, issn = {2223-7747}, support = {41771552//National Natural Science Foundation of China/ ; 2022YFS0469//Sichuan Science and Technology Project/ ; }, abstract = {The rhizosphere serves as a critical interface for plant-soil-microorganism interactions. Rhizosphere soil refers to the soil directly adhering to root surfaces, while non-rhizosphere soil denotes the surrounding soil not in direct contact with roots. This study investigated the characteristics of soil microbial community structure, diversity, and enzyme activity dynamics in both rhizosphere and non-rhizosphere soils of Salix cupularis (shrub) across different restoration periods (4, 8, 16, and 24 years) in alpine sandy lands on the eastern Qinghai-Tibet Plateau, with unrestored sandy land as control (CK), while analyzing relationships between soil properties and microbial characteristics. Results demonstrated that with increasing restoration duration, activities of sucrase, urease, alkaline phosphatase, and catalase in Salix cupularis rhizosphere showed increasing trends across periods, with rhizosphere enzyme activities consistently exceeding non-rhizosphere levels. Bacterial Chao1 and Shannon indices followed similar patterns to enzyme activities, revealing statistically significant differences between rhizosphere and non-rhizosphere soils after 8 and 24 years of restoration, respectively. Dominant bacterial phyla ranked by relative abundance were Actinobacteria > Proteobacteria > Acidobacteria > Chloroflexi > Gemmatimonadetes. The relative abundance of Actinobacteria exhibited highly significant positive correlations with carbon, nitrogen, phosphorus, and enzyme activity indicators, indicating that Salix cupularis restoration promoted improvements in soil physicochemical properties and nutrient accumulation, thereby enhancing bacterial community diversity and increasing Actinobacteria abundance. These findings provide fundamental data for restoration ecology and microbial ecology in alpine ecosystems, offering a scientific basis for optimizing ecological restoration processes and improving recovery efficiency in alpine sandy ecosystems.}, }
@article {pmid40647139, year = {2025}, author = {Bach, LG and Braga, GZA and Bedutti, MC and Dias, LMP and Dos Santos, EAR and Tadielo, LE and Silva, ECD and Schmiedt, JA and Alves, VF and De Martinis, ECP and Possebon, FS and Barcellos, VC and Bersot, LDS}, title = {Total Culturable Microbial Diversity of Food Contact Surfaces in Poultry and Fish Processing Industries After the Pre-Operational Cleaning Process.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {13}, pages = {}, pmid = {40647139}, issn = {2304-8158}, support = {001//Coordination for the Improvement of Higher Education - CAPES/ ; Proc.# 3069982022-0//National Council for Scientific and Technological Development/ ; }, abstract = {This study assessed the viable and culturable microbial diversity that remained on equipment surfaces after hygiene procedures in Brazilian poultry and fish slaughterhouses. Food-contact surface samples were collected using sterile swabs in poultry (n = 50) and fish (Oreochromis niloticus, n = 50) slaughterhouses. The swab samples were used to prepare culture plates to recover viable and culturable cells. The grown plates were washed, and the total DNA of the cell suspension was extracted with a commercial kit. Sequencing of the total DNA extracted from cultures was targeted at the V3 and V4 regions of the 16S rRNA. DNA reads were analyzed by QIIME2 software, with results expressed in relative frequency (%RF). Alpha and beta diversity indexes were analyzed considering the spots of sample collection, type of industry, surfaces (smooth or modular), and materials (polypropylene, stainless steel, or polyurethane). The results showed that in the poultry slaughterhouse, the most abundant genera were Acinetobacter (27.4%), Staphylococcus (7.7%), and Pseudomonas (5.3%), while for the fish slaughterhouse, there was a higher abundance of Staphylococcus (27.7%), Acinetobacter (17.2%), and Bacillus (12.5%). Surface characteristics influenced the microbial diversity, with Acinetobacter spp. dominating modular surfaces and Staphylococcus spp. prevailing on smooth surfaces. The results obtained indicate there is an important resident microbiota that persists even after hygiene processes, and surface-specific cleaning strategies should be developed.}, }
@article {pmid40647044, year = {2025}, author = {Park, I and Mannaa, M}, title = {Fermented Foods as Functional Systems: Microbial Communities and Metabolites Influencing Gut Health and Systemic Outcomes.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {13}, pages = {}, pmid = {40647044}, issn = {2304-8158}, support = {2024//This work was supported by Youngsan University research fund of/ ; }, abstract = {Fermented foods represent an intricate ecosystem that delivers live microbes and numerous metabolites, influencing gut health. In this review, we explore how complex microbial communities and metabolites generated during food fermentation modulate the gut microbiome and affect human health. We discuss fermentation-induced biochemical transformations, including enhanced fiber fermentability; nutrient availability; and the synthesis of bioactive metabolites such as short-chain fatty acids, exopolysaccharides, bacteriocins, and modified polyphenols. We describe the dynamic microbial ecology of fermented foods, influenced by ingredient variations, highlighting its effect on health-related metabolic outcomes. Fermented products when consumed transiently introduce beneficial microbes and bioactive compounds into the gut, thereby boosting microbial diversity, resilience, and barrier function. We review clinical and preclinical studies to substantiate the roles of fermented foods in immune regulation, metabolic homeostasis, cognitive function, and inflammation mitigation. Individual variability in response to fermented foods has been emphasized, underscoring the potential for personalized nutrition strategies informed by advanced omics technologies. By integrating microbial ecology, metabolomics, and clinical evidence, this review positions fermented food intake as a strategic dietary intervention for microbiome modulation and health promotion.}, }
@article {pmid40643242, year = {2025}, author = {Nguyen, A and Ustick, LJ and Larkin, AA and Martiny, AC}, title = {Global phylogeography and microdiversity of the marine diazotrophic photoautotrophs Trichodesmium and UCYN-A.}, journal = {mSphere}, volume = {10}, number = {7}, pages = {e0024525}, pmid = {40643242}, issn = {2379-5042}, support = {1046297, 1559002, 1848576, 1948842, 2135035, 2137339//National Science Foundation/ ; //Peter und Traudl Engelhorn Stiftung/ ; 101813-Z7554214//National Oceanic and Atmospheric Administration/ ; T32AI141346/NH/NIH HHS/United States ; 80NSSC21K1654/NASA/NASA/United States ; T32 AI141346/AI/NIAID NIH HHS/United States ; }, mesh = {Nitrogen Fixation ; Phylogeography ; *Genetic Variation ; *Trichodesmium/genetics/classification ; Phylogeny ; *Seawater/microbiology ; Pacific Ocean ; Indian Ocean ; Nitrogenase/genetics ; Atlantic Ocean ; Biodiversity ; }, abstract = {Photoautotrophic diazotrophs, specifically the genera Trichodesmium and UCYN-A, play a pivotal role in marine nitrogen cycling through their capacity for nitrogen fixation. Despite their global distribution, the microdiversity and environmental drivers of these diazotrophs remain underexplored. This study provides a comprehensive analysis of the global diversity and distribution of Trichodesmium and UCYN-A using the nitrogenase gene (nifH) as a genetic marker. We sequenced 954 samples from the Pacific, Atlantic, and Indian Oceans as part of the Bio-GO-SHIP project. Our results reveal significant phylogenetic and biogeographic differences between and within the two genera. Trichodesmium exhibited greater microdiversity compared to UCYN-A, with clades showing region-specific distribution. Trichodesmium clades were primarily influenced by temperature and nutrient availability. They were particularly frequent in regions of phosphorus stress. In contrast, UCYN-A was most frequently observed in regions experiencing iron stress. UCYN-A clades demonstrated more homogeneous distributions, with a single sequence variant within the UCYN-A1 clade dominating across varied environments. The biogeographic patterns and environmental correlations of Trichodesmium and UCYN-A highlight the role of microdiversity in their ecological adaptation and reflect their different ecological strategies. These findings underscore the importance of characterizing the global patterns of fine-scale genetic diversity to better understand the functional roles and distribution of marine nitrogen-fixing photoautotrophs.IMPORTANCEThis study provides insights into the global diversity and distribution of nitrogen-fixing photoautotrophs, specifically Trichodesmium and UCYN-A. We sequenced 954 oceanic samples of the nifH nitrogenase gene and uncovered significant differences in microdiversity and environmental associations between these genera. Trichodesmium showed high levels of sequence diversity and region-specific clades influenced by temperature and nutrient availability. In contrast, UCYN-A exhibited a more uniform distribution, thriving in iron-stressed regions. Quantifying these fine-scale genetic variations enhances our knowledge of their ecological roles and adaptations, emphasizing the need to characterize the genetic diversity of marine nitrogen-fixing prokaryotes.}, }
@article {pmid40640502, year = {2025}, author = {Liu, L and Firrman, JA and Narrowe, AB and Mahalak, KK and Lemons, JMS and Marzorati, M and Duysburgh, C and Rotsaert, C and Van de Wiele, T}, title = {Structural and functional characterization of a porcine intestinal microbial ecosystem developed in vitro.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {24821}, pmid = {40640502}, issn = {2045-2322}, support = {8072-41000-108-00-D//USDA/ ; 8072-41000-108-00-D//USDA/ ; 8072-41000-108-00-D//USDA/ ; 8072-41000-108-00-D//USDA/ ; 8072-41000-108-00-D//USDA/ ; EOS-Homistasis project//FWO-FNR/ ; GOA-Microbes4Immunity//UGent-BOF/ ; }, mesh = {Animals ; Swine ; *Gastrointestinal Microbiome ; Metagenome ; Feces/microbiology ; *Bacteria/genetics/classification ; Metagenomics/methods ; Metabolomics ; *Intestines/microbiology ; Ecosystem ; }, abstract = {The mammalian digestive tract harbors a vast microbial community that has the potential to modulate numerous health-related processes. Multicompartment dynamic gut models have been developed to study microbial communities in a controlled environment. To verify the assumption that the experimental results produced in vitro in a mechanical device would be highly similar to those obtained from an in vivo study, in this study fecal samples from four pigs were inoculated in a simulator of the porcine intestinal microbial ecosystem (SPIME) and cultured until reaching steady state. The composition and structure of the resultant microbial communities, and the metabolites produced were compared with those harvested from the intestine of the same pigs. Taxonomic abundance identification based on shallow shotgun metagenomic sequencing revealed only 12.1% of species or 15% of metagenome-assembled genomes (MAGs) being shared across the colon compartments of the source pigs and the SPIME. Despite these overwhelming compositional shifts, higher functional conservation was indicated as measured by functional richness, MAG-level traits, CAZymes, and untargeted metabolomics. Environmental selection and bacterial functional redundancy were considered the two key elements in microbial compositional shifts and functional preservation.}, }
@article {pmid40639195, year = {2025}, author = {Estrada-Peña, A and Antunes, S and Domingos, A and Esser, H and Földvári, G and Fuehrer, HP and Gargili, A and van Gestel, M and Grandi, G and Kazimirova, M and Kiewra, D and Klemola, T and Kjær, LJ and Kjelland, V and Kubiak, K and de Meneghi, D and Mihalca, AD and Moutailler, S and Potkonjak, A and Prokop, P and Robert, K and Ranka, R and Sainz, A and Sormunen, J and Sotiraki, S and Strube, C and Stuen, S and Široký, P and Tomassone, L and Zintl, A}, title = {Living with ticks: Results of an online survey of the knowledge, attitudes and practices (KAP) regarding ticks and tick-borne pathogens in academic environments across Europe.}, journal = {Ticks and tick-borne diseases}, volume = {16}, number = {4}, pages = {102515}, doi = {10.1016/j.ttbdis.2025.102515}, pmid = {40639195}, issn = {1877-9603}, mesh = {Europe/epidemiology ; *Health Knowledge, Attitudes, Practice ; Animals ; *Tick-Borne Diseases/epidemiology/prevention &amp; control/psychology/microbiology ; Humans ; Surveys and Questionnaires ; Male ; *Ticks/physiology ; Female ; Adult ; Universities ; Tick Bites/epidemiology ; Young Adult ; Middle Aged ; }, abstract = {We prepared a digital questionnaire to capture knowledge, attitudes and practices (KAP) regarding ticks and tick-borne pathogens (TBPs) in 20 languages. The questionnaire was distributed to 21 universities and research institutions in 22 European countries and 9401 valid responses were collected. Most survey participants identified ticks correctly and regarded ticks as a serious health risk. There was also a good level of knowledge regarding tick activity, habitats and the predominant TBPs in the country or region. Moreover, most respondents were familiar with effective tick protection and removal measures. Over 75 % of respondents had been bitten by ticks and up to 12 % of participants had been diagnosed with a tick-borne infection in the past. Respondents from northern and central European countries who reported engaging in outdoor activities more frequently, reported increased frequencies of tick bites and infection with TBPs compared to respondents from southern Europe. Awareness of national information campaigns on ticks and TBPs was also greater among respondents from northern and central European countries than among Mediterranean countries. This study identified knowledge gaps among respondents from some European countries where TBPs have not been prioritised historically. These knowledge gaps should be addressed by reputable bodies to encourage personal protective behaviours without causing alarm and to forestall the spreading of incorrect and unreliable information propagated by some social media sources.}, }
@article {pmid40638961, year = {2025}, author = {Schröer, L and Balcaen, T and Folens, K and Boon, N and De Kock, T and Samari-Kermani, M and Kerckhofs, G and Cnudde, V}, title = {Contrast-Enhanced micro-computed tomography for 3D imaging of biofilms in opaque materials: Insights from water treatment plant sand filters.}, journal = {Water research}, volume = {285}, number = {}, pages = {124152}, doi = {10.1016/j.watres.2025.124152}, pmid = {40638961}, issn = {1879-2448}, abstract = {Microorganisms form biofilms in various environments, including porous media, where they alter substrate properties and fluid flow. Visualizing biofilms in 3D within the pore system is essential to understand their effect. Micro-computed tomography (µCT) is a powerful technique to visualize the pore system, but biofilms are usually invisible due to low contrast with water. Contrast-enhancing staining agents (CESAs) can improve their visibility by changing the attenuation of the biofilm or water phase. Traditional CESAs such as BaSO4, silver-coated microspheres or 1-chloronapthalene proved to be successful, but often stain the water phase and have drawbacks such as sedimentation or toxicity. After the successful use of isotonic Lugol and Hf-WD 1:2 POM on cyanobacteria at the surface, this study investigated the use of those CESAs to stain biofilms within opaque materials and, in particular, on biofilms colonizing field-derived sand filters of water treatment plants. Both CESAs increased the biofilms' visibility, including channels within the Hf-WD 1:2 POM stained biofilms and improved segmentation. Their visualization was consistent with Scanning Electron Microscopy (SEM). The CESAs quickly stained the biofilms, and their effect was stable. Isotonic Lugol enhanced the X-ray attenuation the most but might have caused shrinkage. The use of BaSO4 solution, added for comparison and positive control, was complicated due to its fast precipitation. BaSO4 was unable to visualize the isotonic Lugol-stained biofilms but corresponded with the Hf-WD 1:2 POM-stained biofilms. However, the stability and detail shown by isotonic Lugol and Hf-WD 1:2 POM make the latter two preferred. The study showed the potential of µCT and these CESAs for biofilm visualization and water research. Future research should apply these CESAs and focus on the CESA-biofilm interaction to understand the binding mechanisms and their effect on the structure.}, }
@article {pmid40638158, year = {2025}, author = {Dhara, S and Majhi, J and Mandal, B and Bhadury, P and Bhattacharya, S and Ghorai, SK}, title = {Polydendrorhynchus amaleshii sp. nov., a New Species With Branched Proboscis (Nemertea: Heteronemertea) From the North-East Coastal Bay of Bengal.}, journal = {Zoological science}, volume = {42}, number = {3}, pages = {326-334}, doi = {10.2108/zs240093}, pmid = {40638158}, issn = {0289-0003}, mesh = {Animals ; Phylogeny ; India ; *Invertebrates/classification/anatomy &amp; histology/genetics ; Bays ; Species Specificity ; Animal Distribution ; RNA, Ribosomal, 16S/genetics ; }, abstract = {A new lineid heteronemertean with a branched proboscis, Polydendrorhynchus amaleshii sp. nov., is described as the second member of the genus Polydendrorhynchus Yin and Zeng, 1986, following Polydendrorhynchus zhanjiangensis (Yin and Zeng, 1984). The description is based on specimens collected from the northeastern coastal Bay of Bengal, including the Subarnarekha Estuary and Frazerganj in the Indian Sundarbans mangrove ecosystem. The new species is distinguished from its congener by having up to 56 terminal branchlets of the proboscis and the absence of rhynchocoel compartments. In a maximum-likelihood phylogenetic analysis based on COI and 16S rRNA genes, P. amaleshii and P. zhanjiangensis formed a well-supported clade. Polydendrorhynchus amaleshii represents the ninth nemertean species recorded from India.}, }
@article {pmid40637783, year = {2025}, author = {Philippe, C and Denis, LA and Fonville, M and Devriendt, B and Dufrasne, FE and Obregon, D and Maître, A and Skičková, &#x160; and Cox, E and Sprong, H and Cruz, AC and Mori, M}, title = {Diversity of the Ixodes ricinus Microbiome Across Belgian Ecoregions and Its Association with Pathogen and Symbiont Presence.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {73}, pmid = {40637783}, issn = {1432-184X}, mesh = {*Ixodes/microbiology ; Animals ; *Microbiota ; Belgium ; *Symbiosis ; *Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Nymph/microbiology ; Anaplasma phagocytophilum/isolation &amp; purification/genetics ; Biodiversity ; }, abstract = {Ticks are important vectors of zoonotic pathogens, and their presence can be influenced by the composition of the tick microbiome. In turn, this microbiome is shaped by environmental and ecological factors, as demonstrated in several studies conducted under controlled conditions. However, the extent of these influences under natural ecological conditions remains underexplored. In this study, we investigated the diversity of the microbiome and the prevalence of pathogens in Ixodes ricinus nymphs across three distinct Belgian ecoregions: Sandy Loam, Condroz, and Ardennes. Using real-time quantitative PCR (qPCR) and Oxford Nanopore 16S rRNA sequencing, we assessed how geography and pathogen presence influence tick-associated microbial communities. Our results revealed significant regional differences in microbiome composition and pathogen prevalence. Borrelia burgdorferi sensu lato (s.l.) was most prevalent in the Ardennes (9% (7.4-10.9) vs 3.8% (2.8-5.2) in the Condroz and 2.1% (1.4-3.2) in Sandy Loam) while Anaplasma phagocytophilum was more common in the Sandy Loam region (21.1% (18.7-23.8) vs 4% (3-5.4) in the Condroz and 3.2% (2.2-4.4) in the Ardennes). Endosymbionts such as Midichloria mitochondrii and Spiroplasma ixodetis also exhibited distinct geographic distributions. Network analysis identified potential pathogen-microbiota interactions, with certain bacterial taxa showing positive or negative associations with specific pathogens. Moreover, microbiome composition was influenced not only by ecoregion but also by microorganisms such as Rickettsia helvetica, suggesting that its colonization may actively shape microbial community structure, potentially through competition or facilitation mechanisms. Additionally, microbiome network robustness varied across ecoregions, highlighting the role of ecological context in shaping microbial interactions within ticks. These findings underscore the complex interplay between geography, pathogen presence, and microbial diversity in ticks, highlighting the importance of integrating these interactions to inform microbiome-based strategies for vector control and disease prevention.}, }
@article {pmid40636495, year = {2025}, author = {Chen, F and Cheng, M and Rong, D and Wang, Y and Liang, R and Irfan, M and Kang, Y and Cao, Y}, title = {Metagenomic insights into the microbial communities and functional traits of hot springs in Guizhou Province, China.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1615879}, pmid = {40636495}, issn = {1664-302X}, abstract = {INTRODUCTION: Hot springs were previously believed to be uninhabitable due to their hostile nature. However, recent studies have determined that hot springs not only have a rich microbiota but are also involved in various biogeochemical processes and possess unique characteristics that can be utilized for several biotechnological applications. This study aimed to determine the bacterial taxonomic diversity and functional profiles of 11 hot springs in the Guizhou Province, China.<br><br>METHODS: Illumina high-throughput sequencing was used to sequence the V3-V4 region of the 16S rRNA gene from microorganisms in samples collected from these hot springs. Software such as Mothur, the SILVA ribosomal RNA database, and Quantitative Insights into Microbial Ecology (QIIME) were utilized for taxonomic and operational taxonomic unit (OTU) analysis, while PICRUST2 was employed for functional predictions.<br><br>RESULTS: Guizhou Baili Rhododendron Hot Spring No.1 (BLDJA) had the highest diversity in terms of species richness, while Jianhe Hot Spring (YAS) had the lowest diversity. At the phylum level, the highest reported phyla included Pseudomonadota, Bacillota, Nitrospirota, Bacteroidota, and Actinomycetota, where Pseudomonadota had the highest abundance (92.094%) in Jianhe Hot Spring (YAS) and the lowest (41.238%) in Guizhou Baili Rhododendron Hot Spring No. 2 (BLDJB). Bacillota has the highest abundance (39.178%) in Guizhou Baili Rhododendron Hot Spring No. 2 (BLDJB) and the lowest (0.547%) in Jiutian Hot Spring (SNJT). The highest predicted functions were observed for amino acid metabolism, followed by carbohydrates. Predicted pathways for secondary metabolite and vitamin synthesis, along with stress-adaptation genes, underscore the biotechnological value of these habitats.<br><br>DISCUSSION: This study presents a preliminary survey of 11 hot springs in Guizhou Province, providing important insights into the origin and evolution of microorganisms. Furthermore, studying these microorganisms is crucial for understanding the adaptive mechanisms of life under extreme conditions, such as high temperatures, and for exploring the potential biotechnological applications of these microbes. An in-depth approach combining functional metagenomics and next-generation culturomics is required to fully understand the microbial flora and its potential biotechnological applications.}, }
@article {pmid40634370, year = {2025}, author = {Crombez, E and Van de Peer, Y and Li, Z}, title = {The subordinate role of pseudogenization to recombinative deletion following polyploidization in angiosperms.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {6335}, pmid = {40634370}, issn = {2041-1723}, support = {G0ADO25N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; BOF.BAF.2024.0889.01//Universiteit Gent (UGent)/ ; BOF.MET.2021.0005.01//Universiteit Gent (UGent)/ ; No. 833522//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; }, mesh = {*Polyploidy ; *Pseudogenes/genetics ; Genome, Plant/genetics ; *Magnoliopsida/genetics ; *Gene Deletion ; Evolution, Molecular ; Gene Duplication ; *Recombination, Genetic ; }, abstract = {Extensive gene loss is a hallmark of rediploidization following polyploidization, but its molecular basis remains unclear: whether it occurs primarily through pseudogenization or DNA deletion. Here, we examine pseudogenization in collinear segments from ancient whole-genome multiplications (WGMs) across 12 angiosperms. Although total pseudogenes are abundant, we find far fewer WGM-derived pseudogenes than expected if pseudogenization and DNA deletion contribute equally to gene loss. Simulations of neutrally evolving pseudogenes indicate that, if DNA deletion is absent, pseudogenes should be detectable for far longer than observed in the paleo-polyploid genomes, suggesting gene loss driven by DNA deletion. Analyses of three neo-autopolyploid genomes confirm this pattern: among substantial gene loss, DNA deletions occur on average 1.5 times more frequently than pseudogenization. Our findings imply that gene loss post-polyploidization primarily takes place via DNA deletion, enabled by a genomic environment with an elevated recombination rate created by WGMs. In contrast, small-scale duplications yield scattered duplicated genes, which appear less exposed to deletion and hence result in a high number of pseudogenes. This model is further reinforced by an enrichment of WGM-derived pseudogenes in high recombination regions. Moreover, some pseudogenes may govern a function, as indicated by non-neutral Ka/Ks ratios and overlap with lncRNAs.}, }
@article {pmid40633764, year = {2025}, author = {Kovarova, A and Amadasun, M and Hooban, B and McDonagh, F and Tumeo, A and Ryan, K and Clarke, C and Cormican, M and Miliotis, G}, title = {Characterisation of Citrobacter freundii and Enterobacter cloacae complex isolates co-carrying blaNDM-1 and mcr-9 from three hospitals.}, journal = {Journal of global antimicrobial resistance}, volume = {44}, number = {}, pages = {226-233}, doi = {10.1016/j.jgar.2025.07.003}, pmid = {40633764}, issn = {2213-7173}, abstract = {OBJECTIVES: Antimicrobial resistance (AMR) is a global health concern related to antimicrobial use and the subsequent emergence of resistant organisms, including carbapenemase-producing Enterobacterales (CPE). CPE isolate co-carrying blaNDM-1 and mcr-9.1 have been scarcely reported internationally. The identification of 20 such isolates, including 16 of one species, within a group of three hospitals in one region indicated potential dissemination within and between healthcare facilities.<br><br>METHODS: Twenty isolates were pseudo-anonymised and identified via MALDI-ToF MS. Antimicrobial susceptibility testing was performed by disc diffusion, and Minimal Inhibition Concentration for colistin was carried out using the UMIC system. Short-read sequencing was conducted using the Illumina MiSeq platform, and genomic analysis identified antimicrobial resistance genes, virulence factors and plasmid contigs. Taxonomic classification of draft genomes was bioinformatically assessed using Kraken2.<br><br>RESULTS: This collection comprised of Enterobacter hormaechei (n = 16), Citrobacter freundii (n = 3) and Enterobacter cloacae (n = 1) sourced from patient rectal swabs collected during routine screening (n = 13) or from healthcare-associated environmental sites (n = 7). The E. hormaechei isolates included four different ST types with one unassigned ST. Contig-based plasmid analysis identified 17 plasmid replicon types among the isolates. IncHI2A, IncHI2, and pKPCCAV1321_1 were detected in all isolates. Linked blaNDM-1 and mcr-9.1 gene spread in hospitals likely occurred via plasmid-mediated transfer rather than spread of E. hormaechei.<br><br>CONCLUSIONS: This study represents the first documented instance of blaNDM-1/mcr-9.1 co-occurrence in Europe to date. It highlights the increasing public health threat posed by antimicrobial resistance and underscores the importance of genomic surveillance and clinical screening.}, }
@article {pmid40633699, year = {2025}, author = {Sun, HJ and Zhao, X and Ding, J and Wang, YQ and Wang, WS and Feng, ZH and Zhao, S and Wang, L and Ren, NQ and Yang, SS}, title = {Unveiling dynamics of microbial communities, species interactions, and ecological assembly during low-temperature-induced sludge bulking in full-scale wastewater treatment systems.}, journal = {Bioresource technology}, volume = {435}, number = {}, pages = {132950}, doi = {10.1016/j.biortech.2025.132950}, pmid = {40633699}, issn = {1873-2976}, mesh = {*Sewage/microbiology ; *Wastewater/microbiology ; *Water Purification/methods ; *Cold Temperature ; *Waste Disposal, Fluid/methods ; *Microbiota ; }, abstract = {This study investigated the microbial community characteristics and ecological mechanisms of floating sludge and suspended sludge in a full-scale wastewater treatment plant under low-temperature conditions. Floating sludge exhibited a lower proportion of positive correlations compared to suspended sludge (56.98 % vs. 61.03 %), indicating stronger competition within the microbial community. Null model analysis revealed the roles of deterministic and stochastic processes in shaping the microbial communities, with stochastic processes being dominant. However, deterministic selection played a larger role in floating sludge, highlighting stronger influence of species interactions and temperature fluctuations. Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway analysis revealed stronger energy metabolism in floating sludge, while suspended sludge microbes were more active in material transport. This study reveals distinct microbial and ecological differences between floating and suspended sludge at low temperatures, providing theoretical support for optimizing wastewater treatment and controlling sludge bulking in cold climates.}, }
@article {pmid40632216, year = {2025}, author = {Romano, F and John, U and Laval-Peuto, M and Pitta, P}, title = {Small Things that Make a Big Difference: Single-Cell Transcriptomic of Nanociliates Reveals Genes Potentially Involved in Mixotrophy.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {72}, pmid = {40632216}, issn = {1432-184X}, support = {766327//MixITiN/ ; 766327//MixITiN/ ; 766327//MixITiN/ ; }, mesh = {*Transcriptome ; Phylogeny ; *Haptophyta/genetics/classification ; Mediterranean Sea ; Photosynthesis/genetics ; Single-Cell Analysis ; Food Chain ; }, abstract = {Nanociliates play an important role in the microbial food web of oligotrophic marine systems as grazers of picoplankton on one side, and as prey for microplankton, on the other. However, knowledge on their taxonomy, phylogeny, and trophic strategies is very limited, as well as their potential role as mixotrophs. In the present study, we investigated the transcriptomes of five marine planktonic nanociliates isolated from the Eastern Mediterranean Sea. Our aim was the following: (i) to characterize the phylogenetic placement of these cells using concatenated phylotranscriptomic and (ii) to identify genes potentially involved in mixotrophy by focusing on both photosynthesis and digestion-related genes (phagosome, lysosome). Phylogenetic reconstruction revealed that two cells clustered with Tintinnida, while the other three clustered with Oligotrichida. Reciprocal best hits (RHBs) BlastP analysis indicated the presence of genes related to photosynthesis across all the transcriptomes, while the detection of genes associated with phagosome, lysosome, and generic metabolic pathways provided a more informative insight into the mechanism of mixotrophy. These findings suggest that photosynthesis-related genes alone may not be sufficient indicators of mixotrophic potential in nanociliates and highlight the importance of considering additional cellular pathways involved in phagotrophy. Moreover, these transcriptomes will help to establish a basis for the evaluation of differential gene expression in Oligotrichida, Choreotrichida, and Tintinnida, and a step stone for mixotrophic investigation.}, }
@article {pmid40630186, year = {2025}, author = {Ceretto, A and Weinig, C}, title = {A comparison of 16S rRNA-gene and 16S rRNA-transcript derived microbial communities in bulk and rhizosphere soils.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1608399}, pmid = {40630186}, issn = {1664-302X}, abstract = {Root exudates in a plant's rhizosphere alters microbial community membership and activity, which can in turn alter a plant's health and fitness. In this study we characterized bacterial community composition, using 16S rRNA-gene (DNA) sequencing to define total community membership and 16S rRNA-transcripts (RNA) to define protein synthesis potential (PSP) as a proxy of microbial activity in both rhizosphere and bulk soils of a Wyoming native plant Boechera stricta. Using PSP rather than total microbial membership reveals fine-scale differences in genera between the rhizosphere and control soil communities. This study found DNA community analysis alone disproportionately increased the importance of Saccharibacteria and Gemmatimonadetes phyla in the overall soil community profile, and underestimated the importance of several known root associates (Comamonadaceae, Rhizobacter, and Variovorax), which had elevated PSP in the rhizosphere soil. Thus, the use of DNA-vs. RNA-based community characterization reveals that community composition (DNA) may not completely capture community activity (RNA). Analysis of the PSP community profile also indicated elevated levels of proteins associated with carbohydrate and amino acid metabolism in the rhizosphere-associated bacteria, which may shed light on potential mechanisms by which root exudates shape the rhizosphere soil community.}, }
@article {pmid40626910, year = {2025}, author = {Kust, A and Zorz, J and Paniker, CC and Bouma-Gregson, K and Krishnappa, N and Liu, W and Banfield, JF and Diamond, S}, title = {Model cyanobacterial consortia reveal a consistent core microbiome independent of inoculation source or cyanobacterial host species.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf142}, pmid = {40626910}, issn = {1751-7370}, abstract = {Cyanobacteria are integral to biogeochemical cycles, influence climate processes, and hold promise for commercial applications. In natural habitats, they form complex consortia with other microorganisms, where interspecies interactions shape their ecological roles. Although in vitro studies of these consortia have significantly advanced our understanding, they often lack the biological replication needed for robust statistical analysis of shared microbiome features and functions. Moreover, the microbiomes of many model cyanobacterial strains, which are central to our understanding of cyanobacterial biology, remain poorly characterized. Here, we expanded on existing in vitro approaches by co-culturing five well-characterized model cyanobacterial strains with microorganisms filtered from three distinct freshwater sources, generating 108 stable consortia. Metagenomic analyses revealed that, despite host and inoculum diversity, these consortia converged on a similar set of non-cyanobacterial taxa, forming a 25-species core microbiome. The large number of stable consortia in this study enabled statistical validation of both previously observed and newly identified core microbiome functionalities in micronutrient biosynthesis, metabolite transport, and anoxygenic photosynthesis. Furthermore, core species showed significant enrichment of plasmids, and functions encoded on plasmids suggested plasmid-mediated roles in symbiotic interactions. Overall, our findings uncover the potential microbiomes recruited by key model cyanobacteria, demonstrate that laboratory-enriched consortia retain many taxonomic and functional traits observed more broadly in phototroph-heterotroph assemblages, and show that model cyanobacteria can serve as robust hosts for uncovering functional roles underlying cyanobacterial community dynamics.}, }
@article {pmid40626735, year = {2025}, author = {Kellom, M and Berg, M and Chen, I-MA and Chu, K and Clum, A and Huntemann, M and Ivanova, NN and Kyrpides, NC and Mukherjee, S and Reddy, TBK and Roux, S and Seshadri, R and Szabo, G and Varghese, NJ and Woyke, T and Eloe-Fadrosh, EA}, title = {Tetranucleotide frequencies differentiate genomic boundaries and metabolic strategies across environmental microbiomes.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0174424}, doi = {10.1128/msystems.01744-24}, pmid = {40626735}, issn = {2379-5077}, abstract = {UNLABELLED: Microbiomes are constrained by physicochemical conditions, nutrient regimes, and community interactions across diverse environments, yet genomic signatures of this adaptation remain unclear. Metagenome sequencing is a powerful technique to analyze genomic content in the context of natural environments, establishing concepts of microbial ecological trends. Here, we developed a data discovery tool-a tetranucleotide-informed metagenome stability diagram-that is publicly available in the integrated microbial genomes and microbiomes (IMG/M) platform for metagenome ecosystem analyses. We analyzed the tetranucleotide frequencies from quality-filtered and unassembled sequence data of over 12,000 metagenomes to assess ecosystem-specific microbial community composition and function. We found that tetranucleotide frequencies can differentiate communities across various natural environments and that specific functional and metabolic trends can be observed in this structuring. Our tool places metagenomes sampled from diverse environments into clusters and along gradients of tetranucleotide frequency similarity, suggesting microbiome community compositions specific to gradient conditions. Within the resulting metagenome clusters, we identify protein-coding gene identifiers that are most differentiated between ecosystem classifications. We plan for annual updates to the metagenome stability diagram in IMG/M with new data, allowing for refinement of the ecosystem classifications delineated here. This framework has the potential to inform future studies on microbiome engineering, bioremediation, and the prediction of microbial community responses to environmental change.<br><br>IMPORTANCE: Microbes adapt to diverse environments influenced by factors like temperature, acidity, and nutrient availability. We developed a new tool to analyze and visualize the genetic makeup of over 12,000 microbial communities, revealing patterns linked to specific functions and metabolic processes. This tool groups similar microbial communities and identifies characteristic genes within environments. By continually updating this tool, we aim to advance our understanding of microbial ecology, enabling applications like microbial engineering, bioremediation, and predicting responses to environmental change.}, }
@article {pmid40625615, year = {2025}, author = {Goodall, T and Busi, SB and Griffiths, RI and Jones, B and Pywell, RF and Richards, A and Nowakowski, M and Read, DS}, title = {Soil properties in agricultural systems affect microbial genomic traits.}, journal = {FEMS microbes}, volume = {6}, number = {}, pages = {xtaf008}, pmid = {40625615}, issn = {2633-6685}, abstract = {Understanding the relationships between bacteria, their ecological and genomic traits, and their environment is important to elucidate microbial community dynamics and their roles in ecosystem functioning. Here, we examined the relationships between soil properties and bacterial traits within highly managed agricultural soil systems subjected to arable crop rotations or management as permanent grass. We assessed the bacterial communities using metabarcoding and assigned each amplicon trait scores for rRNA copy number, genome size, and guanine-cytosine (GC) content, which are classically associated with potential growth rates and specialization. We also calculated the niche breadth trait of each amplicon as a measure of social ubiquity within the examined samples. Within this soil system, we demonstrated that pH was the primary driver of bacterial traits. The weighted mean trait scores of the samples revealed that bacterial communities associated with soils at lower pH (<7) tended to have larger genomes (potential plasticity), have more rRNA (higher growth rate potential), and are more ubiquitous (have less niche specialization) than the bacterial communities from higher pH soils. Our findings highlight not only the association between pH and bacterial community composition but also the importance of pH in driving community functionality by directly influencing genomic and niche traits.}, }
@article {pmid40624251, year = {2025}, author = {Karlsson, CJ and Gerlee, P and Rowlett, J}, title = {An adaptive dynamics framework for microbial ecology and evolution.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {24307}, pmid = {40624251}, issn = {2045-2322}, mesh = {*Biological Evolution ; Game Theory ; Models, Biological ; Biodiversity ; *Adaptation, Physiological ; }, abstract = {Adaptive dynamics describes a deterministic approximation of the evolution of scalar- and function-valued traits. We construct an evolutionary process for a game-theoretic model which may describe the evolution of microbes. In our analysis, we demonstrate the existence of solutions to the adaptive dynamics and determined their regularity. Moreover, we identify all stationary solutions and prove that these are precisely the Nash equilibria of the game theoretic model. Numerical examples are provided to highlight the main characteristics of the dynamics. The dynamics are unstable; non-stationary solutions oscillate and perturbations of the stationary solutions do not shrink. Instead, a linear type of branching may occur. This may explain the ever-increasing complexity in microbial biological systems and provide a mechanistic explanation for not only the tremendous biodiversity observed in microbe species but also for the extensive phenotypic variability within species.}, }
@article {pmid40624015, year = {2025}, author = {Wang, C and Zhang, L and Kan, C and He, J and Liang, W and Xia, R and Zhu, L and Yang, J and Jiang, X and Ma, W and Liang, Z and Xiao, Z and Zhang, J and Zhong, J and Sun, X and Chang, D and Wang, Z and Zhang, G and Li, M}, title = {Benefits and challenges of host depletion methods in profiling the upper and lower respiratory microbiome.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {130}, pmid = {40624015}, issn = {2055-5008}, support = {Z211100002121135//Beijing Nova Program/ ; 32100098//National Natural Science Foundation of China/ ; 2021097//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; KCXFZ20211020163545004//Shenzhen Scientific and Technological Foundation/ ; SZZYSM202311009//Sanming Project of Medicine in Shenzen Municipality/ ; 2022YFA1304300//National Key Research and Development Program of China/ ; }, mesh = {Humans ; Bronchoalveolar Lavage Fluid/microbiology ; *Microbiota/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation &amp; purification ; *Respiratory Tract Infections/microbiology/diagnosis ; Oropharynx/microbiology ; *Respiratory System/microbiology ; }, abstract = {Metagenomic sequencing for respiratory pathogen detection faces two challenges: efficient host DNA depletion and the representativeness of upper respiratory samples for lower tract infections. In this study, we benchmarked seven host depletion methods, including a new method (F_ase), using bronchoalveolar lavage fluid (BALF), oropharyngeal swab (OP), and mock samples. All methods significantly increased microbial reads, species richness, genes richness, and genome coverage while reduced bacterial biomass, introduced contamination, and altered microbial abundance. Some commensals and pathogens, including Prevotella spp. and Mycoplasma pneumoniae, were significantly diminished. F_ase demonstrated the most balanced performance. High-resolution microbiomes profiling revealed distinct microbial niche preferences and microbiome disparities between the upper and lower respiratory tract. In pneumonia patients, 16.7% of high-abundance species (>1%) in BALF were underrepresented (<0.1%) in OP, highlighting OP's limitations as lower respiratory proxies. This study underscores both the potential and challenges of metagenomic sequencing in advancing microbial ecology and clinical research.}, }
@article {pmid40622379, year = {2025}, author = {Mars Brisbin, M and Acord, M and Davitt, R and Bent, S and Van Mooy, BAS and Flaum, E and Norlin, A and Turner, J and Krinos, A and Alexander, H and Saito, M}, title = {Exploring the Phaeosphere: Characterizing the microbiomes of Phaeocystis antarctica colonies from the coastal Southern Ocean and laboratory culture.}, journal = {Journal of phycology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jpy.70051}, pmid = {40622379}, issn = {1529-8817}, support = {874439//Simons Foundation/ ; OPP-2224611//National Science Foundation/ ; }, abstract = {Interactions between phytoplankton and bacteria play critical roles in shaping marine ecosystems. However, the intricate relationships within these communities-particularly in rapidly changing polar environments-remain poorly understood. We use targeted methods to directly characterize the microbiomes of individual colonies of Phaeocystis antarctica, a keystone phytoplankton species in the Southern Ocean, and showed that colony microbiomes were consistent across individual colonies collected 108 nautical miles apart. These results suggest that hosting specific colony microbiomes is a shared trait across colony-forming Phaeocystis species, with different species hosting colony microbiomes suited to their respective environments. The bacterial orders Alteromonadales, Oceanospirillales, and Sphingomonadales dominated the microbiomes of all field-collected P. antarctica colonies. The relative abundances of bacterial taxa comprising the majority of field-collected colony microbiomes-for example, Paraglaciecola sp. (Alteromonadales) and Nitrincolaceae (Oceanospirillales)-correlated with Phaeocystis abundance in surface waters, highlighting their potential roles in bloom dynamics and carbon cycling. After a year of laboratory culture, we observed a reduction in colony microbiome diversity, and Caulobacterales, Cellvibrionales, and Rhodobacterales dominated the cultured colony microbiomes. Notably, abundant genera in field-collected colony microbiomes that were lost in culture were psychrophiles. The shift in microbiome structure emphasizes the importance of field-based studies to capture the complexity of microbial interactions, especially for species from polar environments that are difficult to replicate in laboratory conditions. This research provides valuable insights into the ecological significance of prokaryotic interactions with a key phytoplankton species and underscores the necessity of considering these dynamics in the context of climate-driven shifts in marine ecosystems.}, }
@article {pmid40622159, year = {2025}, author = {Hernandez, JB and Hayer, SS and Alvarez, S and Fischer, A and Hassenstab, HR and Cooper, K and Alsafwani, ZW and Benson, AK and Suhr Van Haute, MJ and Izard, J and Song, H-S and Clayton, JB}, title = {Microbiome and metabolome association network analysis identifies Clostridium_sensu_stricto_1 as a stronger keystone genus candidate than Bifidobacterium in the gut of common marmosets.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0021425}, doi = {10.1128/msystems.00214-25}, pmid = {40622159}, issn = {2379-5077}, abstract = {The common marmoset (Callithrix jacchus), a nonhuman primate species, is a model organism of great interest due to its translational value in a variety of research settings, including the field of microbiomics. While the composition of the marmoset's gut microbiome has been somewhat described in captivity, little is known about how gut microbiota interact with each other over time and how they relate to metabolite production. To help answer this, we characterized interactions in the gut microbiome of the common marmoset by calculating the Spearman correlation coefficient between 16S rDNA-derived relative genera abundance data and targeted metabolomics data collected longitudinally from 10 captive marmosets. Association network graphs were used to visualize significant correlations and identify genera and metabolites that have high degree centrality, marking them as more influential within the microbiome. The genus Clostridium_sensu_stricto_1 engaged in the most metabolomic associations, indicating that it potentially plays a gatekeeping role over metabolites involved in microbial growth and signaling. Its associations with downregulated taurine and bile acids further suggest Clostridium_sensu_stricto_1 modifies bile acids to exert its influence. Flavonifractor and several Bacteroidales members had the most bacterial associations and were negatively associated with Bifidobacterium, indicating a potential competitive relationship. To further characterize microbiome interactions, we performed hierarchical clustering on significant within-dataset associations and developed a new "Keystone Candidate Score" metric that identified Clostridium_sensu_stricto_1 and Alloprevotella as the most influential bacteria (so-called candidate keystone genera) in the marmoset gut microbiome.IMPORTANCEPrevious studies have identified significant individuality within the gut microbiome of common marmosets. The reasons for this inter-subject variability and how it relates to health in captivity are poorly understood, owing to a lack of knowledge regarding dynamic interactions between specific microbiota. To that end, this study characterized significant temporal associations between the gut microbiome and metabolome of healthy captive marmosets. Our findings suggest that certain microbial taxa exert a stronger influence within the gut than others. Specifically, Bifidobacterium was the most abundant genus and primary driving force behind subject-specific microbiome differences, while Clostridium_sensu_stricto_1 and bacteria from the order Bacteroidales were the main sources, respectively, for significant bacteria-metabolite and bacteria-bacteria associations. Together, this suggests that Bifidobacterium may compete with the other taxa for resources and a metabolic niche in the marmoset microbiome.}, }
@article {pmid40621946, year = {2025}, author = {Engelberts, JP and Ye, J and Parks, DH and McMaster, ES and McInnes, AS and Woodcroft, BJ and Volmer, JG and McIlroy, SJ and Tyson, GW}, title = {GenomeFISH: genome-based fluorescence in situ hybridization for strain-level visualization of microbial communities.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {40621946}, issn = {1751-7370}, support = {FT210100521//Australian Research Council Fellowships/ ; FT190100211//Australian Research Council Fellowships/ ; FL230100159//Australian Research Council Fellowships/ ; 2022-4087//Heising-Simons Foundation/ ; DP200102310//Australian Government Research Discovery Grant/ ; }, abstract = {Fluorescence in situ hybridization (FISH) is a powerful tool for visualizing the spatial organization of microbial communities. However, traditional FISH has several limitations, including limited phylogenetic resolution, difficulty visualizing certain lineages, and the design and optimization of new probes is time consuming and does not scale to the known diversity of microbial life. Here, we present GenomeFISH, a high-throughput, genome-based FISH approach that can differentiate strains within complex communities. Fluorescent probes are generated from the genomes of single cells, which are obtained from environmental or clinical samples through fluorescence activated single-cell sorting. GenomeFISH can distinguish between strains with up to 99% average nucleotide identity and was successfully applied to visualize strains in mock communities and human fecal samples. Given the superior sensitivity and specificity of GenomeFISH, we envisage it will become widely used for the visualization of complex microbial systems.}, }
@article {pmid40621919, year = {2025}, author = {Reintjes, G and Giljan, G and Fuchs, BM and Arnosti, C and Amann, R}, title = {Using phenotyping to visualize and identify selfish bacteria: a methods guide.}, journal = {Microbiology spectrum}, volume = {13}, number = {8}, pages = {e0160224}, pmid = {40621919}, issn = {2165-0497}, support = {496342779//Deutsche Forschungsgemeinschaft/ ; 840804//Horizon 2020 Framework Programme/ ; OCE-1736772//National Science Foundation/ ; OCE-2022952//National Science Foundation/ ; //Max-Planck-Gesellschaft/ ; }, mesh = {Humans ; *Bacteria/metabolism/classification/isolation &amp; purification/genetics ; Phenotype ; *Polysaccharides/metabolism ; }, abstract = {Polysaccharides are dominant components of plant and algal biomass, whose degradation is typically mediated by heterotrophic bacteria. These bacteria use extracellular enzymes to hydrolyze polysaccharides to oligosaccharides that are then also available to other bacteria. Recently, a new mechanism of polysaccharide processing-"selfish" uptake-has been recognized, initially among gut-derived bacteria. In "selfish" uptake, polysaccharides are bound at the outer membrane, partially hydrolyzed, and transported into the periplasmic space without loss of hydrolysis products, thus limiting the availability of smaller sugars to the surrounding environment. Selfish uptake is widespread in environments ranging from the ocean's cool, oxygen-rich, organic carbon-poor waters to the warm, carbon-rich, anoxic environment of the human gut. In this methods paper, we present a detailed guide to identifying selfish bacteria, including techniques for rapidly visualizing selfish uptake in complex bacterial communities, detecting selfish organisms, and distinguishing their activity from that of other community members.IMPORTANCEUnderstanding the role of heterotrophic bacteria in the degradation of organic matter is critical for comprehending carbon cycling and microbial ecology across different environments. This study highlights the significant prevalence of "selfish uptake" among bacteria-often overlooked by standard microbial activity assessments-and presents the method used to quantify and identify these "selfish" bacteria. Found in diverse habitats such as anoxic gut environments, oxygenated waters, sediments, and soils, their widespread presence underscores the necessity of revisiting current methodologies to include these crucial organisms. By identifying and studying selfish bacteria, we can gain detailed insights into how microbial communities function, how carbon flows through ecosystems, and how these processes impact global biogeochemical cycles.}, }
@article {pmid40621498, year = {2025}, author = {Chong, J and Zhou, Y and Li, Z and Li, X and Zhang, J and Cao, H and Ma, J and Ge, L and Zhong, H and Sun, J}, title = {Hyodeoxycholic acid modulates gut microbiota and bile acid metabolism to enhance intestinal barrier function in piglets.}, journal = {Frontiers in veterinary science}, volume = {12}, number = {}, pages = {1610956}, pmid = {40621498}, issn = {2297-1769}, abstract = {Oral bile acids, particularly hyodeoxycholic acid (HDCA), serve as critical drivers for gut microbial community maturation in mice. In the first study, Cy5-labeled HDCA combined with fluorescence imaging revealed rapid gastrointestinal transit of HDCA in piglets, contrasting with its delayed absorption observed in mice. In the second study, the effects of the oral HDCA supplementation on microbiota-host metabolic interactions were investigated using four piglet model groups: OPM-HDCA (naturally born, raised germ-free (GF), and orally administered HDCA), OPM-CON (naturally born, raised GF, and orally administered PBS), SPF-HDCA (naturally born, raised GF, and received fecal microbiota transplantation (FMT) and HDCA), and SPF-CON (naturally born, raised GF with FMT but no HDCA). The results demonstrated that HDCA administration at 0.2 mg/mL suppressed body weight gain in piglets, which was alleviated by FMT. HDCA significantly altered gut microbiota composition in SPF piglets, markedly increasing the Lactobacillus abundance (37.97% vs. 5.28% in SPF-CON) while decreasing the proportion of Streptococcus (28.34% vs. 38.65%) and pathogenic family Erysipelotrichaceae (0.35% vs. 17.15%). Concurrently, HDCA enhanced intestinal barrier integrity by upregulating tight junction proteins (ZO-1, Claudin, Occludin) and suppressing pro-inflammatory cytokines (TNF-α, IL-1β). Additionally, HDCA significantly upregulated ileal gene expression of CYP7A1 (cytochrome P450 family 7 subfamily A member 1) and TGR5 (G protein-coupled bile acid receptor 1) in both SPF-HDCA and OPM-HDCA groups compared to their respective controls (p < 0.05). These findings demonstrate that HDCA exerts microbiota-dependent effects on growth performance, intestinal barrier function, and bile acid metabolism in piglets. Although 0.2 mg/mL HDCA treatment suppressed body weight gain, it potentially enhanced intestinal barrier integrity by activating the TGR5 signaling pathway and increasing the abundance of beneficial bacteria such as Lactobacillus. These results also highlight the critical role of early-life gut microbiota in nutritional interventions, providing a basis for developing precision nutritional strategies targeting intestinal microbial ecology in piglets.}, }
@article {pmid40619451, year = {2025}, author = {Yan, F and Niu, Z}, title = {Impacts of pollution on coral bacterial and metabolites diversity across Dapeng Cove of South China sea.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {24107}, pmid = {40619451}, issn = {2045-2322}, mesh = {*Anthozoa/microbiology/metabolism ; China ; Animals ; *Bacteria/metabolism/classification/genetics ; Seawater/microbiology/chemistry ; Biodiversity ; Environmental Monitoring ; Oceans and Seas ; }, abstract = {Coastal ecosystems are increasingly threatened by anthropogenic activities, including sewage discharge and tourism-related pollution, which alter microbial diversity and biochemical cycles. This study applied molecular techniques to examine the coral microbial diversity, and metabolite composition of seawater across five sites (A-E) in Dapeng Cove, South China Sea, to assess pollution impacts. Sites A and B, within the yacht tourism area, exhibited high microbial diversity, dominated by Synechococcus and Rhodobacteraceae, with minimal pollution effects. Site C, inside a domestic drainage channel, showed moderate pollution, with elevated nitrite (NO2) and nitrate (NO3) levels, microbial taxa linked to organic matter degradation, and increased hydroxy acids and indoles. Sites D and E, located in main sewage channels, experienced severe pollution, characterized by high salinity, low dissolved oxygen, and dominance of pollution-tolerant bacteria such as Exiguobacterium and Tepidibacter. Metabolite analysis revealed elevated fatty acyls, organonitrogen compounds, and amino acids at these sites, highlighting strong anthropogenic influence. Beta diversity analysis (NMDS and ANOSIM) confirmed distinct microbial community structures, while KEGG pathway analysis indicated shifts in metabolic functions, with enrichment in xenobiotic biodegradation and anaerobic respiration in sewage-impacted areas. These findings underscore the detrimental effects of wastewater discharge on microbial ecology and biochemical functions. Urgent interventions, including improved wastewater management and regular environmental monitoring, are recommended to mitigate pollution effects. Future research integrating multi-omics approaches is necessary to evaluate the long-term ecological consequences of pollution and climate variability on coastal microbial communities.}, }
@article {pmid40614873, year = {2025}, author = {Lu, X and Gao, Y and Liu, X and Sun, Y and Zhen, G}, title = {Unlocking microbial community succession and key influencing factors during bioelectrocatalytically-driven simultaneous removal of ammonia nitrogen and sulfate from wastewater.}, journal = {Bioresource technology}, volume = {435}, number = {}, pages = {132934}, doi = {10.1016/j.biortech.2025.132934}, pmid = {40614873}, issn = {1873-2976}, mesh = {*Ammonia/isolation &amp; purification/metabolism ; *Wastewater/chemistry/microbiology ; *Sulfates/isolation &amp; purification/metabolism ; *Nitrogen/isolation &amp; purification ; Biofilms ; Electrodes ; Oxidation-Reduction ; Bacteria/metabolism ; *Water Purification/methods ; Electrolysis ; Catalysis ; Bioelectric Energy Sources/microbiology ; }, abstract = {Ammonia nitrogen (NH4[+]-N) and sulfate (SO4[2][-]) removal by Anaerobic ammonium oxidation (Anammox) and sulfate-reducing bacteria (SRB) was studied in dual-chamber microbial electrolysis cells (MECs). Appropriate anode potential stimulation promoted biofilm formation and enhanced extracellular polymeric substances fluorescence, facilitating electron transfer. The highest NH4[+]-N removal (81.1 %) was achieved at the anode potential of 0.6 V vs. Ag/AgCl after 50 days, coinciding with the increase in electroactive Candidatus_Brocadia from 1.1 % to 27.4 %. Simultaneously, SO4[2][-] removal reached 77.0 %, supported by cathodic biofilms dominated by SRB (Desulfofustis, Desulfomicrobium, and Desulfatirhabdium). Automated machine learning and principal co-ordinates analysis identified the anode potential as the key factor shaping microbial ecology. The appropriate anode potential (0.4-0.6 V vs. Ag/AgCl) promoted cathodic sulfidogenesis, indirectly enhancing electron flow and supporting Anammox process at the anode. These findings demonstrate that MECs hold great promise for simultaneously enhancing anaerobic ammonia oxidation bacteria and SRB activities, enabling efficient NH4[+]-N and SO4[2][-] removal.}, }
@article {pmid40614496, year = {2025}, author = {Brotto, AC and Kurt, H and Chandran, K}, title = {Impacts of intermittent and continuous aeration modes on performance, substrate dynamics, and microbial ecology of mainstream nitrification processes.}, journal = {Water research}, volume = {285}, number = {}, pages = {124123}, doi = {10.1016/j.watres.2025.124123}, pmid = {40614496}, issn = {1879-2448}, abstract = {Intermittent and continuous aeration strategies in combination with solids retention time (SRT) were investigated in terms of their impact on the performance and ecology of mainstream nitrification. Two lab-scale reactors (R1 and R2) were seeded with the same inoculum and subjected to intermittent aeration and continuous low aeration, respectively at statistically similar air-supply rates. For both reactors, SRT was progressively decreased from 8 d during Phase I to 4 and 2.5 d during Phases II and III, respectively. Compared to R2 (93 ± 4.8 %), R1 achieved more stable and higher ammonia oxidation (99 ± 0.13 %) averaged across SRTs. In R1, Nitrosospira were the dominant AOB, while in R2, AOB were a combination of Nitrosospira and Nitrosomonas. Among NOB, Nitrospira were more abundant than Nitrobacter for both R1 and R2 across SRTs. Intermittent aeration in R1 supported higher relative abundance of Comammox Nitrospira than R2. Notably, the enrichment patterns for nitrifying bacteria in the two reactors reflected distinct drivers (beyond microbial kinetics), including inoculum composition, extant oxygen or nitrogen concentrations or both. Overall, intermittent aeration strategies are integral to the design of biological nitrogen removal processes, although other considerations such as operational feasibility and process emissions might ultimately influence operating strategies.}, }
@article {pmid40614494, year = {2025}, author = {Mol, Z and Waegenaar, F and Pluym, T and Vermeir, P and Van Langenhove, H and De Gusseme, B and Boon, N and Walgraeve, C and Demeestere, K}, title = {Effect of biofilm, temperature and type of source water on the formation of haloanisoles in a pilot drinking water distribution system.}, journal = {Water research}, volume = {285}, number = {}, pages = {124078}, doi = {10.1016/j.watres.2025.124078}, pmid = {40614494}, issn = {1879-2448}, abstract = {Taste and odor deviations in tap water affect many consumers and cause a preference for bottled water. However, since tap water is more sustainable than bottled water, these issues should be solved and prevented rapidly. Haloanisoles (HAs) have a very low odor threshold concentration (sub ng.L[-1]) and are of considerable concern since they are mainly formed in drinking water distribution systems (DWDS). Understanding their formation and influencing factors is a crucial aspect of addressing these odor problems. Therefore, this study uses a DWDS pilot to closely mimic the complex situation in real DWDS and investigates the (microbial) formation of six HAs regarding biofilm cell density and composition, temperature, and type of source water. Ten to thirty times higher formation was observed when a stable biofilm (5 months, 10 times more biomass) was present, compared to a young biofilm (2 weeks). With a spiked halophenol (HP) concentration of 0.1 mg.L[-1], the HA concentrations produced by a young biofilm were already within the OTC range. The mature biofilm contained a higher variety of HA-producing microorganisms and more O-methyltransferase genes to convert the precursors (HPs) into HAs. Higher temperatures (24 °C instead of 16 °C) increased the formation of each HA by a factor of 2 to 4, although still low HP-HA conversion ratios were observed (0.2 %). Regardless of the temperature and the type of source water, a clear pattern is observed in the type of HAs formed, with 2,3,4-trichloroanisole being the most abundant. This study finally investigated the effectiveness of flushing to mitigate these odorous compounds in DWDS and concludes that their partitioning between the biofilm and water phase affects the performance of flushing procedures.}, }
@article {pmid40614303, year = {2025}, author = {Ferrocino, I and Buzzanca, D and Pagiati, L and Kazou, M and Georgalaki, M and Hatzopoulos, I and Tsakalidou, E}, title = {The microbial terroir of the Greek olive varieties.}, journal = {International journal of food microbiology}, volume = {441}, number = {}, pages = {111332}, doi = {10.1016/j.ijfoodmicro.2025.111332}, pmid = {40614303}, issn = {1879-3460}, mesh = {Greece ; *Olea/microbiology/classification ; *Fungi/classification/isolation &amp; purification/genetics ; *Bacteria/classification/isolation &amp; purification/genetics ; *Microbiota ; Food Microbiology ; Fruit/microbiology ; }, abstract = {The microbial terroir of Greek olive varieties remains underexplored. In this study, 62 samples of olive fruits, collected across the harvest period 2019-2020, were analyzed by high-throughput sequencing. The samples represented 38 olive varieties collected from geographically well distributed regions of Greece. Analysis of the bacterial composition revealed that the geographical area was a significant factor in discriminating samples. The core microbiota included Erwinia, Pseudomonas, and members of the Enterobacteriaceae family. Furthermore, a notable variation in bacterial taxa abundances associated with the geographic location was observed. The sampling area was a key discriminant factor for the mycobiota, and the core mycobiota comprised Alternaria, Taphrina, Candida, Wickerhamomyces anomalus and Penicillium. Finally, Redundancy Analysis (RDA) revealed a notable association between environmental characteristics and microbial composition. Specifically, tree age was associated with certain bacterial and fungal taxa (Pearson's correlation p-value adj.[FDR] < 0.05).}, }
@article {pmid40613821, year = {2025}, author = {Saini, N and Ghosh, A and Bhadury, P}, title = {Linking plastic degradation potential and resistance gene abundance in bacterioplankton community of the Sundarbans estuarine ecosystem.}, journal = {FEMS microbiology letters}, volume = {372}, number = {}, pages = {}, doi = {10.1093/femsle/fnaf067}, pmid = {40613821}, issn = {1574-6968}, support = {DST/SJF/E&amp;ASA-01/2017-18//Science and Engineering Research Board/ ; }, mesh = {*Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *Plastics/metabolism ; Biodegradation, Environmental ; Estuaries ; *Plankton/genetics/metabolism/classification ; India ; *Microbiota/genetics ; Ecosystem ; Metagenomics ; }, abstract = {Harnessing microbial capabilities offers a promising and sustainable approach to address the global challenge of plastic waste. However, the potential of mangrove microbiomes to degrade diverse plastic polymers remains largely unexplored. In this metagenomic-based study, surface water microbiomes were analysed from the Indian Sundarbans, part of the world's largest contiguous mangrove ecosystem, revealing 748.21 hits per billion nucleotides associated with plastic-degrading enzymes (PDEs) targeting 17 different polymer types. Of these, 72.9% corresponded to synthetic polymers and 27.1% to natural polymers. The highest number of hits (223) was associated with polyethylene glycol-degrading enzymes, representing 26.7% of the total PDEs hits. Taxonomic analysis revealed Deltaproteobacteria and Gammaproteobacteria as key degraders of diverse synthetic plastic polymers, with Deltaproteobacteria emerging as a previously unreported group. This suggests that surface sediments may serve as reservoirs for novel plastic-degrading microbes. Co-occurrence network analysis indicated possible emerging co-selection or complex associations between PDEs, antibiotic resistance genes (ARGs), and metal resistance genes (MRGs). Notably, zinc resistance genes and aminoglycoside-related ARGs showed more associations with PDEs. While the presence of PDEs offers a promising avenue for bioremediation, their application may be complicated by the concurrent rise of ARGs and MRGs within PDE-harbouring microbes. Thus, it highlights the need for careful assessment when employing microbes for plastic bioremediation.}, }
@article {pmid40610473, year = {2025}, author = {Ivanova, EA and Suleymanov, AR and Nikitin, DA and Semenov, MV and Abakumov, EV}, title = {Machine learning-based mapping of Acidobacteriota and Planctomycetota using 16 S rRNA gene metabarcoding data across soils in Russia.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {23763}, pmid = {40610473}, issn = {2045-2322}, support = {24-44-00006//Russian Science Support Foundation/ ; 24-44-00006//Russian Science Support Foundation/ ; }, mesh = {*Machine Learning ; *Soil Microbiology ; *RNA, Ribosomal, 16S/genetics ; Russia ; *DNA Barcoding, Taxonomic/methods ; Soil/chemistry ; Microbiota/genetics ; *Acidobacteria/genetics/classification ; Ecosystem ; }, abstract = {The soil microbiome plays a crucial role in maintaining healthy ecosystems and supporting sustainable agriculture. Studying its biogeographical structure and distribution is essential for understanding the rates and mechanisms of microbially mediated soil ecosystem services. This study aimed to investigate the spatial distribution patterns of Acidobacteriota and Planctomycetota across soils in Russia, summarizing data from 16S rRNA gene metabarcoding of topsoils. A machine learning approach (Random Forest) was employed to generate digital distribution maps using climatic, topographic, vegetation, geological, and soil variables. Model interpration was performed using variable importance assessment and Shapley values. According to the error metrics, the Acidobacteriota model achieved a root mean squared error (RMSE) of 6.67% and an R[2] of 0.41, while the Planctomycetota model achieved an RMSE of 2.04% and an R[2] of 0.46. Both phyla exhibited similar spatial distribution patterns, with relative abundance decreasing from North to South. For Acidobacteriota, vegetation cover, surface temperature, and soil pH were significant predictors, whereas the relative abundance of Planctomycetota was mainly influenced by climatic variables. Specifically, Acidobacteriota were more abundant in areas with dense vegetation, stable surface temperatures, and acidic soils. In contrast, Planctomycetota showed reduced abundance in regions with higher levels of precipitable water vapor. These results highlight the potential of machine learning techniques to visualize predictive biogeographic patterns in soil microbial taxa abundance at the phylum level. Despite limitations related to the heterogeneous nature of source data, focusing on higher taxonomic ranks less sensitive to methodological variation enabled to identify preliminary large-scale distribution trends of microbial phyla in soils.}, }
@article {pmid40607773, year = {2025}, author = {Tao, Y and Liu, D and Shi, Q and Sun, Q and Liu, C and Zeng, X}, title = {Lead exposure in relation to gut homeostasis, microbiota, and metabolites.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {7}, pages = {e0037225}, pmid = {40607773}, issn = {1098-5336}, support = {701200E003,2024JKZKTS21//The Research Project of Zhejiang Chinese Medical University/ ; }, mesh = {*Lead/toxicity/metabolism ; *Gastrointestinal Microbiome/drug effects ; Humans ; *Homeostasis/drug effects ; *Gastrointestinal Tract/microbiology/drug effects ; Animals ; }, abstract = {Lead (Pb) is a hazardous heavy metal with no known safe threshold for exposure or consumption, posing significant risks to human health. Pb exposure can cause multiple system damage, depending on exposure levels, duration, and its high bioavailability and bioaccumulative potential. Gastrointestinal tract serves as a primary site for Pb absorption, making it particularly vulnerable to Pb-induced damage, including disruption of gut microbiota composition and metabolic function. This study briefly summarizes the detrimental effects of Pb gut homeostasis, microbial ecology, and host metabolism, which, in turn, further contribute to systemic toxicity. Notably, Pb exposure compromises intestinal barrier integrity, increasing gut permeability and facilitating the translocation of harmful biomolecules into systemic circulation, thereby exacerbating organ dysfunction. Importantly, we underscore that dietary and nutritional interventions such as fiber, probiotic, and vitamin C supplementation is a practicable and effective strategy for mitigating or preventing Pb toxicity.}, }
@article {pmid40606160, year = {2025}, author = {Al-Khlifeh, E and Khadem, S and Hausmann, B and Berry, D}, title = {Corrigendum: Microclimate shapes the phylosymbiosis of rodent gut microbiota in Jordan's Great Rift Valley.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1639190}, doi = {10.3389/fmicb.2025.1639190}, pmid = {40606160}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2023.1258775.].}, }
@article {pmid40605266, year = {2025}, author = {Herman, C and Barker, BM and Bartelli, TF and Chandra, V and Krajmalnik-Brown, R and Jewell, M and Li, L and Liao, C and McAllister, F and Nirmalkar, K and Xavier, JB and Caporaso, JG}, title = {A review of engraftment assessments following fecal microbiota transplant.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2525478}, pmid = {40605266}, issn = {1949-0984}, support = {U24 CA248454/CA/NCI NIH HHS/United States ; }, mesh = {*Fecal Microbiota Transplantation ; Humans ; *Gastrointestinal Microbiome ; *Clostridium Infections/therapy/microbiology ; Clostridioides difficile/physiology ; Animals ; Feces/microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {Fecal Microbiota Transplant (FMT) is a treatment for recurrent Clostridium difficile infections and is being explored for other clinical applications, from alleviating digestive and neurological disorders, to restoring microbiomes impacted by cancer treatment. Quantifying the extent of engraftment following an FMT is important in understanding a recipient's response to treatment. Engraftment and clinical response need to be investigated independently to evaluate an FMT's role (or lack thereof) in achieving a clinical response. Standardized bioinformatics methodologies for quantifying engraftment extent would not only improve assessment and understanding of FMT outcomes, but also facilitate comparison of FMT results and protocols across studies. Here we review FMT studies, integrating three concepts from microbial ecology as framework to discuss how these studies approached assessing engraftment extent: 1) Community Coalescence investigates microbiome shifts following FMT engraftment, 2) Indicator Features tracks specific microbiome features as a signal of engraftment, and 3) Resilience examines how resistant post-FMT recipients' microbiomes are to reverting back to baseline. These concepts explore subtly different questions about the microbiome following FMT. Taken together, they provide holistic insight into how an FMT alters a recipient's microbiome composition and provide a clear framework for quantifying and communicating about microbiome engraftment.}, }
@article {pmid40602916, year = {2025}, author = {Puche, E and Roger, B and Vargas-Sánchez, M and Sánchez-Carrillo, S and Rodrigo, MA}, title = {Freshwater macrophyte type (macroalgae versus phanerogams) mainly determines detritus-derived greenhouse gases production: A microcosm experiment.}, journal = {Journal of environmental sciences (China)}, volume = {157}, number = {}, pages = {674-689}, doi = {10.1016/j.jes.2025.01.015}, pmid = {40602916}, issn = {1001-0742}, mesh = {*Greenhouse Gases/analysis/metabolism ; *Seaweed ; Ecosystem ; Methane/analysis ; Fresh Water ; Carbon Dioxide/analysis ; Eutrophication ; *Environmental Monitoring ; *Air Pollutants/analysis ; }, abstract = {Freshwater ecosystems are crucial in the global emissions of greenhouse gases (GHGs) such as CH4. Macrophytes are the main organic matter (i.e., detritus) supplier to the sediment of these systems, thus controlling CH4 production. However, species-specific differences (structure and composition) may determine contrasting patterns of detritus transformation into CH4. Furthermore, eutrophication can affect the degradation and, consequently, CH4 production. We performed a 64-day microcosm experiment with anoxic incubations of detritus from seven phylogenetically different macrophytes (two charophytes, filamentous algae -Spirogyra, Cladophora-, three submerged plants and an amphibious one), under two trophic conditions (oligo- versus eutrophic) and with/without sediment. We assessed the CH4 and CO2 production and the changes in the detritus quality at the end of the experiment. The ranking in the mean cumulative CH4 production was: Chara hispida > Nitella hyalina > Najas marina ≈ Teucrium scordium > Stuckenia pectinata ≈ Myriophyllum spicatum > filamentous algae, and it was related to the detritus quality. GHGs maximum production rates were 1.6 (N. marina)-1.2 (C. hispida) mmol CH4/(g OC·day) and 1.7 (N. marina)-1.5 (C. hispida) mmol CO2/(g OC·day). The CO2:CH4 ratio was biased towards CO2 during the first 10 days (average ratio of 200) and fell afterwards to about 1 for all macrophyte species and treatments. The sediment favored detritus decomposition (probably due to the "positive priming effect"), increasing GHGs production. The influence of nutrient enrichment was not evident. Delving into the macrophyte detritus quality-GHGs production relationship is needed to forecast the GHGs emissions in macrophyte-dominated systems.}, }
@article {pmid40602642, year = {2025}, author = {Pieńkowska, A and Fleischmann, J and Drabesch, S and Merbach, I and Wang, G and Rocha, U and Reitz, T and Marie Muehe, E}, title = {Long-term organic fertilization shields soil prokaryotes from metal stress while mineral fertilization exacerbates it.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {382}, number = {}, pages = {126747}, doi = {10.1016/j.envpol.2025.126747}, pmid = {40602642}, issn = {1873-6424}, mesh = {*Fertilizers/analysis ; *Soil Microbiology ; *Soil Pollutants/analysis/toxicity ; Soil/chemistry ; *Metals/toxicity ; Minerals ; Agriculture ; RNA, Ribosomal, 16S ; }, abstract = {Metal contamination in agricultural soils threatens prokaryote dynamics essential for soil health and crop productivity. Yet, whether fertilization in the long-run affects their resilience to metals remains unclear. This study examined the biogeochemical impacts of realistically low-dose applications of cadmium, zinc, and lead in soils subjected to 119 years of non-fertilization, mineral-fertilization (NPK), organic-fertilization (manure), or combined mineral-organic fertilization. Amended metals remained in the mobile fraction with the order: mineral < unfertilized < mineral + organic < organic, mirroring the effects on soil prokaryotes. In both unfertilized and mineral-fertilized soils, 16S rRNA gene copy numbers declined by 30 % upon metal addition, but recovery timing differed: in unfertilized soil, recovery began after three days, whereas in mineral-fertilized soil, numbers declined until day seven before recovering. This coincided with an increase in metal-resistant taxa, particularly in mineral-fertilized soil, with 10 significantly affected OTUs, and to a lesser extent in unfertilized soil, with 5 affected OTUs. Carbon-, nitrogen-, and phosphorus-mining enzyme activities increased 50-100 % in mineral-fertilized soils, suggesting enhanced nutrient acquisition to mitigate metal toxicity. In contrast, organic-fertilized soil hosted stable enzymatic activities and microbial copy numbers with minimal community shifts (1 affected OTU), indicating greater resistance to metal amendment. Combined mineral-organic fertilization stabilized copy numbers and enzymatic activity upon metal amendment, but 8 OTUs were affected, including specialized nutrient cyclers, suggesting increased availability of previously adsorbed NPK cations. Our findings indicate that organic fertilization shields prokaryotes from metal stress, while mineral fertilization exacerbates it, highlighting the benefits of organic practices for maintaining soil health and productivity.}, }
@article {pmid40602621, year = {2025}, author = {Zhang, Z and Yuan, G and Turgun, X and Turgun, Z and Hou, L and Ye, M and Wang, Y and Xu, X}, title = {Biogeographic Patterns and Ecological Roles of Microorganisms in Sediments Along an Estuarine Salinity Gradient.}, journal = {Environmental microbiology reports}, volume = {17}, number = {4}, pages = {e70139}, pmid = {40602621}, issn = {1758-2229}, support = {2023A1515110368//Guangdong Basic and Applied Basic Research Foundation/ ; XJNUZBS2423//Doctoral Research Foundation of Xinjiang Normal University/ ; 42361144846 and 42461006//National Natural Science Foundation of China/ ; //Tianchi Talents (Xinjiang) Plan Project (Young Doctor)/ ; }, mesh = {*Geologic Sediments/microbiology/chemistry ; *Salinity ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Estuaries ; China ; Biodiversity ; Microbiota ; Ecosystem ; Metagenome ; Phylogeny ; }, abstract = {The distribution patterns and driving mechanisms of microbial biogeographic patterns are fundamental questions in microbiology. This study analysed and compared the bacterial biogeographic patterns in the coastal environment, focusing on the Yangtze Estuary and its adjacent coastal zone. The purpose is to explore the driving mechanisms under spatial distribution, the community assembly processes and potential functions. Our results revealed that the sediment bacterial community structure exhibited a distinct geographical pattern and was significantly influenced by environmental factors. The microbial community displayed a non-random co-occurrence pattern, and the biogeographic patterns were shaped not only by environmental constraints (deterministic processes) but also by stochastic processes resulting from dispersal limitation. The metagenome sequencing analysis revealed a pronounced salinity gradient in the nitrogen-cycling function of the bacterial community. This functional difference appears to be driven by microbial diversity changes from the estuarine region to the ocean, highlighting the key role of microbial ecological characteristics. The findings of this study contribute to a deeper understanding of microbial ecology in estuarine environments, emphasizing the complex interplay between environmental factors and microbial community dynamics in shaping the function of estuarine sediment bacterial communities.}, }
@article {pmid40602118, year = {2025}, author = {Liu, Z and Wen, J and Liu, Z and Su, Z and Wu, Z and Shen, H and Wei, H and Zhang, J}, title = {Tire microplastics rather than polystyrene microplastics reduce soil microbial diversity and network complexity and stability, and induce microbial homogenization.}, journal = {Journal of hazardous materials}, volume = {495}, number = {}, pages = {138945}, doi = {10.1016/j.jhazmat.2025.138945}, pmid = {40602118}, issn = {1873-3336}, abstract = {Microplastics (MPs) pollution poses escalating threats to soil biodiversity, yet its impacts on microbial community structure, stability, and assembly are far from fully understood, limiting the comprehensive assessment of MPs risks. This study investigated effects of polystyrene (PS) and tire particle (TP) MPs (0, 1 %, 5 %; w/w) on soil microbial communities in a maize-planted system, evaluating shifts in diversity, network architecture, and assembly processes. Our results demonstrated that high-concentration (5 %) PS MPs significantly enhanced bacterial α-diversity by promoting some taxa (e.g., Planctomycetes, Betaproteobacteria), and increased bacterial network complexity. In contrast, 5 % TP MPs reduced bacterial and fungal diversity, destabilized bacterial networks, and induced taxonomic homogenization. TP MPs amplified deterministic assembly processes by elevating homogeneous selection contribution while reducing stochastic drift, thereby driving microbial community convergence. Bacterial and fungal community structure shifts under TP MPs correlated with soil stoichiometric alterations, including depleted nitrate nitrogen and available phosphorus, and elevated pH, contents of dissolved organic carbon, ammonium nitrogen, and total carbon. These findings highlight the divergent ecological risks posed by PS and TP MPs, and underscore the urgent need for prioritized mitigation of TP MPs pollution in agroecosystems to preserve microbial functional integrity.}, }
@article {pmid40601059, year = {2025}, author = {Chao, LL and Shih, CM}, title = {Molecular Survey and Genetic Identification of Wolbachia Endosymbionts in Dwelling-Caught Culex quinquefasciatus (Diptera: Culicidae) Mosquitoes from Taiwan.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {69}, pmid = {40601059}, issn = {1432-184X}, support = {NSTC 113-2320-B-037-010; NSTC 114-2923-B-037-001//National Science and Technology Council/ ; }, mesh = {Animals ; *Wolbachia/genetics/classification/isolation &amp; purification/physiology ; *Culex/microbiology ; Taiwan ; *Symbiosis ; Phylogeny ; Female ; Male ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics ; }, abstract = {The genetic identity of Wolbachia endosymbionts was determined in dwelling-caught Culex quinquefasciatus from Taiwan. A total of 370 Cx. quinquefasciatus (245 females and 125 males) was initially screened for Wolbachia infection targeting the universal 16S gene, and the positive samples were further identified their genogroup by a nested-polymerase chain reaction assay to amplify the group-specific Wolbachia surface protein (wsp) gene. In general, 44.59% of Cx. quinquefasciatus was detected with Wolbachia endosymbionts, and 43.2% (54/125) in male and 45.31% (111/245) in female. The group-specific detection was observed in 2.16% (8/370), 41.35% (153/370), and 1.08% (4/370) with groups A, B, and co-infection (A&amp;B), respectively. Phylogenetic analysis revealed that the genetic identities of these Taiwan strains were genetically similar to the groups A and B of Wolbachia with the high sequence homogeneity of 98.7-100% and 96.5-99.8%, respectively. Genetic relatedness is clearly discriminated using both methods of maximum likelihood (ML) and unweighted pair group with arithmetic mean (UPGMA). This study demonstrates the initial genetic identity of Wolbachia endosymbionts with a low prevalence (2.16%) of group A and a high prevalence (41.35%) of group B in dwelling-caught Cx. quinquefasciatus of Taiwan. Because the Cx. quinquefasciatus had been known as a vector for various viral pathogens, the possible impacts of Wolbachia endosymbionts on vector competence of Cx. quinquefasciatus in Taiwan need to be further identified.}, }
@article {pmid40601038, year = {2025}, author = {He, T and Chen, Y and Wang, Y and Peng, Z and Mou, Y and Wang, L}, title = {Responses of Microbial Community to Heterogeneous Dissolved Organic Nitrogen Constituents in the Hyporheic Zones of Treated Sewage-Dominated Rivers.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {71}, pmid = {40601038}, issn = {1432-184X}, support = {2021YFB2600200//National Key Research and Development Project of China/ ; grant number 52170159//National Natural Science Foundation of China/ ; No. BE2022601//Key Research and Development Program of Jiangsu Province/ ; 2016-JNHB-007//the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), and the Six Talent Peaks Project in Jiangsu Province/ ; }, mesh = {*Sewage/microbiology/chemistry ; *Nitrogen/metabolism/analysis ; China ; *Rivers/microbiology/chemistry ; *Microbiota ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; *Microbial Consortia ; }, abstract = {The hyporheic zone (HZ) of treated sewage-dominated rivers serves as a critical biogeochemical hotspot for dissolved organic nitrogen (DON) transformation, yet the mechanisms linking DON chemodiversity to microbial community dynamics remain poorly resolved. This study integrated spectroscopic fingerprinting, machine learning, and partial least squares path modeling (PLS-PM) to unravel the interactions between redox-stratified DON fractions and microbial consortia in two effluent-impacted rivers (Xi'an, China). The results revealed that DOM spectral parameters associated with distinct DON characteristics posed distinct effects on microbial communities, with the communities in oxic zones largely impacted by autobiogenic, aromatic, and protein-like DON, while the communities in suboxic zones were more intensely impacted by the humification degree of DON. Microbial communities exhibited redox-dependent niche differentiation; i.e., keystone taxa in oxic zones (e.g., Gamma-Proteobacteria) drove nitrogen assimilation, while suboxic taxa (e.g., Verrucomicrobia) prioritized stress-resistant D-amino acid metabolism. PLS-PM demonstrated that biomarkers exerted stronger control on nitrogen cycling (|path coefficients|> 0.6, P < 0.05) than keystone taxa, with summer communities showing higher model fit. Treated sewage-derived DON fostered specialized consortia through biochemical trade-offs, i.e., methionine recycling in oxic zones versus peptidoglycan modification in suboxic zones, thus highlighting the critical role of HZ in mitigating nitrogen pollution. These findings advance predictive modeling of DON-microbe interactions in anthropogenically perturbed aquatic ecosystems.}, }
@article {pmid40601033, year = {2025}, author = {Nariman, N and Entling, MH and Krehenwinkel, H and Kennedy, S}, title = {The Microbiome of an Invasive Spider: Reduced Bacterial Richness, but no Indication of Microbial-Mediated Dispersal Behaviour.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {70}, pmid = {40601033}, issn = {1432-184X}, mesh = {Animals ; *Spiders/microbiology/physiology ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; Introduced Species ; Symbiosis ; Europe ; Animal Distribution ; }, abstract = {Mermessus trilobatus, an invasive North American linyphiid spider, has expanded its invasion range up to 1400 km in Europe, accelerating its dispersal speed in less than 40 years. The high heritability of dispersal behaviour and the spatial sorting of high and low dispersers indicate a genetic basis of dispersal behaviour. However, microbial endosymbionts can moderate dispersal behaviour in related species (Rickettsia in Erigone atra). Hence, dispersal behaviour in M. trilobatus might also be dictated by the activity of dispersal-mediating endosymbionts. Here, we investigated the microbiome of invasive M. trilobatus spiders extracted from (1) high- and low-dispersive individuals and (2) spiders originating from locations close to the edge and core of the expansion. We examine the microbiomes for the presence of potential dispersal- and reproduction-mediating bacterial strains and compare the microbial assemblages of spiders based on their dispersal behaviour and locations of origin. The composition of microbial assemblages was similar among spiders of different geographic origins and dispersal behaviour. However, microbial richness was lower in high- than in low-dispersive individuals. Surprisingly, none of the known dispersal- or reproduction-altering endosymbionts of arthropods was identified in any tested spider. This contrasts with published results from North America, where M. trilobatus is a known host of Rickettsia and Wolbachia. Thus, the invasive European population appears to have lost its associated endosymbionts. As endosymbionts can reduce spider mobility, it is possible that their absence facilitates the spread of the invasive spider population. The absence of endosymbionts among the analysed individuals substantiates the role of genetic mechanisms behind the variable dispersal behaviour of invasive M. trilobatus in Europe.}, }
@article {pmid40600875, year = {2025}, author = {Yao, J and Wang, H and Fang, J and Shan, S and Joseph, SD and van Zwieten, L and Zhu, K and Chen, D and Jia, H}, title = {Distribution Hotspots, Formation Mechanisms, and Ecological Effects of Reactive Oxygen Species in Soil and Sediment: A Critical Review.}, journal = {Environmental science &amp; technology}, volume = {59}, number = {27}, pages = {13551-13565}, doi = {10.1021/acs.est.5c00581}, pmid = {40600875}, issn = {1520-5851}, mesh = {*Soil/chemistry ; *Geologic Sediments/chemistry ; *Reactive Oxygen Species/analysis ; Rhizosphere ; Free Radicals/analysis ; Environmental Monitoring ; Carbon Sequestration ; Superoxides/analysis ; Hydrogen Peroxide/analysis ; Hydroxyl Radical/analysis ; Environmental Restoration and Remediation ; Ecological and Environmental Phenomena ; }, abstract = {Reactive oxygen species (ROS), including superoxide radical (O2[•-]), hydrogen peroxide (H2O2), hydroxyl radical ([•]OH), and singlet oxygen ([1]O2), are commonly present in soil and sediment, playing a crucial role in the nutrient biogeochemical cycle, pollutant transformation, and microbial ecology. Previous reviews mainly emphasized ROS toxicity and Fenton chemistry-related reactions, neglecting a comprehensive understanding of ROS distribution and hotspots, formation mechanisms, and ecological effects. Here, the most advanced in situ and ex situ detection methods of ROS in soil and sediment are first summarized to address these gaps. ROS hotspots are identified as active microinterfaces and oxic-anoxic fluctuation zones by graphing the distribution of ROS in soil and sediment. Second, ROS formation processes and mechanisms are outlined, which involve natural organic matter (NOM) and biochar (acting as electron shuttle, geobattery, geoconductor, and photosensitizer), transition metals (mainly via Fenton and Fenton-like reactions), and microbes (producing extracellular ROS and mediating NOM decomposition or metal oxides reduction). Further, as for the ecological effects of ROS, they impact the microbial community, nutrient cycle, and the transformation of organic pollutants and multivalence heavy metals. Finally, we call for more future research that focuses on developing rapid and in situ ROS detection techniques, elucidating the interactive ROS formation mechanisms by trace environmental components, analyzing ecological consequences in ROS hotspots, and practically applying ROS in soil and sediment. A comprehensive understanding of the ROS formation process in soil and sediment is crucial for the study of soil carbon sequestration and natural remediation processes in the context of global green and low-carbon development.}, }
@article {pmid40600175, year = {2025}, author = {Etesami, H}, title = {The dual nature of plant growth-promoting bacteria: Benefits, risks, and pathways to sustainable deployment.}, journal = {Current research in microbial sciences}, volume = {9}, number = {}, pages = {100421}, pmid = {40600175}, issn = {2666-5174}, abstract = {Plant growth-promoting bacteria (PGPB) are pivotal in sustainable agriculture, enhancing crop productivity and reducing reliance on chemical inputs. However, their dual role as beneficial agents and potential stressors remains underexplored. This review examines the paradoxical adverse effects of PGPB, challenging the predominantly optimistic narrative surrounding their use. At the plant level, unintended consequences include hormonal imbalances (e.g., auxin-induced root inhibition), phytotoxic metabolite production (e.g., hydrogen cyanide), and trade-offs between growth and defense mechanisms. At the soil level, risks encompass disrupted microbial diversity, altered nutrient cycling, and horizontal gene transfer that may foster pathogenicity. These outcomes are driven by environmental factors (soil pH and moisture), host-specific interactions, and application practices. Mitigation strategies emphasize rigorous strain selection, optimized dosing, and integrated soil management to balance efficacy with ecological safety. Advances in multi-omics technologies and synthetic consortia design offer predictive insights into strain behavior, while long-term ecological assessments are critical to address legacy impacts. The review underscores the necessity of a nuanced, evidence-based approach to PGPB deployment, harmonizing agricultural benefits with environmental stewardship. By addressing knowledge gaps in microbial ecology and risk assessment, this work supports strategies prioritizing both agricultural resilience and soil biodiversity to ensure PGPB contribute sustainably to global food security.}, }
@article {pmid40600142, year = {2025}, author = {Xia, Y and Lu, L and Wang, L and Qiu, Y and Liu, X and Ge, W}, title = {Multi-omics analyses reveal altered gut microbial thiamine production in obesity.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1516393}, pmid = {40600142}, issn = {1664-302X}, abstract = {OBJECTIVE: Accumulating evidence highlights the important role of B vitamins in maintaining the balance of gut microbial ecology and metabolism, however, few studies have focused on changes in B vitamins homeostasis in the gut and their associations with disease. This study aims to investigate the potential interplay between B vitamins, gut microbiota, and obesity.<br><br>METHODS: We conducted an integrated analysis of fecal shotgun metagenomics, fecal metabolome concerning B vitamins and short chain fatty acids (SCFAs), and obese phenotypes in a cohort of 63 participants, including 31 healthy controls and 32 individuals with obesity.<br><br>RESULTS: Metabolomic analysis identified significantly lower levels of fecal thiamine in individuals with obesity (P Wilcoxon < 0.001). Fecal thiamine levels exhibited a positive correlation with HDL-C and a negative correlation with BMI, DBP, fasting serum insulin, HOMA-IR, triglycerides, and propionic acid. Binary logistics regression suggested that fecal thiamine deficiency may be a potential contributor to the onset of obesity (Odds ratio: 0.295). Metagenomic analysis indicated that the microbial composition in individuals with obesity was characterized by a predominance of potential opportunistic pathogens, a loss of complexity, and a decrease in thiamine-producing bacteria. Integrated analysis indicated that thiamine deficiency was positively associated with the depletion of thiamine auxotrophic bacteria in the obese microbiome. Functional analysis revealed that KOs content for enzymes involved in the microbial production of thiamine were significantly lower in obesity, including tRNA uracil 4-sulfurtransferase (ThiI, P Wilcoxon = 0.001) and nucleoside-triphosphatase (NTPCR, P Wilcoxon = 0.006), both of which were positively associated with fecal thiamine.<br><br>CONCLUSION: Our study highlights the impairment of microbial thiamine production and its broad associations with gut microbiota dysbiosis and obesity-related phenotypes. Our findings provide a rationale for developing treatments that utilize thiamine to prevent obesity by modulating gut microbiota.}, }
@article {pmid40600059, year = {2025}, author = {Liu, J and Yao, P and Liu, J and Ren, G and Zhang, XH and Liu, J}, title = {Habitat and lifestyle affect the spatial dynamics of prokaryotic communities along a river-estuary-sea continuum.}, journal = {mLife}, volume = {4}, number = {3}, pages = {305-318}, pmid = {40600059}, issn = {2770-100X}, abstract = {Microbial biogeography and its controlling mechanisms are central themes in microbial ecology. However, we still lack a comprehensive understanding of how habitats and lifestyles affect microbial biogeography across complex environmental gradients. In this study, we investigated the planktonic (including free-living [FL] and particle-associated [PA] lifestyles) and benthic prokaryotic communities along a river-estuary-sea continuum of the Changjiang River to explore their distinct spatial dynamics. We observed greater community variability across spatial distances than between habitat and lifestyle types. Spatial variations were evident in FL, PA, and benthic communities, with the highest turnover rates observed in benthic communities, followed by PA, and the lowest turnover rates observed in FL. The replacement effect dominated PA and benthic community variations, whereas the richness effect was more significant in FL communities. Microbial assembly was primarily governed by homogeneous selection and dispersal limitation regardless of habitats/lifestyles, with their ratios decreasing as the spatial distance increased, particularly in the FL fraction. Dispersal limitation had a stronger effect on benthic communities compared to planktonic communities. While heterogeneous selection generally played a minor role, its influence became more pronounced over larger spatial distances and with increasing salinity differences. Finally, we showed that abiotic and biotic factors individually exerted a greater influence on PA communities, whereas their interactions had a stronger effect on FL communities. Our results revealed complex spatial dynamics and assembly mechanisms among microorganisms across different habitats and lifestyles, providing insights into the spatial scaling of community assembly across complex environmental gradients.}, }
@article {pmid40598447, year = {2025}, author = {Bulzu, PA and Henriques Vieira, H and Ghai, R}, title = {Lineage-specific expansions of polinton-like viruses in photosynthetic cryptophytes.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {154}, pmid = {40598447}, issn = {2049-2618}, support = {25-15920S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 24-11998S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 20-12496X//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; }, mesh = {*Cryptophyta/virology/genetics ; Metagenomics ; Phylogeny ; Genome, Viral ; Photosynthesis ; *Giant Viruses/genetics/classification ; *DNA Viruses/genetics/classification ; }, abstract = {BACKGROUND: Polinton-like viruses (PLVs) are diverse eukaryotic DNA viral elements (14-40 kb) that often undergo significant expansion within protist genomes through repeated insertion events. Emerging evidence indicates they function as antiviral defense systems in protists, reducing the progeny yield of their infecting giant viruses (phylum Nucleocytoviricota) and influencing the population dynamics and evolution of both viruses and their hosts. While many PLVs have been identified within the genomes of sequenced protists, most were recovered from metagenomic data. Even with the large number of PLVs identified from metagenomic data, their host-virus linkages remain unknown owing to the scarcity of ecologically relevant protist genomes. Additionally, the extent of PLV diversification within abundant freshwater taxa remains undetermined. In order to tackle these questions, high-quality genomes of abundant and representative taxa that bridge genomic and metagenomic PLVs are necessary. In this regard, cryptophytes, which are among the most widely distributed, abundant organisms in freshwaters and have remained largely out of bounds of genomic and metagenomic approaches, are ideal candidates for investigating the diversification of such viral elements both in cellular and environmental context.<br><br>RESULTS: We leveraged long-read sequencing to recover large (200-600&#xa0;Mb), high-quality, and highly repetitive (>&#x2009;60%) genomes of representative freshwater and marine photosynthetic cryptophytes. We uncovered over a thousand complete PLVs within these genomes, revealing vast lineage-specific expansions, particularly in the common freshwater cryptophyte Rhodomonas lacustris. By combining deep sequence homology annotation with biological network analyses, we discern well-defined PLV groups defined by characteristic gene-sharing patterns and the use of distinct strategies for replication and integration within host genomes. Finally, the PLVs recovered from these cryptophyte genomes also allow us to assign host-virus linkages in environmental sequencing data.<br><br>CONCLUSIONS: Our findings provide a primer for understanding the evolutionary history, gene content, modes of replication and infection strategies of cryptophyte PLVs, with special emphasis on their expansion as endogenous viral elements (EVEs) in freshwater bloom-forming R. lacustris. Video Abstract.}, }
@article {pmid40594354, year = {2025}, author = {Flores, SS and Cordovez, V and Arias Giraldo, LM and Leon-Reyes, A and van 't Hof, P and Raaijmakers, JM and Oyserman, BO}, title = {Unveiling diversity and adaptations of the wild tomato Microbiome in their center of origin in the Ecuadorian Andes.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {22448}, pmid = {40594354}, issn = {2045-2322}, support = {CZ07-000440-2018//SENESCYT scholarship/ ; 10093//Chancellor Grant and COCIBA-USFQ/ ; 10093//Chancellor Grant and COCIBA-USFQ/ ; 024.004.014/NWO_/Dutch Research Council/Netherlands ; 024.004.014/NWO_/Dutch Research Council/Netherlands ; }, mesh = {*Solanum lycopersicum/microbiology/genetics ; *Microbiota/genetics ; Soil Microbiology ; Rhizosphere ; Ecuador ; Plant Roots/microbiology ; Biodiversity ; *Adaptation, Physiological ; Phylogeny ; }, abstract = {Microbiome assembly has been studied for many plant species and is recognized as a key driver of plant growth and plant tolerance to (a)biotic stresses. To date, assembly of the tomato rhizosphere microbiome has been investigated primarily for commercial varieties and field soils subjected to agricultural management practices, whereas the microbiome of wild tomato genotypes in their native habitats remains largely unexplored. This research focused on distinct populations of Solanum pimpinellifolium in three natural habitats in the Ecuadorian Andes to identify the taxonomic and functional diversity of their rhizosphere microbiome. The results showed that, despite genotypic differences among the wild tomato populations, different soil types and soil microbiome compositions, the rhizosphere microbiome showed strikingly compositional similarity across the three habitats. Proteobacteria, in particular taxa classified as Enterobacteriaceae, and specific unclassified fungal taxa were highly represented in the rhizosphere of S. pimpinellifolum. Metagenomic analyses suggested that the prevalence of Enterobacteriaceae on wild tomato roots may be explained by several traits, in particular nutrient competition, motility, iron acquisition, membrane transport, stress response, and plant hormone biosynthesis. These results reveal a conserved microbiome signature associated with wild tomato rhizosphere in their center of origin. Just as the genomes of wild crop ancestors provide a valuable source of beneficial traits for breeding cultivated varieties, exploring their microbiome in native environments could uncover microbial taxa and traits that similarly contribute to crop growth and health.}, }
@article {pmid40594086, year = {2025}, author = {Leifels, M and Cheng, D and Cai, J and Nadhirah, N and Mohidin, AF and Santillan, E and Woo, Y and Hill, E and Wu, SW and Boon, N and Favere, J and Whittle, AJ and Wuertz, S}, title = {Biofilm detachment significantly affects biological stability of drinking water during intermittent water supply in a pilot scale water distribution system.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {22408}, pmid = {40594086}, issn = {2045-2322}, support = {3S85419//the FWO Flanders/ ; 3S85419//the FWO Flanders/ ; S006221N//FWO-SBO Biostable project/ ; S006221N//FWO-SBO Biostable project/ ; }, mesh = {*Biofilms/growth &amp; development ; *Drinking Water/microbiology ; *Water Supply ; *Water Microbiology ; RNA, Ribosomal, 16S/genetics ; Pilot Projects ; Flow Cytometry ; Water Quality ; Bacteria/genetics/classification ; Water Purification ; }, abstract = {Intermittent service provision (IWS) in piped drinking water distribution systems is practiced in countries with limited water resources; it leads to stagnant periods during which water drains completely from de-pressurized pipes, increasing the likelihood of biofilm detachment upon reconnection when water is supplied to the consumer and thus affecting water quality. Our study examines the impact of uninterrupted or continuous water supply (CWS) and IWS on microbial communities and biofilm detachment, using data from three 30-day experiments conducted in an above-ground drinking water testbed with 90-m long PVC pipes containing residual monochloramine. Flow cytometry (FCM) revealed a significant increase in total and intact cell concentrations when water was supplied intermittently compared to CWS, and the microbial alpha-diversity was significantly higher in CWS sections by both 16S rRNA gene metabarcoding and phenotypic fingerprinting of flow cytometry data. Nitrate levels in the water were significantly higher during initial intermittent flow due to the activity of nitrifying bacteria in biofilms exposed to stagnant water in pipes. Overall, biofilm detachment significantly affects the biological stability of drinking water delivered through IWS compared to CWS. We developed a novel biofilm detachment potential index derived from FCM data to estimate the minimum amount of water needed to be discarded before microbial cell counts and community composition return to baseline levels.}, }
@article {pmid40589459, year = {2025}, author = {Ametefe, EN and Thorsen, L and Danwonno, H and Agoha, RK and Glover, RLK and Dzogbefia, VP and Jespersen, L}, title = {Molecular Characterization of Culturable Yeasts and Nonspore-Forming Bacteria Associated With Fermented Kapok Seeds (Kantong), a Traditional Food Condiment in Ghana.}, journal = {International journal of food science}, volume = {2025}, number = {}, pages = {6452183}, pmid = {40589459}, issn = {2314-5765}, abstract = {Fermented kapok seeds, known as kantong in northern Ghana, serve as a traditional food condiment which provides flavor and improves the protein content of soups. In this study, the occurrence of yeasts, lactic acid bacteria (LAB), and other nonspore-forming bacteria in kantong was investigated. Microbial enumeration and phenotypic characterizations on isolated strains were performed. Molecular methods were also employed for grouping and identification of strains, and these included random amplification of polymorphic DNA (RAPD) using Escherichia coli phage-derived M13 primer (M13-PCR typing), repetitive element PCR typing (rep-PCR), and 16S rRNA gene sequencing. After a 48-h fermentation period, microbial load ranged from 4.77 ± 0.11 to 8.9 ± 0.1 log10 CFU/g. The pH of the fermenting condiment decreased from 6.5 to 4.7 during the fermentation period. A total of 190 LAB, 53 enterobacteria, and 39 yeasts were identified at species levels using both phenotypic and molecular methods. The LAB included Pediococcus acidilactici, Weissella paramesenteroides, Pediococcus pentosaceus, Weissella confusa, and Lactiplantibacillus plantarum; the enterobacteria isolated were Acinetobacter baumannii, Klebsiella pneumoniae, Enterococcus faecium, Escherichia coli, and Enterobacter cloacae; and the yeasts identified were Nakaseomyces glabratus, Cyberlindnera fabianii, Pichia kudriavzevii, and Saccharomyces cerevisiae. This work presents fermented kapok seeds as a reservoir of microorganisms, some of which could possess some technological properties which could be harnessed to enhance the nutritional value of Ghanaian foods as well as improve gut health as probiotics. It also reveals the presence of enterobacteria in this spontaneous fermentation, thus impacting the safety of the product and the need for starter culture development.}, }
@article {pmid40589000, year = {2025}, author = {Sharma, H and Al Noman, A and Ahmad, I and Tonni, SD and Mim, TJ and Afrose, F and Sharma, PD and Parvez, A and Tamanna, S and Al Azad, M and Pathak, R}, title = {Bridging Mind and Gut: The Molecular Mechanisms of microRNA, Microbiota, and Cytokine Interactions in Depression.}, journal = {Current gene therapy}, volume = {}, number = {}, pages = {}, doi = {10.2174/0115665232361169250617192348}, pmid = {40589000}, issn = {1875-5631}, abstract = {Depression is a complex psychiatric disorder that arises from various underlying biological mechanisms. In this review, the role of microRNAs (miRNAs) in modulating gut microbiotacytokine communication and their potential to unravel the pathophysiology of depression and develop novel therapeutic strategies are discussed. MiRNAs are small non-coding RNA molecules that have emerged as key regulators in the bidirectional signaling of the gut-brain axis by modulating gene expression and fine-tuning an intricate dialogue between the microbiota, immune system, and central nervous system. Results show how gut microbiota can shape miRNA expression in brain regions involved in mood regulation; conversely, evidence is accumulating, elucidating how miRNA perturbations can shape microbial ecology. Gut bacteria-derived short-chain fatty acids (SCFAs) fuel this nexus by exerting effects on neurogenesis, neurotransmitter synthesis, neuroinflammation, affective behavior alterations, and depressive-like phenotypes. Pro-inflammatory cytokines such as IL-6, TNF-α, and IL-1β are also known to be associated with depressive symptoms related to altered expression patterns of specific miRNAs across these disorders. This review exposes the novel potential biomarkers and therapeutic targets/strategies to develop innovative methods in the diagnosis and treatment of depression by exploring bidirectional relations among miRNAs, gut microbiota, and cytokines. The knowledge of these molecular networks and pathways has provided the opportunity for designing new-generation therapeutics such as phytobiotics, probiotics, psychobiotics, diet therapies, and nanomedicine based on miRNAs from a future perspective, which will revolutionize the management of mental disorders.}, }
@article {pmid40586542, year = {2025}, author = {Bruno, JS and Heidrich, V and Restini, FCF and Alves, TMMT and Miranda-Silva, W and Knebel, FH and Cóser, EM and Inoue, LT and Asprino, PF and Camargo, AA and Fregnani, ER}, title = {Dental biofilm serves as an ecological reservoir of acidogenic pathobionts in head and neck cancer patients with radiotherapy-related caries.}, journal = {mSphere}, volume = {10}, number = {7}, pages = {e0025725}, pmid = {40586542}, issn = {2379-5042}, mesh = {Humans ; *Dental Caries/microbiology/etiology ; *Biofilms/growth &amp; development ; *Head and Neck Neoplasms/radiotherapy/complications ; Male ; Female ; *Microbiota ; Middle Aged ; Aged ; *Bacteria/classification/genetics/isolation &amp; purification ; Adult ; *Radiotherapy/adverse effects ; }, abstract = {UNLABELLED: Radiotherapy-related caries (RRC) is an aggressive and debilitating oral toxicity that affects half of the patients who undergo radiotherapy for head and neck cancer. However, the etiology of RRC is not fully established, and there are no clinically validated methods for preventing it. To gain a better understanding of the risk factors and the microbiome's role in causing RRC, we compared clinicopathological characteristics, oncological treatment regimens, oral health condition, and the oral microbiota at three different oral sites of radiotherapy-treated patients with (RRC+) and without radiotherapy-related caries (RRC-). We observed no significant differences between these groups in the clinicopathological characteristics and treatment regimens. However, RRC+ patients were older and had poorer oral health conditions at the start of the radiotherapy treatment, with a lower number of teeth and a higher proportion of rehabilitated teeth. RRC+ patients had lower microbiota diversity and the dental biofilm of RRC+ patients displayed striking alterations in microbiome composition compared to RRC- patients, including enrichment of acidogenic species and altered metabolic potential, with a higher abundance of genes linked to energy-related pathways associated with the synthesis of amino acids and sugars. We also compared the microbiota of RRC+ tissue with conventional caries tissue, revealing lower bacterial diversity and enrichment of Lactobacillaceae members in RRC+. The insights into the irradiated oral microbiota enhance the understanding of RRC etiology and highlight the potential for microbial-targeted therapies in its prevention and treatment.<br><br>IMPORTANCE: This study focuses on a dedicated collection of diverse oral sites to comprehensively investigate microbial differences between patients who develop RRC and those who do not. RRC is a severe oral disease that profoundly impacts on the oral health and overall quality of life of cancer survivors. Leveraging shotgun metagenomics, we characterize the unique microbial variations in in vivo irradiated dental biofilms, unveiling novel insights into the microbial ecology of radiotherapy-treated patients. Furthermore, this research integrates extensive data on oral health and oncological profiles, providing a comprehensive understanding of the intricate relationship between oral microbial communities and the outcomes of radiotherapy-induced toxicity.}, }
@article {pmid40586525, year = {2025}, author = {Taylor, CC and Parks, ST}, title = {There and back again: navigating the return to in-person lab work post-pandemic for the Hybrid Microbial Ecology Course-based Undergraduate Research Experience (H-ME-CURE).}, journal = {Journal of microbiology &amp; biology education}, volume = {}, number = {}, pages = {e0024924}, doi = {10.1128/jmbe.00249-24}, pmid = {40586525}, issn = {1935-7877}, abstract = {The Microbial Ecology Course-based Undergraduate Research Experience (ME-CURE) has evolved over time to accommodate student needs and experiences. Prior to the COVID-19 pandemic, the lab was fully in-person, with a shift to in silico, remote learning from 2020 to 2023. In 2024, the ME-CURE was further adapted to return to in-person learning while maintaining some of the remote learning pedagogy. Significantly, the 2024 Hybrid ME-CURE (H-ME-CURE) built upon the findings of prior iterations of the lab such that students in the 2024 cohort entered with lab isolates, primers, and pathways that were ready for testing. This novel version of the ME-CURE synthesized years of in-person and remote, in silico learning to yield a deeper understanding of microbial pathways and improved molecular data including novel gene sequences for further testing. The goal of this work is to provide the tools that were used to help build the H-ME-CURE by combining past in-person and in silico learning methods of the ME-CURE.}, }
@article {pmid40585502, year = {2025}, author = {Zhu, M and Zhang, F and Qiu, Z and Zhao, S and Gao, S}, title = {White Light Orchestrates Mycoparasitic and Infection Activities by Regulating Expression of Effectors in Trichothecium roseum.}, journal = {Food science &amp; nutrition}, volume = {13}, number = {7}, pages = {e70396}, pmid = {40585502}, issn = {2048-7177}, abstract = {The fungal developmental processes are orchestrated by white light. Despite the genome assembly of Trichothecium roseum being available, the underlying molecular mechanisms of the white light-mediated developments of T. roseum remain obscure. It was found that white light impaired mycoparasitic activities against the wheat powdery mildew fungus and infection processes on tomato fruits in T. roseum. In vitro and in vivo, white light significantly impaired colony expansion and dramatically increased conidiation of T. roseum. RNA-seq analysis of T. roseum conidia was profiled to illustrate the light-mediated expression of genes. A total of 153 and 666 differentially expressed genes were identified between conidia treated with or without white light at 48- and 96-h post inoculation (hpi). Among genome-wide identified effectors, 8 and 36 effectors were differentially regulated by white light at 48 and 96 hpi, respectively. The core effectors, Tro004101, Tro006854, Tro008316, and Tro004104 were commonly downregulated by white light. Notably, white light regulated gene expression in key metabolic pathways including tryptophan metabolism (3 genes) and tyrosine metabolism (5 genes), as well as the HOG-MAPK signaling cascade. These results demonstrated that white light-compromised T. roseum mycoparasitic and infection activities might be achieved by regulating specific effector expression and differentially modulating metabolism and HOG-MAPK pathways. The genes detected by our transcriptome analysis may be crucial for mycoparasitism and infection by T. roseum and thus serve as targets for future functional analysis. Our findings provide new insights into the white light-orchestrated developments of an important agricultural and economical fungus and will potentially support efforts for the study of fungal effectors.}, }
@article {pmid40584121, year = {2025}, author = {Barrero, MAO and Varón-López, M and Peñuela-Sierra, LM}, title = {Competing microorganisms with exclusion effects against multidrug-resistant Salmonella Infantis in chicken litter supplemented with growth-promoting antimicrobials.}, journal = {Veterinary world}, volume = {18}, number = {5}, pages = {1127-1136}, pmid = {40584121}, issn = {0972-8988}, abstract = {BACKGROUND AND AIM: The widespread use of antibiotic growth promoters (AGPs) in poultry production has been implicated in altering gut microbiota and promoting the excretion of multidrug-resistant (MDR) bacteria into the environment. Salmonella enterica serovar Infantis (Salmonella Infantis [S.I]), a prevalent zoonotic pathogen, has demonstrated increasing resistance in poultry systems. This study aimed to evaluate the efficacy of natural control microorganisms (NCM), Bacillus subtilis and Lactobacillus plantarum, in reducing the abundance of MDR S.I in fresh chicken litter from birds raised with or without AGP supplementation. It also examined how physicochemical properties and microbial dynamics influence pathogen persistence.<br><br>MATERIALS AND METHODS: Microcosms were constructed using litter from broilers raised under two dietary regimes (with and without avilamycin). Treatments included combinations of AGP, S.I, and NCM. Bacterial enumeration was performed using selective media, and whole-genome sequencing of S.I was conducted to characterize antimicrobial resistance and virulence genes. Physicochemical parameters (pH, humidity, temperature, and ammonia) were measured and correlated with microbial loads. Antagonistic activity of NCM strains was assessed using agar diffusion assays.<br><br>RESULTS: Genome analysis revealed that S.I carried multiple resistance genes (e.g., blaCTX-M-65, tet(A), and sul1) and efflux systems conferring MDR. In vitro assays showed strong antagonism by L. plantarum and moderate activity by B. subtilis. In microcosms, S.I counts significantly decreased in the presence of both AGP and NCM, indicating synergistic inhibition. Conversely, in the absence of AGP, NCM had a limited effect. Statistical analyses showed strong correlations between microbial groups and physicochemical variables, particularly during later production stages.<br><br>CONCLUSION: The application of B. subtilis and L. plantarum in chicken litter significantly reduced S.I colonization under AGP supplementation, suggesting their potential as biocontrol agents. These findings support the development of integrated litter management strategies to mitigate zoonotic and resistant pathogen dissemination, particularly in AGP-using systems. However, the effectiveness of such interventions may vary across farms due to differences in microbial ecology and environmental conditions.}, }
@article {pmid40583496, year = {2025}, author = {Crull, S and Hammer, E and Mann, AE and O'Connell, LM and Soule, A and Griffith, E and Blouin, T and Brigmon, RL and Richards, VP}, title = {Seasonal Host Shifts for Legionella Within an Industrial Water-Cooling System.}, journal = {Environmental microbiology reports}, volume = {17}, number = {4}, pages = {e70132}, pmid = {40583496}, issn = {1758-2229}, support = {89303321CEM000080//Office of Environmental Management/ ; //The Laboratory Directed Research and Development (LDRD) program within the Savannah River National Laboratory (SRNL)/ ; }, mesh = {Seasons ; *Legionella/genetics/isolation &amp; purification/physiology/classification ; RNA, Ribosomal, 16S/genetics ; *Water Microbiology ; RNA, Ribosomal, 18S/genetics ; Acanthamoeba ; Phylogeny ; }, abstract = {Legionella is a genus of environmental bacteria containing pathogenic species such as Legionella pneumophila that are responsible for Legionnaires' disease, a potentially fatal respiratory infection. Disease aetiology can involve Legionella replication intracellularly within protists and this study aimed to characterise the Legionella-protist relationship to develop novel outbreak prevention targets. Water and sediment samples were collected from a water-cooling tower in South Carolina over a 6-month period. Concomitantly, multiple environmental parameters were recorded. Bacterial and eukaryotic communities were characterised using 16S rRNA gene V4 region and a 252 bp fragment of 18S rRNA gene, respectively. Co-occurrence network analyses were performed to elucidate Legionella-protist correlations through time. We found that Legionella correlated with different protists as the seasons progressed. Acanthamoeba correlated with Legionella in early spring followed by Vannella and Korotnevella in late spring and early summer, and were joined by Echinamoeba in mid-summer. Vannella and Acanthamoeba are known potential hosts for Legionella, while Korotnevella is a potential undocumented host. Of the environmental parameters, temperature showed strong correlation with protists genera, suggesting that Legionella abundance was driven by temperature-dependent protist availability. Our results highlight ecological shifts that are associated with elevated Legionella levels, which offers potential targets to help predict and prevent disease outbreaks.}, }
@article {pmid40583058, year = {2025}, author = {Cornet, L and Zaidi, SS and Li, J and Ngapout, Y and Shakir, S and Meunier, L and Callot, C and Marande, W and Hanikenne, M and Rombauts, S and Van de Peer, Y and Vanderschuren, H}, title = {A BAC-guided haplotype assembly pipeline increases the resolution of the virus resistance locus CMD2 in cassava.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {185}, pmid = {40583058}, issn = {1474-760X}, support = {F.4515.17//Fonds De La Recherche Scientifique - FNRS/ ; 1.B456.20//Fonds De La Recherche Scientifique - FNRS/ ; 833522/ERC_/European Research Council/International ; BOF.MET.2021.0005.01//Universitair Ziekenhuis Gent/ ; }, mesh = {*Manihot/genetics/virology ; *Disease Resistance/genetics ; *Plant Diseases/genetics/virology ; *Haplotypes ; *Chromosomes, Artificial, Bacterial/genetics ; Genome, Plant ; Chromosome Mapping ; }, abstract = {BACKGROUND: Cassava is an important crop for food security in the tropics where its production is jeopardized by several viral diseases, including the cassava mosaic disease (CMD) which is endemic in Sub-Saharan Africa and the Indian subcontinent. Resistance to CMD is linked to a single dominant locus, namely CMD2. The cassava genome contains highly repetitive regions making the accurate assembly of a reference genome challenging.<br><br>RESULTS: In the present study, we generate BAC libraries of the CMD-susceptible cassava cultivar (cv.) 60444 and the CMD-resistant landrace TME3. We subsequently identify and sequence BACs belonging to the CMD2 region in both cultivars using high-accuracy long-read PacBio circular consensus sequencing (ccs) reads. We then sequence and assemble the complete genomes of cv. 60444 and TME3 using a combination of ONT ultra-long reads and optical mapping. Anchoring the assemblies on cassava genetic maps reveals discrepancies in our, as well as in previously released, CMD2 regions of the cv. 60444 and TME3 genomes. A BAC-guided approach to assess cassava genome assemblies significantly improves the synteny between the assembled CMD2 regions of cv. 60444 and TME3 and the CMD2 genetic maps. We then performed repeat-unmasked gene annotation on CMD2 assemblies and identify 81 stress resistance proteins present in the CMD2 region, among which 31 were previously not reported in publicly available CMD2 sequences.<br><br>CONCLUSIONS: The BAC-assessed approach improved CMD2 region accuracy and revealed new sequences linked to virus resistance, advancing our understanding of cassava mosaic disease resistance.}, }
@article {pmid40581745, year = {2025}, author = {Richter, I and Büttner, H and Hertweck, C}, title = {Endofungal bacteria as hidden facilitators of biotic interactions.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {40581745}, issn = {1751-7370}, support = {//Deutsche Forschungsgemeinschaft/ ; 390713860//Germany's Excellence Strategy - EXC 2051/ ; 239748522//SFB 1127 ChemBioSys/ ; }, mesh = {*Symbiosis ; *Fungi/physiology ; *Bacteria/metabolism/genetics/classification ; Humans ; Plants/microbiology ; *Bacterial Physiological Phenomena ; Animals ; *Microbial Interactions ; Ecosystem ; }, abstract = {Fungi play pivotal roles in ecology and human health, driving nutrient cycling, supporting antibiotic production, and posing threats through toxin production. Less well-recognized, however, is their ability to harbour endosymbiotic bacteria. Advances in genomics and microscopy have revealed the prevalence of endofungal bacteria across diverse fungal phyla, though their functions are primarily inferred from genomic and transcriptomic studies. Recent functional research has begun to shed light on their influence on fungal pathogenicity, physiology, and ecology. These findings raise fundamental questions about the establishment and benefits of bacterial-fungal endosymbiosis, as well as the role of endosymbionts in mediating fungal interactions with other organisms. This review provides an in-depth analysis of the molecular mechanisms involved in the establishment and persistence of these symbioses. It also summarizes the current understanding of how endofungal bacteria impact fungal interactions with other organisms. For instance, endofungal bacteria contribute to the beneficial effects of fungi on plant health and fitness, protect fungal hosts from fungivorous predators, and enhance fungal virulence against plants, animals, and humans. These discoveries highlight the need for holistic investigations into bacterial-fungal endosymbiosis to fully understand their role in natural ecosystems. A deeper understanding of these multipartite partnerships offers exciting opportunities to improve ecosystem management, food safety, disease control, and crop productivity.}, }
@article {pmid40580837, year = {2025}, author = {Zhou, B and Niu, C and Mao, W and Wang, X and Wu, Z and Wang, Z}, title = {An electrochemical anaerobic dynamic membrane bioreactor for enhanced sludge digestion: Unveiling molecular interactions and microbial mechanisms.}, journal = {Water research}, volume = {285}, number = {}, pages = {124080}, doi = {10.1016/j.watres.2025.124080}, pmid = {40580837}, issn = {1879-2448}, abstract = {This study investigated the effects of stepwise external voltages on an electrochemical anaerobic dynamic membrane bioreactor (EC-AnDMBR) for anaerobic digestion of waste activated sludge. Increasing the applied voltage greatly mitigated membrane fouling, reduced the transmembrane pressure increase rate and enhanced both volatile solids digestion and biogas production. The dynamic membrane structure became looser with fewer biofouling substances, attributed to a 42.6 % increase in the sludge-membrane interaction energy barrier at higher voltages. Electrochemical analysis revealed improved electroactivity of the anaerobic sludge, as evidenced by increased conductivity and reduced internal resistance. The proton-coupled electron transfer (PCET) pathway was promoted, indicated by a significant increase in the hydrogen/deuterium kinetic isotope effect from 616 to 25,990. Molecular simulations of dissolved organic matter (DOM) showed an enrichment of amide and quinone groups, along with stronger hydrogen-bonding and π-cation interactions, which may contribute to the PCET process. Moreover, elevated voltages promoted more deterministic microbial community assembly and reduced upstream microbial immigration. Gene upregulation in organic metabolism, electron/proton transport, and methanogenesis further supported enhanced digestion performance via PCET pathway. These findings offer valuable insights into the molecular mechanisms and microbial ecology of EC-AnDMBR systems, advancing the development of more efficient and sustainable sludge treatment technologies.}, }
@article {pmid40578101, year = {2025}, author = {Liu, B and Jia, M and Nauwynck, W and Wang, J and Kundu, K and Springael, D and Boon, N}, title = {Hydrogen-powered bacteria enhance organic micropollutant degradation under starvation conditions.}, journal = {Water research}, volume = {285}, number = {}, pages = {124052}, doi = {10.1016/j.watres.2025.124052}, pmid = {40578101}, issn = {1879-2448}, abstract = {Organic micropollutants (OMPs) occur in natural aquatic environments at trace concentrations with suspected adverse effects on the ecosystem and human health. Microbial biodegradation plays a crucial role in OMP-elimination from drinking water resources. However, long-term OMP-biodegradation remains challenging since the metabolic activity of degrading strains is restricted by energy-limited conditions in treatment systems. Molecular hydrogen (H2) has been identified as a universally available energy source utilized by various bacteria under nutrient-starved conditions, and it can be hypothesized that H2 might also support OMP-degrading microbes when other energy carriers are scarce. The potential of H2 as a supporting energy source for OMP-degradation was tested by examining its effect on the biodegradation of 2,6-dichlorobenzamide (BAM) by Aminobacter niigataensis MSH1 and on the physiological status of the MSH1 cells during both nongrowth-linked (500 μg BAM/L) and growth-linked (10,000 μg BAM/L) regimes. MSH1 cells used as inoculum were either not or pre-exposed to H2 and were harvested at different growth phases. During the nongrowth-linked BAM biodegradation, MSH1 pre-exposed to H2 exhibited a 1.2 to 1.5-fold higher initial specific BAM biodegradation rate, resulting in more rapid BAM removal, likely due to the retention of more metabolically active cells, as suggested by a cell vitality assay. During the growth-linked biodegradation, MSH1 pre-exposed to H2 demonstrated accelerated growth with a 1.5-fold higher maximum specific growth rate, which coincided with an improved BAM removal. The positive effects of H2 were only evident for MSH1 cells harvested either at the stationary and/or starvation phase. Evidence of H2 metabolism was supported by H2 consumption measurements. Collectively, this study reveals that microbial H2 metabolism enables OMP-degrading bacteria to sustain metabolic activity under starvation conditions, offering a novel strategy to enhance long-term OMP-biodegradation.}, }
@article {pmid40577691, year = {2025}, author = {Quellhorst, HE and Ponce, MA and Holguin Rocha, AF and Sakka, MK and Tsintzou, G and Maille, JM and Vagelas, I and Madesis, P and Athanassiou, CG and Scully, ED and Zhu, KY and Morrison, WR}, title = {The capacity of 3 stored product insect species to vector microbes after increasing dispersal periods.}, journal = {Journal of economic entomology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jee/toaf123}, pmid = {40577691}, issn = {1938-291X}, support = {2024-67012-42439//USDA-NIFA/ ; }, abstract = {Prostephanus truncatus (Horn) (Coleoptera: Bostrichidae), Rhyzopertha dominica (F.) (Coleoptera: Bostrichidae), and Sitophilus zeamais Motschulsky (Coleoptera: Curculionidae) are 3 important stored product pests of maize, but there has been little work evaluating how they vector microbes. While there has been some work assessing the microbial ecology of S. zeamais, none has directly assessed whether they transfer microbes to new food patches. Thus, we evaluated the ability of both species to vector microbes when given the opportunity to forage on sterilized potato dextrose agar dishes after a 0, 24, or 72 h dispersal period in a sterilized container. We subsequently photographed the dishes at 3 and 5 d after introduction and quantified the microbial growth using ImageJ. In addition, we isolated unique morphotypes of fungi, extracted DNA and amplified the internal transcribed spacer 5/4 intergenic spacer region, then sequenced to determine fungal identity. We found that 3 species readily vectored several plant pathogenic microbes, including 21 taxa from more than 11 genera, notably Aspergillus spp. Increasing dispersal period (0, 24, 72 h) resulted in a third less microbial growth (mean microbial growth or mean greyscale value from 0 to 255) by S. zeamais after 72 h, while for P. truncatus it resulted in a 2.7-fold increase in microbial growth. Dispersal by S. zeamais (0, 24, 72 h) resulted in 6.6-fold more microbial growth than dispersal by P. truncatus. There was 1.5- to 3.7-fold more microbial growth after 5 d than 3 d by each species. This research has important implications for food safety in the postharvest environment, especially for maize production, storage, and processing.}, }
@article {pmid40577531, year = {2025}, author = {Duxbury, SJN and Raguideau, S and Cremin, K and Richards, L and Medvecky, M and Rosko, J and Coates, M and Randall, K and Chen, J and Quince, C and Soyer, OS}, title = {Niche formation and metabolic interactions contribute to stable diversity in a spatially structured cyanobacterial community.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf126}, pmid = {40577531}, issn = {1751-7370}, abstract = {Understanding how microbial communities maintain stable compositional diversity is a key question in microbial ecology. Studies from pairwise interactions and synthetic communities indicate that metabolic interactions and spatial organisation can influence diversity, but the relevance of these factors in more complex communities is unclear. Here we used a cyanobacterial enrichment community that consistently forms millimetre-scale granular structures, to investigate compositional diversity and its stability. Over a year of passaging in media without significant carbon source, we found stable co-existence of 17 species belonging to diverse bacterial phyla. Metagenomic analysis revealed polysaccharide breakdown genes and complementary vitamin biosynthesis pathways in these species. Supporting these findings, we show growth of several isolated species on cyanobacterial slime components and experimentally verify vitamin exchanges between two members of the community. Several species had genes for (an)oxygenic photosynthesis and sulfur cycling, the expression of which we verified via meta transcriptomics. Consistent with this, we found that the granular structures displayed oxygen gradients with anoxic interiors. Cyanobacteria and other bacteria were distributed on the periphery and insides of these structures, respectively. Perturbation of the community via glucose addition resulted in fold increases of the heterotrophs, whereas disturbing the community by continual shaking led to fold reductions in several heterotrophs, including anoxygenic phototrophs. In contrast, removal of vitamins supplementation did not consistently alter species coverages, due to predicted vitamin sharing amongst community members. Taken together, these findings indicate that spatial organisation, microenvironment niche formation and metabolic interactions contribute to community compositional diversity and stability.}, }
@article {pmid40577477, year = {2025}, author = {Li, B and Jiang, L and Johnson, T and Wang, G and Sun, W and Wei, G and Jiao, S and Gu, J and Tiedje, J and Qian, X}, title = {Global health risks lurking in livestock resistome.}, journal = {Science advances}, volume = {11}, number = {26}, pages = {eadt8073}, pmid = {40577477}, issn = {2375-2548}, mesh = {*Livestock/microbiology ; Animals ; *Global Health ; Humans ; Manure/microbiology ; Anti-Bacterial Agents/pharmacology ; Risk Assessment ; *Metagenome ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; }, abstract = {Livestock farming consumes more than 70% of global antibiotics annually, making livestock manures an important vector of anthropogenically influenced antibiotic resistance genes (ARGs). The global pattern of the livestock resistome, its driving mechanisms, and transmission potential to the clinic are not well assessed. We analyzed 4017 livestock manure metagenomes from 26 countries and constructed a comprehensive catalog of livestock ARGs and metagenome-assembled genomes. Livestock resistome is a substantial reservoir of known (2291 subtypes) and latent ARGs (3166 subtypes) and is highly connectable to human resistomes. We depicted the global pattern of livestock resistome and prevalence of clinically critical ARGs, highlighting the role of farm and human antibiotic stewardship in shaping livestock resistome. We developed a risk-assessment framework by integrating mobility potential, clinical significance, and host pathogenic relevance, and prioritized higher risk livestock ARGs, producing a predictive global map of livestock resistome risks that can help guide research and policy.}, }
@article {pmid40576334, year = {2025}, author = {Lee, EM and Srinivasan, S and Purvine, SO and Fiedler, TL and Leiser, OP and Proll, SC and Minot, SS and Djukovic, D and Raftery, D and Johnston, C and Fredricks, DN and Deatherage Kaiser, BL}, title = {Syntrophic bacterial and host-microbe interactions in bacterial vaginosis.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {40576334}, issn = {1751-7370}, support = {P41 GM103493/GM/NIGMS NIH HHS/United States ; S10 OD021562/OD/NIH HHS/United States ; R01 AI061628/AI/NIAID NIH HHS/United States ; U19 AI113173/AI/NIAID NIH HHS/United States ; S10OD021562/RI/ORIP NIH HHS/United States ; R01AI061628/NH/NIH HHS/United States ; GM103493/GM/NIGMS NIH HHS/United States ; U19 AI113173/NH/NIH HHS/United States ; }, mesh = {Female ; *Vaginosis, Bacterial/microbiology ; Humans ; Vagina/microbiology ; *Host Microbial Interactions ; *Bacteria/metabolism/classification/genetics/isolation &amp; purification ; Formates/metabolism ; Adult ; Putrescine/metabolism ; Proteomics ; Microbiota ; Bacterial Proteins/metabolism ; }, abstract = {Bacterial vaginosis (BV) is a common, polymicrobial condition of the vaginal microbiota that is associated with symptoms such as malodor and excessive discharge, along with increased risk of various adverse sequelae. Host-bacteria and bacteria-bacteria interactions are thought to contribute to the condition, but many of these functions have yet to be elucidated. Using untargeted metaproteomics, we identified 1068 host and 1418 bacterial proteins in a set of cervicovaginal lavage samples collected from 20 participants with BV and 9 who were negative for the condition. We identified Dialister micraerophilus as a major producer of malodorous polyamines and identified a syntrophic interaction between this organism and Fannyhessea vaginae that leads to increased production of putrescine, a metabolite characteristic of BV. Although formate synthesis has not previously been noted in BV, we discovered diverse bacteria associated with the condition express pyruvate formate-lyase enzymes in vivo and confirm these organisms secrete formic acid in vitro. Sodium hypophosphite efficiently inhibited this function in multiple taxa. We also found that the fastidious organism Coriobacteriales bacterium DNF00809 can metabolize formic acid secreted by Gardnerella vaginalis, representing another syntrophic interaction. We noted an increased abundance of the host epithelial repair protein transglutaminase 3 in the metaproteomic data, which we confirmed by enzyme-linked immunosorbent assay. Other proteins identified in our samples implicate Finegoldia magna and Parvimonas micra in the production of malodorous trimethylamine. Some bacterial proteins identified represent novel targets for future therapeutics to disrupt BV communities and promote vaginal colonization by commensal lactobacilli.}, }
@article {pmid40573780, year = {2025}, author = {Zhang, S and Luo, Z and Peng, J and Wu, X and Meng, X and Qin, Y and Zhu, F}, title = {Analysis of Cadmium Accumulation Characteristics Affected by Rhizosphere Bacterial Community of Two High-Quality Rice Varieties.}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {12}, pages = {}, pmid = {40573780}, issn = {2223-7747}, support = {2024YFD2301400//the National Key Research and Development Program of China/ ; 2024CX09//the Agricultural Science and Technology Innovation Project of Hunan Province, China/ ; }, abstract = {Cadmium-contaminated rice poses serious health risks through the bioaccumulation of Cd (cadmium) from soil to edible grains. Cd contamination disrupts soil microbial ecology and alters microbial diversity. However, the role of cultivar-specific rhizosphere microbial communities in modulating Cd uptake remains unclear. In this study, we aimed to elucidate the mechanism underlying variety-dependent rhizosphere microecological remodeling and Cd accumulation in two independently selected late rice varieties, Yuzhenxiang (YZX) and Xiangwanxian 12 (XWX12). Combining physiological and metagenomic analyses, we revealed variety-specific correlations between root Cd accumulation and dynamic changes in soil pH, soil available phosphorus, and rhizosphere bacteria. The key bacterial genera (Variibacter, Nitrospira) showed differential enrichment patterns under Cd stress. In contrast, Galella and Anaeromyxobacter likely reduce Cd bioavailability by modulating phosphorus availability. Overall, this study elucidates that rice cultivars indirectly shape Cd accumulation patterns via rhizosphere microbial remodeling, providing novel insights for microbial remediation strategies in Cd-contaminated farmland.}, }
@article {pmid40572127, year = {2025}, author = {Mohammadi, T and Ely, B}, title = {Dolichocephalovirinae Phages Exist as Episomal Pseudolysogens Across Diverse Soil Bacteria.}, journal = {Microorganisms}, volume = {13}, number = {6}, pages = {}, pmid = {40572127}, issn = {2076-2607}, abstract = {Interactions between bacteria and bacteriophages are important for the maintenance of soil communities. In this study, we characterized the giant bacteriophages found within diverse soil bacteria and 14 additional phages isolated directly from soil samples. Based on their genome sizes and genetic composition, we concluded that these phages belong to the Dolichocephalovirinae subfamily. In addition, we used pulsed-field gel electrophoresis to show that the genomes of these phages were present as episomal pseudolysogens in the cytoplasm of their host cells. These findings suggest that episomal phages are important components of soil microbial ecosystems. Understanding the interactions between bacteriophages and bacteria is essential for microbial ecology, as they influence nutrient cycling, community composition, and host evolution. Furthermore, these phage-bacteria dynamics offer potential applications in plant disease control, as bacteriophages could serve as biocontrol agents against soilborne pathogens, promoting sustainable agricultural practices.}, }
@article {pmid40569388, year = {2025}, author = {Dellicour, S and Gámbaro, F and Jacquot, M and Lequime, S and Baele, G and Gilbert, M and Pybus, OG and Suchard, MA and Lemey, P}, title = {Comparative performance of viral landscape phylogeography approaches.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {26}, pages = {e2506743122}, pmid = {40569388}, issn = {1091-6490}, support = {/WT_/Wellcome Trust/United Kingdom ; R01 AI153044/AI/NIAID NIH HHS/United States ; R01 AI162611/AI/NIAID NIH HHS/United States ; U19 AI135995/AI/NIAID NIH HHS/United States ; }, mesh = {Phylogeography/methods ; *RNA Viruses/genetics ; Phylogeny ; Genome, Viral ; Computer Simulation ; }, abstract = {The rapid evolution of RNA viruses implies that their evolutionary and ecological processes occur on the same time scale. Genome sequences of these pathogens therefore can contain information about the processes that govern their transmission and dispersal. Landscape phylogeographic approaches use phylogeographic reconstructions to investigate the impact of environmental factors and variables on the spatial spread of viruses. Here, we extend and improve existing approaches and develop three novel landscape phylogeographic methods that can test the impact of continuous environmental factors on the diffusion velocity of viral lineages. In order to evaluate the different methods, we also implemented two simulation frameworks to test and compare their statistical performance. The results enable us to formulate clear guidelines for the use of three complementary landscape phylogeographic approaches that have sufficient statistical power and low rates of false positives. Our open-source methods are available to the cientific community and can be used to investigate the drivers of viral spread, with potential benefits for understanding virus epidemiology and designing tailored intervention strategies.}, }
@article {pmid40569073, year = {2025}, author = {Kobiałka, M and Świerczewski, D and Walczak, M and Urbańczyk, W}, title = {Extremely distinct microbial communities in closely related leafhopper subfamilies: Typhlocybinae and Eurymelinae (Cicadellidae, Hemiptera).}, journal = {mSystems}, volume = {10}, number = {7}, pages = {e0060325}, pmid = {40569073}, issn = {2379-5077}, support = {2021/43/D/NZ8/02183//National Science Centre, Poland/ ; }, mesh = {Animals ; *Hemiptera/microbiology/classification ; *Microbiota ; Symbiosis ; In Situ Hybridization, Fluorescence ; High-Throughput Nucleotide Sequencing ; *Bacteria/classification/genetics/isolation &amp; purification ; Phylogeny ; }, abstract = {UNLABELLED: Among the Hemiptera insects, a widespread way of feeding is sucking sap from host plants. Due to their nutrient-poor diet, these insects enter into obligate symbiosis with their microorganisms involved in the synthesis of components essential for host survival. However, within the Cicadellidae family, there is a relatively large group of mesophyll feeders-Typhlocybinae-that is considered to be devoid of obligate symbiotic companions. In this work, we examine the composition of microorganisms in this subfamily and compare the results with their close relatives-the Eurymelinae subfamily. To study the microbiome, we used high-throughput next-generation sequencing (NGS, Illumina) and advanced microscopic techniques, such as transmission electron microscopy (TEM) and fluorescence in situ hybridization (FISH), in a confocal microscope. In the bodies of Typhlocybinae insects, we did not detect the presence of microorganisms deemed to be obligate symbionts. Their microbial communities consist of facultative symbionts, mainly alphaproteobacteria such as Wolbachia or Rickettsia as well as others that can be considered as facultative, including Spiroplasma, Acidocella, Arsenophonus, Sodalis, Lariskella, Serratia, Cardinium, and Asaia. On the other hand, the Eurymelinae group is characterized by a high diversity of microbial communities, both obligate and facultative, similar to other Cicadomorpha. We find co-symbionts involved in the synthesis of essential amino acids such as Karelsulcia, betaproteobacteria Nasuia, or gammaproteobacteria Sodalis. In other representatives, we observed symbiotic yeast-like fungi from the family Ophiocordycipitaceae or Arsenophonus bacteria inhabiting the interior of Karelsulcia bacteria. Additionally, we investigated some aspects of symbiont transmission and the phylogeny of symbiotic organisms and their hosts.<br><br>IMPORTANCE: The Typhlocybinae and Eurymelinae leafhoppers differ significantly in their symbiotic communities. They have different diets, as Typhlocybinae insects feed on parenchyma, which is richer in nutrients, while Eurymelinae, like most representatives of Auchenorrhyncha, consume sap from the phloem fibers of plants. Our work presents comprehensive studies of 42 species belonging to the two above-mentioned, and so far poorly known, Cicadomorpha subfamilies. Phylogenetic studies indicate that the insects from the studied groups have a common ancestor. The diet shift in the Typhlocybinae leafhoppers contributed to major changes in the composition of microorganisms inhabiting the body of these insects. Research on the impact of diet on the microbiome and the subsequent consequences on the evolution and adaptation of organisms plays an important role in the era of climate change.}, }
@article {pmid40567269, year = {2025}, author = {Mohamadi Nasrabadi, A and Eckstein, D and Mettke, P and Ghanem, N and Kallies, R and Schmidt, M and Mothes, F and Schaefer, T and Graefe, R and Bandara, CD and Maier, M and Liebert, UG and Richnow, H and Herrmann, H}, title = {A Virus Aerosol Chamber Study: The Impact of UVA, UVC, and H2O2 on Airborne Viral Transmission.}, journal = {Environment &amp; health (Washington, D.C.)}, volume = {3}, number = {6}, pages = {648-658}, pmid = {40567269}, issn = {2833-8278}, abstract = {The COVID-19 pandemic highlighted the urgent need to control airborne virus transmission, particularly in indoor environments with limited ventilation. This study evaluates the effectiveness of UVA and UVC irradiation, along with hydrogen peroxide (H2O2), in inactivating aerosolized viruses. A 19 m[3] virus aerosol simulation chamber, replicating indoor conditions, was used to simulate human respiratory emissions by aerosolizing Escherichia phage T4 (T4 phages) embedded in a pig mucin medium that mimics respiratory aerosols. Results showed a clear, dose-dependent reduction in viral genome copies with UVC exposure, where a dose of 129.9 mJ/cm[2] reduced over 99% of the viral genome copies. Although less efficient, UVA still contributed to virus inactivation, reducing detectable phages to 20% at 513.30 J/cm[2]. Mucin provided a protective effect, making virus removal more challenging. Hydrogen peroxide enhanced disinfection, with 1.6 ppm reducing viral genome copies by 78%, and higher concentrations (up to 16 ppm) achieving over 99% reduction in the dark condition. The combination of UVA/UVC with H2O2 further enhanced disinfection, eliminating detectable virus genome copies entirely. These findings underscore the potential for using combined UV light and chemical treatments to effectively mitigate airborne viral transmission in enclosed spaces.}, }
@article {pmid40566942, year = {2025}, author = {Kara, K and Yilmaz Öztaş, S and Baytok, E}, title = {In Vitro Ruminal Metagenomic Profiles and Ruminal Fermentation Variables of Aromatic Plant Pulps.}, journal = {Veterinary medicine and science}, volume = {11}, number = {4}, pages = {e70447}, pmid = {40566942}, issn = {2053-1095}, support = {TSA-2023-13007//Erciyes University Scientific Research Projects Unit/ ; }, mesh = {*Fermentation ; *Rumen/microbiology/metabolism/physiology ; Animals ; Cattle ; Metagenomics ; Animal Feed/analysis ; *Metagenome ; Gastrointestinal Microbiome ; Digestion ; }, abstract = {BACKGROUND: Aromatic plant residues remaining after aromatic oil extraction represent a promising alternative feed source due to their rich bioactive compound content and fibrous structure. However, their fermentative behaviour and microbial degradability in the rumen require evaluation.<br><br>OBJECTIVE: This study aimed to determine the nutrient composition, in vitro ruminal gas production, digestibility characteristics and fermentation end-products of aromatic plant pulps (sage, thyme, lavender and yarrow) obtained via hydrodistillation.<br><br>METHODS: Dried pulps were analysed for nutrient contents and subjected to in vitro ruminal fermentation for 24&#xa0;h. Gas production estimated metabolizable energy (ME), net energy for lactation (NEL), organic matter digestibility (OMd), ammonia nitrogen (NH3-N) and short-chain fatty acid (SCFA) profiles were evaluated. Microbial community composition was assessed via 16S rRNA-based metagenomics.<br><br>RESULTS: Yarrow pulp had the highest gas production, ME, NEL, OMd and SCFA concentrations (AA, BA, IVA, T-SCFA) (p&#xa0;<&#xa0;0.05). Thyme pulp exhibited the highest NH3-N levels (75.14&#xa0;mg/L), suggesting high rumen-degradable protein content. Sage pulp had the lowest NH3-N levels (60.93&#xa0;mg/L). Microbial composition shifted with fibre content; higher lignin (in lavender) was associated with lower Bacteroidota and higher Firmicutes abundance. Methanogenic archaea (Methanobrevibacter) were least abundant in thyme pulp (p&#xa0;<&#xa0;0.05).<br><br>CONCLUSION: Due to their fermentability and favourable microbial responses, aromatic plant pulps, particularly yarrow, show promise as functional ruminant feed ingredients. These byproducts may enhance ruminal fibre utilization while modulating microbial ecology and reducing methane-associated archaea.}, }
@article {pmid40564363, year = {2025}, author = {Luo, G and Cheng, Y and Xu, Y and Liu, J and Yang, W and Liu, J and Guo, B and Zhu, H}, title = {Monochromatic Light Impacts the Growth Performance, Intestinal Morphology, Barrier Function, Antioxidant Status, and Microflora of Yangzhou Geese.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {12}, pages = {}, pmid = {40564363}, issn = {2076-2615}, support = {32202622//National Natural Science Foundation of China/ ; 32102542//National Natural Science Foundation of China/ ; CX(24)1012//Jiangsu Agricultural Science and Technology Innovation Fund/ ; 2025SKLAB6-17//Open project of State Key Laboratory of Animal Biotech Breeding/ ; }, abstract = {This study investigates the effect of monochromatic light on the body weight (BW), melatonin concentration and its receptors expression levels, intestinal health, and gut microorganisms of Yangzhou geese. Green light (GL) significantly increased BW, melatonin and its receptor expression levels, villus height (VH) and villus height/crypt depth (VH/CD) ratio, superoxide dismutase (SOD), catalase (CAT), and total antioxidant capacity (T-AOC) activities, as well as the abundance of Synergistota and Prevotellaceae_UCG-001, compared with white light (WL). Blue light (BL) significantly increased the mRNA expression of melatonin membrane receptor 1a (Mel1a) and nuclear receptor 1α (RORα), VH and VH/CD ratio, CAT activity, cecal microbes diversity, and decreased malondialdehyde (MDA) levels. Red light (RL) significantly decreased average daily feed intake, reduced the abundances of Synergistota and Prevotellaceae_UCG-001, and increased Mel1a and RORα mRNA expression levels, MDA content, and cecum microbial diversity. Moreover, melatonin levels were significantly higher in the GL and BL groups compared to RL. Furthermore, the mRNA expression levels of Claudin-10, Occludin, and occludens-1 (ZO-1) were significantly upregulated under GL or BL exposures compared to the WL group, whereas RL only enhanced the expression levels of ZO-1. Spearman's correlation analysis revealed that the relative abundance of Prevotellaceae_UCG-001 exhibited positive correlations with BW, melatonin and its receptors expression, gut health, and antioxidant capacity. Overall, these findings suggested that GL exposure enhanced melatonin synthesis and its receptors expression, modulated intestinal homeostasis and microbial ecology, and ultimately increased goose BW.}, }
@article {pmid40562244, year = {2025}, author = {Costa, BF and Sawaya, C and Buren, JV and Smith, AL}, title = {Investigating anaerobic digestion microbiome resilience to high PFOA and PFOS mixtures during cometabolism.}, journal = {Bioresource technology}, volume = {435}, number = {}, pages = {132877}, doi = {10.1016/j.biortech.2025.132877}, pmid = {40562244}, issn = {1873-2976}, mesh = {*Fluorocarbons/metabolism ; *Alkanesulfonic Acids/metabolism ; Anaerobiosis ; *Microbiota/drug effects ; *Caprylates/metabolism ; Bioreactors/microbiology ; Methane/metabolism ; Sewage/microbiology ; Biodegradation, Environmental ; Biofuels ; }, abstract = {Anaerobic digestion (AD) is a reducing environment with high microbial diversity and potential for biotransformation of PFAS. Yet, their fate and impact on the microbial community remains poorly understood. This study evaluated the long-term impact (100 d) of perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS) spiked at10 mg/L (low) and 100 mg/L (high), respectively. Although resilient to complete system failure, high PFAS concentrations disrupted AD, evidenced by 25-50 % reduction in methane content, 45 -48 % reduction in cumulative biogas production, and accumulation of butyric acid. No significant decrease in PFAS concentration was observed in the liquid fraction after 100 d relative to the kill controls, indicating PFAS adsorption behavior. However, PFAS concentrations were temporally variable. Microbial community analysis revealed enrichment of notable AD groups, such as Firmicutes, Synergistetes, and Methanomassillicoccus phyla in high PFAS reactors, which underscores the potential for the microbiome adaptation and informs future strategies for PFAS-contaminated sludge treatment.}, }
@article {pmid40561955, year = {2025}, author = {Yasin, MU and Muhammad, S and Chen, N and Hannan, F and Afzal, M and Haider, Z and Ali, B and Ahmad, I and Rehman, M and Gan, Y}, title = {Nano-engineered biochar enhances soil microbial interactions and maize transcriptomic pathways for cadmium detoxification.}, journal = {Journal of hazardous materials}, volume = {495}, number = {}, pages = {139029}, doi = {10.1016/j.jhazmat.2025.139029}, pmid = {40561955}, issn = {1873-3336}, abstract = {Cadmium (Cd) contamination threatens agroecosystems and food security by degrading soil health, inducing plant oxidative stress, and reducing crop yields. Sustainable strategies integrating biochar (BC) with nanoparticles (NPs) for Cd immobilization and soil-plant-microbe restoration remain underexplored. Here, we demonstrate the efficacy of BC, nano-silicon (nSi), and nano-iron (nFe) to immobilize Cd, improve soil health and reprogram maize stress responses in Cd-contaminated soil. Soil Cd bioavailability, microbial networks, and maize transcriptomes were analyzed under varying BC-nSi-nFe formulations. Among these formulations, the BC + 25 % nSi + 75 % nFe + Cd (T6) composite reduced bioavailable Cd by 21 %, raised soil pH from 6.21 to 6.98, and enhanced soil enzyme activities (118-139 %). T6 improved maize biomass (115-119 %), reduced shoot Cd accumulation (78 %), and suppressed oxidative stress (67-75 % ROS reduction). This study presents transcriptomic evidence showing that BC-NPs composites mitigate Cd stress and modulate maize antioxidant defense and phytohormone signaling pathways, offering new insights into the molecular mechanisms underlying improved plant resilience. Soil microbial networks shifted toward metal-resistant taxa, with enriched glutathione metabolism and nitrogen fixation. BC-NPs composites offer a multidimensional remediation strategy, integrating nanomaterial science, microbial ecology, and plant molecular biology to mitigate Cd toxicity. This approach enhances soil-plant resilience, supporting sustainable agriculture in contaminated ecosystems.}, }
@article {pmid40561631, year = {2025}, author = {Ma, X and Li, Y and Niu, L and Grossart, HP and Shang, J and Zheng, J and Wu, J}, title = {Salinity regulates nutrient cycling via top-down and bottom-up forces in artificial cut-off tidal channels: Insights from multitrophic microbiota.}, journal = {Water research}, volume = {285}, number = {}, pages = {124037}, doi = {10.1016/j.watres.2025.124037}, pmid = {40561631}, issn = {1879-2448}, abstract = {Artificial cut-off of natural tidal meanders for flood control has substantially altered microbial communities and their role in nutrient cycling, yet the lack of comprehensive investigations into these specific anthropogenic impacts introduces greater uncertainty regarding the resultant water quality of nutrient-enriched estuaries. Here, we investigated how planktonic multitrophic microbiota and their mediated nutrient cycling respond to artificial meander cut-off using the environmental DNA (eDNA) approach. Results showed that despite the decline in α diversity of multitrophic microbiota, the nutrient cycling potential of the water column was enhanced 2.91-fold in the straight tidal channel. The artificial cut-off restructured the microbial food web, with trophic transfer efficiency from basal species to protozoa increasing. Salinity was identified to be the key environmental driver, mitigating the negative impact of decreased biodiversity on estuarine nutrient cycling potential by intensifying protozoan predation on heterotrophic bacteria (top-down forces). Additionally, salinity further enhanced environmental selection (bottom-up forces), reducing heterotrophic bacterial diversity while promoting the proliferation of functional microbial taxa, such as Comamonadaceae, Chitinophagaceae, and Rhodocyclaceae. This study offers novel insights into nutrient cycling in artificial straight tidal channels and provides critical foundations for optimizing restoration and management strategies in anthropogenically modified tidal river.}, }
@article {pmid40560449, year = {2025}, author = {de Meireles, DA and Souza, T and de A A Carneiro, K and da S Fraga, V and de O Dias, B and da S Batista, D and Martins, EL and de Lima, AFL and Dos Santos Nascimento, G and Campos, MCC}, title = {Treated Wastewater Irrigation Enhances Plant Biomass, Soil Fertility, and Rhizosphere Microbial Activity in C4 and CAM species Grown on a Degraded Planosol.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {7}, pages = {804}, doi = {10.1007/s10661-025-14271-4}, pmid = {40560449}, issn = {1573-2959}, mesh = {*Wastewater/chemistry ; *Agricultural Irrigation/methods ; *Soil Microbiology ; *Soil/chemistry ; *Rhizosphere ; Biomass ; *Waste Disposal, Fluid/methods ; Brazil ; }, abstract = {The Brazilian semi-arid region, marked by erratic rainfall and severely degraded soils, presents critical challenges for sustainable agriculture. In this context, the reuse of treated domestic wastewater-collected from a septic tank and anaerobic filter system-offers a promising strategy to enhance plant productivity and rehabilitate soil conditions, particularly within the Caatinga biome. This study evaluated the long-term (four-year) effects of irrigation with pure water versus treated domestic wastewater on plant dry biomass, soil fertility, and rhizospheric microbial activity in a degraded Planosol. Two plant types were assessed: a C4 species (Mimosa caesalpiniifolia) and a CAM species (Opuntia atropes). Results demonstrated that treated wastewater irrigation significantly increased dry biomass, with a 12.18% increase in the C4 species and a 29.33% increase in the CAM species. Soil chemical fertility improved notably, with wastewater application raising soil pH by 5.0%, increasing soil organic carbon by 87.9%, and enhancing nutrient availability, including nitrogen, potassium, magnesium, and sodium. A 37.5% reduction in exchangeable aluminum further indicated mitigation of soil acidity. Microbial responses varied between species: while soil respiration increased in both rhizospheres-more prominently in CAM species-microbial biomass carbon rose significantly in the C4 rhizosphere but declined in CAM, suggesting species-specific microbial interactions. These findings support the potential of treated domestic wastewater as a nutrient-rich, low-cost irrigation alternative for improving plant performance and soil quality in semi-arid degraded lands. Nevertheless, potential risks-including salinity build-up and pathogen persistence-necessitate long-term monitoring and further environmental safety assessments. By integrating plant physiology, soil chemistry, and microbial ecology, this study offers a comprehensive approach to evaluating wastewater reuse as a sustainable agricultural and ecological restoration practice in the Caatinga biome.}, }
@article {pmid40559796, year = {2025}, author = {Popov, IV and Peshkova, DA and Lukbanova, EA and Tsurkova, IS and Emelyantsev, SA and Krikunova, AA and Malinovkin, AV and Chikindas, ML and Ermakov, AM and Popov, IV}, title = {Gut Microbiota Dynamics in Hibernating and Active Nyctalus noctula: Hibernation-Associated Loss of Diversity and Anaerobe Enrichment.}, journal = {Veterinary sciences}, volume = {12}, number = {6}, pages = {}, pmid = {40559796}, issn = {2306-7381}, support = {23-14-00316//Russian Science Foundation/ ; 075-10-2025-017//Ministry of Science and Higher Education of the Russian Federation/ ; }, abstract = {Hibernation in mammals entails profound physiological changes that are known to impact host-associated microbial communities, yet its effects on the gut microbiota of synanthropic bats remain underexplored. In this study, we investigated the gut bacterial composition and diversity of Nyctalus noctula before and during hibernation using high-throughput 16S rRNA amplicon sequencing. Fecal samples from individually banded bats were collected under controlled conditions at a rehabilitation center and analyzed for alpha and beta diversity, as well as differential taxonomic abundance. Hibernation was associated with a marked reduction in microbial diversity according to the Shannon and Simpson indices and a distinct restructuring of gut communities based on the Bray-Curtis dissimilarity index. Active bats exhibited a diverse microbiota enriched in facultative anaerobes, including Lactococcus, Enterococcus, and Escherichia-Shigella, while hibernating individuals were dominated by obligate anaerobes, such as Romboutsia and Paeniclostridium. These findings suggest a contraction and functional specialization of the gut microbiota during torpor, potentially reflecting adaptations to fasting, hypothermia, and reduced gut motility. Our results demonstrate that the bat's gut microbiome is highly responsive to physiological status and underscore the importance of microbial ecology for understanding the host's energy balance and health under seasonal contexts.}, }
@article {pmid40559651, year = {2025}, author = {Wimmer, BC and Dwan, C and De Medts, J and Duysburgh, C and Rotsaert, C and Marzorati, M}, title = {Undaria pinnatifida Fucoidan Enhances Gut Microbiome, Butyrate Production, and Exerts Anti-Inflammatory Effects in an In Vitro Short-Term SHIME[®] Coupled to a Caco-2/THP-1 Co-Culture Model.}, journal = {Marine drugs}, volume = {23}, number = {6}, pages = {}, pmid = {40559651}, issn = {1660-3397}, support = {n.a.//Marinova Pty Ltd., 249 Kennedy Drive, Cambridge, TAS 7170, Australia/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Polysaccharides/pharmacology/isolation &amp; purification ; *Undaria/chemistry ; *Anti-Inflammatory Agents/pharmacology ; Caco-2 Cells ; Coculture Techniques ; *Butyrates/metabolism ; THP-1 Cells ; Colon/microbiology/drug effects ; Feces/microbiology ; Cytokines/metabolism ; Adult ; Fatty Acids, Volatile/metabolism ; Edible Seaweeds ; }, abstract = {Fucoidans have demonstrated a wide range of bioactivities including immune modulation and benefits in gut health. To gain a deeper understanding on the effects of fucoidan from Undaria pinnatifida (UPF) on the colonic microbiome, the short-term Simulator of the Human Intestinal Microbial Ecosystem[®], a validated in vitro gut model, was applied. Following a three-week intervention period on adult faecal samples from three healthy donors, microbial community activity of the colonic microbiota was assessed by quantifying short-chain fatty acids while composition was analysed utilising 16S-targeted Illumina sequencing. Metagenomic data were used to describe changes in community structure. To assess the secretion of cytokines, co-culture experiments using Caco-2 and THP1-Blue™ cells were performed. UPF supplementation over a three-week period had a profound butyrogenic effect while also enriching colonic microbial diversity, consistently stimulating saccharolytic genera, and reducing genera linked with potentially negative health effects in both regions of the colon. Mild immune modulatory effects of UPF were also observed. Colonic fermentation of UPF showed anti-inflammatory properties by inducing the secretion of the anti-inflammatory cytokines IL-6 and IL-10 in two out of three donors in the proximal and distal colon. In conclusion, UPF supplementation may provide significant gut health benefits.}, }
@article {pmid40558970, year = {2025}, author = {Vieira, RIM and Peixoto, ADS and Monclaro, AV and Ricart, CAO and Filho, EXF and Miller, RNG and Gomes, TG}, title = {Fungal Coculture: Unlocking the Potential for Efficient Bioconversion of Lignocellulosic Biomass.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {11}, number = {6}, pages = {}, pmid = {40558970}, issn = {2309-608X}, support = {00193-00002388/2023-21//Foundation for Research Support of the Federal District/ ; }, abstract = {Microbial decomposition of persistent natural compounds such as phenolic lignin and polysaccharides in plant cell walls plays a crucial role in the global carbon cycle and underpins diverse biotechnological applications. Among microbial decomposers, fungi from the Ascomycota and Basidiomycota phyla have evolved specialized mechanisms for efficient lignocellulosic biomass degradation, employing extracellular enzymes and synergistic fungal consortia. Fungal coculture, defined as the controlled, axenic cultivation of multiple fungal species or strains in a single culture medium, is a promising strategy for industrial processes. This approach to biomass conversion offers potential for enhancing production of enzymes, biofuels, and other high-value bioproducts, while enabling investigation of ecological dynamics and metabolic pathways relevant to biorefinery operations. Lignocellulosic biomass conversion into fuels, energy, and biochemicals is central to the bioeconomy, integrating advanced biotechnology with sustainable resource use. Recent advancements in -omics technologies, including genomics, transcriptomics, and proteomics, have facilitated detailed analysis of fungal metabolism, uncovering novel secondary metabolites and enzymatic pathways activated under specific growth conditions. This review highlights the potential of fungal coculture systems to advance sustainable biomass conversion in alignment with circular bioeconomy goals.}, }
@article {pmid40557448, year = {2025}, author = {Lingua, MS and Sabatino, ME and Cuatrin, A and Salvucci, E and Blajman, JE and Páez, RB and Wunderlin, DA and Baroni, MV}, title = {From waste to worth: stability, bioaccessibility, and cellular antioxidant activity of microencapsulated red grape pomace phenolics.}, journal = {Journal of the science of food and agriculture}, volume = {}, number = {}, pages = {}, doi = {10.1002/jsfa.70010}, pmid = {40557448}, issn = {1097-0010}, support = {//This work was supported by the National Institute of Agricultural Technology (INTA, Argentina) (Projects 2019-PD-I152-A537 and 2019-PE-I150-A5) and the National Agency of Scientific and Technological Promotion (FONCyT, Argentina), and Argentine Wine Corporation (COVIAR) (Project PICTO-COVIAR-2017-0123)./ ; }, abstract = {BACKGROUND: Red grape pomace (RGP) is a recognized winery by-product due to its phenolic profile with valuable antioxidant power and beneficial health properties. Following the latest trends in food science and technology, this study valorizes the use of RGP to obtain a food ingredient rich in antioxidant phenolics. An integrated approach was proposed, investigating the production by spray drying of easy-to-handle microparticles, rich in stable compounds with antioxidant properties demonstrated after simulated digestion using in vitro assays and Caco-2 cells. The changes in microbiota composition after fermentation were also studied.<br><br>RESULTS: Among investigated wall materials, maltodextrin/skimmed milk powder (1:1) 300&#x2009;g&#x2009;L[-1] offered the highest drying yield, appropriate moisture, solubility, and adequate microparticle morphology, as well as the best stability of polyphenols. Encapsulation improved the protection of phenolic compounds and the in vitro antioxidant capacity during 120&#x2009;days of storage at 4 and 25&#x2009;&#xb0;C, as compared to those unencapsulated. Microencapsulated polyphenols bioaccessibility was evident in 15 out of 22 compounds initially quantified, with 6.6% potentially absorbed. The polyphenols from microcapsules modulated positively the microbial ecology after colonic fermentation. Those derived from intestinal digestion demonstrated the highest capacity to reduce the reactive oxygen species under oxidative stress conditions in Caco-2 cells.<br><br>CONCLUSION: RGP could be used in the development of new food ingredients as a potential candidate for health promotion. This represents the first report on the benefits of RGP microcapsules as a food ingredient, validating its final biological effects in a cellular model considering the processing and digestion effects. &#xa9; 2025 Society of Chemical Industry.}, }
@article {pmid40556136, year = {2025}, author = {Long, Y and Li, Y and Zhang, J and Liu, J and Han, Q and Cao, Y and Jiang, Y and Liu, C and Hu, Y and Wang, G and Zhang, X and Jin, J and Semenov, M and Han, G and Liu, X and Yu, Z}, title = {Unconventional Nitrogen Fixation and Adaptive Genomics of a New Neorhizobium glycines sp. nov., A Promising Soybean Symbiont.}, journal = {Plant, cell &amp; environment}, volume = {}, number = {}, pages = {}, doi = {10.1111/pce.70046}, pmid = {40556136}, issn = {1365-3040}, support = {//This study was funded by the National Key R &amp; D Program of China (2021YFD1500400), Strategic Priority Research Program of Chinese Academy of Sciences (XDA28020201), National Natural Science Foundation of China (32172123, 42207399)./ ; }, }
@article {pmid40555367, year = {2025}, author = {McGrath, AH and Steinberg, PD and Egan, S and Kjelleberg, S and Marzinelli, EM}, title = {Disruption of host-associated and benthic microbiota affects reproductive output and settlement of a habitat-forming macroalga.}, journal = {Proceedings. Biological sciences}, volume = {292}, number = {2049}, pages = {20250729}, pmid = {40555367}, issn = {1471-2954}, support = {//University of Sydney/ ; //Australian Research Council/ ; //Ecological Society of Australia/ ; }, mesh = {*Microbiota/drug effects ; Reproduction ; Ecosystem ; *Rhodophyta/microbiology/physiology ; Anti-Bacterial Agents/pharmacology ; }, abstract = {The reproduction and establishment of habitat-forming species are key processes affecting their persistence and associated biodiversity. In marine systems, microbial communities associated with habitat-forming macroalgae can influence various aspects of host performance; however, the role of these microorganisms in influencing macroalgal reproduction and settlement is poorly understood. Using a dominant habitat-forming macroalga on Australian rocky shores, Hormosira banksii, we manipulated host- and benthic-associated microbiota to determine the relative importance of microorganisms to reproductive output (number of viable eggs released) and settlement (settlement and morphogenesis of algal zygotes). Disruption of the host microbiota using antibiotics decreased reproductive output after 2 weeks, with the effect dependent on the type of antibiotic used. Disruption of host- and benthic-associated microbiota, in combination, caused a significant decrease in settlement of H. banksii zygotes, with the combined disruption having the greatest impact on settlement success. Our results demonstrate the importance of host-associated microbiota in macroalgal reproduction and an interactive effect of host- and benthic-associated microbiota on settlement-a key ecological process with important implications for host fitness and potentially ecosystem persistence.}, }
@article {pmid40553410, year = {2025}, author = {Bota, JL and Baum, C and Gawronski, S and Grafe, TU and Kerth, G and Schöner, MG and Schöner, CR}, title = {UV treatment of the digestive fluid of Nepenthes hemsleyana pitcher plants affects their digestive process, possibly via reducing microbial inquilines.}, journal = {Oecologia}, volume = {207}, number = {7}, pages = {108}, pmid = {40553410}, issn = {1432-1939}, support = {SCHO1740/1-1//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Ultraviolet Rays ; Animals ; Digestion/radiation effects ; }, abstract = {Interactions with microbes are ubiquitous, and many of them are essential for the survival and success of plants. In Nepenthes pitcher plants, they occur as part of a diverse community of organisms, so-called inquilines, that live inside the digestive fluid of the pitcher traps. However, evidence is ambiguous regarding the role of microbial inquilines: they may complement the plants' prey digestion, fix atmospheric N, act as competitors that reduce plant-available nutrients or affect the plants in other ways unrelated to the breakdown of prey. In a field experiment on Borneo, we investigated the effect of UV disinfection of the digestive fluid on prey digestion of N. hemsleyana that captures and digests insects as well as bat faeces in its pitchers. We show that in the short term, the photosynthetic performance of plants with UV-treated digestive fluids decreases compared to untreated plants, likely due to lower abundances of microbial inquilines. However, at the end of 2 months, responses of pitcher plants with UV-treated and untreated digestive fluids tend to equalise. Nutrient source, whether from insects or bat faeces, does not influence prey digestion. We expect our findings to be a starting point for unveiling the ecological role of microbial inquilines in pitcher plants and how they interact with other inquiline groups of higher trophic levels. Ultimately, this will also help to improve understanding of the functioning and evolution of convergent interactions in other carnivorous plants.}, }
@article {pmid40553254, year = {2025}, author = {Wu, BX and Ma, JY and Huang, XC and Liang, XS and Ning, BL and Wu, Q and Wang, SZ and Zhou, JH and Fu, WB}, title = {Acupuncture as A Potential Therapeutic Approach for Tourette Syndrome: Modulation of Neurotransmitter Levels and Gut Microbiota.}, journal = {Chinese journal of integrative medicine}, volume = {31}, number = {8}, pages = {735-742}, pmid = {40553254}, issn = {1993-0402}, mesh = {Animals ; *Tourette Syndrome/therapy/microbiology/metabolism ; *Gastrointestinal Microbiome ; *Neurotransmitter Agents/metabolism ; *Acupuncture Therapy ; Male ; Mice, Inbred C57BL ; Mice ; }, abstract = {OBJECTIVE: To investigate the effects of acupuncture on the neurotransmitter levels and gut microbiota in a mouse model of Tourette syndrome (TS).<br><br>METHODS: Thirty-six male C57/BL6 mice were randomly divided into 4 groups using a random number table method: 3,3'-iminodipropionitrile (IDPN) group, control group, acupuncture group, and tiapride group, with 9 mice in each group. In the IDPN group, acupuncture group, and tiapride group, mice received daily intraperitoneal injections of IDPN (300 mg/kg body weight) for 7 consecutive days to induce stereotyped behaviors. Subsequently, in the acupuncture intervention group, standardized acupuncture treatment was administered for 14 consecutive days to IDPN-induced TS model mice. The selected acupoints included Baihui (DU 20), Yintang (DU 29), Waiguan (SJ 5), and Zulinqi (GB 41). In the tiapride group, mice were administered tiapride (50 mg/kg body weight) via oral gavage daily for 14 consecutive days. The control group, IDPN group, and acupuncture group received the same volume of saline orally for 14 consecutive days. Stereotypic behaviors were quantified through behavioral assessments. Neurotransmitter levels, including dopamine (DA), glutamate (Glu), and aspartate (ASP) in striatal tissue were measured using enzyme-linked immunosorbent assay. Dopamine transporter (DAT) expression levels were additionally quantified through quantitative polymerase chain reaction (qPCR). Gut microbial composition was analyzed through 16S ribosomal RNA gene sequencing, while metabolic profiling was conducted using liquid chromatography-mass spectrometry (LC-MS).<br><br>RESULTS: Acupuncture administration significantly attenuated stereotypic behaviors, concurrently reducing striatal levels of DA, Glu and ASP concentrations while upregulating DAT expression compared with untreated TS controls (P<0.05 or P<0.01). Comparative analysis identified significant differences in Muribaculaceae (P=0.001), Oscillospiraceae (P=0.049), Desulfovibrionaceae (P=0.001), and Marinifilaceae (P=0.014) following acupuncture intervention. Metabolomic profiling revealed alterations in 7 metabolites and 18 metabolic pathways when compared to the TS mice, which involved various amino acid metabolisms associated with DA, Glu, and ASP.<br><br>CONCLUSIONS: Acupuncture demonstrates significant modulatory effects on both central neurotransmitter systems and gut microbial ecology, thereby highlighting its dual therapeutic potential for TS management through gut-brain axis regulation.}, }
@article {pmid40548738, year = {2025}, author = {Mattelin, V and Van Landuyt, J and Kerkhof, F-M and Minnebo, Y and Boon, N}, title = {Integrating taxonomic and phenotypic information through FISH-enhanced flow cytometry for microbial community dynamics analysis.}, journal = {Microbiology spectrum}, volume = {13}, number = {8}, pages = {e0197324}, pmid = {40548738}, issn = {2165-0497}, support = {1288224N//Fonds Wetenschappelijk Onderzoek/ ; HBC.2019.2622//Agentschap Innoveren en Ondernemen/ ; BOF.BAS.2022.0014.01//Bijzonder Onderzoeksfonds UGent/ ; 30770923//Fonds Wetenschappelijk Onderzoek/ ; }, mesh = {*Flow Cytometry/methods ; *In Situ Hybridization, Fluorescence/methods ; *Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Humans ; *Microbiota ; Phenotype ; Gastrointestinal Microbiome ; Biodiversity ; Ecosystem ; }, abstract = {UNLABELLED: Flow cytometry is a powerful tool to monitor microbial communities, as it allows tracking both changes in the subpopulations and cell numbers at high throughput and a low sample cost. This information can be combined in a phenotypic fingerprint that can be leveraged for diversity analysis. However, as isogenic individuals can manifest phenotypic diversity, for example, due to differing physiological state and phenotypic plasticity, combining the phenotypic information with taxonomic information adds an extra dimension for describing the dynamics of a microbial community. In this research, taxonomic information was incorporated in the microbial fingerprint through fluorescent in situ hybridization (FISH) at a single-cell level. To validate this concept and explore its versatility, two ecosystems with different micro-biodiversity were considered. In the first environment, marine bacteria were monitored for plastic biodegradation in a trickling filter, and in the second, an in vitro simulated human gut microbiome was followed over time. Samples were prepared using different (staining) methods, including FISH, and beta diversity analysis was used to evaluate the level of distinction between differently treated groups in both environments. As a reference to correlate increased distinction with the incorporation of taxonomic information, 16S rRNA gene sequencing was used. Finally, a predictive algorithm was trained to correctly classify samples in the differently treated groups. The results showed that the implementation of FISH in flow cytometry provides more information on a single-cell level to answer specific scientific questions, like distinguishing between phenotypically similar communities or following a specific taxonomic group over time.<br><br>IMPORTANCE: Understanding microbial communities is crucial for elucidating their role in maintaining ecosystem health and stability. Researchers are increasingly interested in studying microbial communities by looking at not just their genetic makeup but also their physical traits and functions. In our study, we used common techniques like fluorescence in situ hybridization and flow cytometry, along with advanced data analysis, to better understand these communities. This combination allowed us to gather and use data more effectively, demonstrating that these easy-to-use methods, when paired with proper analysis, can enhance our understanding of changing microbial ecosystems.}, }
@article {pmid40545777, year = {2025}, author = {VanWallendael, A and Wijewardana, C and Bonnette, J and Vormwald, L and Fritschi, FB and Boe, A and Chambers, S and Mitchell, RB and Rouquette, FM and Wu, Y and Fay, PA and Jastrow, JD and Lovell, JT and Juenger, TE and Lowry, DB}, title = {Local adaptation of both plant and pathogen: an arms-race compromise in switchgrass rust.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.70313}, pmid = {40545777}, issn = {1469-8137}, support = {DE-AC02-06CH11357//Biological and Environmental Research/ ; DE-SC0014156//Biological and Environmental Research/ ; DE-SC0017883//Biological and Environmental Research/ ; DE-SC0018409//Biological and Environmental Research/ ; 1832042//Division of Environmental Biology/ ; DE-AC02-05CH11231//Joint Genome Institute/ ; }, abstract = {In coevolving species, parasites locally adapt to host populations as hosts locally adapt to resist parasites. Parasites often outpace host local adaptation since they have rapid life cycles, but host diversity, the strength of selection, and external environmental influence can result in complex outcomes. To better understand local adaptation in host-parasite systems, we examined locally adapted switchgrass (Panicum virgatum), and its leaf rust pathogen (Puccinia novopanici) across a latitudinal range in North America. We grew switchgrass genotypes in 10 replicated multiyear common gardens, measuring rust severity from natural infection in a 'host reciprocal transplant' framework for testing local adaptation. We conducted genome-wide association mapping to identify genetic loci associated with rust severity. Genetically differentiated rust populations were locally adapted to northern and southern switchgrass, despite host local adaptation to environmental conditions in the same regions. Rust resistance was polygenic, and distinct loci were associated with rust severity in the north and south. We narrowed a previously identified large-effect quantitative trait locus for rust severity to a candidate YELLOW STRIPE-LIKE gene and linked numerous other loci to defense-related genes. Overall, our results suggest that both hosts and parasites can be simultaneously locally adapted, especially when parasites impose less selection than other environmental factors.}, }
@article {pmid40542918, year = {2025}, author = {Zhang, W and Li, XJ and Liu, F and Zhang, J and Tian, J and Gao, Y}, title = {Fungen: clustering and correcting long-read metatranscriptomic data for exploring eukaryotic microorganisms.}, journal = {Science China. Life sciences}, volume = {}, number = {}, pages = {}, pmid = {40542918}, issn = {1869-1889}, abstract = {Long-read metatranscriptomics is a powerful and cost-effective technology for elucidating the genetic diversity and expression dynamics of active eukaryotic microorganisms by characterizing full-length transcripts. However, its potential has been limited by the lack of high-quality reference genomes and high sequencing error rates. We present Fungen, a reference-free tool that constructs accurate transcripts from long-read metatranscriptomic data through read clustering and error correction. Fungen achieves superior accuracy in transcript determination while significantly reducing memory usage and offering a 22 to 56-fold speed improvement over existing methods. This novel approach overcomes the challenges posed by sequence similarity among closely related species, enabling the analysis of deeply sequenced metatranscriptomes by generating reliable gene clusters and accurate sequences. Two applications showcase Fungen's capabilities to perform high-resolution taxonomic assignments and gene profiling in marine direct RNA datasets, as well as resolving reliable annotation identities in full-length rRNA targeted sequencing datasets. When applied to soil metatranscriptomic data, Fungen offers valuable insights into the in situ fungal composition and gene expression dynamics, revealing specialized life strategies of plant-pathogenic fungi in soil environments. Overall, Fungen provides a fast, scalable, and accurate solution for analyzing complex metatranscriptomic datasets, paving the way for a comprehensive understanding of eukaryotic diversity and function from long-read sequencing data.}, }
@article {pmid40542710, year = {2025}, author = {Susukida, S and Miyazawa, K and Ichikawa, H and Muto, K and Yoshimi, A and Kumagai, T and Kato, Y and Abe, K}, title = {Improved Mixing Properties of Stirred Fermentation of an Aspergillus oryzae Hyphal Dispersion Mutant.}, journal = {Biotechnology and bioengineering}, volume = {122}, number = {9}, pages = {2389-2399}, pmid = {40542710}, issn = {1097-0290}, support = {//This study was supported by the Institute for Fermentation, Grant/Award Number: L-2018-2-014; Japan Science and Technology Agency-Adaptable and Seamless Technology Transfer Program through target-driven R&amp;D, Grant/Award Number: JPMJTM19Y4; JSPS KAKENHI, Grant/Award Number: JP20H02895; and New Energy and Industrial Technology Development Organization, Grant/Award Number: JPNP20011./ ; }, mesh = {*Aspergillus oryzae/genetics/metabolism/growth &amp; development/physiology ; *Fermentation ; *Bioreactors/microbiology ; *Hyphae/genetics/metabolism/growth &amp; development ; Hydrodynamics ; }, abstract = {The complexity of mechanical and biological processes in filamentous fungal fermentation remains a major obstacle to improving product yield. We previously demonstrated that the AGΔ-GAGΔ strain of Aspergillus oryzae, lacking both α-1,3-glucan (AG) and galactosaminogalactan (GAG), had improved hyphal dispersion, reduced culture viscosity, and increased recombinant protein production. Here, we applied computational fluid dynamics (CFD) and multi-omics analysis to characterize the AGΔ-GAGΔ strain during fermentation in a stirred-tank bioreactor. CFD simulations revealed large gas cavities behind the impeller blades and severe compartmentalization in both wild-type and AGΔ-GAGΔ cultures. However, shear stress distribution was broader and gas cavity formation was lower in the AGΔ-GAGΔ strain than in the wild type. The simulation results were consistent with measurements of volumetric oxygen mass transfer coefficients (KLa) and mixing times. Transcriptome analysis revealed upregulation of TCA-cycle genes in AGΔ-GAGΔ relative to the wild type. Analysis of intracellular and extracellular metabolites indicated distinct metabolic profiles associated with oxygen availability. Our findings highlight the critical role of hydrodynamics in fungal fermentation and demonstrate the potential of strain engineering for improving mixing characteristics.}, }
@article {pmid40540980, year = {2025}, author = {Noviello, D and Amoroso, C and Vecchi, M and Facciotti, F and Caprioli, F}, title = {Curing inflammatory bowel diseases: breaking the barriers of current therapies- emerging strategies for a definitive treatment.}, journal = {Current opinion in immunology}, volume = {95}, number = {}, pages = {102593}, doi = {10.1016/j.coi.2025.102593}, pmid = {40540980}, issn = {1879-0372}, mesh = {Humans ; *Inflammatory Bowel Diseases/therapy/immunology/etiology ; Animals ; Gastrointestinal Microbiome/immunology ; Fecal Microbiota Transplantation ; Hematopoietic Stem Cell Transplantation ; Intestinal Mucosa/immunology ; }, abstract = {Chronic intestinal inflammation in inflammatory bowel diseases (IBD) reflects the interplay of genetic predisposition, immune dysregulation, microbial imbalance, and epithelial barrier defects. Current therapies for IBD primarily focus on controlling inflammation necessitating lifelong treatment and face a 'therapeutic ceiling' due to primary and secondary loss of efficacy over time. Immune-mediated approaches do not address additional pathogenic mechanisms, such as impairment of epithelial barrier and gut microbial ecology. Thus, innovative strategies are required to foster the field closer to a definitive cure. This review discusses novel strategies to overcome current therapeutic limitations, including immune reset via hematopoietic stem cell transplantation and B cell-targeted therapies, antigen-specific interventions such as chimeric antigen receptor T cells and tolerogenic vaccines, and intestinal epithelial barrier restoration. We also explore microbiota-based strategies - ranging from fecal microbiota transplantation to engineered consortia and bacteriophages - and discuss the adjunctive role of diet. Together, we outline a potential research roadmap toward a potential cure for IBD.}, }
@article {pmid40540566, year = {2025}, author = {Woods, PH and Speth, DR and Laso-Pérez, R and Utter, DR and Ruff, SE and Orphan, VJ}, title = {Identification of key steps in the evolution of anaerobic methanotrophy in Candidatus Methanovorans (ANME-3) archaea.}, journal = {Science advances}, volume = {11}, number = {25}, pages = {eadq5232}, pmid = {40540566}, issn = {2375-2548}, mesh = {*Methane/metabolism ; Anaerobiosis ; Phylogeny ; *Evolution, Molecular ; Genome, Archaeal ; *Archaea/genetics/metabolism ; Metagenomics ; Gene Transfer, Horizontal ; }, abstract = {Despite their large environmental impact and multiple independent emergences, the processes leading to the evolution of anaerobic methanotrophic archaea (ANME) remain unclear. This work uses comparative metagenomics of a recently evolved but understudied ANME group, "Candidatus Methanovorans" (ANME-3), to identify evolutionary processes and innovations at work in ANME, which may be obscured in earlier evolved lineages. We identified horizontal transfer of hdrA homologs and convergent evolution in carbon and energy metabolic genes as potential early steps in Methanovorans evolution. We also identified the erosion of genes required for methylotrophic methanogenesis along with horizontal acquisition of multiheme cytochromes and other loci uniquely associated with ANME. The assembly and comparative analysis of multiple Methanovorans genomes offers important functional context for understanding the niche-defining metabolic differences between methane-oxidizing ANME and their methanogen relatives. Furthermore, this work illustrates the multiple evolutionary modes at play in the transition to a globally important metabolic niche.}, }
@article {pmid40539105, year = {2025}, author = {Zhang, Z and Shi, Z and Zheng, L and Zhang, H}, title = {Remediation of acetochlor-contaminated maize field soil using Serratia odorifera AC-1 fertilizer: effects on soil microbial communities.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1510157}, pmid = {40539105}, issn = {1664-302X}, abstract = {Acetochlor is a chloroacetamide herbicide that is widely applied in corn fields. Nevertheless, the long-term usage of acetochlor in the soil leads to residues, which severely affect the germination of corn seeds and the growth of seedlings, and even exert an influence on the soil microbial community. Microbial degradation of acetochlor is the principal approach for restoring the soil microbial ecology. In this study, the Serratia odorifera AC-1 strain was isolated and identified from the soil for the degradation of residual acetochlor in the soil. To enhance the degradation efficiency, a solid microbial agent was prepared by using activated carbon as a carrier and the AC-1 strain at a 1:1 ratio and applied to the soil for degradation and remediation experiments. The content of the microbial cells in the solid microbial agent was 1.49 × 106 CFU/g after 120 days of preparation. The application of the AC-1 solid microbial agent significantly influenced the relative abundance of soil microbial communities (Actinobacteria, Firmicutes, and Proteobacteria), increasing the diversity of bacterial populations in the soil. The experimental results indicated that after the application of the AC-1 solid microbial agent, the plant height, stem diameter, and photosynthetic efficiency of corn seedlings under acetochlor stress were significantly elevated. When the application rate of the AC-1 solid microbial agent was 5.00 mg/kg, the stem diameter of corn increased by 56.4% compared with the control group. When the acetochlor concentration in the soil was 6.65 mg/kg, the DT50 value of the AC-1 solid microbial agent was 2.28 days. This study clarified the degradation mechanism and remediation capacity of the Serratia odorifera AC-1 strain in acetochlor-contaminated soil and proposed a new strategy to improve the stability and degradation efficiency of the microbial strain by optimizing the immobilization technology of the strain on activated carbon. This research provides a scientific basis and technical guidance for the future application of bioremediation technology in the field environment to remove pesticide residues, restore soil health, and enhance crop productivity.}, }
@article {pmid40537563, year = {2025}, author = {Embury, EL and Romero-Olivares, AL}, title = {Fungi Follow Flora, Bacteria Track the Seasons: A Tale of a Changing Landscape.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {68}, pmid = {40537563}, issn = {1432-184X}, support = {R16 GM146585/GM/NIGMS NIH HHS/United States ; 1R16GM146585//National Institute of General Medical Sciences of the National Institutes of Health/ ; 2312226//National Science Foundation Building Research Capacity in Biology/ ; }, mesh = {Seasons ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Fungi/classification/genetics/isolation &amp; purification ; Desert Climate ; *Microbiota ; Ecosystem ; Grassland ; Soil/chemistry ; Biomass ; Biodiversity ; }, abstract = {Microbes play critical roles in dryland ecosystems, driving nutrient cycling, soil stability, and plant interactions. Despite their ecological importance, few studies have examined how microbial communities respond to vegetation changes in arid landscapes. In the northern extent of the Chihuahuan Desert, the encroachment of woody shrubs into grasslands has been occurring since the 1800s, largely driven by extensive livestock grazing and increased drought levels. In this study, we investigated how microbial communities respond to both biotic (i.e., vegetation) and abiotic (i.e., seasonality) factors, how they assemble in a changing landscape, and which taxa may be particularly responsive to shrub encroachment or even facilitating this transformation. We assessed microbial communities using soil surface samples across five distinct seasonal periods in a grassland-to-shrubland gradient in the Jornada Experimental Range in the Chihuahuan Desert through the use of phospholipid fatty-acid analysis and DNA metabarcoding techniques. Our findings reveal that bacterial and fungal biomass are significantly influenced by seasonal changes, with strong correlations to humidity and temperature fluctuations. We also found that fungal community assembly and diversity were highly impacted by vegetation whereas seasons were more impactful on bacteria. Our results support the idea that microbes may be playing a crucial role in facilitating the grassland-to-shrubland transition. Overall, our study highlights the complex interactions between microbial communities and biotic and abiotic factors in dryland systems. These findings are essential for understanding the future of dryland ecosystems undergoing shrub encroachment and provide a critical foundation for guiding restoration efforts, particularly those looking to incorporate microbial-mediated solutions.}, }
@article {pmid40536564, year = {2025}, author = {Parret, L and Simoens, K and Horemans, B and De Vrieze, J and Smets, I}, title = {Establishing a co-culture aggregate of N-cycle bacteria to elucidate flocculation in biological wastewater treatment.}, journal = {Applied microbiology and biotechnology}, volume = {109}, number = {1}, pages = {149}, pmid = {40536564}, issn = {1432-0614}, support = {C24/18/043//KU Leuven/ ; FWO-G032321N//Fonds Wetenschappelijk Onderzoek/ ; FWO- 1191022N//Fonds Wetenschappelijk Onderzoek/ ; }, mesh = {Flocculation ; *Wastewater/microbiology ; Coculture Techniques/methods ; Sewage/microbiology ; *Bacteria/metabolism/growth &amp; development ; Bioreactors/microbiology ; Alginates ; *Water Purification/methods ; *Nitrogen/metabolism ; Nitrification ; Microbial Consortia ; }, abstract = {Biological flocculation is a complex phenomenon that is often treated as a black box. As a result, flocculation problems are usually remediated without knowledge of the exact causes. We show that it is feasible to exploit a model (N-cycle) consortium with reduced complexity to fundamentally study bioflocculation. Strong nitrifier microcolonies were formed during oxic/anoxic cycles in sequencing batch reactors, using alginate entrapment as a cell retention system. After the release of these aggregates into suspension, macroclusters with flocs of the denitrifier were observed. These results suggest that a living model of a full-scale activated sludge floc can be built through the use of this bottom-up approach. By eliminating shifts in the microbial community, the applied experimental conditions have a more direct effect on the observations. Key Points ∙ Studying flocculation with a model consortium is feasible ∙ Alginate entrapment leads to strong microcolony formation of nitrifiers ∙ FISH by itself is not suitable to study aggregation of a coculture.}, }
@article {pmid40536143, year = {2025}, author = {Timmis, K and Williams, P and Karahan, ZC and López-García, P and Rainey, P and Chavarria, M and Greening, C and Steward, K and Hallsworth, JE and Pereira, CS and Giraldo, R and Verstraete, W and Jonjić, S and Ramos, JL and Nunes, O and Ventosa, A and Armstrong, R and Sessitsch, A and Ron, E and Wang, H}, title = {Journals Operating Predatory Practices Are Systematically Eroding the Science Ethos: A Gate and Code Strategy to Minimise Their Operating Space and Restore Research Best Practice.}, journal = {Microbial biotechnology}, volume = {18}, number = {6}, pages = {e70180}, pmid = {40536143}, issn = {1751-7915}, mesh = {*Periodicals as Topic/standards ; Peer Review, Research/standards ; Humans ; }, abstract = {Scientific research seeks to extend knowledge and understanding, an activity that perhaps more than any other advances society and humanity. In essence, it is the search for truth. But, because it seeks new knowledge, there is little or no benchmark for appraisal of the plausibility or validity of the immediate conclusions drawn from new information gained, no instant confirmation. For this and other reasons, the science ethos requires the highest level of rigour to ensure the highest level of probability that new findings are true, or at least the most plausible under the prevailing circumstances and state of knowledge. Research is only as good as its degree of rigour. Rigour comes through intensive and comprehensive scientific training and mentoring that teaches critical and agnostic evaluation of new results, self-scrutiny and self-criticism. Additional rigour comes via independent scrutiny and validation: peer review of results and interpretations submitted as publications, and peer repetition of key experiments. However, the current proliferation of publication vehicles whose business model is based on maximisation of papers published, and the revenue stream of article processing charges (APCs) they generate, is promoting an insidious degradation of rigour and quality standards of reviewing-editing practices. Such predatory practices result in the systematic degradation of research quality and its "truthfulness". Moreover, they undermine the science ethos and threaten to create a new generation of scientists that lack this ethos. These trends will inevitably progressively erode public trust in scientists and the research ecosystem. This Editorial is a call for action to all actors, in particular leaders, in scientific research to oppose predatory practices in science dissemination-to restrict the operational space of those responsible for such practices-in order to restore and maintain research rigour and the science ethos and to prevent a downward spiral of research quality. It proposes two linked actionable solutions to the problem, one for the "pull" element of predatory practices and one for the "push" element of research ecosystem management practices, especially those promoting the publish or perish mentality, that drive authors to publish in journals with predatory practices. To counter the "pull", we propose a solution based on the principle of prevention, rather than cure, and list a number of essential policy decisions and actions that should be taken at all levels of the science chain/cloud to achieve this. A central plank of the concept is journal accreditation, without which a journal would be ineligible for payment of APCs from public funds. For accreditation, a journal would need to convincingly demonstrate adoption of a prescribed journal code of conduct. Ideally, accreditation would also be required for inclusion in journal indexing and ranking services and bibliographic databases. To counter the "push", we propose a top-down imposition of a cultural change in science management that ensures merit-based success of scientists and their careers, research best practice, improved education and mentoring of younger scientists in the science ethos and greater support of them in their careers. This must include explicit recognition of the crucial role of peer reviewing for the good health of the research enterprise, its incentivisation and appropriate appreciation of the time and effort involved. To orchestrate this change, we propose the creation of a multi-stakeholder alliance whose brief is to develop the framework and implementation strategy for changes in the research ecosystem. This Editorial also exhorts all actors to embrace the principle of publish less, publish better and to use public funding provided by tax revenues more effectively to perpetually raise the bar of science quality, dissemination and potential to advance humanity.}, }
@article {pmid40534981, year = {2025}, author = {Hodgson, RJ and Cando-Dumancela, C and Liddicoat, C and Ramesh, SA and Edwards, RA and Breed, MF}, title = {Strong Host Modulation of Rhizosphere-to-Endosphere Microbial Colonisation in Natural Populations of the Pan-Palaeotropical Keystone Grass Species, Themeda triandra.}, journal = {Ecology and evolution}, volume = {15}, number = {6}, pages = {e71595}, pmid = {40534981}, issn = {2045-7758}, abstract = {Soil microbiota can colonise plant roots through a two-step selection process, involving recruitment of microbiota first from bulk soil into plant rhizospheres, then into root endospheres. This process is poorly understood in all but a few model species (e.g., Arabidopsis), which is surprising given its fundamental role in plant and soil ecology. Here, we examined the microbial community assembly processes across the rhizospheres and root endospheres in eight natural populations of the pan-palaeotropical C4 grass, Themeda triandra, in southern Australia. Using a space-for-time substitution approach, we assessed whether bacterial root colonisation patterns conformed to the two-step model and tested whether community assembly was driven more by deterministic or stochastic processes. Our results show that the two-step selection process shaped bacterial recruitment dynamics across these natural T. triandra populations, and we provide clear evidence that host plants influence microbial assembly via deterministic pressures that produce strong community convergence within endospheres. These findings highlight the central role of host filtering in shaping a conserved 'core' endosphere microbiome. However, limited understanding of these endosphere communities constrains efforts to harness these important relationships to, for example, improve plant propagation and revegetation practices.}, }
@article {pmid40533683, year = {2025}, author = {Rios-Reyes, A and Gonzalez-Lozano, KJ and Cabral-Miramontes, JP and Hernandez-Gonzalez, JJ and Rios-Sosa, A and Alvarez-Gutierrez, PE and Mireles-Torres, SP and Batista-García, RA and Arechiga-Carvajal, ET}, title = {Exploration of Plant and Microbial Life at "El Chichonal" Volcano with a Sustainable Agriculture Prospection.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {67}, pmid = {40533683}, issn = {1432-184X}, support = {700634//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; 2055419//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; 1081508//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; 315114//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; 252373/SEP-CONACYT//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; CBF2023-2024-3120//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; }, mesh = {*Soil Microbiology ; *Bacteria/classification/isolation &amp; purification/genetics/metabolism ; *Fungi/isolation &amp; purification/classification/genetics ; Agriculture ; Soil/chemistry ; *Volcanic Eruptions ; Bacillus cereus/isolation &amp; purification/genetics ; Plant Roots/microbiology ; Microbiota ; }, abstract = {Active volcanic environments represent extreme habitats with underexplored potential for microbial bioprospecting. This study aimed to characterize pioneer vegetation and associated microbial diversity in the crater of "El Chichonal" volcano, with an emphasis on their potential applications in sustainable agriculture. A physicochemical analysis of the soil was performed, identifying acidic and nutrient-poor conditions. Three pioneer plant species were described: Tibouchina longifolia (dominant) and Poaceae spp. (co-dominant), and Palhinhaea cernua (non-dominant). A total of 311 microorganisms were predominantly bacteria, were isolated from soil, root, stem, and water samples. Bacillus cereus and Priestia megaterium were molecularly identified, and in vitro assays demonstrated their ability to fix nitrogen, produce auxins, and antagonize fungal pathogens (Alternaria solani, Botrytis cinerea, and Colletotrichum gloeosporioides). These results suggest that microorganisms adapted to extreme volcanic environments could be promising sources of plant growth-promoting bacteria (PGPB) with application in biological control.}, }
@article {pmid40533475, year = {2025}, author = {Wollrab, S and Schmidt, SR and Woodhouse, J and Kasprzak, P and Berger, SA and Beyer, U and Bodenlos, M and Dalchow, J and Degebrodt, M and Ganzert, L and Gonsiorczyk, T and Huth, E and Kiel, C and Küchler, L and Krienitz, L and Lentz, M and Mach, E and Mallok, U and Nejstgaard, JC and Papke, M and Penske, A and Pinnow, S and Roßberg, R and Ronneberger, D and Sachtleben, M and Scheffler, A and Grossart, HP and Casper, P and Gessner, MO and Koschel, R}, title = {Fifty years of limnological data on Lake Stechlin, a temperate clearwater lake.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1028}, pmid = {40533475}, issn = {2052-4463}, abstract = {We present 50 years of monitoring data on water quality of Lake Stechlin, a deep, dimictic hardwater lake in northeastern Germany known for its exceptionally clear water. Although located in a forested catchment, the lake has undergone major changes in recent decades, including a period of massive heating of surface water when receiving cooling water from a nearby nuclear power plant (1966-1990), accompanied by a greatly shortened water residence time from more than 40 years to less than 300 days. These changes are superimposed by a long-term trend of surface water warming and a concomitant decrease in winter ice cover. Total phosphorus concentrations have quadrupled since 2010 and zones of deep-water oxygen depletion have greatly expanded. The presented dataset covers basic water-chemical and physical records taken at monthly to fortnightly intervals from 1970 to 2020, documenting limnological changes during that period. Furthermore, it serves as a valuable basis to assess and project potential consequences of climate change and other types of environmental change on deep clearwater lakes in temperate climates.}, }
@article {pmid40531665, year = {2025}, author = {Phithakrotchanakoon, C and Kitikhun, S and Siriarchawatana, P and Charoenyingcharoen, P and Jeennor, S and Nilsakha, T and Chanpet, A and Vorajinda, T and Mayteeworakoon, S and Yukphan, P and Ingsriswang, S}, title = {Flavobacterium mekongense sp. nov., isolated from the Mekong River in Thailand.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {75}, number = {6}, pages = {}, doi = {10.1099/ijsem.0.006815}, pmid = {40531665}, issn = {1466-5034}, mesh = {Thailand ; *Flavobacterium/classification/genetics/isolation &amp; purification ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Rivers/microbiology ; Fatty Acids/chemistry/analysis ; DNA, Bacterial/genetics ; Base Composition ; Bacterial Typing Techniques ; Sequence Analysis, DNA ; Vitamin K 2/analogs &amp; derivatives/chemistry/analysis ; Nucleic Acid Hybridization ; Genome, Bacterial ; Phospholipids/analysis/chemistry ; *Water Microbiology ; }, abstract = {Two Gram-stain-negative, aerobic, non-motile, non-gliding, rod-shaped bacterial strains, designated as TBRC 19031[T] and TBRC 19032, were isolated from water samples collected from the Mekong River, Thailand. Strain TBRC 19031[T] was obtained from Chiang Saen in the upstream section near the borders with China and Myanmar, while TBRC 19032 originated from Khong Chiam, in the downstream section where the river exits Thailand. Colonies of both strains were circular, smooth and deep yellow on Reasoner's 2A agar and did not produce flexirubin-type pigments. Phylogenetic analysis with 16S rRNA gene sequences placed both strains within the genus Flavobacterium, showing the highest sequence similarity to Flavobacterium cheonhonense ARSA-15[T] (98.29% for TBRC 19031[T] and 98.22% for TBRC 19032). However, whole-genome comparisons between the strains and F. cheonhonense ARSA-15[T] revealed average nt identity (89.39% and 89.29%), average aa identity (92.84% and 92.95%) and digital DNA-DNA hybridization (35.00% and 34.70%). The predominant fatty acids were iso-C15:1, iso-C15:0 and iso-C15:0 3-OH, and menaquinone MK-6 was the major respiratory quinone. The major polar lipids of both strains included phosphatidylethanolamine, steryl ester and diacylglycerol. The genome sizes were 3.02 and 3.04 Mbp, with G+C contents of 38.3% and 38.2% for TBRC 19031[T] and TBRC 19032, respectively. Comparative genomic analyses revealed the absence of genes involved in sulphate reduction and denitrification pathways and the presence of a gene encoding phosphatidylinositol synthase, distinguishing them from other Flavobacterium within the clade. Ecological profiling using public metagenomic datasets showed that both strains were associated with lotic freshwater environments. This study not only introduces Flavobacterium mekongense sp. nov. as a new species but also provides broader insights into the ecology, metabolism and environmental distribution of freshwater Flavobacterium. The genomic features identified here offer promising leads for future studies in microbial ecology, comparative genomics and functional gene mining in aquatic ecosystems. The type strain is TBRC 19031[T] (TBRC 19031[T]=NBRC 117006[T]).}, }
@article {pmid40531656, year = {2025}, author = {Bou Orm, E and Mukherjee, S and Rifa, E and Créach, A and Grec, S and Bayle, S and Benezet, JC and Bergeret, A and Malhautier, L}, title = {Enhancing Biodiversity-Function Relationships in Field Retting: Towards Key Microbial Indicators for Retting Control.}, journal = {Environmental microbiology reports}, volume = {17}, number = {3}, pages = {e70102}, pmid = {40531656}, issn = {1758-2229}, mesh = {*Biodiversity ; *Fungi/classification/genetics/enzymology/isolation &amp; purification/metabolism ; *Bacteria/classification/genetics/enzymology/isolation &amp; purification/metabolism ; *Cannabis/microbiology/metabolism ; Pectins/metabolism ; Glycoside Hydrolases/metabolism ; Microbiota ; }, abstract = {Hemp field retting is a bioprocess that facilitates fibre extraction by degrading pectin and other matrix components surrounding fibre bundles. However, traditional methods rely on empirical practices, often resulting in inconsistent fibre quality. This study investigates the biodiversity-function relationship in the hemp retting ecosystem to identify microbial and enzymatic indicators for improved process control. Over six weeks of field retting, we monitored bacterial and fungal community dynamics using high-throughput sequencing and assessed enzymatic activity profiles. Our results revealed a sequential enzymatic pattern: pectinases (e.g., polygalacturonase) dominated early stages, followed by hemicellulases (β-xylosidase, β-galactosidase), and later cellulases. These enzymatic shifts were reflected in the changes in microbial community composition, with pectinolytic bacteria (e.g., Proteobacteria) dominating the initial phases and cellulolytic fungi (e.g., Ascomycota) becoming more prevalent later. Our results identified specific microbial taxa correlated with optimal retting, suggesting their potential as bioindicators for monitoring retting. Specifically, key bacterial genera such as Pseudomonas and Sphingomonas, and fungal genera like Cladosporium, were associated with distinct enzymatic profiles. Our findings offer new insights into the microbial ecology of retting, providing both microbial and enzymatic indicators that could inform the development of monitoring strategies for process control, ultimately contributing to more consistent hemp fibre production.}, }
@article {pmid40530365, year = {2025}, author = {Akdur Öztürk, E and Guadano-Procesi, I and Figueiredo, AM and Godfrey, A and Gentekaki, E and Tsaousis, AD and Carmena, D and Dogruman-Al, F}, title = {A protocol for mapping Blastocystis epidemiology and diagnostics from One Health perspective.}, journal = {Open research Europe}, volume = {5}, number = {}, pages = {133}, pmid = {40530365}, issn = {2732-5121}, abstract = {Blastocystis is a globally prevalent gut protist colonising over a billion people worldwide, yet its epidemiology, transmission dynamics, and clinical significance remain underexplored. This protocol represents the first step of a large-scale effort to map Blastocystis epidemiology and diagnostic practices across Europe through the COST Action CA21105: Blastocystis under One Health. By assessing diagnostic methodologies across clinical, veterinary, and environmental sectors, this work sets the foundation for future research and standardisation. Here, we highlight key findings, challenges, and a roadmap for improving Blastocystis detection, ultimately influencing global health policies and microbial ecology studies.}, }
@article {pmid40530126, year = {2025}, author = {Wu, WJ and Wang, K and Yang, YV and Yang, X}, title = {Identification of neuronal synapse-related signatures and potential therapeutic drugs in colorectal cancer based on machine learning algorithms and molecular docking.}, journal = {Translational cancer research}, volume = {14}, number = {5}, pages = {2737-2757}, pmid = {40530126}, issn = {2219-6803}, abstract = {BACKGROUND: Nervous system-cancer interactions can regulate tumorigenesis, invasion, and metastasis. However, specific biomarkers for targeting neuron synapse in colorectal cancer (CRC) remain unexplored. This study aims to develop a neuronal synapse-related signature (NSRS) to predict survival in CRC patients, identify potential therapeutic drugs, and explore its clinical applications.<br><br>METHODS: We collected neuronal synapse genes (NSGs) from the Molecular Signatures Database (MSigDB) and published mass spectrometry data. Using weighted gene co-expression network analysis (WGCNA) and least absolute shrinkage and selection operator Cox regression (LASSO-Cox), we identified prognostic NSGs and constructed a NSRS through multivariate Cox regression. Functional enrichment analysis revealed the molecular characteristics of NSRS subgroups. Additionally, xCell and ESTIMATE algorithms quantified the abundance of 54 cell subtypes and assessed the tumor immune microenvironment (TIME) of the two NSRS subgroups. Finally, drug prediction and molecular docking identified candidate drugs with therapeutic potential.<br><br>RESULTS: Seven key prognostic NSGs were identified, and an independent, stable NSRS model was constructed. Kaplan-Meier survival curves indicated that the high NSRS group had poorer outcomes (log-rank test, P<0.05). Functional enrichment analysis revealed significant enrichment of epithelial-mesenchymal transition, hypoxia, and inflammation features in the high NSRS group. xCell and ESTIMATE analyses showed a more complex TIME and lower tumor purity in the high NSRS group, highlighting the role of neuro-tumor interactions in CRC. Drug prediction and molecular docking suggested alprostadil, dihydroergocristine, and nocodazole as candidate drugs for CRC treatment.<br><br>CONCLUSIONS: This is the first study to develop neuron synapse-related biomarkers from the perspective of neuron-cancer interactions using machine learning. We constructed a robust NSRS model and identified candidate drugs targeting prognostic NSGs, providing new insights into CRC prognosis and treatment.}, }
@article {pmid40529576, year = {2025}, author = {Sanz-López, C and Amato, M and Torrent, D and Borrego, M and Anza, M and Bibiso, M and Grijalva-Vallejos, N and Vilanova, C and Porcar, M and Pascual, J}, title = {Microbial ecology of selected traditional Ethiopian fermented products.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1570914}, pmid = {40529576}, issn = {1664-302X}, abstract = {The consumption of traditional fermented foods and beverages plays an important role in the diet of Ethiopia, providing significant nutritional and health benefits to the local population. The present study aimed to investigate the microbial ecology and diversity of nine types of fermented products. These include two foods (Kotcho and Injera), one food condiment (Datta), and six beverages (Tej, Tella, Cheka, Kinito, Borde, and Shamita). A combination of metataxonomic and culturomic approaches was used to achieve a comprehensive characterization of the bacterial communities, together with a thorough physicochemical characterization of the fermented products. This study provides one of the most comprehensive microbial characterizations of a wide selection of Ethiopian fermented products, highlighting that some bacterial species involved in the fermentation processes could contribute to the safety and nutritional quality of fermented foods and, based on previous studies, could also play a key role in enhancing their potential probiotic properties.}, }
@article {pmid40529573, year = {2025}, author = {Ma, R and Zhang, Z and Wang, J and Han, Y and Li, K and Hou, M and Lei, Y and Xiong, S and Yang, B and Zhi, X and Jiao, Y and Lin, T and Zhang, S and Li, Y}, title = {Mitigating gaseous nitrogen emissions in cotton fields through green manure and reduced nitrogen fertilization.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1615142}, pmid = {40529573}, issn = {1664-302X}, abstract = {Integrating green manure with reduced nitrogen (N) fertilization is a promising strategy to mitigate N emissions in intensive cotton cultivation, however, the underlying mechanisms remain poorly understood. This study investigated the effects of three green manure incorporation patterns-no green manure (NG), Orychophragmus violaceus (OVG), and Vicia villosa (VVG)-combined with four N reduction levels (100, 50, 25%, and conventional) on gaseous N emissions (NH3 and N2O), soil physicochemical properties, and bacterial community characteristics using a cotton field experiment in the Yellow River Basin. Results showed that OVG incorporation with 25% N reduction (N2 treatment) significantly reduced total gaseous N emissions by 36.07% on average during the cotton growth period, reducing NH3 and N2O emissions by 13.31-54.11% and 32.25-68.77%, respectively, compared with N2 application without OVG. OVG application also increased the relative abundance of Proteobacteria (28.10%), enhanced heterogeneous selection in bacterial community assembly (200%), and increased the complexity of co-occurrence networks, compared with NG. Compared with conventional N fertilization (N3 treatment), ≥50% N reduction significantly lowered NH3 (>25.51%) and N2O (>32.76%) emissions, reduced the relative abundance of Acidobacteria (-20.23%), simplified co-occurrence networks, and increased homogeneous selection in bacterial assembly (50.00%). Integrating green manure with 25% N reduction substantially reduced gaseous N emissions, which was associated with the enhanced microbial biomass carbon (MBC) and facilitated recruitment of key bacterial taxa (e.g., Sphingosinicella, Azohydromonas, Phototrophicus) within the microbial co-occurrence network. These findings provide insight into how green manure application coupled with N reduction can mitigate gaseous N losses and reshape soil microbial ecology, offering a theoretical basis for sustainable nutrient management during cotton production.}, }
@article {pmid40528722, year = {2025}, author = {Gao, D and Guo, X and Yang, Z and Li, H and Chen, Y and Yang, X and Song, L and Yang, X and Yang, J and Zhou, C}, title = {Effects of Sibiraea laevigate maxim polysaccharides on intestinal flora in immunosuppressed mice.}, journal = {Journal of the science of food and agriculture}, volume = {}, number = {}, pages = {}, doi = {10.1002/jsfa.14433}, pmid = {40528722}, issn = {1097-0010}, support = {//The program of Science and Technology Department of Gansu Province (2024ZDPC001, 24YFFA026, 23CXGP0002)/ ; //The innovation Drive assistance project of Gansu for Science and Technology Association (GXH20240328-3)/ ; 2023QB-001//The Young Doctor Fund of Gansu Province/ ; //The youth science and technology talent innovation project of Lanzhou (2023-QN-69)./ ; //The Fundamental Research Funds for the Central Universities of Northwest Minzu University (31920240125-01)./ ; 2024RCXM45//The key talent project of Gansu Province (2024)/ ; }, abstract = {BACKGROUND: The intestinal microbial ecology plays a significant role in maintaining normal physiological function processes and significantly influences the immune system. However, research regarding its effects on gut flora and in vivo immunomodulation is insufficient.<br><br>RESULTS: In this study, cyclophosphamide was administered to mice to establish an immunosuppressed mouse model. The regulatory effects of Sibiraea laevigata maxim polysaccharides (SLMPs) on immunity and intestinal microbiota in the immunosuppressed mouse model were investigated. The results indicated that SLMPs could mitigate spleen and thymus damage, protect immune organs, increase the levels of leukocytes, lymphocytes, neutrophils and monocytes in mouse blood and upregulate the levels of IL-2, IFN-&#x3b3;, TNF-&#x3b1; and IgA in mouse serum. Furthermore, SLMPs can restore intestinal microbial imbalance and enhance the diversity of gut microorganisms in immunosuppressed mice.<br><br>CONCLUSION: The findings from this study indicated that SLMPs could enhance immunity and improve the structure and abundance of intestinal flora in mice. These results provide a theoretical basis for the further development and utilization of SLMPs in immunomodulatory adjuvants and functional foods, thereby promoting their application in these fields. &#xa9; 2025 Society of Chemical Industry.}, }
@article {pmid40528265, year = {2025}, author = {Selak, L and Meier, DV and Marinović, M and Čačković, A and Kajan, K and Pjevac, P and Orlić, S}, title = {Salinization alters microbial methane cycling in freshwater sediments.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {73}, pmid = {40528265}, issn = {2524-6372}, support = {DOK-2018-09-1550//Hrvatska Zaklada za Znanost/ ; IP-2020-02-9021//Hrvatska Zaklada za Znanost/ ; }, abstract = {Climate change-induced salinization poses a global threat to freshwater ecosystems and challenges microbial communities driving crucial biogeochemical processes, particularly methane cycling. This study examined the impact of salinization and the accompanying sulfate concentration increases on microbial community dynamics and methane cycling in coastal freshwater lake sediments. We show that sulfate enrichment in sediment profiles enables the proliferation of distinct sulfate-reducing bacteria (SRB) that reshape microbial niches by competing with methanogens and promoting sulfate-dependent anaerobic oxidation of methane (AOM). Freshwater SRB clusters, which compete with some methanogens for substrates but also degrade organic compounds into methanogenesis precursors, are replaced by the SEEP-SRB groups that form syntrophic relationships with ANME-1 in salinized sediments. As seawater intrudes and reshapes microbial communities, a methane pocket forms that escapes both aerobic and anaerobic oxidation. Underneath this methane pocket, SRB play a key role in enabling sulfate-dependent AOM, facilitating methane consumption at higher sediment depths. While all microorganisms demonstrated some physiological adaptability potential to elevated osmotic stress, SRB exhibited the highest resilience to increased salinity. These findings highlight how salinization-induced geochemical shifts, particularly sulfate enrichment, directly affect microbial community assembly and impact methane cycling in coastal freshwater ecosystems.}, }
@article {pmid40528093, year = {2025}, author = {Goswami, R and Sarkar, A and Bandyopadhyay, B and Sadhukhan, S}, title = {Exploring microbial diversity in the Kharasinpur hot spring of West Bengal, India.}, journal = {Molecular biology reports}, volume = {52}, number = {1}, pages = {608}, pmid = {40528093}, issn = {1573-4978}, mesh = {*Hot Springs/microbiology ; India ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/isolation &amp; purification/classification ; Phylogeny ; Biodiversity ; Water Microbiology ; Microbiota/genetics ; Hydrogen-Ion Concentration ; Iron/analysis ; }, abstract = {BACKGROUND: Hot springs are natural geothermal environments that harbour thermophilic microorganisms with significant biotechnological potential. Despite extensive studies on many Indian hot springs, Kharasinpur Hot Spring in West Bengal remains totally unexplored in terms of microbial diversity and physicochemical properties.<br><br>METHODS: A total of seven bacterial isolates were obtained from water samples collected at the Kharasinpur Hot Spring. These isolates underwent morphological, physiological, biochemical, and molecular characterization through 16S rRNA gene sequencing. Water samples were analyzed for physicochemical parameters such as temperature, pH, total hardness, iron concentration, salt content, and total dissolved solids (TDS).<br><br>RESULTS: The water temperature was recorded at 65&#xa0;&#xb0;C with a slightly alkaline pH (7.24). The 16S rRNA analysis identified isolates belonging to the phyla Pseudomonadota (e.g., Pseudomonas sp., Hydrogenophaga sp.) and Bacillota (e.g., Staphylococcus sp., Neobacillus sp.). The high iron content in the hot spring water was notable and rendered it unsafe for direct human consumption.<br><br>CONCLUSION: This study provides novel insights into the microbial diversity and physicochemical characteristics of a relatively unstudied Indian hot spring. The findings contribute to broader research efforts on hot spring ecosystems in India, enhancing our understanding of their microbial ecology and potential health implications.}, }
@article {pmid40528049, year = {2025}, author = {Blair, EM and Margalith, NJ and O'Malley, MA}, title = {Microbial Enrichments Contribute to Characterization Of Desert Tortoise Gut Microbiota.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {66}, pmid = {40528049}, issn = {1432-184X}, support = {DE-SC0020420//U.S. Department of Energy/ ; DE-SC0020420//U.S. Department of Energy/ ; DE-SC0020420//U.S. Department of Energy/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Turtles/microbiology ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Desert Climate ; Fatty Acids, Volatile/metabolism ; Lignin/metabolism ; DNA, Bacterial/genetics ; Biomass ; }, abstract = {Desert tortoises play ecologically significant roles, including plant seed dispersal and mineral cycling, and yet little is known about microbial members that are critical to their gut and overall health. Tortoises consume recalcitrant plant material, which their gut microbiota degrades and converts into usable metabolites and nutrients for the tortoise. Findings from tortoise gut microbiomes may translate well into biotechnological applications as these microbes have evolved to efficiently degrade recalcitrant substrates and generate useful products. In this study, we cultivated microbial communities from desert tortoise fecal samples following a targeted anaerobic enrichment for microbes involved in deconstruction and utilization of plant biomass. We employed 16S rRNA amplicon sequencing to compare cultivated communities to initial fecal source material and found high abundances of Firmicutes and Bacteroidota typically associated with biomass deconstruction in all cultivated samples. Significantly decreased microbial diversity was observed in the cultivated microbial communities, yet several key taxa thrived in lignocellulose enrichments, including Lachnospiraceae and Enterococcus. Additionally, cultivated communities produced short-chain fatty acids under anaerobic conditions, and their growth and metabolic output provide evidence of their viability in the initial fecal communities. Overall, this study adds to the limited understanding of reptilian herbivore microbiota, and offers a path towards biotechnological translation based on the ability of the cultivated communities to convert lignocellulose directly to acetate, propionate, and butyrate.}, }
@article {pmid40527958, year = {2025}, author = {Jendrusch, MA and Yang, ALJ and Cacace, E and Bobonis, J and Voogdt, CGP and Kaspar, S and Schweimer, K and Perez-Borrajero, C and Lapouge, K and Scheurich, J and Remans, K and Hennig, J and Typas, A and Korbel, JO and Sadiq, SK}, title = {AlphaDesign: a de novo protein design framework based on AlphaFold.}, journal = {Molecular systems biology}, volume = {}, number = {}, pages = {}, pmid = {40527958}, issn = {1744-4292}, support = {de.NBI project: 031A537B//Bundesministerium f&#xfc;r Bildung und Forschung (BMBF)/ ; contract 95826//Volkswagen Foundation (VolkswagenStiftung)/ ; 93874-1//Volkswagen Foundation (VolkswagenStiftung)/ ; COFUND grant nr. 847543//EC | Horizon Europe | Excellent Science | HORIZON EUROPE Marie Sklodowska-Curie Actions (MSCA)/ ; }, abstract = {De novo protein design is of fundamental interest to synthetic biology, with a plethora of computational methods of various degrees of generality developed in recent years. Here, we introduce AlphaDesign, a hallucination-based computational framework for de novo protein design developed with maximum generality and usability in mind, which combines AlphaFold with autoregressive diffusion models to enable rapid generation and computational validation of proteins with controllable interactions, conformations and oligomeric state without the requirement for class-dependent model re-training or fine-tuning. We apply our framework to design and systematically validate in vivo active inhibitors of a family of bacterial phage defense systems with toxic effectors called retrons, paving the way towards efficient, rational design of novel proteins as biologics.}, }
@article {pmid40525968, year = {2025}, author = {Lopez-Echartea, E and Dusek, N and Misialek, M and Mahmud-Un-Nabi, MA and Williamson, R and Marathe, K and Geddes, BA}, title = {Culturomics from field-grown crop plants using dilution to extinction, two-step library preparation and amplicon sequencing.}, journal = {Microbiology (Reading, England)}, volume = {171}, number = {6}, pages = {}, pmid = {40525968}, issn = {1465-2080}, mesh = {RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation &amp; purification/growth &amp; development ; *Zea mays/microbiology ; *Microbiota/genetics ; Phylogeny ; DNA, Bacterial/genetics ; Plant Roots/microbiology ; *Pisum sativum/microbiology ; *Crops, Agricultural/microbiology ; High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA ; Gene Library ; Soil Microbiology ; }, abstract = {Culturomics approaches have advanced microbial research by enabling the high-throughput isolation and characterization of a broader range of bacterial taxa, including some previously considered unculturable. Here, we present the testing and optimization of a protocol for isolating and identifying hundreds of cultivable microbes from field-grown plants. This protocol was tested and optimized using the root microbiomes of field-grown corn and pea plants under varying environmental conditions in ND, USA. By employing dilution-to-extinction culturing and a two-step barcoding PCR strategy targeting the V4 region of the 16S rRNA gene, we identified over 200 unique bacterial isolates. The optimized bioinformatic pipeline, built around the DADA2 package, ensured accurate amplicon sequence variant detection and taxonomy assignment. The resulting bacterial isolates span diverse phylogenetic groups, including plant-associated taxa known for promoting plant growth and mitigating stress. Our findings highlight the value of culturomics in generating microbial collections for synthetic community design and advancing plant-microbe interaction research. The protocol's scalability, cost-effectiveness and robust performance demonstrate its potential for widespread application in agricultural microbiome studies.}, }
@article {pmid40525847, year = {2025}, author = {Kroos, L and Wall, D and Islam, ST and Whitworth, DE and Muñoz-Dorado, J and Higgs, PI and Singer, M and Mauriello, EM and Treuner-Lange, A and Søgaard-Andersen, L and Kaimer, C and Elías-Arnanz, M and Stojković, EA and Müller, R and Volz, C and Velicer, GJ and Nan, B}, title = {Milestones in the development of Myxococcus xanthus as a model multicellular bacterium.}, journal = {Journal of bacteriology}, volume = {207}, number = {7}, pages = {e0007125}, pmid = {40525847}, issn = {1098-5530}, mesh = {*Myxococcus xanthus/physiology/genetics/growth &amp; development/cytology ; History, 20th Century ; History, 21st Century ; Models, Biological ; }, abstract = {From the humblest of beginnings (i.e. a pile of dry cow dung) over 80 years ago, the Gram-negative bacterium Myxococcus xanthus has emerged as a premier model system for studying diverse fields of bacteriology, including multicellular development, sporulation, motility, cell-envelope biogenesis, spatiotemporal regulation, signaling, photoreception, kin recognition, social evolution, and predation. As the flagship representative of myxobacteria found in varied terrestrial and aquatic environments, M. xanthus research has evolved into a collaborative global effort, as reflected by the contributions to this article. In celebration of the upcoming 50th anniversary of the International Conference on the Biology of Myxobacteria, this review highlights the historical and ongoing contributions of M. xanthus as a multifaceted model bacterium.}, }
@article {pmid40524759, year = {2025}, author = {Lacerda, AL and Proietti, MC and Kessler, F and Mendes, CR and Secchi, ER and Taylor, JD}, title = {Oceanic regions shape the composition of the Antarctic plastisphere.}, journal = {Communications earth &amp; environment}, volume = {6}, number = {1}, pages = {462}, pmid = {40524759}, issn = {2662-4435}, abstract = {Antarctica, once considered pristine, is increasingly threatened by plastic pollution, with debris found in its waters, sediments, sea ice, and biota. Here, we provide a comprehensive molecular survey of both prokaryotic and eukaryotic diversity on plastics around the Antarctic Peninsula, addressing a gap in existing research. Using eDNA metabarcoding, we identified diverse communities, with Pseudomonadota and Bacteroidota dominating prokaryotic communities, while Gyrista (mostly diatoms), Fungi and Arthropods were prevalent among eukaryotes. Geographic location significantly influenced community composition, with differences between the Bransfield Strait and the Gerlache Strait/Bellingshausen Sea. Polymer type and plastic shape did not impact species richness or community structure. These findings offer new insights into the complexity of the Antarctic plastisphere, highlighting potential impacts on biodiversity, ecosystem functions, and the broader implications of marine plastic pollution.}, }
@article {pmid40524188, year = {2025}, author = {Perillo, VL and Nute, M and Sapoval, N and Curry, KD and Golia, L and Yin, Y and Ogilvie, HA and Nakhleh, L and Segarra, S and Bhaya, D and Cuadrado, DG and Treangen, TJ}, title = {A survey of computational approaches for characterizing microbial interactions in microbial mats.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {168}, pmid = {40524188}, issn = {1474-760X}, support = {EF-2126387//National Science Foundation/ ; BBSRC-NSF/BIO #1921429//National Science Foundation/ ; NSF#2125965//National Science Foundation/ ; PICT 2020-302//Fondo para la Investigaci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; Pampa Azul A8 Programa "Investigaci&#xf3;n//Ministerio de Ciencia, Tecnolog&#xed;a e Innovaci&#xf3;n/ ; Desarrollo e Innovaci&#xf3;n en Ciencias del Mar"//Ministerio de Ciencia, Tecnolog&#xed;a e Innovaci&#xf3;n/ ; Proposal 503441//Joint Genome Institute/ ; proposal: 10.46936/10.25585/60001132//Joint Genome Institute/ ; }, mesh = {*Microbial Interactions ; *Computational Biology/methods ; *Microbiota ; Ecosystem ; Bacteria/genetics/metabolism ; }, abstract = {In this review, we use microbial mat communities as a general model system to highlight the strengths and limitations of current computational methods for analyzing interactions between members of microbial ecosystems. We describe the factors that make this environment have such a high degree of interaction, and we explore different categories of both laboratory and computational tools for studying these interactions. For each tool, we describe efforts to apply them to microbial mats in the past and, in the process, argue that genome-scale metabolic models have breakthrough potential for modeling microbial interactions in microbial mats.}, }
@article {pmid40523669, year = {2025}, author = {Prakash, O and Chauhan, A and Green, SJ}, title = {The Study of Microbial Physiology Under Microoxic Conditions Is Critical but Neglected.}, journal = {Environmental microbiology reports}, volume = {17}, number = {3}, pages = {e70108}, pmid = {40523669}, issn = {1758-2229}, support = {2200615//BioXFEL Science and Technology Center/ ; DE-FE0032198//DOE's University Training &amp; Research Program University Coal Research (UCR)/ ; 0000602538//The Department of Energy/ ; //Major Research Project (MJRP) intramural grant from Symbiosis International (Deemed University)/ ; 1901371//National Science Foundation/ ; 2200615//National Science Foundation/ ; W911NF2210145//Department of Defence contract/ ; }, mesh = {Anaerobiosis ; Aerobiosis ; *Oxygen/metabolism ; *Bacteria/metabolism/genetics/growth &amp; development ; Ecosystem ; *Bacterial Physiological Phenomena ; Humans ; }, abstract = {During the early evolution of life on Earth, the environment was largely free of molecular oxygen, and only anaerobic life existed. With the subsequent oxidation of oceans and the atmosphere, a wide range of environmental niches, ranging from anoxic to microoxic/hypoxic and oxic, developed. Despite this broad range of natural environments, microbiology as a field has focused on the physiology, metabolism, and genetics of aerobic microorganisms, with less attention paid to anaerobes and much less attention paid to microaerophiles. The disparity in studies between aerobic and anaerobic conditions is rampant in host-associated systems, particularly in human health, and studies of microorganisms in intermediate oxygen conditions between fully aerobic and fully anoxic conditions are exceedingly rare. Studies on the physiological behaviour, metabolism, growth response, and drug susceptibility patterns of commensal and pathogenic organisms are almost totally neglected in microoxic conditions. Furthermore, microorganisms from microaerobic and microoxic ecosystems have been less robustly explored in terms of physiology, growth, and metabolism. In this work, we highlight the importance of understanding the physiological and metabolic behaviours of microorganisms under hypoxic or microoxic conditions.}, }
@article {pmid40522148, year = {2025}, author = {Fejes, R and Séneca, J and Pjevac, P and Lutnik, M and Weisshaar, S and Pilat, N and Steiner, R and Wagner, KH and Woodman, RJ and Bondonno, CP and Hodgson, JM and Berry, D and Wolzt, M and Neubauer, O}, title = {Increased Nitrate Intake From Beetroot Juice Over 4 Weeks Changes the Composition of the Oral, But Not the Intestinal Microbiome.}, journal = {Molecular nutrition &amp; food research}, volume = {}, number = {}, pages = {e70156}, doi = {10.1002/mnfr.70156}, pmid = {40522148}, issn = {1613-4133}, support = {//Austrian Science Fund (FWF)/ ; KLI 858//Clinical Research (KLIF) program/ ; }, abstract = {Inorganic dietary nitrate, metabolized through an endogenous pathway involving nitrate reducing bacteria, improves cardiovascular health, but its effects on the oral and intestinal microbiomes of older adults with treated hypertension are unknown. Our study investigated the effects of nitrate from beetroot juice on the oral and intestinal microbiomes of this population. A randomized, double-blind, placebo-controlled crossover trial was conducted with 15 participants (age range: 56-71 years), who consumed nitrate-rich or nitrate-depleted (placebo) beetroot juice for 4 weeks. The oral microbiome analysis revealed an increase in Neisseria and a decrease in Veillonella relative abundance (for both, PERMANOVA p < 0.001), with no significant changes in the intestinal microbiome composition. Our findings suggest that an increased dietary nitrate intake from a vegetable source may selectively modulate the oral microbiome and promote an increased abundance of nitrate-reducing species, which was previously associated with improved cardiovascular health outcomes.}, }
@article {pmid40521244, year = {2025}, author = {Addo, M and Apaame, S and Ghanney, MA and Adu, HK and DeWitt, ME and Addo, SO}, title = {Hepatitis B Infection in Outpatients and Pregnant Women Visiting a Mission Hospital in Ghana.}, journal = {Public health challenges}, volume = {4}, number = {2}, pages = {e70071}, pmid = {40521244}, issn = {2769-2450}, abstract = {Millions of individuals worldwide suffer from hepatitis B, a serious, potentially fatal liver infection brought on by the hepatitis B virus (HBV). Although vaccines are available for HBV, infections continue to persist in Ghana. This study reports the prevalence of HBV infections in outpatients and pregnant women attending antenatal care at the Seventh-day Adventist (SDA) Hospital in Gbawe, Ghana. This retrospective cohort study involved the review of de-identified medical records of outpatients and pregnant women who visited the hospital between 2022 and 2024. Data on their HBV infection status, sex and age were analysed using R version 4.4.1. A total of 531 outpatients and 768 pregnant women visited the hospital during the study period. The prevalence of HBV infection was 7.5% in outpatients and 3.9% in pregnant women. It was observed that outpatients were more likely to be hepatitis B surface antigen (HBsAg) positive (OR = 2.0, 95%CI = 1.24-3.28, p = 0.005). It was also seen that HBV prevalence increased from 2022 to 2023 and decreased in 2024. There is a need for more educational campaigns to raise awareness of HBV infections, especially in pregnant women due to the risk of mother-to-child transmission. Furthermore, vaccinations need to be made affordable and easily accessible to the general population to ensure maximum coverage within the country.}, }
@article {pmid40518732, year = {2025}, author = {Mota de Almeida, FJ and Rakhimova, O and Romani Vestman, N and Lee, NM and Brundin, M}, title = {In situ imaging and microbiome analysis of calculus-like deposits at the root apex: A case report of refractory apical periodontitis.}, journal = {International endodontic journal}, volume = {58}, number = {9}, pages = {1474-1487}, pmid = {40518732}, issn = {1365-2591}, support = {7003589//Region of V&#xe4;sterbotten (Sweden)/ ; 977100//Region of V&#xe4;sterbotten (Sweden)/ ; RV-967705//Region of V&#xe4;sterbotten (Sweden)/ ; }, mesh = {Humans ; Biofilms ; *Dental Calculus/microbiology/diagnostic imaging ; High-Throughput Nucleotide Sequencing ; In Situ Hybridization, Fluorescence ; *Microbiota ; *Periapical Periodontitis/microbiology/diagnostic imaging ; *Tooth Apex/microbiology/diagnostic imaging ; }, abstract = {AIM: This case report explored the application of next-generation sequencing (NGS) and fluorescence in situ hybridization (FISH) to visualize and characterize microbial populations in a refractory endodontic infection with apical calculus-like deposits, a rarely reported phenomenon.<br><br>SUMMARY: Histopathologic analysis revealed bacterial biofilms and calcifications on the root surface, with Gram-positive bacteria predominant in both hard and soft tissues. Microbial sequencing showed Pseudomonadota dominated hard tissues, whereas Bacillota were prevalent in soft tissues, with distinct genera like Lactibacterium and Streptococcus identified. FISH imaging confirmed spatially distributed bacterial taxa, including Actinomycetota and Chloroflexota, within the biofilm, aligning with NGS findings. Notably, Bacteroidota was exclusive to soft tissues, whereas Chloroflexota was detected only in hard tissues. The presence of extensive calculus-like deposits on the root surface provided new insights into the microbial complexity of persistent endodontic infections and their management.<br><br>KEY LEARNING POINTS: The combination of NGS and FISH provided unprecedented insights into the microbial composition of refractory endodontic infections, revealing a diverse and spatially organized ecosystem. Distinct microbial compositions in hard and soft tissues emphasize the importance of targeted therapeutic strategies for endodontic infections. The presence of unique bacterial taxa and biofilms in calculus-like deposits offers new avenues for research into the pathogenesis and persistence of endodontic infections.}, }
@article {pmid40511921, year = {2025}, author = {Mayer, L and Nikolov, G and Kunert, M and Horn, M and Willemsen, A}, title = {Mimivirus transcription and translation occur at well-defined locations within amoeba host cells.}, journal = {Journal of virology}, volume = {99}, number = {7}, pages = {e0055425}, pmid = {40511921}, issn = {1098-5514}, support = {891572//Marie Sklodowska-Curie Actions/ ; 101039843/ERC_/European Research Council/International ; 10.55776/COE7//Austrian Science Fund/ ; }, mesh = {*Mimiviridae/genetics/physiology ; Virus Replication ; *Transcription, Genetic ; *Protein Biosynthesis ; In Situ Hybridization, Fluorescence/methods ; RNA, Viral/genetics ; *Acanthamoeba/virology ; RNA, Messenger/genetics/metabolism ; *Amoeba/virology ; Cytoplasm/virology ; Genome, Viral ; }, abstract = {Many giant viruses replicate in the cytoplasm in viral factories. How exactly these viral factories are established and where the different steps of the replication cycle occur remain largely obscure. We have developed a single-molecule messenger RNA fluorescence in situ hybridization (smFISH) protocol for giant viruses in an Acanthamoeba host. Combined with other labeling techniques (FUNCAT, DiD, rRNA FISH, and DAPI), we show the Mimivirus transcription and translation sites during an infection cycle in the amoeba host cell. Although viral mRNA localization changes depend on the infection stage, transcription occurs at well-defined spots within the viral factory. The original viral cores released within the cytoplasm most likely define these spots. When transported outside of the viral factory, the translation of viral mRNA takes place in a well-defined ring surrounding it. With this study, we obtained novel insights into giant virus replication, of which the methods are widely applicable to other viruses for the visualization and quantification of RNA molecules.IMPORTANCEGiant viruses have massive particle and genome sizes, which are known to infect unicellular eukaryotes. Although most viruses replicate in the host cell's nucleus, the giant Mimivirus replicates in viral factories established in the host cell's cytoplasm. Before this study, the location of the various steps in the Mimivirus replication cycle was largely unknown. By developing new protocols to label giant virus mRNA, protein synthesis, host cell membranes and rRNA, we demonstrate that Mimivirus transcription occurs at well-defined sites within the viral factory. In contrast, translation takes place directly outside of it. This is different from other viruses known to have a cytoplasmic life cycle. These results bring us a step closer to understanding how the genome complexity of viruses influences the virus-host interactions and viral replication strategies.}, }
@article {pmid40510670, year = {2025}, author = {Barnhart, EP and Douterelo, I and Morgan, MJ and Puzon, GJ}, title = {Editorial: Microbial ecology supporting growth of free-living amoebae in natural and engineered water systems.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1620877}, doi = {10.3389/fmicb.2025.1620877}, pmid = {40510670}, issn = {1664-302X}, }
@article {pmid40509663, year = {2025}, author = {van Dijk, JR and Geelhoed, JS and Geerlings, N and Choyikutty, JA and Boschker, HTS and Verbruggen, E and Meysman, FJR}, title = {Inactive "Ghost" Cells Do Not Affect Motility and Long-Range Electron Transport in Filamentous Cable Bacteria.}, journal = {Environmental microbiology}, volume = {27}, number = {6}, pages = {e70117}, pmid = {40509663}, issn = {1462-2920}, support = {G038819N//Fonds Wetenschappelijk Onderzoek/ ; S004523N//Fonds Wetenschappelijk Onderzoek/ ; //Universiteit Antwerpen/ ; PRINGLE 101046719//HORIZON EUROPE European Innovation Council/ ; EMBO ALTF 102-2023//European Molecular Biology Organization/ ; }, mesh = {Electron Transport ; *Bacteria/metabolism/cytology ; Oxidation-Reduction ; Sulfur/metabolism ; *Bacterial Physiological Phenomena ; }, abstract = {Cable bacteria are multicellular filamentous microorganisms that perform electrogenic sulphur oxidation over centimetre-long distances. These filaments contain so-called "ghost cells", which display a highly reduced cytoplasmic content and a lack of metabolic activity. However, the origin and abundance of these ghost cells are not well understood, raising questions about their formation and potential impact on the functioning of the entire filaments. Here, we quantified the abundance of ghost cells in cable bacteria via a targeted propidium iodide staining technique and investigated their morphology and possible origin. Microscopy revealed that ghost cells are present in filaments under in situ conditions, and hence, they are not an artefact from filament sampling. Interestingly, filaments containing ghost cells retained gliding motility, as well as the capacity for long-distance electron transport, thus suggesting that the functionality of the filament as a whole remains largely unaffected by the presence of these ghost cells. Noteworthy is the higher frequency of ghost cells near the ends of filaments, and within filament fragments retrieved from oxic environments. Our findings provide new insights into the adaptive strategies of filamentous bacteria, highlighting their ability to maintain functionality at the organism level despite the fact that some individual cells are no longer metabolically active.}, }
@article {pmid40509476, year = {2025}, author = {Bemis, DH and Camphausen, CE and Liu, E and Dantus, JJ and Navarro, JA and Dykstra, KL and Paltrowitz, LA and Dzhelmach, M and Joerg, M and Tamelessio, P and Belenky, P}, title = {Nutrient Availability and Pathogen Clearance Impact Microbiome Composition in a Gnotobiotic Kimchi Model.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {11}, pages = {}, pmid = {40509476}, issn = {2304-8158}, abstract = {Kimchi is a fermented Korean food typically made with napa cabbage, garlic, radish, ginger, and chili pepper. It is becoming increasingly popular due to its flavor, high fiber content, and purported probiotic benefits. The microbial ecology of the fermentation community has been extensively studied, though what's less understood is how its microbial community changes when nutrients or pathogens are introduced. To study this, we used gnotobiotic cabbage media inoculated with a kimchi starter culture as a model system. These inoculated samples were exposed to E. coli or Bacillus cereus, with or without added nutrients in the form of tryptic soy broth (TSB). We tracked pH, colony-forming units (CFUs), and community composition over time. We also used Oxford Nanopore sequencing to analyze the 16S rRNA gene (V4-V9), followed by use of the Emu algorithm for taxonomic assignments. As expected, LABs suppressed pathogens, but this effect was weaker early on in the nutrient-rich condition. Pathogen exposure changed the overall community-Lactobacillus species became more common, and Leuconostoc mesenteroides less so. Interestingly, adding nutrients alone caused similar microbial shifts to those seen with pathogen exposure. This could suggest that nutrient levels have a larger impact on the final microbiome structure than direct microbial competition. Together, these findings suggest that monitoring total microbial composition, and not just the presence of pathogens, may be important for ensuring kimchi fermentation reproducibility.}, }
@article {pmid40507003, year = {2025}, author = {Karkala, A and Kotoulas, SC and Tzinas, A and Massa, E and Mouloudi, E and Gkakou, F and Pataka, A}, title = {The Lung Microbiome and Its Impact on Obstructive Sleep Apnea: A Diagnostic Frontier.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {15}, number = {11}, pages = {}, pmid = {40507003}, issn = {2075-4418}, abstract = {Obstructive sleep apnea (OSA), a prevalent disorder characterized by recurrent upper airway collapse, is increasingly recognized as a systemic inflammatory condition influenced by microbial dysregulation. Emerging evidence underscores the lung microbiome as a mediator in OSA pathophysiology, where dysbiotic shifts driven by intermittent hypoxia, oxidative stress and mechanical airway trauma amplify inflammatory cascades and perpetuate respiratory instability. This review synthesizes current knowledge on the bidirectional interplay between OSA and lung microbial communities. It aims to highlight how hypoxia-induced alterations in microbial ecology disrupt immune homeostasis, while inflammation-driven mucosal injury fosters pathogenic colonization. Clinical correlations between specific taxa like Streptococcus and Prevotella, and disease severity, suggest microbial signatures as novel biomarkers for OSA progression and treatment response. Furthermore, oxidative stress markers and pro-inflammatory cytokines emerge as potential diagnostic tools that bridge microbial dysbiosis with sleep-related outcomes. However, challenges persist in sampling standardization of the low-biomass lower airways, as well as in causative mechanisms linking microbial dysbiosis to OSA pathophysiology. By integrating microbial ecology with precision sleep medicine, this paradigm shift promises to transform OSA management from mechanical stabilization to holistic ecosystem restoration.}, }
@article {pmid40504771, year = {2025}, author = {Augustijn, HE and Reitz, ZL and Zhang, L and Boot, JA and Elsayed, SS and Challis, GL and Medema, MH and van Wezel, GP}, title = {Genome mining based on transcriptional regulatory networks uncovers a novel locus involved in desferrioxamine biosynthesis.}, journal = {PLoS biology}, volume = {23}, number = {6}, pages = {e3003183}, pmid = {40504771}, issn = {1545-7885}, mesh = {*Deferoxamine ; *Gene Regulatory Networks ; Gene Expression Regulation, Bacterial ; *Streptomyces coelicolor/genetics/metabolism ; *Genome, Bacterial ; Multigene Family ; Bacterial Proteins/genetics/metabolism ; Operon ; Computational Biology ; Iron/metabolism ; Data Mining ; }, abstract = {Bacteria produce a plethora of natural products that are in clinical, agricultural and biotechnological use. Genome mining has uncovered millions of biosynthetic gene clusters (BGCs) that encode their biosynthesis, the vast majority of them lacking a clear product or function. Thus, a major challenge is to predict the bioactivities of the molecules these BGCs specify, and how to elicit their expression. Here, we present an innovative strategy whereby we harness the power of regulatory networks combined with global gene expression patterns to predict BGC functions. Bioinformatic analysis of all genes predicted to be controlled by the iron master regulator DmdR1 combined with co-expression data, led to identification of the novel operon desJGH that plays a key role in the biosynthesis of the iron overload drug desferrioxamine (DFO) B in Streptomyces coelicolor. Deletion of either desG or desH strongly reduces the biosynthesis of DFO B, while that of DFO E is enhanced. DesJGH most likely act by changing the balance between the DFO precursors. Our work shows the power of harnessing regulation-based genome mining to functionally prioritize BGCs, accelerating the discovery of novel bioactive molecules.}, }
@article {pmid40504377, year = {2025}, author = {Zhang, J and Zhao, Z and Zhu, C and Wang, E and Brunel, B and Li, S and Zheng, Q and Feng, Z and Zhang, H}, title = {Diverse Peanut Bradyrhizobial Communities in Chinese Soils: Insights from Eastern, Central, and Northern Henan Province.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {65}, pmid = {40504377}, issn = {1432-184X}, support = {2024M761756//China Postdoctoral Science Foundation/ ; Yuzutong[2023]No.11//Central Plains Youth Top Talent Project/ ; Sabbatical Year SIP20200726//IPN, Mexico/ ; }, mesh = {*Arachis/microbiology ; China ; *Bradyrhizobium/genetics/classification/isolation &amp; purification ; Phylogeny ; *Soil Microbiology ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics ; Polymorphism, Restriction Fragment Length ; Symbiosis ; Soil/chemistry ; Root Nodules, Plant/microbiology ; Bacterial Proteins/genetics ; }, abstract = {Henan province is a major peanut-producing area in China, but research on rhizobia nodulating peanut have been limited to southern Henan, which accounts for only less than half of the province. A collection of 212 strains of peanut rhizobia was obtained from six field sites in eastern, central, and northern Henan, Central China, by using peanut as a trap host under glasshouse conditions. PCR-RFLP analysis of ribosomal IGS sequences classified the 212 strains into 28 distinct types. Phylogenetic analyses of the 16S rRNA, atpD, gyrB, dnaK, and rpoB genes from 30 representative strains of the 28 IGS types identified revealed the presence of Bradyrhizobium. liaoningense, B. yuanmingense, B. zhengyangense, and two novel Bradyrhizobium genospecies. This composition differs from the peanut rhizobia community found in southern Henan. B. liaoningense was the dominant species, covering 49% of the total isolates across the field sites, while B. zhengyangense accounting for 27%, B. yuanmingense for 7% and the two novel Bradyrhizobium genospecies for 17%. Phylogenetic analysis showed that the symbiosis-related nodC and nifH gene sequences clustered into six groups: three associated exclusively with the peanut host (symbiovar arachidis and two unnamed group), three originating from other legume hosts (sv. glycinearum, cajani and retamae). Through the principal component analysis (PCA) between IGS types or species and soil physicochemical properties and environmental factors, it showed that IGS types 1, 3, 5, 8, 9, 12, 14, 15, 18, and 21 positively correlated with AveTmax, AveTmin, AN and AP. IGS types 4, 11, 16, 17, 20, 25, and 26 were positively associated with Alt, AvePrecp, and pH. IGS types 2, 7, 10, 22, 24, and 27 correlated with AP, while remaining types exhibited correlations with OM. In addition, B. yuanmingense, B. liaoningense, and Bradyrhizobium genosp. I positively affected by AveTmax, AP, AN, and AK. Bradyrhizobium genosp. II positively correlated with AK, AN, and OM while B. zhengyangense mainly affected by AvePrecp and pH. The alkaline soil pH in this study differs greatly from the acid soils in southern Henan, explaining the inconsistency between the species of peanut rhizobia detected in southern Henan and the rest of the province. The symbiotic effect assay demonstrated that all representative strains successfully formed nodules and exhibited a significant increase in symbiotic efficiency. Representative strains revealed diverse abiotic stress tolerance to NaCl, acidity, alkalinity, temperature and drought. It conducted a comprehensive collection of peanut rhizobia in eastern, central, and northern Henan province, identifying two putative novel Bradyrhizobium species and isolating rhizobial strains with high symbiotic efficiency and robust stress tolerance. This study is a necessary basic for the producing and application of peanut rhizobial inoculant in this main agricultural province.}, }
@article {pmid40504009, year = {2025}, author = {Schroer, HW and Markland, K and Ling, F and Just, CL}, title = {Hydraulic Connectivity and Hydrochemistry Influence Microbial Community Structure in Agriculturally Affected Alluvial Aquifers in the Midwestern United States.}, journal = {Environmental science &amp; technology}, volume = {59}, number = {24}, pages = {12279-12291}, pmid = {40504009}, issn = {1520-5851}, mesh = {*Groundwater/microbiology ; *Microbiota ; Midwestern United States ; Drinking Water ; }, abstract = {Alluvial aquifers can provide ecosystem services and drinking water, but much remains unknown about human effects on aquifer microbiomes. Therefore, we used amplicon sequencing and hydrochemical characterization to pair microbial communities with environmental conditions across 37 alluvial aquifer wells. The study region spanned eastern Iowa and southern Minnesota (USA) and contained a combination of drinking water and monitoring wells. In terms of microbial ecology, dominant phyla across the wells included Proteobacteria, Bacteroidota, Patescibacteria, Planctomycetota, and Nitrospirota. Tritium, an indicator of infiltration and surface water influence, was the highest correlated variable with the Shannon index (α-diversity) by the Spearman rank sum (ρ = 0.60) and one of only four significant environmental variables in the constrained correspondence analysis. We built random forest regression models to predict tritium concentrations from microbial family relative abundance (held-out testing coefficient of determination (R[2]) = 0.77 and mean absolute percentage error = 7%) and interpreted the models with Shapley additive explanation values. The most important families for predicting tritium concentrations were Nitrosopumilaceae and Methylomirabilaceae. Upwelling methane could contribute to the unusual coupling of ammonia oxidation by Nitrosopumilaceae with simultaneous nitrite-dependent methane oxidation by Methylomirabilaceae. Taken together, we illuminate the relationship among hydrochemistry, hydraulic connectivity, and alluvial aquifer microbiomes.}, }
@article {pmid40502102, year = {2025}, author = {Baty, JJ and Drozdick, AK and Pfeiffer, JK}, title = {P. aeruginosa rhamnolipids stabilize human rhinovirus 14 virions.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40502102}, issn = {2692-8205}, support = {R37 AI074668/AI/NIAID NIH HHS/United States ; T32 AI007520/AI/NIAID NIH HHS/United States ; }, abstract = {Many mammalian viruses encounter bacteria and bacterial molecules over the course of infection. Previous work has shown that the microbial ecology of the gut plays an integral role in poliovirus and coxsackievirus infection, where bacterial glycans can facilitate virus-receptor interactions, enhance viral replication, and stabilize viral particles. However, how airway bacteria alter respiratory viral infection is less understood. Therefore, we investigated whether a panel of airway bacteria affect rhinovirus stability. We found that Pseudomonas aeruginosa, an opportunistic airway pathogen, protects human rhinovirus 14 from acid or heat inactivation. Further investigation revealed that P. aeruginosa rhamnolipids, glycolipids with surfactant properties, are necessary and sufficient for stabilization of rhinovirus virions. Taken together, this work demonstrates that specific molecules produced by an opportunistic airway pathogen can influence a respiratory virus.}, }
@article {pmid40501655, year = {2025}, author = {Chen, J and Pfeifer, K and Steensen, K and Crooke, AM and Wolfram, M and Bobonis, J and Lopatina, A and Bartlau, N and Hussain, FA and Balskus, EP and Polz, MF and Blainey, PC}, title = {Bacterial peptide deformylase inhibitors induce prophages in competitors.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40501655}, issn = {2692-8205}, support = {R01 GM132564/GM/NIGMS NIH HHS/United States ; }, abstract = {While antibiotics mediate chemical warfare among microbes, their roles in the wild extend beyond direct growth inhibition(1). Some antibiotics have the potential to mediate interference competition by triggering a bacterial stress response that subsequently activates endogenous viruses integrated in bacterial genomes (prophages). Canonically, this activation is regulated by the SOS response upon DNA damage. Here we show that a metabolite produced by natural isolates of Vibrio ordalii circumvents the SOS response by directly triggering prophage induction in other Vibrio species, co-occurring in the same environment. While the metabolite was previously classified as a broad-spectrum antibiotic, we observe how it acts as a peptide deformylase inhibitor that specifically induces certain prophages, even when target bacterial cells carry multiple other prophages. Its biosynthetic gene cluster, or ord cluster, also encodes its own peptide deformylase (OrdE) which provides self-immunity to producer strains. Likewise, among natural Vibrio isolates that carry similar prophages, resistance against the ord metabolite was found in those that had acquired a divergent second peptide deformylase. Finally, we show that prophage induction by the ord cluster prevents slower-growing producer strains from being outcompeted by their otherwise fast-growing competitors if they carry an inducible prophage. Thus, we demonstrate how natural products play additional impactful roles in communities beyond antibiotic activity and that prophage induction serves as an interference competition strategy, sustaining community diversity.}, }
@article {pmid40500964, year = {2025}, author = {Li, S and Wang, T and Liu, M and Ma, T and Li, Y and Liu, J and Liu, Y and Shen, W and Ma, J and Wang, X and Han, X and Wang, H and Zhang, X}, title = {α-Linolenic Acid-Rich Flaxseed Oil Improves Polycystic Ovary Syndrome via Regulating Lipid Metabolism by GPR120-cAMP Pathway and Restoring Gut Microecology.}, journal = {Molecular nutrition &amp; food research}, volume = {}, number = {}, pages = {e70136}, doi = {10.1002/mnfr.70136}, pmid = {40500964}, issn = {1613-4133}, support = {82460793//National Natural Science Foundation of China/ ; 82160691//National Natural Science Foundation of China/ ; 2023AAC03216//Ningxia Natural Science Foundation, China/ ; 2023BEG02011//Key Research and Development Program of Ningxia/ ; 2022BSB03112//Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; XZ2021003//Key Laboratory of Fertility Preservation and Maintainance of Ministry of Education of Ningxia Medical University/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; }, abstract = {Polycystic ovary syndrome (PCOS) is a common endocrine disorder that affects metabolic and reproductive health in women. α-Linolenic acid (ALA)-rich flaxseed oil as a dietary food has been suggested to offer potential therapeutic benefits in managing metabolic disturbances associated with PCOS. This study investigates the effects of ALA-rich flaxseed oil on lipid metabolism and gut microecology in a PCOS rat model. The PCOS model was induced in rats using letrozole, and the animals were then administered ALA-rich flaxseed oil. Metabolomics, transcriptomics, 16S rRNA sequencing, hormonal levels, and markers of metabolic health were assessed. Results showed that ALA-rich flaxseed oil significantly improved lipid metabolism by reducing serum cholesterol and triglycerides. In addition, we found that the improvement in lipid metabolism may be associated with the activation of the GPR120-cAMP pathway. Furthermore, gut microbiota analysis revealed a restoration of gut microbial ecology, with a shift toward a more balanced and healthy microbial composition. ALA-rich flaxseed oil shows promising potential as a dietary intervention for managing metabolic disturbances in PCOS. Its effects on lipid metabolism and gut microecology highlight its nutritional relevance, offering new insights into the dietary management of PCOS and its associated metabolic disorders.}, }
@article {pmid40500753, year = {2025}, author = {Bograd, A and Oppenheimer-Shaanan, Y and Levy, A}, title = {Plasmids, prophages, and defense systems are depleted from plant microbiota genomes.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {163}, pmid = {40500753}, issn = {1474-760X}, support = {1535/20//Israeli Science Foundation/ ; 1535/20//Israeli Science Foundation/ ; 1535/20//Israeli Science Foundation/ ; 1001695377//Israeli Ministry of Innovation, Science, and Technology/ ; 1001695377//Israeli Ministry of Innovation, Science, and Technology/ ; 1001695377//Israeli Ministry of Innovation, Science, and Technology/ ; 81259//Israel Innovation Authority/ ; 81259//Israel Innovation Authority/ ; 81259//Israel Innovation Authority/ ; 12-12-0008//Ministry of Agriculture and Rural Development/ ; 12-12-0008//Ministry of Agriculture and Rural Development/ ; 12-12-0008//Ministry of Agriculture and Rural Development/ ; ZN4041//Volkswagen Stiftung/ ; ZN4041//Volkswagen Stiftung/ ; ZN4041//Volkswagen Stiftung/ ; }, mesh = {*Prophages/genetics ; *Plasmids/genetics ; *Plants/microbiology ; *Genome, Bacterial ; *Microbiota/genetics ; Metagenome ; *Bacteria/genetics/virology ; }, abstract = {Plant-associated bacteria significantly impact plant growth and health. Understanding how bacterial genomes adapt to plants can provide insights into their growth promotion and virulence functions. Here, we compare 38,912 bacterial genomes and 6073 metagenomes to explore the distribution of mobile genetic elements and defense systems in plant-associated bacteria. We reveal a consistent taxon-independent depletion of prophages, plasmids, and defense systems in plant-associated bacteria, particularly in the phyllosphere, compared to other ecosystems. The mobilome depletion suggests the presence of unique ecological constraints or molecular mechanisms exerted by plants to control the bacterial mobilomes independently of bacterial immunity.}, }
@article {pmid40500405, year = {2025}, author = {Chen, TK and Shiau, YJ}, title = {Effects of Soil Properties and Seasonal Variations on Microbial Communities in Constructed Wetlands.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {64}, pmid = {40500405}, issn = {1432-184X}, support = {110-2313-B-002-033-MY3//National Science and Technology Council/ ; }, mesh = {*Wetlands ; Seasons ; *Soil Microbiology ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Soil/chemistry ; Denitrification ; *Microbiota ; Biodiversity ; Nitrates/analysis ; Sulfates/analysis ; Nitrification ; }, abstract = {Constructed wetlands (CWs) are important ecosystems with numerous benefits such as wastewater treatment, wildlife habitat protection, and stormwater remediation. However, the development of soil microbial communities in CWs over time remains understudied. This study comprehensively investigates microbial diversity and community composition in three constructed wetlands, focusing on the influence of wetland age, soil depth, and environmental factors. The results indicate that both soil depth and seasonal variations significantly affect alpha diversity, particularly in surface soils. The predominant microbial communities, including nitrifying and denitrifying communities, were identified across the studied wetlands. Moreover, sulfate-rich conditions may promote sulfur autotrophic denitrification. Redundancy analysis and multiple linear regression highlighted the distinction between autotrophic and heterotrophic denitrifiers. Soluble organic carbon was identified as a major factor influencing heterotrophic denitrifying bacteria, while sulfate and nitrate levels were more closely associated with autotrophic denitrifying bacteria. Overall, these findings provide valuable insights into microbial community dynamics in CWs and can help optimize wetland management strategies for improved nutrient removal efficiency.}, }
@article {pmid40499249, year = {2025}, author = {McDonagh, F and Murray, EK and Hallahan, B and Miliotis, G}, title = {Systematic examination of off-target effects of antipsychotic medications associated with microbiome disruption and heightened bacterial infection risks.}, journal = {Journal of psychiatric research}, volume = {189}, number = {}, pages = {171-183}, doi = {10.1016/j.jpsychires.2025.05.046}, pmid = {40499249}, issn = {1879-1379}, abstract = {OBJECTIVE: This systematic review aims to critically evaluate the link between antipsychotic drugs and bacterial infection risk, emphasising antimicrobial properties of antipsychotics, and microbiome changes that might heighten susceptibility to bacterial infections.<br><br>METHODS: A systematic literature search was conducted across PubMed, Scopus, and Google Scholar, up to March 2024. Peer-reviewed articles that investigated the relationship between antipsychotics, their antimicrobial effects, microbiome alterations, and bacterial infection risk were included. Data extracted included antipsychotic type, infection risks, patient demographics, and study methodologies. Risk-of-bias assessments were performed using tools such as the Newcastle-Ottawa Scale and the SYRCLE risk-of-bias tool.<br><br>RESULTS: The review analysed twenty-six studies detailing antimicrobial properties of antipsychotics, four studies on antipsychotic-induced microbiome alterations, and thirty-one studies assessing bacterial infection risk associated with antipsychotics. First-generation antipsychotics were observed to have broad antimicrobial properties, whereas second-generation antipsychotics primarily affected commensal bacteria. At least four antipsychotics were observed to disrupt the gut microbiota. A heightened risk of infection was observed among psychiatric cohorts as well as off-label antipsychotics use, with clozapine linked to a substantial increase in respiratory infection risk.<br><br>DISCUSSION: Although antipsychotics remain indispensable in psychiatric care, their association with an increased risk of bacterial infections underscores the need for judicious prescribing and vigilant monitoring. The review identifies significant knowledge gaps attributable to inconsistent research methodologies, small study cohorts, lack of controls, and focus on a limited range of antipsychotics. Further standardised research is essential to deepen our understanding of these associations and to inform improved prescribing practices and risk mitigation strategies.}, }
@article {pmid40498465, year = {2025}, author = {Samimi, A and Hengoju, S and Martin, K and Rosenbaum, MA}, title = {Advancing droplet-based microbiological assays: optofluidic detection meets multiplexed droplet generation.}, journal = {The Analyst}, volume = {150}, number = {14}, pages = {3137-3146}, doi = {10.1039/d5an00130g}, pmid = {40498465}, issn = {1364-5528}, mesh = {*Microfluidic Analytical Techniques/instrumentation/methods ; High-Throughput Screening Assays/instrumentation ; *Microbiological Techniques/instrumentation/methods ; }, abstract = {Microbiological assays are crucial in understanding microbial ecology and developing new bioproducts. Given the significance of these assays, there is a growing interest in developing high throughput experimentation methods capable of assay multiplexing to enhance the accuracy and efficiency. In this study, we integrate a multiplexed droplet generation set-up into an optofluidic detection chip to facilitate rapid and high throughput analysis of microbiological assays. The optofluidic detection set-up at the same time enables fast and sensitive assessment of droplet condition and content, providing analysis scalability in a high throughput manner. Employing the integration, we produced unique fluorescence barcoded droplets containing defined concentrations of various carbon sources, allowing the simultaneous investigation of microbial growth and metabolic capacity under different experimental conditions. We successfully validated the robustness of the established setup in analyzing and distinguishing different fluorescence barcodes. Our findings highlight the potential of the integrated platform for a broader range of applications in high throughput drug screening, environmental monitoring, and microbiology research.}, }
@article {pmid40498364, year = {2025}, author = {Castledine, M and Esom, C and Van Nieuwenhuyse, B and Djebara, S and Merabishvili, M and Pirnay, JP and Buckling, A}, title = {Predicting clinical phage therapy outcomes in vitro: results using mixed versus single isolates from an MRSA case study.}, journal = {Journal of applied microbiology}, volume = {136}, number = {6}, pages = {}, doi = {10.1093/jambio/lxaf144}, pmid = {40498364}, issn = {1365-2672}, support = {NE/V012347/1//NERC/ ; NE/S000771/1//NERC/ ; }, mesh = {Humans ; Anti-Bacterial Agents/therapeutic use ; *Methicillin-Resistant Staphylococcus aureus/virology/isolation &amp; purification ; *Phage Therapy/methods ; *Staphylococcal Infections/therapy/microbiology ; *Staphylococcus Phages/physiology ; Treatment Outcome ; }, abstract = {AIMS: In phage therapy case studies, 1-3 bacteria isolates are typically tested against phages (phagogram). However, as bacteria populations differ in their susceptibility to phages and antibiotics, the strains selected may not represent how the infecting population will respond to treatment. Our aim was to assess whether the effects of phage on single or a mix of isolates in vitro show more comparable results to that observed during a clinical case study.<br><br>METHODS AND RESULTS: The patient presented with a methicillin resistant Staphylococcus aureus infection (MRSA). In this previously published case study, phage therapy alongside antibiotics rapidly cleared blood cultures of bacteria while localized regions, including the lungs, took longer to clear of bacteria. In this follow-up study, mixed isolates were more likely to persist than single isolates in vitro, more closely representing the lung, but not blood, infections. These results may reflect the different degrees of genetic diversity of the infecting bacteria in these sites.<br><br>CONCLUSIONS: For this patient, phage therapy predictions were significantly affected by whether we used mixed versus single isolates, but the predictive precision depended on the site of in vivo infection.}, }
@article {pmid40495815, year = {2025}, author = {Abiriga, D and Odong, R and Bakyayita, GK and Semyalo, R and Okello, W and Grossart, HP}, title = {The microbiology of Uganda's large freshwater lakes experiencing anthropogenic and climatic perturbations: why it matters-a review.}, journal = {Proceedings. Biological sciences}, volume = {292}, number = {2048}, pages = {20243072}, pmid = {40495815}, issn = {1471-2954}, mesh = {Uganda ; *Lakes/microbiology ; *Climate Change ; *Anthropogenic Effects ; *Water Microbiology ; Biodiversity ; Bacteria ; }, abstract = {Intensification of pollution of African water resources due to human activities together with climate change has serious implications for Africa's blue economy, biodiversity and human health. Despite these overwhelming threats, there is limited research as evidenced by the underrepresentation of Africa-based data in global ecological and biochemical models. This review, therefore, aims to highlight key challenges and existing research gaps, particularly in Ugandan freshwater ecosystems. We focus on lake microbiology as this scientific field has been greatly underrepresented. Aquatic microorganisms are situated at the base of lake food webs and thus play crucial roles in the evolution and maintenance of water quality, attenuation of pollutants, and control of biogeochemical cycling through the microbial loop. Until now, the microbiology of Ugandan lakes has not been systematically studied. Thus, many open fundamental microbial ecology questions need to be urgently addressed to generate valuable information to advance future research, education, management and policy in Uganda and beyond. These include, but are not limited to: identification of microbial taxa and functional genes in relation to anthropogenic and climatic influence; seasonal and spatial variation in species diversity and functions; diversity and functions of planktonic, sediment, biofilm and mat communities; antimicrobial resistance burden; plastisphere communities; and geomicrobiology.}, }
@article {pmid40493213, year = {2025}, author = {Vila Duplá, M}, title = {Advancements in Algal Microbiome Research: A Game-Changer for Climate Resilience and Invasion Success?.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {63}, pmid = {40493213}, issn = {1432-184X}, mesh = {*Microbiota ; *Climate Change ; *Seaweed/microbiology ; *Introduced Species ; }, abstract = {While marine microbiomes have been getting more attention in recent years, they remain understudied compared to those of terrestrial systems. With the refinement of molecular methods, microbiome research has extended to other key marine organisms such as macroalgae. The microbiome plays a key role in macroalgal health, adaptation to environmental conditions, and resilience to climate stressors. The main factors affecting the algal microbiome are host specificity (genetics, functional profile, phylum and species identity), life stage, morphology, thallus region, and tissue age. Other significant drivers of microbiome community structure include spatiotemporal distribution and environmental conditions, especially as global stressors intensify with climate change. The mechanisms through which the microbiome of invasive seaweeds might enhance their competitiveness over native species are still unclear. However, there is evidence that, like climate resilience, invasive potential is linked to the functional flexibility of associated microbiota, allowing the host to adapt to the new environmental conditions. The main objective of this review was to synthesize the current understanding of the macroalgal microbiome and propose future directions in microbiome research based on identified shortcomings. Based on the knowledge gaps detected, there is an urgent need for multi-factorial experimental studies that link host and microbiome gene expression through chemical signals under future climate change scenarios, standardization of analytical methods, and a focus on underrepresented geographical regions and species. While algal microbiome research holds great promise for predicting and mitigating the effects of climate change and invasive species, embracing new tools and tackling ecologically relevant mechanistic and applied questions will be essential to advancing this field.}, }
@article {pmid40492114, year = {2025}, author = {Zhang, Y and Fan, J and Zhao, J and Zhu, H and Xia, Y and Xu, H}, title = {A telomere-associated molecular landscape reveals immunological, microbial, and therapeutic heterogeneity in colorectal cancer.}, journal = {Frontiers in molecular biosciences}, volume = {12}, number = {}, pages = {1615533}, pmid = {40492114}, issn = {2296-889X}, abstract = {BACKGROUND: Colorectal cancer (CRC) ranks among the most prevalent malignancies of the gastrointestinal tract and remains a leading cause of cancer-related mortality worldwide. Although telomere biology has been increasingly implicated in immune modulation and tumor progression, its clinical significance in CRC remains poorly understood.<br><br>METHODS: We developed a telomere score, termed TELscore, by integrating transcriptomic and intratumoral microbiome profiles from publicly available colorectal cancer (CRC) cohorts. To comprehensively characterize TELscore subgroups, we performed pathway enrichment analysis, tumor immune microenvironment (TIME) profiling, and microbiome niche assessment. Whole-slide histopathological images (WSIs) and immunohistochemical (IHC) staining were utilized to visualize immune features, including tertiary lymphoid structures (TLSs), across subgroups. Patients were stratified into high and low TELscore categories, and the predictive robustness was validated across multiple independent training and validation cohorts. Chemotherapeutic drug sensitivity was evaluated using pharmacogenomic data from the Genomics of Drug Sensitivity in Cancer (GDSC) database. Furthermore, the predictive capacity of TELscore for immunotherapy response was independently assessed in an external cohort. Finally, single-cell RNA sequencing (scRNA-seq) analysis was conducted to further dissect the cellular landscape and immunological heterogeneity within the TME.<br><br>RESULTS: TELscore stratified patients into two biologically and clinically distinct subgroups. The high TELscore group, which exhibited significantly shorter DFS, showed marked enrichment of tumorigenic pathways such as EMT, along with a distinctly immunosuppressive TME. This was reflected by elevated ESTIMATE/TIDE scores and corroborated by CIBERSORT, which revealed increased infiltration of M0 macrophages and upregulation of immunosuppressive signatures. In contrast, the low TELscore group was enriched for cell cycle related pathways, including E2F targets and the G2/M checkpoint, and demonstrated higher infiltration of pro-inflammatory M1 macrophages. 16S rRNA sequencing further revealed a divergent intratumoral microbiome between subgroups, the high TELscore group harbored significantly greater relative abundance of Selenomonas and Lachnoclostridium, two pathogenic genera previously associated with colorectal tumorigenesis. Complementary histopathological assessment via WSI demonstrated a marked absence of intraTLSs in high TELscore tumors. From a therapeutic standpoint, high TELscore tumors exhibited reduced sensitivity to standard chemotherapeutic agents-including Fluorouracil, Irinotecan, Oxaliplatin, and Docetaxel-as reflected by elevated IC50 values. Conversely, these tumors demonstrated increased susceptibility to MAPK pathway inhibitors, such as Selumetinib and Trametinib. Notably, TELscore also served as a robust predictor of immunotherapy response, which was validated in the IMvigor210 cohort. Finally, scRNA analysis highlighted profound cellular and functional divergence between TELscore subgroups. We identified intensified intercellular communication between inflammatory macrophages and fibroblasts, reinforcing the presence of an immunosuppressive niche.<br><br>CONCLUSION: TELscore is a robust stratification tool that captures the interplay between tumor biology, immune characteristics, and microbial ecology in colorectal cancer. By identifying clinically relevant subtypes with distinct therapeutic vulnerabilities, TELscore offers a powerful framework to advance personalized treatment and precision oncology.}, }
@article {pmid40488407, year = {2025}, author = {Grossman, AS and Lei, L and Botting, JM and Liu, J and Nahar, N and Liu, J and McLean, JS and He, X and Bor, B}, title = {Saccharibacteria deploy two distinct type IV pili, driving episymbiosis, host competition, and twitching motility.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {40488407}, issn = {1751-7370}, support = {R01 DE023810/DE/NIDCR NIH HHS/United States ; T90 DE026110-07/DE/NIDCR NIH HHS/United States ; 1S10OD034405-01/GF/NIH HHS/United States ; R01 AI087946/AI/NIAID NIH HHS/United States ; 1S10OD023603-01A1/GF/NIH HHS/United States ; R01 DE031274/DE/NIDCR NIH HHS/United States ; R01 AI152421/AI/NIAID NIH HHS/United States ; R01AI152421//National Institute of Allergy and Infectious Diseases/ ; S10 OD023603/OD/NIH HHS/United States ; T90 DE026110/DE/NIDCR NIH HHS/United States ; S10 OD034405/OD/NIH HHS/United States ; 1R01DE023810/DE/NIDCR NIH HHS/United States ; 1R01DE031274/DE/NIDCR NIH HHS/United States ; }, mesh = {*Fimbriae, Bacterial/genetics/physiology ; *Symbiosis ; In Situ Hybridization, Fluorescence ; }, abstract = {All cultivated Patescibacteria, also known as the candidate phyla radiation, are obligate episymbionts residing on other microbes. Despite being ubiquitous in many diverse environments, including mammalian microbiomes, molecular mechanisms of host identification and binding amongst ultrasmall bacterial episymbionts remain largely unknown. Type 4 pili are well conserved in this group and could potentially facilitate these symbiotic interactions. To test this hypothesis, we genetically targeted pili genes in Saccharibacteria Nanosynbacter lyticus strain TM7x to assess their essentiality and roles in symbiosis. Our results revealed that N. lyticus assembles two distinct type 4 pili: a nonessential thin pilus that has the smallest diameter of any type 4 pili and contributes to host-binding and episymbiont growth; and an essential thick pilus involved in twitching motility. To understand the role of these pili in vivo we developed Saccharibacteria competition assays and species-specific Fluorescence in situ hybridization probes. Competition between different Saccharibacteria within mock communities demonstrated consistent competitive outcomes that were not driven by priority effects but were dependent on the thin pilus. Collectively, our findings demonstrate that Saccharibacteria encode unique extracellular pili that enable their underexplored episymbiotic lifestyle and competitive fitness within a community.}, }
@article {pmid40487916, year = {2025}, author = {Okazaki, Y and Nishikawa, Y and Wagatsuma, R and Takeyama, H and Nakano, SI}, title = {Contrasting defense strategies of oligotrophs and copiotrophs revealed by single-cell-resolved virus-host pairing of freshwater bacteria.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf086}, pmid = {40487916}, issn = {2730-6151}, abstract = {Characterizing virus-host pairs and the infection state of individual cells is the major technical challenge in microbial ecology. We addressed these challenges using state-of-the-art single-cell genome technology (SAG-gel) combined with extensive metagenomic datasets targeting the bacterial and viral communities in Lake Biwa. From two water layers and two seasons, we obtained 862 single-cell amplified genomes (SAGs), including 176 viral (double-stranded DNA phage) contigs, which identified novel virus-host pairs involving dominant freshwater lineages. The viral infection rate, estimated by mapping the individual SAG's raw reads to viral contigs, showed little variation among samples (12.1%-18.1%) but significant variation in host taxonomy (4.2%-65.3%), with copiotrophs showing higher values than oligotrophs. The high infection rates of copiotrophs were attributed to collective infection by diverse viruses, suggesting weak density-dependent virus-host selection, presumably due to their nonpersistent interactions with viruses resulting from fluctuating abundance. In contrast, the low infection rates of oligotrophs supported the idea that their codominance with viruses is achieved by genomic microdiversification, which diversifies the virus-host specificity, sustained by their large population size and persistent density-dependent fluctuating selection. Notably, we discovered viruses infecting CL500-11, the dominant bacterioplankton lineage in deep freshwater lakes worldwide. These viruses showed extremely high read coverages in cellular and virion metagenomes but were detected in <1% of host cells, suggesting a low infection rate and high burst size. Overall, we revealed highly diverse virus-host interactions within and between host lineages that were overlooked at the metagenomic resolution.}, }
@article {pmid40487326, year = {2025}, author = {Bornbusch, SL and Dami, KA}, title = {Connecting microbial ecology to human fertility and reproduction: perspectives from the reproductive microbiomes of animals.}, journal = {F&amp;S reports}, volume = {6}, number = {Suppl 1}, pages = {45-49}, pmid = {40487326}, issn = {2666-3341}, abstract = {In all vertebrates, reproduction occurs in the context of host-associated microbiomes, which are increasingly recognized for their contributions to reproductive success. Although host-associated microbiomes are species specific, synthesizing patterns in microbial ecology across human and animal taxa provides perspectives for understanding the factors that shape microbial communities and their contributions to reproduction. Additionally, the fertility and reproductive physiology of animals under human care-particularly endangered species-is often meticulously monitored to maximize reproductive opportunities. In this mini-review, we examine current knowledge on reproductive microbiomes in animals, focusing, when available, on the sparse literature for wildlife species. We suggest ways in which studying animal microbial ecology may advance human fertility and reproduction by focusing on 3 microbial communities-vaginal, milk, and seminal microbiomes-which represent a large portion of literature and have clear implications for reproductive health. We identify avenues of future research that will further strengthen the linkages between reproductive research in wildlife species and humans and provide potential guidelines for practical applications of microbiome science to human reproductive health.}, }
@article {pmid40483289, year = {2025}, author = {Swain, PP and Subudhi, E and Sahoo, RK}, title = {Heavy Metals and Carbapenem-Resistant Klebsiella pneumoniae in a River System of Odisha, India: Correlation and Integrated Risk Assessment.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {62}, pmid = {40483289}, issn = {1432-184X}, support = {523/2020(BSR)//University Grants Commission/ ; }, mesh = {*Metals, Heavy/analysis ; *Rivers/microbiology/chemistry ; India ; *Klebsiella pneumoniae/drug effects/genetics/isolation &amp; purification ; Risk Assessment ; *Water Pollutants, Chemical/analysis ; *Carbapenems/pharmacology ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Wastewater/microbiology ; Environmental Monitoring ; Humans ; Microbial Sensitivity Tests ; }, abstract = {The unregulated release of heavy metals and antibiotics into rivers has the potential to significantly impact human health. Infections caused by healthcare-associated pathogen, carbapenem-resistant Klebsiella pneumoniae (CRKP), present a critical challenge to clinical practitioners due to its resistance to last-line antibiotics. In this study, we investigated co-contamination of heavy metals (As, Cd, Cr, Mn, and Pb) and CRKP isolates in water samples from multiple sites along the river receiving wastewater discharge from urban areas of twin-city, Odisha. We used a composite risk scoring framework integrating chemical risks (based on hazard indices (HI) of heavy metals) and biological risks (based on the proportion of CRKP isolates exhibiting multidrug-resistant phenotypes and their multiple antibiotic resistance (MAR) index. Furthermore, Spearman's correlations and redundancy analysis (RDA) were employed to assess the association between heavy metals and antibiotic resistance genes (ARGs). From the total CRKP isolates identified (n = 91), 90.1% and 9.89% exhibited multidrug resistant (MDR) and extensively drug-resistant (XDR) phenotypes, respectively. Sites D2 and C2 were flagged as high-risk sites based on their composite risk scores of 0.735 and 0.699, respectively. Positive correlations were observed between heavy metals and ARGs (blaOXA-48, blaTEM, and blaSHV). The findings raise concern regarding the potential threat of CRKP and heavy metal pollution in river water while also emphasizing the need for integrated assessment to control their release into the environment.}, }
@article {pmid40482721, year = {2025}, author = {Araujo, ASF and Pereira, APA and de Medeiros, EV and Mendes, LW}, title = {Root architecture and the rhizosphere microbiome: Shaping sustainable agriculture.}, journal = {Plant science : an international journal of experimental plant biology}, volume = {359}, number = {}, pages = {112599}, doi = {10.1016/j.plantsci.2025.112599}, pmid = {40482721}, issn = {1873-2259}, mesh = {*Rhizosphere ; *Plant Roots/microbiology/anatomy &amp; histology/growth &amp; development ; *Microbiota ; Soil Microbiology ; *Crops, Agricultural/microbiology/growth &amp; development ; *Agriculture ; Plant Breeding ; }, abstract = {Understanding root architecture and exudation is fundamental for enhancing crop productivity and promoting sustainable agriculture. Historically, plant researchers have focused on above-ground traits to increase yield and reduce input dependence. However, below-ground traits, especially those related to the root system, are equally critical yet often overlooked due to phenotyping challenges. Root architecture, including some root traits, i.e., lateral root density, root hair abundance, and root tip number, plays central roles in plant establishment, stress tolerance, and the recruitment of beneficial microbes in the rhizosphere. Root exudates, a complex array of chemical compounds released by roots, vary with plant species, developmental stage, and environmental conditions. These compounds act as signals and nutrients, shaping the composition and function of rhizosphere microbial communities. In turn, the microbiome of rhizosphere contributes to plant health by facilitating nutrient uptake, enhancing stress resilience, and providing defense against pathogens. Integrating root traits into breeding programs offers promising opportunities to select for genotypes that are more efficient in recruiting beneficial microbes. Heritable root traits, such as increased branching, finer roots, and higher exudation capacity, can enhance microbiome assembly and stability. The assessment of genes can also regulate of these traits and represent targets for genomics-assisted selection. Some strategies, such as microbiome engineering, particularly through the design of synthetic microbial communities (SynComs), can be used to modulate root architecture and optimize plant-microbe interactions. Despite these promising outcomes, challenges remain in translating SynCom applications to the field due to environmental variability, native microbial competition, and limited understanding of host genetic controls. This review discusses how root architecture shapes the rhizosphere microbiome and explores strategies, such as trait-based breeding and microbiome engineering, for advancing sustainable crop production.}, }
@article {pmid40481550, year = {2025}, author = {Zhu, F and Ying, H and Siadat, SD and Fateh, A}, title = {The gut-lung axis and microbiome dysbiosis in non-tuberculous mycobacterial infections: immune mechanisms, clinical implications, and therapeutic frontiers.}, journal = {Gut pathogens}, volume = {17}, number = {1}, pages = {40}, pmid = {40481550}, issn = {1757-4749}, abstract = {Non-tuberculous mycobacteria (NTM) are emerging pathogens of global concern, particularly in regions with declining tuberculosis rates. This review synthesizes current evidence on the epidemiology, immune pathogenesis, and microbiome interactions underlying NTM infections. The rising incidence of NTM is driven by environmental factors, immunocompromised populations, and advanced diagnostics. Clinically, NTM manifests as pulmonary, lymphatic, skin/soft tissue, or disseminated disease, with Mycobacterium avium complex (MAC) and M. abscessus being predominant pathogens. Host immunity, particularly Th1 responses mediated by IL-12/IFN-γ and TLR2 signaling, is critical for controlling NTM, while dysregulated immunity (e.g., elevated Th2 cytokines, PD-1/IL-10 pathways) exacerbates susceptibility. Emerging research highlights the gut-lung axis as a pivotal mediator of disease, where microbiome dysbiosis-marked by reduced Prevotella and Bifidobacterium-impairs systemic immunity and promotes NTM progression. Short-chain fatty acids (SCFAs) and microbial metabolites like inosine modulate macrophage and T-cell responses, offering therapeutic potential. Studies reveal distinct airway microbiome signatures in NTM patients, characterized by enriched Streptococcus and Prevotella, and reduced diversity linked to worse outcomes. Despite advances, treatment remains challenging due to biofilm formation, antibiotic resistance, and relapse rates. This review underscores the need for microbiome-targeted therapies, personalized medicine, and longitudinal studies to unravel causal relationships between microbial ecology and NTM pathogenesis.}, }
@article {pmid40481438, year = {2025}, author = {Babalola, OO and Osuji, IE and Akanmu, AO}, title = {Amplicon-based metagenomic survey of microbes associated with the organic and inorganic rhizosphere soil of Glycine max L.}, journal = {BMC genomic data}, volume = {26}, number = {1}, pages = {40}, pmid = {40481438}, issn = {2730-6844}, abstract = {OBJECTIVES: The metagenomic dataset of 16S rRNA and ITS gene amplicons of DNA were obtained from the cultivated soybean rhizosphere of organic and inorganic treatments. The organic treatments consisted of poultry waste, and cow dung treatments while the inorganic consisted of samples from untreated soybean plots and the bulk. Amplicon sequencing was performed on the Illumina platform, and the raw sequence data were processed and analyzed using Quantitative Insights Into Microbial Ecology (QIIME 2 version 2019.1.).<br><br>DATA DESCRIPTION: The analysis revealed a metagenomic library from soybean rhizospheric soils, providing insights into diversity and distribution of the bacterial and fungal community diversities. The most predominant bacteria phylum taxa across the treatments were Proteobacteria, Firmicutes, Actinobacteriota and Bacteriodota, while those for fungi were Ascomycota, Basidiomycota and Glomeromycota. The dataset provides insights into how different organic fertilization sources affect the structure, composition, and diversity of the microbiome in the soybean rhizosphere. The sequences have been deposited in the Sequence Read Archive (SRA) of the National Center for Biotechnology Information (NCBI) with assigned bioproject accession numbers; 16S rRNA (SRP540791) and ITS (SRP541849).}, }
@article {pmid40480043, year = {2025}, author = {Keating, C and Trego, A and O'Flaherty, V and Ijaz, UZ}, title = {Microbiomes of high-rate anaerobic digestors reveal 'Study'-specific factors and limitations of synthetic wastewater.}, journal = {Water research}, volume = {282}, number = {}, pages = {123931}, doi = {10.1016/j.watres.2025.123931}, pmid = {40480043}, issn = {1879-2448}, mesh = {*Wastewater/microbiology ; *Microbiota ; *Bioreactors/microbiology ; Anaerobiosis ; Archaea/genetics ; Bacteria/genetics ; Waste Disposal, Fluid ; }, abstract = {Anaerobic digestion (AD) is a key technology for the treatment of organic wastes and the production of renewable energy. The stability of the process hinges on the underlying microbial populations. Amplicon sequencing is increasingly used to characterise AD microbiomes, yet sequencing efforts have not translated to process engineering of the microbiome or prediction of failure using microbial tools. Using high-rate biofilm wastewater bioreactors as a study system, we aimed to i) discern trends in archaeal and bacterial diversity, ii) identify a core AD microbiome, iii) determine the functional stability of AD microbiomes, and iv) correlate taxa to experimental conditions. We analysed amplicon sequencing data from 32 high-rate anaerobic digestor studies (> 1258 samples) at various operational conditions and applied a suite of statistical microbiome tools. We found that taxonomic archaeal diversity was highly study dependent, while functional diversity was highly shared across studies. A core AD microbiome was identified with > 100 bacterial genera and 6 archaeal genera which were present at > 1 % relative abundance in at least 50 % of samples. Interestingly, we observed that microbiome stability was significantly impacted by the choice of real or synthetic wastewater, with synthetic wastewaters yielding a more stable and less complex microbiome. This was correlated to the abundances of 37 taxa in the synthetic wastewater, including 3 key methanogens (Methanothrix, Methanobacterium, and Methanosphaerula). This suggests that when synthetic wastewater is used in experimental studies, it may not result in an AD microbiome representative of real wastewater treatment systems.}, }
@article {pmid40476717, year = {2025}, author = {Baer, J and Little, M and Aquino, J and van der Geer, A and Sánchez-Quinto, A and Ballard, A and Lawrence, C and Carilli, J and Hartmann, A and Rohwer, F}, title = {Viralization as a microbial approach for enhancing coral reef restoration.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {40476717}, issn = {1751-7370}, support = {2209377//National Science Foundation/ ; CR20-5175//United States Department of Defense Environmental Security Technology Certification Program/ ; 9207//Gordon and Betty Moore Foundation/ ; S10 OD026929/OD/NIH HHS/United States ; 2022717//National Science Foundation/ ; }, mesh = {*Coral Reefs ; Animals ; *Anthozoa/virology/growth &amp; development/microbiology ; *Viruses/isolation &amp; purification ; Seawater/chemistry/virology ; *Environmental Restoration and Remediation/methods ; }, abstract = {Coral reef ecosystems rely on microorganisms to carry out biogeochemical processes essential to the survival of corals and the reef food web. However, widespread shifts from coral to algal dominance as a result of anthropogenic pressures have promoted microbial communities that compromise reef health through deoxygenation and disease. These degraded reefs become locked in a "microbialized" state characterized by high microbial biomass, low oxygen, and heightened pathogenic activity that stymie efforts to outplant corals onto the reef, a common approach applied to restore these ecosystems. Over 18 months, we compared viral and microbial dynamics alongside physical and chemical parameters ("water quality") between two coral outplanting sites and two midwater reef mesocosms called Coral Arks. Seafloor sites exhibited microbialization, whereas Arks maintained conditions with higher viral abundances and virus-to-microbe ratios, smaller and less abundant microorganisms, and consistently higher dissolved oxygen, water flow, and light availability. These conditions, which we term "viralized", supported enhanced coral growth and survival, greater benthic diversity, increased coral recruitment, reduced turf and macroalgae, and higher fish abundance compared to outplanting sites. Despite these benefits, analysis of microbial carbon metabolism genes revealed an underlying trend towards microbialization at both sites, reflecting larger-scale regional decline. These findings emphasize that microbial and physicochemical conditions are drivers of reef restoration outcomes; to be successful, restoration strategies must target the underlying environmental factors that support coral survival and resilience. We identify key microbial and physical variables-such as oxygen levels, flow, and viral activity-associated with viralized reef states, which should serve as focal points for developing new interventions and technologies aimed at creating conditions conducive to reef recovery.}, }
@article {pmid40474779, year = {2025}, author = {Green, N and Norwood, A and Sidhe, C and Mutlow, A and Aymen, J and Stiles, R and Bushell, J and Lim, T and Culver, E and Reeder, N and Timmer, M and Connelly, F and Charbonneau, J and McCall, W and Koenig, L and Stein, M and Geist, N and Lambert, MR and Hernández-Gómez, O}, title = {Shell Lesion Prevalence and Bacteriome Associations in Threatened Western Pond Turtles (Actinemys marmorata and Actinemys pallida) in California, USA.}, journal = {Journal of wildlife diseases}, volume = {61}, number = {3}, pages = {574-586}, pmid = {40474779}, issn = {1943-3700}, mesh = {Animals ; *Turtles/microbiology ; California/epidemiology ; *Animal Shells/microbiology/pathology/injuries ; Endangered Species ; *Bacteria/isolation &amp; purification/classification ; }, abstract = {Bacteriome characterization studies can provide insights into the microbial ecology associated with disease. We collected western pond turtles (Actinemys marmorata and Actinemys pallida) from six San Francisco Bay Area, California, USA, ponds; assessed their shells for lesions; and collected shell swabs and keratin scrape samples to evaluate bacteriome differences between the whole shell (swabs) and the affected tissues (scrapes). We quantified shell lesion type and prevalence by using visual inspections of photographs collected of the plastron and carapace and then applied 16S rRNA amplicon sequencing to characterize the associated bacteriomes of shells that observed pits, ulcerations, or no lesions. We observed shell lesions at high frequencies throughout our sites, with larger individuals (>100-mm plastron length) more likely to possess injuries. We saw no differences in alpha diversities between shells presenting with lesions and those on which we did not observe lesions; however, swab samples showed higher bacterial richness than keratin scrapes. The bacterial composition within the scrapes was influenced by pond location and then lesion presence. We observed a higher relative abundance of Actinobacteriota, Bacteroidota, Cyanobacteria, and Deinococcota in the shell keratin microflora of turtles with shell lesions. Because western pond turtles are under consideration for listing under the Endangered Species Act of 1973 in the USA, understanding patterns of shell disease pathologies and the bacteria associated with disease is imperative for the management of current populations.}, }
@article {pmid40474000, year = {2025}, author = {Cottam, DE and Cosgrove, DW and Megía-Palma, R and Žagar, A and Blázquez-Castro, S and Faria, JF and Turner, AE and Silva, DO and Pie, MR}, title = {Does the Gut Microbiome of the Insular Lizard Gallotia galloti Reflect Variation in Sex, Environment, and Population Genetic Differentiation?.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {61}, pmid = {40474000}, issn = {1432-184X}, mesh = {Animals ; *Lizards/microbiology/genetics ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Male ; Female ; Spain ; *Bacteria/classification/genetics/isolation &amp; purification ; Environment ; Genetic Variation ; Genetics, Population ; Sex Factors ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Despite their critical role in maintaining organismal health, the factors driving intraspecific variation in gut microbiotas in the wild are poorly understood. Gallotia galloti is a lizard endemic to the Canary Islands characterized by substantial phenotypic and genetic differentiation across populations, as well as by its ability to occur across considerably different environmental conditions. However, the extent to which such diversity is reflected in their gut microbiota is still unknown. Here, we use metabarcoding of fecal samples to explore how the gut microbiome of G. galloti reflects variation in sex, environment, human footprint, and subspecies identity. Fecal samples of 47 individuals were obtained across 13 locations to reflect the extent of intraspecific variation in the species. We found no evidence for consistent differences in microbiota richness across the studied groups, regardless of whether analyses were carried out at the genus, family, or phylum levels. Moreover, neither the richness nor composition of the microbiota was associated with variation in mean annual temperature, annual precipitation, and human footprint. Our results suggest that the generalist diet of G. galloti exposes them to a broad range of food items that provide a common template across the island, despite ecological and historical differences between populations.}, }
@article {pmid40473091, year = {2025}, author = {Santos, FSA and Corgosinho, PHC and de Abreu, FVS and Vaca-Sánchez, MS and Cuevas-Reyes, P and de Faria, ML and Valério, HM and Borges, MAZ}, title = {Assessing the impact of different scale removal methods on the geometric morphometrics of Aedes aegypti wings.}, journal = {Acta tropica}, volume = {268}, number = {}, pages = {107686}, doi = {10.1016/j.actatropica.2025.107686}, pmid = {40473091}, issn = {1873-6254}, mesh = {Animals ; *Aedes/anatomy &amp; histology ; *Wings, Animal/anatomy &amp; histology ; Sodium Hydroxide ; Glycerol ; }, abstract = {This work aimed to test different treatments for removing wing scales from Aedes aegypti, and evaluate through geometric morphometrics, if these treatments can modify the wing venation morphometric pattern. The treatments were wing agitation in mineral water and NaOH (sodium hydroxide) saline solution using a mini-ultrasound, and manual wing scales removal using a size zero (0) tip brush. We propose an alternative method for mounting wings on slides using glycerin. We conclude that glycerin use for slide mounting provides better optics and translucency, and that treatments with NaOH saline solution and water can impair morphometric analysis of wings. The size zero (0) tip brush treatment efficiently removed wing scales, improving wing structure visualization without causing significant modifications to the specimens.}, }
@article {pmid40471139, year = {2025}, author = {Gawish, R and Varada, R and Deckert, F and Hladik, A and Steinbichl, L and Cimatti, L and Milanovic, K and Jain, M and Torgasheva, N and Tanzer, A and De Paepe, K and Van de Wiele, T and Hausmann, B and Lang, M and Pechhacker, M and Ibrahim, N and De Vries, I and Brostjan, C and Sixt, M and Gasche, C and Boon, L and Berry, D and Jantsch, MF and Pereira, FC and Vesely, C}, title = {Filamin A editing in myeloid cells reduces intestinal inflammation and protects from colitis.}, journal = {The Journal of experimental medicine}, volume = {222}, number = {9}, pages = {}, pmid = {40471139}, issn = {1540-9538}, support = {57-B28//Austrian Science Fund/ ; V 1025-B//Austrian Science Fund/ ; DOC32-B28//Austrian Science Fund/ ; F8007//Austrian Science Fund/ ; P32678//Austrian Science Fund/ ; //Medical University of Vienna/ ; }, mesh = {*Filamins/genetics/metabolism ; Animals ; *Myeloid Cells/metabolism/pathology ; Humans ; *Colitis/genetics/pathology/prevention &amp; control ; *Inflammation/pathology/genetics ; Mice ; Mice, Inbred C57BL ; Neutrophils/metabolism ; *RNA Editing ; Macrophages/metabolism ; Male ; }, abstract = {Patho-mechanistic origins of ulcerative colitis are still poorly understood. The actin cross-linker filamin A (FLNA) impacts cellular responses through interaction with cytosolic proteins. Posttranscriptional A-to-I editing generates two forms of FLNA: genome-encoded FLNAQ and FLNAR. FLNA is edited in colon fibroblasts, smooth muscle cells, and endothelial cells. We found that the FLNA editing status determines colitis severity. Editing was highest in healthy colons and reduced during murine and human colitis. Mice that exclusively express FLNAR were highly resistant to DSS-induced colitis, whereas fully FLNAQ animals developed severe inflammation. While the genetic induction of FLNA editing influenced transcriptional states of structural cells and microbiome composition, we found that FLNAR exerts protection specifically via myeloid cells, which are physiologically unedited. Introducing fixed FLNAR did not hamper cell migration but reduced macrophage inflammation and rendered neutrophils less prone to NETosis. Thus, loss of FLNA editing correlates with colitis severity, and targeted editing of myeloid cells serves as a novel therapeutic approach in intestinal inflammation.}, }
@article {pmid40469738, year = {2025}, author = {Amen, R and Ganzert, L and Friedl, T and Rybalka, N and Wagner, D}, title = {From single pioneers to complex pro- and eukaryotic microbial networks in soils along a glacier forefield chronosequence in continental Antarctica.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1576898}, pmid = {40469738}, issn = {1664-302X}, abstract = {INTRODUCTION: In the extremely dry and oligotrophic soils of East Antarctica, where low temperatures and humidity result in minimal biological turnover rates, extracellular DNA (eDNA) can persist over extended timescales. Differentiating between sequences from living, potentially active cells (intracellular DNA, or iDNA) and those from ancient, non-living organisms (eDNA) is crucial for accurately assessing the current microbial community and understanding historical microbial dynamics.<br><br>METHODS: This study was conducted along a chronosequence in the Larsemann Hills, East Antarctica, where soil samples were collected from sites at varying distances from the glacier. By employing DNA separation methods, we distinguished iDNA, which represents living cells, from eDNA derived from dead organisms. High-throughput sequencing was used to characterize bacterial and eukaryotic communities across different successional stages.<br><br>RESULTS: The DNA separation approach revealed distinct bacterial and eukaryotic community structures along the glacier transect. Actinobacteria were consistently abundant across all sites, while other phyla such as Chloroflexi, Gemmatimonadetes, and Proteobacteria thrived in extreme, nutrient-poor environments. Early successional stages were characterized by the simultaneous colonization of green algae Trebouxiophyceae and cryophilic fungi, alongside nitrogen-fixing bacteria, which contributed to initial soil development. The study also identified three distinct modes of microbial distribution, reflecting varying degrees of activity and adaptability.<br><br>DISCUSSION: Our findings provide new insights into microbial dynamics in extreme habitats and propose new hypotheses for microbial colonization in newly exposed soils. Moreover, they contribute to the ongoing debate in microbial ecology regarding the viability of dormant or dead cells and emphasize the need for refining DNA-based methods and exploring functional pathways to deepen our understanding of microbial succession in polar regions.}, }
@article {pmid40469504, year = {2025}, author = {Van Den Bossche, T and Armengaud, J and Benndorf, D and Blakeley-Ruiz, JA and Brauer, M and Cheng, K and Creskey, M and Figeys, D and Grenga, L and Griffin, TJ and Henry, C and Hettich, RL and Holstein, T and Jagtap, PD and Jehmlich, N and Kim, J and Kleiner, M and Kunath, BJ and Malliet, X and Martens, L and Mehta, S and Mesuere, B and Ning, Z and Tanca, A and Uzzau, S and Verschaffelt, P and Wang, J and Wilmes, P and Zhang, X and Zhang, X and Li, L and , }, title = {The microbiologist's guide to metaproteomics.}, journal = {iMeta}, volume = {4}, number = {3}, pages = {e70031}, pmid = {40469504}, issn = {2770-596X}, support = {R35 GM138362/GM/NIGMS NIH HHS/United States ; }, abstract = {Metaproteomics is an emerging approach for studying microbiomes, offering the ability to characterize proteins that underpin microbial functionality within diverse ecosystems. As the primary catalytic and structural components of microbiomes, proteins provide unique insights into the active processes and ecological roles of microbial communities. By integrating metaproteomics with other omics disciplines, researchers can gain a comprehensive understanding of microbial ecology, interactions, and functional dynamics. This review, developed by the Metaproteomics Initiative (www.metaproteomics.org), serves as a practical guide for both microbiome and proteomics researchers, presenting key principles, state-of-the-art methodologies, and analytical workflows essential to metaproteomics. Topics covered include experimental design, sample preparation, mass spectrometry techniques, data analysis strategies, and statistical approaches.}, }
@article {pmid40468430, year = {2025}, author = {Khoiri, AN and Costa, NR and Crusciol, CAC and Pariz, CM and Costa, C and Calonego, JC and de Castilhos, AM and de Souza, DM and de Lima Meirelles, PR and Cru, IV and Moretti, LG and Bossolani, JW and Kuramae, EE}, title = {Pigeon pea-mediated soil microbial shifts improve agroecosystem multifunctionality in long-term maize-palisade grass intercropping.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {60}, pmid = {40468430}, issn = {2524-6372}, support = {#2014/21772-4 and #2014/14935-4//S&#xe3;o Paulo Research Foundation (FAPESP)/ ; #458225/2014-2//National Council for Scientific and Technological Development (CNPq)/ ; 1378/14//Funda&#xe7;&#xe3;o Agrisus/ ; }, abstract = {BACKGROUND: Intercropping systems enhance agricultural sustainability by promoting ecosystem multifunctionality (EMF). This study examined the impact of adding pigeon pea (M + PG + PP) into a maize-palisade grass (M + PG) intercropping system under a no-till system (NTS) on soil microbial communities and ecosystem services. After five consecutive growing seasons, bulk soil samples from a soybean-based crop-livestock system were analyzed using metagenomics.<br><br>RESULTS: The inclusion of pigeon pea significantly improved the EMF index, with higher plant productivity and slightly enhanced outcomes in soil health, lamb meat productivity, and climate protection. The M&#x2009;+&#x2009;PG&#x2009;+&#x2009;PP treatment enriched Bradyrhizobium spp., which were positively correlated with soil health, plant productivity, and EMF index. Functional analysis indicated that M&#x2009;+&#x2009;PG&#x2009;+&#x2009;PP treatment enhanced nitrogen metabolism, biofilm formation, and exopolysaccharide (EPS) biosynthesis, improving soil fertility and microbial activity. Similarly, functional analysis of microbial plant growth-promoting traits revealed that the M&#x2009;+&#x2009;PG&#x2009;+&#x2009;PP treatment promoted microbial functions related to nitrogen and iron acquisition, sulfur assimilation, and plant colonization, all essential for plant growth and nutrient cycling. In contrast, the M&#x2009;+&#x2009;PG treatment primarily enhanced pathways related to competitive exclusion and phytohormone production.<br><br>CONCLUSIONS: These findings highlight the importance of incorporating legumes such as pigeon pea into intercropping systems to optimize ecosystem services, enhance soil health, and promote long-term agricultural productivity and sustainability.}, }
@article {pmid40467851, year = {2025}, author = {Rakotonindrina, V and Andriamananjara, A and Razafimbelo, T and Okamoto, T and Sarr, PS}, title = {Land Cover and Seasonal Variations Shape Soil Microbial Communities and Nutrient Cycling in Madagascar Tropical Forests.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {60}, pmid = {40467851}, issn = {1432-184X}, mesh = {*Soil Microbiology ; Seasons ; Madagascar ; *Forests ; Soil/chemistry ; Tropical Climate ; Nitrogen/analysis/metabolism ; Carbon/analysis ; *Microbiota ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Fungi/genetics/classification/isolation &amp; purification/metabolism ; RNA, Ribosomal, 16S/genetics ; Phosphorus/analysis/metabolism ; Trees ; Ecosystem ; }, abstract = {Understanding how land cover and seasonal variations influence soil microbial communities and nutrient cycling is crucial for sustainable land management in tropical forests. However, such investigations are limited in Madagascar's tropical ecosystems. This study investigated the impacts of land cover types and seasonal variations on soil properties and microbial communities in the tropical forest region of Andasibe, Madagascar. Soil samples were collected from four land cover types-tree fallow (TSA), shrub fallow (SSA), eucalyptus forest (EUC), and degraded land (TM)-across three seasonal periods: the dry season, the start of the rainy season, and the end of the rainy season. Both land cover and sampling season affected soil pH and available P, whereas total nitrogen, soil organic carbon, and the C/N ratio were affected only by land cover. The soil organic carbon and total nitrogen concentrations were greater in TM. NextSeq sequencing of the 16S rRNA gene and ITS regions of the nuclear rRNA operon revealed distinct microbial community compositions across land covers, with greater diversity in the TSA and SSA. Bacteria are more sensitive to seasonal changes than are fungi, with phosphate-solubilizing (gcd) and phosphate-mineralizing (phoD) genes being more abundant in the rainy season, emphasizing the role of microbes in nutrient availability under different climatic conditions. Principal component analysis highlighted SSA as a hotspot for microbial activity, reinforcing the potential of shrub ecosystems in soil restoration. These findings reveal strong land cover and seasonal effects on soil microbial functions, with implications for nutrient cycling, ecosystem resilience, and sustainable land management in tropical forest landscapes.}, }
@article {pmid40467767, year = {2025}, author = {Yan, Z and Yao, Y and Xu, Q and He, X and Zhou, X and Wang, H}, title = {Dietary microbiota-mediated shifts in gut microbial ecology and pathogen interactions in giant pandas (Ailuropoda melanoleuca).}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {864}, pmid = {40467767}, issn = {2399-3642}, mesh = {Animals ; *Ursidae/microbiology ; *Gastrointestinal Microbiome ; *Diet/veterinary ; Feces/microbiology ; *Bacteria/genetics/classification ; }, abstract = {The impact of dietary microorganisms on host microbiota is recognized, but the underlying mechanisms remain unclear. This study examined the effects of bamboo surface microbiota, including virulence factors, antibiotic resistance genes (ARGs), and mobile genetic elements from different bamboo parts (leaves, shoots, and culms), on giant panda gut microbiota using three pairs of twins. Results showed that bamboo and fecal samples shared 1670 microbial species, with shoot surface microbiota contributing the highest proportion (21%, Bayesian source tracking) of contemporaneous gut microbiota, primarily by increasing abundances of Escherichia coli and ARGs. Klebsiella pneumoniae and Salmonella enterica also showed high co-occurrence in both bamboo and fecal samples, indicating potential colonization. Additionally, Streptococcus suis, Acinetobacter, and Mycobacterium progressively declined in fecal samples as bamboo shoot intake increased, suggesting these microbes are likely transient. The findings emphasize the impact of foodborne microorganisms on the host and the importance of conservation management.}, }
@article {pmid40467587, year = {2025}, author = {Xiong, S and Xie, B and Yin, N and Zhu, H and Gao, H and Xu, X and Xiao, K and Cai, X and Sun, G and Sun, X and Cui, Y and Van de Wiele, T and Zhu, Y}, title = {Prenatal exposure to trace elements impacts mother-infant gut microbiome, metabolome and resistome during the first year of life.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {5186}, pmid = {40467587}, issn = {2041-1723}, support = {No. L232076//Natural Science Foundation of Beijing Municipality (Beijing Natural Science Foundation)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; Female ; Pregnancy ; Infant ; *Trace Elements/adverse effects ; *Metabolome/drug effects ; Feces/microbiology ; *Prenatal Exposure Delayed Effects/microbiology/metabolism ; Adult ; Male ; Metagenomics ; Hair/chemistry ; *Maternal Exposure/adverse effects ; Infant, Newborn ; Bacteria/genetics/classification/drug effects ; Copper ; }, abstract = {Infancy is a critical window for the colonization of gut microbiome. However, xenobiotic impacts on gut microbiome development in early life remain poorly understood. Here, we recruit 146 mother-infant pairs and collect stool samples at 3, 6, and 12 months after delivery for amplicon sequencing (N = 353), metagenomics (N = 65), and metabolomics (N = 198). Trace elements in maternal hair samples (N = 119) affect diversity and composition of the infant gut microbiome. Shannon diversity in 3 month-old infants is correlated positively with selenium and negatively with copper, and relative abundance of Bifidobacterium increases under high exposure to aluminum and manganese. During the first year of life, infants and their paired mothers have distinct microbial diversity and composition, and their bacterial community structures gradually approach. here are 56 differential metabolites between the first and second visit and 515 differential metabolites between the second and third visit. The typical profile of antibiotic resistance genes (ARGs) significantly differs between infants and their mothers. High levels of copper and arsenic exposure may induce the enrichment of ARGs in the infant gut. Our findings highlight the dynamics of the gut microbiome, metabolites, and ARG profiles of mother-infant pairs after delivery, associated with prenatal exposure to trace elements.}, }
@article {pmid40467261, year = {2025}, author = {Cabezas-Terán, K and Grootaert, C and Van Camp, J and Ortiz, J and Ruales, J and Donoso, S and Van de Wiele, T}, title = {Bioaccessibility of β-carotene during in vitro co-digestion of encapsulated mango peel carotenoids with milk.}, journal = {Food research international (Ottawa, Ont.)}, volume = {214}, number = {}, pages = {116576}, doi = {10.1016/j.foodres.2025.116576}, pmid = {40467261}, issn = {1873-7145}, mesh = {*Mangifera/chemistry ; *beta Carotene/pharmacokinetics/metabolism ; *Milk/chemistry/metabolism ; *Digestion ; Animals ; Biological Availability ; *Fruit/chemistry ; *Carotenoids ; Particle Size ; }, abstract = {β-carotene is a carotenoid with provitamin A activity whose digestive stability and bioaccessibility prior to intestinal absorption are important to fully exploit its health benefits. Microencapsulation protects carotenoids, but there is a lack of information on the extent to which its characteristics and interactions with complex food matrices could impact the carotenoid micellization during digestion. We evaluated the effect of milk fat content on the in vitro bioaccessibility of β-carotene from microparticles containing carotenoids from mango peel. The microparticles tested contained solvent-extracted carotenoids and supercritical fluid-extracted carotenoids, and were separately co-digested with whole, semi-skimmed and skimmed milks. Bioaccessibility was assessed using an in vitro digestion method adapted to carotenoids. β-carotene recoveries after in vitro digestions ranged from 79.6 to 102.2 %, with the highest values corresponding mainly to microparticles with the lowest initial β-carotene concentration. β-carotene bioaccessibilities ranged from 8.8 to 75.5 %, the highest values being obtained mainly when the microparticles were co-digested with whole milk, especially when those containing supercritical fluid-extracted carotenoids were used. The bioaccessibility-enhancing effect of the milk fat was explained by the higher concentration of free fatty acids in the micellar phase, while the better results in the microparticles containing supercritical-fluid-extract was attributed to the lower initial concentration of β-carotene. In conclusion, increasing the milk fat content increased the bioaccessibility of encapsulated β-carotene from mango peel, further determining that, a lower initial concentration of β-carotene in the microparticles resulted in higher bioaccessibility.}, }
@article {pmid40467013, year = {2025}, author = {Valmas, MI and Kormas, K and Karpouzas, DG and Konstantinidis, KT and Rozman, SD and Udiković-Kolić, N and Remus-Emsermann, MNP and Vasileiadis, S}, title = {Targeted analysis of metagenomes: divide and conquer.}, journal = {Biotechnology advances}, volume = {83}, number = {}, pages = {108619}, doi = {10.1016/j.biotechadv.2025.108619}, pmid = {40467013}, issn = {1873-1899}, mesh = {*Metagenomics/methods ; *Metagenome/genetics ; High-Throughput Nucleotide Sequencing/methods ; Microbiota/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {The rapidly developing field of targeted analysis of metagenomes focuses on retrieving information about specific genes and/or genome(s) from environmental DNA. The traditional shotgun sequencing methods overemphasise dominant microorganisms and often fail to confidently assign the entirety of the analysed genetic material to specific species, genomovars, or strains. The ultimate goal of the targeted methods is to overcome this limitation of throughput and precision of current shotgun metagenomics when analysing complex microbial communities in the quest of refined information. Here, we discuss recent technological advances that are designed to focus the analytical power of diagnostic tools like sequencing, towards phylogenetically or functionally distinct and rare microbial groups and enhance e.g. the confidence in the assignment of genetic elements to their respective owning organisms. We specifically showcase the capabilities of these technological advances for targeted analysis of metagenomes, identify suitable related applications, discuss methodological limitations, and propose solutions for addressing these limitations. This review aspires to inspire highly relevant experimental designs in the future that will unlock unknown and important aspects of microbial ecology, and the yet-uncultivated microbial majority.}, }
@article {pmid40465274, year = {2025}, author = {Hassen, B and Hammami, S}, title = {Environmental phages: ecosystem dynamics, biotechnological applications and their limits, and future directions.}, journal = {Journal of applied microbiology}, volume = {136}, number = {6}, pages = {}, doi = {10.1093/jambio/lxaf136}, pmid = {40465274}, issn = {1365-2672}, support = {//IRESA/ ; }, mesh = {*Bacteriophages/physiology/genetics ; *Ecosystem ; *Biotechnology/methods/trends ; Gene Transfer, Horizontal ; Bacteria/virology ; *Environmental Microbiology ; }, abstract = {Phages, the most abundant biological entities on Earth, play a crucial role in various microbial ecosystems, significantly impacting biogeochemical cycles and bacterial evolution. They inhabit diverse environments, including soil, water, and extreme conditions, where they contribute to the contribute to regulating microbial populations, facilitate genetic exchange, and aid in nutrient cycling. Recent research has highlighted their potential in addressing antibiotic resistance, enhancing wastewater treatment, promoting agricultural sustainability, and tackling environmental issues. However, their ability to disseminate antibiotic resistance genes through horizontal gene transfer raises important concerns, warranting a thorough assessment of their ecological and biotechnological applications. This review synthesizes current knowledge on the diversity, ecological roles, and practical uses of environmental phages, emphasizing both their benefits and limitations. By analyzing recent findings and real-world applications, it provides insights into the challenges encountered and future directions for leveraging phages in environmental management, biotechnology, and healthcare.}, }
@article {pmid40464990, year = {2025}, author = {Peng, Z and Kang, C and Xu, Y and Zhang, C and Zhang, Y and Yan, B and Wang, S and Guo, X and Wan, X and Lv, C and Huang, L and Guo, L and Wang, H}, title = {Effects of Wild and Domesticated Seeds on the Colonization of Rhizosphere Microorganisms in Atractylodes lancea.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {59}, pmid = {40464990}, issn = {1432-184X}, support = {2023YFC3503804//National Key Research and Development Program of China/ ; 2023YFC3503804//National Key Research and Development Program of China/ ; 2023YFC3503804//National Key Research and Development Program of China/ ; 2023YFC3503804//National Key Research and Development Program of China/ ; ZZ18-YO-051, ZZ13-YQ-096//Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; ZZ18-YO-051, ZZ13-YQ-096//Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; ZZ18-YO-051, ZZ13-YQ-096//Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; ZZ18-YO-051, ZZ13-YQ-096//Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; CI2021A03903, CI2021A03905, CI2021B013//Scientific and technological innovation project of China Academy of Chinese Medical Sciences/ ; CI2021A03903, CI2021A03905, CI2021B013//Scientific and technological innovation project of China Academy of Chinese Medical Sciences/ ; CI2021A03903, CI2021A03905, CI2021B013//Scientific and technological innovation project of China Academy of Chinese Medical Sciences/ ; CI2021A03903, CI2021A03905, CI2021B013//Scientific and technological innovation project of China Academy of Chinese Medical Sciences/ ; No: ZYYCXTD-D-202005//Innovation Team and Talents Cultivation Program of National Administration of Traditional Chinese Medicine/ ; No: ZYYCXTD-D-202005//Innovation Team and Talents Cultivation Program of National Administration of Traditional Chinese Medicine/ ; No: ZYYCXTD-D-202005//Innovation Team and Talents Cultivation Program of National Administration of Traditional Chinese Medicine/ ; No: ZYYCXTD-D-202005//Innovation Team and Talents Cultivation Program of National Administration of Traditional Chinese Medicine/ ; }, mesh = {*Rhizosphere ; *Seeds/microbiology/growth &amp; development ; *Soil Microbiology ; *Atractylodes/microbiology/growth &amp; development ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; Seedlings/microbiology/growth &amp; development ; Plant Roots/microbiology ; Domestication ; Endophytes/classification/isolation &amp; purification/genetics ; Plant Leaves/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The domestication of plant species has played a pivotal role in shaping human civilization, yet it has also contributed to a significant reduction in the genetic diversity of crop varieties. This reduction may have profound implications for the formation and establishment of rhizosphere microbial communities in plants. This study systematically investigates microbiome dynamics during seed development in wild and domesticated Atractylodes lancea. The seeds from both wild and domesticated A. lancea exhibited shared microbial genera, while their communities were changed significantly. However, when A. lancea seeds from wild and domesticated germinated into seedlings under identical microbiological conditions, the leaves and root endophytic microbial and rhizosphere microbiome displayed similar genus. Remarkably, the rhizosphere microbial communities of the seedlings consistently enriched Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Paenibacillus, Variovorax, Conexibacter, and norank_f__Micropepsaceae. And this convergence likely arises from the shared chemotype of A. lancea and exposure to identical environmental microbiomes. In summary, this study delineates the transmission processes of A. lancea seed endophytes and identifies the dynamic patterns of microbial shifts during its development from seed to seedling. These findings contribute to a broader understanding of plant-microbe interactions and the role of microbial ecology in crop improvement.}, }
@article {pmid40463892, year = {2025}, author = {Shepherd, RM and Oliverio, AM}, title = {The Biogeography of Apicomplexan Parasites in Tropical Soils.}, journal = {Ecology and evolution}, volume = {15}, number = {6}, pages = {e71478}, pmid = {40463892}, issn = {2045-7758}, abstract = {Parasitic protists such as Apicomplexa, an abundant group of soil protists, contribute to ecosystem processes and nutrient cycling in belowground soil systems through their obligate symbioses with soil Metazoa. Yet despite the importance of soil parasites, the biodiversity and biogeography of Apicomplexa in belowground systems remain poorly characterized. Leveraging 205 soils collected across a rainfall gradient spanning the isthmus of Panama, we sought to understand the distribution of soil Apicomplexa lineages and how abiotic (e.g., soil and climatic) and biotic (e.g., soil Metazoa) factors relate to their diversity and structure. Apicomplexa were highly heterogeneous across the samples and comprised 30% of the soil protist community on average. Soil pH, along with phosphorus and magnesium, best explained the overall distribution of Apicomplexa. Soil Metazoa distributions also corresponded to Apicomplexa distributions, and many Metazoan taxa co-occurred with particular Apicomplexa, which may reflect ecological interactions (such as parasitism) or shared habitat preferences. These results highlight the potential roles of both soil and climatic variables and putative hosts in structuring parasite distributions in belowground tropical systems. Our work builds a broader understanding of Apicomplexa biodiversity in tropical soils and sheds light on environmental factors that may contribute to shaping their distribution in belowground systems. These results help inform our understanding of the importance of parasites in tropical forest soils.}, }
@article {pmid40463148, year = {2025}, author = {Usman, H and Molaei, M and House, S and Haase, MF and Dennis, CL and Niepa, THR}, title = {Magnetically Responsive Nanocultures for Direct Microbial Assessment in Soil Environments.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.05.17.654660}, pmid = {40463148}, issn = {2692-8205}, abstract = {UNLABELLED: Cultivating microorganisms in native-like conditions is vital for bioprospecting and accessing currently unculturable species. However, there remains a gap in scalable tools that can both mimic native microenvironments and enable targeted recovery of microbes from complex settings. Such approaches are essential to advance our understanding of microbial ecology, predict community functions, and discover novel biotherapeutics. We present magnetic nanocultures-a high-throughput microsystem for isolating and growing environmental microbes under near-native conditions. These nanoliter-scale bioreactors are encapsulated in semi-permeable membranes that form magnetic polymeric microcapsules using iron oxide nanoparticles within polydimethylsiloxane-based shells. This design offers mechanical stability and magnetic actuation, enabling efficient retrieval from soil-like environments. The nanocultures are optimized for optical and biological properties to support microbial encapsulation, growth, and sorting. Our study demonstrates the feasibility of using magnetically responsive microenvironments to cultivate elusive microbes, offering a promising platform for discovering previously uncultured or unknown microbial species.<br><br>TEASER: Engineered magnetic nanocultures support microbial growth and magnetic separation from complex environments.}, }
@article {pmid40462960, year = {2025}, author = {Wheeler, KM and Oh, MW and Fusco, J and Mershon, A and Kim, E and De Oliveira, A and Rahme, LG}, title = {MvfR shapes Pseudomonas aeruginosa Interactions in Polymicrobial Contexts: Implications for Targeted Quorum Sensing Inhibition.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40462960}, issn = {2692-8205}, support = {R01 AI177555/AI/NIAID NIH HHS/United States ; }, abstract = {Infections often occur in complex niches consisting of multiple bacteria. Despite the in-creasing awareness, there is a fundamental gap in understanding which interactions govern mi-crobial community composition. Pseudomonas aeruginosa is frequently isolated from monomicrobi-al and polymicrobial human infections. This pathogen forms polymicrobial infections with other ESKAPEE pathogens and defies eradication by conventional therapies. By analyzing the competi-tion within cocultures of P. aeruginosa and representative secondary pathogens that commonly co-infect patients, we demonstrate the antagonism of P. aeruginosa against other ESKAPEE pathogens and the contribution of this pathogen's multiple quorum sensing (QS) systems in these interac-tions. QS is a highly conserved bacterial cell-to-cell communication mechanism that coordinates collective gene expressions at the population level, and it is also involved in P. aeruginosa virulence. Using a collection of P. aeruginosa QS mutants of the three major systems, LasR/LasI, MvfR/PqsABCDE, and RhlR/RhlI and mutants of several QS-regulated functions, we reveal that MvfR and, to a lesser extent, LasR and RhlR control competition between P. aeruginosa and other microbes, possibly through their positive impact on pyoverdine, pyochelin, and phenazine genes. We show that MvfR inhibition alters competitive interspecies interactions and preserves the coexistence of P. aeruginosa with ESKAPEE pathogens tested while disarming the pathogens' ability to form biofilm and adhere to lung epithelial cells. Our results highlight the role of MvfR inhibition in modulating microbial competitive interactions across multiple species, while simultaneously atten-uating virulence traits. These findings reveal the complexity and importance of QS in interspecies interactions and underscore the impact of the anti-virulence approach in microbial ecology and its importance for treating polymicrobial infections.}, }
@article {pmid40462143, year = {2025}, author = {Kindtler, NL and Sheikh, S and Zervas, A and Ellegaard-Jensen, L and Feld, L and Scheel, M and Jiménez, FC and da Fonseca, RR and Laursen, KH and Jacobsen, CS and Ekelund, F}, title = {Small sample amounts from rhizosphere of barley maintain microbial community structure and diversity revealed by total RNA sequencing.}, journal = {Plant methods}, volume = {21}, number = {1}, pages = {79}, pmid = {40462143}, issn = {1746-4811}, abstract = {Total RNA sequencing is a crucial technique in microbial ecology for profiling active microbial communities in various environments, including the rhizosphere. Since total RNA sequencing yields both 16 S and 18 S ribosomal RNA (rRNA), it is effective for taxonomic profiling of the full microbial community in a sample. However, the effectiveness of this approach with limited initial sample amounts remains unclear. In this study, we grew barley in a growth system designed for highly controlled plant experiments using an inert growth medium inoculated with a soil microbiome. Our objectives were two-fold: firstly, to test the feasibility of extracting total RNA from the rhizosphere of barley grown in an inert growth medium consisting of sand and perlite. Secondly, we aimed to address the challenge of extracting comprehensive taxonomic information from minimal amounts of rhizosphere samples from barley plants, using three different amounts of freeze-dried rhizosphere material: 10, 40, and 200 mg. We showed that although smaller sample amounts yielded lower concentrations of extracted RNA, this did not significantly influence the diversity or composition of the rhizosphere microbiome as indicated by SSU rRNA. Our results demonstrate that total RNA sequencing, focusing on SSU rRNA, robustly captures the taxonomic diversity of active rhizosphere microbial communities, even in small initial sample amounts. Effective use of smaller samples opens new possibilities for detailed studies in environments where sample quantity is limited. We also conclude that the growth system applied in this experiment is suitable for highly controlled plant experiments focusing on total RNA extraction from the rhizosphere.}, }
@article {pmid40461733, year = {2025}, author = {Ruiz-Blas, F and Friese, A and Bartholomäus, A and Henny, C and Russell, JM and Kallmeyer, J and Vuillemin, A}, title = {The Deep Subsurface Biosphere and its Substrates Along a One-Million-Year Ferruginous Lake Archive.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {58}, pmid = {40461733}, issn = {1432-184X}, support = {KA 2293/8-1//Deutsche Forschungsgemeinschaft/ ; VU 94/1-1//Deutsche Forschungsgemeinschaft/ ; P2GEP2_148621//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; }, mesh = {*Lakes/microbiology/chemistry ; *Geologic Sediments/microbiology/chemistry ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism ; Indonesia ; *Archaea/genetics/classification/isolation &amp; purification ; Phylogeny ; Iron/analysis/metabolism ; Biodiversity ; }, abstract = {Lake Towuti, Indonesia, is an ancient stratified lake with ferruginous (iron-rich, sulfate-poor) anoxic bottom water conditions and a long depositional record affected by redox changes in the water column and sediments. As modern analogue of Earth's early ferruginous oceans, it enables the study of an active microbial subsurface biosphere and its role in organic matter and iron mineralization. Combining 16S rRNA genes, cell counts, pore water geochemistry, and bulk sediment profiles from a 100-m-long core, we present the first comprehensive characterization of the deep subsurface biosphere along a one-million-year lacustrine archive. Electron acceptors in the pore water became depleted at shallow depths, resulting in a drastic decrease in cell densities in the fermentative zone, where Bathyarchaeia dominate the microbial community composition. Although alpha and beta diversity reflected initial depletion of substrates during burial, they also varied across successive lithologies, indicating that sediment composition subsequent to deposition also affects diversity. The upper sediments (0-20 mblf) sheltered a dense and diverse microbial community involved in organic matter remineralization, actively producing and converting volatile fatty acids into carbon dioxide and methane. Deeper sediments (20-70 mblf) contained low-diversity microbial communities adapted to nutrient scarcity. In contrast, deepest lacustrine sediments (70-100 mblf) contained an increased microbial diversity reflecting greater availability of organic matter of terrestrial origin. Despite Bathyarchaeia being prime constituents of the deep subsurface biosphere, increased diversity in 16S rRNA gene composition was observed in discrete sediment layers (tephra, diatom ooze, peat). This demonstrated that depositional conditions remained traceable, while stratified microbial communities drove reductive diagenesis.}, }
@article {pmid40461630, year = {2025}, author = {Koch, M and Lado, S and Bodner-Adler, B and Carlin, G and Pacífico, C and Bauer, C and Cartwright, R and Seki, D and Steininger, C and Makristathis, A and Umek, W}, title = {Women suffering from overactive bladder syndrome exhibit a higher urethral viral abundance compared to healthy controls: a pilot study.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {19484}, pmid = {40461630}, issn = {2045-2322}, support = {1815//OeNB Jubil&#xe4;umsfonds/ ; }, mesh = {Humans ; Female ; *Urinary Bladder, Overactive/virology/microbiology ; Pilot Projects ; Middle Aged ; *Urethra/virology/microbiology ; Microbiota ; Case-Control Studies ; Prospective Studies ; Adult ; Phylogeny ; Aged ; Bacteria/genetics ; Virome ; *Viruses/genetics/isolation &amp; purification/classification ; High-Throughput Nucleotide Sequencing ; }, abstract = {The interactions between the human bacterial microbiome and essential bodily functions are well established for organ systems such as the oral cavity, gut, and female reproductive tract. However, the urinary microbiome, particularly its viral component, remains largely unexplored. Emerging evidence suggests that the urinary microbiome may play a significant role in the development of overactive bladder syndrome (OAB). This study aims to fill this knowledge gap by investigating the potential link between the urethral virome and female overactive bladder syndrome, and by aligning these findings with the bacterial microbiome. Prospective pilot study including 15 patients with overactive bladder syndrome and five controls. Current urinary tract infection and antibiotic therapy within the last two months were ruled out and controls were matched to cases by age and body mass index. Urethral swabs (Copan eSwab[®] urethra) were taken from each participant at one single time point. Subsequent viral isolation, purification, and enrichment were conducted using the ViPEP method. Next-generation sequencing was performed on pooled samples, followed by bioinformatic analysis to identify and classify viral contigs. Phylogenetic analysis was conducted to assess genetic relationships among identified viral sequences. The bacterial microbiome was analyzed by sequencing of the variable V3-4 region of the eubacterial 16 S rDNA gene on the Illumina MiSeq platform. We identified twenty-one viruses and bacteriophages only in pooled urethral swab samples of the OAB group, but no valid detections were retained in the control group after analysis. The most abundant human virus in urethral swab samples was human papilloma virus, whereas the most abundant bacteriophages belong to the family of Siphoviridae. In the bacterial microbiome analysis, we identified statistically higher levels of Veillonella and Bacteroides in OAB samples. Results of this pilot study suggest a difference in the urethral virome between women with OAB and healthy controls. When looking deeper into the detected virus families and species, we might postulate a unique microbial pattern of OAB patients. This pattern suggests an interplay of immunosuppression, autoimmune processes and a larger diversity of bacterial and viral microbes. Current evidence strongly suggests a disturbance of the healthy microbiome of the urogenital tract in patients with OAB, leading to subclinical chronic inflammation and thus typical OAB symptoms. Further research should focus on interventions aimed at restoring a healthy microbiome in OAB patients to mitigate inflammation and improve symptom control.}, }
@article {pmid40459550, year = {2025}, author = {Wu, Y and Zhang, F and Zhang, S and Zhang, J and Zhao, S and Qiu, Z and Zhu 朱, M&#x58a8;}, title = {Curvularia spicifera causing black rot on Ipomoea batatas in China.}, journal = {Plant disease}, volume = {}, number = {}, pages = {}, doi = {10.1094/PDIS-03-25-0477-PDN}, pmid = {40459550}, issn = {0191-2917}, abstract = {Ipomoea batatas (sweet potato) is an annual herb originating from South America and the large and small Antilles. It is widely cultivated in tropical and subtropical regions around the world and is widely grown in most parts of China. As an edible plant with rich nutrition, I. batatas has high economic and medicinal value (Suhendy et al. 2023). In September 2023, black rot-like disease signs and symptoms were observed on the roots of I. batatas in a farmland (about 6667 m2) located in Kaifeng city, Henan Province, China. The roots showed irregular brown or dark spots on the surface, extending to the internal center, and brown to black necrosis. Additionally, above-ground parts of infected plants showed symptoms such as yellowing and wilting of leaves, brown spots on stems, and stunted growth. Around 80 % of monitored plant roots (n = 200) exhibited the symptoms. Infected roots were cut into pieces and then placed on potato dextrose agar (PDA) (light/dark, 16 h/8 h; temperature, 18°C). After a period of 3-10 days, single hyphal tips of each fungal colony were placed on PDA and incubated for another 5-10 days (Paul et al. 2021). Colonies of the fungal pathogen on PDA reached 50 mm in diameter within 7 days, dark gray on the inner side, dark brown extending to the edge, irregular round edge, with abundant aerial mycelium, cotton-like, irregularly convex upward, undulating. The conidia were brown, ellipsoid to oval, 8 to 19 × 3 to 6 μm (n = 50). Morphologically similar isolates with characteristics consistent with those of Curvularia spicifera (Cui et al. 2020) were recovered from 87% of symptomatic root tissues (n=100). The internal transcribed spacer (ITS) region and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene from three independent isolates (CSZM202101, CSZM202102, and CSZM202103) of the fungus were amplified and sequenced with primers ITS1/ITS4 (Seliger et al. 1990) and GAPDH1/GAPDH3R (Bradshaw et al. 2022) according to a previously reported method (Zhu et al. 2022). The resulting sequences were deposited in GenBank (Accession No. OR885691, PV056889, PV056568, PQ839726, PV072835 and PV02836). BLASTn analysis showed that the ITS and GAPDH sequences had 100% (ITS, 516/516; GAPDH, 508/508) identity with C. spicifera (OQ845826 and CBS 274.52 JN192387) from maize (Ram et al. 2024) and pearl millet (S. et al. 2024), respectively. The phylogenetic analysis clearly illustrated that these isolates clustered with the sequences of a representative reference strain of C. spicifera(CBS 274.52, GenBank accession number JN192387). Therefore, the morphological, molecular and phylogenetic analysis indicated that the pathogen was C. spicifera. To complete Koch's postulates, pathogenicity experiments were carried out by inoculating spore suspension (106 spores mL-1) into the wounded roots (n=10) of I. batatas plants. Sterile distilled water treated wounded roots (n=10) served as control. One to two days after inoculation, visible mycelia were produced at the inoculation sites of I. batatas. Inoculated roots showed black rot signs 21 days post-inoculation; controls were unaffected. This was confirmed in three repeated pathogenicity tests. To our knowledge, this is the first report of black rot caused by C. spicifera on I. batatas in China. The emergence of the black rot pathogen could harm valuable food crops and reduce agricultural productivity in China. Accurate identification of the black rot fungus is essential for devising effective disease management strategies and supporting future control of C. spicifera in China.}, }
@article {pmid40459301, year = {2025}, author = {Zhang, J and Guo, Z and Liu, J and Pan, X and Huang, Y and Cui, X and Wang, Y and Jin, Y and Sheng, J}, title = {Capabilities and Limitations of Air-Dried Soils in Microbial Biogeography: A Regional-Scale Comparative Analysis.}, journal = {Environmental microbiology}, volume = {27}, number = {6}, pages = {e70111}, doi = {10.1111/1462-2920.70111}, pmid = {40459301}, issn = {1462-2920}, support = {KFJ-SW-YW043-2//Field Station Basic Research Project of the Chinese Academy of Sciences/ ; 42107145//National Natural Science Foundation of China/ ; 42407410//National Natural Science Foundation of China/ ; 0270756100ZX//Jiangsu Agricultural Biodiversity Cultivation and Utilization Research Center/ ; CX (22) 2002//Jiangsu Agricultural Science and Technology Innovation Fund/ ; CX (23) 3105//Jiangsu Agricultural Science and Technology Innovation Fund/ ; 3220220039//Pilot Project for Mineral-Land Integration of Jiangsu Province/ ; //Jiangsu Provincial Territorial Ecological Monitoring/ ; }, mesh = {*Soil Microbiology ; *Soil/chemistry ; China ; *Bacteria/classification/genetics/isolation &amp; purification ; *Desiccation ; Biodiversity ; *Microbiota ; }, abstract = {Air-dried soil archives offer valuable potential for studying long-term microbial dynamics, yet systematic evaluations across large spatial scales with paired fresh-soil comparisons remain limited. Here, we systematically evaluated the effects of 1-month air-drying on microbial biogeography across 244 paddy fields in eastern China. Results showed that air-drying significantly altered communities by reducing diversity through the elimination of rare taxa while enriching desiccation-resistant phyla like Firmicutes, Chloroflexi and Actinobacteria. These compositional shifts further triggered functional bias, enhancing fermentation/methanogenesis pathways while suppressing nitrogen cycling processes. Despite these alterations, air-dried samples maintained remarkable fidelity to key ecological patterns observed in fresh soils. Multivariate analyses demonstrated strong structural concordance between paired samples, with soil pH consistently emerging as the primary environmental driver in both data sets. This preservation of biogeographical relationships occurred despite significant changes in underlying ecological mechanisms. Air-dried soil communities exhibited increased stochastic assembly, reduced niche breadth and simplified co-occurrence networks with altered keystone taxa, indicative of a two-phase process: deterministic filtering of drought-sensitive taxa followed by stochastic reorganisation among survivors. Overall, our findings provide a framework for utilising soil archives in microbial ecology, showing that while air-drying introduces predictable distortions, samples retain essential ecological information for reconstructing historical microbial-environmental relationships at large scales.}, }
@article {pmid40456365, year = {2025}, author = {Zhao, X and Van Overbeek, L and Burgess, CM and Holden, N and Brennan, F and Johannessen, GS and Allende, A and Höfte, M and Cottyn, B and Pothier, JF and Schikora, A and Uyttendaele, M}, title = {Human Pathogenic Microorganisms in Fresh Produce Production: Lessons Learned When Plant Science Meets Food Safety.}, journal = {Journal of food protection}, volume = {88}, number = {7}, pages = {100551}, doi = {10.1016/j.jfp.2025.100551}, pmid = {40456365}, issn = {1944-9097}, mesh = {Humans ; *Food Safety ; Food Microbiology ; Food Contamination/prevention &amp; control ; }, abstract = {To enhance control of human pathogenic microorganisms in plant production systems, an EU COST Action (HUPLANTcontrol CA16110) was initiated, bringing together microbiologists in food, environmental, and plant microbial ecology. This article summarizes the outcomes of multiple workshops and the four main lessons learned: (i) many terminologies need further explanation to facilitate multidisciplinary communication on the behavior of human pathogens from preharvest plant production to postharvest food storage, (ii) the complexity of bacterial taxonomy pushes microbial hazard identification for greater resolution of characterization (to subspecies, or even strain level) needing a multimethod approach, (iii) hazard characterization should consider a range of factors to evaluate the weight of evidence for adverse health effects in humans, including strain pathogenicity, host susceptibility, and the impact of the plant, food, or human gut microbiome, (iv) a wide diversity of microorganisms in varying numbers and behaviors coexist in the plant microbiome, including good (beneficial for plant or human health), bad (established human or plant pathogens), or ugly (causing spoilage or opportunistic disease). In conclusion, active listening in communication and a multiperspective approach are the foundation for every successful conversation when plant science meets food safety.}, }
@article {pmid40456197, year = {2025}, author = {Song, W and Lin, L and Oh, S and Grossart, HP and Yang, Y}, title = {Tire wear particles in aquatic environments: From biota to ecosystem impacts.}, journal = {Journal of environmental management}, volume = {388}, number = {}, pages = {126059}, doi = {10.1016/j.jenvman.2025.126059}, pmid = {40456197}, issn = {1095-8630}, mesh = {*Ecosystem ; Biota ; Microplastics ; *Water Pollutants, Chemical ; Animals ; }, abstract = {Tire wear particles (TWPs), mainly generated through friction between tires and road surfaces, represent a major source of traffic-related microplastic pollution, posing threats to biota and ecosystem functions. These particles are a complex mixture of toxic compounds, including heavy metals (e.g., zinc) and organic compounds (e.g., 6-PPD), and their diverse leachates exacerbate their ecological impacts. This review collates current knowledge on the occurrence of TWPs and their leachates in aquatic systems, emphasizing their toxicological effects on species and cascading ecological consequences at the community and ecosystem levels. TWP concentrations in aquatic environments span several orders of magnitude, ranging from 10[-5] to 10[4] mg/L in water via pyrolysis-GC/MS. TWPs and their leachates induce oxidative stress, DNA damage, and alter immune responses of aquatic biota, while disrupting feeding behavior, reproduction, and survival. At the ecosystem level, TWPs and their leachates cause shifts in species composition, reduce biodiversity, and alter trophic interactions, destabilizing natural food web dynamics through selective pressure that promotes tolerant taxa and triggers cascading ecological effects. Their presence significantly influences carbon and nitrogen cycling, with environmentally relevant concentrations could promote primary producers, while higher concentrations inhibit photosynthetic nitrogen-fixing biota, disrupt microbial communities, and impair processes such as denitrification and carbon mineralization. Their toxicological and ecological impacts are likely to be intensified by global environmental change, highlighting the need for long-term studies under realistic environmental conditions to better understand underlying mechanisms and develop effective mitigation strategies.}, }
@article {pmid40453667, year = {2025}, author = {Yang, H and Shao, C and Liu, Z and Zhang, X and Liu, Y and Xiao, J and Tang, L}, title = {Cold- and hot-classified botanical drugs differentially modulate gut microbiota: linking TCM emic classification to microbial ecology.}, journal = {Frontiers in pharmacology}, volume = {16}, number = {}, pages = {1545619}, pmid = {40453667}, issn = {1663-9812}, abstract = {INTRODUCTION: Traditional Chinese Medicine (TCM) classifies botanical drugs based on their thermal properties (an emic classification system), categorizing them as "cold" (e.g., "clearing heat" for anti-inflammatory effects) or "hot" (e.g., "warming the middle" for metabolic enhancement). However, the specific roles of these botanical drugs in restoring gut microbiota dysbiosis remain unclear. This study aimed to explore whether TCM-classified cold and hot botanical drugs differentially restore gut microbiota dysbiosis and host physiology in antibiotic-treated mice.<br><br>METHODS: Mice with antibiotic-induced dysbiosis were treated with eight TCM-classified botanical drugs (four cold: Rheum palmatum L., Scutellaria baicalensis Georgi, Senna alexandrina Mill., Coptis chinensis Franch.; four hot: Codonopsis pilosula (Franch.) Nannf., Astragalus membranaceus (Fisch.) Bunge, Angelica sinensis (Oliv.) Diels, Panax ginseng C.A.Mey.) for 20&#xa0;days. Gut microbiota were analyzed via 16S rRNA sequencing on days 5, 10, 15, and 20, alongside physiological parameters including blood glucose, serum lipids, TNF-&#x3b1;, adiponectin, and intestinal histomorphology.<br><br>RESULTS: By day 20, all botanical drugs restored the diversity and ranking of dominant genera (those with >10% abundance, such as Lactobacillus and unclassified Muribaculaceae). However, cold-classified drugs, traditionally associated with anti-inflammatory effects, selectively enriched anti-inflammatory taxa, including Akkermansia and Bifidobacterium. In contrast, hot-classified drugs, linked to metabolic enhancement, promoted metabolic-modulating genera such as Clostridia and Eubacterium coprostanoligenes. These differential enrichments corresponded with the therapeutic principles defined by TCM: cold-classified drugs reduced serum TNF-&#x3b1; levels (P < 0.01), demonstrating anti-inflammatory effects, whereas hot-classified drugs improved lipid profiles (TG: P < 0.001), thereby promoting metabolic modulation.<br><br>DISCUSSION: TCM-classified cold and hot botanical drugs universally stabilize dominant microbiota while differentially modulating low-abundance taxa. The enrichment of Akkermansia (cold) and Clostridia (hot) offers a microbiota-driven validation of TCM's empirical classification framework. These findings connect traditional knowledge with microbial ecology, underscoring the potential of TCM-guided microbiota modulation for precision therapies.}, }
@article {pmid40450024, year = {2025}, author = {Masigol, H and Solbach, MD and Pourmoghaddam, MJ and Ahadi, R and Mostowfizadeh-Ghalamfarsa, R and Taheri, SR and Tobias-Hünefeldt, SP and Bonkowski, M and Grossart, HP}, title = {A glimpse into Oomycota diversity in freshwater lakes and adjacent forests using a metabarcoding approach.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {19124}, pmid = {40450024}, issn = {2045-2322}, mesh = {*Lakes/microbiology ; *DNA Barcoding, Taxonomic/methods ; *Biodiversity ; *Forests ; *Oomycetes/genetics/classification/isolation &amp; purification ; Ecosystem ; Germany ; Phylogeny ; Fresh Water/microbiology ; }, abstract = {Oomycota, a diverse group of fungus-like protists, play key ecological roles in aquatic and terrestrial ecosystems, yet their habitat-specific diversity and distribution remain poorly understood. This study investigates the diversity of two major Oomycota classes, Saprolegniomycetes and Peronosporomycetes, in two freshwater lakes and their adjacent forests in northeastern Germany. Using a combination of targeted metabarcoding and traditional isolation techniques, we analyzed samples from six habitats, including soil (forest), rotten leaves (forest and shoreline), sediments (shoreline), and surface waters (littoral and pelagic zones). Metabarcoding revealed 401 Oomycota OTUs, with Pythium, Globisporangium, and Saprolegnia as dominant genera. Culture-based methods identified 110 strains, predominantly from surface water and sediment, with Pythium sensu lato and Saprolegnia as the most frequent taxa. Alpha and beta diversity analyses highlighted distinct community structures influenced by lake and habitat type, with significant co-occurrence of Saprolegniomycetes and Peronosporomycetes across habitats. This study provides the first comprehensive metabarcoding-based exploration of Oomycota biodiversity in interconnected freshwater and terrestrial ecotones, uncovering previously unrecognized patterns of habitat-specific diversity.}, }
@article {pmid40448709, year = {2025}, author = {Samaniego, T and La Torre, R and Orjeda, G and Ramirez, JL}, title = {Lima Megacity's Influence on Aquatic Microbial Communities in the Rímac River: Dominance Over Spatial and Seasonal Variations.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {57}, pmid = {40448709}, issn = {1432-184X}, support = {B2110006i//Universidad Nacional Mayor de San Marcos/ ; B2110006i//Universidad Nacional Mayor de San Marcos/ ; B2110006i//Universidad Nacional Mayor de San Marcos/ ; }, mesh = {*Rivers/microbiology ; Seasons ; *Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Peru ; *Microbiota ; *Water Microbiology ; Environmental Monitoring ; DNA, Bacterial/genetics ; Biodiversity ; }, abstract = {The Rímac River, a vital watershed on the Peruvian coast, is confronted with substantial environmental challenges stemming from intensive exploitation and widespread contamination. As the primary source of water for Lima, supplying approximately 80% of the city's needs, the river is heavily impacted by pollutants from domestic, hospital, industrial, and mining effluents. These contaminants introduce microbiota that pose significant public health risks. This study utilizes 16S rRNA gene metabarcoding to characterize the bacterial communities along the Rímac River, examining both spatial (upper, middle, and lower basins) and temporal (dry and rainy seasons) variations. Over a year-long sampling period, DNA sequencing revealed pronounced microbiological differences between the Metropolitan and Regional zones, primarily driven by anthropogenic activities. Key findings include a significant reduction in microbial diversity and an increase in pathogenic bacteria within the Metropolitan zone, while the influence of seasonal variations and altitudinal gradients was comparatively minor. Betaproteobacteria emerged as the most abundant class across most samples. Notably, Aliarcobacter cryaerophilus, an indicator of fecal contamination and a potential public health hazard, was predominantly detected in the Metropolitan zone. These results underscore the necessity for comprehensive monitoring of the Rímac River's microbiota, incorporating advanced molecular techniques to effectively track and mitigate pollution. The study emphasizes the urgent need for robust water quality management strategies to protect this critical resource, ensuring the health and sustainability of Lima and its surrounding regions.}, }
@article {pmid40446899, year = {2025}, author = {Fang, P and Ye, S and Luo, Z and Guo, R and Jiang, Y and Liu, L and Li, S and Xiao, F}, title = {Nanoplastics under the charge effects: Unveiling the potential threats to amphibian (Rana nigromaculata) growth, intestinal damage and microbial ecology.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {381}, number = {}, pages = {126566}, doi = {10.1016/j.envpol.2025.126566}, pmid = {40446899}, issn = {1873-6424}, mesh = {Animals ; *Microplastics/toxicity ; Larva/drug effects/growth &amp; development ; *Intestines/drug effects ; *Ranidae/growth &amp; development ; *Water Pollutants, Chemical/toxicity ; Gastrointestinal Microbiome/drug effects ; Oxidative Stress ; }, abstract = {Nanoplastics (NPs) are contaminants that may be found in charged forms in the environment, capable of accumulating in aquatic organisms and affecting their health. This study compared the effects of positively charged Polystyrene-NPs (PS-NH2, 30 nm) and negatively charged Polystyrene-NPs (PS-COOH, 30 nm) at 6 and 60 mg/L on the growth and development of black-spotted frog tadpoles (Rana nigromaculata), as well as on intestinal damage and microbial ecology. The results demonstrated that exposure to both types of NPs significantly reduced the survival rate of tadpoles, while significantly increased their body weight and body length. Compared to PS-COOH, PS-NH2 exposure resulted in more adverse intestinal tissue damage, manifested by more severe intestinal oxidative stress. Furthermore, exposure to PS-NH2 significantly reduced the abundance and diversity of the microbiome associated with gut function and nutrient absorption, thereby indirectly causing more severe intestinal damage and growth changes. In addition, functional prediction and gene transcription analysis showed that exposure to charged PS-NPs caused changes in genes associated with glycolysis and lipid metabolism, indicating that the glucose-lipid metabolism of tadpoles is impacted. This study revealed the effects of different charged NPs exposure on the growth of tadpoles and their intestinal toxicity, clarified the potential connections between gut microbiota and glucose-lipid metabolism, and provided a new perspectives on the health risks of NPs in amphibians.}, }
@article {pmid40446767, year = {2025}, author = {Adyari, B and Liao, X and Yan, X and Qiu, Y and Grossart, HP and Li, L and Yu, T and Mao, G and Liu, K and Su, J and Liu, Y and Hu, A}, title = {Anthropogenic gene dissemination in Tibetan Plateau rivers: sewage-driven spread, environmental selection, and microeukaryotic inter-trophic driving factors.}, journal = {Water research}, volume = {284}, number = {}, pages = {123887}, doi = {10.1016/j.watres.2025.123887}, pmid = {40446767}, issn = {1879-2448}, mesh = {*Sewage/microbiology ; *Rivers/microbiology ; Tibet ; Bacteria/genetics ; }, abstract = {The spread of anthropogenic genes, such as antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), virulence factor genes (VFGs), and antibiotic-resistant bacteria (ARBs), is a growing public health concern. However, the role of anthropogenic activities in the dissemination of these genes and bacteria in Tibetan Plateau rivers is still unclear. In this study, we analyzed 138 metagenomic samples from water and sediment across nine Tibetan rivers, along with sewage samples from 21 wastewater treatment plants (WWTPs), at both the gene and contig levels, to investigate the spread of the sewage-enriched genes and their bacterial hosts (contigs) in Tibetan rivers. Overall, sewage input was positively correlated with increased the abundance of an average 56 % and 17 % of detected genes in water and sediment, respectively. However, FEAST source tracking analysis revealed that the overall contribution of sewage across all rivers was significantly lower than that of water and sediment. Additionally, sewage's impact varied across rivers, with the Yarlung Zangbo, the largest river, exhibiting limited influence despite receiving inputs from smaller rivers and WWTPs. Neutral community model (NCM) suggested that neutral processes and negative selection predominantly governed the spread of majority of highly abundant sewage-enriched genes and contigs, suggesting restricted environmental spread. In contrast, a subset of genes over-represented relative to neutral expectations (above-neutral prediction) showed lower overall abundance but higher richness, potentially reflecting selection that favor their retention in certain downstream environments. Furthermore, sewage-enriched genes and contigs in water, regardless of their community assembly processes, were linked to microbial interaction modules dominated by microeukaryotic groups associated with sewage, including consumer protists (ciliate), human parasites (e.g., Naegleria), algae, and fungi. These interactions may facilitate the dissemination of antimicrobial resistance in aquatic environments, though this pattern was less pronounced in sediment.}, }
@article {pmid40446743, year = {2025}, author = {Jansriphibul, K and Krohn, C and Ball, AS}, title = {Sources of variability for viability PCR using propidium monoazide.}, journal = {Microbiological research}, volume = {298}, number = {}, pages = {128224}, doi = {10.1016/j.micres.2025.128224}, pmid = {40446743}, issn = {1618-0623}, mesh = {*Propidium/analogs &amp; derivatives/chemistry ; *Azides/chemistry ; *Microbial Viability ; *Polymerase Chain Reaction/methods/standards ; DNA, Bacterial/isolation &amp; purification/genetics ; *Bacteria/genetics/isolation &amp; purification ; Environmental Microbiology ; }, abstract = {The molecular detection of microorganisms in environmental samples relies on PCR-associated molecular workflows that typically cannot differentiate live from dead microbes. Understanding the microbial functions of complex communities can be significantly hindered by presence of the dead microbes. Using propidium monoazide (PMA), PMA-based viability PCR, is arguably the most convenient method to differentiate viability status apart. Errors from variabilities of non-standardized practices and a lack of understanding of the PMA mechanism deter the viability PCR approach. This review discusses the sources of variability in each of four key sequential steps: pre-analysis, PMA activation, DNA extraction and PCR. An analysis of previous literature on optimization of PMA-based viability PCR indicates that often only one source of variability is considered. However, all steps are interrelated and should be considered together when understanding and mitigating unwanted variability, especially in the PMA activation and PCR steps. Research gaps in PMA are addressed, such as the chemical mechanisms of PMA and possible by-products interferences, internal standard spiking and recommendations for future research.}, }
@article {pmid40446651, year = {2025}, author = {O'Connor, L and Minogue, E and Carolan, S and Darcy, G and Chueiri, A and Faherty, M and Morton, J and Mc Donagh, F and Singh, NK and Venkateswaran, K and Miliotis, G and Smith, TJ}, title = {Rapid detection of the novel human pathogen Pantoea piersonii: advancements in methodology.}, journal = {Diagnostic microbiology and infectious disease}, volume = {113}, number = {2}, pages = {116905}, doi = {10.1016/j.diagmicrobio.2025.116905}, pmid = {40446651}, issn = {1879-0070}, mesh = {Humans ; *Pantoea/isolation &amp; purification/genetics/classification ; Sensitivity and Specificity ; *Real-Time Polymerase Chain Reaction/methods ; RNA, Ribosomal, 16S/genetics ; *Enterobacteriaceae Infections/diagnosis/microbiology ; DNA, Bacterial/genetics ; *Molecular Diagnostic Techniques/methods ; }, abstract = {Pantoea piersonii a novel bacterium isolated from the International Space Station (ISS) presents a unique challenge for microbial monitoring in spaceflight and more recently in clinical environments. Identification of the organism currently involves culture, followed by whole genome sequencing and analysis of generated sequences. Since the MALDI-TOF profile of this pathogen is absent from the database and 16S rRNA sequencing fails to resolve its identity to the nearest neighbour, a definitive genetic marker is required for unambiguous identification of the organism. Given the increase in the number of reported clinical cases, there exists a need for a rapid method for identification of the organism which could be utilised in a range of environments including the clinical setting. This study describes the design, development and validation of a specific and sensitive real-time PCR assay for the specific detection of P. piersonii. The assay targets a unique region of the malate dehydrogenase gene, confirmed through comparative genomic analysis. We demonstrate the performance of the assay in terms of analytical specificity, sensitivity, and robustness, ensuring its suitability for both space microbiology applications and clinical use.}, }
@article {pmid40445193, year = {2025}, author = {Cisneros, M and Blanco-Fuertes, M and Lluansí, A and Brotons, P and Henares, D and Pérez-Argüello, A and González-Comino, G and Ciruela, P and Mira, A and Muñoz-Almagro, C}, title = {Synergistic inhibition of pneumococcal growth by Dolosigranulum pigrum and Corynebacterium pseudodiphtheriticum: insights into nasopharyngeal microbial interactions.}, journal = {Microbiology spectrum}, volume = {13}, number = {7}, pages = {e0013825}, pmid = {40445193}, issn = {2165-0497}, support = {PI19/00104//Instituto de Salud Carlos III/ ; PI23/00049//Instituto de Salud Carlos III/ ; FI 24/00206//Instituto de Salud Carlos III/ ; }, mesh = {*Nasopharynx/microbiology ; *Streptococcus pneumoniae/growth &amp; development/isolation &amp; purification/genetics ; *Corynebacterium/physiology/isolation &amp; purification ; Humans ; *Pneumococcal Infections/microbiology ; *Microbial Interactions ; *Carnobacteriaceae/physiology/isolation &amp; purification ; *Antibiosis ; Child, Preschool ; Child ; }, abstract = {Streptococcus pneumoniae is a nasopharynx colonizer that can invade sterile tissues, causing invasive pneumococcal disease (IPD). Dolosigranulum pigrum and Corynebacterium pseudodiphtheriticum are commensal bacteria commonly isolated from the nasopharynx of healthy children, potentially playing a protective role. This study aims to analyze the effects of D. pigrum and C. pseudodiphtheriticum on S. pneumoniae in vitro growth. Pneumococcal strains were collected from IPD patients and healthy carriers in Catalonia (2016-2023). D. pigrum and C. pseudodiphtheriticum strains were isolated from a healthy child's nasopharynx. S. pneumoniae was co-cultured with each commensal bacterium in triplicate experiments. Pneumococcal growth was quantified using a real-time PCR assay targeting the lytA gene. The effect of commensal bacteria on pneumococcal growth was evaluated using a linear mixed-effect regression model. Twenty-eight pneumococcal strains expressing 24 different serotypes and 27 clonal types were analyzed (18 isolated in blood and 10 in nasopharyngeal aspirate). Pneumococcal growth was decreased by D. pigrum (β = -0.763, 95% confidence interval [CI]: -0.94 to -0.59, P < 0.0001) and C. pseudodiphtheriticum (β = -0.583, 95% CI: -0.76 to -0.41, P < 0.0001). The combined presence of both had a stronger inhibitory effect (β = -0.971, 95% CI: -1.15 to -0.79, P < 0.0001). No association was found between isolation site or serotype with pneumococcal growth. D. pigrum and C. pseudodiphtheriticum significantly reduced pneumococcal growth, with a synergistic effect when combined. This antagonistic effect supports the potential protective factor of healthy nasopharyngeal microbiota against IPD and the development of these microorganisms as probiotics.IMPORTANCEInvasive pneumococcal disease (IPD) is a significant worldwide health challenge. The present study highlights the significant inhibitory effect of two commensal bacteria, Dolosigranulum pigrum and Corynebacterium pseudodiphtheriticum, on pneumococcal growth, with a stronger effect observed when both bacteria are present together. Through testing different strains of S. pneumoniae and the implementation of a robust statistical model, this research advances in the knowledge of microbial ecology and provides evidence to support the development of the use of these commensal bacteria as probiotics. These results emphasize the possibility of using the nasopharyngeal microbiota's natural interactions to mitigate the risk of IPD.}, }
@article {pmid40444437, year = {2025}, author = {Pan, Y and Tao, Y and Yang, X and Du, S and Ding, H and Li, J and Jia, H and Chen, H}, title = {Underlying mechanisms of spatial distribution of prokaryotic community in surface seawater from Arctic Ocean to the Sea of Japan.}, journal = {Microbiology spectrum}, volume = {13}, number = {7}, pages = {e0051725}, pmid = {40444437}, issn = {2165-0497}, support = {41906113//National Natural Science Foundation of China/ ; 2023A004//Shenzhen Municipal Science and Technology Innovation Council | Shenzhen Science and Technology Innovation Program ()/ ; JCYJ20220530150201003//Shenzhen Municipal Science and Technology Innovation Council | Shenzhen Science and Technology Innovation Program ()/ ; }, mesh = {Japan ; *Seawater/microbiology ; Arctic Regions ; *Bacteria/classification/genetics/isolation &amp; purification ; Phylogeny ; *Microbiota ; Temperature ; Biodiversity ; Oceans and Seas ; Ecosystem ; Salinity ; Archaea/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Microorganisms play critical roles in marine ecosystems, so understanding the factors shaping microbial communities across various oceanic regions is essential for predicting ecosystem resilience and biogeochemical cycles. This study investigated the marine prokaryotic communities across 22 stations spanning the Arctic Ocean, the Chukchi Sea, the Bering Sea, and the Sea of Japan, with an emphasis on how environmental factors shape these communities. Results showed that the microbial alpha diversity generally declines with increasing latitude, though Arctic Ocean stations exhibited higher Chao 1 indices compared to the Bering Sea. Beta diversity analyses revealed that temperature and salinity were key factors associated with community composition variation across latitudes. Proteobacteria and Cyanobacteria were the dominant phyla showing opposite distribution trends across sampling stations. Cold-adapted oligotrophs such as Planktomarina and the SAR11 clade thrived in Arctic waters, while Sphingomonas, known for pollutant degradation, was more abundant in the Sea of Japan. Temperature was positively correlated to the relative abundance of Sphingomonas. At broad spatial scales, stochastic processes dominated community assembly of microbial phylogenetic diversity, while in specific regions like the Arctic Ocean, deterministic homogeneous selection appeared to shape microbial communities; and temperature showed a pronounced influence on phylogenetic turnover across all samples. Co-occurrence networks identified several key taxa, such as Polaribacter_1, Candidatus_Aquiluna, and NS5_marine_group. Overall, the study underscores temperature's role in shaping microbial community diversity, composition, and assembly processes across latitudinal gradients, highlighting unique community adaptations to extreme environments.IMPORTANCEMicrobes are the invisible engines of ocean health, recycling nutrients and sustaining marine life. This research helps us understand how climate factors like temperature shape these microscopic communities, which differ starkly between icy Arctic waters and warmer seas. As oceans warm due to climate change, microbial populations and their critical roles in cleaning pollutants or supporting food webs could shift dramatically. The study suggests Arctic microbes are uniquely adapted to cold, low-nutrient conditions, making them vulnerable to warming. By linking temperature to microbial diversity, this work provides clues to predict how marine ecosystems might respond to climate shifts, informing efforts to protect ocean biodiversity and processes vital to Earth's carbon and nutrient cycles.}, }
@article {pmid40442489, year = {2025}, author = {Ostap-Chec, M and Antoł, W and Bajorek, D and Berbeć, E and Moroń, D and Rapacz, M and Miler, K}, title = {Meta-Analysis and Experimental Evidence Reveal No Impact of Nosema ceranae Infection on Honeybee Carbohydrate Consumption.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {56}, pmid = {40442489}, issn = {1432-184X}, support = {Preludium 2021/41/N/NZ8/02917//Narodowe Centrum Nauki/ ; }, mesh = {Animals ; Bees/microbiology/physiology/metabolism ; *Nosema/physiology ; Hemolymph/chemistry/metabolism ; Feeding Behavior ; Trehalose/metabolism/analysis ; *Carbohydrate Metabolism ; }, abstract = {Honeybees (Apis mellifera) are indispensable pollinators for ecosystem stability and agricultural productivity. However, they face numerous challenges, including pathogens threatening their survival and ecosystem services. Among these pathogens, Nosema ceranae, a microsporidian parasite, causes significant damage to the intestinal tract and induces energetic imbalances in the organism, posing a major threat to both individual bees and entire colonies. In response to infections, bees often engage in behavioral defenses, such as self-medicating with antimicrobial substances available in their environment. We hypothesized that bees infected with N. ceranae might compensate behaviorally by increasing their carbohydrate consumption. To test this hypothesis, we conducted a meta-analysis of existing studies comparing sugar consumption in healthy and infected bees, complemented by an experimental study. In our experiment, we measured sugar intake and quantified trehalose levels in the hemolymph, a key indicator of energy reserves. Both the meta-analysis and experimental results consistently showed no significant differences in sugar consumption between healthy and infected bees. Similarly, trehalose levels in the hemolymph remained comparable between the two groups. Our findings suggest that the infection caused by N. ceranae does not elicit compensatory feeding behavior in honeybees. Moreover, the meta-analysis revealed significant gaps in current research, particularly a lack of studies focusing on forager bees, which face the highest energetic demands among colony members. Our findings call for future studies on the energetic effects of nosemosis and studies conducted under natural or semi-natural conditions.}, }
@article {pmid40440849, year = {2025}, author = {Ramadoss, R and Nishad, AK and Moovarkumudalvan, B and Shomar, B}, title = {Bacterial composition of dust deposited in Qatar: A seasonal study.}, journal = {The Science of the total environment}, volume = {985}, number = {}, pages = {179766}, doi = {10.1016/j.scitotenv.2025.179766}, pmid = {40440849}, issn = {1879-1026}, mesh = {Qatar ; *Dust/analysis ; Seasons ; *Bacteria/classification ; *Air Microbiology ; *Environmental Monitoring ; RNA, Ribosomal, 16S/analysis ; *Microbiota ; *Air Pollutants/analysis ; }, abstract = {Dust storms in the Middle East threaten public health by deteriorating air quality and transporting microorganisms over vast distances. This study analyzes seasonal variations in dust-borne bacterial diversity on photovoltaic (PV) panels using 16S rRNA gene sequencing and bioinformatics to assess community composition and metabolic potential. Our findings suggest that seasonal ecological factors have potential effects on the composition of the airborne bacterial community. In Qatar, the high atmospheric CO2 levels associated with hydrocarbon refining had promoted the growth of hydrocarbon-degrading bacteria belonging to the phyla Campilobacterota, Proteobacteria, and Bacteroidota. High temperatures and photothermal reactions of summer conditions have favored sulfur-metabolizing bacteria. Conversely, milder temperatures, increased humidity, reduced wind speed, and a decline in summer-favoring bacteria had contributed to the increased abundance of the phyla Patescibacteria, Firmicutes, and Actinobacteriota during other seasons. This study had also identified dust borne pathogenic bacteria associated with human and plant diseases, highlighting the need for environmental surveillance to monitor microbial diversity and its shifts driven by ecological factors. This knowledge is crucial for public health, environmental protection, sustainable farming and advancing our understanding of microbial ecology.}, }
@article {pmid40439420, year = {2025}, author = {Park, J and Kohn, E and Schenk, S and Davis, KM and Clark, JS and Parfrey, LW}, title = {An experimental test of the influence of microbial manipulation on sugar kelp (Saccharina latissima) supports the core influences host function hypothesis.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {6}, pages = {e0030125}, pmid = {40439420}, issn = {1098-5336}, mesh = {*Kelp/microbiology/growth &amp; development ; *Bacteria/isolation &amp; purification/classification/genetics ; *Microbiota ; Edible Seaweeds ; Laminaria ; }, abstract = {UNLABELLED: Kelp are valued for a wide range of commercial products and their role in kelp forest ecosystems, making kelp cultivation a rapidly expanding economic sector. Microbes associated with kelp and other macroalgae play a critical role in processes such as nutrient exchange, chemical signaling, and defense against pathogens. Thus, manipulating the microbiome to enhance macroalgal growth and resilience is a promising yet underexplored approach for sustainable kelp cultivation. The core microbiome hypothesis suggests that the bacteria that are consistently found on a host (the core microbes) are likely to have a disproportionate impact on host biology, making them an attractive target for microbiome manipulation. In this study, we surveyed wild Saccharina latissima and their surrounding environment to identify core bacterial taxa, compared them to cultivated kelp, and experimentally tested how cultured bacterial isolates affect kelp development. We found that core bacteria are nearly absent in cultivated juvenile sporophytes in nurseries, but eventually colonize them after outplanting to ocean farm sites. Bacterial inoculants had both positive and negative effects on kelp development. Notably, the strength of association of a bacterial genus with kelp in the wild positively correlated with its impact on gametophyte settlement and sporophyte development in kelp co-culture experiments, aligning with predictions from the core microbiome influences host function hypothesis. These findings affirm the feasibility of using microbial manipulations to improve current kelp aquaculture practices and provide a framework for developing these techniques.<br><br>IMPORTANCE: Microorganisms consistently associated with hosts are widely thought to be more likely to impact host biology and health. However, this intuitive concept has not been experimentally evaluated. This study formalizes this concept as the Core Microbiome Influences Host Function hypothesis and experimentally tests this hypothesis in sugar kelp (Saccharina). The distribution of bacteria on wild kelp and core microbes was first identified by compiling a broad dataset of the kelp microbiome sampled across space and time. Bacterial cultures were isolated from the surface of sugar kelp and individually grown in laboratory co-culture with sugar kelp spores to assess the ability of bacterial isolates to influence kelp growth and development. In support of the core influences host function hypothesis, isolates belonging to bacterial genera that are more strongly associated with wild sugar kelp are more likely to influence development in laboratory experiments.}, }
@article {pmid40437905, year = {2025}, author = {Ni, J and Yang, Z and Sun, X and Cui, Q and Zhang, R and Lu, H and Wu, Z and Zhu, J and Mao, H and Liu, K and Tang, C and Wang, C and Xing, C and Zhu, J}, title = {Probiotic Akkermansia muciniphila alleviates acute kidney injury by protecting the intestinal barrier and modulating gut microbiota and metabolites.}, journal = {Journal of biomedical research}, volume = {}, number = {}, pages = {1-12}, doi = {10.7555/JBR.39.20250162}, pmid = {40437905}, issn = {1674-8301}, abstract = {Acute kidney injury (AKI) is a critical condition with limited effective therapies. Akkermansia muciniphila (A. muciniphila) is a probiotic with multiple beneficial effects, including epithelial cell tight junctions regulation. Since renal pathophysiology is associated with gut barrier integrity, we hypothesized that A. muciniphila may have potential preventive effects on AKI. We established a lipopolysaccharide (LPS)-induced AKI mouse model to evaluate the effects of A. muciniphila. Our findings showed that pretreatment with A. muciniphila significantly attenuated kidney injury, as evidenced by reduced serum creatinine and urea nitrogen levels, alongside diminished tubular necrosis and apoptosis. A. muciniphila preserved the intestinal barrier integrity and induced marked shifts in gut microbial ecology and the metabolome. A. muciniphila induced notably an increase in the relative abundance of phylum Proteobacteria while a decrease of Bacteroidetes. At the genus level, Prevotella, Faecalibaculum, Moraxella and Lactobacillus were more abundant in A. muciniphila-pretreated mice. Metabolomic analysis revealed that A. muciniphila altered the gut metabolome affecting modulation of pathways, including tyrosine metabolism, alanine/aspartate/glutamate homeostasis, cancer-related carbon flux, and GABAergic synaptic signaling. In conclusion, our findings demonstrate A. muciniphila's renoprotective effects through gut-kidney axis modulation, laying the foundation for subsequent studies to verify the connection between gut microbiota and AKI.}, }
@article {pmid40436193, year = {2025}, author = {Lacerda, AL and Casotti, R and Briand, JF and Lenoble, V and Muniategui-Lorenzo, S and Kessler, F and Barre, A and Moscoso-Pérez, CM and Fernández-González, V and Andrade-Garda, JM and Murano, C and Donnarumma, V and Oreste, E and Joyce, H and Hannon, C and Nash, R and Orange, F and Frias, J and Pedrotti, ML}, title = {The plastisphere: a comprehensive description of geographic and temporal community patterns across the Mediterranean Sea and the Atlantic Ocean.}, journal = {Environmental research}, volume = {282}, number = {}, pages = {121929}, doi = {10.1016/j.envres.2025.121929}, pmid = {40436193}, issn = {1096-0953}, mesh = {Atlantic Ocean ; Mediterranean Sea ; *Plastics ; Bacteria/classification ; *Microbiota ; Environmental Monitoring ; RNA, Ribosomal, 18S ; *Water Pollutants, Chemical/analysis ; }, abstract = {Plastic pollution is a global ecological threat, not only as physical debris but also as a novel substrate hosting microbial communities, known as "plastisphere". Polymer type (virgin vs. recycled), combined with environmental variations, may influence both early and mature colonization stages. While biogeography has been identified as a key driver of the plastisphere community structure, prior research often relied on isolated studies with no methodological standardization or on opportunistic sampling. Here, this study stands out by conducting a simultaneous and harmonized investigation across environmentally distinct sites in the Mediterranean Sea and the Atlantic Ocean. Three polymers (LDPE, PP-PC, PLA) were incubated in situ, across six locations. Using standardized protocols and eDNA metabarcoding (16S and 18S rRNA), we assessed how biogeography, environmental variables, polymer type, and exposure time shape the diversity and composition of prokaryotic and eukaryotic communities colonizing plastics. Incubations lasted up to one year, with sampling at 7, 30 and 90 days, covering all four seasons. Microbial colonization in all plastics occurred within 7 days, but community richness and maturity fluctuated across sites and seasons. Proteobacteria, Bacteroidia and Planctomycetes were the dominant prokaryotes, while Ciliophora, Cercozoa and Dinoflagellata dominated eukaryotes. Taxa with potential for plastic biodegradation (e.g., Oleibacter, Alcanivorax) and pathogenicity (e.g., Pseudomonas, Candida) were identified, highlighting the plastisphere's ecological role. This dataset represents the most comprehensive assessment of marine plastisphere diversity to date, allowing the understanding of species occurrence and their interactions, influence on ecological processes and the emerging health risks of the plastisphere, which should be considered when developing global strategies to mitigate ocean plastic pollution.}, }
@article {pmid40435560, year = {2025}, author = {Fazio, NA and Albertin, W and Masneuf-Pomarede, I and Randazzo, CL and Caggia, C}, title = {Structure of culturable indigenous yeast population and genetic diversity of Saccharomyces cerevisiae and non-Saccharomyces yeasts during spontaneous fermentation of Etna vineyards grapes.}, journal = {International journal of food microbiology}, volume = {440}, number = {}, pages = {111282}, doi = {10.1016/j.ijfoodmicro.2025.111282}, pmid = {40435560}, issn = {1879-3460}, mesh = {*Vitis/microbiology ; Fermentation ; *Genetic Variation ; *Wine/microbiology ; *Saccharomyces cerevisiae/genetics/isolation &amp; purification/metabolism/classification ; *Yeasts/genetics/isolation &amp; purification/classification/metabolism/growth &amp; development ; Italy ; Microsatellite Repeats ; Farms ; }, abstract = {The microbial diversity of indigenous yeasts plays a fundamental role in the spontaneous fermentation of wines, contributing to the concept of microbial terroir and potentially influencing the sensory profile of the final product. This study explores the yeast ecology and genetic diversity of Saccharomyces cerevisiae and non-Saccharomyces yeasts in four wineries located on two different sides of Mount Etna, a region of unique viticultural significance due to its volcanic soils and diverse microclimatic conditions. A total of 454 yeast isolates were obtained from spontaneous fermentations of different grape varieties, and identified as belonging to 18 distinct species. The spontaneous fermentation was characterized by an initial dominance of non-Saccharomyces yeasts, especially Hanseniaspora uvarum and Metschnikowia pulcherrima, followed by a gradual dominance of S. cerevisiae at later stages. Microsatellite genotyping revealed significant genetic diversity among S. cerevisiae strains, with some distinct genetic patterns associated with Italian winery environments. Additionally, H. uvarum exhibited significant genetic variation but lacked clear geographic clustering, suggesting complex ecological and enological interactions. Statistical analyses of microbial diversity indices indicated that vineyard-specific factors, including altitude, soil composition, and agronomic practices, may influence yeast community structure among the four wineries. These findings provide new insights into the microbial ecology of Etna wines and highlight the potential of indigenous yeast populations for maintaining and enhancing regional wine identity.}, }
@article {pmid40432969, year = {2025}, author = {Wang, JQ and Yu, T and Qiu, HY and Ji, SW and Xu, ZQ and Cui, QC and Li, HF and Liang, WF and Feng, S and Fu, CT and Gao, X and Han, ZZ and Tian, WN and Li, JX and Xue, SJ}, title = {Differential impact of spotted fever group rickettsia and anaplasmosis on tick microbial ecology: evidence from multi-species comparative microbiome analysis.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1589263}, pmid = {40432969}, issn = {1664-302X}, abstract = {Tick-borne diseases (TBDs) pose a significant public health challenge, as their incidence is increasing due to the effects of climate change and ecological shifts. The interplay between tick-borne pathogens and the host microbiome is an emerging area of research that may elucidate the mechanisms underlying disease susceptibility and severity. To investigate the diversity of microbial communities in ticks infected with vertebrate pathogens, we analyzed the microbiomes of 142 tick specimens. The presence of Rickettsia and Anaplasma pathogens in individual samples was detected through PCR. Our study aimed to elucidate the composition and variation of microbial communities associated with three tick species, which are known vectors for various pathogens affecting both wildlife and humans. We employed high-throughput sequencing techniques to characterize the microbial diversity and conducted statistical analyses to assess the correlation between the presence of specific pathogens and the overall microbial community structure. Pathogen screening revealed an overall positivity rate of 51.9% for Anaplasma and 44.6% for spotted fever group rickettsia (SFGR). Among the three tick species (Dermacentor silvarum, Haemaphysalis concinna, and Haemaphysalis japonica) analyzed, D. silvarum (the predominant species) exhibited the highest pathogen prevalence. The results indicate significant variation in microbial diversity between tick samples, with the presence of Anaplasma and SFGR associated with distinct changes in the microbial community composition. These findings underscore the complex interactions between ticks and their microbial inhabitants, enriching our understanding of tick-borne diseases.}, }
@article {pmid40431577, year = {2025}, author = {Jia, J and Bao, P and Yu, Q and Li, N and Ren, H and Chen, Q and Yan, P}, title = {Lactobacillus Re-Engineers Gut Microbiota to Overcome E. coli Colonization Resistance in Mice.}, journal = {Veterinary sciences}, volume = {12}, number = {5}, pages = {}, pmid = {40431577}, issn = {2306-7381}, support = {KCXF20201221173205015//the Shenzhen Science and Technology Program/ ; TCYC-TP2023//Xinjiang Tianchi introduction of talent research Program/ ; }, abstract = {The intestinal health and functionality of animals play pivotal roles in nutrient digestion and absorption, as well as in maintaining defense against pathogenic invasions. These biological processes are modulated by various determinants, including husbandry conditions, dietary composition, and gut microbial ecology. The excessive use of anthropogenic antibiotics may disrupt intestinal microbiota composition, potentially leading to dysbiosis that directly compromises host homeostasis. While Lactobacillus species are recognized for their immunomodulatory properties, their precise mechanisms in regulating host anti-inflammatory gene expression and influencing mucosal layer maturation, particularly regarding E. coli colonization resistance, require further elucidation. To investigate the regulatory mechanisms of Lactobacillus in relation to intestinal architecture and function during E. coli infection, we established a colonic infection model using Bal b/c mice, conducting systematic analyses of intestinal morphology, inflammatory mediator profiles, and microbial community dynamics. Our results demonstrate that Lactobacillus supplementation (Pediococcus acidilactici) effectively mitigated E. coli O78-induced enteritis, with co-administration during infection facilitating the restoration of physiological parameters, including body mass, intestinal histoarchitecture, and microbial metabolic functions. Microbiome profiling revealed that the Lactobacillus intervention significantly elevated Lactococcus abundance while reducing Weissella populations (p < 0.05), concurrently enhancing metabolic pathways related to nutrient assimilation and environmental signal processing (including translation mechanisms, ribosomal biogenesis, amino acid transport metabolism, and energy transduction systems; p < 0.05). Mechanistically, Lactobacillus administration attenuated E. coli-induced intestinal pathology through multiple pathways: downregulating pro-inflammatory cytokine expression (IL-1β, IL-1α, and TNF-α), upregulating epithelial junctional complexes (Occludin, Claudin-1, and ZO-1), and stimulating mucin biosynthesis (MUC1 and MUC2; p < 0.05). These modifications collectively enhanced mucosal barrier integrity and promoted epithelial maturation. This investigation advances our comprehension of microbiota-host crosstalk during enteropathogenic infections under probiotic intervention, offering valuable insights for developing novel nutritional strategies and microbial management protocols in animal husbandry.}, }
@article {pmid40431542, year = {2025}, author = {Karukayil Gopalakrishnan, N and Pappuswamy, M and Meganathan, G and Shanmugam, S and Pushparaj, K and Balasubramanian, B and Kim, IH}, title = {Influence of Probiotic Administration in Canine Feed: A Comprehensive Review.}, journal = {Veterinary sciences}, volume = {12}, number = {5}, pages = {}, pmid = {40431542}, issn = {2306-7381}, abstract = {Dogs are cherished companions, and in today's world, pets are increasingly regarded as family members. Pet owners are placing growing emphasis on their animals' health, particularly for dogs. Probiotics, which are living bacteria that benefit the host when given in sufficient quantities, have drawn a lot of interest in the veterinary nutrition community due to their beneficial effects on companion animals, including dogs. This study emphasizes the advantages of adding probiotics to canine diets in order to enhance the health of the gut flora and the technologies used to incorporate probiotics into canine feed. It looks at the best ways to deal with common dog health problems, highlighting probiotics as a helpful substitute for antibiotics, which can have serious adverse effects, encourage bacterial resistance, and disturb the gut's microbial ecology, which is necessary for digesting. Such disruptions are linked to chronic inflammatory enteropathy and obesity in dogs. This paper also examines biotechnological advancements in probiotic incorporation methods in dog feed, aiming to optimize their health benefits. Probiotic feed supplements may thus represent a promising approach to advancing canine health care, providing a natural adjunct to conventional treatments and preventive measures.}, }
@article {pmid40431287, year = {2025}, author = {Zhong, J and Ran, Q and Han, Y and Gan, L and Dong, C}, title = {Biosynthetic Mechanisms of Plant Chlorogenic Acid from a Microbiological Perspective.}, journal = {Microorganisms}, volume = {13}, number = {5}, pages = {}, pmid = {40431287}, issn = {2076-2607}, support = {32360029//the National Science Foundation of China/ ; 32400111//the National Science Foundation of China/ ; Qiankehe Foundation-ZK (2024) General 091//he Guizhou Provincial Basic Research Program (Natural Science)/ ; }, abstract = {Chlorogenic acid (CGA), a phenolic compound with diverse bioactivities, plays a crucial role in plant defense mechanisms and has significant therapeutic potential in human inflammatory and cardiovascular diseases. The biosynthesis and accumulation of CGA in plants result from a complex interplay between internal factors (e.g., hormones, enzymes, and genes) and external factors (e.g., microbial interactions, drought, and temperature fluctuations). This review systematically investigates the influence of microbes on internal regulatory factors governing CGA biosynthesis in plants. CGA is synthesized through four distinct metabolic pathways, with hormones, enzymes, and genes as key regulators. Notably, microbes enhance CGA biosynthesis by improving plant nutrient uptake, supplying essential hormones, regulating the expression of related enzymes and genes, and the interaction between bacteria and fungi. In addition, our review summarizes the challenges currently present in the research and proposes a series of innovative strategies. These include in-depth investigations into the molecular mechanisms of microbial regulation of plant gene expression, gene editing, development of microbial inoculants, construction of synthetic microbial communities, and exogenous application of plant hormones.}, }
@article {pmid40431158, year = {2025}, author = {Mirete, S and Sánchez-Costa, M and Díaz-Rullo, J and González de Figueras, C and Martínez-Rodríguez, P and González-Pastor, JE}, title = {Metagenome-Assembled Genomes (MAGs): Advances, Challenges, and Ecological Insights.}, journal = {Microorganisms}, volume = {13}, number = {5}, pages = {}, pmid = {40431158}, issn = {2076-2607}, support = {PID2021-126114NB-C43//Spanish Ministry of Science and Innovation which also included European Regional Development Fund (FEDER)/ ; }, abstract = {Metagenome-assembled genomes (MAGs) have revolutionized microbial ecology by enabling the genome-resolved study of uncultured microorganisms directly from environmental samples. By leveraging high-throughput sequencing, advanced assembly algorithms, and genome binning techniques, researchers can reconstruct microbial genomes without the need for cultivation. These methodological advances have expanded the known microbial diversity, revealing novel taxa and metabolic pathways involved in key biogeochemical cycles, including carbon, nitrogen, and sulfur transformations. MAG-based studies have identified microbial lineages form Archaea and Bacteria responsible for methane oxidation, carbon sequestration in marine sediments, ammonia oxidation, and sulfur metabolism, highlighting their critical roles in ecosystem stability. From a sustainability perspective, MAGs provide essential insights for climate change mitigation, sustainable agriculture, and bioremediation. The ability to characterize microbial communities in diverse environments, including soil, aquatic ecosystems, and extreme habitats, enhances biodiversity conservation and supports the development of microbial-based environmental management strategies. Despite these advancements, challenges such as assembly biases, incomplete metabolic reconstructions, and taxonomic uncertainties persist. Continued improvements in sequencing technologies, hybrid assembly approaches, and multi-omics integration will further refine MAG-based analyses. As methodologies advance, MAGs will remain a cornerstone for understanding microbial contributions to global biogeochemical processes and developing sustainable interventions for environmental resilience.}, }
@article {pmid40427685, year = {2025}, author = {Chen, Z and Zhong, Y and Chen, L and Liu, W and Lin, C and Chen, Y and Wang, X}, title = {HGF Aggravated Periodontitis-Associated Gut Barrier and Microbial Dysfunction: Implications for Oral-Gut Axis Regulation.}, journal = {Biology}, volume = {14}, number = {5}, pages = {}, pmid = {40427685}, issn = {2079-7737}, support = {81700985//National Natural Science Foundation of China/ ; 2024A03J0138//Guangzhou Municipal Science and Technology Bureau/ ; 02-408-2304-05037XM and 02-408-240603131063//Plan on Enhancing Scientific Research in Guangzhou Medical University/ ; 202201020203//Guangzhou Science and Technology Program/ ; }, abstract = {While periodontitis is increasingly linked to systemic disorders through the oral-gut axis, the molecular mediators driving gut microbiota dysbiosis and barrier disruption remain elusive. Hepatocyte growth factor (HGF), a novel regulator of inflammatory bone loss in periodontitis, may serve as a critical communicator between oral infection and distal intestinal pathology. This study investigates how HGF overexpression modulates the gut microbial ecosystem and intestinal barrier integrity in a transgenic periodontitis model. In this study, we combined 16S rRNA sequencing of fecal microbiota with comprehensive gut barrier assessments, including systemic markers (D-lactate, LPS, and DAO ELISA), structural integrity (villous morphology), and molecular analysis (ZO-1, occludin, and NOD2 immunohistochemistry), using HGF-overexpressing transgenic (HGF-Tg) mice with periodontitis. The results demonstrated that HGF increased gut permeability in the context of periodontitis, as evidenced by elevated serum levels of D-lactate and LPS compared to wild type (WT) mice. In addition, gut villous morphology disorder was observed in HGF-Tg mice with periodontitis. HGF also diminished the protein level of occludin and upregulated NOD2 expression in mice with periodontitis. Moreover, HGF-Tg mice with periodontitis exhibited significant dysbiosis of gut microbiota, with reduced levels of probiotics (e.g., Faecalibaculum). Notably, HGF also increased the enrichment of the periodontitis-associated pathogens (e.g., Desulfovibrio and Streptococcus) in the gut. Microbial functions, particularly metabolic pathways, were significantly altered by HGF when periodontitis occurred. Some microorganisms like g_Desulfovibrio may play a role in gut barrier disorder in HGF-Tg mice with periodontitis. Overall, our findings position HGF as a novel orchestrator of oral-gut crosstalk, where its overexpression reshapes gut microbial ecology toward a "leaky gut" phenotype to compromise intestinal barrier integrity, further deepening our understanding of the oral-gut axis.}, }
@article {pmid40427319, year = {2025}, author = {Xu, C and Guo, X and Li, L}, title = {Metagenomic Comparison of Gut Microbes of Lemur catta in Captive and Semi-Free-Range Environments.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {10}, pages = {}, pmid = {40427319}, issn = {2076-2615}, abstract = {In order to protect endangered species, many zoos adopt diverse rearing models to achieve optimal conservation outcomes. This study employed metagenomic approaches to assess differences in the fecal microbiome of captive and semi-free-ranging ring-tailed lemurs (Lemur catta). The results show that captivity significantly altered the microbial community structure. The inter-individual variability in the microbial community within the captive-bred (CB) group was lower than that in the semi-free-ranging (FR) group, yet these individuals harbored a higher abundance of potential pathogens (Treponema_D). In contrast, microbial genera associated with fiber degradation and short-chain fatty acid production in the FR group were significantly elevated (Faecalibacterium, Roseburia, and Megamonas) as compared to the CB group. Environmental variations between the two rearing systems led to distinct profiles in microbial functions and carbohydrate-active enzyme gene composition. Notably, the FR group of lemurs exhibited an increased abundance of enzyme genes associated with the degradation of complex polysaccharides (cellulose, hemicellulose, and pectin), suggesting that their diet, rich in natural plant fibers, enhances the capacity of their gut microbiota to extract essential energy and nutrients. Conversely, the CB group displayed a more homogeneous microbial community with a higher prevalence of potential pathogens, implying that a captive lifestyle may negatively impact gastrointestinal health. These findings offer valuable insights into the influence of rearing conditions on gut microbial ecology and its potential implications for the health management of ring-tailed lemurs.}, }
@article {pmid40426572, year = {2025}, author = {Touati, A and Ibrahim, NA and Mairi, A and Kirat, H and Basher, NS and Idres, T}, title = {One Health at Risk: Plasmid-Mediated Spread of mcr-1 Across Clinical, Agricultural, and Environmental Ecosystems.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {14}, number = {5}, pages = {}, pmid = {40426572}, issn = {2079-6382}, support = {IMSIU-DDRSP2501//Deanship of Scientific Research at Imam Mohammad Ibn Saud Islamic University (IMSIU)/ ; }, abstract = {The global dissemination of plasmid-mediated mcr genes, which confer resistance to the last-resort antibiotic colistin, represents a critical public health challenge driven by the interplay of clinical, agricultural, and environmental factors. This review examines the genetic and ecological dynamics of mcr-bearing plasmids, focusing on their role in disseminating colistin resistance across diverse bacterial hosts and ecosystems. Key plasmid families demonstrate distinct evolutionary strategies, including IncI2, IncHI2, and IncX4. IncI2 plasmids favor stability in livestock and clinical settings. IncHI2 plasmids, on the other hand, leverage transposons to co-select for multidrug resistance, while IncX4 plasmids achieve global dissemination through streamlined, conjugation-efficient architectures. The pervasive spread of mcr genes is exacerbated by their integration into chromosomes via mobile genetic elements and co-selection with resistance to other antibiotic classes, amplifying multidrug-resistant phenotypes. Environmental reservoirs, food chains, and anthropogenic practices further facilitate cross-niche transmission, underscoring the interconnectedness of resistance under the One Health framework. Addressing this crisis requires coordinated strategies, including reducing colistin misuse in agriculture, enhancing surveillance of high-risk plasmid types, and fostering international collaboration to preserve antimicrobial efficacy and mitigate the threat of untreatable infections.}, }
@article {pmid40423845, year = {2025}, author = {Pérez-Gómez, O and Domínguez-Maqueda, M and García-Márquez, J and Moriñigo, M&#xc1; and Tapia-Paniagua, ST}, title = {Metabolite-Driven Modulation of Biofilm Formation in Shewanella: Insights from Shewanella sp. Pdp11 Extracellular Products.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {55}, pmid = {40423845}, issn = {1432-184X}, support = {PID2020-113637RB-C21//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2020-113637RB-C21//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2020-113637RB-C21//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2020-113637RB-C21//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2020-113637RB-C21//Ministerio de Ciencia e Innovaci&#xf3;n/ ; }, mesh = {*Shewanella/metabolism/physiology/genetics ; *Biofilms/growth &amp; development/drug effects ; Glycogen/metabolism ; }, abstract = {Biofilm formation is a survival strategy for bacteria, contributing to their persistence in natural and industrial environments. In this study, we investigated the ability of extracellular products (ECPs) produced by the probiotic strain Shewanella sp. Pdp11 under different culture conditions to inhibit biofilm formation in pathogenic and environmental Shewanella strains. ECPs from specific culture conditions altered biofilm formation in several Shewanella strains, with Shewanella hafniensis P14 displaying the highest sensitivity. Metabolomic analysis of the ECPs identified glycogen as a key metabolite associated with biofilm inhibition. Further genomic analysis of S. hafniensis P14 revealed an interruption in its glycogen synthesis pathway, suggesting a dependency on external glycogen-related metabolites for biofilm development. These findings demonstrate that Shewanella sp. Pdp11 ECPs can modify biofilm formation across multiple Shewanella strains, particularly in S. hafniensis P14 through glycogen-associated mechanisms.}, }
@article {pmid40423805, year = {2025}, author = {Meehan, DE and O'Toole, PW}, title = {A Review of Diet and Foraged Pollen Interactions with the Honeybee Gut Microbiome.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {54}, pmid = {40423805}, issn = {1432-184X}, support = {GOIPG/2024/5035//Taighde &#xc9;ireann/ ; 12/RC/2273_P2/SFI_/Science Foundation Ireland/Ireland ; }, mesh = {Bees/microbiology/physiology ; Animals ; *Gastrointestinal Microbiome ; *Pollen/metabolism ; *Diet ; }, abstract = {The honeybee Apis mellifera is a globally vital pollinator for flowering plants and crops, but it is currently facing mounting threats to survival due to habitat anthropization, emerging pathogens, and climate change. Over the past decade, increasing research efforts to understand and combat these challenges have led to an exploration of the honeybee gut microbiome-a relatively simple and highly conserved community of commensals which has a range of effects on the host. Researchers have now unravelled the main functional roles of this microbiome which include innate immune system stimulation, metabolism of dietary compounds, and mediation of host development and behaviour. Key amongst these is its role in aiding nutrition through the metabolism of complex carbohydrates and by degradation of otherwise indigestible pollen compounds. Increasingly, research is indicating that a diverse and high-quality pollen diet is key to maintaining healthy colonies and a stable microbiome. However, colonies can struggle to meet these dietary needs, particularly if they are located in anthropized ecosystems. Disruptions to honeybee diets or a reduction in the availability of diverse foraging options can significantly alter the composition of the microbiome, shifting it towards an abnormal state that leaves the honeybee more vulnerable to infection. Seasonal changes, primarily the overwintering period, also induce shifts in microbiome composition and are periods of time when a colony is particularly vulnerable to pathogenic infection. A comprehensive understanding of the effect these variables have on both microbiome composition and colony health is key to tackling the unprecedented environmental challenges that honeybees now face. This review summarises recent research which has elucidated the functional role of the gut microbiome in metabolism and how the composition of this bacterial community can alter due to seasonal change, anthropized landscapes, and dietary shifts. Finally, we also discuss recent studies investigating the effect that dietary supplementation has on the gut microbiome and the application of probiotic candidates for improving colony resilience and strength.}, }
@article {pmid40423261, year = {2025}, author = {Rotsaert, C and Minnebo, Y and Duysburgh, C and Liu, LS and Mahalak, KK and Firman, J and Mattei, LM and Moustafa, AM and Bittinger, K and Hu, W and Marzorati, M and Michiels, J and Van de Wiele, T}, title = {Digestive parameters and gut microbiota load and composition along the in vivo piglet gastrointestinal tract.}, journal = {Journal of animal science}, volume = {}, number = {}, pages = {}, doi = {10.1093/jas/skaf107}, pmid = {40423261}, issn = {1525-3163}, abstract = {The increased attention towards the role of the gut microbiome in health and disease for both animals and humans has fuelled the demand for more relevant and accurate research models. In this study, we present an overview of biochemical and microbial parameters measured throughout the digestive tract of ten TopigsNorsvin x German Piétrain piglets to better understand the in vivo dynamics of digestive and fermentative processes in different gastrointestinal segments, as pigs are suggested to be a representative animal model for the human gastrointestinal tract. Our key findings include region-specific and significantly differing (P < 0.001) pH profiles, with the stomach having the lowest pH (3.36 ± 0.72) and the ileum the highest (7.24 ± 0.18). Dry matter content also varied significantly (P < 0.001), with the stomach having the highest (27.8 ± 2.4%) and the duodenum the lowest (10.6 ± 0.7%). The average total transit time was 12 hours and 45 minutes ± 1 hour and 42 minutes. Enzyme activities (pepsin, trypsin, amylase) showed interindividual differences. Amino acid levels varied among piglets, with total concentrations averaging 7.04 x 102 ± 2.29 x 102 µg mL-1 in the duodenum, 1.19 x 103 ± 2.69 x 102 µg mL-1 in the jejunum and 9.39 x 102 ± 2.54 x 102 µg mL-1 in the ileum. Bile acid concentrations varied strongly between piglets, with high levels in the gall bladder and varying levels throughout the digestive tract. Short-chain fatty acid concentrations increased significantly (P < 0.001) along the digestive tract, with the highest levels in the large intestine. The microbial load increased consistently (P < 0.001) along the digestive tract, with the highest loads in the rectum (6.82 x 1010 ± 2.88 x 1010 cells mL-1). The highest microbial diversity was observed in the lower intestine (i.e. caecum, colon and rectum), with significant shifts in microbial community composition, especially from the ileum to the caecum. This study provides valuable insights into the digestive and microbiological parameters of the porcine gut, confirming the pig's relevance as a model for gastrointestinal research. The findings can inform the development of in vitro or ex vivo models, reducing ethical constraints of animal studies and aiding in the assessment of dietary interventions on gut health.}, }
@article {pmid40422247, year = {2025}, author = {Wheeler, KM and Oh, MW and Fusco, J and Mershon, A and Kim, E and De Oliveira, A and Rahme, LG}, title = {MvfR Shapes Pseudomonas aeruginosa Interactions in Polymicrobial Contexts: Implications for Targeted Quorum-Sensing Inhibition.}, journal = {Cells}, volume = {14}, number = {10}, pages = {}, pmid = {40422247}, issn = {2073-4409}, support = {R01 AI177555/AI/NIAID NIH HHS/United States ; 5R01AI177555-02/GF/NIH HHS/United States ; N/A//Massachusetts General Hospital Research Scholar Award/ ; }, mesh = {*Quorum Sensing/genetics ; *Pseudomonas aeruginosa/pathogenicity/physiology/genetics/metabolism ; Humans ; *Bacterial Proteins/metabolism/genetics ; Biofilms/growth &amp; development ; Virulence ; Gene Expression Regulation, Bacterial ; Microbial Interactions ; Pseudomonas Infections/microbiology ; }, abstract = {Infections often occur in complex niches consisting of multiple bacteria. Despite the increasing awareness, there is a fundamental gap in understanding which interactions govern microbial community composition. Pseudomonas aeruginosa is frequently isolated from monomicrobial and polymicrobial human infections. This pathogen forms polymicrobial infections with other ESKAPEE pathogens and defies eradication by conventional therapies. By analyzing the competition within co-cultures of P. aeruginosa and representative secondary pathogens that commonly co-infect patients, we demonstrate the antagonism of P. aeruginosa against other ESKAPEE pathogens and the contribution of this pathogen's multiple quorum-sensing (QS) systems in these interactions. QS is a highly conserved bacterial cell-to-cell communication mechanism that coordinates collective gene expressions at the population level, and it is also involved in P. aeruginosa virulence. Using a collection of P. aeruginosa QS mutants of the three major systems, LasR/LasI, MvfR/PqsABCDE, and RhlR/RhlI, and mutants of several QS-regulated functions, we reveal that MvfR and, to a lesser extent, LasR and RhlR, control competition between P. aeruginosa and other microbes, possibly through their positive impact on pyoverdine, pyochelin, and phenazine genes. We show that MvfR inhibition alters competitive interspecies interactions and preserves the coexistence of P. aeruginosa with the ESKAPEE pathogens tested while disarming the pathogens' ability to form biofilm and adhere to lung epithelial cells. Our results highlight the role of MvfR inhibition in modulating microbial competitive interactions across multiple species, while simultaneously attenuating virulence traits. These findings reveal the complexity and importance of QS in interspecies interactions and underscore the impact of the anti-virulence approach in microbial ecology and its importance for treating polymicrobial infections.}, }
@article {pmid40421462, year = {2025}, author = {Liu, RZ and Zhao, XY and Feng, B and Zhao, WS and Li, MY and Yu, XF and Hu, SP and Li, RP and Gao, JL and Borjigin, Q}, title = {Research on soil bacterial community assembly and function under different straw returning practices in arid and semi-arid agricultural ecosystems over multiple years.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1590686}, pmid = {40421462}, issn = {1664-302X}, abstract = {INTRODUCTION: Straw return has gained attention for its potential to improve soil quality and crop yields, particularly in semi-arid regions like the Tumu Chuan Plain Irrigation Area. Soil bacteria play a crucial role in regulating soil biological processes, and understanding how straw return affects bacterial populations can guide better agricultural management practices.<br><br>METHODS: We investigated the impact of continuous straw return on soil bacterial communities using 16S rRNA gene sequencing. Four treatments were applied: Farmers' shallow rotation (CK), straw incorporated with deep tillage (DPR), straw incorporated with subsoiling (SSR), and no-tillage mulching straw return (NTR). Bacterial community structure, metabolic pathways, and assembly mechanisms were analyzed using Bugbase and PICRUSt2 for phenotypic and metabolic pathway predictions.<br><br>RESULTS: The study found that straw return practices significantly altered the relative abundance and life history strategies of bacterial phyla, mainly influenced by soil organic matter (SOM) and enzyme activity. The K-strategist to r-strategist ratio was highest in CK (2.06) and lowest in SSR (1.89). DPR and NTR treatments significantly changed bacterial community structure compared to CK (p < 0.05), resembling SSR. Predictions showed that DPR and NTR enhanced carbohydrate and amino acid metabolism and promoted more stable bacterial networks, with homogenous selection and drift effects. Bacterial aggregation in all treatments was driven by random processes, with varying aggregation levels: CK (20%), DPR (38.6%), SSR (16.5%), and NTR (30.7%).<br><br>DISCUSSION: The study demonstrates that continuous straw return practices significantly impact soil bacterial communities. DPR and NTR notably improved microbial diversity, bacterial cooperation, and ecosystem stability. These findings provide valuable insights for sustainable agricultural practices in semi-arid regions, enhancing soil microbial ecology and soil health through strategic straw return.}, }
@article {pmid40419814, year = {2025}, author = {Srivastava, AK and Riaz, A and Jiang, J and Li, X and Uzair, M and Mishra, P and Zeb, A and Zhang, J and Singh, RP and Luo, L and Chen, S and Yang, S and Zhao, Y and Xie, X}, title = {Advancing Climate-Resilient Sorghum: the Synergistic Role of Plant Biotechnology and Microbial Interactions.}, journal = {Rice (New York, N.Y.)}, volume = {18}, number = {1}, pages = {41}, pmid = {40419814}, issn = {1939-8425}, support = {[2022]091//Guizhou Provincial Youth Science and Technology Talents Growth Project/ ; }, abstract = {Climate-related problems such as drought stress, extreme temperature, erratic rainfall patterns, soil degradation, heatwaves, flooding, water logging, pests and diseases afflict the production and sustainability of sorghum. These challenges may be addressed by adopting climate-resilient practices and using advanced agronomic techniques. These challenges are being addressed through innovative applications of plant biotechnology and microbiology, which offer targeted solutions to enhance sorghum's resilience. For instance, biotechnological tools like CRISPR/Cas9 enable precise genetic modifications to improve drought and heat tolerance, while microbial inoculants, such as plant growth-promoting rhizobacteria (PGPR) and arbuscular mycorrhizal fungi (AMF), enhance nutrient uptake and stress tolerance through symbiotic interactions. However, biotechnological tools lead to the development of sorghum varieties with heat, drought and salinity tolerance, while marker-assisted selection significantly accelerates breeding for stress-resilient traits. When genetic engineering is introduced, genes encoding heat shock proteins, Osmo protectants and antioxidant pathways are introduced to increase plant resistance to abiotic stress. These compounds stabilise cellular structures, protect enzymes, and maintain osmotic balance, enhancing the plant's ability to survive and function in adverse environmental conditions. At the same time, it is reported that microbiology offers beneficial microbes, nitrogen-fixing bacteria, phosphate-solubilizing microorganisms, and arbuscular mycorrhizal fungi that help enhance nutrient availability, soil health and water uptake. Combinations of endophytes and microbial inoculants enhance plant immunity to pests and diseases while increasing tolerance to stress. Biocontrol agents such as Bacillus and Trichoderma contain suppression of pathogens and need less dependence on the use of chemical pesticides. On top of that, genetic modification increases the nutritional quality of sorghum biofortified. This is where biotechnology and microbiology work together to deliver sustainable farming systems reducing environmental impacts, boosting yields and securing food supply under environmental stresses. This review aims to examine the synergistic integration of plant biotechnology and microbial interactions as a strategy to enhance sorghum's resilience to climate-induced stresses, including drought, elevated temperatures, and nutrient-deficient soils. It highlights recent advancements in biotechnological tools such as gene editing, marker-assisted selection, and tissue culture, alongside the emerging role of plant-beneficial microbes in promoting stress tolerance and improving soil health. By synthesizing current knowledge across these disciplines, this review seeks to outline a framework for future research that harnesses the intersection of biotechnology and microbial ecology to support the sustainable improvement of sorghum resilience.}, }
@article {pmid40419768, year = {2025}, author = {Keegstra, JM and Landry, ZC and Zweifel, ST and Roller, BRK and Baumgartner, DA and Carrara, F and Martínez-Pérez, C and Clerc, EE and Ackermann, M and Stocker, R}, title = {Risk-reward trade-off during carbon starvation generates dichotomy in motility endurance among marine bacteria.}, journal = {Nature microbiology}, volume = {10}, number = {6}, pages = {1393-1403}, pmid = {40419768}, issn = {2058-5276}, support = {542395FY22//Simons Foundation/ ; 542379FY22//Simons Foundation/ ; GBMF9197//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 205321 207488//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 51NF40 225148//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; }, mesh = {*Carbon/metabolism ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; *Seawater/microbiology ; *Aquatic Organisms/physiology/metabolism ; Biomass ; Carbon Cycle ; *Bacterial Physiological Phenomena ; }, abstract = {Copiotrophic marine bacteria contribute to the control of carbon storage in the ocean by remineralizing organic matter. Motility presents copiotrophs with a risk-reward trade-off: it is highly beneficial in seeking out sparse nutrient hotspots, but energetically costly. Here we studied the motility endurance of 26 marine isolates, representing 18 species, using video microscopy and cell tracking over 2 days of carbon starvation. We found that the trade-off results in a dichotomy among marine bacteria, in which risk-averse copiotrophs ceased motility within hours ('limostatic'), whereas risk-prone copiotrophs converted ~9% of their biomass per day into energy to retain motility for the 2 days of observation ('limokinetic'). Using machine learning classifiers, we identified a genomic component associated with both strategies, sufficiently robust to predict the response of additional species with 86% accuracy. This dichotomy can help predict the prevalence of foraging strategies in marine microbes and inform models of ocean carbon cycles.}, }
@article {pmid40417422, year = {2025}, author = {Roothans, N and Pabst, M and van Diemen, M and Herrera Mexicano, C and Zandvoort, M and Abeel, T and van Loosdrecht, MCM and Laureni, M}, title = {Long-term multi-meta-omics resolves the ecophysiological controls of seasonal N2O emissions during wastewater treatment.}, journal = {Nature water}, volume = {3}, number = {5}, pages = {590-604}, pmid = {40417422}, issn = {2731-6084}, abstract = {Nitrous oxide (N2O) is the third most important greenhouse gas and originates primarily from natural and engineered microbiomes. Effective emission mitigations are currently hindered by the largely unresolved ecophysiological controls of coexisting N2O-converting metabolisms in complex communities. To address this, we used biological wastewater treatment as a model ecosystem and combined long-term metagenome-resolved metaproteomics with ex situ kinetic and full-scale operational characterization over nearly 2 years. By leveraging the evidence independently obtained at multiple ecophysiological levels, from individual genetic potential to actual metabolism and emergent community phenotype, the cascade of environmental and operational triggers driving seasonal N2O emissions has ultimately been resolved. We identified nitrifier denitrification as the dominant N2O-producing pathway and dissolved O2 as the prime operational parameter, paving the way to the design and fostering of robust emission control strategies. This work exemplifies the untapped potential of multi-meta-omics in the mechanistic understanding and ecological engineering of microbiomes towards reducing anthropogenic impacts and advancing sustainable biotechnological developments.}, }
@article {pmid40413948, year = {2025}, author = {Pholtaisong, J and Kongsinkaew, C and On-Mee, T and Chittapun, S and Pornpukdeewattana, S and Todhanakasem, T and Kunyanee, K and Panya, A and Phonsatta, N and Yingcharoen, P and Charoenrat, T}, title = {Natural versus Saccharomyces boulardii self-induced anaerobic coffee fermentation: Effects on physicochemical properties and microbial ecology, and their influence on volatile profiles and sensory attributes across roast levels.}, journal = {Food chemistry}, volume = {488}, number = {}, pages = {144871}, doi = {10.1016/j.foodchem.2025.144871}, pmid = {40413948}, issn = {1873-7072}, mesh = {Fermentation ; *Volatile Organic Compounds/metabolism/chemistry/analysis ; Taste ; *Coffee/microbiology/chemistry/metabolism ; Humans ; *Saccharomyces boulardii/metabolism ; Anaerobiosis ; *Coffea/microbiology/chemistry/metabolism ; Bacteria/metabolism/isolation &amp; purification/classification/genetics ; Flavoring Agents/metabolism/chemistry ; }, abstract = {This study investigates the effects of natural self-induced anaerobic fermentation (NSIAF) and Saccharomyces boulardii self-induced anaerobic fermentation (SSIAF) on Arabica coffee during wet processing. Over 24 h of fermentation, NSIAF exhibited greater microbial diversity, higher titratable acidity, and increased reducing sugar consumption, while SSIAF provided a more controlled microbial environment dominated by S. boulardii. Volatile compound analysis identified 207 compounds, with lighter roasts showing the greatest number of significantly different compounds between NSIAF and SSIAF treatments. Sensory evaluation revealed a higher cupping score for NSIAF at a light roast (82.08 ± 0.14) compared to SSIAF (81.58 ± 0.14), reflecting distinct flavor characteristics imparted by each fermentation process. Both methods achieved specialty coffee standards (≥80 points), highlighting the potential of NSIAF for complex and diverse profiles and the suitability of SSIAF for consistency and controlled fermentation.}, }
@article {pmid40413198, year = {2025}, author = {Brandão Gontijo, J and Huang, L and Levintal, E and Prieto García, C and Erikson, CB and Coyotl, A and Horwath, WR and Dahlke, HE and Mazza Rodrigues, JL}, title = {Depth-dependent Metagenome-Assembled Genomes of Agricultural Soils under Managed Aquifer Recharge.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {858}, pmid = {40413198}, issn = {2052-4463}, support = {7975//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 2021-38420-34070//United States Department of Agriculture | National Institute of Food and Agriculture (NIFA)/ ; }, mesh = {*Soil Microbiology ; *Groundwater ; Agriculture ; *Metagenome ; Microbiota ; Bacteria/genetics/classification ; Metagenomics ; California ; Archaea/genetics ; Soil ; }, abstract = {Managed Aquifer Recharge (MAR) systems, which intentionally replenish groundwater aquifers with excess water, are critical for addressing water scarcity exacerbated by demographic shifts and climate variability. To date, little is known about the functional diversity of the soil microbiome at different soil depth inhabiting agricultural soils used for MAR. Knowing the functional diversity is pivotal in regulating nutrient cycling and maintaining soil health. Metagenomics, particularly Metagenome-Assembled Genomes (MAGs), provide a powerful tool to explore the diversity of uncultivated soil microbes, facilitating in-depth investigations into microbial functions. In a field experiment conducted in a California vineyard, we sequenced soil DNA before and after water application of MAR. Through this process, we assembled 146 medium and 14 high-quality MAGs, uncovering a wide array of archaeal and bacterial taxa across different soil depths. These findings advance our understanding of the microbial ecology and functional diversity of soils used for MAR, contributing to the development of more informed and sustainable land management strategies.}, }
@article {pmid40412969, year = {2025}, author = {Yan, W and Gu, L and Yue, X and Zhong, H and Wang, D}, title = {Vertical distribution of intracellular protoporphyrin IX in coastal sediment cores: Implications for sedimentology and microbial community composition.}, journal = {Journal of environmental sciences (China)}, volume = {156}, number = {}, pages = {712-724}, doi = {10.1016/j.jes.2024.11.014}, pmid = {40412969}, issn = {1001-0742}, mesh = {*Geologic Sediments/chemistry/microbiology ; *Protoporphyrins/analysis ; *Microbiota ; RNA, Ribosomal, 16S ; *Environmental Monitoring ; }, abstract = {Protoporphyrin IX (PPIX), a basic porphyrin system found in nature, all "porphyrin-type" tetrapyrroles with a biological function are biosynthetically derived thereof. PPIX is a metalloprosthetic group of numerous proteins involved in diverse metabolic and respiratory processes across all domains of life, and is thus considered essential for respiring organisms. Determining the biotic and abiotic factors that influence marine microbial growth and community structure is critical for understanding global biogeochemical cycles. Here, we present vertical profiles of intracellular PPIX and four derivative products (Chlorophyll-a/b and Pheophytin-a/b) from two coastal sediment cores, alongside ancillary geochemical and 16S rRNA microbial community data. Our findings indicated that PPIX is present in the natural sediment environment and displays a decreasing trend with depth, revealing a significant positive correlation with both organic matter and microbial abundance. Co-occurrence networks revealed that the environmental distribution of PPIX was positively correlated with the microbial porphyrin producer (high genetic completeness), but negatively correlated with auxotrophs (absence or low genetic completeness). It emphasized the critical role of PPIX as a biological molecule involved in key physiological processes. These results suggest that PPIX is a prominent component of the shared extracellular metabolite pool, especially in anoxic marine sediments where it exists at physiologically relevant concentrations for microbial metabolism. This study highlighted the significance of PPIX in microbial ecology and its potential impact on biogeochemical cycles in marine sedimentary environments.}, }
@article {pmid40412391, year = {2025}, author = {Breyer, E and Stix, C and Kilker, S and Roller, BRK and Panagou, F and Doebke, C and Amano, C and Saavedra, DEM and Coll-García, G and Steger-Mähnert, B and Dachs, J and Berrojalbiz, N and Vila-Costa, M and Sobrino, C and Fuentes-Lema, A and Berthiller, F and Polz, MF and Baltar, F}, title = {The contribution of pelagic fungi to ocean biomass.}, journal = {Cell}, volume = {188}, number = {15}, pages = {3992-4002.e13}, doi = {10.1016/j.cell.2025.05.004}, pmid = {40412391}, issn = {1097-4172}, mesh = {*Biomass ; *Fungi/metabolism/genetics ; Oceans and Seas ; *Seawater/microbiology ; Archaea ; Bacteria ; Carbon Cycle ; Ergosterol ; In Situ Hybridization, Fluorescence ; }, abstract = {Metagenomic analysis has recently unveiled the widespread presence of pelagic fungi in the global ocean, yet their quantitative contribution to carbon stocks remains elusive, hindering their incorporation into biogeochemical models. Here, we revealed the biomass of pelagic fungi in the open-ocean water column by combining ergosterol extraction, Calcofluor-White staining, catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH), and microfluidic mass sensor techniques. We compared fungal biomass with the biomass of other more studied microbial groups in the ocean such as archaea and bacteria. Globally, fungi contributed 0.32 Gt C (CI: 0.19-0.46), refining previous uncertainty estimates from two orders of magnitude to less than one. While fungal biomass was lower than that of bacteria, it exceeded that of the archaea (archaea:fungi:bacteria biomass ratio of 1:9:44). Collectively, our findings reveal the important contribution of fungi to open-ocean biomass and, consequently, the marine carbon cycle, emphasizing the need for their inclusion in biogeochemical models.}, }
@article {pmid40411587, year = {2025}, author = {Kelleher, LA and Anderson, Z and Stratford, JA and Fortunato, CS}, title = {Deciphering Soil Microbial Dynamics in Northeastern American Grasslands with Goldenrods (Solidago sp.).}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {53}, pmid = {40411587}, issn = {1432-184X}, mesh = {*Soil Microbiology ; *Grassland ; Rhizosphere ; *Bacteria/classification/genetics/isolation &amp; purification ; Soil/chemistry ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Pennsylvania ; *Solidago/microbiology ; Plant Roots/microbiology ; Biodiversity ; Hydrogen-Ion Concentration ; }, abstract = {Grasslands are important centers of biodiversity; however, these ecosystems have been in decline. Although many methods for grassland restoration have been developed, the abundant microbial communities in these regions are understudied and could be used to assist in these efforts. In this study, we aimed to understand how microbial communities varied by soil type, grassland site, and environmental conditions. Samples were taken from rhizosphere soil (attached to plant roots), proximal soil (close to the plant roots), and from bulk cores at Ricketts Glen State Park and Nescopeck State Park in northeastern Pennsylvania, USA, during June and August of 2021 and 2022. Rhizosphere soil samples were taken from the native common grassland plant, Solidago rugosa. 16S rRNA gene sequencing revealed that pH as well as soil type (bulk, proximal, or rhizosphere) significantly influenced the microbial community composition of each soil. Each soil type had its own distinct microbial communities, and proximal soil was identified as a transition zone between rhizosphere and bulk microbial communities. We also observed that the rhizosphere communities were dependent upon geography, as these communities were significantly different between grasslands even though the plant species remained the same. Our results highlight the complex nature of soil microbial communities and how many factors, including pH, soil type, and geography, can be overlayed to impact soil microbes. Results suggest future avenues of conservation research through modification and regulation of specific soil microbial communities in order to aid in the rehabilitation of these diminished regions.}, }
@article {pmid40410028, year = {2025}, author = {Vareschi, S and Jaut, V and Vijay, S and Allen, RJ and Schreiber, F}, title = {Antimicrobial efflux and biofilms: an interplay leading to emergent resistance evolution.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2025.04.012}, pmid = {40410028}, issn = {1878-4380}, abstract = {The biofilm mode of growth and drug efflux are both important factors that impede the treatment of bacterial infections with antimicrobials. Decades of work have uncovered the mechanisms involved in both efflux and biofilm-mediated antimicrobial tolerance, but links between these phenomena have only recently been discovered. Novel findings show how efflux impacts global cellular physiology and antibiotic tolerance, underpinned by phenotypic heterogeneity. In addition efflux can mediate cell-to-cell interactions, relevant in biofilms, via mechanisms including efflux of signaling molecules and metabolites, signaling using pump components and the establishment of local antibiotic gradients via pumping. These recent findings suggest that biofilm antibiotic tolerance and efflux are closely coupled, with synergistic effects leading to the evolution of antimicrobial resistance in the biofilm environment.}, }
@article {pmid40408931, year = {2025}, author = {Conall Holohan, B and Trego, A and Keating, C and Bressani-Ribeiro, T and Chernicharo, CL and Daigger, G and Galdi, SM and Knörle, U and Paissoni, E and Robles, A and Rogalla, F and Shin, C and Soares, A and Smith, AL and Szczuka, A and Hughes, D and O'Flaherty, V}, title = {Anaerobic microbial core for municipal wastewater treatment - the sustainable platform for resource recovery.}, journal = {Current opinion in biotechnology}, volume = {94}, number = {}, pages = {103317}, doi = {10.1016/j.copbio.2025.103317}, pmid = {40408931}, issn = {1879-0429}, mesh = {*Wastewater/microbiology ; Anaerobiosis ; *Water Purification/methods ; *Waste Disposal, Fluid/methods ; }, abstract = {The requirement for carbon neutrality and bioresource recovery has shifted our views on water treatment from health and pollution avoidance to one of sustainability with water and nutrient circularity. Despite progress, the current process of wastewater treatment is linear, based on core aerobic microbiology, which is unlikely to be carbon neutral due to its large use of energy and production of waste sludge. Here, we outline a shift from aerobic to anaerobic microbiology at the core of wastewater treatment and resource recovery, illustrating the state-of-the-art technologies available for this paradigm shift. Anaerobic metabolism primarily offers the benefit of minimal energy input (up to 50% reduction) and minimal biomass production, resulting in up to 95% less waste sludge compared with aerobic treatment, which is increasingly attractive, given dialogue surrounding emerging contaminants in biosolids. Recent innovative research solutions have made ambient (mainstream) anaerobic treatment a ready substitute for the aerobic processes for municipal wastewater in temperate regions. Moreover, utilising anaerobic treatment as the core carbon removal step allows for more biological downstream resource recovery with several opportunities to couple the process with (anaerobic) nitrogen and phosphorus recovery, namely, potential mainstream anaerobic ammonium oxidation (anammox) and methane oxidation (N-DAMO). Furthermore, these technologies can be mixed and matched with membranes and ion-exchange systems, high-value biochemical production, and/or water reuse installations. As such, we propose the reconfiguration of the wastewater treatment plant of the futurewith anaerobic microbiology. Mainstream anaerobic treatment at the core of a truly sustainable platform for modern municipal wastewater treatment, facilitating circular economy and net-zero carbon goals.}, }
@article {pmid40408805, year = {2025}, author = {Bi, W and Butardo, V and Sha, G and Zhang, H and Wu, X and Wang, L}, title = {Microbial degradation and pollutant control in aerobic composting and anaerobic digestion of organic wastes: A review.}, journal = {Waste management (New York, N.Y.)}, volume = {204}, number = {}, pages = {114894}, doi = {10.1016/j.wasman.2025.114894}, pmid = {40408805}, issn = {1879-2456}, mesh = {*Composting/methods ; Anaerobiosis ; Biodegradation, Environmental ; Aerobiosis ; *Refuse Disposal/methods ; *Waste Management/methods ; }, abstract = {Aerobic composting (AC) and anaerobic digestion (AD) are promising technologies for organic waste treatment, but their efficiency and safety are influenced by complex waste composition and persistent contaminants. This review identifies the advances in understanding microbial community dynamics, enzymatic degradation pathways, and the fate of contaminants during AC and AD processes. The findings indicate that substrate composition shapes dominant microbial populations and their degradative enzymes, with this correlation potentially useful for predicting functional microbial communities. Additionally, AC shows advantages in antibiotic elimination while AD excels in heavy metal immobilization, with both contributing to removing certain antibiotic resistance genes (ARGs). The strategic manipulation of environmental conditions, particularly temperature and oxygen levels, can drive microbial succession to optimize organic matter decomposition while minimizing ARG proliferation. Economic analyses reveal that AC offers lower operational costs and AD generates valuable by-products with potential energy recovery from organic waste. Case studies indicate that integrating both technologies can overcome individual limitations and enhance degradation efficiency compared to conventional single-technology approaches. This work proposes a comprehensive framework for developing coupled AC-AD systems to achieve more efficient and safer organic waste valorization than conventional single-technology approaches. This review has important implications for advancing sustainable waste management practices and mitigating the spread of antibiotic resistance in the environment.}, }
@article {pmid40408146, year = {2025}, author = {Fontanarrosa, P and Clare, C and Fedorec, AJH and Barnes, CP}, title = {MIMIC: a Python package for simulating, inferring, and predicting microbial community interactions and dynamics.}, journal = {Bioinformatics (Oxford, England)}, volume = {41}, number = {5}, pages = {}, pmid = {40408146}, issn = {1367-4811}, support = {BB/W013770/1//Bioengineered Cells &amp; Systems/ ; BB/T008709/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Software ; *Microbiota ; Bayes Theorem ; *Computational Biology/methods ; *Microbial Interactions ; Machine Learning ; Computer Simulation ; }, abstract = {SUMMARY: The study of microbial communities is vital for understanding their impact on environmental, health, and technological domains. The Modelling and Inference of MICrobiomes Project (MIMIC) introduces a Python package designed to advance the simulation, inference, and prediction of microbial community interactions and dynamics. Addressing the complex nature of microbial ecosystems, MIMIC integrates a suite of mathematical models, including previously used approaches such as Generalized Lotka-Volterra (gLV), Gaussian Processes (GP), and Vector Autoregression (VAR) plus newly developed models for integrating multi-omic data, to offer a versatile framework for analyzing microbial dynamics. By leveraging Bayesian inference and machine learning techniques, MIMIC provides the ability to infer the dynamics of microbial communities from empirical data, facilitating a deeper understanding of their complex biological processes, unveiling possible unknown ecological interactions, and enabling the design of microbial communities. Such insights could help to advance microbial ecology research, optimizing biotechnological applications, and contribute to environmental sustainability and public health strategies. MIMIC is designed for flexibility and ease of use, aiming to support researchers and practitioners in microbial ecology and microbiome research.<br><br>MIMIC is freely available under the MIT License at https://github.com/ucl-cssb/MIMIC. It is implemented in Python (version 3.7 or higher) and is compatible with Windows, macOS, and Linux operating systems. MIMIC depends on standard Python libraries including NumPy, SciPy, and PyMC. Comprehensive examples and tutorials (including the main text demonstrations) are provided as Jupyter notebooks in the examples/directory and at the MIMIC Docs website, along with detailed installation instructions and real-world data use cases. The software will remain freely available for at least two years following publication. A code snapshot for this publication is also available at Zenodo: https://doi.org/10.5281/zenodo.15149003.}, }
@article {pmid40407874, year = {2025}, author = {Velthuis, M and Zoccarato, L and Veraart, AJ and Monaghan, MT and Funke, E and Verdonschot, P and Grossart, HP and Hilt, S}, title = {Light-Driven Changes in Macrophyte Tissue Quality Affect the Composition of Associated Microbial Communities.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {52}, pmid = {40407874}, issn = {1432-184X}, support = {Veni.202.053//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; }, mesh = {Biofilms/growth &amp; development/radiation effects ; *Fungi/classification/genetics/radiation effects/isolation &amp; purification ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Microbiota/radiation effects ; *Light ; *Hydrocharitaceae/microbiology/radiation effects/chemistry/metabolism ; Nitrogen/metabolism/analysis ; Carbon/metabolism/analysis ; Phosphorus/metabolism/analysis ; Biodiversity ; Plant Leaves/microbiology ; Phenols/analysis/metabolism ; }, abstract = {Microbial biofilms are important components in macrophyte decomposition, and their composition depends on the decomposition stage and host plant quality. Here, we investigated how macrophyte tissue quality (i.e., C:N:P stoichiometry and phenolic contents) influences epiphytic microbial biofilms during litter decomposition. Consecutive experiments were conducted to (1) modify the C:N:P stoichiometry and phenolic content of the freshwater macrophyte Elodea nuttallii by manipulating light and nutrient availability and (2) test how the modified tissue quality affected epiphytic microbial biofilm diversity and community composition before and during macrophyte decomposition. Our results showed that shading led to lower C:N ratios (28.6 to 12.6) and higher phenolic content (10.8 to 19.2 µg/mg dry weight). Simultaneously, shading affected the epiphytic bacterial and fungal community composition, and these shifts correlated with the macrophyte C:N ratio. While no effects of macrophyte tissue quality on decomposition rates were observed, the epiphytic bacterial community composition on the litter was significantly affected by light treatment, time, and their interaction. Bacterial community composition shifted from a high abundance of Comamonadaceae to a more diverse community over time. Overall bacterial diversity was lower on the litter grown in the shaded mesocosms. Fungal diversity and community composition during litter decomposition were not affected by litter quality. Overall, our results reveal a structuring role of macrophyte tissue quality on its associated microbial biofilm and uniquely show a continuation of light-driven changes in epiphytic bacterial community composition after exposure. We conclude that light-driven changes in C:N stoichiometry are a crucial factor in shaping epiphytic microbial communities during macrophyte decomposition.}, }
@article {pmid40407873, year = {2025}, author = {Van Heurck, B and Cardenas, DV and Hylén, A and Jankowska, E and Cole, DB and Montserrat, F and Kreuzburg, M and Romaniello, SJ and Meysman, FJR}, title = {Microbial Community Structure in Contrasting Hawaiian Coastal Sediments.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {51}, pmid = {40407873}, issn = {1432-184X}, mesh = {*Geologic Sediments/microbiology/chemistry ; Hawaii ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; *Seawater/microbiology/chemistry ; Bays/microbiology/chemistry ; Biodiversity ; }, abstract = {Microbe-mineral interactions play a fundamental role in marine sediments and global biogeochemical cycles. Here, we investigated the sediment microbial communities in two contrasting field sites on Big Island, Hawaii (USA), that differ in their bay morphology and sediment grain size distributions: Papakōlea Beach (exposed, finer sediment) and Richardson Ocean Park (sheltered, coarser sediment). We selected three stations within each bay and characterized the mineral and chemical composition of the sediment and porewater, and used 16S rRNA amplicon sequencing of the V4V5 hypervariable region to investigate the naturally occurring microbial communities. Microbial community structure differed significantly between the two bays, rather than within each bay, whereby microbial diversity was markedly lower at Papakōlea compared to Richardson. We correlated environmental variables to microbial community structure in order to identify the key drivers of community differences between and within the two bays. Our study suggests that differing physico-chemical properties of the sediment and porewater, resulting from the contrasting bay morphologies and geophysical drivers, are the main factors influencing microbial community structure in these two bays. Papakōlea Beach is a naturally occurring "green sand" beach, due to its high olivine content. This site was selected in the broader context of a field campaign investigating olivine as a source mineral for ocean alkalinity enhancement (OAE), a carbon dioxide removal technology. Our results highlight the complexity of marine sediment environments, with implications for the monitoring, reporting and verification of future field trials involving olivine addition for ocean alkalinity enhancement.}, }
@article {pmid40406230, year = {2025}, author = {Li, M and Meng, Z and Li, J and Zhang, X and Wang, Y and Li, X and Yang, Y and Li, Y and Yang, X and Chen, X and Fan, Y}, title = {Stochastic processes dominate the community assembly of ectomycorrhizal fungi associated with Betula platyphylla in Inner Mongolia, China.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19364}, pmid = {40406230}, issn = {2167-8359}, mesh = {*Mycorrhizae/genetics/classification/isolation &amp; purification ; China ; *Soil Microbiology ; *Betula/microbiology ; Stochastic Processes ; Biodiversity ; Rhizosphere ; DNA, Fungal/genetics ; Mycobiome ; }, abstract = {The maintenance and driving mechanisms of microbial community structure have become important research focuses in microbial ecology. Therefore, clarifying the assembly of ectomycorrhizal (EM) fungal communities can provide a relevant basis for studying forest diversity, ecological diversity, and ecological evolution. Betula platyphylla is a typical EM dependent tree species with characteristics such as renewal ability and strong competitive adaptability, and it plays a crucial ecological function in Inner Mongolia. However, the research on EM fungi's diversity and community assembly is very limited. We investigated EM fungal communities associated with B. platyphylla from 15 rhizosphere soil samples across five sites in Inner Mongolia. The fungal rDNA ITS2 region was sequenced using Illumina Miseq sequencing. A total of 295 EM fungal OTUs belonging to two phyla, three classes, nine orders, 20 families, and 31 genera were identified, of which Russula, Cortinarius, and Sebacina were the most dominant taxa. Significant differences existed in the composition of dominant genera of EM fungi across the five sites, and the relative abundances of dominant genera also showed significant differences among the sites. The β NTI and NCM fitting analyses suggest that stochastic processes mainly determine the EM fungal community assembly. Our study indicates that B. platyphylla harbors a high EM fungal diversity and highlights the important role of the stochastic process in driving community assembly of mutualistic fungi associated with B. platyphylla in north China.}, }
@article {pmid40405772, year = {2025}, author = {Onghena, L and Heldens, A and De Paepe, K and Antwi, M and Van Vlierberghe, H and Raevens, S and Verhelst, X and Hoorens, A and Devisscher, L and van Nieuwenhove, Y and Van de Wiele, T and Geerts, A and Lefere, S}, title = {The double-edged sword of metabolic and bariatric surgery: extending the biliary limb can trigger bacterial translocation, sepsis, and liver inflammation - an experimental study.}, journal = {International journal of surgery (London, England)}, volume = {111}, number = {7}, pages = {4239-4251}, pmid = {40405772}, issn = {1743-9159}, mesh = {Animals ; *Bacterial Translocation ; Mice ; *Bariatric Surgery/adverse effects/methods ; Humans ; Male ; *Sepsis/etiology ; Mice, Inbred C57BL ; *Postoperative Complications/etiology ; Disease Models, Animal ; Gastric Bypass/adverse effects ; Female ; Gastrointestinal Microbiome ; }, abstract = {BACKGROUND: Metabolic and bariatric surgery (MBS) procedures with extended biliary limb length are gaining popularity to expedite weight loss but can induce liver failure. We aimed to investigate the underlying pathophysiology for this potentially fatal complication.<br><br>MATERIALS AND METHODS: We compared mouse models of vertical sleeve plication, sleeve gastrectomy, Roux-en-Y gastric bypass (RYGB), and one-anastomosis gastric bypass with three biliary limb lengths (25%&#xa0;=&#xa0;&#x3a9; 1 , 50%&#xa0;=&#xa0;&#x3a9; 2 , 75%&#xa0;=&#xa0;&#x3a9; 3) by analyzing mortality, weight loss, metabolic and liver health, bacterial translocation, inflammation, and biliary and fecal microbiome. Gut decontamination with oral antibiotics (amoxicillin, vancomycin, neomycin, and metronidazole) was performed in a subset of &#x3a9; 3 mice. Liver histology from mice with different biliary limb lengths was compared to samples from human patients who developed liver failure following biliopancreatic diversion or RYGB.<br><br>RESULTS: RYGB and &#x3a9; 1&amp;2 significantly improved glucose intolerance and liver steatosis compared to sham surgery. However, extending the biliary limb (&#x3a9; 3) resulted in 100% mortality. The &#x3a9; 3 procedure induced bacterial translocation of Enterococcus genus to the spleen and biliary fluid, consistent with increased serum lipopolysaccharide levels and terminal ileum, biliary limb, and hepatic inflammation. Liver histology in &#x3a9; 3 mice was characterized by mediovesicular steatosis, closely resembling the histological picture observed in patients with liver failure after MBS. Oral gut decontamination significantly improved &#x3a9; 3 1-week-survival from 31.3% to 80.0%, prevented bacterial overgrowth in biliary fluid and spleen, and decreased liver damage.<br><br>CONCLUSION: Mortality in longer biliary limb MBS surgery is caused by bacterial overgrowth, translocation, and gut-liver axis inflammation, which were reversed by oral gut decontamination with antibiotics.}, }
@article {pmid40405300, year = {2025}, author = {He, T and Moukarzel, R and Fu, M and Yang, M and Du, R and Zhao, J and Liu, J and Wu, J and Deng, W and Zhu, Y and Yang, M and Zhu, S and Du, F}, title = {Rain-shelter cultivation promotes grapevine health by altering phyllosphere microecology in rainy areas.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {56}, pmid = {40405300}, issn = {2524-6372}, support = {32360712//National Natural Science Foundation of China/ ; 32360712//National Natural Science Foundation of China/ ; 32360712//National Natural Science Foundation of China/ ; 32360712//National Natural Science Foundation of China/ ; 32360712//National Natural Science Foundation of China/ ; 32360712//National Natural Science Foundation of China/ ; 32360712//National Natural Science Foundation of China/ ; 32360712//National Natural Science Foundation of China/ ; 202101BD070001-125//Yunnan Province Agricultural Joint Special Project/ ; 202101BD070001-125//Yunnan Province Agricultural Joint Special Project/ ; 202101BD070001-125//Yunnan Province Agricultural Joint Special Project/ ; 202101BD070001-125//Yunnan Province Agricultural Joint Special Project/ ; 202101BD070001-125//Yunnan Province Agricultural Joint Special Project/ ; 202101BD070001-125//Yunnan Province Agricultural Joint Special Project/ ; 202101BD070001-125//Yunnan Province Agricultural Joint Special Project/ ; 202101BD070001-125//Yunnan Province Agricultural Joint Special Project/ ; 202101BD070001-125//Yunnan Province Agricultural Joint Special Project/ ; 2018HA009//Yunnan Provincial Academician Exploration Funding Project/ ; }, abstract = {Grapes are a globally significant fruit crop, but their cultivation is often challenged by leaf diseases, which limit industrial productivity. Rain-shelter cultivation has emerged as a sustainable agricultural strategy to mitigate these challenges. This study examines the effects of rain-shelter cultivation, compared to open-air cultivation, on the microclimate within the grape canopy and the microbial ecology of the grape phyllosphere. The research focused on two cultivation methods: rain-shelter and open-air cultivation. Key environmental factors such as temperature, relative humidity, and light intensity within the grape canopy were measured during the growing season. The study also explored how these conditions influence the biodiversity, stability, and functional roles of phyllosphere microbiota, particularly focusing on the community assembly processes of bacteria and oomycetes, and the efficacy of culturable microorganisms in combating grape leaf diseases. The results showed that rain-shelter cultivation signifcantly reduced leaf humidity, increased canopy temperature, and decreased light intensity, regardless of weather conditions. This approach led to a significant decrease in the incidence of grape downy mildew without affecting the overall Shannon diversity index of phyllosphere microbes. At the Class level, there was a reduction in Cystobasidiomycetes, Bacteroidia, Brocadiae, and Phycisphaerae, while Oligoflexia levels are significantly increased under rain-shelter conditions. Genus-level analysis revealed significant reductions in plant pathogens such as Erysiphe, Alternaria, and Cercospora. The study found that rain-shelter cultivation shifts fungal community assembly from stochastic to deterministic processes, while bacterial networks showed increased stability. Additionally, the beneficial microorganism Pseudomonas aeruginosa exhibited a preventive effect against grape leaf diseases, enhancing grape berry quality by increasing puncture resistance and leaf internode length. These findings provide understanding of the complex relationship between grape canopy microclimate, disease management, and microbial dynamics suggesting rain-shelter cultivation as a viable strategy for sustainable grape production, it offers insights into the research and development of future biological control agents.}, }
@article {pmid40404904, year = {2025}, author = {Scheelings, TF and Kodikara, S and Beale, DJ and Van, TTH and Moore, RJ and Skerratt, LF}, title = {Pondering Ponds: Exploring Correlations Between Cloacal Microbiota and Blood Metabolome in Freshwater Turtles.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {50}, pmid = {40404904}, issn = {1432-184X}, mesh = {Animals ; *Turtles/microbiology/blood ; *Metabolome ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; RNA, Ribosomal, 16S/genetics ; *Cloaca/microbiology ; *Ponds/microbiology ; *Microbiota ; Gastrointestinal Microbiome ; Fresh Water ; }, abstract = {The gut microbiota of vertebrates significantly influences host physiology, yet little is known about how habitat factors shape microbiotas in non-human species, especially freshwater turtles. This study explores the relationship between cloacal microbiota and serum metabolome in eastern longneck turtles (Chelodina longicollis), marking the first such investigation in chelonians. By comparing microbiotas from two distinct pond environments, we applied a multi-omics approach combining 16S rRNA sequencing and metabolomic profiling. Results showed that location influenced microbial composition and metabolic profiles, with dominant bacterial phyla Pseudomonadota, Actinomycetota, and Bacillota, and distinct families linked to differences in microbial diversity. Notably, turtles from one pond displayed an unusually high proportion of Actinomycetota. We also found a clear connection between microbiota diversity and metabolome, suggesting certain bacterial combinations impact host physiology. These findings offer important insights into the complex interaction between microbial communities and metabolism in freshwater turtles, a highly threatened group. This research emphasises the value of integrating microbiota and metabolomic data in conservation strategies and highlights the need for further longitudinal studies to explore the dynamic host-microbiota relationship in these understudied species.}, }
@article {pmid40403739, year = {2025}, author = {Kramer, SJ and Jones, EL and Estapa, ML and Paul, NL and Rynearson, TA and Santoro, AE and Sudek, S and Durkin, CA}, title = {Sinking particles exporting diatoms and Hacrobia predict the magnitude of oceanic POC flux.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {40403739}, issn = {1751-7370}, support = {#986836//Simons Foundation Postdoctoral Fellowship in Marine Microbial Ecology/ ; 80NSSC21K0015//NASA Ocean Biology and Biogeochemistry/ ; 80NSSC18K1431//NASA Ocean Biology and Biogeochemistry/ ; 80NSSC17K0716//NASA Ocean Biology and Biogeochemistry/ ; }, mesh = {*Seawater/microbiology/chemistry ; *Phytoplankton/genetics/metabolism/classification ; *Diatoms/metabolism/genetics/classification ; RNA, Ribosomal, 18S/genetics ; Pacific Ocean ; Atlantic Ocean ; *Carbon/metabolism/analysis ; Ecosystem ; Sequence Analysis, DNA ; }, abstract = {Carbon flux to the deep sea can be dictated by surface ocean phytoplankton community composition, but translating surface ocean observations into quantitative predictions of carbon export requires additional consideration of the underlying ecosystem drivers. Here, we used genetic tracers of phytoplankton detected in surface seawater and within sinking particles collected in the mesopelagic ocean to identify mechanistic links between surface communities and carbon export in the North Pacific and North Atlantic Oceans. Phytoplankton 18S rRNA gene sequences were sampled over a 1-month period in surface seawater and within bulk-collected and individually isolated sinking particles using mesopelagic sediment traps (100-500 m). Nearly all phytoplankton amplicon sequence variants exported from the surface were packaged in large (>300 μm) particles. Individually, each of these particles contained only a few distinct phytoplankton amplicon sequence variants, but collectively, large particles transported about half of the surface taxonomic diversity into the mesopelagic. The relative sequence abundances of the surface community detected within particles were quantitatively related to measured carbon fluxes: a linear model based on the relative sequence abundance of just two pigment-based phytoplankton taxa, diatoms and photosynthetic Hacrobia, was predictive of carbon flux magnitude. These two taxa were also enriched in the ecologically distinct particle classes that had the greatest influence on carbon export magnitude. As global, hyperspectral ocean color satellites begin to quantify these taxonomic groups in the surface ocean, the relationship of these taxa to carbon fluxes demonstrated here may help in developing more accurate algorithms to estimate global carbon export in the ocean.}, }
@article {pmid40402470, year = {2025}, author = {Moukarzel, R and Waller, LP and Jones, EE and Ridgway, HJ}, title = {Arbuscular mycorrhizal fungal symbiosis in New Zealand ecosystems: challenges and opportunities.}, journal = {Letters in applied microbiology}, volume = {78}, number = {5}, pages = {}, doi = {10.1093/lambio/ovaf070}, pmid = {40402470}, issn = {1472-765X}, mesh = {*Mycorrhizae/physiology/genetics/classification ; New Zealand ; *Symbiosis ; *Ecosystem ; *Plants/microbiology ; Soil Microbiology ; }, abstract = {Arbuscular mycorrhizal fungi (AMF) are obligate biotrophs that form a symbiotic and mutualistic relationship with most terrestrial plants, playing an important role in plant growth, nutrient acquisition, and ecosystem stability. This review synthesizes current knowledge on AMF colonization in plants within New Zealand ecosystems, including the challenges and opportunities of molecular identification techniques used in characterizing AMF communities in natural and managed systems. The ecosystem services provided by AMF, such as improved growth parameters, enhanced nutrition, and disease control, are discussed in detail, highlighting their significance in sustainable agriculture and natural ecosystems. Additionally, the role of AMF in invasion ecology was examined, revealing their dual potential to either facilitate or hinder invasive plant species. Despite significant advances in understanding AMF biology, future research is needed to explore the underlying mechanisms of AMF-plant interactions and to address the challenges caused by changing environmental conditions. This review focused on the importance of AMF in promoting ecosystem resilience and suggests avenues for future research to harness their full potential in agricultural and ecological contexts.}, }
@article {pmid40402324, year = {2025}, author = {Mizeriene, G and Lygis, V and Prospero, S}, title = {Oomycete Diversity and Ecology in Declining Alder Stands in Switzerland.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {49}, pmid = {40402324}, issn = {1432-184X}, support = {Project Code 14.035//Sciex-NMSch Fellowship/ ; }, mesh = {Switzerland ; *Alnus/microbiology/parasitology ; *Oomycetes/classification/isolation &amp; purification/genetics ; *Biodiversity ; *Soil Microbiology ; Plant Diseases/microbiology ; Rhizosphere ; Phytophthora/isolation &amp; purification/classification/genetics ; Phylogeny ; Pythium/isolation &amp; purification/genetics/classification ; }, abstract = {In this study, we assessed the occurrence and diversity of four oomycete genera (Phytophthora, Phytopythium, Pythium, and Globisporangium) in 13 declining alder (Alnus glutinosa and A. incana) stands in Switzerland. For this, we sampled and analyzed soil from tree rhizosphere, water from streams and rivers along which the stands were located, and symptomatic alder bark. The overall isolation rate was 47.2%, with a total of 400 oomycete isolates recovered at all 13 sites. The highest incidence of oomycete isolates was in soil samples (baiting, 82.5% isolation rate), followed by water (baiting, 14.7%), and bark (direct isolation, 2.7%). Of all recovered oomycete isolates, 90.3% could be successfully assigned to a known species, for a total of 23 species identified, including both preferential saprotrophs and pathogens. Among all genera, Phytophthora was the most abundant with 273 isolates (75.6%), followed by Phytopythium, Pythium, and Globisporangium. Oomycete species diversity showed a significant variation among substrates. Only one species-Phytophthora lacustris-was abundant in all substrates, while 16 species were restricted to a specific substrate, mainly soil. The rhizosphere of symptomatic alder trees harbored the most diverse oomycete community, highlighting once again the importance of soil as a reservoir for these microorganisms. Only two Phytophthora species were isolated from alder bark lesions, namely, P. × alni, the known causal agent of alder decline, and P. lacustris. The low recovery rate of P. × alni might be due to attempts to isolate it from old, inactive lesions, but may also suggest that alder decline might be caused by other oomycetes infecting the root system of the trees.}, }
@article {pmid40402315, year = {2025}, author = {Mitchell, JK and Matthee, S and Ndhlovu, A and Miller, M and Buss, P and Matthee, CA}, title = {The Microbiome and Coxiella Diversity Found in Amblyomma hebraeum and Dermacentor rhinocerinus Ticks Sampled from White Rhinoceros.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {48}, pmid = {40402315}, issn = {1432-184X}, mesh = {Animals ; *Microbiota ; *Perissodactyla/parasitology/microbiology ; *Amblyomma/microbiology ; *Coxiella/genetics/classification/isolation &amp; purification ; *Dermacentor/microbiology ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; South Africa ; Coxiella burnetii/genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; Bacteria/classification/genetics/isolation &amp; purification ; Female ; Male ; }, abstract = {The microbiome and the prevalence of the pathogenic bacterium Coxiella burnetii in ticks associated with white rhinoceros, Ceratotherium simum, is unknown. Targeted Illumina 16S rRNA amplicon sequencing was used to characterize the bacterial microbiome diversity found within 40 Amblyomma hebraeum and 40 Dermacentor rhinocerinus ticks collected from 40 white rhinoceros individuals in the Kruger National Park, South Africa. Specific emphasis was also given to further investigate the prevalence of the pathogenic C. burnetti in these tick species. At the phylum level, Proteobacteria dominated both tick microbiomes, followed by Actinobacteria and Firmicutes; Coxiella was the most abundant genus within A. hebraeum and Rickettsia within D. rhinocerinus. While alpha diversity did not differ significantly between the two tick species, beta diversity revealed significant species-specific differences in bacterial community composition. Additionally, there was no correlation between sampling region and microbiome diversity or composition for either tick species. Twenty-five Coxiella amplicon sequence variants (ASVs) were identified, forming three distinct monophyletic Coxiella clades and a fourth single ASV lineage. The Coxiella clades showed a correlation to tick species identity with D. rhinocerinus harboring significantly greater Coxiella diversity than A. hebraeum-potentially indicative of different coevolutionary pathways between the bacteria and their respective hosts. PCR of the IS1111 transposase gene for 238 ticks detected a 66.1% (56.7-74.4%) prevalence for C. burnetii in D. rhinocerinus compared to 55.8% in A. hebraeum (46.5-64.8%). These findings support a notion that each tick species is characterized by its own microbiome community composition and that both A. hebraeum and D. rhinocerinus may act as reservoirs and potential vectors of C. burnetii to white rhinoceros.}, }
@article {pmid40402178, year = {2025}, author = {Salazar, J and González, J and Riofrío, R and Siavichay, F and Carrera, M and Mogrovejo, A and Barrera-Galicia, G and Valdez-Tenezaca, A}, title = {MALDI-TOF Mass Spectrometry Characterization of Culturable Microbiota Associated with the Skin of Amphibians from the Southern Andes Mountains of Ecuador.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {47}, pmid = {40402178}, issn = {1432-184X}, support = {PICCIITT19-11//Universidad Cat&#xf3;lica de Cuenca/ ; PICCIITT19-11//Universidad Cat&#xf3;lica de Cuenca/ ; PICCIITT19-11//Universidad Cat&#xf3;lica de Cuenca/ ; }, mesh = {Ecuador ; Animals ; *Skin/microbiology ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; *Microbiota ; *Bacteria/classification/isolation &amp; purification/genetics ; *Fungi/classification/isolation &amp; purification/genetics ; *Anura/microbiology ; Biodiversity ; }, abstract = {Ecuador is recognized for having a high diversity of anuran species, which are distributed mainly south of the Andes mountains. However, due to their geographic location and accessibility, there are few studies related to the culturable microbiota of these amphibians in this region. The objective of this study was to explore the bacterial and fungal biodiversity present on the skin of wild anuran species in the southern Andes of Ecuador and to observe whether geographical barriers in the region could increase the variability of the culturable microbiota through MALDI-TOF mass spectrometry. This analysis revealed the presence of 29 bacterial taxa and 9 fungal taxa, consisting mainly of: Pseudomonas chlororaphis (28%), Acinetobacter iwoffii (14%), Pseudomonas fluorescens (14%), and Hortaea werneckii (26.4%), Fusarium solani (20.5%), Syncephalastrum spp. (20.5%), respectively. Diversity varied across the five sampling locations, with geographic location proving to be a significant driver of diversity. Some of the most abundant bacterial and fungal genera have important associations with skin diseases in wildlife and humans. This work represents a glimpse into the complex biodiversity of bacteria and fungi that inhabit the skin substrate, and further studies will be needed to better understand bacterial and fungal biodiversity with potential implications for establishing conservation strategies, along with the development of necessary animal protection measures.}, }
@article {pmid40401940, year = {2025}, author = {Nieves-Morales, R and Paez-Diaz, JA and Rivera-Lopez, EO and Pérez-Santos, N and Borrero-Villabol, SJ and Rodríguez-Ramos, J and Nieves-Rivera, AM and Rios-Velazquez, C}, title = {Characterization of fungal communities in Puerto Rican caves using internal transcribed spacer sequencing.}, journal = {Microbiology resource announcements}, volume = {14}, number = {6}, pages = {e0002225}, pmid = {40401940}, issn = {2576-098X}, abstract = {Cave ecosystems harbor unique and diverse microbial ecology, with fungal communities playing important roles. This study utilizes internal transcribed spacer across seven caves in the northern limestone karst belt area of Puerto Rico to investigate fungal composition. This enhances scientific understanding of subterranean microbial dynamics and supports conservation efforts.}, }
@article {pmid40401939, year = {2025}, author = {Darden, B and Johnson, G and Busch, G and Sharma, I}, title = {Draft genome sequence of Vreelandella neptunia strain 04GJ23 isolated from the underwater Hawaii seamounts.}, journal = {Microbiology resource announcements}, volume = {14}, number = {6}, pages = {e0088224}, pmid = {40401939}, issn = {2576-098X}, support = {2205569//National Science Foundation/ ; }, abstract = {We report a draft genome sequence for Vreelandella neptunia strain 04GJ23 isolated from the underwater Hawaii seamounts. The whole-genome sequence will help understand the ecology and evolution of various ecotypes that are physiologically distinct from the surrounding environments.}, }
@article {pmid40401933, year = {2025}, author = {Das, J and Pal, S and Negi, A and Sundharam, SS and Yadav, A and Subramanian, S and Sinha, SK and Samanta, J and Krishnamurthi, S}, title = {Genomic insights into novel predatory myxobacteria isolated from human feces.}, journal = {Microbiology spectrum}, volume = {13}, number = {7}, pages = {e0214724}, pmid = {40401933}, issn = {2165-0497}, support = {MLP044//Council of Scientific and Industrial Research, India/ ; }, mesh = {Humans ; *Feces/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Myxococcales/genetics/classification/isolation &amp; purification ; *Genome, Bacterial/genetics ; DNA, Bacterial/genetics ; Inflammatory Bowel Diseases/microbiology ; Genomics ; Gastrointestinal Microbiome ; }, abstract = {Myxobacteria are Gram-negative, spore-forming predatory bacteria isolated from diverse environmental samples that feed on other microbes for their survival and growth. However, no reports of cultured representatives from the human gut have been published to date, although previous investigations have revealed the presence of myxobacterial operational taxonomic units (OTUs) in skin and fecal samples. In this study, three myxobacterial strains designated as O35, O15, and Y35 were isolated and purified from fecal samples of two inflammatory bowel disease (IBD) patients. The 16S rRNA gene sequence analysis and phylogeny identified the strains as Myxococcus spp. belonging to two different clades. Genome-based phylogeny and overall genome-related indices, i.e., average amino acid identity and percentage of conserved proteins, confirmed the heterogeneity within the genus and placed the three strains within two different clades separated at the level of different genera. Digital DNA-DNA hybridization and average nucleotide identity values indicated that they belonged to two novel Myxococcus spp. The analysis of meta-barcoding data from IBD and control cohorts detected OTU lineages closely affiliated to the three novel strains. Based on evidence from detailed structural and functional genomics, we propose the novel species Myxococcus faecalis sp. nov. O35[T] and a new genus Pseudomyxococcus gen. nov. to accommodate the novel species Pseudomyxococcus flavus sp. nov. Y35[T]. Overall, these findings provide new information about the occurrence of myxobacteria in the human gut and lay the foundations for a new classification scheme for myxobacterial taxa.IMPORTANCEMyxobacteria have been described from a variety of niches ranging from terrestrial to marine habitats and are known to harbor a diverse portfolio of bioactive molecules. However, to date, there has been no report of isolating culturable representatives from the human gut. This study describes novel myxobacteria from the human gut based on phylogenomics and phenotypic description. The findings are complemented by sequence-based data, wherein operational taxonomic unit (OTU) lineages closely affiliated with the isolated strains have been identified, thus opening a Pandora's box of opportunities for research into the microbial ecology and functional potential of these taxa in the gut ecosystem. Additionally, the study also seeks to establish a new systematic framework, expanding our understanding of myxobacterial taxonomy.}, }
@article {pmid40400674, year = {2025}, author = {Kokociński, M and Graco-Roza, C and Jasser, I and Karosienė, J and Kasperovičienė, J and Kobos, J and Koreivienė, J and Mankiewicz-Boczek, J and Soininen, J and Szczurowska, A}, title = {Environmental factors determining the distribution patterns of invasive Raphidiopsis raciborskii and R. mediterranea in central east Europe.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1533716}, pmid = {40400674}, issn = {1664-302X}, abstract = {OBJECTIVE: In recent decades, the invasive cyanobacteria Raphidiopsis raciborskii and Raphidiopsis mediterranea have expanded their distribution globally, particularly in temperate regions. Understanding the ecological drivers of Raphidiopsis distribution is imperative to addressing the challenges associated with these species. Here, we aimed to characterize the distribution and biomass of R. raciborskii and R. mediterranea across 112 lakes in Poland and Lithuania in relation to local and regional factors.<br><br>RESEARCH DESIGN AND METHODS: Integrated water samples were collected from 102 Polish and 10 Lithuanian lakes from different regions for phytoplankton and chemical analyses. The lakes varied in surface area, and exhibited diverse mixing regimes, trophic states, and morphometries. Phytoplankton was identified and quantified using a Fuchs-Rosenthal or Nageotte chamber. Additionally, we characterized the degree of human pressures the climatic constraints experienced by each lake.<br><br>RESULTS: R. raciborskii occurrence has increased in eastern regions of Poland but biomass is relatively low compared to western Poland, likely due to lower air temperatures and nutrient concentrations, especially phosphorus. In contrast, R. mediterranea only occurred in a small number of lakes in Poland, and in a single lake in Lithuania, with no relation to measured local and regional variables.<br><br>CONCLUSIONS: Our study shows contrasting patterns in the distribution of two invasive cyanobacteria species in Europe, highlighting the importance of climate and nutrients to the distribution of R. raciborskii, the most widespread species, and providing relevant information for decision making and conservation strategies.}, }
@article {pmid40399330, year = {2025}, author = {Liang, X and Yang, S and Radosevich, M and Wang, Y and Duan, N and Jia, Y}, title = {Bacteriophage-driven microbial phenotypic heterogeneity: ecological and biogeochemical importance.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {82}, pmid = {40399330}, issn = {2055-5008}, support = {42377306//National Natural Science Foundation of China/ ; 2023JH3/10200009//Natural Science Foundation of Liaoning Province/ ; No.KLFES-2027//CAS Key Laboratory of Forest Ecology and Silviculture, Institute of Applied Ecology, Chinese Academy of Sciences/ ; No.KLFES-2027//CAS Key Laboratory of Forest Ecology and Silviculture, Institute of Applied Ecology, Chinese Academy of Sciences/ ; }, mesh = {*Bacteriophages/physiology ; Phenotype ; *Bacteria/virology/metabolism/genetics ; Ecosystem ; *Host Microbial Interactions ; *Microbiota ; }, abstract = {Bacteriophages (phages) reprogram host metabolism and generate phenotypic heterogeneity, yet the mechanisms and ecological implications remain poorly understood representing a major knowledge gap in microbial ecology. This review explores how phage infection alters microbial physiology, contributes to single-cell variation, and influences population dynamics. We highlight the potential consequences of phage-driven heterogeneity for microbial community structure and biogeochemical cycling, underscoring the importance of integrating phage-host interactions into ecological and ecosystem models.}, }
@article {pmid40398824, year = {2025}, author = {Massaro, A and Peruzzo, A and Zacometti, C and Zancato, M and Piro, R and Losasso, C and Tata, A and Peron, G}, title = {Exploring the crosstalk between gut microbiota and stool metabolome in omnivorous, vegetarian, and vegan diets: A pilot study.}, journal = {The Journal of nutritional biochemistry}, volume = {144}, number = {}, pages = {109965}, doi = {10.1016/j.jnutbio.2025.109965}, pmid = {40398824}, issn = {1873-4847}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Pilot Projects ; *Feces/chemistry/microbiology ; *Diet, Vegan ; *Diet, Vegetarian ; Adult ; Male ; *Metabolome ; Female ; Middle Aged ; Young Adult ; Metabolomics ; }, abstract = {Gut microbiota (GM) and fecal metabolome are shaped by different dietary regimens. Nevertheless, outlining generalized patterns is challenging, due to the intrinsic heterogeneity of individual dietary choices. In this work, the fecal metabolome of adult volunteers consuming omnivorous (n=44), vegetarian (n=29), and vegan diets (n=25) for at least 12 months was characterized. The crosstalk among diet, GM and fecal metabolome was also investigated correlating metabolomics and metataxonomics data. Untargeted metabolomic profiles were correlated with metataxonomics data previously acquired on the same stool samples. The sphingomyelin SM(d18:2/18:1-2OH) and phosphoethanolamines from animal-based food were associated to the omnivorous diet and were negatively correlated to beneficial Bacteroides ovatus and Odoribacter genus. Plant glycerides, sterols, triterpenes, and oleic-linoleic acid were associated with the vegan diet. Oleic-linoleic acid was positively correlated with Alistipes putredinis. Chenodeoxycholic acid, a primary bile acid, was identified as a marker of vegan diet, while ketolithocholic acid, a secondary bile acid, was associated to the omnivorous diet. This latter was also negatively correlated to B.ovatus. Overall, results confirm that assessing markers of dietary regimens instead of specific food categories is challenging, especially if volunteers' diet is not strictly monitored. However, the integration of metabolomics and metataxonomic data allows to better understand the effects of specific food components on the GM and represents a suitable approach for further molecular investigation in nutrition.}, }
@article {pmid40394467, year = {2025}, author = {Van Hee, S and Segurado Luchsinger, AE and Cusumano, A and Masschelein, J and Jacquemyn, H and Lievens, B}, title = {Correction: The plant-beneficial fungus Trichoderma harzianum T22 modulates plant metabolism and negatively affects Nezara viridula.}, journal = {BMC plant biology}, volume = {25}, number = {1}, pages = {671}, pmid = {40394467}, issn = {1471-2229}, }
@article {pmid40394206, year = {2025}, author = {Khurshid, H and Jamshaid, MB and Salahuudin, Z and Sibtain, K and Fayyaz, I and Ameer, A and Kerbiriou, C and Mckirdy, S and Malik, SN and Gerasimidis, K and Noreen, Z and Javed, S and Tariq, A and Ijaz, UZ and Tariq, A}, title = {Gut microbial ecology and function of a Pakistani cohort with Iron deficiency Anemia.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {17532}, pmid = {40394206}, issn = {2045-2322}, support = {EP/V030515/1//Engineering and Physical Sciences Research Council/ ; MR/Z50628X/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Anemia, Iron-Deficiency/microbiology/epidemiology ; *Gastrointestinal Microbiome ; Humans ; Pakistan/epidemiology ; Female ; Adult ; RNA, Ribosomal, 16S/genetics ; Cohort Studies ; Iron/metabolism ; Bacteria/genetics/classification ; Diet ; }, abstract = {Iron deficiency anemia (IDA) is a major public health concern among women of reproductive age leading to high maternal mortality. Pakistan being one of the Lower -Middle income countries (LMIC) is facing this challenge tremendously. The objective of this study is to determine the impact of IDA on gut microbial diversity as well as its relationship with microbial metabolites.16 S rRNA gene profiling of healthy and IDA affected meconium samples was performed with additional meta-data collected through questionnaire. The anemia was linked to different dietary parameters through chi-square test of independence and Generalized Linear Latent Variable Model (GLLVM). Anaerobic bacterial genera such as Coprococcus, Anaerovoracaceae, strongly associated with anemia and negatively correlated with red meat and fish consumption. Moreover, these microbes positively correlated with branched short chain fatty acids (BSCFAs) production. BSCFAs have strong implications in metabolic disorders. This study provides a snapshot of how anemia modulates gut microbial diversity and microbial metabolites production which may have an impact on iron metabolism.}, }
@article {pmid40393817, year = {2025}, author = {Pantigoso, HA and Ossowicki, A and Stringlis, IA and Carrión, VJ}, title = {Hub metabolites at the root-microbiome interface: unlocking plant drought resilience.}, journal = {Trends in plant science}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tplants.2025.04.007}, pmid = {40393817}, issn = {1878-4372}, abstract = {Drought is one of the most devastating environmental challenges, severely affecting agriculture, ecosystems, and global food security. Effective strategies to predict and mitigate drought are limited. The root-soil-microbiome interface is pivotal in mediating plant resilience to drought. Recent studies highlight dynamics between plant root exudates and microbial communities, influencing stress tolerance through chemical signaling under drought. By integrating plant molecular biology, root chemistry, and microbiome research, we discuss insights into how these mechanisms can be harnessed to enhance crop resilience. Here, we focus on the interplay between plants and their microbiomes with metabolites as a central point of interactions. We synthesize recent developments, identify critical knowledge gaps, and propose future directions to leverage plant-microbe interactions to improve plant drought tolerance.}, }
@article {pmid40393246, year = {2025}, author = {Liu, X and Li, Y and Yuan, C and Zhao, Y and Zhou, L and Yan, Y and Ren, J and Liu, Q}, title = {Sophocarpine suppresses MAPK-mediated inflammation by restoring gut microbiota in colorectal cancer.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {143}, number = {}, pages = {156833}, doi = {10.1016/j.phymed.2025.156833}, pmid = {40393246}, issn = {1618-095X}, mesh = {*Gastrointestinal Microbiome/drug effects ; *Colorectal Neoplasms/drug therapy/microbiology ; Animals ; Humans ; Mice ; *Alkaloids/pharmacology ; Fecal Microbiota Transplantation ; Inflammation/drug therapy ; Cell Line, Tumor ; Male ; Mice, Inbred BALB C ; *Antineoplastic Agents, Phytogenic/pharmacology ; MAP Kinase Signaling System/drug effects ; Dysbiosis/drug therapy ; Xenograft Model Antitumor Assays ; Mice, Nude ; p38 Mitogen-Activated Protein Kinases/metabolism ; Matrines ; }, abstract = {BACKGROUND: Colorectal cancer (CRC), as one of the most common cancers globally, poses a significant challenge to public health due to its high incidence and mortality rates. This underscores the need for continuous exploration of new therapeutic targets and effective drugs. Sophocarpine (SC), a natural compound derived from traditional Chinese medicine, holds considerable therapeutic potential in the treatment of CRC, however, the relevant mechanisms remains unclear.<br><br>PURPOSE: This study aims to explore the anti-tumor effects of SC against CRC by modulating gut microbiota, and uncover potential mechanisms linking SC's therapeutic effects to gut microbiota regulation by analyzing the impact of SC on microbiota composition and CRC progression.<br><br>MATERIAL: This study explores the impact of SC on the gut microbiota in CRC by constructing subcutaneous xenograft tumors of CRC and integrating 16S rRNA sequencing and RNA transcriptomic sequencing. The fecal microbiota transplantation (FMT) mouse model was used to validate the biological function of SC in correcting gut microbiota dysbiosis to treat CRC. Subsequently, we conducted in vitro studies on the molecular mechanisms by which SC regulates the gut microbiota as an effective hallmark of CRC treatment, using lipopolysaccharide (LPS) to simulate an inflammatory gut microbiota environment and P38 MAPK knockdown cell line.<br><br>RESULTS: SC significantly inhibited CRC cell proliferation with IC50 values of 2.547&#xb1;0.256 &#x3bc;M for HCT116 and 2.851&#xb1;0.332 &#x3bc;M for LoVo cells. In vivo experiments demonstrated that SC effectively suppressed tumor growth in xenograft models. 16S rRNA sequencing revealed that SC modulated gut microbiota composition, particularly affecting Bacteroides and Alistipes populations. SC significantly reduced the levels of inflammatory factors and inhibited the MAPK signaling pathway, as evidenced by decreased p-JNK, p-p38 MAPK, and p-NF-&#x3ba;B p65 expression.<br><br>CONCLUSIONS: Current clinical practice still lacks effective therapeutic agents targeting CRC through gut microbiota modulation. This study presents the first evidence that SC, a natural compound, exhibits dual-action therapeutic efficacy against CRC progression by simultaneously modulating gut microbial composition and suppressing MAPK pathway-mediated inflammatory responses. These findings highlight SC's novel therapeutic potential as a promising microbiota-regulating candidate for CRC intervention, offering an innovative approach that bridges microbial ecology with cancer signaling pathways.}, }
@article {pmid40387954, year = {2025}, author = {Warren, ML and Tsuji, K and Decker, LE and Kishi, M and Yang, J and Howe, AC and Fukami, T}, title = {Bacteria in Honeybee Crops Are Decoupled from Those in Floral Nectar and Bee Mouths.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {46}, pmid = {40387954}, issn = {1432-184X}, support = {1656518//National Science Foundation Graduate Research Fellowship Program/ ; }, mesh = {Bees/microbiology ; Animals ; *Plant Nectar ; *Bacteria/classification/isolation &amp; purification/genetics ; *Flowers/microbiology ; Japan ; *Mouth/microbiology ; Seasons ; Gastrointestinal Microbiome ; }, abstract = {Bacteria in the honeybee gut are a well-recognized factor affecting bee health. However, the primary focus of this research has been the hindgut, while the crop, or honey stomach, is assumed to be dominated by environmentally acquired transient taxa that matter little to the bees. To evaluate this assumption, we examined bacterial taxa in the crop and mouth of Apis mellifera and A. cerana japonica foragers and in the nectar of Prunus mume flowers visited by the bees in the Minabe-Tanabe region of Japan. We found that in bacterial composition, the crop was distinct from both the mouth and the nectar, whereas mouth and nectar samples were indistinguishable. Furthermore, the crop remained similar in bacterial composition and diversity, while the mouth showed a sharp drop in alpha diversity and a large increase in beta diversity, from summer to winter. These results refute the conventional assumption, suggesting instead that the crop contains a conserved bacterial community largely distinct from environmental taxa. We also found that strains of a crop-associated species, Apilactobacillus kunkeei, could be season- and host species-specific. Together, these findings suggest that crop-associated bacterial communities should be studied further to better understand the relationship between honeybees and their gut bacteria.}, }
@article {pmid40387916, year = {2025}, author = {González-Villalobos, E and de Almeida Kumlien, ACM and Sànchez-Melsió, A and Balcázar, JL}, title = {Bacteriophages as Vehicles for Antibiotic Resistance Genes in the Onyar River, Spain.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {41}, pmid = {40387916}, issn = {1432-184X}, support = {CVU: 441304//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; 792686//European Union's Horizon 2020 Research and Innovation Programme under the Marie Sk&#x142;odowska-Curie/ ; SGR 01282//Generalitat de Catalunya/ ; }, mesh = {Spain ; *Rivers/microbiology/virology ; *Bacteriophages/genetics ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects/virology/isolation &amp; purification ; *Drug Resistance, Bacterial/genetics ; Geologic Sediments/microbiology/virology ; *Genes, Bacterial ; *Drug Resistance, Microbial/genetics ; DNA, Viral/genetics ; }, abstract = {This study aimed to investigate the presence and abundance of antibiotic resistance genes (ARGs) in bacterial and phage DNA fractions from sediment samples collected from the Onyar River, both before and after its passage through the urban area of Girona (northeast Spain). Genes conferring resistance to β-lactams, fluoroquinolones, macrolides, sulfonamides, and tetracyclines were quantified using quantitative PCR. Our findings showed that ARGs are present in both bacterial and phage DNA fractions, with a higher abundance in the bacterial fraction. Notably, our analysis revealed an increased abundance of the sulfonamide resistance gene sulI in the phage DNA fraction when comparing samples collected before and after the river's passage through the city. Although similar trends were observed for other ARGs (e.g., qnrS and sulII), these differences were not statistically significant (p > 0.05). These findings emphasize the importance of phages as potential reservoirs or vehicles for ARGs in environmental settings. Further research is needed to elucidate the factors that influence gene transfer dynamics and the persistence of ARGs within phages.}, }
@article {pmid40385475, year = {2025}, author = {Li, J and Zhou, L and Xiao, Z}, title = {Advances in the study of Ophiopogon japonicus polysaccharides: structural characterization, bioactivity and gut microbiota modulation regulation.}, journal = {Frontiers in pharmacology}, volume = {16}, number = {}, pages = {1583711}, pmid = {40385475}, issn = {1663-9812}, abstract = {Ophiopogon japonicus polysaccharides (OJPS), the principal bioactive constituents isolated from Ophiopogon japonicus, demonstrate substantial physiological efficacy. OJPS is characterized by a high molecular weight, typically ranging from 2.48 to 324.7 kDa. Emerging evidence indicates that OJPS modulates the composition and structural organization of the gut microbiota, thereby maintaining intestinal barrier integrity and enhancing both gastrointestinal and systemic homeostasis. Moreover, OJPS and its metabolic derivatives engage in dynamic interactions with microbial communities, mediating cellular signaling cascades and endocrine regulation to elicit hypoglycemic effects. Despite these findings, comprehensive analyses of OJPS extraction and purification methodologies, structural elucidation, biological functionalities, and mechanistic insights into its crosstalk with the gut microbiota remain scarce. This review systematically synthesizes contemporary knowledge pertaining to the preparation, structural attributes, bioactivity, and mechanistic underpinnings of OJPS, with particular emphasis on its dual regulatory role in host physiology and gut microbial ecology.}, }
@article {pmid40384051, year = {2025}, author = {Khafagy, ES and Saqr, AA and Almutairy, BK and Aldawsari, MF and Lila, ASA and Ibrahim, TS and Hegazy, WAH and Salem, IM}, title = {Repurposing Nitroimidazoles: A New Frontier in Combatting Bacterial Virulence and Quorum Sensing via In Silico, In Vitro, and In Vivo Insights.}, journal = {Drug development research}, volume = {86}, number = {3}, pages = {e70101}, doi = {10.1002/ddr.70101}, pmid = {40384051}, issn = {1098-2299}, support = {//The authors extend their appreciation to Prince Sattam bin Abdulaziz University for funding this research work through the project number (PSAU/2024/03/29653)./ ; }, mesh = {*Quorum Sensing/drug effects ; Animals ; Biofilms/drug effects ; *Drug Repositioning ; Humans ; Molecular Docking Simulation ; Virulence/drug effects ; *Nitroimidazoles/pharmacology ; Mice ; *Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; HeLa Cells ; Chromobacterium/drug effects ; Molecular Dynamics Simulation ; Pseudomonas aeruginosa/drug effects ; Female ; Indoles/metabolism ; }, abstract = {The global antibiotic resistance crisis demands innovative strategies targeting bacterial virulence rather than survival. Quorum sensing (QS), a key regulator of virulence and biofilm formation, offers a promising avenue to mitigate resistance by disarming pathogens without bactericidal pressure. This study investigates the repurposing of nitroimidazoles as anti-QS and anti-virulence agents at subminimum inhibitory concentrations (sub-MICs). In Silico analyses, including molecular docking and molecular dynamics (MD) simulations, were performed to investigate ligand-receptor interactions with structurally distinct Lux-type QS receptors and assess binding stability and conformational dynamics over time. In Vitro assays evaluated the effects of representative nitroimidazoles, metronidazole (MET) and secnidazole (SEC), on QS-controlled phenotypes, including violacein production in Chromobacterium violaceum and biofilm formation and protease activity in Pseudomonas aeruginosa, Acinetobacter baumannii, Salmonella enterica, and Proteus mirabilis. In Vivo efficacy was assessed using a murine infection model and HeLa cell invasion assays. Molecular docking revealed high-affinity binding to QS receptors, corroborating their mechanistic interference. Sub-MIC MET/SEC significantly suppressed violacein synthesis, biofilm biomass, and protease secretion in Gram-negative pathogens. Both compounds reduced bacterial invasiveness in HeLa cells and In Vivo protected mice from lethal P. aeruginosa infections. Crucially, nitroimidazoles attenuated virulence without affecting bacterial viability, preserving microbial ecology. These findings position nitroimidazoles as dual-function agents; antimicrobial at bactericidal doses and anti-virulence at sub-MICs. Their validated efficacy across In Silico, In Vitro, and In Vivo models underscores their potential as adjunctive therapies, bridging the gap between drug repurposing and next-generation anti-infective development.}, }
@article {pmid40383311, year = {2025}, author = {Zhu, L and Huang, K and Bai, T and Xia, H}, title = {Bacteriophages enhance the transformation of dissolved organic matter during vermicomposting of sludge.}, journal = {Bioresource technology}, volume = {432}, number = {}, pages = {132694}, doi = {10.1016/j.biortech.2025.132694}, pmid = {40383311}, issn = {1873-2976}, mesh = {*Sewage/microbiology/chemistry ; *Bacteriophages/physiology/metabolism ; *Composting/methods ; *Organic Chemicals/metabolism ; Biodegradation, Environmental ; Carbon ; Solubility ; }, abstract = {Vermicomposting is an eco-friendly technology for treating sewage sludge, however its efficiency in transforming biological material is often constrained. This study investigates the potential of bacteriophages to enhance the transformation of dissolved organic matter (DOM) during sludge vermicomposting. Fresh dewatered sludge treated with bacteriophages (VP) were compared to untreated controls (CK) over a 30 days' vermicomposting. The results showed that bacteriophage inoculation led to a 58.17 % reduction in dissolved organic carbon (DOC), significantly higher than the 10.67 % reduction in the CK group (P < 0.05). Additionally, the DOM stability indices in the VP treatment were significantly decreased by 30.95 % (P < 0.05), alongside an increased humification rate. Partial least squares path modeling (PLS-PM) revealed that bacteriophages played a pivotal role in accelerating DOM degradation by selectively lysing specific bacterial populations and altering DOM transformation pathways.}, }
@article {pmid40382531, year = {2025}, author = {Hasegawa, R and Poulin, R and Salloum, PM}, title = {Testing for Consistency in Co-occurrence Patterns Among Bacterial Taxa Across the Microbiomes of Four Different Trematode Parasites.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {45}, pmid = {40382531}, issn = {1432-184X}, support = {202460294//Japan Society for the Promotion of Science/ ; UOO2113//Marsden Fund/ ; UOO2113//Marsden Fund/ ; }, mesh = {Animals ; *Trematoda/microbiology/classification ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; *Snails/parasitology/microbiology ; Phylogeny ; }, abstract = {Elucidating the specific processes and drivers of community assembly in the host microbiome is essential to fully understand host biology. Toward this goal, an important first step is to describe co-occurrence patterns among different microbial taxa, which can be driven by numerous factors, such as host identity. While host identity can be an important influential factor on co-occurrence patterns, a limited number of studies have explored the relative importance of host identity after controlling for other environmental factors. Here, we examined microbial co-occurrence patterns in four phylogenetically distinct trematode species living within the same snail species, collected concomitantly from the same habitat. Our previous study determined that all these trematodes shared some bacterial taxa, and the relative abundance of microbial taxa differed among trematodes, possibly due to differences in their eco-physiological traits. Here, we specifically predict that pairwise microbial co-occurrence patterns also vary among trematode host species. Our results showed that co-occurrence patterns among eight microbial families varied greatly among the four trematode hosts, with some microbial families co-occurring in some trematode species, whereas no such patterns were observed in other trematodes. Our study suggests that the habitat identity (trematode species) and its associated biotic characteristics, such as physiological and ecological traits, can determine co-occurrence patterns among microbial taxa, with substantial effects on local community composition.}, }
@article {pmid40382475, year = {2025}, author = {Yang, Q and Downey, R and Stark, JS and Johnstone, GJ and Mitchell, JG}, title = {The Microbial Ecology of Antarctic Sponges.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {44}, pmid = {40382475}, issn = {1432-184X}, mesh = {*Porifera/microbiology ; Animals ; Antarctic Regions ; *Microbiota ; Symbiosis ; *Bacteria/classification/genetics/isolation &amp; purification ; Archaea/classification/genetics/isolation &amp; purification ; Ecosystem ; Fungi/classification/genetics/isolation &amp; purification ; }, abstract = {Microbial communities in Antarctic marine sponges have distinct taxonomic and functional profiles due to low temperatures, seasonal days and nights, and geographic isolation. These sponge holobionts contribute to nutrient cycling, structural habitat formation, and benthic ecosystem resilience. We review Antarctic sponge holobiont knowledge, integrating culture-based and molecular data across environmental and taxonomic gradients. Although microbiome data exist for only a fraction of the region's 593 known sponge species, these hosts support diverse symbionts spanning at least 63 bacterial, 5 archaeal, and 6 fungal phyla, highlighting the complexity and ecological significance of these understudied polar microbiomes. A conserved core microbiome, dominated by Proteobacteria, Bacteroidetes, Nitrospinae, and Planctomycetes, occurs across Antarctic sponges, alongside taxa shaped by host identity, depth, and environment. Metagenomic data indicate microbial nitrogen cycling, chemoautotrophic carbon fixation, and stress tolerance. Despite these advances, major knowledge gaps remain, particularly in deep-sea and sub-Antarctic regions, along with challenges in taxonomy, methodological biases, and limited functional insights. We identify key research priorities, including developing standardised methodologies, expanded sampling across ecological and depth gradients, and integrating multi-omics with environmental and host metadata. Antarctic sponge holobionts provide a tractable model for investigating microbial symbiosis, functional adaptation, and ecosystem processes in one of Earth's most rapidly changing marine environments.}, }
@article {pmid40380820, year = {2025}, author = {Lakamp, AD and Neujahr, AC and Fernando, SC and Snelling, WM and Spangler, ML}, title = {Short communication: imputation accuracy of host genomic data from metagenomic sequence information.}, journal = {Journal of animal science}, volume = {103}, number = {}, pages = {}, pmid = {40380820}, issn = {1525-3163}, mesh = {Animals ; Cattle/genetics ; *Metagenomics/methods ; Genotype ; Sequence Analysis, DNA/veterinary ; }, abstract = {Metagenomic sequencing is the process of extracting all the genomic information from a given sample. Most metagenomic studies remove any host reads as a matter of course. However, host reads can be used as the basis for genotype imputation to obtain whole genomic sequences. The accuracy of these imputed genotypic calls from a bovine ocular sample was determined by comparing results to those from a commercial array. Overall, imputed genotype calls proved to have a high concordance with array genotype calls (average concordance of 83% and correlation of 0.81 with no filtering). Accuracy increased as filters for host read depth and imputed call confidence were implemented. With filters in place, the average percent concordance was 98% (88% to 99%) while the mean correlation was 0.98 (0.89 to 0.99). Further, identity verification of the metagenomic samples can be carried out if the host is genotyped on another platform.}, }
@article {pmid40379949, year = {2025}, author = {Onaka, H}, title = {Unlocking hidden bioactive compounds: from indolocarbazole and RiPP biosynthesis to the activation of cryptic secondary metabolism via microbial interactions.}, journal = {The Journal of antibiotics}, volume = {78}, number = {7}, pages = {395-407}, pmid = {40379949}, issn = {1881-1469}, mesh = {*Carbazoles/metabolism/pharmacology/chemistry ; *Secondary Metabolism ; *Actinobacteria/metabolism ; Streptomyces/metabolism ; Biological Products/metabolism ; Anti-Bacterial Agents/biosynthesis ; Biosynthetic Pathways ; }, abstract = {Actinomycetes, particularly Streptomyces, are soil microorganisms that produce diverse secondary metabolites with pharmaceutical applications, such as antibiotics and anticancer drugs. These metabolites play important roles in microbial competition and survival. This review highlights three major aspects of actinomycete secondary metabolism: (1) the biosynthesis of indolocarbazoles, (2) the biosynthesis of RiPPs (ribosomally synthesized and post-translationally modified peptides), and (3) the activation of secondary metabolism through microbial interactions. Indolocarbazoles, including staurosporine and rebeccamycin, are potent inhibitors of kinases and DNA topoisomerase I, with potential as anticancer agents. Their biosynthetic pathways involve multiple enzymatic steps, notably carbon-carbon bond formation catalyzed by cytochrome P450 enzymes. RiPPs such as goadsporin and lactazole are highly modular peptide natural products; structural gene modification enables the generation of diverse analogs. A cell-free one-pot synthesis platform has been developed for efficient analog production. To activate cryptic biosynthetic pathways, we employed a combined-culture strategy using actinomycetes and mycolic acid-containing bacteria, resulting in the discovery of 42 novel compounds. Genetic and physiological data indicate that physical contact, rather than diffusible signaling, is essential for induction. These insights emphasize the importance of microbial interactions in natural product biosynthesis and offer new directions for drug discovery through synthetic biology and microbial ecology.}, }
@article {pmid40376461, year = {2025}, author = {Davis, RA and Mafune, KK and Winkler, MKH}, title = {Biodegradable hydrogels and microbial consortia as a treatment for soil dysbiosis.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1565940}, pmid = {40376461}, issn = {1664-302X}, abstract = {Terrestrial microbial communities drive many soil processes and can be pushed into a state of dysbiosis upon disturbance. This dysregulation negatively impacts soil biogeochemical cycles, which threatens plant and soil health. Effective treatment of soil dysbiosis requires simultaneous restoration of multiple system components, addressing both the physical structure of soil and its microbial communities. Hydrogels with microbial consortia simultaneously remedy soil hydrodynamics while promoting microbial reestablishment. The purpose of this review is to shed light on soil management practices through the lens of soil dysbiosis. This is important to address not only for soil health and crop productivity, but also to mitigate climate change through improved soil carbon sequestration and reduced greenhouse gas emissions. This review positions hydrogels and microbes as tools for the treatment of soil dysbiosis, contributing to agricultural and climate resilience.}, }
@article {pmid40373669, year = {2025}, author = {Rescan, M and Gros, M and Borrego, CM}, title = {Multidimensional tolerance landscapes reveal antibiotic-environment interactions affecting population dynamics of wastewater bacteria.}, journal = {Water research}, volume = {282}, number = {}, pages = {123720}, doi = {10.1016/j.watres.2025.123720}, pmid = {40373669}, issn = {1879-2448}, mesh = {*Wastewater/microbiology ; *Anti-Bacterial Agents/pharmacology ; Escherichia coli/drug effects ; Temperature ; Salinity ; Sewage/microbiology ; *Bacteria/drug effects ; Population Dynamics ; }, abstract = {City sewers harbor diverse bacterial communities that are continuously exposed to a myriad of antibiotic residues resulting from human consumption and excretion. Despite their sub-inhibitory concentrations in sewage, these pharmaceutical residues affect the growth rate and the yield of susceptible wastewater-associated bacteria. Moreover, environmental conditions in sewers are complex, including variations in temperature and, in many coastal city sewers, salinity. These variables can modulate antibiotic tolerance and therefore affect the dynamics of microbial populations. To explore such interactions between antibiotics and abiotic environmental factors, we built continuous multivariate tolerance landscapes for three bacterial species commonly detected in sewage: Escherichia coli, the emerging pathogen Streptococcus suis, and a typical sewer dweller, Arcobacter cryaerophilus. We projected their intrinsic growth rate and carrying capacity onto a complex environment including temperature, salinity, and a range of concentrations of two antibiotics frequently measured in urban wastewater (ciprofloxacin and azithromycin). We revealed that antibiotic tolerance was maximal at salinities close to seawater for both E. coli and S. suis, and that the direction of the interaction between antibiotics and temperature is species dependent. In E. coli, we additionally observed a third-order interaction among salinity, temperature and antibiotics, highlighting the limits of predicting field dynamics of bacterial populations using standard laboratory measures. We projected these tolerance curves onto time series data of temperature and conductivity measured in the sewers of Barcelona. Our model highlights that low concentrations of antibiotics could exclude the most sensitive species, while interactions between antibiotics, temperature, and salinity substantially affected the dynamics of the more tolerant ones.}, }
@article {pmid40373649, year = {2025}, author = {Rosa-Masegosa, A and Vilchez-Vargas, R and Gorrasi, S and Monteoliva-García, A and Gonzalez-Martinez, A and Gonzalez-Lopez, J and Muñoz-Palazon, B}, title = {Unraveling the composition and succession of the microbial community in aerobic granular sludge treating urban wastewater with high load from hospital effluent.}, journal = {Chemosphere}, volume = {381}, number = {}, pages = {144483}, doi = {10.1016/j.chemosphere.2025.144483}, pmid = {40373649}, issn = {1879-1298}, mesh = {*Wastewater/microbiology/chemistry ; *Sewage/microbiology ; *Waste Disposal, Fluid/methods ; *Water Pollutants, Chemical/analysis/metabolism ; Bioreactors/microbiology ; Hospitals ; Bacteria/classification/genetics ; Fungi/classification ; *Microbiota ; Cities ; Aerobiosis ; Pharmaceutical Preparations/analysis ; }, abstract = {The treatment of wastewater containing high concentrations of pharmaceutical compounds is a challenge that has not yet been fully resolved. In this study, the occurrence of pharmaceutical and the bacterial and fungal communities were investigated during the treatment of urban wastewater including the hospital effluents using aerobic granular sludge technology. The physic-chemical results pointed out the capability of this technology to remove high rates of organic matter (97 %), total suspended solids (90 %), and nitrogen (85 %) without compromising the granular integrity and properties. The obtained data of pharmaceuticals remarked that the influent concentration had a strong effect on the removal ratio. The better average pharmaceutical removal performances were for carbamazepine (60-85 %), ketoprofen(50-60 %), cyclophosphamide(∼70 %), and trimethoprim(70 %), while the most recalcitrant compound was diclofenac. The molecular analysis exposed the relevance of endogenous microbial loads in the raw wastewater, especially in the start-up period. The mature granules demonstrated the strong selection of granules-forming bacteria, whereas the fungal populations took a longer period to be stable in granular biomass. Once the reactor was stable, the system was able to compete successfully with the influent microorganisms and avoid the spreading of pathogen microorganisms in the effluent, achieving excellent macro-pollutant and micro-pollutant removal ratios.}, }
@article {pmid40373419, year = {2025}, author = {Orsi, AS and Lemos Junior, WJF and Alegbeleye, OO and Muniz, DC and Horita, CN and Sant'Ana, AS}, title = {Sodium chloride reduction in meat processing: Microbial shifts, spoilage risks, and metagenomic insights.}, journal = {Meat science}, volume = {226}, number = {}, pages = {109848}, doi = {10.1016/j.meatsci.2025.109848}, pmid = {40373419}, issn = {1873-4138}, mesh = {*Meat Products/microbiology/analysis ; *Food Microbiology ; *Sodium Chloride/analysis ; *Food Handling/methods ; Animals ; Metagenomics ; Microbiota ; Bacteria ; Food Preservation/methods ; }, abstract = {This review evaluated the impact of sodium chloride (NaCl) reduction or substitution on the microbial ecology of meat products, with a focus on how these changes affect shelf life and safety. Reducing NaCl in fresh meat products promotes the growth of psychrotrophic spoilage bacteria, such as Pseudomonas sp., which thrive at low temperatures, and mesophilic pathogens like Escherichia coli and Staphylococcus aureus, particularly under inadequate storage conditions. In cured and fermented meats, such as salami, lowering NaCl levels disrupts the balance of salt-tolerant microorganisms, notably lactic acid bacteria (LAB) and coagulase-negative staphylococci, potentially leading to increased spoilage and pathogen proliferation. In smoked meats, the combination of reduced NaCl and altered microbial ecology, including a shift toward LAB dominance, may weaken the inhibitory effects on spore-forming bacteria like Clostridium botulinum. Additionally, using metagenomics, we explore the shifts in microbial communities observed in studies involving meat, revealing critical insights into the composition and diversity of bacteria in meat products, as well as the gaps in research on the impact of NaCl reduction and/or substitution on the microbiota. This review provides a comprehensive understanding of these microbial shifts, highlighting the distinct responses of psychrotrophic, mesophilic, and LAB groups to NaCl modification and the need to understand the effects of these alternatives on the meat product microbiome, as well as the neglected microorganisms that can affect the quality and safety of these products.}, }
@article {pmid40372110, year = {2025}, author = {Rohrhofer, J and Wolflehner, V and Schweighardt, J and Koidl, L and Stingl, M and Zehetmayer, S and Séneca, J and Pjevac, P and Untersmayr, E}, title = {Gastrointestinal Barrier Disruption in Post-COVID Syndrome Fatigue Patients.}, journal = {Allergy}, volume = {}, number = {}, pages = {}, doi = {10.1111/all.16593}, pmid = {40372110}, issn = {1398-9995}, support = {//WE&amp;ME Foundation/ ; //Medizinisch-Wissenschaftlicher Fond des Buergermeisters der Bundeshauptstadt Wien/ ; }, abstract = {BACKGROUND: Post-COVID Syndrome (PCS) is the term for a condition with persistent symptoms in a proportion of COVID-19 patients after asymptomatic, mild, or severe disease courses. Numbers vary, but the current estimate is that after COVID-19 approximately 10% develop PCS. The aim of our study was to evaluate the impact of SARS-CoV-2 infection on the gastrointestinal (GI) tract and associations with the development of PCS with fatigue, post-exertional malaise (PEM), orthostatic dysregulation, autonomous dysregulation, and/or neurocognitive dysregulation.<br><br>METHODS: By combining medical record data from a prospective observational study with symptom analysis before, during, and after SARS-CoV-2 infection, we aimed to identify potential risk factors and predictive markers for PCS. Additionally, we analyzed blood, saliva, and stool samples from this well-characterized PCS patient cohort to biologically validate our findings.<br><br>RESULTS: We identified significant associations between pre-existing GI complaints and the development of PCS Fatigue. PCS patients showed higher LBP/sCD14 ratios, lower IL-33 levels, and higher IL-6 levels compared to control groups. Our results highlight the critical role of the GI tract in PCS development of post-viral Fatigue.<br><br>CONCLUSION: We propose that the viral infection disrupts pathways related to the innate immune response and GI barrier function, evidenced by intestinal low-grade inflammation and GI barrier leakage. Monitoring GI symptoms and markers before, during, and after SARS-CoV-2 infection is crucial for identifying predictive clinical phenotypes in PCS. Understanding the interaction between viral infections, immune responses, and gut integrity could lead to more effective diagnostic and treatment strategies, ultimately reducing the burden on PCS patients.}, }
@article {pmid40367785, year = {2025}, author = {Wang, Y and Huang, S and He, J and Feng, Z and Wu, W and Guo, C and He, J}, title = {Unveiling the dynamic viral landscape across developmental stages of cold seep ecosystems: Implications for global marine biogeochemistry.}, journal = {Journal of hazardous materials}, volume = {494}, number = {}, pages = {138594}, doi = {10.1016/j.jhazmat.2025.138594}, pmid = {40367785}, issn = {1873-3336}, mesh = {*Ecosystem ; *Viruses/genetics/classification ; *Geologic Sediments/virology ; *Seawater/virology ; Metagenomics ; }, abstract = {Cold seeps are methane-rich ecosystems playing pivotal roles in global biogeochemical cycling, yet their viral communities remain underexplored. We present the first comprehensive viral metagenomic analysis across developmental stages of the Haima Cold Seep. Characterizing viral assemblages from chemoautotrophic, mature, and extinct seep sediments revealed 4272 viral operational taxonomic units, with 77 % representing novel lineages, highlighting cold seeps' unique viral diversity. Viral community structure and diversity varied significantly by seep stage, with highest diversity in the chemoautotrophic stage. While Siphoviridae and Microviridae dominated, their relative abundances shifted with maturity. Gammaproteobacteria emerged as predominant viral hosts, exhibiting distinct interaction patterns across stages. Notably, the chemoautotrophic stage harbored the highest abundance and diversity of virus-encoded auxiliary metabolic genes (AMGs; ∼450 AMGs), with significantly enriched carbohydrate metabolism and central carbon pathway genes (2.2-fold and 1.8-fold higher respectively, p < 0.005), amino acid metabolism (1.9-fold, p = 0.003), and sulfur relay system genes (2.0-fold, p = 0.002). In contrast, the mature stage exhibited distinct enrichment in energy metabolism genes (up to 3.9-fold difference between sites, p < 0.001) and xenobiotics degradation pathways, suggesting stage-specific viral impacts on biogeochemical cycling. Lytic lifestyles prevailed across stages, indicating dynamic virus-host interactions during seep development. These findings unveil complex viral ecology in cold seeps, with potential influences on microbial community structure and biogeochemical processes. Providing a foundation for understanding viral roles in cold seep ecosystem functioning and biogeochemical cycles, this study has implications for marine microbial ecology and environmental biotechnology.}, }
@article {pmid40366158, year = {2025}, author = {Geonczy, SE and Hillary, LS and Santos-Medellín, C and Sorensen, JW and Emerson, JB}, title = {Patchy burn severity explains heterogeneous soil viral and prokaryotic responses to fire in a mixed conifer forest.}, journal = {mSystems}, volume = {10}, number = {6}, pages = {e0174924}, pmid = {40366158}, issn = {2379-5077}, mesh = {*Soil Microbiology ; Forests ; *Fires ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; Soil/chemistry ; *Tracheophyta ; *Viruses/genetics/classification/isolation &amp; purification ; Microbiota ; Metagenome ; Virome ; }, abstract = {UNLABELLED: Effects of fire on soil viruses and virus-host dynamics are largely unexplored, despite known microbial contributions to biogeochemical processes and ecosystem recovery. Here, we assessed how viral and prokaryotic communities responded to a prescribed burn in a mixed conifer forest. We sequenced 91 viral-size fraction metagenomes (viromes) and 115 16S rRNA gene amplicon libraries from 120 samples: four samples at five timepoints (two before fire and three after fire) at six sites (four treatment, two control). We hypothesized that compositional differences would be most significant between burned and unburned soils, but instead, plot location best distinguished viral communities, more than treatment (burned or not), depth (0-3 or 3-6 cm), or timepoint. For both viruses and prokaryotes, some burned communities resembled unburned controls, while others were significantly different, revealing heterogeneous responses to fire. These patterns were explained by burn severity, here defined by soil chemistry. Viral but not prokaryotic richness decreased significantly with burn severity, and low viromic DNA yields indicated substantial loss of viral biomass at higher severity. The relative abundances of Firmicutes, Actinobacteriota, and the viruses predicted to infect them increased significantly with burn severity, suggesting survival and viral infection of these fire-responsive and potentially spore-forming taxa. The degree of burn severity experienced by each patch of soil, rather than burn status alone, differed over mere meters in the same fire. Therefore, our analyses highlight the importance of high-resolution, paired biogeochemical data to explain soil community responses to fire.<br><br>IMPORTANCE: The impact of fire on the soil microbiome, particularly on understudied soil viral communities, warrants investigation, given known microbial contributions to biogeochemical processes and ecosystem recovery. Here, we collected 120 soil samples before and after a prescribed burn in a mixed conifer forest to assess the impacts of this disturbance on soil viral and prokaryotic communities. We show that simple categorical comparisons of burned and unburned areas were insufficient to reveal the underlying community response patterns. The patchy nature of the fire (indicated by soil chemistry data) led to significant changes in viral and prokaryotic community composition in areas of high burn severity, while communities that experienced lower burn severity were indistinguishable from those in unburned controls. Our results highlight the importance of considering highly resolved burn severity and biogeochemical measurements, even in nearby soils after the same fire, in order to understand soil microbial responses to prescribed burns.}, }
@article {pmid40366134, year = {2025}, author = {Gilbert, NE and Kimbrel, JA and Samo, TJ and Siccardi, AJ and Stuart, RK and Mayali, X}, title = {A bloom of a single bacterium shapes the microbiome during outdoor diatom cultivation collapse.}, journal = {mSystems}, volume = {10}, number = {6}, pages = {e0037525}, pmid = {40366134}, issn = {2379-5077}, support = {SCW1039//U.S. Department of Energy/ ; 1939//Joint Genome Institute/ ; 50220//Facilities Integrating collaborations for User Science/ ; }, mesh = {*Diatoms/growth &amp; development/microbiology ; *Microbiota ; *Eutrophication ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification ; *Flavobacteriaceae/genetics/metabolism ; Metagenomics ; }, abstract = {Algae-dominated ecosystems are fundamentally influenced by their microbiome. We lack information on the identity and function of bacteria that specialize in consuming algal-derived dissolved organic matter in high algal density ecosystems such as outdoor algal ponds used for biofuel production. Here, we describe the metagenomic and metaproteomic signatures of a single bacterial strain that bloomed during a population-wide crash of the diatom, Phaeodactylum tricornutum, grown in outdoor ponds. 16S rRNA gene data indicated that a single Kordia sp. strain (family Flavobacteriaceae) contributed up to 93% of the bacterial community during P. tricornutum demise. Kordia sp. expressed proteins linked to microbial antagonism and biopolymer breakdown, which likely contributed to its dominance over other microbial taxa during diatom demise. Analysis of accompanying downstream microbiota (primarily of the Rhodobacteraceae family) provided evidence that cross-feeding may be a pathway supporting microbial diversity during diatom demise. In situ and laboratory data with a different strain suggested that Kordia was a primary degrader of biopolymers during algal demise, and co-occurring Rhodobacteraceae exploited degradation molecules for carbon. An analysis of 30 Rhodobacteraceae metagenome assembled genomes suggested that algal pond Rhodobacteraceae commonly harbored pathways to use diverse carbon and energy sources, including carbon monoxide, which may have contributed to the prevalence of this taxonomic group within the ponds. These observations further constrain the roles of functionally distinct heterotrophic bacteria in algal microbiomes, demonstrating how a single dominant bacterium, specialized in processing senescing or dead algal biomass, shapes the microbial community of outdoor algal biofuel ponds.IMPORTANCEAquatic biogeochemical cycles are dictated by the activity of diverse microbes inhabiting the algal microbiome. Outdoor biofuel ponds provide a setting analogous to aquatic algal blooms, where monocultures of fast-growing algae reach high cellular densities. Information on the microbial ecology of this setting is lacking, and so we employed metagenomics and metaproteomics to understand the metabolic roles of bacteria present within four replicated outdoor ponds inoculated with the diatom Phaeodactylum tricornutum. Unexpectedly, after 29 days of cultivation, all four ponds crashed concurrently with a "bloom" of a single taxon assigned to the Kordia bacterial genus. We assessed how this dominant taxon influenced the chemical and microbial fate of the ponds following the crash, with the hypothesis that it was primarily responsible for processing senescent/dead algal biomass and providing the surrounding microbiota with carbon. Overall, these findings provide insight into the roles of microbes specialized in processing algal organic matter and enhance our understanding of biofuel pond microbial ecology.}, }
@article {pmid40366070, year = {2025}, author = {Herz, CT and Kulterer, OC and Prager, M and Marculescu, R and Prager, G and Kautzky-Willer, A and Hacker, M and Trajanoski, S and Köfeler, HC and Gallé, B and Haug, AR and Berry, D and Kiefer, FW}, title = {Bariatric surgery promotes recruitment of brown fat linked to alterations in the gut microbiota.}, journal = {European journal of endocrinology}, volume = {192}, number = {5}, pages = {603-611}, doi = {10.1093/ejendo/lvaf081}, pmid = {40366070}, issn = {1479-683X}, support = {P 27391//Austrian Science Fund/ ; 17094//Medical Scientific Fund of the Mayor of the City of Vienna/ ; //Austrian Diabetes Association Research Fund/ ; }, mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; *Adipose Tissue, Brown/metabolism/diagnostic imaging ; *Bariatric Surgery ; Energy Metabolism/physiology ; Fatty Acids, Volatile/metabolism/blood ; *Gastrointestinal Microbiome/physiology ; *Obesity, Morbid/surgery/metabolism/microbiology ; Positron Emission Tomography Computed Tomography ; Weight Loss/physiology ; }, abstract = {OBJECTIVE: The mechanisms of bariatric surgery-induced weight loss and metabolic improvements are still incompletely understood and reach beyond malabsorption or calorie restriction. We sought to investigate the effect of bariatric surgery on brown adipose tissue (BAT) activity and a potential connection with changes in energy metabolism, the gut microbiota, and short-chain fatty acid (SCFA) composition.<br><br>METHODS: We included 32 subjects (25 females) with morbid obesity and analyzed their metabolic profile, gut microbiota composition, circulating SCFAs, energy expenditure, and cold-induced BAT activity using [18F]Fluorodeoxyglucose-positron emission tomography-computed tomography before and up to 1 year after bariatric surgery.<br><br>RESULTS: Twelve months after surgery, the percentage of individuals with active BAT had increased from 28% to 53%. The BAT-negative (BATneg) individuals who had an adverse metabolic profile at baseline compared with subjects with active BAT (BATpos) showed a greater metabolic benefit after surgery. While no changes in overall gut bacterial diversity were observed between BATpos and BATneg, the abundance of 3 specific bacterial families, including Akkermansiaceae, Pasteurellaceae, and Carnobacteriaceae, was distinctly regulated between BAT groups. The bacterial genera most strongly increased in BATpos vs BATneg subjects were all positively correlated with BAT volume and BAT activity. Finally, circulating concentrations of the SCFAs acetate, butyrate, and propionate rose after bariatric surgery and were related to bacterial genera such as Akkermansia, Dialister, and Lachnospiraceae FCS020 group, all known SCFA producers.<br><br>CONCLUSIONS: Bariatric surgery helps recruit active BAT in individuals with obesity and is linked to distinct alterations in the gut microbiome and SCFA composition.<br><br>TRIAL REGISTRATION NUMBER: ClinicalTrials.gov (NCT03168009).}, }
@article {pmid40361280, year = {2025}, author = {Wan, SH and Xu, Y and Xu, W and Leung, SKK and Yu, EYN and Yung, CCM}, title = {Environmental Heterogeneity Drives Ecological Differentiation in Vibrio Populations Across Subtropical Marine Habitats.}, journal = {Environmental microbiology}, volume = {27}, number = {5}, pages = {e70107}, pmid = {40361280}, issn = {1462-2920}, support = {AoE/P-601/23-N//Research Grants Council of Hong Kong/ ; }, mesh = {*Vibrio/genetics/classification/isolation &amp; purification ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Seawater/microbiology ; *Ecosystem ; Hong Kong ; Temperature ; Salinity ; Chaperonin 60/genetics ; Bays/microbiology ; }, abstract = {Elucidating how environmental gradients structure bacterial communities remains fundamental to microbial ecology. We investigated Vibrio population dynamics across contrasting subtropical marine environments in Hong Kong over a year period. Using an integrated approach combining cultivation techniques with molecular analyses of Hsp60 and 16S rRNA genes, we characterised the population structure between a coastal site (Clear Water Bay) and an estuarine site (Deep Bay). The estuarine environment consistently harboured higher Vibrio abundances (10[4]-10[7] copies/mL) compared to coastal waters (10[2]-10[4] copies/mL), with significantly greater phylogenetic diversity. Multivariate analyses revealed salinity as the primary driver of community differentiation between sites, while temperature governed seasonal succession patterns. Phylogenetic analysis of 1521 Vibrio isolates identified three distinct ecological groups corresponding to specific temperature-salinity niches, with evidence of habitat-specific thermal adaptations among closely related strains. Experimental characterisation of thermal performance curves confirmed physiological differentiation between warm- and cool-temperature adapted strains despite high genetic similarity (> 97% Hsp60 gene sequence identity). Several abundant species detected via amplicon sequencing (including V. navarrensis and V. mimicus) displayed site-specific ecotypes but remained uncultivated, highlighting methodological constraints in community characterisation. Our findings demonstrate how environmental heterogeneity drives fine-scale ecological differentiation in Vibrio populations, providing insights into mechanisms of bacterial adaptation in dynamic marine environments.}, }
@article {pmid40359204, year = {2025}, author = {Ghyselinck, J and Verstrepen, L and Rakebrandt, M and Marynissen, S and Daminet, S and Marzorati, M}, title = {In vitro fermentation of yeast cell walls (mannan-oligosaccharide) and purified β-glucans modulates the colonic microbiota of dogs with inflammatory bowel disease and demonstrates protective effects on barrier integrity and anti-inflammatory properties.}, journal = {PloS one}, volume = {20}, number = {5}, pages = {e0322877}, pmid = {40359204}, issn = {1932-6203}, mesh = {Animals ; Dogs ; *Inflammatory Bowel Diseases/microbiology/veterinary ; *Gastrointestinal Microbiome/drug effects ; *Mannans/metabolism/pharmacology ; *beta-Glucans/pharmacology/metabolism ; Prebiotics ; *Saccharomyces cerevisiae/metabolism/chemistry ; *Cell Wall/metabolism/chemistry ; Humans ; Fermentation ; *Colon/microbiology ; Caco-2 Cells ; *Anti-Inflammatory Agents/pharmacology ; *Oligosaccharides/metabolism ; RNA, Ribosomal, 16S/genetics ; Intestinal Mucosa ; }, abstract = {Inflammatory bowel disease (IBD) is characterized by a disruption of intestinal homeostasis, chronic inflammation, and dysbiosis. Prebiotic supplementation may be useful for managing IBD in dogs. The aim of the study is to investigate the effects of two prebiotics, Biolex MB40 or Leiber Beta-S, on the gut microbiota isolated from three dogs with IBD, using the Colon-on-a-plate technology. Biolex MB40 and Leiber Beta-S contain concentrated 1,3-1,6- β-D-glucan isolated from the Saccharomyces cerevisiae cell walls. Biolex MB40 also contains mannan-oligosaccharide (MOS). Wells of the Colon-on-a-plate set up were inoculated with fecal suspensions and supplemented with either Biolex MB40 and Leiber Beta-S, or no test product (blank). Following 48h incubation, bacterial metabolites were measured and 16S rRNA targeted gene sequencing was performed. Colonic supernatants were added to a Caco-2/THP1 co-culture model to evaluate their effects on barrier integrity upon inflammation-induced barrier disruption and interleukin (IL)-10 production. Acetate and propionate concentrations were significantly increased versus blank with Biolex MB40, and biologically relevant numerical increases were observed with Leiber Beta-S supplementation. A donor-dependent, biologically relevant increase in butyrate was observed with both test products versus blank. Alpha diversity and microbiota biomass were increased, as well as the abundance of the five predominant phyla with both test products relative to blank. The greatest increases in abundance were observed for the Bacteroidetes and Firmicutes phyla. Fermentation of both test products had a protective effect on the gut epithelial barrier (measured by transepithelial electrical resistance) that was donor dependent. IL-10 production was significantly increased with Biolex MB40 supplementation for all donors, and with Leiber Beta-S supplementation for one donor. These in vitro findings confirm a prebiotic effect for both products and suggest that supplementation with either Biolex MB40 or Leiber Beta-S may have beneficial effects on the gut microbiota of dogs with IBD.}, }
@article {pmid40358239, year = {2025}, author = {Waegenaar, F and Pluym, T and Vermeulen, E and De Gusseme, B and Boon, N}, title = {Impact of flushing procedures on drinking water biostability and invasion susceptibility in distribution systems.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {6}, pages = {e0068625}, pmid = {40358239}, issn = {1098-5336}, support = {1S02022N//Fonds Wetenschappelijk Onderzoek/ ; 1S26823N//Fonds Wetenschappelijk Onderzoek/ ; S006221N//Fonds Wetenschappelijk Onderzoek/ ; }, mesh = {*Drinking Water/microbiology ; Belgium ; *Water Purification/methods ; *Bacteria/drug effects/growth &amp; development ; *Water Microbiology ; Water Supply ; Halogenation ; Sodium Hypochlorite/pharmacology ; Chlorine ; }, abstract = {UNLABELLED: Ensuring high-quality drinking water remains challenging, as complaints about odors, discoloration, or contamination persist. In Belgium and beyond, traditional flushing is a common curative strategy that involves discharging large water volumes through hydrants while the network remains in use. In some cases, free chlorine (0.5 mg/L) is added, and consumers are advised not to drink the water. However, flushing can alter water biostability, potentially increasing susceptibility to microbial invasion. This study used a pilot-scale drinking water distribution system with three identical 100 m polyvinyl chloride(PVC) loops (DN 80 mm) to assess the impact of flushing with and without chlorination as practiced in chlorinated networks. Loop 1 was flushed with tap water and sodium hypochlorite (NaOCl), followed by two non-chlorinated flushes, loop 2 was unflushed, and loop 3 underwent three flushes. Biostability was assessed using online flow cytometry, and susceptibility to bacterial invasion (Aeromonas media, Pseudomonas putida, and Serratia fonticola) was evaluated in the days following flushing. The water had a 7-day residence time. Results showed that chlorinated flushing promoted microbial regrowth (3.8 × 10[5] vs 2.0 × 10[5] and 1.6 × 10[5] cells/mL for loops 1, 2, and 3, respectively), primarily of resident Sphingopyxis spp. Biofilm cell densities (~4 × 10[6] cells/cm[2]) remained stable across conditions. Bacterial indicators declined over time, with P. pudita and S. fonticola surviving longer (>100 hours) than A. media (13 hours). Decay rates were highest in chlorinated loops, likely due to increased microbial competition. For example, the decay constant of S. fonticola at 20°C was -0.082 h[-1], -0.042 h[-1], and -0.027 h[-1] for loops 1, 2, and 3, respectively.<br><br>IMPORTANCE: Traditional flushing is used as a curative strategy to solve unwanted quality issues during distribution, yet its impact on microbial biostability remains poorly understood. This study provides critical insights into how traditional flushing, both with and without chlorination, influences microbial regrowth and susceptibility to invasion. Findings reveal that chlorinated flushing promotes the regrowth of resident drinking water bacteria while accelerating the decay of introduced unwanted bacterial indicators, emphasizing the complex trade-off between microbial control and system stability. Understanding these dynamics is essential for optimizing flushing procedures, minimizing unintended consequences, and improving distribution system resilience.}, }
@article {pmid40358205, year = {2025}, author = {An, Y and Garcia, SL and Hambäck, PA}, title = {Microbial transfer through fecal strings on eggs affects leaf beetle microbiome dynamics.}, journal = {mSystems}, volume = {10}, number = {6}, pages = {e0172324}, pmid = {40358205}, issn = {2379-5077}, support = {#2019-4980//Vetenskapsr&#xe5;det/ ; }, mesh = {Animals ; *Coleoptera/microbiology ; *Gastrointestinal Microbiome ; *Feces/microbiology ; Female ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; *Ovum/microbiology ; Larva/microbiology ; }, abstract = {UNLABELLED: Gut microbiomes of holometabolous insects can be strongly affected by metamorphosis. Previous studies suggest that microbiome colonization and community development often rely on specialized transmission routes between host life stages. However, there is a lack of comparative studies of microbial community dynamics from different transmission mechanisms. We compared the gut microbial community dynamics across life stages in five Galerucella species that differ in their potential microbial transfer mechanism by sequencing amplicons of the 16S rRNA gene. Females of three of the studied species place a fecal string on top of the egg, which may enhance the transfer of gut microbes, whereas females of the two other species do not. We found that the α-diversity was more stable between life stages in fecal string-placer species compared with the non-fecal string-placer species. Moreover, there were consistent microbiome differences between species, with multiple taxa in each species consistently appearing in all life stages. Fecal strings placed on eggs seem to play an important role in the diversity and dynamics of gut bacteria in Galerucella species, facilitating the vertical transfer of gut bacteria between host insect generations. Alternative, but less efficient, transmission routes appear to occur in non-fecal string-placer species.<br><br>IMPORTANCE: We explore the consequences of having different mechanisms for transferring and establishing the gut microbiome between generations on gut microbial community dynamics. This process is often problematic in holometabolous insects, which have a complete metamorphosis between larval and adult stages. In our previous research, we found that females of some species within the genus Galerucella (Chrysomelidae) place a fecal string on the eggs, which is later consumed by the hatching larvae, whereas other species in the same genus do not have this behavior. In this paper, we therefore quantify the microbial community dynamics across all life stages in five Galerucella beetles (three with and two without fecal strings). Our results also indicate that the dynamics are much more stable in the species with fecal strings, particularly in the early life stages.}, }
@article {pmid40356667, year = {2025}, author = {Martínez-Mota, R and Vásquez-Aguilar, AA and Hernández-Rodríguez, D and Suárez-Domínguez, EA and Krömer, T}, title = {Close neighbors, not intruders: investigating the role of tank bromeliads in shaping faunal microbiomes.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19376}, pmid = {40356667}, issn = {2167-8359}, mesh = {Animals ; *Diptera/microbiology ; Larva/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Mexico ; *Bromeliaceae/microbiology ; *Bacteria/genetics/classification ; Ecosystem ; }, abstract = {BACKGROUND: Tropical montane cloud forests contain high levels of epiphyte diversity. Epiphytic tank bromeliads play an important role in the functioning of these ecosystems and provide a microhabitat for many species of invertebrates. Microbial ecology theory suggests that the environment serves as a source of microbes for animals, but the contribution of this factor to the composition of an animal microbiome varies. In this study, we examined the extent to which tank bromeliads (Tillandsia multicaulis) serve as a source of microbes for two species of fly larvae in a cloud forest fragment in central Veracruz, Mexico.<br><br>METHODS: We used 16S rRNA sequencing to characterize the bacterial communities in the organic matter within bromeliad tanks and in the whole bodies (surface and gut) of larvae from two fly taxa (Austrophorocera sp., Tachinidae, and Copestylum sp., Syrphidae) that inhabit these bromeliads. To assess the contribution of bromeliads to the microbiome of the fly larvae, we conducted fast expectation-maximization microbial source tracking (FEAST) analysis.<br><br>RESULTS: The bacterial communities in bromeliad tanks were primarily composed of Pseudomonadota, Acidobacteriota, Bacteroidota, Verrucomicrobiota, and Spirochaetota. Similarly, communities of the fly larvae contained Pseudomonadota, Bacteroidota, Bacillota, and Actinomycetota. Bromeliad tanks exhibited the highest bacterial richness, followed by Copestylum and Austrophorocera larvae. Beta diversity analyses indicated that bacterial communities clustered by species. We found a modest contribution of bromeliads to the fly microbiome, with nearly 30% of the larvae microbiome traced to the organic matter deposited in the tanks.<br><br>CONCLUSIONS: Our data suggest that the microbiome of flies, which inhabit tank bromeliads during their larval stage, is nourished to some extent by the bacterial communities present in the organic matter within the tank.}, }
@article {pmid40356640, year = {2025}, author = {Sun, Z and Hu, Y and Yang, YX and Lei, MY and Han, ZM and Cheng, L and Wang, W and Han, M and Lyu, ZL and Yang, LM}, title = {Changes in the diversity of ginseng endophyte flora driven by Fusarium solani.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1554706}, pmid = {40356640}, issn = {1664-302X}, abstract = {Endophytic flora serves a crucial function as a secondary line of defense against pathogen invasion in plants. To investigate the mechanisms underlying the relationship between changes in endophytic flora and ginseng root rot, exhumate beneficial endophytic bacteria, and explore biological management approaches for ginseng root rot. In this study, we used Illumina high-throughput sequencing and bioinformatics analysis to investigate the characteristics and differences in endophytic microbial community structure between healthy ginseng (HG) and diseased ginseng (BLS) after Fusarium solani infection. The findings revealed that as ginseng root rot increased, the diversity and richness of endophytic bacterial communities increased before decreasing, but the diversity and richness of endophytic fungal communities decreased. The dominating bacterial phylum in ginseng roots was Proteobacteria, which declined in quantity as the disease progressed. Ascomycota was the dominating fungal phylum among endophytes, and its prevalence grew as the disease progressed. At the genus level, the relative abundance of Rhodococcus, Stenotrophomonas, Variovorax, and Achromobacter species increased with the occurrence of ginseng root rot, in contrast, Pantoea and Pseudomonas species decreased in relative abundance as the prevalence of ginseng root rot increased. The relative abundance of the pathogenic fungi Gibberella, Nectria, Ilyonectria, and Alternaria in ginseng roots increased as the disease progressed. Endophytic fungal LEfSe research revealed that Neonectria was the particular biomarker discovered in the highly susceptible group. Additionally, commensal nutrient-type fungi appeared to be absent in moderately susceptible ginseng, but pathognomic nutrient-type fungi grew, coupled with potentially pathogenic fungi, exacerbating the condition. These results suggest that there is a pattern of response of ginseng endophytic microbial diversity to disease infestation. In this work, we investigated the impact of varying degrees of root rot on ginseng's endophytic flora structure. The study's findings give a theoretical framework for understanding the microecological processes of ginseng root rot via the lens of microbial ecology and applying biological control tools.}, }
@article {pmid40356172, year = {2025}, author = {Cardinali, F and Rampanti, G and Harasym, J and Lucci, P and Ferrocino, I and Pacetti, D and Fanesi, B and Milanović, V and Garofalo, C and Petruzzelli, A and Savelli, D and Gabucci, C and Aquilanti, L and Osimani, A}, title = {Comprehensive profiling of smoked cheese from raw goat's milk handcrafted in Lower Silesia (Poland).}, journal = {Food research international (Ottawa, Ont.)}, volume = {211}, number = {}, pages = {116398}, doi = {10.1016/j.foodres.2025.116398}, pmid = {40356172}, issn = {1873-7145}, mesh = {*Cheese/microbiology/analysis ; Animals ; Goats ; Fatty Acids/analysis ; Volatile Organic Compounds/analysis ; Poland ; *Milk/microbiology/chemistry ; *Food Microbiology ; *Food Handling/methods ; Consumer Behavior ; Humans ; *Smoke ; Colony Count, Microbial ; }, abstract = {This study aimed to explore the distinctive characteristics of smoked cheese made from raw goat's milk, labelled "Produkt polski" and crafted in the Lower Silesia region of Poland. A comprehensive range of analyses was performed, including physico-chemical and morpho-textural evaluations, microbial counts, and a metataxonomic investigation to uncover the microbial diversity occurring in the cheese. The volatile organic compounds (VOCs) and the total fatty acid composition were also determined. Additionally, a consumer test based on a hedonic scale was conducted to capture the subjective experience of the product's appeal. The cheese samples revealed water activity (aw) ranging between 0.901 ± 0.003 and 0.926 ± 0.001, with pH levels between 5.08 ± 0.15 and 5.44 ± 0.01. Regarding fatty acid composition, all of the smoked cheeses displayed a similar profile, with saturated fatty acids dominating (SFA, ∼75 %), followed by monounsaturated (MUFA, ∼22 %) and polyunsaturated fatty acids (PUFA, ∼3 %). Microbial analysis revealed thriving populations, including lactococci (up to 8.63 ± 0.07 log colony-forming units g[-1]), thermophilic cocci (up to 6.85 ± 0.08 log cfu g[-1]), lactobacilli (up to 9.50 ± 0.04 log cfu g[-1]), enterococci (up to 5.93 ± 0.00 log cfu g[-1]), and eumycetes (up to 2.68 ± 0.48 log cfu g[-1]). Metataxonomic analysis identified dominant bacterial taxa such as Lactobacillus, Lactococcus, and Leuconostoc, as well as Carnobacterium and Lacticaseibacillus. Among the 24 lactic acid bacteria cultures isolated, the closest relatives to Enterococcus, Lacticaseibacillus, Lactococcus, and Leuconostoc were identified. Some isolates demonstrated promising pro-technological traits, positioning them as potential adjunct cultures for improving fermented dairy products. The volatile profile of the smoked cheese was particularly intriguing, with a total of 87 VOCs detected, categorized as esters (18), ketones (14), hydrocarbons (11), acids (10), phenols (11), alcohols (8), furans (5), lactones (4), aldehydes (3), and other compounds (3). Sensory evaluation revealed a moderate appreciation for the cheese's appearance, whereas the smoked flavor elicited the most varied scores, highlighting its strong impact on consumer preference.}, }
@article {pmid40356145, year = {2025}, author = {Wang, S and Zheng, C and Bu, C and Guo, D and Zhang, C and Xie, Q and Pan, J and Sun, J and Chen, W and Jiang, S and Zhai, Q}, title = {Role of sn-2 palmitate on the development of the infant gut microbiome: A metagenomic insight.}, journal = {Food research international (Ottawa, Ont.)}, volume = {211}, number = {}, pages = {116488}, doi = {10.1016/j.foodres.2025.116488}, pmid = {40356145}, issn = {1873-7145}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; *Infant Formula/chemistry ; Infant ; Feces/microbiology ; *Metagenomics/methods ; Milk, Human/chemistry ; Female ; Male ; Breast Feeding ; *Palmitates/pharmacology ; Infant, Newborn ; Phylogeny ; }, abstract = {The infant gut microbiome, which develops from birth, has profound and lasting effects on human health. Its establishment in early life is influenced by events such as delivery mode and feeding type. This study examined the effects of formula milk enriched with sn-2 palmitate on the gut microbiota of healthy term infants. We conducted a 16-week comparative analysis of three feeding groups: infants receiving high sn-2 palmitate formula (n = 30), regular vegetable oil formula (n = 32), and breast milk (n = 30). Using shotgun metagenomic sequencing of fecal samples, we performed a comprehensive assessment of the gut microbiota. While overall microbial composition and diversity were comparable across groups, the functional profile of the microbiome in infants receiving sn-2 palmitate-enriched formula more closely resembled that of breastfed infants compared to the control formula group. This similarity extended to microbial species interactions, virulence gene abundance, and metabolic pathway expression patterns. In addition, sn-2 palmitate promoted the proliferation of Bifidobacterium breve and enhanced the robustness of the gut microbial ecology. Notably, the phylogenetic analysis of B. breve strains in the sn-2 palmitate group showed closer alignment with the breastfed group compared to the control group. These findings suggest that sn-2 palmitate-enriched formula may confer gut microbiota functional benefits that more closely resemble those of breast milk compared to control formula milk. This study provides scientific evidence for the development of future functional infant formulas.}, }
@article {pmid40354775, year = {2025}, author = {Frazier, CF and Harris, TD and DelSontro, T and Grossart, HP and Sturm, BSM and Murry, JM and Ising, A}, title = {Phytoplankton abundance and methane emissions are minimally impacted by environmentally-relevant glyphosate concentrations in small-scale outdoor mesocosms.}, journal = {Water research}, volume = {283}, number = {}, pages = {123764}, doi = {10.1016/j.watres.2025.123764}, pmid = {40354775}, issn = {1879-2448}, mesh = {Glyphosate ; *Glycine/analogs &amp; derivatives/toxicity ; *Methane/metabolism ; *Phytoplankton/drug effects ; Herbicides ; *Water Pollutants, Chemical ; Ecosystem ; Phosphorus ; Nitrogen ; }, abstract = {Glyphosate is one of the most widely applied agrochemicals in North America and can be directly transported via runoff into non-target aquatic habitats. Yet, our understanding of how this herbicide affects aquatic ecosystems is limited; past studies have often focused on single species effects and/or used herbicide concentrations several orders of magnitude higher than what has been reported in contaminated aquatic systems. Further, glyphosate in aquatic systems has the potential to alter greenhouse gas emissions (methane) if it is broken down for phosphate utilization by bacteria under specific environmental conditions (i.e., oxygen, nutrient concentrations). In this study, we assessed the temporal changes in nutrients, phytoplankton, copy number of genes associated with breakdown of glyphosate or production of methane (phnJ, mcrA), and methane concentrations in 12-day mesocosms with amendments of glyphosate, nitrogen, and/or phosphorus. We found glyphosate at environmentally-relevant concentrations (∼4 ug/L) did not confer changes in overall ratios and total concentrations of nutrients, or abundance of any major phytoplankton group (cyanobacteria, diatoms, green algae), methane concentration or flux, or gene copy numbers of phnJ and mcrA. Our results suggest that the relatively low concentrations of glyphosate we used (relative to levels used in toxicological studies) did not cause major changes over short time periods in mesocosms, and that the potential for glyphosate to increase greenhouse gas emissions in aquatic systems requires specific conditions to occur and may not be universal in contaminated systems.}, }
@article {pmid40354740, year = {2025}, author = {Rodrigo, MA and Puche, E and Muñoz-Colmenares, M and Sánchez-Carrillo, S}, title = {Vascular macrophytes versus charophytes: how the macrophyte type and warming affect the sediment microbial community and the production of greenhouse gases.}, journal = {Journal of environmental management}, volume = {386}, number = {}, pages = {125654}, doi = {10.1016/j.jenvman.2025.125654}, pmid = {40354740}, issn = {1095-8630}, mesh = {*Greenhouse Gases ; *Geologic Sediments/microbiology ; Global Warming ; Carbon Dioxide ; Ecosystem ; Microbiota ; }, abstract = {In the global warming context, adaptive management strategies involve the conservation and restoration of inland waters by planning the reintroduction of macrophytes to substantially mitigate greenhouse gas emissions (GHG). The selection of appropriate species is crucial. We studied the influence of two submerged macrophyte species on GHG production, sediment-oxygen microprofiles, and microbial community composition under two thermal regimes by means of a microcosm experiment. We chose the phanerogam Myriophyllum spicatum, more typical of meso-eutrophic habitats, and the charophyte Chara hispida, more frequent in oligotrophic waters and belonging to a much less studied macrophyte group, which, moreover, exhibit contrasting functional traits (i.e., roots versus rhizoids). The presence of both macrophyte types considerably reduced the diurnal diffusive CO2 emissions due to their photosynthetic activity compared to bare-sediment situations. The radial oxygen loss of M. spicatum roots provided aerobic-microaerobic conditions beyond the first sediment centimeter, in contrast to more anoxic sediments created by C. hispida. As a result of this, each type of macrophyte determined a particular sediment microbiome. Despite dissolved CH4 being greater in the presence of plants, no statistical differences in CH4 diffusive flux caused by the presence or absence of plants was found. We demonstrated how the presence, or not, of macrophytes is more important than warming (in our case with a temperature difference of 3 °C) in relation to GHG emissions. Both species, being perennial, provide ecosystem services year-round and are strong candidates for management strategies aimed at transforming new or restored aquatic ecosystems into carbon sinks.}, }
@article {pmid40353721, year = {2025}, author = {Pellitier, PT and Kling, MM and Qin, C and Van Nuland, ME and Zhu, K and Peay, KG}, title = {Wind Patterns Influence the Dispersal and Assembly of North American Soil Fungal Communities.}, journal = {Ecology letters}, volume = {28}, number = {5}, pages = {e70130}, doi = {10.1111/ele.70130}, pmid = {40353721}, issn = {1461-0248}, support = {1845544//Directorate for Biological Sciences/ ; 1926335//Directorate for Biological Sciences/ ; 2010897//Directorate for Biological Sciences/ ; 2244711//Directorate for Biological Sciences/ ; }, mesh = {*Wind ; *Soil Microbiology ; *Fungi/physiology/genetics ; North America ; *Mycobiome ; Spores, Fungal/physiology ; Climate Change ; Models, Biological ; }, abstract = {Wind is the primary dispersal mechanism of most fungal spores but is rarely considered in studies of fungal communities, limiting inference of assembly mechanisms and forecasting responses to climate change. We compiled wind-connectivity models-'windscapes'-to model potential dispersal of fungal spores at the continental scale and linked them with a molecular dataset of North American soil fungi. Our analyses demonstrate that prevailing windflow patterns exhibit a significantly stronger signal on fungal community structure than do geographic distances amongst sites. Notably, the signature of wind was detectable for mushrooms and fungi producing primarily wind-dispersed spores. Contrastingly, fungi primarily reliant on animal dispersal exhibited a strong signature of geographic distance but not wind-connectivity. Additionally, we show that directionally 'downwind' sites are more diverse than comparatively 'upwind' sites. Altogether, our findings suggest that future wind patterns will shape the adaptation potential of fungal communities dispersing into suitable climatic niches.}, }
@article {pmid40353658, year = {2025}, author = {Laso-Pérez, R and Rivas-Santisteban, J and Fernandez-Gonzalez, N and Mundy, CJ and Tamames, J and Pedrós-Alió, C}, title = {Nitrogen cycling during an Arctic bloom: from chemolithotrophy to nitrogen assimilation.}, journal = {mBio}, volume = {16}, number = {6}, pages = {e0074925}, pmid = {40353658}, issn = {2150-7511}, support = {FJC2019-041362-I, RyC2021-031775-I//Ministerio de Ciencia e Innovaci&#xf3;n (MCIN)/ ; PID2019-110011RB-C33, PID2023-146919NB-C21//MEC | Agencia Estatal de Investigaci&#xf3;n (AEI)/ ; }, mesh = {Arctic Regions ; *Nitrogen/metabolism ; *Bacteria/metabolism/genetics/classification ; *Nitrogen Cycle ; *Archaea/metabolism/genetics/classification ; Phytoplankton/growth &amp; development/metabolism ; Metagenomics ; Canada ; *Chemoautotrophic Growth ; Seasons ; Metagenome ; }, abstract = {In the Arctic, phytoplankton blooms are recurring phenomena occurring during the spring-summer seasons and influenced by the strong polar seasonality. Bloom dynamics are affected by nutrient availability, especially nitrogen, which is the main limiting nutrient in the Arctic. This study aimed to investigate the changes in an Arctic microbial community using omics approaches during a phytoplankton bloom focusing on the nitrogen cycle. Using metagenomic and metatranscriptomic samples from the Dease Strait (Canada) from March to July (2014), we reconstructed 176 metagenome-assembled genomes. Bacteria dominated the microbial community, although archaea reached up to 25% of metagenomic abundance in early spring, when Nitrososphaeria archaea actively expressed genes associated with ammonia oxidation to nitrite (amt, amo, nirK). The resulting nitrite was presumably further oxidized to nitrate by a Nitrospinota bacterium that highly expressed a nitrite oxidoreductase gene (nxr). Since May, the constant increase in chlorophyll a indicated the occurrence of a phytoplankton bloom, promoting the successive proliferation of different groups of chemoorganotrophic bacteria (Bacteroidota, Alphaproteobacteria, Gammaproteobacteria). These bacteria showed different strategies to obtain nitrogen, whether it be from organic or inorganic sources, according to the expression patterns of genes encoding transporters for nitrogen compounds. In contrast, during summer, the chemolithotrophic organisms thriving during winter reduced their relative abundance and the expression of their catabolic genes. Based on our functional analysis, we see a transition from a community where nitrogen-based chemolitotrophy plays a relevant role to a chemoorganotrophic community based on the carbohydrates released during the phytoplankton bloom, where different groups seem to specialize in different nitrogen sources.IMPORTANCEThe Arctic is one of the environments most affected by anthropogenic climate change. It is expected that the rise in temperature and change in ice cover will impact the marine microbial communities and the associated biogeochemical cycles. In this regard, nitrogen is the main nutrient limiting Arctic phytoplankton blooms. In this study, we combine genetic and expression data to study the nitrogen cycle at the community level over a time series covering from March to July. Our results indicate the importance of different taxa (from archaea to bacteria) and processes (from chemolithoautotrophy to incorporation of different nitrogen sources) in the cycling of nitrogen during this period. This study provides a baseline for future research that should include additional methodologies like biogeochemical analysis to fully understand the changes occurring on these communities due to global change.}, }
@article {pmid40352645, year = {2025}, author = {Quinn, LK and Sharma, K and Faber, KT and Orphan, VJ}, title = {Clear as mud redefined: Tunable transparent mineral scaffolds for visualizing microbial processes below ground.}, journal = {PNAS nexus}, volume = {4}, number = {5}, pages = {pgaf118}, pmid = {40352645}, issn = {2752-6542}, abstract = {Microbes inhabiting complex porous microenvironments in sediments and aquifers catalyze reactions that are critical to global biogeochemical cycles and ecosystem health. However, the opacity and complexity of porous sediment and rock matrices have considerably hindered the study of microbial processes occurring within these habitats. Here, we generated microbially compatible, optically transparent mineral scaffolds to visualize and investigate microbial colonization and activities occurring in these environments, in laboratory settings and in situ. Using inexpensive synthetic cryolite mineral, we produced optically transparent scaffolds mimicking the complex 3D structure of sediments and rocks by adapting a suspension-based, freeze-casting technique commonly used in materials science. Fine-tuning of parameters, such as freezing rate and choice of solvent, provided full control of pore size and architecture. The combined effects of scaffold porosity and structure on the movement of microbe-sized particles, tested using velocity tracking of fluorescent beads, showed diverse yet reproducible behaviors. The scaffolds we produced are compatible with epifluorescence microscopy, allowing the fluorescence-based identification of colonizing microbes by DNA-based staining and fluorescence in situ hybridization (FISH) to depths of 100 µm. Additionally, Raman spectroscopy analysis indicates minimal background signal in regions used for measuring deuterium and [13]C enrichment in microorganisms, highlighting the potential to directly couple D2O or [13]C stable isotope probing and Raman-FISH for quantifying microbial activity at the single-cell level. To demonstrate the relevance of cryolite scaffolds for environmental field studies, we visualized their colonization by diverse microorganisms within rhizosphere sediments of a coastal seagrass plant using epifluorescence microscopy. The tool presented here enables highly resolved, spatially explicit, and multimodal investigations into the distribution, activities, and interactions of underground microbes typically obscured within opaque geological materials until now.}, }
@article {pmid40352477, year = {2025}, author = {Coltman, BL and Motheramgari, K and Tatto, N and Gasser, B}, title = {Identification and functional analysis of growth rate associated long non-coding RNAs in Komagataella phaffii.}, journal = {Computational and structural biotechnology journal}, volume = {27}, number = {}, pages = {1693-1705}, pmid = {40352477}, issn = {2001-0370}, abstract = {Long non-coding RNAs (lncRNAs) are a regulatory feature that have been reported to operate on both transcriptional and translational levels. With DNA-based prediction still limited, lncRNAs are most reliably identified through genome-guided mapping of RNA-Seq data. Reports of lncRNAs in yeast have been increasing in recent years and changes in their expression levels have often been associated with stressful conditions. As the transition to near zero-growth conditions likely imposes stress, we used RNA-Seq data from the non-conventional, biotechnologically established yeast Komagataella phaffii, cultivated in glucose-limited retentostats, to identify the expression of lncRNAs. Using an adapted bioinformatics pipeline, we identified 168 mostly novel lncRNAs from the K. phaffii retentostat RNA-Seq data, 36 of which demonstrate likely growth-associated expression changes. lncRNA expression levels were associated to that of possible interaction partners, in both cis and trans, suggesting potential roles in regulatory adaptations. Our analysis indicates that lncRNAs likely contribute to how K. phaffii responds to changing environmental conditions, as exemplified here by the adaptation to extremely slow growth.}, }
@article {pmid40349898, year = {2025}, author = {Moghaddam, ZS and Dehghan, A and Halimi, S and Najafi, F and Nokhostin, A and Naeini, AE and Akbarzadeh, I and Ren, Q}, title = {Bacterial Extracellular Vesicles: Bridging Pathogen Biology and Therapeutic Innovation.}, journal = {Acta biomaterialia}, volume = {200}, number = {}, pages = {1-20}, doi = {10.1016/j.actbio.2025.05.028}, pmid = {40349898}, issn = {1878-7568}, mesh = {*Extracellular Vesicles/metabolism ; Humans ; *Bacteria/metabolism ; Animals ; Drug Delivery Systems ; *Host-Pathogen Interactions ; }, abstract = {The main role of bacterial extracellular vesicles (BEVs) has been associated with various processes such as intercellular communication and host-pathogen interactions. This comprehensive review explores the multifaceted functions of BEVs across different biological domains, emphasizing their dual nature as contributors to disease and potential vehicles for therapeutic intervention. We examine the intricate interactions of BEVs within bacterial communities and between bacteria and hosts, their involvement in disease development through cargo delivery mechanisms, and their beneficial impact on microbial ecology. The review also highlights BEVs' applications in biomedical field, where they are revolutionizing vaccine development, targeted drug delivery, and cancer therapy. By utilizing the inherent properties of BEVs for controlled drug release, targeted antigen delivery, and immune modulation, they offer a promising frontier in precision medicine. In addition, the diagnostic potential of BEVs is explored through their utility as biomarkers, providing valuable insights into disease states and treatment efficacy. Looking forward, this review underscores the challenges and opportunities in translating BEV research to clinical practice, promoting the need of standardized methods in BEV characterization and scaling up production. The diverse abilities of BEVs, ranging from contributing to pathogen virulence to driving therapeutic innovation, highlight their potential as a cornerstone in the future of biomedical advancements. STATEMENT OF SIGNIFICANCE: Bacterial extracellular vesicles (BEVs) are emerging as pivotal players in both pathogenesis and therapeutic innovation. This review explores their dual nature as agents of disease and as promising biomaterials for biomedical applications, and provides a comprehensive survey on their involvement in disease mechanisms and microbial ecology, and their potential in biomedical applications such as vaccine development, targeted drug delivery, cancer therapy, and diagnosis. It highlights the complex interactions of BEVs within bacterial communities and between bacteria and hosts. This review also addresses current advancements, challenges, and opportunities in translating BEV research into clinical practice. The insights presented here position BEVs as a cornerstone in the future of biomedical advancements, advocating for standardized methods in BEV characterization and scalable production techniques.}, }
@article {pmid40348966, year = {2025}, author = {Van Hee, S and Segurado Luchsinger, AE and Cusumano, A and Masschelein, J and Jacquemyn, H and Lievens, B}, title = {The plant-beneficial fungus Trichoderma harzianum T22 modulates plant metabolism and negatively affects Nezara viridula.}, journal = {BMC plant biology}, volume = {25}, number = {1}, pages = {615}, pmid = {40348966}, issn = {1471-2229}, support = {C24E/19/052//KU Leuven/ ; }, mesh = {*Hypocreales/physiology ; Animals ; Plant Leaves/metabolism/microbiology ; Herbivory ; Metabolome ; *Capsicum/microbiology/metabolism ; Plant Roots/microbiology/metabolism ; Plant Defense Against Herbivory ; }, abstract = {BACKGROUND: Plant-beneficial fungi play an important role in enhancing plant health and resistance against biotic and abiotic stresses. Although extensive research has focused on their role in eliciting plant defences against pathogens, their contribution to induced resistance against herbivorous insects and the underlying mechanisms remain poorly understood. In this study, we used insect bioassays and untargeted metabolomics to investigate the impact of root inoculation of sweet pepper with the plant-beneficial fungus Trichoderma harzianum T22 on direct defence responses against the insect herbivore Nezara viridula.<br><br>RESULTS: We observed reduced relative growth rate of N. viridula on leaves of fungus-inoculated plants, with no change in mortality. Untargeted metabolomic analyses revealed that inoculation with T. harzianum did not affect the leaf metabolome in the absence of herbivory five weeks after inoculation. However, compared to non-inoculated plants, inoculated plants exhibited significant metabolic alterations in herbivore-damaged leaves following N. viridula feeding, while changes in the metabolic profile of distant leaves were less pronounced. Notably, metabolites involved in the shikimate-phenylpropanoid pathway, known to be involved in plant defence responses, displayed higher accumulation in damaged leaves of inoculated plants compared to non-inoculated plants.<br><br>CONCLUSION: Our results indicate that root inoculation with T. harzianum T22 affects plant defences against N. viridula, leading to reduced insect performance. Metabolite-level effects were primarily observed in damaged leaves, suggesting that the priming effect mainly results in localized metabolite accumulation at the site of attack. Future research should focus on identifying the detected compounds and determining their role in impairing N. viridula performance.}, }
@article {pmid40347612, year = {2025}, author = {Rodríguez-Seijo, A and Pérez-Rodríguez, P and Arias-Estévez, M and Gómez-Armesto, A and Conde-Cid, M and Santás-Miguel, V and Campillo-Cora, C and Ollio, I and Lloret, E and Martínez-Martínez, S and Zornoza, R and Waeyenberge, L and Schrader, S and Brandt, KK and Loit, K and Põldmets, M and Shanskiy, M and Peltoniemi, K and Hagner, M and Calviño, DF}, title = {Occurrence, persistence and risk assessment of pesticide residues in European wheat fields: A continental scale approach.}, journal = {Journal of hazardous materials}, volume = {494}, number = {}, pages = {138291}, doi = {10.1016/j.jhazmat.2025.138291}, pmid = {40347612}, issn = {1873-3336}, mesh = {*Triticum ; *Pesticide Residues/analysis ; Risk Assessment ; Europe ; *Soil Pollutants/analysis ; Environmental Monitoring ; Agriculture ; Organic Agriculture ; }, abstract = {Pesticide residues in agricultural soils represent an environmental concern that requires special attention due to their potential ecological and public health risks. We analyzed 614 pesticides in 188 wheat fields across Europe subjected to both conventional and organic farming systems. At least one pesticide residue was detected in 141 soils. Seventy-eight pesticides or their metabolites were detected. The presence of pesticides was significantly higher in both number and concentration in conventional fileds (up to 0.98 mg kg[-1]) compared to organically managed sites (up to 0.40 mg kg[-1]). A total of 88 % of conventional fields and 63 % of organic fields contained two or more pesticides. Conversion from conventional to organic farming does not guarantee that soils will be pesticide-free in the short term. Fenbutatin oxide was the most frequently detected pesticide in both farming systems, followed by AMPA. Other substances, such as boscalid, epoxiconazole, diflufenican, tebuconazole, dinoterb, bixafen, and DEET, were found in ≥ 10 % of samples. Some Persistent Organic Pollutants, including dieldrin, endosulfan sulphate, and chlorpyrifos, were also detected. Ecological risks were higher in conventionally managed fields, with 46 % exhibiting high-risk levels, compared to just 1 % in organic fields. Epoxiconazole and boscalid were the substances with the highest risk levels.}, }
@article {pmid40347236, year = {2025}, author = {Qi, W and Song, W and Qi, R and Li, Y and Yang, H and Li, Y and Chang, Z}, title = {Land Use Types Drive the Distinct Patterns of Bacterial and Fungal Communities in Soils from the Semi-arid Area.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {43}, pmid = {40347236}, issn = {1432-184X}, support = {2021-XBQNXZ-001//The West Light Foundation of Chinese Academy of Science/ ; DD20242544//The Ecological Protection and Restoration Support Survey Project of China Geological Survey/ ; }, mesh = {*Soil Microbiology ; China ; *Bacteria/classification/isolation &amp; purification/genetics ; *Fungi/classification/isolation &amp; purification/genetics ; Soil/chemistry ; Biodiversity ; Grassland ; Ecosystem ; Desert Climate ; Agriculture ; *Microbiota ; Farms ; Mycobiome ; }, abstract = {Land types and ways of utilization significantly influence soil microbial communities in arid and semi-arid regions, which are vital for nutrient cycling and ecosystem functionality. In this study, the soil bacterial and fungal communities of five land types, including natural grasslands, farmlands, artificial grasslands, uncultivated lands, and riverbeds in the semi-arid lower reaches of the Heihe River, China, were investigated. Farmlands exhibited the highest bacterial Chao1 richness and Shannon diversity, while uncultivated soils had the lowest bacterial Chao1 richness. Fungal diversity was highest in uncultivated soils compared to farmlands. Principal coordinate analysis (PCoA) showed distinct microbial community structures across land types, with Actinobacteria, Proteobacteria, Firmicutes, and Chloroflexi dominating bacterial communities, and Ascomycota and Basidiomycota dominating fungal communities. Life history strategies revealed distinct patterns between bacterial and fungal communities within farmland soils and artificial grassland soils. Microbial community assembly in natural grasslands was primarily deterministic, with limited stochastic influence, while farmlands exhibited mixed assembly processes. Co-occurrence network analysis showed more stable and cooperative microbial networks in natural grasslands, while farmland networks were more competitive and reliant on key species. These findings provide important insights into the role of land use in shaping microbial diversity and ecosystem function, offering guidance for sustainable land management in semi-arid oasis regions.}, }
@article {pmid40347194, year = {2025}, author = {Su, QY and Zhang, JT and Gao, HJ and Zhang, Y and Luo, J and Cao, TY and Yang, MY and Zhang, SX}, title = {Mechanism and clinical utility of abatacept in the treatment of rheumatoid arthritis.}, journal = {Expert opinion on drug safety}, volume = {}, number = {}, pages = {1-12}, doi = {10.1080/14740338.2025.2505542}, pmid = {40347194}, issn = {1744-764X}, abstract = {INTRODUCTION: Abatacept, a biological disease-modifying antirheumatic drug(bDMARD), has demonstrated unique and effective therapeutic properties for rheumatoid arthritis (RA).<br><br>AREAS COVERED: This review offers an in-depth examination of the mechanism by which abatacept exerts its effects in RA treatment and assesses its efficacy and safety based on a range of studies. We conducted a comprehensive search of PubMed, Embase databases, Web of Science, the Cochrane Library, MEDLINE, Wanfang Data, and CNKI from the time the databases were created until 30 July 2024.<br><br>EXPERT OPINION: By modulating the CD28 and CD80/CD86 costimulatory signaling pathways, abatacept is instrumental in regulating immune cells and cytokines implicated in the pathogenesis RA. Longitudinal studies have highlighted its capacity to mitigate disease advancement and maintain joint functionality. The most frequently reported adverse effects associated with abatacept are headache, nausea, and upper respiratory tract infections, which are typically self-resolving. The incidence of serious infections was not high, mainly various types of bacterial pneumonia. Comparative safety analyses of abatacept with other DMARDs yield encouraging results. As our understanding of the mechanism of action of abatacept improves, we may be able to better identify appropriate biologic therapies and advanced combination therapies for RA patients and ultimately improve patient outcomes.}, }
@article {pmid40346393, year = {2025}, author = {Leiter, N and Wohlschläger, M and Versen, M and Harter, SD and Kießlich, T and Lederer, F and Clauß, S and Schlosser, D and Armanu, EG and Eberlein, C and Heipieper, HJ and Löder, MGJ and Laforsch, C}, title = {Effects of defined organic layers on the fluorescence lifetime of plastic materials.}, journal = {Analytical and bioanalytical chemistry}, volume = {417}, number = {16}, pages = {3651-3663}, pmid = {40346393}, issn = {1618-2650}, support = {FKZ 031B0828A//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 391977956 - SFB 1357//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Plastics/chemistry/analysis ; *Microplastics/analysis/chemistry ; Microscopy, Fluorescence/methods ; Spectrometry, Fluorescence/methods ; Fluorescence ; Environmental Monitoring/methods ; Polyethylene Terephthalates/chemistry ; }, abstract = {Plastics have become an integral part of modern life, and linked to that fact, the demand for and global production of plastics are still increasing. However, the environmental pollution caused by plastics has reached unprecedented levels. The accumulation of small plastic fragments-microplastics and nanoplastics-potentially threatens organisms, ecosystems, and human health. Researchers commonly employ non-destructive analytical methods to assess the presence and characteristics of microplastic particles in environmental samples. However, these techniques require extensive sample preparation, which represents a significant limitation and hinders a direct on-site analysis. In this context, previous investigations showed the potential of fluorescence lifetime imaging microscopy (FLIM) for fast and reliable identification of microplastics in an environmental matrix. However, since microplastics receive an environmental coating after entering nature, a challenge arises from organic contamination on the surface of microplastic particles. How this influences the fluorescence signal and the possibility of microplastic detection are unknown. To address this research gap, we exposed acrylonitrile butadiene styrene (ABS) and polyethylene terephthalate (PET) plastic samples to peptides, proteins, bacteria, and a filamentous fungus to induce organic contamination and mimic environmental conditions. We analyzed the fluorescence spectra and lifetimes of the samples using fluorescence spectroscopy and frequency-domain fluorescence lifetime imaging microscopy (FD-FLIM), respectively. Our results demonstrate that reliably identifying and differentiating ABS and PET was possible via FD-FLIM, even in the presence of these biological contaminations. These findings highlight the potential of this technique as a valuable tool for environmental monitoring and plastic characterization, offering a rapid and efficient alternative to currently used analytical methods.}, }
@article {pmid40345255, year = {2025}, author = {Feng, J and Zhang, C and Bao, J and Xu, Q and Gan, Y and Hu, Y}, title = {A modified variable flip angle release device for endoscopic titanium clips.}, journal = {Endoscopy}, volume = {57}, number = {S 01}, pages = {E396-E397}, pmid = {40345255}, issn = {1438-8812}, support = {2024GZL-CX58//Xiamen High-quality Development Medical Innovation Fund/ ; }, }
@article {pmid40343125, year = {2025}, author = {Tóth, VR}, title = {The impact of epiphytic algae on the foliar traits of Potamogeton perfoliatus.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1561709}, pmid = {40343125}, issn = {1664-462X}, abstract = {This study investigated the effect of epiphyton on foliar traits of a submerged rooted macrophyte, Potamogeton perfoliatus, in a shallow freshwater lake, highlighting its influence on the ecological dynamics of littoral zones in aquatic ecosystems. It was shown that the limnological characteristics of the sampling sites (water chlorophyll-a, total suspended matter and coloured dissolved organic matter content) had no significant effect on the average values of epiphytic algal content found on pondweed leaves, while influencing the plasticity of these data. The responses of morphological and physiological traits of submerged macrophytes to accumulated epiphyton demonstrate the complexity of their relationship: epiphyton colonisation had no relevant effect on leaf morphology (except leaf length) and leaf pigment content (except Chl-a/Chl-b ratio), however, this study highlights the significant influence of epiphytic algal biomass on photophysiological traits of submerged macrophyte leaves, as 5 out of 6 photophysiological traits were affected. The results highlight the importance of considering epiphyte colonisation when seeking to understand the ecological functioning of littoral aquatic ecosystems. Furthermore, the complex interactions between epiphytes and submerged rooted macrophytes should be considered in integrated lake management and environmental protection policies. These interactions play an important, though ambiguous role in shaping habitat variability and overall ecosystem health in littoral zones.}, }
@article {pmid40341906, year = {2025}, author = {Shoemaker, WR and Sánchez, &#xc1; and Grilli, J}, title = {Macroecological patterns in experimental microbial communities.}, journal = {PLoS computational biology}, volume = {21}, number = {5}, pages = {e1013044}, pmid = {40341906}, issn = {1553-7358}, mesh = {*Models, Biological ; *Ecology/methods ; Biodiversity ; Ecosystem ; *Microbiota/physiology ; Computational Biology ; }, abstract = {Ecology has historically benefited from the characterization of statistical patterns of biodiversity within and across communities, an approach known as macroecology. Within microbial ecology, macroecological approaches have identified universal patterns of diversity and abundance that can be captured by effective models. Experimentation has simultaneously played a crucial role, as the advent of high-replication community time-series has allowed researchers to investigate underlying ecological forces. However, there remains a gap between experiments performed in the laboratory and macroecological patterns documented in natural systems, as we do not know whether these patterns can be recapitulated in the lab and whether experimental manipulations produce macroecological effects. This work aims at bridging the gap between experimental ecology and macroecology. Using high-replication time-series, we demonstrate that microbial macroecological patterns observed in nature exist in a laboratory setting, despite controlled conditions, and can be unified under the Stochastic Logistic Model of growth (SLM). We found that demographic manipulations (e.g., migration) impact observed macroecological patterns. By modifying the SLM to incorporate said manipulations alongside experimental details (e.g., sampling), we obtain predictions that are consistent with macroecological outcomes. By combining high-replication experiments with ecological models, microbial macroecology can be viewed as a predictive discipline.}, }
@article {pmid40338317, year = {2025}, author = {Graziosi, S and Deloche, L and Januario, M and Selosse, MA and Deveau, A and Bach, C and Chen, Z and Murat, C and Iotti, M and Rech, P and Zambonelli, A}, title = {Newly Designed Fluorescence In Situ Hybridization Probes Reveal Previously Unknown Endophytic Abilities of Tuber magnatum in Herbaceous Plants.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {42}, pmid = {40338317}, issn = {1432-184X}, support = {K272X8 - CUP J53D23010090006//European Union - NextGenerationEU under the National Recovery and Resilience Plan (PNRR) - Mission 4 Education and research - Component 2 From research to business - Investment 1.1 Notice Prin 2022 - DD N. 104 del 2/2/2022, from title "Interactions of the white truffle Tuber magnatum with soil microbiome and plants"/ ; K272X8 - CUP J53D23010090006//European Union - NextGenerationEU under the National Recovery and Resilience Plan (PNRR) - Mission 4 Education and research - Component 2 From research to business - Investment 1.1 Notice Prin 2022 - DD N. 104 del 2/2/2022, from title "Interactions of the white truffle Tuber magnatum with soil microbiome and plants"/ ; ANR-11-LABX-0002-01//The French National Research Agency (ANR), 'Investissements d'Avenir' program, Lab of Excellence ARBRE, UMR IaM./ ; ANR-11-LABX-0002-01//The French National Research Agency (ANR), 'Investissements d'Avenir' program, Lab of Excellence ARBRE, UMR IaM./ ; ANR-11-LABX-0002-01//The French National Research Agency (ANR), 'Investissements d'Avenir' program, Lab of Excellence ARBRE, UMR IaM./ ; ANR-11-LABX-0002-01//The French National Research Agency (ANR), 'Investissements d'Avenir' program, Lab of Excellence ARBRE, UMR IaM./ ; }, mesh = {*Endophytes/genetics/isolation &amp; purification/physiology ; *In Situ Hybridization, Fluorescence/methods ; Plant Roots/microbiology ; *Mycorrhizae/genetics/isolation &amp; purification/physiology ; *Ascomycota/genetics/isolation &amp; purification/physiology ; Symbiosis ; Italy ; Polymerase Chain Reaction ; Hyphae/genetics ; }, abstract = {Tuber magnatum Picco (the Italian white truffle) is the most valuable and widely appreciated truffle. It is an ectomycorrhizal fungus known to associate with many broadleaf tree species. However, its mycorrhizae are rarely observed in the field, suggesting possible alternative symbiotic strategies, such as endophytism with non-ectomycorrhizal plants. In order to test potential endophytic interactions of T. magnatum with wild plants, a combination of polymerase chain reaction (PCR) and Fluorescence In Situ Hybridization (FISH) approaches were used. Specific FISH probes for T. magnatum were designed, tested in vitro on hyphae and/or ectomycorrhizae, and selected for their specificity. These probes were then used on a wide variety root samples of wild plants collected from three T. magnatum production areas in Italy and previously tested for the presence of T. magnatum mycelium using PCR-specific primers. Molecular analyses detected the presence of T. magnatum in 21 of 100 plant samples analyzed. FISH analysis confirmed the extracellular presence of active T. magnatum hyphae inside the root system of Carex pendula Huds plant. This study provides the first evidence of T. magnatum acting as an endophyte in an herbaceous plant. The newly designed, highly specific T. magnatum FISH probes can be used for further investigations to confirm the endophytic tendencies of T. magnatum and to understand their influence on the life cycle and biology of this fungus.}, }
@article {pmid40336837, year = {2025}, author = {Couch, CE and Xavier, R and Beechler, BR}, title = {Editorial: Parasite, host, and microbiome interactions in natural host systems.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1589627}, doi = {10.3389/fmicb.2025.1589627}, pmid = {40336837}, issn = {1664-302X}, }
@article {pmid40335733, year = {2025}, author = {Guo, Y and Tian, L and Zhu, X and Liu, S and Wang, L and Li, W}, title = {Antagonism of Bacillus velezensis ZGE166 Against the Pathogenic Fungi Causing Corm Rot Disease in Saffron (Crocus sativus L.).}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {40}, pmid = {40335733}, issn = {1432-184X}, mesh = {*Bacillus/physiology/genetics/isolation &amp; purification ; *Crocus/microbiology/growth &amp; development ; Rhizosphere ; *Plant Diseases/microbiology/prevention &amp; control ; Soil Microbiology ; *Antibiosis ; *Fungi/physiology ; Genome, Bacterial ; Phylogeny ; }, abstract = {Saffron can be infected with pathogenic fungi that cause corm rot as it grows and multiplies, which can reduce the quality and yield of saffron. Corm rot has become one of the most serious diseases of saffron. In this study, rhizosphere bacteria were isolated from saffron rhizosphere soil, and bacteria exhibiting antagonistic effects against corm rot pathogenic fungi were screened using in vitro plate co-culture assays and dual-compartment agar plate systems. Selected strains were further evaluated for hydrolase activity determination and PGP potential assessment. Among them, Bacillus velezensis showed the best disease resistance activity. The degradative enzyme production and some beneficial characteristics of Bacillus velezensis for plant growth promotion were evaluated. It was found that Bacillus velezensis possesses nitrogen fixing, NH3-producing, IAA production, and ACC-deaminating enzymes. The whole genome sequence of this strain was annotated and analyzed. The genome of Bacillus velezensis consists of a circular chromosome of 3,908,025 bp base pairs, with a guanine and cytosine content of 46.64%. There are 3737 protein-coding genes, including 86 tRNA genes, 27 rRNA genes, and 85 sRNA genes. The genome also contains four genomic islands, two pre-phages, and one transposon. The prediction of the secondary metabolic accumulation gene cluster demonstrated that the genome sequence of ZGE166 encodes 12 gene clusters involved in the synthesis of secondary metabolites, including macrolactin H, bacillaene, fengycin, difficidin, and bacillibactin. In summary, strain ZGE166 Bacillus velezensis has the potential to be developed as a biological agent.}, }
@article {pmid40335388, year = {2025}, author = {Dwivedi, SL and Vetukuri, RR and Kelbessa, BG and Gepts, P and Heslop-Harrison, P and Araujo, ASF and Sharma, S and Ortiz, R}, title = {Exploitation of rhizosphere microbiome biodiversity in plant breeding.}, journal = {Trends in plant science}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tplants.2025.04.004}, pmid = {40335388}, issn = {1878-4372}, abstract = {Climate change-induced stresses are perceived by plants at the root-soil interface, where they are alleviated through interactions between the host plant and the rhizosphere microbiome. The recruitment of specific microbiomes helps mitigate stress, increases resistance to pathogens, and promotes plant growth, development, and reproduction. The structure of the rhizosphere microbiome is shaped by crop domestication and variations in ploidy levels. Here we list key genes that regulate rhizosphere microbiomes and host genetic traits. We also discuss the prospects for rigorous analysis of symbiotic interactions, research needs, and strategies for systematically utilizing microbe-crop interactions to improve crop performance. Finally, we highlight challenges of maintaining live rhizosphere microbiome collections and mining heritable variability to enhance interactions between host plants and their rhizosphere microbiomes.}, }
@article {pmid40334664, year = {2025}, author = {Sandin, MM and Renaudie, J and Suzuki, N and Not, F}, title = {Extant diversity, biogeography, and evolutionary history of Radiolaria.}, journal = {Current biology : CB}, volume = {35}, number = {11}, pages = {2524-2538.e6}, doi = {10.1016/j.cub.2025.04.032}, pmid = {40334664}, issn = {1879-0445}, mesh = {*Biological Evolution ; *Biodiversity ; *Fossils ; Phylogeny ; *Plankton/classification/physiology/genetics ; Phylogeography ; }, abstract = {Since Ernst Haeckel and the Challenger expedition (1872-1876), Radiolaria have been known as ubiquitous and abundant star-shaped oceanic plankton. Their exquisite biomineralized skeletons left an extensive fossil record extremely valuable for biostratigraphic and paleo-environmental research. In contemporary oceans, there is growing evidence that Radiolaria are significant contributors to marine food webs and global biogeochemical cycles. Here we provide a comprehensive morpho-molecular framework to assess the extant diversity, biogeography, and evolutionary history of Radiolaria. Our analyses reveal that half of radiolarian diversity is morphologically undescribed, with a large part forming three hyper-diverse environmental clades, named Rad-A, Rad-B, and Rad-C. We suggest that most of this undescribed diversity comprises skeleton-less life forms or endosymbionts, explaining their elusive, yet abundant, nature. Phylogenetic analyses highlight the need for a major revision of high-level Radiolaria taxonomy, including placement of Collodaria within the order Nassellaria. Global metabarcoding surveys show that Radiolaria contributes more than 12% to the total eukaryotic community, displaying distinct biogeographic patterns with the skeleton-less lineages at depth and photosymbiont-bearing lineages in the surface. Fossil calibration of a molecular clock revealed the first appearance of Radiolaria ∼760 million years ago (mya), the development of the skeleton in the early Paleozoic (∼500 mya), and the onset of photosymbiotic relationships during the mid to late Mesozoic (∼140 mya), related to geological periods of oligotrophy and anoxia. The results presented here provide a robust framework for developing new perspectives on early eukaryotic diversification, paleo-environmental impacts on plankton evolution, and marine microbial ecology in rapidly evolving ecosystems.}, }
@article {pmid40333193, year = {2025}, author = {Hodžić, A and Kunert, M and Berry, D}, title = {Protocol for the visualization of bacteria in the tick gut using whole-mount fluorescence in situ hybridization.}, journal = {STAR protocols}, volume = {6}, number = {2}, pages = {103814}, pmid = {40333193}, issn = {2666-1667}, mesh = {*In Situ Hybridization, Fluorescence/methods ; Animals ; *Bacteria/isolation &amp; purification/genetics ; *Ticks/microbiology ; *Gastrointestinal Tract/microbiology ; }, abstract = {The tick gut harbors a relatively diverse microbial community that includes commensal, beneficial, and pathogenic bacterial species. Here, we present a protocol for the visualization of bacteria in the tick gut using whole-mount fluorescence in situ hybridization. We describe steps for tick dissection, tissue fixation, hybridization, washing, and mounting. We then detail procedures for microscopy imaging of the whole-mounted samples. Although the procedure is designed for gut tissue samples, it can be readily modified for use with other tissue types. For complete details on the use and execution of this protocol, please refer to Hodžić et al.[1].}, }
@article {pmid40333163, year = {2025}, author = {Touati, A and Ibrahim, NA and Idres, T}, title = {Disarming Staphylococcus aureus: Review of Strategies Combating This Resilient Pathogen by Targeting Its Virulence.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {4}, pages = {}, pmid = {40333163}, issn = {2076-0817}, support = {IMSIU-DDRSP2501//The Deanship of Scientific Research at Imam Mohammad Ibn Saud Islamic University (IMSIU)/ ; }, mesh = {Humans ; *Staphylococcal Infections/microbiology/drug therapy ; Virulence/drug effects ; *Staphylococcus aureus/drug effects/pathogenicity/physiology ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Biofilms/drug effects/growth &amp; development ; *Virulence Factors/antagonists &amp; inhibitors/metabolism ; Quorum Sensing/drug effects ; Methicillin-Resistant Staphylococcus aureus/drug effects/pathogenicity ; Animals ; }, abstract = {Staphylococcus aureus is a formidable pathogen notorious for its antibiotic resistance and diverse virulence mechanisms, including toxin production, biofilm formation, and immune evasion. This article explores innovative anti-virulence strategies to disarm S. aureus by targeting critical virulence factors without exerting bactericidal pressure. Key approaches include inhibiting adhesion and biofilm formation, neutralizing toxins, disrupting quorum sensing (e.g., Agr system inhibitors), and blocking iron acquisition pathways. Additionally, interventions targeting two-component regulatory systems are highlighted. While promising, challenges such as strain variability, biofilm resilience, pharmacokinetic limitations, and resistance evolution underscore the need for combination therapies and advanced formulations. Integrating anti-virulence strategies with traditional antibiotics and host-directed therapies offers a sustainable solution to combat multidrug-resistant S. aureus, particularly methicillin-resistant strains (MRSA), and mitigate the global public health crisis.}, }
@article {pmid40333144, year = {2025}, author = {Plewa-Tutaj, K and Chmielewska, Z and Twarużek, M and Kosicki, R and Soszczyńska, E}, title = {An Analysis of the Mycotoxins, Cytotoxicity, and Biodiversity of Airborne Molds Belonging to Aspergillus Genera Isolated from the Zoological Garden.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {4}, pages = {}, pmid = {40333144}, issn = {2076-0817}, support = {"MINIATURA 6," grant 2022/06/X/NZ8/00430//National Science Centre, Poland/ ; }, mesh = {*Mycotoxins/toxicity/analysis ; *Aspergillus/isolation &amp; purification/classification/genetics/metabolism ; *Air Microbiology ; *Biodiversity ; Animals ; Humans ; }, abstract = {The present study aimed to identify airborne molds of the Aspergillus genus and to determine the secondary metabolite profiles and toxicity of dominant fungal species isolated from various locations in the Wroclaw Zoological Garden. Air samples were collected using a MAS-100 air sampler and analyzed for fungal colony-forming units (CFU). Morphological and molecular methods, including ITS sequencing, were employed for dominant mold identification. The most frequently encountered species were A. fumigatus and A. niger, while A. pseudoglaucus and A. nomius were the least common. The high prevalence of species from sections Nigri, Flavi, and Fumigati suggests their adaptability to the zoo environment. A total of 17 Aspergillus isolates were analyzed for both their capacity to induce cellular toxicity and their production of mycotoxins. The results indicated that all isolates exhibited cellular toxicity, with 70.6% displaying levels of toxicity that were medium to high. Furthermore, the mycotoxicological analysis revealed that only A. fumigatus strains were capable of producing mycotoxins, specifically gliotoxin. The study underscores the discrepancy between the levels of toxicity and the production of mycotoxins, thereby suggesting the presence of additional cytotoxic metabolites. These findings emphasize the need for a comprehensive understanding of the complex interplay between fungal metabolites and their consequences for human health.}, }
@article {pmid40333133, year = {2025}, author = {Niculescu, AG and Mitache, MM and Grumezescu, AM and Chifiriuc, MC and Mihai, MM and Tantu, MM and Tantu, AC and Popa, LG and Grigore, GA and Cristian, RE and Popa, MI and Vrancianu, CO}, title = {From Microbial Ecology to Clinical Challenges: The Respiratory Microbiome's Role in Antibiotic Resistance.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {4}, pages = {}, pmid = {40333133}, issn = {2076-0817}, support = {CNFIS-FDI-2024-F-0484 INOVEX//University of Bucharest/ ; Pillar III, Component C9/Investment no. 8 (I8) - contract CF 68//; Ministry of Research, Innovation and Digitalization through the National Recovery and Resilience Plan (PNRR) of Romania/ ; project no. 23020101, Contract no. 7N from 3 January 2023//The core program within the National Research Development and Innovation Plan, 2022-2027', carried out with the support of the Ministry of Research, Innovation and Digitalization (MCID)/ ; }, mesh = {Humans ; *Microbiota/drug effects ; Anti-Bacterial Agents/pharmacology/therapeutic use ; *Respiratory Tract Infections/microbiology/drug therapy ; *Drug Resistance, Microbial ; Probiotics ; *Drug Resistance, Bacterial ; *Respiratory System/microbiology ; }, abstract = {Antibiotic resistance represents a growing public health threat, with airborne drug-resistant strains being especially alarming due to their ease of transmission and association with severe respiratory infections. The respiratory microbiome plays a pivotal role in maintaining respiratory health, influencing the dynamics of antibiotic resistance among airborne pathogenic microorganisms. In this context, this review proposes the exploration of the complex interplay between the respiratory microbiota and antimicrobial resistance, highlighting the implications of microbiome diversity in health and disease. Moreover, strategies to mitigate antibiotic resistance, including stewardship programs, alternatives to traditional antibiotics, probiotics, microbiota restoration techniques, and nanotechnology-based therapeutic interventions, are critically presented, setting an updated framework of current management options. Therefore, through a better understanding of respiratory microbiome roles in antibiotic resistance, alongside emerging therapeutic strategies, this paper aims to shed light on how the global health challenges posed by multi-drug-resistant pathogens can be addressed.}, }
@article {pmid40332344, year = {2025}, author = {Figueiredo, JEF and Marins, MS and Silva, FC and Ribeiro, VP and Diniz, GdFD and Rodrigues, VA and Oliveira-Paiva, CA and Lana, UGdP and Ferreira, LVS and Sousa Tinoco, SMd and Cruz-Magalhães, V}, title = {Draft genome of the endophytic Bacillus velezensis CNPMS-22 isolated from maize leaves.}, journal = {Microbiology resource announcements}, volume = {14}, number = {6}, pages = {e0127924}, pmid = {40332344}, issn = {2576-098X}, abstract = {Bacillus velezensis has been widely used as a biocontrol agent and plant growth promoter in agricultural bio-inputs. The genome of the endophytic bacterial strain CNPMS-22 isolated from maize leaves was sequenced, and the results showed that the strain is a Bacillus velezensis species.}, }
@article {pmid40329925, year = {2025}, author = {Razzaq Meo, S and Van de Wiele, T and Defoirdt, T}, title = {Indole signaling in Escherichia coli: a target for antivirulence therapy?.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2499573}, pmid = {40329925}, issn = {1949-0984}, mesh = {*Indoles/metabolism/pharmacology ; *Escherichia coli/drug effects/metabolism/pathogenicity/genetics ; Humans ; *Signal Transduction/drug effects ; *Escherichia coli Infections/microbiology/drug therapy ; Virulence/drug effects ; Quorum Sensing/drug effects ; *Anti-Bacterial Agents/pharmacology ; Virulence Factors/metabolism/genetics/antagonists &amp; inhibitors ; Animals ; Escherichia coli Proteins/metabolism/genetics ; Biofilms/drug effects/growth &amp; development ; }, abstract = {Pathogenic Escherichia coli are a major cause of infections in both humans and animals, leading to conditions such as severe diarrheal diseases, urinary tract infections, enteritis, and septicemia. To combat bacterial infections, antibiotics are widely utilized. However, the extensive and inappropriate use of antibiotics has fueled the development and spread of antibiotic resistance, posing a significant challenge to the effective treatment of E. coli. There is consequently an urgent need to explore alternative therapies to control such infections. This review provides an overview of the recent findings concerning indole signaling in E. coli. E. coli uses indole as a quorum sensing molecule, and indole signaling has been reported to decrease various virulence factors in pathogenic E. coli, including motility, biofilm formation, adherence to host cells, expression of the LEE pathogenicity island, and formation of attaching and effacing lesions. This makes indole signaling an interesting target for the development of new therapeutics in the framework of antivirulence therapy. Both natural and synthetic indole analogues have been explored as potential virulence inhibitors. This alternative approach could be advantageous, as it will exert less selective pressure for resistance development than conventional antibiotics.}, }
@article {pmid40329550, year = {2025}, author = {Jenkins, GB and Boyd, ES and Danchin, A and Hervé, V and Huggett, MJ and Sánchez, &#xc1; and Trevorrow, P}, title = {Environmental Microbiology and Environmental Microbiology Reports: Two Journals, One Goal.}, journal = {Environmental microbiology}, volume = {27}, number = {5}, pages = {e70078}, doi = {10.1111/1462-2920.70078}, pmid = {40329550}, issn = {1462-2920}, }
@article {pmid40329526, year = {2025}, author = {Ory, F and Dainat, B and Würgler, O and Wenger, F and Roetschi, A and Braillard, L and Charrière, JD and Dietemann, V}, title = {Ecology and Pathogenicity for Honey Bee Brood of Recently Described Paenibacillus melissococcoides and Comparison With Paenibacillus dendritiformis, Paenibacillus thiaminolyticus.}, journal = {Environmental microbiology reports}, volume = {17}, number = {3}, pages = {e70089}, pmid = {40329526}, issn = {1758-2229}, mesh = {Bees/microbiology ; Animals ; *Paenibacillus/pathogenicity/genetics/isolation &amp; purification/classification ; Virulence ; Spores, Bacterial ; Paenibacillus larvae ; Phylogeny ; Larva/microbiology ; }, abstract = {Honey bee colonies contain thousands of individuals living in close proximity in a thermally homeostatic nest, creating ideal conditions for the thriving of numerous pathogens. Among the bacterial pathogens, Paenibacillus larvae infects larvae via the nutritive jelly that adult workers feed them, causing the highly contagious American foulbrood disease. Further Paenibacillus species were anecdotally found in association with honey bees, including when affected by another disease, European foulbrood (EFB). However, their pathogenicity remains largely unknown. Our results indicate that Paenibacillus dendritiformis, Paenibacillus thiaminolyticus and newly described Paenibacillus melissococcoides are pathogenic towards honey bee brood and that their virulence correlates with their sporulation ability, which confers them resistance to the bactericidal properties of the nutritive jelly. Our survey occasionally but increasingly detected P. melissococcoides in confirmed and idiopathic cases of EFB but never in healthy colonies, suggesting that this bacterium is an emerging pathogen of honey bee brood. Overall, our results suggest that virulence traits allowing a pathogenic or opportunistically pathogenic habit towards honey bee brood are frequent in Paenibacillus spp., but that their degree of adaptation to this host varies. Our study clarifies the ecology of this ubiquitous genus, especially when infecting honey bees.}, }
@article {pmid40327698, year = {2025}, author = {Clegg, T and Gross, T}, title = {Cross-feeding creates tipping points in microbiome diversity.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {19}, pages = {e2425603122}, pmid = {40327698}, issn = {1091-6490}, mesh = {*Microbiota/physiology ; *Biodiversity ; *Models, Biological ; }, abstract = {A key unresolved question in microbial ecology is how the extraordinary diversity of microbiomes emerges from the interactions among their many functionally distinct populations. This process is driven in part by the cross-feeding networks that help to structure these systems, in which consumers use resources to fuel their metabolism, creating by-products which can be used by others in the community. Understanding the effects of cross-feeding presents a major challenge, as it creates complex interdependencies between populations which can be hard to untangle. We address this problem using the tools of network science to develop a structural microbial community model. Using methods from percolation theory, we identify feasible community states for cross-feeding network structures in which the needs of consumers are met by metabolite production across the community. We identify tipping points at which small changes in structure can cause the catastrophic collapse of cross-feeding networks and abrupt declines in microbial community diversity. Our results are an example of a well-defined tipping point in a complex ecological system and provide insight into the fundamental processes shaping microbiomes and their robustness. We further demonstrate this by considering how network attacks affect community diversity and apply our results to show how the apparent difficulty in culturing the microbial diversity emerges as an inherent property of their cross-feeding networks.}, }
@article {pmid40327084, year = {2025}, author = {Zhang, M and Hu, Y and Ma, Y and Hou, T and Wang, J and Che, Q and Chen, B and Wang, Q and Feng, G}, title = {Soil Bacterial Diversity and Community Structure of Cotton Rhizosphere under Mulched Drip-Irrigation in Arid and Semi-arid Regions of Northwest China.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {39}, pmid = {40327084}, issn = {1432-184X}, mesh = {*Gossypium/microbiology/growth &amp; development ; *Rhizosphere ; *Soil Microbiology ; China ; *Bacteria/classification/genetics/isolation &amp; purification ; Soil/chemistry ; *Agricultural Irrigation/methods ; Biodiversity ; Desert Climate ; Microbiota ; Alkaline Phosphatase/genetics ; }, abstract = {Xinjiang is situated in an arid and semi-arid region, where abundant heat and sunlight create highly favorable conditions for cotton cultivation. Xinjiang's cotton output accounts for nearly one-quarter of global production. Moreover, the implementation of advanced planting techniques, such as 'dwarfing, high-density, early-maturing' strategies combined with mulched drip irrigation, ensures stable and high yields in this region. Despite these advancements, limited research has focused on the microbial mechanisms in cotton fields employing these advanced planting methods. In this study, high-throughput sequencing technology was utilized to investigate the diversity and composition of bacterial and phoD (Alkaline phosphatases encoding gene) communities in the rhizosphere of cotton grown under different yield levels in Xinjiang Province, China. The Mantel test, redundancy analysis (RDA) and partial least squares path modeling (PLS-PM) were employed to explore the interactions between soil bacterial and phoD communities, their network structures, and environmental factors. The bacterial and phoD communities in the cotton rhizosphere were predominantly composed of nine bacterial phyla (i.e., Proteobacteria, Actinobacteria, Acidobacteria, Gemmatimonadetes, Chloroflexi, Bacteroidetes, Rokubacteria, Firmicutes, and Nitrospirae) and five phoD phyla (i.e., Proteobacteria, Actinobacteria, Planctomycetes, Acidobacteria, and Firmicutes), respectively. Alpha diversity analysis indicated that the medium yield cotton field (MYF) exhibited higher bacterial richness and diversity indices compared to low yield (LYF) and high yield (HYF) fields. The symbiotic network analysis of LYF revealed greater values of average degree, number of edges, and modularity, suggesting a more complex network structure in both bacterial and phoD communities. The Mantel test, RDA, and PLS-PM model identified soil pH, electrical conductivity (EC), organic phosphorus (OP), available phosphorus (AP), total nitrogen (TN), microbial biomass carbon (MBC), and clay content as the main driving factors influencing changes in the rhizosphere bacterial community diversity and network structure. These findings provide a theoretical basis for future research aimed at improving soil quality and cotton yield.}, }
@article {pmid40324073, year = {2025}, author = {Hoffman, PF}, title = {Ecosystem relocation on Snowball Earth: Polar-alpine ancestry of the extant surface biosphere?.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {20}, pages = {e2414059122}, pmid = {40324073}, issn = {1091-6490}, support = {EAR-0417422//NSF (NSF)/ ; }, mesh = {*Ecosystem ; Earth, Planet ; Oceans and Seas ; Ice Cover ; Fossils ; Biological Evolution ; }, abstract = {Geological observations informed by climate dynamics imply that the oceans were 99.9% covered by light-blocking ice shelves during two discrete, self-reversing Snowball Earth epochs spanning a combined 60 to 70 Myr of the Cryogenian Period (720 to 635 Ma). The timescale for initial ice advances across the tropical oceans is ~300 y in an ice-atmosphere-ocean general circulation model in Cryogenian paleogeography. Areas of optically thin oceanic ice are usually invoked to account for fossil marine phototrophs, including macroscopic multicellular eukaryotes, before and after each Snowball, but different taxa. Ecosystem relocation is a scenario that does not require thin marine ice. Assume that long before Cryogenian Snowballs, diverse supra- and periglacial biomes were established in polar-alpine regions. When the Snowball onsets occurred, those biomes migrated in step with their ice margins to the equatorial zone of net sublimation. There, they prospered and evolved, their habitat areas expanded, and the cruelty of winter reduced. Nutrients were supplied by dust (loess) derived from cozonal ablative lands where surface winds were strong. When each Snowball finally ended, those biomes were mostly inundated by the meltwater-dominated and rapidly warming lid of a nutrient-rich but depauperate ocean. Some taxa returned to the mountaintops while others restocked the oceans. This ecosystem relocation scenario makes testable predictions. The lineages required for post-Cryogenian biotic radiations should be present in modern polar-alpine biomes. Legacies of polar-alpine ancestry should be found in the genomes of living organisms. Examples of such tests are highlighted herein.}, }
@article {pmid40323108, year = {2025}, author = {Oz, A and Mairesse, O and Raikin, S and Hanani, H and Mor, H and Dafny Yelin, M and Sharon, I}, title = {Pear flower and leaf microbiome dynamics during the naturally occurring spread of Erwinia amylovora.}, journal = {mSphere}, volume = {10}, number = {5}, pages = {e0001125}, pmid = {40323108}, issn = {2379-5042}, support = {Accelerator project//The JCA Foundation/ ; }, mesh = {*Erwinia amylovora/genetics ; *Pyrus/microbiology ; *Flowers/microbiology ; *Microbiota ; *Plant Diseases/microbiology ; *Plant Leaves/microbiology ; Bacteria/classification/genetics ; }, abstract = {Erwinia amylovora is the causal pathogen of fire blight, a contagious disease that affects apple and pear trees and other members of the family Rosaceae. In this study, we investigated the community dynamics of the pear flower microbiome in an agricultural setting during the naturally occurring infection of E. amylovora. Five potential factors were considered: collection date, the flower's phenological stage, location on the tree, location within the orchard, and pear cultivar. The phenological stage and the collection date were identified as the most important factors associated with pear flower microbiome composition, while the location of the tree in the orchard and the flower's location on the tree had a marginal effect. The leaf microbiome reflected that of the abundant phenological stage on each date. The flower microbiome shifted toward E. amylovora dominating the community as time and phenological stages progressed, leading to a decreased community diversity. The E. amylovora population was represented almost exclusively by six amplicon sequence variants (ASVs) with similar proportions throughout the entire collection period. Other taxa, including Pseudomonas, Pantoea, Lactobacillus, and Sphingomonas, were represented by dozens of ASVs, and different succession patterns in their populations were observed. Some of the taxa identified include known antagonists to E. amylovora. Overall, our results suggest that flower physiology and the interaction with the environment are strongly associated with the pear flower microbiome and should be considered separately. Taxon-specific succession patterns under E. amylovora spread should be considered when choosing candidates for antagonist-based treatments for fire blight.IMPORTANCEThe spread of pathogens in plants is an important ecological phenomenon and has a significant economic impact on agriculture. Flowers serve as the entry point for E. amylovora, but members of the flower microbiome can inhibit or slow down the proliferation and penetration of the pathogen. Knowledge about leaf and flower microbiome response to the naturally occurring spread of E. amylovora is still lacking. The current study is the first to describe the Rosaceae flower microbiome dynamics during the naturally occurring infection of E. amylovora. Unlike previous studies, the study design enabled us to evaluate the contribution of five important environmental parameters to community composition. We identified different ASV succession patterns across different taxa in the flower consortia throughout the season. These results contribute to our understanding of plant microbial ecology during pathogen spread and can help improve biological treatments for fire blight.}, }
@article {pmid40322584, year = {2025}, author = {Zschaubitz, E and Schröder, H and Glackin, CC and Vogel, L and Labrenz, M and Sperlea, T}, title = {A benchmark analysis of feature selection and machine learning methods for environmental metabarcoding datasets.}, journal = {Computational and structural biotechnology journal}, volume = {27}, number = {}, pages = {1636-1647}, pmid = {40322584}, issn = {2001-0370}, abstract = {Next-Generation Sequencing methods like DNA metabarcoding enable the generation of large community composition datasets and have grown instrumental in many branches of ecology in recent years. However, the sparsity, compositionality, and high dimensionality of metabarcoding datasets pose challenges in data analysis. In theory, feature selection methods improve the analyzability of eDNA metabarcoding datasets by identifying a subset of informative taxa that are relevant for a certain task and discarding those that are redundant or irrelevant. However, general guidelines on selecting a feature selection method for application to a given setting are lacking. Here, we report a comparison of feature selection methods in a supervised machine learning setup across 13 environmental metabarcoding datasets with differing characteristics. We evaluate workflows that consist of data preprocessing, feature selection and a machine learning model by their ability to capture the ecological relationship between the microbial community composition and environmental parameters. Our results demonstrate that, while the optimal feature selection approach depends on dataset characteristics, feature selection is more likely to impair model performance than to improve it for tree ensemble models like Random Forests. Furthermore, our results show that calculating relative counts impairs model performance, which suggests that novel methods to combat the compositionality of metabarcoding data are required.}, }
@article {pmid40322503, year = {2025}, author = {Mandal, A and Ghosh, A and Kumar, G and Bhadury, P}, title = {Dataset of benthic foraminiferal community structure from sediment eDNA of Sundarbans mangrove ecosystem.}, journal = {Data in brief}, volume = {60}, number = {}, pages = {111554}, pmid = {40322503}, issn = {2352-3409}, abstract = {Sundarbans, the world's largest contiguous mangrove wetland, a UNESCO World Heritage Site and a RAMSAR site formed on the delta of Ganga-Brahmaputra-Meghna (GBM) and influenced by coastal water entering from the Bay of Bengal contribute immensely to biodiversity and blue economy. To track the changes driven by natural and anthropogenic stressors, sediment based environmental DNA (eDNA) biomonitoring of benthic foraminifera communities, an important biological group sensitive to changes, has been initiated along with estimation of dissolved nutrients from estuarine surface water of Sundarbans. In pre-monsoon of 2022 (June), sediment cores and surface water were collected as well as in situ environmental parameters were measured from two pre-designated sampling points of Sundarbans to elucidate the benthic foraminifera community based on sediment eDNA approach. Based on Oxford Nanopore Technologies (ONT) sequencing in MinION platform, high abundance of Sorites sp., Elphidium excavatum, Textularia gramen, Quinqueloculina sp. and Trochammina hadai were detected. The increasing nutrient concentrations and elucidated benthic foraminiferal signals can contribute towards tracking the state of ecological health of Sundarbans. This study is aimed at generating baseline information on mangrove benthic foraminifera communities using sediment eDNA based high-throughput sequencing.}, }
@article {pmid40319780, year = {2025}, author = {Attiani, V and Smidt, H and van der Wielen, PWJJ}, title = {Investigating spatial and temporal dynamics in microbial community composition of multiple full-scale slow sand filters in drinking water treatment.}, journal = {Water research}, volume = {282}, number = {}, pages = {123751}, doi = {10.1016/j.watres.2025.123751}, pmid = {40319780}, issn = {1879-2448}, mesh = {*Water Purification ; *Drinking Water/microbiology ; Filtration ; *Sand ; RNA, Ribosomal, 16S/genetics ; Microbiota ; Netherlands ; Bacteria ; }, abstract = {Slow sand filters (SSFs) are essential for producing high-quality and sustainable drinking water, relying on chemical, physical, and microbial processes to remove nutrients, organic matter, and pathogens. Despite numerous studies on the physical and chemical mechanisms in SSFs, the microbial processes and dynamics remain poorly understood. This study bridges this knowledge gap by investigating the spatial and temporal dynamics of prokaryotic communities within SSFs, by analysing different depths and the top layer, the Schmutzdecke (SCM), over time in full-scale SSFs from different drinking water treatment plants in The Netherlands. Utilising 16S ribosomal RNA gene-targeted amplicon sequencing and quantitative PCR, we observed a horizontally uniform prokaryotic community at each depth at all analysed SSFs, suggesting effective influent water and nutrient distribution, regardless of filter size or influent inlet design. Vertically, however, the prokaryotic composition varied significantly, with the SCM showing higher biomass and diversity compared to the deeper layers. This study identified a core prokaryotic community, including the families Nitrospiraceae, Pirellulaceae, Nitrosomonadaceae, Gemmataceae, and Vicinamibacteriaceae, consistent across various depths and SSFs, and in the SCMs of different ages. Their presence suggests a central role in supporting key biological processes in SSFs such as organic matter degradation and nitrification. Additionally, the relative abundance of archaea increased with sand depth in all SSFs, suggesting their adaptation to lower-nutrient conditions found in deeper layers. Analysis of the SCM over time showed that after scraping, the prokaryotic community gradually adapted, with minimal biomass increase during the first 3.6 years, eventually evolving into a mature, diverse, and even prokaryotic community. Our findings highlight the presence of spatially distinct microbial communities at various depths of SSFs, suggesting the removal of specific compounds in distinct sand layers. Moreover, the persistence of a core prokaryotic community across different SSFs, SCM maturation stages, and even after disturbances like scraping, demonstrates that the biology in SSFs is resilient and likely ensures reliable SSF performance. It also implies possibilities for earlier SSF operational restart after cleaning than is conventionally done, but with continuous monitoring of water quality parameters to ensure microbial safety. These findings lay the groundwork for future research to focus on these microorganisms and their functional potential.}, }
@article {pmid40319213, year = {2025}, author = {Liu, Y and Hu, Y and Ma, B and Wang, Z and Wei, B}, title = {Gut Microbiota and Exercise: Probiotics to Modify the Composition and Roles of the Gut Microbiota in the Context of 3P Medicine.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {38}, pmid = {40319213}, issn = {1432-184X}, mesh = {*Probiotics/administration &amp; dosage/pharmacology ; Humans ; *Gastrointestinal Microbiome/drug effects/physiology ; *Exercise/physiology ; Athletic Performance/physiology ; Precision Medicine ; Animals ; }, abstract = {Prolonged and intense physical activity can trigger stress response mechanisms across various physiological systems-including the cardiovascular, respiratory, gastrointestinal, musculoskeletal, and neuroendocrine systems-disrupting energy metabolism, immune function, redox balance, and hormonal regulation. Critically, when not accompanied by adequate recovery, such exertion may impair rather than enhance athletic performance. In parallel, there has been growing interest in probiotics as natural, safe, and accessible dietary supplements with the potential to support performance and recovery. Emerging evidence highlights the pivotal role of the gut microbiome in mediating communication along the gut-brain and gut-muscle axes, thereby influencing not only metabolic and immune functions but also neuromuscular adaptation and fatigue resistance. This review explores the mechanisms through which probiotics may enhance exercise performance, mitigate exercise-induced fatigue, and improve physiological adaptation via modulation of inflammation, oxidative stress, and metabolic signaling pathways. Framed within the context of predictive, preventive, and personalized medicine (3P medicine), this paper emphasizes the diagnostic and therapeutic potential of personalized probiotic strategies in optimizing athletic performance through the qualitative and quantitative assessment of microbiota and host responses.}, }
@article {pmid40316823, year = {2025}, author = {Ben Ammar, FE and Hkiri, AE and Zaafouri, K and Saidane Bchir, F and Hamdi, M}, title = {Enhanced growth of Chlorella sorokiniana on ash-enriched treated wastewater for large-scale lipid and chlorophyll a production using a hybrid raceway photobioreactor.}, journal = {Environmental science and pollution research international}, volume = {32}, number = {21}, pages = {12610-12629}, pmid = {40316823}, issn = {1614-7499}, mesh = {*Chlorella ; *Wastewater ; *Photobioreactors ; Lipids ; Chlorophyll A ; Microalgae ; Biomass ; }, abstract = {Nutrient concentration in microalgal cultivation media greatly influences microalgal growth and macromolecules production. In the present study, treated urban wastewater was used as a medium for Chlorella sorokiniana, incorporating mineral components and ashes in batch culture. The aim was to assess the combined effect of nutrients on microalgal growth, Chlorophyll a content, and lipid production using customized experimental design and response surface methodology. Another objective was to evaluate response improvement after using hybrid raceway photobioreactor HRPBR. The results showed that the highest microalgal biomass growth as well as the highest Chlorophyll a and lipid concentrations was obtained using 2015 mg. L[-1]of NaNO3 and 2086.76 mg. L[-1] of NaHCO3 with a mineral solution concentration of 120 mg. L[-1]. After the HRPBR cultivation, Chlorophyll a content increased from 40.26 to 65.04 mg. L[-1] and the lipid content rose from 37 to 40% and then to 68% under starvation conditions. In these circumstances, the FA profile of Chlorella sorokiniana became in line with the requirements of the European biodiesel standard. Thus, the low-cost nutrient sources for culture medium formulation can be used to culture C. sorokiniana as an efficient strain for sustainable and cost-effective biofuel production.}, }
@article {pmid40312782, year = {2025}, author = {Kynast, D and Reverey, F and Ganzert, L and Grossart, HP and Lischeid, G and Kolb, S}, title = {Detectable land use impact on methanotrophs and methanogens in kettle hole sediments but not on net methane production potentials.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {6}, pages = {}, pmid = {40312782}, issn = {1574-6941}, support = {465808595//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Methane/metabolism ; *Geologic Sediments/microbiology ; *Archaea/metabolism/classification/genetics/isolation &amp; purification ; Microbiota ; *Bacteria/metabolism/classification/genetics/isolation &amp; purification ; Soil Microbiology ; Soil/chemistry ; Agriculture ; Biodiversity ; Forests ; }, abstract = {Kettle holes (KHs) are dynamic freshwater systems and potential sources of the greenhouse gas methane. Due to their small size (<1 hectare), KHs are subject to inorganic and organic matter input from their terrestrial surroundings, governed by land use. Matter inputs include inorganic solutes that are alternative electron acceptors and impact on methanotrophs and methanogens. Thus, they might affect methane net production. We sampled 10 kettle hole sediments embedded in landscapes with either agricultural or forest land use and determined their (i) potential net methane production rates, (ii) the composition of their microbial communities, and (iii) physicochemical soil parameters. Potential net methane production did not significantly differ by land use type but between single KHs. However, land use type had a strong impact on methanotroph and methanogen and on total bacterial and archaeal microbiota structure. Relative abundances of methanotrophs and methanogens were significantly higher in agricultural KHs, and their relative abundances were among the most influential variables projecting net methane production potentials along with nutrient status and water content. Land use type was thus identified as a major factor that impacts the structure and biodiversity of general and methane-cycling microbiota, but it did not affect net methane production potentials.}, }
@article {pmid40312547, year = {2025}, author = {Hu, L and Zhang, K and Xu, Y and Zheng, X and Waterman, JM and Ouyang, X and Wu, Z and Shen, Z and He, Y and Ma, B and Robert, CAM and Raaijmakers, JM and Ye, M and Erb, M and Xu, J}, title = {Herbivory-induced green leaf volatiles increase plant performance through jasmonate-dependent plant-soil feedbacks.}, journal = {Nature plants}, volume = {11}, number = {5}, pages = {1001-1017}, pmid = {40312547}, issn = {2055-0278}, support = {32372775//National Natural Science Foundation of China (National Science Foundation of China)/ ; 200355//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; }, mesh = {*Oxylipins/metabolism ; *Cyclopentanes/metabolism ; *Herbivory ; *Volatile Organic Compounds/metabolism ; *Plant Leaves/metabolism ; *Zea mays/physiology/metabolism/growth &amp; development ; Soil Microbiology ; Soil/chemistry ; Animals ; Rhizosphere ; }, abstract = {Plants influence each other chemically by releasing leaf volatiles and root exudates, but whether and how these two phenomena interact remains unknown. Here we demonstrate that volatiles that are released by herbivore-attacked leaves trigger plant-soil feedbacks, resulting in increased performance of different plant species. We show that this phenomenon is due to green leaf volatiles that induce jasmonate-dependent systemic defence signalling in receiver plants, which results in the accumulation of beneficial soil bacteria in the rhizosphere. These soil bacteria then increase plant growth and enhance plant defences. In maize, a cysteine-rich receptor-like protein kinase, ZmCRK25, is required for this effect. In four successive year-field experiments, we demonstrate that this phenomenon can suppress leaf herbivore abundance and enhance maize growth and yield. Thus, volatile-mediated plant-plant interactions trigger plant-soil feedbacks that shape plant performance across different plant species through broadly conserved defence signalling mechanisms and changes in soil microbiota. This phenomenon expands the repertoire of biologically relevant plant-plant interactions in space and time and holds promise for the sustainable intensification of agriculture.}, }
@article {pmid40310547, year = {2025}, author = {Calcagnile, M and Quarta, E and Sicuro, A and Pecoraro, L and Schiavone, R and Tredici, SM and Talà, A and Corallo, A and Verri, T and Stabili, L and Alifano, P}, title = {Effect of Bacillus velezensis MT9 on Nile Tilapia (Oreochromis Niloticus) Intestinal Microbiota.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {37}, pmid = {40310547}, issn = {1432-184X}, support = {ARS01_01053//Ministero dell'Istruzione e del Merito/ ; ARS01_01053//Ministero dell'Istruzione e del Merito/ ; CUP B83C22002930006//European Union Next Generation EU (PNRR)/ ; }, mesh = {Animals ; *Bacillus/physiology/genetics ; *Cichlids/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Probiotics/administration &amp; dosage/pharmacology ; RNA, Ribosomal, 16S/genetics ; Aquaculture ; Bacteria/classification/genetics/isolation &amp; purification ; Animal Feed/analysis ; }, abstract = {In recent years, there has been a growing interest in the use of probiotics in aquaculture, due to their effectiveness on production, safety, and environmental friendliness. Probiotics, used as feed additives and as an alternative to antibiotics for disease prevention, have been shown to be active as growth promoters, improving survival and health of farmed fish. In this study, we have investigated the ability of the strain Bacillus velezensis MT9, as potential probiotic, to modulate the intestinal microbiota of the Nile tilapia (Oreochromis niloticus) fed with the Bacillus velezensis-supplemented feed in an experimental aquaculture plant. The analysis of the microbial community of the Nile tilapia by culture-based and 16S rRNA gene metabarcoding approaches demonstrated that B. velezensis MT9 reshapes the fish intestinal microbiota by reducing the amounts of opportunistic Gram-negative bacterial pathogens belonging to the phylum of Proteobacterium (Pseudomonadota) and increasing the amounts of beneficial bacteria belonging to the phyla Firmicutes (Bacillota) and Actinobacteria (Actinomycetota). Specifically, dietary supplementation of Nile tilapia with B. velezensis MT9 resulted in an increase in the relative abundance of bacteria of the genus Romboutsia, which has a well-documented probiotic activity, and a decrease in the relative abundance of Gammaproteobacteria of the genera Aeromonas and Vibrio, which include opportunistic pathogens for fish, and Escherichia/Shigella, which may pose a risk to consumers. The whole genome sequence of B. velezensis MT9 was then determined. Genome analysis revealed several peculiarities of B. velezensis MT9 compared to other B. velezensis reference strains including specific metabolic traits, differences in two-component and quorum sensing systems as well as the potential ability to produce a distinct array of secondary metabolites, which could explain the strong ability of this strain to modulate the intestinal microbiota of the Nile tilapia.}, }
@article {pmid40309103, year = {2025}, author = {Cong, X and Liu, X and Zhou, D and Xu, Y and Liu, J and Tong, F}, title = {Characterization and comparison of the fecal bacterial microbiota in Red Back Pine Root Snake (Oligodon formosanus) and Chinese Slug-Eating Snake (Pareas chinensis).}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1575405}, pmid = {40309103}, issn = {1664-302X}, abstract = {INTRODUCTION: The gastrointestinal tracts and oral cavities of animals harbor complex microbial communities that assist hosts in nutrient absorption and immune responses, thereby influencing behavior, development, reproduction, and overall health.<br><br>METHODS: We utilized metagenomic sequencing technology to conduct a detailed analysis of the fecal bacterial communities of six Red Back Pine Root Snakes (Oligodon formosanus, XT) and three Chinese Slug-Eating Snakes (Pareas chinensis, Z) individuals. The microbial composition was assessed through taxonomic profiling, alpha diversity analysis, and functional annotation using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database.<br><br>RESULTS: The results indicated that Proteobacteria, Bacteroidetes, Firmicutes, Verrucomicrobia, Actinobacteria, and Fusobacteria were the dominant phyla in XT samples, while Z samples additionally contained Patescibacteria. Alpha diversity analysis revealed significant differences in species abundance at the family level, with Z samples exhibiting higher microbial richness than XT. Furthermore, KEGG analysis showed that XT had higher functional gene abundance in pathways related to transcription, translation, environmental adaptation, membrane transport, cellular communities (prokaryotes), motility, and replication/repair compared to Z.<br><br>DISCUSSION: This study provides a comparative analysis of their gut microbiomes, offering valuable insights for future research on zoonotic diseases, host-microbe interactions, and ecological, evolutionary, behavioral, and seasonal influences on snake microbiota. These findings contribute to a broader understanding of microbial ecology in reptiles and its implications for conservation and disease dynamics.}, }
@article {pmid40307095, year = {2025}, author = {Zhang, D and Gao, JT and Zhou, SG}, title = {Microbial electrotaxis: rewiring environmental microbiomes.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2025.04.005}, pmid = {40307095}, issn = {1878-4380}, abstract = {Electric fields in sediments and soils are critical yet overlooked drivers of microbial ecology. This review examines the importance of electrotaxis in shaping microbial community dynamics and ecology models, surpassing traditional frameworks centered on chemotaxis. We analyze evidence that electric field gradients influence microbial community structure, function, and biogeochemical cycles in natural environments. Current mechanistic models, primarily based on eukaryotic systems, insufficiently explain bacterial electrotactic responses, necessitating new conceptual frameworks that integrate electrochemical and biological perspectives. We also evaluate its applications in environmental and microbiome engineering, with future research recommendations and methodologies in electrotaxis research. This synthesis aims to establish electrotaxis as an essential consideration in microbial ecology, presenting both challenges and opportunities for advancing our understanding of microbial ecosystems.}, }
@article {pmid40305681, year = {2025}, author = {Bennett, BD and Meier, DAO and Lanclos, VC and Asrari, H and Coates, JD and Thrash, JC}, title = {Polyhydroxybutyrate production by freshwater SAR11 (LD12).}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {40305681}, issn = {1751-7370}, mesh = {Phylogeny ; *Fresh Water/microbiology ; *Hydroxybutyrates/metabolism ; *Polyhydroxyalkanoates/metabolism/biosynthesis ; Escherichia coli/genetics/metabolism ; *Alphaproteobacteria/metabolism/genetics/classification ; Bacterial Proteins/genetics/metabolism ; Gene Transfer, Horizontal ; Polyhydroxybutyrates ; }, abstract = {SAR11 bacteria (order Pelagibacterales) are oligotrophs and often the most abundant bacterioplankton in aquatic environments. A subset of sequenced SAR11 genomes, predominantly in the brackish and freshwater SAR11 subclades, contain homologs of pha genes, which in other organisms confer the ability to store carbon and energy via polyhydroxyalkanoate (PHA) polymers. Here, we investigated the relevance of PHA production to SAR11 biology. Phylogenetics showed that Pha proteins occurred on a long branch and provided evidence for origin at the common ancestor of the brackish IIIa and freshwater LD12 subclades, followed by horizontal transfer within SAR11. Using the LD12 representative "Candidatus Fonsibacter ubiquis" strain LSUCC0530, we found that many LSUCC0530 cells contained a single Nile red-staining granule, confirmed that the cells produced polyhydroxybutyrate, a common form of PHA, and estimated the total polyhydroxybutyrate content in the cells. We heterologously expressed the LSUCC0530 phaCAB locus in Escherichia coli, finding it to be functional and the likely origin of the polyhydroxybutyrate. We also determined that, irrespective of changes to carbon, nitrogen, and phosphorus concentrations, a similar fraction of LSUCC0530 cells generated polyhydroxybutyrate granules and expression of the phaCAB locus remained constant. We suggest that polyhydroxybutyrate synthesis in LSUCC0530 may be constitutively active due to the slow growth dynamics and minimal regulation that characterize SAR11 bacteria. This work characterizes polymer storage in SAR11, providing new insights into the likely fitness advantage for cells harboring this metabolism.}, }
@article {pmid40304437, year = {2025}, author = {Kardish, MR and Stachowicz, JJ}, title = {More Than a Stick in the Mud: Eelgrass Leaf and Root Bacterial Communities Are Distinct From Those on Physical Mimics.}, journal = {Environmental microbiology reports}, volume = {17}, number = {3}, pages = {e70086}, pmid = {40304437}, issn = {1758-2229}, support = {//UC Davis Center for Population Biology/ ; OCE 1829992//National Science Foundation/ ; //National Science Foundation GRFP/ ; TG-DEB160008//Extreme Science and Engineering Discovery Environment (XSEDE)/ ; //Gordon and Betty Moore Foundation/ ; }, mesh = {*Zosteraceae/microbiology ; *Plant Roots/microbiology ; *Plant Leaves/microbiology ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; RNA, Ribosomal, 16S/genetics ; }, abstract = {We examine the role of physical structure versus biotic interactions in structuring host-associated microbial communities on a marine angiosperm, Zostera marina, eelgrass. Across several months and sites, we compared microbiomes on physical mimics of eelgrass roots and leaves to those on intact plants. We find large, consistent differences in the microbiome of mimics and plants, especially on roots, but also on leaves. Key taxa that are more abundant on leaves have been associated with microalgal and macroalgal disease and merit further investigation to determine their role in mediating plant-microalgal-pathogen interactions. Root associated taxa were associated with sulphur and nitrogen cycling, potentially ameliorating environmental stresses for the plant. Our work identifies targets for future work on the functional role of the seagrass microbiome in promoting the success of these angiosperms in the sea through identifying components of microbial communities that are specific to seagrasses.}, }
@article {pmid40303429, year = {2025}, author = {Zhao, C and Zhang, J and Chen, Y and Yang, L and Chen, H and Liang, Y and Wang, W and He, S and Luo, Y and Zhang, J and Zhang, H and Yang, S and Guo, G and Dai, W and Yang, Z and Chen, J and Zhou, Y and Khan, WU and Liu, G and Jiang, Y and Zhu, T and Xu, Y and García-Caparros, P and Van de Peer, Y and Xue, JY and Chen, C and Zhang, L and Chen, F}, title = {Water lily pond: a multiomics database for water lilies.}, journal = {Horticulture research}, volume = {12}, number = {6}, pages = {uhaf076}, pmid = {40303429}, issn = {2662-6810}, }
@article {pmid40302853, year = {2025}, author = {Gharbi, D and Neumann, FH and Podile, K and McDonald, M and Linde, JH and Frampton, M and Liebenberg, JL and Cilliers, S and Mmatladi, T and Nkosi, P and Paledi, K and Piketh, S and Staats, J and Burger, RP and Havenga, H and Garland, RM and Bester, P and Lebre, PH and Ricci, C}, title = {Exposure to outdoor aerospora and associated respiratory health risks among adults in Potchefstroom, North-West province, South Africa.}, journal = {Frontiers in allergy}, volume = {6}, number = {}, pages = {1568669}, pmid = {40302853}, issn = {2673-6101}, abstract = {BACKGROUND: Data on allergic rhinitis and respiratory health metrics are limited for South Africa, with grass pollen as a key outdoor aeroallergen. Exotic trees such as plane trees and ragweed produce highly allergenic pollen, dominating indigenous trees and weeds. Pollen allergy prevalence data is lacking in cities of North-West province such as Potchefstroom.<br><br>OBJECTIVES: This study aimed to (i) assess the prevalence of allergies to major aeroallergens, including Poaceae (grasses), Cupressus/Hesperocyparis (cypresses), Platanus (plane tree), Ulmus (elm), Quercus (oak), Betula (birch), Olea (olive), Artemisia (sagebrush), Amaranthus (amaranth), Plantago (plantain), Morus (mulberry), and Ambrosia (ragweed), along with fungal spores such as Alternaria, Cladosporium, and Penicillium/Aspergillus, and (ii) investigate the monthly incidence of major aeroallergens and reactivity levels in sensitized adults in Potchefstroom.<br><br>METHODS: Skin prick tests (SPTs) were performed on 202 adults aged 18-64 years with confirmed allergic symptoms during a field campaign at North-West University (NWU)'s Potchefstroom campus. A test panel of grass, weed, tree, and fungal spore extracts previously identified via aerobiological monitoring was used. Symptom scores were recorded using ISAAC questionnaires; Spearman's statistical correlation between symptom frequency and monthly aeroallergen concentrations were analyzed.<br><br>RESULTS: Among the participants, 184 (91%) exhibited positive SPT reactions: 104 (57%) are monosensitized to pollen, 45 (24%) to fungal spores, and 35 (19%) are polysensitized. Aeroallergen prevalence was higher in females (73%) than in males (27%). The most common pollen allergens were Cynodon dactylon (Bermuda grass) (85%), Zea mays (maize) (46%), Platanus spp. (plane tree) (35%), and Ulmus campestris (field elm) (33%). Among fungal spores, Alternaria was the most common (93%), followed by Cladosporium (27%). A significant and positive statistical correlation was found between allergic rhinitis symptoms and monthly pollen concentrations of Betula, Morus, Platanus, and Quercus.<br><br>DISCUSSION &amp; CONCLUSION: This pilot study linked aeroallergens detected in Potchefstroom with allergy profiles of local residents. The findings highlight the need for more comprehensive regional studies that integrate allergen testing with aerobiological data. Raising awareness and implementing health strategies are essential for managing allergic rhinitis in South Africa. More affordable and available SPTs kits, adapted to allergy prevalence in South Africa, are strongly suggested.}, }
@article {pmid40301344, year = {2025}, author = {Zhu, C and Wu, L and Ning, D and Tian, R and Gao, S and Zhang, B and Zhao, J and Zhang, Y and Xiao, N and Wang, Y and Brown, MR and Tu, Q and ,  and Ju, F and Wells, GF and Guo, J and He, Z and Nielsen, PH and Wang, A and Zhang, Y and Chen, T and He, Q and Criddle, CS and Wagner, M and Tiedje, JM and Curtis, TP and Wen, X and Yang, Y and Alvarez-Cohen, L and Stahl, DA and Alvarez, PJJ and Rittmann, BE and Zhou, J}, title = {Global diversity and distribution of antibiotic resistance genes in human wastewater treatment systems.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {4006}, pmid = {40301344}, issn = {2041-1723}, support = {EF-2025558//National Science Foundation (NSF)/ ; 32371724//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82202299//National Natural Science Foundation of China (National Science Foundation of China)/ ; 61872218//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Wastewater/microbiology ; Humans ; Sewage/microbiology ; *Drug Resistance, Microbial/genetics ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; *Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Water Purification ; *Drug Resistance, Bacterial/genetics ; Interspersed Repetitive Sequences/genetics ; }, abstract = {Antibiotic resistance poses a significant threat to human health, and wastewater treatment plants (WWTPs) are important reservoirs of antibiotic resistance genes (ARGs). Here, we analyze the antibiotic resistomes of 226 activated sludge samples from 142 WWTPs across six continents, using a consistent pipeline for sample collection, DNA sequencing and analysis. We find that ARGs are diverse and similarly abundant, with a core set of 20 ARGs present in all WWTPs. ARG composition differs across continents and is distinct from that of the human gut and the oceans. ARG composition strongly correlates with bacterial taxonomic composition, with Chloroflexi, Acidobacteria and Deltaproteobacteria being the major carriers. ARG abundance positively correlates with the presence of mobile genetic elements, and 57% of the 1112 recovered high-quality genomes possess putatively mobile ARGs. Resistome variations appear to be driven by a complex combination of stochastic processes and deterministic abiotic factors.}, }
@article {pmid40301151, year = {2025}, author = {Kaufmann, H and Salvador, C and Salazar, VW and Cruz, N and Dias, GM and Tschoeke, D and Campos, L and Sawabe, T and Miyazaki, M and Maruyama, F and Thompson, F and Thompson, C}, title = {Genomic Repertoire of Twenty-Two Novel Vibrionaceae Species Isolated from Marine Sediments.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {36}, pmid = {40301151}, issn = {1432-184X}, mesh = {*Geologic Sediments/microbiology ; *Vibrionaceae/genetics/classification/isolation &amp; purification ; *Genome, Bacterial ; Phylogeny ; Japan ; *Seawater/microbiology ; Genetic Variation ; }, abstract = {The genomic repertoire of vibrios has been extensively studied, particularly regarding their metabolic plasticity, symbiotic interactions, and resistance mechanisms to environmental stressors. However, little is known about the genomic diversity and adaptations of vibrios inhabiting deep-sea marine sediments. In this study, we investigated the genomic diversity of vibrios isolated from deep-sea core sediments collected using a manned submersible off Japan. A total of 50 vibrio isolates were obtained and characterized phenotypically, and by genome sequencing. From this total, we disclosed 22 novel species examining genome-to-genome distance, average amino acid identity, and phenotypes (Alivibrio: 1; Enterovibrio: 1; Photobacterium: 8; Vibrio: 12). The novel species have fallen within known clades (e.g., Fisheri, Enterovibrio, Profundum, and Splendidus) and novel clades (JAMM0721, JAMM0388, JAMM0395). The 28 remainder isolates were identified as known species: Aliivibrio sifiae (2), A. salmonicida (1), Enterovibrio baiacu (1), E. norvegicus (1), Photobacterium profundum (3), P. angustum (1), P. chitiniliticum (1), P. frigidiphilum (1), Photobacterium indicum (1), P. sanguinicancri (1). P. swingsii (2), Vibrio alginolyticus (3), V. anguillarum (1), V. campbellii (1), V. fluvialis (1), V. gigantis (1), V. lentus (1), V. splendidus (4), and V. tasmaniensis (1). Genomic analyses revealed that all 50 vibrios harbored genes associated with high-pressure adaptation, including sensor kinases, chaperones, autoinducer-2 (AI-2) signaling, oxidative damage repair, polyunsaturated fatty acid biosynthesis, and stress response mechanisms related to periplasmic and outer membrane protein misfolding under heat shock and osmotic stress. Additionally, alternative sigma factors, trimethylamine oxide (TMAO) respiration, and osmoprotectant acquisition pathways were identified, further supporting their ability to thrive in deep-sea environments. Notably, the genomes exhibited a high prevalence of antibiotic resistance genes, with antibiotic efflux pumps being the most abundant group. The ugd gene expanded in number in some novel species (Photobacterium satsumensis sp. nov. JAMM1754: 4 copies; Vibrio makurazakiensis sp. nov. JAMM1826: 3 copies). This gene may confer antibiotic (polymyxin) resistance to these vibrios.}, }
@article {pmid40301143, year = {2025}, author = {Weitzman, CL and Day, K and Brown, GP and Gibb, K and Christian, K}, title = {Differential Temporal Shifts in Skin Bacteria on Wild and Captive Toads.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {35}, pmid = {40301143}, issn = {1432-184X}, support = {DP210102176//Australian Research Council/ ; DP210102176//Australian Research Council/ ; DP210102176//Australian Research Council/ ; DP210102176//Australian Research Council/ ; DP210102176//Australian Research Council/ ; }, mesh = {Animals ; *Skin/microbiology ; Seasons ; *Bacteria/classification/isolation &amp; purification/genetics ; *Bufo marinus/microbiology ; *Microbiota ; Ecosystem ; Australia ; Animals, Wild/microbiology ; Animals, Zoo/microbiology ; }, abstract = {Skin bacteria on amphibian hosts play an important role in host health, but those communities are also constantly shifting based on environmental and host-related feedback. On some hosts, stability of skin communities depends on relatively abundant taxa, with less abundant taxa more readily entering and exiting the system. Cane toads (Rhinella marina) have invaded widespread, diverse tropical ecosystems, with varying ecology, physiology, and behaviour in different environments. In this study, we described temporal patterns of skin bacterial communities on cane toads at a site in northern Australia through the wet and dry seasons over two years. Toads in the wild population were paired with a captive-held population, housed in a semi-natural environment, to detect effects of time and season on wild toads, explore bacterial transience and volatility in skin taxa, and determine the extent to which skin communities on captive toads represent those on the wild population. We found community differences by captivity status, sampling timepoint, and season, with increased richness in the wet season on wild toads. Bacterial communities also became more similar among individuals (lower dispersion) in the wet season. Captive toads harboured more stable communities over time, likely owing to the reduced bacterial reservoirs experienced while in captivity. We propose that cane toads, with varied movement patterns among their diverse invaded habitats, provide an interesting direction for future work understanding the influences of habitat and movement on skin microbes, and the flexibility of microbial symbiotic interactions in invasive hosts.}, }
@article {pmid40300605, year = {2025}, author = {Lopez, JA and McKeithen-Mead, S and Shi, H and Nguyen, TH and Huang, KC and Good, BH}, title = {Abundance measurements reveal the balance between lysis and lysogeny in the human gut microbiome.}, journal = {Current biology : CB}, volume = {35}, number = {10}, pages = {2282-2294.e11}, doi = {10.1016/j.cub.2025.03.073}, pmid = {40300605}, issn = {1879-0445}, support = {R35 GM146949/GM/NIGMS NIH HHS/United States ; }, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Bacteriophages/physiology/genetics ; *Lysogeny ; Mice ; Animals ; *Bacteria/virology/genetics ; *Virome ; }, abstract = {The human gut contains diverse communities of bacteriophage, whose interactions with the broader microbiome and potential roles in human health are only beginning to be uncovered. Here, we combine multiple types of data to quantitatively estimate gut phage population dynamics and lifestyle characteristics in human subjects. Unifying results from previous studies, we show that an average human gut contains a low ratio of phage particles to bacterial cells (∼1:100) but a much larger ratio of phage genomes to bacterial genomes (∼4:1), implying that most gut phage are effectively temperate (e.g., integrated prophage and phage-plasmids). By integrating imaging and sequencing data with a generalized model of temperate phage dynamics, we estimate that phage induction and lysis occur at a low average rate (∼0.001-0.01 per bacterium per day), imposing only a modest fitness burden on their bacterial hosts. Consistent with these estimates, we find that the phage composition of a diverse synthetic community in gnotobiotic mice can be quantitatively predicted from bacterial abundances alone while still exhibiting phage diversity comparable to native human microbiomes. These results provide a foundation for interpreting existing and future studies on links between the gut virome and human health.}, }
@article {pmid40299544, year = {2025}, author = {Veenhof, RJ and McGrath, AH and Champion, C and Dworjanyn, SA and Marzinelli, EM and Coleman, MA}, title = {The role of microbiota in kelp gametophyte development and resilience to thermal stress.}, journal = {Journal of phycology}, volume = {61}, number = {3}, pages = {633-649}, pmid = {40299544}, issn = {1529-8817}, support = {//The University of Sydney/ ; DP200100201//Australian Research Council/ ; //NSW Climate Change Fund/ ; //Holsworth Wildlife Research Endowment/ ; }, mesh = {*Microbiota ; *Kelp/microbiology/growth &amp; development/physiology ; *Germ Cells, Plant/growth &amp; development/microbiology ; Hot Temperature ; Stress, Physiological ; }, abstract = {Ocean warming is driving profound changes in the ecology of marine habitat formers such as kelps, with negative implications for the biodiversity and ecosystem services they support. Thermal stress can disturb associated microbiota that are essential to the healthy functioning of kelp, but little is known about how this process influences early-life stages. Because kelps have a biphasic life cycle, thermal stress dynamics of adult sporophyte microbiota may not reflect those of the free-living haploid gametophyte. We investigated the role of microbial disruption under thermal stress on gametophytes of the kelp Ecklonia radiata and compared sporophyte and gametophyte microbiota. The microbiota of gametophytes changed significantly when the microbiome was disrupted and under increased temperature (26°C), in which putative generalist bacterial taxa proliferated and bacterial families associated with nitrogen fixation decreased. Concurrently, the survival of gametophytes decreased to <10%, and surviving gametophytes did not become fertile when the microbiome was disrupted. The length of gametophytes decreased under both microbial disruption and thermal stress. Taken together, this suggests that the associated microbiota of Ecklonia gametophytes is important for their survival, fertility, and response to warming. Gametophyte and parental sporophyte microbiota were also distinct from the water column but not each other, suggesting vertical transmission of microbiota from one life stage to the next. This study furthers our understanding of the role of microbiota in gametophyte stress tolerance as well as the acquisition of microbiota, which may prove vital in protecting and increasing the stress resilience of these foundation species.}, }
@article {pmid40298441, year = {2025}, author = {Peng, S-X and Gao, S-M and Lin, Z-L and Luo, Z-H and Zhang, S-Y and Shu, W-S and Meng, F and Huang, L-N}, title = {Biogeography and ecological functions of underestimated CPR and DPANN in acid mine drainage sediments.}, journal = {mBio}, volume = {16}, number = {6}, pages = {e0070525}, pmid = {40298441}, issn = {2150-7511}, support = {no. 31870111//National Natural Science Foundation of China/ ; no. 41830318//National Natural Science Foundation of China/ ; no. 32300001//National Natural Science Foundation of China/ ; no. 2022A1515010625//Natural Science Foundation of Guangdong Province/ ; no. 2021A1515012468//Natural Science Foundation of Guangdong Province/ ; }, mesh = {*Bacteria/classification/genetics/isolation &amp; purification/metabolism ; China ; *Archaea/genetics/classification/isolation &amp; purification/metabolism ; *Geologic Sediments/microbiology ; Metagenomics ; Metagenome ; Mining ; Phylogeny ; Acids ; Phylogeography ; }, abstract = {Recent genomic surveys have uncovered candidate phyla radiation (CPR) bacteria and DPANN archaea as major microbial dark matter lineages in various anoxic habitats. Despite their extraordinary diversity, the biogeographic patterns and ecological implications of these ultra-small and putatively symbiotic microorganisms have remained elusive. Here, we performed metagenomic sequencing on 90 geochemically diverse acid mine drainage sediments sampled across southeast China and recovered 282 CPR and 189 DPANN nonredundant metagenome-assembled genomes, which collectively account for up to 28.6% and 31.2% of the indigenous prokaryotic communities, respectively. We found that, remarkably, geographic distance represents the primary factor driving the large-scale ecological distribution of both CPR and DPANN organisms, followed by pH and Fe. Although both groups might be capable of iron reduction through a flavin-based extracellular electron transfer mechanism, significant differences are found in their metabolic capabilities (with complex carbon degradation and chitin degradation being more prevalent in CPR whereas fermentation and acetate production being enriched in DPANN), indicating potential niche differentiation. Predicted hosts are mainly Acidobacteriota, Bacteroidota, and Proteobacteria for CPR and Thermoplasmatota for DPANN, and extensive, unbalanced metabolic exchanges between these symbionts and putative hosts are displayed. Together, our results provide initial insights into the complex interplays between the two lineages and their physicochemical environments and host populations at a large geographic scale.IMPORTANCECandidate phyla radiation (CPR) bacteria and DPANN archaea constitute a significant fraction of Earth's prokaryotic diversity. Despite their ubiquity and abundance, especially in anoxic habitats, we know little about the community patterns and ecological drivers of these ultra-small, putatively episymbiotic microorganisms across geographic ranges. This study is facilitated by a large collection of CPR and DPANN metagenome-assembled genomes recovered from the metagenomes of 90 sediments sampled from geochemically diverse acid mine drainage (AMD) environments across southeast China. Our comprehensive analyses have allowed first insights into the biogeographic patterns and functional differentiation of these major enigmatic prokaryotic groups in the AMD model system.}, }
@article {pmid40297467, year = {2025}, author = {Deep, A and Sieber, G and Boden, L and David, GM and Baikova, D and Buchner, D and Starke, J and Stach, TL and Reinders, T and Hadžiomerović, U and Beszteri, S and Probst, AJ and Boenigk, J and Beisser, D}, title = {A metatranscriptomic exploration of fungal and bacterial contributions to allochthonous leaf litter decomposition in the streambed.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19120}, pmid = {40297467}, issn = {2167-8359}, mesh = {*Plant Leaves/metabolism/microbiology ; *Bacteria/genetics/metabolism ; *Fungi/genetics/metabolism ; *Rivers/microbiology ; Ecosystem ; Alnus ; Transcriptome ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The decomposition of organic matter is essential for sustaining the health of freshwater ecosystems by enabling nutrient recycling, sustaining food webs, and shaping habitat conditions, which collectively enhance ecosystem resilience and productivity. Bacteria and fungi play a crucial role in this process by breaking down coarse particulate organic matter (CPOM), such as leaf litter, into nutrients available for other organisms. However, the specific contribution of bacteria and their functional interactions with fungi in freshwater sediments have yet to be thoroughly explored. In the following study, we enriched organic matter through the addition of alder (Alnus glutinosa) leaves into artificial stream channels (AquaFlow mesocosms). We then investigated enzyme expression, metabolic pathways, and community composition of fungi and bacteria involved in the degradation of CPOM through metatranscriptomics and amplicon sequencing. Enzymes involved in the degradation of lignin, cellulose, and hemicellulose were selectively upregulated with increased organic matter. Analysis of ITS and 16S rRNA gene sequences revealed that during decomposition, fungal communities were predominantly composed of Basidiomycota and Ascomycota, while bacterial communities were largely dominated by Pseudomonadota and Bacteroidota. The similar gene expression patterns of CPOM degradation related enzymes observed between bacteria and fungi indicate potential functional interaction between these microbial groups. This correlation in enzyme expression may indicate that bacteria and fungi are jointly involved in the breakdown of coarse particulate organic matter, potentially through mutualistic interaction. This study uncovers the specific enzymatic activities of bacteria and fungi and the importance of microbial interactions in organic matter decomposition, revealing their central role in facilitating nutrient cycling and maintaining the ecological health and stability of freshwater ecosystems.}, }
@article {pmid40294427, year = {2025}, author = {Ran, X and Wang, T and Zhou, M and Li, Z and Wang, H and Tsybekmitova, GT and Guo, J and Wang, Y}, title = {A Novel Perspective on the Instability of Mainstream Partial Nitrification: The Niche Differentiation of Nitrifying Guilds.}, journal = {Environmental science &amp; technology}, volume = {59}, number = {18}, pages = {8922-8938}, doi = {10.1021/acs.est.5c01214}, pmid = {40294427}, issn = {1520-5851}, mesh = {*Nitrification ; Bacteria/metabolism ; Nitrogen ; Wastewater ; Nitrites/metabolism ; Ammonia/metabolism ; }, abstract = {Short-cut biological nitrogen removal (sBNR) favors the paradigm shift toward energy-positive and carbon-neutral wastewater treatment processes. Partial nitrification (PN) is a key approach to provide nitrite for anammox or denitritation during sBNR, and its stability is the precondition for achieving robust nitrogen removal performance. However, maintaining a stable mainstream PN process has been a long-standing challenge. This review analyzes the mainstream PN process from a microbial ecology perspective, focusing on the niche differentiation among nitrifiers. First, we propose that mainstream PN systems are ecologically unstable, and the failure of the mainstream PN process due to the reactivation of nitrite-oxidizing bacteria (NOB) can be regarded as a behavior to restore system stabilization. Thus, maintaining mainstream PN systems primarily relies on enhancing the niche differentiation between ammonia-oxidizing bacteria (AOB) and NOB. We then summarize the realized niches of indigenous nitrifiers within nitrification systems and discuss their ecophysiological characteristics (e.g., cell structure and substrate affinity) that define their specific ecological niches. By comparing the niche breadths of AOB and NOB on various niche axes, we further discuss their niche differentiation and identify the different responses of AOB (resistance) and NOB (resilience) to exogenous perturbations. Finally, we propose outlook for achieving a stable mainstream PN process through an ecological lens. This review provides ecological insights into the instability of the mainstream PN process, which is intended to guide the derivation of optimized strategies from a single-factor approach to integrated solutions.}, }
@article {pmid40294268, year = {2025}, author = {Sun, W and Wang, J and Wang, G and Jiang, L and Feng, W and Dang, S and Li, M and Jiao, S and Wei, G and Gu, J and Tiedje, JM and Qian, X}, title = {Exposure and health risks of livestock air resistomes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {18}, pages = {e2403866122}, pmid = {40294268}, issn = {1091-6490}, support = {42277412 and 42207463//NSF of China/ ; 2024RS-CXTD-68//Shaanxi Innovation Support Program/ ; }, mesh = {Animals ; *Livestock/microbiology ; Humans ; *Air Microbiology ; Anti-Bacterial Agents/pharmacology ; Farms ; Swine ; China ; Chickens ; *Drug Resistance, Microbial/genetics ; *Occupational Exposure ; *Drug Resistance, Bacterial/genetics ; Europe ; }, abstract = {Most of the global antibiotic consumption is by the livestock industry, making livestock farms a hotspot of antibiotic resistance genes (ARGs). Farm air poses direct ARG exposure to workers, but the health risks of air resistomes remain unclear. We evaluated the human exposure and health risks of air resistomes in pig and chicken farms and compared air resistomes in Chinese farms to those in European farms given their long-term restrictions on use of antibiotics in livestock. We found that livestock air was highly enriched in ARGs, with each cell harboring seven times more ARGs than urban air. The daily ARG inhalation of farm workers was equivalent to several years of ARG inhalation by urban residents. ARGs encoding resistance to last-resort antibiotics such as mcr-1 and tetX were detected in farm air, and tetX variants were prevalent in both Chinese and European farms. ARGs in livestock air were highly associated with mobile genetic elements, and conjugation experiments confirmed their cross-phyla transferability. The projected resistome risk of farm air was significantly higher than well-recognized ARG hotspots like air from hospitals, sewage treatment plants, and from animal manures. The diversity, abundance, and risk score of air resistomes in Chinese farms were significantly higher than those in European farms, suggesting that long-term restriction of antibiotic use mitigates antibiotic resistance in the livestock environment. Our results underscore the high exposure of farm workers to ARGs via farm air and highlight its role in ARG dissemination, supporting the importance of antibiotic stewardship practices in combating antibiotic resistance.}, }
@article {pmid40293502, year = {2025}, author = {Cao, X and Liu, H and Zhang, R and Wen, Y and Ma, L and Xu, Z and Wen, L and Zhuo, Y and Liu, D and Wang, L}, title = {Composition, Predicted Functions, and Co-occurrence Networks of Bacteria and Fungi in Hummock Wetlands of Northeastern Inner Mongolia, China.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {34}, pmid = {40293502}, issn = {1432-184X}, support = {YSS2021007//the Funds of Yinshanbeilu Grassland Eco-hydrology National Observation and Research Station/ ; 32160279, 32161143025, 31960249//the National Natural Science Funds, P.R. China/ ; 2022YFHH0017//Science and Technology Major Project of Inner Mongolia/ ; 2022EEDSKJZDZX010, 2022EEDSKJXM005//Ordos Science and Technology Plan/ ; }, mesh = {China ; *Wetlands ; *Soil Microbiology ; Soil/chemistry ; Ecosystem ; *Bacteria/classification/genetics/isolation &amp; purification ; *Fungi/classification/genetics/isolation &amp; purification ; }, abstract = {Wetland microhabitats, varying in water table position, pH, and biochemical properties, have been understudied in terms of their influence on soil microbial community structure. This study employed amplicon-based gene sequencing to investigate the responses of both fungal and bacterial communities to habitat changes in northeastern Inner Mongolia, China. The results showed that while α-diversity indices (Shannon and Chao1) did not significantly differ between hummocks and hollows, β-diversity analyses revealed distinct microbial community structures in these habitats. Bacterial communities were primarily influenced by soil pH, EC, and AP, whereas fungal communities were affected by pH, AKP, MBC, MBN, and AP. Bacterial interactions were predominant in hollows, whereas fungal interactions were predominant in hummocks. Hummocks significantly enhanced amino acid metabolism function, whereas hollows significantly increased the abundance of endophyte-litter saprotroph-soil saprotroph-undefined saprotroph. This study underscores the importance of habitats in regulating microbial networks and functions, thereby enhancing our understanding of the influence of microhabitats, such as hummocks, on wetland ecosystem structure and function.}, }
@article {pmid40287826, year = {2025}, author = {Gerhardt, K and Ruiz-Perez, CA and Rodriguez-R, LM and Jain, C and Tiedje, JM and Cole, JR and Konstantinidis, KT}, title = {FastAAI: efficient estimation of genome average amino acid identity and phylum-level relationships using tetramers of universal proteins.}, journal = {Nucleic acids research}, volume = {53}, number = {8}, pages = {}, pmid = {40287826}, issn = {1362-4962}, support = {DBI1356288NSF//NSF/ ; }, mesh = {Phylogeny ; *Genome, Bacterial ; *Software ; *Bacteria/genetics/classification ; *Amino Acids/genetics ; *Computational Biology/methods ; }, abstract = {Estimation of whole-genome relatedness and taxonomic identification are two important bioinformatics tasks in describing environmental or clinical microbiomes. The genome-aggregate Average Nucleotide Identity is routinely used to derive the relatedness of closely related (species level) microbial and viral genomes, but it is not appropriate for more divergent genomes. Average Amino-acid Identity (AAI) can be used in the latter cases, but no current AAI implementation can efficiently compare thousands of genomes. Here we present FastAAI, a tool that estimates whole-genome pairwise relatedness using shared tetramers of universal proteins in a matter of microseconds, providing a speedup of up to 5 orders of magnitude when compared with current methods for calculating AAI or alternative whole-genome metrics. Further, FastAAI resolves distantly related genomes related at the phylum level with comparable accuracy to the phylogeny of ribosomal RNA genes, substantially improving on a known limitation of current AAI implementations. Our analysis of the resulting AAI matrices also indicated that bacterial lineages predominantly evolve gradually, rather than showing bursts of diversification, and that AAI thresholds to define classes, orders, and families are generally elusive. Therefore, FastAAI uniquely expands the toolbox for microbiome analysis and allows it to scale to millions of genomes.}, }
@article {pmid40287775, year = {2025}, author = {Ren, H and Hong, H and Zha, B and Lamlom, SF and Qiu, H and Cao, Y and Sun, R and Wang, H and Ma, J and Zhang, H and Sun, L and Yang, Q and Zhou, C and Liu, X and Wang, X and Zhang, C and Zhang, F and Zhao, K and Yuan, R and Abdelghany, AM and Zhang, B and Zheng, Y and Wang, J and Lu, W}, title = {Soybean productivity can be enhanced by understanding rhizosphere microbiota: evidence from metagenomics analysis from diverse agroecosystems.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {105}, pmid = {40287775}, issn = {2049-2618}, mesh = {*Rhizosphere ; *Metagenomics/methods ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Glycine max/microbiology/growth &amp; development ; *Microbiota/genetics ; China ; Fungi/classification/genetics/isolation &amp; purification ; Plant Roots/microbiology ; Archaea/classification/genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: Microbial communities associated with roots play a crucial role in the growth and health of plants and are constantly influenced by plant development and alterations in the soil environment. Despite extensive rhizosphere microbiome research, studies examining multi-kingdom microbial variation across large-scale agricultural gradients remain limited.<br><br>RESULTS: This study investigates the rhizosphere microbial communities associated with soybean across 13 diverse geographical locations in China. Using high-throughput shotgun metagenomic sequencing on the BGISEQ T7 platform with 10 GB per sample, we identified a total of 43,337 microbial species encompassing bacteria, archaea, fungi, and viruses. Our analysis revealed significant site-specific variations in microbial diversity and community composition, underscoring the influence of local environmental factors on microbial ecology. Principal coordinate analysis (PCoA) indicated distinct clustering patterns of microbial communities, reflecting the unique environmental conditions and agricultural practices of each location. Network analysis identified 556 hub microbial taxa significantly correlated with soybean yield traits, with bacteria showing the strongest associations. These key microorganisms were found to be involved in critical nutrient cycling pathways, particularly in carbon oxidation, nitrogen fixation, phosphorus solubilization, and sulfur metabolism. Our findings demonstrate the pivotal roles of specific microbial taxa in enhancing nutrient cycling, promoting plant health, and improving soybean yield, with significant positive correlations (r&#x2009;= 0.5, p&#x2009;= 0.039) between microbial diversity and seed yield.<br><br>CONCLUSION: This study provides a comprehensive understanding of the diversity and functional potential of rhizosphere microbiota in enhancing soybean productivity. The findings underscore the importance of integrating microbial community dynamics into crop management strategies to optimize nutrient cycling, plant health, and yield. While this study identifies key microbial taxa with potential functional roles, future research should focus on isolating and validating these microorganisms for their bioremediation and biofertilization activities under field conditions. This will provide actionable insights for developing microbial-based agricultural interventions to improve crop resilience and sustainability. Video Abstract.}, }
@article {pmid40287657, year = {2025}, author = {De Maayer, P and Green, T and Jordan, S and Smits, THM and Coutinho, TA}, title = {Pan-genome analysis of the Enterobacter hormaechei complex highlights its genomic flexibility and pertinence as a multidrug resistant pathogen.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {408}, pmid = {40287657}, issn = {1471-2164}, support = {310030L_204333//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 310030L_204333//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 310030L_204333//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 310030L_204333//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 310030L_204333//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; }, mesh = {*Enterobacter/genetics/classification/drug effects/pathogenicity ; *Genome, Bacterial ; Phylogeny ; *Drug Resistance, Multiple, Bacterial/genetics ; *Genomics/methods ; Anti-Bacterial Agents/pharmacology ; DNA Transposable Elements ; Plasmids/genetics ; }, abstract = {BACKGROUND: Enterobacter hormaechei is of increasing concern as both an opportunistic and nosocomial pathogen, exacerbated by its evolving multidrug resistance. However, its taxonomy remains contentious, and little is known about its pathogenesis and the broader context of its resistome. In this study, a comprehensive comparative genomic analysis was undertaken to address these issues.<br><br>RESULTS: Phylogenomic analysis revealed that E. hormaechei represents a complex, comprising three predicted species, E. hormaechei, E. hoffmannii and E. xiangfangensis, with the latter putatively comprising three distinct subspecies, namely oharae, steigerwaltii and xiangfangensis. The species and subspecies all display open and distinct pan-genomes, with diversification driven by an array of mobile genetic elements including numerous plasmid replicons and prophages, integrative conjugative elements (ICE) and transposable elements. These elements have given rise to a broad, relatively conserved set of pathogenicity determinants, but also a variable set of secretion systems. The E. hormaechei complex displays a highly mutable resistome, with most taxa being multidrug resistant.<br><br>CONCLUSIONS: This study addressed key issues pertaining to the taxonomy of the E. hormaechei complex, which may contribute towards more accurate identification of strains belonging to this species complex in the clinical setting. The pathogenicity determinants identified in this study could serve as a basis for a deeper understanding of E. hormaechei complex pathogenesis and virulence. The extensive nature of multidrug resistance among E. hormaechei complex strains highlights the need for responsible antibiotic stewardship to ensure effective treatment of these emerging pathogens.}, }
@article {pmid40287646, year = {2025}, author = {He, L and Zou, Q and Wang, Y}, title = {metaTP: a meta-transcriptome data analysis pipeline with integrated automated workflows.}, journal = {BMC bioinformatics}, volume = {26}, number = {1}, pages = {111}, pmid = {40287646}, issn = {1471-2105}, support = {62102269//National Natural Science Foundation of China/ ; }, mesh = {*Metagenomics/methods ; Computational Biology/methods ; *Software ; *Gene Expression Profiling/methods ; *Microbiota ; Data Collection ; Quality Control ; Workflow ; RNA, Untranslated ; Molecular Sequence Annotation ; Rhizosphere ; Automation ; }, abstract = {BACKGROUND: The accessibility of sequencing technologies has enabled meta-transcriptomic studies to provide a deeper understanding of microbial ecology at the transcriptional level. Analyzing omics data involves multiple steps that require the use of various bioinformatics tools. With the increasing availability of public microbiome datasets, conducting meta-analyses can reveal new insights into microbiome activity. However, the reproducibility of data is often compromised due to variations in processing methods for sample omics data. Therefore, it is essential to develop efficient analytical workflows that ensure repeatability, reproducibility, and the traceability of results in microbiome research.<br><br>RESULTS: We developed metaTP, a pipeline that integrates bioinformatics tools for analyzing meta-transcriptomic data comprehensively. The pipeline includes quality control, non-coding RNA removal, transcript expression quantification, differential gene expression analysis, functional annotation, and co-expression network analysis. To quantify mRNA expression, we rely on reference indexes built using protein-coding sequences, which help overcome the limitations of database analysis. Additionally, metaTP provides a function for calculating the topological properties of gene co-expression networks, offering an intuitive explanation for correlated gene sets in high-dimensional datasets. The use of metaTP is anticipated to support researchers in addressing microbiota-related biological inquiries and improving the accessibility and interpretation of microbiota RNA-Seq data.<br><br>CONCLUSIONS: We have created a conda package to integrate the tools into our pipeline, making it a flexible and versatile tool for handling meta-transcriptomic sequencing data. The metaTP pipeline is freely available at: https://github.com/nanbei45/metaTP .}, }
@article {pmid40287414, year = {2025}, author = {Bull, F and Tavaddod, S and Bommer, N and Perry, M and Brackley, CA and Allen, RJ}, title = {Different factors control long-term versus short-term outcomes for bacterial colonisation of a urinary catheter.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {3940}, pmid = {40287414}, issn = {2041-1723}, support = {682237 EVOSTRUC//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council(H2020 Excellent Science - European Research Council)/ ; EXC 2051 - Project-ID 390713860//Deutsche Forschungsgemeinschaft(German Research Foundation)/ ; EP/L015110/1//RCUK | Engineering and Physical Sciences Research Council(EPSRC)/ ; }, mesh = {*Urinary Catheters/microbiology/adverse effects ; Humans ; *Urinary Tract Infections/microbiology/prevention &amp; control/etiology ; *Catheter-Related Infections/microbiology/prevention &amp; control ; *Urinary Catheterization/adverse effects ; Computer Simulation ; *Bacteria/growth &amp; development ; Urinary Bladder/microbiology ; Models, Theoretical ; Models, Biological ; Time Factors ; }, abstract = {Urinary catheters are used extensively in hospitals and long-term care and they are highly prone to infection. Understanding the pathways by which bacteria colonise a urinary catheter could guide strategies to mitigate infection, but quantitative models for this colonisation process are lacking. Here we present a mathematical model for bacterial colonisation of a urinary catheter that integrates population dynamics and fluid dynamics. The model describes bacteria migrating up the outside surface of the catheter, spreading into the bladder and being swept through the catheter lumen. Computer simulations of the model reveal that clinical outcomes for long-term versus short-term catheterisation are controlled by different factors: the rate of urine production by the kidneys as opposed to urethral length, catheter surface properties and bacterial motility. Our work may help explain variable susceptibility to catheter-associated urinary tract infection (CAUTI) among individuals and the mixed success of antimicrobial surface coatings. Our model suggests that for long-term catheterised patients, increasing fluid intake or reducing residual urine volume in the bladder may help prevent infection, while antimicrobial surface coatings are predicted to be effective only for short-term catheterised patients. Therefore, different catheter management strategies could be rationally targeted to long-term vs short-term catheterised patients.}, }
@article {pmid40286617, year = {2025}, author = {Kang, S and Lee, JY and Natsagdorj, A and Matsuki, A and Cho, KS}, title = {Functional adaptation of PM2.5 microbiomes to varying environmental conditions in Northeast Asia: Ulaanbaatar, Seoul, and Noto.}, journal = {The Science of the total environment}, volume = {979}, number = {}, pages = {179495}, doi = {10.1016/j.scitotenv.2025.179495}, pmid = {40286617}, issn = {1879-1026}, mesh = {*Particulate Matter/analysis ; *Microbiota ; *Environmental Monitoring ; *Air Pollutants/analysis ; Fungi ; Bacteria ; *Air Microbiology ; Seoul ; }, abstract = {This study examined the bacterial and fungal communities associated with PM2.5 collected from three geographically distinct locations in Northeast Asia-Ulaanbaatar (high pollution), Seoul (moderate pollution), and Noto (low pollution)-which collectively represent a gradient of urbanization and environmental conditions during the spring sampling period from March 15 to April 7, 2022. Ulaanbaatar exhibited the highest abundance of both bacteria and fungi, yet exhibited the lowest fungal diversity. In contrast, Noto exhibited the lowest microbial abundance but the highest fungal diversity, while Seoul displayed intermediate values. Dominant bacterial genera, including Caldalkalibacillus, Halomonas, and Nesterenkonia, demonstrated notable resilience across all three locations, highlighting their adaptability to diverse environmental conditions. The dominant fungal genera were Cladosporium and Candida. Analyses revealed significant correlations between microbial community structures and environmental factors. In Ulaanbaatar, microbial communities were strongly associated with meteorological parameters such as temperature, humidity, and wind speed. In Seoul, stronger correlations were observed with polycyclic aromatic hydrocarbons (PAHs). Noto exhibited weaker correlations with both meteorological factors and organic compounds. Across all sites, bacteria consistently showed broader niche breadths compared to fungi, reflecting their greater metabolic versatility and resource utilization capacity. Both bacterial and fungal niche breadths generally increased at intermediate concentrations of alkanes and DCAs but declined at extreme concentrations, suggesting optimal survival ranges. These findings highlight the complex interplay of environmental factors and pollutants in shaping microbial community structures and functional diversity across diverse geographical settings during the spring season.}, }
@article {pmid40285533, year = {2025}, author = {Liao, X and Wang, H and Wu, D and Grossart, HP and Yang, X and Li, L and Wang, Y and Li, S and Li, J and Cao, M and Chen, N and Hu, A}, title = {Geographical and Environmental Factors Differentially Shape Planktonic Microbial Community Assembly and Resistomes Composition in Urban Rivers.}, journal = {Global change biology}, volume = {31}, number = {4}, pages = {e70211}, doi = {10.1111/gcb.70211}, pmid = {40285533}, issn = {1365-2486}, support = {//the Ocean Negative Carbon Emissions (ONCE) Program/ ; 2021QZKK0103//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; 2019QZKK0503//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; 2023YFC3804904//National Key Research and Development Program/ ; }, mesh = {*Microbiota ; *Plankton ; China ; *Rivers/microbiology ; Bacteria/genetics/drug effects ; Urbanization ; }, abstract = {Global urbanization accelerates pollution challenges in urban rivers, including increased transmission of bacterial antibiotic resistance genes (ARGs), severely threatening the health of aquatic ecosystems and human health. Yet, systematic knowledge of differences in distribution and community assembly patterns of bacterial resistance across urban rivers at a continental scale is still insufficient. In this study, we conducted extensive sampling in nine representative urban rivers across China. We used amplicon and shotgun metagenomic sequencing, state-of-the-art bioinformatics, and multivariate statistics to investigate distribution patterns and community assembly mechanisms of planktonic microbiomes (i.e., bacterioplankton and planktonic microeukaryotes), including their resistomes, i.e., ARGs and metal resistance genes (MRGs). Geographical and environmental factors played a pivotal role in shaping distribution patterns of planktonic microbiomes vs. resistomes in the studied urban rivers. Phylogenetic-bin-based null model analysis (iCAMP) indicated that planktonic microbiomes, dominated by dispersal limitation and drift, tend toward spatial heterogeneity. In contrast, planktonic resistomes, driven by deterministic processes, display more similar distribution patterns. Cross-validated Mantel tests revealed that geographical factors (i.e., geographic distance) were the primary regulators of planktonic microbial community assembly, while environmental factors (i.e., temperature) control assembly processes of planktonic resistomes. Our findings provide crucial insights into the mechanisms driving the biogeographical distribution and community assembly of planktonic microbial entities in urban rivers at a continental scale, offering valuable implications for mitigating and managing the spread of ARGs from the environment to humans.}, }
@article {pmid40284744, year = {2025}, author = {Yahya, R and Albaqami, A and Alzahrani, A and Althubaiti, SM and Alhariri, M and Alrashidi, ET and Alhazmi, N and Al-Matary, MA and Alharbi, N}, title = {Comprehensive Genomic Analysis of Klebsiella pneumoniae and Its Temperate N-15-like Phage: From Isolation to Functional Annotation.}, journal = {Microorganisms}, volume = {13}, number = {4}, pages = {}, pmid = {40284744}, issn = {2076-2607}, support = {NRC21R/053/02//King Abdullah International Medical Research Center/ ; }, abstract = {Antibiotic resistance to Klebsiella pneumoniae poses a major public health threat, particularly in intensive care unit (ICU) settings. The emergence of extensively drug-resistant (XDR) strains complicates treatment options, requiring a deeper understanding of their genetic makeup and potential therapeutic targets. This research delineated an extensively drug-resistant (XDR) Klebsiella pneumoniae strain obtained from an ICU patient and telomeric temperate phage derived from hospital effluent. The bacteria showed strong resistance to multiple antibiotics, including penicillin (≥16 μg/mL), ceftriaxone (≥32 μg/mL), and meropenem (≥8 μg/mL), which was caused by SHV-11 beta-lactamase, NDM-1 carbapenemase, and porin mutations (OmpK37, MdtQ). The strain was categorized as K46 and O2a types and carried virulence genes involved in iron acquisition, adhesion, and immune evasion, as well as plasmids (IncHI1B_1_pNDM-MAR, IncFIB) and eleven prophage regions, reflecting its genetic adaptability and resistance dissemination. The 172,025 bp linear genome and 46.3% GC content of the N-15-like phage showed strong genomic similarities to phages of the Sugarlandvirus genus, especially those that infect K. pneumoniae. There were structural proteins (11.8%), DNA replication and repair enzymes (9.3%), and a toxin-antitoxin system (0.4%) encoded by the phage genome. A protelomerase and ParA/B partitioning proteins indicate that the phage is replicating and maintaining itself in a manner similar to the N15 phage, which is renowned for maintaining a linear plasmid prophage throughout lysogeny. Understanding the dynamics of antibiotic resistance and pathogen development requires knowledge of phages like this one, which are known for their temperate nature and their function in altering bacterial virulence and resistance profiles. The regulatory and structural proteins of the phage also provide a model for research into the biology of temperate phages and their effects on microbial communities. The importance of temperate phages in bacterial genomes and their function in the larger framework of microbial ecology and evolution is emphasized in this research.}, }
@article {pmid40284675, year = {2025}, author = {Li, M and Liu, X and Chen, W and Xu, H and Huang, F and Yao, Q and Jia, X and Huang, Y}, title = {Alleviating Effect of Lactiplantibacillus plantarum HYY-S10 on Colitis in Mice Based on an Analysis of the Immune Axis in the Intestine.}, journal = {Microorganisms}, volume = {13}, number = {4}, pages = {}, pmid = {40284675}, issn = {2076-2607}, support = {32302242//the National Natural Science Foundation of China/ ; 2022A1515110426//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2023B0202040002//Guangdong Provincial Key Research and Development Program/ ; 2022B1212010015//Key Laboratory Project of Guangdong Province/ ; }, abstract = {The pathogenesis of ulcerative colitis (UC) has been fundamentally associated with intestinal microbiota dysbiosis and disruption of immune homeostasis. This study systematically investigates the therapeutic potential of Lactiplantibacillus plantarum HYY-S10 (HYY-S10), a novel strain isolated from De'ang sour tea in Yun an, China, with a focus on its mechanisms for alleviating colitis through the modulation of gut microbiota. Using a dextran sulfate sodium (DSS)-induced colitis model in C57BL/6J mice, our findings demonstrated that seven days of oral supplementation with HYY-S10 (1 × 10[8] CFU/mL, 0.2 mL/10 g body weight) significantly improved Disease Activity Index (DAI) scores and attenuated characteristic colitis symptoms, including progressive weight loss, rectal bleeding, and abnormal stool consistency. Administration of HYY-S10 exhibited significant immunomodulatory effects characterized by the downregulation of pro-inflammatory mediators (such as IL-1β, IL-6, IFN-γ, and LPS) while concomitantly upregulating anti-inflammatory IL-10 expression. Additionally, the strain enhanced intestinal antioxidant capacity by increasing GSH-Px activity, which collectively contributed to the reduction in intestinal inflammation. Furthermore, HYY-S10 demonstrated multifaceted protective effects by ameliorating oxidative stress through the restoration of redox homeostasis and modulation of gut microbial ecology. Probiotic intervention significantly increased short-chain fatty acids (SCFAs) production and notably enhanced the relative abundance of beneficial taxa, including Akkermansia and Ruminococcus_B, while restoring microbial diversity and ecological stability. Collectively, our results demonstrate that HYY-S10 alleviates experimental colitis by modulating the intestinal immune axis and microbiota composition, providing mechanistic insights to support its potential as a probiotic-based therapeutic strategy for UC.}, }
@article {pmid40284595, year = {2025}, author = {Frazier, AN and Willis, W and Robbe, H and Ortiz, A and Koziel, JA}, title = {Characterization and Assembly Dynamics of the Microbiome Associated with Swine Anaerobic Lagoon Manure Treated with Biochar.}, journal = {Microorganisms}, volume = {13}, number = {4}, pages = {}, pmid = {40284595}, issn = {2076-2607}, support = {3090-31630-006//USDA-ARS CRIS/ ; }, abstract = {Biochar has significant potential for livestock microbiomes and crop agriculture regarding greenhouse gas emissions reduction. Therefore, a pilot study was designed to investigate the effect of biochar application on the surface of swine manure from an open lagoon and the associated microbial communities. Samples were collected from four different treatment groups: control (n = 4), coarse biochar (n = 4), fine biochar (n = 4), and ultra-fine biochar (n = 4). Additionally, aged manure in bulk was collected (n = 4) to assess alterations from the control group. The method of 16S rRNA amplicon sequencing along with microbial analyses was performed. Diversity was significantly different between aged manure in bulk samples and all treatment groups (Kruskal-Wallis; p < 0.05). Additionally, distinct community compositions were seen using both weighted and unweighted UniFrac distance matrices (PERMANOVA; p < 0.01). Differential abundance analysis revealed four distinct features within all treatment groups that were enriched (q < 0.001): Idiomarina spp., Geovibrio thiophilus, Parapusillimonas granuli, and an uncultured Gammaproteobacteria species. Similarly, Comamonas spp. and Brumimicrobium aurantiacum (q-value < 0.001) were significantly depleted by all the treatments. Stochastic and functional analyses revealed that biochar treatments were not deterministically altering assembly patterns, and functional redundancy was evident regardless of compositional shifts.}, }
@article {pmid40280843, year = {2025}, author = {Araujo, ASF and Pereira, APA and de Medeiros, EV and Mendes, LW}, title = {Plant-microbe interactions: plants modulating their defenses.}, journal = {Trends in plant science}, volume = {30}, number = {8}, pages = {806-808}, doi = {10.1016/j.tplants.2025.04.001}, pmid = {40280843}, issn = {1878-4372}, mesh = {Gene Expression Regulation, Plant ; Host-Pathogen Interactions ; *Plant Diseases/microbiology/immunology ; *Plant Immunity/genetics ; *Plants/microbiology/immunology/genetics ; }, abstract = {Plant immunity is mediated by multiple factors, including microbial interactions and gene expression. Keppler et al. identified a set of microbe-responsive genes (general non-self response genes) whose expression or products affect bacterial strain abundance and enhance immunity. We explore how these genes shape alternative plant defense strategies for sustainable agriculture.}, }
@article {pmid40280003, year = {2025}, author = {Cholet, F and Vignola, M and Quinn, D and Ijaz, UZ and Sloan, WT and Smith, CJ}, title = {Microbial ecology of drinking water biofiltration based on 16S rRNA sequencing: A meta-analysis.}, journal = {Water research}, volume = {281}, number = {}, pages = {123684}, doi = {10.1016/j.watres.2025.123684}, pmid = {40280003}, issn = {1879-2448}, mesh = {*Filtration ; *RNA, Ribosomal, 16S/genetics ; *Water Purification/methods ; *Drinking Water/microbiology ; Microbiota ; }, abstract = {Biofiltration, a sustainable water treatment technology relying on microbial processes to remove contaminants, offers a promising approach to achieving the United Nations Sustainable Goal 6 of universal access to clean water and sanitation by 2030. However, a key barrier to optimising biofiltration is the incomplete understanding of the biological mechanisms governing its performance. Despite numerous studies examining how engineering decisions impact biofilter performance and the associated microbiome, the significant influence of geographical location on microbial communities raises the question of whether these findings are universally applicable or location-specific. To address this, we conducted a meta-analysis of 15 biofilter microbiomes using 16S rRNA high-throughput sequencing (HTS) data, mainly originating from rapid gravity and/or granular activated carbon (GAC) filters. Despite different types and scales, results highlight geographical location as the major contributor to microbiome dissimilarity in biofilter samples (Top and Bottom) (R[2]∼ 0.5; p-value<0.001). The same was observed for influent waters (PERMANOVA R[2]= 0.76; p-value<0.001), indicating location-specific microbiomes as opposed to differences driven by different biofilter operating parameters. Irrespective of location, the higher percentage of the microbiome was assembled through deterministic processes (∼55 %) compared to stochastic processes (∼45 %). Finally, our findings suggest that the depth stratification of biofilter microbiomes may be associated with the enrichment of taxa capable of metabolising more complex organic carbon in deeper filter layers (10 enriched pathways in biofilter Bottom layers compared to 3 at the Top). These insights provide a broader understanding of biofiltration microbiomes and offer possible research avenues for targeted and effective biofilter design strategies.}, }
@article {pmid40279085, year = {2025}, author = {Zheng, F and Zhao, J and Yuan, Z and Gao, Y and Li, Y and Li, Y and Geng, Y and Qiang, Y}, title = {Interpretable drug-target affinity prediction based on pre-trained models' output as embeddings and based on structure-aware cross-attention for feature fusion.}, journal = {Molecular diversity}, volume = {29}, number = {4}, pages = {3537-3554}, pmid = {40279085}, issn = {1573-501X}, support = {U21A20469//National Natural Science Foundation of China/ ; 82170716//National Natural Science Foundation of China/ ; 62376183//National Natural Science Foundation of China/ ; 202304051001009//the special fund for Science and Technology Innovation Teams of Shanxi Province/ ; 2020-PT320-005//National Health Commission Key Laboratory of Pneumoconiosis/ ; }, mesh = {*Proteins/chemistry/metabolism ; Models, Molecular ; Protein Binding ; Software ; }, abstract = {The characteristics of protein pockets can better capture the interaction information between proteins and small molecules, thereby improving the performance of drug-target interaction (DTI) prediction tasks. However, pocket data typically need to be predicted using software such as AlphaFold, which would entail a massive workload for datasets ranging from tens of thousands to hundreds of thousands of samples. Moreover, feature representation networks for 3D pocket data are computationally intensive. To address this, we propose simulating 3D pocket data using sequence data through feature fusion of two different objects based on structure cross-attention (CASD). Additionally, precise feature representation is a prerequisite for accurately identifying pocket information. We introduce a method that leverages the output of the last layer of a pre-trained model as an embedding layer for training a new model from scratch. This approach not only incorporates prior knowledge from the pre-trained model but also expands model capacity, enabling more accurate feature representation. Furthermore, we enhance the multimodal representation of small molecule compounds using feature fusion based on structure cross-attention for the same object (CASS), further improving feature representation capabilities. Our cross-attention mechanisms operate at the token-level or node-level, allowing fine-grained capture of interactions between amino acids and atoms. This enables the identification of the contribution score of each atom or amino acid to the task, making our model interpretable for drug-target prediction. Experimental validation demonstrates that our model achieves state-of-the-art predictive performance.}, }
@article {pmid40277367, year = {2025}, author = {Thapa, BS and Flynn, TM and Jensvold, ZD and Kemner, KM and Sladek, MF and O'Loughlin, EJ and Marshall, CW}, title = {Effects of soluble electron shuttles on microbial iron reduction and methanogenesis.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {5}, pages = {e0222224}, pmid = {40277367}, issn = {1098-5336}, support = {DE-AC02-06CH11357//U.S. Department of Energy (DOE)/ ; }, mesh = {Oxidation-Reduction ; *Iron/metabolism ; *Methane/metabolism ; *Bacteria/metabolism/classification/genetics ; Electron Transport ; Electrons ; Quinones/metabolism ; Acetates/metabolism ; Riboflavin/metabolism ; Archaea/metabolism ; Microbiota ; }, abstract = {In many aquatic and terrestrial ecosystems, iron (Fe) reduction by microorganisms is a key part of biogeochemical cycling and energy flux. The presence of redox-active electron shuttles in the environment potentially enables a phylogenetically diverse group of microbes to use insoluble iron as a terminal electron acceptor. We investigated the impact that different electron shuttles had on respiration, microbial physiology, and microbial ecology. We tested eight different electron shuttles, seven quinones and riboflavin, with redox potentials between 0.217 and -0.340 V. Fe(III) reduction coupled with acetate oxidation was observed with all shuttles. Once Fe(III) reduction began to plateau, a rapid increase in acetate consumption was observed and coincided with the onset of methane production, except in the incubations with the shuttle 9,10-anthraquinone-2-carboxylic acid (AQC). The rates of iron reduction, acetate consumption, methanogenesis, and the microbial communities varied significantly across the different shuttles independent of redox potential. In general, shuttles appeared to reduce the overall diversity of the community compared to no shuttle controls, but certain shuttles were exceptions to this trend. Geobacteraceae were the predominant taxonomic family in all enrichments except in the presence of AQC or 1,2-dihydroxyanthraquinone (AQZ), but each shuttle enriched a unique community significantly different from the no shuttle control conditions. This suggests that the presence of different redox-active electron shuttles can have a large influence on the microbial ecology and total carbon flux in the environment.IMPORTANCEIron is the fourth most abundant element in the Earth's crust, and the reduction of iron by microbes is an important component of global biogeochemical cycles. A phylogenetically diverse group of microbes is capable of conserving energy with oxidized iron as a terminal electron acceptor, but the environmental conditions favoring certain taxonomic clades in iron-reducing environments are unclear. One complicating factor often overlooked in small-scale enrichments is the influence of soluble, redox-active electron shuttles on the rate and microbial ecology of iron reduction. We tested the effects of eight different electron shuttles on microbial physiology and ecology in iron-reducing enrichments derived from a local wetland. Each electron shuttle varied the microbial activity and enriched for a microbial community distinct from the no shuttle control condition. Therefore, in complex subsurface environments with many redox-active compounds present, we propose electron shuttles as a reason for the coexistence of multiple clades of iron-reducing bacteria.}, }
@article {pmid40277363, year = {2025}, author = {Wang, Y and Yang, L and Wu, W and Feng, Z and He, J and Guo, C and He, J}, title = {Bacillus haimaensis sp. nov.: a novel cold seep-adapted bacterium with unique biosynthetic potential.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {5}, pages = {e0245624}, pmid = {40277363}, issn = {1098-5336}, support = {No. 2022B1111030001//Guangdong key Research and Developement program/ ; No. CARS-46//China Agricultural Research System/ ; No. 32473201//National Natural Science Foundation of China/ ; No. 2022YFE0203900//National Key Research and Development Program of China/ ; No. 2023A1515110395//Guangdong Province Basic and Applied Basic Research Found project/ ; No. 2024B1212040007//Science and Technology Plan Project of Guangdong Province/ ; }, mesh = {*Bacillus/genetics/classification/isolation &amp; purification/physiology/metabolism ; Phylogeny ; *Geologic Sediments/microbiology ; China ; Genome, Bacterial ; *Seawater/microbiology ; Cold Temperature ; Multigene Family ; RNA, Ribosomal, 16S/genetics ; Adaptation, Physiological ; }, abstract = {Deep-sea cold seeps harbor unique microbial communities that play crucial roles in biogeochemical cycles and possess potential biotechnological applications. Herein, we report the isolation, characterization, and genomic analysis of a novel Bacillus species, Bacillus haimaensis sp. nov. (type strain CSS-39[T], CCTCC M20241382), obtained from sediments collected at a depth of 1,350 m in the Haima cold seep, South China Sea. Phylogenomic analysis, revealing an average nucleotide identity of 87.78% and a digital DNA-DNA hybridization value of 34.0% with its closest relative B. tianshenii DSM 25879[T], confirms the taxonomic novelty of the genus Bacillus. The complete 4.54 Mb genome of B. haimaensis reveals adaptations to the cold seep environment, including enhanced nutrient acquisition capabilities and stress response mechanisms. Comparative genomic analysis identifies 27 unique gene clusters related to spore germination and sulfate assimilation, suggesting specialized metabolic strategies for this extreme habitat. Furthermore, six biosynthetic gene clusters, including a novel lassopeptide cluster, indicate a potential for secondary metabolite production. Phenotypic characterization demonstrates the strain's ability to utilize diverse carbon sources and tolerate a wide range of environmental conditions. Our findings provide insights into microbial adaptations to deep-sea cold seeps and highlight the potential of B. haimaensis for biotechnological applications in bioremediation and natural product discovery. This study expands our understanding of microbial diversity in extreme marine environments and offers a new model bacterium for investigating bacterial adaptations to deep-sea ecosystems.IMPORTANCEThe discovery of Bacillus haimaensis sp. nov. in the Haima cold seep of the South China Sea represents a significant advancement in our understanding of microbial adaptations to extreme marine environments. This novel species exhibits remarkable metabolic versatility and unique genomic features, providing insights into bacterial survival strategies in nutrient-variable, high-pressure deep-sea ecosystems. Comprehensive genomic analysis reveals distinctive biosynthetic gene clusters, suggesting untapped potential for discovering novel natural product. Furthermore, B. haimaensis exhibits promising capabilities for aromatic compound degradation, indicating potential applications in marine bioremediation. This work not only expands our knowledge of microbial diversity in understudied deep-sea habitats but also highlights the biotechnological promise of extremophiles. The adaptive mechanisms elucidated in B. haimaensis, particularly those related to sporulation and sulfate assimilation, contribute to our broader understanding of microbial ecology in cold seeps and may inform future research on climate change impacts on deep-sea ecosystems.}, }
@article {pmid40276016, year = {2025}, author = {Papazlatani, C and Wagner, A and Chen, Z and Zweers, H and de Boer, W and Garbeva, P}, title = {Enhancement of production of pathogen-suppressing volatiles using amino acids.}, journal = {Current research in microbial sciences}, volume = {8}, number = {}, pages = {100385}, pmid = {40276016}, issn = {2666-5174}, abstract = {Bacterial volatile organic compounds can play a significant role in antagonistic interactions. Enhancing the production of bacterial volatiles that suppress the growth of soil-borne phytopathogenic fungi, has perspective as a sustainable disease control strategy. In the present study, we explored the potential of stimulating Burkholderia AD24 and Paenibacillus AD87 to produce volatiles that suppress the growth of the plant pathogenic fungi Fusarium culmorum PV and Rhizoctonia solani AG2.2IIIb. We provided the bacterial strains with a mixture of amino acids that can serve as precursor molecules in metabolic routes leading to emission of suppressive bacterial volatiles. Only Burkholderia AD24 was stimulated to produce a volatile blend that led to higher suppression of both pathogens. Subsequent analysis of the volatile composition emitted by Burkholderia AD24 in the presence of amino acids, showed higher abundance of antifungal compounds, including sulfur compounds (DMDS), pyrazines (2,5-dimethyl pyrazine) and carbohydrates (3-methyl-1-butanol). Follow-up trials with single amino acids revealed a pathogen specific response effect. When Burkholderia AD24 was cultivated in the presence of glutamine and asparagine, the emitted volatile blend suppressed the growth of F. culmorum, whereas when cultivated in the presence of glycine, glutamine, arginine and lysine the volatile blend suppressed the growth of R. solani. Analysis of the volatile blend composition showed differences between the amino acid treatments. Our findings show that amino acid precursor molecules can stimulate the production of fungistatic volatiles but the sensitivity of the fungal pathogens to these bacterial volatiles varies. This should be considered in future application strategies.}, }
@article {pmid40275504, year = {2025}, author = {Ekemezie, SC and Davis, CC and Russo, MV and Carpenter, LP and Russell, AL}, title = {Pollen-microbe interactions in nectar weakly influence bee foraging behavior.}, journal = {Integrative and comparative biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/icb/icaf017}, pmid = {40275504}, issn = {1557-7023}, abstract = {Plant-pollinator interactions are frequently affected by microbes that grow on flowers. Bacteria and yeast commonly grow within floral nectar, which is a sugar-rich floral reward often sought out by pollinators. Nectar is also commonly contaminated with protein-rich pollen. Microbes can induce this pollen to germinate or burst within the nectar, which potentially results in pollen nutrients being made available to nectar foraging pollinators. Yet whether pollen-microbe interactions in nectar impact pollinator behavior remains unknown. We therefore investigated how a common nectar yeast (Metschnikowia reukaufii) and bacteria (Acinetobacter nectaris) affected pollen germination and bursting within artificial nectar and effects on bumble bee (Bombus impatiens) foraging behavior. We found that both bacteria and yeast reduced the proportion of intact pollen in nectar, with bacteria inducing the most germination and bursting. Although microbes may thus potentially increase the quality of the nectar reward via increased access to pollen nutrients, we did not observe effects on bee flower preference. Similarly, bees did not show increased constancy (i.e., fidelity to one flower type across flower visits) to nectar contaminated with pollen and microbes. In contrast, bees were much more likely to reject flowers with nectar contaminated with pollen and yeast alone or together, relative to flowers that offered uncontaminated nectar. Altogether, our work suggests pollen-microbe interactions within nectar may have relatively minor influences on pollinator foraging behavior. We discuss possible explanations and implications of these results for plant and pollinator ecology.}, }
@article {pmid40273553, year = {2025}, author = {Ballan, D and Picot, A and Rolland, N and Bovo, C and Prévost, C and Coton, E and Mounier, J}, title = {Diversity of spoilage microorganisms associated with fresh fruits and vegetables in French households.}, journal = {International journal of food microbiology}, volume = {437}, number = {}, pages = {111204}, doi = {10.1016/j.ijfoodmicro.2025.111204}, pmid = {40273553}, issn = {1879-3460}, mesh = {*Vegetables/microbiology ; France ; *Fruit/microbiology ; *Bacteria/isolation &amp; purification/classification/genetics ; *Fungi/isolation &amp; purification/classification/genetics ; *Food Microbiology ; Family Characteristics ; Seasons ; Biodiversity ; Food Contamination/analysis ; }, abstract = {Food loss and waste generated throughout the food chain are major concerns in today's society. A high level of food waste occurs at the household's level and fresh fruit and vegetable (FFV) spoilage caused by microbial growth accounts for a large part of these losses. While numerous studies focused on spoilage microorganism diversity from primary production to distribution, little is known about those involved at the household level. In this context, this study aimed at investigating which FFV are usually wasted depending on the season and storage conditions at households, and identifying the microorganisms associated with spoiled FFV. During two periods (summer and autumn), 346 spoiled FFV samples were collected using a citizen science approach in 49 households in the Brest area (Finistère, Brittany, France). About three quarters of spoiled FFV collected originated from room temperature storage and 75 % were collected during summer. Among the studied samples, 75 % showed microbial growth after plating onto agar-based medium, and therefore, were likely spoiled because of microbial spoilage. Overall, 183 molds, 31 yeasts and 96 bacteria were isolated and identified using MALDI-TOF MS and sequencing. Among the 42 different mold species identified, Penicillium spp. were the most common representing more than 50 % of mold isolates followed by Botrytis (12.4 %), Mucor (8.6 %) and Cladosporium (7.6 %) spp. Hanseniaspora uvarum and Aureobasidium pullulans were the most prevalent yeast species while bacterial isolates showed the highest diversity of all identified organisms (49 species) with Pseudomonas spp., enterobacteria and lactic acid bacteria representing the most frequently isolated taxa. This study shows for the first time the microbial diversity associated with spoiled FFV of which a large proportion were stored at room temperature, suggesting that a better usage of FFV refrigeration could help reduce FFV waste in households.}, }
@article {pmid40270585, year = {2025}, author = {Zheng, Z and Gong, Z and Zhang, R and Lin, X and Hong, W and Song, L}, title = {Potential pathogens drive ARGs enrichment during biofilms formation on environmental surfaces.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf057}, pmid = {40270585}, issn = {2730-6151}, abstract = {The enrichment of antibiotic resistance genes (ARGs) on environmental surfaces is a fundamental question in microbial ecology. Understanding the processes driving ARG variations can provide clues into their transfer mechanisms between phases and offer insights for public health management. In this study, we examined microbiota, potential pathogen, and ARG dynamics on two common environment surfaces-polyvinyl chloride (PVC) and carbon steel (CS)-under environmental stress (induced by landfill leachate flow) in a Center for Disease Control and Prevention Biofilm Reactor using metagenomics and quantitative polymerase chain reaction-Chip techniques. Contrary to the expected changes in biofilms morphology and physiochemical properties, microbiota, potential pathogens, and ARGs exhibited a divergence-convergence pattern, primarily shaped by attachment surface properties and, subsequently, biofilm maturity during biofilms formation. During this process, ARG levels in biofilms gradually increased to and exceeded the levels in the surrounding environment, but with a distinct structure (P < .05). Furthermore, 1.93- and 3.05-fold increases in the concentrations of mobile genetic elements intI-1 in PVC and CS biofilms, respectively, suggested their important role in the transfer and spread of ARGs within the biofilm matrix. Although potential pathogens were less abundant (3.48%-5.63%) in the biofilms microbiota, they accounted for 18.28%-45.16% of the ARG hosts and harbored multiple ARGs. Pathogens significantly impacted ARG enrichment (Procrustes analysis: P = .0136, M[2] = 0.34) although microbiota development also influenced this process (P = .0385, M[2] = 0.67). These results suggest that pathogens are key in shaping ARG enrichment in biofilms. Our findings provide dynamic insights into resistome enrichment on environmental surfaces.}, }
@article {pmid40270532, year = {2025}, author = {Ma, J and Wang, M and Sun, Y and Zheng, Y and Lai, S and Zhang, Y and Wu, Y and Jiang, C and Shen, F}, title = {Cockroach Microbiome Disrupts Indoor Environmental Microbial Ecology with Potential Public Health Implications.}, journal = {Environment &amp; health (Washington, D.C.)}, volume = {3}, number = {4}, pages = {380-391}, pmid = {40270532}, issn = {2833-8278}, abstract = {Cockroaches pose a significant global public health concern. However, besides the well-recognized cockroach-induced allergy, the potential impact of the cockroach microbiome on human health through various means is not yet fully elucidated. This study aimed to clarify the health impacts of cockroaches by investigating the microbial interactions among cockroaches, the indoor environment, and humans. We simultaneously collected cockroach, indoor environment (indoor air and floor dust), and human (exhaled breath condensate and skin) samples from residential areas in five cities representing distinct climate zones in China. The 16S rDNA sequencing results revealed that cockroaches harbor diverse bacterial populations that vary across different cities. The prevalence of potential pathogenic bacteria (PPB) in cockroaches ranged from 1.1% to 58.9%, with dominant resistance genes conferring resistance to tetracycline, macrolide, and beta-lactam. The relationships between the cockroach microbiome and the associated environmental and human microbiomes were explored by using fast expectation-maximization microbial source tracking (FEAST). The potential contribution of cockroach bacteria to the floor dust-borne microbiome and indoor airborne microbiome was estimated to be 5.6% and 1.3%, respectively. Similarly, the potential contribution of cockroach PPB to the floor dust-borne microbiome and indoor airborne microbiome was calculated to be 4.0% and 1.2%, respectively. In residences with cockroach infestations, the contribution of other sources to the indoor environment was slightly increased. Collectively, the role of cockroaches in the transmission of microorganisms, particularly pathogenic bacteria and antibiotic resistance genes, cannot be overlooked.}, }
@article {pmid40268300, year = {2025}, author = {Goyal, A and Chure, G}, title = {Paradox of the Sub-Plankton: Plausible Mechanisms and Open Problems Underlying Strain-Level Diversity in Microbial Communities.}, journal = {Environmental microbiology}, volume = {27}, number = {4}, pages = {e70094}, pmid = {40268300}, issn = {1462-2920}, mesh = {*Biodiversity ; *Microbiota ; *Bacteria/genetics/classification ; Gene Transfer, Horizontal ; Genetic Variation ; Ecosystem ; Biological Evolution ; }, abstract = {Microbial communities are often complex and highly diverse, typically with dozens of species sharing spatially-restricted environments. Within these species, genetic and ecological variation often exists at a much finer scale, with closely related strains coexisting and competing. While the coexistence of strains in communities has been heavily explored over the past two decades, we have no self-consistent theory of how this diversity is maintained. This question challenges our conventional understanding of ecological coexistence, typically framed around species with clear phenotypic and ecological differences. In this review, we synthesise plausible mechanisms underlying strain-level diversity (termed microdiversity), focusing on niche-based mechanisms such as nutrient competition, neutral mechanisms such as migration, and evolutionary mechanisms such as horizontal gene transfer. We critically assess the strengths and caveats of these mechanisms, acknowledging key gaps that persist in linking genetic similarity to ecological divergence. Finally, we highlight how the origin and maintenance of microdiversity could pose a major challenge to conventional ecological thinking. We articulate a call-to-arms for a dialogue between well-designed experiments and new theoretical frameworks to address this grand conceptual challenge in understanding microbial biodiversity.}, }
@article {pmid40267173, year = {2025}, author = {Bull, CT and Salgado-Salazar, C and Romberg, MK and Allen, C and Kantor, M and Handoo, Z and Aboughanem-Sabanadzovic, N and Sabanadzovic, S and Coutinho, T}, title = {Plant Pathogen Name Game: Cross Kingdom Review for the Naming of Biotic Agents Associated with Plants.}, journal = {Annual review of phytopathology}, volume = {}, number = {}, pages = {}, doi = {10.1146/annurev-phyto-111424-090412}, pmid = {40267173}, issn = {1545-2107}, abstract = {To communicate across scientific disciplines, regulatory bodies, and the agricultural community, the naming of plant pathogens assigned to specific taxa is critical. Here, we provide an overview of the nomenclatural systems governing the naming of plant-pathogenic nematodes, fungi, oomycetes, prokaryotes, and viruses. Although we focus on the nature of the nomenclatural codes, we briefly discuss fundamental principles of taxonomy, including classification and identification. Key elements of the codes of nomenclature that ensure stability and clarity when naming species of pathogens are defined. When comparing the practice of nomenclature across different kingdoms, the classification and nomenclatural systems differ, and thus unique challenges are faced. We provide guidance from the codes and current practice for naming novel species. When there are nomenclatural conflicts, international committees play a critical role in their resolution. They also play a role in updating the codes to reflect new advancements in science. With this review, we aim to assist plant pathologists, journal editors, and those in related fields by providing an entrée to the legalistic requirements of the codes. Authors must consult and follow the rules of the appropriate code for any proposal of new or new combinations of names. To those interested in naming new species (or renaming the current ones), we recommend collaborations with experts in the field of taxonomy to ensure that rules for accurate and consistent naming practices and procedures are followed and to increase the likelihood that the proposed nomenclature is correct and acceptable.}, }
@article {pmid40266732, year = {2025}, author = {Duque-Granda, D and Vivero-Gómez, RJ and González Ceballos, LA and Junca, H and Duque, SR and Aroca Aguilera, MC and Castañeda-Espinosa, A and Cadavid-Restrepo, G and Gómez, GF and Moreno-Herrera, CX}, title = {Exploring the Diversity of Microbial Communities Associated with Two Anopheles Species During Dry Season in an Indigenous Community from the Colombian Amazon.}, journal = {Insects}, volume = {16}, number = {3}, pages = {}, pmid = {40266732}, issn = {2075-4450}, support = {Hermes 57545//Universidad Nacional de Colombia/ ; }, abstract = {Malaria disease affects millions of people annually, making the Amazon Basin a major hotspot in the Americas. While traditional control strategies rely on physical and chemical methods, the Anopheles microbiome offers a promising avenue for biological control, as certain bacteria can inhibit parasite development and alter vector immune and reproductive systems, disrupting the transmission cycle. For this reason, this study aimed to explore the bacterial communities in An. darlingi and An. triannulatus s.l., including breeding sites, immature stages, and adults from San Pedro de los Lagos (Leticia, Amazonas) through next-generation sequencing of the 16S rRNA gene. The results revealed a higher bacterial genus richness in the L1-L2 larvae of An. triannulatus s.l. Aeromonas and Enterobacter were prevalent in most samples, with abundances of 52.51% in L3-L4 larvae and 48.88% in pupae of An. triannulatus s.l., respectively. In breeding site water, Verrucomicrobiota bacteria were the most dominant (52.39%). We also identified Delftia (15.46%) in An. triannulatus s.l. pupae and Asaia (98.22%) in An. triannulatus, linked to Plasmodium inhibition, and Elizabethkingia, in low abundances, along with Klebsiella and Serratia, known for paratransgenesis potential. Considering the high bacterial diversity observed across the different mosquito life stages, identifying bacterial composition is the first step towards developing new strategies for malaria control. However, the specific roles of these bacteria in anophelines and the malaria transmission cycle remain to be elucidated.}, }
@article {pmid40266381, year = {2025}, author = {Cuny, MAC and Gloder, G and Bourne, ME and Kalisvaart, SN and Verreth, C and Crauwels, S and Cusumano, A and Lievens, B and Poelman, EH}, title = {Parasitoid Calyx Fluid and Venom Affect Bacterial Communities in Their Lepidopteran Host Labial Salivary Glands.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {33}, pmid = {40266381}, issn = {1432-184X}, support = {ALWOP.368//Netherlands Organization for Scientific Research/ ; ALWOP.368//Netherlands Organization for Scientific Research/ ; ALWOP.368//Netherlands Organization for Scientific Research/ ; ALWOP.368//Netherlands Organization for Scientific Research/ ; ALWOP.368//Netherlands Organization for Scientific Research/ ; G.0961.19 N//Flemish Fund for Scientific Research/ ; G.0961.19 N//Flemish Fund for Scientific Research/ ; G.0961.19 N//Flemish Fund for Scientific Research/ ; G.0961.19 N//Flemish Fund for Scientific Research/ ; }, mesh = {Animals ; *Salivary Glands/microbiology ; *Wasps/physiology ; *Bacteria/classification/genetics/isolation &amp; purification/drug effects ; *Microbiota ; Larva/parasitology/microbiology ; Host-Parasite Interactions ; *Butterflies/microbiology/parasitology ; Hemolymph/microbiology ; Polydnaviridae/physiology ; *Wasp Venoms/pharmacology ; *Moths/microbiology/parasitology ; }, abstract = {The influence of gut and gonad bacterial communities on insect physiology, behaviour, and ecology is increasingly recognised. Parasitism by parasitoid wasps alters many physiological processes in their hosts, including gut bacterial communities. However, it remains unclear whether these changes are restricted to the gut or also occur in other tissues and fluids, and the mechanisms underlying such changes are unknown. We hypothesise that host microbiome changes result from the injection of calyx fluid (that contain symbiotic viruses known as polydnaviruses) and venom during parasitoid oviposition and that these effects vary by host tissue. To test this, we microinjected Pieris brassicae caterpillars with calyx fluid and venom from Cotesia glomerata, using saline solution and natural parasitism by C. glomerata as controls. We analysed changes in the bacterial community composition in the gut, regurgitate, haemolymph, and labial salivary glands of the host insects. Multivariate analysis revealed distinct bacterial communities across tissues and fluids, with high diversity in the salivary glands and haemolymph. Parasitism and injection of calyx fluid and venom significantly altered bacterial communities in the salivary glands. Differential abundance analysis showed that parasitism affected bacterial relative abundance in the haemolymph, and that Wolbachia was only found in the haemolymph of parasitized caterpillars. Altogether, our findings reveal that parasitism influences the host haemolymph microbiome, and both parasitism and injection of calyx fluid and venom drive changes in the bacterial community composition within the host salivary glands. Given that the composition of salivary glands can influence plant response to herbivory, we discuss these results in the broader context of plant-parasitoid interactions.}, }
@article {pmid40262702, year = {2025}, author = {Zhang, S and Sun, C}, title = {Ecological divergence of marine bacteria Alteromonas mediterranea.}, journal = {Molecular phylogenetics and evolution}, volume = {208}, number = {}, pages = {108359}, doi = {10.1016/j.ympev.2025.108359}, pmid = {40262702}, issn = {1095-9513}, mesh = {*Phylogeny ; *Alteromonas/genetics/classification ; Ecosystem ; Evolution, Molecular ; Seawater/microbiology ; Sequence Analysis, DNA ; Gene Transfer, Horizontal ; Ecotype ; Phylogeography ; }, abstract = {Alteromonas mediterranea, originally designated as A. macleodii, is a deep-sea ecotype that plays an important ecological role in the ocean. However, a comprehensive understanding of their biogeographic distribution and evolutionary histories remains limited. In this study, our analysis indicated that A. mediterranea members could adapt contrasting marine ecosystems and flourish in nutrient-rich habitats such as feces and coral reefs. No significant correlations between the relative abundance of A. mediterranea members and the environmental variables were identified. Phylogenetic analysis and geographic patterns of A. mediterranea strains suggested that they could be clustered into two clades (clade Ⅰ and clade Ⅱ). In contrast, many distinct genomic traits exist between these clades, such as the complete genes encoding cytochrome o ubiquinol oxidase only involved in clade Ⅱ. Genes were more likely to be lost in the evolutionary history of A. mediterranea relatives. Gene loss might be a major force in all phylogenetic groups driving the distinct clades. Adaptation to different biotopes resulted in the functional differentiation of A. mediterranea members, with the loss of genes encoding carbohydrate-active enzymes. Genes acquired horizontally from unclassified bacteria, and Proteobacteria represented by Gammaproteobacteria played key roles in the functional diversification of A. mediterranea in marine habitats. Given these data, these results are useful for information supplementation of A. mediterranea strains, particularly for making significant advances in understanding marine microbial ecology within different clonal frames using genome-wide recruitments.}, }
@article {pmid40262432, year = {2025}, author = {Wu, G and Zhang, H and Huang, T and Song, Y and Liu, X and Liu, X and Wang, X and Pei, T and Xu, G and Wang, Z}, title = {Hydraulic and thermal performance trigger the deterministic assembly of water microbiomes: From biogeographical homogenization to machine learning model.}, journal = {Water research}, volume = {282}, number = {}, pages = {123626}, doi = {10.1016/j.watres.2025.123626}, pmid = {40262432}, issn = {1879-2448}, mesh = {*Machine Learning ; *Microbiota ; *Water Microbiology ; Temperature ; Drinking Water/microbiology ; Seasons ; }, abstract = {Water quality at the point of consumption has long been a health issue because of the potential for microbial ecology. However, research on water hydraulic performance remains in its infancy, and in particular, little is known about the effects of thermal performance during winter. This study explored the effects of stagnation and municipal heating on microbial communities in tap water, focusing on spatial and temporal variations in microbial community composition. The results revealed that stagnation significantly alters the microbial community, especially in heating areas, where the temperature exacerbates microbial growth. Furthermore, hydraulic and thermal performance drive deterministic assembly processes in microbial communities, as evidenced by the reductions in β-diversity, normalized stochasticity ratio (NST), and neutral community model (NCM) fit. Machine learning models revealed that stagnation time greater than 8 h results in increased community abundance because of longer exposure to organic matter and nutrients. The study finding illustrate the importance of environmental influences on microbial community dynamics, and provide valuable insights into the water microbial community, particularly in areas with prolonged stagnation.}, }
@article {pmid40261360, year = {2025}, author = {Cho, KH and Kwon, Y and Kasani, PH and Lee, SG and Jeong, SJ}, title = {Influence of Maternal Weight Dynamics Prior to and Throughout Gestation on Early Infant Gut Microbiome Colonization.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {32}, pmid = {40261360}, issn = {1432-184X}, support = {HR22C1605//Korea Health Technology R&amp;D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health &amp; Welfare, Republic of Korea/ ; }, mesh = {Humans ; Female ; *Gastrointestinal Microbiome ; Pregnancy ; *Bacteria/classification/genetics/isolation &amp; purification ; Infant, Newborn ; RNA, Ribosomal, 16S/genetics ; Adult ; Body Mass Index ; Feces/microbiology ; *Gestational Weight Gain ; Male ; Meconium/microbiology ; Infant ; *Body Weight ; }, abstract = {This study is aimed at exploring the relationship between maternal weight categories, including pre-pregnancy body mass index (P-BMI) and gestational weight gain (GWG), and the composition of the infant gut microbiome in the early days of life. We recruited 71 mother-infant pairs from Kangwon National University Hospital and Bundang CHA Hospital, collecting meconium samples from the infants within the first 5 days postpartum. Using 16S ribosomal RNA gene sequencing (V3-V4 region), this study assessed microbial diversity and the relative abundance of specific bacterial taxa in these initial stool samples. Participants were categorized into groups based on maternal P-BMI and GWG, enabling a comprehensive comparison of the microbiota composition in the infants' meconium across different maternal weight metrics. Our analysis identified significant variations in the infant gut microbiome correlated with maternal weight categories. Key findings include a differential abundance of genera such as Sphingobacteriaceae, Bacillaceae, Cytophagaceae, and Alteromonadaceae across maternal P-BMI groups, whereas Moraxellaceae and Rhodospirillaceae varied across GWG groups. In the P-BMI category, infants born to overweight mothers demonstrated a higher abundance of Pseudopedobacter, and a lower abundance of Citrobacter and Lachnospira, while infants in the underweight group showed a higher abundance of Lachnospira and Weissella. In the normal weight group, Citrobacter and Pseudopedobacter were more abundant. Within the GWG category, infants in the inadequate group showed a higher abundance of Klebsiella, whereas the normal group showed a higher abundance of Holdemania. The composition of the infant gut microbiome in the early postnatal period is significantly influenced by maternal weight categories. Understanding the role of maternal weight in shaping early microbial colonization may provide insights into developing strategies to optimize infant health outcomes through targeted interventions before and during pregnancy.}, }
@article {pmid40261136, year = {2025}, author = {Elias Masiques, N and De Vrieze, J and Hemeryck, LY and Vanhaecke, L and De Smet, S and Van Hecke, T}, title = {Dietary fiber mitigates the differential impact of beef and chicken meat consumption on rat intestinal health.}, journal = {Food &amp; function}, volume = {16}, number = {10}, pages = {3949-3962}, doi = {10.1039/d5fo00900f}, pmid = {40261136}, issn = {2042-650X}, mesh = {Animals ; Rats ; *Dietary Fiber/metabolism ; Male ; Chickens ; Gastrointestinal Microbiome ; Cattle ; *Red Meat/analysis ; Oxidative Stress ; Colon/metabolism/microbiology ; Rats, Wistar ; Oligosaccharides/metabolism ; *Meat/analysis ; Fermentation ; Bacteria/classification/isolation &amp; purification/genetics/metabolism ; }, abstract = {In this rat feeding study, it was hypothesized that the impact of red (vs. white) meat consumption on gut health is more pronounced in fiber-deprived diets, whereas fiber-rich diets may attenuate meat-related differences. For this purpose, rats were fed a red (beef) or white (chicken) meat diet with and without fructo-oligosaccharides (FOS) for three weeks. Gut health was assessed through colonic microbiota, fermentation metabolites, oxidative stress, inflammation, DNA adducts and histology. In rats on the fiber-deprived diets, beef consumption resulted in higher abundance of mucin-degrading bacteria Akkermansia and lower blood glutathione levels compared to chicken-fed rats. Adding FOS to the meat diets modulated the gut microbiota and fermentation metabolites, affected oxidative stress and inflammation markers in tissues and blood, increased colon length, and reduced fat deposition and liver weight. Thus, results showed that the dietary context should be considered when evaluating the impact of red meat consumption on gut health.}, }
@article {pmid40260087, year = {2025}, author = {Matsumura, E and Kato, H and Hara, S and Ohbayashi, T and Ito, K and Shingubara, R and Kawakami, T and Mitsunobu, S and Saeki, T and Tsuda, S and Minamisawa, K and Wagai, R}, title = {Single-cell genomics of single soil aggregates: methodological assessment and potential implications with a focus on nitrogen metabolism.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1557188}, pmid = {40260087}, issn = {1664-302X}, abstract = {Soil particles in plant rooting zones are largely clustered to form porous structural units called aggregates where highly diverse microorganisms inhabit and drive biogeochemical cycling. The complete extraction of microbial cells and DNA from soil is a substantial task as certain microorganisms exhibit strong adhesion to soil surfaces and/or inhabit deep within aggregates. However, the degree of aggregate dispersion and the efficacy of extraction have rarely been examined, and thus, adequate cell extraction methods from soil remain unclear. We aimed to develop an optimal method of cell extraction for single-cell genomics (SCG) analysis of single soil aggregates by focusing on water-stable macroaggregates (diameter: 5.6-8.2 mm) from the topsoil of cultivated Acrisol. We postulated that the extraction of microorganisms with distinct taxonomy and functions could be achieved depending on the degree of soil aggregate dispersion. To test this idea, we used six individual aggregates and performed both SCG sequencing and amplicon analysis. While both bead-vortexing and sonication dispersion techniques improved the extractability of bacterial cells compared to previous ones, the sonication technique led to more efficient dispersion and yielded a higher number and more diverse microorganisms than the bead technique. Furthermore, the analyses of nitrogen cycling and exopolysaccharides-related genes suggested that the sonication-assisted extraction led to the greater recovery of microorganisms strongly attached to soil particles and/or inhabited the aggregate subunits that were more physically stable (e.g., aggregate core). Further SCG analysis revealed that all six aggregates held intact microorganisms holding the genes (potentials) to convert nitrate into all possible nitrogen forms while some low-abundance genes showed inter-aggregate heterogeneity. Overall, all six aggregates studied showed similarities in pore characteristics, phylum-level composition, and microbial functional redundancy. Together, these results suggest that water-stable macroaggregates may act as a functional unit in soil and show potential as a useful experimental unit in soil microbial ecology. Our study also suggests that conventional methods employed for the extraction of cells and DNA may not be optimal. The findings of this study emphasize the necessity of advancing extraction methodologies to facilitate a more comprehensive understanding of microbial diversity and function in soil environments.}, }
@article {pmid40259028, year = {2025}, author = {Hsieh, YE and Yang, SY and Liu, SL and Wang, SW and Wang, WL and Tang, SL and Yang, SH}, title = {Microbial Community Shifts and Nitrogen Utilization in Peritidal Microbialites: The Role of Salinity and pH in Microbially Induced Carbonate Precipitation.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {31}, pmid = {40259028}, issn = {1432-184X}, support = {MOST 111-2621-B-029 -002 -MY3//National Science and Technology Council, Taiwan/ ; MOST 110-2611-M-002-024//National Science and Technology Council/ ; }, mesh = {*Carbonates/metabolism/chemistry ; Hydrogen-Ion Concentration ; Salinity ; *Nitrogen/metabolism ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; *Microbiota ; *Seawater/microbiology/chemistry ; *Geologic Sediments/microbiology/chemistry ; RNA, Ribosomal, 16S/genetics ; Chemical Precipitation ; }, abstract = {Microbialites have the potential to record environmental changes and act as biosignatures of past geochemical conditions. As such, they could be used as indicators to decipher ancient rock records. Modern microbialites are primarily found in environments where competitors and destructors are absent or where biogeochemical conditions favor their continuous formation. Many previous studies have essentially focused on the role of photosynthetic microbes in controlling pH and carbonate speciation and potentially overlooked alternative non-photosynthetic pathways of carbonate precipitation. Given that microbial activity induces subtle geochemical changes, microbially induced carbonate precipitation (MICP) can involve several mechanisms, from extracellular polymeric substances (EPS), sulfate reduction, anaerobic oxidation of methane, to nitrogen cycling processes, such as ammonification, ureolysis, and denitrification. Moreover, the peritidal zone where temperate microbialites are mostly found today, is under the influence of both freshwater and seawater, arguing for successive biogeochemical processes leading to mineral saturation, and questioning interpretations of fossil records. This study investigates microbialites in three tide pools from the peritidal zone of Fongchueisha, Hengchun, Taiwan, to address the influence of salinity on microbial community composition and carbonate precipitation mechanisms. Microbial samples were collected across varying salinity gradients at multiple time points and analyzed using next-generation sequencing (NGS) of bacterial 16S and eukaryotic 18S rRNA genes. Our results indicate that dominant bacterial groups, including Cyanobacteria and Alphaproteobacteria, were largely influenced by salinity variations, albeit pH exhibited stronger correlation with community composition. Combining our results on geochemistry and taxonomic diversity over time, we inferred a shift in the trophic mode under high salinity conditions, during which the use of urea and amino acids as a nitrogen source outcompetes diazotrophy, ureolysis and ammonification of amino acids reinforcing carbonate precipitation dynamics by triggering an increase in both pH and dissolved inorganic carbon.}, }
@article {pmid40258091, year = {2025}, author = {Hashem, I and Wang, J and Van Impe, JFM}, title = {A Discretized Overlap Resolution Algorithm (DORA) for resolving spatial overlaps in individual-based models of microbes.}, journal = {PLoS computational biology}, volume = {21}, number = {4}, pages = {e1012974}, pmid = {40258091}, issn = {1553-7358}, mesh = {*Algorithms ; *Models, Biological ; Computational Biology/methods ; Computer Simulation ; Biofilms/growth &amp; development ; }, abstract = {Individual-based modeling (IbM) is an instrumental tool for simulating spatial microbial growth, with applications in both microbial ecology and biochemical engineering. Unlike Cellular Automata (CA), which use a fixed grid of cells with predefined rules for interactions, IbMs model the individual behaviors of cells, allowing complex population dynamics to emerge. IbMs require more detailed modeling of individual interactions, which introduces significant computational challenges, particularly in resolving spatial overlaps between cells. Traditionally, this is managed using arrays or kd-trees, which require numerous pairwise comparisons and become inefficient as population size increases. To address this bottleneck, we introduce the Discretized Overlap Resolution Algorithm (DORA), which employs a grid-based framework to efficiently manage overlaps. By discretizing the simulation space further and assigning circular cells to specific grid units, DORA transforms the computationally intensive pairwise comparison process into a more efficient grid-based operation. This approach significantly reduces the computational load, particularly in simulations with large cell populations. Our evaluation of DORA, through simulations of microbial colonies and biofilms under varied nutrient conditions, demonstrates its superior computational efficiency and ability to accurately capture microbial growth dynamics compared to conventional methods. DORA's grid-based strategy enables the modeling of densely populated microbial communities within practical computational timeframes, thereby expanding the scope and applicability of individual-based modeling.}, }
@article {pmid40257249, year = {2025}, author = {Maggiori, C and John, Z and Bower, DM and Millan, M and Hahn, AS and McAdam, A and Johnson, SS}, title = {Draft genome sequence of a member of a putatively novel Rubrobacteraceae genus from lava tubes in Lava Beds National Monument.}, journal = {Microbiology resource announcements}, volume = {14}, number = {5}, pages = {e0133524}, pmid = {40257249}, issn = {2576-098X}, support = {/NASA/NASA/United States ; }, abstract = {We report the draft genome sequence of a member of a potentially novel genus of Rubrobacteraceae isolated from Golden Dome Cave in Lava Beds National Monument. Members of this family are known to inhabit thermophilic environments. The metagenome-assembled genome presented here helps illuminate the genetic capacity of basaltic lava tube environments.}, }
@article {pmid40253969, year = {2025}, author = {Achouri, H and Derguini, A and Idres, T and Selamoglu, Z and Hamadi, NB and Jalouli, M and Elfalleh, W and Bendif, H and Badraoui, R and Boufahja, F and Dellali, M}, title = {Impact of climate change on the toxicity of bisphenol A in Mytilus galloprovincialis and assessment of phycoremediation using Nannochloropsis salina via a multi-biomarker strategy and modeling.}, journal = {Marine pollution bulletin}, volume = {216}, number = {}, pages = {118010}, doi = {10.1016/j.marpolbul.2025.118010}, pmid = {40253969}, issn = {1879-3363}, mesh = {Animals ; *Mytilus/drug effects ; *Benzhydryl Compounds/toxicity ; *Phenols/toxicity ; *Water Pollutants, Chemical/toxicity ; Biomarkers/metabolism ; *Climate Change ; *Stramenopiles ; Oxidative Stress ; Lipid Peroxidation ; Bisphenol A Compounds ; }, abstract = {In the current study, the mussels Mytilus galloprovincialis, exposed to four varying temperatures (17, 20, 23, and 26 °C), were contaminated with 50 μg/L of bisphenol A both with and without Nannochloropsis salina. The toxicity evaluation is determined by quantifying various biomarkers related to oxidative stress, neurotoxicity, and cellular damage. The key findings indicate that the toxicity of bisphenol A is heightened by rising temperature. The impact of bisphenol A is most evident at 26 °C, leading to excessive production of reactive oxygen species, depletion of non-enzymatic antioxidants, and activation of antioxidant enzymes (catalase and glutathione-S-transferase). The rise in malondialdehyde levels confirms lipid peroxidation caused by bisphenol A and intensified by thermal stress. These findings have been supported by strong molecular interactions between bisphenol A and lectin mytilec apo-form and proximal thread matrix protein 1 from M. galloprovincialis following the computational modeling assay. The incorporation of N. salina as a food additive helped, firstly, to mitigate the stress effects and, secondly, resulted in a noticeable enhancement of oxidative balance and filtration ability, along with decreased lipid peroxidation.}, }
@article {pmid40252751, year = {2025}, author = {Tuts, L and Heyndrickx, M and Becue, I and Boon, N and De Maesschalck, P and Rasschaert, G}, title = {Tracking antibiotics and antibiotic-resistant E. coli in the aquatic environment linked to agriculture.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {374}, number = {}, pages = {126265}, doi = {10.1016/j.envpol.2025.126265}, pmid = {40252751}, issn = {1873-6424}, mesh = {*Escherichia coli/drug effects ; *Anti-Bacterial Agents/analysis ; *Environmental Monitoring ; *Agriculture ; *Water Pollutants, Chemical/analysis ; *Drug Resistance, Bacterial ; Groundwater/microbiology/chemistry ; Water Microbiology ; }, abstract = {The application of manure to fertilize agricultural land is associated with the introduction of antibiotic residues and bacteria, including antibiotic-resistant bacteria, which can reach surface water through runoff and drainage and groundwater through leaching from the soil. This was investigated by sampling 50 surface water locations (before and after fertilization) and 50 groundwater wells for the presence of antibiotic residues and the presence of antibiotic-resistant bacteria. For the latter, Escherichia coli and extended-spectrum β-lactamase (ESBL) producing E. coli were used as indicators and profiled for antibiotic resistance. The presence of a wide range of antibiotic residues, though at low concentrations (0.01-10 μg/L), in freshwater ecosystems highlights the extensive spread of these substances. Only 16 % of the samples were consistently free of antibiotic residues throughout both sampling periods. Notably, the frequent occurrence of sulfonamides and lincomycin in surface waters raises concerns as their concentrations occasionally exceed the predicted no-effect levels for antimicrobial resistance selection. Maximum concentrations were reported at 8.83 μg/L and 1.60 μg/L for sulfamethoxazole and lincomycin, respectively. Additionally, resistance patterns in E. coli indicate increased resistance to sulfamethoxazole following the fertilization period, suggesting that the application of manure on fields contributes to a rise in antibiotic resistance from 20 % to 48 %. Although antibiotic contamination in groundwater is less prevalent, antibiotic resistance remains widespread. In particular, ESBL-producing E. coli exhibit heightened resistance levels, not limited to β-lactam antibiotics. The detection of resistance to critical last-resort antibiotics such as carbapenems and colistin further emphasizes the urgency of addressing antibiotic resistance in environmental contexts. This study highlights the need for continued monitoring and the implementation of legislation to reduce antibiotic pollution and tackle resistance in aquatic ecosystems.}, }
@article {pmid40251008, year = {2025}, author = {Rizaludin, MS and Díaz, ASL and Zweers, H and Raaijmakers, JM and Garbeva, P}, title = {Foliar infections by Botrytis cinerea modulate the tomato root volatilome and microbiome.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {5}, pages = {}, pmid = {40251008}, issn = {1574-6941}, support = {024.004.014/NWO_/Dutch Research Council/Netherlands ; }, mesh = {*Plant Roots/microbiology/chemistry/metabolism ; *Botrytis/physiology ; *Solanum lycopersicum/microbiology/genetics/chemistry ; *Microbiota ; *Volatile Organic Compounds/metabolism/analysis ; *Plant Diseases/microbiology ; Rhizosphere ; Bacteria/classification/genetics/isolation &amp; purification ; Plant Leaves/microbiology ; Soil Microbiology ; }, abstract = {The fungal pathogen Botrytis cinerea causes significant damage to aboveground plant parts, but its impact on root chemistry and microbiome composition is less understood. This study investigated how B. cinerea foliar infection influences the root volatilome and microbiome of two tomato genotypes: wild Solanum pimpinellifolium and domesticated Solanum lycopersicum var. Moneymaker. In the absence of infection, wild tomato roots emitted higher levels of monoterpenes such as α-pinene and terpinene compared to domesticated tomato roots. The fungal infection induced elevated levels of benzyl alcohol and benzofuran in the root headspace and/or rhizosphere of both genotypes, alongside genotype-specific changes. Multivariate analyses revealed that B. cinerea significantly altered bacterial and fungal community compositions in the rhizosphere and rhizoplane, with stronger bacterial community shifts in the rhizoplane. Taxa depletion and enrichment were observed, particularly among Proteobacteria and Ascomycota. Mantel tests showed significant correlations between rhizoplane bacterial community compositions and root-associated volatilome. Notably, enriched bacterial taxa such as Pelomonas and Comamonadaceae positively correlated with benzyl alcohol and benzofuran levels in the root volatilome. These findings demonstrate that B. cinerea foliar infection might induce profound changes in root-associated volatilome and microbiome composition, highlighting its systemic effects on plant root chemistry and microbiome composition.}, }
@article {pmid40250533, year = {2025}, author = {Rosario Rodero, MD and Steyer, JP and Pérez-Bernal, MF and Verstraete, W and Escudié, R and Capson-Tojo, G}, title = {Dinitrogen fixation by open purple non-sulfur bacteria cultures for protein production: Diazotrophy boosts photoheterotrophic uptake rates.}, journal = {Bioresource technology}, volume = {430}, number = {}, pages = {132554}, doi = {10.1016/j.biortech.2025.132554}, pmid = {40250533}, issn = {1873-2976}, mesh = {*Nitrogen Fixation/physiology ; Biomass ; Rhodopseudomonas/metabolism ; Nitrogen/metabolism ; Heterotrophic Processes ; Light ; *Bacterial Proteins/biosynthesis ; }, abstract = {Purple non-sulfur bacteria (PNSB) offer a sustainable alternative to current inefficient protein production systems thanks to their high yields. This study explored the potential of specialized diazotrophic PNSB open cultures for protein production, benchmarking their performance against ammonium-grown PNSB and other diazotrophs. While diazotrophic yields (0.85-0.93 gCODbiomass·gCODsubstrate[-1]; COD being chemical oxygen demand) were slightly lower than non-diazotrophic (∼1.0), they were over double those of heterotrophic-diazotrophic rhizobacteria, with full N recovery as biomass (∼1.0 gNbiomass·gNfixed[-1]). Photoheterotrophic-diazotrophic uptake rates were the fastest ever reported for PNSB and any other diazotroph (e.g., 5.20 ± 0.83 vs. 2.64 ± 0.34 gCODsubstrate·gCODbiomass[-1]·d[-1] for PNSB on NH4[+]). Optimal rates required high light intensities, aligning with diazotrophic energy demands. Photoheterotrophic-diazotrophic conditions were highly selective, enriching a specialized Rhodopseudomonas palustris strain. Biomass protein contents and essential amino acid metrics confirmed nutritional suitability for humans. This work lays the background for exploiting PNSB's potential to address global protein demands through sustainable nitrogen fixation.}, }
@article {pmid40248914, year = {2025}, author = {Zhang, RG and Shang, HY and Milne, RI and Almeida-Silva, F and Chen, H and Zhou, MJ and Shu, H and Jia, KH and Van de Peer, Y and Ma, YP}, title = {SOI: robust identification of orthologous synteny with the Orthology Index and broad applications in evolutionary genomics.}, journal = {Nucleic acids research}, volume = {53}, number = {7}, pages = {}, pmid = {40248914}, issn = {1362-4962}, support = {2022YFF1301700//National Key Research and Development Program/ ; KIBXD202401//Kunming Institute of Botany, Chinese Academy of Sciences/ ; //Light of West China/ ; 202101BC070003//Key Basic Research Programs of Yunnan Province/ ; 2022SJ07X-03//PSESP/ ; }, mesh = {*Synteny/genetics ; *Genomics/methods ; *Evolution, Molecular ; *Genome, Plant ; Phylogeny ; Polyploidy ; Algorithms ; Plants/genetics ; }, abstract = {With the explosive growth of whole-genome datasets, accurate detection of orthologous synteny has become crucial for reconstructing evolutionary history. However, current methods for identifying orthologous synteny face great limitations, particularly in scaling with varied polyploidy histories and accurately removing out-paralogous synteny. In this study, we developed a scalable and robust approach, based on the Orthology Index (OI), to effectively identify orthologous synteny. Our evaluation across a large-scale empirical dataset with diverse polyploidization events demonstrated the high reliability and robustness of the OI method. Simulation-based benchmarks further validated the accuracy of our method, showing its superior performance against existing methods across a wide range of scenarios. Additionally, we explored its broad applications in reconstructing the evolutionary histories of plant genomes, including the inference of polyploidy, identification of reticulation, and phylogenomics. In conclusion, OI offers a robust, interpretable, and scalable approach for identifying orthologous synteny, facilitating more accurate and efficient analyses in plant evolutionary genomics.}, }
@article {pmid40248762, year = {2025}, author = {Flores, C and Millard, S and Seekatz, AM}, title = {Bridging Ecology and Microbiomes: Applying Ecological Theories in Host-associated Microbial Ecosystems.}, journal = {Current clinical microbiology reports}, volume = {12}, number = {1}, pages = {9}, pmid = {40248762}, issn = {2196-5471}, support = {R35 GM150609/GM/NIGMS NIH HHS/United States ; }, abstract = {PURPOSE OF REVIEW: This review explores the application of classical ecological theory to host-associated microbiomes during initial colonization, maintenance, and recovery. We discuss unique challenges of applying these theories to host-associated microbiomes and host factors to consider going forward.<br><br>RECENT FINDINGS: Recent studies applying community ecology principles to host microbiomes continue to demonstrate a role for both selective and stochastic processes in shaping host-associated microbiomes. However, ecological frameworks developed to describe dynamics during homeostasis do not necessarily apply during diseased or highly perturbed states, where large variations can potentially lead to alternate stable states.<br><br>SUMMARY: Despite providing valuable insights, the application of ecological theories to host-associated microbiomes has some unique challenges. The integration of host-specific factors, such as genotype or immune dynamics in ecological models or frameworks is crucial for understanding host microbiome assembly and stability, which could improve our ability to predict microbiome outcomes and improve host health.}, }
@article {pmid40247944, year = {2025}, author = {Sun, Y and Sun, S and Zahid, MS and Qiu, Q and Wang, L and Wang, S}, title = {Root-applied brassinosteroid and salicylic acid enhance thermotolerance and fruit quality in heat-stressed 'Kyoho' grapevines.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1563270}, pmid = {40247944}, issn = {1664-462X}, abstract = {INTRODUCTION: The increasingly severe global greenhouse effect has become an irreversible trend, significantly impacting viticulture regions through heat stress during various grape growth stages, especially under protected cultivation conditions where high temperatures frequently occur. Therefore, studying the impact of heat stress on grapevine growth and fruit quality across the entire growth and development period, along with effective mitigation measures, is crucial.<br><br>METHODS: In this study, three-year-old 'Kyoho' grapevines were used as experimental materials, with four treatment groups: a control group, a hightemperature group (heat stress, HT), a high-temperature + brassinolide group (BR), and a high-temperature + salicylic acid group (SA). During the flowering, young berry swelling, and veraison stages, BR and SA were applied via nutrient solutions every seven days.<br><br>RESULTS: The results demonstrated that BR restored the maximum photosynthetic rate (Amax) to 96.14% of CK by the 18th day of flowering, significantly outperforming SA's recovery rate of 86.64%. Both treatments maintained light saturation points (1200 &#x3bc;mol&#x2022;m[&#x207b;&#xb2;]&#x2022;s[&#x207b;&#xb9;]) and CO2 saturation thresholds equivalent to CK. The decline in PSII photochemical efficiency (Fv/Fm) was reduced from 18% in HT to 5-8% in BR/SA-treated groups, with BR showing minimal deviation (2.3%) from CK during veraison, effectively mitigating PSII photoinhibition caused by heat stress. Furthermore, both treatments reduced leaf malondialdehyde (MDA) content, minimizing membrane lipid peroxidation, while increasing soluble protein (SP) content to protect leaves. Under heat stress, BR notably improved the fruit set rate by 22.67% compared to HT (SA: 13%), promoted berry expansion, and enhanced the accumulation of sugars and anthocyanins in the fruit skin, with SA showing similar, though slightly less pronounced, effects.<br><br>DISCUSSION: These findings provide valuable theoretical insights into the use of exogenous hormones in root nutrient solutions as a strategy to mitigate the adverse effects of heat stress in grape production.}, }
@article {pmid40247820, year = {2025}, author = {Liu, M and Yao, X and Wang, H and Xu, X and Kong, J and Wang, Y and Chen, W and Bai, H and Wang, Z and Setati, ME and Crauwels, S and Blancquaert, E and Fan, P and Liang, Z and Dai, Z}, title = {Carposphere microbiota alters grape volatiles and shapes the wine grape typicality.}, journal = {The New phytologist}, volume = {246}, number = {5}, pages = {2280-2294}, doi = {10.1111/nph.70152}, pmid = {40247820}, issn = {1469-8137}, support = {NXNYYZ202101//Agricultural Breeding Project of Ningxia Hui Autonomous Region/ ; U20A2041//National Natural Science Foundation of China/ ; JCTD-2022-06//CAS Youth Interdisciplinary Team/ ; 2021YFE0109500//National Key Research and Development Program of China/ ; YSBR-093//CAS Project for Young Scientists in Basic Research/ ; }, mesh = {*Vitis/microbiology/genetics/metabolism ; *Volatile Organic Compounds/metabolism ; *Microbiota ; Fruit/microbiology/genetics/metabolism ; *Wine/microbiology ; Sphingomonas/physiology ; Transcriptome/genetics ; Metabolome ; Gene Expression Regulation, Plant ; }, abstract = {While specific environments are known to shape plant metabolomes and the makeup of their associated microbiome, it is as yet unclear whether carposphere microbiota contribute to the characteristics of grape fruit flavor of a particular wine region. Here, carposphere microbiomes and berry transcriptomes and metabolomes of three grape cultivars growing at six geographic sites were analyzed. The composition of the carposphere microbiome was determined mainly by environmental conditions, rather than grape genotype. Bacterial microbiota likely contributed to grape volatile profiles. Particularly, candidate operational taxonomic units (OTUs) in genus Sphingomonas were highly correlated with grape C6 aldehyde volatiles (also called green leaf volatiles, GLVs), which contribute to a fresh taste. Furthermore, a core set of expressed genes was enriched in lipid metabolism, which is responsible for bacterial colonization and C6 aldehyde volatile synthesis activation. Finally, a similar grape volatile profile was observed after inoculating the berry skin of two grape cultivars with Sphingomonas sp., thus providing evidence for the hypothetical microbe-metabolite relationship. These results provide novel insight into how the environment-microbiome-plant quality (E × Mi × Q) interaction may shape berry flavor and thereby typicality, serving as a foundation for decision-making in vineyard microbial management.}, }
@article {pmid40247656, year = {2025}, author = {Bonazzi, E and De Barba, C and Lorenzon, G and Maniero, D and Bertin, L and Barberio, B and Facciotti, F and Caprioli, F and Scaldaferri, F and Zingone, F and Savarino, EV}, title = {Recent developments in managing luminal microbial ecology in patients with inflammatory bowel disease: from evidence to microbiome-based diagnostic and personalized therapy.}, journal = {Expert review of gastroenterology &amp; hepatology}, volume = {19}, number = {5}, pages = {563-576}, doi = {10.1080/17474124.2025.2495087}, pmid = {40247656}, issn = {1747-4132}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Precision Medicine ; Animals ; Fecal Microbiota Transplantation ; *Colitis, Ulcerative/therapy/microbiology/diagnosis ; *Inflammatory Bowel Diseases/therapy/microbiology/diagnosis ; *Crohn Disease/therapy/microbiology/diagnosis ; }, abstract = {INTRODUCTION: Inflammatory bowel disease (IBD), including Crohn's disease and ulcerative colitis, is a chronic condition characterized by abnormal immune responses and intestinal inflammation. Emerging evidence highlights the vital role of gut microbiota in IBD's onset and progression. Recent advances have shaped diagnostic and therapeutic strategies, increasingly focusing on microbiome-based personalized care. Methodology: this review covers studies from 2004 to 2024, reflecting the surge in research on luminal microbial ecology in IBD. Human studies were prioritized, with select animal studies included for mechanistic insights. Only English-language, peer-reviewed articles - clinical trials, systematic reviews, and meta-analyses - were considered. Studies without clinical validation were excluded unless offering essential insights. Searches were conducted using PubMed, Scopus, and Web of Science.<br><br>AREAS COVERED: we explore mechanisms for managing IBD-related microbiota, including microbial markers for diagnosis and novel therapies such as fecal microbiota transplantation, metabolite-based treatments, and precision microbiome modulation. Additionally, we review technologies and diagnostic tools used to analyze gut microbiota composition and function in clinical settings. Emerging data supporting personalized therapeutic strategies based on individual microbial profiles are discussed.<br><br>EXPERT OPINION: Standardized microbiome research integration into clinical practice will enhance precision in IBD care, signaling a shift toward microbiota-based personalized medicine.}, }
@article {pmid40246153, year = {2025}, author = {Bharathan, A and Arafath, Y and Fathima, A and Hassan, S and Singh, P and Kiran, GS and Selvin, J}, title = {Implication of environmental factors on the pathogenicity of Vibrio vulnificus: Insights into gene activation and disease outbreak.}, journal = {Microbial pathogenesis}, volume = {204}, number = {}, pages = {107591}, doi = {10.1016/j.micpath.2025.107591}, pmid = {40246153}, issn = {1096-1208}, mesh = {*Vibrio vulnificus/pathogenicity/genetics/drug effects ; Humans ; *Vibrio Infections/epidemiology/microbiology ; *Disease Outbreaks ; Virulence Factors/genetics ; Climate Change ; Virulence/genetics ; Gene Expression Regulation, Bacterial ; Temperature ; Anti-Bacterial Agents/therapeutic use/pharmacology ; Animals ; Biofilms/growth &amp; development ; }, abstract = {Climate change, particularly rising sea surface temperatures and altered salinity levels has contributed to the increased prevalence of Vibrio vulnificus infections in humans and marine life. This opportunistic pathogen thrives in warm, estuarine environments, and its virulence is influenced by temperature-dependent gene expression, such as the activation of pVvBt2. Elevated temperatures and iron availability enhance pathogenicity by upregulating key virulence factors, including hemolysin, exotoxins, and biofilm-associated genes. Climate-driven shifts in microbial ecology have also facilitated the global expansion of V. vulnificus, leading to more frequent outbreaks and an increasing threat to public health. The unregulated use of antibiotics has also contributed to the emergence of resistant strains, complicating treatment strategies. This review explores the complex interplay between climate change and the molecular mechanisms driving V. vulnificus pathogenicity, global gene expression responses, and the implications for disease outbreaks. We also discuss current and emerging therapeutic approaches, including antibiotic stewardship and vaccine development, to mitigate the rising health risks posed by this climate-sensitive pathogen.}, }
@article {pmid40244660, year = {2025}, author = {Narla, AV and Hwa, T and Murugan, A}, title = {Dynamic coexistence driven by physiological transitions in microbial communities.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {16}, pages = {e2405527122}, pmid = {40244660}, issn = {1091-6490}, support = {R35 GM151211/GM/NIGMS NIH HHS/United States ; R35GM151211//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; 542387//Simons Foundation (SF)/ ; 2029480//NSF | BIO | Division of Molecular and Cellular Biosciences (MCB)/ ; 2317138//NSF | MPS | Division of Physics (PHY)/ ; }, mesh = {*Ecosystem ; *Models, Biological ; Biomass ; *Microbiota/physiology ; *Microbial Interactions/physiology ; Bacteria/growth &amp; development ; }, abstract = {Microbial ecosystems are commonly modeled by fixed interactions between species in steady exponential growth states. However, microbes in exponential growth often modify their environments so strongly that they are forced out of the growth state into stressed, nongrowing states. Such dynamics are typical of ecological succession in nature and serial-dilution cycles in the laboratory. Here, we introduce a phenomenological model, the Community State Model, to gain insight into the dynamic coexistence of microbes due to changes in their physiological states during cyclic succession. Our model specifies the growth preference of each species along a global ecological coordinate, taken to be the biomass density of the community, but is otherwise agnostic to specific interactions (e.g., nutrient starvation, stress, aggregation), in order to focus on self-consistency conditions on combinations of physiological states, "community states," in a stable ecosystem. We identify three key features of such dynamical communities that contrast starkly with steady-state communities: enhanced community stability through staggered dominance of different species in different community states, increased tolerance of community diversity to fast growing species dominating distinct community states, and increased requirement of growth dominance by late-growing species. These features, derived explicitly for simplified models, are proposed here as principles aiding the understanding of complex dynamical communities. Our model shifts the focus of ecosystem dynamics from bottom-up studies based on fixed, idealized interspecies interaction to top-down studies based on accessible macroscopic observables such as growth rates and total biomass density, enabling quantitative examination of community-wide characteristics.}, }
@article {pmid40243315, year = {2025}, author = {Weng, L and Cui, Y and Jian, W and Zhang, Y and Pang, L and Cao, Y and Zhou, Y and Liu, W and Lin, H and Tao, Y}, title = {Inter-kingdom interactions and environmental influences on the oral microbiome in severe early childhood caries.}, journal = {Microbiology spectrum}, volume = {13}, number = {6}, pages = {e0251824}, pmid = {40243315}, issn = {2165-0497}, support = {31901116//National Natural Science Foundation of China/ ; 2022A1515012345//Basic and Applied Basic Research Foundation of Guangdong Province/ ; }, mesh = {Humans ; *Dental Caries/microbiology ; *Microbiota/genetics ; Child, Preschool ; Saliva/microbiology/chemistry ; *Bacteria/classification/genetics/isolation &amp; purification ; Male ; Female ; *Mouth/microbiology ; RNA, Ribosomal, 16S/genetics ; Dental Plaque/microbiology ; Fungi/classification/genetics/isolation &amp; purification ; Hydrogen-Ion Concentration ; Candida albicans/isolation &amp; purification ; }, abstract = {UNLABELLED: Dental caries arise from intricate interactions among oral microorganisms, impacting ecological stability and disease progression. In this study, we aimed to investigate the microbial diversity and inter-kingdom interactions in severe early childhood caries (S-ECC) and assess the influence of environmental factors such as salivary pH and trace elements. We analyzed 61 children aged 3-4 years with complete deciduous dentition, evaluating salivary pH, buffering capacity, and trace elements (iron, fluoride). We examined the performance of 16S rRNA V1-V9 regions gene and internal transcribed spacer (ITS) primers for bacteria and fungi from plaque and saliva to characterize community compositions and diversity. Findings revealed significant shifts in bacterial diversity in S-ECC saliva samples, marked by decreased diversity and elevated abundance of cariogenic species, particularly Streptococcus mutans. Candida albicans was notably more prevalent in the S-ECC group, implicating its potential role in pathogenesis. Iron and fluoride concentrations showed no significant correlation with microbial community structure. Network analyses uncovered complex intra- and inter-kingdom interactions, underscoring cooperative and competitive dynamics. S-ECC children exhibited higher abundances of bacteria (Streptococcus mutans, Granulicatella, Actinomyces) and fungi (Candida albicans), with specific microbial taxa associated with reduced salivary pH.<br><br>IMPORTANCE: This study illuminates the intricate relationship between bacteria and fungi within the oral microbial community of children, specifically highlighting differences between those with S-ECC and those without caries. Through an extensive analysis of the microbial composition in both saliva and dental plaque, we identified a significant increase in the abundance of specific bacterial taxa (e.g., S. mutans, Granulicatella, Actinomyces) and fungal species (e.g., C. albicans) in the oral cavities of children with S-ECC. This finding underscores the potential role of these microorganisms in the development of caries. Contrary to previous studies that emphasize the importance of iron and fluoride in oral health, our research found no significant correlation between the concentrations of these elements and the composition of oral microbial communities. This result challenges conventional understanding and opens new avenues for future research. Additionally, our findings revealed an association between Veillonella sp., Propionibacterium sp., and Candida sp. and reduced salivary pH. This provides novel insights into the relationship between the oral microenvironment and caries development. The implications of our findings are substantial for the development of prevention and intervention strategies targeting childhood caries. They also underscore the critical need for a deeper exploration of oral microbial interactions and their environmental influences.}, }
@article {pmid40241747, year = {2025}, author = {Takahashi, M and Hiraoka, S and Matsumoto, Y and Shibagaki, R and Ujihara, T and Maeda, H and Seo, S and Nagasaki, K and Takeuchi, H and Matsuzaki, S}, title = {Host-encoded DNA methyltransferases modify the epigenome and host tropism of invading phages.}, journal = {iScience}, volume = {28}, number = {4}, pages = {112264}, pmid = {40241747}, issn = {2589-0042}, abstract = {Restriction modification (RM) systems are ubiquitous bacterial defense systems; however, some phages evade RM system and adapt to their bacterial hosts. In such cases, phages are thought to stochastically acquire DNA methylation from host-encoded DNA methyltransferases (MTases), facilitating host adaptation. However, no studies have directly compared the methylomes of host bacteria and their infecting phages. Here, we demonstrate the epigenetic landscape of adapted phages with diverse infection histories, focusing on the broad host-range phage KHP30T as its adapts to three Helicobacter pylori strains. Using a multistage infection system, we observed that the adapted phages displayed significantly high titers against the last infected H. pylori strain, suggesting an attendant change in host tropism. Single-molecule real-time sequencing revealed that methylated motifs were predominantly shared between the adapted phages and their most recent host. Our findings enhance our understanding of epigenetic phage-host interactions, which have significant implications for microbial ecology.}, }
@article {pmid40240613, year = {2025}, author = {Dhungana, I and Nguyen, NH}, title = {Legacy of Repeated Cultivation Drives Cyclical Microbial Community Development in a Tropical Oxisol Soil.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {30}, pmid = {40240613}, issn = {1432-184X}, support = {HAW08042-H//U.S. Department of Agriculture/ ; }, mesh = {*Soil Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification/growth &amp; development ; *Fungi/classification/growth &amp; development/genetics/isolation &amp; purification ; Soil/chemistry ; Agriculture/methods ; Zea mays/growth &amp; development/microbiology ; *Archaea/classification/growth &amp; development/genetics/isolation &amp; purification ; *Microbiota ; Tropical Climate ; Crops, Agricultural/growth &amp; development/microbiology ; Lactuca/growth &amp; development/microbiology ; Mustard Plant/growth &amp; development/microbiology ; }, abstract = {Agricultural practices and the crop being actively cultivated are some of the most important contributors to soil microbial community assembly processes in agroecosystems. However, it is not well-understood how the cultivation of diverse crop species can directionally shift complex soil microbial communities, especially under continuous monoculture systems. Here, we conducted a field experiment to assess how three crop species (Lactuca sativa, Brassica juncea, and Zea mays) may shift soil microbial (bacteria/archaea and fungi) communities when planted in a monoculture and repeatedly grown for three cycles in a tropical Oxisol soil. We found that while plant species made limited contributions to microbial community differentiation, repeated cultivation was a strong driver of community development over time. The bacterial/archaeal communities exhibited a cyclical community development pattern, initially with strong differentiation that attenuated to a steady state at the end of the three cycles. In contrast, fungal communities generally developed more linearly and may have only started to stabilize after three cropping cycles. These developments may speak to the stronger legacy effects on fungal communities. Together, these results highlight the differences between how bacteria/archaea and fungal communities develop, especially in tropical, underdeveloped, intensively degraded, or marginal soils.}, }
@article {pmid40239902, year = {2025}, author = {Ma, H and Chen, S and Lv, L and Ye, Z and Yang, J and Wang, B and Zou, J and Li, J and Ganigué, R}, title = {Large-sized aerobic granular biofilm: stable biotechnology to improve nitrogen removal and reduce sludge yield.}, journal = {Bioresource technology}, volume = {429}, number = {}, pages = {132543}, doi = {10.1016/j.biortech.2025.132543}, pmid = {40239902}, issn = {1873-2976}, mesh = {*Sewage/microbiology ; *Biofilms/growth &amp; development ; *Nitrogen/isolation &amp; purification/metabolism ; Aerobiosis ; Bioreactors/microbiology ; *Biotechnology/methods ; Biomass ; }, abstract = {Three parallel sequencing batch reactors (control, small-sized polyurethane sponge (PUS) (3.0 mm), and large-sized PUS (10.0 mm)) were used to investigate aerobic granular biofilm (AGB) characteristics. Results show that 10.0 mm PUS facilitated rapid formation of large-sized AGB (AGBL), which exhibited higher biomass concentration (8.5 g/L) and faster settling velocity (69.2-159.3 m/h) than aerobic granular sludge (AGS) (3.2 g/L and 38.6-80.0 m/h). The AGBL system also maintained long-term structural stability with a lower instability coefficient (0.004-0.018 min[-1]) than AGS (0.053-0.090 min[-1]). Additionally, during long-term operation, the AGBL system achieved excellent removal efficiencies for NH4[+]-N (99.6 ± 0.4 %) and total nitrogen (92.3 ± 2.6 %), and exhibited a lower sludge yield (0.05 gVSS/gCOD) than AGS (0.14 gVSS/gCOD). The larger size and compact structure of AGBL increased anoxic/anaerobic zones, enriching denitrifying and hydrolytic/fermentative bacteria. These findings highlight AGBL with large PUS as a more promising biotechnology for practical applications than conventional AGS.}, }
@article {pmid40238873, year = {2025}, author = {Bukhdruker, S and Gushchin, I and Shevchenko, V and Kovalev, K and Polovinkin, V and Tsybrov, F and Astashkin, R and Alekseev, A and Mikhaylov, A and Bukhalovich, S and Bratanov, D and Ryzhykau, Y and Kuklina, D and Caramello, N and Rokitskaya, T and Antonenko, Y and Rulev, M and Stoev, C and Zabelskii, D and Round, E and Rogachev, A and Borshchevskiy, V and Ghai, R and Bourenkov, G and Zeghouf, M and Cherfils, J and Engelhard, M and Chizhov, I and Rodriguez-Valera, F and Bamberg, E and Gordeliy, V}, title = {Proteorhodopsin insights into the molecular mechanism of vectorial proton transport.}, journal = {Science advances}, volume = {11}, number = {16}, pages = {eadu5303}, pmid = {40238873}, issn = {2375-2548}, mesh = {*Protons ; *Rhodopsins, Microbial/chemistry/metabolism ; Hydrogen Bonding ; Models, Molecular ; Proton Pumps/chemistry/metabolism ; Protein Conformation ; }, abstract = {Bacterial proton pumps, proteorhodopsins (PRs), are a major group of light-driven membrane proteins found in marine bacteria. They are functionally and structurally distinct from archaeal and eukaryotic proton pumps. To elucidate the proton transfer mechanism by PRs and understand the differences to nonbacterial pumps on a molecular level, high-resolution structures of PRs' functional states are needed. In this work, we have determined atomic-resolution structures of MAR, a PR from marine actinobacteria, in various functional states, notably the challenging late O intermediate state. These data and information from recent atomic-resolution structures on an archaeal outward proton pump bacteriorhodopsin and bacterial inward proton pump xenorhodopsin allow for deducing key universal elements for light-driven proton pumping. First, long hydrogen-bonded chains characterize proton pathways. Second, short hydrogen bonds allow proton storage and inhibit their backflow. Last, the retinal Schiff base is the active proton donor and acceptor to and from hydrogen-bonded chains.}, }
@article {pmid40238292, year = {2025}, author = {Zhang, Y and Lin, H and Xiong, Y and Zhang, Z and Zeng, L and Liu, Z}, title = {Fu Brick Tea Protects the Intestinal Barrier and Ameliorates Colitis in Mice by Regulating Gut Microbiota.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {7}, pages = {}, pmid = {40238292}, issn = {2304-8158}, support = {2024HX118//Horizontal project of Shaoyang University/ ; 2024JJ7497//Foundation regional joint fund of Hunan Province natural Science/ ; 202401001313//The teaching reform research project of Hunan Province in 2024/ ; 2022YFE0111200//Innovation and transformation of key technologies for efficient preparation of catechin oxidation polymerization products/ ; }, abstract = {Ulcerative colitis (UC) pathogenesis is strongly linked to gut microbiota dysbiosis and compromised intestinal barrier integrity. Emerging evidence suggests that targeted dietary interventions may restore microbial homeostasis and ameliorate colitis progression. In this study, we evaluated the therapeutic potential of Fu Brick tea (FBT) using a dextran sulfate sodium (DSS)-induced murine colitis model. The results indicated that oral administration of FBT extract significantly improved the disease index, reduced inflammatory response, protected intestinal barrier protein (e.g., ZO-1), and maintained intestinal structure integrity. Furthermore, FBT intake increased the diversity of gut microbiota, promoted the growth of beneficial bacteria (e.g., Akkermansia), inhibited the proliferation of harmful bacteria (e.g., Desulfovibrioceae, Escherichia, and Helicobacter), restored intestinal homeostasis, and alleviated colitis symptoms including diarrhea. These findings position FBT as a promising nutraceutical candidate for UC management via multi-target modulation of mucosal immunity and microbial ecology.}, }
@article {pmid40238218, year = {2025}, author = {Zhadyra, S and Tao, F and Xu, P}, title = {Exploring the Microbiome and Functional Metabolism of Fermented Camel Milk (Shubat) Using Metagenomics.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {7}, pages = {}, pmid = {40238218}, issn = {2304-8158}, abstract = {Shubat is a traditional fermented camel milk drink that originated in Central Asia, with especially deep cultural roots in Kazakhstan. However, systematic studies on the microbial ecology and functional genes of Shubat remain scarce. As a distinctive fer-mented food, its microbial diversity and functional properties have not been fully ex-plored. This study investigates the microbial diversity and functional potential of Shubat by using advanced metagenomic techniques. Its microbial community is mainly composed of bacteria (96.6%), with Lactobacillus, Lactococcus, and Streptococcus being the dominant genera. Functional annotations through EggNOG, KEGG, and CAZy databases highlighted the metabolic versatility of Shubat's microbiota. Key pathways included amino acid and carbohydrate metabolism, vitamin biosynthesis, and central carbon metabolism, emphasizing their roles in fermentation and nutritional enhancement. The identification of various enzymes related to chemical synthesis further emphasizes the contribution of the microbiota to Shubat's unique flavor and texture. This study not only provides an important basis for the scientific understanding of Shubat but also expands the application possibilities of fermented food in the field of health and nutrition and confers modern value and significance to traditional food. This integration of science and tradition has not only facilitated the development of food microbiology but also paved new pathways for the global dissemination of traditional foods and the development of functional foods.}, }
@article {pmid40237447, year = {2025}, author = {Choudoir, MJ and Ishaq, SL and Beiko, RG and Silva, DS and Allen-Vercoe, E and O'Doherty, KC}, title = {The case for microbiome stewardship: what it is and how to get there.}, journal = {mSystems}, volume = {10}, number = {5}, pages = {e0006225}, pmid = {40237447}, issn = {2379-5077}, support = {//University of Guelph Institute of Environmental Research/ ; R15 DK133826/DK/NIDDK NIH HHS/United States ; 191753/CAPMC/CIHR/Canada ; //Canada Research Chairs/ ; 7004439, ME022329//U.S. Department of Agriculture's National Institute of Food and Agriculture/ ; //Natural Sciences and Engineering Research Council of Canada/ ; NIH/NIDDK 1R15DK133826-01/NH/NIH HHS/United States ; }, mesh = {Animals ; Humans ; Agriculture ; Anti-Bacterial Agents ; Ecosystem ; *Microbiota ; Public Health ; }, abstract = {Microbiomes are essential for human, animal, plant, and ecosystem health. Despite widespread recognition of the importance of microbiomes, there is little attention paid to monitoring and safeguarding microbial ecologies on policy levels. We observe that microbiomes are deteriorating owing to practices at societal levels such as pesticide use in agriculture, air and water pollution, and overuse of antibiotics. Potential policy on these issues would cross multiple domains such as public health, environmental protection, and agriculture. We propose microbiome stewardship as a foundational concept that can act across policy domains to facilitate healthy microbiomes for human and ecosystem health. We examine challenges to be addressed and steps to take toward developing meaningful microbiome stewardship.}, }
@article {pmid40235320, year = {2025}, author = {Bahram Wlia, A and Majedi, S}, title = {Optimizing hygiene and microbial aspect of paper recycling: a sustainable approach for environmental conservation.}, journal = {Cellular and molecular biology (Noisy-le-Grand, France)}, volume = {71}, number = {3}, pages = {151-157}, doi = {10.14715/cmb/2025.71.3.18}, pmid = {40235320}, issn = {1165-158X}, mesh = {*Recycling/methods ; *Paper ; *Hygiene ; *Bacteria/isolation &amp; purification/classification/genetics ; *Conservation of Natural Resources/methods ; Iraq ; Waste Management/methods ; }, abstract = {This study explores microbial dynamics in paper recycling, emphasizing the significance of sustainable practices for environmental preservation. Samples were collected from various urban waste sources in Erbil city, Kurdistan Region, Iraq, including materials such as pizza boxes, cigarette packets, and coffee cups. Pure bacterial colonies were isolated using standard methods, and their morphological and physiological traits were characterized through biochemical tests. Identification of bacterial species followed established protocols. The study identified diverse bacterial species associated with paper waste, highlighting potential hygiene concerns in the recycling process. The findings of this study contribute to understanding the microbial ecology associated with paper waste and recycling processes. By optimizing hygiene measures and gaining insights into the microbial communities present, this research underscores the importance of sustainable practices in paper recycling to mitigate environmental impacts and promote a healthier ecosystem. Policies for future waste management and reduction of environmental risks have been proposed.}, }
@article {pmid40234253, year = {2025}, author = {Yao, B and Mou, X and Li, Y and Lian, J and Niu, Y and Liu, J and Lu, J and Li, Y and Li, Y and Wang, X}, title = {Distinct Assembly Patterns of Soil Bacterial and Fungal Communities along Altitudinal Gradients in the Loess Plateau's Highest Mountain.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {29}, pmid = {40234253}, issn = {1432-184X}, support = {23JRRA672//Youth Science and Technology Fund Program of Gansu Province/ ; 2023449//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; 22JR5RA076//Gansu Province Natural Science Foundation Program/ ; }, mesh = {*Soil Microbiology ; *Altitude ; *Bacteria/classification/genetics/isolation &amp; purification ; *Fungi/classification/genetics/isolation &amp; purification ; Soil/chemistry ; Ecosystem ; *Microbiota ; Biodiversity ; *Mycobiome ; China ; High-Throughput Nucleotide Sequencing ; }, abstract = {A critical issue in microbial ecology is quantifying the relative contributions of deterministic and stochastic processes to microbial community assembly, and predicting ecosystem function by understanding the ecological processes of community composition is an integral part. However, the mechanisms driving microbial community assembly along altitudinal gradients in mountain ecosystems remain largely unexplored. Here, we used high-throughput sequencing to examine the structural characteristics and diversity maintenance mechanisms of soil bacterial and fungal communities along an altitudinal gradient (2632-3661 m) in Mahan Mountain, the highest peak of the Loess Plateau. Proteobacteria, Acidobacteriota and Actinobacteriota dominated the bacterial communities, while Ascomycota, Basidiomycota and Mortierellomycota were the predominant fungal groups. Although elevation did not significantly affect bacterial and fungal alpha diversity, notable shifts in community structure were observed along the altitudinal gradients. Bacterial communities were predominantly shaped by deterministic processes, leading to pronounced structural and compositional differentiation across altitudes. In contrast, fungal community assembly was primarily determined by a combination of deterministic and stochastic processes, leading to small pronounced structural divergence. The interplay of topography, climate, and soil conditions influenced the altitudinal distribution and community structure of soil bacteria in this mountain ecosystem.}, }
@article {pmid40230839, year = {2025}, author = {Zhao, T and Wang, C and Liu, Y and Li, B and Shao, M and Zhao, W and Zhou, C}, title = {The role of polysaccharides in immune regulation through gut microbiota: mechanisms and implications.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1555414}, pmid = {40230839}, issn = {1664-3224}, mesh = {*Gastrointestinal Microbiome/immunology ; Humans ; *Polysaccharides/immunology/metabolism ; Animals ; Fatty Acids, Volatile/metabolism ; *Immunomodulation ; Cytokines/metabolism ; }, abstract = {Polysaccharides, as complex carbohydrates, play a pivotal role in immune modulation and interactions with the gut microbiota. The diverse array of dietary polysaccharides influences gut microbial ecology, impacting immune responses, metabolism, and overall well-being. Despite their recognized benefits, there is limited understanding of the precise mechanisms by which polysaccharides modulate the immune system through the gut microbiota. A comprehensive search of Web of Science, PubMed, Google Scholar, and Embase up to May 2024 was conducted to identify relevant studies. This study employs a systematic approach to explore the interplay between polysaccharides and the gut microbiota, focusing on cytokine-mediated and short-chain fatty acid (SCFA)-mediated pathways. The findings underscore the significant role of polysaccharides in shaping the composition and function of the gut microbiota, thereby influencing immune regulation and metabolic processes. However, further research is necessary to elucidate the detailed molecular mechanisms and translate these findings into clinical applications.}, }
@article {pmid40229524, year = {2025}, author = {Sakae, K and Kitagami, Y and Matsuda, Y}, title = {Rhizosphere Bacterial Communities Alter in Process to Mycorrhizal Developments of a Mixotrophic Pyrola japonica.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {28}, pmid = {40229524}, issn = {1432-184X}, support = {2023-4099//Japan Science Society/ ; JRMJSP2137//Japan Science and Technology Agency/ ; 24K01796//Japan Society for the Promotion of Science/ ; }, mesh = {*Mycorrhizae/growth &amp; development/physiology ; *Rhizosphere ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Plant Roots/microbiology ; *Ericaceae/microbiology/growth &amp; development ; *Microbiota ; Biodiversity ; DNA, Bacterial/genetics ; }, abstract = {Rhizosphere bacteria work in synergy with mycorrhizal fungi to promote plant growth. The community structure of rhizosphere bacteria may be influenced by continuous changes in fungal associations with host plants. Asiatic herbaceous plant Pyrola japonica (Ericaceae) forms arbutoid mycorrhizas without fungal mantles, with its mycorrhizal development being visually distinguishable at the cellular level. This study aimed to investigate roles of rhizosphere bacteria and their community shifts along with mycorrhizal developments. We examined bacterial communities at three different developmental stages of mycorrhizal roots-limited, full, and digested-via a partial 16S rRNA amplicon sequencing. Both α- and β-diversities in the full condition were significantly lower than those in the limited and digested conditions. Significant clusters of bacterial compositions were found among all treatments. In terms of ecological processes of community assembly, communities in limited conditions and bulk soil were influenced by both deterministic and stochastic processes, whereas those in full and digested conditions were regulated only by stochastic ways. Furthermore, the order Rhizobiales and Actinomycetales known as mycorrhizal helper bacteria were characterized in the full and digested conditions through phylogenetic analysis and detection of indicator taxa. These results suggest that mycorrhizal fungi may play ecologically important roles not only as temporal drivers initiating the formation rhizosphere bacterial communities but also as key founders exerting continuous influences to establish priority effects. Moreover, the rhizosphere bacterial community remains after mycorrhizal degeneration and their historical continuity may contribute to maintaining plant-mycorrhizal fungi-bacterial associations.}, }
@article {pmid40228732, year = {2025}, author = {Zhang, R and Gong, C and Gao, Y and Chen, Y and Zhou, L and Lou, Q and Zhao, Y and Zhuang, H and Zhang, J and Shan, S and Wang, X and Qian, X and Lei, L and Wong, MH}, title = {Reducing antibiotic resistance genes in soil: The role of organic materials in reductive soil disinfestation.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {374}, number = {}, pages = {126245}, doi = {10.1016/j.envpol.2025.126245}, pmid = {40228732}, issn = {1873-6424}, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Genes, Bacterial ; }, abstract = {Increasing attention has been given to the role of reductive soil disinfestation (RSD) on antibiotic resistance genes (ARGs) in soil. The selection of organic materials in RSD is crucial to the effectiveness of the RSD method. However, the effects of distinct organic materials on ARGs remains unclear. In this study, we selected straw and rapeseed meal as the organic materials in RSD and explored their effects on ARGs. The results showed that using straw significantly reduced the abundance of ARGs, high-risk ARGs, and mobile genetic elements (MGEs) by 31.5 %-65.8 %, while using rapeseed meal led to ARGs enrichment. Structural equation modeling (SEM) analysis identified MGEs and microbial communities as the primary drivers of ARGS changes under different organic materials. The abundance of MGEs was effectively controlled in straw treatments, reducing the potential for horizontal gene transfer of ARGs. Bacterial diversity was significantly lower in the straw treatments compared to the rapeseed meal treatments, potentially leading to a reduced abundance of ARGs host bacteria. Network co-occurrence analysis further revealed that Symbiobacteraceae and Bacillus were potential bacterial hosts of ARGs. In straw treatments, these genera' abundance decreased by 12 %-100 % compared to the control (CK) and rapeseed meal groups, further inhibiting the spread of ARGs. These findings demonstrate that RSD with straw as the organic material is more effective in mitigating ARGs compared to rapeseed meal, providing insights into controlling soil antibiotic resistance risks and utilizing agricultural waste resources.}, }
@article {pmid40227232, year = {2025}, author = {Prochera, A and Muppirala, AN and Kuziel, GA and Soualhi, S and Shepherd, A and Sun, L and Issac, B and Rosenberg, HJ and Karim, F and Perez, K and Smith, KH and Archibald, TH and Rakoff-Nahoum, S and Hagen, SJ and Rao, M}, title = {Enteric glia regulate Paneth cell secretion and intestinal microbial ecology.}, journal = {eLife}, volume = {13}, number = {}, pages = {}, pmid = {40227232}, issn = {2050-084X}, support = {Fellowship//Schmidt Family Foundation/ ; K08 DK110532/DK/NIDDK NIH HHS/United States ; R01DK135707/NH/NIH HHS/United States ; Fellowship//National Defense Science and Engineering Graduate/ ; P30 DK034854/DK/NIDDK NIH HHS/United States ; R01 DK135707/DK/NIDDK NIH HHS/United States ; Graduate Research Fellowship Program//National Science Foundation/ ; K08DK110532/NH/NIH HHS/United States ; R01 DK130836/DK/NIDDK NIH HHS/United States ; Odyssey Award//Smith Family Foundation/ ; R01DK130836/NH/NIH HHS/United States ; }, mesh = {Animals ; *Paneth Cells/metabolism/physiology ; Mice ; *Neuroglia/physiology/metabolism ; *Gastrointestinal Microbiome/physiology ; Humans ; Myelin Proteolipid Protein/metabolism/genetics ; *Intestinal Mucosa/metabolism/microbiology ; *Enteric Nervous System/physiology ; Mice, Inbred C57BL ; Male ; Female ; }, abstract = {Glial cells of the enteric nervous system (ENS) interact closely with the intestinal epithelium and secrete signals that influence epithelial cell proliferation and barrier formation in vitro. Whether these interactions are important in vivo, however, is unclear because previous studies reached conflicting conclusions (Prochera and Rao, 2023). To better define the roles of enteric glia in steady state regulation of the intestinal epithelium, we characterized the glia in closest proximity to epithelial cells and found that the majority express the gene Proteolipid protein 1 (PLP1) in both mice and humans. To test their functions using an unbiased approach, we genetically depleted PLP1[+] cells in mice and transcriptionally profiled the small and large intestines. Surprisingly, glial loss had minimal effects on transcriptional programs and the few identified changes varied along the gastrointestinal tract. In the ileum, where enteric glia had been considered most essential for epithelial integrity, glial depletion did not drastically alter epithelial gene expression but caused a modest enrichment in signatures of Paneth cells, a secretory cell type important for innate immunity. In the absence of PLP1[+] glia, Paneth cell number was intact, but a subset appeared abnormal with irregular and heterogenous cytoplasmic granules, suggesting a secretory deficit. Consistent with this possibility, ileal explants from glial-depleted mice secreted less functional lysozyme than controls with corresponding effects on fecal microbial composition. Collectively, these data suggest that enteric glia do not exert broad effects on the intestinal epithelium but have an essential role in regulating Paneth cell function and gut microbial ecology.}, }
@article {pmid40223273, year = {2025}, author = {Yang, SY and Han, SM and Lee, JY and Kim, KS and Lee, JE and Lee, DW}, title = {Advancing Gut Microbiome Research: The Shift from Metagenomics to Multi-Omics and Future Perspectives.}, journal = {Journal of microbiology and biotechnology}, volume = {35}, number = {}, pages = {e2412001}, pmid = {40223273}, issn = {1738-8872}, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; Metagenomics/trends ; Multiomics/trends ; *Host Microbial Interactions/physiology ; *Translational Research, Biomedical/methods/trends ; Precision Medicine/methods/trends ; }, abstract = {The gut microbiome, a dynamic and integral component of human health, has co-evolved with its host, playing essential roles in metabolism, immunity, and disease prevention. Traditional microbiome studies, primarily focused on microbial composition, have provided limited insights into the functional and mechanistic interactions between microbiota and their host. The advent of multi-omics technologies has transformed microbiome research by integrating genomics, transcriptomics, proteomics, and metabolomics, offering a comprehensive, systems-level understanding of microbial ecology and host-microbiome interactions. These advances have propelled innovations in personalized medicine, enabling more precise diagnostics and targeted therapeutic strategies. This review highlights recent breakthroughs in microbiome research, demonstrating how these approaches have elucidated microbial functions and their implications for health and disease. Additionally, it underscores the necessity of standardizing multi-omics methodologies, conducting large-scale cohort studies, and developing novel platforms for mechanistic studies, which are critical steps toward translating microbiome research into clinical applications and advancing precision medicine.}, }
@article {pmid40222749, year = {2025}, author = {Belda, I and Izquierdo-Gea, S and Benitez-Dominguez, B and Ruiz, J and Vila, JCC}, title = {Wine Fermentation as a Model System for Microbial Ecology and Evolution.}, journal = {Environmental microbiology}, volume = {27}, number = {4}, pages = {e70092}, pmid = {40222749}, issn = {1462-2920}, support = {//Center for Computational, Evolutionary and Human Genomics, Stanford University. Postdoc Fellowship to Jean CC VIla/ ; FPU21/06830//Spanish Ministry of Science, Innovation and Universities/ ; PID2019-105834GA-I00//Agencia Estatal de Investigaci&#xf3;n/ ; PID2022-138343NB-I00//Agencia Estatal de Investigaci&#xf3;n/ ; PRE2022-103063//Agencia Estatal de Investigaci&#xf3;n/ ; }, mesh = {*Wine/microbiology ; *Fermentation ; *Biological Evolution ; Microbiota ; *Bacteria/metabolism/genetics ; Ecosystem ; Models, Biological ; Ecology ; }, abstract = {In vitro microbial communities have proven to be invaluable model systems for studying ecological and evolutionary processes experimentally. However, it remains unclear whether quantitative insights obtained from these laboratory systems can be applied to complex communities assembling and evolving in their natural ecological context. To bridge the gap between the lab and the 'real-world', there is a need for laboratory model systems that better approximate natural and semi-natural ecosystems. Wine fermentation presents an ideal system for this purpose, balancing experimental tractability with rich ecological and evolutionary dynamics. In this perspective piece we outline the key features that make wine fermentation a fruitful model system for ecologists and evolutionary biologists. We highlight the diversity of environmentally mediated interactions that shape community dynamics during fermentation, the complex evolutionary history of wine microbial populations, and the opportunity to study the impact of complex ecologies on evolutionary dynamics. By integrating knowledge from both wine research and microbial ecology and evolution we aim to enhance understanding and foster collaboration between these fields.}, }
@article {pmid40220383, year = {2025}, author = {Li, C and Zhu, L and Axe, L and Li, M}, title = {Acclimation of sludge-derived biofilms for effective removal of emerging contaminants: Impacts of inoculum source and carbon supplementation.}, journal = {Journal of hazardous materials}, volume = {492}, number = {}, pages = {138235}, doi = {10.1016/j.jhazmat.2025.138235}, pmid = {40220383}, issn = {1873-3336}, mesh = {*Biofilms ; *Sewage/microbiology ; *Carbon ; *Water Pollutants, Chemical/metabolism ; Biodegradation, Environmental ; Sulfamethoxazole/metabolism ; Carbamazepine/metabolism ; Waste Disposal, Fluid/methods ; Acclimatization ; }, abstract = {Contaminants of emerging concern (CECs) have gathered significant public attention due to their widespread occurrence, high persistence, and increasing exposure potential. In this study, we used polyethylene biocarriers for acclimating biofilms from singular or combined activated sludges collected from three wastewater treatment plants (R, P, and L) over 5 month-long cycles. The acclimated biofilms achieved an average removal rate at 0.333, 0.313, and 0.185 week[-1] for N, N-diethyl-meta-toluamide (DEET), sulfamethoxazole (SMX), and carbamazepine (CBZ), respectively, when external carbon was supplemented, which were significantly higher (p < 0.05) than biofilms that did not receive external carbons. Metabolite screening revealed SMX transformation through ipso-hydroxylation and acetyl conjugation, while CBZ degradation could be initiated by epoxidation. Significant but slower degradation rates (0.024∼0.031 week[-1]) were observed for aminotriazole (AMT), lidocaine (LDC), and trimethoprim (TMP), whereas atrazine (ATZ) exhibited minimal removal, highlighting its high recalcitrance. Biofilms acclimated from individual R and P sludges, with external carbon supplementation, attained the greatest removal efficiencies for 7 CECs. Multivariate statistical correlations (p < 0.05) identified potential degraders, including Sphingomonas and Zoogolea for AMT, Labrys and Koazkia for CBZ, and Asprobacter, unclassified Cyclobacteriaceae (ELB16-189) and Bryobacteraceae (Fen-178) for LDC. Abundance distribution of potential degraders among biofilms revealed that Sludge R favored the enrichment of key degraders for AMT, CBZ and LDC, while Sludge P was more conducive to acclimating CBZ degraders. This study advances our understanding of strategies in biofilm acclimation to improve CEC removal and provides insights into degradation pathways and associated microbial communities for future research.}, }
@article {pmid40220189, year = {2025}, author = {Knoppersen, RS and Bose, T and Coutinho, TA and Hammerbacher, A}, title = {Inside the Belly of the Beast: Exploring the Gut Bacterial Diversity of Gonipterus sp. n. 2.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {27}, pmid = {40220189}, issn = {1432-184X}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Eucalyptus/parasitology/chemistry ; *Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Diet ; South Africa ; *Coleoptera/microbiology/physiology ; Gas Chromatography-Mass Spectrometry ; Introduced Species ; Biodiversity ; }, abstract = {The Eucalyptus snout beetle (Gonipterus sp. n. 2) is a destructive invasive pest of Eucalyptus plantations, responsible for significant defoliation and wood yield losses globally. Native to Australia, this beetle has adapted to thrive on diverse Eucalyptus hosts, overcoming their chemical defences. However, the mechanisms by which Gonipterus tolerates or utilises these plant defence metabolites remain poorly understood. In South Africa, Gonipterus sp. n. 2 poses a significant threat to Eucalyptus plantations by causing extensive defoliation and leading to substantial reductions in growth and wood production. This study investigates the relationship between diet, host Eucalyptus species, and the gut microbiome of Gonipterus sp. n. 2. Using controlled feeding experiments, beetles were reared on artificial, semi-artificial, and natural diets, as well as two Eucalyptus genotypes with distinct secondary metabolite profiles. High-throughput 16S rDNA sequencing and gas chromatography-mass spectrometry (GC-MS) revealed significant shifts in gut bacterial diversity and composition across diets. Natural diets supported the most diverse microbial communities, while artificial diets fostered a homogenised microbiome dominated by opportunistic taxa like Serratia. Host-specific effects were observed in frass microbiota, with substantial biotransformation of monoterpenes into less toxic derivatives. The results highlight the plasticity of Gonipterus gut microbiota, which enables metabolic adaptability and resilience in diverse environments. This microbial flexibility underpins the invasiveness of Gonipterus, emphasising the role of gut symbionts in overcoming host chemical defences. Understanding these interactions offers novel insights for microbiome-targeted pest management strategies, providing a sustainable approach to mitigate the impact of Gonipterus on global Eucalyptus forestry.}, }
@article {pmid40216640, year = {2025}, author = {Huttunen, KL and Malazarte, J and Jyväsjärvi, J and Lehosmaa, K and Muotka, T}, title = {Temporal Beta Diversity of Bacteria in Streams: Network Position Matters But Differently for Bacterioplankton and Biofilm Communities.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {26}, pmid = {40216640}, issn = {1432-184X}, support = {356403//Research Council of Finland/ ; 318230//Research Council of Finland/ ; 318230//Research Council of Finland/ ; }, mesh = {*Biofilms/growth &amp; development ; *Rivers/microbiology/chemistry ; *Bacteria/classification/genetics/isolation &amp; purification ; *Biodiversity ; *Plankton/classification/genetics ; Soil Microbiology ; Ecosystem ; Seasons ; }, abstract = {Concern about biodiversity loss has yielded a surge of studies on temporal change in α-diversity, whereas temporal β-diversity has gained less interest. We sampled bacterioplankton, biofilm, and riparian soil bacteria repeatedly across the open-water season in a pristine stream network to determine the level of temporal β-diversity in relation to stream network position and environmental variability. We tested the hypothesis that aquatic bacterial communities in isolated and environmentally heterogenous headwaters exhibit high temporal β-diversity while the better-connected and environmentally more stable mainstem sections support more stable communities, and soil communities bear no relationship to network position. As expected, temporal β-diversity decreased from headwaters toward mainstems for bacterioplankton. Against expectations, an opposite pattern was observed for biofilm. For bacterioplankton, temporal β-diversity was positively related to temporal variability in water chemistry. For biofilm bacteria, temporal variability was negatively related to variability in temperature. Temporal β-diversity of soil communities did not show any response to stream network position, but was strongly related to variability in the soil environment. The two aquatic habitats and riparian soils supported distinctly different bacterial communities. The number of ASVs shared between the soil and the aquatic communities decreased along the network, and more so for bacterioplankton. The higher temporal variability of bacterial communities in the headwaters likely results from temporally variable input of propagules from riparian soil, emphasizing the role of land-water connection and network position to bacterioplankton community composition. Overall, bacterial communities exhibited high temporal variability, highlighting the importance of temporal replication to fully capture their network-scale biodiversity.}, }
@article {pmid40214404, year = {2025}, author = {Nilsen, T and Pettersen, R and Keeley, NB and Ray, JL and Majaneva, S and Stokkan, M and Hervik, A and Angell, IL and Snipen, LG and Sundt, M&#xd8; and Rudi, K}, title = {Association of Microbial Networks with the Coastal Seafloor Macrofauna Ecological State.}, journal = {Environmental science &amp; technology}, volume = {59}, number = {15}, pages = {7517-7529}, pmid = {40214404}, issn = {1520-5851}, mesh = {Animals ; Aquaculture ; Archaea ; Ecosystem ; Iceland ; *Microbiota ; Norway ; *Aquatic Organisms/microbiology ; }, abstract = {Recent evidence suggests that there is a major switch in coastal seafloor microbial ecology already at a mildly deteriorated macrofaunal state. This knowledge is of critical value in the management and conservation of the coastal seafloor. We therefore aimed to determine the relationships between seafloor microbiota and macrofauna on a regional scale. We compared prokaryote, macrofauna, chemical, and geographical data from 1546 seafloor samples, which varied in their exposure to aquaculture activities along the Norwegian and Icelandic coasts. We found that the seafloor samples contained either a network centralized by a sulfur oxidizer (42.4% of samples, n = 656) or a network centralized by an archaeal ammonium oxidizer (44.0% of samples, n = 681). Very few samples contained neither network (9.8% of samples, n = 151) or both (3.8% of samples, n = 58). Samples with a sulfur oxidizer network had a 10-fold higher risk of macrofauna loss (odds ratios, 95% CI: 9.5 to 15.6), while those with an ammonium oxidizer network had a 10-fold lower risk (95% CI: 0.068 to 0.11). The sulfur oxidizer network was negatively correlated to distance from Norwegian aquaculture sites (Spearman rho = -0.42, p < 0.01) and was present in all Icelandic samples (n = 274). The ammonium oxidizer network was absent from Icelandic samples and positively correlated to distance from Norwegian aquaculture sites (Spearman rho = 0.67, p < 0.01). Based on 356 high-quality metagenome-assembled genomes (MAGs), we found that bicarbonate-dependent carbon fixation and low-affinity oxygen respiration were associated with the ammonium oxidizer network, while the sulfur oxidizer network was associated with ammonium retention, sulfur metabolism, and high-affinity oxygen respiration. In conclusion, our findings highlight the critical roles of microbial networks centralized by sulfur and ammonium oxidizers in mild macrofauna deterioration, which should be included as an essential part of seafloor surveillance.}, }
@article {pmid40209676, year = {2025}, author = {Schell, LD and Carmody, RN}, title = {An energetic framework for gut microbiome-mediated obesity induced by early-life exposure to antibiotics.}, journal = {Cell host &amp; microbe}, volume = {33}, number = {4}, pages = {470-483}, doi = {10.1016/j.chom.2025.03.009}, pmid = {40209676}, issn = {1934-6069}, mesh = {*Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/adverse effects/pharmacology ; *Obesity/chemically induced/microbiology/etiology/metabolism ; Animals ; Humans ; *Energy Metabolism/drug effects ; Female ; Mice ; Male ; }, abstract = {Early-life antibiotic (ELA) exposure has garnered attention for its potential role in modulating obesity risk, although outcomes from mouse experiments and human epidemiological studies often vary based on dosage and sex. Low-dose (subtherapeutic) antibiotics can enhance energy availability through moderate alterations in gut microbiome profile, while high-dose (therapeutic) antibiotics substantially deplete the gut microbiota, thereby contributing to short-term negative energy balance. In this perspective, we propose a framework to understand how these distinct impacts of antibiotics on the gut microbiome during critical developmental windows shape long-term obesity risk through their influence on host energy balance. Using this framework, we then propose several hypotheses to explain variation in ELA-induced obesity outcomes across males and females. We conclude by discussing the evolutionary implications of ELAs, positing that the response of the gut microbiome to ELAs may signal energy availability and environmental volatility, influencing metabolic programming and adaptive traits across generations.}, }
@article {pmid40208324, year = {2025}, author = {Mazzella, V and Zahn, G and Dell'Anno, A and Pons, LN}, title = {Marine Mycobiomes Colonize Mediterranean Sponge Hosts in a Random Fashion.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {25}, pmid = {40208324}, issn = {1432-184X}, support = {C63C22000520001//National Recovery and Resilience Plan (NRRP)/ ; C63C22000520001//National Recovery and Resilience Plan (NRRP)/ ; C63C22000520001//National Recovery and Resilience Plan (NRRP)/ ; }, mesh = {Animals ; *Porifera/microbiology ; *Fungi/classification/genetics/isolation &amp; purification ; Mediterranean Sea ; *Mycobiome ; *Seawater/microbiology ; Phylogeny ; Biodiversity ; DNA Barcoding, Taxonomic ; DNA, Fungal/genetics ; Ecosystem ; }, abstract = {Marine sponges are widespread, sessile, filter-feeding animals, known for living in association with complex prokaryotic communities structured by host species. Though marine fungi are ubiquitous across marine environments, little is known about sponge-associated fungal communities (mycobiome). Indeed, aside from a few studies based on the isolation of fungal strains for biotechnological purposes, little information is available to understand the diversity and structure of sponge mycobiome. Here, a metabarcoding approach based on the ITS1 marker was applied to examine the structure and composition of fungal communities associated with four Mediterranean sponges. The species: Petrosia ficiformis, Chondrosia reniformis, Crambe crambe, and Chondrilla nucula were analyzed along with the surrounding seawater, revealing Aspergillus (1-56%), Cladosporium (1-75%), Malassezia (1-38.5%), and Pennicillium (1.5-36%) as the most represented fungal genera. Our data showed high intra-specific variability and no clear core mycobiome within each of the sponge species host, suggesting stochastic and perhaps transient community membership. This study sheds light on one of the most abundant yet least understood components of the marine ecosystem. Unraveling the dynamics of fungal interactions within sponge holobionts is essential to advance our understanding of their ecological roles and functions. By addressing the enigmatic nature of sponge-associated fungi, this research opens new avenues for exploring their contributions to marine ecosystems and resolving the many unanswered questions in this field.}, }
@article {pmid40208265, year = {2025}, author = {DiPietri, VT and Grady, ZS and Frost, AN and Stitzel, SE and Sivey, JD}, title = {Toilet Bowl Cleaning Tablets as Sources of Chlorine, Bromine, and Disinfection Byproducts in Wastewater.}, journal = {Environmental science &amp; technology}, volume = {59}, number = {15}, pages = {7646-7655}, doi = {10.1021/acs.est.4c12026}, pmid = {40208265}, issn = {1520-5851}, mesh = {*Chlorine/analysis ; *Wastewater/chemistry ; *Bromine/analysis ; Disinfection ; *Water Pollutants, Chemical/analysis ; Tablets ; *Disinfectants/analysis ; }, abstract = {Commercial toilet bowl cleaning tablets were examined in laboratory systems to characterize their release of active halogens and their potential to form trihalomethanes (THMs) when combined with synthetic sewage. Active halogens (e.g., HOCl, HOBr, and reactive halamines) were quantified via derivatization with 1,3,5-trimethoxybenzene prior to analysis by liquid chromatography. The effects of several variables on halogen release profiles were examined, including pH, ionic strength, temperature, tank solution volume, flushing frequency, and tablet brand. Changes in pH resulted in modest or no appreciable changes in halogen release profiles. Release of active halogens increased as ionic strength decreased and as temperature increased. Tank volume, flushing frequency, and tablet brand had pronounced impacts on halogen release profiles. Maximum measured active chlorine and bromine concentrations in toilet tank water were 189 mg/L as Cl2 and 164 mg/L as Cl2, respectively. Active halogens persisted in toilet bowl water for >24 h. When toilet-tablet-treated water was combined with synthetic sewage, THMs formed at up to 219 ppb with bromine incorporation factors up to 2.86. Active halogens and highly brominated THMs released into wastewater from toilet tablets could have implications for downstream microbial ecology, septic system performance, and overall water quality.}, }
@article {pmid40206699, year = {2025}, author = {Connors, E and Gallagher, KL and Dutta, A and Oliver, M and Bowman, JS}, title = {Suspended detrital particles support a distinct microbial ecosystem in Palmer Canyon, Antarctica, a coastal biological hotspot.}, journal = {Polar biology}, volume = {48}, number = {2}, pages = {62}, pmid = {40206699}, issn = {0722-4060}, support = {S10 OD026929/OD/NIH HHS/United States ; }, abstract = {UNLABELLED: The coastal region of the Western Antarctic Peninsula is considered a biological hotspot with high levels of phytoplankton productivity and krill biomass. Recent in situ observations and particle modeling studies of Palmer Canyon, a deep bathymetric feature in the region, demonstrated the presence of a recirculating eddy that traps particles, retaining a distinct particle layer over the summer season. We applied metagenomic sequencing and Imaging Flow Cytobot (IFCB) analysis to characterize the microbial community in the particle layer. We sampled across the upper water column (< 200 m) along a transect to identify the locations of increased particle density, categorizing particles into either living cells or cellular detritus via IFCB. An indicator species analysis of community composition demonstrated the diatom Corethron and the bacteria Sulfitobacter were significantly highly abundant in samples with high levels of living cells, while the mixotrophic dinoflagellate Prorocentrum texanum and prokaryotes Methanomassiliicoccales and Fluviicola taffensis were significantly more abundant in samples with high detritus within the particle layer. From our metagenomic analysis, the significantly differentially abundant metabolic pathway genes in the particle layer of Palmer Canyon included pathways for anaerobic metabolism, such as methanogenesis and sulfate reduction. Overall, our results indicate that distinct microbial species and metabolic pathway genes are present in the retained particle layer of Palmer Canyon.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00300-025-03380-y.}, }
@article {pmid40205489, year = {2025}, author = {Soares, A and Rassner, SME and Edwards, A and Farr, G and Blackwell, N and Sass, H and Persiani, G and Schofield, D and Mitchell, AC}, title = {Hydrogeological and geological partitioning of iron and sulfur cycling bacterial consortia in subsurface coal-based mine waters.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {5}, pages = {}, pmid = {40205489}, issn = {1574-6941}, support = {//S&#xea;r Cymru/ ; NE/V012991/1//Natural Environment Research Council/ ; }, mesh = {*Sulfur/metabolism ; *Iron/metabolism ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Coal/microbiology ; *Groundwater/microbiology/chemistry ; *Microbial Consortia ; Oxidation-Reduction ; Seasons ; Phylogeny ; Sulfides/metabolism ; Wales ; Coal Mining ; Mining ; }, abstract = {Pyrite oxidation drives iron and sulfur availability across Earth's subsurface and is partly microbially mediated. Subsurface microbial communities accelerate this process at circumneutral pH directly by weathering pyritic surfaces and indirectly by causing changes to the surrounding microenvironment, thereby further accelerating pyrite weathering. However, our understanding of community structure dynamics and associated biogeochemistry in Fe- and S-rich lithologies, e.g. pyritic coal, is limited. Here, we present the first comprehensive regional and seasonal genus-level survey of bacterial groundwater communities in a pyritic coal-based aquifer in the South Wales Coalfield (SWC), using 16S rRNA gene amplicon sequencing. Seasonal changes in community structure were limited, suggesting limited influence of surface processes on subsurface communities. Instead, hydrogeologically distinct mine water blocks (MWB) and coal rank largely explained bacterial community structure variation across sites. Fe(II)-oxidizing Betaproteobacteriales genera Gallionella and Sideroxydans dominated the bacterial communities across nine sites and seven MWBs, while three sites within a single MWB, were dominated by S-oxidizing Epsilonbacteraeota genera Sulfuricurvum and Sulfurovum. The cooccurrence of pairs of Fe(II)- and S-oxidizing bacterial genera suggests functional redundancy, which coupled with genus-specific morphologies and life strategies, indicates the importance of distinct environmental and ecological niches within the SWC groundwater at seasonal and regional scales.}, }
@article {pmid40205473, year = {2025}, author = {Rodriguez-Cruz, UE and Ochoa-Sánchez, M and Eguiarte, LE and Souza, V}, title = {Running against the clock: exploring microbial diversity in an extremely endangered microbial oasis in the Chihuahuan Desert.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {5}, pages = {}, pmid = {40205473}, issn = {1574-6941}, support = {//DGAPA/ ; IG200319//UNAM/ ; //Instituto de Ecolog&#xed;a, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; }, mesh = {RNA, Ribosomal, 16S/genetics ; *Biodiversity ; *Bacteria/classification/genetics/isolation &amp; purification ; Desert Climate ; *Microbiota/genetics ; Phylogeny ; Ecosystem ; Groundwater/microbiology ; }, abstract = {The Cuatro Ciénegas Basin is a biodiversity hotspot known for its unique biodiversity. However, this ecosystem is facing severe anthropogenic threats that are drying its aquatic systems. We investigated microbial communities at three sites with different physicochemical and environmental characteristics (Pozas Rojas, Archean Domes, and the Churince system) within the basin to explore potential connections to deep aquifers and determine if the sites shared microorganisms. Utilizing 16S rRNA gene data, we identified a core microbiota between Pozas Rojas (PR) and Archean Domes (AD). Sulfur reduction appears to shape the microbial connectivity among sites, since sulfur-reducing bacteria has the highest prevalence between samples from PR and AD: Halanaerobium sp. (88.46%) and Desulfovermiculus halophilus (65%); and between the Churince system and AD: Halanaerobium sp. (63%) and D. halophilus (60%). Furthermore, metagenome-assembled genomes from Ectothiorhodospira genus were found in both AD and Churince, suggesting microbial dispersal. An important finding is that microbial diversity in the AD system declined, from 2016 to 2023 the ecosystem lost 29 microbial phyla. If this trend continues, the basin will lose most of its water, resulting in the loss of various prokaryotic lineages and potential biotechnological solutions, such as enzymes or novel antibiotics. Our findings highlighting the need for water extraction regulations to preserve the basin's biodiversity.}, }
@article {pmid40205253, year = {2025}, author = {Dasgupta, M and Paul, R and Chowdhury, P and Mondal, S and Ahmed, J and Mukherjee, C and Das, S and Tribedi, P}, title = {Management of Enterococcus faecalis biofilms: a combinatorial approach with phytochemical.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {56}, number = {2}, pages = {1131-1143}, pmid = {40205253}, issn = {1678-4405}, support = {TNU/R&amp;D/MP/2021/010//The Neotia University/ ; }, mesh = {*Biofilms/drug effects/growth &amp; development ; *Enterococcus faecalis/drug effects/physiology ; Microbial Sensitivity Tests ; *Anti-Bacterial Agents/pharmacology ; *Phytochemicals/pharmacology ; *Benzoquinones/pharmacology ; *Benzaldehydes/pharmacology ; Humans ; }, abstract = {The rapid emergence of antimicrobial resistance in Enterococcus faecalis infections was primarily due to their robust biofilm formation, highlighting the urgent need for meaningful strategies. Since combinatorial application of natural phytochemical often offer promising outcomes in dealing with microbial infections, present study indicated the pharmacological, antimicrobial and antibiofilm potential of combinatorial strategies of natural phytochemical involving cuminaldehyde and thymoquinone against E. faecalis. Towards this direction, in silico analysis suggested that both compounds could show favourable oral bioavailability and high GI absorption, with a considerable solubility and drug-likeness profiles. Furthermore, in vitro antimicrobial assay indicated that the minimum inhibitory concentrations (MIC) of cuminaldehyde and thymoquinone were found to be 500 µg/mL and 30 µg/mL, respectively against E. faecalis. Thereafter, the fractional inhibitory concentration (FIC) index score of 0.73 indicated an additive effect prevailed between cuminaldehyde and thymoquinone, enhancing their antimicrobial potential. Thereafter, sub-MIC doses of cuminaldehyde (40 µg/mL) and thymoquinone (8 µg/mL) were selected to assess their antibiofilm potential. Though the compounds were able to show antibiofilm activity separately, their combination was significantly more effective, reduced biofilm formation by approximately 80%, and decreased production of extracellular polymeric substance (EPS) and protein content by ~ 76% and ~ 70%, respectively. Further studies revealed that the antibiofilm activity of the test compounds could likely to be attributed to the accumulation of reactive oxygen species (ROS) and enhancement of membrane permeability. Taken together, all this experimental observation revealed that combination of these natural compounds could potentially improve the treatment outcomes of biofilm-borne infections of E. faecalis.}, }
@article {pmid40203032, year = {2025}, author = {Timilsina, S and Iruegas-Bocardo, F and Jibrin, MO and Sharma, A and Subedi, A and Kaur, A and Minsavage, GV and Huguet-Tapia, JC and Klein-Gordon, J and Adhikari, P and Adhikari, TB and Cirvilleri, G and de la Barrera, LBT and Bernal, E and Creswell, TC and Doan, TTK and Coutinho, TA and Egel, DS and Félix-Gastélum, R and Francis, DM and Kebede, M and Ivey, ML and Louws, FJ and Luo, L and Maynard, ET and Miller, SA and Nguyen, NTT and Osdaghi, E and Quezado-Duval, AM and Roach, R and Rotondo, F and Ruhl, GE and Shutt, VM and Thummabenjapone, P and Trueman, C and Roberts, PD and Jones, JB and Vallad, GE and Goss, EM}, title = {Diversification of an emerging bacterial plant pathogen; insights into the global spread of Xanthomonas euvesicatoria pv. perforans.}, journal = {PLoS pathogens}, volume = {21}, number = {4}, pages = {e1013036}, pmid = {40203032}, issn = {1553-7374}, mesh = {*Xanthomonas/genetics/pathogenicity/classification ; *Plant Diseases/microbiology ; *Solanum lycopersicum/microbiology ; *Genetic Variation ; Phylogeny ; }, abstract = {Emerging and re-emerging plant diseases continue to present multifarious threats to global food security. Considerable recent efforts are therefore being channeled towards understanding the nature of pathogen emergence, their spread and evolution. Xanthomonas euvesicatoria pv. perforans (Xep), one of the causal agents of bacterial spot of tomato, rapidly emerged and displaced other bacterial spot xanthomonads in many tomato production regions around the world. In less than three decades, it has become a dominant xanthomonad pathogen in tomato production systems across the world and presents a compelling example for understanding diversification of recently emerged bacterial plant pathogens. Although Xep has been continuously monitored in Florida since its discovery, the global population structure and evolution at the genome-scale is yet to be fully explored. The objectives of this work were to determine genetic diversity globally to ascertain if different tomato production regions contain genetically distinct Xep populations, to examine genetic relatedness of strains collected in tomato seed production areas in East Asia and other production regions, and to evaluate variation in type III secretion effectors, which are critical pathogenicity and virulence factors, in relationship to population structure. We used genome data from 270 strains from 13 countries for phylogenetic analysis and characterization of type III effector gene diversity among strains. Our results showed notable genetic diversity in the pathogen. We found genetically similar strains in distant tomato production regions, including seed production regions, and diversification over the past 100 years, which is consistent with intercontinental dissemination of the pathogen in hybrid tomato production chains. Evolution of the Xep pangenome, including the acquisition and loss of type III secreted effectors, is apparent within and among phylogenetic lineages. The apparent long-distance movement of the pathogen, together with variants that may not yet be widely distributed, poses risks of emergence of new variants in tomato production.}, }
@article {pmid40202691, year = {2025}, author = {Pimentel, AC and Cesar, CS and Martins, AHB and Martins, M and Cogni, R}, title = {Wolbachia Offers Protection Against Two Common Natural Viruses of Drosophila.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {24}, pmid = {40202691}, issn = {1432-184X}, mesh = {Animals ; *Wolbachia/physiology ; *Drosophila melanogaster/virology/microbiology ; *Drosophila/virology/microbiology ; Symbiosis ; Female ; }, abstract = {Wolbachia pipientis is a maternally transmitted endosymbiont infecting more than half of terrestrial arthropod species. Wolbachia can express parasitic phenotypes such as manipulation of host reproduction and mutualist phenotypes such as protection against RNA virus infections. Because Wolbachia can invade populations by reproductive manipulation and block virus infection, it is used to modify natural insect populations. However, the ecological importance of virus protection is not yet clear, especially due to scarce information on Wolbachia protection against viruses that are common in nature. We used systemic infection to investigate whether Wolbachia protects its host by suppressing the titer of DMELDAV and DMelNora virus, two viruses that commonly infect Drosophila melanogaster flies in natural populations. Antiviral protection was tested in three systems to assess the impact of Wolbachia strains across species: (1) a panel of Wolbachia strains transfected into Drosophila simulans, (2) two Wolbachia strains introgressed into the natural host D. melanogaster, and (3) two native Wolbachia strains in their natural hosts Drosophila baimaii and Drosophila tropicalis. We showed that certain Wolbachia strains provide protection against DMelNora virus and DMELDAV, and this protection is correlated with Wolbachia density, which is consistent with what has been observed in protection against other RNA viruses. Additionally, we found that Wolbachia does not protect its original host, D. melanogaster, from DMELDAV infection. While native Wolbachia can reduce DMELDAV titers in D. baimaii, this effect was not detected in D. tropicalis. Although the Wolbachia protection-induced phenotype seems to depend on the virus, the specific Wolbachia strain, and the host species, our findings suggest that antiviral protection may be one of the mutualistic effects that helps explain why Wolbachia is so widespread in arthropod populations.}, }
@article {pmid40201423, year = {2025}, author = {Boden, L and Bludau, D and Sieber, G and Deep, A and Baikova, D and David, GM and Hadžiomerović, U and Stach, TL and Boenigk, J}, title = {The impact of elevated temperature and salinity on microbial communities and food selectivity in heterotrophic nanoflagellates in the Boye River.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf049}, pmid = {40201423}, issn = {2730-6151}, abstract = {Microbial predator-prey interactions play a crucial role in aquatic food webs. Bacterivorous protists not only regulate the quantity and biomass of bacterial populations but also profoundly influence the structure of bacterial communities. Consequently, alterations in both the quantity and quality of protist bacterivory can influence the overall structure of aquatic food webs. While it is well-documented that changes in environmental conditions or the occurrence of abiotic stressors can lead to shifts in microbial community compositions, the impact of such disturbances on food selection remains unknown. Here, we investigated the effects of elevated temperature and salinization on food selectivity of heterotrophic nanoflagellates by monitoring the uptake of preselected target bacteria via catalyzed reporter deposition fluorescence in situ hybridization and fluorescence microscopy. Our results indicate that salinization, but not increased temperature, significantly increased the flagellates' selection against Microbacterium lacusdiani (Actinomycetota). However, the effect of the reduced grazing pressure was counterbalanced by the negative effect of increased salinity on the growth of Actinomycetota. Our results suggest that the effect of stressors on the feeding behavior of protistan predators may strongly affect the composition of their prey community, when bacterial taxa are concerned that are less sensitive to the particular stressor.}, }
@article {pmid40200306, year = {2025}, author = {Bindels, LB and Watts, JEM and Theis, KR and Carrion, VJ and Ossowicki, A and Seifert, J and Oh, J and Shao, Y and Hilty, M and Kumar, P and Hildebrand, F and Lovejoy, C and Wigley, P and Yu, K and Zhang, M and Zhang, T and Walter, J and Desai, MS and Huws, SA and Schriml, LM and Ravel, J and Fricke, WF and Eloe-Fadrosh, EA and Lee, CK and Clavel, T}, title = {A blueprint for contemporary studies of microbiomes.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {95}, pmid = {40200306}, issn = {2049-2618}, mesh = {*Microbiota ; *Publishing/standards ; }, abstract = {This editorial piece co-authored by the Senior Editors at Microbiome aims to highlight current challenges in the field of environmental and host-associated microbiome research. We also take the opportunity to clarify our expectations for the articles submitted to the journal. At Microbiome, we are seeking studies that provide either new mechanistic insights into the role of microbiomes in health and environmental systems or substantial conceptual or technical advances. Manuscripts need to meet high standards of language accuracy, quality of microbiome analyses, and data and protocol availability, including detailed reporting of wet-lab and in silico protocols, all of which can critically enhance transparency and reproducibility. We think that such efforts are essential to push the boundaries of our knowledge on microbiomes in a concerted, international effort.}, }
@article {pmid40197060, year = {2025}, author = {Giacomini, JJ and Torres-Morales, J and Dewhirst, FE and Borisy, GG and Mark Welch, JL}, title = {Spatial ecology of the Neisseriaceae family in the human oral cavity.}, journal = {Microbiology spectrum}, volume = {13}, number = {5}, pages = {e0327524}, pmid = {40197060}, issn = {2165-0497}, support = {R01 DE016937/DE/NIDCR NIH HHS/United States ; R01 DE022586/DE/NIDCR NIH HHS/United States ; R01 DE030136/DE/NIDCR NIH HHS/United States ; }, abstract = {The human oral microbiome is a diverse ecosystem in which bacterial species have evolved to occupy specific niches within the oral cavity. The Neisseriaceae family, which includes human oral species in the genera Neisseria, Eikenella, Kingella, and Simonsiella, plays a significant role in both commensal and pathogenic relationships. In this study, we investigate the distribution and functional adaptations of Neisseriaceae species across oral habitats, focusing on their site tropisms and ecological roles. We employed a metapangenomic approach in which a curated set of reference genomes representing Neisseriaceae diversity was used for competitive mapping of metagenomic reads. Our analysis revealed distinct habitat preferences among Neisseriaceae species, with Kingella oralis, Neisseria elongata, and Neisseria mucosa primarily found in dental plaque; Neisseria subflava on the tongue dorsum; and Neisseria cinerea in the keratinized gingiva. Functional enrichment analyses identified genes and pathways underpinning habitat-specific adaptations. Plaque specialists showed metabolic versatility, with adaptations in nitrogen metabolism, including nitrate reduction and denitrification, lysine degradation, and galactose metabolism. Tongue dorsum specialists exhibited adaptations including enhanced capabilities for amino acid biosynthesis, short-chain fatty acid and glycerol transport, as well as lipopolysaccharide glycosylation, which may aid in resisting antimicrobial peptides and maintaining membrane integrity. These findings provide insights into the ecological roles and adaptive strategies of Neisseriaceae species within the human oral microbiome and establish a foundation for exploring functional specialization and microbial interactions in these niches.IMPORTANCEUnraveling the distribution and functional adaptations of Neisseriaceae within the human oral microbiome is essential for understanding the roles of these abundant and prevalent commensals in both health and disease. Through a metapangenomic approach, we uncovered distinct habitat preferences of various Neisseriaceae taxa across the oral cavity and identified key genetic traits that may drive their habitat specialization and role in host-microbe interactions. These insights enhance our understanding of the microbial dynamics that shape oral microbial ecology, offering potential pathways for advancing oral health research.}, }
@article {pmid40197052, year = {2025}, author = {Liu, S and Ru, J and Guo, X and Gao, Q and Deng, S and Lei, J and Song, J and Zhai, C and Wan, S and Yang, Y}, title = {Altered precipitation and nighttime warming reshape the vertical distribution of soil microbial communities.}, journal = {mSystems}, volume = {10}, number = {5}, pages = {e0124824}, pmid = {40197052}, issn = {2379-5077}, support = {32161123002//MOST | National Natural Science Foundation of China (NSFC)/ ; 2019QZKK0503//the Second Tibetan Plateau Scientific Expedition and Research (STEP) program/ ; 20223BBG74S02//the Key Technology R&amp;D Program of JiangXi Province grant/ ; KY-23ZK01//the Hainan Institute of National Park grant/ ; }, mesh = {*Soil Microbiology ; *Microbiota ; Bacteria/genetics/classification ; *Rain ; China ; Fungi/genetics/classification ; Climate Change ; Soil/chemistry ; Grassland ; Biodiversity ; }, abstract = {Soil depth determines microbial community composition. Yet, it remains largely unexplored how climate changes affect the vertical distribution of soil microbial communities. Here, we investigated the effects of altered precipitation and nighttime warming on microbial communities in the topsoils (0-20 cm) and subsoils (20-50 cm) of a temperate grassland in Inner Mongolia, China. As commonly observed under nutrient scarcity conditions, bacterial and fungal α-diversity and network complexity decreased with soil depth. However, protistan α-diversity and network complexity increased, which was attributed to less niche overlap and smaller body size. Strikingly, the slopes of linear regressions of microbial α-diversity/network complexity and soil depth were all reduced by altered precipitation. Microbial community composition was significantly influenced by both depth and reduced precipitation, and to a lesser extent by nighttime warming and elevated precipitation. The ribosomal RNA gene operon (rrn) copy number, a genomic proxy of bacterial nutrient demand, decreased with soil depth, and the percentages of positive network links were higher in the subsoil, supporting the "hunger game" hypothesis. Both reduced precipitation and nighttime warming decreased the rrn copy number in the subsoils while increasing the percentages of positive links, enhancing potential niche sharing among bacterial species. The stochasticity level of bacterial and fungal community assemblies decreased with soil depth, showing that depth acted as a selection force. Altered precipitation increased stochasticity, attenuating the depth's filtering effect and diminishing its linear relationship with microbial diversity. Collectively, we unveiled the predominant influence of altered precipitation in affecting the vertical distribution of soil microbial communities.IMPORTANCEUnderstanding how climate change impacts the vertical distribution of soil microbial communities is critical for predicting ecosystem responses to global environmental shifts. Soil microbial communities exhibit strong depth-related stratification, yet the effects of climate change variables, such as altered precipitation and nighttime warming, on these vertical patterns have been inadequately studied. Our research uncovers that altered precipitation disrupts the previously observed relationships between soil depth and microbial diversity, a finding that challenges traditional models of soil microbial ecology. Furthermore, our study provides experimental support for the hunger game hypothesis, highlighting that oligotrophic microbes, characterized by lower ribosomal RNA gene operon (rrn) copy numbers, are selectively favored in nutrient-poor subsoils, fostering increased microbial cooperation for resource exchange. By unraveling these complexities in soil microbial communities, our findings offer crucial insights for predicting ecosystem responses to climate change and for developing strategies to mitigate its adverse impacts.}, }
@article {pmid40196585, year = {2025}, author = {Dellicour, S and Gámbaro, F and Jacquot, M and Lequime, S and Baele, G and Gilbert, M and Pybus, OG and Suchard, MA and Lemey, P}, title = {Comparative performance of novel viral landscape phylogeography approaches.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40196585}, issn = {2692-8205}, support = {/WT_/Wellcome Trust/United Kingdom ; R01 AI153044/AI/NIAID NIH HHS/United States ; R01 AI162611/AI/NIAID NIH HHS/United States ; U19 AI135995/AI/NIAID NIH HHS/United States ; }, abstract = {The fast rate of evolution in RNA viruses implies that their evolutionary and ecological processes occur on the same time scale. Genome sequences of these pathogens can therefore contain information about the processes that govern their transmission and dispersal. In particular, landscape phylogeographic approaches use phylogeographic reconstructions to investigate the impact of environmental factors and variables on the spatial spread of viruses. Here, we extend and improve existing approaches and develop three novel landscape phylogeographic methods that can test the impact of continuous environmental factors on the diffusion velocity of viral lineages. In order to evaluate the different methods, we also implemented two simulation frameworks to test and compare their statistical performance. The results enable us to formulate clear guidelines for the use of three complementary landscape phylogeographic approaches that have sufficient statistical power and low rates of false positives. Our open-source methods are available to the scientific community and can be used to investigate the drivers of viral spread, with potential benefits for understanding virus epidemiology and designing tailored intervention strategies.}, }
@article {pmid40195174, year = {2025}, author = {Burazerović, J and Jovanović, M and Savković, &#x17d; and Breka, K and Stupar, M}, title = {Finding the Right Host in the Darkness of the Cave-New Insights into the Ecology and Spatio-temporal Dynamics of Hyperparasitic Fungi (Arthrorhynchus nycteribiae, Laboulbeniales).}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {23}, pmid = {40195174}, issn = {1432-184X}, support = {451- 03- 66/2024- 03/200178; 451- 03- 65/2024- 03/ 200178//Ministry of Science, Technological Development and Innovation of the Republic of Serbia/ ; 451- 03- 66/2024- 03/200178; 451- 03- 65/2024- 03/ 200178//Ministry of Science, Technological Development and Innovation of the Republic of Serbia/ ; 451- 03- 66/2024- 03/200178; 451- 03- 65/2024- 03/ 200178//Ministry of Science, Technological Development and Innovation of the Republic of Serbia/ ; 451- 03- 66/2024- 03/200178; 451- 03- 65/2024- 03/ 200178//Ministry of Science, Technological Development and Innovation of the Republic of Serbia/ ; }, mesh = {Animals ; *Chiroptera/parasitology/microbiology ; *Caves/microbiology ; *Ascomycota/genetics/isolation &amp; purification/physiology/classification ; *Diptera/microbiology ; Serbia ; Male ; Female ; Phylogeny ; }, abstract = {The aim of this study was to determine the presence of the hyperparasitic fungus Arthrorhynchus nycteribiae and to analyze its spatio-temporal pattern in the two bat flies (Penicillidia conspicua and P. dufourii) parasitizing on bats. We collected 612 samples of bat flies from 400 bats in 20 caves in the Central Balkans. Hyperparasite was identified based on morphological and molecular analyses of rDNA genes (LSU and SSU). A. nycteribiae was reported for the first time in Bosnia and Herzegovina and Montenegro, and confirmed in Serbia. Of the 20 sites examined, we found A. nycteribiae at 11 sites. The prevalence of A. nycteribiae infection in the bats examined was approximately 17%. Miniopterus schreibersii harbored the highest number of bat flies and was the only bat species hosting the infected bat flies of the species P. conspicua. Our results showed significant differences in infection patterns during the different seasons: the highest prevalence of bat flies with hyperparasitic fungi was found in the summer season (23%) and the lowest in spring (2%). Female bat fly hosts showed a significantly higher prevalence of infection than male bat flies. This study makes an important contribution to the knowledge of the distribution of A. nycteribiae and to the understanding of complex parasite-host relationships in the poorly studied areas of the Central Balkans.}, }
@article {pmid40194740, year = {2025}, author = {Nieman, DC and Sakaguchi, CA and Williams, JC and Lawson, J and Lambirth, KC and Omar, AM and Mulani, FA and Zhang, Q}, title = {Gut Prevotella copri abundance linked to elevated post-exercise inflammation.}, journal = {Journal of sport and health science}, volume = {14}, number = {}, pages = {101039}, pmid = {40194740}, issn = {2213-2961}, abstract = {PURPOSE: This study aimed to examine the linkage between gut microbiome taxa and exercise-induced inflammation.<br><br>METHODS: Twenty-five cyclists provided 4 stool samples during a 10-week period and cycled vigorously for 2.25 h at 67% maximal oxygen uptake (VO2max) in a laboratory setting. Blood samples were collected pre- and post-exercise, with additional samples collected at 1.5-h, 3-h, and 24-h post exercise. Primary outcomes included stool microbiome composition and alpha diversity via whole genome shotgun (WGS) sequencing (averaged from 4 stool samples) and a targeted panel of 75 plasma oxylipins. A total of 5719 taxa were identified, and the 339 that were present in more than 20% of stool samples were used in the analysis. Alpha diversity was calculated by evenness, and the Analysis of Composition of Microbiomes (ANCOM) differential abundance analysis was performed using Quantitative Insights Into Microbial Ecology-2 (QIIME2). A composite variable was calculated from 8 pro-inflammatory oxylipins generated from arachidonic acid (ARA) and cytochrome P-450 (CYP).<br><br>RESULTS: ARA-CYP oxylipins were significantly elevated for at least 3-h post-exercise (p < 0.001); they were strongly and positively related to Prevotella copri (P. copri) abundance (R[2]&#x202f;=&#x202f;0.676, p < 0.001) and negatively related to gut microbiome alpha diversity (R[2]&#x202f;=&#x202f;0.771, p < 0.001).<br><br>CONCLUSION: This analysis revealed for the first time a novel, positive relationship between gut microbiome P. copri abundance in cyclists and post-exercise pro-inflammatory oxylipins. These data demonstrate that about two-thirds of the wide variance in inflammation following prolonged and intensive exercise is largely explained by the abundance of a single gut bacterial species: P. copri.}, }
@article {pmid40186763, year = {2025}, author = {Huang, YD and Zhao, XL and Lin, Y and Ouyang, XM and Cheng, XS and Liang, LY and Huo, YN and Xie, GJ and Lin, JH and Jazag, A and Guleng, B}, title = {Mindin orchestrates the macrophage-mediated resolution of liver fibrosis in mice.}, journal = {Hepatology international}, volume = {}, number = {}, pages = {}, pmid = {40186763}, issn = {1936-0541}, support = {No. 81970460//National Natural Science Foundation of China/ ; No. 2023J011598//Natural Science Foundation of Fujian Province/ ; }, abstract = {BACKGROUND &amp; AIMS: Liver disease that progresses to cirrhosis is an enormous health problem worldwide. The extracellular matrix protein Mindin is known to have immune functions, but its role in liver homeostasis remains largely unexplored. We aimed to characterize the role of Mindin in the regulation of liver fibrosis.<br><br>APPROACH &amp; RESULTS: Mindin was upregulated in mice with carbon tetrachloride (CCl4) or thioacetamide (TAA)-induced liver fibrosis, and was primarily expressed in hepatocytes. Global Mindin knockout mice were generated, which were susceptible to liver fibrosis. Notably, Mindin failed to activate hepatic stellate cells directly; however, it played a role in promoting the recruitment and phagocytosis of macrophages, and caused a phenotypic switch toward restorative macrophages during liver fibrosis. Furthermore, Mindin was found to bind to the &#x3b1;M-I domain of CD11b/CD18 heterodimeric receptors. To further explore this mechanism, we created Mindin and CD11b double-knockout (DKO) mice. In DKO mice, phagocytosis was further reduced, and liver fibrosis was markedly exacerbated.<br><br>CONCLUSIONS: Mindin promotes the resolution of liver fibrosis and the Mindin/CD11b axis might represent a novel target for the macrophage-mediated regression of liver fibrosis.}, }
@article {pmid40186595, year = {2025}, author = {Pérez, J and Boyero, L and Pearson, RG and Gessner, MO and Tonin, A and López-Rojo, N and Rubio-Ríos, J and Correa-Araneda, F and Alonso, A and Cornejo, A and Albariño, RJ and Anbalagan, S and Barmuta, LA and Boulton, AJ and Burdon, FJ and Caliman, A and Callisto, M and Campbell, IC and Cardinale, BJ and Carneiro, LS and Casas, JJ and Chará-Serna, AM and Chauvet, E and Colón-Gaud, C and Davis, AM and de Eyto, E and Degebrodt, M and Díaz, ME and Douglas, MM and Encalada, AC and Figueroa, R and Flecker, AS and Fleituch, T and Frainer, A and García, EA and García, G and García, PE and Giller, PS and Gómez, JE and Gonçalves, JF and Graça, MAS and Hall, RO and Hamada, N and Hepp, LU and Hui, C and Imazawa, D and Iwata, T and Junior, ESA and Landeira-Dabarca, A and Leal, M and Lehosmaa, K and M'Erimba, CM and Marchant, R and Martins, RT and Masese, FO and Maul, M and McKie, BG and Medeiros, AO and Middleton, JA and Muotka, T and Negishi, JN and Ramírez, A and Rezende, RS and Richardson, JS and Rincón, J and Serrano, C and Shaffer, AR and Sheldon, F and Swan, CM and Tenkiano, NSD and Tiegs, SD and Tolod, JR and Vernasky, M and Wanderi, EW and Watson, A and Yule, CM}, title = {Positive Feedback on Climate Warming by Stream Microbial Decomposers Indicated by a Global Space-For-Time Substitution Study.}, journal = {Global change biology}, volume = {31}, number = {4}, pages = {e70171}, doi = {10.1111/gcb.70171}, pmid = {40186595}, issn = {1365-2486}, support = {UAL18-RNM-B006-B//2014-2020 Operational Programme FEDER Andalusia/ ; IT951-16//Eusko Jaurlaritza/ ; IT1471-22//Eusko Jaurlaritza/ ; UIDB/04292/2020//Funda &#xe7; &#xe3;o para a Ci &#xea;ncia e a Tecnologia, Portugal/ ; //UAL-HIPATIA/ ; }, mesh = {*Rivers/microbiology ; *Climate Change ; Temperature ; *Global Warming ; Plants/metabolism ; Carbon Cycle ; }, abstract = {Decomposition of plant litter is a key ecological process in streams, whose contribution to the global carbon cycle is large relative to their extent on Earth. We examined the mechanisms underlying the temperature sensitivity (TS) of instream decomposition and forecast effects of climate warming on this process. Comparing data from 41 globally distributed sites, we assessed the TS of microbial and total decomposition using litter of nine plant species combined in six mixtures. Microbial decomposition conformed to the metabolic theory of ecology and its TS was consistently higher than that of total decomposition, which was higher than found previously. Litter quality influenced the difference between microbial and total decomposition, with total decomposition of more recalcitrant litter being more sensitive to temperature. Our projections suggest that (i) warming will enhance the microbial contribution to decomposition, increasing CO2 outgassing and intensifying the warming trend, especially in colder regions; and (ii) riparian species composition will have a major influence on this process.}, }
@article {pmid40185870, year = {2025}, author = {Ripoll, J and Stenger, PL and Nuñez, NF and Demenois, J and Stokes, A and Gourmelon, V and Dinh, K and Robert, N and Drouin, J and Mournet, P and Léopold, A and Read, J and Gardes, M and Maggia, L and Carriconde, F}, title = {Unexpected microbial diversity in new Caledonia's ultramafic ecosystems with conservation implications in a biodiversity hotspot.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {11564}, pmid = {40185870}, issn = {2045-2322}, support = {IAC-SLN Research Collaboration N&#xb0;DE2013-041//Soci&#xe9;t&#xe9; Le Nickel (SLN-Eramet Group)/ ; agreement CSF N&#xb0;1PS2013-CNRT.IAC/BIOINDIC//CNRT "Nickel &amp; son Environnement"/ ; }, mesh = {New Caledonia ; *Biodiversity ; *Soil Microbiology ; *Ecosystem ; Mycorrhizae/genetics/classification ; Conservation of Natural Resources ; Fungi/genetics/classification ; *Bacteria/genetics/classification ; }, abstract = {Soils harbour an incredible diversity of microorganisms that play crucial roles in ecosystem functioning. However, this biodiversity remains largely overlooked, with a poor understanding of how patterns form across landscapes. An eDNA metabarcoding approach was used to identify potential overarching patterns in fungal and bacterial communities from ultramafic ecosystems in New Caledonia, a renowned biodiversity hotspot. Our comprehensive analysis revealed several key findings, notably an important microbial diversity in the extreme environments of iron crust soils. Clear tendencies in phyla composition were also observed, with the fungal groups Ascomycota and Mucoromycota acting as potential indicators of land degradation (only in lateritic soils for Mucoromycota). For bacteria, Chloroflexi was characteristic of open vegetation, while Proteobacteria and Cyanobacteria were observed in higher relative abundances in the closed vegetation. The ectomycorrhizal fungal functional group was also found to be rich and unique, with a hypothetical endemism rate of 87%, and over-represented by the Cortinarius genus in rainforests and maquis (shrublands) dominated by ectomycorrhizal plants. Finally, each ultramafic Massif demonstrated a unique microbial community. Thus, our findings provide valuable insights into microbial ecology and emphasize the need for tailored conservation strategies for this biodiversity hotspot.}, }
@article {pmid40184705, year = {2025}, author = {Barrantes-Jiménez, K and Lejzerowicz, F and Tran, T and Calderón-Osorno, M and Rivera-Montero, L and Rodríguez-Sánchez, C and Wikmark, OG and Eiler, A and Grossart, HP and Arias-Andrés, M and Rojas-Jiménez, K}, title = {Anthropogenic imprint on riverine plasmidome diversity and proliferation of antibiotic resistance genes following pollution and urbanization.}, journal = {Water research}, volume = {281}, number = {}, pages = {123553}, doi = {10.1016/j.watres.2025.123553}, pmid = {40184705}, issn = {1879-2448}, mesh = {*Plasmids/genetics ; *Rivers/microbiology ; *Urbanization ; *Drug Resistance, Microbial/genetics ; Bacteria/genetics ; }, abstract = {Plasmids are key determinants in microbial ecology and evolution, facilitating the dissemination of adaptive traits and antibiotic resistance genes (ARGs). Although the molecular mechanisms governing plasmid replication, maintenance, and transfer have been extensively studied, the specific impacts of urbanization-induced pollution on plasmid ecology, diversity, and associated ARGs in tropical regions remain underexplored. This study investigates these dynamics in a tropical aquatic ecosystem, providing novel insights into how pollution shapes plasmid composition and function. In contrast to the observed decrease in chromosomal diversity, we demonstrate that pollution associated with urbanization increases the diversity and taxonomic composition of plasmids within a bacterial community (plasmidome). We analyzed eighteen water and sediment metagenomes, capturing a gradient of pollution and ARG contamination along a tropical urban river. Plasmid and chromosomal diversity profiles were found to be anti-correlated. Plasmid species enrichment along the pollution gradient led to significant compositional differences in water samples, where differentially abundant species suggest plasmid maintenance within specific taxonomic classes. Additionally, the diversity and abundance of ARGs related to the plasmidome increased concomitantly with the intensity of fecal and chemical pollution. These findings highlight the critical need for targeted plasmidome studies to better understand plasmids' environmental spread, as their dynamics are independent of chromosomal patterns. This research is crucial for understanding the consequences of bacterial evolution, particularly in the context of environmental and public health.}, }
@article {pmid40184632, year = {2025}, author = {Huang, Y and Mao, X and Zheng, X and Zhao, Y and Wang, D and Wang, M and Chen, Y and Liu, L and Wang, Y and Polz, MF and Zhang, T}, title = {Longitudinal dynamics and cross-domain interactions of eukaryotic populations in wastewater treatment plants.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {40184632}, issn = {1751-7370}, support = {17212124//Hong Kong GRF/ ; }, mesh = {*Eukaryota/classification/genetics/isolation &amp; purification ; *Sewage/microbiology/virology/parasitology ; *Wastewater/microbiology ; Hong Kong ; Metagenomics ; Animals ; Biodiversity ; Phylogeny ; }, abstract = {Activated sludge is a large reservoir of novel microorganisms and microbial genetic diversity. While much attention has been given to the profile and functions of prokaryotes, the eukaryotic diversity remains largely unexplored. In this study, we analysed longitudinal activated sludge samples spanning 13 years from the largest secondary wastewater treatment plants in Hong Kong, unveiling a wealth of eukaryotic taxa and 681 856 non-redundant protein-coding genes, the majority (416 044) of which appeared novel. Ciliophora was the most dominant phylum with a significant increase after a transient intervention (bleaching event). Our metagenomic analysis reveals close linkage and covariation of eukaryotes, prokaryotes, and prokaryotic viruses (phages), indicating common responses to environmental changes such as transient intervention and intermittent fluctuations. Furthermore, high-resolution cross-domain relationships were interpreted by S-map, demonstrating a predatory role of Arthropoda, Ascomycota, Mucoromycota, and Rotifera. This high-resolution profile of microbial dynamics expands our knowledge on yet-to-be-cultured populations and their cross-domain interactions and highlights the ecological importance of eukaryotes in the activated sludge ecosystem.}, }
@article {pmid40183581, year = {2025}, author = {Aminian-Dehkordi, J and Dickson, A and Valiei, A and Mofrad, MRK}, title = {MetaBiome: a multiscale model integrating agent-based and metabolic networks to reveal spatial regulation in gut mucosal microbial communities.}, journal = {mSystems}, volume = {10}, number = {5}, pages = {e0165224}, pmid = {40183581}, issn = {2379-5077}, mesh = {*Gastrointestinal Microbiome/physiology ; *Metabolic Networks and Pathways ; *Intestinal Mucosa/microbiology/metabolism ; *Metabolomics/methods ; Models, Biological ; Humans ; Computer Simulation ; }, abstract = {Mucosal microbial communities (MMCs) are complex ecosystems near the mucosal layers of the gut essential for maintaining health and modulating disease states. Despite advances in high-throughput omics technologies, current methodologies struggle to capture the dynamic metabolic interactions and spatiotemporal variations within MMCs. In this work, we present MetaBiome, a multiscale model integrating agent-based modeling (ABM), finite volume methods, and constraint-based models to explore the metabolic interactions within these communities. Integrating ABM allows for the detailed representation of individual microbial agents each governed by rules that dictate cell growth, division, and interactions with their surroundings. Through a layered approach-encompassing microenvironmental conditions, agent information, and metabolic pathways-we simulated different communities to showcase the potential of the model. Using our in-silico platform, we explored the dynamics and spatiotemporal patterns of MMCs in the proximal small intestine and the cecum, simulating the physiological conditions of the two gut regions. Our findings revealed how specific microbes adapt their metabolic processes based on substrate availability and local environmental conditions, shedding light on spatial metabolite regulation and informing targeted therapies for localized gut diseases. MetaBiome provides a detailed representation of microbial agents and their interactions, surpassing the limitations of traditional grid-based systems. This work marks a significant advancement in microbial ecology, as it offers new insights into predicting and analyzing microbial communities.IMPORTANCEOur study presents a novel multiscale model that combines agent-based modeling, finite volume methods, and genome-scale metabolic models to simulate the complex dynamics of mucosal microbial communities in the gut. This integrated approach allows us to capture spatial and temporal variations in microbial interactions and metabolism that are difficult to study experimentally. Key findings from our model include the following: (i) prediction of metabolic cross-feeding and spatial organization in multi-species communities, (ii) insights into how oxygen gradients and nutrient availability shape community composition in different gut regions, and (iii) identification of spatiallyregulated metabolic pathways and enzymes in E. coli. We believe this work represents a significant advance in computational modeling of microbial communities and provides new insights into the spatial regulation of gut microbiome metabolism. The multiscale modeling approach we have developed could be broadly applicable for studying other complex microbial ecosystems.}, }
@article {pmid40179176, year = {2025}, author = {Lentsch, V and Woller, A and Rocker, A and Aslani, S and Moresi, C and Ruoho, N and Larsson, L and Fattinger, SA and Wenner, N and Barazzone, EC and Hardt, WD and Loverdo, C and Diard, M and Slack, E}, title = {Vaccine-enhanced competition permits rational bacterial strain replacement in the gut.}, journal = {Science (New York, N.Y.)}, volume = {388}, number = {6742}, pages = {74-81}, pmid = {40179176}, issn = {1095-9203}, support = {176954/SNSF_/Swiss National Science Foundation/Switzerland ; 180953/SNSF_/Swiss National Science Foundation/Switzerland ; 865730/ERC_/European Research Council/International ; }, mesh = {Animals ; Female ; Mice ; Adaptive Immunity ; Administration, Oral ; *Antibiosis ; Antibodies, Bacterial/immunology ; *Escherichia coli/immunology/growth &amp; development/physiology ; Escherichia coli Infections/prevention &amp; control/immunology/microbiology ; Gastrointestinal Microbiome ; Immunity, Mucosal ; Mice, Inbred C57BL ; *Salmonella typhimurium/immunology/growth &amp; development/physiology ; *Salmonella Vaccines/immunology/administration &amp; dosage ; Vaccination ; }, abstract = {Colonization of the intestinal lumen precedes invasive infection for a wide range of enteropathogenic and opportunistic pathogenic bacteria. We show that combining oral vaccination with engineered or selected niche-competitor strains permits pathogen exclusion and strain replacement in the mouse gut lumen. This approach can be applied either prophylactically to prevent invasion of nontyphoidal Salmonella strains, or therapeutically to displace an established Escherichia coli. Both intact adaptive immunity and metabolic niche competition are necessary for efficient vaccine-enhanced competition. Our findings imply that mucosal antibodies have evolved to work in the context of gut microbial ecology by influencing the outcome of competition. This has broad implications for the elimination of pathogenic and antibiotic-resistant bacterial reservoirs and for rational microbiota engineering.}, }
@article {pmid40177466, year = {2025}, author = {Hwang, J and Hayward, A and Sofen, LE and Pitz, KJ and Chavez, FP and Edwards, BR}, title = {Daily microbial rhythms of the surface ocean interrupted by the new moon-a lipidomic study.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf044}, pmid = {40177466}, issn = {2730-6151}, abstract = {Lipids are essential biomolecules for cell physiology and are commonly used as biomarkers to elucidate biogeochemical processes over a large range of environments and timescales. Here, we use high-temporal-resolution lipidomic analysis to characterize the surface ocean community in the productive upwelling region overlying the Monterey Bay Canyon. We observed a strong diel signal with a drawdown of lipids at night and an increase during the day that seemed to correspond to wholesale removal of lipids from the surface ocean as opposed to internal metabolism. Individual lipid species were organized into coregulated groups that were interpreted as representing different phytoplankton guilds. Concentrations of long-chained triacylglycerols (TAGs) showed unique patterns over the course of five days. TAGs were used to estimate the amount of energy cycled through the surface ocean. These calculations revealed diurnal carbon cycling that was on scales comparable to net primary production. The diel pattern dissipated from most lipid modules on Day 3 as tidal forcing increased at our site with the advent of the new moon. Pigment analysis indicated that the community shifted from a diatom-dominated community to a more diverse assemblage, including more haptophytes, chlorophytes, and Synechococcus during the new moon. The shift in community appears to promote higher nutritional quality of biomass, with more essential fatty acids in the surface ocean during the spring tide. This analysis showcases the utility of lipidomics in characterizing community dynamics and underscores the importance of considering both diel and tidal timescales when sampling in productive coastal regions.}, }
@article {pmid40177465, year = {2025}, author = {Krause, SMB and van den Berg, NI and Brenzinger, K and Zweers, H and Bodelier, PLE}, title = {Beyond methane consumption: exploring the potential of methanotrophic bacteria to produce secondary metabolites.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf030}, pmid = {40177465}, issn = {2730-6151}, abstract = {Microbial methane-consuming communities significantly impact biogeochemical processes and greenhouse gas emissions. In this study, we explored secondary metabolites produced by methane-oxidizing bacteria (MOB) and their ecological roles. We analyzed the volatile profiles of four MOB strains under controlled conditions and conducted a meta-analysis using high-quality genomes from 62 cultured MOB strains and 289 metagenome-assembled genomes to investigate their potential for producing secondary metabolites. Results show species-specific volatile production, such as germacrene by Methylobacter luteus, which may play a role in the regulation of environmental methane consumption. The meta-analysis revealed that biosynthetic gene clusters (BGCs) for terpenes and β-lactones were more prevalent in the Methylocystaceae and/or Beijerinckiaceae families, while aryl polyene BGCs were dominant in the Methylococcaceae family, reflecting habitat-specific adaptations. These findings advance our understanding of the metabolic capabilities of MOB and underscore the importance of integrating experimental data with genomic and metabolomic analyses to elucidate their ecology, environmental interactions, and contributions to methane cycling.}, }
@article {pmid40177402, year = {2025}, author = {Pellengahr, F and Corella-Puertas, E and Mattelin, V and Saadi, N and Bertella, F and Boulay, AM and van der Meer, Y}, title = {Modeling marine microplastic emissions in Life Cycle Assessment: characterization factors for biodegradable polymers and their application in a textile case study.}, journal = {Frontiers in toxicology}, volume = {7}, number = {}, pages = {1494220}, pmid = {40177402}, issn = {2673-3080}, abstract = {INTRODUCTION: With the continuous increase of plastics production, it is imperative to carefully examine their environmental profile through Life Cycle Assessment (LCA). However, current LCA modeling is not considering the potential impacts of plastic emissions on the biosphere. To integrate plastic emissions into LCA, characterization factors are needed that commonly consist of three elements: a fate factor, an exposure factor, and an effect factor. In this context, fate factors quantify the distribution and longevity of plastics in the environment. Research on these fate factors is still limited, especially for biodegradable polymers. Hence, the main objective of this research was to determine the fate factors of biodegradable polymers [poly (lactic acid), poly (butylene succinate), and poly (ε-caprolactam)] based on primary experimental data for the marine environment.<br><br>METHODS: The validity of former research is tested by comparing the degradation evolution of i. macro- and microplastic particles, ii. two different grades of the polymer, and iii. different temperature levels. The degradation data are obtained by monitoring the oxygen consumption over a period of six months in natural seawater. The determined degradation rates are combined with sedimentation, resuspension, and deep burial rates to obtain fate factors. These fate factors are used to develop polymer-specific characterization factors. The resulting characterization factors are tested in an LCA case study of a synthetic sports shirt made from biodegradable polymer fibers. It allows to assess the relative importance of microplastic impacts compared to other life cycle impacts.<br><br>RESULTS AND DISCUSSION: Comparing the resulting specific surface degradation rates indicates that microplastic degradation rates could be overestimated when using macroplastic degradation data. Pertaining to the case study, the results show that the impact on ecosystem quality by microplastic emissions could account for up to 30% of the total endpoint category. Overall, this work aims to foster interdisciplinary collaboration to leverage the accuracy of LCA studies and thus provide guidance for novel material development.}, }
@article {pmid40175811, year = {2025}, author = {Alexander, NR and Brown, RS and Duwadi, S and Womble, SG and Ludwig, DW and Moe, KC and Murdock, JN and Phillips, JL and Veach, AM and Walker, DM}, title = {Leveraging Fine-Scale Variation and Heterogeneity of the Wetland Soil Microbiome to Predict Nutrient Flux on the Landscape.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {22}, pmid = {40175811}, issn = {1432-184X}, support = {DEB 1933925//National Science Foundation/ ; EF-2125065//National Science Foundation/ ; sub-award 220858//Natural Resource Conservation Services/ ; Molecular Biosciences Program//Middle Tennessee State University/ ; }, mesh = {*Wetlands ; *Soil Microbiology ; *Microbiota ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Soil/chemistry ; Nitrogen/metabolism ; *Nutrients/metabolism ; Nitrogen Cycle ; Phosphorus/metabolism ; Ecosystem ; Agriculture ; }, abstract = {Shifts in agricultural land use over the past 200 years have led to a loss of nearly 50% of existing wetlands in the USA, and agricultural activities contribute up to 65% of the nutrients that reach the Mississippi River Basin, directly contributing to biological disasters such as the hypoxic Gulf of Mexico "Dead" Zone. Federal efforts to construct and restore wetland habitats have been employed to mitigate the detrimental effects of eutrophication, with an emphasis on the restoration of ecosystem services such as nutrient cycling and retention. Soil microbial assemblages drive biogeochemical cycles and offer a unique and sensitive framework for the accurate evaluation, restoration, and management of ecosystem services. The purpose of this study was to elucidate patterns of soil bacteria within and among wetlands by developing diversity profiles from high-throughput sequencing data, link functional gene copy number of nitrogen cycling genes to measured nutrient flux rates collected from flow-through incubation cores, and predict nutrient flux using microbial assemblage composition. Soil microbial assemblages showed fine-scale turnover in soil cores collected across the topsoil horizon (0-5 cm; top vs bottom partitions) and were structured by restoration practices on the easements (tree planting, shallow water, remnant forest). Connections between soil assemblage composition, functional gene copy number, and nutrient flux rates show the potential for soil bacterial assemblages to be used as bioindicators for nutrient cycling on the landscape. In addition, the predictive accuracy of flux rates was improved when implementing deep learning models that paired connected samples across time.}, }
@article {pmid40175529, year = {2025}, author = {Pascoal, F and Branco, P and Torgo, L and Costa, R and Magalhães, C}, title = {Definition of the microbial rare biosphere through unsupervised machine learning.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {544}, pmid = {40175529}, issn = {2399-3642}, mesh = {*Unsupervised Machine Learning ; *Microbiota ; Machine Learning ; }, abstract = {The microbial rare biosphere, composed of low-abundance microorganisms in a community, lacks a standardized delineation method for its definition. Currently, most studies rely on arbitrary thresholds to define the microbial rare biosphere (e.g., 0.1% relative abundance per sample), hampering comparisons across studies. To address this challenge, we present ulrb (Unsupervised Learning based Definition of the Rare Biosphere), available as an R package. ulrb uses unsupervised machine learning to optimally classify taxa into abundance categories (e.g., rare, intermediate, or abundant) within microbial communities. We show that ulrb is more consistent than threshold-based approaches and can be applied to data derived from common microbial ecology protocols and non-microbial studies. ulrb can be used to identify different types of rarity and is statistically valid for the analysis of various dataset sizes. In conclusion, ulrb discerns rare from abundant organisms in a user-independent manner, finding applicability in selected ecological datasets.}, }
@article {pmid40174026, year = {2024}, author = {Shimano, S and Hiruta, SF and Sánchez-Chávez, DI and Pfingstl, T}, title = {Coastal mites (Oribatida, Ameronothridae) found far from the coast in moss growing on the Cathédrale Notre-Dame de Paris, France, fifty years after their first discovery in this historic site.}, journal = {Zootaxa}, volume = {5556}, number = {1}, pages = {62-71}, doi = {10.11646/zootaxa.5556.1.6}, pmid = {40174026}, issn = {1175-5334}, mesh = {Animals ; *Mites/classification/genetics/anatomy &amp; histology/growth &amp; development/ultrastructure ; Male ; Animal Distribution ; Female ; Ecosystem ; France ; Phylogeny ; Body Size ; Animal Structures/growth &amp; development/anatomy &amp; histology ; Organ Size ; *Bryophyta/parasitology ; }, abstract = {A species of oribatid mite, Ameronothrus maculatus (Michael, 1882), was collected from moss growing on the building of the Cathédrale Notre-Dame de Paris. This species of Ameronothridae is usually found in coastal Holarctic environments. The specimens were studied by Scanning Electron Microscope and could be clearly assigned to this taxon. This population was first discovered by F. Grandjean approximately 50 years ago, and the present record demonstrates that it has persisted despite its habitat being a tourist destination visited by over 14 million people annually. The record of this species far upstream and on anthropogenic structures is rare but not out of the ordinary in Northern Europe where its distribution can reach far beyond the edges of the estuaries. For further confirmation, we obtained DNA sequences for the COI gene (1554 bp, LC848687), and they were almost identical to those of an earlier found and sequenced specimen of A. maculatus from Germany, differing by only a single base. As supplemental information on A. maculatus from Paris, the region includes whole nucleic ribosomal RNA genes (18S, 5.8S, and 28S, LC848688), partial elongation factor 1 alpha (LC848689), and the complete nucleotide sequence of mitochondrion were also determined.}, }
@article {pmid40172536, year = {2025}, author = {Madison, JD and Osborne, OG and Ellison, A and Garvey Griffith, CN and Gentry, L and Gross, H and Gratwicke, B and Grayfer, L and Muletz-Wolz, CR}, title = {Probiotic colonization of Xenopus laevis skin causes short-term changes in skin microbiomes and gene expression.}, journal = {Infection and immunity}, volume = {93}, number = {5}, pages = {e0056924}, pmid = {40172536}, issn = {1098-5522}, support = {IOS-2131060//National Science Foundation/ ; IOS-2131061//National Science Foundation/ ; BB/W013517/1//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; }, mesh = {Animals ; *Probiotics/pharmacology/administration &amp; dosage ; *Skin/microbiology/immunology ; *Xenopus laevis/microbiology/immunology/genetics ; *Microbiota/drug effects ; RNA, Ribosomal, 16S/genetics ; Batrachochytrium ; Transcriptome ; }, abstract = {Probiotic therapies have been suggested for amelioration efforts of wildlife disease such as chytridiomycosis caused by Batrachochytrium spp. in amphibians. However, there is a lack of information on how probiotic application affects resident microbial communities and immune responses. To better understand these interactions, we hypothesized that probiotic application would alter microbial community composition and host immune expression in Xenopus laevis. Accordingly, we applied three amphibian-derived and anti-Batrachochytrium bacteria strains (two Pseudomonas spp. and one Stenotrophomonas sp.) to X. laevis in monoculture and also as a cocktail. We quantified microbial community structure using 16S rRNA gene sequencing. We also quantified genes involved in X. laevis immune responses using quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) and skin transcriptomics over 1 and 3-week periods. All probiotic treatments successfully colonized X. laevis skin for 3 weeks, but with differential amplicon sequence variant (ASV) sequence counts over time. Bacterial community and immune gene effects were most pronounced at week 1 post-probiotic exposure and decreased thereafter. All probiotic treatments caused initial changes to bacterial community alpha and beta diversity, including reduction in diversity from pre-exposure anti-Batrachochytrium bacterial ASV relative abundance. Probiotic colonization by Pseudomonas probiotic strain RSB5.4 reduced expression of regulatory T cell marker (FOXP3, measured with RT-qPCR) and caused the greatest gene expression changes detected by transcriptomics. Single bacterial strains and mixed cultures, therefore, altered amphibian microbiome-immune interactions. This work will help to improve our understanding of the role of the microbiome-immune interface underlying both disease dynamics and emergent eco-evolutionary processes.IMPORTANCEAmphibian skin microbial communities have an important role in determining disease outcomes, in part through complex yet poorly understood interactions with host immune systems. Here we report that probiotic-induced changes to the Xenopus laevis frog skin microbial communities also result in significant alterations to these animals' immune gene expression. These findings underscore the interdependence of amphibian skin immune-microbiome interactions.}, }
@article {pmid40170918, year = {2025}, author = {Hager, K and Luo, ZH and Montserrat-Diez, M and Ponce-Toledo, RI and Baur, P and Dahlke, S and Andrei, AS and Bulzu, PA and Ghai, R and Urich, T and Glatzel, S and Schleper, C and Rodrigues-Oliveira, T}, title = {Diversity and environmental distribution of Asgard archaea in shallow saline sediments.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1549128}, pmid = {40170918}, issn = {1664-302X}, abstract = {In recent years, our understanding of archaeal diversity has greatly expanded, especially with the discovery of new groups like the Asgard archaea. These archaea show diverse phylogenetic and genomic traits, enabling them to thrive in various environments. Due to their close relationship to eukaryotes, a large number of metagenomic studies have been performed on Asgard archaea. Research on the fine scale distribution, diversity and quantification in saline aquatic sediments where they mostly occur, has, however, remained scarce. In this study, we investigated depths of shallow saline sediment cores from three distinct European environments: the Baltic Sea near Hiddensee, the coastal Lake Techirghiol in Romania, and an estuarine canal in Piran, Slovenia. Based on 16S rDNA amplicon sequencing, we observe variation in the relative abundance and occurrence of at least seven different Asgard groups that are distinct between the three environments and in their depth distribution. Lokiarchaeia and Thorarchaeia emerge as dominant Asgard groups across all sites, reaching maximal relative abundances of 2.28 and 2.68% of the total microbial communities respectively, with a maximal abundance of all Asgard reaching approx. 5.21% in Hiddensee. Quantitative PCR assays provide insights into the absolute abundance of Lokiarchaeia, supporting distinct patterns of distribution across depths in different sediments. Co-occurrence network analysis indicates distinct potential microbial partners across different Asgard groups. Overall, our study shows that Asgard archaea are found as a stable component in shallow sediment layers and have considerably diversified on macro- and microscales.}, }
@article {pmid40168336, year = {2025}, author = {Brangsch, H and Marcordes, S and Busch, A and Weber, M and Wolf, SA and Semmler, T and Höper, D and Calvelage, S and Linde, J and Barth, SA}, title = {Comparative genomics of Mycobacterium avium subsp. hominissuis strains within a group of captive lowland tapirs.}, journal = {PloS one}, volume = {20}, number = {4}, pages = {e0320499}, pmid = {40168336}, issn = {1932-6203}, mesh = {Animals ; *Mycobacterium avium/genetics/isolation &amp; purification/classification ; *Perissodactyla/microbiology ; Polymorphism, Single Nucleotide ; *Genome, Bacterial ; *Genomics ; Phylogeny ; Multilocus Sequence Typing ; Whole Genome Sequencing ; }, abstract = {Within a group of three captive lowland tapirs (Tapirus terrestris) suffering from clinically apparent mycobacteriosis, non-tuberculous Mycobacterium avium subsp. hominissuis (MAH) strains were isolated from the animals and the tapir's enclosure. Based on MIRU-VNTR findings, which identified two closely related INMV profiles (124 and 246), a micro-evolutionary event was assumed, and four available MAH strains were submitted to whole genome sequencing (short- and long-read technologies). Surprisingly, the differences based on single nucleotide polymorphisms (SNPs) were exceptionally high between the four strains, i.e., between 841 and 11,166 bases, due to a strong impact of homologous recombination. Thus, an ad hoc core genome multilocus sequence typing (cgMLST) scheme was created and pangenome analysis was conducted for determining the genomic similarity between the strains. The INMV246 isolate obtained from sputum on the enclosure floor and one INMV124 isolate of tapir #2 showed the highest congruence, suggesting that both originated from a shared source. The other two INMV124 isolates were genomically distinct from these strains. Nevertheless, in all four strains two plasmids were detected, which were highly conserved between the strains. The study showed that the genomic variability between MAH strains isolated from the same site within a short period of time can be exceptionally high and the influence of homologous recombination needs to be considered when determining MAH strain relationships, particularly via SNP analyses.}, }
@article {pmid40167801, year = {2025}, author = {Banu, S and Valero, KCW and Rivero, F}, title = {Simulated Heat Waves Affect Cell Fate and Fitness in the Social Amoeba Dictyostelium discoideum.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {21}, pmid = {40167801}, issn = {1432-184X}, support = {#101044202/ERC_/European Research Council/International ; }, mesh = {*Dictyostelium/genetics/growth &amp; development/physiology/cytology ; *Hot Temperature ; Protozoan Proteins/genetics/metabolism ; Spores, Protozoan/growth &amp; development/genetics ; }, abstract = {The effects of heatwaves at organism and population levels have been widely investigated; however, little is known about how they affect the development of cell populations and the fitness of the resulting organism. Disruptions caused by heatwaves are especially critical during early developmental stages in organisms lacking parental developmental protection or care. Here we use the social amoeba Dictyostelium discoideum, a soil microbe with a life cycle that transitions between single-cell and multicellular stages. D. discoideum thrives optimally at 22 °C and elevated temperatures impair (27 °C) or completely arrest (30 °C) growth, development, and spore yield. We established a simulated heatwave model in which vegetative cells were exposed to 27 °C for 3 days and studied the effects on the expression of early and cell type specific developmental genes using real-time quantitative PCR. A single heatwave severely impaired the expression of cyclic AMP-dependent early developmental gene markers (carA, acaA, pkaR, gtaC, tgrC1, and csaA) as well as that of prespore markers (cotB and spiA), while the expression of the prestalk marker ecmA was less affected. When mixed with heat-stressed cells, reporter cells expressing β-galactosidase grown at 22 °C preferentially occupy the spore mass of the fruiting body. Chimera assays of wild-type and reporter cells grown at optimal temperature or subjected to a heatwave confirmed a decreased fitness (contribution to chimeric fruiting bodies). We conclude that exposure of unprotected organisms at the single cell stage to a single heatwave has the potential to negatively impact their ability to cope with environmental extremes.}, }
@article {pmid40167318, year = {2025}, author = {Détain, A and Suzuki, H and Wijffels, RH and Leborgne-Castel, N and Hulatt, CJ}, title = {Snow algae exhibit diverse motile behaviors and thermal responses.}, journal = {mBio}, volume = {16}, number = {5}, pages = {e0295424}, pmid = {40167318}, issn = {2150-7511}, support = {No. 319352//Norwegian Research Council/ ; No. 349485//Norwegian Research Council/ ; }, mesh = {*Snow/microbiology ; Temperature ; Microbiota ; Eutrophication ; Phototaxis ; }, abstract = {Snow algal blooms influence snow and glacier melt dynamics, yet the mechanisms involved in community assemblage, development, and dispersal are not well understood. While microbial swimming behavior contributes significantly to the productivity and organization of aquatic and terrestrial microbiomes, the potential impact of algal cell motility in melting snow on the formation of visible, large-scale surface bloom patterns is largely unknown. Here, using video tracking and phototaxis experiments of unique isolates, we evaluated the motility of diverse snow algal taxa from green, red, and golden colored snow blooms in response to light and thermal gradients. We show that many species are efficient cryophilic microswimmers with speed thermal optima below 10°C although taxa with cryotolerant swimming traits were also identified. The significant motility of snow algae at low temperatures, a result of specialized adaptations, supports the importance of active movement in the life histories of algae inhabiting snow meltwater. However, diversity in swimming performance and behavior reveal a range of evolutionary outcomes and sensitivity of motile life stages to dynamic environments.IMPORTANCESwimming motility is a fundamental mechanism that controls the assembly, structure, and productivity of microbiomes across diverse environments and is highly sensitive to temperature. Especially, the role of cell swimming activity in algal bloom formation at the very low temperatures of snowmelt has been hypothesized, but not studied. By examining the movement patterns of snow algae and modeling the thermal response curves of swimming speed, the data reveal the key role of active cell movement that may have further important impacts on the microbial ecology and melt rates of snow and ice in polar and alpine regions.}, }
@article {pmid40162837, year = {2025}, author = {Major, SR and Polinski, JM and Penn, K and Rodrigue, M and Harke, MJ}, title = {Novel and diverse features identified in the genomes of bacteria isolated from a hydrothermal vent plume.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {4}, pages = {e0259324}, pmid = {40162837}, issn = {1098-5336}, support = {22-08846//Dalio Foundation/ ; }, mesh = {*Hydrothermal Vents/microbiology ; *Genome, Bacterial ; *Bacteria/genetics/isolation &amp; purification/classification ; Phylogeny ; Multigene Family ; Seawater/microbiology ; Gene Transfer, Horizontal ; }, abstract = {Hydrothermal vent plumes (HVPs), formed by high-temperature vent emissions, are rich in compounds that support chemosynthesis and serve as reservoirs of microbial diversity and genetic innovation. Through turbulence, mixing, and interaction with subsea currents, vent communities are thought to disperse across ocean basins. In this study, we focused on the plume of the Moytirra hydrothermal vent field, a relatively unexplored site, to investigate its microbial inhabitants. We cultured bacteria from the Moytirra HVP using 11 different media types and performed complete genome sequencing on 12 isolates. Our analyses revealed four putatively novel species from the Thalassobaculum, Sulfitobacter, Idiomarina, and Christiangramia genera. Comparative genomics identified unique genomic islands containing biosynthetic gene clusters, including a novel Non-Ribosomal Peptide Synthetase/Polyketide Synthase cluster, toxin-antitoxin systems, and evidence of horizontal gene transfer facilitated by prophages. These findings underscore the potential of HVPs as a source of novel microbial species and biotechnologically relevant genes, contributing to our understanding of the biodiversity and genetic complexity of these extreme environments.IMPORTANCEHydrothermal vents are dynamic environments that offer unique nutrients for chemosynthetic organisms to drive biology in the deep-sea. The dynamics of these ecosystems are thought to drive genomic innovation in resident populations. Hydrothermal vent plumes (HVPs) mix with surrounding water, carrying local microbiota with them and dispersing for hundreds of kilometers. This study isolated bacteria from a HVP to capture a genomic snapshot of the microbial community, revealing four putatively novel species of bacteria within three taxonomic classes. The addition of these genomes to public databases provides valuable insights into the genomic function, architecture, and novel biosynthetic gene clusters of bacteria found in these extreme environments.}, }
@article {pmid40162703, year = {2025}, author = {Souza Beraldo, C}, title = {An interactive art activity to promote student reflection and learning about host-microbe interactions.}, journal = {Journal of microbiology &amp; biology education}, volume = {26}, number = {1}, pages = {e0006325}, pmid = {40162703}, issn = {1935-7877}, abstract = {The use of art in science teaching can effectively help students understand complex and abstract concepts, particularly in the fields of Microbiology and Microbial Ecology, where the study objects-the microbes-are invisible to human eyes. To explore how different factors shape host-microbe interactions, I developed the activity MicrobiART, which uses mixed art materials to create analogies that illustrate the dynamic relationships between hosts, microbes, and their environments. MicrobiART was presented as an alternative session at a PhD students' conference in Espoo, Finland. Participants were invited to combine papers, balls, and paint-representing hosts, microbes, and environmental factors, respectively-to create paintings that depict the outcomes of these interactions. The completed artworks were then displayed in a mini exhibition. Following this session, participants were invited to engage in discussion to identify patterns in the paintings and reflect on the analogies' meanings and limitations. The activity is adaptable to various age groups and to both non-specialist and specialist audiences. Anecdotal evidence suggests that participants understood how interaction outcomes depend on the specific combination of players (host, microbes, and environment), while also recognizing emergent patterns. For instance, interactions within the same environment often share similar colors, contrasting with those from a different environment. Moreover, participants found the experience enjoyable, particularly due to its interactive and aesthetic appeal. These findings highlight the value of integrating science and art in science communication, especially in conference spaces: such integration fosters connections, inspires new ideas and teaching approaches, and provides a relaxed setting for discussion.}, }
@article {pmid40161817, year = {2025}, author = {Band, VI and Gribonika, I and Stacy, A and Bouladoux, N and Mistry, S and Burns, A and Perez-Chaparro, PJ and Chau, J and Enamorado, M and Nagai, M and Bhushan, V and Golec, DP and Schwartzberg, PL and Hourigan, SK and Nita-Lazar, A and Belkaid, Y}, title = {Sulfide is a keystone metabolite for gut homeostasis and immunity.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40161817}, issn = {2692-8205}, support = {ZIA AI001115/ImNIH/Intramural NIH HHS/United States ; ZIA AI001132/ImNIH/Intramural NIH HHS/United States ; }, abstract = {Hydrogen sulfide is a gaseous, reactive molecule specifically enriched in the gastrointestinal tract. Here, we uncover a non-redundant role for sulfide in the control of both microbial and immune homeostasis of the gut. Notably, depletion of sulfide via both pharmaceutical and dietary interventions led to a profound collapse of CD4 T cells in the ileum of the small intestine lamina propria and significant impact on microbial ecology. As a result, mice with reduced sulfide within the gut were deficient in their ability to mount T cell dependent antibody responses to oral vaccine. Mechanistically, our results support the idea that sulfide could act directly on CD4 T cells via enhanced AP-1 activation, leading to heightened proliferation and cytokine production. This study uncovers sulfides as keystone components in gut ecology and provides mechanistic insight between diet, gut sulfide production and mucosal immunity.}, }
@article {pmid40160925, year = {2025}, author = {Amirmijani, A and Pordel, A and Dehghani, K and Pourmoghaddam, MJ and Masigol, H and Grossart, HP}, title = {Two new pestalotioid fungi from tropical fruits in Iran.}, journal = {MycoKeys}, volume = {115}, number = {}, pages = {221-240}, pmid = {40160925}, issn = {1314-4049}, abstract = {In a survey of tropical plant diseases in southern and southeastern Iran, samples of diseased Mangiferaindica and Psidiumguava leaves with necrotic symptoms were collected between 2021 and 2022. Six representative isolates of Neopestalotiopsis and Robillarda (three isolates for each) were studied using morphological characteristics as well as multi-locus phylogenetic analysis based on (i) the internal transcribed spacer (ITS) region of the nuclear rDNA, (ii) part of the translation elongation factor 1-alpha (tef1), and (iii) the β-tubulin (tub2). After morphological investigation, our phylogenetic analysis revealed that the Neopestalotiopsis and Robillarda isolates under study differed from all previously described species within these genera. Based on our polyphasic approach, two new species, including Neopestalotiopsisguava sp. nov. from necrotic Mangiferaindica and Robillardakhodaparastii sp. nov. from Psidiumguava are described and illustrated from Iran.}, }
@article {pmid40157674, year = {2025}, author = {Wu, X and Yu, D and Ma, Y and Fang, X and Sun, P}, title = {Function and therapeutic potential of Amuc_1100, an outer membrane protein of Akkermansia muciniphila: A review.}, journal = {International journal of biological macromolecules}, volume = {308}, number = {Pt 4}, pages = {142442}, doi = {10.1016/j.ijbiomac.2025.142442}, pmid = {40157674}, issn = {1879-0003}, mesh = {Humans ; Animals ; Gastrointestinal Microbiome/drug effects ; *Bacterial Outer Membrane Proteins/pharmacology/therapeutic use/chemistry ; Akkermansia ; Probiotics/therapeutic use ; }, abstract = {The gut microbiota-derived protein Amuc_1100, a key outer membrane component of Akkermansia muciniphila, has emerged as a groundbreaking therapeutic agent with unique structural and functional properties. Amuc_1100 exerts multifaceted immune-metabolic effects through novel mechanisms, including modulation of TLR2/4 and JAK/STAT pathways. This review highlights its unique multi-component structure that enables synergistic biological activity, and its pharmacological properties, which underlies its ability to enhance intestinal barrier integrity, restore microbiota balance, and suppress systemic inflammation. Crucially, Amuc_1100 demonstrates unprecedented therapeutic versatility across both intestinal disorders (e.g., inflammatory bowel disease, antibiotic-associated diarrhea) and extraintestinal conditions-notably improving neuropsychiatric symptoms via gut-serotonin axis regulation, combating cancer through CD8+ T cell activation, and mitigating cardiotoxicity via gut-heart immune crosstalk. Emerging innovations in targeted delivery systems, including gut-retentive nano-formulations and engineered probiotic vectors, further amplify its clinical potential. We critically evaluate recent advances distinguishing Amuc_1100's mechanisms from live bacterial interventions. By synthesizing evidence from preclinical models, this work positions Amuc_1100 as a prototype for next-generation microbiome-derived therapeutics, bridging microbial ecology with precision medicine.}, }
@article {pmid40152585, year = {2025}, author = {Wang, F and Luo, J and Zhang, Z and Liu, Y and Sheng, Dh and Zhuo, L and Li, Y-z}, title = {Differential crosstalk between toxin-immunity protein homologs divides Myxococcus nonself siblings into close and distant social relatives.}, journal = {mBio}, volume = {16}, number = {5}, pages = {e0390224}, pmid = {40152585}, issn = {2150-7511}, support = {2022FY101100//Science &amp; Technology Fundamental Resources Investigation Program/ ; 32070030//MOST | National Natural Science Foundation of China (NSFC)/ ; 32270073//MOST | National Natural Science Foundation of China (NSFC)/ ; ZR2022QC001//Natural Science Foundation of Shandong Province ()/ ; BK20230248//JST | Natural Science Foundation of Jiangsu Province(Jiangsu Natural Science Foundation)/ ; }, mesh = {*Myxococcus xanthus/genetics/physiology/immunology ; *Bacterial Toxins/genetics/metabolism ; *Bacterial Proteins/genetics/metabolism ; *Toxin-Antitoxin Systems ; Microbial Interactions ; }, abstract = {Many bacteria discriminate self and nonself using toxins and their corresponding immunity proteins. The toxin-immunity systems often include homologs, potentially creating crosstalk with unknown influences on kin discrimination. In this study, we investigated the kinship controlled by four homologous toxin-immunity systems in the social bacterium Myxococcus xanthus. We determined that the four homologous systems each play an independent role in the discrimination of self and nonself. However, the immunity proteins inactivate not only the corresponding nuclease toxin proteins but also some non-corresponding toxin proteins, depending on their sequence and structural similarities. The nonself relatives controlled by toxin-immunity proteins with or without crosstalk exhibit differential co-growth and collaborative behaviors. We concluded that differential crosstalk between toxin-immunity protein homologs can divide bacterial nonself lineages into close and distant relatives displaying differential collaboration and antagonistic behaviors.IMPORTANCEThis study significantly contributes to our knowledge of kin selection and social behavior in bacteria. The interactions between four homologous toxin-immunity protein systems of Myxococcus xanthus were investigated, and evidence was obtained that these systems can distinguish between self and nonself cells within a species. Importantly, this study revealed that nonself lineages, which display varying degrees of genetic relatedness, can co-grow and collaborate in distinct patterns. This discovery implies that the differential crosstalk between homologous toxin-immunity proteins can mimic the degree of kinship; through this activity, bacteria can differentiate close and distant relatives. This novel insight into bacterial social dynamics and kin discrimination supports kin selection theory and enriches our knowledge on microbial interactions and evolutionary strategies. These findings have broad implications for microbial ecology, evolution, and the development of cooperation strategies.}, }
@article {pmid40151948, year = {2025}, author = {Šulčius, S and Alzbutas, G and Lukashevich, V}, title = {Cyanophage Lysis of the Cyanobacterium Nodularia spumigena Affects the Variability and Fitness of the Host-Associated Microbiome.}, journal = {Environmental microbiology}, volume = {27}, number = {4}, pages = {e70042}, doi = {10.1111/1462-2920.70042}, pmid = {40151948}, issn = {1462-2920}, support = {S-LL-21-10//Lietuvos Mokslo Taryba/ ; }, mesh = {*Microbiota ; *Bacteriophages/physiology ; *Cyanobacteria/virology/metabolism/genetics/physiology ; *Bacteriolysis ; }, abstract = {Cyanobacteria are intricately linked with its microbiome through multiple metabolic interactions. We assessed how these interactions might be affected by cyanophage infection and lysis in cyanobacterium Nodularia spumigena. The genome-scale metabolic models and analysis of putative metabolic interactions revealed a bidirectional cross-feeding potential within the N. spumigena microbiome, with heterotrophic bacteria exhibiting a greater level of trophic dependency on the cyanobacterium. Our results indicate that microbes associated with N. spumigena rely on the supply of various amino acids, reduced carbon compounds and protein synthesis cofactors released by the cyanobacterial host. We observed that compositional changes in the N. spumigena microbiome were associated with the multiplicity of infection and increased with increasing initial viral load. Higher mortality of N. spumigena led to decreased variability in the relative abundances of bacteria, suggesting an indirect restriction of their niche space. Lysis of N. spumigena resulted in a substantial decline in the estimated absolute abundances of heterotrophic bacteria, indicating reduced fitness of co-occurring bacteria in the absence of N. spumigena. Altogether, we demonstrate how a gradual increase in viral pressure on the photosynthetic host propagates through the co-occurring microbial community, disrupting cooperative nature and microbial connectivity within the N. spumigena microbiome.}, }
@article {pmid40149089, year = {2025}, author = {Nussbaumer-Pröll, A and Hausmann, B and Weber, M and Pjevac, P and Berry, D and Zeitlinger, M}, title = {A Pilot Study on the Impact of Cranberry and Ascorbic Acid Supplementation on the Urinary Microbiome of Healthy Women: A Randomized Controlled Trial.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {14}, number = {3}, pages = {}, pmid = {40149089}, issn = {2079-6382}, abstract = {Background: The collection of microorganisms that colonize the human genital and urinary tract is referred to as the genitourinary microbiome. Urinary tract infections (UTIs), which predominantly affect women, are linked to alterations in the genitourinary microbiome. Cranberries (Vaccinium oxycoccos), rich in proanthocyanidins, and ascorbic acid (vitamin C), known for their urinary acidification properties, are commonly used for UTI prevention. However, their effects on the genitourinary microbiome remain inadequately characterized. This pilot study assesses the genitourinary microbiome composition in healthy women and evaluates the influence of cranberry and ascorbic acid supplementation. Methods: In a randomized, controlled, and open-label trial, 27 healthy women in their reproductive age (18-40 years) were assigned to three groups: cranberry (n = 8), ascorbic acid (n = 10), and control (n = 9). Urine samples were collected at three time points and processed for 16S rRNA gene amplicon-based microbial community composition analysis. Microbiome composition was compared within and between groups, and between study visits. Results: Sufficient microbial DNA was extracted from all midstream urine samples. The genitourinary microbiome was predominantly composed of Lactobacillus spp., as reported previously. No significant shifts in microbial composition were observed in response to cranberry or ascorbic acid supplementation, and no statistically significant differences were detected between the intervention and control groups or between study visits. Conclusion: The genitourinary microbiome of healthy women remained stable during cranberry or ascorbic acid supplementation. Further studies in patients with recurrent UTIs are needed to explore the potential impacts of these supplements on the genitourinary microbiome in disease states.}, }
@article {pmid40149015, year = {2025}, author = {Fournier, P and Pellan, L and Jaswa, A and Cambon, MC and Chataigner, A and Bonnard, O and Raynal, M and Debord, C and Poeydebat, C and Labarthe, S and Delmotte, F and This, P and Vacher, C}, title = {Revealing microbial consortia that interfere with grapevine downy mildew through microbiome epidemiology.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {37}, pmid = {40149015}, issn = {2524-6372}, support = {20-PCPA-0010//Agence Nationale de la Recherche/ ; }, abstract = {BACKGROUND: Plant and soil microbiomes can interfere with pathogen life cycles, but their influence on disease epidemiology remains understudied. Here, we analyzed the relationships between plant and soil microbiomes and long-term epidemiological records of grapevine downy mildew, a major disease caused by the oomycete Plasmopara viticola.<br><br>RESULTS: We found that certain microbial taxa were consistently more abundant in plots with lower disease incidence and severity and that the microbial community composition could predict disease incidence and severity. Microbial diversity was not strongly linked to epidemiological records, suggesting that disease incidence and severity is more related to the abundance of specific microbial taxa. These key taxa were identified in the topsoil, where the pathogen's oospores overwinter, and in the phyllosphere, where zoospores infect leaves. By contrast, the leaf endosphere, where the pathogen's mycelium develops, contained few taxa of interest. Surprisingly, the soil microbiota was a better predictor of disease incidence and severity than the leaf microbiota, suggesting that the soil microbiome could be a key indicator of the dynamics&#xa0;of this primarily aerial disease.<br><br>CONCLUSION: Our study integrates long-term epidemiological data with microbiome profiles of healthy plants to reveal fungi and bacteria relevant for the biocontrol of grapevine downy mildew. The resulting database provides a valuable resource for designing microbial consortia with potential biocontrol activity. The framework can be applied to other crop systems to guide the development of biocontrol strategies and reduce pesticide use in agriculture.}, }
@article {pmid40148178, year = {2025}, author = {Hodžić, A and Duscher, GG and Alić, A and Beck, R and Berry, D}, title = {Peritrophic matrix: an important determinant of vector competence in hematophagous arthropods.}, journal = {Trends in parasitology}, volume = {41}, number = {5}, pages = {374-386}, doi = {10.1016/j.pt.2025.03.005}, pmid = {40148178}, issn = {1471-5007}, mesh = {Animals ; *Arthropod Vectors/immunology/physiology ; *Arthropods/immunology/physiology/parasitology ; Immunity, Innate ; }, abstract = {The peritrophic matrix (PM) is a non-cellular, glycan-rich structure that lines the gut epithelium of most invertebrates, including arthropod vectors that transmit diseases of public health and veterinary concern. This semipermeable barrier, functionally analogous to the vertebrate mucosal layer, separates the gut lumen from epithelial cells and provides protection against invading pathogens and their toxins. Beyond its mechanical protective role in the gut, the PM plays a crucial part in arthropod innate immunity. Here, we summarize the most recent advances in understanding the molecular mechanisms of vector-pathogen interactions in blood-feeding arthropods and discuss the significance of the PM in modulating vector competence. This knowledge could contribute to the development of novel strategies to control vector-borne infections.}, }
@article {pmid40147302, year = {2025}, author = {Keneally, C and Chilton, D and Dornan, TN and Kidd, SP and Gaget, V and Toomes, A and Lassaline, C and Petrovski, R and Wood, L and Brookes, JD}, title = {Multi-omics reveal microbial succession and metabolomic adaptations to flood in a hypersaline coastal lagoon.}, journal = {Water research}, volume = {280}, number = {}, pages = {123511}, doi = {10.1016/j.watres.2025.123511}, pmid = {40147302}, issn = {1879-2448}, mesh = {*Floods ; Salinity ; RNA, Ribosomal, 16S/genetics ; Geologic Sediments/microbiology ; Metabolomics ; Microbiota ; Multiomics ; }, abstract = {Microorganisms drive essential biogeochemical processes in aquatic ecosystems and are sensitive to both salinity and hydrological changes. As climate change and anthropogenic activities alter hydrology and salinity worldwide, understanding microbial ecology and metabolism becomes increasingly important for managing aquatic ecosystems. Biogeochemical processes were investigated on sediment microbial communities during a significant flood event in the hypersaline Coorong lagoon, South Australia (the largest in the Murray-Darling Basin since 1956). Samples from six sites across a salinity gradient were collected before and during flooding in 2022. To assess changes in microbial taxonomy and metabolic function, 16S rRNA amplicon sequencing was employed alongside untargeted liquid chromatography-mass spectrometry (LC-MS) to assess changes in microbial taxonomy and metabolic function. Results showed a decrease in microbial richness and diversity during flooding, especially in hypersaline conditions. Pre-flood communities were enriched with osmolyte-degrading and methanogenic taxa, alongside osmoprotectant metabolites, such as glycine betaine and choline. Flood conditions favored taxa such as Halanaerobiaceae and Beggiatoaceae, inducing inferred metagenomic shifts indicative of sulfur cycling and nitrogen reduction pathways, while also enriching a greater diversity of metabolites including Gly-Phe dipeptides and guanine. This study demonstrates that integrating metabolomics with microbial community analysis enhances understanding of ecosystem responses to disturbance. These findings suggest microbial communities rapidly change in response to salinity reductions while maintaining key biogeochemical functions. Such insights are valuable for ecosystem management and predictive modelling under environmental stressors such as flooding.}, }
@article {pmid40146382, year = {2025}, author = {Nain, D and Rana, A and Raychoudhury, R and Sen, R}, title = {Parasite-Induced Replacement of Host Microbiota: Impact of Xenos gadagkari Parasitization on the Microbiota of Polistes wattii.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {20}, pmid = {40146382}, issn = {1432-184X}, support = {DST/INSPIRE/03/2021/000175, IF200146//Department of Science and Technology, Ministry of Science and Technology, India/ ; 1061830779//Council of Scientific and Industrial Research, India/ ; CRG-2021/007010//Science and Engineering Research Board/ ; }, mesh = {Animals ; *Wasps/microbiology/physiology/parasitology ; *Microbiota ; Female ; Male ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; Seasons ; *Host-Parasite Interactions ; }, abstract = {The study of microbiota of social insects under different ecological conditions can provide important insights into the role of microbes in their biology and behavior. Polistes is one of the most widely distributed and extensively studied genera of social wasps, yet a comprehensive study on the microbiota of any species of Polistes or any primitively eusocial wasp is missing. Polistes wattii is an Asian wasp, which hibernates in winter and exhibits a biannual nest founding strategy. It is often parasitized by the strepsipteran endoparasite/parasitoid Xenos gadagkari, which changes the morpho-physiology and behavior of their hosts. In this study, we employ 16S rRNA amplicon sequencing, using the Oxford Nanopore platform, to study the microbial community of P. wattii and investigate the effects of seasonality, sex, and Xenos parasitism. We show that the microbiota differs in females from solitary foundress spring nests and multiple foundress summer nests. The microbiota also differs in males and females. Finally, we show that X. gadagkari parasitism replaces and homogenizes the microbiota of P. wattii. Unlike the unparasitized wasps, the microbiota of X. gadagkari parasitoids and parasitized wasps are dominated by Wolbachia and Providencia. Although the normal microbiota of P. wattii resembles that of highly eusocial vespid wasps, we show that the microbiota of parasitized P. wattii becomes more like the microbiota of strepsipterans. Therefore, it appears that X. gadagkari and other such strepsipteran parasitoids may have a bigger impact on the biology of their hosts than previously thought.}, }
@article {pmid40146077, year = {2025}, author = {Savchenko, V and Yu, XA and Polz, MF and Böttcher, T}, title = {Chitinivorax: The New Kid on the Block of Bacterial 2-Alkyl-4(1H)-quinolone Producers.}, journal = {ACS chemical biology}, volume = {20}, number = {4}, pages = {960-966}, pmid = {40146077}, issn = {1554-8937}, mesh = {*Quinolones/metabolism/chemistry ; Multigene Family ; Phylogeny ; *Comamonadaceae/metabolism/genetics ; }, abstract = {2-Alkyl-4(1H)-quinolones play a key role in bacterial communication, regulating biofilm formation, and virulence. Their antimicrobial properties also support bacterial survival and interspecies competition in microbial communities. In addition to the human pathogen Pseudomonas aeruginosa various species of Burkholderia and Pseudoalteromonas are known to produce 2-alkyl-4(1H)-quinolones. However, the evolutionary relationships of their biosynthetic gene clusters remain largely unexplored. To address this, we investigated the phylogeny of 2-alkyl-4(1H)-quinolone biosynthetic gene clusters, leading to the discovery of Chitinivorax as a fourth genus capable of producing 2-alkyl-4(1H)-quinolones, expanding our knowledge of the diversity of bacteria involved in quinolone-biosynthesis.}, }
@article {pmid40143451, year = {2025}, author = {Jenkins, G and Boyd, ES and Danchin, A and Hervé, V}, title = {Microbiome Notes-Building a Library of Descriptive Microbial Ecology.}, journal = {Environmental microbiology reports}, volume = {17}, number = {2}, pages = {e70085}, pmid = {40143451}, issn = {1758-2229}, }
@article {pmid40142506, year = {2025}, author = {Govaert, M and Duysburgh, C and Kesler, B and Marzorati, M}, title = {Effects of NatureKnit™, a Blend of Fruit and Vegetable Fibers Rich in Naturally Occurring Bound Polyphenols, on the Metabolic Activity and Community Composition of the Human Gut Microbiome Using the M-SHIME[®] Gastrointestinal Model.}, journal = {Microorganisms}, volume = {13}, number = {3}, pages = {}, pmid = {40142506}, issn = {2076-2607}, support = {Not applicable//VDF FutureCeuticals, Inc./ ; }, abstract = {This study evaluated the impact of a proprietary blend of fruit and vegetable fibers rich in naturally occurring bound polyphenols (commercially marketed as NatureKnit[TM]), compared to purified fibers (inulin and psyllium), on the human gut microbiome using the validated M-SHIME[®] gastrointestinal model. A short-term single-stage colonic M-SHIME[®] experiment (with fecal inoculum from three healthy human donors) was used to evaluate the test products compared to a negative control. Samples were assessed for pH, gas pressure, short-chain fatty acid (SCFA) production, lactate, and ammonium from 0 h to 48 h. Microbial community composition was assessed at 0 h (negative control only), 24 h, and 48 h (lumen) or 48 h (mucosal). All test products were fermented well in the colon as demonstrated by decreases in pH and increases in gas pressure over time; these changes occurred faster with the purified fibers, whereas NatureKnit™ demonstrated slow, steady changes, potentially indicating a gentler fermentation process. SCFA production significantly increased over the course of the 48 h experiment with all test products versus negative control. SCFA production was significantly greater with NatureKnit™ versus the purified fibers. Shifts in the microbial community composition were observed with all test products versus negative control. At the conclusion of the 48 h experiment, the absolute bacterial abundance and the richness of observed bacterial taxa in the lumen compartment was significantly greater with NatureKnit™ compared with inulin, psyllium, and negative control. Overall, NatureKnit™ demonstrated greater or similar prebiotic effects on study measures compared with established prebiotic fibers.}, }
@article {pmid40142410, year = {2025}, author = {Hassen, AI and Muema, EK and Diale, MO and Mpai, T and Bopape, FL}, title = {Non-Rhizobial Endophytes (NREs) of the Nodule Microbiome Have Synergistic Roles in Beneficial Tripartite Plant-Microbe Interactions.}, journal = {Microorganisms}, volume = {13}, number = {3}, pages = {}, pmid = {40142410}, issn = {2076-2607}, support = {A-089//Department of Agriculture Land Reform and Rural Development/ ; }, abstract = {Microbial symbioses deal with the symbiotic interactions between a given microorganism and another host. The most widely known and investigated microbial symbiosis is the association between leguminous plants and nitrogen-fixing rhizobia. It is one of the best-studied plant-microbe interactions that occur in the soil rhizosphere and one of the oldest plant-microbe interactions extensively studied for the past several decades globally. Until recently, it used to be a common understanding among scientists in the field of rhizobia and microbial ecology that the root nodules of thousands of leguminous species only contain nitrogen-fixing symbiotic rhizobia. With the advancement of molecular microbiology and the coming into being of state-of-the-art biotechnology innovations, including next-generation sequencing, it has now been revealed that rhizobia living in the root nodules of legumes are not alone. Microbiome studies such as metagenomics of the root nodule microbial community showed that, in addition to symbiotic rhizobia, other bacteria referred to as non-rhizobial endophytes (NREs) exist in the nodules. This review provides an insight into the occurrence of non-rhizobial endophytes in the root nodules of several legume species and the beneficial roles of the tripartite interactions between the legumes, the rhizobia and the non-rhizobial endophytes (NREs).}, }
@article {pmid40141768, year = {2025}, author = {Ghobashy, MOI and Al-Otaibi, AS and Alharbi, BM and Alshehri, D and Ghabban, H and Albalawi, DA and Alenzi, AM and Alatawy, M and Alatawi, FA and Algammal, AM and Mir, R and Mahrous, YM}, title = {Metagenomic Characterization of Microbiome Taxa Associated with Coral Reef Communities in North Area of Tabuk Region, Saudia Arabia.}, journal = {Life (Basel, Switzerland)}, volume = {15}, number = {3}, pages = {}, pmid = {40141768}, issn = {2075-1729}, support = {Research no.0144-1444-S//Deanship of Research and Graduate Studies at University of Tabuk/ ; }, abstract = {The coral microbiome is highly related to the overall health and the survival and proliferation of coral reefs. The Red Sea's unique physiochemical characteristics, such a significant north-south temperature and salinity gradient, make it a very intriguing research system. However, the Red Sea is rather isolated, with a very diversified ecosystem rich in coral communities, and the makeup of the coral-associated microbiome remains little understood. Therefore, comprehending the makeup and dispersion of the endogenous microbiome associated with coral is crucial for understanding how the coral microbiome coexists and interacts, as well as its contribution to temperature tolerance and resistance against possible pathogens. Here, we investigate metagenomic sequencing targeting 16S rRNA using DNAs from the sediment samples to identify the coral microbiome and to understand the dynamics of microbial taxa and genes in the surface mucous layer (SML) microbiome of the coral communities in three distinct areas close to and far from coral communities in the Red Sea. These findings highlight the genomic array of the microbiome in three areas around and beneath the coral communities and revealed distinct bacterial communities in each group, where Pseudoalteromonas agarivorans (30%), Vibrio owensii (11%), and Pseudoalteromonas sp. Xi13 (10%) were the most predominant species in samples closer to coral (a coral-associated microbiome), with the domination of Pseudoalteromonas_agarivorans and Vibrio_owensii in Alshreah samples distant from coral, while Pseudoalteromonas_sp._Xi13 was more abundant in closer samples. Moreover, Proteobacteria such as Pseudoalteromonas, Pseudomonas and Cyanobacteria were the most prevalent phyla of the coral microbiome. Further, Saweehal showed the highest diversity far from corals (52.8%) and in Alshreah (7.35%) compared to Marwan (1.75%). The microbial community was less diversified in the samples from Alshreah Far (5.99%) and Marwan Far (1.75%), which had comparatively lower values for all indices. Also, Vibrio species were the most prevalent microorganisms in the coral mucus, and the prevalence of these bacteria is significantly higher than those found in the surrounding saltwater. These findings reveal that there is a notable difference in microbial diversity across the various settings and locales, revealing that geographic variables and coral closeness affect the diversity of microbial communities. There were significant differences in microbial community composition regarding the proximity to coral. In addition, there were strong positive correlations between genera Pseudoalteromonas and Vibrio in close-to-coral environments, suggesting that these bacteria may play a synergistic role in Immunizing coral, raising its tolerance towards environmental stress and overall coral health.}, }
@article {pmid40138093, year = {2025}, author = {Demeulenaere, &#xc9;}, title = {In search of the microbial path to Terroir: a place-based history of the ecologization of French cheese microbiology, 1990-2000s.}, journal = {History and philosophy of the life sciences}, volume = {47}, number = {2}, pages = {22}, pmid = {40138093}, issn = {1742-6316}, support = {EXORIGINS//Emergence(s) Ville de Paris/ ; }, mesh = {*Cheese/microbiology/history ; France ; History, 20th Century ; *Food Microbiology/history ; Animals ; Milk/microbiology ; Laboratories/history ; }, abstract = {At the crossroads between food studies and science and technology studies, this paper analyzes the role of laboratories located within traditional cheese territories in the ecologization of cheese microbiology in France at the turn of the twentieth century. The paper argues that their connectedness with Protected Designation of Origin raw-milk cheese organizations advocating for a strong understanding of terroir played a key role in challenging the modern strain-by-strain approach and fostering a shift towards a new research object: microbial communities in their ecologies. Modernization and standardization in cheese production from the 1950s onwards laid indeed on the improvement of hygiene to get "cleaner" milks, and on lab research on microbial strains to develop selected starter cultures. This led to a dramatic loss of microbial abundance within raw milks, which progressively provoked milk processing issues, as well as a loss of cheese typicality, an issue for place-based cheeses. To face it, the modernist approach promoted more laboratorial research on microbial strains to develop new starter cultures and the diversification of microbial collections, within an ex-situ conservation framework. In contrast, microbiologists conducting applied research for raw-milk terroir cheeses investigated environmental microbial reservoirs, microbial fluxes, as well as farming practices that favor "natural seeding" and enrich milk native microflora. A new approach emerged, namely "practice-driven microbial ecology" (écologie microbienne dirigée), which enacts the dynamic and ubiquitous properties of microbial life. The paper offers a situated account on the "microbial (ecology) turn" described by other authors, highlighting the ecological approach developed in the 1990s-2000s by French microbiologists in search of "the microbial path to terroir".}, }
@article {pmid40137691, year = {2025}, author = {Maitre, A and Mateos-Hernandez, L and Kratou, M and Egri, N and Maye, J and Juan, M and Hodžić, A and Obregón, D and Abuin-Denis, L and Piloto-Sardinas, E and Fogaça, AC and Cabezas-Cruz, A}, title = {Effects of Live and Peptide-Based Antimicrobiota Vaccines on Ixodes ricinus Fitness, Microbiota, and Acquisition of Tick-Borne Pathogens.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {3}, pages = {}, pmid = {40137691}, issn = {2076-0817}, mesh = {Animals ; *Ixodes/microbiology/immunology ; *Microbiota/immunology ; Mice ; *Bacterial Vaccines/immunology/administration &amp; dosage ; Vaccines, Subunit/immunology/administration &amp; dosage ; Staphylococcus epidermidis/immunology ; *Lyme Disease/prevention &amp; control/immunology/microbiology ; Borrelia burgdorferi Group/immunology ; Vaccines, Attenuated/immunology/administration &amp; dosage ; Female ; *Tick-Borne Diseases/prevention &amp; control/microbiology/immunology ; }, abstract = {This study explored the effects of antimicrobiota vaccines on the acquisition of Borrelia and Rickettsia, and on the microbiota composition of Ixodes ricinus ticks. Using a murine model, we investigated the immunological responses to live Staphylococcus epidermidis and multi-antigenic peptide (MAP) vaccines. Immunized mice were infected with either Borrelia afzelii or Rickettsia helvetica, and subsequently infested with pathogen-free I. ricinus nymphs. We monitored the tick feeding behavior, survival rates, and infection levels. Additionally, we employed comprehensive microbiota analyses, including the alpha and beta diversity assessments and microbial co-occurrence network construction. Our results indicate that both live S. epidermidis and MAP vaccines elicited significant antibody responses in mice, with notable bactericidal effects against S. epidermidis. The vaccination altered the feeding patterns and fitness of the ticks, with the Live vaccine group showing a higher weight and faster feeding time. Microbiota analysis revealed significant shifts in the beta diversity between vaccine groups, with distinct microbial networks and taxa abundances observed. Notably, the MAP vaccine group exhibited a more robust and complex network structure, while the Live vaccine group demonstrated resilience to microbial perturbations. However, the effects of antimicrobiota vaccination on Borrelia acquisition appeared taxon-dependent, as inferred from our results and previous findings on microbiota-driven pathogen refractoriness. Staphylococcus-based vaccines altered the microbiota composition but had no effect on B. afzelii infection, and yielded inconclusive results for R. helvetica. In contrast, previous studies suggest that E. coli-based microbiota modulation can induce a pathogen-refractory state, highlighting the importance of both bacterial species and peptide selection in shaping microbiota-driven pathogen susceptibility. However, a direct comparison under identical experimental conditions across multiple taxa is required to confirm this taxon-specific effect. These findings suggest that antimicrobiota vaccination influences tick fitness and microbiota assembly, but its effects on pathogen transmission depend on the bacterial taxon targeted and the selected peptide epitopes. This research provides insights into the need for strategic bacterial taxon selection to enhance vaccine efficacy in controlling tick-borne diseases.}, }
@article {pmid40134242, year = {2025}, author = {Trombley, J and Celenza, JL and Frey, SD and Anthony, MA}, title = {Arbuscular Mycorrhizal Fungi Boost Development of an Invasive Brassicaceae.}, journal = {Plant, cell &amp; environment}, volume = {48}, number = {7}, pages = {4928-4937}, pmid = {40134242}, issn = {1365-3040}, support = {//This study was supported by the Dick George Invasives Fund awarded to S.D.F. and M.A.A. M.A.A. was supported by a Vienna Science and Technology Fund (WWTF) Vienna Research Groups for Young Investigators grant awarded to MAA (VRG22-007)./ ; }, mesh = {*Mycorrhizae/physiology ; *Introduced Species ; *Brassicaceae/growth &amp; development/microbiology ; Symbiosis ; Plant Roots/microbiology/growth &amp; development ; Glucosinolates/metabolism ; Nitrogen/metabolism ; }, abstract = {Invasive plant growth is affected by interactions with arbuscular mycorrhizal fungi (AMF). AMF are mutualists of most land plants but suppress the growth of many plants within the Brassicaceae, a large plant family including many invasive species. Alliaria petiolata (garlic mustard) is a nonnative, nonmycorrhizal Brassicaceae distributed throughout North America in forest understories where native species rely on AMF. If AMF suppress growth of garlic mustard, it may be possible to inoculate AMF to manage invasions. Here, we show that in contrast to expectation, garlic mustard growth nearly doubled in response to AMF inoculation under both laboratory and field conditions. This effect was negatively linked to investments in glucosinolates, a class of defensive compounds. In contrast to typical symbiosis, AMF did not produce arbuscules where nutrient exchange occurs in roots, but AMF inoculation increased plant and soil nitrogen availability. Our findings reveal an adjacent pathway by which AMF promote invasive plant growth without classic symbiotic exchanges. Prior assumptions that garlic mustard suppresses AMF are inadequate to explain invasion success since it benefits from interactions with AMF. This study is the first to demonstrate extensive growth promotion following AMF inoculation in mustard plants, with important implications for invasion biology and agriculture.}, }
@article {pmid40131450, year = {2025}, author = {Sun, L and Guan, W and Tai, X and Qi, W and Zhang, Y and Ma, Y and Sun, X and Lu, Y and Lin, D}, title = {Research Progress on Microbial Nitrogen Conservation Technology and Mechanism of Microorganisms in Aerobic Composting.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {19}, pmid = {40131450}, issn = {1432-184X}, support = {32160756//National Natural Science Foundation of China/ ; GAUfx-04J03//Fuxi Foundation of Gansu Agricultural University/ ; 23CXNN0007//Gansu Province Science and Technology Plan Project Technology Innovation Guidance Program - LuGan Science and Technology Collaboration topic/ ; 2023-3-66//Science and Technology Plan Project of Lanzhou city/ ; GNKJ-2024-46//Research and Application of Supporting Technologies for Gansu Pig Industry/ ; GAU-XKTD-2022-24//The Discipline Team Project of Gansu Agricultural University/ ; }, mesh = {*Composting/methods ; *Nitrogen/metabolism ; *Soil Microbiology ; Aerobiosis ; *Bacteria/metabolism/genetics ; Manure/microbiology ; Soil/chemistry ; Animals ; }, abstract = {With economic development and improvements in living standards, the demand for livestock products has steadily increased, resulting in the generation of large amounts of livestock manure, which seriously pollutes the ecological environment and poses a threat to human health. High-temperature aerobic composting is an effective method for treating livestock manure; however, traditional composting processes often lead to considerable nitrogen loss, reduced efficiency of soil conditioners, and increased emissions of harmful gases. The incorporation of physical, chemical, and biological additives can effectively retain nitrogen within the compost. Among these, microbial agents are particularly noteworthy as they precisely regulate the microbial community structure associated with nitrogen transformation during aerobic composting, altering the abundance of functional genes and enzyme activities involved in nitrogen transformation. This approach significantly reduces nitrogen loss and harmful gas emissions. This paper reviews the application effects of microbial agents on nitrogen retention during aerobic composting and explores the underlying regulatory mechanisms, aiming to provide theoretical guidance and new research directions for the application of microbial agents in enhancing nitrogen retention during aerobic composting.}, }
@article {pmid40129674, year = {2025}, author = {Hussain, N and Al Haddad, AHI and Abbass, S and Alfahl, Z}, title = {The potential impact of habitual sleep quality on glycaemic control and inflammation: A study on geriatric patients recently diagnosed with type 2 diabetes mellitus (T2DM).}, journal = {Sleep medicine: X}, volume = {9}, number = {}, pages = {100139}, pmid = {40129674}, issn = {2590-1427}, abstract = {Sleep quality and its relationship with glycaemic control is of particular interest in the context of geriatric diabetes. We aimed to investigate the potential impact of habitual sleep quality on glycaemic control status among geriatric patients recently diagnosed with type 2 diabetes mellitus (T2DM). A total of 193 geriatric patients recently diagnosed with T2DM in a tertiary-care hospital were selected. A developed questionnaire was used to assess various aspects of sleep quality. Glycaemic control was evaluated through fasting blood glucose levels, HbA1c measurements and number of admissions to the hospital for hypoglycaemic or hyperglycaemic episodes. Patients were divided into Poor Sleep Quality (PSQ, n = 132) and Adequate Sleep Quality (ASQ, n = 61) groups. The PSQ group exhibited significantly worse sleep outcomes, including longer sleep latency (35 ± 9.2 min vs. 15 ± 6.4 min), shorter sleep duration (5 h 42 min vs. 7 h 18 min) and greater use of sleep medications (72 % vs. 22 %). Glycaemic control, measured by HbA1c, was worse in the PSQ group (8.7 ± 1.9 vs. 7.2 ± 1.2; p < 0.01), which also had more frequent severe hypoglycaemic (35 ± 1.4 vs. 8 ± 2.1; p = 0.02) and ketoacidotic episodes (72 ± 1.0 vs. 5 ± 1.1; p = 0.01). These findings suggest an association between poor sleep quality and poorer glycaemic control, with more frequent diabetes-related complications, highlighting the need for further research to explore potential causal relationships and targeted interventions in this population.}, }
@article {pmid40127879, year = {2025}, author = {Mirsalami, SM and Mirsalami, M}, title = {Assessing microbial ecology and antibiotic resistance genes in river sediments.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {130}, number = {}, pages = {105738}, doi = {10.1016/j.meegid.2025.105738}, pmid = {40127879}, issn = {1567-7257}, mesh = {*Geologic Sediments/microbiology ; *Rivers/microbiology ; Phylogeny ; *Bacteria/genetics/classification/drug effects ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Anthropogenic activities greatly affect the Karon River leading to deterioration of water quality. This investigation utilizes environmental genomic techniques to delineate microbial populations, examine functional genomics, and evaluate the occurrence of virulence determinants and antibiotic resistance genes (ARGs) in fluvial sediment. Taxonomic assessment identified that Firmicutes were the predominant phyla, with Bacillus being the most abundant genus across samples. Functional analysis revealed the metabolic capabilities of sediment-associated bacteria, linking them to biogeochemical processes and potential health impacts. The S2 samples exhibited the highest virulence factor genes, while the S3 samples had the most ARGs (30), highlighting concerns about pathogenicity. Analyzing ARGs provides critical insights into environmental data collected, such as water quality parameters (e.g., nutrient concentrations, pH) or pollution levels, prevalence, and distribution of these resistance factors within the sediment samples, helping to identify potential hotspots of antibiotic resistance in the Karon River ecosystem. The study identified similar operational taxonomic units (OTUs) across sampling sites at the phylogenetic level, indicating a consistent presence of certain microbial taxa. However, the lack of variation in functional classification suggests that while these taxa may be present, they are not exhibiting significant differences in metabolic capabilities or functional roles. These findings emphasize the significance of metagenomic methods in understanding microbial ecology and antibiotic resistance in aquatic environments, suggesting a need for further research into the restoration of microbial functions related to ARGs and virulence factors.}, }
@article {pmid40121181, year = {2025}, author = {Eaton, WD and McGee, KM and Glahn, A and Lemenze, A and Soteropoulos, P}, title = {Use of a logging road in a Costa Rican forest changes the composition and stability of soil microbial decomposer communities, and the conversion of organic carbon into biomass.}, journal = {Journal of applied microbiology}, volume = {136}, number = {4}, pages = {}, doi = {10.1093/jambio/lxaf075}, pmid = {40121181}, issn = {1365-2672}, support = {//Pace University Dyson College Office of the Dean/ ; }, mesh = {*Soil Microbiology ; Costa Rica ; *Forests ; Biomass ; *Carbon/metabolism/analysis ; *Fungi/metabolism/classification/genetics/isolation &amp; purification ; Soil/chemistry ; Actinobacteria/metabolism/genetics/isolation &amp; purification ; Nitrogen/analysis/metabolism ; Acidobacteria/metabolism/genetics/isolation &amp; purification ; *Forestry ; Trees ; }, abstract = {AIMS: The effects of a tropical forest logging road on soil C and N, and the compositions of Actinobacteria, Acidobacteria, and wood rot/lignin-degrading fungal (WRT/LD) decomposer communities were evaluated.<br><br>METHODS AND RESULTS: Soils from a healthy Costa Rican old growth forest before Hurricane Otto and from an adjacent, recently formed logging road built after Hurricane Otto were collected over 4 years and assessed for C and N metrics, and characteristics of the three decomposer communities determined by Illumina amplicon sequencing methods. The Logging Road negatively impacted the soil total organic C, respiration, biomass C, qCO2, and total N, while the Actinobacterial and Acidobacterial communities changed from stable compositions of copiotrophic taxa in the rich forest soil to stable compositions of oligotrophic taxa in the poor logging road soil, and the WRT/LD community changed from stable compositions of copiotrophic taxa in the forest soils to an unstable community of oligotrophic taxa with almost no overlap in genera between logging road soils.<br><br>CONCLUSIONS: The logging road negatively influenced 3 decomposer communities and associated C and N metrics, with the two bacterial communities taxonomically stabilizing, but the fungal community taxonomically diverging into an unstable composition over time. Monitoring efforts are on-going to provide local forest land managers with potential indicators of soil ecosystem damage and recovery.}, }
@article {pmid40120670, year = {2025}, author = {San-Blas, E and Cornejo, MJ and Guerra, M and Olivares, M and Faundez, S and Bastidas, B and Morales-Montero, P and Pizarro, L and Aponte, H and Castaneda-Alvarez, C and Lankin, G}, title = {Where are my nematodes? labelling and visualising entomopathogenic nematodes in vivo using carbon quantum dots.}, journal = {Journal of invertebrate pathology}, volume = {211}, number = {}, pages = {108317}, doi = {10.1016/j.jip.2025.108317}, pmid = {40120670}, issn = {1096-0805}, mesh = {Animals ; *Quantum Dots ; *Nematoda ; Carbon ; *Staining and Labeling/methods ; }, abstract = {Identifying single or groups of animals has significantly advanced our understanding of animal biology and ecology. However, labelling is extremely difficult in small animals, like soil invertebrates. Due to the complexity of current methods, the dynamics and interactions of these populations are often studied indirectly. Labelling nematodes or microarthropods such as collembolans or soil acari has been challenging due to the high cost, potential toxicity, genetic modification requirements, cellular processes interference, and photobleaching. In this scenario, no methods can be applied to large numbers of microorganisms at once due to their mentioned practical and biological limitations and cost. In this work we show that quantum carbon dots (Cdots) are effective for labelling infective juveniles (IJs) of entomopathogenic nematodes (EPNs). In in vitro assays the IJs gradually acquired fluorescence, as Cdots accumulated in the lysosome-related organelles from their intestine cells, peaking at day 14, and with no lethal or sub-lethal effects on IJs. Fluorescence was clearly distinguishable from the natural auto-fluorescence of non-labelled IJs and persisted for months in IJs transferred to water. We and non-experts easily differentiated between similar species of EPNs and between two strains of S. feltiae placed in the same matrix (soil or water). We demonstrated for the first time the feasibility of labelling large numbers of IJs (hundreds of thousands/millions) with Cdots at minimal cost without any adverse effects for over a year. Our findings could be the starting point for detailed and large-scale field investigations on nematodes and other small organisms, allowing deeper understanding of their roles in soil ecosystems. This method provides a cost-effective and reliable tool for advancing research in the ecology of soil invertebrates, such as the interactions occurring in communities or between specific organisms, movement and dispersal, population dynamics or ecosystem services in a cryptic environment difficult to study.}, }
@article {pmid40119062, year = {2025}, author = {Acharya, P and Yegon, MJ and Haferkemper, L and Misteli, B and Griebler, C and Vitecek, S and Attermeyer, K}, title = {Leaf Conditioning and Shredder Activity Shape Microbial Dynamics on Fine Particulate Organic Matter Produced During Decomposition of Different Leaf Litter in Streams.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {18}, pmid = {40119062}, issn = {1432-184X}, mesh = {*Plant Leaves/metabolism/chemistry/microbiology ; Acer/metabolism/chemistry ; Animals ; *Rivers/microbiology/chemistry ; Fatty Acids/analysis ; Bacteria/metabolism/classification/genetics/isolation &amp; purification ; Fagus/metabolism ; *Microbiota ; *Particulate Matter/metabolism ; Larva/microbiology ; Alnus/metabolism ; Feces/microbiology/chemistry ; Ecosystem ; Carbon/analysis ; }, abstract = {Leaf litter decomposition (LLD) is a key ecosystem function where invertebrate shredders produce large amounts of fine particulate organic matter (FPOM) that serves as a substrate for microbial assemblages. Here, we explore the shredder-produced FPOM composition and activity of FPOM-associated microbial communities in response to different leaf species and their conditioning. In a laboratory experiment, we fed leaves of different elemental compositions (alder, beech and maple), conditioned under oxic or anoxic conditions, to caddisfly larvae (Sericostoma sp.). We hypothesized differences in FPOM elemental and fatty acid composition and FPOM-associated microbial activity among the leaf species, conditioning, and two types of shredder-produced FPOM, i.e. shredded leaves and faecal pellets. Our results suggest that leaf conditioning and shredder activity play pivotal roles in shaping FPOM composition and FPOM-associated microbial activity. We observed lower C/N ratios with high-C/N litter (beech and maple leaves) after conditioning and no change in the elemental composition of the faecal pellets compared to the leaves. However, we observed differences in microbial fatty acid proportions and composition on leaves and faecal pellets with significantly higher fractions of bacterial fatty acids on faecal pellets than on leaves. We also noted a significant impact of leaf conditioning on the microbial activity of shredded leaves and faecal pellets, with a higher microbial growth efficiency observed on faecal pellets compared to ingested leaves. These findings highlight the crucial influence of leaf species and conditioning on the activity of shredder-produced FPOM, emphasizing the complex interplay between leaf properties and fate and microbial processes in streams.}, }
@article {pmid40118512, year = {2025}, author = {Gomes, IB}, title = {The overlooked interaction of emerging contaminants and microbial communities: a threat to ecosystems and public health.}, journal = {Journal of applied microbiology}, volume = {136}, number = {4}, pages = {}, doi = {10.1093/jambio/lxaf064}, pmid = {40118512}, issn = {1365-2672}, support = {//FCT/ ; UIDB/00511/2020//MCTES/ ; }, mesh = {*Public Health ; Humans ; *Ecosystem ; *Microbiota ; Animals ; *Microbial Interactions ; One Health ; *Environmental Pollutants ; Bacteria ; Biodegradation, Environmental ; }, abstract = {CONTEXT AND AIMS: Emerging contaminants (ECs) and microbial communities should not be viewed in isolation, but through the One Health perspective. Both ECs and microorganisms lie at the core of this interconnected framework, as they directly influence the health of humans, animals, and the environment.The interactions between ECs and microbial communities can have profound implications for public health, affecting all three domains. However, these ECs-microorganism interactions remain underexplored, potentially leaving significant public health and ecological risks unrecognized. Therefore, this article seeks to alert the scientific community to the overlooked interactions between ECs and microbial communities, emphasizing the pivotal role these interactions may play in the management of 'One Health.'<br><br>RESULTS: The most extensively studied interaction between ECs and microbial communities is biodegradation. However, other more complex and concerning interactions demand attention, such as the impact of ECs on microbial ecology (disruptions in ecosystem balance affecting nutrient and energy cycles) and the rise and spread of antimicrobial resistance (a growing global health crisis). Although these ECs-microbial interactions had not been extensively studied, there are scientific evidence that ECs impact on microbial communities may be concerning for public health and ecosystem balance.<br><br>CONCLUSIONS: So, this perspective summarizes the impact of ECs through a One Health lens and underscores the urgent need to understand their influence on microbial communities, while highlighting the key challenges researchers must overcome. Tackling these challenges is vital to mitigate potential long-term consequences for both ecosystems and public health.}, }
@article {pmid40118002, year = {2025}, author = {Wan, W and Grossart, HP and Wu, QL and Xiong, X and Yuan, W and Zhang, W and Zhang, Q and Liu, W and Yang, Y}, title = {Global meta-analysis deciphering ecological restoration performance of dredging: Divergent variabilities of pollutants and hydrobiontes.}, journal = {Water research}, volume = {280}, number = {}, pages = {123506}, doi = {10.1016/j.watres.2025.123506}, pmid = {40118002}, issn = {1879-2448}, mesh = {Ecosystem ; *Environmental Restoration and Remediation ; Water Pollutants, Chemical ; Geologic Sediments ; }, abstract = {Global "Sustainable Development Goals" propose ambitious targets to protect water resource and provide clean water, whereas comprehensive understanding of restoration performance and ecological mechanisms are lacking for dredging adopted for purifying polluted waterbodies and maintaining navigation channels. Here, we conducted a global meta-analysis to estimate ecological restoration consequence of dredging as pollution mitigation and navigation channel maintenance measures using a dataset compiled from 191 articles covering 696 studies and 84 environmental and ecological parameters (e.g., pollutants and hydrobiontes). We confirm that dredging shows negative influences on 77.50% pollutants in the BA model (before dredging vs. after dredging) and 84.21% pollutants in the CI model (control vs. impact) as well as on sediment nutrient fluxes. Additionally, 57.14% attributes (i.e., richness, diversity, biomass, and density) of hydrobiontes in the BA model and 89.47% attributes of hydrobiontes in the CI model responded negatively to dredging. As a result, 76.32% of the pollutants and 61.11% of the hydrobiont attributes responded uniformly to dredging in the BA and CI models. Our findings emphasize that dredging generally decreases pollutants and mitigates algal blooms, controlling phosphorus is easier than controlling nitrogen by dredging, and attributes (i.e., richness, diversity, and biomass) of hydrobiontes (i.e., zooplankton, phytoplankton, and zoobenthos) are density-dependent in dredging-disturbed environments. Our findings broaden our knowledge on ecological restoration performance of dredging as a mitigation measure in global aquatic ecosystems, and these findings might be helpful to use and optimize dredging to efficiently and sustainably purify polluted aquatic ecosystems.}, }
@article {pmid40116066, year = {2025}, author = {Cusenza, BS and Scelfo, G and Licata, G and Capri, FC and Vicari, F and Alduina, R and Villanova, V}, title = {First Insights Into the Biological and Physical-Chemical Diversity of Various Salt Ponds of Trapani, Sicily.}, journal = {Environmental microbiology reports}, volume = {17}, number = {2}, pages = {e70075}, pmid = {40116066}, issn = {1758-2229}, support = {MSCA_0000011//Next Generation EU/ ; }, mesh = {*Ponds/microbiology/chemistry ; Sicily ; *Archaea/genetics/classification/isolation &amp; purification ; *Bacteria/genetics/classification/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Salinity ; Biodiversity ; *Microbiota ; Phylogeny ; DNA, Archaeal/genetics ; Sodium Chloride/analysis ; DNA, Bacterial/genetics ; Ecosystem ; }, abstract = {The salt ponds of Trapani, Sicily, represent an extreme and under-explored ecosystem characterised by varying salinity gradients and environmental conditions. These ponds, integral to traditional salt extraction, include cold, driving, hot and crystallizer ponds, each hosting diverse microbial communities. This study aimed to explore the biological and physical-chemical diversity of 11 ponds during the salt production season in Trapani. We conducted comprehensive physical-chemical characterizations, including measurements of pH, conductivity, viscosity, density, organic carbon and ion concentration. Microbial DNA was extracted from salt pond waters and subjected to metabarcoding of 16S rRNA genes to determine the diversity of archaea and bacteria. High-throughput sequencing revealed significant variations in microbial communities across different pond types and seasons. Cold ponds showed a higher diversity of moderately halophilic organisms, while crystallizer and feeding ponds were dominated by extreme halophiles, particularly archaeal genus Halorubrum and Haloquadratum and bacterial genus Salinibacter. Statistical analyses indicated that environmental parameters, especially salinity and temperature, significantly influenced microbial community composition. Our findings enhance the understanding of microbial ecology in saline environments and highlight the potential of halophilic microorganisms. This study provides a foundation for future research into the functional roles of these microorganisms and their industrial applications.}, }
@article {pmid40113629, year = {2025}, author = {Moldovan, OT and Levei, E and Ferreira, RL and Silva, MS and Mirea, IC}, title = {Exploring the Bacteriome Diversity and Use as a Proxy for Climate Change and Human Impacts on Groundwater in Temperate and Tropical Countries.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {17}, pmid = {40113629}, issn = {1432-184X}, support = {PN-III-P4-ID-PCCF-2016-0016 (DARKFOOD)//Ministry of Research and Innovation, CNCS - UEFISCDI/ ; GA N&#xb0;101052342//Biodiversa+, the European Biodiversity Partnership/ ; CNPq n. 302925/2022-8//National Council for Scientific and Technological Development/ ; }, mesh = {*Groundwater/microbiology ; *Climate Change ; *Bacteria/classification/genetics/isolation &amp; purification ; Brazil ; *Caves/microbiology ; Romania ; Humans ; Tropical Climate ; Biodiversity ; Seasons ; *Microbiota ; Ecosystem ; RNA, Ribosomal, 16S/genetics ; Environmental Monitoring ; }, abstract = {This research investigates bacterial communities in various cave pool water and substrates from Brazil and Romania for their use as indicators of environmental impacts on groundwater. Regional and seasonal differences were observed even if, at the phylum level, common bacteria for both countries were found. Distinct patterns emerged at the genus level due to the different climates (tropical vs. temperate) and ecosystems. Chemoautotrophic conditions define an utterly different groundwater bacteriome than oligotrophic conditions independent of the temperature. Bacteria as a proxy for climate change were explored using seasonal changes in Romanian caves; specific genera become dominant in summer months, such as Acinetobacter, Paeniglutamicibacter, Polaromonas, and Saccharimonadales, indicating processes that occur during the low-water season. Climate change, particularly dryness, is expected to exacerbate these variations, threatening the stability of groundwater ecosystems. The research also identified anthropic pollution indicators (Vogesella, Cutibacterium) and potential decontaminants (Bacillus) in Brazilian cave waters. Anthropic pollution indicators, like Pseudoarthrobacter. were also found in Romanian caves. Other key bacteria genera, such as Flavobacterium, Pseudomonas, and Acinetobacter, are chemolithotrophs or involved in the nitrogen cycle, which is critical in supplying nutrients for the cave food web. Marked differences between water and substrate microbiomes within the same pools suggested that substrates may play a crucial, underexplored role in groundwater ecosystem processes. Our study found unassigned taxa, 3 phyla, 2 families, and 832 genera (> 40%) in the studied pools. The results underscore the need to further explore groundwater microbiomes as potentially crucial yet fragile ecosystems in the face of climate change and human impacts.}, }
@article {pmid40112476, year = {2025}, author = {Xu, RZ and Cao, JS and Cheng, S and Luo, JY and Ni, BJ and Fang, F and Liu, W and Wang, P}, title = {Heterotrophic nitrification-aerobic denitrification strains: An overlooked microbial interaction nexus in the anaerobic-swing-anoxic-oxic (ASAO) plug-flow system.}, journal = {Journal of environmental management}, volume = {380}, number = {}, pages = {125030}, doi = {10.1016/j.jenvman.2025.125030}, pmid = {40112476}, issn = {1095-8630}, mesh = {*Denitrification ; *Nitrification ; Nitrogen/metabolism ; Anaerobiosis ; Aerobiosis ; Heterotrophic Processes ; Bioreactors/microbiology ; Bacteria/metabolism ; Oxygen ; Phosphorus/metabolism ; }, abstract = {This study aims to clarify the overlooked functions of heterotrophic nitrification-aerobic denitrification (HNAD) bacteria in a novel anaerobic-swing-anoxic-oxic (ASAO) continuous plug-flow system. The dissolved oxygen (DO) levels and aerated hydraulic retention time (HRT) varied in the swing zones, providing a more diverse redox environment. High nitrogen (85.0 %) and phosphorus (80.0 %) removal were achieved by enriched HNAD bacteria (e.g., Thauera and Malikia) and phosphate accumulating organisms (PAO, e.g., Rhodocyclus and Azonexus) under middle DO level (1.0-2.0 mg/L) and longer aerated HRT (5.0 h). More importantly, microbial network revealed that HNAD bacteria became a connection point for other functional microorganisms associated with pollutant metabolism, and promoted the cooperation and functional evolution of microbial communities. The microbial ecology analysis captured the high importance of homogeneous selection, diffusion restriction, and drift for microbial community assembly in the ASAO system. Among them, HNAD bacteria contributed to both deterministic and stochastic processes, whereas the community assembly of PAO was mainly affected by the deterministic processes. The upregulation of denitrification genes (i.e., napA, napB, nirS, norB and norC) further confirmed the nitrogen removal contribution of aerobic denitrification by HNAD bacteria. Through this study, a comprehensive analysis of microbial interactions in the ASAO system was achieved, providing valuable insights into the targeted regulation of functional microorganisms in wastewater biological treatment processes.}, }
@article {pmid40112457, year = {2025}, author = {Liu, J and Xu, G and Zhao, S and He, J}, title = {Microbiomes of coastal sediments and plastispheres shaped by microplastics and decabrominated diphenyl ether.}, journal = {Water research}, volume = {280}, number = {}, pages = {123417}, doi = {10.1016/j.watres.2025.123417}, pmid = {40112457}, issn = {1879-2448}, mesh = {*Geologic Sediments/microbiology ; *Microplastics ; *Microbiota/drug effects ; *Halogenated Diphenyl Ethers ; Water Pollutants, Chemical ; }, abstract = {Deciphering the impact of microplastic and persistent organic pollutants (POPs) co-contamination on coastal sediment is critical for developing effective remediation strategies for polluted sites yet remains underexplored. This study investigated the interactions between microplastics, decabrominated diphenyl ether (deca-BDE), and their co-contamination effects on the evolvement of coastal sediment and plastisphere microbiomes for over 2 years. Results showed that deca-BDE was naturally debrominated in sediments via diverse pathways, with microplastic polystyrene stimulating the debromination rate by up to 78.7 ± 10.0 %. The putative OHRB Dehalobacter and uncultured Dehalococcoidia populations were identified responsible for the complete debromination. Co-exposure to microplastics and deca-BDE induced significant shifts in community composition, diversity, and function in the sediment microbiomes, while plastisphere microbiomes exhibited distinct compositions and functional profiles, specializing in pathogenicity, pollutant degradation, and biogeochemical cycling. The type of plastics and the presence of deca-BDE influenced the plastisphere composition. Changes in sediment properties and debromination activity profoundly shaped microbial communities, with deterministic assembly dominating the plastisphere. Co-contamination increased the complexity, modularity, and stability of the plastisphere networks, creating unique niches for OHRB. These findings highlight the intricate interplay between microplastics, deca-BDE, and microbiomes, with significant implications for ecosystem health and remediation efforts.}, }
@article {pmid40109964, year = {2025}, author = {Figueiredo, JEF and Diniz, GFD and Marins, MS and Silva, FC and Ribeiro, VP and Lanza, FE and de Oliveira-Paiva, CA and Cruz-Magalhães, V}, title = {Bacillus velezensis CNPMS-22 as biocontrol agent of pathogenic fungi and plant growth promoter.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1522136}, pmid = {40109964}, issn = {1664-302X}, abstract = {INTRODUCTION: Bacillus velezensis is a ubiquitous bacterium with potent antifungal activity and a plant growth promoter. This study investigated the potential of B. velezensis CNPMS-22 as a biocontrol agent against phytopathogenic fungi under diverse experimental conditions and its potential as a plant growth promoter. Genome sequencing and analysis revealed putative genes involved in these traits.<br><br>METHODS: This research performed in vitro experiments to evaluate the CNPMS-22 antagonistic activity against 10 phytopathogenic fungi using dual culture in plate (DCP) and inverted sealed plate assay (ISP). Greenhouse and field tests evaluated the ability of CNPMS-22 to control Fusarium verticillioides in maize plants in vivo. The CNPMS-22 genome was sequenced using the Illumina HiSeq 4,000 platform, and genomic analysis also included manual procedures to identify genes of interest accurately.<br><br>RESULTS: CNPMS-22 showed antifungal activity in vitro against all fungi tested, with notable reductions in mycelial growth in both DCP and ISP experiments. In the ISP, volatile organic compounds (VOCs) produced by CNPMS-22 also altered the mycelium coloration of some fungi. Scanning electron microscopy revealed morphological alterations in the hyphae of F. verticillioides in contact with CNPMS-22, including twisted, wrinkled, and ruptured hyphae. Eight cluster candidates for synthesizing non-ribosomal lipopeptides and ribosomal genes for extracellular lytic enzymes, biofilm, VOCs, and other secondary metabolites with antifungal activity and plant growth promoters were identified by genomic analysis. The greenhouse and field experiments showed that seed treatment with CNPMS-22 reduced Fusarium symptoms in plants and increased maize productivity.<br><br>CONCLUSION: Our findings highlight the CNPMS-22's potential as bioinoculant for fungal disease control and plant growth with valuable implications for a sustainable crop productivity.}, }
@article {pmid40109356, year = {2025}, author = {Kantor, RS and Kennedy, LC and Miller, SE and Favere, J and Nelson, KL}, title = {Reverse Osmosis in an Advanced Water Treatment Train Produces a Simple, Consistent Microbial Community.}, journal = {ACS ES&amp;T engineering}, volume = {5}, number = {3}, pages = {772-781}, pmid = {40109356}, issn = {2690-0645}, abstract = {Potable water reuse has become a key component of water sustainability planning in arid regions. Many advanced water purification facilities use reverse osmosis (RO) as part of treatment, including as a barrier for microorganisms; however, regrowth after RO treatment has been observed. Questions remain about the identity, source, and survival mechanisms of microorganisms in RO permeate, but the extremely low biomass of this water is a limitation for common microbiological methods. Here, we performed high-throughput sequencing on samples collected throughout a potable reuse train, including samples collected by filtering large volumes of RO permeate and biomass collected from RO membranes during an autopsy. We observed a stable, consistent microbial community across three months and in two parallel RO trains. RO permeate samples contained Burkholderiaceae at high relative abundance, including one Aquabacterium sp. that accounted for 29% of the community, on average. Like most other RO permeate microorganisms, this sequence was not seen in upstream samples and we suggest that biofilm growing on unit process infrastructure, rather than active treatment breakthrough, was the primary source. A metagenome-assembled genome corresponding to Aquabacterium sp. from RO permeate was found to lack most sugar-utilization pathways and to be able to consume low molecular weight organic molecules, potentially those that pass through RO.}, }
@article {pmid40107140, year = {2025}, author = {Quattrocelli, P and Piccirillo, C and Kuramae, EE and Pullar, RC and Ercoli, L and Pellegrino, E}, title = {Synergistic interaction of phosphate nanoparticles from fish by-products and phosphate-solubilizing bacterial consortium on maize growth and phosphorus cycling.}, journal = {The Science of the total environment}, volume = {973}, number = {}, pages = {179082}, doi = {10.1016/j.scitotenv.2025.179082}, pmid = {40107140}, issn = {1879-1026}, mesh = {*Zea mays/growth &amp; development ; *Phosphorus/metabolism ; *Phosphates/metabolism ; *Nanoparticles/chemistry ; *Fish Products ; Bacteria/metabolism ; Microbial Consortia ; Animals ; }, abstract = {Phosphate nanomaterials, such as hydroxyapatite/β-tricalcium nanoparticles (nHAs) derived from food industry by-products, offer a sustainable alternative to enhance P-use efficiency in agriculture. However, their limited solubility remains a challenge. This study first investigated the mechanisms of P solubilization of salmon and tuna bones (SnHAs and TnHAs) in fifteen strains of phosphate-solubilizing bacteria (PSB) by an in vitro system. Then, best-performing strains were assembled in a consortium and tested in vivo on maize. We hypothesized that combining nHAs and the PSB consortium inoculated as seed coating (SC) outperforms single treatments alone in promoting plant growth and P cycling, and ensures the establishment in plant-soil system without a bacterial reinforcement (BR) by an additional inoculum suspension. The synergistic effect of nHAs and PSB was proved, improving maize root (+22 %) and total plant biomass (+29 %), as well as P (+32 %) and K (66 %) uptake compared to single treatments. With nHAs and SC, P-use efficiency and recovery increased by 25 % and three-fold, respectively, compared to nHAs alone or with bacterial reinforcement. Consistently, root and substrate bacterial biomass were associated with nHAs plus SC, while nHAs alone or with PSB upregulated PHT1;1 and PHT1;2 transporter genes in maize. Finally, linking the in vitro and in vivo system, we demonstrated that propionic acid production and P-solubilization efficiency of PSB co-applied with nHAs are key drivers of maize growth and P uptake. Our findings indicated that co-applying nHAs and PSB through SC offers a sustainable strategy to improve maize P-use efficiency.}, }
@article {pmid40106821, year = {2025}, author = {Yang, CC and Washio, J and Lin, YC and Hsu, ML and Wang, DH and Tsai, FT and Lin, YM and Tu, HF and Chang, HC and Takahashi, N}, title = {Microbiome Signatures and Dysbiotic Patterns in Oral Cancer and Precancerous Lesions.}, journal = {Oral diseases}, volume = {}, number = {}, pages = {}, doi = {10.1111/odi.15317}, pmid = {40106821}, issn = {1601-0825}, support = {112-2314-B-A49-027//the National Science and Technology Council, Taiwan/ ; 111-2314-B-A49-028-MY2//the National Science and Technology Council, Taiwan/ ; 111-2314-B-A49-026-MY3//the National Science and Technology Council, Taiwan/ ; 112-2314-B-A49-058//the National Science and Technology Council, Taiwan/ ; 111-2314-B-A49-087-MY3//the National Science and Technology Council, Taiwan/ ; 21H03151//the Japan Society for the Promotion of Science/ ; 20K10241//the Japan Society for the Promotion of Science/ ; 23K18349//the Japan Society for the Promotion of Science/ ; 23K21499//the Japan Society for the Promotion of Science/ ; //the National Yang Ming Chiao Tung University and Ministry of Education (MOE), Taiwan/ ; }, abstract = {BACKGROUND: The oral microbiome has been shown to be associated with the development of oral squamous cell carcinoma (OSCC). Research has primarily focused on elucidating the oncogenic mechanisms of specific pathogens by comparing the microbiomes of OSCC and normal tissues. However, the characteristics of the microbiome in the precancerous state remain less understood, as does the influence of metabolic and environmental factors on OSCC-associated microbiomes.<br><br>METHODS: In this study, we analyzed mucosa-associated microbiomes in normal, precancerous, and OSCC lesions from a cohort of 51 patients using 16S rRNA amplicon sequencing. We investigated compositional changes in the microbiome, including the specific abundances and co-occurrences of OSCC-associated bacteria.<br><br>RESULTS: Our findings indicate that the microbiome associated with precancerous lesions is indistinguishable from that of the normal mucosa, whereas the OSCC microbiome significantly differs from both normal and precancerous conditions. Specifically, the OSCC microbiome harbors less Streptococcus, coupled with an increase in amino-acid-degrading anaerobes such as Fusobacterium and Prevotella. The metabolic properties of individual microbes reported suggest that the overrepresentation of OSCC-specific bacteria is a result of metabolic adaptation to tumor microenvironments, although this possibility needs to be experimentally confirmed.<br><br>CONCLUSIONS: Our results demonstrate oral microbiome patterns across OSCC progression, offering insights into microbial ecological perspectives.}, }
@article {pmid40106330, year = {2025}, author = {Maguire, M and DeLappe, N and Clarke, C and Touhy, A and Carlino-MacDonald, U and Hutson, A and Cormican, M and Brennan, W and Devane, G and Morris, D and Coughlan, SC and Miliotis, G and Russo, TA and Burke, LP}, title = {Genomic and phylogenetic analysis of hypervirulent Klebsiella pneumoniae ST23 in Ireland.}, journal = {Microbial genomics}, volume = {11}, number = {3}, pages = {}, doi = {10.1099/mgen.0.001373}, pmid = {40106330}, issn = {2057-5858}, support = {I01 BX004677/BX/BLRD VA/United States ; R21 AI141826/AI/NIAID NIH HHS/United States ; }, mesh = {*Klebsiella pneumoniae/genetics/pathogenicity/classification/isolation &amp; purification/drug effects ; Animals ; *Klebsiella Infections/microbiology/epidemiology ; Humans ; Virulence/genetics ; Ireland/epidemiology ; Mice ; *Phylogeny ; beta-Lactamases/genetics ; Retrospective Studies ; Bacterial Proteins/genetics ; Microbial Sensitivity Tests ; Female ; Genome, Bacterial ; Anti-Bacterial Agents/pharmacology ; Genomics ; Male ; Genotype ; Aged ; }, abstract = {Hypervirulent Klebsiella pneumoniae (hvKp) has emerged as a pathogen of global concern associated with invasive community-acquired infections. The combination of hypervirulence and carbapenem resistance can result in severe and difficult-to-treat infections. This retrospective study aimed to investigate the spread of hvKp sequence type 23 (ST23) in Ireland and the convergence of hypervirulent (hv) and antimicrobial resistance genotypes. Short-read sequences (PE300) for 90 K. pneumoniae ST23 isolates were generated by the Galway Reference Laboratory Services (GRLS). Isolates were from screening swabs (n=59), invasive infections (n=18), non-invasive sites (n=12) and the hospital environment (n=1). The virulence and resistance content were assessed genomically using Kleborate (v2.2.0), ABRicate (v1.0.1) and Platon (v1.6). The in vivo virulence of the isolates was assessed using a murine model. All isolates were genotypically hv with 88/90 isolates having a maximal Kleborate virulence score of 5 including carriage of key genes. Eighty-two per cent of isolates (74/90) carried a carbapenemase gene (bla OXA-48/bla OXA-181/bla NDM-1), and 42% carried resistance genes to 3 or more antimicrobial classes. Core genomic delineation revealed the isolates to be clonal with similar resistance and virulence profiles. Two distinct clusters of Irish isolates were detected consisting of 82/90 of the isolates. Isolates associated with carriage and infection demonstrated similar in vivo virulence. An established clone of hvKp ST23 is circulating within Ireland and causing both colonization and infection of patients. The lack of reliable screening methods for hvKp makes its detection and control in the healthcare setting challenging.}, }
@article {pmid40100630, year = {2025}, author = {Feng, W and Wan, X and Zhang, Y and Quensen, J and Williams, TA and Thompson, M and Streeter, M and Zhang, Y and Jiao, S and Wei, G and Zhu, Y and Gu, J and Tiedje, JM and Qian, X}, title = {Diversification, niche adaptation, and evolution of a candidate phylum thriving in the deep Critical Zone.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {12}, pages = {e2424463122}, pmid = {40100630}, issn = {1091-6490}, mesh = {Phylogeny ; *Soil Microbiology ; *Bacteria/genetics/classification/metabolism ; *Adaptation, Physiological ; *Microbiota/genetics ; *Biological Evolution ; Genome, Bacterial ; Energy Metabolism ; Evolution, Molecular ; }, abstract = {The deep subsurface soil microbiome encompasses a vast amount of understudied phylogenetic diversity and metabolic novelty, and the metabolic capabilities and ecological roles of these communities remain largely unknown. We observed a widespread and relatively abundant bacterial phylum (CSP1-3) in deep soils and evaluated its phylogeny, ecology, metabolism, and evolutionary history. Genome analysis indicated that members of CSP1-3 were actively replicating in situ and were widely involved in the carbon, nitrogen, and sulfur cycles. We identified potential adaptive traits of CSP1-3 members for the oligotrophic deep soil environments, including a mixotrophic lifestyle, flexible energy metabolisms, and conservation pathways. The ancestor of CSP1-3 likely originated in an aquatic environment, subsequently colonizing topsoil and, later, deep soil environments, with major CSP1-3 clades adapted to each of these distinct niches. The transition into the terrestrial environment was associated with genome expansion, including the horizontal acquisition of a range of genes for carbohydrate and energy metabolism and, in one lineage, high-affinity terminal oxidases to support a microaerophilic lifestyle. Our results highlight the ecology and genome evolution of microbes in the deep Critical Zone.}, }
@article {pmid40099901, year = {2025}, author = {Lysenko, V and Machushynets, NV and van Dam, JL and Sterk, FAC and Speer, A and Ram, AFJ and Slingerland, CJ and Van Wezel, GP and Martin, NI}, title = {Total Synthesis, Structure Elucidation, and Bioactivity Evaluation of the Cyclic Lipopeptide Natural Product Paenilipoheptin A.}, journal = {Organic letters}, volume = {27}, number = {12}, pages = {2826-2831}, pmid = {40099901}, issn = {1523-7052}, mesh = {*Lipopeptides/chemistry/pharmacology/chemical synthesis ; Molecular Structure ; *Biological Products/chemistry/pharmacology/chemical synthesis ; *Microbial Sensitivity Tests ; *Anti-Bacterial Agents/pharmacology/chemistry/chemical synthesis ; Peptides, Cyclic/chemistry/chemical synthesis/pharmacology ; Antifungal Agents/pharmacology/chemistry/chemical synthesis ; Gram-Positive Bacteria/drug effects ; Stereoisomerism ; }, abstract = {In this study, we further investigated the structure of the recently reported cyclic lipopeptide natural product paenilipoheptin A. Here, we disclose the first total synthesis of the compound, allowing for its complete structural assignment. The route developed employs automated SPPS, providing access to the compound in quantities suitable for antibacterial and antifungal testing. These studies unequivocally establish the stereochemical framework of paenilipoheptin A and further reveal that the compound possesses moderate activity against Gram-positive bacteria.}, }
@article {pmid40099188, year = {2025}, author = {Silverio, MP and Schultz, J and Parise, MTD and Parise, D and Viana, MVC and Nogueira, W and Ramos, RTJ and Góes-Neto, A and Azevedo, VAC and Brenig, B and Bonelli, RR and Rosado, AS}, title = {Genomic and phenotypic insight into antimicrobial resistance of Pseudomonas fluorescens from King George Island, Antarctica.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1535420}, pmid = {40099188}, issn = {1664-302X}, abstract = {The genus Pseudomonas includes metabolically versatile microorganisms occupying diverse niches, from environmental habitats to plant pathogens, and has clinically significant strains. For this reason, Pseudomonas spp. might act as a reservoir of antimicrobial resistance genes, which have been detected even in isolated environments. The aim of this study was to report the antimicrobial susceptibility profile of 25 Pseudomonas fluorescens isolates from soil samples collected on King George Island (Antarctic Peninsula), and to select non-clonal isolates with unusual phenotypes for whole genome sequencing (WGS). Six classes of antimicrobials were assessed with disk diffusion and colistin with minimum inhibitory concentration (MIC) by broth microdilution. In order to confirm the discrepant phenotypes, MIC by agar dilution was performed for the beta-lactams aztreonam, ceftazidime, cefepime and the aminoglycoside neomycin. The genus Pseudomonas was confirmed by matrix-assisted laser desorption/ionization - time of flight (MALDI-TOF) and the clonal relationships were examined using repetitive extragenic palindromic polymerase chain reaction (BOX-PCR), from which 14 strains were selected for WGS. Antimicrobial susceptibility testing revealed that all strains were susceptible to neomycin and exhibited varying degrees of intermediate or full resistance to aztreonam and colistin. Additionally, 11 strains demonstrated intermediate resistance to ceftazidime, and six were resistant to cefepime. The genomic analysis identified various efflux pumps, predominantly from the ABC transporter and resistance-nodulation-division families. Resistance genes were detected against eight classes of antimicrobials, listed by prevalence: beta-lactams, tetracyclines, polymyxins, aminoglycosides, fosmidomycin, fosfomycin, quinolones, and chloramphenicol. Genes associated with heavy-metal resistance, prophages, and adaptations to extreme environments were also investigated. One notable isolate exhibited not only the highest number of pathogenicity and resistance islands, but also presented a carbapenemase-encoding gene (bla PFM-2) in its genome. Overall, one plasmid was identified in a distinct isolate, which did not exhibit antimicrobial resistance determinants. The genotypic and phenotypic findings are consistent, suggesting that efflux pumps play a critical role in antimicrobial extrusion. This study offers valuable insight into the evolution of antimicrobial resistance in P. fluorescens, particularly in extreme environments, such as Antarctica. By exploring the antimicrobial resistance mechanisms in P. fluorescens, the study sheds light on how isolated ecosystems drive the natural evolution of resistance genes.}, }
@article {pmid40098226, year = {2025}, author = {Frühe, L and Klein, SG and Angulo-Preckler, C and Martynova, A and Alamoudi, T and García, JVA and Arossa, S and Breavington, J and Frappi, S and Laiolo, E and Lim, KK and Parry, AJ and Re, E and Rosas, DER and Rodrigue, M and Steckbauer, A and Pieribone, VA and Qurban, MA and Duarte, CM}, title = {Particle-Associated Bacterioplankton Communities Across the Red Sea.}, journal = {Environmental microbiology}, volume = {27}, number = {3}, pages = {e70075}, pmid = {40098226}, issn = {1462-2920}, support = {//National Center of Wildlife/ ; //King Abdullah University of Science and Technology/ ; }, mesh = {Indian Ocean ; *Bacteria/classification/genetics/isolation &amp; purification ; *Seawater/microbiology ; *Plankton/classification/genetics/isolation &amp; purification ; Biodiversity ; Ecosystem ; Saudi Arabia ; Phylogeny ; DNA Barcoding, Taxonomic ; }, abstract = {Pelagic particle-associated bacterioplankton play crucial roles in marine ecosystems, influencing biogeochemical cycling and ecosystem functioning. However, their diversity, composition, and dynamics remain poorly understood, particularly in unique environments such as the Red Sea. In this study, we employed eDNA metabarcoding to comprehensively characterise bacterioplankton communities associated with pelagic particles in a three-dimensional assessment spanning depths from the surface to a depth of 2300 m along the full length of the eastern Red Sea within the exclusive economic zone of the Kingdom of Saudi Arabia. Our results reveal a diverse assemblage of taxa, with Pseudomonadota, Cyanobacteriota, and Planctomycetota being the dominant phyla. We identified pronounced spatial variability in community composition among five major Red Sea geographical regions, with a third of all amplicon sequence variants being unique to the Southern Red Sea in contrast to a relatively homogenous distribution along the water column depth gradient. Our findings contribute to a deeper understanding of microbial ecology in the Red Sea and provide valuable insights into the factors governing pelagic particle-associated bacterioplankton communities in this basin.}, }
@article {pmid40097839, year = {2025}, author = {Blanco, S and Viso, R and Borrego-Ramos, M and López-Flores, R and Mota-Echeandía, D and Tierra, M and Herrero, J and C Castañeda, }, title = {The Ecology of Benthic Diatom Assemblages in Saline Wetlands of the Ebro Basin, NE Spain.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {16}, pmid = {40097839}, issn = {1432-184X}, support = {TED2021-130303B-I00//MCIN/AEI/ ; }, mesh = {*Diatoms/classification/physiology ; *Wetlands ; Spain ; Biodiversity ; Ecosystem ; Salinity ; Electric Conductivity ; }, abstract = {Benthic diatoms play a crucial role in aquatic ecosystems as indicators of environmental conditions and contributors to primary productivity. This study explores the ecology of benthic diatom assemblages in saline wetlands in NE Spain, focusing on the relationships between community parameters, species distributions, and environmental factors, particularly conductivity. Samples were collected from several wetlands representing a range of conductivity and trophic state. A total of 25 diatom taxa were identified, with assemblages dominated by halophilous species. Non-metric multidimensional scaling analysis revealed electrical conductivity (EC) as a primary factor shaping diatom communities, with nutrient levels as a secondary influence. Species exhibited varying responses to the EC gradient, with some showing overlapping niches and others clearly separated. The study found strong correlations between species abundance, occupancy, and their contribution to dissimilarity between sampling sites. More abundant and widespread species were key drivers of community structure and differentiation. Additionally, a significant relationship was observed between taxa occurrence and niche breadth, measured as EC tolerance. Species with broader tolerances tended to have higher occupancy rates, supporting ecological theories about generalist strategies in variable environments. Contrary to some previous research, rare taxa (3-5% in relative abundance) had a negligible effect on assemblage segregation among habitats. The findings suggest that both environmental filtering based on EC tolerance and species' inherent characteristics play important roles in shaping diatom community composition across these saline wetlands. This study contributes to our understanding of diatom ecology in saline habitats and highlights the importance of considering both local abundance and environmental tolerance in ecological studies of these communities. The insights gained can inform more accurate ecological models and improve our understanding of species distribution and community dynamics in saline aquatic ecosystems.}, }
@article {pmid40097820, year = {2025}, author = {Blanchette, RA and Rajtar, NN and Lochridge, AG and Held, BW}, title = {Intercontinental movement of exotic fungi on decorative wood used in aquatic and terrestrial aquariums.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {9142}, pmid = {40097820}, issn = {2045-2322}, support = {no number//Minnesota Invasive Terrestrial Plants and Pests Center, University of Minnesota/ ; }, mesh = {*Wood/microbiology ; *Fungi/isolation &amp; purification/genetics/classification ; Plant Diseases/microbiology ; United States ; Introduced Species ; }, abstract = {The intercontinental movement of fungi or fungus-like organisms brings nonnative species into areas where they may become invasive pathogens of trees and other plants. In the past century, many examples such as Dutch elm disease, sudden oak death, laurel wilt, and others have resulted in large economic losses and ecological disasters. Although various safeguards to prevent the transport of potential pathogens have been in effect, new avenues of introduction have occurred causing new disease outbreaks. This study examined fungi in wood shipped from Asia that is used for decorative purposes in aquatic and terrestrial aquariums. From 44 imported wood samples, 202 cultures representing 123 different fungal taxa were obtained and identified using molecular methods. These included 31 species not previously reported in the United States, 21 potential plant pathogens, 37 species of wood decay fungi and 24 taxa with a 97% sequence match or less to known isolates suggesting these are unknown species. The results demonstrate that wood used for decorative purposes in aquariums harbor large numbers of diverse fungi that remain viable during shipping and storage. These fungi are currently being imported into areas where they are not native, and they may pose serious biosecurity threats to the United States and other countries around the world.}, }
@article {pmid40097298, year = {2025}, author = {Morin, C and Alfahl, Z}, title = {A systematic review on the utility of wastewater surveillance for monitoring yellow fever virus and other arboviruses.}, journal = {Journal of applied microbiology}, volume = {136}, number = {3}, pages = {}, doi = {10.1093/jambio/lxaf066}, pmid = {40097298}, issn = {1365-2672}, support = {02-303952//Applied Microbiology International Summer Studentship/ ; }, mesh = {*Wastewater/virology ; *Yellow fever virus/isolation &amp; purification/genetics ; *Arboviruses/isolation &amp; purification/genetics ; Humans ; *Environmental Monitoring/methods ; Yellow Fever/virology ; }, abstract = {AIMS: This review aims to examine wastewater surveillance for the detection of yellow fever virus (YFV) and related arboviruses, focusing on concentration and extraction methodology, viral decay kinetics, and quantification techniques.<br><br>METHODS: A literature search was conducted across 5 databases: PubMed, Science Direct, Web of Science, Embase, and Google Scholar following the PRISMA guidelines. Studies included were original scientific articles published between April 2014 and April 2024. Human research studies investigating wastewater surveillance and YFV or other arboviruses/flaviviruses were assessed.<br><br>RESULTS: A total of 17 studies were included in this review. YFV was not detected in population-based wastewater samples; however, successful detection of similar viruses suggests potential for YFV monitoring with wastewater surveillance. YFV-spiked wastewater studies reveal similar concentration efficiency and decay rates between arboviruses. Effective concentration methods for YFV likely include centrifugation ultrafiltration and solid pellet extraction. YFV and arboviruses decay faster at higher temperatures, though YFV remains detectable for several days at these temperatures.<br><br>CONCLUSIONS: Wastewater surveillance presents a promising approach for monitoring YFV and other arboviruses. However, further research is needed to overcome existing limitations and enhance its effectiveness.}, }
@article {pmid40092580, year = {2025}, author = {Li, G and Wang, Z and Wu, C and Wang, D and Han, I and Lee, J and Kaeli, DR and Dy, JG and Weinberger, KQ and Gu, AZ}, title = {Towards high-accuracy bacterial taxonomy identification using phenotypic single-cell Raman spectroscopy data.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf015}, pmid = {40092580}, issn = {2730-6151}, abstract = {Single-cell Raman Spectroscopy (SCRS) emerges as a promising tool for single-cell phenotyping in environmental ecological studies, offering non-intrusive, high-resolution, and high-throughput capabilities. In this study, we obtained a large and the first comprehensive SCRS dataset that captured phenotypic variations with cell growth status for 36 microbial strains, and we compared and optimized analysis techniques and classifiers for SCRS-based taxonomy identification. First, we benchmarked five dimensionality reduction (DR) methods, 10 classifiers, and the impact of cell growth variances using a SCRS dataset with both taxonomy and cellular growth stage labels. Unsupervised DR methods and non-neural network classifiers are recommended for at a balance between accuracy and time efficiency, achieved up to 96.1% taxonomy classification accuracy. Second, accuracy variances caused by cellular growth variance (<2.9% difference) was found less than the influence from model selection (up to 41.4% difference). Remarkably, simultaneous high accuracy in growth stage classification (93.3%) and taxonomy classification (94%) were achievable using an innovative two-step classifier model. Third, this study is the first to successfully apply models trained on pure culture SCRS data to achieve taxonomic identification of microbes in environmental samples at an accuracy of 79%, and with validation via Raman-FISH (fluorescence in situ hybridization). This study paves the groundwork for standardizing SCRS-based biotechnologies in single-cell phenotyping and taxonomic classification beyond laboratory pure culture to real environmental microorganisms and promises advances in SCRS applications for elucidating organismal functions, ecological adaptability, and environmental interactions.}, }
@article {pmid40090302, year = {2025}, author = {Wang, J and Hu, Y and An, L and Wang, J and Wu, F and Gu, J and Wang, X and Tiedje, JM}, title = {An efficient strategy for BDD electrode drive electro-catalysis triggering active species on lincomycin and antibiotic resistance genes removal: Electron transfer based on calculation modeling.}, journal = {Journal of hazardous materials}, volume = {491}, number = {}, pages = {137915}, doi = {10.1016/j.jhazmat.2025.137915}, pmid = {40090302}, issn = {1873-3336}, mesh = {Electrodes ; *Anti-Bacterial Agents/chemistry ; Electron Transport ; *Water Pollutants, Chemical/chemistry ; Genes, Bacterial ; Electrochemical Techniques ; Catalysis ; *Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; }, abstract = {Identifying the degradation pathway and the final by-products is essential, as their ecological risks are pertinent to the advancement of this technology and its potential application in practical environmental pollution treatment. Elucidating the reaction mechanisms of the degradation system represents the most effective strategy for controlling this process. This study thoroughly revealed that indirect oxidation predominates throughout the electrochemical system, while direct oxidation serves a significant auxiliary role under the synergistic influence. It elucidates the critical importance of electron transfer behavior at the electrode surface for pollutant degradation and unveil potential mechanisms underlying primary degradation reactions via integrating charge density differences and Bader atomic charge analysis. In situ electrochemical infrared spectroscopy (In situ EC-FTIR) and density functional calculation (DFT) were used to analyze the final by-product generation path. It further elucidated the correlation between antibiotic resistance gene (ARGs) and binding strength among base pairs. The oxidative stress process of antibiotic resistance bacteria (ARB) was explained in detail. To comprehensively assess the impact of electrochemical treatment on environmental microbial communities, combined horizontal gene transfer (HGT) experiments were conducted to confirm that electrolytically treated wastewater does not induce ecological stress effects on microorganisms. Finally, a small cyclic electrochemical system was employed to evaluate both ecological impacts and economic benefits associated with wastewater treatment, thereby providing a novel theoretical framework for this domain.}, }
@article {pmid40087979, year = {2025}, author = {Van den Wyngaert, S and Cerbin, S and Garzoli, L and Grossart, HP and Gsell, AS and Kraberg, A and Lepère, C and Neuhauser, S and Stupar, M and Tarallo, A and Cunliffe, M and Gachon, C and Gavrilović, A and Masigol, H and Rasconi, S and Selmeczy, GB and Schmeller, DS and Scholz, B and Timoneda, N and Trbojević, I and Wilk-Woźniak, E and Reñé, A}, title = {ParAquaSeq, a Database of Ecologically Annotated rRNA Sequences Covering Zoosporic Parasites Infecting Aquatic Primary Producers in Natural and Industrial Systems.}, journal = {Molecular ecology resources}, volume = {25}, number = {6}, pages = {e14099}, pmid = {40087979}, issn = {1755-0998}, support = {PID2020-112978GB-I00//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; CA20125//European Cooperation in Science and Technology/ ; 451-03-66/2024-03/200178//Ministarstvo Prosvete, Nauke i Tehnolo&#x161;kog Razvoja/ ; 239548-051//RANNIS Icelandic Research Fund/ ; 340659//Research Council of Finland/ ; 346387//Research Council of Finland/ ; 101086521//European Commission/ ; IR0000005//European Commission/ ; NKFIH KKP 144068//National Laboratory for Water Science and Water Security/ ; RRF-2.3.1-21-2022-00008//National Laboratory for Water Science and Water Security/ ; Y0801-B16//Austrian Science Fund/ ; //AXA Research Fund/ ; ANR-21-BIRE-0002-01//Agence Nationale de la Recherche/ ; 101052342//Biodiversa+/ ; CIR-01_00028//Italian Ministry of University and Research/ ; GR1540/33-1//Deutsche Forschungsgemeinschaft/ ; GR1540/47-1//Deutsche Forschungsgemeinschaft/ ; GR1540/48-1//Deutsche Forschungsgemeinschaft/ ; GR1540/51-1//Deutsche Forschungsgemeinschaft/ ; CEX2019-000928-S//AEI/ ; }, mesh = {*Aquatic Organisms/parasitology ; *RNA, Ribosomal/genetics ; Microalgae/parasitology ; *Parasites/genetics/classification ; *Databases, Genetic ; }, abstract = {Amplicon sequencing tools such as metabarcoding are commonly used for thorough characterisation of microbial diversity in natural samples. They mostly rely on the amplification of conserved universal markers, mainly ribosomal genes, allowing the taxonomic assignment of barcodes. However, linking taxonomic classification with functional traits is not straightforward and requires knowledge of each taxonomic group to confidently assign taxa to a given functional trait. Zoosporic parasites are highly diverse and yet understudied, with many undescribed species and host associations. However, they can have important impacts on host populations in natural ecosystems (e.g., controlling harmful algal blooms), as well as on industrial-scale algae production, e.g. aquaculture, causing their collapse or economic losses. Here, we present ParAquaSeq, a curated database of available molecular ribosomal sequences belonging to zoosporic parasites infecting aquatic vascular plants, macroalgae and photosynthetic microorganisms, i.e. microalgae and cyanobacteria. These sequences are aligned with ancillary data and other information currently available, including details on their hosts, occurrence, culture availability and associated bibliography. The database includes 1131 curated sequences from marine, freshwater and industrial or artificial environments, and belonging to 13 different taxonomic groups, including Chytridiomycota, Oomycota, Phytomyxea, and Syndiniophyceae. The curated database will allow a comprehensive analysis of zoosporic parasites in molecular datasets to answer questions related to their occurrence and distribution in natural communities. Especially through meta-analysis, the database serves as a valuable tool for developing effective mitigation and sustainable management strategies in the algae biomass industry, but it will also help to identify knowledge gaps for future research.}, }
@article {pmid40086056, year = {2025}, author = {Liang, L and Dang, B and Ouyang, X and Zhao, X and Huang, Y and Lin, Y and Cheng, X and Xie, G and Lin, J and Mi, P and Ye, Z and Guleng, B and Cheng, SC}, title = {Dietary succinate supplementation alleviates DSS-induced colitis via the IL-4Rα/Hif-1α Axis.}, journal = {International immunopharmacology}, volume = {152}, number = {}, pages = {114408}, doi = {10.1016/j.intimp.2025.114408}, pmid = {40086056}, issn = {1878-1705}, mesh = {Animals ; *Succinic Acid/therapeutic use/pharmacology ; *Colitis/chemically induced/immunology/drug therapy ; Dextran Sulfate ; Mice ; *Hypoxia-Inducible Factor 1, alpha Subunit/metabolism/genetics ; Mice, Inbred C57BL ; Dietary Supplements ; Mice, Knockout ; Monocytes/immunology ; Colon/immunology/drug effects/pathology ; Male ; Disease Models, Animal ; Humans ; Signal Transduction ; Cytokines/metabolism ; Interleukin-4 Receptor alpha Subunit ; }, abstract = {Inflammatory bowel disease (IBD) remains a pressing global health challenge, necessitating novel therapeutic strategies. Succinate, a metabolite known for its role in type 2 immunity and tuft cell activation in the small intestine, presents its potential in IBD management. However, its impact on colonic inflammation has not been explored. Here, we demonstrate that succinate administration induces a type 2 immune response, significantly alleviating dextran sulfate sodium (DSS)-induced colonic inflammation. Succinate enhances antibacterial capacity, reduces intestinal permeability, and reshapes the colonic cytokine milieu. Mechanistically, succinate promotes myeloid cell expansion in peripheral blood, mesenteric lymph nodes, and the colonic lamina propria. The protective effects of succinate were abolished in Ccr2[-/-] mice, confirming the role of monocyte recruitment, but persisted in Rag1[-/-] mice, indicating independence from adaptive immunity. Adoptive transfer of monocytes from succinate-treated donors mitigated intestinal inflammation in recipient mice. Transcriptomic analysis revealed heightened expression of Il1b and Il6, and higher lactate production in monocytes upon lipopolysaccharide (LPS) stimulation, highlighting a reprogrammed pro-inflammatory trained immunity phenotype. Finally, we identify the IL-4Rα/Hif-1α axis is critical for succinate-mediated protection. These findings reveal the ability of succinate to reprogram monocytes into protective intestinal macrophages via induction of type 2 response, restoring homeostasis through enhanced barrier function and immune modulation. Our study positions thus uncover succinate as a promising therapeutic candidate for IBD.}, }
@article {pmid40085655, year = {2025}, author = {Muratore, D and Gilbert, NE and LeCleir, GR and Wilhelm, SW and Weitz, JS}, title = {Diel partitioning in microbial phosphorus acquisition in the Sargasso Sea.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {11}, pages = {e2410268122}, pmid = {40085655}, issn = {1091-6490}, support = {OCE-1829641//National Science Foundation (NSF)/ ; OCE-1829636//National Science Foundation (NSF)/ ; 721231//Simons Foundation (SF)/ ; }, mesh = {*Phosphorus/metabolism ; *Phytoplankton/metabolism/genetics ; *Seawater/microbiology ; *Cyanobacteria/metabolism/genetics ; Nitrogen/metabolism ; Ecosystem ; *Bacteria/metabolism/genetics ; Oceans and Seas ; Pacific Ocean ; }, abstract = {The daily cycle of photosynthetic primary production at the base of marine food webs is often limited by the availability of scarce nutrients. Microbial competition for these scarce resources can be alleviated insofar as the intensity of nutrient uptake and assimilation activities are distributed heterogeneously across organisms over periodic input cycles. Recent analysis of community transcriptional dynamics in the nitrogen-limited subtropical North Pacific gyre revealed evidence of temporal partitioning of nitrogen uptake and assimilation between eukaryotic phytoplankton, cyanobacteria, and heterotrophic bacteria over day-night cycles. Here, we present results from a Lagrangian metatranscriptomic time series survey in the Sargasso Sea and demonstrate temporally partitioned phosphorus uptake in this phosphorus-limited environment. In the Sargasso, heterotrophic bacteria, eukaryotic phytoplankton, and cyanobacteria express genes for phosphorus assimilation during the morning, day, and dusk, respectively. These results support the generality of temporal niche partitioning as an emergent mechanism that can structure uptake of limiting nutrients and facilitate coexistence of diverse microbes in open ocean ecosystems.}, }
@article {pmid40085287, year = {2025}, author = {Micciulla, JL and Baubin, C and Fierer, N}, title = {Effects of Geosmin on the Behavior of Soil Protists.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {14}, pmid = {40085287}, issn = {1432-184X}, support = {2126106//National Science Foundation/ ; }, mesh = {*Soil/parasitology/chemistry ; *Soil Microbiology ; *Naphthols/metabolism/pharmacology ; *Acanthamoeba castellanii/physiology/drug effects ; *Ciliophora/physiology/drug effects ; Bacteria/metabolism ; Cercozoa/physiology/drug effects ; }, abstract = {Geosmin is a volatile organic compound (VOC) produced by a range of different soil microorganisms, and is most commonly recognized for its characteristic "earthy" scent evident after rainfall. Though it remains unclear why microorganisms produce geosmin, we know that exposure to geosmin can influence behaviors across a wide range of organisms, serving as both an attractant and a repellant, but geosmin effects on soil protists remain largely unstudied. We investigated how soil protists respond to geosmin exposures, focusing on representatives of three morphological groups of protists, Colpoda sp. (ciliate), Cercomonas sp. (flagellate), and Acanthamoeba castellanii (naked amoeba), testing the hypothesis that geosmin production by bacteria influences soil protist behavior. We conducted experiments to evaluate protist excystment (waking up) and predation responses to geosmin-producing (Streptomyces coelicolor M145) and non-producing (S. coelicolor J3003) bacteria, as well as synthetic geosmin. All three protists excysted at higher rates when exposed to geosmin-producing bacteria or synthetic geosmin, while no significant excystment occurred with the non-producing strains or in the absence of synthetic geosmin. Protist feeding preferences were also affected, with two of the three protists (Cercomonas sp. and A. castellanii) less likely to predate geosmin-producing versus non-producing bacterial strains. Our findings suggest that soil protists can detect geosmin as a signal indicating favorable soil conditions and geosmin production by bacteria may serve as a deterrent to predation by protists. More generally, our results highlight the ecological significance of geosmin in the soil food web and its role in mediating bacteria-protist interactions.}, }
@article {pmid40085262, year = {2025}, author = {Castelli, M and Petroni, G}, title = {An Evolutionary-Focused Review of the Holosporales (Alphaproteobacteria): Diversity, Host Interactions, and Taxonomic Re-ranking as Holosporineae Subord. Nov.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {15}, pmid = {40085262}, issn = {1432-184X}, mesh = {Phylogeny ; *Biological Evolution ; Animals ; *Alphaproteobacteria/classification/genetics/physiology ; *Biodiversity ; *Host Microbial Interactions ; }, abstract = {The order Holosporales is a broad and ancient lineage of bacteria obligatorily associated with eukaryotic hosts, mostly protists. Significantly, this is similar to other evolutionary distinct bacterial lineages (e.g. Rickettsiales and Chlamydiae). Here, we provide a detailed and comprehensive account on the current knowledge on the Holosporales. First, acknowledging the up-to-date phylogenetic reconstructions and recent nomenclatural proposals, we reevaluate their taxonomy, thus re-ranking them as a suborder, i.e. Holosporineae, within the order Rhodospirillales. Then, we examine the phylogenetic diversity of the Holosporineae, presenting the 20 described genera and many yet undescribed sub-lineages, as well as the variety of the respective environments of provenance and hosts, which belong to several different eukaryotic supergroups. Noteworthy representatives of the Holosporineae are the infectious intranuclear Holospora, the host manipulator 'Caedimonas', and the farmed shrimp pathogen 'Candidatus Hepatobacter'. Next, we put these bacteria in the broad context of the whole Holosporineae, by comparing with the available data on the least studied representatives, including genome sequences. Accordingly, we reason on the most probable evolutionary trajectories for host interactions, host specificity, and emergence of potential pathogens in aquaculture and possibly humans, as well as on future research directions to investigate those many open points on the Holosporineae.}, }
@article {pmid40084873, year = {2025}, author = {Soh, M and Er, S and Low, A and Jaafar, Z and de Boucher, R and Seedorf, H}, title = {Spatial and temporal changes in gut microbiota composition of farmed Asian seabass (Lates calcarifer) in different aquaculture settings.}, journal = {Microbiology spectrum}, volume = {13}, number = {5}, pages = {e0198924}, pmid = {40084873}, issn = {2165-0497}, abstract = {UNLABELLED: The microbiota composition of healthy farmed fishes remains poorly characterized for many species. This study explores the influence of the external environment and innate factors that may shape the gut microbiota of farmed Asian seabass, Lates calcarifer. The α-diversity based on Shannon, Simpson, and Chao1 indices was lower for fishes reared in sea cages and tanks than for fishes that experienced a transfer from sea cages to tanks. Longitudinal analyses of gut segments revealed no significant differences in alpha diversity between segments within the same containment type, except for the Chao1 index between the stomach and pyloric cecum of sea-caged fishes. β-diversity analysis using weighted UniFrac distance and Bray-Curtis dissimilarity demonstrated that fish reared in the same containment type shared similar microbial communities. PERMANOVA tests confirmed that containment type, farm, and batch significantly influenced these distances. Containment type accounted for 10.4% of the observed diversity, farm for 29.8%, and batch for 10.7%. Genera comprising potential pathogens such as Aeromonas, Flavobacterium, and Vibrio were differentially abundant along the guts of fish from different containment types and particularly increased in tanks. Microbiota changes were observed with host age and gut segment, with differentially abundant microbial genera identified along the gut and as the seabass grew. Comparing the hindgut microbiota of Asian seabass to other species of farmed fishes revealed host-specific clustering as indicated by PERMANOVA. Overall, these findings underscore the significance of containment conditions on the gut microbiota of Asian seabass, with broad implications for aquaculture practices.<br><br>IMPORTANCE: Understanding the microbiota composition of healthy farmed fishes is crucial for optimizing aquaculture practices. This study highlights the significant influence of containment conditions on the gut microbiota of farmed Asian seabass (Lates calcarifer). By demonstrating that gut microbiota diversity and community composition are shaped by containment type, farm location, and batch, the research provides valuable insights into how external environmental factors and innate host factors interact to influence fish health. The findings, particularly the differential abundance of potential pathogens in various containment types, underscore the need for tailored management strategies in aquaculture. This research not only advances our knowledge of fish microbiota but also has broad implications for improving the sustainability and productivity of aquaculture practices.}, }
@article {pmid40084850, year = {2025}, author = {Machushynets, NV and Lysenko, V and Du, C and Slingerland, CJ and Elsayed, SS and Liles, MR and Martin, NI and van Wezel, GP}, title = {Exploring the Chemical Space of Paenibacillus NRPs and Discovery of Paenilipoheptin B.}, journal = {Organic letters}, volume = {27}, number = {12}, pages = {2821-2825}, pmid = {40084850}, issn = {1523-7052}, mesh = {*Paenibacillus/chemistry/metabolism ; Molecular Structure ; *Lipopeptides/chemistry ; Peptide Synthases/metabolism/chemistry ; Nuclear Magnetic Resonance, Biomolecular ; }, abstract = {A combination of genomic and metabolomic analyses paired with molecular networking was applied to a collection of Paenibacillus spp. to identify the producers of a little-studied class of lipopeptides known as paenilipoheptins. Mass spectrometry and NMR spectroscopy allowed revision of the structure of previously reported paenilipoheptin A and elucidation of the structure of novel paenilipoheptin B.}, }
@article {pmid40083115, year = {2025}, author = {Dodds, IL and Watts, EC and Schuster, M and Buscaill, P and Tumas, Y and Holton, NJ and Song, S and Stuttmann, J and Joosten, MHAJ and Bozkurt, T and van der Hoorn, RAL}, title = {Immunity gene silencing increases transient protein expression in Nicotiana benthamiana.}, journal = {Plant biotechnology journal}, volume = {23}, number = {5}, pages = {1768-1770}, pmid = {40083115}, issn = {1467-7652}, support = {BB/R017913/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/S003193/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; DDT00060/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; DDT00230/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 101019324/ERC_/European Research Council/International ; }, }
@article {pmid40082592, year = {2025}, author = {Thomas, PW and Kothamasi, D}, title = {Hunting dog behaviour is a key driver impacting harvest quantity and quality of truffles.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {8662}, pmid = {40082592}, issn = {2045-2322}, mesh = {Animals ; Humans ; Dogs ; *Ascomycota/physiology/growth &amp; development ; *Hunting ; *Behavior, Animal ; Seasons ; }, abstract = {Truffles are an iconic food that have long held high regard. Here we explore the seasonality and eco-physiological interactions affecting truffle quality and quantity across time and space. Collaborating with professional truffle hunters working eight different locations, detailed metrics of 3180 recovered truffles from 236 hunt events and spanning a full fruiting period, were recorded. Contrary to expectations, truffle weight showed no correlation with climate variables, suggesting a limited influence of environmental factors such as temperature and precipitation on truffle size. We also found that truffle maturity and damage from mycophagy were strongly linked, with deeper truffles being more mature but also more susceptible to damage. Finally, we observe that scent-dog behaviour significantly impacts the quantity and quality of recovered truffles, and we address the necessity of considering this in truffle ecophysiology studies. Alongside advances in our biological understanding, we make recommendations of how training methods can be improved to lead to greater detection and quality targeting with immediate socioeconomic impact. These findings highlight the complex interplay between truffle physiology, environmental factors, and human and animal behaviours, emphasizing the need for further considered research to enhance our understanding of truffle biology and to improve truffle cultivation practices.}, }
@article {pmid40080573, year = {2025}, author = {Shumilova, O and Sukhodolov, A and Osadcha, N and Oreshchenko, A and Constantinescu, G and Afanasyev, S and Koken, M and Osadchyi, V and Rhoads, B and Tockner, K and Monaghan, MT and Schröder, B and Nabyvanets, J and Wolter, C and Lietytska, O and van de Koppel, J and Magas, N and Jähnig, SC and Lakisova, V and Trokhymenko, G and Venohr, M and Komorin, V and Stepanenko, S and Khilchevskyi, V and Domisch, S and Blettler, M and Gleick, P and De Meester, L and Grossart, HP}, title = {Environmental effects of the Kakhovka Dam destruction by warfare in Ukraine.}, journal = {Science (New York, N.Y.)}, volume = {387}, number = {6739}, pages = {1181-1186}, doi = {10.1126/science.adn8655}, pmid = {40080573}, issn = {1095-9203}, mesh = {Humans ; *Ecosystem ; Geologic Sediments/chemistry ; Ukraine ; *Warfare ; *Disasters ; }, abstract = {The use of water as a weapon in highly industrialized areas in the Russo-Ukrainian war has resulted in catastrophic economic and environmental damages. We analyze environmental effects caused by the military destruction of the Kakhovka Dam. We link field, remote sensing, and modeling data to demarcate the disaster's spatial-temporal scales and outline trends in reestablishment of damaged ecosystems. Although media attention has focused on the immediate impacts of flooding on society, politics, and the economy, our results show that toxic contamination within newly exposed sediments of the former reservoir bed poses a largely overlooked long-term threat to freshwater, estuarine, and marine ecosystems. The continued use of water as a weapon may lead to even greater risks for people and the environment.}, }
@article {pmid40080167, year = {2025}, author = {Kouakou, AK and Collart, P and Perron, T and Kolo, Y and Gay, F and Brauman, A and Brunel, C}, title = {Soil Microbial Recovery to the Rubber Tree Replanting Process in Ivory Coast.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {13}, pmid = {40080167}, issn = {1432-184X}, support = {(PFI : 7250A1, Centre de co&#xfb;t : 210F2CVNB)//Institut Fran&#xe7;ais du Caoutchouc/ ; ARTS, 2019//IRD PhD Grant Program/ ; }, mesh = {*Soil Microbiology ; *Hevea/growth &amp; development ; Cote d'Ivoire ; Soil/chemistry ; Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Agriculture/methods ; RNA, Ribosomal, 18S/genetics ; Trees ; }, abstract = {The resistance and resilience of soil microbial communities to an environmental disturbance are poorly documented, due to the lack on onfield diachronic experiments, limiting our ability to design adapted agroecological practices. This is especially true in rubber plantations, one of the most planted tree in tropical areas. We aimed to understand (1) how soil disturbances occurring during the rubber replanting phase affect the soil microbiome, (2) how agricultural practices combining legumes cover crops and tree logging residues shape community resilience and (3) how microbial responses vary across different edaphic contexts. In two plantations with distinct soil properties in Ivory Coast, soil microbial communities were surveyed every 6 months for 24 months after soil perturbation. Community structure, functioning and networks were described based on a 16S/18S rRNA gene investigation. Prokaryotes were generally more resistant to soil perturbation than microeukaryote communities. Prokaryotic resilience dynamics were faster than those of microeukaryotes, the latter being deeply modulated by cover treatments. These specific dynamics were exacerbated in the sandy site. Co-occurrence network modelling provided useful insights into microbial resilience trajectories. We argue that this tool should be more widely used to describe microbial community dynamics. Practices involving a combination of logging residues and legume cover crops have shown beneficial effects on the community resilience in the sandy site and appears as promising agroecological practices. However, the major influence of soil texture warns of the need to consider pedological context when designing pertinent agroecological practices.}, }
@article {pmid40078544, year = {2025}, author = {Acciardo, AS and Arnet, M and Gholizadeh Doonechaly, N and Ceccato, A and Rodriguez, P and Tran, HNH and Wenning, Q and Zimmerman, E and Hertrich, M and Brixel, B and Magnabosco, C}, title = {Spatial and temporal groundwater biogeochemical variability help inform subsurface connectivity within a high-altitude Alpine catchment (Riale di Ronco, Switzerland).}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1522714}, pmid = {40078544}, issn = {1664-302X}, abstract = {Accessing the deep terrestrial subsurface (greater than 1 km below the surface) presents significant practical challenges, leaving these ecosystems largely uncharacterized despite their extensive presence beneath Earth's landmasses. In this study, we introduce the BedrettoLab Deep Life Observatory (DELOS), a new underground laboratory to study the biogeochemical diversity of groundwater in a high-altitude Alpine catchment tens of meters to 1.6 km underground. Biogeochemical monitoring of DELOS over spatial and temporal scales highlight three dominant ecotypes throughout DELOS: (1) Shallow groundwater with low electrical conductivity enriched in Leptospirillia; (2) High-inflow fault zones enriched in ultra-small bacteria and archaea; (3) Bicarbonate-enriched waters that are enriched in Candidatus Kryptonia and Spirochaetota. Despite a consistent lithology throughout DELOS, groundwater from fractures that are spatially near each other are not always represented by the same ecotype and can be more similar to groundwater emitted from fractures thousands of meters away. Despite this heterogeneity, the biological and hydrochemical compositions of the groundwater of individual fractures remained relatively stable throughout the course of a 1-year monitoring period. An exception to this trend occurred after a series of seismic events near one groundwater-bearing fracture. Here, the microbial community and hydrochemical composition of the groundwater changed after the seismic events but returned to the site's "baseline" composition within 3 weeks. Taken together, these findings provide new insights into the spatial and temporal heterogeneity of deep subsurface ecosystems and the subsurface connectivity of an Alpine subsurface environment.}, }
@article {pmid40077554, year = {2025}, author = {Smirani, N and Bouazizi, S and Bettaieb, E and Torkhani, R and Hamdi, M}, title = {Effect of Environmentally Friendly Betalain Extraction Methods on Antioxidant Compounds of Tunisian Opuntia stricta Fruit.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {5}, pages = {}, pmid = {40077554}, issn = {2304-8158}, abstract = {This study focuses on the extraction of betalain compounds from Opuntia stricta as a natural alternative to synthetic colorants and sustainable environmentally friendly technology solutions. Non-conventional extraction technologies including microwave (MW) and ultrasound (US) were used alone or in combination. The extraction process was conducted for both undried Opuntia stricta (OS) and dried Opuntia stricta (DOS) plant material at two distinct drying temperatures, 40 °C and 60 °C, to assess the stability of betalain molecules. The colorant's potential was evaluated by determining the betalain content, total phenolic content, and antioxidant activity. The MW (2 min) and MW (2 min) + US (10 min) extraction processes yielded the greatest betalain content in OS fresh weight (FW), with 48.54 ± 0.29 mg/100 g FW and 51.01 ± 0.16 mg/100 g FW, respectively. Furthermore, the results showed a considerable drop in betalain content when the plant material was dried at 40 °C and 60 °C, with reduction rates of 53.75% and 24.82%, respectively, compared to the betalain content before the drying process. The LC-DAD-ESI-MS analysis supported this result, revealing the presence of 17-decarboxy betanin, 17-decarboxy neobetanin, and Cyclo-dopa5-O-βglucoside in DOS at 40 °C. This study highlights the potential future in the sustainable green extraction of betalain compounds with less heat degradation to offer a stable natural colorant.}, }
@article {pmid40072629, year = {2025}, author = {Dyczko, D and Szymański, DM and Szymański, D and Kupczak, M and Kolenda, K}, title = {First European record of Rickettsia bellii in Amblyomma rotundatum from Rhinella marina imported to Poland.}, journal = {Experimental &amp; applied acarology}, volume = {94}, number = {3}, pages = {43}, pmid = {40072629}, issn = {1572-9702}, mesh = {Animals ; Poland ; *Amblyomma/microbiology ; *Rickettsia/isolation &amp; purification/genetics ; Female ; *Tick Infestations/veterinary/parasitology ; }, abstract = {This study reports on the first documented case of Amblyomma rotundatum ticks, a species typically found in the Americas, parasitising an imported toad in Poland. A total of 12 ticks were collected from a single Rhinella marina toad. These ticks were identified as female specimens of A. rotundatum using an examination of morphological characteristics and a molecular analysis. Polymerase chain reaction testing revealed that 75.0% (9/12) of these females were positive for Rickettsia spp. Sequencing of positive samples confirmed the presence of R. bellii. However, no DNA evidence of Borrelia spp. and Anaplasma spp. was detected in the tested ticks. Nevertheless, given the limited number of tick specimens collected from a single host, further research is required to elucidate the pathogen profile of a tick species. This finding represents the second European report of A. rotundatum associated with exported animals, underscoring the importance of vigilance in monitoring the potential spread of ticks and tick-borne pathogens through the global wildlife trade.}, }
@article {pmid40072582, year = {2025}, author = {Barjau-Aguilar, M and Reyes-Hernández, AMJ and Merino-Ibarra, M and Vilaclara, G and Ramírez-Zierold, JA and Alcántara-Hernández, RJ}, title = {Diversity and Structure of the Prokaryotic Community in Tropical Monomictic Reservoir.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {12}, pmid = {40072582}, issn = {1432-184X}, support = {CVU: 747276//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; CVU: 1249011//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; CF-2023-G-155//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; CVU: 41120//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; UNAM, PAPIIT-IN207702//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; UNAM-PAPIIT IN217622//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; }, mesh = {*Archaea/classification/genetics/isolation &amp; purification ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; RNA, Ribosomal, 16S/genetics ; *Biodiversity ; Nitrogen/analysis ; Phosphorus/analysis ; *Fresh Water/microbiology/chemistry ; Tropical Climate ; Oxygen/analysis ; Phylogeny ; *Microbiota ; Water Microbiology ; Eutrophication ; }, abstract = {Bacteria and Archaea are microorganisms that play key roles in the biogeochemical transformations that control water quality in freshwater ecosystems, such as in reservoirs. In this study, we characterize the prokaryotic community of a high-relevance tropical eutrophic reservoir using a 16S rRNA gene survey during a low-water level fluctuation period mainly used for storage, associating the distribution of these microorganisms with the hydrogeochemical conditions of the water column. Our findings revealed that diversity and structure of the prokaryotic community exhibited spatio-temporal variations driven by the annual circulation-stratification hydrodynamic cycle and are significantly correlated with the concentrations of dissolved oxygen (DO), soluble reactive phosphorus (SRP), and dissolved inorganic nitrogen (DIN). During the heterotrophic circulation, the breakdown of thermal gradient leads to a homogeneous distribution of the nutrients, where the presence of DO promotes the dominance of aerobic and facultative heterotrophic bacteria such as Bacteroidota, Actinobacteriota, and Verrucomicrobiota. Also, the autotrophic circulation was characterized by an increase of DO and NO3[-] concentrations, with abundant Cyanobacteria. Finally, during the stratification, the presence of prokaryotes associated with the metabolism of CH4 was detected, mainly in the hypolimnion, as well as others related to sulfate reduction and nitrification. This study shows the diversity of the prokaryotic community in tropical eutrophic reservoirs, and how the continuous monitoring with metabarcoding techniques can provide critical insights for a deeper understanding of the biogeochemical dynamics and improve the water resource management in the future.}, }
@article {pmid40070274, year = {2025}, author = {Cidan, Y and Wang, J and Wang, H and Xu, C and Zhu, Y and Khan, MK and Basang, W and Li, K}, title = {Composition and diversity of rumen mycobiota in Jiani yaks (Bos grunniens jiani): insights into microbial ecology and functions.}, journal = {Animal biotechnology}, volume = {36}, number = {1}, pages = {2476539}, doi = {10.1080/10495398.2025.2476539}, pmid = {40070274}, issn = {1532-2378}, mesh = {Animals ; *Rumen/microbiology ; Cattle/microbiology ; *Fungi/genetics/classification/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; *Mycobiome ; *Gastrointestinal Microbiome ; }, abstract = {This study aimed to explore the diversity and functions of rumen mycobiota in 14‑ (PLf) and 15‑rib (DLf) Jiani yaks using ITS sequencing. A total of 1,079,105 and 1,086,799 filtered sequences were obtained for the PLf and DLf groups, respectively, with 491 ASVs common to both. No significant difference regarding the α‑diversity of mycobiota within the two groups was observed. While β‑diversity analysis indicated that the abundance of fifteen (15) genera in the PLf group and two (2) genera in the DLf group was found to be significantly different (p < 0.05). 16S rRNA sequencing results indicated that at the phylum level, in 14 ribs yaks Ascomycota, Basidiomycota, and Olpidiomycota, while in 15 rib yaks, Neocallimastigomycota, Mortierellomycota, and Rozellomycota were found to be significantly different (p < 0.05). At the genus level, Rhodotorula, Kluyveromyces, Comoclathris, Arthrinium, Cladophialophora, Seimatosporium, Lambertella, and Sphacelotheca in 14 rib yaks, and Orpinomyces, Ustilago, Fusarium, Aspergillus, Caecomyces, Alternaria, Trichoderma and Acremonium in 15 rib yaks were found to be significantly (p < 0.05) different. Predictive functional analysis based on ruminal fungal DNA sequences from 15‑rib yaks (DLf) demonstrated that genes involved in energy metabolism were upregulated. This study sheds novel insights into how genetic variations influence gut mycobiota in Jiani yak.}, }
@article {pmid40068413, year = {2025}, author = {Yang, H and Cappitelli, F and Li, X}, title = {Pollution gradients shape structure and functions of stone heritage bacterial communities at global scale.}, journal = {The Science of the total environment}, volume = {971}, number = {}, pages = {179087}, doi = {10.1016/j.scitotenv.2025.179087}, pmid = {40068413}, issn = {1879-1026}, mesh = {*Bacteria/classification ; *Microbiota/drug effects ; *Environmental Monitoring ; Particulate Matter/analysis ; Biodiversity ; }, abstract = {Previous studies mainly focused on the impact of climatic conditions on stone heritage microbial communities, while ignoring a global ecological perspective of pollution on heritage microorganisms. In particular, there is a lack of detailed analysis of the impact of pollution levels on microbial metabolic function. In this study, >6000 bacterial OTUs from 17 world cultural heritage sites were considered. The microbial diversity indexes and potential functions under different pollution levels were analyzed. The results show that particulate matter pollution, such as PM2.5, has an effect on the microbial community in heritage sites comparable to that of temperature and precipitation. High concentrations of particulate matter increased bacterial richness and facilitated the introduction of unique species. Among them, phototrophic bacteria (e.g., Cyanobacteria) and some heterotrophic bacteria (e.g., Actinobacteria and Proteobacteria) formed the core of the microbial community. However, high concentrations of particulate matter reduced the complexity and stability of microbial ecological networks, favoring pollution-tolerant species. Furthermore, elevated particulate concentrations partially suppressed the expression of certain metabolic pathways, particularly genes related to denitrification (e.g., nosZ and nirS). This study reveals the long-term impact of polluted environments on the diversity and potential functions of microbial communities, providing a theoretical basis for developing sustainable strategies for cultural heritage conservation.}, }
@article {pmid40066860, year = {2025}, author = {Defoirdt, T}, title = {Resistance to quorum sensing inhibition spreads more slowly during host infection than antibiotic resistance.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2476582}, pmid = {40066860}, issn = {1949-0984}, mesh = {*Quorum Sensing/drug effects ; *Anti-Bacterial Agents/pharmacology ; Humans ; *Drug Resistance, Bacterial ; *Bacteria/drug effects ; *Bacterial Infections/microbiology/drug therapy ; Animals ; }, abstract = {Antibiotic resistance is a rising problem and new and sustainable strategies to combat bacterial (intestinal) infections are therefore urgently needed. One promising strategy under intense investigation is the inhibition of quorum sensing, bacterial cell-to-cell communication with small molecules. A key question with respect to the application of quorum sensing inhibition is whether it will impose selective pressure for the spread of resistance. It was recently shown that resistance to quorum sensing inhibition will spread more slowly during infection of a host than resistance to traditional antibiotics.}, }
@article {pmid40065660, year = {2025}, author = {Guislain, ALN and Nejstgaard, JC and Köhler, J and Sperfeld, E and Mischke, U and Skjelbred, B and Grossart, HP and Lyche Solheim, A and Gessner, MO and Berger, SA}, title = {Cell size explains shift in phytoplankton community structure following storm-induced changes in light and nutrients.}, journal = {Ecology}, volume = {106}, number = {3}, pages = {e70043}, pmid = {40065660}, issn = {1939-9170}, support = {731065//European Commission/ ; 871081//European Commission/ ; 01LC1501//German Federal Ministry of Education and Research (BMBF)/ ; GE 1775/2-1//German Research Foundation (DFG)/ ; 603378//the European Commission under its 7th Framework Programme/ ; SAW-2015-IGB-1//Leibniz Association/ ; K45/2017//Leibniz Association/ ; 033L041B//BMBF Infrastructure/ ; }, mesh = {*Phytoplankton/physiology/cytology ; *Light ; *Ecosystem ; Nutrients ; }, abstract = {Understanding the mechanisms driving community structure and dynamics is crucial in the face of escalating climate change, including increasing incidences of extreme weather. Cell size is a master trait of small organisms that is subject to a trade-off between resistance to grazing and competition for resources, and thus holds potential to explain and predict community dynamics in response to disturbances. Here, we aimed at determining whether cell size can explain shifts in phytoplankton communities following changes in nutrient and light conditions resulting from storm-induced inputs of nutrients and colored dissolved organic matter (cDOM) to deep clearwater lakes. To ensure realistic environmental conditions, we used a crossed gradient design to conduct a large-scale enclosure experiment over 6 weeks. Cell size explained phytoplankton community structure when light availability declined as a result of cDOM supply. Initially unimodal, with small-celled species accounting for up to 60% of the total community biovolume, the cell-size distribution gradually shifted toward large-celled species as light levels declined following cDOM addition. Neither nutrients nor mesozooplankton affected the shift in cell-size distribution. These results suggest a distinct competitive advantage of larger over smaller species at reduced light levels following cDOM inputs during storm events. Importantly, the clustering of species in two distinct size classes implies that interspecific size differences matter as much as cell size per se to understand community dynamics. Given that shifts in cell-size distribution have strong implications for food-web structure and biogeochemical cycles, our results point to the importance of analyzing cell-size distributions of small organisms as an essential element to forecast community and ecosystem dynamics in response to environmental change.}, }
@article {pmid40064943, year = {2025}, author = {Roegiers, I and Gheysens, T and Minsart, M and De Clercq, P and Vanbeversluys, K and Rać, N and Stroka, G and de Croock, J and Van de Wiele, T and Dubruel, P and Arroyo, MC}, title = {GelMA as scaffold material for epithelial cells to emulate the small intestinal microenvironment.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {8214}, pmid = {40064943}, issn = {2045-2322}, support = {3G062519//Fonds Wetenschappelijk Onderzoek/ ; 1S51925N//Fonds Wetenschappelijk Onderzoek/ ; 40007505//Excellence Of Science (F.W.O.-F.R.S.-FNRS.)/ ; }, mesh = {Humans ; *Tissue Scaffolds/chemistry ; Caco-2 Cells ; *Epithelial Cells/cytology/metabolism ; Hydrogels/chemistry ; *Intestine, Small/cytology ; *Gelatin/chemistry ; Cell Survival/drug effects ; Permeability ; *Cellular Microenvironment ; Biocompatible Materials/chemistry ; Intestinal Mucosa ; Cell Adhesion ; Coculture Techniques ; }, abstract = {Host-microbe interactions in the intestine play a significant role in health and disease. Novel scaffolds for host cells, capable of potentially supporting these intricate interactions, are necessary to improve our current systems for mimicking host-microbiota interplay in vitro/ex vivo. In this research paper, we study the application of gelatin methacrylamide (GelMA) as scaffold material for intestinal epithelial cells in terms of permeability, mechanical strength, and biocompatibility. We investigated whether the degree of substitution (DS) of GelMA influences the permeability and found that both high and low DS GelMA show sufficient permeability of biorelevant transport markers. Additionally, we researched epithelial cell adherence and viability, as well as mechanical characteristics of different concentrations of GelMA. All concentrations of hydrogel show long-term biocompatibility for the mono- and co-cultures, despite the goblet-like cells (LS174T) showing lower performance than enterocyte-like cells (Caco-2). The mechanical strength of all hydrogel concentrations was in a physiologically relevant range to be used as scaffold material for intestinal cells. Lastly, we examined the effect of the two sterilization methods, ethylene oxide (EO) and 70% ethanol followed by UVC (EtOH/UVC). We found that the impact of the two methods on the mechanical characteristics was minimal, and we did not find a significant effect between the two methods on cell viability and confluency of Caco-2 cells seeded on the GelMA hydrogels. Based on these results, we conclude that GelMA is a suitable material as a scaffold for intestinal cell types in terms of permeability, mechanical strength and biocompatibility. These findings contribute to the growing field of in vitro modeling of the gut and moves the field further to ensuring more translatable research on host-microbe interactions.}, }
@article {pmid40062895, year = {2025}, author = {McDonald, MD and Lewis, KL and Gentry, TJ}, title = {No-tillage systems promote bacterial photosynthetic gene expression in low carbon, semi-arid surface soils.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {4}, pages = {e0018425}, pmid = {40062895}, issn = {1098-5336}, support = {//Texas A&amp;M AgriLife Research Air Quality Initiative/ ; }, mesh = {*Soil Microbiology ; *Carbon/metabolism/analysis ; *Photosynthesis/genetics ; *Soil/chemistry ; *Agriculture/methods ; *Bacteria/genetics/metabolism ; Triticum/growth &amp; development ; Crops, Agricultural/growth &amp; development ; }, abstract = {Managing soils in semi-arid agricultural croplands generally focuses on reducing wind erosion, increasing fertility, and storing carbon. Thus, converting conventionally tilled systems to no-tillage and cover-cropped systems are often the first steps towards a conservation management approach across the growing area of semi-arid croplands. From a soil biological perspective, introducing cover crops to semi-arid soils has been shown to alter microbial community structure, which may lead to changes in the biogeochemical pathways expressed in these soils. In this study, we examined the impact of single-species wheat cover cropping and no-tillage on microbial gene expression after 4 and 5 years of implementation. We sequenced the metatranscriptomes of three production systems with varying levels of conservation management: conventional tillage winter fallow, no-tillage winter fallow, and no-tillage with a winter wheat cover crop. Removing tillage was the biggest factor altering microbial gene expression in this study, specifically resulting in upregulation of several photosystem-associated functions. These functions were taxonomically linked to organisms that make up the early stages of biological soil crusts, which may introduce additional benefits to these semi-arid agricultural systems beyond a reduction in wind erosion. Implementing a cover crop did not clearly alter gene expression beyond the effect of tillage removal; however, it did indicate a potential to reduce fungal disease incidence in 1 year of the study. These alterations of microbial activities and selection for potentially beneficial functions should be considered and further studied to aid in maintaining sustainable croplands for our changing climate.IMPORTANCEEliminating tillage from semi-arid agricultural soils has the potential to significantly alter the activities of the soil bacterial community compared with conventionally tilled soils. A major driver of this change was the activities of biological soil crust forming organisms that can provide several environmental benefits to the soil ecosystem beyond the typically associated benefits of conservation management. Furthermore, this study revealed that the implementation of a cover crop regime on no-tillage soils does not confer a major change in the function of the organisms present. Overall, the study reported here reveals that soil management practices aimed at reducing wind erosion and improving sustainability will positively impact the function of the microbial community and suggests that future investigations into the consequences of these functional changes may provide valuable services to these agricultural ecosystems.}, }
@article {pmid40062772, year = {2025}, author = {Connolly, JP and Kelly, L}, title = {The physical biogeography of Fusobacterium nucleatum in health and disease.}, journal = {mBio}, volume = {16}, number = {4}, pages = {e0298924}, pmid = {40062772}, issn = {2150-7511}, support = {T32 GM007491/GM/NIGMS NIH HHS/United States ; 5T32GM007491-46//HHS | National Institutes of Health (NIH)/ ; //Elsa U. Pardee Foundation (EUPF)/ ; }, mesh = {*Fusobacterium nucleatum/genetics/isolation &amp; purification/classification/physiology ; Humans ; *Colorectal Neoplasms/microbiology ; Female ; Male ; *Fusobacterium Infections/microbiology ; Crohn Disease/microbiology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Metagenome ; Gingiva/microbiology ; Genome, Bacterial ; }, abstract = {UNLABELLED: Fusobacterium nucleatum (Fn) is an oral commensal inhabiting the human gingival plaque that is rarely found in the gut. However, in colorectal cancer (CRC), Fn can be isolated from stool samples and detected in metagenomes. We hypothesized that ecological characteristics of the gut are altered by disease, enabling Fn to colonize. Multiple genomically distinct populations of Fn exist, but their ecological preferences are unstudied. We identified six well-separated populations in 133 Fn genomes and used simulated metagenomes to demonstrate sensitive detection of populations in human oral and gut metagenomes. In 9,560 samples from 11 studies, Fn population C2 animalis is elevated in gut metagenomes from CRC and Crohn's disease patients and is observed more frequently in CRC stool samples than in the gingiva. Polymorphum, the most prevalent gingival Fn population, is significantly increased in Crohn's stool samples; this effect was significantly stronger in male hosts than in female. We find polymorphum genomes are enriched for biosynthetic gene clusters and fluoride exporters, while C2 animalis are high in iron transporters. Fn populations thus associate with specific clinical and demographic phenotypes and harbor distinct functional features. Ecological differences in closely related groups of bacteria inform microbiome impacts on human health.<br><br>IMPORTANCE: Fusobacterium nucleatum is a bacterium normally found in the gingiva. F. nucleatum generally does not colonize the healthy gut, but is observed in approximately a third of colorectal cancer (CRC) patient guts. F. nucleatum's presence in the gut during CRC has been linked to worse prognosis and increased tumor proliferation. Here, we describe the population structure of F. nucleatum in oral and gut microbiomes. We report substantial diversity in gene carriage among six distinct populations of F. nucleatum and identify population disease and body-site preferences. We find the C2 animalis population is more common in the CRC gut than in the gingiva and is enriched for iron transporters, which support gut colonization in known pathogens. We find that C2 animalis is also enriched in Crohn's disease and type 2 diabetes, suggesting ecological commonalities between the three diseases. Our work shows that closely related bacteria can have different associations with human physiology.}, }
@article {pmid40062764, year = {2025}, author = {Watkins, E and Lin, J and Lingohr-Smith, M and Yong, C and Tangirala, K and Collins, K}, title = {Biological, Clinical, and Sociobehavioral Factors Associated with Disproportionate Burden of Bacterial Vaginosis in the United States: A Comprehensive Literature Review.}, journal = {Journal of women's health (2002)}, volume = {34}, number = {5}, pages = {644-652}, doi = {10.1089/jwh.2024.0583}, pmid = {40062764}, issn = {1931-843X}, mesh = {Humans ; *Vaginosis, Bacterial/epidemiology/microbiology/ethnology ; Female ; United States/epidemiology ; Prevalence ; Vagina/microbiology ; Risk Factors ; Microbiota ; Black or African American/statistics &amp; numerical data ; White ; }, abstract = {Background: Bacterial vaginosis (BV), a common gynecological infection characterized by reduced lactic acid-producing bacteria and increased anerobic bacteria in the vaginal microbiome, is associated with adverse health outcomes. Methods: A PubMed search for English-language articles about BV in the USA and factors contributing to disparities in BV risk, with an emphasis on the role of the vaginal microbiome, published from August 2012 to August 2022, identified 760 articles. Results: Among the 52 articles meeting the prespecified criteria, BV prevalence varied among different populations and disproportionately impacted Black women (49-51%), Hispanic ethnicity (32-43%), and women of reproductive age (30%). Differences in microbial ecology and host genetics were important factors underlying these disparities. Colonization of BV-associated bacteria was more common in women of color than in non-Hispanic White women. Other factors linked with disproportionate burden included multiple/same-sex partners, obesity, immunosuppression, and C-section birth. Conclusions: BV prevalence was multifactorial, with some populations having higher prevalence rates and distinctive microbiome profiles that may predispose them to the condition. BV treatment and recurrence prevention were challenging due to the complex interplay of biological, clinical, and sociobehavioral factors. Understanding these disparate risk factors is critical to reducing BV burden.}, }
@article {pmid40062709, year = {2025}, author = {Jeong, IJ and Hong, JK and Bae, YJ and Lee, TK}, title = {Enhancing Bacterial Phenotype Classification Through the Integration of Autogating and Automated Machine Learning in Flow Cytometric Analysis.}, journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology}, volume = {107}, number = {3}, pages = {203-213}, doi = {10.1002/cyto.a.24923}, pmid = {40062709}, issn = {1552-4930}, support = {2020R1C1C100624912//National Research Foundation of Korea/ ; }, mesh = {*Flow Cytometry/methods ; *Machine Learning ; *Bacteria/classification/isolation &amp; purification ; Phenotype ; Escherichia coli ; }, abstract = {Although flow cytometry produces reliable results, the data processing from gating to fingerprinting is prone to subjective bias. Here, we integrated autogating with Automated Machine Learning in flow cytometry to enhance the classification of bacterial phenotypes. We analyzed six bacterial strains prevalent in the soil and groundwater- Bacillus subtilis , Burkholderia thailandensis , Corynebacterium glutamicum , Escherichia coli , Pseudomonas putida , and Pseudomonas stutzeri . Using the H2O-AutoML framework, we applied gradient-boosting machine (GBM) models to classify bacteria across different metabolic phases. Our results demonstrated an overall classification accuracy of 82.34% for GBM. Notably, accuracy varied across metabolic phases, with the highest observed during the late log (88.06%), lag (88.43%), and early log phases (89.37%), whereas the stationary phase showed a slightly lower accuracy of 80.73%. P. stutzeri exhibited consistently high sensitivity and specificity across all the phases, which indicated that it was the most distinctly identifiable strain. In contrast, E. coli showed low sensitivity, particularly in the stationary phase, which indicated challenges in its classification. Overall, this study with incorporating autogating and the AutoML framework, substantially reduces subjective biases and enhances the reproducibility and accuracy of microbial classification. Our methodology offers a robust framework for microbial classification in flow cytometric analysis, paving the way for more precise and comprehensive analyses of microbial ecology.}, }
@article {pmid40060716, year = {2025}, author = {Zhao, Y and Yuan, X and Ran, W and Zhao, Z and Su, D and Song, Y}, title = {The Ecological Restoration Strategies in Terrestrial Ecosystems Were Reviewed: A New Trend Based on Soil Microbiomics.}, journal = {Ecology and evolution}, volume = {15}, number = {3}, pages = {e70994}, pmid = {40060716}, issn = {2045-7758}, abstract = {Soil microorganisms play a pivotal role in the biogeochemical cycle and serve as crucial indicators of ecological restoration in terrestrial ecosystems. The soil microbial community is regarded as a pivotal participant in environmental processes, offering both positive and negative feedback to diverse media within the ecosystem. This community can serve as a potential indicator in ecological monitoring and restoration processes. Consequently, an increasing number of scholars are directing their research towards the field of soil microbial ecology in diverse ecosystems and fragile areas, with the aim of elucidating the intricate interactions between microbes and vegetation. However, the implementation of soil microbiome in ecological restoration remains in the experimental stage due to the interference of extreme events and the complexity of governance measures. Consequently, a comprehensive evaluation of existing research is imperative. This review aims to address the ecological crises currently experienced by diverse terrestrial ecosystems and to provide a comprehensive overview of the specific practices of soil microorganisms in the context of ecological restoration. We also incorporate them into fragile habitats and identify urgent issues that need to be addressed in the ecological restoration process of fragile areas.}, }
@article {pmid40060289, year = {2025}, author = {Sarkar, A and Bhattacharjee, S}, title = {Biofilm-mediated bioremediation of xenobiotics and heavy metals: a comprehensive review of microbial ecology, molecular mechanisms, and emerging biotechnological applications.}, journal = {3 Biotech}, volume = {15}, number = {4}, pages = {78}, pmid = {40060289}, issn = {2190-572X}, abstract = {Environmental pollution, driven by rapid industrialization and urbanization, has emerged as a critical global challenge in the twenty-first century. This comprehensive review explores the potential of bacterial biofilms in bioremediation, focusing on their ability to degrade and transform a wide array of pollutants, including heavy metals, persistent organic pollutants (POPs), oil spills, pesticides, and emerging contaminants, such as pharmaceuticals and microplastics. The unique structural and functional characteristics of biofilms, including their extracellular polymeric substance (EPS) matrix, enhanced genetic exchange, and metabolic cooperation, contribute to their superior pollutant degradation capabilities compared to planktonic bacteria. Recent advancements in biofilm-mediated bioremediation include the application of genetically engineered microorganisms, nanoparticle-biofilm interactions, and innovative biofilm reactor designs. The CRISPR-Cas9 system has shown promise in enhancing the degradative capabilities of biofilm-forming bacteria while integrating nanoparticles with bacterial biofilms demonstrates significant improvements in pollutant degradation efficiency. As global pollution rises, biofilm-based bioremediation emerges as a cost-effective and environmentally friendly approach to address diverse contaminants. This review signifies the need for further research to optimize these techniques and harness their full potential in addressing pressing environmental challenges.}, }
@article {pmid40060287, year = {2025}, author = {Maity, A and Das, A and Roy, R and Malik, M and Das, S and Paul, P and Sarker, RK and Sarkar, S and Dasgupta, A and Chakraborty, P and Tribedi, P}, title = {Development of novel strategies against the threats of drug-resistant Escherichia coli: an in silico and in vitro investigation.}, journal = {3 Biotech}, volume = {15}, number = {4}, pages = {77}, pmid = {40060287}, issn = {2190-572X}, abstract = {UNLABELLED: Escherichia coli (E. coli) biofilms pose alarming threats in healthcare due to their invulnerability to drug therapy. Stand-alone therapies of antimicrobial compounds/antibiotics are not particularly effective against those resistant strains. However, combination therapy of compounds could be used to deal with such threats. Towards this direction, the natural compound cuminaldehyde was employed in combination with the aminoglycoside antibiotic tobramycin to target the biofilm-forming multidrug-resistant (MDR) clinical strains of E. coli, which were isolated from urine samples of patient's at Suraksha Diagnostic Private Limited (Kolkata, India). At first, an integrated in silico approach (PASS online, Swiss ADME, PROTOX 3.0, and OSIRIS) was explored to predict the potential biological activities, and other relevant pharmacokinetic parameters of cuminaldehyde and tobramycin. The in silico analysis suggested that tobramycin might not be bioavailable orally due to its molecular size, polarity, and poor GI absorption. However, cuminaldehyde was well absorbed in the GI but could cause irritation if swallowed in LD50 amounts. Further, in vitro assessments were performed to analyse the antimicrobial and antibiofilm activity of both compounds, alone and in combination, against clinical strains of E. coli. The results suggested that cuminaldehyde and tobramycin together could show an additive effect against the clinical strains of E. coli. The combination of the compounds showed a substantial decrease in minimum inhibitory concentration (MIC) and biofilm formation compared to individual application. The present study indicates that combinatorial application involving cuminaldehyde and tobramycin could inhibit the formation of biofilms in E. coli, potentially aiding in the management of microbial infections.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-025-04246-0.}, }
@article {pmid40058043, year = {2025}, author = {Zhong, Q and Santás-Miguel, V and Cruz-Paredes, C and Rousk, J}, title = {Does the land-use impact the risk of inducing antibiotic tolerance by heavy metal pollution?.}, journal = {Journal of environmental management}, volume = {379}, number = {}, pages = {124883}, doi = {10.1016/j.jenvman.2025.124883}, pmid = {40058043}, issn = {1095-8630}, mesh = {*Metals, Heavy ; *Anti-Bacterial Agents/pharmacology ; Soil Microbiology ; *Soil Pollutants ; Soil/chemistry ; Agriculture ; Forests ; Tetracycline ; Copper ; Bacteria/drug effects ; }, abstract = {The rise of antibiotic-resistant soil microbial communities is a critical global issue. Evidence suggests that heavy metals can select or co-select for tolerance to metals and antibiotics in soil bacteria, but it is unclear if this tolerance varies with land use. We tested the potential of bacterial communities to develop resistance to copper (Cu) or tetracycline (Tet) after amending soils from pristine forests, contaminated forests, and agricultural lands with 3000 mg kg[-1] Cu and 6000 mg kg[-1] tetracycline, separately. Results showed that bacterial communities of unamended contaminated forest soils had the highest initial tolerance to Cu, while unamended agricultural soils exhibited the highest initial tolerance to tetracycline. The inducibility of bacterial resistance to antibiotics after Cu amendment varied by land use. In pristine forests, Cu amendment significantly increased microbial tetracycline resistance, as indicated by bacterial community tolerance, likely due to higher biodiversity. In contaminated forests, Cu amendment did not induce tetracycline-resistance, as indicated by unchanged bacterial community tolerance, possibly because of existing metal pollution and compromised bacterial communities by metal pollution. In agricultural soils, microbial tetracycline resistance as indicated by bacterial community tolerance developed slowly, becoming evident only after 42 days. These findings reveal significant differences in environmental risks related to soil metal pollution across different land uses, highlighting the need for systematic studies on the mechanisms of bacterial resistance to antibiotics in metal-contaminated soils due to their human health implications.}, }
@article {pmid40052378, year = {2025}, author = {Mise, K and Masuda, Y and Senoo, K and Itoh, H}, title = {Betaproteobacterial clade II nosZ activated under high N2O concentrations in paddy soil microcosms.}, journal = {Journal of applied microbiology}, volume = {136}, number = {3}, pages = {}, doi = {10.1093/jambio/lxaf055}, pmid = {40052378}, issn = {1365-2672}, support = {JPNP18016//New Energy and Industrial Technology Development Organization/ ; JPMJMI20E5//JST-Mirai Program/ ; }, mesh = {*Soil Microbiology ; *Nitrous Oxide/metabolism ; RNA, Ribosomal, 16S/genetics ; *Oxidoreductases/genetics/metabolism ; *Betaproteobacteria/genetics/metabolism/classification/enzymology ; Soil/chemistry ; Phylogeny ; Oryza ; }, abstract = {AIMS: Microbial communities in paddy soils act as potential sinks of nitrous oxide (N2O), a notorious greenhouse gas, but their potential to reduce external N2O is unclear. The direct observation of N2O reduction in submerged field soils is technically difficult. Here, we aimed to identify soil microbial clades that underpin the strong N2O mitigation capacity.<br><br>METHODS AND RESULTS: We constructed paddy soil microcosms with external N2O amendment that enabled the simultaneous evaluation of N2O reductase gene (nosZ) transcripts and N2O consumption. Although the amount of N2O amended was large, it was mostly consumed after 6-8 days of microcosm incubation. Metatranscriptomic sequencing revealed that betaproteobacterial nosZ, especially those classified as clade II nosZ belonging to the orders Rhodocyclales or Nitrosomonadales, occupied&#xa0;>50% of the nosZ transcripts in three of the five paddy soils used. On the other hand, publicly available shotgun metagenomic sequences of 46 paddy soils were not dominated by betaproteobacterial clade II nosZ sequences, although they were ubiquitous. The same applied to the 16S rRNA sequences of Rhodocyclales or Nitrosomonadales.<br><br>CONCLUSIONS: The results indicated that betaproteobacterial N2O reducers potentially serve as powerful N2O sinks. Betaproteobacteria holding clade II nosZ can be targets of biostimulation, although further studies are required to understand their ecophysiology.}, }
@article {pmid40049093, year = {2025}, author = {Fonvielle, J and Thuile Bistarelli, L and Tao, Y and Woodhouse, JN and Shatwell, T and Villalba, LA and Berger, SA and Kyba, CCM and Nejstgaard, JC and Jechow, A and Kupprat, F and Stephan, S and Walles, TJW and Wollrab, S and Hölker, F and Dittmar, T and Gessner, MO and Singer, GA and Grossart, HP}, title = {Skyglow increases cyanobacteria abundance and organic matter cycling in lakes.}, journal = {Water research}, volume = {278}, number = {}, pages = {123315}, doi = {10.1016/j.watres.2025.123315}, pmid = {40049093}, issn = {1879-2448}, mesh = {*Lakes/microbiology ; *Cyanobacteria ; Ecosystem ; Light ; Carbon Cycle ; }, abstract = {Artificial light propagating towards the night sky can be scattered back to Earth and reach ecosystems tens of kilometres away from the original light source. This phenomenon is known as artificial skyglow. Its consequences on freshwaters are largely unknown. In a large-scale lake enclosure experiment, we found that skyglow at levels of 0.06 and 6 lux increased the abundance of anoxygenic aerobic phototrophs and cyanobacteria by 32 (±22) times. An ecosystem metabolome analysis revealed that skyglow increased the production of algal-derived metabolites, which appeared to stimulate heterotrophic activities as well. Furthermore, we found evidence that skyglow decreased the number of bacteria-bacteria interactions. Effects of skyglow were more pronounced at night, suggesting that responses to skyglow can occur on short time scales. Overall, our results call for considering skyglow as a reality of increasing importance for microbial communities and carbon cycling in lake ecosystems.}, }
@article {pmid40048904, year = {2025}, author = {Chen, L and Zhao, B and Zhang, M and Yan, Y and Nie, C and Yu, K and Tu, Z and Xia, Y}, title = {Micron-scale heterogeneity reduction leads to increased interspecies competition in thermophilic digestion microbiome.}, journal = {Water research}, volume = {279}, number = {}, pages = {123419}, doi = {10.1016/j.watres.2025.123419}, pmid = {40048904}, issn = {1879-2448}, mesh = {*Microbiota ; Anaerobiosis ; Bioreactors/microbiology ; }, abstract = {Microbial spatial heterogeneity is an important determinant of larger-scale community properties, whereas most studies neglect it and therefore only provide average information, potentially obscuring the signal of microbial interactions. Our study takes a step toward addressing this problem by characterizing the spatial heterogeneity of a microbiome with micron-scale resolution. Micron-scale single clusters (40-70 μm) were randomly collected from lab-scale anaerobic digestion (AD) biosystems, and a comparative analysis was performed to evaluate differences between mesophilic and thermophilic systems. Here we reveal a cascading effect from high-temperature selection to global microbial interactions. We observed that thermophilic communities exhibited less spatial heterogeneity than mesophilic communities, which we attribute to the considerable extinction of low-abundant species by high-temperature selection. Then, the low spatial heterogeneity and the high-temperature selection acting in conjunction resulted in a high proportion of competitive interactions in thermophilic communities. Unexpectedly, however, the thermophilic AD, characterized by lower micron-scale spatial heterogeneity, showed more efficient synergistic and syntrophic cooperations involving around Clostridiales, which significantly enhanced hydrolysis performance under thermophilic conditions. In addition, the fact that high temperatures favor slower growers, along with functional redundancy-related competitive advantage, led to the selection of more proficient methanogens in more competitive environments, which are also potentially associated with enhanced methanogenic performance. In summary, our findings underscore the significance of micron-scale resolution for revealing the microbial ecology in spatially structured environments.}, }
@article {pmid40047954, year = {2025}, author = {Sobhy, IS and Goelen, T and Wäckers, F and Verstrepen, KJ and Wenseleers, T and Jacquemyn, H and Lievens, B}, title = {Impact of Nectar Composition and Nectar Yeasts on Volatile Emissions and Parasitoid Behavior.}, journal = {Journal of chemical ecology}, volume = {51}, number = {2}, pages = {29}, pmid = {40047954}, issn = {1573-1561}, support = {C3 grant (IOF-C32/15/020)//KU Leuven/ ; }, mesh = {Animals ; *Volatile Organic Compounds/metabolism/analysis/chemistry ; *Plant Nectar/chemistry/metabolism ; Female ; *Wasps/physiology ; *Metschnikowia/metabolism/physiology ; Fermentation ; *Aphids/parasitology/physiology ; Amino Acids/analysis/metabolism ; Gas Chromatography-Mass Spectrometry ; *Yeasts ; }, abstract = {Nectar yeasts can significantly influence the scent of floral nectar and therefore the foraging behavior of flower-visiting insects. While these effects likely depend on nectar chemistry and yeast species, their joint impact on nectar volatile profiles and associated insect responses remain poorly understood. Here, we used four synthetic nectar types varying in sugar and amino acid concentration and two specialist nectar yeasts (Metschnikowia gruessii and Metschnikowia reukaufii) to investigate how nectar composition and yeast species affect volatile profiles and the olfactory responses of the generalist aphid parasitoid Aphidius ervi. Olfactometer assays showed that A. ervi females significantly preferred fermented nectars with high amino acid-low sugar content (HL) and low amino acid-high sugar (LH) content, regardless being fermented by M. gruessii or M. reukaufii, over non-inoculated nectars. This effect was not observed for nectars with low amino acid-low sugar (LL) and high amino acid-high sugar (HH) content. Moreover, LL nectar fermented with M. gruessii became even repellent to the parasitoids. GC-MS analysis of volatile organic compounds (VOCs) revealed that VOC profiles of fermented nectars depended significantly on nectar type (i.e., chemical composition), yeast species, and their interaction. Whereas propyl acetate, isobutyl acetate, styrene, α-guaiene and pentyl-octanoate were associated with the LH fermented nectars, ethyl acetate and E-methyl isoeugenol were mainly associated with the HL fermented nectars, suggesting possible involvement in A. ervi attraction to these nectars. In contrast, isopropyl-hexadecanoate was associated with the non-attractive or repellent LL fermented nectars. Altogether, our results indicate that nectar composition has a strong impact on nectar scent when fermented by specialist nectar yeasts and subsequently on insect foraging behavior.}, }
@article {pmid40046987, year = {2025}, author = {Scott, WT and Rockx, S and Mariën, Q and Regueira, A and Candry, P and Ganigué, R and Koehorst, JJ and Schaap, PJ}, title = {Implementation of a Clostridium luticellarii genome-scale model for upgrading syngas fermentations.}, journal = {Computational and structural biotechnology journal}, volume = {27}, number = {}, pages = {649-660}, pmid = {40046987}, issn = {2001-0370}, abstract = {Syngas fermentation is a powerful platform for converting waste streams into sustainable carboxylic acid precursors for value-added biochemicals. Steel mills produce significant syngas, yet industrial microbial syngas valorization remains unrealized. The most promising syngas-converting biocatalysts consist of Clostridia species, such as Clostridium kluyveri, Clostridium autoethanogenum, and Clostridium ljungdahlii. Clostridium luticellarii, a recently discovered species, shares close phylogenetic ties with these organisms. Preliminary metabolic studies suggest its potential for syngas acetogenesis as well as chain elongation. In this study, we create iSJ444, a constraint-based metabolic model of C. luticellarii using iHN637 of a close relative C. ljungdahlii as a starting point. Model predictions support hypothesized methanol and syngas pathways from the metabolic characterization studies; however, the use of propionate could not be accurately predicted. Thermodynamic Flux Analysis (TFA) reveals that C. luticellarii maintains stable energy dissipation across most reactions when exposed to varying pH, with significant increases observed in reactions associated with the Wood-Ljungdahl pathway (WLP), such as the HACD1 reaction, at higher pH (6.5), suggesting an adaptive role in energy management under neutral conditions. Flux sampling simulations exploring metabolic flux distributions show that C. luticellarii might fit into syngas fermenting platforms. In both cases, high hydrogen-to-carbon source ratios result in better production of (iso)butyrate and caproate. We present a minimal genome-scale metabolic model of C. luticellarii as a foundation for further exploration and optimization. Although our predictions of its metabolic behavior await experimental validation, they underscore the potential of C. luticellarii to enhance syngas fermentation platforms.}, }
@article {pmid40045231, year = {2025}, author = {Agyapong, D and Propster, JR and Marks, J and Hocking, TD}, title = {Cross-validation for training and testing co-occurrence network inference algorithms.}, journal = {BMC bioinformatics}, volume = {26}, number = {1}, pages = {74}, pmid = {40045231}, issn = {1471-2105}, support = {2125088//National Science Foundation/ ; }, mesh = {*Algorithms ; *Microbiota ; *Computational Biology/methods ; }, abstract = {BACKGROUND: Microorganisms are found in almost every environment, including soil, water, air and inside other organisms, such as animals and plants. While some microorganisms cause diseases, most of them help in biological processes such as decomposition, fermentation and nutrient cycling. Much research has been conducted on the study of microbial communities in various environments and how their interactions and relationships can provide insight into various diseases. Co-occurrence network inference algorithms help us understand the complex associations of micro-organisms, especially bacteria. Existing network inference algorithms employ techniques such as correlation, regularized linear regression, and conditional dependence, which have different hyper-parameters that determine the sparsity of the network. These complex microbial communities form intricate ecological networks that are fundamental to ecosystem functioning and host health. Understanding these networks is crucial for developing targeted interventions in both environmental and clinical settings. The emergence of high-throughput sequencing technologies has generated unprecedented amounts of microbiome data, necessitating robust computational methods for network inference and validation.<br><br>RESULTS: Previous methods for evaluating the quality of the inferred network include using external data, and network consistency across sub-samples, both of which have several drawbacks that limit their applicability in real microbiome composition data sets. We propose a novel cross-validation method to evaluate co-occurrence network inference algorithms, and new methods for applying existing algorithms to predict on test data. Our method demonstrates superior performance in handling compositional data and addressing the challenges of high dimensionality and sparsity inherent in real microbiome datasets. The proposed framework also provides robust estimates of network stability.<br><br>CONCLUSIONS: Our empirical study shows that the proposed cross-validation method is useful for hyper-parameter selection (training) and comparing the quality of inferred networks between different algorithms (testing). This advancement represents a significant step forward in microbiome network analysis, providing researchers with a reliable tool for understanding complex microbial interactions. The method's applicability extends beyond microbiome studies to other fields where network inference from high-dimensional compositional data is crucial, such as gene regulatory networks and ecological food webs. Our framework establishes a new standard for validation in network inference, potentially accelerating discoveries in microbial ecology and human health.}, }
@article {pmid40044467, year = {2025}, author = {Sharma, P and Reitz, T and Singh, SP and Worrich, A and Muehe, EM}, title = {Going beyond improving soil health: cover plants as contaminant removers in agriculture.}, journal = {Trends in plant science}, volume = {30}, number = {5}, pages = {539-552}, doi = {10.1016/j.tplants.2025.01.009}, pmid = {40044467}, issn = {1878-4372}, mesh = {*Agriculture/methods ; *Soil/chemistry ; *Biodegradation, Environmental ; *Soil Pollutants/metabolism ; *Plants/metabolism ; }, abstract = {Agriculture faces the increasing demands of a growing global population amid simultaneous challenges to soils from climate change and human-induced contamination. Cover plants are vital in sustainable agriculture, contributing to soil health improvement, erosion prevention, and enhanced climate resilience, but their role in contaminant management is underexplored. Herein we review the utilization of cover plants for remediating contaminants such as metals, organic pollutants, nitrate, antibiotics, antimicrobial resistance genes, plastics, and salts. We explore phytoremediation strategies - including phytoextraction, phytodegradation, and phytostabilization - in cover plant management. We highlight the challenges of selecting effective cover plants and the need for biomass removal of non-biodegradable contaminants, and we advocate incorporating phytoremediation concepts into sustainable agricultural management practices beyond nutrient cycling and climate resilience.}, }
@article {pmid40042720, year = {2025}, author = {Zhang, H and Zhang, H and Du, H and Zhang, Y and Zhang, M and Yu, X and Xu, Y}, title = {Unraveling the multiple interactions between phages, microbes and flavor in the fermentation of strong-flavor Baijiu.}, journal = {Bioresources and bioprocessing}, volume = {12}, number = {1}, pages = {14}, pmid = {40042720}, issn = {2197-4365}, abstract = {The fermentation process of strong-flavor Baijiu represents a complex and unique ecosystem, characterized by the involvement of various microorganisms that drive intricate biochemical reactions, ultimately contributing to the distinct flavor profile of the Baijiu. Viruses may affect the succession of microorganisms and thus affect the style and quality of the product. However, the interaction between viruses and microorganisms during the fermentation of Baijiu is still unclear. Here we combined viral metagenomics and amplicon sequencing, physicochemical analysis, and GC-MS detection with temporal sampling to study the dynamics of viral and microbial communities, physicochemical properties, and flavor compounds during strong-flavor Baijiu fermentation. Viral metagenomic analysis revealed 513 viral operational taxonomic units (vOTUs), encompassing 34 viral families. Principal coordinates analysis (PCoA) demonstrated significant differences in vOTUs at different fermentation stages. Notably, the microbial community exhibited distinct succession patterns at various fermentation stages; it changed rapidly during the initial five days, with similarities observed between days 10 and 20. Volatile profile analysis identified 38 flavor components in fermented grains, comprising 16 ester compounds, 11 alcohols, and 8 acids, with the majority formed between days 10 and 30. The Spearman's rank correlation analysis revealed that Peduoviridae exhibited a negative correlation with Gluconobacter. Genomoviridae showed a negative correlation with Issatchenkia, Penicillium, and Monascus. These findings highlight the potential for complex interactions between viruses and microbial communities during Baijiu fermentation, underscoring the importance of considering viral communities in studies of the microbial ecology of fermented foods.}, }
@article {pmid40042690, year = {2025}, author = {Zhang, T and Wang, XL and Zhou, J and Zhou, W and Zhou, SQ}, title = {Construction of Phosphate-Solubilizing Microbial Consortium and Its Effect on the Remediation of Saline-Alkali Soil.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {11}, pmid = {40042690}, issn = {1432-184X}, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Phosphates/metabolism ; Phosphorus/metabolism ; *Microbial Consortia ; *Bacteria/metabolism/classification/genetics/isolation &amp; purification ; Arachis/growth &amp; development ; Alkalies/metabolism ; Calcium Sulfate/metabolism ; Salinity ; Nitrogen/analysis/metabolism ; Hydrogen-Ion Concentration ; }, abstract = {In this study, phosphate solubilizing bacteria (PSB) with good phosphate-solubilizing capability were isolated from phosphogypsum (PG) storage yard, and phosphate-solubilizing bacteria without antagonistic effect were selected to construct phosphate solubilizing microbial consortium (PSMC), and the synergistic effect of PSMC and PG on the physical and chemical properties of saline-alkali soil, soil enzyme activity, soil bacterial diversity, and the growth index and biomass of peanut plants were explored. The results showed that the effect of phosphorus containing soil amendment on saline-alkali soil was better than that of single PSMC or PG. In the T6 group (untreated saline-alkali soil (1.5 kg) + PSMC stock solution (15 mL) + PG (6.0 g)), the pH of saline-alkali soil decreased from 8.54 to 7.03, the content of organic matter increased by 6.64%, the content of alkali hydrolyzable nitrogen, available phosphorus and available potassium increased by 81.68%, 60.31%, and 42.03%, respectively, and the activity of alkaline phosphatase increased by 94.95%. In addition, the electrical conductivity value in T4 group (untreated saline-alkali soil (1.5 kg) + PSMC stock solution (15 mL) + PG (3.0g)) decreased significantly by 20.21%. The diversity and richness of bacterial community in T4 group were the highest, and the growth of peanut plants was the best. The fresh weight of roots and stems increased by 73.34% and 116.6%, respectively. In conclusion, the phosphorus containing soil conditioner prepared by PSMC and PG can effectively improve the soil environment of saline-alkali soil and promote the resource utilization of saline alkali soil.}, }
@article {pmid40042528, year = {2025}, author = {Zaki, H and Hussein, MA and El-Dawy, EGAM}, title = {Diversity and Symbiotic Associations of Endophytic Fungi in Calotropis procera (Aiton) W.T. Aiton (Asclepiadaceae) Across Three Egyptian Regions: Phenotypic Characterization and Mitotic Activity.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {10}, pmid = {40042528}, issn = {1432-184X}, mesh = {*Endophytes/physiology/classification/isolation &amp; purification/genetics ; Egypt ; *Fungi/classification/physiology/isolation &amp; purification/genetics ; *Symbiosis ; *Biodiversity ; Soil Microbiology ; *Calotropis/microbiology/physiology ; Mitosis ; Phenotype ; }, abstract = {Endophytic fungi are essential contributors to fungal biodiversity, playing key roles in plant defense against pathogens, alleviation of abiotic stress, and promotion of growth. This study conducted a comprehensive survey of the phenotypic characterization of Calotropis procera and its associated endophytic fungi across three regions in Egypt: Qena-Safaga, Qena, and Qena-Kosseir. Positive and significant Pearson correlations among plant morphological traits suggest intrinsic connections. Fungal species diversity exhibited significant variation across the three regions examined. Particularly, the Qena-Kosseir region demonstrated the highest fungal species richness both in soil samples and endophytic fungi. Unique to this region, Allocanariomyces tritici, Aspergillus terreus, Chaetomium globosum, C. murorum, Cladosporium cladosporioides, C. sphaerospermum, Fusarium proliferatum, Penicillium crustosum, P. granulatum, P. spinuloseum, and Roussoella intermedia were identified as endophytes. Additionally, compared to other regions, the Qena-Kosseir area exhibited the presence of Aspergillus fumigatus, A. ochraceus, A. ornatus, A. sclerotiocabonarus, Drechslera halodes, Emericella echinulata, Fusarium oxysporum, and Macrophomina phaseolina in soil samples, underscoring its distinct fungal community composition. Furthermore, antimitotic assays using the Allium cepa test revealed distinct effects of endophytic extracts on various mitotic stages. Of the 33 treatments, 11 showed an increase in the mitotic index (MI), indicating a potential positive effect on plant growth and cell division. This study offers valuable insights into the diversity and functional roles of endophytic fungi associated with C. procera, highlighting their promising applications in sustainable agriculture and plant health management.}, }
@article {pmid40042412, year = {2025}, author = {Hicks, LC and Leizeaga, A and Cruz Paredes, C and Brangarí, AC and Tájmel, D and Wondie, M and Sandén, H and Rousk, J}, title = {Simulated Climate Change Enhances Microbial Drought Resilience in Ethiopian Croplands but Not Forests.}, journal = {Global change biology}, volume = {31}, number = {3}, pages = {e70065}, pmid = {40042412}, issn = {1365-2486}, support = {2016-06327//Vetenskapsr&#xe5;det/ ; 2020-03858//Vetenskapsr&#xe5;det/ ; CTS 22:2131//Carl Tryggers Stiftelse f&#xf6;r Vetenskaplig Forskning/ ; 2022-00672//Svenska Forskningsr&#xe5;det Formas/ ; 2023-02438//Svenska Forskningsr&#xe5;det Formas/ ; KAW 2022.0175//Knut och Alice Wallenbergs Stiftelse/ ; KAW 2023.0384//Knut och Alice Wallenbergs Stiftelse/ ; }, mesh = {*Climate Change ; *Droughts ; Ethiopia ; *Forests ; *Soil Microbiology ; Fungi/growth &amp; development ; *Microbiota ; Soil/chemistry ; Bacteria/growth &amp; development ; Crops, Agricultural ; }, abstract = {Climate change and land-use change represent a dual threat to terrestrial ecosystem functioning. In the tropics, forest conversion to agriculture is occurring alongside warming and more pronounced periods of drought. Rainfall after drought induces enormous dynamics in microbial growth (potential soil carbon storage) and respiration (determining carbon loss), affecting the ecosystem carbon budget. We investigated how legacies of drought and warming affected microbial functional (growth and respiration) and structural (16S and ITS amplicon) responses after drought. Rain shelters and open-top chambers (OTCs) were used to simulate drought and warming in tropical cropland and forest sites in Ethiopia. Rain shelters reduced soil moisture by up to 25 vol%, with a bigger effect in the forest, while OTCs increased soil temperature by up to 6°C in the cropland and also reduced soil moisture but had no clear effect in the forest. Soils from these field treatments were then exposed to a standardized drought cycle to test how microbial community traits had been shaped by the different climate legacies. Microbial growth started increasing immediately after rewetting in all soils, reflecting a resilient response and indicating that microbial communities perceived the perturbation as relatively mild. Fungi recovered faster than bacteria, and the recovery of fungal growth was generally accelerated in soils with a legacy of drought. Microbial community functions and structures were both more responsive in the cropland than in forest soils, and a legacy of drought particularly enhanced microbial growth and respiration responses in the cropland but not the forest. Microbial communities in cropland soils also used carbon with a higher efficiency after rewetting. Together, these results suggest contrasting feedbacks to climate change determined by land use, where croplands will be associated with mitigated losses of soil carbon by microorganisms in response to future cycles of drought, compared to forests where soil carbon reservoirs remain more sensitive.}, }
@article {pmid40042334, year = {2025}, author = {Venturini, AM and Gontijo, JB and Berrios, L and Rodrigues, JLM and Peay, KG and Tsai, SM}, title = {Linking soil microbial genomic features to forest-to-pasture conversion in the Amazon.}, journal = {Microbiology spectrum}, volume = {13}, number = {4}, pages = {e0156124}, pmid = {40042334}, issn = {2165-0497}, support = {2014/50320-4//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo (FAPESP)/ ; DEB 1952687//National Science Foundation (NSF)/ ; 2015/13546-7//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo (FAPESP)/ ; 2018/14974-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo (FAPESP)/ ; 140032/2015-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; 133769/2015-1//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; 311008/2016-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; 314806/2021-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; Finance Code 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior (CAPES)/ ; DEB 1442214//National Science Foundation (NSF)/ ; //Canadian Institute for Advanced Research (CIFAR)/ ; 2109481//National Science Foundation (NSF)/ ; //Stanford Doerr School of Sustainability Discovery grant/ ; }, mesh = {*Soil Microbiology ; Brazil ; Forests ; *Bacteria/genetics/classification/isolation &amp; purification ; *Archaea/genetics/classification/isolation &amp; purification ; Metagenome ; Genome, Bacterial ; Phylogeny ; Soil/chemistry ; Base Composition ; Genome, Archaeal ; Genomics ; }, abstract = {Amazonian soil microbial communities are known to be altered by land-use change. However, attempts to understand these impacts have focused on broader community alterations or the response of specific microbial groups. Here, we recovered and characterized 69 soil bacterial and archaeal metagenome-assembled genomes (MAGs) from three forests and three pastures of the Eastern Brazilian Amazon and evaluated the impacts of land conversion on their genomic features. Pasture MAGs had significantly higher GC content (64.9% vs 60.2%), genome size (4.0 vs 3.1 Mbp), and number of coding sequences (4,058 vs 3,306) compared to forest genomes. Taxonomically, MAGs belonged to eight phyla; however, most (90%) had low similarity to previously known species, indicating potentially novel taxa at multiple levels. We also observed that the functional profiles associated with biogeochemical cycling and carbohydrate-active enzyme genes were impacted by forest conversion, with pasture MAGs exhibiting a notably higher number of both gene groups. Together, these data constitute the largest single-sourced genomic data set from upland soils of the Brazilian Amazon to date and increase the known MAG richness in these soils by 78%. Our data, therefore, not only add to a neglected yet emerging field but, importantly, highlight that land-use change has drastic impacts on the genomic characteristics and functional traits of dominant soil microbes.IMPORTANCEThe Brazilian Amazon is facing unprecedented threats, including increasing deforestation and degradation, which together impact half of the original forest area. Soil microorganisms are sensitive indicators of land-use change, linked to a rise in microbial methane emissions and antibiotic-resistance genes in the Amazon. However, most Amazonian soil microbes remain unknown, and little attention has been given to their genomes. Using sequencing and bioinformatics, we recovered and characterized 69 soil bacterial and archaeal genomes (metagenome-assembled genomes). These abundant members of the microbial communities diverged across forests and pastures in terms of taxonomic and functional traits. Forest conversion favors organisms with specific genomic features - increased GC content, genome size, and gene number - selecting for microorganisms that can thrive under altered conditions. Our paper helps us understand the intricate relationships between microbes and the environment, which are crucial pieces of information for comprehensive soil health assessments and future policy formulation.}, }
@article {pmid40041707, year = {2025}, author = {Liu, X and Gong, X and Ma, K and Song, W and Zhou, J and Wang, M and Li, Y and Ji, M and Li, Y and Han, H and Wang, Y and Tu, Q}, title = {Resolving ecological drivers of temporal variations of β-diversity across intertidal microbiomes.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf025}, pmid = {40041707}, issn = {2730-6151}, abstract = {Resolving the ecological drivers mediating the diversity patterns of microbial communities across space and through time is a central issue in microbial ecology. Both regional species pools and local community assembly contribute to the spatial turnover of biodiversity. In this study, we extended the concept of regional species pool to temporal, and investigated the seasonal dynamics of intertidal microbiomes across four microbial domains/kingdoms (bacteria, archaea, fungi, and protists). The results showed that the seasonal variations of microbial β-diversity were primarily governed by community assembly processes rather than temporal species pools. Different microbial domains/kingdoms were structured by different ecological processes, with homogeneous selection as the major process for all of them. Additionally, bacteria and fungi were critically shaped by drift, and protists by drift and homogeneous dispersal. Among various factors, temperature was important in shaping the temporal patterns of microbial β-diversity. The fluctuation in temperature was strongly associated with fungi and protists, resulting in high drift of community composition. This study demonstrated that community assembly processes governed the dynamic seasonal β-variations of intertidal microbiomes, expanding our understanding from spatial ecology.}, }
@article {pmid40041671, year = {2025}, author = {Zernadji, W and Rahmani, F and Jebri, S and Hamdi, M and Khammassi, M and Dhib, S and Hmaied, F}, title = {Distribution of Microbial Contaminants of Minimally Processed Salads Produced in Tunisia: Need to Strengthen Good Hygiene Practices.}, journal = {International journal of food science}, volume = {2025}, number = {}, pages = {9570620}, pmid = {40041671}, issn = {2314-5765}, abstract = {The microbiological safety of ready-to-eat (RTE) salads is considered as a major concern due to the absence of lethal treatments during processing. In this study, we aimed to investigate the microbiological quality of RTE salads commercialized in Tunisia and to determine the antibiotic resistance of isolated pathogens, in particular Staphylococcus aureus (S. aureus). A total of 100 samples were analyzed for total aerobic bacteria, total coliforms, Escherichia coli (E. coli), yeasts and molds, Salmonella spp., Listeria monocytogenes (L. monocytogenes), and S. aureus as well as norovirus (NoV) GI and GII using specific standard methods described by the International Organization for Standardization (ISO). All samples presented unacceptable microbiological quality due to high concentrations of total aerobic bacteria and yeasts (> 10[6] CFU/g) and total coliforms (> 10[4] CFU/g). E. coli and molds were detected at unsatisfactory levels in 4% and 12% of samples, respectively. The pathogens Salmonella spp. and L. monocytogenes were not detected. S. aureus were detected at unsatisfactory levels in 6% of samples. S. aureus isolates were resistant to more than five antibiotic classes. Thus, RTE salads could be a vehicle of multiresistant S. aureus. The total prevalence of NoV GII was 2% (mean 3.81 ± 0.30 Log GC/25 g), and no NoV GI-positive samples were identified. This study showed that the microbiological quality of RTE salads commercialized in Tunisia was unacceptable, highlighting the need to ensure good agricultural and hygiene practices from farm to fork to improve the quality and safety of these products.}, }
@article {pmid40037241, year = {2025}, author = {Lu, Z and Zeng, J and Wang, L and Zhu, D and Cheng, X and Huang, D and Zhang, J and Yuan, L}, title = {The influence of turbulence caused by hydraulic structures on the community assembly of epilithic biofilms in rivers.}, journal = {Journal of environmental management}, volume = {378}, number = {}, pages = {124645}, doi = {10.1016/j.jenvman.2025.124645}, pmid = {40037241}, issn = {1095-8630}, mesh = {*Biofilms ; *Rivers/microbiology ; Ecosystem ; Hydrodynamics ; }, abstract = {The assembly mechanisms of riverine biofilm communities in river systems represent a central question in aquatic microbial ecology. However, the influence of turbulence on the assembly of generalists and specialists within biofilms remains poorly understood. This study aimed to address this gap by examining a river with multiple spur dikes, using high-throughput sequencing, ecological network analysis, and partial least squares path modeling to explore the assembly process and community structure of biofilms. The results revealed that turbulence intensity (0.029 m/s) and kinetic energy (0.0018 m[2]/s[2]) were significantly higher at the heads of spur dikes compared to the tails. Notably, hydrodynamic parameters explained 6.50% of biofilm community variance, highlighting their underappreciated role as deterministic drivers of microbial assembly. Habitat specialists exhibited heightened sensitivity to hydrodynamic fluctuations, occupying central positions in co-occurrence networks. Additionally, turbulence intensity and kinetic energy emerged as the primary drivers of community assembly, influencing critical ecological processes such as homogeneous selection, drift and dispersal limitation. At the head of spur dikes, a high turbulence region, the weakened impact of homogeneous selection, combined with an increase in dispersal limitation, created conditions that particularly favored habitat generalists. Conversely, low turbulence dike tails supported specialist proliferation via strengthened deterministic selection and nutrient-driven niche partitioning. Furthermore, the partial least squares path modeling confirmed that turbulence dominates the assembly process of microbial specialists and generalists. This study revealed the pivotal role of turbulence in shaping biofilm assembly and driving the spatial differentiation of generalists and specialists, offering fresh insights into the complex interplay between hydrodynamics and microbial ecology in rivers impacted by hydraulic structures. These findings significantly enhance the understanding of biofilm assembly mechanisms and their broader implications for effective river ecosystem management.}, }
@article {pmid40036370, year = {2025}, author = {Duysburgh, C and Nicolas, C and Van den Broeck, M and Lloret, F and Monginoux, P and Rème, C and Marzorati, M}, title = {A specific blend of prebiotics and postbiotics improved the gut microbiome of dogs with soft stools in the in vitro Simulator of the Canine Intestinal Microbial Ecosystem.}, journal = {Journal of animal science}, volume = {103}, number = {}, pages = {}, pmid = {40036370}, issn = {1525-3163}, mesh = {Animals ; Dogs/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Feces/microbiology ; *Prebiotics/administration &amp; dosage ; Animal Feed/analysis ; Diet/veterinary ; Bacteria/classification ; Male ; }, abstract = {The Simulator of the Canine Intestinal Microbial Ecosystem (SCIME) allows for the study of the long-term effects of food, supplements, or ingredients on the canine gut microbiome in a simulated proximal and distal colon. This model has been used to evaluate the impact of repeated administration of a test product blend composed of a mixture of baobab fruit pulp, acacia gum, heat-killed Lactobacillus helveticus HA-122, and specific fractions of selected inactivated yeast strains (including Saccharomyces cerevisiae AQP 12260 and AQP 12988 and Cyberlindnera jadinii AQP 12549), on the activity and composition of the gut microbiome of canine donors with soft stools. The SCIME colonic reactors were inoculated with fecal material from 3 different canine donors. After 2 d of stabilization, the 8-d parallel control/treatment period was initiated; reactors were fed with SCIME nutritional medium with or without test product. Changes in microbial metabolic activity were assessed by measuring levels of acetate, propionate, butyrate, lactate, branched short-chain fatty acids, and ammonium. Changes in microbial community composition were assessed using 16S-targeted Illumina sequencing. Overall, test product supplementation resulted in increased saccharolytic fermentation, as evidenced by increases in the health-promoting bacterial metabolites such as propionate (donor-dependent), acetate, and butyrate (donor-dependent) as well as increased abundances of several saccharolytic fermenting microbes, including Bifidobacterium. Conversely, proteolytic bacteria like Proteobacteria were reduced with the test product compared to control. Repeated supplementation with the test product was therefore able to induce-in vitro-a positive modulation of the microbiome originated from dogs with soft stools.}, }
@article {pmid40035794, year = {2025}, author = {Vieira, AR and Camacho, F and Sousa, ML and Luelmo, S and Santarém, N and Cordeiro-da-Silva, A and Leão, PN}, title = {The Cyanobacterial Oxadiazine Nocuolin A Shows Broad-Spectrum Toxicity Against Protozoans and the Nematode C. elegans.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {9}, pmid = {40035794}, issn = {1432-184X}, support = {2022.04572.PTDC//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2021.04285.CEECIND/CP1663/CT0004//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 952374//Horizon 2020/ ; }, mesh = {Animals ; *Cyanobacteria/chemistry/metabolism ; *Caenorhabditis elegans/drug effects ; *Dictyostelium/drug effects ; }, abstract = {Cyanobacteria, known to be rich sources of valuable natural products (NPs) with relevant biological properties, are a unique subject to study the interplay between chemistry and ecology. Cultivation of cyanobacteria as isolated strains may only reveal a small fraction of their NPs. In contrast, investigating microbial interactions from an ecological perspective is a particularly fruitful approach to unveil both new chemistry and bioactivity. Cyanobacteria and amoebae are known to co-exist in diverse environments, but the interaction between these organisms has been poorly investigated. Defense strategies against grazer organisms may rely on morphological changes including biofilm formation or increased motility; however, secretion of toxic metabolites seems to be more effective on this regard. Among the most structurally unique cyanobacterial secondary metabolites is nocuolin A, an 1,2,3-oxadiazine metabolite isolated from the cyanobacterial strain Nodularia sp. LEGE 06071 that exhibits potent anti-proliferative activity against several human cancer lines, associated with impairment of mitochondrial oxidative phosphorylation. In this work, we show that nocuolin A is toxic against two well-known model amoebae, Acanthamoeba and Dictyostelium, leading to amoebae encystation and decrease in viability. In addition, in lawn grazing assays, we observed that Nodularia sp. LEGE 06071, the producer strain of nocuolin A, was not grazed by amoeba, while a related strain, which does not produce detectable levels of nocuolin A, was. These results support the possible involvement of nocuolin A as a chemical mediator during the interaction between these organisms. Furthermore, we show that this cyanobacterial metabolite also exhibits potent toxicity against other protozoan organisms and a free-living nematode, making it an interesting broad-spectrum scaffold for the development of antiprotozoal or anti-helminthic drugs.}, }
@article {pmid40034844, year = {2024}, author = {Thompson, MA and Valentine, DL and Peng, X}, title = {Size fractionation informs microbial community composition and interactions in the eastern tropical North Pacific Ocean.}, journal = {FEMS microbes}, volume = {5}, number = {}, pages = {xtae028}, pmid = {40034844}, issn = {2633-6685}, abstract = {Marine microorganisms are drivers of biogeochemical cycles in the world's oceans, including oxygen minimum zones (OMZs). Using a metabarcoding survey of the 16S rRNA gene, we investigated prokaryotic communities, as well as their potential interactions with fungi, at the coastal, offshore, and peripheral OMZ of the eastern tropical North Pacific. Water samples were collected along a vertical oxygen gradient, and large volumes were filtered through three size fractions, 0.22, 2, and 22 µm. The changes in community composition along the oxygen gradient were driven by Planctomycetota, Bacteroidota, Verrucomicrobiota, and Gammaproteobacteria; most are known degraders of marine polysaccharides and usually associated with the large particle-associated (LPA) community. The relative abundance of Nitrososphaerota, Alphaproteobacteria, Actinomycetota, and Nitrospinota was high in free-living and small particle-associated (SPA) communities. Network analyses identified putative interactions between fungi and prokaryotes in the particle-associated fractions, which have been largely overlooked in the ocean. In the SPAnetwork analysis, fungal amplicon sequence variants (ASVs) had exclusively negative connections with SAR11 nodes. In the LPA network analysis, fungal ASVs displayed both negative and positive connections with Pseudomonadota, SAR324, and Thermoplasmatota. Our findings demonstrate the utility of three-stage size-fractioned filtration in providing novel insights into marine microbial ecology.}, }
@article {pmid40033656, year = {2025}, author = {Orr, JA and Armitage, DW and Letten, AD}, title = {Coexistence Theory for Microbial Ecology, and Vice Versa.}, journal = {Environmental microbiology}, volume = {27}, number = {3}, pages = {e70072}, pmid = {40033656}, issn = {1462-2920}, support = {DE230100373//Australian Research Council/ ; DP220103350//Australian Research Council/ ; DE250100656//Australian Research Council/ ; }, mesh = {*Ecology/methods ; *Microbiota ; Ecosystem ; Models, Biological ; Bacteria ; }, abstract = {Classical models from theoretical ecology are seeing increasing uptake in microbial ecology, but there remains rich potential for closer cross-pollination. Here we explore opportunities for stronger integration of ecological theory into microbial research (and vice versa) through the lens of so-called "modern" coexistence theory. Coexistence theory can be used to disentangle the contributions different mechanisms (e.g., resource partitioning, environmental variability) make to species coexistence. We begin with a short primer on the fundamental concepts of coexistence theory, with an emphasis on the relevance to microbial communities. We next present a systematic review, which highlights the paucity of empirical applications of coexistence theory in microbial systems. In light of this gap, we then identify and discuss ways in which: (i) coexistence theory can help to answer fundamental and applied questions in microbial ecology, particularly in spatio-temporally heterogeneous environments, and (ii) experimental microbial systems can be leveraged to validate and advance coexistence theory. Finally, we address several unique but often surmountable empirical challenges posed by microbial systems, as well as some conceptual limitations. Nevertheless, thoughtful integration of coexistence theory into microbial ecology presents a wealth of opportunities for the advancement of both theoretical and microbial ecology.}, }
@article {pmid40028056, year = {2025}, author = {Vignolle, A and Zehl, M and Kirkegaard, RH and Vignolle, GA and Zotchev, SB}, title = {Secondary Metabolite Biosynthesis Potential of Streptomyces Spp. from the Rhizosphere of Leontopodium nivale Subsp. alpinum.}, journal = {ACS omega}, volume = {10}, number = {7}, pages = {7163-7171}, pmid = {40028056}, issn = {2470-1343}, abstract = {Bacteria of the phylum Actinomycetota, particularly those of the genus Streptomyces, are prolific producers of secondary metabolites (SMs), many of which have been developed into antibiotics, immunosuppressants, and cancer therapeutics. With high rediscovery rates, the attention has shifted to Streptomyces from unique ecological niches for the discovery of new SMs. The plant rhizosphere is one such niche, characterized by complex chemical interactions between the plant and its rhizobiome, which can elicit the production of SMs in Streptomyces. In the present study, 18 Streptomyces strains were previously isolated from the rhizosphere of the rare alpine medicinal plant Leontopodium nivale subsp. alpinum were investigated for their capacity to produce secondary metabolites. Genomes of these strains were analyzed for the presence of SM biosynthetic gene clusters (BGCs). In total, 551 BGCs were detected, of which 217 could not be linked to known SMs. These isolates were cultivated in different media known to support the production of SMs, and 15 out of the 54 methanolic extracts from these cultures exhibited antimicrobial activities. Subsequent liquid chromatography-mass spectrometry analyses of the bioactive extracts led to a putative identification of 69 known SMs as well as 16 potentially new molecules. The results of this study may provide a basis for the discovery of unique molecules with the potential to be developed as drugs against a variety of human diseases.}, }
@article {pmid40025674, year = {2025}, author = {Abdolahpur Monikh, F and Quik, JTK and Wiesner, MR and Tapparo, A and Pastore, P and Grossart, HP and Akkanen, J and Kortet, R and Kukkonen, JVK}, title = {Importance of Attachment Efficiency in Determining the Fate of PS and PVC Nanoplastic Heteroaggregation with Natural Colloids Using a Multimedia Model.}, journal = {Environmental science &amp; technology}, volume = {59}, number = {9}, pages = {4674-4683}, pmid = {40025674}, issn = {1520-5851}, mesh = {*Polyvinyl Chloride/chemistry ; Colloids/chemistry ; *Polystyrenes/chemistry ; Silicon Dioxide/chemistry ; Calcium Chloride/chemistry ; Models, Chemical ; Nanoparticles ; }, abstract = {Here, we assessed the heteroaggregation of polystyrene (PS) and poly(vinyl chloride) (PVC) nanoplastics with SiO2 as a model of natural colloids. Homoaggregation and heteroaggregation were evaluated as a function of CaCl2 (0-100 mM) and natural organic matter (NOM) (50 mg L[-1]) at a designated concentration of nanoplastics (200 μg L[-1]). Critical coagulation concentrations (CCC) of nanoplastics were determined in homoaggregation and heteroaggregation experiments with SiO2 and CaCl2. The attachment efficiency (α) was calculated by quantifying the number of nanoplastics in the presence of CaCl2, NOM, and SiO2 using single-particle inductively coupled plasma mass spectrometry (spICP-MS) and pseudo-first-order kinetics. The calculated α was fed into the SimpleBox4Plastics model to predict the fate of nanoplastics across air, water, soil, and sediment compartments. Nanoplastics exhibited high stability against homoaggregation, while significant heteroaggregation with SiO2 occurred at CaCl2 concentrations above 100 mM. The influence of NOM was also evaluated, showing a reduction in heteroaggregation with SiO2 for both nanoplastic types. Sensitivity analysis indicated that the degradation half-life of the tested nanoplastics had a more significant impact on persistence than did α. The results emphasize the environmental stability of nanoplastics, particularly in freshwater and soil compartments, and the critical role of NOM and emission pathways in determining their fate.}, }
@article {pmid40024538, year = {2025}, author = {Sliti, A and Kim, RH and Lee, D and Shin, JH}, title = {Whole genome sequencing and In silico analysis of the safety and probiotic features of Lacticaseibacillus paracasei FMT2 isolated from fecal microbiota transplantation (FMT) capsules.}, journal = {Microbial pathogenesis}, volume = {202}, number = {}, pages = {107405}, doi = {10.1016/j.micpath.2025.107405}, pmid = {40024538}, issn = {1096-1208}, mesh = {*Probiotics/adverse effects ; *Whole Genome Sequencing ; Genome, Bacterial ; *Fecal Microbiota Transplantation ; Humans ; *Lacticaseibacillus paracasei/genetics/isolation &amp; purification/classification ; Phylogeny ; Computer Simulation ; Virulence Factors/genetics ; Feces/microbiology ; Capsules ; Plasmids/genetics ; Prophages/genetics ; Multigene Family ; Gastrointestinal Microbiome ; Clustered Regularly Interspaced Short Palindromic Repeats ; }, abstract = {Lacticaseibacillus paracasei is widely used as a probiotic supplement and food additive in the medicinal and food industries. However, its application requires careful evaluation of safety traits associated with probiotic pathogenesis, including the transfer of antibiotic-resistance genes, the presence of virulence and pathogenicity factors, and the potential disruptions of the gut microbiome and immune system. In this study, we conducted whole genome sequencing (WGS) of L. paracasei FMT2 isolated from fecal microbiota transplantation (FMT) capsules and performed genome annotation to assess its probiotic and safety attributes. Our comparative genomic analysis assessed this novel strain's genetic attributes and functional diversity and unraveled its evolutionary relationships with other L. paracasei strains. The assembly yielded three contigs: one corresponding to the chromosome and two corresponding to plasmids. Genome annotation revealed the presence of 2838 DNA-coding sequences (CDS), 78 ribosomal RNAs (rRNAs), 60 transfer RNAs (tRNAs), three non-coding RNAs (ncRNAs), and 126 pseudogenes. The strain lacked antibiotic resistance genes and pathogenicity factors. Two intact prophages, one Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) region, and three antimicrobial peptide gene clusters were identified, highlighting the genomic stability and antimicrobial potential of the strain. Furthermore, genes linked to probiotic functions, such as mucosal colonization, stress resistance, and biofilm formation, were characterized. The pan-genome analysis identified 3358 orthologous clusters, including 1775 single-copy clusters, across all L. paracasei strains. Notably, L. paracasei FMT2 contained many unique singleton genes, potentially contributing to its distinctive probiotic properties. Our findings confirm the potential of L. paracasei FMT2 for food and therapeutic applications based on its probiotic profile and safety.}, }
@article {pmid40022977, year = {2025}, author = {Noiset, P and Héger, M and Salmon, C and Kwapong, P and Combey, R and Thevan, K and Warrit, N and Rojas-Oropeza, M and Cabirol, N and Zaragoza-Trello, C and Rasmussen, C and Nkoba, K and Vereecken, NJ}, title = {Ecological and evolutionary drivers of stingless bee honey variation at the global scale.}, journal = {The Science of the total environment}, volume = {969}, number = {}, pages = {178945}, doi = {10.1016/j.scitotenv.2025.178945}, pmid = {40022977}, issn = {1879-1026}, mesh = {*Honey/analysis ; Bees ; Animals ; Biological Evolution ; }, abstract = {Stingless bee honey (SBH) is a prime natural product consumed and used for diverse medicinal and traditional purposes by local communities across the (sub-)tropics. Despite its ecological and cultural significance, the drivers of its compositional variation within and among species remain poorly understood, particularly throughout Asia and sub-Saharan Africa. Addressing this issue at the global scale has the potential to inform broader and less explored eco-evolutionary and how variation in SBH across the (sub-)tropics has led human communities to develop diverse and sometimes specific patterns of practices that are now integral to their cultural and economic life. In this study, we aimed to disentangle the roles of evolutionary and environmental drivers of SBH compositional variation using a sampling design that combines honey profiling by H1-NMR spectroscopy with the collection of honeys from honey bees and stingless bees at the global scale. The results show a clear differentiation between the chemical composition and functional diversity of honey bee and stingless bee honeys, mainly due to the production of a range of bioproducts during sugar fermentation. The study of compositional variation of stingless bee honey showed that the role of ecological and evolutionary drivers and their joint effects varied within each tropical region, preventing the identification of a clear continental, phylogenetic or ecological pattern. We provide the first global and comprehensive characterization of SBH composition, a prerequisite for defining and accepting SBH in the different Codex Alimentarius. We also highlight the need for more interdisciplinary and trans-sectoral research adopting a holistic approach to investigate stingless bee honey characteristics.}, }
@article {pmid40022770, year = {2025}, author = {Attiani, V and Smidt, H and van der Wielen, PWJJ}, title = {Impact of environmental and process conditions on the microbial ecology and performance of full-scale slow sand filters in drinking water treatment.}, journal = {Water research}, volume = {277}, number = {}, pages = {123328}, doi = {10.1016/j.watres.2025.123328}, pmid = {40022770}, issn = {1879-2448}, mesh = {*Drinking Water/microbiology ; *Water Purification/methods ; *Filtration/methods ; *Sand/chemistry ; Netherlands ; Water Microbiology ; }, abstract = {Slow sand filters (SSFs) are commonly used for treating drinking water, effectively removing contaminants such as particles, organic matter, and microorganisms. However, the ecological dynamics of prokaryotic communities within SSFs remain poorly understood. This study investigated the top sand layer, the Schmutzdecke (SCM), along with the influent and effluent water of full-scale SSFs at four drinking water treatment plants (DWTPs) in the Netherlands. These plants use SSFs as the final step in their treatment to produce unchlorinated drinking water. Two DWTPs treat surface water after dune infiltration and do not apply advanced oxidation processes prior the SSF. In contrast, the other two DWTPs treat reservoir-stored surface water and incorporate ozonation or UV and activated carbon filtration as part of their treatment train. All SSFs consistently reduced biomass in the effluent compared to the influent, confirming their role in biomass load reduction. Key biological and chemical parameters showed that pretreatment with dune infiltration produced more biologically stable drinking water compared to reservoir storage. Moreover, while SSFs act as polishing filters when treating dune-infiltrated surface water, they significantly alter the prokaryotic community and biological stability of the water when treating reservoir-stored surface water. Prokaryotic communities in the SCM and water samples showed distinct compositions rather than merely the accumulation of microorganisms in the SCM from the influent water, demonstrating that SSF are active ecosystems different from water. The SCM exhibited a higher relative abundance of the genera SWB02, Gemmata, Pedomicrobium, Nitrospira, and mle1-7, while in the water samples the genus Candidatus Omnitrophus was relatively more abundant. Moreover, each DWTP hosts a unique prokaryotic profiles in both the SCM and water samples. Source water, upstream treatment and/or the biological stability of the influent water are identified as potential causes affecting the prokaryotic communities in SSFs that affect the microbial water quality of the effluent water.}, }
@article {pmid40016229, year = {2025}, author = {Chang, J and Costa, OYA and Sun, Y and Wang, J and Tian, L and Shi, S and Wang, E and Ji, L and Wang, C and Pang, Y and Yao, Z and Ye, L and Zhang, J and Chen, H and Cai, Y and Chen, D and Song, Z and Rong, J and Raaijmakers, JM and Tian, C and Kuramae, EE}, title = {Domesticated rice alters the rhizosphere microbiome, reducing nitrogen fixation and increasing nitrous oxide emissions.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {2038}, pmid = {40016229}, issn = {2041-1723}, mesh = {*Oryza/microbiology/metabolism/genetics ; *Nitrous Oxide/metabolism ; *Rhizosphere ; *Microbiota/genetics ; *Nitrogen Fixation/genetics ; Soil Microbiology ; Plant Roots/microbiology/metabolism ; Domestication ; Metagenomics ; Soil/chemistry ; Nitrogenase/metabolism/genetics ; Bacteria/genetics/metabolism ; Nitrogen/metabolism ; }, abstract = {Crop domestication has revolutionized food production but increased agriculture's reliance on fertilizers and pesticides. We investigate differences in the rhizosphere microbiome functions of wild and domesticated rice, focusing on nitrogen (N) cycling genes. Shotgun metagenomics and real-time PCR reveal a higher abundance of N-fixing genes in the wild rice rhizosphere microbiomes. Validation through transplanting rhizosphere microbiome suspensions shows the highest nitrogenase activity in soils with wild rice suspensions, regardless of planted rice type. Domesticated rice, however, exhibits an increased number of genes associated with nitrous oxide (N2O) production. Measurements of N2O emissions in soils with wild and domesticated rice are significantly higher in soil with domesticated rice compared to wild rice. Comparative root metabolomics between wild and domesticated rice further show that wild rice root exudates positively correlate with the frequency and abundance of microbial N-fixing genes, as indicated by metagenomic and qPCR, respectively. To confirm, we add wild and domesticated rice root metabolites to black soil, and qPCR shows that wild rice exudates maximize microbial N-fixing gene abundances and nitrogenase activity. Collectively, these findings suggest that rice domestication negatively impacts N-fixing bacteria and enriches bacteria that produce the greenhouse gas N2O, highlighting the environmental trade-offs associated with crop domestication.}, }
@article {pmid40012773, year = {2025}, author = {Sun, P and Wu, Y and Zhu, P and Wang, J and Yu, X and Guo, W}, title = {Spartina alterniflora invasion significantly alters the assembly and structure of soil bacterial communities in the Yellow River Delta.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1525632}, pmid = {40012773}, issn = {1664-302X}, abstract = {Soil microbial communities are integral to almost all terrestrial biogeochemical cycles, which are essential to coastal wetland functioning. However, how soil bacterial community assembly, composition, and structure respond to native and non-native plant invasions in coastal wetlands remains unclear. In this study of the coastal wetlands of the Yellow River Delta in China, the assembly, community composition, and diversity of soil bacterial communities associated with four wetland plant species (Phragmites australis, Spartina alterniflora, Suaeda salsa, and Tamarix chinensis) and four soil depths (0-10 cm, 10-20 cm, 20-30 cm, and 30-40 cm) were characterized using high-throughput sequencing. Plant species identity, as well as environmental factors, rather than soil depth, was found to play predominant roles in shaping the diversity and structure of wetland soil bacterial communities. S. alterniflora invasion altered bacterial community structure and increased bacterial diversity. Phragmites australis-associated bacterial communities were enriched with sulfate-reducing bacteria such as Desulfurivibrio and Desulfuromonas. In comparison, S. alterniflora-associated bacterial communities were enriched with both sulfate-reducing bacteria (SEEP-SRB1) and sulfate-oxidizing bacteria (Sulfurimonas), which maintained a dynamic balance in the local sulfur-cycle, and thereby enhanced S. alterniflora growth. In addition, stochastic processes dominated the assembly of soil bacterial communities associated with all four plant species, but were most important for the S. alterniflora community. The S. alterniflora-associated bacterial community also showed stronger interactions and more extensive connections among bacterial taxa; a co-occurrence network for this community had the greatest average clustering coefficient, average degree, modularity, and number of links and nodes, but the lowest average path length. Altogether, individual plant species had distinct effects on soil bacterial community assembly and structure, with the invasive species having the strongest impact. These results provide insights into microbial ecology and inform management strategies for coastal wetland restoration.}, }
@article {pmid40008244, year = {2025}, author = {Xu, LL and McIlroy, SE and Ni, Y and Guibert, I and Chen, J and Rocha, U and Baker, DM and Panagiotou, G}, title = {Chemical pollution drives taxonomic and functional shifts in marine sediment microbiome, influencing benthic metazoans.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycae141}, pmid = {40008244}, issn = {2730-6151}, abstract = {Microbial communities in marine sediments contribute significantly to the overall health and resiliency of marine ecosystems. However, increased human disturbance undermines biodiversity and, hence, natural functionality provided by marine sediments. Here, through a deep shotgun metagenomics sequencing of the sediment microbiome and COI metabarcoding of benthic metazoans, we demonstrate that >50% of the microorganisms' and metazoan's taxonomic variation can be explained by specific chemical pollution indices. Interestingly, there was a significant correlation between the similarity in microbiome communities' taxonomical and functional attributes and the similarity of benthic metazoans community composition. Furthermore, mediation analysis was conducted to evaluate the microbiome-mediated indirect effect, suggesting that microbial species and functions accounted for 36% and 26%, respectively, of the total effect of pollution on the benthic metazoans. Our study introduces a multi-level perspective for future studies in urbanized coastal areas to explore marine ecosystems, revealing the impact of pollution stress on microbiome communities and their critical biogeochemical functions, which in turn may influence macrofaunal composition.}, }
@article {pmid40005728, year = {2025}, author = {Yi, S and Wu, H and Lin, Y and Cha, X and Shang, Y}, title = {Antibiotic Resistance Profiles and Genomic Analysis of Endophytic Bacteria Isolates from Wild Edible Fungi in Yunnan.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, pmid = {40005728}, issn = {2076-2607}, support = {R21 AG050009/AG/NIA NIH HHS/United States ; 32260624//the National Natural Science Foundation of China/ ; 202202AG050009//Yunnan Major Scientific and Technological Projects/ ; }, abstract = {The use of antibiotics has led to the emergence of antibiotic resistance, posing significant challenges in the prevention, control, and treatment of microbial diseases, while threatening public health, the environment, and food safety. In this study, the antibiotic resistance phenotypes and genotypes of 56 endophytic bacteria isolates from three species of wild edible fungi in Yunnan were analyzed using the Kirby-Bauer disk diffusion method and PCR amplification. The results revealed that all isolates were sensitive to ofloxacin, but resistance was observed against 17 other antibiotics. Specifically, 55, 53, and 51 isolates exhibited resistance to amoxicillin, penicillin, and vancomycin, respectively. Antibiotic resistance gene (ARG) detection indicated that the sulfonamide sul1 gene had the highest detection rate (53.57%). Excluding the ARG that was not detected, the lowest detection rates were the sulfonamide sul2 and sul3 genes, both at 1.79%. Among six tetracycline resistance genes, only tetK and tetM were detected. For β-lactam antibiotics, blaTEM, blaVIM, and blaSHV genes were present, while blaOXA was absent. In aminoglycoside resistance genes, aadB was not detected, while detection rates for aac(3')-IIa, acrB, and aadA1 were 3.57%, 1.79%, and 37.5%, respectively. The chloramphenicol Cat gene was detected at a rate of 14.29%, whereas floR was absent. For polypeptide resistance, VanC was detected at 3.57%, with EmgrB not detected. All three quinolone genes were detected, with detection rates of 8.92% for GyrA, 39.29% for GyrB, and 37.5% for ParC. Through phylogenetic analysis, 12 isolates that are closely related to ten common foodborne pathogenic bacteria were further selected for whole-genome sequencing and assembly. Gene annotations revealed that each isolate contained more than 15 ARGs and over 30 virulence factors. Notably, the detection rate of antibiotic resistance phenotypes was higher than that of genotypes, highlighting the importance of studying phenotypic antibiotic resistance that lacks identifiable ARGs. This study enriches the research on endophytes in wild edible fungi and provides new data for microbial ecology and antibiotic resistance research. It also offers critical insights for monitoring microbial antibiotic resistance in wild edible fungi and potentially other food sources, contributing to more effective strategies for ecological protection, sustainable agricultural development, and public health security.}, }
@article {pmid40005607, year = {2025}, author = {Li, S and Zhuang, W and Feng, X and Warren, A and Gong, J}, title = {Morphology and Molecular Phylogeny of Four Anaerobic Ciliates (Protista, Ciliophora, Armophorea), with Report of a New Species and a Unique Arrangement Pattern of Dikinetids in Family Metopidae.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, pmid = {40005607}, issn = {2076-2607}, support = {41976086, 42276094//National Natural Science Foundation of China/ ; }, abstract = {The diversity of anaerobic ciliates is greatly underestimated owing to the limitation in sampling and cultivation when compared with their aerobic counterparts. In this study, four anaerobic ciliates, viz. Brachonella abnormalis sp. nov., Brachonella contorta (Levander, 1894) Jankowski, 1964, Metopus contortus (Quennerstedt, 1867) Kahl, 1932, and Metopus major Kahl, 1932, were investigated by live observation, protargol staining and 18S rRNA gene sequencing. B. abnormalis sp. nov. can be separated from its congeners by a combination of the following features: bullet-shaped cell with a life size of about 130-190 × 90-120 μm, dikinetids distributed along dorsal dome kineties, highly developed adoral zone comprised of 87-107 polykinetids, making about 450° spiralization around the long axis. The present work demonstrates that two known species, M. contortus and M. major, have a special trait never previously reported, viz. short, regularly arranged preoral dome dikinetids. Species with short, regularly arranged dome dikinetids appear in divergent clades in SSU rRNA gene trees, which may infer that this trait evolved several times. Phylogenetic analyses based on SSU rRNA gene sequence data also support the monophyly of the genus Brachonella and the paraphyly of the order Metopida, respectively.}, }
@article {pmid40005589, year = {2025}, author = {Warkhade, Y and Schaerer, LG and Bigcraft, I and Hazen, TC and Techtmann, SM}, title = {Diversity and Distribution of Hydrocarbon-Degrading Genes in the Cold Seeps from the Mediterranean and Caspian Seas.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, pmid = {40005589}, issn = {2076-2607}, support = {Merck Future Insight Prize//Merck KGaA/ ; }, abstract = {Marine cold seeps are unique ecological niches characterized by the emergence of hydrocarbons, including methane, which fosters diverse microbial communities. This study investigates the diversity and distribution of hydrocarbon-degrading genes and organisms in sediments from the Caspian and Mediterranean Seas, utilizing 16S rRNA and metagenomic sequencing to elucidate microbial community structure and functional potential. Our findings reveal distinct differences in hydrocarbon degrading gene profiles between the two seas, with pathways for aerobic and anaerobic hydrocarbon degradation co-existing in sediments from both basins. Aerobic pathways predominate in the surface sediments of the Mediterranean Sea, while anaerobic pathways are favored in the surface sediments of the anoxic Caspian Sea. Additionally, sediment depths significantly influence microbial diversity, with variations in gene abundance and community composition observed at different depths. Aerobic hydrocarbon-degrading genes decrease in diversity with depth in the Mediterranean Sea, whereas the diversity of aerobic hydrocarbon-degrading genes increases with depth in the Caspian Sea. These results enhance our understanding of microbial ecology in cold seep environments and have implications for bioremediation practices targeting hydrocarbon pollutants in marine ecosystems.}, }
@article {pmid40003826, year = {2025}, author = {Castañeda-Espinosa, A and Duque-Granda, D and Cadavid-Restrepo, G and Murcia, LM and Junca, H and Moreno-Herrera, CX and Vivero-Gómez, RJ}, title = {Study of Bacterial Communities in Water and Different Developmental Stages of Aedes aegypti from Aquatic Breeding Sites in Leticia City, Colombian Amazon Biome.}, journal = {Insects}, volume = {16}, number = {2}, pages = {}, pmid = {40003826}, issn = {2075-4450}, support = {57545//Universidad Nacional de Colombia/ ; }, abstract = {Aedes aegypti is a key vector in the transmission of arboviral diseases in the Colombian Amazon. This study aimed to characterize microbiota composition using DNA extracted from water in artificial breeding sites, immature stages, and adults of Ae. aegypti in Leticia, Amazonas. Additionally, the physicochemical water variables were correlated with the bacterial communities present. Eight artificial breeding sites were identified, with bucket, plant pot, and tire being the most frequent. The breeding sites exhibited similar physicochemical profiles, with significant temperature and salinity differences (p-value < 0.03). The most representative bacterial genera included Ottowia (82%), Xanthobacter (70.59%), and Rhodocyclaceae (92.78%) in breeding site water; Aquabacterium (61.07%), Dechloromonas (82.85%), and Flectobacillus (58.94%) in immature stages; and Elizabethkingia (70.89%) and Cedecea (39.19%) in males and females of Ae. aegypti. Beta diversity analysis revealed distinct clustering between adults and the water and immature communities (p-value < 0.001). Multivariate analysis showed strong correlations among bacterial communities, breeding sites, and physicochemical variables such as tire and drum cover which exhibited high levels of total dissolved solids, conductivity, and salinity associated with Flectobacillus, Leifsonia, Novosphingobium, Ottowia, and Rhodobacter. Bacterial genera such as Mycobacterium, Escherichia, Salmonella, and Clostridium, present in artificial breeding sites, are associated with public health relevance. This study provides insights into bacterial community dynamics across Ae. aegypti's life cycle and underscores the importance of water physicochemical and biological characteristics for developing new vector control strategies.}, }
@article {pmid40003751, year = {2025}, author = {Rampanti, G and Cardinali, F and Ferrocino, I and Milanović, V and Garofalo, C and Osimani, A and Aquilanti, L}, title = {Deciphering the Microbiota of Edible Insects Sold by Street Vendors in Thailand Using Metataxonomic Analysis.}, journal = {Insects}, volume = {16}, number = {2}, pages = {}, pmid = {40003751}, issn = {2075-4450}, abstract = {The aim of the present study was to investigate the microbiota of processed ready-to-eat (fried or boiled) edible insects sold by street vendors at local green markets in Thailand (Bangkok and Koh Samui). To this end, samples of 4 insect species (rhino beetle adults, silkworm pupae, giant waterbugs adults, and black scorpions) were collected and analyzed through viable counting and metataxonomic analysis. Enterobacteriaceae showed counts below 1 log cfu g[-1] in all samples, except for black scorpions, which showed elevated counts reaching up to 4 log cfu g[-1]. Total mesophilic aerobes counts were up to 8 log cfu g[-1] in all the analyzed samples. Counts below 1 log cfu g[-1] were observed for Escherichia coli, Staphylococcus aureus, sulfite-reducing clostridia viable cells and spores, and Bacillus cereus. All the samples showed the absence of Listeria monocytogenes and Salmonella spp. According to metataxonomic analysis, 14 taxa were consistently present across all insect samples, including Dellaglioa algida, Latilactobacillus curvatus, Latilactobacillus sakei, Acetobacteraceae, Apilactobacillus kunkeei, Bombilactobacillus spp., Enterobacteriaceae, Gilliamella spp., Lactobacillus spp., Lactobacillus apis, Streptococcus thermophilus, Lacticaseibacillus rhamnosus, Lactiplantibacillus plantarum, and Weissella spp. Minority taxa included Alcaligenes spp., Brochothrix thermosphacta, Psychrobacter spp., Staphylococcus saprophyticus, Lactobacillus melliventris, Pediococcus spp., Levilactobacillus brevis, and Snodgrassella alvi.}, }
@article {pmid39998093, year = {2025}, author = {Varini, C and Manganelli, M and Scardala, S and Antonelli, P and Losasso, C and Testai, E}, title = {An Update of Tetrodotoxins Toxicity and Risk Assessment Associated to Contaminated Seafood Consumption in Europe: A Systematic Review.}, journal = {Toxins}, volume = {17}, number = {2}, pages = {}, pmid = {39998093}, issn = {2072-6651}, support = {project n. RF-2021-12373885//Ministry of Health of Italy/ ; }, mesh = {Risk Assessment ; Europe ; *Food Contamination/analysis ; *Seafood/analysis ; Humans ; Animals ; *Tetrodotoxin/toxicity/analysis ; }, abstract = {Following the occurrence of Tetrodotoxins (TTXs) in Europe-a group of neurotoxins identified in Asia, where fatalities occurred after the ingestion of contaminated pufferfish-the EFSA proposed a limit of 44 µg of TTX/kg of shellfish meat in mollusks in 2017, to protect heavy consumers. The limit was based on an acute reference dose (ARfD) derived from the few available data on TTX toxicity. TTX is expected to increase with sea-surface warming; indeed, it has been found in spring/summer in mollusks in Europe, with concentrations often exceeding this limit. Due to the numerous uncertainties of the EFSA's ARfD, we conducted a systematic review to provide an update on TTX toxicity. Out of 12,741 articles retrieved from PubMed, Science Direct, and Scopus since 2017, only 17 were eligible for data extraction. Our results show that they are not sufficient to modify the EFSA's conclusions. Furthermore, our analysis of occurrence data in European seafood, to assess the current risk of exposure to TTX, reveals several gaps, such as different LODs/LOQs and seasonal monitoring not allowing comparisons between areas and too few analyzed sites. However, the presence of positive samples exceeding the EFSA limit indicates a potential risk even for general consumers, highlighting the urgency to address these knowledge gaps.}, }
@article {pmid39996333, year = {2025}, author = {Medeiros, W and Kralova, S and Oliveira, V and Ziemert, N and Sehnal, L}, title = {Antarctic bacterial natural products: from genomic insights to drug discovery.}, journal = {Natural product reports}, volume = {42}, number = {5}, pages = {774-787}, doi = {10.1039/d4np00045e}, pmid = {39996333}, issn = {1460-4752}, mesh = {*Biological Products/chemistry/pharmacology/metabolism ; Antarctic Regions ; *Drug Discovery ; *Bacteria/genetics/chemistry/metabolism ; Genomics ; Molecular Structure ; }, abstract = {Covering: up to the end of 2024Microbial life dominates the extreme continent Antarctica, playing a pivotal role in ecosystem functioning and serving as a reservoir of specialized metabolites known as natural products (NPs). NPs not only contribute to microbial adaptation to harsh conditions but also modulate microbial community structure. Long-term isolation and environmental pressures have shaped the genomes of Antarctic bacteria, suggesting that they also encode unique NPs. Since NPs are also an important source of drugs, we argue that investigating Antarctic bacterial NPs is essential not only for understanding their ecological role and evolution, but also for discovering new chemical structures, biosynthetic mechanisms, and potential new drugs. Yet, despite advances in omics technologies and increased scientific activities in Antarctica, relatively few new bacterial NPs have been discovered. The lack of systematic research activities focused on the exploration of Antarctic bacteria and their NPs constitutes a big problem considering the climate change issue, to which ecosystems in polar regions are the most sensitive areas on the Earth. Here, we highlight the currently available data on Antarctic bacteria, their biosynthetic potential, and the successful NP discoveries, while addressing the challenges in NP research and advocating for systematic, collaborative efforts aligned with the Antarctic Treaty System and the Antarctic Conservation Biogeographic Regions.}, }
@article {pmid39992142, year = {2025}, author = {Sun, L and Wang, Q and Huang, J and Wang, H and Yu, Z}, title = {Disrupting the balance: how acne duration impacts skin microbiota assembly processes.}, journal = {Microbiology spectrum}, volume = {13}, number = {4}, pages = {e0260324}, pmid = {39992142}, issn = {2165-0497}, support = {32000054, 32170071//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {Humans ; *Acne Vulgaris/microbiology ; *Skin/microbiology ; *Microbiota/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; Female ; Male ; Adult ; Young Adult ; Skin Microbiome ; }, abstract = {Growing interest in the impact of microbial balance on health has driven studies on the ecological processes shaping the skin microbiota. Skin diseases, which alter the skin's local environment, can disrupt the microbial structure and interact with the disease itself. However, research on microbial assembly in diseased skin remains limited. In this study, we applied ecological models to characterize the processes shaping the skin microbiota in acne patients, considering the impact of disease duration on both skin pores and surfaces using bacterial amplicon sequencing. Our results revealed a significant shift in microbial diversity on the skin surface of patients with long-term acne. Further microbial community analyses showed a transition in ecological processes from healthy to diseased skin. Microbial communities on the skin surfaces of healthy controls and individuals with short-duration acne were primarily driven by heterogeneous selection, whereas microbial drift dominated the assembly process in the long-duration groups. Using the Sloan neutral model, we classified amplicon sequence variants (ASVs) into high-effect and low-effect groups based on relative abundance and sample occurrence. High-effect ASVs, likely exerting a greater ecological influence, were predominantly represented by Cutibacterium across all acne-affected skin groups, while Staphylococcus became enriched among high-effect ASVs in patients with long-term acne. Functional profiling further demonstrated that high-effect ASVs were significantly enriched in motility-related pathways. Additionally, we observed a reduction in microbial network complexity on skin surfaces as disease duration increased. Overall, the ecological dynamics of skin microbial communities may offer valuable insights into the mechanisms underlying disease onset and persistence.IMPORTANCEThe skin microbiota plays a critical role in acne development, yet the processes governing microbial assembly during acne progression remain poorly understood. Previous studies predominantly focused on factors such as acne severity, location, and duration in relation to skin microbial structure, with little attention given to the ecological mechanisms shaping the communities. In this study, we applied ecological models to investigate the processes influencing microbial assembly of skin microbiota in acne patients with varying disease durations and examined functions of ecologically important non-neutral amplicon sequence variants (ASVs). Our findings reveal a transition in ecological processes from deterministic to neutral processes as acne duration increased, with non-neutral ASVs potentially contributing to acne pathogenicity and persistence. These insights contribute to a deeper understanding of the ecological dynamics underlying acne and indicate that targeting these non-neutral ASVs or their associated functions may serve as the basis for future therapeutic strategies.}, }
@article {pmid39992122, year = {2025}, author = {Li, X and Wang, H and Zang, Y and Xue, S and Xin, J and Liu, L and Tang, X and Chen, J}, title = {Exploring the structure and assembly of seagrass microbial communities in rhizosphere and phyllosphere.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {3}, pages = {e0243724}, pmid = {39992122}, issn = {1098-5336}, support = {42176154,42206117//MOST | National Natural Science Foundation of China (NSFC)/ ; U1806213//MOST | NSFC | National Natural Science Foundation of China-Shandong Joint Fund (-)/ ; 2019YFD0901204//MOST | National Key Research and Development Program of China (NKPs)/ ; ZR2024QD017//| Natural Science Foundation of Shandong Province ()/ ; }, mesh = {*Rhizosphere ; *Zosteraceae/microbiology ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; Plant Leaves/microbiology ; *Soil Microbiology ; Ecosystem ; }, abstract = {Microbial community assembly and interactions are pivotal research areas within microbial ecology, yet relevant studies in seagrass rhizospheres and phyllosphere remain relatively scarce. In this study, we utilized high-throughput sequencing technology to investigate the microbial communities in different periods and microhabitats (rhizosphere and phyllosphere) of two seagrass species (Zostera marina and Phyllospadix iwatensis). Our findings suggest that microhabitats have a more pronounced impact on the composition of seagrass-associated microbial communities compared to periods and species. Further investigations reveal that the phyllosphere microbial community exhibits a more intricate co-occurrence network and interactions than the rhizosphere microbial community. Keystone taxa show distinct functional roles in different microhabitats of seagrasses. Additionally, we observed that differences in seagrass microhabitats influence community assembly, with the rhizosphere microbial community being more influenced by deterministic processes (heterogeneous selection) compared to the phyllosphere. These findings contribute to our understanding of the intricate interactions between seagrasses and their associated microbial communities, providing valuable insights into their distribution patterns and microhabitat preferences.IMPORTANCEStudying the community structure and assembly of different microhabitats in seagrass beds contributes to revealing the complexity and dynamic processes of seagrass ecosystems. In the rhizosphere microhabitat of seagrasses, microbial communities may assist in disease resistance or enhance nutrient uptake efficiency in seagrasses. On the other hand, in the microhabitat on the surface of seagrass blades, microorganisms may be closely associated with the physiological functions and nutrient cycling of seagrass blades. Therefore, understanding the structure and assembly mechanisms of rhizosphere and phyllosphere microbial communities is crucial for exploring the interactions between seagrass and microbial communities, as well as for enhancing our comprehension of the stability and resilience of seagrass bed ecosystems.}, }
@article {pmid39991271, year = {2025}, author = {Morales, SE and Tobias-Hünefeldt, SP and Armstrong, E and Pearman, WS and Bogdanov, K}, title = {Marine phytoplankton impose strong selective pressures on in vitro microbiome assembly, but drift is the dominant process.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf001}, pmid = {39991271}, issn = {2730-6151}, abstract = {Phytoplankton are known ecosystem engineers that modulate ocean community assembly processes, but the universality and extent of their microbiome control remains unclear. We used in vitro incubations and 16S ribosomal RNA gene amplicon sequencing to test the influence of Southern and South Pacific oceans dominant phytoplankton on assembly processes and community successions in response to phytoplankton blooms. Phytoplankton grown with reduced-diversity cultures or supplemented with exogenously added microbiomes showed reduced diversity, suggesting environmental filtering. Community profiles were distinct under all culture conditions, further confirming strong selection for specific microbiomes based on phytoplankton. Analysis of core, abundant, and rare organisms in each culture condition showed a conserved response in which core organisms were enriched under conditions of exogenously added phytoplankton. Progression through phytoplankton growth phases selected first for rare and abundant organisms, with increased selection for core members during the exponential phase and relaxing of selection during the death phase, as seen throughout incubations for microbiome-only controls. Surprisingly, selection process quantification identified drift as the dominant process across all conditions and growth phases, with homogenous selection and dispersal limitation accounting for the remainder. Altogether, using Southern Ocean-derived model organisms we confirmed the role phytoplankton play in community assembly but also demonstrated that stochastic processes still predominately drive community selection.}, }
@article {pmid39988434, year = {2025}, author = {Howells, G and Sezmis, AL and Blake, C and McDonald, MJ}, title = {Co-Existence Slows Diversification in Experimental Populations of E. coli and P. fluorescens.}, journal = {Environmental microbiology}, volume = {27}, number = {2}, pages = {e70061}, pmid = {39988434}, issn = {1462-2920}, support = {APP1186140//National Health and Medical Research Council/ ; DP220103548//Australian Research Council/ ; }, mesh = {*Pseudomonas fluorescens/genetics/growth &amp; development/physiology ; *Escherichia coli/genetics/growth &amp; development/physiology ; Coculture Techniques ; Adaptation, Physiological ; Genome, Bacterial ; Whole Genome Sequencing ; }, abstract = {Microbes grown in heterogeneous laboratory environments can rapidly diversify into multiple, coexisting variants. While the genetic and evolutionary mechanisms of laboratory adaptive radiations are well studied, how the presence of other species alters the outcomes of diversification is less well understood. To test the effect of co-culture growth on the Pseudomonas fluorescens SBW25 adaptive radiation, Escherichia coli and P. fluorescens were cultured in monoculture and co-culture for 8 weeks. In P. fluorescens monoculture, Wrinkly and Smooth Spreader types rapidly evolved and were maintained over 8 weeks, while E. coli monocultures evolved two colony types, a big and a small colony variant. In contrast, we found that in co-culture, E. coli did not evolve small colony variants. Whole genome sequencing revealed the genetic basis of possible co-culture specific adaptations in both E. coli and P. fluorescens. Altogether, our data support that the presence of multiple species changed the outcome of adaptive radiation.}, }
@article {pmid39987915, year = {2025}, author = {De Luca, G and Barakat, M and Verméglio, A and Achouak, W and Heulin, T}, title = {The Bacterial Genus Ramlibacter: Betaproteobacteria Capable of Surviving in Oligotrophic Environments Thanks to Several Shared Genetic Adaptation Traits.}, journal = {Environmental microbiology}, volume = {27}, number = {2}, pages = {e70059}, pmid = {39987915}, issn = {1462-2920}, mesh = {Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Adaptation, Physiological/genetics ; Genome, Bacterial ; Soil Microbiology ; *Burkholderiaceae/genetics/physiology/classification ; }, abstract = {Ramlibacter tataouinensis, the type species of the genus Ramlibacter, is renowned for its ability to thrive in hot, arid and nutrient-poor desert soils. To investigate whether its adaptive properties are shared across all 20 currently described Ramlibacter species found in diverse terrestrial and aquatic habitats worldwide, we conducted a comprehensive analysis of 16S rRNA sequences and genomic information available from the literature. Our study encompassed approximately 40 deposited genomes, allowing us to propose a genomic phylogeny that aligns with the 16S rRNA phylogeny. Our findings reveal several conserved features across the genus Ramlibacter. This includes the presence of light sensors, environmental sensing networks, organic carbon and phosphate acquisition systems and the ability to store carbon and energy in the form of polyhydroxyalkanoate or polyphosphate granules. These shared traits rationalise the widespread distribution of Ramlibacter in oligotrophic terrestrial and aquatic environments. They also explain the genus' ability to withstand desiccation, endure extended periods of starvation, and survive in nutrient-depleted conditions. Notably, certain adaptive features are further enhanced in several species by their pleiomorphism and ability to form cysts. Overall, our study not only highlights the ecological adaptations of Ramlibacter species but also extends our understanding of microbial ecology in oligotrophic environments.}, }
@article {pmid39987257, year = {2025}, author = {Zhang, X and Ta, N and Yi, S and Xiong, H}, title = {Intolerance of uncertainty and mental health in patients with IBD: the mediating role of maladaptive coping.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {6464}, pmid = {39987257}, issn = {2045-2322}, mesh = {Humans ; *Adaptation, Psychological ; Female ; Male ; *Inflammatory Bowel Diseases/psychology ; Uncertainty ; Adult ; *Mental Health ; Middle Aged ; Anxiety/psychology ; Surveys and Questionnaires ; Depression/psychology ; Young Adult ; }, abstract = {The aim of this study was to investigate the relationship between intolerance of uncertainty (IU) and mental health in patients with Inflammatory Bowel Disease (IBD), and to explore the mediating role of coping styles. A questionnaire was administered to adult patients with IBD, which included general demographic information, the Intolerance of Uncertainty Scale, the Generalized Anxiety Disorder-7, and the Patient Health Questionnaire-9. The study ultimately included validated questionnaires from 163 IBD patients. Intolerance of uncertainty was significantly and positively correlated with anxiety (r = 0.738, p < 0.01) and depression (r = 0.683, p < 0.01). The mediating effect of adaptive coping style was not significant. The maladaptive coping style partially mediated the relationship between IU and anxiety, as well as between IU and depression, with the mediating effect size of 25.5% and 34.2%, respectively. Our findings emphasize the impact of the inability to tolerate uncertainty on the mental health of patients with IBD. It suggests that interventions can be implemented to enhance IBD patients' tolerance of uncertainty and to modify their maladaptive coping styles to promote mental health. This offers a valuable framework for psychological interventions for IBD patients.}, }
@article {pmid39985718, year = {2025}, author = {Gufwan, LA and Peng, L and Gufwan, NM and Lan, S and Wu, L}, title = {Enhancing Soil Health Through Biocrusts: A Microbial Ecosystem Approach for Degradation Control and Restoration.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {8}, pmid = {39985718}, issn = {1432-184X}, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Ecosystem ; Fungi/metabolism ; *Environmental Restoration and Remediation/methods ; Biodiversity ; Lichens ; Cyanobacteria ; Microbiota ; Bryophyta ; Biodegradation, Environmental ; }, abstract = {Escalating global concerns about soil degradation, driven by erosion, salinization, compaction, pollution, and organic matter loss, highlights the critical need for sustainable remediation. Biocrusts-complex communities of cyanobacteria, algae, lichens, bryophytes, and fungi-play a pivotal role in soil stabilization, erosion prevention, and nutrient cycling. This study presents recent advancements in biocrust application for soil management and restoration, focusing on artificial biocrusts as a nature-based solution biotechnology. It emphasizes their effectiveness in enhancing soil quality, biodiversity, and ecosystem functionality. Researchers are leveraging these microbial communities to develop strategies that improve soil health and rehabilitate degraded landscapes. The review concludes that biocrusts are a viable strategy for boosting soil resilience and enhancing soil health against environmental stressors. It recommends future research on their long-term ecological impacts and methods to enhance their functionality.}, }
@article {pmid39978646, year = {2025}, author = {Kij, A and Kieronska-Rudek, A and Bar, A and Czyzynska-Cichon, I and Strus, M and Kozien, L and Wiecek, G and Zeber-Lubecka, N and Kulecka, M and Kwiatkowski, G and Przyborowski, K and Mohaissen, T and Sternak, M and Buczek, E and Zakrzewska, A and Proniewski, B and Kus, K and Franczyk-Zarow, M and Kostogrys, RB and Pieterman, EJ and Princen, HMG and Chlopicki, S}, title = {Low phylloquinone intake deteriorates endothelial function in normolipidemic and dyslipidaemic mice.}, journal = {The Journal of nutritional biochemistry}, volume = {140}, number = {}, pages = {109867}, doi = {10.1016/j.jnutbio.2025.109867}, pmid = {39978646}, issn = {1873-4847}, mesh = {Animals ; Male ; Mice, Inbred C57BL ; *Endothelium, Vascular/physiopathology/drug effects/metabolism ; *Vitamin K 1/administration &amp; dosage/blood ; *Dyslipidemias/physiopathology/metabolism ; Mice ; Vitamin K 2/analogs &amp; derivatives/metabolism ; Liver/metabolism ; Vasodilation/drug effects ; Aorta/metabolism ; Gastrointestinal Microbiome ; Dietary Supplements ; }, abstract = {While the plasma phylloquinone (PK) concentration is inversely correlated with cardiovascular risk, the involvement of PK in regulating endothelial function has not been directly investigated. Therefore, in this study we assessed the effects of short-term treatment with PK-deficient diets (5-10 weeks) on endothelial function in normolipidemic 14-week-old male C57BL/6JCmd mice and age-matched dyslipidaemic male E3L.CETP mice. Our results show that in normolipidemic mice dietary PK deficiency was associated with a marked reduction of PK levels in the plasma and liver (liquid chromatography-mass spectrometry measurements) and with impaired endothelium-dependent vasodilation assessed in vivo by magnetic resonance imaging (MRI). Dietary PK deficiency-induced endothelial dysfunction was fully reversed by PK supplementation. In dyslipidaemic E3L.CETP mice, dietary PK deficiency exacerbated preexisting endothelial dysfunction. Furthermore, dietary PK deficiency decreased menaquinone-4 (MK-4) levels in the aorta but did not affect blood coagulation (calibrated automated thrombography), microbiota composition (culturing and next-generation sequencing), and gut menaquinone production. In conclusion, our study demonstrated for the first time that sufficient dietary PK intake supports endothelial function in normolipidemic and dyslipidaemic mice indicating nutritional significance of dietary PK in the maintenance of endothelial function in humans.}, }
@article {pmid39976768, year = {2025}, author = {Kauserud, H and Martin-Sanchez, PM and Estensmo, EL and Botnen, S and Morgado, L and Maurice, S and Høiland, K and Skrede, I}, title = {Yeasts Prefer Daycares and Molds Prefer Private Homes.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {7}, pmid = {39976768}, issn = {1432-184X}, support = {741332//Horizon 2020/ ; PID2021-123184OA-I00//MICIN/AEI, Spain/ ; }, mesh = {*Fungi/classification/isolation &amp; purification/genetics ; *Yeasts/isolation &amp; purification/classification/genetics ; Humans ; Dust/analysis ; *Air Pollution, Indoor/analysis ; *Child Day Care Centers ; *Mycobiome ; Norway ; *Air Microbiology ; *Housing ; DNA, Fungal/genetics ; Child ; Child, Preschool ; }, abstract = {Worldwide, people spend most of their time indoors; in their homes, workplaces, schools, and daycares. Indoor fungi can cause negative health effects due to the production of toxins or volatiles that trigger the immune system of the occupants. To what degree indoor fungi (mycobiomes) differ between buildings with different usage is poorly known. Here, we compare the indoor mycobiomes in 123 children's daycare centers and 214 private homes throughout Norway, as revealed by metabarcoding of DNA extracted from dust samples collected by community scientists. Although the fungal richness per se was similar in dust samples from daycares and homes, the fungal community composition differed. Yeast fungi, distributed mainly across the orders Saccharomycetales, Filobasidiales, and Tremellales, were proportionally more abundant in the daycares, while filamentous fungi, including spore-producing molds such as Aspergillus, Penicillum, and Cladosporium, were relatively more abundant in homes. Number of occupants, which is considerably higher in daycares, correlated significantly with the fungal community shift. We hypothesize that the density of occupants and their age distribution drive the systematic difference of yeasts and filamentous fungi in the two building types.}, }
@article {pmid39972634, year = {2025}, author = {de Sousa, T and Silva, C and Igrejas, G and Hébraud, M and Poeta, P}, title = {The Interactive Dynamics of Pseudomonas aeruginosa in Global Ecology.}, journal = {Journal of basic microbiology}, volume = {65}, number = {4}, pages = {e70004}, doi = {10.1002/jobm.70004}, pmid = {39972634}, issn = {1521-4028}, support = {//This work was supported by grant 2020.05332.BD, and the projects UI/00772 and LA/P/0059/2020 funded by the Portuguese Foundation for Science and Technology (FCT)./ ; }, mesh = {*Pseudomonas aeruginosa/genetics/drug effects/physiology ; Humans ; Ecosystem ; *Pseudomonas Infections/microbiology ; Animals ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Biodiversity ; Ecology ; }, abstract = {Pseudomonas aeruginosa is an opportunistic bacterium widely distributed in both natural and urban environments, playing a crucial role in global microbial ecology. This article reviews the interactive dynamics of P. aeruginosa across different ecosystems, highlighting its capacity for adaptation and resistance in response to environmental and therapeutic pressures. We analyze the mechanisms of antibiotic resistance, including the presence of resistance genes and efflux systems, which contribute to its persistence in both clinical and nonclinical settings. The interconnection between human, animal, and environmental health, within the context of the One Health concept, is discussed, emphasizing the importance of monitoring and sustainable management practices to mitigate the spread of resistance. Through a holistic approach, this work offers insights into the influence of P. aeruginosa on public health and biodiversity.}, }
@article {pmid39971349, year = {2025}, author = {Russo, CJ and Husain, K and Murugan, A}, title = {Soft Modes as a Predictive Framework for Low-Dimensional Biological Systems Across Scales.}, journal = {Annual review of biophysics}, volume = {54}, number = {1}, pages = {401-426}, pmid = {39971349}, issn = {1936-1238}, support = {R35 GM151211/GM/NIGMS NIH HHS/United States ; }, mesh = {*Models, Biological ; Animals ; Humans ; }, abstract = {All biological systems are subject to perturbations arising from thermal fluctuations, external environments, or mutations. Yet, while biological systems consist of thousands of interacting components, recent high-throughput experiments have shown that their response to perturbations is surprisingly low dimensional: confined to only a few stereotyped changes out of the many possible. In this review, we explore a unifying dynamical systems framework-soft modes-to explain and analyze low dimensionality in biology, from molecules to ecosystems. We argue that this soft mode framework makes nontrivial predictions that generalize classic ideas from developmental biology to disparate systems, namely phenocopying, dual buffering, and global epistasis. While some of these predictions have been borne out in experiments, we discuss how soft modes allow for a surprisingly far-reaching and unifying framework in which to analyze data from protein biophysics to microbial ecology.}, }
@article {pmid39970705, year = {2025}, author = {Yuan, K and Xu, H and Li, S and Coker, OO and Liu, W and Wang, L and Zhang, X and Yu, J}, title = {Intraneoplastic fungal dysbiosis is associated with colorectal cancer progression and host gene mutation.}, journal = {EBioMedicine}, volume = {113}, number = {}, pages = {105608}, pmid = {39970705}, issn = {2352-3964}, mesh = {Humans ; *Colorectal Neoplasms/pathology/genetics/microbiology/etiology ; *Dysbiosis/microbiology ; *Mutation ; Disease Progression ; Female ; Male ; Middle Aged ; *Fungi/genetics/classification ; Microsatellite Instability ; Aged ; Adenoma/microbiology/genetics/pathology ; Proto-Oncogene Proteins p21(ras)/genetics ; }, abstract = {BACKGROUND: The relationship between intraneoplastic fungi and colorectal cancer (CRC) progression remains largely unclear. Here, we investigated fungal community changes in adenoma and CRC and their correlation with host genetic mutations.<br><br>METHODS: We obtained 261 tissue biopsies from two geographically distinct cohorts of CRC and adenoma patients, with each individual contributing 2-5 biopsies from lesions and 2 from adjacent normal tissues. 18S ribosomal RNA gene sequencing was used for microbial profiling. Host genetic alterations including KRAS mutations and microsatellite instability (MSI) were detected concurrently.<br><br>FINDINGS: Intra-neoplastic fungal composition significantly differed between CRC and adenoma in two independent cohorts, with enrichment of highly variable fungi (HVF) in CRC. Six HVFs exhibited higher abundances in adenoma and CRC compared to adjacent normal tissues with Malassezia showing a progressive increase from adenoma to CRC. Fungi intratumoral heterogeneity index also increased from adenoma through stages I to IV of CRC. Intra-tumoral fungi-fungi co-abundance analysis indicated stronger positive interactions in CRC than in adenoma, with increasingly robust links among intra-tumoral fungi along adenoma-CRC progression, primarily driven by Malassezia and Aspergillus. Furthermore, fungal heterogeneity was significantly correlated with host genetic mutations, with higher risk indices in CRC tissues harboring KRAS and MSI mutations. Thirteen fungi stratified CRC samples with KRAS mutations, achieving an area under the curve (AUC) of 0.86, while those associated with MSI status showed an AUC of 0.89.<br><br>INTERPRETATION: This study demonstrates that intraneoplastic fungal community alterations occur between adenoma and CRC, with increasing heterogeneity associated with host genetic mutations, emphasizing the role of fungal dysbiosis in CRC.<br><br>FUNDING: This work was supported by RGC Research Impact Fund Hong Kong (R4032-21F); RGC-CRF (C4008-23W); Strategic Seed Funding Collaboration Research Scheme CUHK (3133344); Strategic Impact Enhancement Fund CUHK (3135509); Impact case for RAE CUHK (3134277).}, }
@article {pmid39970561, year = {2025}, author = {Gullì, M and Cangioli, L and Frusciante, S and Graziano, S and Caldara, M and Fiore, A and Klonowski, AM and Maestri, E and Brunori, A and Mengoni, A and Pihlanto, A and Diretto, G and Marmiroli, N and Bevivino, A}, title = {The relevance of biochar and co-applied SynComs on maize quality and sustainability: Evidence from field experiments.}, journal = {The Science of the total environment}, volume = {968}, number = {}, pages = {178872}, doi = {10.1016/j.scitotenv.2025.178872}, pmid = {39970561}, issn = {1879-1026}, mesh = {*Zea mays/growth &amp; development/physiology ; *Charcoal ; Fertilizers ; *Agriculture/methods ; *Soil Microbiology ; Soil/chemistry ; Mycorrhizae ; Microbiota ; }, abstract = {Adoption of sustainable maize cropping practices is urgently needed. Synthetic microbial communities (SynComs) made of plant growth-promoting microorganisms (PGPMs), coupled with biochar from residual biomass, offer an environmentally compatible alternative to inorganic fertilizers and may improve soil fertility. This article extends in a two-year field trial with preliminary results obtained in previous pot experiments, monitoring plant physiology, soil biology and chemistry, and kernel metabolomics. Here, we report the synergistic effect of the co-application of biochar, SynComs, and arbuscular mycorrhizal fungi on the soil microbiome, maize growth, and kernel metabolomic profile. SynComs application did not affect the diversity and richness of soil microbial communities; therefore, it posed a low risk of long-term effects on soil microbial ecology. With SynComs and biochar co-application to the soil, the physiology of maize plants was characterized by higher chlorophyll content, ear weight, and kernel weight. The combination of SynComs and biochar also affected the kernel metabolome, resulting in enriched health-beneficial and anti-stress metabolites. Since the preliminary evidence on the environmental and economic impact of these new associations was more favorable than that of conventional fertilizers, it seems reasonable that their large-scale implementation can eventually favor the transition to more sustainable agriculture.}, }
@article {pmid39970001, year = {2025}, author = {Vo, L and Avgidis, F and Mattingly, HH and Edmonds, K and Burger, I and Balasubramanian, R and Shimizu, TS and Kazmierczak, BI and Emonet, T}, title = {Nongenetic adaptation by collective migration.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {8}, pages = {e2423774122}, pmid = {39970001}, issn = {1091-6490}, support = {R01 GM138533/GM/NIGMS NIH HHS/United States ; R01 GM106189/GM/NIGMS NIH HHS/United States ; R01GM138533//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R01GM106189//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; F31 GM149174/GM/NIGMS NIH HHS/United States ; F31GM149174-01//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; }, mesh = {*Escherichia coli/physiology/genetics ; *Adaptation, Physiological ; *Chemotaxis/physiology ; Phenotype ; Escherichia coli Proteins/metabolism/genetics ; }, abstract = {Cell populations must adjust their phenotypic composition to adapt to changing environments. One adaptation strategy is to maintain distinct phenotypic subsets within the population and to modulate their relative abundances via gene regulation. Another strategy involves genetic mutations, which can be augmented by stress-response pathways. Here, we studied how a migrating bacterial population regulates its phenotypic distribution to traverse diverse environments. We generated isogenic Escherichia coli populations with varying distributions of swimming behaviors and observed their phenotype distributions during migration in liquid and porous environments. We found that the migrating populations became enriched with high-performing swimming phenotypes in each environment, allowing the populations to adapt without requiring mutations or gene regulation. This adaptation is dynamic and rapid, reversing in a few doubling times when migration ceases. By measuring the chemoreceptor abundance distributions during migration toward different attractants, we demonstrated that adaptation acts on multiple chemotaxis-related traits simultaneously. These measurements are consistent with a general mechanism in which adaptation results from a balance between cell growth generating diversity and collective migration eliminating underperforming phenotypes. Thus, collective migration enables cell populations with continuous, multidimensional phenotypes to flexibly and rapidly adapt their phenotypic composition to diverse environmental conditions.}, }
@article {pmid39963424, year = {2024}, author = {Höner Zu Siederdissen, C and Spangenberg, J and Bisdorf, K and Krautwurst, S and Srivastava, A and Marz, M and Taubert, M}, title = {Nanopore sequencing enables novel detection of deuterium incorporation in DNA.}, journal = {Computational and structural biotechnology journal}, volume = {23}, number = {}, pages = {3584-3594}, pmid = {39963424}, issn = {2001-0370}, abstract = {Identifying active microbes is crucial to understand their role in ecosystem functions. Metabolic labeling with heavy, non-radioactive isotopes, i.e., stable isotope probing (SIP), can track active microbes by detecting heavy isotope incorporation in biomolecules such as DNA. However, the detection of heavy isotope-labeled nucleotides directly during sequencing has, to date, not been achieved. In this study, Oxford nanopore sequencing was utilized to detect heavy isotopes incorporation in DNA molecules. Two isotopes widely used in SIP experiments were employed to label a bacterial isolate: deuterium (D, as D2O) and carbon-13 ([13]C, as glucose). We hypothesize that labeled DNA is distinguishable from unlabeled DNA by changes in the nanopore signal. To verify this distinction, we employed a Bayesian classifier trained on signal distributions of short oligonucleotides (k-mers) from labeled and unlabeled sequencing reads. Our results show a clear distinction between D-labeled and unlabeled reads, based on changes in median and median absolute deviation (MAD) of the nanopore signals for different k-mers. In contrast, [13]C-labeled DNA cannot be distinguished from unlabeled DNA. For D, the model employed correctly predicted more than 85% of the reads. Even when metabolic labeling was conducted with only 30% D2O, 80% of the obtained reads were correctly classified with a 5% false discovery rate. Our work demonstrates the feasibility of direct detection of deuterium incorporation in DNA molecules during Oxford nanopore sequencing. This finding represents a first step in establishing the combined use of nanopore sequencing and SIP for tracking active organisms in microbial ecology.}, }
@article {pmid39962695, year = {2025}, author = {Peng, SW and Zhang, GY and Jiao, YY}, title = {[Microbial Ecology in the Mask-derived Plastisphere in a Water Environment].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {46}, number = {2}, pages = {1193-1202}, doi = {10.13227/j.hjkx.202402057}, pmid = {39962695}, issn = {0250-3301}, mesh = {*Masks/microbiology ; *Microplastics/analysis ; *Water Microbiology ; COVID-19/prevention &amp; control ; *Microbiota ; *Ecosystem ; }, abstract = {As a result of the impact of COVID-19 and other respiratory diseases, the regular use of medical masks and the associated risk that the mask waste enters the water environment have increased, and the mask-derived microplastics are finally posing a potential impact on the aquatic ecological environment. This study explored the microbial diversity, function, assembly mechanism, and ecological network in the plastisphere derived from different layers of masks. The results indicated that the plastisphere in each layer had a unique microbial community, and the community richness gradually increased over time. The functions of microbial communities in the plastisphere, including pathogenicity, phototrophy, compound degradation, and the functions related to the cycling of carbon, nitrogen, and sulfur, changed significantly over time. As to the microbial assembly mechanism in the plastisphere, stochastic processes were more dominant （NST>0.5）, but the influence of deterministic processes gradually grew. The ecological network results indicated that all the plastispheres exhibited a high number of modules and high modularity, and the complexity of the microbial community gradually decreased with colonization time. This study indicates that the mask-derived plastisphere has a unique ecological process, which strengthens our understanding of the ecological effects and microbial colonization processes of the mask-derived plastisphere.}, }
@article {pmid39961999, year = {2025}, author = {Popov, IV and Popov, IV and Chebotareva, IP and Tikhmeneva, IA and Peshkova, DA and Krikunova, AA and Tkacheva, EV and Algburi, AR and Abdulhameed, AM and Jargalsaikhan, A and Ganbold, O and Chikindas, ML and Venema, K and Ermakov, AM}, title = {Differences in gut microbiota composition, diversity, and predicted functional activity between wild and captive zoo Carollia perspicillata in a One Health perspective.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {56}, number = {2}, pages = {1291-1302}, pmid = {39961999}, issn = {1678-4405}, support = {075-10-2021-093//Ministry of Science and Higher Education of the Russian Federation/ ; 23-14-00316//Russian Science Foundation/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Animals, Zoo/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Animals, Wild/microbiology ; *Chiroptera/microbiology ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; Russia ; Panama ; }, abstract = {Bats play an important role in global microbial ecology, as they are the host of various microbes. Carollia perspicillata is one of the most popular bat species in zoos. The influence of the captive environment on the gut microbiota of this species is underinvestigated. In this study, we compared gut microbiota composition, diversity, and the potential functional activity of wild and captive C. perspicillata from Panama and Russia (Moscow Zoo), respectively, based on high-throughput 16S rRNA sequencing data. The abundance of 13 bacterial phyla and 35 bacterial genera significantly differed. Environment- and farm animal health-related bacteria (Mannheimia, unclassified Pasteurellaceae, Staphylococcus, and Mycoplasma) dominated wild bats, while bacteria important for public health (Bacteroides, Clostridium sensu stricto 1, and Acinetobacter) were higher in zoo bats. We also observed significantly greater alpha diversity in zoo bats, while there were no significant differences in beta diversity. These findings were accompanied by significant differences in the abundance of 32 functional pathways of gut bacteria, which are probably associated with the different diets of wild and zoo bats. This study shows that the rearing environment significantly affects the gut microbiota of C. perspicillata and highlights that the outcomes of microbiome research of captive bats need to be interpreted with care. Such differences in gut bacterial communities should be the basis for the development of new handling and veterinary care protocols, and also be the justification for further studies of the impact of microbiota of wild and zoo bats on One Health.}, }
@article {pmid39961275, year = {2025}, author = {Wang, A and Bong, CW and Tao, S and Ye, X and Liu, B and Liang, H and Zheng, X and Wong, YY and Loh, KH and Li, H and Chen, K and Lim, SH and Lee, CW}, title = {Evaluation of heavy metal pollution and ecological risk of surface sediments in a tropical mountainous River-Estuary-Shelf Continuum system: A case study of the Selangor River, Malaysia.}, journal = {Marine environmental research}, volume = {205}, number = {}, pages = {107017}, doi = {10.1016/j.marenvres.2025.107017}, pmid = {39961275}, issn = {1879-0291}, mesh = {*Metals, Heavy/analysis ; *Water Pollutants, Chemical/analysis ; *Geologic Sediments/chemistry ; *Rivers/chemistry ; *Environmental Monitoring ; Malaysia ; *Estuaries ; Risk Assessment ; }, abstract = {As human activities continue to increase, the global production of pollutants has increased significantly, with the majority of pollutants being transported to the ocean via rivers, resulting in intensified pollution in estuaries and coastal areas. To maintain a healthy marine ecological environment, it is necessary to consider rivers, estuaries, and coastal seas as integrated systems and implement pollution management based on the concept of land-ocean integration. In this study, heavy metal elements in the surface sediments of Selangor River-Estuary-Coastal Shelf Continuum were collected and analysed to assess their pollution levels and potential ecological risks. The results show that the heavy metal content is high in the downstream and estuarine regions, with a general decreasing trend observed from nearshore to offshore in the coastal shelf area. The heavy metal pollution assessment indicates that the surface sediments of the Selangor River-Estuary-Coastal Shelf continuum were contaminated, with the most severe pollution occurring downstream and within the estuary. The pollution levels gradually decrease after exiting the estuary. The ecological risk associated with heavy metal pollution in rivers, estuaries, and southeastern coastal areas was classified as moderate to serious, whereas other areas exhibited only slight ecological risks. Specifically, As causes serious pollution in the river and estuary, with moderate-to-serious pollution in the coastal shelf area and moderate-to-serious ecological risks, mainly originating from mining within the river basin. Pb causes moderate pollution in the river, estuary, and coastal areas, with slight ecological risks due to mining within the river basin and inputs from nearby rivers, ports, and industrial activities. Other heavy metals cause minor pollution and pose minimal ecological risks.}, }
@article {pmid39961017, year = {2025}, author = {Colman, DR and Templeton, AS and Spear, JR and Boyd, ES}, title = {Microbial ecology of serpentinite-hosted ecosystems.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {39961017}, issn = {1751-7370}, support = {80NSSC21K0489//NASA Exobiology and Evolutionary Biology program/ ; }, mesh = {*Ecosystem ; *Microbiota ; Bacteria/genetics/classification ; }, abstract = {Serpentinization, the collective set of geochemical reactions initiated by the hydration of ultramafic rock, has occurred throughout Earth history and is inferred to occur on several planets and moons in our solar system. These reactions generate highly reducing conditions that can drive organic synthesis reactions potentially conducive to the emergence of life, while concomitantly generating fluids that challenge life owing to hyperalkalinity and limited inorganic carbon (and oxidant) availability. Consequently, the serpentinite-hosted biosphere offers insights into the earliest life, the habitable limits for life, and the potential for life on other planets. However, the support of abundant microbial communities by serpentinites was only recognized ~20 years ago with the discovery of deep-sea hydrothermal vents emanating serpentinized fluids. Here, we review the microbial ecology of both marine and continental serpentinization-influenced ecosystems in conjunction with a comparison of publicly available metagenomic sequence data from these communities to provide a global perspective of serpentinite microbial ecology. Synthesis of observations across global systems reveal consistent themes in the diversity, ecology, and functioning of communities. Nevertheless, individual systems exhibit nuances due to local geology, hydrology, and input of oxidized, near-surface/seawater fluids. Further, several new (and old) questions remain including the provenance of carbon to support biomass synthesis, the physical and chemical limits of life in serpentinites, the mode and tempo of in situ evolution, and the extent that modern serpentinites serve as analogs for those on early Earth. These topics are explored from a microbial perspective to outline key knowledge-gaps for future research.}, }
@article {pmid39960660, year = {2025}, author = {Gomi, R and Adachi, F}, title = {Quinolone Resistance Genes qnr, aac(6')-Ib-cr, oqxAB, and qepA in Environmental Escherichia coli: Insights into Their Genetic Contexts from Comparative Genomics.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {6}, pmid = {39960660}, issn = {1432-184X}, support = {JP22K18038//JSPS KAKENHI/ ; 22B006//Kurita Water and Environment Foundation, Japan/ ; 2230113//Sumitomo Foundation, Japan/ ; JPMEERF20235R01//Environment Research and Technology Development Fund/ ; }, mesh = {*Escherichia coli/genetics/drug effects/isolation &amp; purification ; *Quinolones/pharmacology ; *Anti-Bacterial Agents/pharmacology ; *Escherichia coli Proteins/genetics ; *Drug Resistance, Bacterial/genetics ; Genome, Bacterial ; Genomics ; Plasmids/genetics ; }, abstract = {Previous studies have reported the occurrence of transferable quinolone resistance determinants in environmental Escherichia coli. However, little is known about their vectors and genetic contexts. To gain insights into these genetic characteristics, we analyzed the complete genomes of 53 environmental E. coli isolates containing one or more transferable quinolone resistance determinants, including 20 sequenced in this study and 33 sourced from RefSeq. The studied genomes carried the following transferable quinolone resistance determinants alone or in combination: aac(6')-Ib-cr, oqxAB, qepA1, qnrA1, qnrB4, qnrB7, qnrB19, qnrD1, qnrS1, and qnrS2, with qnrS1 being predominant. These resistance genes were detected on plasmids of diverse replicon types; however, aac(6')-Ib-cr, qnrS1, and qnrS2 were also detected on the chromosome. The genetic contexts surrounding these genes included not only those found in clinical isolates but also novel contexts, such as qnrD1 embedded within a composite transposon-like structure bounded by Tn3-derived inverted-repeat miniature elements (TIMEs). This study provides deep insights into mobile genetic elements associated with transferable quinolone resistance determinants, highlighting the importance of genomic surveillance of antimicrobial-resistant bacteria in the environment.}, }
@article {pmid39954521, year = {2025}, author = {Hernández-Villamor, D and Li, P and Aydogan, M and Verhelst, M and Van de Wiele, T and Rabaey, K and Prévoteau, A}, title = {Low electrode potentials enhance current generation by Geobacter sulfurreducens biofilms: A high-throughput study.}, journal = {Biosensors &amp; bioelectronics}, volume = {276}, number = {}, pages = {117232}, doi = {10.1016/j.bios.2025.117232}, pmid = {39954521}, issn = {1873-4235}, mesh = {*Geobacter/physiology/growth &amp; development/metabolism ; *Biofilms/growth &amp; development ; Electrodes ; *Bioelectric Energy Sources/microbiology ; Electron Transport ; *Biosensing Techniques ; Oxidation-Reduction ; }, abstract = {The microbial species Geobacter sulfurreducens uses different extracellular electron transfer (EET) pathways depending on the potential of the final electron acceptor, yet a complete understanding of EET mechanisms and the impact of thermodynamically limiting potentials remains elusive. Here, we employ a custom-designed high-throughput system that enables the simultaneous and continuous execution of 128 parallel experiments to investigate the complete spectrum of potentials ([-0.25 to 0] V vs. SHE) impacting the metabolic energy generation in axenic G. sulfurreducens electroactive biofilms (EABs). These were grown for 500 h in three consecutive stages and characterized electrochemically. The EABs grown on electrodes poised below the apparent midpoint potential ([-0.18 to -0.16] V) grew slower than those grown at conventional, non-limiting potential (0 V), developing 50% smaller biofilms and 2.4-fold higher anodic plateau currents on average ([0.1 vs. 0.04] mA cm[-2]). These also exhibited enhanced charge transport coupled to higher average concentrations of charge carriers ([1.6 vs. 0.4] mMe[-]), the latter impacting linearly the anodic plateau current. Low- and high-potential redox pools were discriminated with the former comprising 50%-70% of storable charge. Overall, these findings strongly suggest an overexpression of charge carriers in G. sulfurreducens EABs cultivated at lower potentials and highlight the useful contribution of high-throughput tools for boosting research in electromicrobiology.}, }
@article {pmid39954444, year = {2025}, author = {He, M and Tang, R and Guan, F and Peng, W and Lu, J and Li, K and Zhou, L and Wang, Y and Yuan, Y}, title = {Methanogenic response of paddy soils exposed to zinc oxide nanoparticles and sulfurized products.}, journal = {Journal of hazardous materials}, volume = {489}, number = {}, pages = {137608}, doi = {10.1016/j.jhazmat.2025.137608}, pmid = {39954444}, issn = {1873-3336}, mesh = {*Zinc Oxide/toxicity/chemistry ; *Soil Microbiology ; *Methane/biosynthesis ; Soil/chemistry ; *Soil Pollutants/toxicity ; *Metal Nanoparticles/toxicity ; RNA, Ribosomal, 16S/genetics ; Oryza ; *Sulfides/toxicity ; *Nanoparticles/toxicity ; }, abstract = {The use of zinc oxide nanoparticles (ZnO NPs) in agriculture is expanding, yet their effects on microbial ecology in flooded paddy soils remain unclear. This study examined the influence of ZnO NPs and their sulfide derivatives (S-ZnO NPs) on methane production in paddy soils. Results showed that ZnO NPs at a concentration of 1000 mg/kg significantly inhibited methane production by 28.97 % in an acid soil and by 26.83 % in an alkaline soil. S-ZnO NPs at the same concentration did not significantly affect methane production in the alkaline soil and increased it by 15.33 % in the acid soil. High-throughput sequencing revealed that ZnO NPs significantly altered the microbial community structure, affecting the prevalence of methanogenic organisms like Methanosarcina in the acid soil and Methanobacterium in the alkaline soil. Quantitative PCR analysis showed a reduction in the expression of methanogenic gene (mcrA) and total bacterial 16S rRNA genes with ZnO NPs exposure, but S-ZnO NPs had a lesser impact on these genes. This research highlights the more toxic impact of ZnO NPs compared to S-ZnO NPs on methane production and microbial communities in paddy soils, emphasizing the necessity for careful evaluation of nanoparticles in agricultural use to avoid ecological disturbances.}, }
@article {pmid39954056, year = {2025}, author = {Ren, Z and Gao, H and Martyniuk, N and Ren, H and Xiong, X and Luo, W}, title = {Dual-Domain Primary Succession of Bacteria in Glacier Forefield Streams and Soils of a Maritime and Continental Glacier.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {5}, pmid = {39954056}, issn = {1432-184X}, support = {2023YFF1303700//National Key Research and Development Program of China/ ; }, mesh = {*Soil Microbiology ; *Ice Cover/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Rivers/microbiology ; China ; Ecosystem ; Biodiversity ; Soil/chemistry ; RNA, Ribosomal, 16S/genetics ; Microbiota ; }, abstract = {Glaciers retreat rapidly and create newly exposed terrestrial and aquatic habitats in glacier forefields, where primary succession proceeds synchronously in glacier forefields. Here, we introduced the "Dual-Domain Primary Succession" concept to examine the parallel yet distinct primary succession processes in soil and stream ecosystems within glacier forefields, by focusing on Hailuogou Glacier and Urumqi Glacier No.1 in China. Findings showed that soil bacterial communities exhibited higher α-diversity with a decreasing pattern in Hailuogou Glacier, in contrast to Urumqi Glacier No.1, which displayed lower and unimodally distributed α-diversity along the glacier forefield chronosequence (GFC). A similar pattern emerged in streams, except for an increasing α-diversity trend in Urumqi Glacier No.1 stream along the GFC. Additionally, α-diversity in streams changed more rapidly than in soils for Hailuogou Glacier, but more slowly for Urumqi Glacier No.1. Along GFC, both soil and stream bacterial communities experienced spatial variations, primarily due to species turnover. The succession of community composition was evident at the OTU level, with each module in the co-occurrence network consisting of OTUs enriched at specific successional stages. A substantial number of OTUs shared between paired soil and stream samples showed a decreasing trend along the GFC, while β-diversity increased. The results suggested that bacterial communities have a similar succession pattern but in different pace between soil and stream while having distinct successional trajectories between the studied glaciers. This study highlighted the "Dual-Domain Primary Succession" in glacier forefields, but further studies with more glaciers are necessary to make broader generalizations.}, }
@article {pmid39953673, year = {2025}, author = {Kotsakis, GA and Ganesan, SM}, title = {Microbial Dysbiosis, Titanium Release, and Peri-implantitis.}, journal = {Journal of dental research}, volume = {104}, number = {5}, pages = {473-480}, pmid = {39953673}, issn = {1544-0591}, support = {R01 DE031746/DE/NIDCR NIH HHS/United States ; }, mesh = {Humans ; *Peri-Implantitis/microbiology/immunology/etiology ; *Dysbiosis/microbiology/immunology ; *Titanium/adverse effects ; *Dental Implants/adverse effects/microbiology ; Microbiota ; }, abstract = {The peri-implant mucosal barrier is a unique microenvironment where host-microbiome interactions take place on the surface of an implanted biomaterial. Therefore, peri-implant immunity not only is quintessential to oral health but also contributes to the maintenance of the biomaterial-tissue equilibrium in health. This review delves into the intricate interplay between host factors, biomaterial properties, and the microbiome with a focus on the mechanisms underlying peri-implant dysbiosis. Investigations into this complex milieu have led to the emerging understanding of titanium particles released from the implant as significant exposomes. When biomaterial breakdown occurs, implant degradation products form particles that are released in the peri-implant crevice, exerting profound effects on the local immune surveillance. Comparative analyses with natural dentition highlight the distinct immune responses elicited by titanium particles, thereby implicating them as a key modulator of peri-implant dysbiosis that differentiates peri-implant from periodontal inflammation. Nonetheless, disruptions in the homeostatic balance of host-biomaterial interactions are linked to pathogenic shifts of the peri-implant microbiome that are correlated with titanium particles in humans. Collectively, it is now well established that to elucidate the mechanisms governing peri-implant dysbiosis, this triangle of host-microbiome-biomaterial has to be conjointly investigated. This review highlights findings from studies that have underscored the multifaceted nature of peri-implant dysbiosis, emphasizing the intricate crosstalk between host immunity, biomaterial characteristics, and microbial ecology. These findings suggest that the titanium particle exposome may alter key inflammatory cascades in the peri-implant tissues including toll-like receptor activation and inflammasome and complement signaling, which lead to nonresolving destructive inflammation. The presence of abiotic danger signals in the form of implant degradation products in peri-implant tissues may make antimicrobial monotherapies largely ineffective for managing peri-implantitis. In turn, the future of peri-implantitis therapy seems to lie in the development of targeted host modulatory interventions against titanium-mediated inflammatory pathways.}, }
@article {pmid39952886, year = {2025}, author = {Araujo, ASF and Pereira, APA and de Medeiros, EV and Mendes, LW}, title = {Restoring unbalanced rhizosphere: microbiome transplants combatting leaf diseases.}, journal = {Trends in plant science}, volume = {30}, number = {5}, pages = {451-453}, doi = {10.1016/j.tplants.2025.01.011}, pmid = {39952886}, issn = {1878-4372}, mesh = {*Microbiota ; *Plant Diseases/microbiology/prevention &amp; control ; *Plant Leaves/microbiology ; *Rhizosphere ; *Soil Microbiology ; }, abstract = {Similar to humans, plants experience microbiome imbalance, which increases their vulnerability to pathogens. In a recent study, Ketehouli et al. applied a soil microbiome transplant (SMT) to restore the microbiome balance, which potentially reduced the severity of leaf diseases. Here, we examine this approach, highlighting its limitation and offering perspectives on its use for controlling leaf diseases in plants.}, }
@article {pmid39952771, year = {2025}, author = {Cantuti Gendre, J and Le Marrec, C and Chaillou, S and Omhover-Fougy, L and Landaud, S and Dugat-Bony, E}, title = {Exploring viral diversity in fermented vegetables through viral metagenomics.}, journal = {Food microbiology}, volume = {128}, number = {}, pages = {104733}, doi = {10.1016/j.fm.2025.104733}, pmid = {39952771}, issn = {1095-9998}, mesh = {*Vegetables/virology/microbiology ; Metagenomics ; Fermentation ; *Fermented Foods/virology/microbiology ; *Bacteriophages/genetics/classification/isolation &amp; purification ; Bacteria/classification/genetics/isolation &amp; purification ; Brassica/virology/microbiology ; Microbiota ; *Viruses/classification/genetics/isolation &amp; purification ; Food Microbiology ; Biodiversity ; RNA Viruses/genetics/classification/isolation &amp; purification ; Virome ; DNA Viruses/genetics/classification/isolation &amp; purification ; Daucus carota/virology/microbiology ; }, abstract = {Fermented vegetables are traditionally produced using the endogenous microorganisms present in raw ingredients. While the diversity of bacteria and fungi in fermented vegetables has been relatively well studied, phage communities remain largely unexplored. In this study, we collected twelve samples of fermented cabbage, carrot, and turnip after fermentation and analyzed the microbial and viral communities using shotgun and viral metagenomic approaches. Assessment of the viral diversity also benefited from epifluorescence microscopy to estimate viral load. The viral metagenomics approach targeted dsDNA, ssDNA, and RNA viruses. The microbiome of fermented vegetables was dominated by lactic acid bacteria and varied according to the type of vegetable used as raw material. The analysis of metagenome-assembled-genomes allowed the detection of 22 prophages of which 8 were present as free particles and therefore detected in the metaviromes. The viral community, estimated to range from 5.28 to 7.57 log virus-like particles per gram of fermented vegetables depending on the sample, was mainly composed of dsDNA viruses, although ssDNA and non-bacterial RNA viruses, possibly originating from the phyllosphere, were also detected. The dsDNA viral community, primarily comprising bacteriophages, varied depending on the type of vegetable used for fermentation. The bacterial hosts predicted for these phages mainly belonged to Lactobacillaceae and Enterobacteriaceae families. These results highlighted the complex microbial and viral composition of fermented vegetables, which varied depending on the three types of vegetables used as raw material. Further research is needed to deepen our understanding of the impact of these viruses on the microbial ecology of fermented vegetables and on the quality of the final products.}, }
@article {pmid39952743, year = {2025}, author = {Wu, Y and Ma, F and Tan, S and Niu, A and Chen, Y and Liu, Y and Qiu, W and Wang, G}, title = {The aprD-mutated strain modulates the development of Pseudomonas fragi population but has limited effects on the spoilage profiles of native residents.}, journal = {Food microbiology}, volume = {128}, number = {}, pages = {104708}, doi = {10.1016/j.fm.2024.104708}, pmid = {39952743}, issn = {1095-9998}, mesh = {*Bacterial Proteins/genetics/metabolism ; Chickens/microbiology ; Animals ; *Pseudomonas fragi/genetics/growth &amp; development/metabolism ; *Meat/microbiology ; Biofilms/growth &amp; development ; Mutation ; Food Microbiology ; Pseudomonas/genetics ; }, abstract = {Extracellular enzymes produced by predominant bacteria exert important roles in inducing and accelerating spoilage, with their secretion regulated by specific genes. In Pseudomonas fragi, the aprD gene is a recognized regulator for secreting an alkaline extracellular protease. However, limited studies have focused on this gene in P. fragi population and its impact on meat microbial community structure and function. This study addressed this gap by monitoring the changes in biological properties of P. fragi populations and analyzing the discrepancies in spoilage phenotypes and microbial community structures of chilled chicken among groups differentiated by the initial prevalence of aprD-positive strains. The results showed that aprD-positive strains were disseminated in P. fragi populations, and its prevalence was associated with significant increases in swimming motility and biofilm formation capacities in specific groups. In situ contamination experiments revealed varying spoilage characteristics and community compositions among groups by day 3 of storage. Correlation analysis demonstrated a strong association between spoilage phenotypes and certain bacterial genera, such as Pseudomonadaceae_Pseudomonas and Carnobacterium. However, the microbial community structure and spoilage characteristics of samples from each group were not significantly different on the 5th day of storage. These findings suggest that even a small number of aprD mutants can significantly affect the assembly of the chilled meat microbial community. Nonetheless, the regulatory effect of aprD on spoilage at the strain and population levels of P. fragi is negligible in the context of complex natural microbiota. This work underscores the complex interactions between specific bacterial genes and the broader microbial ecology in refrigerated meat environments, providing deeper insights into the meat spoilage mechanisms.}, }
@article {pmid39951503, year = {2025}, author = {Bauermann, J and Benzi, R and Nelson, DR and Shankar, S and Toschi, F}, title = {Turbulent mixing controls fixation of growing antagonistic populations.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {7}, pages = {e2417075122}, pmid = {39951503}, issn = {1091-6490}, mesh = {*Models, Biological ; *Saccharomyces cerevisiae/growth &amp; development/physiology ; Population Dynamics ; *Antibiosis/physiology ; Computer Simulation ; *Bacteria/growth &amp; development ; }, abstract = {Unlike coffee and cream that homogenize when stirred, growing micro-organisms (e.g., bacteria, baker's yeast) can actively kill each other and avoid mixing. How do such antagonistic interactions impact the growth and survival of competing strains, while being spatially advected by turbulent flows? By using numerical simulations of a continuum model, we study the dynamics of two antagonistic strains that are dispersed by incompressible turbulent flows in two spatial dimensions. A key parameter is the ratio of the fluid transport time to that of biological reproduction, which determines the winning organism that ultimately takes over the whole population from an initial heterogeneous state, a process known as fixation. By quantifying the probability and mean time for fixation along with the spatial structure of concentration fluctuations, we demonstrate how turbulence raises the threshold for biological nucleation and antagonism suppresses flow-induced mixing by depleting the population at interfaces. Our work highlights the unusual biological consequences of the interplay of turbulent fluid flows with antagonistic population dynamics, with potential implications for marine microbial ecology and origins of biological chirality.}, }
@article {pmid39950593, year = {2025}, author = {Kiesewetter, KN and Rawstern, AH and Cline, E and Ortiz, GR and Santamaria, F and Coronado-Molina, C and Sklar, FH and Afkhami, ME}, title = {Microbes in reconstructive restoration: Divergence in constructed and natural tree island soil fungi affects tree growth.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {35}, number = {1}, pages = {e70007}, pmid = {39950593}, issn = {1939-5582}, support = {//South Florida Water Management District/ ; 1922521//Division of Environmental Biology/ ; 2030060//Division of Environmental Biology/ ; //National Science Foundation Graduate Research Fellowship Program/ ; //University of Miami Dissertation Year Fellowship/ ; //USDA NIFA Predoctoral Fellowship/ ; }, mesh = {*Soil Microbiology ; *Trees/growth &amp; development/microbiology ; *Fungi/physiology/classification ; *Microbiota ; *Conservation of Natural Resources ; *Environmental Restoration and Remediation ; }, abstract = {As ecosystems face unprecedented change and habitat loss, pursuing comprehensive and resilient habitat restoration will be integral to protecting and maintaining natural areas and the services they provide. Microbiomes offer an important avenue for improving restoration efforts as they are integral to ecosystem health and functioning. Despite microbiomes' importance, unresolved knowledge gaps hinder their inclusion in restoration efforts. Here, we address two critical gaps in understanding microbial roles in restoration-fungal microbiomes' importance in "reconstructive" restoration efforts and how management and restoration decisions interactively impact fungal communities and their cascading effects on trees. We combined field surveys, microbiome sequencing, and greenhouse experiments to determine how reconstructing an iconic landscape feature-tree islands-in the highly imperiled Everglades impacts fungal microbiomes and fungal effects on native tree species compared with their natural counterparts under different proposed hydrological management regimes. Constructed islands used in this research were built from peat soil and limestone collected from deep sloughs and levees nearby the restoration sites in 2003, providing 18 years for microbiome assembly on constructed islands. We found that while fungal microbiomes from natural and constructed tree islands exhibited similar diversity and richness, they differed significantly in community composition. These compositional differences arose mainly from changes to which fungal taxa were present on the islands rather than changes in relative abundances. Surprisingly, ~50% of fungal hub taxa (putative keystone fungi) from natural islands were missing on constructed islands, suggesting that differences in community composition of constructed island could be important for microbiome stability and function. The differences in fungal composition between natural and constructed islands had important consequences for tree growth. Specifically, these compositional differences interacted with hydrological regime (treatments simulating management strategies) to affect woody growth across the four tree species in our experiment. Taken together, our results demonstrate that reconstructing a landscape feature without consideration of microbiomes can result in diverging fungal communities that are likely to interact with management decisions leading to meaningful consequences for foundational primary producers. Our results recommend cooperation between restoration practitioners and ecologists to evaluate opportunities for active management and restoration of microbiomes during future reconstructive restoration.}, }
@article {pmid39945937, year = {2025}, author = {Gharbi, D and Neumann, FH and Staats, J and McDonald, M and Linde, JH and Mmatladi, T and Podile, K and Piketh, S and Burger, R and Garland, RM and Bester, P and Lebre, PH and Ricci, C}, title = {Prevalence of aeroallergen sensitization in a polluted and industrialized area: a pilot study in South Africa's Vaal Triangle.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {3}, pages = {287}, pmid = {39945937}, issn = {1573-2959}, support = {ST-POC-2312-61906//Grand Challenges Canada/ ; ST-POC-2312-61906//South African Medical Research Council/ ; }, mesh = {South Africa/epidemiology ; Humans ; *Allergens/analysis/immunology ; Male ; Adult ; Female ; Pilot Projects ; Adolescent ; Prevalence ; Middle Aged ; Young Adult ; *Air Pollutants/analysis ; *Hypersensitivity/epidemiology ; *Air Pollution/statistics &amp; numerical data ; Pollen ; *Environmental Exposure/statistics &amp; numerical data ; Skin Tests ; }, abstract = {This pioneering study evaluates the prevalence of aeroallergens reactivity among atopic populations living in the Vaal Triangle Airshed Priority Area (VTAPA), South Africa. A total of 138 volunteers (51 males and 87 females), of African, colored, white, and Asian ethnicity, and with a mean (range) age of 22 (18-56) years were participating in the study. The study was conducted on the North-West University (NWU) campus in Vanderbijlpark/VTAPA. The International Study of Asthma and Allergies in Childhood questionnaire was utilized for pre-screening to identify individuals with probable allergic dispositions. Subsequently, skin prick testing was conducted using commercial aeroallergen extracts for all confirmed participants with allergy symptoms. One hundred six participants were clinically diagnosed with pollen and fungal spore allergies. The highest allergy prevalence was attributed to Cynodon dactylon ((L.) Pers) (Bermuda grass) (41.5%), followed by Lolium perenne (L.) (ryegrass), grass mix, and Zea mays (L.) (maize) (31.1%), respectively. Moreover, among the tree allergens, Olea (L.) (olive tree) was the most prevalent allergen (20; 18.8%), followed by Platanus (L.) (plane tree) (18; 16.9%). Among the weeds, 16 (15.1%) participants were allergic to the weed mix (Artemisia (L.) (wormwood), Chenopodium (Link) (goosefoot), Salsola (L.) (saltwort), Plantago (L.) (plantain), and 11 (10.3%) to Ambrosia (L.) (ragweed)). Regarding the fungal spores, Alternaria (Fr.) (9; 8.5%) followed by Cladosporium (Link) (5; 4.7%) had the highest skin sensitivity. In this pilot study, our findings provide insights into the prevalence of allergic responses in the study population-underlining the strong impact of allergens of exotic plants-and contribute to the existing aerobiological data in South Africa.}, }
@article {pmid39945839, year = {2025}, author = {Márquez-Sanz, R and Garrido-Benavent, I and Durán, J and de Los Ríos, A}, title = {The Establishment of a Terrestrial Macroalga Canopy Impacts Microbial Soil Communities in Antarctica.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {4}, pmid = {39945839}, issn = {1432-184X}, support = {PID2019-105469RB-C22//AEI, MICINN/ ; TED2021-130908A-C43//Agencia Estatal de Investigaci&#xf3;n/ ; CNS2023-145367//EU Next Generation PRTR program/ ; PCI2023-143393//EIG EU-CELAC 2022/ ; 20224AT022//Consejo Superior de Investigaciones Cient&#xed;ficas/ ; RYC2020-029331-I//Ministerio de Ciencia e Innovaci&#xf3;n/ ; }, mesh = {Antarctic Regions ; *Soil Microbiology ; *Fungi/classification/genetics/isolation &amp; purification ; Soil/chemistry ; *Bacteria/classification/genetics/isolation &amp; purification ; Phylogeny ; *Chlorophyta/growth &amp; development/physiology/classification ; *Microbiota ; Nitrogen/analysis ; Ecosystem ; }, abstract = {Prasiola is a genus of foliose green algae that forms extensive cryptogamic canopies that contribute to the greening of ice-free areas in the Antarctic tundra. To better understand the impact of Prasiola canopy establishment on colonization in these areas, this study compared the taxonomic and functional structures of bacterial and fungal communities in adjacent soils with and without extensive Prasiola colonization. DNA metabarcoding was employed to analyze the microbial community structure in these soils and in the canopy. Additionally, a phylogenetic study of Prasiola samples was conducted to characterize the taxonomic composition of the analyzed canopies, revealing the presence of Prasiola crispa (Lightfoot) Kützing and P. antarctica Kützing. Key soil attributes were assessed to examine the canopy's influence. Higher pH and carbon, nitrogen, and organic matter contents were found in Prasiola-covered soils than in bare soils. Furthermore, Prasiola canopy establishment not only influenced abiotic soil properties but also shaped soil microbial community structure and its functions. For instance, while Actinobacteriota predominated in bacterial communities both within the Prasiola canopy and beneath it, Bacteroidota dominated in the bare soil. Despite significant variability across soil types, fungal communities showed a trend of higher abundances in certain Ascomycetes, such as Helotiales, Hypocreales, or Xylariales, in soils beneath Prasiola compared to bare soils. Regarding functional diversity, covered soils exhibited a statistically significant lower potential for bacterial methanogenesis and autotrophic CO2 fixation compared to bare soils. Finally, lichenized fungi, plant pathogens, and fungal wood saprotrophs tended to be more abundant in covered soils.}, }
@article {pmid39943131, year = {2025}, author = {Frazier, AN and Ferree, L and Belk, AD and Al-Lakhen, K and Cramer, MC and Metcalf, JL}, title = {Stochasticity Highlights the Development of Both the Gastrointestinal and Upper-Respiratory-Tract Microbiomes of Neonatal Dairy Calves in Early Life.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {3}, pages = {}, pmid = {39943131}, issn = {2076-2615}, abstract = {The microbiome of dairy calves undergoes extensive change due to various forces during the first weeks of life. Importantly, diseases such as bovine respiratory disease (BRD) and calf diarrhea can have profound impacts on the early-life microbiome. Therefore, a longitudinal, repeated-measures pilot study was designed to characterize the establishment of nasal and fecal microbiomes of dairy calves, assess the governing forces of microbial assembly, and evaluate how disease states impact these microbial ecologies. Dairy calves (n = 19) were clinically evaluated for gastrointestinal and respiratory disease across three weeks beginning at age ≤ seven days old. Fecal (n = 57) and nasal (n = 57) microbial samples were taken for paired-end 16S rRNA gene amplicon sequencing. Taxonomy and diversity analyses were used to characterize early-life nasal and fecal microbiomes. Stochasticity and determinism were measured using normalized stochasticity testing (NST) and Dirichlet multinomial model (DMM). All analyses were tested for statistical significance. Clinical diarrhea was observed in 11 of the 19 calves. Clinical BRD was not independently observed among the cohort; however, two calves presented clinical signs of both BRD and diarrhea. Taxonomic analysis revealed that fecal samples were highlighted by Bacteroidaceae (40%; relative abundance), Ruminococcaceae (13%), and Lachnospiraceae (10%), with changes in diversity (Kruskal-Wallis; p < 0.05) and composition (PERMANOVA; p < 0.05). Clinical diarrhea reduced diversity in the fecal microbiome but did not impact composition. Nasal samples featured Moraxellaceae (49%), Mycoplasmataceae (16%), and Pasteurellaceae (3%). While no diversity changes were seen in nasal samples, compositional changes were observed (p < 0.05). NST metrics (Kruskal-Wallis; p > 0.01) and DMM (PERMANOVA; p < 0.01) revealed that stochastic, neutral theory-based assembly dynamics govern early-life microbial composition and that distinct microbial populations drive community composition in healthy and diarrheic calves.}, }
@article {pmid39942291, year = {2025}, author = {Santás-Miguel, V and Lalín-Pousa, V and Conde-Cid, M and Rodríguez-Seijo, A and Pérez-Rodríguez, P}, title = {Use of Biopowders as Adsorbents of Potentially Toxic Elements Present in Aqueous Solutions.}, journal = {Materials (Basel, Switzerland)}, volume = {18}, number = {3}, pages = {}, pmid = {39942291}, issn = {1996-1944}, support = {ED481D-2021/016//Conseller&#xed;a de Cultura, Educaci&#xf3;n e Universidade (Xunta de Galicia)/ ; IJC2020-044197-I//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; IJC2020-044426-I//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; 101112754//MRV4SOC project/ ; ED481B-2022-081//Xunta de Galicia/ ; }, abstract = {This study examines the adsorption and desorption behaviors of phosphorus (P), arsenic (As), fluoride (F), and chromium (Cr) in aqueous solutions on green materials such as cork bark (CB) and pine bark (PB). These materials are characterized by active functional groups and net negative charges on their surfaces and porous structures. The evaluation considers variations in contaminant concentrations (0.01-10 mM) and pH (3.5-12). Cork bark exhibited higher adsorption capacity for As and F, while PB was more effective for P and Cr. Adsorption isotherms followed the Freundlich and Langmuir models, indicating surface heterogeneity and multilayer adsorption for most potentially toxic elements (PTEs). Desorption tests demonstrated low rates, with CB retaining up to 99% of F and 85% of As, and PB achieving up to 86% retention for Cr and 70% for P. The influence of pH was minimal for As, P, and F, but acidic conditions significantly enhanced Cr adsorption, showing similar behavior for both biopowders. These findings suggest that CB and PB biopowders are promising, environmentally friendly biosorbents for the removal of PTEs from aqueous solutions. Their effectiveness varies depending on the specific contaminant. This study highlights the potential of these natural materials for sustainable applications in water treatment and soil remediation.}, }
@article {pmid39942061, year = {2025}, author = {Di Biase, M and Scicchitano, D and Valerio, F and Lonigro, SL and Cifarelli, V and Ostante, G and D'Antuono, I and Candela, M and Ferrara, M}, title = {Microbial Ecology and Nutritional Features in Liquid Sourdough Containing Hemp Flour Fermented by Lactic Acid Bacterial Strains.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {3}, pages = {}, pmid = {39942061}, issn = {2304-8158}, support = {MicroBHE Project//IBISBA - IT/ ; DAB.AD005.225//FOE - 2021/ ; }, abstract = {Hemp seed flour (Cannabis sativa) is a non-traditional matrix alternative to wheat for baked goods production. The aim of this study was to investigate the microbiota of two liquid sourdoughs (SLs) based on hemp or a wheat-hemp mixture, before and after spontaneous or piloted fermentation (Lactiplantibacillus plantarum ITM21B or Weissella cibaria C43-11 used as starters). Culture-dependent and -independent (high-throughput sequencing of bacterial phylogenetic V3-V4 regions of the 16S rRNA gene) methods, were used to evaluate the microbial community. The effect of fermentation on the content of bioactive molecules (polyphenols, organic acids, proteins, and amino acids) was also investigated. Results indicated that the microbial community of all SLs was mainly (99.7 ÷ 100%) composed of Firmicutes and Proteobacteria, and the latter was the unique phylum before fermentation in formulations produced exclusively with hemp flour. Two PCoA plots (Test adonis with pseudo-F ratio, p > 0.05) showed no significance difference between the microbial communities of the formulations. However, the relative abundance variation at the family level in the wheat-hemp-based mixture SLs showed a significant enrichment of the Lactobacillaceae family (Kruskal-Wallis test, p = 0.04). Moreover, results confirmed hemp seed flour as a suitable fermentation substrate to obtain microbial consortia allowing for an increase in organic acids, especially lactic acid (9.12 ± 1.22 and 7.45 ± 0.75 mmol/kg with Lpb. plantarum and W. cibaria, respectively), in both piloted fermentations, and in polyphenols by 21% and amino acids by 158% in SL fermented by the C43-11 strain.}, }
@article {pmid39937305, year = {2025}, author = {Argentino, ICV and Godoy, MG and Seldin, L and Jurelevicius, D}, title = {Distribution of Bacillota in Water and Sediments from Aquatic Environments.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {3}, pmid = {39937305}, issn = {1432-184X}, mesh = {*Geologic Sediments/microbiology ; RNA, Ribosomal, 16S/genetics ; Brazil ; Microbiota ; Phylogeny ; *Water Microbiology ; *Seawater/microbiology ; *Fresh Water/microbiology ; DNA, Bacterial/genetics ; Biodiversity ; }, abstract = {The phylum Bacillota comprises metabolically diverse bacteria with potential relevance in several fields. Although some genera, such as Bacillus and others, have been extensively studied, the distribution of Bacillota in the environment is still poorly understood. This study aimed to analyze the distribution of Bacillota present in water and sediment samples from different environments. For this purpose, water (W) and sediment (S) samples were collected from different marine environments (Dois Rios Beach - DR, Abraão Beach - AB, Massambaba Beach - MB, and Guanabara Bay - GB), freshwater lagoons (Jacarepiá Lagoon- JL) and hypersaline lagoons (Vermelha Lagoon - VL), all of which are located in Rio de Janeiro, Brazil. The microbial communities present in each sample were determined by sequencing 16S rRNA-encoding genes. The distribution and diversity of Bacillota were analyzed via QIIME2. The results revealed that Bacillota represented an average of 1% of the microbial community of aquatic microbiomes and were unevenly distributed in aquatic water and sediment. The highest abundances of Bacillota were detected in JL_S and VL_S, and the lowest abundances were observed in MB_W and AB_W. Only sequences related to the Bacilli and Clostridia classes were identified. The main Bacillota genera identified were Bacillus and an unidentified Clostridiales order genus. The VL_S and JL_S samples had the highest numbers of exclusive Bacillota genera. On the other hand, 15 Bacillota genera, which are generally observed in the human and animal guts, were found only in anthropogenically impacted GB_W and AB_W. The obtained results revealed how Bacillota are distributed in different aquatic environments.}, }
@article {pmid39936183, year = {2025}, author = {Brait, N and Hackl, T and Lequime, S}, title = {detectEVE: Fast, Sensitive and Precise Detection of Endogenous Viral Elements in Genomic Data.}, journal = {Molecular ecology resources}, volume = {25}, number = {4}, pages = {e14083}, pmid = {39936183}, issn = {1755-0998}, mesh = {*Computational Biology/methods ; *Genomics/methods ; *Software ; Genome, Viral ; *Viruses/genetics ; Sensitivity and Specificity ; }, abstract = {Endogenous viral elements (EVEs) are fragments of viral genomic material embedded within the host genome. Retroviruses contribute to the majority of EVEs because of their genomic integration during their life cycle; however, the latter can also arise from non-retroviral RNA or DNA viruses, then collectively known as non-retroviral (nr) EVEs. Detecting nrEVEs poses challenges because of their sequence and genomic structural diversity, contributing to the scarcity of specific tools designed for nrEVEs detection. Here, we introduce detectEVE, a user-friendly and open-source tool designed for the accurate identification of nrEVEs in genomic assemblies. detectEVE deviates from other nrEVE detection pipelines, which usually classify sequences in a more rigid manner as either virus-associated or not. Instead, we implemented a scaling system assigning confidence scores to hits in protein sequence similarity searches, using bit score distributions and search hints related to various viral characteristics, allowing for higher sensitivity and specificity. Our benchmarking shows that detectEVE is computationally efficient and accurate, as well as considerably faster than existing approaches, because of its resource-efficient parallel execution. Our tool can help to fill current gaps in both host-associated fields and virus-related studies. This includes (i) enhancing genome annotations with metadata for EVE loci, (ii) conducting large-scale paleo-virological studies to explore deep viral evolutionary histories, and (iii) aiding in the identification of actively expressed EVEs in transcriptomic data, reducing the risk of misinterpretations between exogenous viruses and EVEs.}, }
@article {pmid39935057, year = {2025}, author = {Ruiz-Ruiz, P and Mohedano-Caballero, P and De Vrieze, J}, title = {Ectoine production through a marine methanotroph-microalgae culture allows complete biogas valorization.}, journal = {Journal of environmental management}, volume = {375}, number = {}, pages = {124223}, doi = {10.1016/j.jenvman.2025.124223}, pmid = {39935057}, issn = {1095-8630}, mesh = {*Biofuels ; *Microalgae/metabolism ; Methane/metabolism ; *Amino Acids, Diamino/metabolism ; Carbon Dioxide/metabolism ; }, abstract = {Methanotrophs have recently emerged as a promising platform for producing bio-based chemicals, like ectoine, from biogas, offering an economical alternative to glucose. However, most studies have focused solely on CH4 consumption, often overlooking the CO2, which is both produced by methanotrophs and present in biogas, despite its potential as a carbon source for microorganisms, such as microalgae. In this study, marine methanotrophic-microalgal cultures were enriched from environmental samples collected at the North Sea coast to explore ectoine production from both CH4 and CO2 in biogas. The sediment-derived culture exhibited the highest CH4 removal efficiency and CO2 uptake, and was selected for further experiments. The culture was primarily composed of Methylobacter marinus, Methylophaga marina, and the microalga Picochlorum oklahomensis. Gas consumption, growth, and ectoine production were evaluated under varying salinity levels and osmotic stress. The NaCl concentrations above 6% negatively impacted CH4 oxidation and inhibited ectoine synthesis, while osmotic shocks enhanced ectoine accumulation, with a maximum ectoine content of 51.3 mgectoine gVSS[-1] at 4.5% NaCl. This study is the first to report ectoine production from methanotroph-microalgal cultures, showing its potential for biogas valorization into high-value bio-based chemicals, like ectoine, marking a significant step toward sustainable biogas utilization.}, }
@article {pmid39934529, year = {2025}, author = {Roy, R and Das, A and Ganguly, D and Chakraborty, P and Paul, P and Das, S and Maity, A and Malik, M and Tribedi, P}, title = {Cuminaldehyde synergistically enhances the antimicrobial and antibiofilm potential of gentamicin: A direction towards an effective combination for the control of biofilm-linked threats of Staphylococcus aureus.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {56}, number = {2}, pages = {1033-1048}, pmid = {39934529}, issn = {1678-4405}, support = {TNU/R&amp;D/M/11//The Neotia University/ ; }, mesh = {*Biofilms/drug effects ; *Gentamicins/pharmacology ; *Staphylococcus aureus/drug effects/physiology ; *Anti-Bacterial Agents/pharmacology ; Drug Synergism ; Microbial Sensitivity Tests ; Humans ; Staphylococcal Infections/microbiology/drug therapy ; *Benzaldehydes/pharmacology ; Reactive Oxygen Species/metabolism ; }, abstract = {Staphylococcus aureus, a Gram-positive, coccus-shaped bacterium often causes several infections on human hosts by exploiting biofilm. This current work investigates a potential strategy to manage the threats of biofilm-linked infections by embracing a combinatorial approach involving cuminaldehyde (phytochemical) and gentamicin (antibiotic). Despite showing antimicrobial properties individually, cuminaldehyde and gentamicin could exhibit enhanced antimicrobial potential when used together against S. aureus. The fractional inhibitory concentration index (FICI = 0.36) suggested that the selected compounds (cuminaldehyde and gentamicin) offered synergistic interaction while showing antimicrobial potential against the same organism. A series of experiments indicated that the selected compounds (cuminaldehyde and gentamicin) showed substantial antibiofilm potential against S. aureus when combined. The increased antibiofilm potential was linked to the accumulation of reactive oxygen species (ROS) and increased cell membrane permeability. Additionally, the combination of the selected compounds (cuminaldehyde and gentamicin) also impeded the cell surface hydrophobicity of S. aureus, aiding in the prevention of biofilm formation. The present study also showed that combining the mentioned compounds (cuminaldehyde and gentamicin) notably reduced the secretion of several virulence factors from S. aureus. Furthermore, the current research showed that these compounds (cuminaldehyde and gentamicin) could also exhibit antibiofilm potential against the clinical strains of Methicillin-Resistant S. aureus (MRSA). Taken together, this innovative approach not only enhances the potential of existing standard antibiotics but also opens up new therapeutic possibilities for combating biofilm-related infections.}, }
@article {pmid39933594, year = {2025}, author = {Verdon, N and Popescu, O and Titmuss, S and Allen, RJ}, title = {Habitat fragmentation enhances microbial collective defence.}, journal = {Journal of the Royal Society, Interface}, volume = {22}, number = {223}, pages = {20240611}, pmid = {39933594}, issn = {1742-5662}, support = {//Deutsche Forschungsgemeinschaft/ ; //H2020 European Research Council/ ; //Engineering and Physical Sciences Research Council/ ; }, mesh = {*Ecosystem ; *Models, Biological ; *Bacteria ; }, abstract = {Microbes often inhabit complex, spatially partitioned environments such as host tissue or soil, but the effects of habitat fragmentation on microbial ecology and infection dynamics are poorly understood. Here, we investigate how habitat fragmentation impacts a prevalent microbial collective defence mechanism: enzymatic degradation of an environmental toxin. Using a theoretical model, we predict that habitat fragmentation can strongly enhance the collective benefits of enzymatic toxin degradation. For the example of [Formula: see text]-lactamase-producing bacteria that mount a collective defence by degrading a [Formula: see text]-lactam antibiotic, we find that realistic levels of habitat fragmentation can allow a population to survive antibiotic doses that greatly exceed those required to kill a non-fragmented population. This 'habitat-fragmentation rescue' is a stochastic effect that originates from variation in bacterial density among different subpopulations and demographic noise. We also study the contrasting case of collective enzymatic foraging, where enzyme activity releases nutrients from the environment; here we find that increasing habitat fragmentation decreases the lag time for population growth but does not change the ecological outcome. Taken together, this work predicts that stochastic effects arising from habitat fragmentation can greatly enhance the effectiveness of microbial collective defence via enzymatic toxin degradation.}, }
@article {pmid39928396, year = {2025}, author = {Nakajima, M and Nakai, R and Hirakata, Y and Kubota, K and Satoh, H and Nobu, MK and Narihiro, T and Kuroda, K}, title = {Minisyncoccus archaeiphilus gen. nov., sp. nov., a mesophilic, obligate parasitic bacterium and proposal of Minisyncoccaceae fam. nov., Minisyncoccales ord. nov., Minisyncoccia class. nov. and Minisyncoccota phyl. nov. formerly referred to as Candidatus Patescibacteria or candidate phyla radiation.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {75}, number = {2}, pages = {}, pmid = {39928396}, issn = {1466-5034}, mesh = {*Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Bacterial Typing Techniques ; DNA, Bacterial/genetics ; Base Composition ; Methanospirillum/growth &amp; development ; Symbiosis ; DNA, Archaeal/genetics ; Fatty Acids/chemistry/analysis ; }, abstract = {In the domain Bacteria, one of the largest, most diverse and environmentally ubiquitous phylogenetic groups, Candidatus Patescibacteria (also known as candidate phyla radiation/CPR), remains poorly characterized, leaving a major knowledge gap in microbial ecology. We recently discovered a novel cross-domain symbiosis between Ca. Patescibacteria and Archaea in highly purified enrichment cultures and proposed Candidatus taxa for the characterized species, including Ca. Minisyncoccus archaeophilus and the corresponding family Ca. Minisyncoccaceae. In this study, we report the isolation of this bacterium, designated strain PMX.108[T], in a two-strain co-culture with a host archaeon, Methanospirillum hungatei strain DSM 864[T] (JF-1[T]), and hereby describe it as the first representative species of Ca. Patescibacteria. Strain PMX.108[T] was isolated from mesophilic methanogenic sludge in an anaerobic laboratory-scale bioreactor treating synthetic purified terephthalate- and dimethyl terephthalate-manufacturing wastewater. The strain could not grow axenically and is obligately anaerobic and parasitic, strictly depending on M. hungatei as a host. The genome was comparatively large (1.54 Mbp) compared to other members of the clade, lacked some genes involved in the biosynthesis pathway and encoded type IV pili-related genes associated with the parasitic lifestyle of ultrasmall microbes. The G+C content of the genomic DNA was 36.6 mol%. Here, we report the phenotypic and genomic properties of strain PMX.108[T]; we propose Minisyncoccus archaeiphilus gen. nov., sp. nov. to accommodate this strain. The type strain of the species is PMX.108[T] (=JCM 39522[T]). We also propose the associated family, order, class and phylum as Minisyncoccaceae fam. nov. Minisyncoccales nov., Minisyncoccia class. nov. and Minisyncoccota phyl. nov. within the bacterial kingdom Bacillati.}, }
@article {pmid39924526, year = {2025}, author = {Díez López, C and Van Herreweghen, F and De Pessemier, B and Minnebo, Y and Taelman, S and Judge, K and Ransley, K and Hammond, C and Batson, M and Stock, M and Van Criekinge, W and Van de Wiele, T and Macmaster, A and Callewaert, C}, title = {Unravelling the hidden side of laundry: malodour, microbiome and pathogenome.}, journal = {BMC biology}, volume = {23}, number = {1}, pages = {40}, pmid = {39924526}, issn = {1741-7007}, support = {HBC.2020.2292//Agentschap Innoveren en Ondernemen/ ; FWO19/PSD/084//Fonds Wetenschappelijk Onderzoek/ ; }, mesh = {*Microbiota ; *Odorants/analysis ; Volatile Organic Compounds/analysis ; Humans ; *Clothing ; *Laundering ; Skin/microbiology ; Bacteria/genetics ; }, abstract = {BACKGROUND: Recent trends towards lower washing temperatures and a reduction in the use of bleaching agents in laundry undoubtedly benefit our environment. However, these conditions impair microbial removal on clothes, leading to malodour generation and negative impacts on consumer well-being. Clothing undergoes cycles of wearing, washing and drying, with variable exposure to microorganisms and volatilomes originating from the skin, washing machine, water and laundry products. Laundry malodour is therefore a complex problem that reflects its dynamic ecosystem. To date, comprehensive investigations that encompass the evaluation of both microbial community and malodorous volatile organic compounds throughout all stages of the wash-wear-dry cycle are scarce. Furthermore, the microbial and malodour profiles associated with extended humid-drying conditions are poorly defined.<br><br>RESULTS: Here we present olfaction-directed chemical and microbiological studies of synthetic T-shirts after wearing, washing and drying. Results show that although washing reduces the occurrence of known malodour volatile organic compounds, membrane-intact bacterial load on clothing is increased. Skin commensals are displaced by washing machine microbiomes, and for the first time, we show that this shift is accompanied by an altered pathogenomic profile, with many genes involved in biofilm build-up. We additionally highlight that humid-drying conditions are associated with characteristic malodours and favour the growth of specific Gram-negative bacteria.<br><br>CONCLUSIONS: These findings have important implications for the development of next-generation laundry products that enhance consumer well-being, while supporting environmentally friendly laundry practices.}, }
@article {pmid39915510, year = {2025}, author = {Rabbani, G and Afiq-Rosli, L and Lee, JN and Waheed, Z and Wainwright, BJ}, title = {Effects of life history strategy on the diversity and composition of the coral holobiont communities of Sabah, Malaysia.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {4459}, pmid = {39915510}, issn = {2045-2322}, mesh = {Animals ; *Anthozoa/microbiology/physiology ; Malaysia ; *Microbiota ; Biodiversity ; Symbiosis ; Coral Reefs ; Bacteria/genetics/classification ; Climate Change ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Coral-associated microbes have essential roles in promoting and regulating host function and health. As climate change advances and other environmental perturbations increasingly impact corals, it is becoming ever more important that we understand the composition of the microbial communities hosted. Without this baseline it is impossible to assess the magnitude and direction of any future changes in microbial community structure. Here, we characterised both the bacterial and Symbiodiniaceae communities in four coral species (Diploastrea heliopora, Porites lutea, Pachyseris speciosa, and Pocillopora acuta) collected from Sabah, Malaysia. Our findings reveal distinct microbial communities associated with different coral species tending to reflect the varied life history strategies of their hosts. Microbial communities could be differentiated by collection site, with shifts in Symbiodiniaceae communities towards more stress tolerant types seen in samples collected on the shallow Sunda Shelf. Additionally, we identified a core microbiome within species and a more discrete core between all species. We show bacterial and Symbiodiniaceae communities are structured by host species and appear to be influenced by host life history characteristics. Furthermore, we identified a core microbiome for each species finding that several amplicon sequence variants were shared between hosts, this suggests a key role in coral health regardless of species identity. Given the paucity of work performed in megadiverse regions such as the Coral Triangle, this research takes on increased importance in our efforts to understand how the coral holobiont functions and how it could be altered as climate change advances.}, }
@article {pmid39914458, year = {2025}, author = {Wenger, A and Bakkeren, E and Granato, E and Tecon, R and Mitri, S and Möbius, W}, title = {MEEhubs2024: A hub-based conference on microbial ecology and evolution fostering sustainability.}, journal = {FEMS microbiology letters}, volume = {372}, number = {}, pages = {}, pmid = {39914458}, issn = {1574-6968}, support = {51NF40_180575/SNSF_/Swiss National Science Foundation/Switzerland ; BB/V004328/1//BBSRC/ ; 51NF40_180575//NCCR Microbiomes/ ; }, mesh = {*Congresses as Topic ; Humans ; *Ecology ; *Biological Evolution ; *Microbiology ; Europe ; }, abstract = {Scientific conferences are essential to academic exchange. However, related air travel contributes to greenhouse gas emissions, while expensive registration and travel costs limit the participation of early career researchers and those from low-income countries. Virtual conferences offer promising solutions for reducing emissions and enhancing accessibility and inclusivity but often limit networking and personal interaction. Hybrid multi-hub conferences, which combine virtually connected in-person venues with individual virtual participation, combine the benefits of both conference formats. Thus, we present and discuss MEEhubs2024, a multi-hub conference on microbial ecology and evolution held in January 2024. During this 3-day conference, attendees participated virtually or at one of six hubs in Europe and North America. We analyzed the participants' and organizers' feedback to create a template and provide insights into the scientific community's adoption of this new conference format, which was positively evaluated by most participants. Because technical, logistical, and structural challenges remain, including limited opportunities to interact and network across hubs and participation modes, we provide recommendations for improvement, such as hiring technical hosts and offering virtual-only social activities. Finally, we used the participants' feedback to reflect on conference expectations, highlighting research gaps and the need for organizers to define and communicate goals when organizing conferences.}, }
@article {pmid39914213, year = {2025}, author = {Ma, R and Huang, Z and Jiang, Y and Zhao, A and Yu, G and Lin, C and Zhu, L and Zhang, X and Li, X and Wang, C}, title = {Regulation of ethanol production from anaerobic fermentation of food waste using aromatic alcohol-based quorum-sensing molecules.}, journal = {Journal of environmental management}, volume = {376}, number = {}, pages = {124382}, doi = {10.1016/j.jenvman.2025.124382}, pmid = {39914213}, issn = {1095-8630}, mesh = {Fermentation ; *Quorum Sensing ; *Ethanol/metabolism ; Anaerobiosis ; Phenylethyl Alcohol/analogs &amp; derivatives ; Food Loss and Waste ; }, abstract = {Quorum-sensing molecules (QSMs) are used to regulate microbial metabolites to effectively improve food waste anaerobic fermentation to produce high-value products of ethanol and lactic acid. In this study, low concentrations (25 and 50 μmol/L) of aromatic alcohol favored the synthesis of ethanol and lactic products. Among the aromatic alcohol QSMs, 50 μmol/L of tyrosol enhanced the yield of products. The correlations between substrate composition indicators confirmed that tyrosol was conducive to the anaerobic fermentation of food waste. The regulation mechanism of tyrosol, such as microbial diversity in anaerobic fermentation, was analyzed from the perspective of microbial ecology. The result revealed that tyrosol increased the microbial diversity in the system. Limosilactobacillus, Weissella, and Pediococcus were the dominant bacterial species in the early stages of fermentation, whereas Clostridiaceae and Bacillus were dominant in the later stages. Meanwhile, the main dominant fungal species were Saccharomyces, Aspergillus, and Pichia. The results of this study show that using QSMs, including tyrosol, to regulate the physiological characteristics of anaerobic fermentation microorganisms, promote the synthesis of cell metabolites, and regulate the diversity and succession of microbial communities is a feasible measure. This approach improves the resource utilization efficiency of anaerobic fermentation technology for food waste, which is significant for promoting sustainable development.}, }
@article {pmid39913585, year = {2025}, author = {Pertierra, LR and Convey, P and Barbosa, A and Biersma, EM and Cowan, D and Diniz-Filho, JAF and de Los Ríos, A and Escribano-Álvarez, P and Fraser, CI and Fontaneto, D and Greve, M and Griffiths, HJ and Harris, M and Hughes, KA and Lynch, HJ and Ladle, RJ and Liu, XP and le Roux, PC and Majewska, R and Molina-Montenegro, MA and Peck, LS and Quesada, A and Ronquillo, C and Ropert-Coudert, Y and Sancho, LG and Terauds, A and Varliero, G and Vianna, JA and Wilmotte, A and Chown, SL and Olalla-Tárraga, M&#xc1; and Hortal, J}, title = {Advances and shortfalls in knowledge of Antarctic terrestrial and freshwater biodiversity.}, journal = {Science (New York, N.Y.)}, volume = {387}, number = {6734}, pages = {609-615}, doi = {10.1126/science.adk2118}, pmid = {39913585}, issn = {1095-9203}, mesh = {Antarctic Regions ; *Biodiversity ; Animals ; *Fresh Water ; Invertebrates/physiology ; Vertebrates ; }, abstract = {Antarctica harbors many distinctive features of life, yet much about the diversity and functioning of Antarctica's life remains unknown. Evolutionary histories and functional ecology are well understood only for vertebrates, whereas research on invertebrates is largely limited to species descriptions and some studies on environmental tolerances. Knowledge on Antarctic vegetation cover showcases the challenges of characterizing population trends for most groups. Recent community-level microbial studies have provided insights into the functioning of life at its limits. Overall, biotic interactions remain largely unknown across all groups, restricted to basic information on trophic level placement. Insufficient knowledge of many groups limits the understanding of ecological processes on the continent. Remedies for the current situation rely on identifying the caveats of each ecological discipline and finding targeted solutions. Such precise delimitation of knowledge gaps will enable a more aware, representative, and strategic systematic conservation planning of Antarctica.}, }
@article {pmid39912641, year = {2025}, author = {Hamovit, N and RoyChowdhury, T and Akob, DM and Zhang, X and McCarty, G and Yarwood, S}, title = {Comparative assessment of a restored and natural wetland using [13]C-DNA SIP reveals a higher potential for methane production in the restored wetland.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {3}, pages = {e0216124}, pmid = {39912641}, issn = {1098-5336}, support = {2017-67003-26484//U.S. Department of Agriculture (USDA)/ ; }, mesh = {*Wetlands ; *Methane/metabolism ; *Soil Microbiology ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics/analysis ; Carbon Isotopes/analysis ; *Archaea/metabolism/genetics/classification ; Oxidation-Reduction ; Maryland ; Microbiota ; }, abstract = {Wetlands are the largest natural source of methane (CH4), a potent greenhouse gas produced by methanogens. Methanogenesis rates are controlled by environmental factors such as redox potential, temperature, and carbon and electron acceptor availability and are presumably dependent on the composition of the active methanogen community. We collected intact soil cores from a restored and natural freshwater depressional wetland on Maryland's Delmarva Peninsula (USA) to assess the effects of wetland restoration and redox shifts on microbial processes. Intact soil cores were incubated under either saturated (anoxic) or unsaturated (oxic) conditions and amended with [13]C-acetate for quantitative stable isotope probing (qSIP) of the 16S rRNA gene. Restored wetland cores supported a distinct community of methanogens compared to natural cores, and acetoclastic methanogens putatively identified in the genus Methanosarcina were among the most abundant taxa in restored anoxic and oxic cores. The active microbial communities in the restored wetland cores were also distinguished by the unique presence of facultatively anaerobic bacteria belonging to the orders Firmicutes and Bacteroidetes. In natural wetland incubations, methanogen populations were not among the most abundant taxa, and these communities were instead distinguished by the unique presence of aerobic bacteria in the phyla Acidobacteria, Actinobacteria, and class Alphaproteobacteria. Iron-reducing bacteria, in the genus Geobacter, were active across all redox conditions in both the restored and the natural cores, except the natural oxic-anoxic condition. These findings suggest an overall higher potential for methanogenesis in the restored wetland site compared to the natural wetland site, even when there is evidence of Fe reduction.IMPORTANCEMethane (CH4) is a potent greenhouse gas with an atmospheric half-life of ~10 years. Wetlands are the largest natural emitters of CH4, but CH4 dynamics are difficult to constrain due to high spatial and temporal variability. In the past, wetlands were drained for agriculture. Now, restoration is an important strategy to increase these ecosystems' potential for sequestering carbon. However, the consequences of wetland restoration on carbon biogeochemistry are under-evaluated, and a thorough assessment of the active microbial community as a driver of biogeochemical changes is needed. Particularly, the effects of seasonal flooding/drying cycles in geographically isolated wetlands might have implications for CH4 emissions in both natural and restored wetlands. Here, we found that active microbial communities in natural and restored wetlands responded differently to flooding and drying regimes, resulting in differences in CH4 production potentials. Restored wetlands had a higher potential for CH4 production compared to natural wetlands. Our results show that controls on CH4 production in a restored wetland are complex, and dynamics of active microbial communities are linked to seasonal dry-wet cycles.}, }
@article {pmid39912591, year = {2025}, author = {Porras-Socias, P and Mattiussi, R and Silveira, KA and O'Flaherty, V}, title = {Methan-o-poly: a giant collaborative game to "digest" the microbiology of green biogas production.}, journal = {Journal of microbiology &amp; biology education}, volume = {26}, number = {1}, pages = {e0011624}, pmid = {39912591}, issn = {1935-7877}, abstract = {In an era of rapid change and global challenges, impactful educational experiences about sustainability become imperative. Especially in organic waste conversion bioprocess such as anaerobic digestion (AD). Here proposed, is a gamified approach to learn AD and hidden microbial interactions, bringing to real-life size an invisible phenomenon. In Methan-o-poly, participants roleplay cooperating microbes within a bioreactor engaged in four sequential mini-games to mimic organic waste degradation and methane production. Perturbations in the activity simulate real challenges, enhancing adaptability and problem-solving skills. Overall, this cooperative game promotes motivation, collaboration, and experiential learning. Its initial implementation received positive feedback across various age groups, enhancing green education initiatives.}, }
@article {pmid39911734, year = {2025}, author = {Jia, C and Li, J and Li, Z and Zhang, L}, title = {Influence of high-load shocks on achieving mainstream partial nitrification: Microbial community succession.}, journal = {Water research X}, volume = {27}, number = {}, pages = {100304}, pmid = {39911734}, issn = {2589-9147}, abstract = {Driving microbial community succession through the regulation of operational strategies is crucial for achieving partial nitrification (PN) in municipal wastewater. However, at present, there is a decoupling between the strategic regulation of PN systems and the succession characteristics of the microbial community. This study examined the correlation between microbial community succession and PN performance under two high-load shocks (HLS1 and HLS2) treating actual sewage. During HLS1, the influent organic loading rate (OLR) and nitrogen loading rate (NLR) increased from 116.7 ± 37.7 to 219.7 ± 24.7 mg COD/(g VSS·d) and 0.21±0.02 to 0.33±0.02 kg N/m[3]/d respectively, with the nitrite concentration and nitrite accumulation ratio only reaching 11.7 ± 2.7 mg/L and 49.3 ± 13.9 %, respectively. During HLS2, the influent OLR and NLR increased from 123.5 ± 17.2 to 300.3 ± 49.2 mg COD/(g VSS·d) and 0.19±0.03 to 0.32±0.03 kg N/m[3]/d respectively, resulting in a nitrite accumulation ratio of 89.4 ± 10.7 %. The system achieved efficient PN performance and sustained for 124 days. High-throughput sequencing results showed that community diversity remained consistently high, and the community composition returned to its initial state following a minor succession during HLS1. During HLS2, the high-load shock reduced the richness and evenness of the microbial community. The community underwent succession in a new direction, leading to community composition and function changes. The results indicate that the realization, stabilization, and disruption of PN are influenced not only by operational parameters but also by microbial community structure.}, }
@article {pmid39911603, year = {2025}, author = {Sikombe, TW and Linnemann, AR and Moonga, HB and Quilitz, S and Schoustra, SE and Smid, EJ and Alekseeva, A}, title = {Odor-active aroma compounds in traditional fermented dairy products: The case of mabisi in supporting food and nutrition security in Zambia.}, journal = {Current research in food science}, volume = {10}, number = {}, pages = {100976}, pmid = {39911603}, issn = {2665-9271}, abstract = {Aroma is a key sensory attribute that determines consumer preference and acceptability of foods. The aroma of fermented dairy products comprises the volatile organic compounds (VOCs) produced by the activity of fermenting microbes and the compounds originally present in unfermented raw milk. A unique combination of specific compounds detectable by human olfactory senses creates the distinct odor profile of fermented products. This study investigated the influence of different production methods on the VOCs responsible for the odor-active compounds, and the microbial communities present in mabisi, a traditional Zambian fermented dairy product. The VOCs and microbial community composition of four mabisi variants were investigated using GC-O-MS and PTR-QiTOF-MS techniques, and 16S rRNA amplicon sequencing, respectively. A panel of three assessors identified the odor-active compounds from the GC-O-MS, and the compound's quantitative aspects were obtained by the PTR-QiTOF-MS. Twelve volatile compounds were identified as odor-active compounds during the GC-O-MS analysis. The most prominent were ketones and esters, which imparted a buttery and fruity aroma, respectively. The PTR-QiTOF-MS run identified and quantified a total of 390 m/z peaks, 55 of which were tentatively identified. 16S rRNA amplicon sequencing revealed a diverse microbial community, with Lactococcus species dominating. While the VOC profiles showed significant variation in functionality among the variants, minor differences were observed in microbial composition. The study confirms that high compound concentration does not necessarily correlate with compound odor activity. Our findings offer insights into the significance of aromas and microbial ecology to support optimization strategies for upscaling traditional fermented products.}, }
@article {pmid39911488, year = {2024}, author = {Vaselek, S and Alten, B}, title = {Microbial ecology of sandflies-the correlation between nutrition, Phlebotomus papatasi sandfly development and microbiome.}, journal = {Frontiers in veterinary science}, volume = {11}, number = {}, pages = {1522917}, pmid = {39911488}, issn = {2297-1769}, abstract = {The role and the impact of the microbial component on the biology, ecology, and development of sandflies is largely unknown. We evaluated the impact of larval nutrition on laboratory-reared sandflies in correlation to the abundance of food, light starvation, and food with/without live microbiome, by monitoring the survival and development of immature stages, and the longevity of adult sandflies. Within this study we examined 360 larvae, 116 pupae, and 120 adult flies of Phlebotomus papatasi for the microbial gut content. The data showed that the presence of a live and diverse microbiome plays a role in the development and survival of larvae. The mortality rate of the larvae was higher, and larval development was longer for sandflies maintained on microbiome-depleted medium, in comparison to the larvae fed with medium containing alive and complex microbiome. Actively feeding larvae reduce microbial abundance and diversity of the medium. The microbial content of the larval gut depends on the composition of the rearing medium, indicating a potential attraction to certain bacteria. The microbial content of the pupa gut was severely diminished, with overall survival of two bacterial species in adult insects - Ochrobactrum intermedium (found in 95% of dissected adults) and Bacillus subtilis (16%). Further microbial studies may aid in developing biological control methods for sandfly larval or adult stages.}, }
@article {pmid39909903, year = {2025}, author = {Panico, SC and Alberti, G and Foscari, A and Sciabbarrasi, GL and Tomao, A and Incerti, G}, title = {Bacterial and Fungal Communities Respond Differently to Changing Soil Properties Along Afforestation Dynamic.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {2}, pmid = {39909903}, issn = {1432-184X}, mesh = {*Soil Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Soil/chemistry ; *Fungi/classification/genetics/isolation &amp; purification ; Italy ; Biodiversity ; Grassland ; Nitrogen/analysis ; Forests ; Carbon/analysis ; Phosphorus/analysis ; Microbiota ; *Mycobiome ; }, abstract = {Spontaneous afforestation following land abandonment has been increasingly recognized as a nature-based solution to mitigate climate change and provide measurable benefits to biodiversity. However, afforestation effects on biodiversity, particularly on soil microbial communities, are still poorly characterized, with most previous studies focusing on artificial plantations rather than forest rewilding dynamics. Here, we assessed changes in topsoil physical-chemical properties and related dynamics of bacterial and fungal community composition and structure following spontaneous afforestation of abandoned grasslands in Northeast Italy over the last 70 years. With a space-for-time approach, we selected four chronosequences representing different successional stages: grassland, early (2000-2020), intermediate (1978-2000), and late (1954-1978). Results showed that spontaneous afforestation progressively reduced topsoil pH and total phosphorus (P), while soil organic carbon (SOC), nitrogen (N), and C:N ratio increased. Correspondingly, the overall α-diversity of the fungal community, assessed by ITS DNA metabarcoding, progressively decreased after an initial increase from grassland conditions, following substrate acidification and trophic specialization. Bacterial diversity, assessed by 16S DNA metabarcoding, was highest at the initial stages, then progressively decreased at later stages, likely limited by lower organic matter quality. Shifts of fungal community composition included an increase of ectomycorrhizal Basidiomycota linked to topsoil's higher SOC, N, and C:N ratio. Differently, bacterial community composition responded substantially to pH, with topsoil acidity favoring Proteobacteria (Pseudomonadota) and Acidobacteria (Acidobacteriota) at the late afforestation stages. Our findings provide a first contribution to clarify how fungi and bacteria respond to spontaneous afforestation. This is particularly relevant in the context of climate change mitigation, considering the fundamental role of microorganisms in shaping soil carbon storage dynamics.}, }
@article {pmid39907926, year = {2025}, author = {Breedt, G and Korsten, L and Gokul, JK}, title = {Enhancing multi-season wheat yield through plant growth-promoting rhizobacteria using consortium and individual isolate applications.}, journal = {Folia microbiologica}, volume = {}, number = {}, pages = {}, pmid = {39907926}, issn = {1874-9356}, abstract = {In recent decades, there has been a growing interest in harnessing plant growth-promoting rhizobacteria (PGPR) as a possible mechanism to mitigate the environmental impact of conventional agricultural practices and promote sustainable agricultural production. This study investigated the transferability of promising PGPR research from maize to another Poaceae cereal crop, wheat. This multi-seasonal study evaluated the wheat grain yield effect of Lysinibacillus sphaericus (T19), Paenibacillus alvei (T29) when applied i. individually, ii. as a consortium with Bacillus safensis (S7), and iii. at a 75% reduced fertilizer rate. Whole genome sequencing allowed annotation of genes linked to plant growth promotion, providing potential genomic explanations for the observed in-field findings. Application of the consortium compared to a commercial PGPR showed significantly increased wheat yield by 30.71%, and 25.03%, respectively, in season one, and 63.92% and 58.45%, respectively, under reduced fertilizer rates in season two. Individual application of T19 and T29 showed varying results, with T19 increasing wheat yield by 9.33% and 16.22% during seasons three and four but a substantial reduction (33.39%) during season five. T29 exhibited yield increases during season three (9.31%) and five (5.61%) but led to a significant reduction (21.15%) in season four. Genomic analysis unveiled a spectrum of plant growth-promoting genes including those associated with ammonification, phosphate solubilization, ethylene, siderophore, catalase, and superoxide dismutase production. These findings offer valuable insights into the mechanisms behind observed field results, with potential implications for advancing sustainable agriculture and crop productivity in evolving agricultural landscapes.}, }
@article {pmid39905550, year = {2025}, author = {Martínez Rendón, C and Braun, C and Kappelsberger, M and Boy, J and Casanova-Katny, A and Glaser, K and Dumack, K}, title = {Enhancing microbial predator-prey detection with network and trait-based analyses.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {37}, pmid = {39905550}, issn = {2049-2618}, mesh = {*Food Chain ; Antarctic Regions ; *Microbiota ; Animals ; Predatory Behavior ; Bacteria/classification/genetics ; Eukaryota ; }, abstract = {BACKGROUND: Network analyses are often applied to microbial communities using sequencing survey datasets. However, associations in such networks do not necessarily indicate actual biotic interactions, and even if they do, the nature of the interactions commonly remains unclear. While network analyses are valuable for generating hypotheses, the inferred hypotheses are rarely experimentally confirmed.<br><br>RESULTS: We employed cross-kingdom network analyses, applied trait-based functions to the microorganisms, and subsequently experimentally investigated the found putative predator-prey interactions to evaluate whether, and to what extent, correlations indicate actual predator-prey relationships. For this, we investigated algae and their protistan predators in biocrusts of three distinct polar regions, i.e., Svalbard, the Antarctic Peninsula, and Continental Antarctica. Network analyses using FlashWeave indicated that 89, 138, and 51 correlations occurred between predatory protists and algae, respectively. However, trait assignment revealed that only 4.7-9.3% of said correlations link predators to actually suitable prey. We further confirmed these results with HMSC modeling, which resulted in similar numbers of 7.5% and 4.8% linking predators to suitable prey for full co-occurrence and abundance models, respectively. The combination of network analyses and trait assignment increased confidence in the prediction of predator-prey interactions, as we show that 82% of all experimentally investigated correlations could be verified. Furthermore, we found that more vicious predators, i.e., predators with the highest growth rate in co-culture with their prey, exhibit higher stress and betweenness centrality - giving rise to the future possibility of determining important predators from their network statistics.<br><br>CONCLUSIONS: Our results support the idea of using network analyses for inferring predator-prey interactions, but at the same time call for cautionary consideration of the results, by combining them with trait-based approaches to increase confidence in the prediction of biological interactions. Video Abstract.}, }
@article {pmid39903999, year = {2025}, author = {Mondal, A and Parvez, SS and Majumder, A and Sharma, K and Das, B and Bakshi, U and Alam, M and Banik, A}, title = {Co-inoculation of Trichoderma and tea root-associated bacteria enhance flavonoid production and abundance of mycorrhizal colonization in tea (Camellia sinensis).}, journal = {Microbiological research}, volume = {293}, number = {}, pages = {128084}, doi = {10.1016/j.micres.2025.128084}, pmid = {39903999}, issn = {1618-0623}, mesh = {*Camellia sinensis/microbiology/metabolism ; *Flavonoids/biosynthesis ; *Plant Roots/microbiology ; *Mycorrhizae/growth &amp; development ; Soil Microbiology ; Rhizosphere ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Microbiota ; *Trichoderma/physiology/growth &amp; development ; India ; Symbiosis ; Plant Leaves/microbiology/metabolism ; Tea/microbiology ; Phylogeny ; }, abstract = {Tea is one of the most popular nonalcoholic beverages, that contains several medicinally important flavonoids. Due to seasonal variation and various environmental stresses, the overall consistency of tea flavonoids affects the tea quality. To combat stress, plants stimulate symbiotic relationships with root-associated beneficial microbiomes that sustain nutrient allocation. Therefore, a study has been designed to understand the role of the tea root microbiome in sustaining tea leaf flavonoid production. To enumerate the microbiome, tea root and rhizoplane soil were collected from 3 years of healthy plants from Jalpaiguri district, West Bengal, India. A culture-independent approach was adopted to identify root and rhizosphere microbial diversity (BioSample: SAMN31404869; SRA: SRS15503027 [rhizosphere soil metagenome] BioSample: SAMN31404868;SRA:SRS15503030 [root metagenome]. In addition to diverse microbes, four mycorrhiza fungi, i.e., Glomus intraradices, Glomus irregulare, Paraglomus occultum and Scutellospora heterogama were predominant in collected root samples. A culture-dependent approach was also adopted to isolate several plant growth-promoting bacteria [Bacillus sp. D56, Bacillus sp. D42, Bacillus sp. DR15, Rhizobium sp. DR23 (NCBI Accession: OR821747-OR821750)] and one fungal [Trichoderma sp. AM6 (NCBI Accession:OM915414)] strain. A pot experiment was designed to assess the impact of that isolated microbiome on tea seedlings. After six months of microbiome inoculation, tea plants' physicochemical and transcriptional parameters were evaluated. The results confer that the microbiome-treated treatments [(T1-without any microbial inoculation; NCBI Accession: SAMN33591153), Trichoderma sp. AM6 (T2; NCBI Accession: SAMN33591155) and Trichoderma sp. AM6 +VAM containing tea root+synthetic microbial consortia (T5; NCBI Accession: SAMN33591154)] could enhance the total flavonoid content in tea seedlings by upregulating certain transcripts associated with the flavonoid biosynthesis pathway of tea.}, }
@article {pmid39902955, year = {2025}, author = {Li, Q and Marietou, A and Andersen, FF and Hosek, J and Scavenius, C and Zhang, J and Schwab, C}, title = {In vitro investigations on the impact of fermented dairy constituents on fecal microbiota composition and fermentation activity.}, journal = {Microbiology spectrum}, volume = {13}, number = {3}, pages = {e0219324}, pmid = {39902955}, issn = {2165-0497}, support = {00//M&#xe6;lkeafgiftsfonden (Milk Tax Fund)/ ; 00//Brodrene Hartmann Fonden/ ; }, mesh = {*Feces/microbiology ; Fermentation ; Lactose/metabolism ; *Gastrointestinal Microbiome ; Humans ; beta-Galactosidase/genetics/metabolism ; Streptococcus thermophilus/metabolism/genetics ; RNA, Ribosomal, 16S/genetics ; *Cultured Milk Products/microbiology ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Butyrates/metabolism ; *Dairy Products/microbiology ; }, abstract = {UNLABELLED: Fermented dairy constitutes a major dietary source and contains lactose as the main carbohydrate and living starter cultures, which can encounter the intestinal microbiota after ingestion. To investigate whether dairy-related nutritional and microbial modulation impacted intestinal microbiota composition and activity, we employed static fecal microbiota fermentations and a dairy model system consisting of lactose and Streptococcus thermophilus wild type and β-galactosidase deletion mutant. In addition, we conducted single-culture validation studies. 16S rRNA gene-based microbial community analysis showed that lactose increased the abundance of Bifidobacteriaceae and Anaerobutyricum and Faecalibacterium spp. The supplied lactose was hydrolyzed within 24 h of fermentation and led to higher expression of community-indigenous β-galactosidases. Targeted protein analysis confirmed that bifidobacteria contributed most β-galactosidases together with other taxa, including Escherichia coli and Anaerobutyricum hallii. Lactose addition led to higher (P < 0.05) levels of butyrate compared to controls, likely due to lactate-based cross-feeding and direct lactose metabolism by butyrate-producing Anaerobutyricum and Faecalibacterium spp. Representatives of both genera used lactose to produce butyrate in single cultures. When supplemented at around 5.5 log cells mL[-1], S. thermophilus or its β-galactosidase-negative mutant outnumbered the indigenous Streptococcaceae population at the beginning of fermentation but had no impact on lactose utilization and final short-chain fatty acid profiles.<br><br>IMPORTANCE: The consumption of fermented food has been linked to positive health outcomes, possibly due to interactions of food components with the intestinal microbiota. This study brings forward new insights into how major constituents of fermented dairy affect intestinal microbial ecology and activity when supplied together or alone. We provide evidence that lactose availability increased the production of butyrate by fecal microbiota through cross-feeding and did not observe a contribution of starter cultures to lactose metabolism, possibly due to a lack of competitiveness. The methodological setup used in this study can be implemented in future investigations to determine the impact of other fermented foods and their major components on intestinal microbiota composition and activity.}, }
@article {pmid39897492, year = {2025}, author = {Keleher, JG and Strope, TA and Estrada, NE and Griggs Mathis, AM and Easson, CG and Fiore, C}, title = {Freshwater sponges in the southeastern U.S. harbor unique microbiomes that are influenced by host and environmental factors.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e18807}, pmid = {39897492}, issn = {2167-8359}, mesh = {*Porifera/microbiology ; Animals ; *Microbiota ; *Fresh Water/microbiology ; North Carolina ; *Bacteria/classification/genetics/isolation &amp; purification ; Symbiosis ; }, abstract = {Marine, and more recently, freshwater sponges are known to harbor unique microbial symbiotic communities relative to the surrounding water; however, our understanding of the microbial ecology and diversity of freshwater sponges is vastly limited compared to those of marine sponges. Here we analyzed the microbiomes of three freshwater sponge species: Radiospongilla crateriformis, Eunapius fragilis, and Trochospongilla horrida, across four sites in western North Carolina, U.S.A. Our results support recent work indicating that freshwater sponges indeed harbor a distinct microbiome composition compared to the surrounding water and that these varied across sampling site indicating both environmental and host factors in shaping this distinct community. We also sampled sponges at one site over 3 months and observed that divergence in the microbial community between sponge and water occurs at least several weeks after sponges emerge for the growing season and that sponges maintain a distinct community from the water as the sponge tissue degrades. Bacterial taxa within the Gammproteobacteria, Alphproteobacteria, Bacteroidota (Flavobacteriia in particular), and Verrucomicrobia, were notable as enriched in the sponge relative to the surrounding water across sponge individuals with diverging microbial communities from the water. These results add novel information on the assembly and maintenance of microbial communities in an ancient metazoan host and is one of few published studies on freshwater sponge microbial symbiont communities.}, }
@article {pmid39890664, year = {2025}, author = {Zhou, Y and Jiang, P and Ding, Y and Zhang, Y and Yang, S and Liu, X and Cao, C and Luo, G and Ou, L}, title = {Deciphering the Distinct Associations of Rhizospheric and Endospheric Microbiomes with Capsicum Plant Pathological Status.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {1}, pmid = {39890664}, issn = {1432-184X}, support = {2023YFD1201502//National Key Research and Development Program of China/ ; 42107262//National Natural Science Foundation of China/ ; CARS-24-A05//China Agriculture Research System of MOF and MARA/ ; }, mesh = {*Capsicum/microbiology ; *Rhizosphere ; *Soil Microbiology ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; *Plant Diseases/microbiology ; Fungi/classification/isolation &amp; purification/genetics ; Endophytes/classification/genetics/physiology/isolation &amp; purification ; Plant Roots/microbiology ; Biodiversity ; }, abstract = {Exploring endospheric and rhizospheric microbiomes and their associations can help us to understand the pathological status of capsicum (Capsicum annuum L.) for implementing appropriate management strategies. To elucidate the differences among plants with distinct pathological status in the communities and functions of the endospheric and rhizospheric microbiomes, the samples of healthy and diseased capsicum plants, along with their rhizosphere soils, were collected from a long-term cultivation field. The results indicated a higher bacterial richness in the healthy rhizosphere than in the diseased rhizosphere (P < 0.05), with rhizospheric bacterial diversity surpassing endospheric bacterial diversity. The community assemblies of both the endospheric and rhizospheric microbiomes were driven by a combination of stochastic and deterministic processes, with the stochastic processes playing a primary role. The majority of co-enriched taxa in the healthy endophyte and rhizosphere mainly belonged to bacterial Proteobacteria, Actinobacteria, and Firmicutes, as well as fungal Ascomycota. Most of the bacterial indicators, primarily Alphaproteobacteria and Actinobacteria, were enriched in the healthy rhizosphere, but not in the diseased rhizosphere. In addition, most of the fungal indicators were enriched in both the healthy and diseased endosphere. The diseased endophyte constituted a less complex and stable microbial community than the healthy endophyte, and meanwhile, the diseased rhizosphere exhibited a higher complexity but lower stability than the healthy rhizosphere. Notably, only a microbial function, namely biosynthesis of other secondary metabolites, was higher in the healthy endophytes than in the diseased endophyte. These findings indicated the distinct responses of rhizospheric and endospheric microbiomes to capsicum pathological status, and in particular, provided a new insight into leveraging soil and plant microbial resources to enhance agriculture production.}, }
@article {pmid39890294, year = {2025}, author = {Baker, JM and Dickson, RP}, title = {The Microbiome and Pulmonary Immune Function.}, journal = {Clinics in chest medicine}, volume = {46}, number = {1}, pages = {77-91}, doi = {10.1016/j.ccm.2024.10.006}, pmid = {39890294}, issn = {1557-8216}, mesh = {Humans ; *Microbiota/immunology ; *Lung/immunology/microbiology ; *Lung Diseases/immunology/microbiology ; }, abstract = {In the last decade, the lung microbiome field has matured into a promising area of translational and clinical research due to emerging evidence indicating a role for respiratory microbiota in lung immunity and pathogenesis. Here, we review recent insights pertaining to the lung microbiome's relationship with pulmonary immune function. We discuss areas of future investigation that will be essential to the development of immunomodulatory therapies targeting the respiratory microbiome.}, }
@article {pmid39889603, year = {2025}, author = {Fu, P and Zhai, J and Yang, X and Gao, J and Ren, Z and Guo, B and Qi, P}, title = {Distribution and influencing factors of antibiotic resistance genes in two mussel species along the coasts of the East China Sea and the Yellow Sea.}, journal = {Journal of hazardous materials}, volume = {488}, number = {}, pages = {137399}, doi = {10.1016/j.jhazmat.2025.137399}, pmid = {39889603}, issn = {1873-3336}, mesh = {Animals ; China ; *Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; *Mytilus/microbiology ; Bacteria/genetics ; Anti-Bacterial Agents/pharmacology ; Oceans and Seas ; Microbiota ; Aquaculture ; }, abstract = {Antibiotic resistance genes (ARGs) raise a global public health concern. The ARGs profile in marine aquaculture environments was well reported, yet it is poorly revealed in marine bivalves. This study investigated the microbiota, resistome, and environmental factors within the digestive glands of two mussel species (Mytilus coruscus and Mytilus galloprovincialis) cultivated in the East China Sea and Yellow Sea. The microbial communities in the digestive glands of mussels exhibit significant variations across different sampling sites and between the two seas. The three bacterial phyla that predominated in all samples were Firmicutes, Bacteroidota, and Proteobacteria. A total of 88 ARGs were detected, with aminoglycoside resistance genes and multidrug resistance genes being the dominant categories. Analysis revealed that the quinolone resistance gene qnrB, associated with clinically relevant human pathogens, was ubiquitous in all samples. Members of the Enterobacteriaceae family may serve as a reservoir for qnrB within the investigated environment. The distribution of ARGs shows potential associations with the composition of microbial communities in the digestive glands, environmental factors, and mobile genetic elements (MGEs). These findings enhance the elucidation of microbial ecology and antibiotic resistance in marine aquaculture.}, }
@article {pmid39885242, year = {2025}, author = {Grafmüller, J and Möllmer, J and Muehe, EM and Kammann, CI and Kray, D and Schmidt, HP and Hagemann, N}, title = {Publisher Correction: Granulation compared to co-application of biochar plus mineral fertilizer and its impacts on crop growth and nutrient leaching.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {3796}, doi = {10.1038/s41598-025-87051-2}, pmid = {39885242}, issn = {2045-2322}, }
@article {pmid39884152, year = {2025}, author = {Maphosa, S and Steyn, M and Lebre, PH and Gokul, JK and Convey, P and Marais, E and Maggs-Kölling, G and Cowan, DA}, title = {Rhizosphere bacterial communities of Namib Desert plant species: Evidence of specialised plant-microbe associations.}, journal = {Microbiological research}, volume = {293}, number = {}, pages = {128076}, doi = {10.1016/j.micres.2025.128076}, pmid = {39884152}, issn = {1618-0623}, mesh = {*Rhizosphere ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Desert Climate ; Phylogeny ; Plant Roots/microbiology ; *Microbiota ; *Plants/microbiology ; Namibia ; DNA, Bacterial/genetics ; Soil/chemistry ; Biodiversity ; }, abstract = {Rhizosphere microbial communities are intimately associated with plant root surfaces. The rhizosphere microbiome is recruited from the surrounding soil and is known to impact positively on the plant host via enhanced resistance to pathogens, increased nutrient availability, growth stimulation and increased resistance to desiccation. Desert ecosystems harbour a diversity of perennial and annual plant species, generally exhibiting considerable physiological adaptation to the low-water environment. In this study, we explored the rhizosphere bacterial microbiomes associated with selected desert plant species. The rhizosphere bacterial communities of 11 plant species from the central Namib Desert were assessed using 16S rRNA gene-dependent phylogenetic analyses. The rhizosphere microbial community of each host plant species was compared with control soils collected from their immediate vicinity, and with those of all other host plants. Rhizosphere and control soil bacterial communities differed significantly and were influenced by both location and plant species. Rhizosphere-associated genera included 67 known plant growth-promoting taxa, including Rhizobium, Bacillus, Microvirga, Kocuria and Paenibacillus. Other than Kocuria, these genera constituted the 'core' rhizosphere bacterial microbiome, defined as being present in > 90 % of the rhizosphere communities. Nine of the 11 desert plant species harboured varying numbers and proportions of species-specific microbial taxa. Predictive analyses of functional pathways linked to rhizosphere microbial taxa showed that these were significantly enriched in the biosynthesis or degradation of a variety of substances such as sugars, secondary metabolites, phenolic compounds and antimicrobials. Overall, our data suggest that plant species in the Namib Desert recruit unique taxa to their rhizosphere bacterial microbiomes that may contribute to their resilience in this extreme environment.}, }
@article {pmid39883228, year = {2024}, author = {Han, JR and Li, S and Li, WJ and Dong, L}, title = {Mining microbial and metabolic dark matter in extreme environments: a roadmap for harnessing the power of multi-omics data.}, journal = {Advanced biotechnology}, volume = {2}, number = {3}, pages = {26}, pmid = {39883228}, issn = {2948-2801}, support = {32270076//National Natural Science Foundation of China/ ; 2022xjkk1200//The Third Xinjiang Scientific Expedition Program/ ; 2022B0202110001//The Key-Area Research and Development Program of Guangdong Province/ ; }, abstract = {Extreme environments such as hyperarid, hypersaline, hyperthermal environments, and the deep sea harbor diverse microbial communities, which are specially adapted to extreme conditions and are known as extremophiles. These extremophilic organisms have developed unique survival strategies, making them ideal models for studying microbial diversity, evolution, and adaptation to adversity. They also play critical roles in biogeochemical cycles. Additionally, extremophiles often produce novel bioactive compounds in response to corresponding challenging environments. Recent advances in technologies, including genomic sequencing and untargeted metabolomic analysis, have significantly enhanced our understanding of microbial diversity, ecology, evolution, and the genetic and physiological characteristics in extremophiles. The integration of advanced multi-omics technologies into culture-dependent research has notably improved the efficiency, providing valuable insights into the physiological functions and biosynthetic capacities of extremophiles. The vast untapped microbial resources in extreme environments present substantial opportunities for discovering novel natural products and advancing our knowledge of microbial ecology and evolution. This review highlights the current research status on extremophilic microbiomes, focusing on microbial diversity, ecological roles, isolation and cultivation strategies, and the exploration of their biosynthetic potential. Moreover, we emphasize the importance and potential of discovering more strain resources and metabolites, which would be boosted greatly by harnessing the power of multi-omics data.}, }
@article {pmid39883081, year = {2025}, author = {Shin, GY and Asselin, JA and Smith, A and Aegerter, B and Coutinho, T and Zhao, M and Dutta, B and Mazzone, J and Neupane, R and Gugino, B and Hoepting, C and Khanal, M and Malla, S and Nischwitz, C and Sidhu, J and Burke, AM and Davey, J and Uchanski, M and Derie, ML and du Toit, LJ and Stresow-Cortez, S and Bonasera, JM and Stodghill, P and Kvitko, B}, title = {Plasmids encode and can mobilize onion pathogenicity in Pantoea agglomerans.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {39883081}, issn = {1751-7370}, support = {2019-51181-30013//Specialty Crops Research Initiative Award/ ; //National Institute of Food and Agriculture/ ; //U.S. Department of Agriculture/ ; }, mesh = {*Onions/microbiology ; *Pantoea/genetics/pathogenicity ; *Plasmids/genetics ; *Plant Diseases/microbiology ; Phylogeny ; Genome, Bacterial ; Virulence ; Multigene Family ; Virulence Factors/genetics ; }, abstract = {Pantoea agglomerans is one of four Pantoea species reported in the USA to cause bacterial rot of onion bulbs. However, not all P. agglomerans strains are pathogenic to onion. We characterized onion-associated strains of P. agglomerans to elucidate the genetic and genomic signatures of onion-pathogenic P. agglomerans. We collected >300 P. agglomerans strains associated with symptomatic onion plants and bulbs from public culture collections, research laboratories, and a multi-year survey in 11 states in the USA. Combining the 87 genome assemblies with 100 high-quality, public P. agglomerans genome assemblies we identified two well-supported P. agglomerans phylogroups. Strains causing severe symptoms on onion were only identified in Phylogroup II and encoded the HiVir pantaphos biosynthetic cluster, supporting the role of HiVir as a pathogenicity factor. The P. agglomerans HiVir cluster was encoded in two distinct plasmid contexts: (i) as an accessory gene cluster on a conserved P. agglomerans plasmid (pAggl), or (ii) on a mosaic cluster of plasmids common among onion strains (pOnion). Analysis of closed genomes revealed that the pOnion plasmids harbored alt genes conferring tolerance to Allium thiosulfinate defensive chemistry and many harbored cop genes conferring resistance to copper. We demonstrated that the pOnion plasmid pCB1C can act as a natively mobilizable pathogenicity plasmid that transforms P. agglomerans Phylogroup I strains, including environmental strains, into virulent pathogens of onion. This work indicates a central role for plasmids and plasmid ecology in mediating P. agglomerans interactions with onion plants, with potential implications for onion bacterial disease management.}, }
@article {pmid39882875, year = {2025}, author = {Cross, K and Beckman, N and Jahnes, B and Sabree, ZL}, title = {Microbiome metabolic capacity is buffered against phylotype losses by functional redundancy.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {2}, pages = {e0236824}, pmid = {39882875}, issn = {1098-5336}, support = {IOS 2312818//National Science Foundation (NSF)/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics/analysis ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; Phylogeny ; Diet ; }, abstract = {UNLABELLED: Many animals contain a species-rich and diverse gut microbiota that likely contributes to several host-supportive services that include diet processing and nutrient provisioning. Loss of microbiome taxa and their associated metabolic functions as result of perturbations may result in loss of microbiome-level services and reduction of metabolic capacity. If metabolic functions are shared by multiple taxa (i.e., functional redundancy), including deeply divergent lineages, then the impact of taxon/function losses may be dampened. We examined to what degree alterations in phylotype diversity impact microbiome-level metabolic capacity. Feeding two nutritionally imbalanced diets to omnivorous Periplaneta americana over 8 weeks reduced the diversity of their phylotype-rich gut microbiomes by ~25% based on 16S rRNA gene amplicon sequencing, yet PICRUSt2-inferred metabolic pathway richness was largely unaffected due to their being polyphyletic. We concluded that the nonlinearity between taxon and metabolic functional losses is due to microbiome members sharing many well-characterized metabolic functions, with lineages remaining after perturbation potentially being capable of preventing microbiome "service outages" due to functional redundancy.<br><br>IMPORTANCE: Diet can affect gut microbiome taxonomic composition and diversity, but its impacts on community-level functional capabilities are less clear. Host health and fitness are increasingly being linked to microbiome composition and further modeling of the relationship between microbiome taxonomic and metabolic functional capability is needed to inform these linkages. Invertebrate animal models like the omnivorous American cockroach are ideal for this inquiry because they are amenable to various diets and provide high replicates per treatment at low costs and thus enabling rigorous statistical analyses and hypothesis testing. Microbiome taxonomic composition is diet-labile and diversity was reduced after feeding on unbalanced diets (i.e., post-treatment), but the predicted functional capacities of the post-treatment microbiomes were less affected likely due to the resilience of several abundant taxa surviving the perturbation as well as many metabolic functions being shared by several taxa. These results suggest that both taxonomic and functional profiles should be considered when attempting to infer how perturbations are altering gut microbiome services and possible host outcomes.}, }
@article {pmid39882867, year = {2025}, author = {Asmus, AE and Gaire, TN and Schweisthal, KJ and Staben, SM and Noyes, NR}, title = {Microbiome characterization of two fresh pork cuts during production in a pork fabrication facility.}, journal = {Microbiology spectrum}, volume = {13}, number = {3}, pages = {e0220924}, pmid = {39882867}, issn = {2165-0497}, mesh = {Animals ; *Microbiota/genetics ; Swine ; RNA, Ribosomal, 16S/genetics ; Food Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Red Meat/microbiology ; *Pork Meat/microbiology ; Salmonella/isolation &amp; purification/genetics/classification ; *Meat/microbiology ; Food Handling ; }, abstract = {The goal of this study was to characterize the microbial profile of two different fresh pork cuts, bootjack (BJ) trim and tenderloin (TL), through a 16S rRNA sequencing workflow developed specifically for investigating low-biomass fresh meat within a commercial production schedule. Additionally, this study aimed to determine a baseline Salmonella prevalence and enumeration profile across these two fresh pork cuts. Results showed that microbiome diversity was different between the BJ and TL, and also differed significantly by processing date. The relative abundance of key bacterial genera associated with food safety and spoilage was also different between the two meat types. However, over the course of the production shift, changes in the meat microbiome were limited in both the BJ and TL. The crude prevalence and enumerated burden of Salmonella were lower than what has been previously reported in similar fresh pork cuts, and all of the Salmonella-positive samples occurred on just two processing windows of 1-2 days each. Taken together, the results of this study suggest that the microbial profile of two fresh pork cuts is significantly different even within the same plant at the same time points, and that day-to-day variability within the production process likely influences both the fresh pork microbiome and Salmonella profile of these two meat types.IMPORTANCEModern pork processing involves a series of processes that begin with the handling and transport of the live animals, proceed through harvest and fabrication, and end with the packaging and distribution of fresh pork to the consumer. Each step in this process can alter the microbial community of fresh pork and influence the meat's safety and shelf life. However, little is known about the microbial ecology of individual, unprocessed pork cuts and if the diversity of the meat microbiome remains consistent throughout a production schedule. Additionally, the crude prevalence and enumeration of Salmonella have not been well established for individual fresh pork cuts throughout a production schedule. A more thorough understanding of the microbial profile at different stages of pork production will help processors determine processing steps that impact the microbial characteristics of fresh pork. This insight will help processors implement targeted intervention strategies to enhance food safety and quality.}, }
@article {pmid39880965, year = {2025}, author = {Contreras-Negrete, G and Valiente-Banuet, A and Molina-Freaner, F and Partida-Martínez, LP and Hernández-López, A}, title = {Agricultural Practices and Environmental Factors Drive Microbial Communities in the Mezcal-Producing Agave angustifolia Haw.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {181}, pmid = {39880965}, issn = {1432-184X}, support = {CV549242//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; 319061//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; }, mesh = {*Agave/microbiology/growth &amp; development ; *Soil Microbiology ; *Fungi/classification/genetics/isolation &amp; purification ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; *Agriculture/methods ; RNA, Ribosomal, 16S/genetics ; *Alcoholic Beverages/microbiology ; Mexico ; Rhizosphere ; Biodiversity ; }, abstract = {Mezcal, a traditional Mexican alcoholic beverage, has been a vital source of livelihood for indigenous and rural communities for centuries. However, increasing international demand is exerting pressure on natural resources and encouraging intensive agricultural practices. This study investigates the impact of management practices (wild, traditional, and conventional) and environmental factors on the microbial communities associated with Agave angustifolia, a key species in mezcal production. High-throughput sequencing of the 16S rRNA and ITS2 gene regions revealed distinct prokaryotic and fungal community structures across different plant compartments (endosphere, episphere, and soil), identifying 8214 prokaryotic and 7459 fungal ASVs. Core microbial communities were dominated by Proteobacteria, Actinobacteria, Ascomycota, and Basidiomycota. Alpha diversity analyses showed significant increases in prokaryotic diversity from the endosphere to soil, while fungal diversity remained stable. Notably, conventional management practices were associated with reductions in beneficial microbial taxa. Environmental factors such as precipitation and temperature significantly influenced microbial diversity and composition, especially in the rhizosphere. Beta diversity patterns underscored the strong impact of plant compartment, with management practices and aridity further shaping microbial communities. These results reveal the intricate interactions between management practices, environmental conditions, and microbial diversity, providing valuable insights for the sustainable cultivation of A. angustifolia.}, }
@article {pmid39880083, year = {2025}, author = {Vande Moortele, T and Verschaffelt, P and Huang, Q and Doncheva, NT and Holstein, T and Jachmann, C and Dawyndt, P and Martens, L and Mesuere, B and Van Den Bossche, T}, title = {PathwayPilot: A User-Friendly Tool for Visualizing and Navigating Metabolic Pathways.}, journal = {Molecular &amp; cellular proteomics : MCP}, volume = {24}, number = {3}, pages = {100918}, pmid = {39880083}, issn = {1535-9484}, mesh = {*Software ; *Metabolic Networks and Pathways ; Humans ; *Proteomics/methods ; Gastrointestinal Microbiome ; User-Computer Interface ; Proteome/metabolism ; *Computational Biology/methods ; Caloric Restriction ; }, abstract = {Metaproteomics, the study of collective proteomes in environmental communities, plays a crucial role in understanding microbial functionalities affecting ecosystems and human health. Pathway analysis offers structured insights into the biochemical processes within these communities. However, no existing tool effectively combines pathway analysis with peptide- or protein-level data. We here introduce PathwayPilot, a web-based application designed to improve metaproteomic data analysis by integrating pathway analysis with peptide- and protein-level data, filling a critical gap in current metaproteomics bioinformatics tools. By allowing users to compare functional annotations across different samples or multiple organisms within a sample, PathwayPilot provides valuable insights into microbial functions. In the re-analysis of a study examining the effects of caloric restriction on gut microbiota, the tool successfully identified shifts in enzyme expressions linked to short-chain fatty acid biosynthesis, aligning with its original findings. PathwayPilot's user-friendly interface and robust capabilities make it a significant advancement in metaproteomics, with the potential for widespread application in microbial ecology and health sciences. All code is open source under the Apache2 license and is available at https://pathwaypilot.ugent.be.}, }
@article {pmid39878512, year = {2025}, author = {Flanagan, K and Gassner, K and Lang, M and Ozelyte, J and Hausmann, B and Crepaz, D and Pjevac, P and Gasche, C and Berry, D and Vesely, C and Pereira, FC}, title = {Human-derived microRNA 21 regulates indole and L-tryptophan biosynthesis transcripts in the gut commensal Bacteroides thetaiotaomicron.}, journal = {mBio}, volume = {16}, number = {3}, pages = {e0392824}, pmid = {39878512}, issn = {2150-7511}, support = {ZK-57//Austrian Science Fund (FWF)/ ; }, mesh = {*MicroRNAs/genetics/metabolism ; Humans ; *Tryptophan/biosynthesis ; *Gastrointestinal Microbiome/genetics ; *Bacteroides thetaiotaomicron/metabolism/genetics ; Feces/microbiology ; Irritable Bowel Syndrome/microbiology ; Gene Expression Regulation, Bacterial ; Indoles ; }, abstract = {UNLABELLED: In the gut, microRNAs (miRNAs) produced by intestinal epithelial cells are secreted into the lumen and can shape the composition and function of the gut microbiome. Crosstalk between gut microbes and the host plays a key role in irritable bowel syndrome (IBS) and inflammatory bowel diseases, yet little is known about how the miRNA-gut microbiome axis contributes to the pathogenesis of these conditions. Here, we investigate the ability of miR-21, a miRNA that we found decreased in fecal samples from IBS patients, to associate with and regulate gut microbiome function. When incubated with the human fecal microbiota, miR-21 revealed a rapid internalization or binding to microbial cells, which varied in extent across different donor samples. Fluorescence-activated cell sorting and sequencing of microbial cells incubated with fluorescently labeled miR-21 identified organisms belonging to the genera Bacteroides, Limosilactobacillus, Ruminococcus, or Coprococcus, which predominantly interacted with miR-21. Surprisingly, these and other genera also interacted with a miRNA scramble control, suggesting that physical interaction and/or uptake of these miRNAs by gut microbiota is not sequence-dependent. Nevertheless, transcriptomic analysis of the gut commensal Bacteroides thetaiotaomicron revealed a miRNA sequence-specific effect on bacterial transcript levels. Supplementation of miR-21, but not of small RNA controls, resulted in significantly altered levels of many cellular transcripts and increased transcription of a biosynthetic operon for indole and L-tryptophan, metabolites known to regulate host inflammation and colonic motility. Our study identifies a novel putative miR-21-dependent pathway of regulation of intestinal function through the gut microbiome with implications for gastrointestinal conditions.<br><br>IMPORTANCE: The mammalian gut represents one of the largest and most dynamic host-microbe interfaces. Host-derived microRNAs (miRNAs), released from the gut epithelium into the lumen, have emerged as important contributors to host-microbe crosstalk. Levels of several miRNAs are altered in the stool of patients with irritable bowel syndrome or inflammatory bowel disease. Understanding how miRNAs interact with and shape gut microbiota function is crucial as it may enable the development of new targeted treatments for intestinal diseases. This study provides evidence that the miRNA miR-21 can rapidly associate with diverse microbial cells form the gut and increase levels of transcripts involved in tryptophan synthesis in a ubiquitous gut microbe. Tryptophan catabolites regulate key functions, such as gut immune response or permeability. Therefore, this mechanism represents an unexpected host-microbe interaction and suggests that host-derived miR-21 may help regulate gut function via the gut microbiota.}, }
@article {pmid39878482, year = {2025}, author = {Rodriguez-Garcia, C and Wall, H and Ottesen, E and Grainy, J}, title = {Characterization of extended-spectrum beta-lactamase-producing Enterobacteriaceae from recreational water in Athens, GA, using an undergraduate laboratory module.}, journal = {Journal of microbiology &amp; biology education}, volume = {26}, number = {1}, pages = {e0005624}, pmid = {39878482}, issn = {1935-7877}, abstract = {We present a laboratory module that uses isolation of antibiotic-resistant bacteria from locally collected stream water samples to introduce undergraduate students to basic microbiological culture-based and molecular techniques. This module also educates them on the global public health threat of antibiotic-resistant organisms. Through eight laboratory sessions, students are involved in quality testing of water sources from their neighborhoods, followed by isolation of extended-spectrum beta-lactamase-producing Enterobacteriaceae. By the end of the module, students should be able to isolate Enterobacteriaceae from the environment using selective and differential media, identify isolates using biochemical tests, characterize antibiotic resistance phenotypes using Kirby Bauer and MIC tests, and evaluate the presence of select beta-lactamase genes of interest using PCR. To complement laboratory sessions, students participated in a weekly flipped classroom session with collaborative peer discussions and activities to reinforce concepts applied in the laboratory. Learning outcomes were measured over four semesters with concept checks, in-lecture activities, exams, and laboratory reports. We hypothesized that more than 50% of the student population would achieve each learning objective through the implementation of this authentic research laboratory module. Here, we highlight specific questions used to assess learning objective comprehension and demonstrate that each learning objective was achieved by 65%-100% of the student population. We present a ready-to-adapt module with flexible resources that can be implemented in courses across disciplines in biology, microbiology, environmental sciences, and public health.}, }
@article {pmid39876091, year = {2025}, author = {Tocarruncho, OI and Neuta, Y and Lesmes, Y and Castillo, DM and Leal, S and Chambrone, L and Lafaurie, GI}, title = {Submucosal Microbiome Profiles in Paired and Unpaired Samples From Healthy and Peri-Implantitis Dental Implants.}, journal = {Clinical implant dentistry and related research}, volume = {27}, number = {1}, pages = {e13423}, doi = {10.1111/cid.13423}, pmid = {39876091}, issn = {1708-8208}, support = {490-21//Research Vice Rectory of Universidad El Bosque/ ; }, mesh = {Humans ; *Peri-Implantitis/microbiology ; *Microbiota ; Cross-Sectional Studies ; Male ; Middle Aged ; Female ; *Dental Implants/microbiology ; RNA, Ribosomal, 16S ; Adult ; Aged ; }, abstract = {BACKGROUND: This cross-sectional study aimed to compare the composition of the submucosal microbiome of peri-implantitis with paired and unpaired healthy implant samples.<br><br>METHODS: We evaluated submucosal plaque samples obtained in 39 cases, including 13 cases of peri-implantitis, 13 cases involving healthy implants from the same patient (paired samples), and 13 cases involving healthy implants from different individuals (unpaired samples). The patients were evaluated using next-generation genomic sequencing (Illumina) based on 16S rRNA gene amplification. The sequences were grouped according to the amplicon sequence variant (ASV) to define the taxonomic categories. Alpha diversity was analyzed using Shannon's and Simpson's indices, while beta diversity was evaluated using principal coordinate analysis, analysis of similarities, and permutational multivariate variance analysis. Additionally, UniFrac distances were evaluated using Quantitative Insights into Microbial Ecology 2. Finally, we evaluated between-group differences in the taxonomic components.<br><br>RESULTS: There were no significant between-group differences in alpha diversity. The average bacterial ratios of Filifactor alocis, Porphyromona endodontalis, Tannerella forsythia, Treponema denticola, Peptostreptococcaceae [Eubacterium nodatum], Desulfobulbus sp. HTM 041, and Mogibacterium timidum significantly differed between peri-implantitis samples and unpaired samples from the healthy implants (p&#x2009;<&#x2009;0.05). However, there were few differences in the microbiota between peri-implantitis samples and those paired with healthy implants in the same patient.<br><br>CONCLUSIONS: Future studies comparing the microbiome compositions using sequencing techniques between healthy implants and implants with peri-implantitis should focus on retrieving samples from the same patient, especially in individuals with a history of periodontitis.}, }
@article {pmid39873755, year = {2025}, author = {Mwaheb, MA and El-Aziz, BMA and Abd-Elhalim, BT and El-Kassim, NA and Radwan, TEE}, title = {Correction to: Study of Different Cultivated Plants Rhizosphere Soil Fungi-Mediated Pectinase: Insights into Production, Optimization, Purification, Biocompatibility, and Application.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {180}, doi = {10.1007/s00248-025-02498-0}, pmid = {39873755}, issn = {1432-184X}, }
@article {pmid39871445, year = {2025}, author = {Zahir, Z and Khan, F and Hall, BD}, title = {Sulfate and Dissolved Organic Carbon Concentrations Drive Distinct Microbial Community Patterns in Prairie Wetland Ponds.}, journal = {Environmental microbiology reports}, volume = {17}, number = {1}, pages = {e70069}, pmid = {39871445}, issn = {1758-2229}, support = {//Agricultural Development Fund/ ; //Natural Sciences and Engineering Research Council of Canada/ ; //Faculty of Graduate Studies and Research, University of Regina/ ; //Government of Canada/ ; }, mesh = {*Wetlands ; *Sulfates/analysis ; *Ponds/microbiology/chemistry ; *Carbon/analysis/metabolism ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Phylogeny ; *Microbiota ; Geologic Sediments/microbiology/chemistry ; }, abstract = {Prairie wetland ponds on the Great Plains of North America offer a diverse array of geochemical scenarios that can be informative about their impact on microbial communities. These ecosystems offer invaluable ecological services while experiencing significant stressors, primarily through drainage and climate change. In this first study systematically combining environmental conditions with microbial community composition to identify various niches in prairie wetland ponds, sediments had higher microbial abundance but lower phylogenetic diversity in ponds with lower concentrations of dissolved organic carbon ([DOC]; 10-18 mg/L) and sulfate ([SO4 [2-]]; 37-58 mg/L) in water. As [DOC] and [SO4 [2-]] increased, there was an initial decline in abundance but not phylogenetic diversity. Maximum values of both abundance and phylogenetic diversity occurred between 56 and 115 mg/L [DOC] and 5,000-6,000 mg/L [SO4 [2-]] and decreased thereafter in ponds with 150-180 mg/L and 8,000-14,000 mg/L [DOC] and [SO4 [2-]], respectively. These findings confirm that environmental variables shape the microbial communities and that key microbial taxa involved in sulfur and carbon cycling dominated these ponds potentially impacting vital biogeochemical processes such as bioavailability of heavy metals, carbon sequestration, and methane emissions.}, }
@article {pmid39871406, year = {2025}, author = {Noell, SE and Abbaszadeh, J and Richards, H and Labat Saint Vincent, M and Lee, CK and Herbold, CW and Stott, MB and Cary, SC and McDonald, IR}, title = {Antarctic Geothermal Soils Exhibit an Absence of Regional Habitat Generalist Microorganisms.}, journal = {Environmental microbiology}, volume = {27}, number = {1}, pages = {e70032}, pmid = {39871406}, issn = {1462-2920}, support = {18-UOW-028//Marsden Fund/ ; }, mesh = {Antarctic Regions ; *Soil Microbiology ; *Ecosystem ; *Bacteria/classification/genetics/isolation &amp; purification ; *Archaea/classification/genetics/isolation &amp; purification ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Hot Springs/microbiology ; }, abstract = {Active geothermal systems are relatively rare in Antarctica and represent metaphorical islands ideal to study microbial dispersal. In this study, we tested the macro-ecological concept that high dispersal rates result in communities being dominated by either habitat generalists or specialists by investigating the microbial communities on four geographically separated geothermal sites on three Antarctic volcanoes (Mts. Erebus, Melbourne, and Rittman). We found that the microbial communities at higher temperature (max 65°C) sites (Tramway Ridge on Erebus and Rittmann) were unique from each other and were dominated by a variety of novel Archaea from class Nitrososphaeria, while lower temperature (max 50°C) sites (Western Crater on Erebus and Melbourne) had characteristically mesophilic communities (Planctomycetes, Acidobacteriota, etc.) that were highly similar. We found that 97% of the detected microbial taxa were regional habitat specialists, with no generalists, with community assembly driven by high dispersal rates and drift (25% and 30% of community assembly, respectively), not environmental selection. Our results indicate that for microbial communities experiencing high dispersal rates between isolated communities, habitat specialists may tend to out-compete habitat generalists.}, }
@article {pmid39871020, year = {2025}, author = {Zhang, Z and Zhang, Q and Guo, X and Zeng, Z and Wang, Y and Zhang, P and Gao, D and Deng, G and Sun, G and Yang, Y and Wang, J}, title = {Forest Soil pH and Dissolved Organic Matter Aromaticity Are Distinct Drivers for Soil Microbial Community and Carbon Metabolism Potential.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {177}, pmid = {39871020}, issn = {1432-184X}, support = {2023A1515110368//Guangdong Basic and Applied Basic Research Foundation/ ; 2023B1212060002//Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control/ ; }, mesh = {*Soil Microbiology ; *Forests ; *Carbon/metabolism ; *Soil/chemistry ; Hydrogen-Ion Concentration ; China ; *Microbiota ; Carbon Cycle ; Bacteria/metabolism/classification ; Ecosystem ; Microbial Interactions ; }, abstract = {The ecological niche separation of microbial interactions in forest ecosystems is critical to maintaining ecological balance and biodiversity and has yet to be comprehensively explored in microbial ecology. This study investigated the impacts of soil properties on microbial interactions and carbon metabolism potential in forest soils across 67 sites in China. Using redundancy analysis and random forest models, we identified soil pH and dissolved organic matter (DOM) aromaticity as the primary drivers of microbial interactions, representing abiotic conditions and resource niches, respectively. Our network comparison results highlighted significant differences in microbial interactions between acidic and non-acidic soils, suggesting the critical influences of abiotic conditions on microbial interactions. Conversely, abiotic resource niches played a more pivotal role in shaping the carbon metabolism of soil microbes, supporting the concept that resource niche-based processes drive microbial carbon cycling. Additionally, we demonstrated that microbial interactions contributed significantly to ecosystem function stability and served as potential ecological indicators of microbial functional resilience under environmental stress. These insights emphasize the critical need to preserve microbial interactions for effective forest ecosystem management and projection of ecological outcomes in response to future environmental changes.}, }
@article {pmid39870904, year = {2025}, author = {Stenger, PL and Tribollet, A and Guilhaumon, F and Cuet, P and Pennober, G and Jourand, P}, title = {A Multimarker Approach to Identify Microbial Bioindicators for Coral Reef Health Monitoring-Case Study in La Réunion Island.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {179}, pmid = {39870904}, issn = {1432-184X}, mesh = {*Coral Reefs ; *Microbiota ; *Anthozoa/microbiology ; Animals ; *Bacteria/classification/genetics/isolation &amp; purification ; Reunion ; Fungi/classification/isolation &amp; purification/genetics ; *Seawater/microbiology ; *Environmental Monitoring/methods ; Geologic Sediments/microbiology ; Biodiversity ; Seasons ; Microalgae/classification/isolation &amp; purification/genetics ; Biomarkers/analysis ; }, abstract = {The marine microbiome arouses an increasing interest, aimed at better understanding coral reef biodiversity, coral resilience, and identifying bioindicators of ecosystem health. The present study is a microbiome mining of three environmentally contrasted sites along the Hermitage fringing reef of La Réunion Island (Western Indian Ocean). This mining aims to identify bioindicators of reef health to assist managers in preserving the fringing reefs of La Réunion. The watersheds of the fringing reefs are small, steeply sloped, and are impacted by human activities with significant land use changes and hydrological modifications along the coast and up to mid-altitudes. Sediment, seawater, and coral rubble were sampled in austral summer and winter at each site. For each compartment, bacterial, fungal, microalgal, and protist communities were characterized by high throughput DNA sequencing methodology. Results show that the reef microbiome composition varied greatly with seasons and reef compartments, but variations were different among targeted markers. No significant variation among sites was observed. Relevant bioindicators were highlighted per taxonomic groups such as the Firmicutes:Bacteroidota ratio (8.4%:7.0%), the genera Vibrio (25.2%) and Photobacterium (12.5%) dominating bacteria; the Ascomycota:Basidiomycota ratio (63.1%:36.1%), the genera Aspergillus (40.9%) and Cladosporium (16.2%) dominating fungi; the genus Ostreobium (81.5%) in Chlorophyta taxon for microalgae; and the groups of Dinoflagellata (63.3%) and Diatomea (22.6%) within the protista comprising two dominant genera: Symbiodinium (41.7%) and Pelagodinium (27.8%). This study highlights that the identified bioindicators, mainly in seawater and sediment reef compartments, could be targeted by reef conservation stakeholders to better monitor La Réunion Island's reef state of health and to improve management plans.}, }
@article {pmid39870843, year = {2025}, author = {Li, Q and Shao, H}, title = {The Role of Pathogens in Plant Invasion: Accumulation of Local Pathogens Hypothesis.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {178}, pmid = {39870843}, issn = {1432-184X}, support = {No.2023E01012//Ministry of Science and Technology of the People's Republic of China/ ; 2022D01D02//Science and Technology Department of Xinjiang Uygur Autonomous Region/ ; }, mesh = {*Introduced Species ; *Plants/microbiology ; *Plant Diseases/microbiology ; Soil Microbiology ; Host-Pathogen Interactions ; }, abstract = {In the past decades, dozens of invasion hypotheses have been proposed to elucidate the invasion mechanisms of exotic species. Among them, the accumulation of local pathogens hypothesis (ALPH) posits that invasive plants can accumulate local generalist pathogens that have more negative effect on native species than on themselves; as a result, invasive plants might gain competitive advantages that eventually lead to their invasion success. However, research on this topic is still quite insufficient. In this context, we performed a comprehensive literature survey in order to provide a detailed description of the origin and theoretical framework of ALPH; in addition, challenges in contemporary research such as limitations in technical methods and the complexity of interactions between plants and soil microorganisms, as well as future directions of ALPH research, are also discussed in this review. So far, there are less than ten case studies supporting ALPH; therefore, more work is needed to demonstrate whether ALPH is a suitable hypothesis to elucidate the invasion success of certain plant species.}, }
@article {pmid39868213, year = {2025}, author = {Schechter, MS and Trigodet, F and Veseli, IA and Miller, SE and Klein, ML and Sever, M and Maignien, L and Delmont, TO and Light, SH and Eren, AM}, title = {Quantitative insights into the efficacy of genome-resolved surveys of microbial communities through ribosomal protein phylogeography and EcoPhylo.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39868213}, issn = {2692-8205}, support = {T32 GM007197/GM/NIGMS NIH HHS/United States ; }, abstract = {The increasing availability of microbial genomes is essential to gain insights into microbial ecology and evolution that can propel biotechnological and biomedical advances. Recent advances in genome recovery have significantly expanded the catalogue of microbial genomes from diverse habitats. However, the ability to explain how well a set of genomes account for the diversity in a given environment remains challenging for individual studies or biome-specific databases. Here we present EcoPhylo, a computational workflow to characterize the phylogeography of any gene family through integrated analyses of genomes and metagenomes, and apply this approach to ribosomal proteins to quantify phylogeny-aware genome recovery rates in two genome-resolved investigations of the human gut and oral cavity. Our results demonstrate that EcoPhylo reveals highly resolved, reference-free, multi-domain phylogenies in conjunction with distribution patterns of individual clades across environments, providing a means to assess genome recovery in individual studies and benchmark genome collections.}, }
@article {pmid39868180, year = {2025}, author = {Peters, DI and Shin, IJ and Deever, AN and Kaspar, JR}, title = {Design, Development and Validation of New Fluorescent Strains for Studying Oral Streptococci.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39868180}, issn = {2692-8205}, support = {P30 CA016058/CA/NCI NIH HHS/United States ; R03 DE031766/DE/NIDCR NIH HHS/United States ; }, abstract = {Bacterial strains that are genetically engineered to constitutively produce fluorescent proteins have aided our study of bacterial physiology, biofilm formation, and interspecies interactions. Here, we report on the construction and utilization of new strains that produce the blue fluorescent protein mTagBFP2, the green fluorescent protein sfGFP, and the red fluorescent protein mScarlet-I3 in species Streptococcus gordonii, Streptococcus mutans, and Streptococcus sanguinis. Gene fragments, developed to contain the constitutive promoter Pveg, the fluorescent gene of interest as well as aad9, providing resistance to the antibiotic spectinomycin, were inserted into selected open reading frames on the chromosome that were both transcriptionally silent and whose loss caused no measurable changes in fitness. All strains, except for sfGFP in S. sanguinis, were validated to produce a detectable and specific fluorescent signal. Individual stains, along with extracellular polymeric substances (EPS) within biofilms, were visualized and quantified through either widefield or super-resolution confocal microscopy approaches. Finally, to validate the ability to perform single cell-level analysis using the strains, we imaged and analyzed a triculture mixed-species biofilm of S. gordonii, S. mutans, and S. sanguinis grown with and without addition of human saliva. Quantification of the loss in membrane integrity using a SYTOX dye revealed that all strains had increased loss of membrane integrity with water or human saliva added to the growth media, but the proportion of the population stained by the SYTOX dye varied by species. In all, these fluorescent strains will be a valuable resource for the continued study of oral microbial ecology.}, }
@article {pmid39862387, year = {2025}, author = {Almeida-Silva, F and Van de Peer, Y}, title = {doubletrouble: an R/Bioconductor package for the identification, classification, and analysis of gene and genome duplications.}, journal = {Bioinformatics (Oxford, England)}, volume = {41}, number = {2}, pages = {}, pmid = {39862387}, issn = {1367-4811}, support = {/ERC_/European Research Council/International ; 833522//European Union's Horizon 2020 research and innovation program/ ; }, mesh = {*Software ; *Gene Duplication ; *Genome ; *Genomics/methods ; }, abstract = {SUMMARY: Gene and genome duplications are major evolutionary forces that shape the diversity and complexity of life. However, different duplication modes have distinct impacts on gene function, expression, and regulation. Existing tools for identifying and classifying duplicated genes are either outdated or not user-friendly. Here, we present doubletrouble, an R/Bioconductor package that provides a comprehensive and robust framework for analyzing duplicated genes from genomic data. doubletrouble can detect and classify gene pairs as derived from six duplication modes (segmental, tandem, proximal, retrotransposon-derived, DNA transposon-derived, and dispersed duplications), calculate substitution rates, detect signatures of putative whole-genome duplication events, and visualize results as publication-ready figures. We applied doubletrouble to classify the duplicated gene repertoire in 822 eukaryotic genomes, and results were made available through a user-friendly web interface.<br><br>doubletrouble is available on Bioconductor (https://bioconductor.org/packages/doubletrouble), and the source code is available in a GitHub repository (https://github.com/almeidasilvaf/doubletrouble). doubletroubledb is available online at https://almeidasilvaf.github.io/doubletroubledb/.}, }
@article {pmid39861970, year = {2025}, author = {Saati-Santamaría, Z and Navarro-Gómez, P and Martínez-Mancebo, JA and Juárez-Mugarza, M and Flores, A and Canosa, I}, title = {Genetic and species rearrangements in microbial consortia impact biodegradation potential.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {39861970}, issn = {1751-7370}, support = {//University of Seville from the Ministry of Universities/ ; CLU-2018-04//Regional Government of Castilla y Le&#xf3;n/ ; //European NextGenerationEU program/ ; //University of Salamanca/ ; 101090267//EU Horizon Europe program/ ; ProyExcel_00358//Programa de Excelencia de la Junta de Andaluc&#xed;a/ ; //V Plan Propio de investigaci&#xf3;n of the University Pablo de Olavide/ ; }, mesh = {*Microbial Consortia/genetics ; Biodegradation, Environmental ; Plasmids/genetics ; *Ibuprofen/metabolism ; *Bacteria/genetics/metabolism/classification ; Gene Transfer, Horizontal ; Wastewater/microbiology ; Phylogeny ; }, abstract = {Genomic reorganisation between species and horizontal gene transfer have been considered the most important mechanism of biological adaptation under selective pressure. Still, the impact of mobile genes in microbial ecology is far from being completely understood. Here we present the collection and characterisation of microbial consortia enriched from environments contaminated with emerging pollutants, such as non-steroidal anti-inflammatory drugs. We have obtained and further enriched two ibuprofen-degrading microbial consortia from two unrelated wastewater treatment plants. We have also studied their ability to degrade the drug and the dynamics of the re-organisations of the genetic information responsible for its biodegradation among the species within the consortium. Our results show that genomic reorganisation within microorganisms and species rearrangements occur rapidly and efficiently during the selection process, which may be facilitated by plasmids and/or transposable elements located within the sequences. We show the evolution of at least two different plasmid backbones on samples from different locations, showing rearrangements of genomic information, including genes encoding activities for IBU degradation. As a result, we found variations in the expression pattern of the consortia after evolution under selective pressure, as an adaptation process to the new conditions. This work provides evidence for changes in the metagenomes of microbial communities that allow adaptation under a selective constraint -ibuprofen as a sole carbon source- and represents a step forward in knowledge that can inspire future biotechnological developments for drug bioremediation.}, }
@article {pmid39857259, year = {2025}, author = {Chung, CC and Gong, GC and Tseng, HC and Chou, WC and Ho, CH}, title = {Dominance of Sulfur-Oxidizing Bacteria, Thiomicrorhabdus, in the Waters Affected by a Shallow-Sea Hydrothermal Plume.}, journal = {Biology}, volume = {14}, number = {1}, pages = {}, pmid = {39857259}, issn = {2079-7737}, support = {NSTC 113-2611-M-019-006//National Science and Technology Council of Taiwan/ ; }, abstract = {The shallow-sea hydrothermal vent at Guishan Islet, located off the coast of Taiwan, serves as a remarkable natural site for studying microbial ecology in extreme environments. In April 2019, we investigated the composition of prokaryotic picoplankton communities, their gene expression profiles, and the dissolved inorganic carbon uptake efficiency. Our results revealed that the chemolithotrophs Thiomicrorhabdus spp. contributed to the majority of primary production in the waters affected by the hydrothermal vent plume. The metatranscriptomic analysis aligned with the primary productivity measurements, indicating the significant gene upregulations associated with carboxysome-mediated carbon fixation in Thiomicrorhabdus. Synechococcus and Prochlorococcus served as the prokaryotic photoautotrophs for primary productivity in the waters with lower influence from hydrothermal vent emissions. Thiomicrorhabdus and picocyanobacteria jointly provided organic carbon for sustaining the shallow-sea hydrothermal vent ecosystem. In addition to the carbon fixation, the upregulation of genes involved in the SOX (sulfur-oxidizing) pathway, and the dissimilatory sulfate reduction indicated that energy generation and detoxification co-occurred in Thiomicrorhabdus. This study improved our understanding of the impacts of shallow-sea hydrothermal vents on the operation of marine ecosystems and biogeochemical cycles.}, }
@article {pmid39856188, year = {2025}, author = {Tokodi, N and Łobodzińska, A and Klimczak, B and Antosiak, A and Młynarska, S and Šulčius, S and Avrani, S and Yoshida, T and Dziga, D}, title = {Proliferative and viability effects of two cyanophages on freshwater bloom-forming species Microcystis aeruginosa and Raphidiopsis raciborskii vary between strains.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {3152}, pmid = {39856188}, issn = {2045-2322}, support = {PPN/ULM/2019/1/00219//Narodowa Agencja Wymiany Akademickiej/ ; 2021/41/N/NZ9/02957//Narodowym Centrum Nauki/ ; 2020/38/L/NZ9/00135//Narodowym Centrum Nauki/ ; S-LL-21-10//Research Council of Lithuania/ ; 1386/20//Israel Science Foundation/ ; }, mesh = {*Microcystis/virology/growth &amp; development ; *Bacteriophages/physiology ; Fresh Water/microbiology ; *Cyanobacteria/virology ; Photosynthesis ; Eutrophication ; }, abstract = {Viruses that infect cyanobacteria are an integral part of aquatic food webs, influencing nutrient cycling and ecosystem health. However, the significance of virus host range, replication efficiency, and host compatibility on cyanobacterial dynamics, growth, and toxicity remains poorly understood. In this study, we examined the effects of cyanophage additions on the dynamics and activity of optimal, sub-optimal, and non-permissive cyanobacterial hosts in cultures of Microcystis aeruginosa and Raphidiopsis raciborskii. Our findings reveal that cross-infectivity can substantially reduce the proliferative success of the cyanophage under conditions of high-density of sub-optimal hosts which suggests phage dispersal limitation as a result of shared infections, in turn impairing their top-down control over the host community. Furthermore, we found that cyanophage addition triggers host strain-specific responses in photosynthetic performance, population size and toxin production, even among non-permissive hosts. These non-lytic effects suggest indirect impacts on co-existing cyanobacteria, increasing the overall complexity and variance in many ecologically relevant cyanobacterial traits. The high variability in responses observed with a limited subset of cyanophage-cyanobacteria combinations not only highlights the intricate role of viral infections in microbial ecosystems but also underscores the significant challenges in predicting the composition, toxicity, and dynamics of cyanobacterial blooms.}, }
@article {pmid39855017, year = {2025}, author = {Savadova-Ratkus, K and Grendaitė, D and Karosienė, J and Stonevičius, E and Kasperovičienė, J and Koreivienė, J}, title = {Modelling harmful algal blooms in a mono- and a polydominant eutrophic lake under temperature and nutrient changes.}, journal = {Water research}, volume = {275}, number = {}, pages = {123138}, doi = {10.1016/j.watres.2025.123138}, pmid = {39855017}, issn = {1879-2448}, mesh = {*Lakes/microbiology ; *Harmful Algal Bloom ; Temperature ; Cyanobacteria ; Climate Change ; Nutrients ; Eutrophication ; Phosphorus ; }, abstract = {Cyanobacterial blooms, driven by nutrient loading and temperature, pose significant ecological and economic challenges. This study employs a combined data-driven and trait-based modelling approach to predict changes in cyanobacterial communities in a mono- and a polydominant shallow temperate lakes under varying temperature and nutrient scenarios. Results of the AQUATOX simulation model for two aquatic systems suggest that a 2 °C temperature increase, consistent with Intergovernmental Panel on Climate Change's predictions, may influence cyanobacteria species composition and dominance, with trends indicating a possible shift favouring Nostocales over Oscillatoriales and Chroococcales. Temperature increases by 4 °C clearly promoted the dominance of Nostocales. Nutrient dynamics appear to influence community structure. In a nutrient-rich monodominant lake, temperature was the primary driver, while in a nutrient-limited polydominant lake, phosphorus availability influenced cyanobacteria species dominance. Combined warming and phosphorus alterations significantly affected cyanobacteria bloom intensity and duration, particularly enhancing Nostocales growth. The study highlights the complexity of cyanobacterial responses to climate change, emphasizing the need for more analysis and comprehensive models to predict harmful algal blooms (HABs) in freshwater ecosystems. While the findings suggest that temperature and nutrient availability may be critical drivers of cyanobacterial dominance, additional research across a broader range of systems is necessary.}, }
@article {pmid39854900, year = {2025}, author = {Reid, CJ and Farrell, M and Kirby, JK}, title = {Microbial communities in biosolids-amended soils: A critical review of high-throughput sequencing approaches.}, journal = {Journal of environmental management}, volume = {375}, number = {}, pages = {124203}, doi = {10.1016/j.jenvman.2025.124203}, pmid = {39854900}, issn = {1095-8630}, mesh = {*Soil Microbiology ; Soil/chemistry ; High-Throughput Nucleotide Sequencing ; *Sewage/microbiology ; Microbiota ; }, abstract = {Sustainable reuse of treated wastewater sludge or biosolids in agricultural production requires comprehensive understanding of their risks and benefits. Microbes are central mediators of many biosolids-associated risks and benefits, however understanding of their responses to biosolids remains minimal. Application of biosolids to soils amounts to a coalescence of two distinct microbial communities adapted to vastly different matrices. High-throughput DNA and RNA sequencing (HTS) approaches are required to accurately describe the compositional and functional outcomes of this process as they currently provide the highest possible resolution to deal with complex community-scale phenomena. Furthermore, linkage of HTS data to physicochemical and functional data can reveal biotic and abiotic drivers of coalescence, impacts of biosolids-borne contaminants and the collective downstream implications for soil and plant health. Here we review the current body of literature examining microbial communities in biosolids-amended soils using HTS of total community DNA and RNA. We provide a critical synthesis of soil microbial community composition and functional responses, the physical, chemical and biological drivers of these responses, and the influence of three major biosolids-borne anthropogenic contaminants of concern; antimicrobials and antimicrobial resistance genes, plastics, and per- and polyfluoroalkyl substances (PFAS). Finally, we identify methodological limitations and outstanding research questions precluding a holistic understanding of microbial responses in biosolids-amended soils and envision future research whereby sequence-based microbial ecology is integrated with soil, plant, and contaminant data to preserve soil health, support plant productivity, and remediate contaminants.}, }
@article {pmid39853499, year = {2025}, author = {Lucia, Z and Giulio, G and Matteo, G and Stefano, C and Irene, LP and Paolo, P and Giorgio, B and Hauffe, HC}, title = {More Than Meets the Eye: Unraveling the Interactions Between Skin Microbiota and Habitat in an Opportunistic Amphibian.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {176}, pmid = {39853499}, issn = {1432-184X}, mesh = {Animals ; *Skin/microbiology ; *Microbiota ; *Ecosystem ; *Anura/microbiology ; *Bacteria/classification/isolation &amp; purification/genetics ; Italy ; Batrachochytrium/isolation &amp; purification/genetics ; *Fungi/classification/isolation &amp; purification/genetics ; Wetlands ; Temperature ; Biodiversity ; Hydrogen-Ion Concentration ; Skin Microbiome ; }, abstract = {With amphibians still holding the record as the most threatened class of terrestrial vertebrates, their skin microbiota has been shown to play a relevant role in their survival in a fast-changing world. Yet little is known about how abiotic factors associated with different aquatic habitats impact these skin microorganisms. Here we chose the yellow-bellied toad (Bombina variegata), a small anuran that colonizes a wide range of wetland habitats, to investigate how the diversity and composition of both its bacterial and fungal skin communities vary across different habitats and with water characteristics (temperature, pH, and dissolved oxygen) of these habitats. Skin microbiota was sampled from 14 sites in the Province of Trento (Italy), including natural pools, ephemeral ponds, irrigation tanks, and farm ponds. Interestingly, the diversity of the two microbial components was also highly correlated. Close associations between both the diversity and composition of water and skin communities were noted for each habitat and sampling site, suggesting that water bodies actively contribute to the skin microbiota assemblage. In addition, water pH, temperature, and dissolved oxygen affected both bacterial and fungal diversity of skin. We confirmed the presence of Batrachochytrium dendrobatidis in skin samples of animals collected from eight waterbodies, as well as more than 60 microbial taxa previously associated with resistance to this pathogen. We concluded that both skin bacterial and fungal communities appear to be influenced by each other as well as by environmental communities and conditions, and these relationships connecting the whole ecosystem should be considered in future research concerning amphibian conservation.}, }
@article {pmid39849986, year = {2025}, author = {Liu, Y and Geng, Y and Jiang, Y and Li, P and Li, YZ and Zhang, Z}, title = {Global microbial community biodiversity increases with antimicrobial toxin abundance of rare taxa.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {39849986}, issn = {1751-7370}, support = {SDCX-ZG-202203032//Postdoctoral Innovation Project of Shandong Province/ ; BK20230248//Natural Science Foundation of Jiangsu Province/ ; ZR2022QC001//Science Foundation for Youths of Shandong Province/ ; 32070030//National Natural Science Foundation of China/ ; }, mesh = {*Biodiversity ; *Bacteria/classification/metabolism/drug effects/genetics ; *Anti-Infective Agents/metabolism ; *Toxins, Biological ; *Microbiota ; }, abstract = {One of the central questions in microbial ecology is how to explain the high biodiversity of communities. A large number of rare taxa in the community have not been excluded by abundant taxa with competitive advantages, a contradiction known as the biodiversity paradox. Recently, increasing evidence has revealed the central importance of antimicrobial toxins as crucial weapons of antagonism in microbial survival. The powerful effects of antimicrobial toxins result in simple combinations of microorganisms failing to coexist under laboratory conditions, but it is unclear whether they also have a negative impact on the biodiversity of natural communities. Here, we revealed that microbial communities worldwide universally possess functional potential for antimicrobial toxin production. Counterintuitively, the biodiversity of global microbial communities increases, rather than decreases, as the abundance of antimicrobial toxins in rare taxa rises. Rare taxa may encode more antimicrobial toxins than abundant taxa, which is associated with the maintenance of the high biodiversity of microbial communities amid complex interactions. Our findings suggest that the antagonistic interaction caused by antimicrobial toxins may play a positive role in microbial community biodiversity at the global scale.}, }
@article {pmid39849009, year = {2025}, author = {Calderón-Osorno, M and Rojas-Villalta, D and Lejzerowicz, F and Cortés, J and Arias-Andres, M and Rojas-Jimenez, K}, title = {The influence of depth on the global deep-sea plasmidome.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {2959}, pmid = {39849009}, issn = {2045-2322}, support = {SIA 0483-21//Universidad Nacional de Costa Rica/ ; C1455//Vicerrector&#xed;a de Investigacion de la Universidad Costa Rica/ ; C2650//Vicerrector&#xed;a de Investigacion de la Universidad Costa Rica/ ; C3509//Vicerrector&#xed;a de Investigacion de la Universidad Costa Rica/ ; }, mesh = {*Plasmids/genetics ; *Metagenome ; *Seawater/microbiology ; Ecosystem ; Gammaproteobacteria/genetics ; Alphaproteobacteria/genetics ; Oceans and Seas ; Bacteria/genetics ; Computational Biology/methods ; Indian Ocean ; }, abstract = {Plasmids play a crucial role in facilitating genetic exchange and enhancing the adaptability of microbial communities. Despite their importance, environmental plasmids remain understudied, particularly those in fragile and underexplored ecosystems such as the deep-sea. In this paper we implemented a bioinformatics pipeline to study the composition, diversity, and functional attributes of plasmid communities (plasmidome) in 81 deep-sea metagenomes from the Tara and Malaspina expeditions, sampled from the Pacific, Atlantic, and Indian Oceans at depths ranging from 270 to 4005 m. We observed an association between depth and plasmid traits, with the 270-1000 m range (mesopelagic samples) exhibiting the highest number of plasmids and the largest plasmid sizes. Plasmids of Alphaproteobacteria and Gammaproteobacteria were predominant across the oceans, particularly in this depth range, which also showed the highest species diversity and abundance of metabolic pathways, including aromatic compound degradation. Surprisingly, relatively few antibiotic resistance genes were found in the deep-sea ecosystem, with most being found in the mesopelagic layer. These included classes such as beta-lactamase, biocide resistance, and aminoglycosides. Our study also identified the MOBP and MOBQ relaxase families as prevalent across various taxonomic classes. This research underscores the importance of studying the plasmidome independently from the chromosomal context. Our limited understanding of the deep-sea's microbial ecology, especially its plasmidome, necessitates caution in human activities like mining. Such activities could have unforeseen impacts on this largely unexplored ecosystem.}, }
@article {pmid39848193, year = {2025}, author = {Odales-Bernal, L and González, LML and Ghysels, S and Lobanov, V and De Vrieze, J and Barrera, EL and Ronsse, F}, title = {Optimized hydrothermal carbonization of chicken manure and anaerobic digestion of its process water for better energy management.}, journal = {Journal of environmental management}, volume = {375}, number = {}, pages = {124191}, doi = {10.1016/j.jenvman.2025.124191}, pmid = {39848193}, issn = {1095-8630}, mesh = {*Manure ; Chickens ; Animals ; Anaerobiosis ; Water ; Carbon/chemistry ; Methane ; }, abstract = {Modern poultry production is faced with the challenge of properly managing its associated wastes, in particular chicken manure (CM). There is a need to improve the management of CM through conversion processes that allow the production of value-added products, particularly for energy purposes, such as hydrothermal carbonization (HTC) and anaerobic digestion (AD). The objectives of this study were: i) to optimize the CM-HTC, using response surface methodology with simultaneous optimization of mass yield and higher heating value (HHV), and ii) to evaluate the biomethane potential of the process water generated from hydrochar production under the optimized condition. An analysis of the overall energy potential was also performed. The optimal condition for HTC was 234 °C for 30 min, resulting in hydrochar with an HHV of 14.88 ± 0.22 MJ/kg and a mass yield of 50.00 ± 3.13 wt%. The cumulative methane yield was 179.2 ± 13.1 NmL CH4/g VSadded and 255.5 ± 14.5 NmL CH4/g VSadded for process water at 180 °C and 234 °C, respectively. The addition of hydrochar improved the methane yield by 49.6 ± 10.8%, indicating that this is a valuable option for energy recovery from CM. Overall, the HTC-AD integration approach achieved an energy recovery potential of more than 79%, offering an efficient strategy for CM valorization.}, }
@article {pmid39847340, year = {2025}, author = {Ganley, JG and Seyedsayamdost, MR}, title = {Iron limitation triggers roseoceramide biosynthesis and membrane remodeling in marine roseobacter.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {4}, pages = {e2414434122}, pmid = {39847340}, issn = {1091-6490}, support = {R35 GM152049/GM/NIGMS NIH HHS/United States ; Postdoctoral Fellowship in Marine Microbial Ecology//Simons Foundation (SF)/ ; }, mesh = {*Roseobacter/metabolism ; *Iron/metabolism ; Symbiosis ; *Cell Membrane/metabolism ; Metabolome ; }, abstract = {Chemical communication between marine bacteria and their algal hosts drives population dynamics and ultimately determines the fate of major biogeochemical cycles in the ocean. To gain deeper insights into this small molecule exchange, we screened niche-specific metabolites as potential modulators of the secondary metabolome of the roseobacter, Roseovarius tolerans. Metabolomic analysis led to the identification of a group of cryptic lipids that we have termed roseoceramides. The roseoceramides are elicited by iron-binding algal flavonoids, which are produced by macroalgae that Roseovarius species associate with. Investigations into the mechanism of elicitation show that iron limitation in R. tolerans initiates a stress response that results in lowered oxidative phosphorylation, increased import and catabolism of algal exudates, and reconfiguration of lipid ynthesis to prioritize production of roseoceramides over phospholipids, likely to fortify membrane integrity as well as promote a sessile and symbiotic lifestyle. Our findings add new small molecule words and their "meanings" to the algal-bacterial lexicon and have implications for the initiation of these interactions.}, }
@article {pmid39845484, year = {2024}, author = {Tóth, VR}, title = {Photosynthetic traits of Phragmites australis along an ecological gradient and developmental stages.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1476142}, pmid = {39845484}, issn = {1664-462X}, abstract = {Common reed (Phragmites australis) is a cosmopolitan species, though its dieback is a worldwide phenomenon. In order to assess the evolutionary role of phenotypic plasticity in a successful plant, the values and plasticity of photophysiological traits of Phragmites australis were investigated in the Lake Fertő wetlands at 5 sites with different degrees of reed degradation and along a seasonal sequence. On the one hand, along the established ecological degradation gradient, photophysiological traits of Phragmites changed significantly, affecting plant productivity, although no consistent gradient-type trends were observed. Gradual changes within a season in the values of photosynthetic traits were observed that were recorded in both degraded and stable stands, suggesting a universal response to seasonally changing environmental conditions that could not be overridden by the ecological gradient. On the other hand, reed plants exposed to different levels of degradation showed comparable physiological plasticity; there was no difference in trait variability between stable and degraded stands. This relatively uniform plasticity is likely to contribute to the resilience of reed plants by providing a wider range of adaptive traits under different conditions. In contrast, the 150-200% gradual change in photophysiological trait plasticity with senescence in Phragmites was also demonstrated, reflecting a more dynamic response of the photosynthetic apparatus to seasonal changes. Senescence affected the plasticity of plant traits independently of their degradation status, suggesting a more universal nature of seasonal changes. This research shows that under conditions of conservative resource use determined by stressful habitats, trait values respond to conditions, while trait plasticity shows minimal changes. Furthermore, phenological sequence significantly influenced both the values and the plasticity of the photosynthetic traits studied. Our results underline the impact of ecological degradation on reed physiology and highlight the importance of understanding both trait values and plasticity in plant responses to environmental and seasonal change.}, }
@article {pmid39844349, year = {2025}, author = {Fonseca de Souza, L and Oliveira, HG and Pellegrinetti, TA and Mendes, LW and Bonatelli, ML and Dumaresq, ASR and Sinatti, VVC and Pinheiro, JB and Azevedo, JL and Quecine, MC}, title = {Co-inoculation with Bacillus thuringiensis RZ2MS9 and rhizobia improves the soybean development and modulates soil functional diversity.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {2}, pages = {}, pmid = {39844349}, issn = {1574-6941}, support = {2021/12378-4//FAPESP/ ; 166644/2020-0//National Council for Scientific and Technological Development/ ; 69242/2018-8//H.G.O./ ; 22.1.08498.01.0//T.A.P./ ; }, mesh = {*Glycine max/growth &amp; development/microbiology ; *Soil Microbiology ; *Bacillus thuringiensis/physiology ; Soil/chemistry ; *Rhizobium/physiology ; Biodiversity ; }, abstract = {Despite the beneficial effects of plant growth-promoting rhizobacteria on agriculture, understanding the consequences of introducing foreign microbes into soil taxonomic and functional diversity is necessary. This study evaluated the effects co-inoculation of soybean with Bacillus thuringiensis (Bt) RZ2MS9 and commercial rhizobia on the natural microbial community structure and functional potential. Our results indicated that soybean development was positively influenced by co-inoculation, plants exhibited greater height and a higher number of pods, and no reductions in productivity estimates. Soil prokaryotic diversity and community structure remained unchanged by Bt RZMS9 inoculation or co-inoculation with rhizobia 147 days after sowing. However, functional diversity was influenced by sole Bt inoculation, potentially due to community quorum sensing disruption by N-acyl homoserine lactone hydrolases. The genes enriched by co-inoculation were mostly related to soil phosphorus cycling, with gcd showing the most pronounced increase. The nifA genes increased when rhizobia alone were inoculated, suggesting that this pathway could be affected by Bt RZ2MS9 inoculation. This study demonstrates the synergistic activity of rhizobia and Bt RZ2MS9 on soybean development, without significantly interfering with natural microbial community, presenting a promising approach for sustainable crop management.}, }
@article {pmid39844346, year = {2025}, author = {Melville, DW and Meyer, M and Kümmerle, C and Alvarado-Barrantes, KA and Wilhelm, K and Sommer, S and Tschapka, M and Risely, A}, title = {Delayed feeding disrupts diurnal oscillations in the gut microbiome of a neotropical bat in captivity.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {2}, pages = {}, pmid = {39844346}, issn = {1574-6941}, support = {DFG SO 428/17-1//German Research Foundation/ ; //Ulm University/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Chiroptera/microbiology/physiology ; *Circadian Rhythm ; Feces/microbiology ; *Feeding Behavior ; Hydrogen-Ion Concentration ; Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {Diurnal rhythms of the gut microbiota are emerging as an important yet often overlooked facet of microbial ecology. Feeding is thought to stimulate gut microbial rhythmicity, but this has not been explicitly tested. Moreover, the role of the gut environment is entirely unexplored, with rhythmic changes to gut pH rather than feeding per se possibly affecting gut microbial fluctuations. In this study, we experimentally manipulated the feeding schedule of captive lesser long-nosed bats, Leptonycteris yerbabuenae, to dissociate photic and feeding cues, and measured the faecal microbiota and gut pH every 2 h. We detected strong diurnal rhythms in both microbial alpha diversity and beta diversity as well as in pH within the control group. However, a delay in feeding disrupted oscillations of gut microbial diversity and composition, but did not affect rhythms in gut pH. The oscillations of some genera, such as Streptococcus, which aid in metabolizing nutrients, shifted in accordance with the delayed-feeding cue and were correlated with pH. For other bacterial genera, oscillations were disturbed and no connection to pH was found. Our findings suggest that the rhythmic proliferation of bacteria matches peak feeding times, providing evidence that diurnal rhythms of the gut microbiota likely evolved to optimize their metabolic support to the host's circadian phenotype.}, }
@article {pmid39843903, year = {2025}, author = {Tóth, AB and Terauds, A and Chown, SL and Hughes, KA and Convey, P and Hodgson, DA and Cowan, DA and Gibson, J and Leihy, RI and Murray, NJ and Robinson, SA and Shaw, JD and Stark, JS and Stevens, MI and van den Hoff, J and Wasley, J and Keith, DA}, title = {A dataset of Antarctic ecosystems in ice-free lands: classification, descriptions, and maps.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {133}, pmid = {39843903}, issn = {2052-4463}, support = {LP170101143//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005 Securing Antarctica's Environmental Future//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005 Securing Antarctica's Environmental Future//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005 Securing Antarctica's Environmental Future//Department of Education and Training | Australian Research Council (ARC)/ ; LP170101143//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005 Securing Antarctica's Environmental Future//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005 Securing Antarctica's Environmental Future//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005 Securing Antarctica's Environmental Future//Department of Education and Training | Australian Research Council (ARC)/ ; LP170101143//Department of Education and Training | Australian Research Council (ARC)/ ; }, abstract = {Antarctica, Earth's least understood and most remote continent, is threatened by human disturbances and climate-related changes, underscoring the imperative for biodiversity inventories to inform conservation. Antarctic ecosystems support unique species and genetic diversity, deliver essential ecosystem services and contribute to planetary stability. We present Antarctica's first comprehensive ecosystem classification and map of ice-free lands, which host most of the continent's biodiversity. We used latent variables in factor analyses to partition continental-scale abiotic variation, then biotic variation represented in spatial models, and finally recognised regional-scale variation among biogeographic units. This produced a spatially explicit hierarchical classification with nine Major Environment Units (Tier 1), 33 Habitat Complexes (Tier 2) and 269 Bioregional Ecosystem Types (Tier 3) mapped at 100 m resolution and aligned with 'level 4' of the IUCN Global Ecosystem Typology. This comprehensive ecosystem inventory provides foundational data to inform protected area designation under the Antarctic Treaty's Environmental Protocol and track risks to Antarctic ecosystems. Its tiered structure and workflow accommodate data scarcity and facilitate updates, promoting robustness as knowledge builds.}, }
@article {pmid39840338, year = {2024}, author = {Salerno, B and Cornaggia, M and Sabatino, R and Di Cesare, A and Mantovani, C and Barco, L and Cordioli, B and Bano, L and Losasso, C}, title = {The "best practices for farming" successfully contributed to decrease the antibiotic resistance gene abundances within dairy farms.}, journal = {Frontiers in veterinary science}, volume = {11}, number = {}, pages = {1420282}, pmid = {39840338}, issn = {2297-1769}, abstract = {INTRODUCTION: Farms are significant hotspots for the dissemination of antibiotic-resistant bacteria and genes (ARGs) into the environment and directly to humans. The prevalence of ARGs on farms underscores the need for effective strategies to reduce their spread. This study aimed to evaluate the impact of a guideline on "best practices for farming" aimed at reducing the dissemination of antibiotic resistance.<br><br>METHODS: A guideline focused on prudent antibiotic use, selective therapy, and hygienic and immune-prophylactic practices was developed and provided to the owners of 10 selected dairy farms and their veterinarians. Fecal samples were collected from lactating cows, dry cows, and calves both before and after the implementation of the guideline. ARGs (bla TEM, ermB, sul2, and tetA) were initially screened by end-point PCR, followed by quantification using digital droplet PCR. ARG abundance was expressed in relative terms by dividing the copy number of ARGs by the copy number of the 16S rRNA gene.<br><br>RESULTS: The ARG abundances were higher in lactating cows compared to other categories. Despite similar levels of antibiotic administration (based on veterinary prescription data from the sampled farms) in both sampling campaigns, the total abundance of selected ARGs, particularly bla TEM and tetA, significantly decreased after the adoption of the farming guidelines.<br><br>DISCUSSION: This study highlights the positive impact of prudent antibiotic use and the implementation of farming best practices in reducing the abundance of ARGs. The lactating cow category emerged as a crucial point of intervention for reducing the spread of antibiotic resistance. These findings contribute to ongoing efforts to address antibiotic resistance in farm environments and strengthen the evidence supporting the adoption of good farming practices.}, }
@article {pmid39838963, year = {2024}, author = {Guan, J and Ji, Y and Peng, C and Zou, W and Tang, X and Shang, J and Sun, Y}, title = {GOPhage: protein function annotation for bacteriophages by integrating the genomic context.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {1}, pages = {}, pmid = {39838963}, issn = {1477-4054}, support = {11209823//City University of Hong Kong/ ; }, mesh = {*Bacteriophages/genetics ; *Genome, Viral ; *Viral Proteins/genetics/metabolism/chemistry ; *Molecular Sequence Annotation/methods ; Genomics/methods ; Computational Biology/methods ; }, abstract = {Bacteriophages are viruses that target bacteria, playing a crucial role in microbial ecology. Phage proteins are important in understanding phage biology, such as virus infection, replication, and evolution. Although a large number of new phages have been identified via metagenomic sequencing, many of them have limited protein function annotation. Accurate function annotation of phage proteins presents several challenges, including their inherent diversity and the scarcity of annotated ones. Existing tools have yet to fully leverage the unique properties of phages in annotating protein functions. In this work, we propose a new protein function annotation tool for phages by leveraging the modular genomic structure of phage genomes. By employing embeddings from the latest protein foundation models and Transformer to capture contextual information between proteins in phage genomes, GOPhage surpasses state-of-the-art methods in annotating diverged proteins and proteins with uncommon functions by 6.78% and 13.05% improvement, respectively. GOPhage can annotate proteins lacking homology search results, which is critical for characterizing the rapidly accumulating phage genomes. We demonstrate the utility of GOPhage by identifying 688 potential holins in phages, which exhibit high structural conservation with known holins. The results show the potential of GOPhage to extend our understanding of newly discovered phages.}, }
@article {pmid39838210, year = {2025}, author = {Ouyang, XM and Lin, JH and Lin, Y and Zhao, XL and Huo, YN and Liang, LY and Huang, YD and Xie, GJ and Mi, P and Ye, ZY and Guleng, B}, title = {The SERPINB4 gene mutation identified in twin patients with Crohn's disease impaires the intestinal epithelial cell functions.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {2638}, pmid = {39838210}, issn = {2045-2322}, support = {81970460//National Natural Science Foundation of China/ ; 2023J011598//Natural Science Foundation Program, Fujian Province, China/ ; }, mesh = {Humans ; *Crohn Disease/genetics/pathology ; Male ; Female ; *Mutation ; *Epithelial Cells/metabolism/pathology ; Apoptosis/genetics ; Adult ; Exome Sequencing ; *Intestinal Mucosa/metabolism/pathology ; Genetic Predisposition to Disease ; Cell Proliferation/genetics ; *Serpins/genetics ; Cell Movement/genetics ; }, abstract = {Crohn's disease (CD) is a chronic inflammatory autoimmune disease of unknown etiology. To identify new targets related to the initiation of CD, we screened a pair of twins with CD, which is a rare phenomenon in the Chinese population, for genetic susceptibility factors. Whole-exome sequencing (WES) of these patients revealed a mutation in their SERPINB4 gene. Therefore, we studied a wider clinical cohort of patients with CD or ulcerous colitis (UC), healthy individuals, and those with a family history of CD for this mutation by Sanger sequencing. The single-nucleotide difference in the SERPINB4 gene, which was unique to the twin patients with CD, led to the substitution of lysine by a glutamic acid residue. Functional analysis indicated that this mutation of SERPINB4 inhibited the proliferation, colony formation, wound healing, and migration of intestinal epithelial cells (IECs). Furthermore, mutation of SERPINB4 induced apoptosis and activated apoptosis-related proteins in IECs, and a caspase inhibitor significantly reduced these effects. Transcriptome sequencing revealed that the expression of genes encoding proinflammatory proteins (IL1B, IL6, IL17, IL24, CCL2, and CXCR2) and key proteins in the immune response (S100A9, MMP3, and MYC) was significantly upregulated during SERPINB4 mutant-induced apoptosis. Thus, the heterozygous SERPINB4 gene mutation causes the dysfunction of IECs, which would disrupt the intestinal epithelial barrier and contribute to the development of intestinal inflammation. The activation of SERPINB4 might represent a novel therapeutic target for inflammatory bowel disease.}, }
@article {pmid39838107, year = {2025}, author = {Teso-Pérez, C and López-Gazcón, A and Peralta-Sánchez, JM and Martínez-Bueno, M and Valdivia, E and Fárez-Vidal, ME and Martín-Platero, AM}, title = {Bacteriocin-Producing Enterococci Modulate Cheese Microbial Diversity.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {175}, pmid = {39838107}, issn = {1432-184X}, support = {PEJ2018-003019-A//Plan Estatal de Garant&#xed;a Juvenil (Fondo Social Europeo, Gobierno de Espa&#xf1;a/ ; Group BIO 309//PAIDI Program/ ; A-BIO-083-UGR18//Programa Operativo FEDER Andaluc&#xed;a 2014-2020/ ; }, mesh = {*Cheese/microbiology ; *Bacteriocins/biosynthesis/metabolism ; *Enterococcus/metabolism/genetics/classification/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Food Microbiology ; Biodiversity ; Microbiota ; Animals ; Milk/microbiology ; }, abstract = {Cheese production involves various lactic acid bacteria (LAB) that break down lactose, milk proteins, and fats, producing key nutrients and influencing the cheese's flavor. They form communities that play a crucial role in determining the cheese's organoleptic properties. The composition of cheeses' microbial communities is shaped by physicochemical factors (e.g., temperature, pH, and salinity) and biological factors (i.e. microbial interactions). While starter cultures are introduced to control these communities, non-starter LAB represent a significant portion of the final microbial assemblage, but their interactions remain unclear. LAB often produce bacteriocins, antimicrobial peptides that antagonize other bacteria, but their role within LAB communities is not fully understood. This study aimed to assess the impact of bacteriocin production on LAB diversity in cheese, using Enterococcus as a model organism, a common bacteriocin producer. We analyzed enterocin production of enterococcal isolates by antimicrobial assays and microbial diversity differences in raw milk cheeses by two approaches: 16S RNA gene amplicon metagenomic sequencing for the whole microbial community and multi-locus sequence analysis (MLSA) for the enterococcal diversity. Our results revealed that LAB communities were dominated by lactococci, lactobacilli, and streptococci, with enterococci present in lower numbers. However, cheeses containing bacteriocin-producing enterococci exhibited higher microbial diversity. Interestingly, the highest diversity occurred at low levels of bacteriocin producers, but this effect was not observed within enterococcal populations. These findings suggest that bacteriocin production plays a key role in shaping LAB communities during cheese ripening, although further research is needed to understand its broader implications in other microbial ecosystems.}, }
@article {pmid39836327, year = {2025}, author = {Flores Clavo, R and Suclupe-Campos, DO and Castillo Rivadeneira, L and Velez Chicoma, RLJ and Sánchez-Purihuamán, M and Quispe Choque, KG and Casado Peña, FL and Binatti Ferreira, M and Fantinatti Garboggini, F and Carreño-Farfan, C}, title = {Harnessing PGPRs from Asparagus officinalis to Increase the Growth and Yield of Zea mays L.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {174}, pmid = {39836327}, issn = {1432-184X}, mesh = {*Zea mays/growth &amp; development/microbiology ; *Soil Microbiology ; *Asparagus Plant/microbiology/growth &amp; development ; Plant Roots/microbiology/growth &amp; development ; Rhizosphere ; Peru ; *Bacteria/isolation &amp; purification/genetics/classification/metabolism ; RNA, Ribosomal, 16S/genetics ; Indoleacetic Acids/metabolism ; Salt Tolerance ; Soil/chemistry ; }, abstract = {Microbial biotechnology employs techniques that rely on the natural interactions that occur in ecosystems. Bacteria, including rhizobacteria, play an important role in plant growth, providing crops with an alternative that can mitigate the negative effects of abiotic stress, such as those caused by saline environments, and increase the excessive use of chemical fertilizers. The present study examined the promoting potential of bacterial isolates obtained from the rhizospheric soil and roots of the Asparagus officinalis cultivar UF-157 F2 in Viru, la Libertad, Peru. This region has high soil salinity levels. Seventeen strains were isolated, four of which are major potential plant growth-promoting traits, and were characterized based on their morphological and molecular characteristics. These salt-tolerant bacteria were screened for phosphate solubilization, indole acetic acid, deaminase activity, and molecular characterization by 16S rDNA sequencing. Fifteen samples were from saline soils of A. officinalis plants in the northern coastal desert of San Jose, Lambayeque, Peru. The bacterial isolates were screened in a range of salt tolerances from 3 to 6%. Isolates 05, 08, 09, and 11 presented maximum salt tolerance, ammonium quantification, phosphate solubilization, and IAA production. The four isolates were identified by sequencing the amplified 16S rRNA gene and were found to be Enterobacter sp. 05 (OQ885483), Enterobacter sp. 08 (OQ885484), Pseudomonas sp. 09 (OR398704) and Klebsiella sp. 11 (OR398705). These microorganisms promoted the germination of Zea mays L. plants, increased the germination rates in the treatments with chemical fertilizers at 100% and 50%, and the PGPRs increased the height and length of the roots 40 days after planting. The beneficial effects of salt-tolerant PGPR isolates isolated from saline environments may lead to new species that can be used to overcome the detrimental effects of salt stress on plants. The biochemical response and inoculation of the three isolates prove the potential of these strains as sources of products to develop new compounds, confirming their potential as biofertilizers for saline environments.}, }
@article {pmid39833680, year = {2025}, author = {Sbissi, I and Chouikhi, F and Ghodhbane-Gtari, F and Gtari, M}, title = {Ecogenomic insights into the resilience of keystone Blastococcus Species in extreme environments: a comprehensive analysis.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {51}, pmid = {39833680}, issn = {1471-2164}, mesh = {*Extreme Environments ; Phylogeny ; Genome, Bacterial ; Soil Microbiology ; Genomics ; Stress, Physiological ; Metals, Heavy ; }, abstract = {BACKGROUND: The stone-dwelling genus Blastococcus plays a key role in ecosystems facing extreme conditions such as drought, salinity, alkalinity, and heavy metal contamination. Despite its ecological significance, little is known about the genomic factors underpinning its adaptability and resilience in such harsh environments. This study investigates the genomic basis of Blastococcus's adaptability within its specific microniches, offering insights into its potential for biotechnological applications.<br><br>RESULTS: Comprehensive pangenome analysis revealed that Blastococcus possesses a highly dynamic genetic composition, characterized by a small core genome and a large accessory genome, indicating significant genomic plasticity. Ecogenomic assessments highlighted the genus's capabilities in substrate degradation, nutrient transport, and stress tolerance, particularly on stone surfaces and archaeological sites. The strains also exhibited plant growth-promoting traits, enhanced heavy metal resistance, and the ability to degrade environmental pollutants, positioning Blastococcus as a candidate for sustainable agriculture and bioremediation. Interestingly, no correlation was found between the ecological or plant growth-promoting traits (PGPR) of the strains and their isolation source, suggesting that these traits are not linked to their specific environments.<br><br>CONCLUSIONS: This research highlights the ecological and biotechnological potential of Blastococcus species in ecosystem health, soil fertility improvement, and stress mitigation strategies. It calls for further studies on the adaptation mechanisms of the genus, emphasizing the need to validate these findings through wet lab experiments. This study enhances our understanding of microbial ecology in extreme environments and supports the use of Blastococcus in environmental management, particularly in soil remediation and sustainable agricultural practices.}, }
@article {pmid39830292, year = {2024}, author = {Crous, PW and Wingfield, MJ and Jurjević, &#x17d; and Balashov, S and Osieck, ER and Marin-Felix, Y and Luangsa-Ard, JJ and Mejía, LC and Cappelli, A and Parra, LA and Lucchini, G and Chen, J and Moreno, G and Faraoni, M and Zhao, RL and Weholt, &#xd8; and Borovička, J and Jansen, GM and Shivas, RG and Tan, YP and Akulov, A and Alfenas, AC and Alfenas, RF and Altés, A and Avchar, R and Barreto, RW and Catcheside, DEA and Chi, TY and Esteve-Raventós, F and Fryar, SC and Hanh, LTM and Larsbrink, J and Oberlies, NH and Olsson, L and Pancorbo, F and Raja, HA and Thanh, VN and Thuy, NT and Ajithkumar, K and Akram, W and Alvarado, P and Angeletti, B and Arumugam, E and Khalilabad, AA and Bandini, D and Baroni, TJ and Barreto, GG and Boertmann, D and Bose, T and Castañeda Ruiz, RF and Couceiro, A and Cykowska-Marzencka, B and Dai, YC and Darmostuk, V and da Silva, SBG and Dearnaley, JDW and de Azevedo Santiago, ALCM and Declercq, B and de Freitas, LWS and De la Peña-Lastra, S and Delgado, G and de Lima, CLF and Dhotre, D and Dirks, AC and Eisvand, P and Erhard, A and Ferro, LO and García, D and García-Martín, A and Garrido-Benavent, I and Gené, J and Ghobad-Nejhad, M and Gore, G and Gunaseelan, S and Gusmão, LFP and Hammerbacher, A and Hernández-Perez, AT and Hernández-Restrepo, M and Hofmann, TA and Hubka, V and Jiya, N and Kaliyaperumal, M and Keerthana, KS and Ketabchi, M and Kezo, K and Knoppersen, R and Kolarczyková, D and Kumar, TKA and Læssøe, T and Langer, E and Larsson, E and Lodge, DJ and Lynch, MJ and Maciá-Vicente, JG and Mahadevakumar, S and Mateos, A and Mehrabi-Koushki, M and Miglio, BV and Noor, A and Oliveira, JA and Pereira, OL and Piątek, M and Pinto, A and Ramírez, GH and Raphael, B and Rawat, G and Renuka, M and Reschke, K and Mateo, AR and Saar, I and Saba, M and Safi, A and Sánchez, RM and Sandoval-Denis, M and Savitha, AS and Sharma, A and Shelke, D and Sonawane, H and Souza, MGAP and Stryjak-Bogacka, M and Thines, M and Thomas, A and Torres-Garcia, D and Traba, JM and Vauras, J and Vermaas, M and Villarreal, M and Vu, D and Whiteside, EJ and Zafari, D and Starink-Willemse, M and Groenewald, JZ}, title = {Fungal Planet description sheets: 1697-1780.}, journal = {Fungal systematics and evolution}, volume = {14}, number = {}, pages = {325-577}, pmid = {39830292}, issn = {2589-3831}, support = {P01 CA125066/CA/NCI NIH HHS/United States ; }, abstract = {Novel species of fungi described in this study include those from various countries as follows: Antarctica, Leuconeurospora bharatiensis from accumulated snow sediment sample. Argentina, Pseudocercospora quetri on leaf spots of Luma apiculata. Australia, Polychaetomyces verrucosus on submerged decaying wood in sea water, Ustilaginoidea cookiorum on Scleria levis, Xylaria guardiae as endophyte from healthy leaves of Macaranga tanarius. Belgium, Iodophanus taxi on leaf of Taxus baccata. Belize, Hygrocybe mirabilis on soil. Brazil, Gongronella irregularis from soil, Linodochium splendidum on decaying sheath of Euterpe oleracea, Nothophysalospora agapanthi (incl. Nothophysalospora gen. nov.) on flower stalks of Agapanthus praecox, Phaeosphaeria tabebuiae on leaf of Tabebuia sp., Verrucohypha endophytica (incl. Verrucohypha gen. nov.) from healthy roots of Acrocomia aculeata. Estonia, Inosperma apricum on soil under Quercus robur. Greece, Monosporascus solitarius isolated from surface-sterilised, asymptomatic roots of Microthlaspi perfoliatum. India, Diaporthe neocapsici on young seedling stems of Capsicum annuum, Fuscoporia naditirana on dead wood, Sebacina spongicarpa on soil, Torula kanvae from the gut of a Copris signatus beetle. Iran, Sarcinomyces pruni from twig and petiole tissues of Prunus persica and Prunus armeniaca, Xenodidymella quercicola from leaf spots of Quercus brantii. Italy, Agaricus aereiceps on grass, Agaricus bellui in meadows, Agaricus fabrianensis in urban grasslands, Beaucarneamyces muscorum on moss growing in forest, Xenoanthostomella quercus on leaf litter of Quercus ilex. Netherlands, Alfaria neerlandica on stem lesions of Cortaderia selloana, Neodictyosporium juncicola on culms of Juncus maritimus, Penicillium geertdesnooi from soil under Papaver rhoeas, Russula abscondita on rich calcareous soil with Quercus, Russula multiseptata on rich clay soil with Quercus, Russula purpureopallescens on soil with Populus, Sarocladium caricicola on leaves of Carex riparia. Pakistan, Circinaria shimlaensis on limestone rocks. Panama, Acrocalymma philodendri on leaf spots of Philodendron sp., Caligospora panamaensis on leaf litter, Chlamydocillium simulans associated with a Xylaria sp., Corynesporina panamaensis on leaf litter, Cylindromonium panamaense on twig litter of angiosperm, Cyphellophora panamaensis on twig litter of angiosperm, Microcera panamensis on leaf litter of fern, Pseudotricholoma pusillum in tropical montane forest dominated by Quercus spp., Striaticonidium panamaense on leaf litter, Yunnanomyces panamaensis on leaf litter. Poland, Albocremella abscondita (incl. Albocremella gen. nov.) from rhizoids of liverwort Conocephalum salebrosum. Portugal, Agaricus occidualis in meadows. South Africa, Alternaria elsarustiae on culms of unidentified Poaceae, Capronia capensis on dead twig of unidentified angiosperm, Codinaeella bulbinicola on dead leaves of Bulbine frutescens, Cytospora carpobroticola on leaf of Carpobrotus quadrifidus, Neophaeomoniella watsoniae on leaf of Watsonia sp., Neoplatysporoides aloigena on leaf of Aloe khamiesensis, Nothodactylaria comitabilis on living leaf of Itea rhamnoides, Nothopenidiella beaucarneae (incl. Nothopenidiella gen. nov.) on dead leaves of Beaucarnea stricta, Orbilia kirstenboschensis on dead flower stalks of Agapanthus praecox, Phragmocephala agapanthi on dead flower stalks of Agapanthus praecox, Podocarpigena hagahagaensis (incl. Podocarpigena gen. nov.) on leaf spots of Podocarpus falcatus, Sporisorium enterogonipteri from the gut of Gonipterus sp., Synnemapestaloides searsiae on leaf of Searsia populifolia, Xenophragmocapnias diospyri (incl. Xenophragmocapnias gen. nov.) on leaf spots of Diospyros sp., Yunnanomyces hagahagaensis on leaf spots of Sideroxylon inerme. Spain, Agaricus basicinctus in meadows, Agaricus quercetorum among leaf litter in oak forests, Coprinopsis palaciosii on degraded woody debris, Inocybe complutensis in calcareous loamy soil, Inocybe tanitiae in calcareous sandy soil, Mycena subfragosa on dead leaves of Salix atrocinerea, Pseudobaeospora cortegadensis in laurel forests, Trichoderma sedimenticola from fluvial sediments. Sweden, Inocybe badjelanndana on calcareous soil. Ukraine, Beaucarneamyces lupini on overwintered stems of Lupinus polyphyllus, Protocreopsis globulosa on thallus and apothecia of Lecania cyrtella on bark of Populus sp., Thyridium tiliae on dead twigs of Tilia sp. USA, Cladosporium louisianense, Cyphellophora americana from a bedroom vent, Extremus massachusettsianus from lyse buffer, Myxotrichum tapetae on carpet in basement, Neospissiomyces floridanus (incl. Neospissiomyces gen. nov.) on swab from hospital, Polychaetomyces marinus (incl. Polychaetomyces gen. nov.) on submerged driftwood in sea water, Steccherinum fragrans on hardwood fallen on the beach, Steinbeckomyces carnegieae (incl. Steinbeckomyces gen. nov.) on Carnegiea gigantea, Tolypocladium pennsylvanicum from air sampled in basement. Vietnam, Acidomyces ducanhii from Aglaia flowers, Acidomyces paludis from dead bark of Acacia sp., Phakopsora sageretiae on Sageretia theezans, Puccinia stixis on Stixis scandens. Morphological and culture characteristics are supported by DNA barcodes. Citation: Crous PW, Wingfield MJ, Jurjević Ž, et al. (2024). Fungal Planet description sheets: 1697-1780. Fungal Systematics and Evolution 14: 325-577. doi: 10.3114/fuse.2024.14.19.}, }
@article {pmid39828718, year = {2025}, author = {Wang, Z and Fuad, MTI and Liu, J and Lin, K and Liu, L and Gao, C and Wang, W and Liu, X}, title = {Spatial Patterns of Microbial Communities in Intertidal Sediments of the Yellow River Estuary, China.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {173}, pmid = {39828718}, issn = {1432-184X}, support = {41976131//National Natural Science Foundation of China/ ; }, mesh = {*Geologic Sediments/microbiology ; China ; *Archaea/classification/genetics/isolation &amp; purification ; *Bacteria/classification/genetics/isolation &amp; purification ; *Estuaries ; *Rivers/microbiology ; *Microbiota ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Ecosystem ; Metals, Heavy/analysis ; }, abstract = {Estuarine ecosystems are among the most important natural ecosystems on Earth and contribute substantially to human survival and development. The Yellow River Estuary (YRE) is the second largest estuary in China. Microbial communities play an essential role in the material cycle and energy flow in estuarine ecosystems. To date, our knowledge of the spatial patterns of bacterial and archaeal communities is limited. In this study, we investigated the spatial profile of bacterial and archaeal communities and their co-occurrence patterns, functional roles, and environmental driving factors in the intertidal sediments of the YRE from June to July, 2019. The results showed that Proteobacteria, Bacteroidetes, Chloroflexi, and Planctomycetes were the dominant bacterial phyla, whereas Nanoarchaeaeota, Euryarchaeota and Thaumarchaeota were the dominant archaeal phyla in the intertidal sediments of the YRE. Diversity indices and differential abundance analyses revealed significant (p < 0.05) differences in the bacterial and archaeal communities in the intertidal sediments of the YRE. Bacterial communities demonstrated distinct correlations with heavy metals and pollutants. Six archaeal genera exhibited co-occurrence patterns with bacterial genera. Functions associated with sulfur cycles, disease, and pollution were specific to bacterial communities. This study presents a detailed outline of the spatial patterns of microbial communities in the YRE, enriching our understanding of microbial ecology, especially of bacteria and archaea.}, }
@article {pmid39826456, year = {2025}, author = {Wang, Y and Zhang, F and Yang, L and Zhang, G and Wang, H and Zhu, S and Zhang, H and Guo, T}, title = {Synergy of plastics and heavy metals weakened soil bacterial diversity by regulating microbial functions in the Qinghai-Tibet Plateau.}, journal = {Journal of hazardous materials}, volume = {487}, number = {}, pages = {137241}, doi = {10.1016/j.jhazmat.2025.137241}, pmid = {39826456}, issn = {1873-3336}, mesh = {*Soil Microbiology ; *Metals, Heavy/toxicity/analysis ; *Soil Pollutants/toxicity/analysis ; *Bacteria/drug effects/genetics ; *Plastics/toxicity ; Tibet ; Biodiversity ; Soil/chemistry ; China ; *Microplastics/toxicity ; }, abstract = {How plastics coupled with metals regulate microbial functions-diversity relationships remain unknown in plateau soil environment. Three representative catchments in the Qinghai-Tibet Plateau, focusing on microplastics, their plasticisers, and metals in soils, were investigated. This research explores responses of bacterial diversity and functions to the co-existence of target pollutants, and pathways by which target pollutants regulate the diversity. Soil bacterial beta diversity and functional genes exhibited negative correlations with phthalate esters across three catchments (p < 0.05). Dibutyl phthalate emerged as a primary factor affecting beta diversity, rather than the quantity of microplastics. Additionally, the synergy of cadmium and fiber-shaped microplastics exacerbated the impact on diversity. Structural equation modeling further elucidated that plastics, copper, and iron influenced nirK/nirS genes and phoD gene, subsequently affected cbbL/cbbM genes, and ultimately the diversity. In this context, microplastics, phthalate esters and copper, iron exerted antagonistic effects on one another. Consequently, the co-existence of plastics and cadmium weakened soil bacterial diversity in the Qinghai-Tibet Plateau by disrupting microbial functions, but micronutrients alleviated these negative impacts. This research reveals that the co-existence of plastics and metals regulates soil bacterial diversity in the Qinghai-Tibet Plateau, providing a valuable reference for the protection of microbial ecology in plateau regions.}, }
@article {pmid39826104, year = {2025}, author = {Lin, A and Jiang, A and Huang, L and Li, Y and Zhang, C and Zhu, L and Mou, W and Liu, Z and Zhang, J and Cheng, Q and Wei, T and Luo, P}, title = {From chaos to order: optimizing fecal microbiota transplantation for enhanced immune checkpoint inhibitors efficacy.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2452277}, doi = {10.1080/19490976.2025.2452277}, pmid = {39826104}, issn = {1949-0984}, mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; *Immune Checkpoint Inhibitors/therapeutic use ; *Gastrointestinal Microbiome ; *Neoplasms/therapy/immunology/microbiology ; Animals ; Tumor Microenvironment ; Immunotherapy/methods ; Treatment Outcome ; }, abstract = {The integration of fecal microbiota transplantation (FMT) with immune checkpoint inhibitors (ICIs) presents a promising approach for enhancing cancer treatment efficacy and overcoming therapeutic resistance. This review critically examines the controversial effects of FMT on ICIs outcomes and elucidates the underlying mechanisms. We investigate how FMT modulates gut microbiota composition, microbial metabolite profiles, and the tumor microenvironment, thereby influencing ICIs effectiveness. Key factors influencing FMT efficacy, including donor selection criteria, recipient characteristics, and administration protocols, are comprehensively discussed. The review delineates strategies for optimizing FMT formulations and systematically monitoring post-transplant microbiome dynamics. Through a comprehensive synthesis of evidence from clinical trials and preclinical studies, we elucidate the potential benefits and challenges of combining FMT with ICIs across diverse cancer types. While some studies report improved outcomes, others indicate no benefit or potential adverse effects, emphasizing the complexity of host-microbiome interactions in cancer immunotherapy. We outline critical research directions, encompassing the need for large-scale, multi-center randomized controlled trials, in-depth microbial ecology studies, and the integration of multi-omics approaches with artificial intelligence. Regulatory and ethical challenges are critically addressed, underscoring the imperative for standardized protocols and rigorous long-term safety assessments. This comprehensive review seeks to guide future research endeavors and clinical applications of FMT-ICIs combination therapy, with the potential to improve cancer patient outcomes while ensuring both safety and efficacy. As this rapidly evolving field advances, maintaining a judicious balance between openness to innovation and cautious scrutiny is crucial for realizing the full potential of microbiome modulation in cancer immunotherapy.}, }
@article {pmid39825576, year = {2025}, author = {Fouché, J and Lebre, PH and Melville, HA and Cowan, DA}, title = {The Functional and Structural Succession of Mesic-Grassland Soil Microbiomes Beneath Decomposing Large Herbivore Carcasses.}, journal = {Environmental microbiology}, volume = {27}, number = {1}, pages = {e70022}, pmid = {39825576}, issn = {1462-2920}, mesh = {Animals ; *Soil Microbiology ; *Microbiota ; *Herbivory ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Grassland ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; }, abstract = {Plant detritus is abundant in grasslands but decomposes slowly and is relatively nutrient-poor, whereas animal carcasses are labile and nutrient-rich. Recent studies have demonstrated that labile nutrients from carcasses can significantly alter the long-term soil microbial function at an ecosystem scale. However, there is a paucity of knowledge on the functional and structural response and temporal scale of soil microbiomes beneath large herbivore carcasses. This study compared microbiome functions and structures of soil beneath Connochaetes taurinus (hereafter 'wildebeest') carcasses at various postmortem intervals of decomposition to matched control samples over 18 months. Microbial functions were compared by their community-level physiological profiles determined by sole-carbon substrate utilisation and structures by metagenomic sequences using 16S rRNA gene markers. Overall metabolism and metabolic diversity remained increased and functionally dissimilar to control soils throughout the experimental period, with successive sole-carbon substrate utilisation observed. Conversely, diversity was initially reduced and structurally dissimilar from the control soil but recovered within the experimental period. The study contributes to the knowledge of carcass decomposition by investigating the long-term soil microbiome dynamics resulting from large herbivore carcasses decomposing in a mesic grassland. Microbial functional succession and ecologically relevant bacterial biomarkers of soil beneath the decomposing carcasses were identified for various postmortem intervals.}, }
@article {pmid39825218, year = {2025}, author = {de Freitas, AS and Zagatto, LFG and Rocha, GS and Muchalak, F and Martins, GL and Silva-Zagatto, SDS and Hanada, RE and Muniz, AW and Tsai, SM}, title = {Harnessing the synergy of Urochloa brizantha and Amazonian Dark Earth microbiomes for enhanced pasture recovery.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {27}, pmid = {39825218}, issn = {1471-2180}, support = {2021/10626-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2022/05561-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 01.02.016301.00293/2021//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado do Amazonas/ ; }, mesh = {*Soil Microbiology ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; Soil/chemistry ; Plant Roots/microbiology ; Brazil ; *Poaceae/microbiology/growth &amp; development ; RNA, Ribosomal, 16S/genetics ; Rainforest ; Biodiversity ; DNA, Bacterial/genetics ; }, abstract = {Amazonian Dark Earths (ADEs) are fertile soils from the Amazon rainforest that harbor microorganisms with biotechnological potential. This study aimed to investigate the individual and potential synergistic effects of a 2% portion of ADEs and Urochloa brizantha cv. Marandu roots (Brazil's most common grass species used for pastures) on soil prokaryotic communities and overall soil attributes in degraded soil. We conducted a comprehensive plant succession experiment in the greenhouse, utilizing vase soil samples for next-generation sequencing of 16 S rDNA, enzymatic activity assays, and soil chemical properties analysis. Univariate and multivariate analyses were performed to understand better the prokaryotic interactions within soil environments influenced by ADEs and U. brizantha roots, including differential abundance, diversity, and network analyses. Our findings reveal a complementary relationship between U. brizantha and ADEs, each contributing to distinct positive aspects of soil bacterial communities and quality. The combined influence of U. brizantha roots and ADEs exhibited synergies that enhanced prokaryotic diversity and enzyme activity. This balance supported plant growth and increased the general availability of beneficial bacteria in the soil, such as Chujaibacter and Curtobacterium while reducing the presence of potentially pathogenic taxa. This research provided valuable insights into the intricate dynamics of plant-soil feedback, emphasizing the potential for complementary interactions between specific plant species and unique soil environments like ADEs. The findings highlight the potential for pasture ecological rehabilitation and underscore the benefits of integrating plant and soil management strategies to optimize soil characteristics.}, }
@article {pmid39821365, year = {2025}, author = {Zhang, D and Cai, Y and Sun, Y and Zeng, P and Wang, W and Wang, W and Jiang, X and Lian, Y}, title = {A Real-World Disproportionality Analysis of Histamine H2-Receptors Antagonists (Famotidine): A Pharmacovigilance Study Based on Spontaneous Reports in the FDA Adverse Event Reporting System.}, journal = {Drug development research}, volume = {86}, number = {1}, pages = {e70045}, doi = {10.1002/ddr.70045}, pmid = {39821365}, issn = {1098-2299}, support = {//This study was funded by the National Natural Science Foundation of China (Grant No: 82303109), the Natural Science Foundation of Fujian Province, China (Grant No: 2022J05299), Cross-Strait Postdoctoral Exchange Funding Program of Fujian Province, China (Grant No: 2021B002)./ ; }, mesh = {Humans ; *Pharmacovigilance ; *Adverse Drug Reaction Reporting Systems/statistics &amp; numerical data ; *Histamine H2 Antagonists/adverse effects/administration &amp; dosage ; United States ; United States Food and Drug Administration ; *Famotidine/adverse effects/administration &amp; dosage ; Female ; Male ; Middle Aged ; Adult ; Aged ; Young Adult ; Adolescent ; Databases, Factual ; Child ; }, abstract = {Famotidine is an H2 receptor antagonist and is currently used on a large scale in gastroenterology. However, Famotidine may also cause severe toxicity to organ systems, including the blood system, digestive system, and urinary system. The objective of this study was to scientifically and systematically investigate the adverse events (AEs) of Famotidine in the real world through the FDA Adverse Event Reporting System (FAERS) database. A disproportionality analysis was used to quantify the signals of AEs associated with Famotidine in FAERS data from the first quarter of 2004 to the first quarter of 2023. The clinical features, onset time, oral and intravenous administration and severe consequences of Famotidine induced AEs were further analyzed. Among the four tests, we found several AEs that were not mentioned in the drug label. For example, abdominal pain upper, abdominal discomfort, dyspepsia, liver disorder, gastrooesophageal reflux disease, and rhabdomyolysis. These AEs are consistent with the drug instructions. Interestingly, we found several unreported AEs, such as: cerebral infarction, hypocalcaemia, hallucination, visual, hypomagnesaemia, hypoparathyroidism, diabetes insipidus, vulvovaginal candidiasis, retro-orbital neoplasm, neuroblastoma recurrent, and malignant cranial nerve neoplasm. Most of our findings are consistent with clinical observations and drug labels, and we also found possible new and unexpected AEs signals, which suggest the need for prospective clinical studies to confirm these results and explain their relationships. Our findings provide valuable evidence for further safety studies.}, }
@article {pmid39820572, year = {2025}, author = {Azpiazu-Muniozguren, M and García-Martínez, M and Zabaleta, A and Antiguedad, I and Garaizar, J and Laorden, L and Martinez-Malaxetxebarria, I and Martinez-Ballesteros, I}, title = {Prokaryotic Diversity and Community Distribution in the Complex Hydrogeological System of the Añana Continental Saltern.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {171}, pmid = {39820572}, issn = {1432-184X}, support = {US19/01//Euskal Herriko Unibertsitatea/ ; GIU21/021//Euskal Herriko Unibertsitatea/ ; IT1678-22//Eusko Jaurlaritza/ ; }, mesh = {Spain ; *Archaea/classification/genetics/isolation &amp; purification ; *Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Salinity ; *Biodiversity ; Phylogeny ; *Natural Springs/microbiology ; *Saline Waters ; DNA, Bacterial/genetics ; Rivers/microbiology ; Water Microbiology ; DNA, Archaeal/genetics ; }, abstract = {The Añana Salt Valley (northern Spain) is a continental saltern consisting of a series of natural springs that have been used for salt production for at least 7000 years. This habitat has been relatively understudied; therefore, prokaryotic diversity was investigated through Illumina-based 16S rRNA gene sequencing to determine if the waters within the valley exhibit distinctive microbiological characteristics. Two main types of water were found in the valley: salty (approximately 200 g/L salinity) from the diapiric structure and brackish (≤ 20 g/L salinity) from shallow streams. The beta diversity indices showed that salinity was the primary factor influencing the prokaryotic distribution. However, a niche-specific influence was observed between waters of the same origin, with significant differences in the relative abundance of the ASVs. The microbiome of the saltern revealed that the archaeal domain was mainly restricted to salty waters, while the bacterial domain was ubiquitous throughout the saltern, with a notable prevalence in brackish waters. The main bacterial and archaeal phyla identified were Pseudomonadota and Halobacterota, respectively. The genus Halorubrum was abundant and widespread in salty waters, while Pseudomonas was a significant part of the prokaryote community, mainly in brackish waters. The relative abundance of the genera Haloplanus and Salinibacter increased in the salt ponds used for salt production. The taxa involved in chemoheterotrophy and fermentation were widespread, sharing the same niche. Overall, the location of this saltern on a diapiric structure favors the occurrence of waters with different origins that affect the prokaryotic distribution beyond the niche location in the valley.}, }
@article {pmid39820498, year = {2025}, author = {Luo, H and Xie, K and Dong, P and Zhang, Y and Ren, T and Sui, C and Ma, C and Zhao, C and Dewangan, NK and Gong, Z}, title = {Assessing the Risks of Potential Pathogens and Antibiotic Resistance Genes Among Heterogeneous Habitats in a Temperate Estuary Wetland: a Meta-analysis.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {172}, pmid = {39820498}, issn = {1432-184X}, support = {H2022011//Horizontal scientific research project (microbial-enhanced treatment of petroleum hydrocarbon pollutants: technical and engineering demonstration)/ ; 32303039//National Natural Science Foundation of China/ ; 2021DG700024-KF202425//State Key Laboratory for Managing Biotic and Chemical Threats to the Quality, Safety of Agro-products/ ; 30501466//Top-Notch Talents Program of Henan Agricultural University/ ; 242102111013//Henan Province Science and Technology Key Project/ ; 2023HNUAHEDF009//Initial Scientific Research Fund of Young Teachers in Henan University of Animal Husbandry and Economy/ ; }, mesh = {*Wetlands ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; *Estuaries ; Soil Microbiology ; Geologic Sediments/microbiology ; Ecosystem ; *Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Water Microbiology ; *Drug Resistance, Microbial/genetics ; Microbiota ; }, abstract = {Temperate estuary wetlands act as natural filters for microbiological contamination and have a profound impact on "One Health." However, knowledge of microbiological ecology security across the different habitats in temperate estuarine wetlands remains limited. This study employed meta-analysis to explore the characteristics of bacterial communities, potential pathogens, and antibiotic resistance genes (ARGs) across three heterogeneous habitats (water, soil, and sediment) within the Liaohe Estuary landscape. The diversity and composition of the three bacterial communities differed with biogeography, temperature, and pH, with the highest α-diversity showing a significantly negative correlation along latitude in soil. Furthermore, aminoglycosides were significantly enriched in water and soil, while dihydrofolate was more likely to be enriched in soil. The potential pathogens, Pseudoalteromonas and Planococcus, were dominant in water and sediment, while Stenotrophomonas was the dominant bacterium in soil. The network topology parameter revealed interspecific interactions within the community. PLS-PM highlights the main direct factors affecting the abundance of potential pathogens and the spread of ARGs, while temperature and pH indirectly influence these potential pathogens. This study advances our understanding of bacterial communities in estuarine wetlands, while highlighting the need for effective monitoring to mitigate the risks associated with potential pathogens and ARGs in these ecosystems.}, }
@article {pmid39820407, year = {2025}, author = {Hahn, MW and Kisand, V}, title = {Editorial: FEMS EC Thematic Issue "Aquatic Microbial Ecology".}, journal = {FEMS microbiology ecology}, volume = {101}, number = {2}, pages = {}, pmid = {39820407}, issn = {1574-6941}, abstract = {High relative abundance of yeast (Vishniacozyma, Papiliotrema, and Filobasidium) and bacterial (Massilia) genera found in spinach seeds correlates with suppression of Globisporangium ultimum damping-off infection.}, }
@article {pmid39817738, year = {2025}, author = {Wittlinger, J-P and Castejón, N and Hausmann, B and Berry, D and Schnorr, SL}, title = {Shewanella is a putative producer of polyunsaturated fatty acids in the gut soil of the composting earthworm Eisenia fetida.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {2}, pages = {e0206924}, pmid = {39817738}, issn = {1098-5336}, support = {847693//EC | H2020 | PRIORITY 'Excellent science' | H2020 Marie Sk&#x142;odowska-Curie Actions (MSCA)/ ; }, mesh = {*Oligochaeta/microbiology ; Animals ; *Gastrointestinal Microbiome ; *Fatty Acids, Unsaturated/metabolism/biosynthesis ; Composting ; *Soil Microbiology ; *Shewanella/metabolism/genetics ; RNA, Ribosomal, 16S/analysis/genetics ; Soil/chemistry ; Phylogeny ; Bacteria/classification/genetics/metabolism/isolation &amp; purification ; }, abstract = {Polyunsaturated fatty acids (PUFAs) play a crucial role in aiding bacteria to adapt to extreme and stressful environments. While there is a well-established understanding of their production, accrual, and transfer within marine ecosystems, knowledge about terrestrial environments remains limited. Investigation of the intestinal microbiome of earthworms has illuminated the presence of PUFAs presumably of microbial origin, which contrasts with the surrounding soil. To comprehensively study this phenomenon, a multi-faceted approach was employed, combining fatty acid analysis with amplicon sequencing of the PfaA-KS domain of the anaerobic fatty acid synthase gene (pfa), as well as the 16S rRNA and 18S rRNA genes. This methodology was applied to scrutinize the gut microbiome of Eisenia fetida, its compost-based dietary source, and the resultant castings. This study unveiled a distinct gut soil ecosystem from input compost and output castings in fatty acid profile as well as type and abundance of organisms. 16S sequencing provided insights into the microbial composition, showing increased relative abundance of certain Pseudomonadota, including Shewanellaceae, and Planctomycetota, including Gemmataceae within the gut microbiome compared to input bulk soil compost, while Actinomycetota and Bacillota were relatively enriched compared to the casted feces. Sequencing of the PfaA-KS domain revealed amplicon sequence variants (ASVs) belonging primarily to Shewanella. Intriguingly, the 20C PUFAs were identified only in gut soil samples, though PfaA-KS sequence abundance was highest in output castings, indicating a unique metabolism occurring only in the gut. Overall, the results indicate that Shewanella can explain PUFA enrichment in the gut environment because of the pfa gene presence detected via PfaA-KS sequence data.IMPORTANCEPrior research has demonstrated that earthworm microbiomes can potentially harbor polyunsaturated fatty acids (PUFAs) that are not found within their residing soil environment. Moreover, distinct indicator species have been pinpointed for various microbial genera in earthworm microbiomes. Nevertheless, none of these studies have integrated metataxonomic and fatty acid analyses to explore the origin of PUFA synthesis in any earthworm species, with the objective of identifying the specific organisms and locations responsible for this production. This study suggests that earthworms accumulate PUFAs produced from bacteria, especially Shewanella, activated through the gut ecosystem.}, }
@article {pmid39813101, year = {2025}, author = {Shan, Y and Hao, H and He, J and Hu, N and Liu, P and Zhan, M and Jiao, W and Yin, Y}, title = {Thermal Enhanced Electrokinetic Bacterial Transport in Porous Media.}, journal = {Environmental science &amp; technology}, volume = {59}, number = {3}, pages = {1683-1692}, doi = {10.1021/acs.est.4c07954}, pmid = {39813101}, issn = {1520-5851}, mesh = {Bacteria ; Kinetics ; Porosity ; Soil ; *Soil Microbiology ; }, abstract = {Soil bacterial communities are crucial to various ecosystem services, with significant implications for environmental processes and human health. Delivering functional bacterial strains to target locations enhances the preferred ecological features. However, the delivery process is often constrained by limited bacterial transport through low-permeability soil. Although electrokinetics breaks the bottleneck of bacterial transport in thin porous media, its efficiency remains limited. Here, we tested the hypothesis that thermal effects enhance electrokinetic transport by shifting the net force acting on the bacterium. We found that heating significantly increased electrokinetic transport by 2.75-fold at 1 V cm[-1] through porous media. Thermal enhancement mechanisms were interpreted by the heating shift of net force integrating matrix attractive and electrokinetic forces and verified by the Quartz Crystal Microbalance with Dissipation Monitoring (QCMD) observed adhesion rigidity shift. Thermal-dependent parameters liquid viscosity and dielectric constant were the primary contributors to the net force shift. Their variations reduce the attractive force and augment the electrokinetic forces, resulting in lower adhesion rigidity and enhanced bacterial transport. A mechanism-based approach interlinking electric field strength, thermal effect, and collision efficiency was established to facilitate the application of thermally enhanced electrokinetic bacterial transport. These findings provide new prospects for improving bacterial transport, hence optimizing soil ecosystem functions.}, }
@article {pmid39811355, year = {2025}, author = {Paredes Contreras, BV and Vermelho, AB and Casanova, L and de Alencar Santos Lage, C and Spindola Vilela, CL and da Silva Cardoso, V and Pacheco Arge, LW and Cardoso-Rurr, JS and Correa, SS and Passos De Mansoldo, FR and Pinheiro Pereira Reis-Mansur, MC and Alves da Silva, E and Schultz, J and Rosado, AS}, title = {Enhanced UV-B photoprotection activity of carotenoids from the novel Arthrobacter sp. strain LAPM80 isolated from King George Island, Antarctica.}, journal = {Heliyon}, volume = {11}, number = {1}, pages = {e41400}, pmid = {39811355}, issn = {2405-8440}, abstract = {Antarctica's harsh environmental conditions, characterized by high levels of ultraviolet (UV) radiation, pose challenges for microorganisms. To survive in these extreme cold regions with heightened UV exposure, microorganisms employ various adaptive strategies, including photoprotective carotenoid synthesis. Carotenoids are garnering attention in the skin health industry because of their UV photoprotection potential, given the direct relationship between UV exposure and skin burns, and cancer. Also, there is a growing demand for natural and environmentally friendly photoprotectors, such as microbial-based products, in opposition to synthetic photoprotective agents with known adverse effects. In this study, we assessed the carotenoid-producing abilities of Actinomycetota strains from Antarctic Peninsula soils and the photoprotective carotenoid action on UV irradiation resistance. Among 20 evaluated strains, one exhibited significant carotenoid production and it was identified through genomic analysis as a likely novel Arthrobacter sp. strain, LAPM80. This strain's genome revealed the presence of genes coding for the biosynthesis of decaprenoxanthin C50 carotenoid. The LAPM80 strain exhibited enhanced resistance against UV-B irradiation, correlating with increased total carotenoid production in its stationary growth phase. Chemical characterization of the carotenoid extract identified major components as C50 carotenoids, probably decaprenoxanthin and/or sarcinaxanthin. Scanning electron microscopy revealed minimal surface changes in bacteria during carotenoid-rich phase after UV-B irradiation exposure. These findings highlight the likely ability of LAPM80 strain's C50 carotenoids to improve UV-B iiradiation resistance, indicating their potential for developing natural photoprotective compounds for the dermo-cosmetic industry.}, }
@article {pmid39808188, year = {2025}, author = {Nguyen, MP and Lehosmaa, K and Martz, F and Koskimäki, JJ and Toth, K and Ahonen, SHK and Häggman, H and Pirttilä, AM}, title = {Dynamics of fungal endophytic communities in bilberry (Vaccinium myrtillus L.) fruits through development is shaped by host phenolic compounds.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {1}, pages = {}, pmid = {39808188}, issn = {1574-6941}, support = {//Finnish Cultural Foundation/ ; //European Regional Development Fund/ ; 240208//Alfred Kordelin Foundation/ ; }, mesh = {*Vaccinium myrtillus/microbiology/growth &amp; development/chemistry ; *Phenols/metabolism/analysis ; *Fruit/microbiology/growth &amp; development/chemistry ; *Endophytes/genetics/classification/physiology ; *Fungi/classification/genetics/isolation &amp; purification ; *Mycobiome ; }, abstract = {The physical and chemical properties of wild berry fruits change dramatically during development, and the ripe berries host species-specific endophytic communities. However, the development of fungal endophytic communities during berry ripening is unknown. We studied bilberries (Vaccinium myrtillus L.), valuable natural resources in northern Europe and richest sources of phenolic compounds, to characterize dynamics of the fungal communities over fruit developmental stages (raw, veraison, and ripe). Our focus was to examine the changes in the fruit phenolic compounds associated with the fungal community structure using liquid chromatography-mass spectrometry for phenolic compounds and high-throughput sequencing technology targeting the internal transcribed spacer 2 ribosomal DNA region for endophytic fungi. We found that the fungal diversity increased with the ripening stages. The fungal profile changed dramatically through fruit development, and the veraison stage was a transition stage, where the core mycobiome of fruits changed. The fungal community structure and abundance of the most dominant genera in raw and ripe stages, Monilinia and Cladosporium, respectively, were driven by the bilberry phenolic profile. We conclude that sampling time, tissue age, and phenolic compounds play important roles in the development of fruit fungal community. Moreover, phenolic compounds could be the host's strategy to recruit beneficial microbes.}, }
@article {pmid39807875, year = {2025}, author = {Schloss, PD}, title = {phylotypr: an R package for classifying DNA sequences.}, journal = {Microbiology resource announcements}, volume = {14}, number = {2}, pages = {e0114424}, pmid = {39807875}, issn = {2576-098X}, abstract = {The phylotypr R package implements the popular naive Bayesian classification algorithm that is frequently used to classify 16S rRNA and other gene sequences to taxonomic lineages. A companion data package, phylotyprrefdata, also provides numerous versions of taxonomic databases from the Ribosomal Database Project, SILVA, and greengenes.}, }
@article {pmid39806487, year = {2025}, author = {Dieppa-Colón, E and Martin, C and Kosmopoulos, JC and Anantharaman, K}, title = {Prophage-DB: a comprehensive database to explore diversity, distribution, and ecology of prophages.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {5}, pmid = {39806487}, issn = {2524-6372}, support = {R35 GM143024/GM/NIGMS NIH HHS/United States ; T32 GM135066/GM/NIGMS NIH HHS/United States ; R35GM143024/GM/NIGMS NIH HHS/United States ; T32GM135066/GM/NIGMS NIH HHS/United States ; }, abstract = {BACKGROUND: Viruses that infect prokaryotes (phages) constitute the most abundant group of biological agents, playing pivotal roles in microbial systems. They are known to impact microbial community dynamics, microbial ecology, and evolution. Efforts to document the diversity, host range, infection dynamics, and effects of bacteriophage infection on host cell metabolism are extremely underexplored. Phages are classified as virulent or temperate based on their life cycles. Temperate phages adopt the lysogenic mode of infection, where the genome integrates into the host cell genome forming a prophage. Prophages enable viral genome replication without host cell lysis, and often contribute novel and beneficial traits to the host genome. Current phage research predominantly focuses on lytic phages, leaving a significant gap in knowledge regarding prophages, including their biology, diversity, and ecological roles.<br><br>RESULTS: Here we develop and describe Prophage-DB, a database of prophages, their proteins, and associated metadata that will serve as a resource for viral genomics and microbial ecology. To create the database, we identified and characterized prophages from genomes in three of the largest publicly available databases. We applied several state-of-the-art tools in our pipeline to annotate these viruses, cluster them, taxonomically classify them, and detect their respective auxiliary metabolic genes. In total, we identify and characterize over 350,000 prophages and 35,000 auxiliary metabolic genes. Our prophage database is highly representative based on statistical results and contains prophages from a diverse set of archaeal and bacterial hosts which show a wide environmental distribution.<br><br>CONCLUSION: Given that prophages are particularly overlooked and merit increased attention due to their vital implications for microbiomes and their hosts, we created Prophage-DB to advance our understanding of prophages in microbiomes through a comprehensive characterization of prophages in publicly available genomes. We propose that Prophage-DB will serve as a valuable resource for advancing phage research, offering insights into viral taxonomy, host relationships, auxiliary metabolic genes, and environmental distribution.}, }
@article {pmid39805038, year = {2025}, author = {Wei, L and Van Beeck, W and Hanlon, M and DiCaprio, E and Marco, ML}, title = {Lacto-Fermented Fruits and Vegetables: Bioactive Components and Effects on Human Health.}, journal = {Annual review of food science and technology}, volume = {16}, number = {1}, pages = {289-314}, doi = {10.1146/annurev-food-052924-070656}, pmid = {39805038}, issn = {1941-1421}, mesh = {Humans ; *Fruit/chemistry/microbiology ; *Vegetables/chemistry/microbiology ; Fermentation ; *Fermented Foods/microbiology/analysis ; Food Microbiology ; }, abstract = {Lacto-fermented fruits and vegetables (FVs) such as kimchi, sauerkraut, and fermented olives and nonalcoholic juices have a long history as dietary staples. Herein, the production steps and microbial ecology of lacto-fermented FVs are discussed alongside findings from human and laboratory studies investigating the health benefits of these foods. Lacto-fermented FVs are enriched in beneficial live microbes and bioactive compounds, including lactic and acetic acids, phenolic compounds, bacteriocins, and amino acid derivatives such as indole-3-lactic acid, phenyl-lactic acid, and γ-aminobutyric acid. At least 11 human studies have been performed on kimchi, whereas others have been investigated in only one or two trials. Besides exploring the health benefits, it is imperative to ensure that these foods made either commercially or at home have minimal risk for foodborne illness and exposure to undesired compounds like biogenic amines. Development of starter-culture strains and production protocols can lead to lacto-fermented FVs designed for specific health benefits.}, }
@article {pmid39804671, year = {2025}, author = {Broderick, CM and Benucci, GMN and Bachega, LR and Miller, GD and Evans, SE and Hawkes, CV}, title = {Long-term climate establishes functional legacies by altering microbial traits.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {39804671}, issn = {1751-7370}, mesh = {*Soil Microbiology ; Metagenomics ; *Climate ; Carbon Cycle ; Soil/chemistry ; Droughts ; *Bacteria/genetics/classification/metabolism ; }, abstract = {Long-term climate history can influence rates of soil carbon cycling but the microbial traits underlying these legacy effects are not well understood. Legacies may result if historical climate differences alter the traits of soil microbial communities, particularly those associated with carbon cycling and stress tolerance. However, it is also possible that contemporary conditions can overcome the influence of historical climate, particularly under extreme conditions. Using shotgun metagenomics, we assessed the composition of soil microbial functional genes across a mean annual precipitation gradient that previously showed evidence of strong climate legacies in soil carbon flux and extracellular enzyme activity. Sampling coincided with recovery from a regional, multi-year severe drought, allowing us to document how the strength of climate legacies varied with contemporary conditions. We found increased investment in genes associated with resource cycling with historically higher precipitation across the gradient, particularly in traits related to resource transport and complex carbon degradation. This legacy effect was strongest in seasons with the lowest soil moisture, suggesting that contemporary conditions-particularly, resource stress under water limitation-influences the strength of legacy effects. In contrast, investment in stress tolerance did not vary with historical precipitation, likely due to frequent periodic drought throughout the gradient. Differences in the relative abundance of functional genes explained over half of variation in microbial functional capacity-potential enzyme activity-more so than historical precipitation or current moisture conditions. Together, these results suggest that long-term climate can alter the functional potential of soil microbial communities, leading to legacies in carbon cycling.}, }
@article {pmid39799671, year = {2025}, author = {Mo, Y and Abdolahpur Monikh, F and Jaffer, YD and Mugani, R and Ionescu, D and Chen, G and Yang, J and Grossart, HP}, title = {Effects of tire wear particles on freshwater bacterial-fungal community dynamics and subsequent elemental cycles using microcosms.}, journal = {Journal of hazardous materials}, volume = {487}, number = {}, pages = {137062}, doi = {10.1016/j.jhazmat.2024.137062}, pmid = {39799671}, issn = {1873-3336}, mesh = {*Bacteria/drug effects ; *Fungi/drug effects ; *Fresh Water/microbiology ; Lakes/microbiology ; Geologic Sediments/microbiology ; *Water Microbiology ; }, abstract = {Ecological impacts of tire wear particles (TWPs) on microbial communities and biogeochemical cycles in freshwater remain largely unknown. Here, we conducted a microcosm experiment to investigate interactions between the overlying water and sediment without and with TWPs addition in a rural vs. urban lake system. Our results revealed the degree of change in microbial community diversity in water is higher than that in sediment following TWPs addition. For bacterial communities, TWPs addition changed their composition in the water, but only little in the sediment. For fungal communities, TWPs addition changed their composition both in water and sediments. Furthermore, in water, TWPs addition increased network complexity between bacteria-bacteria, fungi-fungi and bacteria-fungi in the urban system but reduced it in the rural one. In contrast, TWPs presence did not significantly change network complexity among microbial communities in the sediment of both lakes. Isotope labeling analysis uncovered that based on a short-term (6 hours) incubation experiment, TWPs addition did not significantly change carbon nor nitrogen cycling in the water. Yet, certain changes could be observed, especially in the long-term experiment (1 month), indicating that TWPs pollution has the potential to impact elemental cycling and thus ecosystem functions by altering microbial communities. Our results provide new insights into TWPs-induced ecological effects on microorganisms and potential biogeochemical consequences in a rural vs. urban lakes.}, }
@article {pmid39798462, year = {2025}, author = {Kovarova, A and Prole, G and Farrell, ML and Maguire, M and Murphy, LC and Chueiri, A and O'Connor, L and Miliotis, G and Morris, D and Burke, LP}, title = {Antimicrobial resistant Enterobacterales of clinical importance in mute swans.}, journal = {The Science of the total environment}, volume = {961}, number = {}, pages = {178400}, doi = {10.1016/j.scitotenv.2025.178400}, pmid = {39798462}, issn = {1879-1026}, mesh = {*Enterobacteriaceae/drug effects ; Animals ; *Drug Resistance, Bacterial/genetics ; Ireland ; *Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; Feces/microbiology ; Clinical Relevance ; }, abstract = {Urban water environments, including canals, harbours and estuaries are susceptible to contamination with antimicrobials and drug-resistant bacteria through domestic and industrial wastewater discharges and storm water overflows. There is potential for wildlife using these waters to acquire and transmit drug-resistant bacteria and antimicrobial resistance genes (ARGs) of clinical importance. This study aimed to assess clinically important drug-resistant bacteria in urban waterfowl, particularly mute swans. Faecal samples were collected from 17 mute swans in the Greater Dublin Area, Ireland during July, August, October, and November of 2022. Samples were swabbed directly onto agars to select for carbapenem resistant, Extended-spectrum Beta-lactamase (ESBL)-producing, ciprofloxacin resistant and colistin resistant bacteria. Isolates identified by MALDI-TOF as Enterobacterales were tested for susceptibility to a panel of 16 antimicrobials and real-time PCR was employed to detect cefotaximase and carbapenemase genes (CRGs). Drug-resistant isolates were characterised by Whole Genome Sequencing (WGS), including long read sequencing for carbapenemase and mobile colistin resistance (mcr) gene-producing Enterobacterales isolates. Eleven of seventeen (65 %) swan samples were positive for the resistant organism(s) (n = 35), comprising Escherichia coli (n = 32; 82 %) and other Enterobacterales (n = 3). Twenty E. coli (63 %) produced ESBL, with 16/20 (80 %) identified as positive for blaCTX-M-group 1 enzymes, comprising CTX-M-15 (n = 13), CTX-M-55 (n = 2) and CTX-M-1 (n = 1) and 4/20 (20 %) positive for blaCTX-M-group 9 enzymes CTX-M-27 (n = 2) and CTX-M-9 (n = 2). Three E. coli isolates were phenotypically ertapenem resistant, one of which was an ST4450 isolate which carried plasmid encoded blaOXA-181 and blaCMY-141 with blaCTX-M-15 identified chromosomally. One colistin resistant E. coli bore the mcr-1 gene chromosomally. Bioinformatic analysis revealed high-risk pathogenic ESBL E. coli clones including ST38 (n = 3), ST69 (n = 3), and ST131 (n = 2). The study indicates mute swans are a reservoir for drug-resistant Enterobacterales and ARGs of clinical importance and may be a useful sentinel species for antimicrobial resistance (AMR) surveillance in wildlife.}, }
@article {pmid39798088, year = {2025}, author = {Stefanic, P and Stare, E and Floccari, VA and Kovac, J and Hertel, R and Rocha, U and Kovács, &#xc1;T and Mandić-Mulec, I and Strube, ML and Dragoš, A}, title = {Ecology of prophage-like elements in Bacillus subtilis at global and local geographical scales.}, journal = {Cell reports}, volume = {44}, number = {1}, pages = {115197}, doi = {10.1016/j.celrep.2024.115197}, pmid = {39798088}, issn = {2211-1247}, mesh = {*Bacillus subtilis/virology/genetics ; *Prophages/genetics ; Phylogeny ; Genome, Bacterial/genetics ; }, abstract = {Prophages constitute a substantial portion of bacterial genomes, yet their effects on hosts remain poorly understood. We examine the abundance, distribution, and activity of prophages in Bacillus subtilis using computational and laboratory analyses. Genome sequences from the NCBI database and riverbank soil isolates reveal prophages primarily related to mobile genetic elements in laboratory strains. Distinct and previously unknown prophages in local isolates prompt an investigation into factors shaping prophage presence, with phylogenetic relatedness predicting the prophage repertoire slightly better than geographical origin. Data also show that prophages exhibit strong co-occurrence and exclusion patterns within genomes. Laboratory experiments indicate that most predicted prophages are cryptic, as they are not induced under DNA-damaging conditions. Importantly, stress responses increase with the number of predicted prophages, suggesting their influence on host physiology. This study highlights the diversity, integration patterns, and potential roles of prophages in B. subtilis, shedding light on bacterial genome evolution and phage-host dynamics.}, }
@article {pmid39797436, year = {2025}, author = {Shopen Gochev, C and Demory, D and Lopes Dos Santos, A and Carlson, MCG and Gutiérrez-Rodríguez, A and Weitz, JS and Lindell, D}, title = {Cold Surface Waters of the Sub-Antarctic Pacific Ocean Support High Cyanophage Abundances and Infection Levels.}, journal = {Environmental microbiology}, volume = {27}, number = {1}, pages = {e70031}, pmid = {39797436}, issn = {1462-2920}, support = {2679/20//Israel Science Foundation/ ; 639682//Simons Foundation/ ; 721231//Simons Foundation/ ; 721254//Simons Foundation/ ; }, mesh = {*Cyanobacteria/classification/virology ; Pacific Ocean ; *Seawater/chemistry/microbiology/virology ; Bacteriophages ; Cold Temperature ; Iron/analysis ; }, abstract = {Cyanobacterial distributions are shaped by abiotic factors including temperature, light and nutrient availability as well as biotic factors such as grazing and viral infection. In this study, we investigated the abundances of T4-like and T7-like cyanophages and the extent of picocyanobacterial infection in the cold, high-nutrient-low-chlorophyll, sub-Antarctic waters of the southwest Pacific Ocean during austral spring. Synechococcus was the dominant picocyanobacterium, ranging from 4.7 × 10[3] to 1.2 × 10[5] cells∙mL[-1], while Prochlorococcus abundances were relatively low overall, ranging from 1.0 × 10[3] to 3.9 × 10[4] cells∙mL[-1]. Using taxon-specific, single-virus and single-cell polony methods, we found that cyanophages were on average 15-fold, and up to 50-fold, more abundant than cyanobacteria in these waters. T4-like cyanophages (ranging from 1.7 × 10[5] to 6.5 × 10[5] phage·mL[-1]) were 2.7-fold more abundant than T7-like cyanophages (ranging from 3.1 × 10[4] to 2.8 × 10[5] phage·mL[-1]). Picocyanobacteria were primarily infected by T4-like cyanophages with more Synechococcus (4.8%-12.1%) infected than Prochlorococcus (2.5%-6.2%), whereas T7-like cyanophages infected less than 1% of both genera. These infection levels translated to daily mortality in the range of 5.7%-26.2% and 2.9%-14.3% of the standing stock of Synechococcus and Prochlorococcus, respectively. Our findings suggest that T4-like cyanophages are significant agents of cyanobacterial mortality in the cold, low-iron, sub-Antarctic waters of the South Pacific Ocean.}, }
@article {pmid39794865, year = {2025}, author = {Passarelli-Araujo, H and Venancio, TM and Hanage, WP}, title = {Relating ecological diversity to genetic discontinuity across bacterial species.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {8}, pmid = {39794865}, issn = {1474-760X}, mesh = {*Genome, Bacterial ; *Bacteria/genetics/classification ; *Genetic Variation ; Phylogeny ; Mycobacterium tuberculosis/genetics ; Biodiversity ; }, abstract = {BACKGROUND: Genetic discontinuity represents abrupt breaks in genomic identity among species. Advances in genome sequencing have enhanced our ability to track and characterize genetic discontinuity in bacterial populations. However, exploring the degree to which bacterial diversity exists as a continuum or sorted into discrete and readily defined species remains a challenge in microbial ecology. Here, we aim to quantify the genetic discontinuity (δ) and investigate how this metric is related to ecology.<br><br>RESULTS: We harness a dataset comprising 210,129 genomes to systematically explore genetic discontinuity patterns across several distantly related species, finding clear breakpoints which vary depending on the taxa in question. By delving into pangenome characteristics, we uncover a significant association between pangenome saturation and genetic discontinuity. Closed pangenomes are associated with more pronounced breaks, exemplified by Mycobacterium tuberculosis. Additionally, through a machine learning approach, we detect key features such as gene conservation patterns and functional annotations that significantly impact genetic discontinuity prediction.<br><br>CONCLUSIONS: Our study clarifies bacterial genetic patterns and their ecological impacts, enhancing the delineation of species boundaries and deepening our understanding of microbial diversity.}, }
@article {pmid39794276, year = {2025}, author = {Tang, L and Manefield, M}, title = {Aeration promotes Proteobacteria over Firmicutes in macerated food waste, resulting in superior anaerobic digestion efficiency.}, journal = {FEMS microbiology letters}, volume = {372}, number = {}, pages = {}, doi = {10.1093/femsle/fnaf001}, pmid = {39794276}, issn = {1574-6968}, support = {//Department of Planning, Industry and Environment/ ; }, mesh = {Anaerobiosis ; *Proteobacteria/metabolism/genetics ; *Firmicutes/metabolism ; Biofuels ; Food ; Aerobiosis ; Food Loss and Waste ; }, abstract = {Aeration is a common pretreatment method to enhance biogas production via anaerobic digestion of waste organic feedstocks such as unused food. While impacts on downstream anaerobic digestion have been intensively investigated, the consequence of aeration on the microbial community in food waste has not been characterized. Food waste has a low pH resulting from the dominance of lactic acid bacteria within the Firmicutes phylum. This excludes other phylotypes with a higher potential to hydrolyse complex biopolymers in food waste. In this study, we reveal that aeration of macerated food waste results in a dramatic shift away from Firmicutes towards dominance of Proteobacteria that are better known for extracellular enzyme production. Given that hydrolysis is the rate limiting step in anaerobic digestion, this explains why aeration improves the efficiency of biogas production from food waste. The discovery that Proteobacteria dominate microbial communities in aerated food waste opens up opportunities to manipulate extracellular enzyme production through gene expression mechanisms common among Proteobacteria such as quorum sensing.}, }
@article {pmid39792461, year = {2025}, author = {Tan, G and LeCates, CN and Simpson, A and Holtzen, S and Parris, DJ and Stewart, FJ and Stockton, A and , }, title = {Amplicon Sequencing Reveals Diversity in Spatially Separated Microbial Communities in the Icelandic Mars Analog Environment Mælifellssandur.}, journal = {Astrobiology}, volume = {25}, number = {1}, pages = {72-81}, doi = {10.1089/ast.2023.0124}, pmid = {39792461}, issn = {1557-8070}, mesh = {*Mars ; Iceland ; *Extraterrestrial Environment ; *Microbiota/genetics ; Phylogeny ; Exobiology ; RNA, Ribosomal, 16S/genetics ; Geologic Sediments/microbiology ; Bacteria/genetics/classification ; Biodiversity ; Sequence Analysis, DNA ; }, abstract = {Exploration missions to Mars rely on landers or rovers to perform multiple analyses over geographically small sampling regions, while landing site selection is done using large-scale but low-resolution remote-sensing data. Utilizing Earth analog environments to estimate small-scale spatial and temporal variation in key geochemical signatures and biosignatures will help mission designers ensure future sampling strategies meet mission science goals. Icelandic lava fields can serve as Mars analog sites due to conditions that include low nutrient availability, temperature extremes, desiccation, and isolation from anthropogenic contamination. This work reports analysis of samples collected using methods analogous to those of planetary missions to characterize microbial communities at different spatial scales in Mælifellssandur, Iceland, an environment with homogeneity at "remote imaging" resolution (overall temperature, apparent moisture content, and regolith grain size). Although microbial richness did not vary significantly among samples, the phylogenetic composition of the sediment microbiome differed significantly among sites separated by 100 m, which suggests distinct microbial signatures despite apparent homogeneity from remote observations. This work highlights the importance of considering microenvironments in future life-detection missions to extraterrestrial planetary bodies.}, }
@article {pmid39792290, year = {2025}, author = {Foffi, R and Brumley, DR and Peaudecerf, FJ and Stocker, R and Słomka, J}, title = {Slower swimming promotes chemotactic encounters between bacteria and small phytoplankton.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {2}, pages = {e2411074122}, pmid = {39792290}, issn = {1091-6490}, support = {PZ00P2_202188//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (SNF)/ ; ANR-22-CPJ2-0015-01//Agence Nationale de la Recherche (ANR)/ ; GBMF9197//Gordon and Betty Moore Foundation (GBMF)/ ; 542395FY22//Simons Foundation (SF)/ ; 205321_207488//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (SNF)/ ; CRSII5-186422//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (SNF)/ ; 51NF40_180575//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (SNF)/ ; 955910//EC | Horizon Europe | Excellent Science | HORIZON EUROPE Marie Sklodowska-Curie Actions (MSCA)/ ; }, mesh = {*Phytoplankton/physiology ; *Chemotaxis/physiology ; Bacteria/metabolism ; Bacterial Physiological Phenomena ; Models, Biological ; }, abstract = {Chemotaxis enables marine bacteria to increase encounters with phytoplankton cells by reducing their search times, provided that bacteria detect noisy chemical gradients around phytoplankton. Gradient detection depends on bacterial phenotypes and phytoplankton size: large phytoplankton produce spatially extended but shallow gradients, whereas small phytoplankton produce steeper but spatially more confined gradients. To date, it has remained unclear how phytoplankton size and bacterial swimming speed affect bacteria's gradient detection ability and search times for phytoplankton. Here, we compute an upper bound on the increase in bacterial encounter rate with phytoplankton due to chemotaxis over random motility alone. We find that chemotaxis can substantially decrease search times for small phytoplankton, but this advantage is highly sensitive to variations in bacterial phenotypes or phytoplankton leakage rates. By contrast, chemotaxis toward large phytoplankton cells reduces the search time more modestly, but this benefit is more robust to variations in search or environmental parameters. Applying our findings to marine phytoplankton communities, we find that, in productive waters, chemotaxis toward phytoplankton smaller than 2 μm provides little to no benefit, but can decrease average search times for large phytoplankton (∼20 μm) from 2 wk to 2 d, an advantage that is robust to variations and favors bacteria with higher swimming speeds. By contrast, in oligotrophic waters, chemotaxis can reduce search times for picophytoplankton (∼1 μm) up to 10-fold, from a week to half a day, but only for bacteria with low swimming speeds and long sensory timescales. This asymmetry may promote the coexistence of diverse search phenotypes in marine bacterial populations.}, }
@article {pmid39789151, year = {2025}, author = {Frasca, S and Alabiso, A and D'Andrea, MM and Migliore, L}, title = {Uncovering the Fungal Community Composition of Alive and Dead Posidonia oceanica Matte.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {170}, pmid = {39789151}, issn = {1432-184X}, mesh = {*Alismatales/microbiology ; Ascomycota/genetics/classification/metabolism/growth &amp; development ; Mycobiome ; Fungi/genetics/classification/metabolism/isolation &amp; purification ; DNA, Fungal/genetics ; Seawater/microbiology ; Biodegradation, Environmental ; Geologic Sediments/microbiology ; Phylogeny ; }, abstract = {Posidonia oceanica retains a large amount of carbon within its belowground recalcitrant structure, the 'matte,' which is characterized by low oxygen availability and biodegradation. Fungi may play a pivotal role in carbon sequestration within the matte, even if little/no information is available. To fill this gap, we profiled fungal communities from the upper and lower layers of alive and dead matte, by using an ITS2-5.8S rDNA metabarcoding approach. The study was conducted in a shallow coastal stretch of the Aegean Sea (Crete). Then, 184 operational taxonomic units were identified, predominantly belonging to Ascomycota, in alive and dead matte. Nevertheless, their composition significantly differed: the host-specific Posidoniomyces atricolor was dominant in alive but not in dead matte, while fast-growing saprotrophs, potentially accelerating the decomposition rate, increased in dead matte. These findings lay the groundwork for future investigations on the possible increase of biodegradation under the changing environmental conditions.}, }
@article {pmid39788196, year = {2025}, author = {Kim, YT and Huang, YP and Ozturk, G and Hahn, J and Taha, AY and Wang, A and Barile, D and Mills, DA}, title = {Characterization of Bifidobacterium bifidum growth and metabolism on whey protein phospholipid concentrate.}, journal = {Journal of dairy science}, volume = {108}, number = {4}, pages = {3366-3381}, doi = {10.3168/jds.2024-25885}, pmid = {39788196}, issn = {1525-3198}, mesh = {*Bifidobacterium bifidum/metabolism/growth &amp; development ; *Whey Proteins ; Humans ; *Phospholipids/metabolism ; Milk, Human/chemistry ; Animals ; Oligosaccharides/metabolism ; }, abstract = {Whey protein phospholipid concentrate (WPPC) is a co-product generated during the manufacture of whey protein isolate. Whey protein phospholipid concentrate is depleted of simple sugars but contains numerous glycoconjugates embedded in the milk fat globule membrane, suggesting this fraction may serve as a carbon source for growth of bifidobacteria commonly enriched in breastfed infants. In this work, we demonstrate that WPPC can serve as a sole carbon source for the growth of Bifidobacterium bifidum, a species common to the breastfed infant and routinely used as a probiotic. Growth on WPPC fractions resulted in expression of key extracellular glycosyl hydrolases in B. bifidum associated with the catabolism of glycoproteins. Interestingly, this included induction of fucosidase genes in B. bifidum linked to catabolism of fucosylated human milk oligosaccharides even though the WPPC glycan possesses little fucose. Additional growth studies revealed that WPPC-glycan components N-acetylglucosamine or N-acetylgalactosamine were required for pre-activation of B. bifidum toward rapid growth on fucosylated human milk oligosaccharides. Growth on WPPC fractions also resulted in expression of extracellular sialidases in B. bifidum which promoted a consistent release of sialic acid, a well-known component of bovine milk oligosaccharides and glycoconjugates with potential effects on gut microbial ecology and host cognition. These studies suggest WPPC may serve as a promising bioactive component to facilitate probiotic activity for use in infant formulas and other synbiotic applications.}, }
@article {pmid39787750, year = {2025}, author = {Zhang, S and Wang, J and Liu, Z and Xia, X and Wu, X and Li, X and Liu, Y and Xu, Z and Marzadri, A and McDowell, WH and Cai, Y and Yang, Z}, title = {Temperature has an enhanced role in sediment N2O and N2 fluxes in wider rivers.}, journal = {Water research}, volume = {273}, number = {}, pages = {123095}, doi = {10.1016/j.watres.2025.123095}, pmid = {39787750}, issn = {1879-2448}, mesh = {*Rivers/chemistry ; *Geologic Sediments/chemistry ; *Nitrogen ; *Temperature ; *Nitrous Oxide ; China ; Denitrification ; Nitrates ; Bacteria/metabolism ; }, abstract = {Riverine N2O and N2 fluxes, key components of the global nitrogen budget, are known to be influenced by river size (often represented by average river width), yet the specific mechanisms behind these effects remain unclear. This study examined how environmental and microbial factors influenced sediment N2O and N2 fluxes across rivers with varying widths (2.8 to 2,000 m) in China. Sediment acted as sources of both N2O and N2 emissions, with both N2 (0.2 to 20.8 mmol m[-2] d[-1]) and N2O fluxes (0.7-54.2 μmol m[-2] d[-1]) decreasing significantly as river width increased. N2 fluxes were positively correlated with denitrifying bacterial abundance, whereas N2O fluxes, when normalized by the abundance of denitrifying bacteria, were negatively correlated with the abundance of N2O-reducing microbes. Water physicochemical factors, particularly temperature and nitrate, were more important drivers of these fluxes than sediment factors. Nitrate significantly increased denitrifying bacterial abundance, whereas higher temperatures enhanced cell-specific activity. Lower N2O and N2 emissions in wider rivers were attributed to decreased denitrifying microbial abundance and lower denitrification rates, in addition to the commonly assumed reduction in exogenous N2O and N2 inputs. Rolling regression analysis showed that nitrate concentration had a stronger effect on sediment N2O and N2 fluxes in narrower rivers, whereas temperature was more influential in wider rivers. This difference is attributed to more stable nitrate concentrations and decreased nitrogen removal efficiency in wider rivers, while temperature variation remained consistent across all river widths. Beyond sediments, temperature had a greater effect on excess N2O concentrations than nitrate in the overlying water of wider rivers (>165 m), highlighting its broader impact. This study provides new biogeochemical insights into how river width influences sediment N2O and N2 fluxes and highlights the importance of incorporating temperature into flux predictions, particularly for wider rivers.}, }
@article {pmid39786593, year = {2025}, author = {Xu, Y and Liang, J and Qin, L and Niu, T and Liang, Z and Li, Z and Chen, B and Zhou, J and Yu, K}, title = {The Dynamics of Symbiodiniaceae and Photosynthetic Bacteria Under High-Temperature Conditions.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {169}, pmid = {39786593}, issn = {1432-184X}, support = {42090041//National Natural Science Foundation of China/ ; 42090041//National Natural Science Foundation of China/ ; 42090041//National Natural Science Foundation of China/ ; 42090041//National Natural Science Foundation of China/ ; 42090041//National Natural Science Foundation of China/ ; 42090041//National Natural Science Foundation of China/ ; 42090041//National Natural Science Foundation of China/ ; 2018GXNSFAA281328//Guangxi scientific projects/ ; 2018GXNSFAA281328//Guangxi scientific projects/ ; 2018GXNSFAA281328//Guangxi scientific projects/ ; 2018GXNSFAA281328//Guangxi scientific projects/ ; 2018GXNSFAA281328//Guangxi scientific projects/ ; 2018GXNSFAA281328//Guangxi scientific projects/ ; }, mesh = {*Photosynthesis ; *Symbiosis ; *Anthozoa/microbiology/physiology ; China ; *Hot Temperature ; *Dinoflagellida/physiology ; Animals ; *Seasons ; Bacteria/classification/metabolism/genetics ; Cyanobacteria/physiology ; Chlorophyll A/metabolism ; }, abstract = {Coral thermal tolerance is intimately linked to their symbiotic relationships with photosynthetic microorganisms. However, the potential compensatory role of symbiotic photosynthetic bacteria in supporting Symbiodiniaceae photosynthesis under extreme summer temperatures remains largely unexplored. Here, we examined the seasonal variations in Symbiodiniaceae and photosynthetic bacterial community structures in Pavona decussata corals from Weizhou Island, Beibu Gulf, China, with particular emphasis on the role of photosynthetic bacteria under elevated temperature conditions. Our results revealed that Symbiodiniaceae density and Chlorophyll a concentration were lowest during the summer and highest in the winter. Notably, the summer bacterial community was predominately composed of the proteorhodopsin bacterium BD 1-7 _clade, alongside a significant increase in Cyanobacteria, particularly Synechococcus_CC9902 and Cyanobium_PCC-6307, which represented 61.85% and 31.48% of the total Cyanobacterial community, respectively. In vitro experiments demonstrated that Cyanobacteria significantly enhanced Symbiodiniaceae photosynthetic efficiency under high-temperature conditions. These findings suggest that the increased abundance of photosynthetic bacteria during summer may mitigate the adverse physiological effects of reduced Symbiodiniaceae density, thereby contributing to coral stability. Our study highlights a potential synergistic interaction between Symbiodiniaceae and photosynthetic bacteria, emphasizing the importance of understanding these dynamic interactions in sustaining coral resilience against environmental stress, although further research is necessary to establish their role in preventing coral bleaching.}, }
@article {pmid39786575, year = {2025}, author = {McNeal, R and Wells, JD and Tomberlin, JK}, title = {Bernard Greenberg: a legacy in medical, veterinary, and forensic entomology.}, journal = {Journal of medical entomology}, volume = {62}, number = {2}, pages = {231-235}, doi = {10.1093/jme/tjae158}, pmid = {39786575}, issn = {1938-2928}, mesh = {Animals ; History, 20th Century ; *Entomology/history ; *Forensic Entomology/history ; *Diptera/microbiology ; History, 21st Century ; Humans ; United States ; Veterinary Medicine/history ; }, abstract = {Bernard Greenberg was a ground-breaking scientist in the worlds of medical-veterinary and forensic entomology, studying the ability of flies to serve as a vector of human and other vertebrate pathogens. His work also extended beyond these topics, creating key studies on flies and their associated microbial ecology. These efforts led to numerous research publications and two books on flies and their associated microorganisms. Greenberg served a pioneering role in establishing the field of forensic entomology in the USA later in his career, publishing key papers and a book that are highly cited to this day. We present a review of Dr Greenberg's scientific contributions concerning flies and disease, insect/microbe interactions, and insects as forensic indicators.}, }
@article {pmid39779689, year = {2025}, author = {Cottin, A and Dequiedt, S and Djemiel, C and Prévost-Bouré, NC and Tripied, J and Lelièvre, M and Terreau, L and Régnier, T and Karimi, B and Jolivet, C and Bispo, A and Saby, N and Maron, PA and Ranjard, L and Terrat, S}, title = {Harmonized Datasets of microbiological parameters from a French national-scale soil monitoring survey.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {34}, pmid = {39779689}, issn = {2052-4463}, support = {2021PRE00370//Conseil r&#xe9;gional de Bourgogne-Franche-Comt&#xe9; (Regional Council of Burgundy)/ ; }, mesh = {*Soil Microbiology ; France ; *Fungi/genetics ; *Archaea/genetics ; *Bacteria/genetics/classification ; Environmental Monitoring ; Soil ; Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Microbiological datasets and associated environmental parameters from the French soil quality monitoring network (RMQS) offer an opportunity for long-term and large-scale soil quality monitoring. Soils supply important ecosystem services e.g. carbon dynamics/storage or mineral element recycling, supported by the soil microbial diversity (bacteria, archaea and fungi). Based on the 2,240 sites of the 2000-2015 RMQS, molecular tools were applied to characterize soil microbiota. Soil DNA analysis yielded molecular microbial biomass for 2,168 sites, bacterial and fungal qPCR for 2,073 sites, and high-throughput amplicon sequencing of targeted 16S rDNA bacterial and archaeal genes for 1,842 sites. All these datasets were partially or completely unavailable, so raw results files from RMQS microbiological studies were harmonized and published in a Dataverse repository to facilitate their reusability. Altogether, these datasets allow for in-depth studies of soil microbial ecology and biogeography, and will be updated with fungal datasets and the second currently ongoing monitoring campaign (2016-2027).}, }
@article {pmid39779584, year = {2025}, author = {Roy, A and Ray, S}, title = {Molecular Evolution of Paralogous Cold Shock Proteins in E. coli: A Study of Asymmetric Divergence and Protein Functional Networks.}, journal = {Molecular biotechnology}, volume = {}, number = {}, pages = {}, pmid = {39779584}, issn = {1559-0305}, abstract = {Nine homologous Cold Shock Proteins (Csps) have been recognized in the E.coli Cold Shock Domain gene family. These Csps function as RNA chaperones. This study aims to establish the evolutionary relationships among these genes by identifying and classifying their paralogous counterparts. It focuses on the physicochemical, structural, and functional analysis of the genes to explore the phylogeny of the Csp gene family. Computational tools were employed for protein molecular modeling, conformational analysis, functional studies, and duplication-divergence assessments. The research also examined amino acid conservation, protein mutations, domain-motif patterns, and evolutionary residue communities to better understand residual interactions, evolutionary coupling, and co-evolution. H33, M5, W11 and F53 residues were highly conserved within the protein family. It was further seen that residues M5, G17, G58, G61, P62, A64, V67 were intolerant to any kind of mutation whereas G3, D40, G41, Y42, S44, T54, T68, S69 were most tolerable towards substitutions. The study of residue communities displayed that the strongest residue coupling was observed in N13, F18, S27, F31, and W11. It was observed that all the gene pairs except CspF/CspH had new motifs generated over time. It was ascertained that all the gene pairs underwent asymmetric expression divergence after duplication. The Ka/ Ks ratio also revealed that all residues undertook neutral and purifying selection pressure. New functions were seen to develop in gene pairs evident from generation of new motifs. The discovery of new motifs and functions in Csps highlights their adaptive versatility, crucial for E. coli's resilience to environmental stressors and valuable for understanding bacterial stress response mechanisms. These findings will pave the way for future investigations into Csp evolution, with potential applications in microbial ecology and antimicrobial strategy development.}, }
@article {pmid39779304, year = {2025}, author = {Diakaki, M and Andreo Jimenez, B and de Lange, E and Butterbach, P and van der Heijden, L and Köhl, J and de Boer, W and Postma, J}, title = {Spinach seed microbiome characteristics linked to suppressiveness against Globisporangium ultimum damping-off.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {2}, pages = {}, pmid = {39779304}, issn = {1574-6941}, support = {//Ministry of Agriculture/ ; }, mesh = {*Spinacia oleracea/microbiology ; *Seeds/microbiology ; *Microbiota ; *Plant Diseases/microbiology/prevention &amp; control ; *Pythium/physiology ; Bacteria/classification/genetics/isolation &amp; purification ; Fungi/genetics/classification ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Recently we demonstrated that the seed microbiome of certain spinach (Spinacia oleracea) seed lots can confer disease suppression against Globisporangium ultimum damping-off (previously known as Pythium ultimum). We hypothesized that differences in the microbial community composition of spinach seed lots correlate with the levels of damping-off suppressiveness of each seed lot. Here, we show that a large proportion of variance in seed-associated bacterial (16S) and fungal (Internal Transcribed Spacer 1) amplicon sequences was explained by seed lot identity, while 9.8% of bacterial and 7.1% of fungal community variance correlated with disease suppression. More specifically, a higher relative abundance of basidiomycetous dimorphic yeasts such as Vishniacozyma, Filobasidium, and Papiliotrema and of the bacterial genus Massilia was a key feature of suppressive seed microbiomes. We suggest that the abundance of these genera is indicative of seed lot suppressive potential. Seed processing and treatment can become more targeted with indicator taxa being used to evaluate the presence of beneficial seed-associated microbial functions. This process, in turn, could contribute to the sustainable management of seedling diseases. Finally, this study highlights the ubiquity of yeasts in spinach seed microbiota and their potential beneficial roles for seed health.}, }
@article {pmid39777550, year = {2025}, author = {Byers, AK and Wakelin, SA and Condron, L and Black, A}, title = {Land Use Change Disrupts the Network Complexity and Stability of Soil Microbial Carbon Cycling Genes Across an Agricultural Mosaic Landscape.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {167}, pmid = {39777550}, issn = {1432-184X}, mesh = {*Soil Microbiology ; *Carbon Cycle ; New Zealand ; *Agriculture ; *Soil/chemistry ; *Microbiota ; *Bacteria/genetics/classification/metabolism ; Carbon/metabolism ; Gene Regulatory Networks ; Forests ; Ecosystem ; }, abstract = {To understand the effects of agricultural land use change and management on soil carbon (C) cycling, it is crucial to examine how these changes can influence microbial soil C cycling. Network analysis can offer insights into the structure, complexity, and stability of the soil microbiome in response to environmental disturbances, including land use change. Using SparCC-based co-occurrence networks, we studied how land use change impacts the connectivity, complexity, and stability of microbial C-cycling gene networks across an agricultural mosaic landscape in Canterbury, New Zealand. The most densely connected networks were found in land uses that were under the most intensive agricultural management, or under naturally regenerating vegetation. The microbial C-cycling gene networks from both land uses presented high network connectivity, low modularity, and a low proportion of negative gene interactions. In contrast, microbial C-cycling genes from native forests, which had the most stable and undisturbed plant cover, had the lowest network connectivity, highest modularity, and a greater proportion of negative gene interactions. Although the differences in total soil C content between land uses were small, the large effects of land use on the network structure of microbial C-cycling genes may have important implications for long-term microbial soil C cycling. Furthermore, this research highlights the value of using microbial network analysis to study the metabolic gene interactions shaping the functional structure of soil microbial communities in a manner not typically captured by more traditional forms of microbial diversity analysis.}, }
@article {pmid39777152, year = {2024}, author = {Liao, H and Wang, X and Wang, X and Zhang, M and Zhang, Y and Huang, S and Wang, H and Jin, H and Wang, J and Li, X and Yan, J and Schubert, T and Löffler, FE and Yang, Y}, title = {Organohalide respiration: retrospective and perspective through bibliometrics.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1490849}, pmid = {39777152}, issn = {1664-302X}, abstract = {Organohalide-respiring bacteria (OHRB) play a pivotal role in the transformation of organohalogens in diverse environments. This bibliometric analysis provides a timely overview of OHRB research trends and identifies knowledge gaps. Publication numbers have steadily increased since the process was discovered in 1982, with fluctuations in total citations and average citations per publication. The past decade witnessed a peak in publications, underscoring heightened research activity and extensive collaboration. Thematic analysis identified two primary research foci: mechanistic exploration of OHRB and their interplay with environmental factors. Future research should prioritize elucidating the roles OHRB's play in biogeochemical cycling, utilizing synthetic biology tools for enhanced biotransformation, deciphering OHRB's ecological interactions, unraveling their evolutionary pathways, and investigating dehalogenation capabilities in other microorganisms, including archaea. These research directions promise to advance our understanding of microbially-driven organohalide transformations, microbial ecology, and genetic engineering potential, ultimately informing natural organohalide cycling and environmental management strategies.}, }
@article {pmid39775407, year = {2025}, author = {Sun, X and Armstrong, M and Moradi, A and Bhattacharya, R and Antão-Geraldes, AM and Munthali, E and Grossart, HP and Matsuzaki, SS and Kangur, K and Dunalska, JA and Stockwell, JD and Borre, L}, title = {Impacts of climate-induced drought on lake and reservoir biodiversity and ecosystem services: A review.}, journal = {Ambio}, volume = {54}, number = {3}, pages = {488-504}, pmid = {39775407}, issn = {1654-7209}, support = {RGPIN-2019-04315//Natural Sciences and Engineering Research Council of Canada/ ; 1638679//U.S. National Science Foundation (NSF) Macrosystems Biology Program/ ; 722518//HORIZON EUROPE Marie Sklodowska-Curie Actions/ ; LA/P/0007/2020//SusTEC/ ; PRG 1266//Estonian Research Council/ ; JPMEERF20232002//Environmental Restoration and Conservation Agency/ ; 1702991//National Science Foundation/ ; UIDB/00690/2020//CIMO/ ; UIDP/00690/2020//CIMO/ ; PIDDAC//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; }, mesh = {*Droughts ; *Biodiversity ; *Lakes ; *Ecosystem ; *Climate Change ; Conservation of Natural Resources ; }, abstract = {Intensifying extreme droughts are altering lentic ecosystems and disrupting services provisioning. Unfortunately, drought research often lacks a holistic and intersectoral consideration of drought impacts, which can limit relevance of the insights for adaptive management. This literature review evaluated the current state of lake and reservoir extreme drought research in relation to biodiversity and three ecosystem services. The study findings demonstrated that few articles linked or discussed drought implications with one or more ecosystem services, instead focusing primarily on biodiversity. Drought effects on biodiversity varied among species and taxonomic groups. In the limited literature that included ecosystem service provisioning, droughts had a general negative effect. Drinking water supply can decrease and become more costly. Decreasing water flow and volume can reduce hydropower generation. Degraded water quality can also impact recreation. Future intersectoral collaborations and research on intensifying droughts should support adaptive management efforts in mitigating drought impacts.}, }
@article {pmid39774713, year = {2025}, author = {Dobrzyński, J and Kulkova, I and Jakubowska, Z and Wróbel, B}, title = {Non-native PGPB Consortium Altered the Rhizobacterial Community and Slightly Stimulated the Growth of Winter Oilseed Rape (Brassica napus L.) Under Field Conditions.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {168}, pmid = {39774713}, issn = {1432-184X}, support = {DDD.6509.00267.2022.15.//The research was funded by the European Agricultural Fund under the Rural Development Programme for 2014-2020/ ; DDD.6509.00267.2022.15.//The research was funded by the European Agricultural Fund under the Rural Development Programme for 2014-2020/ ; DDD.6509.00267.2022.15.//The research was funded by the European Agricultural Fund under the Rural Development Programme for 2014-2020/ ; DDD.6509.00267.2022.15.//The research was funded by the European Agricultural Fund under the Rural Development Programme for 2014-2020/ ; }, mesh = {*Brassica napus/microbiology/growth &amp; development ; *Soil Microbiology ; Pseudomonas/growth &amp; development/metabolism ; Plant Roots/microbiology/growth &amp; development ; Phosphorus/metabolism ; Bacteria/classification/genetics/isolation &amp; purification/growth &amp; development ; Nitrogen/metabolism ; Rhizosphere ; Microbial Consortia ; Indoleacetic Acids/metabolism ; Microbiota ; Azotobacter/growth &amp; development/metabolism ; }, abstract = {Plant growth-promoting bacteria (PGPB) are among the most promising alternatives to mineral fertilizers. However, little is known about the effects of applied bacteria on the native microbiota, including the rhizobacterial community, which plays a crucial role in bacteria-plant interactions. Therefore, this study is aimed at assessing the effects of PGPB not only on plants but also, importantly, on the native rhizobacterial community of winter oilseed rape. The bacterial consortium, consisting of Pseudomonas sp. KR227 and Azotobacter PBC1 (P2A), slightly promoted plant growth, increasing the root weight by 21.95% and seed yield by 18.94%. This likely results from its ability to produce indole-3-acetic acid (IAA), solubilize phosphorus, and fix nitrogen, as indicated by a 35.76% increase in N-NH4 and a 35.05% increase in available phosphorus (AP). The introduced PGPB altered the rhizobacterial community of rapeseed, increasing the relative abundance of the phylum Proteobacteria and the genus Pseudomonas while decreasing the relative abundance of phylum Verrucomicrobiota (3 weeks after inoculation). Moreover, Proteobacteria were positively correlated with AP, while Verrucomicrobiota were correlated with N-NH4. At the genus level, Flavobacterium and Pseudomonas were positively correlated with AP, whereas Candidatus Udaeobacter showed a positive correlation with N-NH4 and a negative correlation with pH. Importantly, the P2A consortium did not significantly affect the diversity of native rapeseed rhizobacteria. These findings suggest that the tested P2A consortium has potential as a biostimulant in rapeseed cultivation.}, }
@article {pmid39774673, year = {2025}, author = {Chen, SC and Chen, S and Musat, N and Kümmel, S and Ji, J and Lund, MB and Gilbert, A and Lechtenfeld, OJ and Richnow, HH and Musat, F}, title = {Author Correction: Back flux during anaerobic oxidation of butane support archaea-mediated alkanogenesis.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {453}, doi = {10.1038/s41467-024-55458-6}, pmid = {39774673}, issn = {2041-1723}, }
@article {pmid39772705, year = {2025}, author = {Zhou, J and Liu, Z and Wang, S and Li, J and Zhang, L and Liao, Z}, title = {A novel framework unveiling the importance of heterogeneous selection and drift on the community structure of symbiotic microbial indicator taxa across altitudinal gradients in amphibians.}, journal = {Microbiology spectrum}, volume = {13}, number = {2}, pages = {e0419223}, pmid = {39772705}, issn = {2165-0497}, support = {20190ZKK0303//The Second Tibetan Plateau Scientific Expedition and Research Program/ ; 32201424//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {Animals ; *Symbiosis ; *Microbiota/genetics ; *Amphibians/microbiology ; Altitude ; China ; *Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {UNLABELLED: Existing analytical frameworks for community assembly have a noticeable knowledge gap, lacking a comprehensive assessment of the relative contributions of individual or grouped microbial distinct sampling units (DSUs) and distinct taxonomic units (DTUs) to each mechanism. Here, we propose a comprehensive framework for identifying DTUs/DSUs that remarkably contribute to the various mechanisms sustaining microbial community structure. Amphibian symbiotic microbes along an altitudinal gradient from Sichuan Province, China, were employed to examine the proposed statistical framework. In different altitude groups, we found that heterogeneous selection governed the community structure of symbiotic microbes across DSUs, while stochastic processes tended to increase with altitude. For DTUs at phylum and family levels, drift emerged as the dominant mechanism driving the community structure in the most symbiotic microbial taxa, while heterogeneous selection governs the most dominant or indicator taxa. Notably, the relative contribution of heterogeneous selection was significantly positively correlated with the relative abundance and niche breadth of taxa, and negatively correlated with drift. We also detected that community assembly processes remarkably regulate the structure of symbiotic microbial communities and their correlation with environmental variables. Altogether, our modeling framework is a robust and valuable tool that further enlarges our insight into microbiota community assembly.<br><br>IMPORTANCE: Distinguishing the drivers regulating microbial community assembly is essential in microbial ecology. We propose a novel modeling framework to partition the relative contributions of each individual or group of microbial DSUs and DTUs into different underpinning mechanisms. An empirical study on amphibian symbiotic microbes notably enlarges insight into community assembly patterns in the herpetological symbiotic ecosystem and demonstrates that the proposed statistical framework is an informative and sturdy tool to quantify microbial assembly processes at both levels of DSUs and DTUs. More importantly, our proposed modeling framework can provide in-depth insights into microbiota community assembly within the intricate tripartite host-environment-microbe relationship.}, }
@article {pmid39772204, year = {2024}, author = {Obong'o, BO and Ogutu, FO and Hurley, SK and Okiko, GM and Mahony, J}, title = {Exploring the Microbial Ecology of Water in Sub-Saharan Africa and the Potential of Bacteriophages in Water Quality Monitoring and Treatment to Improve Its Safety.}, journal = {Viruses}, volume = {16}, number = {12}, pages = {}, pmid = {39772204}, issn = {1999-4915}, mesh = {Africa South of the Sahara ; *Bacteriophages/physiology ; *Water Quality ; *Water Microbiology ; *Water Purification/methods ; Bacteria/virology ; Humans ; Food Safety/methods ; Biodegradation, Environmental ; }, abstract = {Access to safe water and food is a critical issue in sub-Saharan Africa, where microbial contamination poses significant health risks. Conventional water treatment and food preservation methods have limitations in addressing water safety, particularly for antibiotic-resistant bacteria and other pathogenic microorganisms. This review explores the potential application of bacteriophages as an innovative solution for water treatment and food safety in the region. Bacteriophages specifically infect bacteria and offer a targeted approach to reducing bacterial load, including multidrug-resistant strains, without the drawbacks of chemical disinfectants. This review also highlights the advantages of phage bioremediation, including its specificity, adaptability, and minimal environmental impact. It also discusses various case studies demonstrating its efficacy in different water systems. Additionally, we underscore the need for further research and the development of region-specific phage applications to improve water quality and public health outcomes in sub-Saharan Africa. By integrating bacteriophage strategies into water treatment and food production, the region can address critical microbial threats, mitigate the spread of antimicrobial resistance, and advance global efforts toward ensuring safe water for all.}, }
@article {pmid39771075, year = {2024}, author = {Tapia, Y and Salazar, O and Seguel, O and Suazo-Hernández, J and Urdiales-Flores, D and Aponte, H and Urdiales, C}, title = {Optimizing Heavy Metal Uptake in Carpobrotus aequilaterus Through Electrokinetic Treatment: A Comprehensive Study on Phytoremediation from Mine Tailings.}, journal = {Toxics}, volume = {12}, number = {12}, pages = {}, pmid = {39771075}, issn = {2305-6304}, support = {3220201//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; }, abstract = {Copper mining drives economic growth, with the global demand expected to reach 120 million metric tons annually by 2050. However, mining produces tailings containing heavy metals (HMs), which poses environmental risks. This study investigated the efficacy of phytoremediation (Phy) combined with electrokinetic treatment (EKT) to increase metal uptake in Carpobrotus aequilaterus grown in tailings from the Metropolitan Region of Chile. The plants were exposed to varying voltages and treatment durations. In the control (no EKT), the root metal contents were Fe (1008.41 mg/kg) > Cu (176.38 mg/kg) > Mn (103.73 mg/kg) > Zn (30.26 mg/kg), whereas in the shoots, the order was Mn (48.69 mg/kg) > Cu (21.14 mg/kg) > Zn (17.67 mg/kg) > Fe (27.32 mg/kg). The optimal EKT (15 V for 8 h) significantly increased metal uptake, with roots accumulating Fe (5997.24 mg kg[-1]) > Mn (672 mg kg[-1]) > Cu (547.68 mg kg[-1]) > Zn (90.99 mg kg[-1]), whereas shoots contained Fe (1717.95 mg kg[-1]) > Mn (930 mg kg[-1]) > Cu (219.47 mg kg[-1]) > Zn (58.48 mg kg[-1]). Although EKT enhanced plant growth and biomass, higher voltages stressed the plants. Longer treatments were more effective, suggesting that EK-Phy is a promising method for remediating metal-contaminated tailings.}, }
@article {pmid39770685, year = {2024}, author = {Han, Y and He, J and Li, M and Peng, Y and Jiang, H and Zhao, J and Li, Y and Deng, F}, title = {Unlocking the Potential of Metagenomics with the PacBio High-Fidelity Sequencing Technology.}, journal = {Microorganisms}, volume = {12}, number = {12}, pages = {}, pmid = {39770685}, issn = {2076-2607}, support = {SQ2023YFE0102739//National Key Research and Development Program of China/ ; 2022A1515110819//Youth project of Guangdong Foshan joint fund of the Guangdong Natural Science Foundation/ ; 32170430//National Natural Science Foundation of China/ ; }, abstract = {Traditional methods for studying microbial communities have been limited due to difficulties in culturing and sequencing all microbial species. Recent advances in third-generation sequencing technologies, particularly PacBio's high-fidelity (HiFi) sequencing, have significantly advanced metagenomics by providing accurate long-read sequences. This review explores the role of HiFi sequencing in overcoming the limitations of previous sequencing methods, including high error rates and fragmented assemblies. We discuss the benefits and applications of HiFi sequencing across various environments, such as the human gut and soil, which provides broader context for further exploration. Key studies are discussed to highlight HiFi sequencing's ability to recover complete and coherent microbial genomes from complex microbiomes, showcasing its superior accuracy and continuity compared to other sequencing technologies. Additionally, we explore the potential applications of HiFi sequencing in quantitative microbial analysis, as well as the detection of single nucleotide variations (SNVs) and structural variations (SVs). PacBio HiFi sequencing is establishing a new benchmark in metagenomics, with the potential to significantly enhance our understanding of microbial ecology and drive forward advancements in both environmental and clinical applications.}, }
@article {pmid39770645, year = {2024}, author = {Neviani, E}, title = {The Natural Whey Starter Used in the Production of Grana Padano and Parmigiano Reggiano PDO Cheeses: A Complex Microbial Community.}, journal = {Microorganisms}, volume = {12}, number = {12}, pages = {}, pmid = {39770645}, issn = {2076-2607}, abstract = {Natural whey starter (NWS) is an undefined complex culture used in the production of Grana Padano and Parmigiano Reggiano PDO cheeses. The aim of this review is to discuss, in light of the latest research results, the role of NWS as a primary player in the cheese-making process, considering the microbial community scenario. NWS is traditionally produced by fermenting part of the whey collected at the end of a previous cheese-making process. The method used to produce NWS, based on the back-slopping principle, favors the selection of a microbiota composed mainly of thermophilic lactic acid bacteria. This method of preparation induces the survival of several different species and biotypes. The presence of such a mixture of strains facilitates the development of a natural starter characterized by a remarkable ability to adapt to non-standardized cheese-making parameters. NWS is a microbial community whose activity is not simply the result of the sum of the activities of individual microorganisms, but rather the activity of the community as a whole, in which each individual bacterial cell responds to the presence of the others. According to this traditional protocol, the NWS becomes the 'microbiological bond' between cheeses over time.}, }
@article {pmid39770585, year = {2024}, author = {Heczko, PB and Giemza, M and Ponikiewska, W and Strus, M}, title = {Importance of Lactobacilli for Human Health.}, journal = {Microorganisms}, volume = {12}, number = {12}, pages = {}, pmid = {39770585}, issn = {2076-2607}, support = {RPMP.01.02.01-12-0413/17.//The National Centre for Research and Development/ ; }, abstract = {As an extraordinarily diverse group of bacteria, lactobacilli are now classified into several genera, many of which still include "Lactobacillus" in their names. Despite their names, this group of lactic acid bacteria comprises microorganisms that are crucial for human health, especially during the early development of the human microbiota and immune system. The interactions between lactobacilli and components of the mucosal immunity lead to its shaping and development, which is possibly considered a prime mover in the advancement of the human immune system. Although much of the evidence backing the pivotal role of lactobacilli in maintaining human health comes from studies on probiotics aiming to elucidate the mechanisms of their functional activities and studies on mucosal immunity in germ-free mice, it is justifiable to extend observations on the properties of the individual probiotic Lactobacillus that are related to health benefits onto other strains sharing common characteristics of the species. In this review, we will discuss the acquisition, presence, and functions of lactobacilli in different human microbiota throughout their whole life, including those arising in the amnion and their interactions with mucosal and immune cells. Examples of immune system modulation by probiotic lactobacilli include their colonic competition for available nutrients, interference with colonization sites, competition for binding sites on gut epithelial cells, bacteriocin production, reduction of colonic pH, and nonspecific stimulation of the immune system.}, }
@article {pmid39770454, year = {2024}, author = {Atazhanova, GA and Levaya, YK and Badekova, KZ and Ishmuratova, MY and Smagulov, MK and Ospanova, ZO and Smagulova, EM}, title = {Inhibition of the Biofilm Formation of Plant Streptococcus mutans.}, journal = {Pharmaceuticals (Basel, Switzerland)}, volume = {17}, number = {12}, pages = {}, pmid = {39770454}, issn = {1424-8247}, support = {&#x410;&#x420;23488250//MINISTRY OF SCIENCE AND HIGHER EDUCATION OF REPUBLIC OF KAZAKHSTAN/ ; }, abstract = {This review is devoted to a systematic analysis of studies aimed at investigating plant extracts, essential oils and phytochemical compounds capable of inhibiting Streptococcus mutans biofilm formation. This paper investigates the effect of extracts, essential oils and individual plant compounds on inhibiting the biofilm formation of Streptococcus mutans, one of the major pathogens responsible for the development of dental caries. Using cultural microbiology and molecular biology techniques, the authors describe the mechanisms by which plant samples reduce Streptococcus mutans adhesion and growth. The results show that several plant components have antibacterial properties, contributing to the reduction of Streptococcus mutans colony numbers and inhibiting the synthesis of extract-exopolysaccharide matrices required for biofilm formation. This work highlights the potential of botanicals in inhibiting Streptococcus mutans biofilm formation, which can be applied as natural antimicrobial agents in the prevention and treatment of dental diseases. Views on the use of these plant extracts and their components in dental preparations such as toothpastes, rinses and gels aimed at preventing dental caries are evaluated. The review shows the relevance of the research to optimizing the use of plant extracts, essential oils, individual compounds and their active actions in the control of Streptococcus mutans biofilms.}, }
@article {pmid39769364, year = {2024}, author = {Grzyb, T and Szulc, J}, title = {Deciphering Molecular Mechanisms and Diversity of Plant Holobiont Bacteria: Microhabitats, Community Ecology, and Nutrient Acquisition.}, journal = {International journal of molecular sciences}, volume = {25}, number = {24}, pages = {}, pmid = {39769364}, issn = {1422-0067}, mesh = {*Microbiota ; *Bacteria/genetics/classification/metabolism ; *Plants/microbiology ; Biodiversity ; Ecosystem ; Phosphorus/metabolism ; Nitrogen/metabolism ; Symbiosis ; Nutrients/metabolism ; }, abstract = {While gaining increasing attention, plant-microbiome-environment interactions remain insufficiently understood, with many aspects still underexplored. This article explores bacterial biodiversity across plant compartments, including underexplored niches such as seeds and flowers. Furthermore, this study provides a systematic dataset on the taxonomic structure of the anthosphere microbiome, one of the most underexplored plant niches. This review examines ecological processes driving microbial community assembly and interactions, along with the discussion on mechanisms and diversity aspects of processes concerning the acquisition of nitrogen, phosphorus, potassium, and iron-elements essential in both molecular and ecological contexts. These insights are crucial for advancing molecular biology, microbial ecology, environmental studies, biogeochemistry, and applied studies. Moreover, the authors present the compilation of molecular markers for discussed processes, which will find application in (phylo)genetics, various (meta)omic approaches, strain screening, and monitoring. Such a review can be a valuable source of information for specialists in the fields concerned and for applied researchers, contributing to developments in sustainable agriculture, environmental protection, and conservation biology.}, }
@article {pmid39768235, year = {2024}, author = {Riekeles, M and Santos, B and Youssef, SA and Schulze-Makuch, D}, title = {Viability and Motility of Escherichia coli Under Elevated Martian Salt Stresses.}, journal = {Life (Basel, Switzerland)}, volume = {14}, number = {12}, pages = {}, pmid = {39768235}, issn = {2075-1729}, support = {Scholarship for Max Riekeles//Friedrich-Ebert-Stiftung e.V./ ; }, abstract = {This study investigates the effects of three Martian-relevant salts-sodium chlorate, sodium perchlorate, and sodium chloride-on the viability and motility of Escherichia coli, a model organism for understanding microbial responses to environmental stress. These salts are abundant on Mars and play a crucial role in forming brines, one of the few sources of stable liquid water on the planet. We analyze the survivability under different salt concentrations using colony plating. Additionally, we perform a semi-automated motility analysis, analyzing microbial speeds and motility patterns. Our results show that sodium perchlorate is the most toxic, followed by sodium chlorate, with sodium chloride being the least harmful. Both survivability and motility are affected by salt concentration and exposure time. Notably, we observe a short-lived increase in motility at certain concentrations, particularly under sodium chlorate and sodium perchlorate stress, despite rapid declines in cell viability, suggesting a stress response mechanism. Given that motility might enhance an organism's ability to navigate harsh and variable environments, it holds promise as a key biosignature in the search for life on Mars.}, }
@article {pmid39764393, year = {2024}, author = {Russo, CJ and Husain, K and Murugan, A}, title = {Soft Modes as a Predictive Framework for Low Dimensional Biological Systems across Scales.}, journal = {ArXiv}, volume = {}, number = {}, pages = {}, pmid = {39764393}, issn = {2331-8422}, support = {R35 GM151211/GM/NIGMS NIH HHS/United States ; }, abstract = {All biological systems are subject to perturbations: due to thermal fluctuations, external environments, or mutations. Yet, while biological systems are composed of thousands of interacting components, recent high-throughput experiments show that their response to perturbations is surprisingly low-dimensional: confined to only a few stereotyped changes out of the many possible. Here, we explore a unifying dynamical systems framework - soft modes - to explain and analyze low-dimensionality in biology, from molecules to eco-systems. We argue that this one framework of soft modes makes non-trivial predictions that generalize classic ideas from developmental biology to disparate systems, namely: phenocopying, dual buffering, and global epistasis. While some of these predictions have been borne out in experiments, we discuss how soft modes allow for a surprisingly far-reaching and unifying framework in which to analyze data from protein biophysics to microbial ecology.}, }
@article {pmid39762141, year = {2025}, author = {Nguyen, PN and Rehan, SM}, title = {Supporting wild bee development with a bacterial symbiont.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxae317}, pmid = {39762141}, issn = {1365-2672}, abstract = {AIMS: Wild bees foster diverse microbiota that may determine survival success of developing larvae. Here, we compare survivorship and microbial communities of Ceratina calcarata small carpenter bees reared from eggs across three treatments: maternally collected control provisions with diverse microbiota, sterile provisions, and probiotic provisions supplemented with a beneficial symbiont, Apilactobacillus kunkeei.<br><br>METHODS AND RESULTS: Survival probability and adult masses differed across treatments, with the probiotic treatment resulting in highest survivorship and masses. By comparing the bacterial (16S rRNA), fungal (ITS), and plant (rbcL) communities of adults reared across treatments, we characterized distinct microbial communities across each that suggest the microbiome may be sensitive to microbial succession and competition.<br><br>CONCLUSIONS: We describe positive implications for the usage of probiotics on wild bees. Furthermore, the sensitivity of bee microbiota's relationships to their host, floral resources, and the environment suggests that holistic approaches best encapsulate the complex network of interactions between bees and their microbes.}, }
@article {pmid39760916, year = {2025}, author = {García-Bodelón, &#xc1; and Baković, N and Cano, E and Useros, F and Lara, E and González-Miguéns, R}, title = {Predators in the Dark: Metabarcoding Reveals Arcellinida Communities Associated with Bat Guano, Endemic to Dinaric Karst in Croatia.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {166}, pmid = {39760916}, issn = {1432-184X}, support = {PID2021-128499NB-I00//Spanish Ministry of Science, Innovation and Universities/ ; PID2021-128499NB-I00//Spanish Ministry of Science, Innovation and Universities/ ; PID2021-128499NB-I00//Spanish Ministry of Science, Innovation and Universities/ ; PID2021-128499NB-I00//Spanish Ministry of Science, Innovation and Universities/ ; PID2021-128499NB-I00//Spanish Ministry of Science, Innovation and Universities/ ; Garant&#xed;a Juvenil CM 2021//Comunidad de Madrid (Spain)/ ; Garant&#xed;a Juvenil CM 2021//Comunidad de Madrid (Spain)/ ; Class: UP/I-612-07/21-48/170, Ref. No.: 517-10-1-1-21-3, 16.07.2021//Croatian Ministry of Economy and Sustainable Development/ ; }, mesh = {Croatia ; Animals ; *Chiroptera/microbiology ; *Caves/microbiology ; *Biodiversity ; *DNA Barcoding, Taxonomic ; Ecosystem ; Chironomidae/genetics ; Feces/microbiology ; Electron Transport Complex IV/genetics/analysis ; Geologic Sediments/microbiology ; Phylogeny ; }, abstract = {Karst caves, formed from the dissolution of soluble rocks, are characterized by the absence of photosynthetic activity and low levels of organic matter. Organisms evolve under these particular conditions, which causes high levels of endemic biodiversity in both macroorganism and microbes. Recent research has highlighted the presence of testate amoebae (Arcellinida) group in cave environments. This study investigates the diversity of Arcellinida in Dinaric karstic caves in Croatia, a global diversity hotspot, focusing on the influence of bat guano on community structure. Sediment samples were collected from two independent hydrosystems, and a metabarcoding approach was used to assess Arcellinida diversity at specific and intraspecific levels, using Arcellinid-specific primers to amplify the mitochondrial cytochrome oxidase subunit I (COI) region. Results reveal a significant impact of guano on both specific and intraspecific diversity of Arcellinida. Communities in guano-rich sites displayed higher diversity, abundance, and the presence of unique OTUs and genetic variants not observed in other habitats, highlighting the crucial role of bats as ecosystem engineers. In contrast, sites without guano hosted communities with low abundance and reduced biodiversity. These differences suggest the existence of guano-associated Arcellinida communities. This study provides new insights into the biodiversity of subterranean ecosystems and the ecological roles of Arcellinida in karstic environments.}, }
@article {pmid39760871, year = {2025}, author = {Mwaheb, MA and El-Aziz, BMA and Abd-Elhalim, BT and El-Kassim, NA and Radwan, TEE}, title = {Study of Different Cultivated Plants Rhizosphere Soil Fungi-Mediated Pectinase: Insights into Production, Optimization, Purification, Biocompatibility, and Application.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {165}, pmid = {39760871}, issn = {1432-184X}, mesh = {*Polygalacturonase/metabolism ; *Soil Microbiology ; *Rhizosphere ; Fungi/enzymology/metabolism/isolation &amp; purification/classification/genetics ; Aspergillus/metabolism/enzymology/isolation &amp; purification ; Egypt ; Fungal Proteins/metabolism ; }, abstract = {Microorganisms are preferred as an enzyme source due to their short lifespan, high production rate, affordability, and absence of harmful chemicals in enzymes generated from plant and animal sources. Fungi communities are biological factories for many bioactive compounds such as the important industrial enzyme pectinase. The current study dealt with production, optimization, purification, biocompatibility, and application of fungal pectinase obtained from five plant rhizospheres (banana, jarawa, lemon, tomato, and wheat) at Fayoum Governorate, Egypt. The highest pectinase degrading index (PDI) was scored for FB5, FJ2, and FW1 isolates. Pectinase production was also examined quantitively and the highest output of 1603.67, 1311.22, and 1264.83 U/ml was gained by FB5, FJ1, and FW1 fungal isolates, respectively. The most active pectinase-producing fungi were identified as Aspergillus niveus strain AUMC1624, A. niger strain AUMC16245, and A. brasiliensis strain AUMC16244, respectively. For pectinase production optimization, one factor at a time (OFAT) protocol was applied and revealed that A. niger, A. niveus, and A. brasiliensis reached maximum pectinase levels at 1% pectin after 5, 7, and 7 days, at 40, 45, and 45 °C, respectively. Obtained pectinases were partially purified using ammonium sulfate precipitation (ASP) and organic solvent precipitation (OSP) methods. The highest activity using the ASP method scored at 40-60% saturation with A. niger. The thermostability characterization of A. niger pectinase was reached with relative activities of 61.7, 69.0, 99.9, 91.3, and 90.6% at temperatures ranging between 30 and 70 °C. pH optimized at pH 5-7. The enzyme's molecular weight was approximately 30 kDa. The GC-mass analysis of pectinase end products included acetic acid ethyl ester, hexadecane carbonsaure methylase, and hexadecenoic acid. The biocompatibility was examined using a human skin cell line (HFb-4) for the first time, with a minimal half concentration (IC50) of 151.86 ± 0.76 U/ml. The biocompatible pectinase was applied as a clothes bioscouring agent with different concentrations of 1893.52 U/ml achieving the highest bioscouring with 20.0%.}, }
@article {pmid39760805, year = {2025}, author = {Willemsen, A and Manzano-Marín, A and Horn, M}, title = {Novel High-Quality Amoeba Genomes Reveal Widespread Codon Usage Mismatch Between Giant Viruses and Their Hosts.}, journal = {Genome biology and evolution}, volume = {17}, number = {1}, pages = {}, pmid = {39760805}, issn = {1759-6653}, support = {//European Union's Horizon 2020 research and innovation programme/ ; 891572//Marie Sklodowska-Curie/ ; 101039843//European Union/ ; //European Research Council Executive Agency/ ; //Austrian Science Fund/ ; }, mesh = {*Giant Viruses/genetics ; *Codon Usage ; *Amoeba/virology/genetics ; Genome, Protozoan ; Host Specificity ; Phylogeny ; Acanthamoeba/virology/genetics ; }, abstract = {The need for high-quality protist genomes has prevented in-depth computational and experimental studies of giant virus-host interactions. In addition, our current knowledge of host range is highly biased due to the few hosts used to isolate novel giant viruses. This study presents 6 high-quality amoeba genomes from known and potential giant virus hosts belonging to 2 distinct eukaryotic clades: Amoebozoa and Discoba. We employ their genomic data to investigate the predictability of giant virus host range. Using a combination of long- and short-read sequencing, we obtained highly contiguous and complete genomes of Acanthamoeba castellanii, Acanthamoeba griffini, Acanthamoeba terricola, Naegleria clarki, Vermamoeba vermiformis, and Willaertia magna, contributing to the collection of sequences for the eukaryotic tree of life. We found that the 6 amoebae have distinct codon usage patterns and that, contrary to other virus groups, giant viruses often have different and even opposite codon usage with their known hosts. Conversely, giant viruses with matching codon usage are frequently not known to infect or replicate in these hosts. Interestingly, analyses of integrated viral sequences in the amoeba host genomes reveal potential novel virus-host associations. Matching of codon usage preferences is often used to predict virus-host pairs. However, with the broad-scale analyses performed in this study, we demonstrate that codon usage alone appears to be a poor predictor of host range for giant viruses infecting amoeba. We discuss the potential strategies that giant viruses employ to ensure high viral fitness in nonmatching hosts. Moreover, this study emphasizes the need for more high-quality protist genomes. Finally, the amoeba genomes presented in this study set the stage for future experimental studies to better understand how giant viruses interact with different host species.}, }
@article {pmid39753761, year = {2025}, author = {Peng, Z and van der Heijden, MGA and Liu, Y and Li, X and Pan, H and An, Y and Gao, H and Qi, J and Gao, J and Qian, X and Tiedje, JM and Wei, G and Jiao, S}, title = {Agricultural subsoil microbiomes and functions exhibit lower resistance to global change than topsoils in Chinese agroecosystems.}, journal = {Nature food}, volume = {6}, number = {4}, pages = {375-388}, pmid = {39753761}, issn = {2662-1355}, mesh = {Agriculture ; Bacteria/classification/genetics/isolation &amp; purification ; Biodiversity ; China ; *Climate Change ; Crops, Agricultural/growth &amp; development ; *Ecosystem ; *Microbiota ; *Soil/chemistry ; *Soil Microbiology ; }, abstract = {Soils play a critical role in supporting agricultural production. Subsoils, below 20 cm, underpin fundamental agroecosystem sustainability traits including soil carbon storage, climate regulation and water provision. However, little is known about the ecological stability of subsoils in response to global change. Here we conducted a microcosm experiment to determine whether subsoils were more sensitive to global changes across 40 agricultural ecosystems in China, in combination with a multiple global change factor experiment and an in situ field study. We found that subsoils exhibited greater fluctuation in species diversity, community composition, and complexity of microbial networks and ecosystem functions than topsoils, indicating lower resistance to global changes. Soil biodiversity was a major driver of ecosystem resistance, surpassing climate and soil parameters. A reciprocal microorganism transplant experiment showed that microorganisms isolated from the topsoil are more resistant to global changes than those from subsoil. Our study emphasizes that subsoil ecosystems are sensitive to global changes, underscoring the importance of including subsoils in predictions of agricultural sustainability and crop productivity under changing environmental conditions.}, }
@article {pmid39745433, year = {2025}, author = {Grüterich, L and Woodhouse, JN and Mueller, P and Tiemann, A and Ruscheweyh, H-J and Sunagawa, S and Grossart, H-P and Streit, WR}, title = {Assessing environmental gradients in relation to dark CO2 fixation in estuarine wetland microbiomes.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {1}, pages = {e0217724}, pmid = {39745433}, issn = {1098-5336}, support = {407270017//Deutsche Forschungsgemeinschaft (DFG)/ ; 502681570//Deutsche Forschungsgemeinschaft (DFG)/ ; }, mesh = {*Wetlands ; *Microbiota ; *Carbon Dioxide/metabolism ; *Bacteria/metabolism/genetics/classification ; *Carbon Cycle ; Estuaries ; Soil Microbiology ; }, abstract = {UNLABELLED: The rising atmospheric concentration of CO2 is a major concern to society due to its global warming potential. In soils, CO2-fixing microorganisms are preventing some of the CO2 from entering the atmosphere. Yet, the controls of dark CO2 fixation are rarely studied in situ. Here, we examined the gene and transcript abundance of key genes involved in microbial CO2 fixation along major environmental gradients within estuarine wetlands. A combined multi-omics approach incorporating metabarcoding, deep metagenomic, and metatranscriptomic analyses confirmed that wetland microbiota harbor four out of seven known CO2 fixation pathways, namely, the Calvin cycle, reverse tricarboxylic acid cycle, Wood-Ljungdahl pathway, and reverse glycine pathway. These pathways are transcribed at high frequencies along several environmental gradients, albeit at different levels depending on the environmental niche. Notably, the transcription of the key genes for the reverse tricarboxylic acid cycle was associated with high nitrate concentration, while the transcription of key genes for the Wood-Ljungdahl pathway was favored by reducing, O2-poor conditions. The transcript abundance of the Calvin cycle was favored by niches high in organic matter. Taxonomic assignment of transcripts implied that dark CO2 fixation was mainly linked to a few bacterial phyla, namely, Desulfobacterota, Methylomirabilota, Nitrospirota, Chloroflexota, and Pseudomonadota.<br><br>IMPORTANCE: The increasing concentration of atmospheric CO2 has been identified as the primary driver of climate change and poses a major threat to human society. This work explores the mostly overlooked potential of light-independent CO2 fixation by soil microbes (a.k.a. dark CO2 fixation) in climate change mitigation efforts. Applying a combination of molecular microbial tools, our research provides new insights into the ecological niches where CO2-fixing pathways are most active. By identifying how environmental factors, like oxygen, salinity and organic matter availability, influence these pathways in an estuarine wetland environment, potential strategies for enhancing natural carbon sinks can be developed. The importance of our research is in advancing the understanding of microbial CO2 fixation and its potential role in the global climate system.}, }
@article {pmid39745058, year = {2025}, author = {Doyle, RT and Grieves, LA and Gerstein, AC}, title = {Microbial ecology and evolution.}, journal = {Canadian journal of microbiology}, volume = {71}, number = {}, pages = {1-3}, doi = {10.1139/cjm-2024-0192}, pmid = {39745058}, issn = {1480-3275}, }
@article {pmid39744675, year = {2024}, author = {Mathers, AJ and Li, TJX and He, Q and Narendra, S and Stoesser, N and Eyre, DW and Walker, AS and Barry, KE and Castañeda-Barba, S and Huang, FW and Parikh, H and Kotay, S and Crook, DW and Reidys, C}, title = {Developing a framework for tracking antimicrobial resistance gene movement in a persistent environmental reservoir.}, journal = {npj antimicrobials and resistance}, volume = {2}, number = {1}, pages = {50}, pmid = {39744675}, issn = {2731-8745}, abstract = {Mobile genetic elements are key to the global emergence of antibiotic resistance. We successfully reconstructed the complete bacterial genome and plasmid assemblies of isolates sharing the same bla KPC carbapenemase gene to understand evolution over time in six confined hospital drains over five years. From 82 isolates we identified 14 unique strains from 10 species with 113 bla KPC-carrying plasmids across 16 distinct replicon types. To assess dynamic gene movement, we introduced the 'Composite-Sample Complex', a novel mathematical approach to using probability to capture the directional movement of antimicrobial resistance genes. The Composite Sample Complex accounts for the co-occurrence of both plasmids and chromosomes within an isolate, and highlights likely gene donors and recipients. From the validated model, we demonstrate frequent transposition events of bla KPC from plasmids to other plasmids, as well as integration into the bacterial chromosome within specific drains. We present a novel approach to estimate the directional movement of antimicrobial resistance via gene mobilization.}, }
@article {pmid39744400, year = {2024}, author = {Bradbury, ES and Holland-Moritz, H and Gill, A and Havrilla, CA}, title = {Plant and soil microbial composition legacies following indaziflam herbicide treatment.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1450633}, pmid = {39744400}, issn = {1664-302X}, abstract = {Land stewards in dryland ecosystems across the western U.S. face challenges to manage the exotic grass Bromus tectorum (cheatgrass), which is a poor forage, is difficult to remove, and increases risk of catastrophic fire. Managers may consider using indaziflam (Rejuvra™), a relatively new pre-emergent herbicide, which may reduce cheatgrass cover within drylands. However, few studies have explored the effects of indaziflam on non-target organisms. We tested how indaziflam application impacted cover and biomass of native and exotics within the plant community and composition and diversity of the soil microbiome by comparing untreated and treated arid shrubland sites in Boulder County, Colorado, USA. We found that indaziflam application decreased cheatgrass cover by as much as 80% and increased native plant cover by the same amount. Indaziflam application also was associated with increased soil nitrate (NO3 [-]), decreased soil organic matter, and had a significant effect on the composition of the soil microbiome. Microbial community composition was significantly related to soil NO3 [-], soil organic matter, soil pH, and native species and cheatgrass biomass. An indicator species analysis suggested that indaziflam application shifted microbial communities. In untreated sites, ammonia-oxidizing bacteria Nitrosomonadaceae and nitrogen-digesting Opitutaceae and the fungi Articulospora proliferata were found. While in treated sites, ammonia-oxidizing archaea which are associated with intact drylands, Nitrososphaeraceae and toxin digesters and acidic-soil species Sphingomonas and Acidimicrobiia were significantly associated. Overall, these results demonstrate that indaziflam application can increase native plant recruitment, while also affecting soil properties and the soil microbiome. The findings from this study can be used to inform decision-making during dryland restoration planning process as indaziflam use may have benefits and unknown long-term consequences for the biogeochemistry and microbial ecology of the system.}, }
@article {pmid39742975, year = {2025}, author = {Dougherty, PE and Pedersen, MS and Forero-Junco, LM and Carstens, AB and Raaijmakers, JM and Riber, L and Hansen, LH}, title = {Novel bacteriophages targeting wheat phyllosphere bacteria carry DNA modifications and single-strand breaks.}, journal = {Virus research}, volume = {352}, number = {}, pages = {199524}, pmid = {39742975}, issn = {1872-7492}, mesh = {*Triticum/microbiology/virology ; Phylogeny ; *Bacteriophages/genetics/classification/isolation &amp; purification ; *Erwinia/virology ; Genome, Viral ; *Pseudomonas/virology ; DNA, Viral/genetics ; Microbiota ; Plant Leaves/microbiology ; Metagenome ; }, abstract = {The phyllosphere microbiome can positively or negatively impact plant health and growth, but we currently lack the tools to control microbiome composition. Contributing to a growing collection of bacteriophages (phages) targeting bacteria living in the wheat phyllosphere, we here isolate and sequence eight novel phages targeting common phyllosphere Erwinia and Pseudomonas strains, including two jumbo phages. We characterize genomic, phylogenetic, and morphological traits from these phages and argue for establishing four novel viral genera. We also search the genomes for anti-defense systems and investigate DNA modifications using Nanopore sequencing. In Pseudomonas phage Rembedalsseter we find evidence of 13 motif-associated single-stranded DNA breaks. A bioinformatics search revealed that 60 related Pseudomonas phages are enriched in the same motif, suggesting these single-stranded nicks may be widely distributed in this family of phages. Finally, we also search the Sequence Read Archive for similar phages in public metagenomes. We find close hits to the Erwinia jumbo-phage Kaldavass in a wide variety of plant, food, and wastewater metagenomes including a near-perfect hit from a Spanish spinach sample, illustrating how interconnected geographically distant phages can be.}, }
@article {pmid39742000, year = {2024}, author = {Ford, SE and Slater, GF and Engel, K and Warr, O and Lollar, GS and Brady, A and Neufeld, JD and Lollar, BS}, title = {Deep terrestrial indigenous microbial community dominated by Candidatus Frackibacter.}, journal = {Communications earth &amp; environment}, volume = {5}, number = {1}, pages = {795}, pmid = {39742000}, issn = {2662-4435}, abstract = {Characterizing deep subsurface microbial communities informs our understanding of Earth's biogeochemistry as well as the search for life beyond the Earth. Here we characterized microbial communities within the Kidd Creek Observatory subsurface fracture water system with mean residence times of hundreds of millions to over one billion years. 16S rRNA analysis revealed that biosamplers well isolated from the mine environment were dominated by a putatively anaerobic and halophilic bacterial species from the Halobacteroidaceae family, Candidatus Frackibacter. Contrastingly, biosamplers and biofilms exposed to the mine environment contained aerobic Sphingomonas taxa. δ[13]C values of phospholipid fatty acids and putative functional predictions derived from 16S rRNA gene profiles, imply Candidatus Frackibacter may use carbon derived from ancient carbon-rich layers common in these systems. These results indicate that Candidatus Frackibacter is not unique to hydraulically fracked sedimentary basins but rather may be indigenous to a wide range of deep, saline groundwaters hosted in carbon-rich rocks.}, }
@article {pmid39741633, year = {2024}, author = {Zhang, D and Cai, Y and Sun, Y and Zeng, P and Wang, W and Wang, W and Jiang, X and Lian, Y}, title = {A real-world pharmacovigilance study of Sorafenib based on the FDA Adverse Event Reporting System.}, journal = {Frontiers in pharmacology}, volume = {15}, number = {}, pages = {1442765}, pmid = {39741633}, issn = {1663-9812}, abstract = {AIMS: The primary objective of this study was to closely monitor and identify adverse events (AEs) associated with Sorafenib, a pharmacological therapeutic agent used to treat hepatocellular carcinoma, renal cell carcinoma, and thyroid cancer. The ultimate goal was to optimize patient safety and provide evidence-based guidance for the appropriate use of this drug.<br><br>METHODS: Reports from the FDA Adverse Event Reporting System (FAERS) database were comprehensively collected and analyzed, covering the first quarter of 2004 to the first quarter of 2024. Disproportionality analysis was performed using robust algorithms for effective data mining to quantify the signals associated with Sorafenib-related AEs.<br><br>RESULTS: In total, we identifued 18,624 patients (82,857 AEs in the Sorafenib population) from the collected reports and examined, the occurrence of Sorafenib-induced AEs in 26 organ systems. The study results revealed the presence of the expected AEs, including Diarrhoea, Palmar-plantar erythrodysaesthesia syndrome, Hepatocellular carcinoma, Fatigue, and Rash, which was consistent with the information provided in the drug insert. In addition, unexpected significant AEs, such as Gait inability, Palmoplantar keratoderma and Hyperkeratosis were observed at the preferred term (PT) level. These findings suggest the potential occurrence of adverse reactions not currently documented in drug descriptions.<br><br>CONCLUSION: This study successfully detected new and unforeseen signals associated with Sorafenib-related AEs related to Sorafenib administration, providing important insights into the complex correlations between AEs and Sorafenib use. The results of this study emphasize the critical importance of continuous and vigilant surveillance for the timely identification and effective management of AEs to improve the overall patient safety and wellbeing in the context of Sorafenib therapy.}, }
@article {pmid39739109, year = {2024}, author = {Rovira-Alsina, L and Romans-Casas, M and Perona-Vico, E and Ceballos-Escalera, A and Balaguer, MD and Bañeras, L and Puig, S}, title = {Microbial Electrochemical Technologies: Sustainable Solutions for Addressing Environmental Challenges.}, journal = {Advances in biochemical engineering/biotechnology}, volume = {}, number = {}, pages = {}, pmid = {39739109}, issn = {0724-6145}, abstract = {Addressing global challenges of waste management demands innovative approaches to turn biowaste into valuable resources. This chapter explores the potential of microbial electrochemical technologies (METs) as an alternative opportunity for biowaste valorisation and resource recovery due to their potential to address limitations associated with traditional methods. METs leverage microbial-driven oxidation and reduction reactions, enabling the conversion of different feedstocks into energy or value-added products. Their versatility spans across gas, food, water and soil streams, offering multiple solutions at different technological readiness levels to advance several sustainable development goals (SDGs) set out in the 2030 Agenda. By critically examining recent studies, this chapter uncovers challenges, optimisation strategies, and future research directions for real-world MET implementations. The integration of economic perspectives with technological developments provides a comprehensive understanding of the opportunities and demands associated with METs in advancing the circular economy agenda, emphasising their pivotal role in waste minimisation, resource efficiency promotion, and closed-loop system renovation.}, }
@article {pmid39738334, year = {2024}, author = {Ahadi, R and Bouket, AC and Alizadeh, A and Masigol, H and Grossart, HP}, title = {Globisporangium tabrizense sp. nov., Globisporangium mahabadense sp. nov., and Pythium bostanabadense sp. nov. (Oomycota), three new species from Iranian aquatic environments.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {31701}, pmid = {39738334}, issn = {2045-2322}, mesh = {Iran ; *Phylogeny ; *Pythium/genetics/isolation &amp; purification ; Oomycetes/genetics/classification/isolation &amp; purification ; Cucumis sativus/microbiology ; }, abstract = {During a survey on the biodiversity of oomycetes in aquatic environments in northwest Iran (East Azarbaijan and West Azarbaijan provinces), three Pythium and four Globisporangium isolates were recovered from agricultural water pools and irrigation canals, respectively. Through a polyphasic approach combining morphology and phylogenetic analysis using the nuclear rDNA ITS1-5.8 S-ITS2 (ITS) and partial sequences of the cytochrome c oxidase subunit I and II (COX1 and COX2), three novel species were identified namely Globisporangium tabrizense sp. nov., G. mahabadense sp. nov., and Pythium bostanabadense sp. nov. Furthermore, experiments confirmed the pathogenicity of all identified species on cucumber seedlings, suggesting a pathogenic lifestyle also in aquatic systems. Our research contributes to a better understanding of the diversity, host range and distribution of oomycetes genera Globisporangium and Pythium in northwestern Iran. Detailed morphological descriptions and illustrations are provided for all species.}, }
@article {pmid39737770, year = {2025}, author = {Rawstern, AH and Hernandez, DJ and Afkhami, ME}, title = {Central Taxa Are Keystone Microbes During Early Succession.}, journal = {Ecology letters}, volume = {28}, number = {1}, pages = {e70031}, pmid = {39737770}, issn = {1461-0248}, support = {DEB-1922521//National Science Foundation/ ; DEB-2030060//National Science Foundation/ ; }, mesh = {*Soil Microbiology ; *Microbiota ; Biodiversity ; Bacteria/classification/genetics ; Ecosystem ; }, abstract = {Microorganisms underpin numerous ecosystem processes and support biodiversity globally. Yet, we understand surprisingly little about what structures environmental microbiomes, including how to efficiently identify key players. Microbiome network theory predicts that highly connected hubs act as keystones, but this has never been empirically tested in nature. Combining culturing, sequencing, networks and field experiments, we isolated 'central' (highly connected, hub taxa), 'intermediate' (moderately connected), and 'peripheral' (weakly/unconnected) microbes and experimentally evaluated their effects on soil microbiome assembly during early succession in nature. Central early colonisers significantly (1) enhanced biodiversity (35%-40% richer communities), (2) reshaped trajectories of microbiome assembly and (3) increased recruitment of additional influential microbes by > 60%. In contrast, peripheral microbes did not increase diversity and were transient taxa, minimally affected by the presence of other microbes. This work elucidates fundamental principles of network theory in microbial ecology and demonstrates for the first time in nature that central microbes act as keystone taxa.}, }
@article {pmid39736538, year = {2024}, author = {Radjasa, OK and Steven, R and Natanael, Y and Nugrahapraja, H and Radjasa, SK and Kristianti, T and Moeis, MR and Trinugroho, JP and Suharya, HB and Rachmatsyah, AO and Dwijayanti, A and Putri, MR and de Fretes, CE and Siallagan, ZL and Fadli, M and Opier, RDA and Farahyah, JD and Rahmawati, V and Rizanti, M and Humaira, Z and Prihatmanto, AS and Hananto, ND and Susanto, RD and Chahyadi, A and Elfahmi,  and Priharto, N and Kamarisima,  and Dwivany, FM}, title = {From the depths of the Java Trench: genomic analysis of Priestia flexa JT4 reveals bioprospecting and lycopene production potential.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {1259}, pmid = {39736538}, issn = {1471-2164}, mesh = {*Lycopene/metabolism ; Indonesia ; *Genome, Bacterial ; Bioprospecting ; Genomics/methods ; Phylogeny ; Multigene Family ; Peptide Synthases/genetics/metabolism ; Whole Genome Sequencing ; Carotenoids/metabolism ; Actinobacteria/genetics/metabolism ; }, abstract = {BACKGROUND: The marine environment boasts distinctive physical, chemical, and biological characteristics. While numerous studies have delved into the microbial ecology and biological potential of the marine environment, exploration of genetically encoded, deep-sea sourced secondary metabolites remains scarce. This study endeavors to investigate marine bioproducts derived from deep-sea water samples at a depth of 1,000 m in the Java Trench, Indonesia, utilizing both culture-dependent and whole-genome sequencing methods.<br><br>RESULTS: Our efforts led to the successful isolation and cultivation of a bacterium Priestia flexa JT4 from the water samples, followed by comprehensive genome sequencing. The resultant high-quality draft genome, approximately 4&#xa0;Mb, harbored 5185 coding sequences (CDSs). Notably, 61.97% of these CDSs were inadequately characterized, presenting potential novel CDSs. This study is the first to identify the "open-type" (&#x3b1;&#x2009;<&#x2009;1) pangenome within the genus Priestia. Moreover, our analysis uncovered eight biosynthetic gene clusters (BGCs) using the common genome mining pipeline, antiSMASH. Two non-ribosomal peptide synthetase (NRPS) BGCs within these clusters exhibited the potential to generate novel biological compounds. Noteworthy is the confirmation that the terpene BGC in P. flexa JT4 can produce lycopene, a compound in substantial industrial demand. The presence of lycopene in the P. flexa JT4 cells was verified using Ultra-performance liquid chromatography-mass spectrometry (UPLC-MS/MS) in multiple reaction modes.<br><br>CONCLUSIONS: This study highlights the bioprospecting opportunity to explore novel bioproducts and lycopene compounds from P. flexa JT4. It marks the pioneering exploration of deep-sea bacterium bioprospecting in Indonesia, seeking to unveil novel bioproducts and lycopene compounds through a genome mining approach.}, }
@article {pmid39736196, year = {2025}, author = {Wong, JWH and Balskus, EP}, title = {Small molecules as modulators of phage-bacteria interactions.}, journal = {Current opinion in chemical biology}, volume = {84}, number = {}, pages = {102566}, doi = {10.1016/j.cbpa.2024.102566}, pmid = {39736196}, issn = {1879-0402}, mesh = {*Bacteriophages/physiology/drug effects ; *Bacteria/virology/metabolism/drug effects ; *Small Molecule Libraries/pharmacology/chemistry ; Lysogeny/drug effects ; }, abstract = {Bacteriophages (phages) play a critical role in microbial ecology and evolution. Their interactions with bacteria are influenced by a complex network of chemical signals derived from a wide range of sources including both endogenous bacterial metabolites and exogenous environmental compounds. In this review, we highlight two areas where small molecules play a pivotal role in modulating phage behaviors. First, we discuss how temperate phages respond to various chemical cues that influence the lysis-lysogeny decision, describing recent advances in our understanding of noncanonical cues. Second, we examine the diverse array of small molecules that disrupt phage infection, potentially serving as bacterial defense strategies against their long-standing competitors. Collectively, this growing body of research highlights the intricate molecular mechanisms governing phage-bacteria dynamics, offering new perspectives on the chemical language shaping microbial communities.}, }
@article {pmid39732620, year = {2025}, author = {Berrios, L and Ansell, TB and Dahlberg, PD and Peay, KG}, title = {Standardizing experimental approaches to investigate interactions between bacteria and ectomycorrhizal fungi.}, journal = {FEMS microbiology reviews}, volume = {49}, number = {}, pages = {}, pmid = {39732620}, issn = {1574-6976}, support = {2109481//National Science Foundation/ ; //Canadian Institute for Advanced Research/ ; 1845544//DEB/ ; }, mesh = {*Mycorrhizae/physiology ; *Bacteria ; Soil Microbiology ; Plant Roots/microbiology ; *Microbial Interactions ; }, abstract = {Bacteria and ectomycorrhizal fungi (EcMF) represent two of the most dominant plant root-associated microbial groups on Earth, and their interactions continue to gain recognition as significant factors that shape forest health and resilience. Yet, we currently lack a focused review that explains the state of bacteria-EcMF interaction research in the context of experimental approaches and technological advancements. To these ends, we illustrate the utility of studying bacteria-EcMF interactions, detail outstanding questions, outline research priorities in the field, and provide a suite of approaches that can be used to promote experimental reproducibility, field advancement, and collaboration. Though this review centers on the ecology of bacteria, EcMF, and trees, it by default offers experimental and conceptual insights that can be adapted to various subfields of microbiology and microbial ecology.}, }
@article {pmid39732444, year = {2025}, author = {Correa, SS and Schultz, J and Zahodnik-Huntington, B and Naschberger, A and Rosado, AS}, title = {Carboxysomes: The next frontier in biotechnology and sustainable solutions.}, journal = {Biotechnology advances}, volume = {79}, number = {}, pages = {108511}, doi = {10.1016/j.biotechadv.2024.108511}, pmid = {39732444}, issn = {1873-1899}, mesh = {*Biotechnology/methods ; *Organelles/metabolism ; Carbon Cycle ; Ribulose-Bisphosphate Carboxylase/metabolism ; *Bacteria/metabolism ; Carbonic Anhydrases/metabolism ; Cyanobacteria/metabolism ; Carbon Dioxide/metabolism ; }, abstract = {Some bacteria possess microcompartments that function as protein-based organelles. Bacterial microcompartments (BMCs) sequester enzymes to optimize metabolic reactions. Several BMCs have been characterized to date, including carboxysomes and metabolosomes. Genomic analysis has identified novel BMCs and their loci, often including genes for signature enzymes critical to their function, but further characterization is needed to confirm their roles. Among the various BMCs, carboxysomes, which are found in cyanobacteria and some chemoautotrophic bacteria, and are most extensively investigated. These self-assembling polyhedral proteinaceous BMCs are essential for carbon fixation. Carboxysomes encapsulate the enzymes RuBisCo and carbonic anhydrase, which increase the carbon fixation rate in the cell and decrease the oxygenation rate by RuBisCo. The ability of carboxysomes to concentrate carbon dioxide in crops and industrially relevant microorganisms renders them attractive targets for carbon assimilation bioengineering. Thus, carboxysome characterization is the first step toward developing carboxysome-based applications. Therefore, this review comprehensively explores carboxysome morphology, physiology, and biochemistry. It also discusses recent advances in microscopy and complementary techniques for isolating and characterizing this versatile class of prokaryotic organelles.}, }
@article {pmid39731630, year = {2024}, author = {Fluch, M and Corretto, E and Feldhaar, H and Schuler, H}, title = {Seasonal Changes in the Gut Microbiota of Halyomorpha halys.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {164}, pmid = {39731630}, issn = {1432-184X}, mesh = {Animals ; *Seasons ; *Gastrointestinal Microbiome ; *Heteroptera/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; Symbiosis ; Pantoea/isolation &amp; purification/physiology/genetics/classification ; Phylogeny ; }, abstract = {The gut microbiome plays an important role in insect evolution and ecology. Bacteria support the host's nutrition and defense and therefore play an important role in the fitness of the host. Halyomorpha halys is one of the most important invasive pest species in the world. Native to North-Eastern Asia, this Pentatomid bug has recently invaded North America and Europe, causing significant damage to agricultural production. Although an increasing number of studies investigated the biology of this pest species, little is known about the composition of its gut microbiota. Like many other Pentatomid species, H. halys harbors a primary symbiont called "Candidatus Pantoea carbekii," which produces vitamins and essential amino acids for the host. However, information about the presence of other bacteria is currently lacking. Therefore, we investigated the gut microbiota of H. halys individuals, which were collected in the field across the year using a high-throughput 16S rRNA gene metabarcoding approach. Our results revealed 3309 different ASVs associated with H. halys, with Pantoea being the most abundant symbiont, present in almost all individuals. Additionally, many individuals harbor Commensalibacter, a genus of acetic acid bacterial symbionts. Besides these two predominant taxa, we show a high diversity of microorganisms associated with H. halys with seasonal fluctuations, highlighting a dynamic microbiota that might influence the biology of this species.}, }
@article {pmid39730790, year = {2024}, author = {Struniawski, K and Kozera, R and Trzciński, P and Marasek-Ciołakowska, A and Sas-Paszt, L}, title = {Extreme learning machine for identifying soil-dwelling microorganisms cultivated on agar media.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {31034}, pmid = {39730790}, issn = {2045-2322}, support = {BIOSTRATEG3/344433/16/NCBR/2018//Narodowe Centrum Bada&#x144; i Rozwoju/ ; }, mesh = {*Soil Microbiology ; *Machine Learning ; Agar/chemistry ; Soil/chemistry ; Image Processing, Computer-Assisted/methods ; Culture Media ; }, abstract = {The aim of this research is to create an automated system for identifying soil microorganisms at the genera level based on raw microscopic images of monocultural colonies grown in laboratory environment. The examined genera are: Fusarium, Trichoderma, Verticillium, Purpureolicillium and Phytophthora. The proposed pipeline deals with unprocessed microscopic images, avoiding additional sample marking or coloration. The methodology includes several stages: image preprocessing, segmenting images to isolate microorganisms from the background, calculating features related to image color and texture for classification. Using an extensive dataset of 2866 images from the National Institute of Horticultural Research in Skierniewice the Extreme Learning Machine model was trained and validated. The model showcases high accuracy and computational efficiency compared to other Machine Learning state-of-the art methods e.g. CatBoost, Random Forest or Convolutional Neural Networks. Statistical techniques, including Multivariate Analysis of Variance were employed to confirm significant differences among the datasets, enhancing the model's robustness. Nevertheless, Shapley Additive Explanations values provided transparency into the model's decision-making process. This approach has the potential to improve early detection and management of soil pathogens, promoting sustainable agriculture and demonstrating machine learning's potential in environmental monitoring, microbial ecology or industrial microbiology.}, }
@article {pmid39730187, year = {2025}, author = {Yan, M and Andersen, TO and Pope, PB and Yu, Z}, title = {Probing the eukaryotic microbes of ruminants with a deep-learning classifier and comprehensive protein databases.}, journal = {Genome research}, volume = {35}, number = {2}, pages = {368-378}, pmid = {39730187}, issn = {1549-5469}, mesh = {Animals ; *Ruminants/microbiology/parasitology/genetics ; *Metagenomics/methods ; Metagenome ; *Deep Learning ; *Databases, Protein ; Rumen/microbiology ; Fungi/genetics/classification ; Computational Biology/methods ; *Eukaryota/genetics/classification ; *Gastrointestinal Microbiome/genetics ; }, abstract = {Metagenomics, particularly genome-resolved metagenomics, have significantly deepened our understanding of microbes, illuminating their taxonomic and functional diversity and roles in ecology, physiology, and evolution. However, eukaryotic populations within various microbiomes, including those in the mammalian gastrointestinal (GI) tract, remain relatively underexplored in metagenomic studies owing to the lack of comprehensive reference genome databases and robust bioinformatic tools. The GI tract of ruminants, particularly the rumen, contains a high eukaryotic biomass but a relatively low diversity of ciliates and fungi, which significantly impacts feed digestion, methane emissions, and rumen microbial ecology. In the present study, we developed GutEuk, a bioinformatics tool that improves upon the currently available Tiara and EukRep in accurately identifying eukaryotic sequences from metagenomes. GutEuk is optimized for high precision across different sequence lengths. It can also distinguish fungal and protozoal sequences, further elucidating their unique ecological, physiological, and nutritional impacts. GutEuk was shown to facilitate comprehensive analyses of protozoa and fungi within more than 1000 rumen metagenomes, revealing a greater genomic diversity among protozoa than previously documented. We further curated several ruminant eukaryotic protein databases, significantly enhancing our ability to distinguish the functional roles of ruminant fungi and protozoa from those of prokaryotes. Overall, the newly developed package GutEuk and its associated databases create new opportunities for the in-depth study of GI tract eukaryotes.}, }
@article {pmid39730090, year = {2025}, author = {Nguyen, TV and Kim, NK and Lee, SH and Trinh, HP and Park, HD}, title = {Gene abundance and microbial syntrophy as key drivers of anaerobic digestion revealed through 16S rRNA gene and metagenomic analysis.}, journal = {Chemosphere}, volume = {370}, number = {}, pages = {144028}, doi = {10.1016/j.chemosphere.2024.144028}, pmid = {39730090}, issn = {1879-1298}, mesh = {Anaerobiosis ; *RNA, Ribosomal, 16S/genetics ; Metagenomics ; Wastewater/microbiology ; *Bacteria/genetics/metabolism ; Bioreactors/microbiology ; }, abstract = {Genes in microorganisms influence the biological processes in anaerobic digestion (AD). However, key genes involved in the four metabolic steps (hydrolysis, acidogenesis, acetogenesis, and methanogenesis) remain largely unexplored. This study investigated the abundance and distribution of key functional genes in full-scale anaerobic digesters processing food waste (FWDs) and municipal wastewater (MWDs) through 16S rRNA gene and shotgun metagenomic analysis. Our results revealed that FWDs exhibited a higher abundance of key genes in the metabolic steps, despite having significantly lower microbial diversity compared to MWDs. Pathways and genes associated with syntrophic oxidation of acetate (SAO) and butyrate (SBO) were more present in FWDs. SAO potentially used both the conventional reversed Wood-Ljungdahl pathway and its integration with the glycine cleavage system in FWDs, which complements pathways for acetate oxidation under ammonia stress conditions. Similarly, genes associated with SBO (atoB and croR) were notably more prevalent in FWDs compared to MWDs with an 8.4-fold and 108-fold increase, respectively, indicating the adaptation of SBO bacteria to convert butyrate into acetate. The higher abundance of key genes in FWDs was driven by microbes adapting to the feedstock compositions with higher levels of substrate content, volatile fatty acids, and ammonia. This study quantified the genes central to AD metabolism and uncovered the contributions of microbial diversity, gene abundance, syntrophy, and feedstock characteristics to the functionality of AD processes. These findings enhance understanding of the microbial ecology in AD and provide a foundation for developing innovative strategies to enhance biogas production and waste management.}, }
@article {pmid39726151, year = {2024}, author = {Nieland, MA and Lacy, P and Allison, SD and Bhatnagar, JM and Doroski, DA and Frey, SD and Greaney, K and Hobbie, SE and Kuebbing, SE and Lewis, DB and McDaniel, MD and Perakis, SS and Raciti, SM and Shaw, AN and Sprunger, CD and Strickland, MS and Templer, PH and Vietorisz, C and Ward, EB and Keiser, AD}, title = {Nitrogen Deposition Weakens Soil Carbon Control of Nitrogen Dynamics Across the Contiguous United States.}, journal = {Global change biology}, volume = {30}, number = {12}, pages = {e70016}, doi = {10.1111/gcb.70016}, pmid = {39726151}, issn = {1365-2486}, support = {1831944//Division of Environmental Biology/ ; SC0020382//Biological and Environmental Research/ ; 1845417//National Science Foundation/ ; 2045135//Division of Earth Sciences/ ; //University of Massachusetts Amherst/ ; }, mesh = {*Soil/chemistry ; United States ; *Carbon/metabolism/analysis ; *Nitrogen/metabolism/analysis ; *Soil Microbiology ; *Nitrification ; Forests ; Biomass ; }, abstract = {Anthropogenic nitrogen (N) deposition is unequally distributed across space and time, with inputs to terrestrial ecosystems impacted by industry regulations and variations in human activity. Soil carbon (C) content normally controls the fraction of mineralized N that is nitrified (ƒnitrified), affecting N bioavailability for plants and microbes. However, it is unknown whether N deposition has modified the relationships among soil C, net N mineralization, and net nitrification. To test whether N deposition alters the relationship between soil C and net N transformations, we collected soils from coniferous and deciduous forests, grasslands, and residential yards in 14 regions across the contiguous United States that vary in N deposition rates. We quantified rates of net nitrification and N mineralization, soil chemistry (soil C, N, and pH), and microbial biomass and function (as beta-glucosidase (BG) and N-acetylglucosaminidase (NAG) activity) across these regions. Following expectations, soil C was a driver of ƒnitrified across regions, whereby increasing soil C resulted in a decline in net nitrification and ƒnitrified. The ƒnitrified value increased with lower microbial enzymatic investment in N acquisition (increasing BG:NAG ratio) and lower active microbial biomass, providing some evidence that heterotrophic microbial N demand controls the ammonium pool for nitrifiers. However, higher total N deposition increased ƒnitrified, including for high soil C sites predicted to have low ƒnitrified, which decreased the role of soil C as a predictor of ƒnitrified. Notably, the drop in contemporary atmospheric N deposition rates during the 2020 COVID-19 pandemic did not weaken the effect of N deposition on relationships between soil C and ƒnitrified. Our results suggest that N deposition can disrupt the relationship between soil C and net N transformations, with this change potentially explained by weaker microbial competition for N. Therefore, past N inputs and soil C should be used together to predict N dynamics across terrestrial ecosystems.}, }
@article {pmid39725503, year = {2025}, author = {Belanche, A and Bannink, A and Dijkstra, J and Durmic, Z and Garcia, F and Santos, FG and Huws, S and Jeyanathan, J and Lund, P and Mackie, RI and McAllister, TA and Morgavi, DP and Muetzel, S and Pitta, DW and Yáñez-Ruiz, DR and Ungerfeld, EM}, title = {Feed additives for methane mitigation: A guideline to uncover the mode of action of antimethanogenic feed additives for ruminants.}, journal = {Journal of dairy science}, volume = {108}, number = {1}, pages = {375-394}, doi = {10.3168/jds.2024-25046}, pmid = {39725503}, issn = {1525-3198}, mesh = {*Methane ; Animals ; *Animal Feed ; *Ruminants ; *Rumen/metabolism ; Diet/veterinary ; }, abstract = {This publication aims to provide guidelines of the knowledge required and the potential research to be conducted in order to understand the mode of action of antimethanogenic feed additives (AMFA). In the first part of the paper, we classify AMFA into 4 categories according to their mode of action: (1) lowering dihydrogen (H2) production; (2) inhibiting methanogens; (3) promoting alternative H2-incorporating pathways; and (4) oxidizing methane (CH4). The second part of the paper presents questions that guide the research to identify the mode of action of an AMFA on the rumen CH4 production from 5 different perspectives: (1) microbiology; (2) cell and molecular biochemistry; (3) microbial ecology; (4) animal metabolism; and (5) cross-cutting aspects. Recommendations are provided to address various research questions within each perspective, along with examples of how aspects of the mode of action of AMFA have been elucidated before. In summary, this paper offers timely and comprehensive guidelines to better understand and reveal the mode of action of current and emerging AMFA.}, }
@article {pmid39725195, year = {2025}, author = {Xu, W and Lam, C and Wang, Y and Wan, SH and Ho, PH and Myung, J and Yung, CCM}, title = {Temporal succession of marine microbes drives plastisphere community convergence in subtropical coastal waters.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {367}, number = {}, pages = {125572}, doi = {10.1016/j.envpol.2024.125572}, pmid = {39725195}, issn = {1873-6424}, mesh = {*Plastics/analysis ; *Seawater/microbiology ; Hong Kong ; *Microbiota ; *Water Pollutants, Chemical/analysis ; Ecosystem ; Environmental Monitoring ; Bacteria/classification ; *Water Microbiology ; }, abstract = {Marine plastic pollution is a pervasive environmental issue, with microplastics serving as novel substrates for microbial colonization in aquatic ecosystems. This study investigates the succession of plastisphere communities on four common plastic types (polyethylene, polypropylene, polyethylene terephthalate, and polystyrene) in subtropical coastal waters of Hong Kong SAR. Over a 42-day period, we analysed the temporal development of microbial communities using a three-domain universal metabarcoding method. Our results reveal that temporal succession is a stronger driver of community structure than plastic type, with prokaryotic communities converging across different plastics as biofilms mature. Despite this convergence, plastisphere communities remain distinct from planktonic communities throughout the experiment, suggesting that plastics create unique ecological niches in marine environments. We observed differences in diversity patterns and community composition among prokaryotic, eukaryotic, and chloroplastic communities, highlighting the importance of multi-domain analyses in plastisphere research. Functional predictions suggest potential roles of prokaryotic communities in biogeochemical cycling and possible pathogenicity, highlighting the ecological and public health implications of plastisphere formation. This study provides valuable insights into the dynamics of microbial colonization across domains on marine plastics and enhances our understanding of how these anthropogenic substrates influence microbial ecology in marine ecosystems.}, }
@article {pmid39724890, year = {2024}, author = {Kusradze, I and Rcheulishvili, O and Karumidze, N and Rigvava, S and Rcheulishvili, A and Goliadze, R and Kamashidze, L and Chipurupalli, A and Metreveli, N and Goderdzishvili, M}, title = {PHAGE-BACTERIA INTERACTIONS UNDER METAL STRESS: A STUDY OF THE NOVEL STENOTROPHOMONAS MALTOPHILIA PHAGE VB_STM18.}, journal = {Georgian medical news}, volume = {}, number = {355}, pages = {117-122}, pmid = {39724890}, issn = {1512-0112}, mesh = {*Stenotrophomonas maltophilia/virology/drug effects ; *Cadmium/toxicity ; *Bacteriophages ; Biodegradation, Environmental ; Stress, Physiological/drug effects ; }, abstract = {Stenotrophomonas maltophilia is a highly adaptable gram-negative bacteria, demonstrating resilience in metal-contaminated environment, which makes it a key subject for understanding microbial survival under heavy metal stress. This study investigates the effects of cadmium ions (Cd[2+]) on the growth dynamics, cadmium uptake, and bacteriophage vB_Stm18-host interactions, with implications for environmental microbiology and applied biotechnology. Growth analysis revealed that S. maltophilia tolerates Cd[2+] at 0.01 g/L, although exposure prolonged the lag phase by 3 hours. Despite the initial growth inhibition, the bacterium adapted and achieved control-like growth levels by 18 hours. Bioaccumulation assays showed progressive cadmium uptake, reaching 1876 µg/g at 24 hours, highlighting its potential for bioremediation. The influence of Cd[2+] on phage vB_Stm18's life cycle was assessed through adsorption efficiency and burst size measurements. Short-term exposure to Cd[2+] caused minimal reductions in adsorption efficiency (97% vs. 98% in control) but significantly decreased the burst size to 17 particles per infected cell. Prolonged exposure exacerbated these effects, with adsorption efficiency decreasing to 58% and burst size dropping to 6 particles per infected cell, after 18 hours of pre-incubation. These findings suggest that cadmium alters bacterial surface structures, intracellular processes and disrupts phage replication and release. Therefore, this study sheds light on the molecular interplay between environmental pollutants and microbial systems providing valuable insights into microbial ecology in metal-contaminated habitats as well as informing strategies for optimizing phage therapy and bioremediation under heavy metal stress.}, }
@article {pmid39724159, year = {2024}, author = {Ulbrich, J and Jobe, NE and Jones, DS and Kieft, TL}, title = {Cave Pools in Carlsbad Caverns National Park Contain Diverse Bacteriophage Communities and Novel Viral Sequences.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {163}, pmid = {39724159}, issn = {1432-184X}, support = {NCKRI-NMT Internal Seed Grant Program//National Cave and Karst Research Institute/ ; }, mesh = {*Caves ; *Parks, Recreational ; *Bacteriophages/genetics/isolation &amp; purification/classification ; *Bacteria/genetics/classification/isolation &amp; purification/virology ; *RNA, Ribosomal, 16S/genetics ; California ; Metagenome ; Phylogeny ; Virome ; Biodiversity ; }, abstract = {Viruses are the most abundant biological entities on Earth, and they play a critical role in the environment and biosphere where they regulate microbial populations and contribute to nutrient cycling. Environmental viruses have been the most studied in the ocean, but viral investigations have now spread to other environments. Here, viral communities were characterized in four cave pools in Carlsbad Caverns National Park to test the hypotheses that (i) viral abundance is ten-fold higher than prokaryotic cell abundance in cavern pools, (ii) cavern pools contain novel viral sequences, and (iii) viral communities in pools from developed portions of the cave are distinct from those of pools in undeveloped parts of the same cave. The relationship between viral and microbial abundance was determined through direct epifluorescence microscopy counts. Viral metagenomes were constructed to examine viral diversity among pools, identify novel viruses, and characterize auxiliary metabolic genes (AMGs). Bacterial communities were characterized by 16S rRNA gene amplicon sequencing. Epifluorescence microscopy showed that the ratio of viral-like particles (VLPs) to microorganisms was approximately 22:1 across all sites. Viral communities from pools with higher tourist traffic were more similar to each other than to those from less visited pools, although surprisingly, viruses did not follow the same pattern as bacterial communities, which reflected pool geochemistry. Bacterial hosts predicted from viral sequences using iPHoP showed overlap with both rare and abundant genera and families in the 16S rRNA gene dataset. Gene-sharing network analysis revealed high viral diversity compared to a reference viral database as well as to other aquatic environments. AMG presence showed variation in metabolic potential among the four pools. Overall, Carlsbad Cavern harbors novel viruses with substantial diversity among pools within the same system, indicating that caves are likely an important repository for unexplored viromes.}, }
@article {pmid39723821, year = {2025}, author = {Sanchez, VA and Renner, T and Baker, LJ and Hendry, TA}, title = {Genome evolution following an ecological shift in nectar-dwelling Acinetobacter.}, journal = {mSphere}, volume = {10}, number = {1}, pages = {e0101024}, pmid = {39723821}, issn = {2379-5042}, mesh = {*Acinetobacter/genetics/classification ; *Genome, Bacterial ; *Plant Nectar/metabolism ; Phylogeny ; *Evolution, Molecular ; Ecosystem ; Gene Transfer, Horizontal ; }, abstract = {UNLABELLED: The bacterial genus Acinetobacter includes species found in environmental habitats like soil and water, as well as taxa adapted to be host-associated or pathogenic. High genetic diversity may allow for this habitat flexibility, but the specific genes underlying switches between habitats are poorly understood. One lineage of Acinetobacter has undergone a substantial habitat change by evolving from a presumed soil-dwelling ancestral state to thrive in floral nectar. Here, we compared the genomes of floral-dwelling and pollinator-associated Acinetobacter, including newly described species, with genomes from relatives found in other environments to determine the genomic changes associated with this ecological shift. Following one evolutionary origin of floral nectar adaptation, nectar-dwelling Acinetobacter taxa have undergone reduction in genome size compared with relatives and have experienced dynamic gene gains and losses as they diversified. Gene content changes suggest a shift to metabolism of monosaccharides rather than diverse carbohydrates, and scavenging of nitrogen sources, which we predict to be beneficial in nectar environments. Gene gains appear to result from duplication events, evolutionary divergence, and horizontal gene transfer. Most notably, nectar-dwelling Acinetobacter acquired the ability to degrade pectin from plant pathogens, and the genes underlying this ability have duplicated and are under selection within the clade. We hypothesize that this ability was a key trait for adaptation to floral nectar, as it could improve access to nutrients in the nutritionally unbalanced habitat of nectar. These results identify the genomic changes and traits coinciding with a dramatic habitat switch from soil to floral nectar.<br><br>IMPORTANCE: Many bacteria, including the genus Acinetobacter, commonly evolve to exploit new habitats. However, the genetic changes that underlie habitat switches are often unknown. Floral nectar is home to specialized microbes that can grow in this nutritionally unbalanced habitat. Several specialized Acinetobacter species evolved from soil-dwelling relatives to become common and abundant in floral nectar. Here, we investigate the genomic adaptations required to successfully colonize a novel habitat like floral nectar. We performed comparative genomics analyses between nectar-dwelling Acinetobacter and Acinetobacter species from other environments, like soil and water. We find that although gene loss coincided with the switch to living in nectar, gains of specific genes from other bacteria may have been particularly important for this ecological change. Acinetobacter living in nectar gained genes for degrading pectin, a plant polysaccharide, which may improve access to nutrients in their environment. These findings shed light on how evolutionary novelty evolves in bacteria.}, }
@article {pmid39723138, year = {2024}, author = {Xie, S and Ma, J and Lu, Z}, title = {Bacteroides thetaiotaomicron enhances oxidative stress tolerance through rhamnose-dependent mechanisms.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1505218}, pmid = {39723138}, issn = {1664-302X}, abstract = {This study probes into the unique metabolic responses of Bacteroides thetaiotaomicron (B. thetaiotaomicron), a key player in the gut microbiota, when it metabolizes rhamnose rather than typical carbohydrates. Known for its predominant role in the Bacteroidetes phylum, B. thetaiotaomicron efficiently breaks down poly- and mono-saccharides into beneficial short-chain fatty acids (SCFAs), crucial for both host health and microbial ecology balance. Our research focused on how this bacterium's SCFA production differ when utilizing various monosaccharides, with an emphasis on the oxidative stress responses triggered by rhamnose consumption. Notably, rhamnose use results in unique metabolic byproducts, including substantial quantities of 1,2-propanediol, which differs significantly from those produced during glucose metabolism. Our research reveals that rhamnose consumption is associated with a reduction in reactive oxygen species (ROS), signifying improved resistance to oxidative stress compared to other sugars. This effect is attributed to specific gene expressions within the rhamnose metabolic pathway. Notably, overexpression of the rhamnose metabolism regulator RhaR in B. thetaiotaomicron enhances its survival in oxygen-rich conditions by reducing hydrogen peroxide production. This reduction is linked to decreased expression of pyruvate:ferredoxin oxidoreductase (PFOR). In contrast, experiments with a rhaR-deficient strain demonstrated that the absence of RhaR causes B. thetaiotaomicron cells growing on rhamnose to produce ROS at rates comparable to cells grown on glucose, therefore, losing their advantage in oxidative resistance. Concurrently, the expression of PFOR is no longer suppressed. These results indicate that when B. thetaiotaomicron is cultured in a rhamnose-based medium, RhaR can restrain the expression of PFOR. Although PFOR is not a primary contributor to intracellular ROS production, its sufficient inhibition does reduce ROS levels to certain extent, consequently improving the bacterium's resistance to oxidative stress. It highlights the metabolic flexibility and robustness of microbes in handling diverse metabolic challenges and oxidative stress in gut niches through the consumption of alternative carbohydrates.}, }
@article {pmid39721552, year = {2025}, author = {IJdema, F and Lievens, S and Smets, R and Poma, G and Van Der Borght, M and Lievens, B and De Smet, J}, title = {Modulating the fatty acid composition of black soldier fly larvae via substrate fermentation.}, journal = {Animal : an international journal of animal bioscience}, volume = {19}, number = {1}, pages = {101383}, doi = {10.1016/j.animal.2024.101383}, pmid = {39721552}, issn = {1751-732X}, mesh = {Animals ; Larva/growth &amp; development/metabolism/chemistry ; Fermentation ; *Animal Feed/analysis ; *Simuliidae/growth &amp; development/metabolism ; *Mortierella/metabolism ; *Fatty Acids/metabolism ; Dietary Fiber/metabolism ; Fatty Acids, Omega-6/metabolism ; Fatty Acids, Omega-3/metabolism ; Aquaculture/methods ; }, abstract = {Black soldier fly larvae (BSFL, Hermetia illucens) contain high amounts of proteins and essential amino acids and are therefore an appropriate feed source. However, they lack essential fatty acids (FAs), specifically ω-3 and ω-6, making them a less desirable feed choice for aquaculture. The aim of this study was to increase the ω-3 and ω-6 FA concentrations in BSFL by manipulating the FA composition in their rearing substrate. Specifically, the potential of substrate fermentation using the ω-3 and ω-6 FA-producing fungus Mortierella alpina was assessed. Fermentation of two agricultural side streams (wheat bran (WB) and WB with distiller's dried grains with solubles (DDGS)) increased substrate total crude fat concentration by 2.1 - 4.6%, as well as the concentration of several essential FAs, including the ω-6 FAs arachidonic acid (from less than 0.2 mg/g fat to a maximum of 44.2 mg/g fat) and gamma-linolenic acid (from less than 1.2 mg/g fat to a maximum of 45.8 mg/g fat and the ω-3 FA eicosapentaenoic acid (EPA) (from less than 0.7 mg/g fat to a maximum of 49.9 mg/g fat). Rearing BSFL on feeds from such fermented substrates resulted in similar changes in larval FA composition, specifically a higher concentration of EPA (from less than 0.2 mg/g fat to a maximum of 26.6 mg/g fat in the larvae fed on fermented diets), however, larval growth was reduced. Feeds made from fermented substrates were prone to stickiness and dehydration, possibly limiting larval movement and feeding, thereby affecting larval growth. Furthermore, proximate analysis of the substrates revealed sugar depletion after fermentation, which could be detrimental for larval growth and illustrate important attention points going forward. This study shows that fermentation of agricultural side streams WB and a mixture of WB with DDGS with Mortierella alpina alters their FA profile, increasing their ω-3 and ω-6 FA concentrations and that of BSFL fed with those substrates. Therefore, these results suggest that BSFL with tailor-made FA profiles for a specific application could be successfully produced.}, }
@article {pmid39716780, year = {2025}, author = {Quevedo-Caraballo, S and de Vega, C and Lievens, B and Fukami, T and Álvarez-Pérez, S}, title = {Tiny but mighty? Overview of a decade of research on nectar bacteria.}, journal = {The New phytologist}, volume = {245}, number = {5}, pages = {1897-1910}, pmid = {39716780}, issn = {1469-8137}, support = {//Agentschap Innoveren en Ondernemen/ ; //Fonds Wetenschappelijk Onderzoek/ ; //KU Leuven/ ; PIPF-2023/ECO-29442//Consejer&#xed;a de Educaci&#xf3;n, Ciencia y Universidades, Comunidad de Madrid/ ; CNS2022-135237//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; PID2022-136719NB-I00//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; RYC2018-023847-I//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; //Complutense University of Madrid, Spain/ ; DEB 1737758//Directorate for Biological Sciences/ ; //ESF Investing in your future/ ; }, mesh = {*Plant Nectar/chemistry/metabolism ; *Bacteria/metabolism/genetics ; Microbiota ; *Research ; Animals ; Flowers/microbiology ; }, abstract = {An emerging focus of research at the intersection of botany, zoology, and microbiology is the study of floral nectar as a microbial habitat, referred to as the nectar microbiome, which can alter plant-pollinator interactions. Studies on these microbial communities have primarily focused on yeasts, and it was only about a decade ago that bacteria began to be studied as widespread inhabitants of floral nectar. This review aims to give an overview of the current knowledge on nectar bacteria, with emphasis on evolutionary origin, dispersal mode, effects on nectar chemistry and plant-animal interactions, community assembly, agricultural applications, and their use as model systems in ecological research. We further outline gaps in our understanding of the ecological significance of these microorganisms, their response to environmental changes, and the potential cascading effects.}, }
@article {pmid39716385, year = {2025}, author = {Lu, Z and Entwistle, E and Kuhl, MD and Durrant, AR and Barreto Filho, MM and Goswami, A and Morris, JJ}, title = {Coevolution of marine phytoplankton and Alteromonas bacteria in response to pCO2 and coculture.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {39716385}, issn = {1751-7370}, mesh = {*Phytoplankton/growth &amp; development/genetics/metabolism ; *Carbon Dioxide/metabolism ; *Alteromonas/growth &amp; development/genetics/metabolism ; *Seawater/microbiology/chemistry ; *Biological Evolution ; Diatoms/growth &amp; development/genetics ; Coculture Techniques ; Prochlorococcus/growth &amp; development/genetics ; }, abstract = {As a result of human activity, Earth's atmosphere and climate are changing at an unprecedented pace. Models based on short-term experiments predict major changes will occur in marine phytoplankton communities in the future ocean, but rarely consider how evolution or interactions with other microbes may influence these changes. Here, we experimentally evolved several phytoplankton in coculture with a heterotrophic bacterium, Alteromonas sp. EZ55, under either present-day or predicted future pCO2 conditions. Growth rates of phytoplankton generally increased over time under both conditions, but only Thalassiosira oceanica had evidence of a growth rate tradeoff in the ancestral environment after evolution at elevated pCO2. The growth defects observed in ancestral Prochlorococcus cultures at elevated pCO2 and in axenic culture were diminished after evolution, possibly due to regulatory mutations in antioxidant genes. Except for Prochlorococcus, mutational profiles suggested phytoplankton experienced primarily purifying selection, but most Alteromonas lineages showed evidence of directional selection, where evolution appeared to favor a metabolic switch between growth on small organic acids with cyanobacteria versus catabolism of more complex carbon substrates with eukaryotic phytoplankton. Evolved Alteromonas were also poorer "helpers" for Prochlorococcus, consistent with that interaction being a competitive Black Queen process rather than a true mutualism. This work provides new insights on how phytoplankton will respond to increased pCO2 and on the evolutionary mechanisms governing phytoplankton:bacteria interactions. It also clearly demonstrates that both evolution and interspecies interactions must be considered to predict future marine biogeochemistry.}, }
@article {pmid39715919, year = {2024}, author = {Jiang, ZB and Zhang, H and Tian, JJ and Guo, HH and Zhou, LR and Ma, XL}, title = {The Microbial Diversity of Biological Moss Crust: Application in Saline-Alkali Soil Management.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {162}, pmid = {39715919}, issn = {1432-184X}, support = {82160672//the National Natural Science Foundation of China/ ; 2022AAC05041 and 2023AAC05048//Outstanding Youth Program of Ningxia Natural Science Foundation/ ; 2021BEB04019//the Key R&amp;D Projects in Ningxia/ ; 2021AAC03210 and 2019AAC03113//the Ningxia Natural Science Foundation/ ; }, mesh = {*Soil/chemistry ; *Soil Microbiology ; *Bryophyta/microbiology ; China ; Biodiversity ; Alkalies/analysis ; Salinity ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Chlorophyll/analysis ; }, abstract = {Soil salinization poses a substantial threat to global food security, particularly under the influence of climate change, and is recognized as one of the most urgent challenges in land degradation. This study aims to elucidate the challenges associated with managing arid and semi-arid saline-alkali lands in China's Ningxia province and propose feasible solutions. To assess moss crust colonization, we measured changes in organic matter and chlorophyll levels. Additionally, we investigated the impact of an interlayer composed of Goji berry root bark using liquid chromatography-mass spectrometry analysis, biological enzyme activity analysis, and metagenomic sequencing. A total of 45 endophytes were isolated from the moss crust. The most significant colonization of moss crusts was observed when the Goji berry root bark was used as the interlayer, resulting in a significant increase in chlorophyll content. Several responses were identified as pivotal factors facilitating moss crust growth when the Goji berry root bark was used as the interlayer. In saline-alkali soil, the Goji berry root bark interlayer increased the activities of sucrase, urease, and alkaline phosphatase. Metagenomic data analysis revealed variations in the relative abundance of microorganisms at the phylum level, although these differences were not statistically significant. Evaluation of the impact of physical isolation and moss crust transplantation on the ecological restoration of saline-alkali soil using liquid chromatography-tandem mass spectrometry and metagenomic sequencing indicated that the Goji berry root bark as a physical isolation method promotes moss crust colonization in saline-alkali soil and increases soil organic matter and nutrient elements, offering valuable insights for the ecological management of saline-alkali land and serving as a reference for future research in this field.}, }
@article {pmid39714209, year = {2025}, author = {Payne, PE and Knobbe, LN and Chanton, P and Zaugg, J and Mortazavi, B and Mason, OU}, title = {Uncovering novel functions of the enigmatic, abundant, and active Anaerolineae in a salt marsh ecosystem.}, journal = {mSystems}, volume = {10}, number = {1}, pages = {e0116224}, pmid = {39714209}, issn = {2379-5077}, support = {2342607//National Science Foundation (NSF)/ ; 1643486//National Science Foundation (NSF)/ ; 1438092//National Science Foundation (NSF)/ ; 503678//Joint Genome Institute (JGI)/ ; }, mesh = {*Wetlands ; Rhizosphere ; Metagenome ; Soil Microbiology ; Ecosystem ; Genome, Bacterial ; }, abstract = {Anaerolineae, particularly uncultured representatives, are one of the most abundant microbial groups in coastal salt marshes, dominating the belowground rhizosphere, where over half of plant biomass production occurs. However, this class generally remains poorly understood, particularly in a salt marsh context. Here, novel Anaerolineae metagenome-assembled genomes (MAGs) were generated from the salt marsh rhizosphere representing Anaerolineales, Promineifilales, JAAYZQ01, B4-G1, JAFGEY01, UCB3, and Caldilineales orders. Metagenome and metatranscriptome reads were mapped to annotated MAGs, revealing nearly all Anaerolineae encoded and transcribed genes required for oxidation of carbon compounds ranging from simple sugars to complex polysaccharides, fermentation, and carbon fixation. Furthermore, the majority of Anaerolineae expressed genes involved in anaerobic and aerobic respiration and secondary metabolite production. The data revealed that the belowground salt marsh Anaerolineae in the rhizosphere are important players in carbon cycling, including degradation of simple carbon compounds and more recalcitrant plant material, such as cellulose, using a diversity of electron acceptors and represent an unexplored reservoir of novel secondary metabolites.IMPORTANCEGiven that coastal salt marshes are recognized as biogeochemical hotspots, it is fundamentally important to understand the functional role of the microbiome in this ecosystem. In particular, Anaerolineae are abundant members of the salt marsh rhizosphere and have been identified as core microbes, suggesting they play an important functional role. Yet, little is known about the metabolic pathways encoded and expressed in this abundant salt marsh clade. Using an 'omics-based approach, we determined that Anaerolineae are capable of oxidizing a range of carbon compounds, including simple sugars to complex carbon compounds, while also encoding fermentation and carbon fixation. Surprisingly, Anaerolineae encoded and transcribed genes involved in aerobic respiration, which was unexpected given the reduced nature of the salt marsh rhizosphere. Finally, the majority of Anaerolineae appear to be involved in secondary metabolite production, suggesting that this group represents an unexplored reservoir of novel and important secondary metabolites.}, }
@article {pmid39714150, year = {2025}, author = {Beizman-Magen, Y and Orevi, T and Kashtan, N}, title = {Hydration conditions as a critical factor in antibiotic-mediated bacterial competition outcomes.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {1}, pages = {e0200424}, pmid = {39714150}, issn = {1098-5336}, support = {220020475//James S. McDonnell Foundation (JSMF)/ ; 12-02-0046//The minisitry of Agriculture and rural development, Israel/ ; }, mesh = {*Bacillus/physiology/metabolism/drug effects ; *Pseudomonas syringae/physiology/drug effects ; *Xanthomonas/physiology/drug effects ; *Anti-Bacterial Agents/pharmacology/metabolism ; *Microbial Interactions ; *Water ; *Antibiosis ; }, abstract = {Antibiotic secretion plays a pivotal role in bacterial interference competition; yet, the impact of environmental hydration conditions on such competition is not well understood. Here, we investigate how hydration conditions affect interference competition among bacteria, studying the interactions between the antibiotic-producing Bacillus velezensis FZB42 and two bacterial strains susceptible to its antibiotics: Xanthomonas euvesicatoria 85-10 and Pseudomonas syringae DC3000. Our results show that wet-dry cycles significantly modify the response of the susceptible bacteria to both the supernatant and cells of the antibiotic-producing bacteria, compared to constantly wet conditions. Notably, X. euvesicatoria shows increased protection against both the cells and supernatants of B. velezensis under wet-dry cycles, while P. syringae cells become more susceptible under wet-dry cycles. In addition, we observed a reciprocal interaction between P. syringae and B. velezensis, where P. syringae inhibits B. velezensis under wet conditions. Our findings highlight the important role of hydration conditions in shaping bacterial interference competition, providing valuable insights into the microbial ecology of water-unsaturated surfaces, with implications for applications such as biological control of plant pathogens and mitigating antibiotic resistance.IMPORTANCEOur study reveals that hydration conditions, particularly wet-dry cycles, significantly influence antibiotic-mediated competition between bacterial species. We revealed that the effectiveness of antibiotics produced by Bacillus velezensis against two susceptible bacterial species: Xanthomonas and Pseudomonas varies based on these hydration conditions. Unlike traditional laboratory environments, many real-world habitats, such as soil, plant surfaces, and even animal skin, undergo frequent wet-dry cycles. These conditions affect bacterial competition dynamics and outcomes, with wet-dry cycles providing increased protection for some bacteria while making others more susceptible. Our findings highlight the importance of considering environmental hydration when studying microbial interactions and developing biological control strategies. This research has important implications for improving agricultural practices and understanding natural microbial ecosystems.}, }
@article {pmid39711055, year = {2025}, author = {Mant, D and Orevi, T and Kashtan, N}, title = {Impact of micro-habitat fragmentation on microbial population growth dynamics.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {39711055}, issn = {1751-7370}, support = {//Interdisciplinary Data Science Research/ ; 220020475//James S. McDonnell Foundation/ ; 1322/23//Israel Science Foundation/ ; }, mesh = {*Ecosystem ; *Escherichia coli/growth &amp; development ; Population Dynamics ; }, abstract = {Microbial communities thrive in virtually every habitat on Earth and are essential to the function of diverse ecosystems. Most microbial habitats are not spatially continuous and well-mixed, but rather composed, at the microscale, of many isolated or semi-isolated local patches of different sizes, resulting in partitioning of microbial populations into discrete local populations. The impact of this spatial fragmentation on population dynamics is not well-understood. Here, we study how such variably sized micro-habitat patches affect the growth dynamics of clonal microbial populations and how dynamics in individual patches dictate those of the metapopulation. To investigate this, we developed the μ-SPLASH, an ecology-on-a-chip platform, enabling the culture of microbes in microscopic landscapes comprised of thousands of microdroplets, with a wide range of sizes. Using the μ-SPLASH, we cultured the model bacteria Escherichia coli and based on time-lapse microscopy, analyzed the population dynamics within thousands of individual droplets. Our results reveal that growth curves substantially vary with droplet size. Although growth rates generally increase with drop size, reproductive success and the time to approach carrying capacity, display non-monotonic patterns. Combining μ-SPLASH experiments with computational modeling, we show that these patterns result from both stochastic and deterministic processes, and demonstrate the roles of initial population density, patchiness, and patch size distribution in dictating the local and metapopulation dynamics. This study reveals basic principles that elucidate the effects of habitat fragmentation and population partitioning on microbial population dynamics. These insights deepen our understanding of natural microbial communities and have significant implications for microbiome engineering.}, }
@article {pmid39710833, year = {2024}, author = {Bullington, JA and Langenfeld, K and Phaneuf, JR and Boehm, AB and Francis, CA}, title = {Microbial Community of a Sandy Beach Subterranean Estuary is Spatially Heterogeneous and Impacted by Winter Waves.}, journal = {Environmental microbiology}, volume = {26}, number = {12}, pages = {e70009}, doi = {10.1111/1462-2920.70009}, pmid = {39710833}, issn = {1462-2920}, support = {2024504//National Science Foundation, Understanding the Rules of Life: Microbiome Theory and Mechanisms (URoL:MTM)/ ; //Stanford McGee and Levorsen Research Grant/ ; //ARCO Stanford Graduate Fellowship/ ; }, mesh = {*Microbiota/genetics ; *Estuaries ; *Seasons ; *Bacteria/classification/genetics/isolation &amp; purification ; *RNA, Ribosomal, 16S/genetics ; *Bathing Beaches ; California ; *Seawater/microbiology ; Archaea/genetics/classification ; Phylogeny ; }, abstract = {Subterranean estuaries (STEs) are critical ecosystems at the interface of meteoric groundwater and subsurface seawater that are threatened by sea level rise. To characterize the influence of tides and waves on the STE microbial community, we collected porewater samples from a high-energy beach STE at Stinson Beach, California, USA, over the two-week neap-spring tidal transition during both a wet and dry season. The microbial community, analyzed by 16S rRNA gene (V4) amplicon sequencing, clustered according to consistent physicochemical features found within STEs. The porewater community harbored relatively abundant Proteobacteria, Verrucomicrobiota, and Bacteroidota, as well as members of the archaeal DPANN superphylum and bacterial Candidate Phyla Radiation (CPR). Tidal conditions were not associated with microbial community composition; however, a wave overtopping event significantly impacted the beach microbiome. As a baseline for environmental change, our results elucidate the unique dynamics of a STE microbiome with unprecedented temporal resolution, highlighting the transport of cellular material through beach porewater due to waves.}, }
@article {pmid39710772, year = {2025}, author = {Ali, A and Zhong, X and Wang, Q and Xu, H}, title = {Use of a broad β-diversity for bioassessment of salinity stress on community homogeneity in marine environments.}, journal = {Environmental science and pollution research international}, volume = {32}, number = {3}, pages = {1167-1175}, pmid = {39710772}, issn = {1614-7499}, support = {31672308//The Natural Science Foundation of China/ ; 41076089//The Natural Science Foundation of China/ ; ZR2022QD065//Youth Project of the Natural Science Foundation of Shandong Province, China/ ; }, mesh = {*Salinity ; China ; *Salt Stress ; *Biodiversity ; Ecosystem ; Seawater/chemistry ; }, abstract = {To determine the feasibility of β-diversity measures to evaluate the impact of salinity stress on community homogeneity in marine environments, a 1-month bioassay was conducted using the protozoan assemblage as the test community. The test samples were collected using the slide method in coastal waters of the Yellow Sea, northern China. Five treatments were designed according to a salinity gradient of 9, 19, 29, 39, and 49 PSU. The homogeneity of the test community showed significant variability in both composition and abundance patterns among five treatments. The multivariate dispersion measure on compositional data was linearly associated with the salinity stress compared to those on abundance alone or in combination with occurrence. The traditional β-diversity index represented a different behavior from that of the multivariate dispersion measures. These findings suggest that the composition-based multivariate dispersion may be a useful tool to evaluate the global salinity stress on community homogeneity in marine ecosystems.}, }
@article {pmid39710259, year = {2025}, author = {Callaway, T and Perez, HG and Corcionivoschi, N and Bu, D and Fluharty, FL}, title = {International Symposium on Ruminant Physiology: The holobiont concept in ruminant physiology-More of the same, or something new and meaningful to food quality, food security, and animal health?.}, journal = {Journal of dairy science}, volume = {108}, number = {7}, pages = {7567-7575}, doi = {10.3168/jds.2024-25847}, pmid = {39710259}, issn = {1525-3198}, mesh = {Animals ; *Ruminants/physiology/microbiology ; Gastrointestinal Microbiome ; Humans ; *Food Security ; *Food Quality ; Food Supply ; }, abstract = {The holobiont concept has emerged as an attempt to recognize and describe the myriad interactions and physiological signatures inherent to a host organism, as affected by the microbial communities that colonize and co-inhabit the environment within which the host resides. The field acknowledges and draws upon principles from evolution, ecology, genetics, and biology, and in many respects has been pushed by the advent of high throughput DNA sequencing and, to a lesser extent, other omics-based technologies. Despite the explosion in data generation and analyses, much of our current understanding of the human and ruminant holobiont is based on compositional forms of data and thereby, restricted to describing host phenotypes via associative or correlative studies. So, where to from here? We will discuss some past findings arising from ruminant and human gut microbiota research and seek to evaluate the rationale, progress, and opportunities that might arise from the holobiont approach to the ruminant and human host. In particular, we will consider what is a "good" or "bad" host gastrointestinal microbiome in different scenarios, as well as potential avenues to sustain or alter the holobiont. Although the holobiont approach might improve food quality, food security, and animal health, these benefits will most likely be achieved via a judicious and pragmatic compromise in data generation, both in terms of its scale as well as its generation, in context with the forgotten knowledge of ruminant and human physiology.}, }
@article {pmid39709274, year = {2025}, author = {Kerkar, AU and Sutherland, KR and Thompson, AW}, title = {Non-viral predators of marine picocyanobacteria.}, journal = {Trends in microbiology}, volume = {33}, number = {5}, pages = {558-568}, doi = {10.1016/j.tim.2024.11.010}, pmid = {39709274}, issn = {1878-4380}, mesh = {*Prochlorococcus/physiology/growth &amp; development ; *Synechococcus/physiology/growth &amp; development ; Ecosystem ; *Seawater/microbiology ; Aquatic Organisms ; Food Chain ; }, abstract = {The Earth's most abundant photosynthetic cells, the picocyanobacteria - Prochlorococcus and Synechococcus - play a fundamental global role in aquatic ecosystems. The success of these picocyanobacteria is interpreted through a cross-scale systems framework that integrates bottom-up controls on growth (e.g., nutrients and light), diversity, and the selective pressures and response to predation. While viral predators are well studied and experimentally tractable, the diverse non-viral predators of picocyanobacteria are disconnected from this framework and experimentally challenging, leaving a major gap in understanding the picocyanobacteria. This review presents existing research on non-viral picocyanobacterial predators and promising research frontiers that will expand knowledge of the ecology and evolution of these crucial microorganisms.}, }
@article {pmid39708482, year = {2025}, author = {Zhao, H and Hu, X and Guan, S and Cai, J and Li, W and Zhang, D and Feng, Y and Zhu, W and Marzorati, M and Li, B and Zhang, X and Tian, J}, title = {Capilliposide A alleviates DSS-induced colitis by regulating the intestinal flora and its metabolites of origin.}, journal = {International immunopharmacology}, volume = {146}, number = {}, pages = {113858}, doi = {10.1016/j.intimp.2024.113858}, pmid = {39708482}, issn = {1878-1705}, mesh = {Animals ; Dextran Sulfate ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Saponins/therapeutic use/pharmacology ; Disease Models, Animal ; Colon/pathology/drug effects/microbiology ; *Anti-Inflammatory Agents/therapeutic use/pharmacology ; *Colitis/drug therapy/chemically induced ; Male ; *Triterpenes/therapeutic use/pharmacology ; Mice, Inbred C57BL ; *Colitis, Ulcerative/drug therapy/chemically induced ; Cytokines/metabolism ; Intestinal Mucosa/drug effects ; Humans ; }, abstract = {Ulcerative colitis is a chronic idiopathic inflammatory disease that impacts the mucous membrane of the colon. Lately, the incidence and prevalence of UC has been increasing globally. However, there are significant side effects of existing drugs for UC intervention. Accordingly, there is a pressing demand to explore novel bioactive substances for addressing UC. Natural product saponins have attracted great attention due to their obvious anti-colitis potential. Capilliposide A is a triterpenoid saponin, which is derived from Lysimachia capillipes Hemsl., exhibits good anti-inflammatory activity. Nonetheless, the impact and mechanism of CPS-A on ulcerative colitis remains obscure. This study aimed to investigate the therapeutic effects of CPS-A on the dextran sulphate sodium induced colitis mouse model and explore its mechanism. The efficacy and safety of CPS-A were evaluated in a well-established dextran sodium sulfate (DSS)-induced colitis mice model. Disease progression was monitored via clinical symptoms, histopathological examination, quantification of inflammatory cytokines, and epithelial barrier function evaluation. Plasma samples and intestinal contents were collected for non-targeted metabolomics and 16sRNA sequencing, respectively, to jointly evaluate the mechanism of action. CPS-A alleviated colitis by improving weight, Disease activity index score, histopathology, goblet cell, colon length, and expression of inflammatory factors. Moreover, CPS-A effectively preserved the integrity of the intestinal barrier by enhancing the expression of tight junction proteins and mucin in the colonic tissue of mice. Furthermore, CPS-A exerted a regulatory effect on the composition of the gut microbiota, promoting bacterial richness and diversity. It not only suppressed the abundance of detrimental bacteria while enhancing the abundance of advantageous bacteria, but also modulated the metabolites derived from the intestinal flora. Importantly, correlation analysis shows that these indicators are highly correlated. This study revealed that CPS-A exhibits a favorable therapeutic efficacy against colitis, primarily attributed to its ability to modulate the gut microbiota their associated metabolites as the key mechanisms of action.}, }
@article {pmid39708146, year = {2024}, author = {Zhao, L and Zhang, S and Li, J and Zhang, C and Xiao, R and Bai, X and Xu, H and Zhang, F}, title = {Unveiling Diversity and Function: Venom-Associated Microbes in Two Spiders, Heteropoda venatoria and Chilobrachys guangxiensis.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {156}, pmid = {39708146}, issn = {1432-184X}, mesh = {Animals ; *Spiders/microbiology/physiology ; *Spider Venoms ; *Bacteria/genetics/classification/drug effects/isolation &amp; purification ; Apoptosis ; Symbiosis ; Humans ; Cell Line, Tumor ; High-Throughput Nucleotide Sequencing ; Anti-Inflammatory Agents/pharmacology ; }, abstract = {Spiders are natural predators of agricultural pests, primarily due to the potent venom in their venom glands. Spider venom is compositionally complex and holds research value. This study analyzes the diversity of symbiotic bacteria in spider venom glands and venom, as well as the biological activity of culturable symbiotic bacteria. Focusing on the venom glands and venom of Heteropoda venatoria and Chilobrachys guangxiensis, we identified a diverse array of microorganisms. High-throughput sequencing detected 2151 amplicon sequence variants (ASVs), spanning 31 phyla, 75 classes, and 617 genera. A total of 125 strains of cultivable bacteria were isolated. Using the Oxford cup method, crude extracts from 46 of these strains exhibited inhibitory effects against at least one indicator bacterium. MTT (Thiazolyl blue) assays revealed that the crude extracts from 43 strains had inhibitory effects on tumor cell line MGC-803 growth. Additionally, DAPI (4',6-diamidino-2'-phenylindole) staining and flow cytometry were employed to detect cell apoptosis. The anti-inflammatory activity of nine bacterial strains was assessed using a NO assay kit and enzyme-linked immunosorbent assay (ELISA). This study further investigated the biological activity of venom, exploring the relationship between the venom and the functional activity of venom-associated bacteria.}, }
@article {pmid39708144, year = {2024}, author = {Quevedo-Caraballo, S and Roldán, A and Álvarez-Pérez, S}, title = {Demethylation Inhibitor Fungicides Have a Significantly Detrimental Impact on Population Growth and Composition of Nectar Microbial Communities.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {160}, pmid = {39708144}, issn = {1432-184X}, support = {PIPF-2023/ECO-29442//Consejer&#xed;a de Educaci&#xf3;n, Ciencia y Universidades, Comunidad de Madrid/ ; RYC2018-023847-I, CNS2022-135237//Ministerio de Ciencia e Innovaci&#xf3;n/ ; }, mesh = {*Fungicides, Industrial/pharmacology ; *Plant Nectar ; *Microbiota/drug effects ; Bacteria/classification/drug effects/isolation &amp; purification/genetics ; Demethylation ; Fungi/drug effects/classification/isolation &amp; purification ; Metschnikowia/drug effects ; Flowers/microbiology/growth &amp; development ; }, abstract = {Demethylation inhibitor (DMI) fungicides are a mainstay of modern agriculture due to their widespread use for crop protection against plant-pathogenic fungi. However, DMI residues can disperse and persist in the environment, potentially affecting non-target fungi. Previous research has demonstrated that DMIs and other fungicides inhibit yeast growth in floral nectar microbial communities and decrease fungal richness and diversity of exposed flowers with no apparent effect on bacteria. Nevertheless, the effect of DMIs on the population growth of different species of nectar inhabitants and the dynamics of these microbial communities remains understudied. To address these issues, in this study we created synthetic microbial communities including yeasts (Metschnikowia reukaufii and Metschnikowia pulcherrima) and bacteria (Rosenbergiella epipactidis and Comamonas sp.) and propagated them in culture media containing different DMIs (imazalil, propiconazole, and prothioconazole) at different doses or no fungicide. Our results showed that DMIs have a significant impact on some of the most common microbial inhabitants of floral nectar by favoring the growth of bacteria over yeasts. Furthermore, habitat generalists such as M. pulcherrima and Comamonas sp. were more impacted by the presence of fungicides than the nectar specialists M. reukaufii and R. epipactidis, especially upon dispersal across habitat patches. Future research should determine if the patterns observed in the present study hold true for other species of nectar microbes and explore the interaction between growth limitation due to fungicide presence, dispersal limitation, and other mechanisms involved in community assembly in floral nectar.}, }
@article {pmid39708139, year = {2024}, author = {Zhao, Z and Liu, S and Jiang, S and Zhang, D and Sha, Z}, title = {Diversity and Potential Metabolic Characteristics of Culturable Copiotrophic Bacteria That Can Grow on Low-Nutrient Medium in Zhenbei Seamount in the South China Sea.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {157}, pmid = {39708139}, issn = {1432-184X}, support = {LSKJ202203102//the Science and Technology Innovation Project of Laoshan Laboratory/ ; XDB42000000//the Strategic Priority Research Program of Chinese Academy of Sciences/ ; 42221005//the NSFC Innovative Group Grant/ ; 42376143//the National Natural Science Foundation of China/ ; }, mesh = {*Seawater/microbiology ; China ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification/growth &amp; development ; Gammaproteobacteria/metabolism/genetics/isolation &amp; purification/classification/growth &amp; development ; Phylogeny ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; Nitrates/metabolism ; Culture Media/chemistry ; Nutrients/metabolism ; Alphaproteobacteria/metabolism/genetics/isolation &amp; purification/classification/growth &amp; development ; Vibrio/metabolism/genetics/isolation &amp; purification/growth &amp; development/classification ; }, abstract = {Oligotrophs are predominant in nutrient-poor environments, but copiotrophic bacteria may tolerate conditions of low energy and can also survive and thrive in these nutrient-limited conditions. In the present study, we isolated 648 strains using a dilution plating method after enrichment for low-nutrient conditions. We collected 150 seawater samples at 21 stations in different parts of the water column at the Zhenbei Seamount in the South China Sea. The 648 isolated copiotrophic strains that could grow on low-nutrient medium were in 21 genera and 42 species. A total of 99.4% (644/648) of the bacteria were in the phylum Pseudomonadota, with 73.3% (472/644) in the class Gammaproteobacteria and 26.7% (172/644) in the class Alphaproteobacteria. Among the 42 representative isolates, Pseudoalteromonas arabiensis, Roseibium aggregatum, and Vibrio neocaledonicus were present in all layers of seawater and at almost all of the stations. Almost half of these species (20/42) contained genes that performed nitrate reduction, with confirmation by nitrate reduction testing. These isolates also contained genes that functioned in sulfur metabolism, including sulfate reduction, thiosulfate oxidation, thiosulfate disproportionation, and dimethylsulfoniopropionate degradation. GH23, CBM50, GT4, GT2, and GT51 were the main carbohydrate-active enzymes (CAZymes), and these five enzymes were present in all or almost all of the isolated strains. The most abundant classes of CAZymes were those associated with the degradation of chitin, starch, and cellulose. Collectively, our study of marine copiotrophic bacteria capable of growing on low-nutrient medium demonstrated the diversity of these species and their potential metabolic characteristics.}, }
@article {pmid39708121, year = {2024}, author = {Grisnik, M and Walker, DM}, title = {Bat Cutaneous Microbial Assemblage Functional Redundancy Across a Host-Mediated Disturbance.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {161}, pmid = {39708121}, issn = {1432-184X}, support = {32801-00803//Tennessee Wildlife Resources Agency,United States/ ; }, mesh = {*Chiroptera/microbiology ; Animals ; *Seasons ; *Bacteria/genetics/classification/isolation &amp; purification ; *Skin/microbiology ; *Microbiota ; Ascomycota/genetics/physiology ; Ecosystem ; }, abstract = {Understanding the processes and factors that influence the structure of host-associated microbial assemblages has been a major area of research as these assemblages play a role in host defense against pathogens. Previous work has found that bacterial taxa within bat cutaneous microbial assemblages have antifungal capabilities against the emerging fungal pathogen, Pseudogymnoascus destructans. However, our understanding of natural fluctuations in these cutaneous microbial assemblages over time due to shifts in host habitat is lacking. The objective of this work was to understand how the taxonomic and functional bat cutaneous microbial assemblage responds to seasonal shifts in host habitat. We hypothesized that at the community level, there will be turnover in taxonomic structure but functional redundancy across seasons. On a finer scale, we hypothesized that there will be differences in the relative abundance of functional genes that code for select pathways across seasons. Results showed that, on a broad scale, the bat cutaneous microbial assemblage is seasonally taxonomically dynamic but functionally redundant. Additionally, although there was almost complete taxonomic turnover between winter and summer bat microbial assemblages, there was no difference in assemblage structure across winters. This functional redundancy was also observed at finer scales, with no differences in the abundance of genes within pathways of hypothesized importance across seasons or winters. Taken together, results suggest species sorting mechanisms correlated with shifts in host habitat use, drive taxonomic but not functional host-associated cutaneous microbial community assembly.}, }
@article {pmid39708106, year = {2024}, author = {Singh, S and Singh, AK and Pradhan, B and Tripathi, S and Kumar, KS and Chand, S and Rout, PR and Shahid, MK}, title = {Harnessing Trichoderma Mycoparasitism as a Tool in the Management of Soil Dwelling Plant Pathogens.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {158}, pmid = {39708106}, issn = {1432-184X}, mesh = {*Trichoderma/physiology ; *Soil Microbiology ; *Plant Diseases/microbiology/prevention &amp; control ; Pest Control, Biological/methods ; Agriculture/methods ; Plants/microbiology ; Biological Control Agents ; Soil/chemistry ; }, abstract = {Maintaining and enhancing agricultural productivity for food security while preserving the ecology and environment from the harmful effects of toxicants is the main challenge in modern monoculture farming systems. Microbial biological agents can be a promising substitute for traditional synthetic pesticides to manage plant diseases. Trichoderma spp. are soil-dwelling ascomycete fungi and are common biocontrol agents against diverse phytopathogens. Trichoderma-based biocontrol techniques can regulate and control soil-borne plant diseases through mechanisms such as mycoparasitism, the production of antibiotics and hydrolytic enzymes, rhizo-sphere competence, the effective competition for available resources, induction of plant resistance and facilitation of plant growth. Numerous secondary metabolites produced by Trichoderma spp. are reported to prevent the development of soil-borne plant disease. Thus, Trichoderma spp. may have direct and indirect biological impacts on the targeted plant pathogens. Furthermore, this review discusses the convenient implications and challenges of applying Trichoderma-based strategies in agricultural settings. Overall, the assessment underscores the potential of Trichoderma as a sustainable and effective tool for mitigating soil-borne pathogens, highlighting avenues for future research and applications.}, }
@article {pmid39708073, year = {2024}, author = {Han, GH and Yu, J and Kang, MJ and Park, MJ and Noh, CH and Kim, YJ and Kwon, KK}, title = {Correction to: Phylosymbiosis in Seven Wild Fish Species Collected Off the Southern Coast of Korea: Skin Microbiome Most Strongly Reflects Evolutionary Pressures.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {159}, doi = {10.1007/s00248-024-02478-w}, pmid = {39708073}, issn = {1432-184X}, }
@article {pmid39708062, year = {2024}, author = {Nonthijun, P and Tanunchai, B and Schroeter, SA and Wahdan, SFM and Alves, EG and Hilke, I and Buscot, F and Schulze, ED and Disayathanoowat, T and Purahong, W and Noll, M}, title = {Feels Like Home: A Biobased and Biodegradable Plastic Offers a Novel Habitat for Diverse Plant Pathogenic Fungi in Temperate Forest Ecosystems.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {155}, pmid = {39708062}, issn = {1432-184X}, mesh = {*Forests ; *Fungi/genetics/metabolism/classification ; *Biodegradable Plastics/metabolism ; *Trees/microbiology ; Soil Microbiology ; Plant Diseases/microbiology ; Biodegradation, Environmental ; Ecosystem ; Soil/chemistry ; Plant Leaves/microbiology ; }, abstract = {Poly(butylene succinate-co-adipate) (PBSA), a biodegradable plastic, is significantly colonized and degraded by soil microbes under natural field conditions, especially by fungal plant pathogens, raising concerns about potential economic losses. This study hypothesizes that the degradation of biodegradable plastics may increase the presence and abundance of plant pathogens by serving as an additional carbon source, ultimately posing a risk to forest ecosystems. We investigated (i) fungal plant pathogens during the exposure of PBSA in European broadleaved and coniferous forests (two forest types), with a specific focus on potential risk to tree health, and (ii) the response of such fungi to environmental factors, including tree species, soil pH, nutrient availability, moisture content, and the physicochemical properties of leaf litter layer. Next-generation sequencing (NGS) revealed that PBSA harbored a total of 318 fungal plant pathogenic amplicon sequence variants (ASVs) belonging to 108 genera. Among the identified genera (Alternaria, Nectria, Phoma, Lophodermium, and Phacidium), some species have been reported as causative agents of tree diseases. Plenodomus was present in high relative abundances on PBSA, which have not previously been associated with disease in broadleaved and coniferous forests. Furthermore, the highest number of fungal plant pathogens were detected at 200 days of PBSA exposure (112 and 99 fungal plant pathogenic ASV on PBSA degraded under Q. robur and F. sylvatic-dominated forest, respectively), which was double compared mature leaves and needles from the same forest sites. These findings suggest that PBSA attracts fungal plant pathogens in forests as an additional carbon source, potentially leading to increased disease outbreaks and disrupting the stability of forest ecosystems. The fungal plant pathogenic community compositions were mainly shaped by forest type, PBSA exposure time, site locations, leaf litter layer water content, and N:P ratio from leaf litter layer in both forest types. This study provides valuable insights into the potential risks posed by biodegradable plastic degradation in forests after 200 and 400 days of exposure, respectively. Further comprehensive evaluations of their effects on tree health and ecosystems, ideally on a long-term basis, are needed. These evaluations should include integrating microbial investigation, soil health monitoring, and ecosystem interaction assessments. Nevertheless, it should be noted that our interpretation of plant pathogens is solely based on high-throughput sequencing, bioinformatics, and annotation tools.}, }
@article {pmid39703713, year = {2024}, author = {Sheng, Y and Zeng, X and Zhao, L and Li, Y}, title = {Editorial: Microbial involvement in biogeochemical cycling and contaminant transformations at land-water ecotones.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1525521}, pmid = {39703713}, issn = {1664-302X}, }
@article {pmid39701829, year = {2025}, author = {McAlister, JS and Blum, MJ and Bromberg, Y and Fefferman, NH and He, Q and Lofgren, E and Miller, DL and Schreiner, C and Candan, KS and Szabo-Rogers, H and Reed, JM}, title = {An interdisciplinary perspective of the built-environment microbiome.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {1}, pages = {}, pmid = {39701829}, issn = {1574-6941}, support = {CCF 2200140//U.S. National Science Foundation/ ; }, mesh = {*Microbiota ; *Built Environment ; Humans ; Interdisciplinary Research ; }, abstract = {The built environment provides an excellent setting for interdisciplinary research on the dynamics of microbial communities. The system is simplified compared to many natural settings, and to some extent the entire environment can be manipulated, from architectural design to materials use, air flow, human traffic, and capacity to disrupt microbial communities through cleaning. Here, we provide an overview of the ecology of the microbiome in the built environment. We address niche space and refugia, population, and community (metagenomic) dynamics, spatial ecology within a building, including the major microbial transmission mechanisms, as well as evolution. We also address landscape ecology, connecting microbiomes between physically separated buildings. At each stage, we pay particular attention to the actual and potential interface between disciplines, such as ecology, epidemiology, materials science, and human social behavior. We end by identifying some opportunities for future interdisciplinary research on the microbiome of the built environment.}, }
@article {pmid39701529, year = {2025}, author = {Firkins, JL and Henderson, EL and Duan, H and Pope, PB}, title = {International Symposium on Ruminant Physiology: Current perspective on rumen microbial ecology to improve fiber digestibility.}, journal = {Journal of dairy science}, volume = {108}, number = {7}, pages = {7511-7529}, doi = {10.3168/jds.2024-25863}, pmid = {39701529}, issn = {1525-3198}, mesh = {Animals ; *Rumen/microbiology/metabolism/physiology ; *Dietary Fiber/metabolism ; *Ruminants/microbiology/physiology ; *Digestion/physiology ; Animal Feed ; Fermentation ; Diet/veterinary ; Bacteria/metabolism ; }, abstract = {Although cellulose has received the most attention, further research is needed for a complete comprehension of other fiber components in forage and nonforage fiber sources corresponding to the array of enzymes needed for depolymerization and resulting fermentation of sugars. Carbohydrate-active enzymes (CAZymes) have been described in detail herein, although new information will no doubt accumulate in the future. Known CAZymes are attributed to taxa that are easily detected via 16S rRNA gene profiling techniques, but such approaches have limitations. We describe how closely related species or strains expand into different niches depending on diet and the dynamic availability of remaining fibrous substrates. Moreover, expression of CAZymes and other enzymes such as in fermentation pathways can shift among strains and even within strains over time of incubation. We describe unique fibrolytic components of bacteria, protozoa, and fungi and emphasize the development of consortia that efficiently increase neutral detergent fiber degradability (NDFD). For example, more powerful genome-centric functional omics approaches combined with expanded bioinformatics and network analyses are needed to expand our current understanding of ruminal function and the bottlenecks that lead to among-study variation in NDFD. Specific examples highlighted include our lack of fundamental understanding why starch limits NDFD, whereas moderate inclusion of rumen-degraded protein, certain supplemental fatty acids (especially palmitic acid), and supplemental sugars sometimes stimulates NDFD. Current and future research must uncover deeper complexity in the rumen microbiome through a combination of approaches described herein to be followed by validation using novel cultivation studies and, ultimately, NDFD measured in vivo for integration with ruminant productivity traits.}, }
@article {pmid39699229, year = {2025}, author = {Anuforo, PC and Würz, B and Wick, LY and Kallies, R}, title = {Draft genome sequences of Pseudomonas chengduensis strain BW1 and Sphingobium sp. strain MK2 isolated from oil sands process-affected water.}, journal = {Microbiology resource announcements}, volume = {14}, number = {2}, pages = {e0067724}, pmid = {39699229}, issn = {2576-098X}, support = {57610608//Deutscher Akademischer Austauschdienst (DAAD)/ ; 57610608//MPR | Petroleum Technology Development Fund (PTDF)/ ; }, abstract = {Draft genomes of two phenanthrene-degrading bacterial isolates from oil sands process-affected water (OSPW) in Alberta, Canada were sequenced. Both isolates grew in close association on agar plates and were difficult to obtain axenically. They represent novel Pseudomonas chengduensis and Sphingobium sp. strains with genomes of 5.5 and 4.1 Mbases length, respectively.}, }
@article {pmid39699221, year = {2025}, author = {Lustermans, JJM and Sereika, M and Burdorf, LDW and Albertsen, M and Schramm, A and Marshall, IPG}, title = {Extracellular electron transfer genes expressed by candidate flocking bacteria in cable bacteria sediment.}, journal = {mSystems}, volume = {10}, number = {1}, pages = {e0125924}, pmid = {39699221}, issn = {2379-5077}, support = {DNRF136//Danmarks Grundforskningsfond (DNRF)/ ; S004523N//Flanders Research FWO/ ; TopBOF//University Antwerp TopBOF program/ ; Microflora Danica//Poul Due Jensens Fond (Poul Due Jensen Foundation)/ ; HORIZON-MSCA-2023-PF-01: 101152850//EC | Horizon Europe | Excellent Science | HORIZON EUROPE Marie Sklodowska-Curie Actions (MSCA)/ ; }, mesh = {*Geologic Sediments/microbiology ; Electron Transport/genetics ; *Bacteria/genetics/metabolism/classification ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Oxidation-Reduction ; Phylogeny ; }, abstract = {UNLABELLED: Cable bacteria, filamentous sulfide oxidizers that live in sulfidic sediments, are at times associated with large flocks of swimming bacteria. It has been proposed that these flocks of bacteria transport electrons extracellularly to cable bacteria via an electron shuttle intermediate, but the identity and activity of these bacteria in freshwater sediment remain mostly uninvestigated. Here, we elucidate the electron exchange capabilities of the bacterial community by coupling metagenomics and metatranscriptomics to 16S rRNA amplicon-based correlations with cable bacteria over 155 days. We identified candidate flocking bacteria as bacteria containing genes for motility and extracellular electron transfer including synthesis genes for potential extracellular electron shuttles: phenazines and flavins. Based on these criteria, 22 MAGs were from candidate flockers, which constituted 21.4% of all 103 MAGs. Of the candidate flocking bacteria, 42.1% expressed extracellular electron transfer genes. The proposed flockers belonged to a large variety of metabolically versatile taxonomic groups: 18 genera spread across nine phyla. Our data suggest that cable bacteria in freshwater sediments engage in electric relationships with diverse exoelectrogenic microbes. This community, found in deeper anoxic sediment layers, is involved in sulfur, carbon, and metal (in particular Fe) cycling and indirectly utilizes oxygen here by extracellularly transferring electrons to cable bacteria.<br><br>IMPORTANCE: Cable bacteria are ubiquitous, filamentous bacteria that couple sulfide oxidation to the reduction of oxygen at up to centimeter distances in sediment. Cable bacterial impact extends beyond sulfide oxidation via interactions with other bacteria that flock around cable bacteria and use them as electron acceptor "shortcut" to oxygen. The exact nature of this interspecies electric interaction remained unknown. With metagenomics and metatranscriptomics, we determined what extracellular electron transport processes co-occur with cable bacteria, demonstrating the identity and metabolic capabilities of these potential flockers. In sediments, microbial activities are sharply divided into anaerobic and aerobic processes, with oxygen reaching only millimeters deep. Cable bacteria extend the influence of oxygen to several centimeters, revealing a new class of anaerobic microbial metabolism with cable bacteria as electron acceptors. This fundamentally changes our understanding of sediment microbial ecology with wide-reaching consequences for sulfur, metal (in particular Fe), and carbon cycling in freshwater and marine sediments.}, }
@article {pmid39698295, year = {2024}, author = {Bovio-Winkler, P and Cabezas, A and Etchebehere, C}, title = {Unveiling the hidden diversity and functional role of Chloroflexota in full-scale wastewater treatment plants through genome-centric analyses.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae050}, pmid = {39698295}, issn = {2730-6151}, abstract = {The phylum Chloroflexota has been found to exhibit high abundance in the microbial communities from wastewater treatment plants (WWTPs) in both aerobic and anaerobic systems. However, its metabolic role has not been fully explored due to the lack of cultured isolates. To address this gap, we use publicly available metagenome datasets from both activated sludge (AS) and methanogenic (MET) full-scale wastewater treatment reactors to assembled genomes. Using this strategy, 264 dereplicated, medium- and high-quality metagenome-assembled genomes (MAGs) classified within Chloroflexota were obtained. Taxonomic classification revealed that AS and MET reactors harbored distinct Chloroflexota families. Nonetheless, the majority of the annotated MAGs (166 MAGs with >85% completeness and < 5% contamination) shared most of the metabolic potential features, including the ability to degrade simple sugars and complex polysaccharides, fatty acids and amino acids, as well as perform fermentation of different products. While Chloroflexota MAGs from MET reactors showed the potential for strict fermentation, MAGs from AS harbored the potential for facultatively aerobic metabolism. Metabolic reconstruction of Chloroflexota members from AS unveiled their versatile metabolism and suggested a primary role in hydrolysis, carbon removal and involvement in nitrogen cycling, thus establishing them as fundamental components of the ecosystem. Microbial reference genomes are essential resources for understanding the potential functional role of uncultured organisms in WWTPs. Our study provides a comprehensive genome catalog of Chloroflexota for future analyses aimed at elucidating their role in these ecosystems.}, }
@article {pmid39697668, year = {2024}, author = {Roy, A and Ghosh, A and Bhadury, P}, title = {Delving deep into the draft genome of Mangrovibacter sp. SLW1, isolated from Sundarbans mangrove.}, journal = {Access microbiology}, volume = {6}, number = {8}, pages = {}, pmid = {39697668}, issn = {2516-8290}, abstract = {Mangrovibacter sp. SLW1, a Gram-negative, aerobic, motile bacterium, was isolated from mangrove litterfall in Sundarbans mangrove. The draft genome is 5.5 Mbp in size with 49.45 mol% guanine-cytosine (GC) content. The linear chromosome of the bacterium consists of 27 contigs with 7339 coding sequences. The detailed in silico analyses of the genome of Mangrovibacter sp. SLW1 provide information on ecological adaptation. The genome is a reservoir for multiple heavy metals and metalloid resistance gene clusters as well as exhibit metabolic capabilities for utilization of a wide range of carbohydrates. It also encodes for tris-catecholate siderophore and can regulate uptake of iron thereby may influence plant growth such as mangrove vegetation.}, }
@article {pmid39695543, year = {2024}, author = {Qin, K and Qing, J and Wang, Q and Li, Y}, title = {Epidemiological shifts in chronic kidney disease: a 30-year global and regional assessment.}, journal = {BMC public health}, volume = {24}, number = {1}, pages = {3519}, pmid = {39695543}, issn = {1471-2458}, support = {82170716//National Natural Science Foundation of China/ ; 82170716//National Natural Science Foundation of China/ ; 82170716//National Natural Science Foundation of China/ ; 82170716//National Natural Science Foundation of China/ ; 2020SYS01//Key Laboratory Construction Plan Project of Shanxi Provincial Health Commission/ ; 2020SYS01//Key Laboratory Construction Plan Project of Shanxi Provincial Health Commission/ ; 2020SYS01//Key Laboratory Construction Plan Project of Shanxi Provincial Health Commission/ ; 2020SYS01//Key Laboratory Construction Plan Project of Shanxi Provincial Health Commission/ ; 2020XM21//Key Project of Shanxi Provincial Health Commission/ ; 2020XM21//Key Project of Shanxi Provincial Health Commission/ ; 2020XM21//Key Project of Shanxi Provincial Health Commission/ ; 2020XM21//Key Project of Shanxi Provincial Health Commission/ ; }, mesh = {Humans ; *Renal Insufficiency, Chronic/epidemiology/mortality ; Male ; Incidence ; *Global Health/statistics &amp; numerical data ; Female ; Middle Aged ; Adult ; Prevalence ; Aged ; *Global Burden of Disease ; Risk Factors ; Disability-Adjusted Life Years ; Adolescent ; Young Adult ; Quality-Adjusted Life Years ; }, abstract = {BACKGROUND: Chronic kidney disease (CKD) presents a growing global health challenge, with significant variability in disease burden across different regions and countries. This study aimed to analyze the trends in incidence, prevalence, mortality, and disability-adjusted life years (DALYs) for CKD from 1990 to 2019, utilizing data from the Global Burden of Disease Study.<br><br>METHODS: We conducted an in-depth study on the global and age-standardized incidence, prevalence, mortality, and DALYs of CKD, and assessed trends over a 30-year period. Additionally, we explored the associations between healthcare access and quality (HAQ), the Socio-Demographic Index (SDI), and CKD. Furthermore, we conducted a detailed analysis of six risk factors closely related to CKD, and based on these findings, provided strong evidence for enhancing the management of CKD.<br><br>RESULTS: In 2019, there were 18,986,903 cases of CKD, with an average annual percent change (AAPC) of 1.82 (95% CI&#x2009;=&#x2009;1.8 to 1.82) in incidence since 1990. The age-standardized incidence rate increased from 192.45 per 100,000 in 1990 to 233.65 per 100,000 in 2019. Prevalence also rose, with a total of 69,729,430 cases in 2019 and an AAPC of 1.19 (95% CI&#x2009;=&#x2009;1.19 to 1.2). Mortality and DALYs have increased correspondingly, with the mortality rate reaching 18.29 per 100,000 and total DALYs at 41,538,592 in 2019. The analysis showed that higher HAQ levels are associated with better outcomes in terms of lower mortality and DALY rates, whereas lower HAQ levels correlate with poorer outcomes. In addition, high fasting plasma glucose and high systolic blood pressure are the main contributors to CKD-related deaths, with their population attributable fraction&#xa0;(PAF) significantly decreasing as the SDI decreases.<br><br>CONCLUSION: The burden of CKD has significantly increased over the past three decades, influenced by demographic changes and variations in healthcare quality and access. Effective public health strategies and improvements in healthcare delivery are needed to address the disparities in CKD outcomes globally.}, }
@article {pmid39695352, year = {2025}, author = {Moore, M and Whittington, HD and Knickmeyer, R and Azcarate-Peril, MA and Bruno-Bárcena, JM}, title = {Non-stochastic reassembly of a metabolically cohesive gut consortium shaped by N-acetyl-lactosamine-enriched fibers.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2440120}, pmid = {39695352}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome ; Infant ; *Bacteria/metabolism/classification/isolation &amp; purification/genetics ; Feces/microbiology ; Lactose/metabolism ; Dietary Fiber/metabolism ; Oligosaccharides/metabolism ; Amino Sugars ; }, abstract = {Diet is one of the main factors shaping the human microbiome, yet our understanding of how specific dietary components influence microbial consortia assembly and subsequent stability in response to press disturbances - such as increasing resource availability (feeding rate) - is still incomplete. This study explores the reproducible re-assembly, metabolic interplay, and compositional stability within microbial consortia derived from pooled stool samples of three healthy infants. Using a single-step packed-bed reactor (PBR) system, we assessed the reassembly and metabolic output of consortia exposed to lactose, glucose, galacto-oligosaccharides (GOS), and humanized GOS (hGOS). Our findings reveal that complex carbohydrates, especially those containing low inclusion (~1.25 gL[-1]) components present in human milk, such as N-acetyl-lactosamine (LacNAc), promote taxonomic, and metabolic stability under varying feeding rates, as shown by diversity metrics and network analysis. Targeted metabolomics highlighted distinct metabolic responses to different carbohydrates: GOS was linked to increased lactate, lactose to propionate, sucrose to butyrate, and CO2, and the introduction of bile salts with GOS or hGOS resulted in butyrate reduction and increased hydrogen production. This study validates the use of single-step PBRs for reliably studying microbial consortium stability and functionality in response to nutritional press disturbances, offering insights into the dietary modulation of microbial consortia and their ecological dynamics.}, }
@article {pmid39694113, year = {2025}, author = {Van Peteghem, L and Matassa, S and Sakarika, M}, title = {Fueling the protein transition: Can waste-derived ethanol enable efficient and high-quality microbial protein production?.}, journal = {Bioresource technology}, volume = {418}, number = {}, pages = {131990}, doi = {10.1016/j.biortech.2024.131990}, pmid = {39694113}, issn = {1873-2976}, mesh = {*Bacterial Proteins/biosynthesis ; Biomass ; *Ethanol/isolation &amp; purification/metabolism ; Fermentation ; *Waste Products ; }, abstract = {Meeting the protein needs of a growing population will require significant resources. In this context, microbial protein (MP) offers a nutritious and versatile protein source from recovered resources. This meta-analysis of over 100 studies examines the efficiency and nutritional quality of MP production using ethanol. Ethanol, a feedstock derived from CO2 and biological waste, is used by various microorganisms, and has an established role in the food sector. Results show that ethanol-based MP production is technically feasible for food applications, reaching biomass concentrations of 14-230 g/L and productivities of 11-13 g/L/h. The protein content of MP correlates with productivity, and the nutritional quality of ethanol-grown MP matches common sources like pork and tofu. Lastly, operational choices affect the techno-economic feasibility of using waste-derived ethanol and other recovered resources. This meta-analysis highlights the potential of ethanol-grown MP, though further research is needed to close existing knowledge gaps.}, }
@article {pmid39693383, year = {2024}, author = {Arrington, EC and Tarn, J and Kivenson, V and Nunn, BL and Liu, RM and Paul, BG and Valentine, DL}, title = {Hydrocarbon metabolism and petroleum seepage as ecological and evolutionary drivers for Cycloclasticus.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrae247}, pmid = {39693383}, issn = {1751-7370}, abstract = {Aqueous-soluble hydrocarbons dissolve into the ocean's interior and structure deep-sea microbial populations influenced by natural oil seeps and spills. n-Pentane is a seawater-soluble, volatile compound abundant in petroleum products and reservoirs and will partially partition to the deep-water column following release from the seafloor. In this study, we explore the ecology and niche partitioning of two free-living Cycloclasticus strains recovered from seawater incubations with n-pentane and distinguish them as an open ocean variant and a seep-proximal variant, each with distinct capabilities for hydrocarbon catabolism. Comparative metagenomic analysis indicates the variant more frequently observed further from natural seeps encodes more general pathways for hydrocarbon consumption, including short-chain alkanes, aromatics, and long-chain alkanes, and also possesses redox versatility in the form of respiratory nitrate reduction and thiosulfate oxidation; in contrast, the seep variant specializes in short-chain alkanes and relies strictly on oxygen as the terminal electron acceptor. Both variants observed in our work were dominant ecotypes of Cycloclasticus observed during the Deepwater Horizon disaster, a conclusion supported by 16S rRNA gene analysis and read-recruitment of sequences collected from the submerged oil plume during active flow. A comparative genomic analysis of Cycloclasticus across various ecosystems suggests distinct strategies for hydrocarbon transformations among each clade. Our findings suggest Cycloclasticus is a versatile and opportunistic consumer of hydrocarbons and may have a greater role in the cycling of sulfur and nitrogen, thus contributing broad ecological impact to various ecosystems globally.}, }
@article {pmid39693347, year = {2024}, author = {Sun, X and Buchanan, PJ and Zhang, IH and San Roman, M and Babbin, AR and Zakem, EJ}, title = {Ecological dynamics explain modular denitrification in the ocean.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {52}, pages = {e2417421121}, pmid = {39693347}, issn = {1091-6490}, support = {LS-FMME-00871981//Simons Foundation (SF)/ ; OCE-2138890 and OCE-2142998//NSF (NSF)/ ; N/A//MIT School of Science MathWorks Science Fellowship/ ; 2125142//NSF (NSF)/ ; }, mesh = {*Denitrification/physiology ; *Oceans and Seas ; *Ecosystem ; Seawater/microbiology/chemistry ; Nitrogen/metabolism ; Nitrous Oxide/metabolism ; Oxygen/metabolism ; Bacteria/metabolism ; }, abstract = {Microorganisms in marine oxygen minimum zones (OMZs) drive globally impactful biogeochemical processes. One such process is multistep denitrification (NO3[-]→NO2[-]→NO→N2O→N2), which dominates OMZ bioavailable nitrogen (N) loss and nitrous oxide (N2O) production. Denitrification-derived N loss is typically measured and modeled as a single step, but observations reveal that most denitrifiers in OMZs contain subsets ("modules") of the complete pathway. Here, we identify the ecological mechanisms sustaining diverse denitrifiers, explain the prevalence of certain modules, and examine the implications for N loss. We describe microbial functional types carrying out diverse denitrification modules by their underlying redox chemistry, constraining their traits with thermodynamics and pathway length penalties, in an idealized OMZ ecosystem model. Biomass yields of single-step modules increase along the denitrification pathway when organic matter (OM) limits growth, which explains the viability of populations respiring NO2[-] and N2O in a NO3[-]-filled ocean. Results predict denitrifier community succession along environmental gradients: Pathway length increases as the limiting substrate shifts from OM to N, suggesting a niche for the short NO3[-]→NO2[-] module in free-living, OM-limited communities, and for the complete pathway in organic particle-associated communities, consistent with observations. The model captures and mechanistically explains the observed dominance and higher oxygen tolerance of the NO3[-]→NO2[-] module. Results also capture observations that NO3[-] is the dominant source of N2O. Our framework advances the mechanistic understanding of the relationship between microbial ecology and N loss in the ocean and can be extended to other processes and environments.}, }
@article {pmid39692747, year = {2025}, author = {Wallace, EJ and O'Dwyer, J and Dolan, EB and Burke, LP and Wylie, R and Bellavia, G and Straino, S and Cianfarani, F and Ciotti, G and Serini, S and Calviello, G and Roche, ET and Mitra, T and Duffy, GP}, title = {Actuation-Mediated Compression of a Mechanoresponsive Hydrogel by Soft Robotics to Control Release of Therapeutic Proteins.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {12}, number = {7}, pages = {e2401744}, pmid = {39692747}, issn = {2198-3844}, support = {713690//Horizon 2020/ ; 812865//Horizon 2020/ ; GOIPD/2020/157//Irish Research Council/ ; 13/RC/2073/SFI_/Science Foundation Ireland/Ireland ; }, mesh = {Animals ; Rats ; *Vascular Endothelial Growth Factor A/administration &amp; dosage ; *Hydrogels/chemistry ; *Robotics/methods ; *Drug Delivery Systems/methods ; Diabetes Mellitus, Experimental/drug therapy ; Male ; Rats, Sprague-Dawley ; }, abstract = {Therapeutic proteins, the fastest growing class of pharmaceuticals, are subject to rapid proteolytic degradation in vivo, rendering them inactive. Sophisticated drug delivery systems that maintain protein stability, prolong therapeutic effects, and reduce administration frequency are urgently required. Herein, a mechanoresponsive hydrogel is developed contained within a soft robotic drug delivery (SRDD) device. In a step-change from previously reported systems, pneumatic actuation of this system releases the cationic therapeutic protein Vascular Endothelial Growth Factor (VEGF) in a bioactive form which is required for therapeutic angiogenesis, the growth of new blood vessels, in numerous clinical conditions. The ability of the SRDD device to release bioactive VEGF in a spatiotemporal manner from the hydrogel is tested in diabetic rats - a model in which angiogenesis is difficult to stimulate. Daily actuation of the SRDD device in the diabetic rat model significantly increased cluster of differentiation 31+ (CD31+) blood vessel number (p = 0.0335) and the diameter of alpha-smooth muscle actin+ (α-SMA+) blood vessels (p = 0.0025) compared to passive release of VEGF from non-actuated devices. The SRDD device combined with the mechanoresponsive hydrogel offers the potential to deliver an array of bioactive therapeutics in a spatiotemporal manner to mimic their natural release in vivo.}, }
@article {pmid39691821, year = {2024}, author = {Ghosh, A and Bhambra, SK and Chandrasekaran, R and Bhadury, P}, title = {Genome description of a potentially new species of Streptomyces isolated from the Indian Sundarbans mangrove.}, journal = {Access microbiology}, volume = {6}, number = {12}, pages = {}, pmid = {39691821}, issn = {2516-8290}, abstract = {A potentially new species of Streptomyces was isolated from station 177 of the Sundarbans Seasonal Time Series in the Indian Sundarbans mangrove. The isolate was cultured from a sediment sample on TYS medium of salinity 15. Sequencing and annotation of the 16S rRNA showed 100% identity against S. laurentii NPS17 against GenBank/ENA/DDBJ. Annotation of the whole genome against the GTDB database showed closest identity with S. terrae SKN60 and belongs to the same clade as S. roseicoloratus TRM44457T and S. laurentii ATCC 31255. The genome is ~7.2 Mb and has a G+C% of 73%. The average amino acid identity was 85.01% with S. roseicoloratus and 80.34% with S. roseolus. The assembly reflected the presence of all essential genes and had 19 biosynthetic gene clusters predicted.}, }
@article {pmid39689568, year = {2025}, author = {Sumerta, IN and Ruan, X and Howell, K}, title = {The forgotten wine: Understanding palm wine fermentation and composition.}, journal = {International journal of food microbiology}, volume = {429}, number = {}, pages = {111022}, doi = {10.1016/j.ijfoodmicro.2024.111022}, pmid = {39689568}, issn = {1879-3460}, mesh = {*Arecaceae/microbiology/chemistry ; Bacteria/metabolism/classification/isolation &amp; purification ; *Fermentation ; Microbiota ; *Wine/microbiology/analysis ; }, abstract = {Palm wine is an alcoholic beverage that has existed for centuries and has important economic and socio-culture values in many tropical and sub-tropical countries. Lesser known than other types of wines, palm wine is made by spontaneous fermentation of palm sap by naturally occurring microbial communities. The palm sap ecosystem has unique microbial composition and diversity, which determines the composition of the eventual wine and is likely affected by geographical distinctiveness. While these features are well understood in grape and rice wine, these features have not been understood in palm wine. Here, we gather information of microbial communities and metabolite profiles from published studies, covering a wide range of methodologies and regions to better understand the causal links between the principal microbial species and major metabolites of palm wine. We assessed palm wine quality across production regions and local practices to provide general characteristics of palm wine and identify specific regional information. These will provide better understandings to the function of microbial communities and metabolite diversity, the contribution of regional variations and to ensure product quality in this unique, yet overlooked, fermented beverage.}, }
@article {pmid39689238, year = {2024}, author = {Yang, Q and Defoirdt, T}, title = {Weak selection for resistance to quorum sensing inhibition during multiple host infection cycles.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39689238}, issn = {1751-7370}, support = {//Special Research Fund of Ghent University/ ; G016823N//Scientific Research Fund of Flanders/ ; }, mesh = {*Quorum Sensing/drug effects ; *Vibrio/drug effects/physiology/genetics ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial ; Animals ; Vibrio Infections/microbiology ; Selection, Genetic ; }, abstract = {Quorum sensing (QS) inhibition is a promising novel approach to control bacterial infections. However, it is not clear whether QS inhibition will impose selective pressure for the spread of resistance against QS inhibition in pathogen populations. Previous research tried to answer this question by using synthetic growth media, and this revealed that whether or not resistance will spread completely depends on the environment in which it is studied. Therefore, the spread of resistance should be studied in the environment where it ultimately matters: in vivo during infection of a host. Here, using QS inhibitor-susceptible and -resistant mimics, we show that resistance to QS inhibition does not spread in host-associated populations of Vibrio campbellii during up to 35 cycles of infection and transmission if the initial frequency of the resistance is low in the pathogen population, whereas it further increases to 100% if it is already prevalent. However, even in the latter case, the resistance spreads at a slower pace than resistance to antibiotics spreads under the same conditions.}, }
@article {pmid39689178, year = {2024}, author = {Li, G and Liu, T and Xie, W and Liu, Z and Li, H and Whalen, JK and Jousset, A and Wei, Z}, title = {Metabolites limiting predator growth wane with prey biodiversity.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {52}, pages = {e2410210121}, pmid = {39689178}, issn = {1091-6490}, support = {32201399//MOST | National Natural Science Foundation of China (NSFC)/ ; 32171640//MOST | National Natural Science Foundation of China (NSFC)/ ; KYQN2023048//MOE | Fundamental Research Funds for the Central Universities (Fundamental Research Fund for the Central Universities)/ ; 2022YFD1500302//MOST | National Key Research and Development Program of China (NKPs)/ ; }, mesh = {Animals ; *Biodiversity ; *Nematoda/physiology ; *Food Chain ; *Predatory Behavior/physiology ; Microbiota/physiology ; Bacteria/metabolism/classification ; Soil Microbiology ; }, abstract = {Predator-prey interactions are a major driver of microbiome dynamics, but remain difficult to predict. While several prey traits potentially impact resistance to predation, their effects in a multispecies context remain unclear. Here, we leverage synthetic bacterial communities of varying complexity to identify traits driving palatability for nematodes, a main consumer of bacteria in soil. We assessed trophic interactions between four nematode species and 122 bacterial isolates, across a gradient of prey biodiversity ranging from single species to 50 species. Nematode size, a proxy for prey palatability, varied strongly with prey community composition and could be predicted by metabolic and morphological properties of the prey. However, the influence of prey traits on predators depended on biodiversity. Secondary metabolites drove palatability in monoculture, but this effect vanished under increasing prey biodiversity, where prey size became the dominant predictors of nematode size. Although idiosyncratic properties are often emphasized in the literatures, our results suggest that in biodiverse assemblages, the composition of available prey and their traits are more reliable predictors of predator-prey interactions. This study offers valuable insights into microbial ecology in the context of predator-prey interactions, as cryptic microbial responses can be guided by deductions based on generalizable biological traits.}, }
@article {pmid39687379, year = {2024}, author = {Lee, D and Oliveira, FCC and Conant, RT and Kim, M}, title = {Microbial community assembly across agricultural soil mineral mesocosms revealed by 16S rRNA gene amplicon sequencing data.}, journal = {Data in brief}, volume = {57}, number = {}, pages = {111125}, pmid = {39687379}, issn = {2352-3409}, abstract = {Increasing atmospheric carbon dioxide (CO2) concentrations are impacting the global climate, resulting in significant interest in soil carbon sequestration as a mitigation strategy. While recognized that mineral-associated organic matter (MAOM) in soils is mainly formed through microbial activity, our understanding of microbial-derived MAOM formation processes remains limited due to the complexity of the soil environment. To gain insights into this issue, we incubated fresh soil samples for 45 days with one of three mineral additions: Sand, Kaolinite+Sand, or Illite+Sand. 16S rRNA V3/V4 gene amplicon sequencing was then conducted on samples using an Illumina NextSeq 2000 flow cell. The reads were analyzed and taxonomically assigned with QIIME2 v2023.5.1 and SILVA 138. The dataset has been made publicly available through NCBI GenBank under BioProject ID PRJNA1124235. This dataset is important and useful as it provides valuable insights into the interactions between soil minerals and microbial communities, which can inform strategies for enhancing soil carbon sequestration and mitigating climate change. Moreover, it serves as a crucial reference for future studies, offering a foundational understanding of microbial dynamics in soil systems and guiding further research in microbial ecology and carbon cycling.}, }
@article {pmid39683937, year = {2024}, author = {Liu, S and Teng, L and Ping, J}, title = {Graphitic Carbon Nitride Confers Bacterial Tolerance to Antibiotics in Wastewater Relating to ATP Depletion.}, journal = {Molecules (Basel, Switzerland)}, volume = {29}, number = {23}, pages = {}, pmid = {39683937}, issn = {1420-3049}, support = {62105175//National Natural Science Foundation of China/ ; ZR2021QF058//Natural Science Foundation of Shandong Province/ ; 2022PY036//The Education and Industry Integration Pilot Project of Qilu University of Technology/ ; 432413/01090//Start-up fund of Tianjin Renai College/ ; }, mesh = {*Graphite/chemistry ; *Wastewater/microbiology/chemistry ; *Anti-Bacterial Agents/pharmacology ; *Adenosine Triphosphate/metabolism ; Nitrogen Compounds/chemistry ; Staphylococcus aureus/drug effects ; Ofloxacin/pharmacology ; Drug Resistance, Bacterial/drug effects ; Reactive Oxygen Species/metabolism ; Microbial Sensitivity Tests ; Water Purification/methods ; }, abstract = {Graphitic carbon nitride (C3N4) is a kind of visible light-responsive photocatalyst that has been of great interest in wastewater treatment. However, its environmental impact and biological effect remains to be elucidated. This study investigated the effect of C3N4 nanosheets on bacterial abundance and antibiotic tolerance in wastewater. Interestingly, as compared to the wastewater containing the antibiotic ofloxacin alone, the wastewater containing both ofloxacin and C3N4 had much higher numbers of total living bacteria, but lower levels of the ofloxacin-resistant bacteria and the ofloxacin-resistant gene qnrS. The model bacterium Staphylococcus aureus was then used to explore the mechanism of C3N4-induced antibiotic tolerance. The nanosheets neither adsorbed the antibiotic nor promoted drug efflux, uncovering that drug adsorption and efflux were not involved in antibiotic tolerance. Further investigations revealed that the nanosheets, like arsenate and menadione, drastically reduced ATP levels and induced the production of reactive oxygen species for enhanced antibiotic tolerance. This study revealed an antibiotic-tolerating mechanism associated with C3N4-induced ATP depletion, and shed a light on the effect of photocatalysts on microbial ecology during their application in wastewater treatment.}, }
@article {pmid39682491, year = {2024}, author = {Suriyasathaporn, W and Kongkaew, A and Intanon, M and Srithanasuwan, A and Saipinta, D and Pangprasit, N and Thongtharb, A and Chuasakhonwilai, A and Chaisri, W}, title = {Non-aureus Staphylococci Cause the Spontaneous Cure or Persistent Infection of Major Bovine Mastitis Pathogens in the Murine Mammary Glands.}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {23}, pages = {}, pmid = {39682491}, issn = {2076-2615}, support = {FF66/017//The Fundamental Fund, Chiang Mai University/ ; }, abstract = {The microbial ecology in mastitis involves the interactions between bacteria and the mammary gland environment. Poor mastitis control, for which understanding these microbial relationships is crucial, increases the risk of mastitis and co-infections. The aim of this study was to determine the pathogenesis and bacterial ecology of murine mammary glands following intramammary infection (IMI) with S. aureus (AU), S. agalactiae (SA), and four isolates of selected non-aureus staphylococci (NAS), as well as co-infections of AU or SA with NAS. Selected NAS demonstrated resistance to growth inhibition after co-culture with AU and SA and were proven to be protective in vitro against AU and SA. Both single infections and co-infections of AU, SA, two selected isolates of S. hominis (NAS1 and NAS2), and two selected isolates of S. chromogens (NAS3 and NAS4) were injected into the murine mammary glands at 10[5] CFU/mL. After 72 h of inoculation, the results showed that AU, AU-NAS2, and AU-NAS3 expressed severe inflammation with clinical signs of mastitis. The persistence of AU was found for AU, NAS3, and AU-NAS3, whereas the persistence of SA was found for SA-NAS1, SA-NAS3, and SA-NAS, although single SA could not persist. Interestingly, NAS2 in both the single- and co-IMIs with AU or SA resulted in a spontaneous cure 72 h after the IMI. In conclusion, some NAS have beneficial results because they can eliminate S. aureus and S. agalactiae, but some NAS have negative effects because they can support persistent S. agalactiae infection. These results may be used to explain both the advantages and disadvantages of NAS on farms with poor mastitis control. In addition, the beneficial S. hominis may initiate natural live antibiotics and reduce antibiotic resistance problems.}, }
@article {pmid39681734, year = {2024}, author = {Rajendran, D and Vinayagam, S and Sekar, K and Bhowmick, IP and Sattu, K}, title = {Symbiotic Bacteria: Wolbachia, Midgut Microbiota in Mosquitoes and Their Importance for Vector Prevention Strategies.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {154}, pmid = {39681734}, issn = {1432-184X}, mesh = {Animals ; Culicidae/microbiology ; Gastrointestinal Microbiome ; *Mosquito Control/methods ; *Mosquito Vectors/microbiology ; Symbiosis ; *Wolbachia/physiology ; }, abstract = {Mosquito-borne illnesses pose a significant threat to eradication under existing vector management measures. Chemo-based vector control strategies (use of insecticides) raise a complication of resistance and environmental pollution. Biological control methods are an alternative approach to overcoming this complication arising from insecticides. The mosquito gut microbiome is essential to supporting the factors that involve metabolic regulation and metamorphic development (from juvenile to adult), as well as the induction of an immune response. The induced immune response includes the JAK-STAT, IMD, and Toll pathways due to the microbial interaction with the midgut cells (MG cells) that prevent disease transmission to humans. The aforementioned sequel to the review provides information about endosymbiont Wolbachia, which contaminates insect cells, including germline and somatic cytoplasm, and inhibits disease-causing pathogen development and transmission by competing for resources within the cell. Moreover, it reduces the host population via cytoplasmic incompatibility (CI), feminization, male killing, and parthenogenesis. Furthermore, the Cif factor in Wolbachia is responsible for CI induction that produces inviable cells with the translocating systems and the embryonic defect-causing protein factor, WalE1 (WD0830), which manipulates the host actin. This potential of Wolbachia can be used to design a paratransgenic system to control vectors in the field. An extracellular symbiotic bacterium such as Asaia, which is grown in the growth medium, is used to transfer lethal genes within itself. Besides, the genetically transferred symbiotic bacteria infect the wild mosquito population and are easily manifold. So, it might be suitable for vector control strategies in the future.}, }
@article {pmid39681034, year = {2025}, author = {Fu, Y and Hu, F and Wang, F and Xu, M and Jia, Z and Amelung, W and Mei, Z and Han, X and Virta, M and Jiang, X and Tiedje, JM}, title = {Field-based evidence for the prevalence of soil antibiotic resistomes under long-term antibiotic-free fertilization.}, journal = {Environment international}, volume = {195}, number = {}, pages = {109202}, doi = {10.1016/j.envint.2024.109202}, pmid = {39681034}, issn = {1873-6750}, mesh = {*Fertilizers/analysis ; *Soil Microbiology ; Anti-Bacterial Agents ; Manure ; Soil/chemistry ; *Drug Resistance, Microbial/genetics ; Agriculture ; }, abstract = {Growing evidence suggests that the use of manure containing residual antibiotics universally leads to an increase in soil antibiotic resistance genes (ARGs). However, there is limited understanding of the influence of long-term antibiotic-free fertilization and the differences between antibiotic-free manure and chemical fertilizer on soil ARGs. This study aimed to quantify the assembly patterns of the antibiotic resistome by in situ probing bacterial community and environmental variations in field soils that have been subjected to long-term exposure to chemical fertilizer and/or manure from animals without antibiotic amendments. Long-term fertilization slightly impacts the diversity of antibiotic resistomes, with 85.5 % of total ARGs and mobile genetic elements (MGEs) being common across all treatment types, while significantly increasing their abundances from 0.68 to a maximum of 0.90 copies/16S rRNA. The rise in ARG abundances was less pronounced when using antibiotic-free manure compared to chemical fertilizer, particularly for Rank Ⅱ ARGs. However, when antibiotic-free manure and chemical fertilizer were combined, a significant increase in nutrients (such as available nitrogen and organic matter) and MGEs occurred, leading to the enrichment of soil microbial populations, especially in certain resistant species, and Rank Ⅰ and Ⅱ ARGs. Despite the influence of various factors like bacterial communities, soil properties, heavy metals, and MGEs, the MGEs had the most significant standardized effects on shaping ARGs through both direct and indirect pathways. Our findings indicates that while of antibiotic-free manure can lower the risk of antibiotic residues and promote sustainable farming practices, it may not fully eliminate the prevalence of ARGs, highlighting the need for more comprehensive strategies to address antibiotic resistance in agriculture rather than simply prohibiting the use of antibiotics.}, }
@article {pmid39680930, year = {2024}, author = {Li, XY and Zhu, CW and Chen, S and Xiang, Q and Lu, C and Lin, XY and Chen, QL}, title = {Elevated CO2 Increased Antibiotic Resistomes in Seed Endophytes: Evidence from a Free-Air CO2 Enrichment (FACE) Experiment.}, journal = {Environmental science &amp; technology}, volume = {58}, number = {52}, pages = {23190-23200}, doi = {10.1021/acs.est.4c09625}, pmid = {39680930}, issn = {1520-5851}, mesh = {*Carbon Dioxide ; Seeds/microbiology ; *Endophytes ; Bacteria ; Fungi ; Anti-Bacterial Agents ; *Drug Resistance, Microbial/genetics ; Microbiota ; Soil Microbiology ; }, abstract = {Climate warming affects antibiotic resistance genes (ARGs) in soil and the plant microbiome, including seed endophytes. Seeds act as vectors for ARG dissemination in the soil-plant system, but the impact of elevated CO2 on seed resistomes remains poorly understood. Here, a free-air CO2 enrichment system was used to examine the impact of elevated CO2 on seed-associated ARGs and seed endophytic bacteria and fungi. Results indicated that elevated CO2 levels significantly increased the relative abundance of seed ARGs and mobile genetic elements (MGEs), especially those related to beta-lactam resistance and MGEs. Increased CO2 levels also influenced the composition of seed bacterial and fungal communities and the complexity of bacteria-fungi interactions. Fungi were more sensitive to changes in the CO2 level than bacteria, with deterministic processes playing a greater role in fungal community assembly. Co-occurrence network analysis revealed a stronger correlation between fungi and ARGs compared to bacteria. The structure equation model (SEM) showed that elevated CO2 directly influenced seed resistomes by altering bacterial composition and indirectly through bacteria-fungi interactions. Together, our work offers new insights into the effects of elevated CO2 on antibiotic resistomes in the seed endosphere, highlighting their increased dissemination potential within soil-plant systems and the associated health risks in a changing environment.}, }
@article {pmid39680691, year = {2025}, author = {Yang, JC and Lagishetty, V and Aja, E and Arias-Jayo, N and Chang, C and Hauer, M and Katzka, W and Zhou, Y and Sedighian, F and Koletic, C and Liang, F and Dong, TS and Situ, J and Troutman, R and Buri, H and Bhute, S and Simpson, CA and Braun, J and Jacob, N and Jacobs, JP}, title = {Biogeographical distribution of gut microbiome composition and function is partially recapitulated by fecal transplantation into germ-free mice.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {39680691}, issn = {1751-7370}, support = {CDA2 IK2CX001717//Crohn's and Colitis Foundation Career Development/ ; //Vatche and Tamar Manoukian Division of Digestive Diseases/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; Mice ; *Fecal Microbiota Transplantation ; Germ-Free Life ; RNA, Ribosomal, 16S/genetics ; *Feces/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Mice, Inbred C57BL ; Colon/microbiology ; Specific Pathogen-Free Organisms ; Male ; }, abstract = {Fecal microbiota transplantation has been vital for establishing whether host phenotypes can be conferred through the microbiome. However, whether the existing microbial ecology along the mouse gastrointestinal tract can be recapitulated in germ-free mice colonized with stool remains unknown. We first identified microbes and their predicted functions specific to each of six intestinal regions in three cohorts of specific pathogen-free mice spanning two facilities. Of these region-specific microbes, the health-linked genus Akkermansia was consistently enriched in the lumen of the small intestine compared to the colon. Predictive functional modeling on 16S rRNA gene amplicon sequencing data recapitulated in shotgun sequencing data revealed increased microbial central metabolism, lipolytic fermentation, and cross-feeding in the small intestine, whereas butyrate synthesis was colon-enriched. Neuroactive compound metabolism also demonstrated regional specificity, including small intestine-enriched gamma-aminobutyric acid degradation and colon-enriched tryptophan degradation. Specifically, the jejunum and ileum stood out as sites with high predicted metabolic and neuromodulation activity. Differences between luminal and mucosal microbiomes within each site of the gastrointestinal tract were largely facility-specific, though there were a few consistent patterns in microbial metabolism in specific pathogen-free mice. These included luminal enrichment of central metabolism and cross-feeding within both the small intestine and the colon, and mucosal enrichment of butyrate synthesis within the colon. Across three cohorts of germ-free mice colonized with mice or human stool, compositional and functional region specificity were inconsistently reproduced. These results underscore the importance of investigating the spatial variation of the gut microbiome to better understand its impact on host physiology.}, }
@article {pmid39679708, year = {2025}, author = {Liu, Z and Jiang, C and Yin, Z and Ibrahim, IA and Zhang, T and Wen, J and Zhou, L and Jiang, G and Li, L and Yang, Z and Huang, Y and Yang, Z and Gu, Y and Meng, D and Yin, H}, title = {Ecological features of microbial community linked to stochastic and deterministic assembly processes in acid mine drainage.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {1}, pages = {e0102824}, pmid = {39679708}, issn = {1098-5336}, support = {2023YFE0114500//MOST | National Key Research and Development Program of China (NKPs)/ ; 92351303//MOST | National Natural Science Foundation of China (NSFC)/ ; BX20230437//Postdoctoral Fellowship Program of CPSF/ ; }, mesh = {*Microbiota ; *Bacteria/genetics/classification/isolation &amp; purification ; *Mining ; Phylogeny ; Acids ; Stochastic Processes ; }, abstract = {UNLABELLED: Ecological processes greatly shape microbial community assembly, but the driving factors remain unclear. Here, we compiled a metagenomic data set of microbial communities from global acid mine drainage (AMD) and explored the ecological features of microbial community linked to stochastic and deterministic processes from the perspective of species niche position, interaction patterns, gene functions, and viral infection. Our results showed that dispersal limitation (DL) (48.5%~93.5%) dominated the assembly of phylogenetic bin in AMD microbial community, followed by homogeneous selection (HoS) (3.1%~39.2%), heterogeneous selection (HeS) (1.4%~22.2%), and drift (DR) (0.2%~2.7%). The dominant process of dispersal limitation was significantly influenced by niche position in temperature (r = -0.518, P = 0.007) and dissolved oxygen (r = 0.471, P = 0.015). Network stability had a significantly negative correlation with the relative importance of dispersal limitation, while it had a positive correlation with selection processes, implying changes in network properties could be mediated by ecological processes. Furthermore, we found that ecological processes were mostly related to the gene functions of energy production and conversion (C), and amino acid transport and metabolism (E). Meanwhile, our results showed that the number of proviruses and viral genes involved in arsenic (As) resistance is negatively associated with the relative importance of ecological drift in phylogenetic bin assembly, implying viral infection might weaken ecological drift. Taken together, these results highlight that ecological processes are associated with ecological features at multiple levels, providing a novel insight into microbial community assembly in extremely acidic environments.<br><br>IMPORTANCE: Unraveling the forces driving community assemblage is a core issue in microbial ecology, but how ecological constraints impose stochasticity and determinism remains unknown. This study presents a comprehensive investigation to uncover the association of ecological processes with species niche position, interaction patterns, microbial metabolisms, and viral infections, which provides novel insights into community assembly in extreme environments.}, }
@article {pmid39679616, year = {2024}, author = {Seki, D and Kirkegaard, R and Osvatic, J and Hausmann, B and Séneca, J and Pjevac, P and Berger, A and J Hall, L and Wisgrill, L and Berry, D}, title = {Gut microbiota genome features associated with brain injury in extremely premature infants.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2410479}, pmid = {39679616}, issn = {1949-0984}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; *Infant, Extremely Premature ; *Brain Injuries/microbiology/genetics ; *Feces/microbiology ; Female ; Male ; Bacteria/genetics/classification/isolation &amp; purification/metabolism ; Genome, Bacterial ; Cohort Studies ; }, abstract = {Severe brain damage is common among premature infants, and the gut microbiota has been implicated in its pathology. Although the order of colonizing bacteria is well described, the mechanisms underlying aberrant assembly of the gut microbiota remain elusive. Here, we employed long-read nanopore sequencing to assess abundances of microbial species and their functional genomic potential in stool samples from a cohort of 30 extremely premature infants. We identify several key microbial traits significantly associated with severe brain damage, such as the genomic potential for nitrate respiration and iron scavenging. Members of the Enterobacteriaceae were prevalent across the cohort and displayed a versatile metabolic potential, including pathogenic and nonpathogenic traits. Predominance of Enterobacter hormaechei and Klebsiella pneumoniae were associated with an overall loss of genomic functional redundancy as well as poor neurophysiological outcome. These findings reveal microbial traits that may be involved in exacerbating brain injury in extremely premature infants and provide suitable targets for therapeutic interventions.}, }
@article {pmid39675658, year = {2025}, author = {Yan, R and Xu, X and Niu, Y and Ying, S and Cai, J and Chen, R and Gu, Y and Kan, H}, title = {Microbial diversity and environmental determinants at Shanghai Hongqiao railway station: A comprehensive microbial assessment.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {366}, number = {}, pages = {125534}, doi = {10.1016/j.envpol.2024.125534}, pmid = {39675658}, issn = {1873-6424}, mesh = {China ; *Railroads ; *Environmental Monitoring ; *Air Microbiology ; *Microbiota ; Seasons ; RNA, Ribosomal, 16S/analysis ; *Air Pollution, Indoor/analysis ; Humans ; SARS-CoV-2 ; }, abstract = {The COVID-19 pandemic has underscored the importance of indoor environmental management in transportation hubs, which are critical for pathogen transmission due to high foot traffic. However, research has primarily focused on subways, with limited studies on train stations. In this study, samples were collected at the Shanghai Hongqiao Railway Station in winter, spring, and summer. Microbial DNA was extracted from collected indoor surfaces and ambient air samples and then analyzed through high-throughput 16S rRNA gene sequencing. Alongside sample collection, environmental data were recorded. Alpha diversity was greatest in winter, followed by summer, and least in spring within the train station environment. Surface samples exhibited higher alpha diversity compared to air samples, with no notable difference between indoor and outdoor air. Beta diversity showed significant variation across seasons and locations, with seasonal changes more pronounced than spatial ones, primarily due to differences between air and surface samples rather than indoor and outdoor environments. Key determinants of microbial community structure included CO2, temperature, illuminance, and passenger volume. The microbial community in train stations originates from various sources, with contributions from both natural elements (like wastewater/sludge, soil, and plants) and human sources (such as gastrointestinal, oral, and dermal flora). This study highlights the microbial ecology of train stations, emphasizing the need for microbial surveillance and management in transportation settings.}, }
@article {pmid39670887, year = {2025}, author = {Vlasselaer, L and Moons, J and De Clercq, T and Lievens, B and De Coninck, B}, title = {Development of a Toolbox to Study Phytophthora cryptogea-Lettuce Interactions: Characterization and Detection of P. cryptogea in Hydroponic Lettuce.}, journal = {Plant disease}, volume = {109}, number = {6}, pages = {1254-1267}, doi = {10.1094/PDIS-09-24-2018-RE}, pmid = {39670887}, issn = {0191-2917}, mesh = {*Lactuca/microbiology/parasitology ; *Phytophthora/genetics/physiology/pathogenicity/isolation &amp; purification ; *Plant Diseases/microbiology/parasitology ; Hydroponics ; Cichorium intybus/microbiology/parasitology ; Host-Pathogen Interactions ; }, abstract = {Climate change poses a major threat to crop production, resulting in the emergence of new pests and diseases. Phytophthora cryptogea has recently emerged as a major concern in hydroponic lettuce cultivation, causing substantial yield and economic losses. This oomycete pathogen thrives in elevated water temperatures induced by warmer weather conditions (e.g., heatwaves), facilitating rapid pathogen propagation. Although the disease is already present for several decades in chicory cultivation, where it originates from the field, its origin in lettuce cultivation remains unclear. To get a better understanding of its origin, we conducted a multilocus sequence analysis using five reference genes (ITS, β-tub, COI, EF1α, and HSP90) and 33 P. cryptogea isolates from various hosts, including chicory and lettuce. Results revealed a clear separation between lettuce and chicory isolates. Furthermore, we developed and implemented a robust disease bioassay and qPCR assay to investigate the interaction between P. cryptogea strains and lettuce. Our findings revealed that while lettuce isolates exhibited the highest virulence, some chicory isolates also caused disease in lettuce, suggesting a potential evolutionary link between P. cryptogea in lettuce and chicory. Our experiments also revealed that even a low concentration of zoospores (100 zoospores/liter) can elicit severe symptoms, underscoring the pathogen's high virulence. Therefore, effective disease management strategies are needed for controlling (the spread of) the disease. Together, this research provides several tools that can be used to enhance our understanding of the interaction between P. cryptogea and its host plants, including the development of proper disease management strategies.}, }
@article {pmid39665561, year = {2025}, author = {Unzueta-Martínez, A and Girguis, PR}, title = {Taxonomic diversity and functional potential of microbial communities in oyster calcifying fluid.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {1}, pages = {e0109424}, pmid = {39665561}, issn = {1098-5336}, support = {2109473//National Science Foundation (NSF)/ ; 9208//Gordon and Betty Moore Foundation (GBMF)/ ; }, mesh = {Animals ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Ostreidae/microbiology ; *Archaea/classification/genetics/isolation &amp; purification/metabolism ; Biomineralization ; Viruses/classification/genetics/isolation &amp; purification ; Calcification, Physiologic ; Metagenomics ; Biodiversity ; Phylogeny ; }, abstract = {UNLABELLED: Creating and maintaining an appropriate chemical environment is essential for biomineralization, the process by which organisms precipitate minerals to form their shells or skeletons, yet the mechanisms involved in maintaining calcifying fluid chemistry are not fully defined. In particular, the role of microorganisms in facilitating or hindering animal biomineralization is poorly understood. Here, we investigated the taxonomic diversity and functional potential of microbial communities inhabiting oyster calcifying fluid. We used shotgun metagenomics to survey calcifying fluid microbial communities from three different oyster harvesting sites. There was a striking consistency in taxonomic composition across the three collection sites. We also observed archaea and viruses that had not been previously identified in oyster calcifying fluid. Furthermore, we identified microbial energy-conserving metabolisms that could influence the host's calcification, including genes involved in sulfate reduction and denitrification that are thought to play pivotal roles in inorganic carbon chemistry and calcification in microbial biofilms. These findings provide new insights into the taxonomy and functional capacity of oyster calcifying fluid microbiomes, highlighting their potential contributions to shell biomineralization, and contribute to a deeper understanding of the interplay between microbial ecology and biogeochemistry that could potentially bolster oyster calcification.<br><br>IMPORTANCE: Previous research has underscored the influence of microbial metabolisms in carbonate deposition throughout the geological record. Despite the ecological importance of microbes to animals and inorganic carbon transformations, there have been limited studies characterizing the potential role of microbiomes in calcification by animals such as bivalves. Here, we use metagenomics to investigate the taxonomic diversity and functional potential of microbial communities in calcifying fluids from oysters collected at three different locations. We show a diverse microbial community that includes bacteria, archaea, and viruses, and we discuss their functional potential to influence calcifying fluid chemistry via reactions like sulfate reduction and denitrification. We also report the presence of carbonic anhydrase and urease, both of which are critical in microbial biofilm calcification. Our findings have broader implications in understanding what regulates calcifying fluid chemistry and consequentially the resilience of calcifying organisms to 21st century acidifying oceans.}, }
@article {pmid39660837, year = {2025}, author = {Lewin, GR}, title = {mSphere of Influence: How the single cell contributes to the collective.}, journal = {mSphere}, volume = {10}, number = {1}, pages = {e0043124}, pmid = {39660837}, issn = {2379-5042}, support = {DP2 AI184733/AI/NIAID NIH HHS/United States ; R00 DE031018/DE/NIDCR NIH HHS/United States ; }, mesh = {*Single-Cell Analysis ; Humans ; *Bacteria/genetics/classification ; *Microbiota/genetics ; RNA-Seq ; }, abstract = {Gina Lewin works in the field of microbial ecology, with a focus on the human microbiota. In this mSphere of Influence article, she reflects on how two papers describing bacterial single-cell RNA-seq-"Prokaryotic single-cell RNA sequencing by in situ combinatorial indexing" by S. B. Blattman, W. Jiang, P. Oikonomou, and S. Tavazoie (Nat Microbiol 5:1192-1201, 2020, https://doi.org/10.1038/s41564-020-0729-6) and "Microbial single-cell RNA sequencing by split-pool barcoding" by A. Kuchina, L. M. Brettner, L. Paleologu, C. M. Roco, et al. (Science 371:eaba5257, 2021, https://doi.org/10.1126/science.aba5257)-impacted her work by developing a new approach to study how single cells of bacteria contribute to ecosystem-level processes.}, }
@article {pmid39659497, year = {2024}, author = {Ritsch, M and Brait, N and Harvey, E and Marz, M and Lequime, S}, title = {Endogenous viral elements: insights into data availability and accessibility.}, journal = {Virus evolution}, volume = {10}, number = {1}, pages = {veae099}, pmid = {39659497}, issn = {2057-1577}, abstract = {Endogenous viral elements (EVEs) are remnants of viral genetic material endogenized into the host genome. They have, in the last decades, attracted attention for their role as potential contributors to pathogenesis, drivers of selective advantage for the host, and genomic remnants of ancient viruses. EVEs have a nuanced and complex influence on both host health and evolution, and can offer insights on the deep evolutionary history of viruses. As an emerging field of research, several factors limit a comprehensive understanding of EVEs: they are currently underestimated and periodically overlooked in studies of the host genome, transcriptome, and virome. The absence of standardized guidelines for ensuring EVE-related data availability and accessibility following the FAIR ('findable, accessible, interoperable, and reusable') principles obstructs our ability to gather and connect information. Here, we discuss challenges to the availability and accessibility of EVE-related data and propose potential solutions. We identified the biological and research focus imbalance between different types of EVEs, and their overall biological complexity as genomic loci with viral ancestry, as potential challenges that can be addressed with the development of a user-oriented identification tool. In addition, reports of EVE identification are scattered between different subfields under different keywords, and EVE sequences and associated data are not properly gathered in databases. While developing an open and dedicated database might be ideal, targeted improvements of generalist databases might provide a pragmatic solution to EVE data and metadata accessibility. The implementation of these solutions, as well as the collective effort by the EVE scientific community in discussing and setting guidelines, is now drastically needed to lead the development of EVE research and offer insights into host-virus interactions and their evolutionary history.}, }
@article {pmid39657855, year = {2025}, author = {Gu, Z and He, L and Liu, T and Xing, M and Feng, L and Luo, G}, title = {Exploring strategies for kitchen waste treatment and remediation from the perspectives of microbial ecology and genomics.}, journal = {Chemosphere}, volume = {370}, number = {}, pages = {143925}, doi = {10.1016/j.chemosphere.2024.143925}, pmid = {39657855}, issn = {1879-1298}, mesh = {Animals ; Oligochaeta/growth &amp; development ; *Composting ; Sewage/microbiology ; Biodegradation, Environmental ; Metagenomics ; Genomics ; *Soil Microbiology ; *Refuse Disposal/methods ; Bacteria/genetics ; Lignin ; }, abstract = {Nowadays, the rapid growth of population has led to a substantial increase in kitchen waste and wasted sludge. Kitchen waste is rich in organic matter, including lignocellulose. Synergistic treatment involving kitchen waste and wasted sludge can enhance treatment process. Vermicomposting can facilitate microbial activities on organic matter. Nevertheless, the underlying mechanisms remain unclear. In this study, metagenomics was used to analyze microbial functional genes in vermicomposting. Redundancy analysis found that TOC, TN and DTN adversely affect earthworm growth and reproduction. The relative abundance of Bacteroidetes and Firmicutes increased with earthworms, thereby potentially augmenting lignocellulose degradation. The predominant functional genes included amino acid, carbohydrate, and inorganic ion conversion and metabolism. Metagenomics analysis demonstrated that GH1, GH3, GH5, GH6, GH9, GH12, GH44, GH48 and GH74, GT41, GT4, GT2, and GT51 were dominant. Furthermore, there was higher abundance of carbohydrate-active enzymes in the vermicomposting, particularly during the later phases (30-45 days). Co-occurrence network revealed that Cellvibrio in the vermicomposting exhibited a relatively dense positive correlation with other microbial groups. The findings elucidated the mechanism of vermicomposting as a promising approach for managing kitchen waste and wasted sludge.}, }
@article {pmid39657789, year = {2025}, author = {Zdouc, MM and Blin, K and Louwen, NLL and Navarro, J and Loureiro, C and Bader, CD and Bailey, CB and Barra, L and Booth, TJ and Bozhüyük, KAJ and Cediel-Becerra, JDD and Charlop-Powers, Z and Chevrette, MG and Chooi, YH and D'Agostino, PM and de Rond, T and Del Pup, E and Duncan, KR and Gu, W and Hanif, N and Helfrich, EJN and Jenner, M and Katsuyama, Y and Korenskaia, A and Krug, D and Libis, V and Lund, GA and Mantri, S and Morgan, KD and Owen, C and Phan, CS and Philmus, B and Reitz, ZL and Robinson, SL and Singh, KS and Teufel, R and Tong, Y and Tugizimana, F and Ulanova, D and Winter, JM and Aguilar, C and Akiyama, DY and Al-Salihi, SAA and Alanjary, M and Alberti, F and Aleti, G and Alharthi, SA and Rojo, MYA and Arishi, AA and Augustijn, HE and Avalon, NE and Avelar-Rivas, JA and Axt, KK and Barbieri, HB and Barbosa, JCJ and Barboza Segato, LG and Barrett, SE and Baunach, M and Beemelmanns, C and Beqaj, D and Berger, T and Bernaldo-Agüero, J and Bettenbühl, SM and Bielinski, VA and Biermann, F and Borges, RM and Borriss, R and Breitenbach, M and Bretscher, KM and Brigham, MW and Buedenbender, L and Bulcock, BW and Cano-Prieto, C and Capela, J and Carrion, VJ and Carter, RS and Castelo-Branco, R and Castro-Falcón, G and Chagas, FO and Charria-Girón, E and Chaudhri, AA and Chaudhry, V and Choi, H and Choi, Y and Choupannejad, R and Chromy, J and Donahey, MSC and Collemare, J and Connolly, JA and Creamer, KE and Crüsemann, M and Cruz, AA and Cumsille, A and Dallery, JF and Damas-Ramos, LC and Damiani, T and de Kruijff, M and Martín, BD and Sala, GD and Dillen, J and Doering, DT and Dommaraju, SR and Durusu, S and Egbert, S and Ellerhorst, M and Faussurier, B and Fetter, A and Feuermann, M and Fewer, DP and Foldi, J and Frediansyah, A and Garza, EA and Gavriilidou, A and Gentile, A and Gerke, J and Gerstmans, H and Gomez-Escribano, JP and González-Salazar, LA and Grayson, NE and Greco, C and Gomez, JEG and Guerra, S and Flores, SG and Gurevich, A and Gutiérrez-García, K and Hart, L and Haslinger, K and He, B and Hebra, T and Hemmann, JL and Hindra, H and Höing, L and Holland, DC and Holme, JE and Horch, T and Hrab, P and Hu, J and Huynh, TH and Hwang, JY and Iacovelli, R and Iftime, D and Iorio, M and Jayachandran, S and Jeong, E and Jing, J and Jung, JJ and Kakumu, Y and Kalkreuter, E and Kang, KB and Kang, S and Kim, W and Kim, GJ and Kim, H and Kim, HU and Klapper, M and Koetsier, RA and Kollten, C and Kovács, &#xc1;T and Kriukova, Y and Kubach, N and Kunjapur, AM and Kushnareva, AK and Kust, A and Lamber, J and Larralde, M and Larsen, NJ and Launay, AP and Le, NT and Lebeer, S and Lee, BT and Lee, K and Lev, KL and Li, SM and Li, YX and Licona-Cassani, C and Lien, A and Liu, J and Lopez, JAV and Machushynets, NV and Macias, MI and Mahmud, T and Maleckis, M and Martinez-Martinez, AM and Mast, Y and Maximo, MF and McBride, CM and McLellan, RM and Bhatt, KM and Melkonian, C and Merrild, A and Metsä-Ketelä, M and Mitchell, DA and Müller, AV and Nguyen, GS and Nguyen, HT and Niedermeyer, THJ and O'Hare, JH and Ossowicki, A and Ostash, BO and Otani, H and Padva, L and Paliyal, S and Pan, X and Panghal, M and Parade, DS and Park, J and Parra, J and Rubio, MP and Pham, HT and Pidot, SJ and Piel, J and Pourmohsenin, B and Rakhmanov, M and Ramesh, S and Rasmussen, MH and Rego, A and Reher, R and Rice, AJ and Rigolet, A and Romero-Otero, A and Rosas-Becerra, LR and Rosiles, PY and Rutz, A and Ryu, B and Sahadeo, LA and Saldanha, M and Salvi, L and Sánchez-Carvajal, E and Santos-Medellin, C and Sbaraini, N and Schoellhorn, SM and Schumm, C and Sehnal, L and Selem, N and Shah, AD and Shishido, TK and Sieber, S and Silviani, V and Singh, G and Singh, H and Sokolova, N and Sonnenschein, EC and Sosio, M and Sowa, ST and Steffen, K and Stegmann, E and Streiff, AB and Strüder, A and Surup, F and Svenningsen, T and Sweeney, D and Szenei, J and Tagirdzhanov, A and Tan, B and Tarnowski, MJ and Terlouw, BR and Rey, T and Thome, NU and Torres Ortega, LR and Tørring, T and Trindade, M and Truman, AW and Tvilum, M and Udwary, DW and Ulbricht, C and Vader, L and van Wezel, GP and Walmsley, M and Warnasinghe, R and Weddeling, HG and Weir, ANM and Williams, K and Williams, SE and Witte, TE and Rocca, SMW and Yamada, K and Yang, D and Yang, D and Yu, J and Zhou, Z and Ziemert, N and Zimmer, L and Zimmermann, A and Zimmermann, C and van der Hooft, JJJ and Linington, RG and Weber, T and Medema, MH}, title = {MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration.}, journal = {Nucleic acids research}, volume = {53}, number = {D1}, pages = {D678-D690}, pmid = {39657789}, issn = {1362-4962}, support = {//Conahcyt Mexico International PhD Studentship/ ; 32170080//National Natural Science Foundation of China/ ; 547394769//German Research Foundation/ ; 101066127//European Union/ ; NNF19SA0059360//Novo Nordisk Foundation INTERACT/ ; //Swedish Pharmaceutical Society PostDoc/ ; F32AT011475/AT/NCCIH NIH HHS/United States ; //Werner Siemens Foundation/ ; 027/E5/PG.02.00.PL/2024//Ministry of Education/ ; ANR-17-EUR-0007//EUR Saclay Plant Sciences-SPS/ ; PROYEXCEL_00012//Spanish "Junta de Andaluc&#xed;a"/ ; 1347411//CONAHCYT/ ; IM230100154//Australian Research Council Industry Fellowship/ ; 1229222N//Research Foundation-Flanders (FWO)/ ; R01 GM146224/GM/NIGMS NIH HHS/United States ; //Swiss Federal Government/ ; OSF.23.1.044//NWO Open Science Project 'BiG-CODEC'/ ; //NWO Merian/ ; R01 GM097142/GM/NIGMS NIH HHS/United States ; 024.004.014//MiCRop Consortium/ ; CZIF2022-007203//Chan Zuckerberg Initiative Foundation/ ; BB/T007222/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; DP230102668//Australian Research Council Discovery Project/ ; 57/0009//Ministry of Education and Science of Ukraine/ ; //Delta Stewardship Council Delta Science Program/ ; T32 GM136629/GM/NIGMS NIH HHS/United States ; //Basic Science Research Program/ ; R01-GM146224/GM/NIGMS NIH HHS/United States ; K12 GM068524/GM/NIGMS NIH HHS/United States ; AUFF-E-2022-9-42//AUFF/ ; 10062709//UK Innovation Funding Agency (UKRI)/ ; CBET-2032243//U.S. National Science Foundation/ ; //University of Illinois/ ; //HZI POF IV Cooperativity and Creativity Project Call/ ; //Horizon Europe Marie Sk&#x142;odowska-Curie Actions Postdoctoral Fellowship/ ; NE/T010959/1//Signals in the Soil/ ; ANR-24-CE20-7299-01//Agence Nationale de la Recherche/ ; DNRF137//Danish National Research Foundation/ ; OCENW.GROOT.2019.063//NWO-XL/ ; BB/V005723/2//BBSRC/ ; 101087181//EU/ ; 101000392//Horizon 2020/ ; 101072485//European Union's Horizon/ ; 10.55776/P 34036//Austrian Science Fund/ ; EP/X03142X/1//United Kingdom Research and Innovation/ ; 23/01956-2//S&#xe3;o Paulo Research Foundation/ ; //Department of Biotechnology/ ; 222676//USDA Evans-Allen Research/ ; //Saarland University/ ; 102022750//SINTEF/ ; //Hans Fischer Society/ ; 21K06336//KAKENHI/ ; CF22-1239//Carlsberg Foundation/ ; ANR-22-CE44-0011-01 UMISYN//Agence Nationale de la Recherche/ ; 495740318//German Research Foundation/ ; 802736//European Union Horizon 2020/ ; //Strathclyde University Global Research Scholarship/ ; NNF22OC0079021//Novo Nordisk Foundation Postdoctoral Fellowship/ ; 101055020-COMMUNITY//ERC Advanced/ ; 101099528//European Innovation Council/ ; GNT2021638//National Health and Medical Research Council/ ; 757173//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; NA22NOS4200050//NERRS/ ; 865738/ERC_/European Research Council/International ; DGE 2241144//NSF GRFP/ ; //National Research Fund of Ukraine/ ; RYC2020-029240-I//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; MR/V022334/1//UKRI Future Leaders Fellowship/ ; 102029187//SEP AGREE/ ; NNF22OC0078997//Novo Nodisk Foundation/ ; F31 ES036421/ES/NIEHS NIH HHS/United States ; KICH1.LWV04.21.013//NWO/ ; DM60066//Italian Ministry of Research/ ; 101117891-MeDiSyn//ERC Starting/ ; //European Union's Horizon 2020 Research/ ; R01 GM123998/GM/NIGMS NIH HHS/United States ; NRF 2018R1A5A2023127//Korea Government (MSIT)/ ; PS00349981//Fulbright/ ; NRF-2020R1A6A1A03044512//Korean Government (MSIT)/ ; 735867//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; 3141-00013A//Innovation Fund Denmark/ ; CFB 2.0//Novo Nordisk Foundation/ ; 21/07038-0//S&#xe3;o Paulo Research Foundation/ ; 2021YFA0909500//National Key Research and Development Program of China/ ; 101072485//European Union's Horizon Europe/ ; OCENW.XL21.XL21.088//NWO-XL/ ; //University Grants Commission/ ; //Natural Science and Research Council of Canada/ ; TTU 09.826//German Center for Infection Research/ ; //European Regional Development Fund/ ; 101072485//Horizon Europe Marie Sk&#x142;odowska-Curie/ ; DNRF137//Danish National Research Foundation CeMiSt/ ; BB/X010953/1//Growing Health Institute Strategic Programme/ ; BB/X01097X/1//BBSRC Institute Strategic Program/ ; 802736//European Union's Horizon 2020/ ; //Alexander von Humboldt-Stiftung/ ; //UK Government Department for Environment, Food &amp; Rural Affairs (DEFRA) Global Centre on Biodiversity for the Climate/ ; //Shanghai Pilot Program for Basic Research - Shanghai Jiao Tong University/ ; 102024676-14//POS BIOINFO 2024/ ; MR/W011247/1//UKRI Future Leaders Fellowship/ ; DGE 21-46756//National Science Foundation Graduate Research Fellowship/ ; 101106349//Marie Sklodowska-Curie/ ; T32-GM136629//Chemical-Biology Interface Training/ ; //University of Sydney/ ; 101000794//SECRETed EU Project Horizon 2020/ ; 2022R1C1C2004118//National Research Foundation of Korea/ ; //Indonesia Endowment Fund for Education Agency (LPDP)/ ; 101130799//European Union's Horizon/ ; 852600//Innovation Program ERC St/ ; //National Agri-Food Biotechnology Institute/ ; //German Academic Scholarship Foundation/ ; 205320_219638/SNSF_/Swiss National Science Foundation/Switzerland ; EXC-2124/1-09.029_0//Cluster of Excellence: Controlling Microbes to Fight Infection/ ; F32 AT011475/AT/NCCIH NIH HHS/United States ; 398967434-TRR 261//Deutsche Forschungsgemeinschaft/ ; 212747/SNSF_/Swiss National Science Foundation/Switzerland ; K445/2022//Leibniz Association/ ; NRF-RS-2024-00352229//Ministry of Science and ICT/ ; //Natural Sciences and Engineering Research Council of Canada Discovery/ ; VI.Veni.202.130//NWO Talent/ ; 106/IV/KS/11/2023//National Research and Innovation Agency/ ; T32GM136583/NH/NIH HHS/United States ; DE-AC02-05CH11231//U.S. Department of Energy/ ; }, mesh = {*Multigene Family ; *Databases, Genetic ; Biosynthetic Pathways/genetics ; Molecular Sequence Annotation ; Biological Products/metabolism/chemistry ; Data Curation ; }, abstract = {Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015. Since its conception, MIBiG has been regularly updated to expand data coverage and remain up to date with innovations in natural product research. Here, we describe MIBiG version 4.0, an extensive update to the data repository and the underlying data standard. In a massive community annotation effort, 267 contributors performed 8304 edits, creating 557 new entries and modifying 590 existing entries, resulting in a new total of 3059 curated entries in MIBiG. Particular attention was paid to ensuring high data quality, with automated data validation using a newly developed custom submission portal prototype, paired with a novel peer-reviewing model. MIBiG 4.0 also takes steps towards a rolling release model and a broader involvement of the scientific community. MIBiG 4.0 is accessible online at https://mibig.secondarymetabolites.org/.}, }
@article {pmid39651958, year = {2024}, author = {Werlang, CA and Sahoo, JK and Cárcarmo-Oyarce, G and Stevens, C and Uzun, D and Putnik, R and Hasturk, O and Choi, J and Kaplan, DL and Ribbeck, K}, title = {Selective Biofilm Inhibition through Mucin-Inspired Engineering of Silk Glycopolymers.}, journal = {Journal of the American Chemical Society}, volume = {146}, number = {50}, pages = {34661-34668}, pmid = {39651958}, issn = {1520-5126}, support = {P41 EB027062/EB/NIBIB NIH HHS/United States ; }, mesh = {*Biofilms/drug effects ; *Mucins/chemistry/metabolism ; *Streptococcus mutans/drug effects ; *Silk/chemistry ; Humans ; Streptococcus sanguis/drug effects ; Streptococcus/drug effects/chemistry ; }, abstract = {Mucins are key components of innate immune defense and possess remarkable abilities to manage pathogenic microbes while supporting beneficial ones and maintaining microbial homeostasis at mucosal surfaces. Their unique properties have garnered significant interest in developing mucin-inspired materials as novel therapeutic strategies for selectively controlling pathogens without disrupting the overall microbial ecology. However, natural mucin production is challenging to scale, driving the need for simpler materials that reproduce mucin's bioactivity. In this work, we generated silk-based glycopolymers with different monosaccharides (GalNAc, GlcNAc, NeuNAc, GlcN, and GalN) and different grafting densities. Using the oral cavity as a model system, we treated in vitro cultures of pathogenic Streptococcus mutans and commensal Streptococcus sanguinis with our glycopolymers, finding that silk-tethered GalNAc uniquely prevented biofilm formation without affecting overall bacterial growth of either species. This relatively simple material reproduced mucin's virulence-neutralizing effects while maintaining biocompatibility. These mucin-inspired materials represent a valuable tool for preventing infection-related harm and offer a strategy for the domestication of pathogens in other environments.}, }
@article {pmid39644970, year = {2025}, author = {Tumeo, A and McDonagh, F and Kovarova, A and Ryan, K and Clarke, C and Miliotis, G}, title = {Draft genome sequence of a co-harbouring blaNDM-5 and mcr-1.1 Escherichia coli phylogroup A isolate associated with patient colonisation in Ireland.}, journal = {Journal of global antimicrobial resistance}, volume = {40}, number = {}, pages = {62-65}, doi = {10.1016/j.jgar.2024.11.018}, pmid = {39644970}, issn = {2213-7173}, mesh = {*Escherichia coli/genetics/isolation &amp; purification/drug effects/classification ; Humans ; Ireland ; *beta-Lactamases/genetics ; *Genome, Bacterial ; *Escherichia coli Infections/microbiology ; Whole Genome Sequencing ; *Escherichia coli Proteins/genetics ; Phylogeny ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Microbial Sensitivity Tests ; Colistin/pharmacology ; Virulence Factors/genetics ; Multilocus Sequence Typing ; Plasmids ; }, abstract = {OBJECTIVES: While Escherichia coli phylogroup-A is typically associated with commensal strains, some isolates can harbour virulence and exhibit multidrug-resistant (MDR) phenotypes. We report the draft genome of a rare instance of carbapenem, fosfomycin and colistin resistant E. coli phylogroup-A, isolated as part of routine screening of a human patient in a clinical setting in Ireland.<br><br>METHODS: E. coli E230738 was identified using MALDI-ToF/MS. Antibiotic susceptibility testing was performed using the Sensititre-EUMDRXXF plate. Whole-genome-sequencing was conducted with NextSeq1000, and genomic analysis identified antibiotic-resistance-genes (ARGs) and virulence-factors (VFs). Phylogenetic analysis was performed using whole-genome-multilocus-sequence-typing (wgMLST).<br><br>RESULTS: E. coli E230738 genome was identified to belong to phylogroup-A/ST10 complex and to harbour 63 ARGs, 17 of which acquired. Resistance to beta-lactams, including carbapenems and cephalosporins was likely due to chromosomally identified blaNDM-5. Colistin resistance appeared associated with acquired mcr-1.1. Despite lacking fosfomycin-inactivating-enzymes, fosfomycin resistance was observed, possibly due to efflux pumps. Forty-seven chromosomal VFs were identified, involved in adhesion and iron acquisition amongst other properties. Plasmid replicons associated with the spread of MDR genes such as IncHI2/HI2A were detected. wgMLST analysis showed the closest relative being a strain from the UK, exhibiting differences in the sequences of 851 genes.<br><br>CONCLUSION: This is a first detected instance of a blaNDM-5 and mcr-1.1 co-occurring in E. coli in Ireland. The MDR profile of E. coli E230738 highlights the growing public health concern posed by the dissemination of MDR E. coli lineages with limited treatment options and underscores the need for clinical screening coupled with genomic surveillance to better understand evolving MDR patterns in E. coli.}, }
@article {pmid39642168, year = {2024}, author = {Champion, C and Momal, R and Le Chatelier, E and Sola, M and Mariadassou, M and Berland, M}, title = {OneNet-One network to rule them all: Consensus network inference from microbiome data.}, journal = {PLoS computational biology}, volume = {20}, number = {12}, pages = {e1012627}, pmid = {39642168}, issn = {1553-7358}, mesh = {*Computational Biology/methods ; Humans ; *Microbiota/physiology ; *Algorithms ; *Gastrointestinal Microbiome/physiology ; Microbial Interactions/physiology ; }, abstract = {Modeling microbial interactions as sparse and reproducible networks is a major challenge in microbial ecology. Direct interactions between the microbial species of a biome can help to understand the mechanisms through which microbial communities influence the system. Most state-of-the art methods reconstruct networks from abundance data using Gaussian Graphical Models, for which several statistically grounded and computationnally efficient inference approaches are available. However, the multiplicity of existing methods, when applied to the same dataset, generates very different networks. In this article, we present OneNet, a consensus network inference method that combines seven methods based on stability selection. This resampling procedure is used to tune a regularization parameter by computing how often edges are selected in the networks. We modified the stability selection framework to use edge selection frequencies directly and combine them in the inferred network to ensure that only reproducible edges are included in the consensus. We demonstrated on synthetic data that our method generally led to slightly sparser networks while achieving much higher precision than any single method. We further applied the method to gut microbiome data from liver-cirrothic patients and demonstrated that the resulting network exhibited a microbial guild that was meaningful in terms of human health.}, }
@article {pmid39641603, year = {2025}, author = {Grimm, H and Lorenz, J and Straub, D and Joshi, P and Shuster, J and Zarfl, C and Muehe, EM and Kappler, A}, title = {Nitrous oxide is the main product during nitrate reduction by a novel lithoautotrophic iron(II)-oxidizing culture from an organic-rich paddy soil.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {1}, pages = {e0126224}, pmid = {39641603}, issn = {1098-5336}, support = {project ID 431072007//Deutsche Forschungsgemeinschaft (DFG)/ ; project ID 390838134//Deutsche Forschungsgemeinschaft (DFG)/ ; }, mesh = {*Nitrous Oxide/metabolism ; Oxidation-Reduction ; *Nitrates/metabolism ; *Soil Microbiology ; *Ferrous Compounds/metabolism ; China ; *Iron/metabolism ; Soil/chemistry ; *Gallionellaceae/metabolism/isolation &amp; purification ; }, abstract = {Microbial nitrate reduction coupled to iron(II) oxidation (NRFeOx) occurs in paddy soils due to high levels of dissolved iron(II) and regular application of nitrogen fertilizer. However, to date, there is no lithoautotrophic NRFeOx isolate or enrichment culture available from this soil environment. Thus, resulting impacts on greenhouse gas emissions during nitrate reduction (i.e., nitrous oxide [N2O]) and on toxic metalloid (i.e., arsenic) mobility can hardly be investigated. We enriched a lithoautotrophic NRFeOx culture, culture HP (Huilongpu paddy, named after its origin), from a paddy soil (Huilongpu Town, China), which was dominated by Gallionella (71%). The culture reduced 0.45 to 0.63 mM nitrate and oxidized 1.76 to 2.31 mM iron(II) within 4 days leading to N2O as the main N-product (62%-88% N2O-N of total reduced NO3[-]-N). Nitrite was present as an intermediate at a maximum of 0.16 ± 0.1 mM. Cells were associated with, but mostly not encrusted by, poorly crystalline iron(III) minerals (ferrihydrite). Culture HP performed best below an iron(II) threshold of 2.5-3.5 mM and in a pH range of 6.50-7.05. In the presence of 100 µM arsenite, only 0%-18% of iron(II) was oxidized. Due to low iron(II) oxidation, arsenite was not immobilized. However, the proportion of N2O-N of total reduced NO3[-]-N decreased from 77% to 30%. Our results indicate that lithoautotrophic NRFeOx occurs even in organic-rich paddy soils, resulting in denitrification and subsequent N2O emissions. The obtained novel enrichment culture allows us to study the impact of lithoautotrophic NRFeOx on arsenic mobility and N2O emissions in paddy soils.IMPORTANCEPaddy soils are naturally rich in iron(II) and regularly experience nitrogen inputs due to fertilization. Nitrogen fertilization increases nitrous oxide emissions as it is an intermediate product during nitrate reduction. Microorganisms can live using nitrate and iron(II) as electron acceptor and donor, respectively, but mostly require an organic co-substrate. By contrast, microorganisms that only rely on nitrate, iron(II), and CO2 could inhabit carbon-limited ecological niches. So far, no isolate or consortium of lithoautotrophic iron(II)-oxidizing, nitrate-reducing microorganisms has been obtained from paddy soil. Here, we describe a lithoautotrophic enrichment culture, dominated by a typical iron(II)-oxidizer (Gallionella), that oxidized iron(II) and reduced nitrate to nitrous oxide, negatively impacting greenhouse gas dynamics. High arsenic concentrations were toxic to the culture but decreased the proportion of nitrous oxide of the total reduced nitrate. Our results suggest that autotrophic nitrate reduction coupled with iron(II) oxidation is a relevant, previously overlooked process in paddy soils.}, }
@article {pmid39637856, year = {2025}, author = {Caty, SN and Alvarez-Buylla, A and Vasek, C and Tapia, EE and Martin, NA and McLaughlin, T and Golde, CL and Weber, PK and Mayali, X and Coloma, LA and Morris, MM and O'Connell, LA}, title = {Alkaloids are associated with increased microbial diversity and metabolic function in poison frogs.}, journal = {Current biology : CB}, volume = {35}, number = {1}, pages = {187-197.e8}, doi = {10.1016/j.cub.2024.10.069}, pmid = {39637856}, issn = {1879-0445}, mesh = {Animals ; *Alkaloids/metabolism ; *Microbiota ; *Anura/microbiology/metabolism ; Skin/microbiology/metabolism ; Bacteria/metabolism/classification/genetics/isolation &amp; purification ; Poison Frogs ; }, abstract = {Shifts in host-associated microbiomes can impact both host and microbes.[1][,][2][,][3][,][4][,][5][,][6] It is of interest to understand how perturbations, like the introduction of exogenous chemicals,[7][,][8][,][9][,][10][,][11][,][12][,][13] impact microbiomes. In poison frogs (family Dendrobatidae), the skin microbiome is exposed to alkaloids that the frogs sequester for defense.[14][,][15][,][16][,][17][,][18][,][19] These alkaloids are antimicrobial[20][,][21][,][22]; however, their effect on the frogs' skin microbiome is unknown. To test this, we characterized microbial communities from field-collected dendrobatid frogs. Then, we conducted a laboratory experiment to monitor the effect of the alkaloid decahydroquinoline (DHQ) on the microbiome of two frog species with contrasting alkaloid loads in nature. In both datasets, we found that alkaloid-exposed microbiomes were more phylogenetically diverse, with an increase in diversity among rare taxa. To better understand the isolate-specific response to alkaloids, we cultured microbial isolates from poison frog skin and found that many isolates exhibited enhanced growth or were not impacted by the addition of DHQ. To further explore the microbial response to alkaloids, we sequenced the metagenomes from high- and low-alkaloid frogs and observed a greater diversity of genes associated with nitrogen and carbon metabolism in high-alkaloid frogs. From these data, we hypothesized that some strains may metabolize the alkaloids. We used stable isotope tracing coupled to nanoSIMS (nanoscale secondary ion mass spectrometry), which supported the idea that some of these isolates are able to metabolize DHQ. Together, these data suggest that poison frog alkaloids open new niches for skin-associated microbes with specific adaptations, such as alkaloid metabolism, that enable survival in this environment.}, }
@article {pmid39637512, year = {2025}, author = {Wilkie, I and Orellana, LH}, title = {Elusive marine Verrucomicrobiota: Seasonally abundant members of the novel genera Seribacter and Chordibacter specialize in degrading sulfated glycans.}, journal = {Systematic and applied microbiology}, volume = {48}, number = {1}, pages = {126562}, doi = {10.1016/j.syapm.2024.126562}, pmid = {39637512}, issn = {1618-0984}, mesh = {Phylogeny ; *Polysaccharides/metabolism ; *Sulfates/metabolism ; RNA, Ribosomal, 16S/genetics ; Genome, Bacterial ; Seasons ; North Sea ; *Seawater/microbiology ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; Metagenome ; }, abstract = {Members of the phylum Verrucomicrobiota play a significant role in various ecosystems, yet they are underrepresented in databases due to their comparatively lower abundance and isolation challenges. The use of cultivation-independent approaches has unveiled their hidden diversity and specialized metabolic capabilities, yet many of these populations remain uncharacterized. In this study, we focus on members of the family MB11C04 associated with North Sea spring blooms. Our analyses revealed recurrent MB11C04 populations with increased abundance in the late stages of spring blooms over ten-years. By examining their genomic content, we identified specialized genetic features for the degradation of complex polysaccharides, particularly sulfated and fucose-rich compounds, suggesting their role in utilizing organic matter during the collapse of the bloom. Furthermore, we describe two novel genera each with a novel species (Seribacter gen. Nov., Chordibacter gen. Nov.) in accordance with the SeqCode initiative based on high quality metagenome-assembled genomes. We also propose a new name for the family MB11C04, Seribacteraceae. Our findings shed light on the ecological significance and metabolic potential of Verrucomicrobiota populations in spring bloom events.}, }
@article {pmid39633812, year = {2024}, author = {Bauchinger, F and Seki, D and Berry, D}, title = {Characteristics of putative keystones in the healthy adult human gut microbiota as determined by correlation network analysis.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1454634}, pmid = {39633812}, issn = {1664-302X}, abstract = {Keystone species are thought to play a critical role in determining the structure and function of microbial communities. As they are important candidates for microbiome-targeted interventions, the identification and characterization of keystones is a pressing research goal. Both empirical as well as computational approaches to identify keystones have been proposed, and in particular correlation network analysis is frequently utilized to interrogate sequencing-based microbiome data. Here, we apply an established method for identifying putative keystone taxa in correlation networks. We develop a robust workflow for network construction and systematically evaluate the effects of taxonomic resolution on network properties and the identification of keystone taxa. We are able to identify correlation network keystone species and genera, but could not detect taxa with high keystone potential at lower taxonomic resolution. Based on the correlation patterns observed, we hypothesize that the identified putative keystone taxa have a stabilizing effect that is exerted on correlated taxa. Correlation network analysis further revealed subcommunities present in the dataset that are remarkably similar to previously described patterns. The interrogation of available metatranscriptomes also revealed distinct transcriptional states present in all putative keystone taxa. These results suggest that keystone taxa may have stabilizing properties in a subset of community members rather than global effects. The work presented here contributes to the understanding of correlation network keystone taxa and sheds light on their potential ecological significance.}, }
@article {pmid39633134, year = {2024}, author = {Han, GH and Yu, J and Kang, MJ and Park, MJ and Noh, CH and Kim, YJ and Kwon, KK}, title = {Phylosymbiosis in Seven Wild Fish Species Collected Off the Southern Coast of Korea: Skin Microbiome Most Strongly Reflects Evolutionary Pressures.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {153}, pmid = {39633134}, issn = {1432-184X}, support = {20210469//Ministry of Oceans and Fisheries/ ; }, mesh = {Animals ; Republic of Korea ; *Microbiota ; *Skin/microbiology ; *Phylogeny ; *RNA, Ribosomal, 16S/genetics ; *Fishes/microbiology ; *Symbiosis ; *Bacteria/classification/genetics/isolation &amp; purification ; Gills/microbiology ; Biological Evolution ; Species Specificity ; }, abstract = {Phylosymbiosis is defined as the relationship in which the microbiome recapitulates the phylogeny of the host and has been demonstrated in a variety of terrestrial organisms, although it has been understudied in fish, the most phylogenetically diverse vertebrate. Given that the species-specificity of fish microbiomes was detected in multiple body parts and differed by body parts, we assumed that the phylogenetic reflection of the microbiome would differ across body parts. Thus, we analyze the difference of phylosymbiotic relationships in the microbial communities found in three body parts (skin, gills, and intestine) of seven wild fish species from four families (Labridae, Sebastidae, Sparidae, and Rajidae) via 16S rRNA gene amplicon sequencing. Fishes were purchased at Docheon port market in Tongyeong City, Korea and were transported to nearby research institutes for aliveness. Mantel tests using dissimilarity values of microbiomes and hosts' divergence times showed that the differences in microbial communities in all three body parts were related to the hosts' divergence time. This pattern was the most pronounced in the skin. Furthermore, fishes from the same family showed similar bacterial compositions on their skins and gills, with clear differences depending on the family, with the exception of Labridae. These results suggest that the skin microbiome is particularly vulnerable to evolutionary pressures. We hypothesized that the evolution of the fish immune system and the difference in feeding habits induced the stronger phylosymbiotic signal in the skin. Collectively, this dataset will be useful for understanding the fish microbiome and give insights into phylosymbiosis of aquatic animals across body parts.}, }
@article {pmid39633061, year = {2024}, author = {Paduano, S and Marchesi, I and Valeriani, F and Frezza, G and Facchini, MC and Romano Spica, V and Bargellini, A}, title = {Characterization by 16S Amplicon Sequencing of Bacterial Communities Overall and During the Maturation Process of Peloids in Two Spas of an Italian Thermal Complex.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {152}, pmid = {39633061}, issn = {1432-184X}, mesh = {*Bacteria/genetics/classification/isolation &amp; purification ; Italy ; *RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Clay/chemistry ; Biodiversity ; High-Throughput Nucleotide Sequencing ; DNA, Bacterial/genetics ; Mineral Waters/microbiology ; Phylogeny ; }, abstract = {Peloids are made by mixing clay materials with thermo-mineral waters, enriched with organic substances from microorganisms during maturation. Their beneficial properties may depend on clay minerals, water characteristics, and microbial components, although strong evidence is lacking. Next Generation Sequencing (NGS) allows a comprehensive approach to studying the entire microbial community, including cultivable and uncultivable bacteria. Our study aims to characterize, by NGS, the bacterial community overall and during the maturation process of thermal muds in two spas (A-B) of an Italian thermal complex. Peloids were produced from sulfurous-bromine-iodine thermal water and clay material: natural mud for spa A and sterile clay for spa B. Thermal waters and peloids at different maturation stages (2/4/6 months) were analyzed for microbiome characterization by 16S amplicon sequencing. Biodiversity profiles showed a low level of similarity between peloids and water used for their maturation. Peloids from spa A showed greater microbial richness than those from spa B, suggesting that natural mud with an existing bacterial community leads to greater biodiversity than sterile clay. Genera involved in sulfur metabolism were prevalent in both spas, as expected considering peloids matured in sulfide-rich water. For all three maturation stages, the prevalent genera were Thiobacillus and Pelobacter in spa A and Thiobacillus, Thauera, Pelobacter, and Desulfuromonas in spa B. Richness and diversity indices showed that the community seemed to stabilize after 2-4 months. The 16S amplicon sequencing to study bacterial communities enables the identification of a biological signature that characterizes a specific thermal matrix, defining its therapeutic and cosmetic properties. The bacterial composition of peloids is affected by the thermal water and the type of clay material used in their formulation and maturation.}, }
@article {pmid39632307, year = {2025}, author = {Delmoitié, B and Sakarika, M and Rabaey, K and De Wever, H and Regueira, A}, title = {Tailoring non-axenic lactic acid fermentation from cheese whey permeate targeting a flexible lactic acid platform.}, journal = {Journal of environmental management}, volume = {373}, number = {}, pages = {123529}, doi = {10.1016/j.jenvman.2024.123529}, pmid = {39632307}, issn = {1095-8630}, mesh = {*Cheese ; Fermentation ; *Whey/metabolism ; *Lactic Acid/metabolism ; Hydrogen-Ion Concentration ; Temperature ; }, abstract = {Lactic acid (LA) is an important biobased platform chemical, with potential applications in synthetising a wide range of chemical products or serving as feedstock for various bioprocesses. Industrial LA production via pure culture fermentation is characterized by high operational costs and utilizes food-grade sugars, thereby reducing the feasibility of LA applications. In this context, our research focussed on valorising the largest dairy side stream, cheese whey permeate, through the use of mixed microbial communities. We evaluated the effect of different operational parameters (temperature, pH and hydraulic retention time) in non-axenic fermentations on productivity, yield, concentration, optical purity, and community. Our findings revealed that operating at mildly thermophilic conditions (45 °C) resulted in highly selective LA production, and significantly augmented the LA yield, and productivity, compared to higher temperatures (50-55 °C). In addition, operating at circumneutral pH conditions (6.0-6.5) led to significantly increased the LA fermentation performance compared to the conventional acid pH conditions (≤5.5). This led to an unprecedented LA productivity of 27.4 g/L/h with a LA yield of 70.0% which is 2.5 times higher compared to previous reported maximum. Additionally, varying pH levels influenced the optical purity of LA: we achieved an optical L-LA purity of 98.3% at pH 6.0-6.5, and an optical D-LA purity of 91.3% at a pH of 5.5. A short hydraulic retention time of less than 12 h was crucial for selective LA production. This process also yielded a microbial biomass composed of 90.3-98.6% Lactobacillus delbrueckii, which could be potentially valorised as probiotic or protein ingredient in food or feed products. Our work shows that by careful selection of operational conditions, the overall performance can be significantly increased compared to the state-of-the-art. These results highlight the potential of non-sterile LA fermentation and show that careful selection of simple reactor operation parameters can maximize process performance. A preliminary assessment suggests that valorising EU cheese whey permeate could increase LA and poly-LA production by 40 and 125 times, respectively. This could also lead to the production of 4,000 kton protein-rich biomass, potentially reducing CO2 emissions linked to EU food and feed production by 4.87% or 2.77% respectively.}, }
@article {pmid39629059, year = {2024}, author = {Pecsi, EL and Forbes, S and Guillemette, F}, title = {Organic Matter Composition as a Driver of Soil Bacterial Responses to Pig Carcass Decomposition in a Canadian Continental Climate.}, journal = {Journal of geophysical research. Biogeosciences}, volume = {129}, number = {12}, pages = {e2024JG008355}, pmid = {39629059}, issn = {2169-8953}, abstract = {Organic by-products are released into the surrounding soil during the terrestrial decomposition of animal remains. The affected area, known as the Cadaver Decomposition Island (CDI), can undergo biochemical changes that contribute to landscape heterogeneity. Soil bacteria are highly sensitive to labile inputs, but it is unknown how they respond to shifts in dissolved organic matter (DOM) quantity and quality resulting from animal decomposition. We aimed to evaluate the relationship between soil DOM composition and bacterial activity/function in CDIs under a Canadian temperate continental climate. This was studied in soils surrounding adult pig carcasses (n = 3) that were surface deposited within a mixed forested environment (Trois-Rivières, Québec) in June 2019. Using fluorescence spectroscopy and dissolved organic carbon analyses, we detected a pulse of labile protein-like DOM during the summer season (day 55). This was found to be an important driver of heightened soil bacterial respiration, cell abundance and potential carbohydrate metabolism. These bacterial disturbances persisted into the cooler autumn season (day 156) and led to the gradual transformation of labile DOM inputs into microbially sourced humic-like compounds. By the spring (day 324), DOM quantities and bacterial measures almost recovered, but DOM quality remained distinct from surrounding vegetal humic signals. All observed effects were spatially constrained to the topsoil (A-horizon) and within 20 cm laterally from the carcasses. These findings provide valuable insight into CDI organic matter cycling within a cold-climate ecosystem. Repeated CDI studies will however be required to capture the changing dynamics resulting from increasing global temperatures.}, }
@article {pmid39628456, year = {2025}, author = {Sinclair, JS and Buchner, D and Gessner, MO and Müller, J and Pauls, SU and Stoll, S and Welti, EAR and Bässler, C and Buse, J and Dziock, F and Enss, J and Hörren, T and Künast, R and Li, Y and Marten, A and Morkel, C and Richter, R and Seibold, S and Sorg, M and Twietmeyer, S and Weis, D and Weisser, W and Wiggering, B and Wilmking, M and Zotz, G and Frenzel, M and Leese, F and Haase, P}, title = {Effects of land cover and protected areas on flying insect diversity.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {39}, number = {4}, pages = {e14425}, pmid = {39628456}, issn = {1523-1739}, support = {//Hessisches Landesamt f&#xfc;r Umwelt und Geologie/ ; //LOEWE Centre for Translational Biodiversity Genomics/ ; 871128//EU Horizon project eLTER PLUS/ ; }, mesh = {Animals ; *Biodiversity ; *Insecta/physiology ; *Conservation of Natural Resources ; Germany ; Biomass ; }, abstract = {Widespread insect losses are a critical global problem. Mitigating this problem requires identifying the principal drivers across different taxa and determining which insects are covered by protected areas. However, doing so is hindered by missing information on most species owing to extremely high insect diversity and difficulties in morphological identification. To address this knowledge gap, we used one of the most comprehensive insect DNA metabarcoding data sets assembled (encompassing 31,846 flying insect species) in which data were collected from a network of 75 Malaise traps distributed across Germany. Collection sites encompass gradients of land cover, weather, and climate, along with differences in site protection status, which allowed us to gain broader insights into how insects respond to these factors. We examined changes in total insect biomass, species richness, temporal turnover, and shifts in the composition of taxa, key functional groups (pollinators, threatened species, and invasive species), and feeding traits. Lower insect biomass generally equated to lower richness of all insects and higher temporal turnover, suggesting that biomass loss translates to biodiversity loss and less stable communities. Spatial variability in insect biomass and composition was primarily driven by land cover, rather than weather or climate change. As vegetation and land-cover heterogeneity increased, insect biomass increased by 50% in 2019 and 56% in 2020 and total species richness by 58% and 33%, respectively. Similarly, areas with low-vegetation habitats exhibited the highest richness of key taxa, including pollinators and threatened species, and the widest variety of feeding traits. However, these habitats tended to be less protected despite their higher diversity. Our results highlight the value of heterogeneous low vegetation for promoting overall insect biomass and diversity and that better protection of insects requires improved protection and management of unforested areas, where many biodiversity hotspots and key taxa occur.}, }
@article {pmid39624182, year = {2024}, author = {Wirth, JS and Katz, LS and Williams, GM and Chen, JC}, title = {primerForge: a Python program for identifying primer pairs capable of distinguishing groups of genomes from each other.}, journal = {Journal of open source software}, volume = {9}, number = {101}, pages = {}, pmid = {39624182}, issn = {2475-9066}, support = {CC999999/ImCDC/Intramural CDC HHS/United States ; }, abstract = {In both molecular epidemiology and microbial ecology, it is useful to be able to categorize specific strains of microorganisms in either an ingroup or an outgroup in a given population, e.g. to distinguish a pathogenic strain of interest from its non-virulent relatives. An "ingroup" refers to a group of microbes that are the primary focus of study or interest. Conversely, an "outgroup" consists of microbes that are closely-related to, but have evolved separately from, the ingroup. While whole genome sequencing and downstream phylogenetic analyses can be employed to do this, these techniques are often slow and can be resource intensive. Additionally, the laboratory would have to sequence the whole genome to use these tools to determine whether or not a new sample is part of the ingroup or outgroup. Alternatively, polymerase chain reaction (PCR) can be used to amplify regions of genetic material that are specific to the strain(s) of interest. PCR is faster, less expensive, and more accessible than whole genome sequencing, so having a PCR-based approach can accelerate the detection of specific strain(s) of microbes and facilitate diagnoses and/or population studies.}, }
@article {pmid39621250, year = {2024}, author = {Lin, X and Lin, C and Li, X and Yao, F and Guo, X and Wang, M and Zeng, M and Yuan, Y and Xie, Q and Huang, X and Jiao, X}, title = {Gut Microbiota Dysbiosis Facilitates Susceptibility to Bloodstream Infection.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {62}, number = {12}, pages = {1113-1124}, pmid = {39621250}, issn = {1976-3794}, support = {201224106490150//Shantou Science and Technology Project/ ; }, mesh = {Humans ; *Dysbiosis/microbiology ; *Gastrointestinal Microbiome ; Male ; Female ; *RNA, Ribosomal, 16S/genetics ; Middle Aged ; *Feces/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Aged ; Adult ; Bacteremia/microbiology ; Disease Susceptibility ; DNA, Bacterial/genetics ; }, abstract = {To study the role of intestinal flora in the development of bloodstream infections (BSIs). 42 patients and 19 healthy controls (HCs) were screened into the study and their intestinal flora was measured by 16S rRNA gene sequencing. The bacterial diversity was significantly lower in the BSI group compared with that in the HCs (P < 0.001), and beta diversity was significantly differentiated between the two groups (PERMANOVA, P = 0.001). The four keystone species [Roseburia, Faecalibacterium, Prevotella, and Enterococcus (LDA > 4)] differed significantly between the two groups. Dysbiosis of fecal microbial ecology is a common condition present in patients with BSI. The proliferation of certain pathogens or reduction of SCFA-producing bacteria would cause susceptibility to BSI.}, }
@article {pmid39619625, year = {2024}, author = {Sakarika, M and Matassa, S and Carvajal-Arroyo, JM and Ganigué, R}, title = {Editorial: Microbial biorefineries for a more sustainable, circular economy.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {12}, number = {}, pages = {1512756}, doi = {10.3389/fbioe.2024.1512756}, pmid = {39619625}, issn = {2296-4185}, }
@article {pmid39612478, year = {2025}, author = {Zhao, Y and Ran, W and Xu, W and Song, Y}, title = {ITS amplicon sequencing revealed that rare taxa of tea rhizosphere fungi are closely related to the environment and provide feedback on tea tree diseases.}, journal = {Microbiology spectrum}, volume = {13}, number = {1}, pages = {e0188924}, pmid = {39612478}, issn = {2165-0497}, support = {32260120//MOST | National Natural Science Foundation of China (NSFC)/ ; Qiankehejichu-ZK [2023] General 257//Guizhou Natural Science Foundation/ ; Qiankehepingtairencai-GCC [2023]032//Training Program for High-level Innovative Talents of Guizhou Province/ ; Qiankehepingtairencai-CXTD [2023]010//Science and Techonlogy Innovation Talent Team Building Project of Guizhou Province/ ; }, mesh = {*Rhizosphere ; *Soil Microbiology ; *Fungi/classification/genetics/isolation &amp; purification ; *Camellia sinensis/microbiology ; *Plant Diseases/microbiology ; China ; Symbiosis ; Tea/microbiology ; High-Throughput Nucleotide Sequencing ; Phylogeny ; }, abstract = {The rhizospheres of plants and soil microorganisms are intricately interconnected. Tea trees are cultivated extensively on the karst plateau of Guizhou Province, China; however, the understanding of the interactions among fungal communities, community taxa, and diseases impacting tea tree in the soil rhizosphere is limited. Our aim is to offer insights for the advancement of modern agriculture in ecologically fragile karst tea gardens, as well as microbiomics concepts for green and sustainable environmental development. This study utilized the internal transcribed spacer high-throughput sequencing technology to explore the symbiotic relationship between rhizosphere fungi and plant disease feedback in multiple tea estates across the Guizhou Plateau. The ecological preferences and environmental thresholds of fungi were investigated via environmental variables. Furthermore, a correlation was established between different taxa and individual soil functions. Research has indicated that tea leaf blight disrupts symbiotic connections among fungal groups. For various taxa, we found that numerous taxa consistently maintained core positions within the community, whereas rare taxa were able to stabilize due to a high proportion of positive effects. Additionally, abundant taxa presented a wider range of environmental feedback, whereas the rare taxon diversity presented a stronger positive association with the soil Z score. This study contributes to our understanding of the importance of rare taxa in plant rhizosphere soil processes. Emphasis should be placed on the role of rare taxa in pest and disease control within green agriculture while also strengthening systematic development and biogeographical research related to rare taxa in this region.IMPORTANCEIn this study, based on internal transcribed spacer high-throughput sequencing, fungal communities in the rhizosphere soil of tea trees and their interactions with the environment in karst areas were reported, and the symbiotic relationships of different fungal taxa and their feedback to the environment were described in detail by using the knowledge of microbial ecology. On this basis, it was found that tea tree diseases affect the symbiotic relationships of fungal taxa. At the same time, we found that rare taxa have stronger cooperative relationships in response to environmental changes and explored their participation in soil processes based on fungal trait sets. This study will provide basic data for the development of modern agriculture in tea gardens and theoretical basis for the sustainable prevention and control of tea tree diseases.}, }
@article {pmid39611982, year = {2024}, author = {Kou, Z and Liu, J and Tohti, G and Zhu, X and Zheng, B and Zhu, Y and Zhang, W}, title = {Distinct Bacterial Communities Within the Nonrhizosphere, Rhizosphere, and Endosphere of Ammodendron bifolium Under Winter Condition in the Takeermohuer Desert.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {151}, pmid = {39611982}, issn = {1432-184X}, support = {2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; }, mesh = {*Rhizosphere ; *Bacteria/classification/genetics/isolation &amp; purification ; *Soil Microbiology ; *Desert Climate ; *Seasons ; Plant Roots/microbiology ; Soil/chemistry ; Microbiota ; }, abstract = {Due to human activities and severe climatic conditions, the population of Ammodendron bifolium, an excellent sand-fixing plant, has gradually decreased in the Takeermohuer Desert. The plant-associated bacteria community can enhance its survival in harsh environments. However, the understanding of A. bifolium-associated bacterial community is still unclear during the harsh winter. We investigated the bacterial community structure from the A. bifolium rhizosphere and nonrhizosphere at different depths (i.e., 0-40 cm, 40-80 cm, 80-120 cm) and from endosphere (i.e., root endosphere and stem endosphere) in winter. At the same time, we analyzed the impact of different compartments and soil factors on the bacterial community structure. Studies have shown that the A. bifolium rhizosphere exhibits higher levels of SOM (soil organic matter), SOC (soil organic carbon), SAN (soil alkaline nitrogen), and SAK (soil available potassium) compared with the nonrhizosphere. The dominant bacterial phyla were Proteobacteria (19.6%), Cyanobacteria (15.9%), Actinobacteria (13.6%), Acidobacteria (9.0%), and Planctomycetota (5.7%) in the desert. Proteobacteria (24.0-30.2%) had the highest relative abundance in rhizosphere, Actinobacteria (18.3-22.6%) had the highest relative abundance in nonrhizosphere, and Cyanobacteria had the highest relative abundance in endosphere. At the genus level, the relative abundance of Pseudomonas (1.2%) in the root endosphere was the highest and the other genera were mostly unclassified. The Chao1 and PD_whole_tree indices showed that the diversity of the bacterial communities decreased from nonrhizosphere, rhizosphere, root endosphere to stem endosphere. Co-occurrence network analyses identified Proteobacteria and Actinobacteria as key species across the three compartments. Additionally, unique keystone species like Cyanobacteria, Verrucomicrobiota, and Desulfobacterota were found only in the endosphere. The bacterial community in the rhizosphere was influenced by factors such as EC (electrical conductivity), STC (soil total carbon), SOM, SOC, STN (soil total nitrogen), SAN, STP (soil total phosphorus), and SAK, while that of the nonrhizosphere was mainly influenced by pH, C/N (STC/STN), SAP, and distance. The study highlighted differences in bacterial community composition, diversity, and influencing factors across the three compartments, which can provide a better understanding of the association/interactions between A. bifolium and bacterial communities and lay a foundation for revealing its adaptability in winter.}, }
@article {pmid39611949, year = {2024}, author = {Makumbi, JP and Leareng, SK and Pierneef, RE and Makhalanyane, TP}, title = {Synergizing Ecotoxicology and Microbiome Data Is Key for Developing Global Indicators of Environmental Antimicrobial Resistance.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {150}, pmid = {39611949}, issn = {1432-184X}, support = {UID 110717//National Research Foundation of South Africa/ ; UID 110717//National Research Foundation of South Africa/ ; }, mesh = {*Microbiota/drug effects ; Humans ; *Ecotoxicology ; Animals ; Risk Assessment ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial ; Public Health ; Drug Resistance, Microbial ; }, abstract = {The One Health concept recognises the interconnectedness of humans, plants, animals and the environment. Recent research strongly supports the idea that the environment serves as a significant reservoir for antimicrobial resistance (AMR). However, the complexity of natural environments makes efforts at AMR public health risk assessment difficult. We lack sufficient data on key ecological parameters that influence AMR, as well as the primary proxies necessary for evaluating risks to human health. Developing environmental AMR 'early warning systems' requires models with well-defined parameters. This is necessary to support the implementation of clear and targeted interventions. In this review, we provide a comprehensive overview of the current tools used globally for environmental AMR human health risk assessment and the underlying knowledge gaps. We highlight the urgent need for standardised, cost-effective risk assessment frameworks that are adaptable across different environments and regions to enhance comparability and reliability. These frameworks must also account for previously understudied AMR sources, such as horticulture, and emerging threats like climate change. In addition, integrating traditional ecotoxicology with modern 'omics' approaches will be essential for developing more comprehensive risk models and informing targeted AMR mitigation strategies.}, }
@article {pmid39611829, year = {2025}, author = {Hameed, A and McDonagh, F and Sengupta, P and Miliotis, G and Sivabalan, SKM and Szydlowski, L and Simpson, A and Singh, NK and Rekha, PD and Raman, K and Venkateswaran, K}, title = {Neobacillus driksii sp. nov. isolated from a Mars 2020 spacecraft assembly facility and genomic potential for lasso peptide production in Neobacillus.}, journal = {Microbiology spectrum}, volume = {13}, number = {1}, pages = {e0137624}, pmid = {39611829}, issn = {2165-0497}, support = {Mars Program Office//NASA | Jet Propulsion Laboratory (JPL)/ ; IBSE//Indian Institute of Technology Madras (IITM)/ ; WSAI//Indian Institute of Technology Madras (IITM)/ ; }, mesh = {*Phylogeny ; *RNA, Ribosomal, 16S/genetics ; *Spacecraft ; *Mars ; Genome, Bacterial ; Fatty Acids/metabolism/analysis ; DNA, Bacterial/genetics ; Genomics ; Base Composition ; Bacillales/genetics/classification/isolation &amp; purification/metabolism ; Soil Microbiology ; Peptides/metabolism ; Whole Genome Sequencing ; }, abstract = {UNLABELLED: During microbial surveillance of the Mars 2020 spacecraft assembly facility, two novel bacterial strains, potentially capable of producing lasso peptides, were identified. Characterization using a polyphasic taxonomic approach, whole-genome sequencing and phylogenomic analyses revealed a close genetic relationship among two strains from Mars 2020 cleanroom floors (179-C4-2-HS, 179-J1A1-HS), one strain from the Agave plant (AT2.8), and another strain from wheat-associated soil (V4I25). All four strains exhibited high 16S rRNA gene sequence similarity (>99.2%) and low average nucleotide identity (ANI) with Neobacillus niacini NBRC 15566[T], delineating new phylogenetic branches within the genus. Detailed molecular analyses, including gyrB (90.2%), ANI (86.4%), average amino acid identity (87.8%) phylogenies, digital DNA-DNA hybridization (32.6%), and percentage of conserved proteins (77.7%) indicated significant divergence from N. niacini NBRC 15566[T]. Consequently, these strains have been designated Neobacillus driksii sp. nov., with the type strain 179-C4-2-HS[T] (DSM 115941[T] = NRRL B-65665[T]). N. driksii grew at 4°C to 45°C, pH range of 6.0 to 9.5, and 0.5% to 5% NaCl. The major cellular fatty acids are iso-C15:0 and anteiso-C15:0. The dominant polar lipids include diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and an unidentified aminolipid. Metagenomic analysis within NASA cleanrooms revealed that N. driksii is scarce (17 out of 236 samples). Genes encoding the biosynthesis pathway for lasso peptides were identified in all N. driksii strains and are not commonly found in other Neobacillus species, except in 7 out of 26 recognized species. This study highlights the unique metabolic capabilities of N. driksii, underscoring their potential in antimicrobial research and biotechnology.<br><br>IMPORTANCE: The microbial surveillance of the Mars 2020 assembly cleanroom led to the isolation of novel N. driksii with potential applications in cleanroom environments, such as hospitals, pharmaceuticals, semiconductors, and aeronautical industries. N. driksii genomes were found to possess genes responsible for producing lasso peptides, which are crucial for antimicrobial defense, communication, and enzyme inhibition. Isolation of N. driksii from cleanrooms, Agave plants, and dryland wheat soils, suggested niche-specific ecology and resilience under various environmentally challenging conditions. The discovery of potent antimicrobial agents from novel N. driksii underscores the importance of genome mining and the isolation of rare microorganisms. Bioactive gene clusters potentially producing nicotianamine-like siderophores were found in N. driksii genomes. These siderophores can be used for bioremediation to remove heavy metals from contaminated environments, promote plant growth by aiding iron uptake in agriculture, and treat iron overload conditions in medical applications.}, }
@article {pmid39611809, year = {2025}, author = {Mermans, F and Chatzigiannidou, I and Teughels, W and Boon, N}, title = {Quantifying synthetic bacterial community composition with flow cytometry: efficacy in mock communities and challenges in co-cultures.}, journal = {mSystems}, volume = {10}, number = {1}, pages = {e0100924}, pmid = {39611809}, issn = {2379-5077}, mesh = {*Flow Cytometry/methods ; RNA, Ribosomal, 16S/genetics ; Coculture Techniques/methods ; *Bacteria/genetics/classification/isolation &amp; purification ; *Microbiota/genetics ; Humans ; DNA, Bacterial/genetics ; }, abstract = {Determination of bacterial community composition in synthetic communities is critical for understanding microbial systems. The community composition is typically determined through bacterial plating or through PCR-based methods, which can be labor-intensive, expensive, or prone to bias. Simultaneously, flow cytometry has been suggested as a cheap and fast alternative. However, since the technique captures the phenotypic state of bacterial cells, accurate determination of community composition could be affected when bacteria are co-cultured. We investigated the performance of flow cytometry for quantifying oral synthetic communities and compared it to the performance of strain specific qPCR and 16S rRNA gene amplicon sequencing. Therefore, axenic cultures, mock communities and co-cultures of oral bacteria were prepared. Random forest classifiers trained on flow cytometry data of axenic cultures were used to determine the composition of the synthetic communities, as well as strain specific qPCR and 16S rRNA gene amplicon sequencing. Flow cytometry was shown to have a lower average root mean squared error and outperformed the PCR-based methods in even mock communities (flow cytometry: 0.11 ± 0.04; qPCR: 0.26 ± 0.09; amplicon sequencing: 0.15 ± 0.01). When bacteria were co-cultured, neither flow cytometry, strain-specific qPCR, nor 16S rRNA gene amplicon sequencing resulted in similar community composition. Performance of flow cytometry was decreased compared with mock communities due to changing phenotypes. Finally, discrepancies between flow cytometry and strain-specific qPCR were found. These findings highlight the challenges ahead for quantifying community composition in co-cultures by flow cytometry.IMPORTANCEQuantification of bacterial composition in synthetic communities is crucial for understanding and steering microbial interactions. Traditional approaches like plating, strain-specific qPCR, and amplicon sequencing are often labor-intensive and expensive and limit high-throughput experiments. Recently, flow cytometry has been suggested as a swift and cheap alternative for quantifying communities and has been successfully demonstrated on simple bacterial mock communities. However, since flow cytometry measures the phenotypic state of cells, measurements can be affected by differing phenotypes. Especially, changing phenotypes resulting from co-culturing bacteria can have a profound effect on the applicability of the technique in this context. This research illustrates the feasibility and challenges of flow cytometry for the determination of community structure in synthetic mock communities and co-cultures.}, }
@article {pmid39609949, year = {2024}, author = {Almela, P and Elser, JJ and Giersch, JJ and Hotaling, S and Rebbeck, V and Hamilton, TL}, title = {Laboratory Experiments Suggest a Limited Impact of Increased Nitrogen Deposition on Snow Algae Blooms.}, journal = {Environmental microbiology reports}, volume = {16}, number = {6}, pages = {e70052}, pmid = {39609949}, issn = {1758-2229}, support = {2113783//National Science Foundation/ ; 2113784//National Science Foundation/ ; }, mesh = {*Nitrogen/metabolism/analysis ; *Snow/chemistry ; *Phosphorus/metabolism/analysis ; *Eutrophication ; *Biomass ; }, abstract = {Snow algal blooms decrease snow albedo and increase local melt rates. However, the causes behind the size and frequency of these blooms are still not well understood. One factor likely contributing is nutrient availability, specifically nitrogen and phosphorus. The nutrient requirements of the taxa responsible for these blooms are not known. Here, we assessed the growth of three commercial strains of snow algae under 24 different nutrient treatments that varied in both absolute and relative concentrations of nitrogen and phosphorus. After 38 days of incubation, we measured total biomass and cell size and estimated their effective albedo reduction surface. Snow algal strains tended to respond similarly and achieved bloom-like cell densities over a wide range of nutrient conditions. However, the molar ratio of nitrogen to phosphorus at which maximum biomass was achieved was between 4 and 7. Our data indicate a high requirement for phosphorus for snow algae and highlights phosphorus availability as a critical factor influencing the frequency and extent of snow algae blooms and their potential contribution to snow melt through altered albedo. Snow algae can thrive across a range of nitrogen (N) and phosphorus (P) conditions, with a higher P requirement for optimal growth. Our study suggests that increased N deposition may have a limited impact on snow algae bloom occurrence and size, emphasising P as a key factor influencing these blooms and their potential to accelerate snow melt by lowering albedo.}, }
@article {pmid39609930, year = {2024}, author = {Paquette, AJ and Bhatnagar, S and Vadlamani, A and Gillis, T and Khot, V and Novotnik, B and De la Hoz Siegler, H and Strous, M and Rattray, JE}, title = {Ecology and biogeochemistry of the microbial underworld in two sister soda lakes.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {98}, pmid = {39609930}, issn = {2524-6372}, abstract = {BACKGROUND: Approximately 3.7 billion years ago, microbial life may have emerged in phosphate-rich salty ponds. Surprisingly, analogs of these environments are present in alkaline lake systems, recognized as highly productive biological ecosystems. In this study, we investigate the microbial ecology of two Canadian soda lake sediment systems characterized by naturally high phosphate levels.<br><br>RESULTS: Using a comprehensive approach involving geochemistry, metagenomics, and amplicon sequencing, we discovered that groundwater infiltration into Lake Goodenough sediments supported stratified layers of microbial metabolisms fueled by decaying mats. Effective degradation of microbial mats resulted in unexpectedly low net productivity. Evaporation of water from Last Chance Lake and its sediments led to saturation of brines and a habitat dominated by inorganic precipitation reactions, with low productivity, low organic matter turnover and little biological uptake of phosphorus, leading to high phosphate concentrations. Highly alkaline brines were found to be dominated by potentially dormant spore-forming bacteria. These saturated brines also hosted potential symbioses between Halobacteria and Nanoarchaeaota, as well as Lokiarchaea and bacterial sulfate reducers. Metagenome-assembled genomes of Nanoarchaeaota lacked strategies for coping with salty brines and were minimal for Lokiarchaea.<br><br>CONCLUSIONS: Our research highlights that modern analogs for origin-of-life conditions might be better represented by soda lakes with low phosphate concentrations. Thus, highly alkaline brine environments could be too extreme to support origin of life scenarios. These findings shed light on the complex interplay of microbial life in extreme environments and contribute to our understanding of early Earth environments.}, }
@article {pmid39608606, year = {2025}, author = {Lee, JY and Jo, YH and Kim, TH and Lee, SE and Hong, ES and Kang, TS}, title = {Microbial and Sensory Characteristics of Traditional Watery Kimchi (Dongchimi) Fortified with Probiotics.}, journal = {Journal of food protection}, volume = {88}, number = {1}, pages = {100422}, doi = {10.1016/j.jfp.2024.100422}, pmid = {39608606}, issn = {1944-9097}, mesh = {*Probiotics ; *Food Microbiology ; *Fermentation ; *Fermented Foods/microbiology ; Humans ; }, abstract = {Dongchimi, a traditional Korean watery kimchi, relies on complex interactions among diverse lactic acid bacteria (LAB) to maintain its freshness and quality. Recently, dongchimi has gained attention as a health-promoting food due to its content of probiotics and prebiotics. In this study, six probiotic strains were employed into dongchimi fermentation, and its sensory and microbial characteristics were evaluated. The LAB-enriched dongchimi demonstrated improved sensory preference (63%) and significantly higher LAB counts (average 5.2 × 10[7] CFU/ml) compared to traditional dongchimi. Furthermore, microbial diversity between the LAB-enriched and traditional dongchimi was analyzed during the fermentation process using both culture-dependent Sanger sequencing and culture-independent metabarcoding techniques, employing 16S ribosomal RNA gene sequences. Lactiplantibacillus plantarum was identified as the dominant probiotic strain in both types of dongchimi, while other probiotics, including Bifidobacterium bifidum, B. animalis, Limosilactobacillus fermentum, and Heyndrickxia coagulans, were exclusively detected in the LAB-enriched dongchimi. In conclusion, Lactiplanti. plantarum and Limosi. fermentum were identified as the most effective probiotics for dongchimi fermentation. These results offer critical insights into the microbial ecology and probiotic strains essential for optimizing synbiotic dongchimi, thereby reinforcing health claims related to probiotics and prebiotics.}, }
@article {pmid39605469, year = {2024}, author = {Woodruff, GC and Moser, KA and Wang, J}, title = {The Bacteria of a Fig Microcommunity.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.11.22.624729}, pmid = {39605469}, issn = {2692-8205}, abstract = {UNLABELLED: Understanding the biotic drivers of diversity is a major goal of microbial ecology. One approach towards tackling this issue is to interrogate relatively simple communities that are easy to observe and perturb. Figs (syconia) of the genus Ficus represent such a system. Here, we describe the microbial communities of Ficus septica figs, which are associated with the nematode Caenorhabditis inopinata (the sister species of the C. elegans genetic model system). In 2019, 38 Ficus septica figs (across 12 plants in Taiwan) were dissected, and metadata such as foundress wasp number and nematode occupancy were collected for each fig. Suspensions derived from interior fig material and fig surface washes were prepared for 16S microbial metabarcoding. Over 3,000 OTUs were detected, and microbial communities were dominated by members of Proteobacteria , Bacteroidota , and Actinobacteriota . Although microbial communities of fig exteriors and interiors can be distinguished, levels of microbial alpha diversity were comparable across these areas of the fig. Nematodes likewise had no detectable impact on microbial alpha diversity, although nematodes were associated with a modest change in microbial community composition. A handful of OTUs (associated with the genera Kosokonia , Ochobactrum , and Stenotrophomonas) revealed potential differential abundance among figs varying in nematode occupancy. Additionally, foundress wasp number was negatively correlated with microbial alpha diversity. These findings set the stage for future studies that directly test the role of nematode and wasp occupancy on microbial communities, as well as investigations that probe nematode-microbe interactions through laboratory experiments. Taken together, these results constitute a fundamental step in characterizing the natural microbial communities of figs and Caenorhabditis nematodes.<br><br>IMPORTANCE: Unraveling why different species live in different places is a longstanding open question in ecology, and it is clear that interspecific interactions among species are a major contributor to species distributions. Ficus figs are a useful system for ecological studies because they are relatively simple microcosms where characterizing animal community composition of multiple samples is straightforward. Additionally, Caenorhabditis inopinata , a close relative of the C. elegans genetic model system, thrives in Ficus septica figs. Here, we tie 16S microbial metabarcoding to nematode and wasp occupancy data to understand the causes of bacterial community composition in F. septica figs. We found that microbial composition, but not total diversity, varies among fig surface and interiors. Likewise, we found that nematode occupancy impacts microbial composition but not alpha diversity. Moreover, we show that as the number of foundress wasps increases, the microbial alpha diversity decreases. Finally, we identified OTUs that are potentially associated with nematode occupancy. Taken together, these results represent a key step in describing a microcommunity wherein ecological genetic hypotheses can be tested, as well as one that can potentially reveal the roles of uncharacterized genes in established model systems.}, }
@article {pmid39605409, year = {2024}, author = {Alexander, AM and Loo, HQ and Askew, L and Raghuram, V and Read, TD and Goldberg, JB}, title = {Intraspecific Diversity of Staphylococcus aureus Populations Isolated from Cystic Fibrosis Respiratory Infections.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39605409}, issn = {2692-8205}, support = {R21 AI148847/AI/NIAID NIH HHS/United States ; T32 AI138952/AI/NIAID NIH HHS/United States ; }, abstract = {Chronic bacterial infections are often polymicrobial, comprising multiple bacterial species or variants of the same species. Because chronic infections may last for decades, they have the potential to generate high levels of intraspecific variation through within-host diversification over time, and the potential for superinfections to occur through the introduction of multiple pathogen populations to the ongoing infection. Traditional methods for identifying infective agents generally involve isolating one single colony from a given sample, usually after selecting for a specific pathogen or antibiotic resistance profile. Isolating a recognized virulent or difficult to treat pathogen is an important part of informing clinical treatment and correlative research; however, these reductive methods alone, do not provide researchers or healthcare providers with the potentially important perspective on the true pathogen population structure and dynamics over time. To begin to address this limitation, in this study, we compare findings on Staphylococcus aureus single colonies versus and pools of colonies taken from fresh sputum samples from three patients with cystic fibrosis to isolates collected from the same sputum samples and processed by the clinical microbiology laboratory. Phenotypic and genotypic analysis of isolated S. aureus populations revealed coexisting lineages in two of three sputum samples as well as population structures that were not reflected in the single colony isolates. Altogether, our observations presented here demonstrate that clinically relevant diversity can be missed with standard sampling methods when assessing chronic infections. More broadly, this work outlines the potential impact that comprehensive population-level sampling may have for both research efforts and more effective treatment practices.}, }
@article {pmid39604741, year = {2024}, author = {de Freitas, AS and Carlos, FS and Martins, GL and Monteiro, GGTN and Roesch, LFW}, title = {Bacterial Resilience and Community Shifts Under 11 Draining-Flooding Cycles in Rice Soils.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {149}, pmid = {39604741}, issn = {1432-184X}, mesh = {*Oryza/microbiology ; *Soil Microbiology ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Floods ; *Soil/chemistry ; Brazil ; Microbiota ; RNA, Ribosomal, 16S/genetics ; Hydrogen-Ion Concentration ; Ecosystem ; }, abstract = {Flooded rice cultivation, accounting for 75% of global rice production, significantly influences soil redox potential, element speciation, pH, and nutrient availability, presenting challenges such as extensive water usage and altered soil properties. This study investigates bacterial community dynamics in rice soils subjected to repeated draining and flooding in Rio Grande do Sul, Brazil. We demonstrate that bacterial communities exhibit remarkable resilience (the capacity to recover after being altered by a disturbance) but cannot remain stable after long-term exposure to environmental changes. The beta diversity analysis revealed four distinct community states after 11 draining/flooding cycles, indicating resilience over successive environment changes. However, the consistent environmental disturbance reduced microbial resilience, causing the bacterial community structure to shift over time. Those differences were driven by substitutions of taxa and functions and not by the loss of diversity. Notable shifts included a decline in Acidobacteria and an increase in Proteobacteria and Chloroflexi. Increased Verrucomicrobia abundance corresponded with lower pH levels. Functional predictions suggested dynamic metabolic responses, with increased nitrification during drained cycles and a surge in fermenters after the sixth cycle. Despite cyclic disturbances, bacterial communities exhibit resilience, contributing to stable ecosystem functioning in flooded rice soils. These findings enhance our understanding of microbial adaptation, providing insights into sustainable rice cultivation and soil management practices.}, }
@article {pmid39603473, year = {2025}, author = {Li, Y and Tao, C and Li, S and Chen, W and Fu, D and Jafvert, CT and Zhu, T}, title = {Feasibility study of machine learning to explore relationships between antimicrobial resistance and microbial community structure in global wastewater treatment plant sludges.}, journal = {Bioresource technology}, volume = {417}, number = {}, pages = {131878}, doi = {10.1016/j.biortech.2024.131878}, pmid = {39603473}, issn = {1873-2976}, mesh = {*Machine Learning ; *Sewage/microbiology ; *Wastewater/microbiology ; Water Purification/methods ; Feasibility Studies ; Bacteria/drug effects/genetics ; Drug Resistance, Microbial/genetics ; Microbiota/drug effects ; China ; Drug Resistance, Bacterial/genetics ; }, abstract = {Wastewater sludges (WSs) are major reservoirs and emission sources of antibiotic resistance genes (ARGs) in cities. Identifying antimicrobial resistance (AMR) host bacteria in WSs is crucial for understanding AMR formation and mitigating biological and ecological risks. Here 24 sludge data from wastewater treatment plants in Jiangsu Province, China, and 1559 sludge data from genetic databases were analyzed to explore the relationship between 7 AMRs and bacterial distribution. The results of the Procrustes and Spearman correlation analysis were unsatisfactory, with p-value exceeding the threshold of 0.05 and no strong correlation (r > 0.8). In contrast, explainable machine learning (EML) using SHapley Additive exPlanation (SHAP) revealed Pseudomonadota as a major contributor (39.3 %-74.2 %) to sludge AMR. Overall, the application of ML is promising in analyzing AMR-bacteria relationships. Given the different applicable occasions and advantages of various analysis methods, using ML as one of the correlation analysis tools is strongly recommended.}, }
@article {pmid39601575, year = {2025}, author = {Maguire, M and Serna, C and Montero Serra, N and Kovarova, A and O'Connor, L and Cahill, N and Hooban, B and DeLappe, N and Brennan, W and Devane, G and Cormican, M and Morris, D and Coughlan, SC and Miliotis, G and Gonzalez-Zorn, B and Burke, LP}, title = {Spatiotemporal and genomic analysis of carbapenem resistance elements in Enterobacterales from hospital inpatients and natural water ecosystems of an Irish city.}, journal = {Microbiology spectrum}, volume = {13}, number = {1}, pages = {e0090424}, pmid = {39601575}, issn = {2165-0497}, support = {773830//EC | Horizon 2020 Framework Programme (H2020)/ ; 18/CRT/6214//Science Foundation Ireland (SFI)/ ; 2017-HW-LS-1//Environmental Protection Agency (EPA)/ ; 2017-HW-LS-1//Health Service Executive (HSE)/ ; }, mesh = {Humans ; *beta-Lactamases/genetics ; Ireland ; *Plasmids/genetics ; *Bacterial Proteins/genetics ; *Carbapenems/pharmacology ; Anti-Bacterial Agents/pharmacology ; Enterobacteriaceae/genetics/drug effects/isolation &amp; purification ; Inpatients ; Enterobacteriaceae Infections/microbiology/epidemiology ; Whole Genome Sequencing ; Wastewater/microbiology ; Genomics ; Ecosystem ; Klebsiella pneumoniae/genetics/drug effects/isolation &amp; purification ; Microbial Sensitivity Tests ; Genome, Bacterial ; Carbapenem-Resistant Enterobacteriaceae/genetics/isolation &amp; purification/drug effects ; Cities ; Spatio-Temporal Analysis ; }, abstract = {Carbapenemase-producing Enterobacterales (CPE) is a diverse group of often multidrug-resistant organisms. Surveillance and control of infections are complicated due to the inter-species spread of carbapenemase-encoding genes (CEGs) on mobile genetic elements (MGEs), including plasmids and transposons. Due to wastewater discharges, urban water ecosystems represent a known reservoir of CPE. However, the dynamics of carbapenemase-bearing MGE dissemination between Enterobacterales in humans and environmental waters are poorly understood. We carried out whole-genome sequencing, combining short- and long-sequencing reads to enable complete characterization of CPE isolated from patients, wastewaters, and natural waters between 2018 and 2020 in Galway, Ireland. Isolates were selected based on their carriage of Class A blaKPC-2 (n = 6), Class B blaNDM-5 (n = 12), and Class D blaOXA-48 (n = 21) CEGs. CEGs were plasmid-borne in all but two isolates. OXA-48 dissemination was associated with a 64 kb IncL plasmid (62%), in a broad range of Enterobacterales isolates from both niches. Conversely, blaKPC-2 and blaNDM-5 genes were usually carried on larger and more variable multireplicon IncF plasmids in Klebsiella pneumoniae and Escherichia coli, respectively. In every isolate, each CEG was surrounded by a gene-specific common genetic environment which constituted part, or all, of a transposable element that was present in both plasmids and the bacterial chromosome. Transposons Tn1999 and Tn4401 were associated with blaOXA-48 and blaKPC-2, respectively, while blaNDM-5 was associated with variable IS26 bound composite transposons, usually containing a class 1 integron.IMPORTANCESince 2018, the Irish National Carbapenemase-Producing Enterobacterales (CPE) Reference Laboratory Service at University Hospital Galway has performed whole-genome sequencing on suspected and confirmed CPE from clinical specimens as well as patient and environmental screening isolates. Understanding the dynamics of CPE and carbapenemase-encoding gene encoding mobile genetic element (MGE) flux between human and environmental reservoirs is important for One Health surveillance of these priority organisms. We employed hybrid assembly approaches for improved resolution of CPE genomic surveillance, typing, and plasmid characterization. We analyzed a diverse collection of human (n = 17) and environmental isolates (n = 22) and found common MGE across multiple species and in different ecological niches. The conjugation ability and frequency of a subset of these plasmids were demonstrated to be affected by the presence or absence of necessary conjugation genes and by plasmid size. We characterize several MGE at play in the local dissemination of carbapenemase genes. This may facilitate their future detection in the clinical laboratory.}, }
@article {pmid39601521, year = {2025}, author = {Atkinson, CGF and Kerns, KA and Hendrickson, EL and He, X and Bor, B and McLean, JS}, title = {Complete genome of Nanosynbacter sp. strain BB002, isolated and cultivated from a site of periodontal disease.}, journal = {Microbiology resource announcements}, volume = {14}, number = {1}, pages = {e0063724}, pmid = {39601521}, issn = {2576-098X}, support = {R01 DE023810/DE/NIDCR NIH HHS/United States ; R01 DE031470/DE/NIDCR NIH HHS/United States ; R01 DE031274/DE/NIDCR NIH HHS/United States ; T90 DE021984/DE/NIDCR NIH HHS/United States ; T90DE021984, R01DE031470, R01DE023810, R01DE031274//HHS | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; }, abstract = {Nanosynbacter sp. strain BB002, was isolated from the human oral cavity on its basibiont bacterial host Actinomyces sp. oral taxon 171 strain F0337, related to Actinomyces oris. As a member of the Saccharibacteria within the candidate phylum radiation group (CPR), its reduced genome facilitates the survival as an ultrasmall (<0.2 μm) epibiont.}, }
@article {pmid39597739, year = {2024}, author = {Sun, X and Liu, Y and He, L and Kuang, Z and Dai, S and Hua, L and Jiang, Q and Wei, T and Ye, P and Zeng, H}, title = {Response of Yields, Soil Physiochemical Characteristics, and the Rhizosphere Microbiome to the Occurrence of Root Rot Caused by Fusarium solani in Ligusticum chuanxiong Hort.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, pmid = {39597739}, issn = {2076-2607}, support = {2023NSFSC1262//the Natural Science Foundation of Sichuan Province of China/ ; SCCXTD-2024-19//Sichuan Innovation Team of the Chinese National Modern Agriculture Industry Technology System/ ; CARS-21-21//National Chinese Medicinal Materials Technology System/ ; 2022ZZCX078//Sichuan Provincial Finance Independent Innovation Project/ ; }, abstract = {Ligusticum chuanxiong Hort. is considered an important medicinal herb with extremely high economic value and medicinal value due to its various effects, including anti-oxidation, sedative action, hepatoprotection, and invigorating blood circulation. However, L. chuanxiong cultivation is hampered by various plant diseases, especially the root rot caused by Fusarium solani, hindering the sustainable development of the L. chuanxiong industry. The occurrence of soil-borne diseases is closely linked to imbalances in the microbial community structure. Here, we studied the yields, rhizosphere microbiota, and soil physiochemical characteristics of healthy and diseased L. chuanxiong plants affected by root rot with high-throughput sequencing and microbial network analysis, aiming to explore the relationships between soil environmental factors, microbiomes, and plant health of L. chuanxiong. According to the results, L. chuanxiong root rot significantly decreased the yields, altered microbial community diversity and composition, enriched more pathogenic fungi, recruited some beneficial bacteria, and reduced microbial interaction network stability. The Mantel test showed that soil organic matter and pH were the major environmental factors modulating plant microbiome assembly. The root rot severity was significantly affected by soil physiochemical properties, including organic matter, cation exchange capacity, available nitrogen, phosphorus, potassium, and pH. Furthermore, two differential microbes that have great potential in the biocontrol of L. chuanxiong root rot were dug out in the obtained results, which were the genera Trichoderma and Bacillus. This study provided a theoretical basis for further studies revealing the microecological mechanism of L. chuanxiong root rot and the ecological prevention and control of L. chuanxiong root rot from a microbial ecology perspective.}, }
@article {pmid39597685, year = {2024}, author = {Zhang, K and Chen, X and Shi, X and Yang, Z and Yang, L and Liu, D and Yu, F}, title = {Endophytic Bacterial Community, Core Taxa, and Functional Variations Within the Fruiting Bodies of Laccaria.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, pmid = {39597685}, issn = {2076-2607}, support = {202205AD160036//the Yunnan Technology Innovation/ ; 42077072//the National Natural Science Foundation of Management Practices China/ ; }, abstract = {Macrofungi do not exist in isolation but establish symbiotic relationships with microorganisms, particularly bacteria, within their fruiting bodies. Herein, we examined the fruiting bodies' bacteriome of seven species of the genus Laccaria collected from four locations in Yunnan, China. By analyzing bacterial diversity, community structure, and function through 16S rRNA sequencing, we observed the following: (1) In total, 4,840,291 high-quality bacterial sequences obtained from the fruiting bodies were grouped into 16,577 amplicon sequence variants (ASVs), and all samples comprised 23 shared bacterial ASVs. (2) The Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium complex was found to be the most abundant and presumably coexisting bacterium. (3) A network analysis revealed that endophytic bacteria formed functional groups, which were dominated by the genera Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Novosphingobium, and Variovorax. (4) The diversity, community structure, and dominance of ecological functions (chemoheterotrophy and nitrogen cycling) among endophytic bacteria were significantly shaped by geographic location, habitat, and fungal genotype, rather than fruiting body type. (5) A large number of the endophytic bacteria within Laccaria are bacteria that promote plant growth; however, some pathogenic bacteria that pose a threat to human health might also be present. This research advances our understanding of the microbial ecology of Laccaria and the factors shaping its endophytic bacterial communities.}, }
@article {pmid39597671, year = {2024}, author = {Skliros, D and Kostakou, M and Kokkari, C and Tsertou, MI and Pavloudi, C and Zafeiropoulos, H and Katharios, P and Flemetakis, E}, title = {Unveiling Emerging Opportunistic Fish Pathogens in Aquaculture: A Comprehensive Seasonal Study of Microbial Composition in Mediterranean Fish Hatcheries.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, pmid = {39597671}, issn = {2076-2607}, support = {5010932//Operational Program Fisheries and Maritime 2014-2020/ ; }, abstract = {The importance of microbial communities in fish hatcheries for fish health and welfare has been recognized, with several studies mapping these communities during healthy rearing conditions and disease outbreaks. In this study, we analyzed the bacteriome of the live feeds, such as microalgae, rotifers, and Artemia, used in fish hatcheries that produce Mediterranean species. Our goal was to provide baseline information about their structure, emphasizing in environmental putative fish pathogenic bacteria. We conducted 16S rRNA amplicon Novaseq sequencing for our analysis, and we inferred 46,745 taxonomically annotated ASVs. Results showed that incoming environmental water plays a significant role in the presence of important taxa that constitute presumptive pathogens. Bio-statistical analyses revealed a relatively stable bacteriome among seasonal samplings for every hatchery but a diverse bacteriome between sampling stations and a distinct core bacteriome for each hatchery. Analysis of putative opportunistic fish pathogenic genera revealed some co-occurrence correlation events and a high average relative abundance of Vibrio, Tenacibaculum, and Photobacterium genera in live feeds, reaching a grand mean average of up to 7.3% for the hatchery of the Hellenic Center of Marine Research (HCMR), 12% for Hatchery A, and 11.5% for Hatchery B. Mapping the bacteriome in live feeds is pivotal for understanding the marine environment and distinct aquaculture practices and can guide improvements in hatchery management, enhancing fish health and sustainability in the Mediterranean region.}, }
@article {pmid39597543, year = {2024}, author = {Wu, D and He, X and Lu, Y and Gao, Z and Chong, Y and Hong, J and Wu, J and Deng, W and Xi, D}, title = {Effects of Different Dietary Combinations on Blood Biochemical Indicators and Rumen Microbial Ecology in Wenshan Cattle.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, pmid = {39597543}, issn = {2076-2607}, abstract = {With the continuous optimization of feed ingredients in livestock production, barley has garnered significant attention as a potential substitute for corn in feed. This study aims to investigate the effects of replacing part of the corn and soybean meal with barley, wheat bran, and rapeseed meal on Wenshan cattle, focusing on the rumen microbial community, blood physiological and biochemical indicators, and growth traits. Through an intensive feeding experiment with two different dietary ratios, we found that adding barley to the diet significantly reduced the host's blood lipid concentration and significantly increased the height, body length, heart girth, and average daily weight gain of Wenshan cattle. Analysis of the rumen microbial community structure showed that the addition of barley significantly affected the relative abundance of Firmicutes, Proteobacteria, and Bacteroidetes, with the relative abundance of Spirochaetes being significantly lower than that of the control group (p < 0.05). The dominant bacterial groups mainly included Acinetobacter, Solibacillus, and Lysinibacillus. In summary, this study reveals the potential of different feed ingredient ratios involving barley, wheat bran, and rapeseed meal in the production performance of Wenshan cattle. By regulating blood physiology and improving the rumen micro-ecological structure, it provides new scientific evidence for optimizing livestock and poultry feeding management strategies. Future research will further explore the optimal application ratio of barley under different feeding conditions and its long-term impact on animal health and production performance.}, }
@article {pmid39597512, year = {2024}, author = {Banerji, A and Brinkman, NE and Davis, B and Franklin, A and Jahne, M and Keely, SP}, title = {Food Webs and Feedbacks: The Untold Ecological Relevance of Antimicrobial Resistance as Seen in Harmful Algal Blooms.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, pmid = {39597512}, issn = {2076-2607}, abstract = {Antimicrobial resistance (AMR) has long been framed as an epidemiological and public health concern. Its impacts on the environment are unclear. Yet, the basis for AMR is altered cell physiology. Just as this affects how microbes interact with antimicrobials, it can also affect how they interact with their own species, other species, and their non-living environment. Moreover, if the microbes are globally notorious for causing landscape-level environmental issues, then these effects could alter biodiversity and ecosystem function on a grand scale. To investigate these possibilities, we compiled peer-reviewed literature from the past 20 years regarding AMR in toxic freshwater cyanobacterial harmful algal blooms (HABs). We examined it for evidence of AMR affecting HAB frequency, severity, or persistence. Although no study within our scope was explicitly designed to address the question, multiple studies reported AMR-associated changes in HAB-forming cyanobacteria (and co-occurring microbes) that pertained directly to HAB timing, toxicity, and phase, as well as to the dynamics of HAB-afflicted aquatic food webs. These findings highlight the potential for AMR to have far-reaching environmental impacts (including the loss of biodiversity and ecosystem function) and bring into focus the importance of confronting complex interrelated issues such as AMR and HABs in concert, with interdisciplinary tools and perspectives.}, }
@article {pmid39596705, year = {2024}, author = {Moraes, BDGC and Martins, RCR and Fonseca, JVDS and Franco, LAM and Pereira, GCO and Bartelli, TF and Cortes, MF and Scaccia, N and Santos, CF and Musqueira, PT and Otuyama, LJ and Pylro, VS and Mariano, L and Rocha, V and Witkin, SS and Sabino, E and Guimaraes, T and Costa, SF}, title = {Impact of Exogenous Lactiplantibacillus plantarum on the Gut Microbiome of Hematopoietic Stem Cell Transplantation Patients Colonized by Multidrug-Resistant Bacteria: An Observational Study.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {11}, pages = {}, pmid = {39596705}, issn = {2079-6382}, support = {FAPESP//001/ ; }, abstract = {Background:Lactiplantibacillus plantarum can inhibit the growth of multidrug-resistant organisms (MDROs) and modulate the gut microbiome. However, data on hematopoietic stem cell transplantation (HSCT) are scarce. Aim: In an observational study, we assessed the impact of L. plantarum on the modulation of the gut microbiome in HSCT patients colonized by MDROs. Methods: Participants were allocated to an intervention group (IG = 22) who received capsules of L. plantarum (5 × 10[9] CFU) twice per day until the onset of neutropenia or a control group (CG = 20). The V4 region of the 16S bacterial rRNA gene was sequenced in 87 stool samples from a subset of 33 patients (IG = 20 and CG = 13). The Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) program was used to predict metagenome functions. Results:L. plantarum demonstrated an average 86% (±11%) drug-target engagement at 43 (±29) days of consumption and was deemed safe, well-tolerated, and associated with an increase in the abundance of the Lactobacillales (p < 0.05). A significant increase in Lactococcus and a reduction in Turicibacter (p < 0.05) were identified on the second week of L. plantarum use. Although Enterococcus abundance had a greater rise in the CG (p = 0.07), there were no significant differences concerning the Gram-negative MDROs. No serious adverse effects were reported in the IG. We observed a greater, non-significant pyruvate fermentation to propanoate I (p = 0.193) relative abundance in the IG compared with the CG. L. plantarum use was safe and tolerable by HSCT patients. Conclusions: While L. plantarum is safe and may impact Enterococcus and Turicibacter abundance, it showed no impact on Gram-negative MDRO abundance in HSCT patients.}, }
@article {pmid39592542, year = {2025}, author = {Kaur, T and Devi, R and Negi, R and Kour, H and Singh, S and Khan, SS and Kumari, C and Kour, D and Chowdhury, S and Kapoor, M and Rai, AK and Rustagi, S and Shreaz, S and Yadav, AN}, title = {Macronutrients-availing microbiomes: biodiversity, mechanisms, and biotechnological applications for agricultural sustainability.}, journal = {Folia microbiologica}, volume = {70}, number = {2}, pages = {293-319}, pmid = {39592542}, issn = {1874-9356}, mesh = {*Microbiota ; Phosphorus/metabolism ; Agriculture ; Soil Microbiology ; *Biodiversity ; Potassium/metabolism ; Nitrogen/metabolism ; *Biotechnology ; *Nutrients/metabolism ; *Bacteria/metabolism/genetics/classification ; Soil/chemistry ; Crops, Agricultural ; }, abstract = {Nitrogen, phosphorus, and potassium are the three most essential micronutrients which play major roles in plant survivability by being a structural or non-structural component of the cell. Plants acquire these nutrients from soil in the fixed (NO3[¯], NH4[+]) and solubilized forms (K[+], H2PO4[-] and HPO4[2-]). In soil, the fixed and solubilized forms of nutrients are unavailable or available in bare minimum amounts; therefore, agrochemicals were introduced. Agrochemicals, mined from the deposits or chemically prepared, have been widely used in the agricultural farms over the decades for the sake of higher production of the crops. The excessive use of agrochemicals has been found to be deleterious for humans, as well as the environment. In the environment, agrochemical usage resulted in soil acidification, disturbance of microbial ecology, and eutrophication of aquatic and terrestrial ecosystems. A solution to such devastating agro-input was found to be substituted by macronutrients-availing microbiomes. Macronutrients-availing microbiomes solubilize and fix the insoluble form of nutrients and convert them into soluble forms without causing any significant harm to the environment. Microbes convert the insoluble form to the soluble form of macronutrients (nitrogen, phosphorus, and potassium) through different mechanisms such as fixation, solubilization, and chelation. The microbiomes having capability of fixing and solubilizing nutrients contain some specific genes which have been reported in diverse microbial species surviving in different niches. In the present review, the biodiversity, mechanism of action, and genomics of different macronutrients-availing microbiomes are presented.}, }
@article {pmid39587684, year = {2025}, author = {DuBose, JG and Crook, TB and Matzkin, LM and Haselkorn, TS}, title = {The relative importance of host phylogeny and dietary convergence in shaping the bacterial communities hosted by several Sonoran Desert Drosophila species.}, journal = {Journal of evolutionary biology}, volume = {38}, number = {2}, pages = {180-189}, doi = {10.1093/jeb/voae143}, pmid = {39587684}, issn = {1420-9101}, support = {//University of Central Arkansas Southwest Energy Research Fellowship program/ ; }, mesh = {Animals ; *Drosophila/microbiology/genetics/classification/physiology ; *Phylogeny ; *Diet ; *Microbiota ; Symbiosis ; Desert Climate ; *Bacteria/classification ; }, abstract = {Complex eukaryotes vary greatly in the mode and extent that their evolutionary histories have been shaped by the microbial communities that they host. A general understanding of the evolutionary consequences of host-microbe symbioses requires that we understand the relative importance of host phylogenetic divergence and other ecological processes in shaping variation in host-associated microbial communities. To contribute to this understanding, we described the bacterial communities hosted by several Drosophila species native to the Sonoran Desert of North America. Our sampling consisted of four species that span multiple dietary shifts to cactophily, as well as the dietary generalist D. melanogaster, allowing us to partition the influences of host phylogeny and extant ecology. We found that bacterial communities were compositionally indistinguishable when considering incidence only but varied when considering the relative abundances of bacterial taxa. Variation in community composition was not explained by host phylogenetic divergence but could be partially explained by dietary variation. In support of the important role of diet as a source of ecological selection, we found that specialist cactophilic Drosophila deviated more from neutral predictions than dietary generalists. Overall, our findings provide insight into the evolutionary and ecological factors that shape host-associated microbial communities in a natural context.}, }
@article {pmid39587399, year = {2024}, author = {Trevathan-Tackett, SM and Kepfer-Rojas, S and Malerba, M and Macreadie, PI and Djukic, I and Zhao, J and Young, EB and York, PH and Yeh, SC and Xiong, Y and Winters, G and Whitlock, D and Weaver, CA and Watson, A and Visby, I and Tylkowski, J and Trethowan, A and Tiegs, S and Taylor, B and Szpikowski, J and Szpikowska, G and Strickland, VL and Stivrins, N and Sousa, AI and Sinutok, S and Scheffel, WA and Santos, R and Sanderman, J and Sánchez-Carrillo, S and Sanchez-Cabeza, JA and Rymer, KG and Ruiz-Fernandez, AC and Robroek, BJM and Roberts, T and Ricart, AM and Reynolds, LK and Rachlewicz, G and Prathep, A and Pinsonneault, AJ and Pendall, E and Payne, R and Ozola, I and Onufrock, C and Ola, A and Oberbauer, SF and Numbere, AO and Novak, AB and Norkko, J and Norkko, A and Mozdzer, TJ and Morgan, P and Montemayor, DI and Martin, CW and Malone, SL and Major, M and Majewski, M and Lundquist, CJ and Lovelock, CE and Liu, S and Lin, HJ and Lillebo, A and Li, J and Kominoski, JS and Khuroo, AA and Kelleway, JJ and Jinks, KI and Jerónimo, D and Janousek, C and Jackson, EL and Iribarne, O and Hanley, T and Hamid, M and Gupta, A and Guariento, RD and Grudzinska, I and da Rocha Gripp, A and González Sagrario, MA and Garrison, LM and Gagnon, K and Gacia, E and Fusi, M and Farrington, L and Farmer, J and de Assis Esteves, F and Escapa, M and Domańska, M and Dias, ATC and de Los Santos, CB and Daffonchio, D and Czyryca, PM and Connolly, RM and Cobb, A and Chudzińska, M and Christiaen, B and Chifflard, P and Castelar, S and Carneiro, LS and Cardoso-Mohedano, JG and Camden, M and Caliman, A and Bulmer, RH and Bowen, J and Boström, C and Bernal, S and Berges, JA and Benavides, JC and Barry, SC and Alatalo, JM and Al-Haj, AN and Adame, MF}, title = {Climate Effects on Belowground Tea Litter Decomposition Depend on Ecosystem and Organic Matter Types in Global Wetlands.}, journal = {Environmental science &amp; technology}, volume = {58}, number = {49}, pages = {21589-21603}, pmid = {39587399}, issn = {1520-5851}, mesh = {*Wetlands ; Tea ; Climate ; Ecosystem ; Carbon ; Temperature ; }, abstract = {Patchy global data on belowground litter decomposition dynamics limit our capacity to discern the drivers of carbon preservation and storage across inland and coastal wetlands. We performed a global, multiyear study in over 180 wetlands across 28 countries and 8 macroclimates using standardized litter as measures of "recalcitrant" (rooibos tea) and "labile" (green tea) organic matter (OM) decomposition. Freshwater wetlands and tidal marshes had the highest tea mass remaining, indicating a greater potential for carbon preservation in these ecosystems. Recalcitrant OM decomposition increased with elevated temperatures throughout the decay period, e.g., increase from 10 to 20 °C corresponded to a 1.46-fold increase in the recalcitrant OM decay rate constant. The effect of elevated temperature on labile OM breakdown was ecosystem-dependent, with tidally influenced wetlands showing limited effects of temperature compared with freshwater wetlands. Based on climatic projections, by 2050 wetland decay constants will increase by 1.8% for labile and 3.1% for recalcitrant OM. Our study highlights the potential for reduction in belowground OM in coastal and inland wetlands under increased warming, but the extent and direction of this effect at a large scale is dependent on ecosystem and OM characteristics. Understanding local versus global drivers is necessary to resolve ecosystem influences on carbon preservation in wetlands.}, }
@article {pmid39587087, year = {2024}, author = {Whalen, ED and Grandy, AS and Geyer, KM and Morrison, EW and Frey, SD}, title = {Microbial trait multifunctionality drives soil organic matter formation potential.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {10209}, pmid = {39587087}, issn = {2041-1723}, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Fungi/metabolism ; *Carbon/metabolism ; Biomass ; Organic Chemicals/metabolism ; }, abstract = {Soil microbes are a major source of organic residues that accumulate as soil organic matter, the largest terrestrial reservoir of carbon on Earth. As such, there is growing interest in determining the microbial traits that drive soil organic matter formation and stabilization; however, whether certain microbial traits consistently predict soil organic matter accumulation across different functional pools (e.g., total vs. stable soil organic matter) is unresolved. To address these uncertainties, we incubated individual species of fungi in soil organic matter-free model soils, allowing us to directly relate the physiological, morphological, and biochemical traits of fungi to their soil organic matter formation potentials. We find that the formation of different soil organic matter functional pools is associated with distinct fungal traits, and that 'multifunctional' species with intermediate investment across this key grouping of traits (namely, carbon use efficiency, growth rate, turnover rate, and biomass protein and phenol contents) promote soil organic matter formation, functional complexity, and stability. Our results highlight the limitations of categorical trait-based frameworks that describe binary trade-offs between microbial traits, instead emphasizing the importance of synergies among microbial traits for the formation of functionally complex soil organic matter.}, }
@article {pmid39586934, year = {2024}, author = {Rong, X and Liu, X and Du, F and Aanderud, ZT and Zhang, Y}, title = {Biocrusts Mediate the Niche Distribution and Diversity of Ammonia-Oxidizing Microorganisms in the Gurbantunggut Desert, Northwestern China.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {148}, pmid = {39586934}, issn = {1432-184X}, support = {2022TSYCCX0007//the Xinjiang Tianshan Youth Talent Top Project/ ; 2022D01D083//the Key Fund Projects of the Natural Science Foundation of Xinjiang/ ; U2003214//the National Natural Science Foundation of China/ ; }, mesh = {*Archaea/genetics/metabolism/classification ; *Desert Climate ; *Ammonia/metabolism ; *Soil Microbiology ; China ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; *Oxidation-Reduction ; Soil/chemistry ; Biodiversity ; Ecosystem ; Seasons ; Microbiota ; Nitrification ; }, abstract = {Biological soil crusts (biocrusts) play pivotal ecological roles in regulating nitrogen cycling within desert ecosystems. While acknowledging the essential role played by ammonia-oxidizing microorganisms in nitrogen transformation, there remains a paucity of understanding concerning how disturbances to biocrusts impact the diversity and spatial distribution patterns among ammonia oxidizer communities within temperate deserts. This investigation delved into assessing how 4 years' worth of removing biocrust influenced niche differentiation between nitrifying archaea and bacteria while also examining its effects on shaping community structures of predominant ammonia-oxidizing archaea (AOA) within the Gurbantunggut Desert soils. Despite notable variations in abundance of ammonia-oxidizing microbes across distinct soil depths throughout different seasons, it became apparent that removing biocrust significantly altered both the abundance and niche pattern for AOA alongside their bacterial counterparts during winter and summer periods. Notably dominating over their bacterial counterparts within desert soils, AOA displayed their highest archaeal to bacterial amoA gene copy ratio (6549-fold higher) at a soil depth of 5-10 cm during summer. Moreover, substantial impacts were observed upon AOA diversity along with compositional changes following such perturbation events. The aftermath saw an emergence of more diffuse yet dynamic AOA communities, especially noticeable amidst winter when nitrogen and water limitations were relatively alleviated. In summary, our findings underscore how interactions between biocrust coverages alongside factors like soil temperature, total carbon content, or NO3[-]_N concentrations govern niches occupied by ammoxidation communities whilst influencing assemblage processes too. The sensitivity shown by dominant AOAs towards biocrust removal further underscores how biocrust coverage influences nitrogen transformation processes while potentially involving other communities and functions in desert ecosystems.}, }
@article {pmid39585925, year = {2024}, author = {Richards, TA and Eme, L and Archibald, JM and Leonard, G and Coelho, SM and de Mendoza, A and Dessimoz, C and Dolezal, P and Fritz-Laylin, LK and Gabaldón, T and Hampl, V and Kops, GJPL and Leger, MM and Lopez-Garcia, P and McInerney, JO and Moreira, D and Muñoz-Gómez, SA and Richter, DJ and Ruiz-Trillo, I and Santoro, AE and Sebé-Pedrós, A and Snel, B and Stairs, CW and Tromer, EC and van Hooff, JJE and Wickstead, B and Williams, TA and Roger, AJ and Dacks, JB and Wideman, JG}, title = {Reconstructing the last common ancestor of all eukaryotes.}, journal = {PLoS biology}, volume = {22}, number = {11}, pages = {e3002917}, pmid = {39585925}, issn = {1545-7885}, support = {R35 GM143039/GM/NIGMS NIH HHS/United States ; }, mesh = {*Eukaryota/genetics ; *Phylogeny ; Eukaryotic Cells/metabolism ; Evolution, Molecular ; Genomics/methods ; Biological Evolution ; }, abstract = {Understanding the origin of eukaryotic cells is one of the most difficult problems in all of biology. A key challenge relevant to the question of eukaryogenesis is reconstructing the gene repertoire of the last eukaryotic common ancestor (LECA). As data sets grow, sketching an accurate genomics-informed picture of early eukaryotic cellular complexity requires provision of analytical resources and a commitment to data sharing. Here, we summarise progress towards understanding the biology of LECA and outline a community approach to inferring its wider gene repertoire. Once assembled, a robust LECA gene set will be a useful tool for evaluating alternative hypotheses about the origin of eukaryotes and understanding the evolution of traits in all descendant lineages, with relevance in diverse fields such as cell biology, microbial ecology, biotechnology, agriculture, and medicine. In this Consensus View, we put forth the status quo and an agreed path forward to reconstruct LECA's gene content.}, }
@article {pmid39583547, year = {2024}, author = {Yang, X and Gänzle, M and Wang, R}, title = {Editorial: How the application of antimicrobial hurdles in meat processing facilities shapes microbial ecology.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1501925}, pmid = {39583547}, issn = {1664-302X}, }
@article {pmid39578630, year = {2024}, author = {Barber, DG and Child, HT and Joslin, GR and Wierzbicki, L and Tennant, RK}, title = {Statistical design approach enables optimised mechanical lysis for enhanced long-read soil metagenomics.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {28934}, pmid = {39578630}, issn = {2045-2322}, support = {CW648947-PT34767//Shell Research Ltd/ ; CW648947-PT34767//Shell Research Ltd/ ; CW648947-PT34767//Shell Research Ltd/ ; CW648947-PT34767//Shell Research Ltd/ ; CW648947-PT34767//Shell Research Ltd/ ; }, mesh = {*Metagenomics/methods ; *Soil Microbiology ; Soil/chemistry ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; }, abstract = {Metagenomic analysis has enabled insights into soil community structure and dynamics. Long-read sequencing for metagenomics can enhance microbial ecology by improving taxonomic classification, genome assembly, and functional annotation. However, protocols for purifying high-molecular weight DNA from soil are not yet optimised. We used a statistical design of experiments approach to enhance mechanical lysis of soil samples, increasing the length of purified DNA fragments. Low energy input into mechanical lysis improved DNA integrity, resulting in longer sequenced reads. Our optimized settings of 4 m s[-1] for 10 s increased fragment length by 70% compared to the manufacturer's recommendations. Longer reads from low intensity lysis produced longer contiguous sequences after assembly, potentially improving a range of down-stream analyses. Importantly, there was minimal bias exhibited in the microbial community composition due to lysis efficiency variations. We therefore propose a framework for improving the fragment lengths of DNA purified from diverse soil types, improving soil science research with long-read sequencing.}, }
@article {pmid39572704, year = {2024}, author = {Li, J and Göbel, F and Hsu, HY and Koch, JN and Hager, N and Flegler, WA and Tanabe, TS and Dahl, C}, title = {YeeE-like bacterial SoxT proteins mediate sulfur import for oxidation and signal transduction.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {1548}, pmid = {39572704}, issn = {2399-3642}, support = {Da 351/8-2//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Da 351/13-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Da 351/14-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {*Sulfur/metabolism ; *Oxidation-Reduction ; *Signal Transduction ; *Bacterial Proteins/metabolism/genetics ; *Gene Expression Regulation, Bacterial ; Biological Transport ; }, abstract = {Many sulfur-oxidizing prokaryotes oxidize sulfur compounds through a combination of initial extracytoplasmic and downstream cytoplasmic reactions. Facultative sulfur oxidizers adjust transcription to sulfur availability. While sulfur-oxidizing enzymes and transcriptional repressors have been extensively studied, sulfur import into the cytoplasm and how regulators sense external sulfur are poorly understood. Addressing this gap, we show that SoxT1A and SoxT1B, which resemble YeeE/YedE-family thiosulfate transporters and are encoded alongside sulfur oxidation and transcriptional regulation genes, fulfill these roles in the Alphaproteobacterium Hyphomicrobium denitrificans. SoxT1A mutants are sulfur oxidation-negative despite high transcription levels of sulfur oxidation genes, showing that SoxT1A delivers sulfur to the cytoplasm for its further oxidation. SoxT1B serves as a signal transduction unit for the transcriptional repressor SoxR, as SoxT1B mutants are sulfur oxidation-negative due to low transcription unless SoxR is also absent. Thus, SoxT1A and SoxT1B play essential but distinct roles in oxidative sulfur metabolism and its regulation.}, }
@article {pmid39572621, year = {2024}, author = {Rabenhorst, SHB and Ferrasi, AC and Barboza, MMO and Melo, VMM}, title = {Microbial composition of gastric lesions: differences based on Helicobacter pylori virulence profile.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {28890}, pmid = {39572621}, issn = {2045-2322}, support = {07939716/2020//Funda&#xe7;&#xe3;o Cearense de Apoio ao Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {Humans ; *Helicobacter pylori/pathogenicity/genetics ; *Helicobacter Infections/microbiology/pathology ; *Stomach Neoplasms/microbiology/pathology ; *Gastritis/microbiology/pathology ; Virulence ; *Gastric Mucosa/microbiology/pathology ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Aged ; Metaplasia/microbiology ; Adult ; Gastrointestinal Microbiome ; }, abstract = {Helicobacter pylori infection is a major risk factor for gastric adenocarcinomas. In the case of the intestinal subtype, chronic gastritis and intestinal metaplasia are well-known sequential steps in carcinogenesis. H. pylori has high genetic diversity that can modulate virulence and pathogenicity in the human host as a cag Pathogenicity Island (cagPAI). However, bacterial gene combinations do not always explain the clinical presentation of the disease, indicating that other factors associated with H. pylori may play a role in the development of gastric disease. In this context, we characterized the microbial composition of patients with chronic gastritis (inactive and active), intestinal metaplasia, and gastric cancer as well as their potential association with H. pylori. To this end, 16 S rRNA metagenomic analysis was performed on gastric mucosa samples from patients with different types of lesions and normal gastric tissues. Our main finding was that H. pylori virulence status can contribute to significant differences in the constitution of the gastric microbiota between the sequential steps of the carcinogenesis cascade. Differential microbiota was observed in inactive and active gastritis dependent of the H. pylori presence and status (p = 0.000575). Pseudomonades, the most abundant order in the gastritis, was associated the presence of non-virulent H. pylori in the active gastritis. Notably, there are indicator genera according to H. pylori status that are poorly associated with diseases and provide additional evidence that the microbiota, in addition to H. pylori, is relevant to gastric carcinogenesis.}, }
@article {pmid39572453, year = {2024}, author = {Méndez, A and Sanmartín, P and Balboa, S and Trueba-Santiso, A}, title = {Environmental Proteomics Elucidates Phototrophic Biofilm Responses to Ornamental Lighting on Stone-built Heritage.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {147}, pmid = {39572453}, issn = {1432-184X}, support = {04_IN606D_2021_2598528//Programa de Doutoramento Industrial - Xunta de Galicia/ ; ED431F 2022/14//FONTES project - Xunta de Galicia/ ; ED431F 2022/14//FONTES project - Xunta de Galicia/ ; ED431C 2022/09//Competitive Reference Group (GRC) grant - GEMAP/ ; ED431C 2022/09//Competitive Reference Group (GRC) grant - GEMAP/ ; RYC2020-029987-I//Ram&#xf3;n y Cajal contract - Spanish State Research Agency (AEI)/ ; ED431C-2021/37//Competitive Reference Group (GRC) - Biogroup/ ; ED431C-2021/37//Competitive Reference Group (GRC) - Biogroup/ ; }, mesh = {*Biofilms/radiation effects/growth &amp; development ; *Proteomics ; Light ; Phototrophic Processes ; Cyanobacteria/metabolism/radiation effects/physiology ; Chlorophyta/radiation effects/metabolism/physiology ; Proteome ; Lighting ; }, abstract = {Recent studies are showing that some lights suitable for illuminating the urban fabric (i.e. that do not include the red, green and blue sets of primary colours) may halt biological colonisation on monuments, mainly that caused by phototrophic subaerial biofilms (SABs), which may exacerbate the biodeterioration of substrates. However, the light-triggered mechanisms that cause changes in the growth of the phototrophs remain unknown. Environmental proteomics could be used to provide information about the changes in the SAB metabolism under stress inflicted by nocturnal lighting. Here, laboratory-produced SABs, composed of Chlorophyta, Streptophyta and Cyanobacteriota, were subjected to three types of lighting used for monuments: cool white, warm white and amber + green (potentially with a biostatic effect). A control without light (i.e. darkness) was also included for comparison. The nocturnal lighting impaired the capacity of the SABs to decompose superoxide radicals and thus protect themselves from oxidative stress. Cool white and warm white light both strongly affected the proteomes of the SABs and reduced the total peptide content, with the extent of the reduction depending on the genera of the organisms involved. Analysis of the photo-damaging effect of amber + green light on the biofilm metabolism revealed a negative impact on photosystems I and II and production of photosystem antenna protein-like, as well as a triggering effect on protein metabolism (synthesis, folding and degradation). This research provides, for the first-time, a description of the proteomic changes induced by lighting on SABs colonising illuminated monuments in urban areas.}, }
@article {pmid39571806, year = {2025}, author = {Graham, A and Thorn, C and McDonagh, M and O'Donnell, C and Nolan, S and Kirwan, SF and O'Connor, S and Nzeteu, CO and Montoya, ACV and Bartle, A and Hall, A and Abberton, C and Friel, R and Waters, SM and O'Flaherty, V}, title = {Development and in-vitro assessment of novel oxygen-releasing feed additives to reduce enteric ruminant methane emissions.}, journal = {The Science of the total environment}, volume = {963}, number = {}, pages = {177598}, doi = {10.1016/j.scitotenv.2024.177598}, pmid = {39571806}, issn = {1879-1026}, mesh = {*Methane/metabolism/analysis ; Animals ; *Animal Feed/analysis ; Ruminants ; Rumen/metabolism ; Oxygen ; Oxidation-Reduction ; Fatty Acids, Volatile ; }, abstract = {Ruminant livestock contribute significantly to global methane production and mitigation of which is of utmost importance. Feed additives represent a cost-effective means of achieving this. A potential target for such additives is rumen Oxidative Reduction Potential (ORP), a parameter which influences CH4 production rates, with methanogenesis occurring optimally at ORPs below -300 mV. Thus, a controlled elevation of rumen ORP represents a potentially benign means of methanogen suppression. This research involved assessing a range of oxygen-releasing compounds for their ability to increase rumen ORP and inhibit methanogenesis, using the in-vitro rumen simulation technique (RUSITEC). Seven potential CH4 inhibitors were tested in a 21-day trial monitoring biogas volume, CH4 content, ORP, digestibility, ammonia, and volatile fatty acids concentration. The additives evaluated included: liquid peroxide (H2O2) and urea hydrogen peroxide (UHP), as well as slower reacting species (calcium and magnesium peroxide), in addition to encapsulated liquid H2O2 for controlled, slow release. Consistent CH4 reductions of >50 % were observed from all additives. Reduced neutral detergent fibre (NDF) digestibility and a reduction in total volatile fatty acids (VFAs) was observed for some treatments, but MgO2 and encapsulated H2O2 reduced CH4 volume by 62 % and 58 %, respectively, and had no detrimental effects on digestibility (p > 0.05) or on VFA production. Ex-situ ORP measurements demonstrated significant increases in ORP upon addition of the additives, with MgO2 and encapsulated H2O2 inducing a more moderate effect suggesting a controlled additive release was achieved with the slow-release format of encapsulated liquid H2O2. Thus, potential slow-release forms deemed suitable to progress to bolus or pellet format in-vivo were identified and could enable a longer-lasting suppression of methanogens within the rumen, facilitating application in both intensive and pasture-based production systems.}, }
@article {pmid39571521, year = {2025}, author = {Zuo, J and Yang, S and Grossart, HP and Xiao, P and Zhang, H and Sun, R and Li, G and Jiang, H and Zhao, Q and Jiao, M and Cheng, Y and Wang, Z and Geng, R and Ma, Z and Li, R}, title = {Sequential decline in cyanobacterial, total prokaryotic, and eukaryotic responses to backward flow in a river connected to Lake Taihu.}, journal = {Water research}, volume = {269}, number = {}, pages = {122784}, doi = {10.1016/j.watres.2024.122784}, pmid = {39571521}, issn = {1879-2448}, mesh = {*Cyanobacteria/physiology ; *Rivers/microbiology ; *Lakes/microbiology ; China ; Ecosystem ; Eukaryota ; }, abstract = {River ecosystems face escalating challenges due to altered flow regimes from human activities, such as urbanization with hydrological modifications. Understanding the role of microbial communities for ecosystems with changing flow regimes is still incomplete and remains at the frontier of aquatic microbial ecology. In particular, influences of riverine backward flow on the aquatic biota remain largely unknown. Therefore, we examined the impact of backward flow on the cyanobacterial, total prokaryotic, and eukaryotic communities in the Changdougang River, which naturally flows into Lake Taihu, through environmental DNA metabarcoding. We analyzed the differences in community diversity, assembly, and ecological network stability among groups under backward, weak, and forward flow direction conditions. Non-metric multidimensional scaling showed higher variations in communities of groups across flow direction conditions than seasonal groups. Variations in alpha and beta diversity showed that cyanobacterial and total prokaryotic communities experienced strong homogenization under backward flow conditions, whereas the ecological uniqueness of the eukaryotic community decreased. Assembly of the three flow-related communities was primarily governed by drift and dispersal limitation in stochastic processes. However, in the cyanobacterial community, homogeneous selection in deterministic processes increased from 22.79 % to 42.86 % under backward flow, aligning with trends observed in the checkerboard score (C-score). More importantly, the topological properties of ecological networks and the degree of average variation revealed higher stability in the cyanobacterial community compared to total prokaryotic and eukaryotic communities. Considering the variations in cohesion, the network stability in the cyanobacterial community decreased under backward flow. Our findings emphasize the distinct and sequentially diminishing responses of cyanobacterial, total prokaryotic, and eukaryotic communities to backward flowing rivers. This knowledge is crucial for maintaining ecological health of rivers, assessing the complex ecological impacts on hydrological engineering, and formulating sustainable water management strategies.}, }
@article {pmid39570409, year = {2024}, author = {Xu, H and Zhang, Y and Fan, D and Meng, S and Fan, L and Song, C and Qiu, L and Li, D and Fang, L and Liu, Z and Bing, X}, title = {Influences of Community Coalescence on the Assembly of Bacterial Communities of the Small-Scale Complex Aquatic System from the Perspective of Bacterial Transmission, Core Taxa, and Co-occurrence Patterns.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {145}, pmid = {39570409}, issn = {1432-184X}, support = {2023JBFR01//Central Public-interest Scientific Institution Basal Research Fund, Freshwater Fisheries Research Center, CAFS/ ; CARS-46//the earmarked fund for CARS/ ; 2023TD18//Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; }, mesh = {*Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; *Aquaculture ; *Rhizosphere ; *Feces/microbiology ; Animals ; Biofilms ; Fishes/microbiology ; Water Microbiology ; Ecosystem ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Recirculating aquaculture and aquaponics are considered sustainable aquaculture models playing important roles in animal-derived protein supply. In these aquaculture systems, microorganisms are crucial for the system stability. The community coalescence by mixing substances and microorganisms from various microhabitats under hydraulic forces is important for shaping the bacterial communities in these small-scale complex systems. However, the influences of community coalescence on bacterial communities remain rarely revealed in these systems. In this study, aquaponics (APS) and recirculating aquaculture (RAS) systems were set up to explore the bacterial community coalescence across different microhabitats, including water, fish feces, biofilter biofilms, and plant rhizosphere environment. Our results showed that diversity and compositions varied across different microhabitats in both systems. However, bacterial transmissions across these microhabitats differed between systems. The core microbiome of the RAS and APS were formed under community coalescence with the highest contribution of bacterial taxa derived from the fish feces. Nevertheless, the plant rhizosphere bacterial community also contributed to the core microbiome of the APS. Furthermore, the core taxa showed a higher average degree than the other nodes in the bacterial community networks in all microhabitats except for the plant rhizosphere environment, implying the important roles of core taxa in maintaining these bacterial community networks. Our results provide new insights into the assembly of bacterial communities under community coalescence in the artificial aquatic ecosystems comprising complex microhabitats, which is vital for developing microbial solutions for regulating the microbial communities to improve system performance in the future.}, }
@article {pmid39570377, year = {2024}, author = {Jensen, IC and Schramm, A and Offenberg, J}, title = {Fungus Fighters: Wood Ants (Formica polyctena) and Their Associated Microbes Inhibit Plant Pathogenic Fungi.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {146}, pmid = {39570377}, issn = {1432-184X}, support = {NNF21OC0071665//Novo Nordisk Fonden/ ; NNF21OC0071665//Novo Nordisk Fonden/ ; 34009-19-1562//Internationalt Center for Forskning i &#xd8;kologisk Jordbrug og F&#xf8;devaresystemer/ ; }, mesh = {*Ants/microbiology/physiology ; Animals ; *Plant Diseases/microbiology/prevention &amp; control ; Malus/microbiology ; Fungi/physiology/classification ; Antibiosis ; Bacteria/classification/drug effects/isolation &amp; purification ; Ascomycota/physiology/drug effects ; }, abstract = {Plant diseases cost the global economy billions of US dollars every year. The problem has mainly been addressed by using chemical pesticides, but recently, the use of ants has shown promising effects against plant pathogens. However, the mechanisms accounting for these effects have not yet been determined. One possible explanation is antimicrobial microorganisms associated with ants. Through controlled laboratory experiments, we investigated the inhibitory effects of wood ants (Formica polyctena) and their associated microorganisms against economically important plant pathogenic fungi. All live ants, extracts from crushed ants, and extracts from washed ants significantly inhibited the apple brown rot (Monilinia fructigena) while yielding the growth of other microbes. Furthermore, all investigated wood ants transferred microorganisms to their surroundings within 10 s when walking across a surface. We isolated the most dominant microorganisms deposited by walking ants and from washed ant extracts (i.e., strains likely found on the surface of ants), resulting in four bacterial cultures and one yeast. Two of these isolates, strain I3 (most closely related to Pseudomonas sichuanensis and P. entomophila) and strain I1b (most closely related to Bacillus mycoides), showed inhibitory effects against apple brown rot and apple scab (Venturia inaequalis), while strain I3 also inhibited gray mold (Botrytis cinerea) and Fusarium head blight (Fusarium graminearum). These results suggest that wood ants have potential as biological control agents against commercially relevant plant pathogens, and that their inhibitory effect might be at least partially caused by antibiotic compounds produced by their associated microorganisms.}, }
@article {pmid39568064, year = {2024}, author = {Sauma-Sánchez, T and Alcorta, J and Tamayo-Leiva, J and Díez, B and Bezuidenhout, H and Cowan, DA and Ramond, JB}, title = {Functional redundancy buffers the effect of poly-extreme environmental conditions on southern African dryland soil microbial communities.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {12}, pages = {}, pmid = {39568064}, issn = {1574-6941}, support = {FBIS160422162807//National Research Foundation/ ; 1210912//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; }, mesh = {*Soil Microbiology ; *Bacteria/genetics/classification ; *Archaea/genetics/classification ; *Microbiota ; *Salinity ; *Fungi/genetics/classification ; Climate Change ; Desert Climate ; Soil/chemistry ; Extreme Environments ; Africa, Southern ; Biodiversity ; }, abstract = {Drylands' poly-extreme conditions limit edaphic microbial diversity and functionality. Furthermore, climate change exacerbates soil desiccation and salinity in most drylands. To better understand the potential effects of these changes on dryland microbial communities, we evaluated their taxonomic and functional diversities in two Southern African dryland soils with contrasting aridity and salinity. Fungal community structure was significantly influenced by aridity and salinity, while Bacteria and Archaea only by salinity. Deterministic homogeneous selection was significantly more important for bacterial and archaeal communities' assembly in hyperarid and saline soils when compared to those from arid soils. This suggests that niche partitioning drives bacterial and archaeal communities' assembly under the most extreme conditions. Conversely, stochastic dispersal limitations drove the assembly of fungal communities. Hyperarid and saline soil communities exhibited similar potential functional capacities, demonstrating a disconnect between microbial structure and function. Structure variations could be functionally compensated by different taxa with similar functions, as implied by the high levels of functional redundancy. Consequently, while environmental selective pressures shape the dryland microbial community assembly and structures, they do not influence their potential functionality. This suggests that they are functionally stable and that they could be functional even under harsher conditions, such as those expected with climate change.}, }
@article {pmid39567391, year = {2024}, author = {Vezina, B and Cooper, HB and Wisniewski, JA and Parker, MH and Jenney, AWJ and Holt, KE and Wyres, KL}, title = {Wild-Type Domestication: Loss of Intrinsic Metabolic Traits Concealed by Culture in Rich Media.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {144}, pmid = {39567391}, issn = {1432-184X}, support = {DP200103364//Australian Research Council/ ; DP200103364//Australian Research Council/ ; APP1176192//National Health and Medical Research Council/ ; }, mesh = {*Klebsiella pneumoniae/genetics/metabolism/growth &amp; development ; *Culture Media/chemistry ; *Genome, Bacterial ; Histidine/metabolism ; Mutation ; Whole Genome Sequencing ; }, abstract = {Bacteria are typically isolated on rich media to maximise isolation success, removing them from their native evolutionary context. This eliminates selection pressures, enabling otherwise deleterious genomic events to accumulate. Here, we present a cautionary tale of these 'quiet mutations' which can persist unnoticed in bacterial culture lines. We used a combination of microbiological culture (standard and minimal media conditions), whole genome sequencing and metabolic modelling to investigate putative Klebsiella pneumoniae L-histidine auxotrophs. Additionally, we used genome-scale metabolic modelling to predict auxotrophies among completed public genomes (n = 2637). Two sub-populations were identified within a K. pneumoniae frozen stock, differing in their ability to grow in the absence of L-histidine. These sub-populations were the same 'strain', separated by eight single nucleotide variants and an insertion sequence-mediated deletion of the L-histidine biosynthetic operon. The His[-] sub-population remained undetected for > 10 years despite its inclusion in independent laboratory experiments. Genome-scale metabolic models predicted 0.8% public genomes contained ≥ 1 auxotrophy, with purine/pyrimidine biosynthesis and amino acid metabolism most frequently implicated. We provide a definitive example of the role of standard rich media culture conditions in obscuring biologically relevant mutations (i.e. nutrient auxotrophies) and estimate the prevalence of such auxotrophies using public genome collections. While the prevalence is low, it is not insignificant given the thousands of K. pneumoniae that are isolated for global surveillance and research studies each year. Our data serve as a pertinent reminder that rich-media culturing can cause unnoticed wild-type domestication.}, }
@article {pmid39567372, year = {2024}, author = {Issifu, S and Acharya, P and Kaur-Bhambra, J and Gubry-Rangin, C and Rasche, F}, title = {Biological Nitrification Inhibitors with Antagonistic and Synergistic Effects on Growth of Ammonia Oxidisers and Soil Nitrification.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {143}, pmid = {39567372}, issn = {1432-184X}, support = {RA 1717/8-1//2019-2020 Bio-divERsA joint call for research proposals, under the BiodivClim ERA-Net COFUND programme, and with the funding organisations German Research Foundation/ ; RA 1717/8-1//2019-2020 Bio-divERsA joint call for research proposals, under the BiodivClim ERA-Net COFUND programme, and with the funding organisations German Research Foundation/ ; URF150571//Royal Society University Research Fellowship/ ; }, mesh = {*Nitrification ; *Soil Microbiology ; *Ammonia/metabolism ; *Soil/chemistry ; Archaea/metabolism/drug effects/growth &amp; development ; Oxidation-Reduction ; Rhizosphere ; Bacteria/metabolism/drug effects/growth &amp; development ; }, abstract = {Biological nitrification inhibition (BNI) refers to the plant-mediated process in which nitrification is inhibited through rhizospheric release of diverse metabolites. While it has been assumed that interactive effects of these metabolites shape rhizosphere processes, including BNI, there is scant evidence supporting this claim. Hence, it was a primary objective to assess the interactive effects of selected metabolites, including caffeic acid (CA), vanillic acid (VA), vanillin (VAN), syringic acid (SA), and phenylalanine (PHE), applied as single and combined compounds, against pure cultures of various ammonia-oxidising bacteria (AOB, Nitrosomonas europaea, Nitrosospira multiformis, Nitrosospira tenuis, Nitrosospira briensis) and archaea (AOA, Nitrososphaera viennensis), as well as soil nitrification. Additionally, benzoic acid (BA) was examined as a novel biological nitrification inhibitor. All metabolites, except SA, tested as single compounds, achieved varied levels of inhibition of microbial growth, with CA exhibiting the highest inhibitory potential. Similarly, all metabolites applied as single compounds, except PHE, inhibited soil nitrification by up to 62%, with BA being the most potent. Inhibition of tested nitrifying microbes was also observed when compounds were assessed in combination. The combinations VA + PH, VA + CA, and VA + VAN exhibited synergism against N. tenuis and N. briensis, while others showed antagonism against N. europaea, N. multiformis, and N. viennensis. Although all combinations suppressed soil nitrification, their interactions against soil nitrification revealed antagonism. Our findings indicate that both antagonism and synergism are possible in rhizospheric interactions involving BNI metabolites, resulting in growth inhibition of nitrifiers and suppression of soil nitrification.}, }
@article {pmid39565130, year = {2025}, author = {Yu, C and Yu, M and Ma, R and Wei, S and Jin, M and Jiao, N and Zheng, Q and Zhang, R and Feng, X}, title = {A novel Alteromonas phage with tail fiber containing six potential iron-binding domains.}, journal = {Microbiology spectrum}, volume = {13}, number = {1}, pages = {e0093424}, pmid = {39565130}, issn = {2165-0497}, mesh = {*Bacteriophages/genetics/metabolism/isolation &amp; purification ; *Iron/metabolism ; *Phylogeny ; *Alteromonas/virology/metabolism/genetics ; Host Specificity ; Viral Tail Proteins/metabolism/genetics ; Genome, Viral/genetics ; Protein Domains ; }, abstract = {Viruses play a vital role in regulating microbial communities, contributing to biogeochemical cycles of carbon, nitrogen, and essential metals. Alteromonas is widespread and plays an essential role in marine microbial ecology. However, there is limited knowledge about the interactions of Alteromonas and its viruses (alterophages). This study isolated a novel podovirus, vB_AmeP-R22Y (R22Y), which infects Alteromonas marina SW-47 (T). Phylogenetic analysis suggested that R22Y represented a novel viral genus within the Schitoviridae family. R22Y exhibited a broad host range and a relatively large burst size, exerting an important impact on the adaptability and dynamics of host populations. Two auxiliary metabolic genes, encoding Acyl carrier protein and AAA domain-containing protein, were predicted in R22Y, which may potentially assist in host fatty acid metabolism and VB12 biosynthesis, respectively. Remarkably, the prediction of the R22Y tail fiber structure revealed six conserved histidine residues (HxH motifs) that could potentially bind iron ions, suggesting that alterophages may function as organic iron-binding ligands in the marine environment. Our isolation and characterization of R22Y complements the Trojan Horse hypothesis, proposes the possible role of alterophages for marine iron biogeochemical cycling, and provides new insights into phage-host interactions in the iron-limited ocean.IMPORTANCEIron (Fe), as an essential micronutrient, is often a limiting factor for microbial growth in marine ecosystems. The Trojan Horse hypothesis suggests that iron in the phage tail fibers is recognized by the host's siderophore-bound iron receptor, enabling the phage to attach and initiate infection. The potential role of phages as iron-binding ligands has significant implications for oceanic trace metal biogeochemistry. In this study, we isolated a new phage R22Y with the potential to bind iron ions, using Alteromonas, a major siderophore producer, as the host. The tail fiber structure of R22Y exhibits six conserved HxH motifs, suggesting that each phage could potentially bind up to 36 iron ions. R22Y may contribute to colloidal organically complexed dissolved iron in the marine environment. This finding provides further insights into the Trojan Horse hypothesis, suggesting that alterophages may act as natural iron-binding ligands in the marine environment.}, }
@article {pmid39563404, year = {2024}, author = {Chari, NR and Muratore, TJ and Frey, SD and Winters, CL and Martinez, G and Taylor, BN}, title = {Long-Term Soil Warming Drives Different Belowground Responses in Arbuscular Mycorrhizal and Ectomycorrhizal Trees.}, journal = {Global change biology}, volume = {30}, number = {11}, pages = {e17550}, doi = {10.1111/gcb.17550}, pmid = {39563404}, issn = {1365-2486}, support = {DEB-1456610//National Science Foundation/ ; DEB-1832110//National Science Foundation/ ; }, mesh = {*Mycorrhizae/physiology ; *Trees/microbiology/physiology/growth &amp; development ; *Soil/chemistry ; *Plant Roots/microbiology ; *Global Warming ; Biomass ; Soil Microbiology ; Carbon/metabolism/analysis ; Nitrogen/metabolism/analysis ; Climate Change ; Temperature ; }, abstract = {The ability of trees to acquire soil nutrients under future climate conditions will influence forest composition and function in a warmer world. Rarely are multiple belowground carbon allocation pathways measured simultaneously in large global change experiments, restricting our understanding of how trees may shift their allocation of resources to different nutrient acquisition mechanisms under future climates. Leveraging a 20-year soil warming experiment, we show that ectomycorrhizal (EM) trees reduce mycorrhizal colonization and root exudation while increasing fine root biomass, while arbuscular mycorrhizal (AM) trees largely maintained their belowground carbon allocation patterns in warmer soils. We suggest that AM trees may be better adapted to thrive under global warming due to higher rates of nitrogen mineralization in warmer soils and the ability of their mycorrhizal symbiont to acquire mineralized inorganic nutrients, whereas EM trees may need to alter their belowground carbon allocation patterns to remain competitive as global temperatures rise.}, }
@article {pmid39561700, year = {2024}, author = {Partida-Martínez, LP}, title = {Laila P. Partida-Martínez.}, journal = {Current biology : CB}, volume = {34}, number = {22}, pages = {R1121-R1122}, doi = {10.1016/j.cub.2024.09.085}, pmid = {39561700}, issn = {1879-0445}, mesh = {*Symbiosis ; Fungi/physiology ; Plants/microbiology ; History, 21st Century ; History, 20th Century ; }, abstract = {Interview with Laila Partida-Martínez, who studies microbial ecology, fungal-bacterial symbioses and plant-microbe interactions at the Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav).}, }
@article {pmid39561304, year = {2024}, author = {Vargas Ribera, PR and Kim, N and Venbrux, M and Álvarez-Pérez, S and Rediers, H}, title = {Evaluation of sequence-based tools to gather more insight into the positioning of rhizogenic agrobacteria within the Agrobacterium tumefaciens species complex.}, journal = {PloS one}, volume = {19}, number = {11}, pages = {e0302954}, pmid = {39561304}, issn = {1932-6203}, mesh = {*Agrobacterium tumefaciens/genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Agrobacterium/genetics ; Genome, Bacterial ; DNA, Bacterial/genetics ; }, abstract = {Rhizogenic Agrobacterium, the causative agent of hairy root disease (HRD), is known for its high phenotypic and genetic diversity. The taxonomy of rhizogenic agrobacteria has undergone several changes in the past and is still somewhat controversial. While the classification of Agrobacterium strains was initially mainly based on phenotypic properties and the symptoms they induced on plants, more and more genetic information has been used along the years to infer Agrobacterium taxonomy. This has led to the definition of the so-called Agrobacterium tumefaciens species complex (Atsc), which comprises several genomospecies. Interestingly, the rhizogenic Agrobacterium strains are found in several of these genomospecies. Nevertheless, even up until today Agrobacterium strains, and in particular rhizogenic agrobacteria, are prone to misclassification and considerable confusion in literature. In this study, we evaluated different phylogenetic analysis approaches for their use to improve Agrobacterium taxonomy and tried to gain more insight in the classification of strains into this complex genus, with a particular focus on rhizogenic agrobacteria. The genome sequence analysis of 580 assemblies, comprising Agrobacterium, Allorhizobium and Rhizobium strains demonstrated that phylogenies based on single marker genes, such as the commonly used 16S rRNA and recA gene, do not provide sufficient resolution for proper delineation of the different genomospecies within the Atsc. Our results revealed that (in silico) multi-locus sequences analysis (MLSA) in combination with average nucleotide identity (ANIb) at a 94.0% threshold delineates genomospecies accurately and efficiently. Additionally, this latter approach permitted the identification of two new candidate genomospecies.}, }
@article {pmid39560406, year = {2024}, author = {Ye, Y-Q and Ye, M-Q and Zhang, X-Y and Huang, Y-Z and Zhou, Z-Y and Feng, Y-J and Du, Z-J}, title = {Description of the first marine-isolated member of the under-represented phylum Gemmatimonadota, and the environmental distribution and ecogenomics of Gaopeijiales ord. nov.}, journal = {mSystems}, volume = {9}, number = {12}, pages = {e0053524}, pmid = {39560406}, issn = {2379-5077}, support = {92351301//MOST | National Natural Science Foundation of China (NSFC)/ ; 32070002//MOST | National Natural Science Foundation of China (NSFC)/ ; 2022FY101100//National Science and Technology Fundamental Resources Investigation Program of China/ ; }, mesh = {*Phylogeny ; *Geologic Sediments/microbiology ; China ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification/metabolism ; DNA, Bacterial/genetics ; }, abstract = {The phylum Gemmatimonadota is widespread but rarely cultured and, in fact, there are only six described species isolated from soil, freshwater, and wastewater treatment. However, no isolates of Gemmatimonadota from marine environment have been described; thus, little is known about the physiology and metabolism of members of the marine lineages. In this study, four novel facultatively anaerobic bacterial strains belonging to Gemmatimonadota were isolated from marine sediments collected from Xiaoshi Island in Weihai, China, using an aerobic enrichment method. The integrated results of phylogenetic and phenotypic characteristics supported that these four strains represent one novel species in a novel genus, for which the name Gaopeijia maritima gen. nov., sp. nov. is proposed, as the first representative of novel taxa, Gaopeijiales ord. nov., Gaopeijiaceae fam. nov. in the class Longimicrobiia. Gaopeijiales was detected in 22,884 out of 95,549 amplicon data sets, mainly from soil. However, the highest mean relative abundances were in sponge (0.7%) and marine sediment (0.35%), showing salt-related character. Most of the Gaopeijiales subgroups potentially belong to the rare bacterial biosphere. The aerobic enrichment in this study could significantly increase the relative abundance of Gaopeijiales (from 0.37% to 2.6%). Furthermore, the metabolic capabilities inferred from high-quality representative Gaopeijiales genomes/MAGs suggest that this group primarily performs chemoorganoheterotrophic metabolism with facultatively anaerobic characteristics and possesses various secondary metabolite biosynthesis gene clusters (BGCs), mirroring those observed in the four novel strains.IMPORTANCEDespite rapid advances in molecular and sequencing technologies, obtaining pure cultures remains a crucial research goal in microbiology, as it is essential for a deeper understanding of microbial metabolism. Gemmatimonadota is a widespread but rarely cultured bacterial phylum. Currently, there are only six cultured strains of this interesting group, all isolated from non-marine environments. Little is known about the physiology and metabolism of members of the marine lineages. Here we isolated and characterized four novel marine strains, and proposed a new order Gaopeijiales within Gemmatimonadota. Furthermore, the global distribution, environmental preference, and metabolic potential of Gaopeijiales are analyzed using public data. Our work enriches the resources available for the under-represented phylum Gemmatimonadota and provides insights into the physiological and metabolic characteristics of the marine lineage (Gaopeijiales) through culturology and omics.}, }
@article {pmid39558480, year = {2024}, author = {Zechner, EL and Kienesberger, S}, title = {Microbiota-derived small molecule genotoxins: host interactions and ecological impact in the gut ecosystem.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2430423}, pmid = {39558480}, issn = {1949-0984}, mesh = {Animals ; Humans ; *Bacteria/drug effects/genetics/metabolism ; Enterotoxins/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Host Microbial Interactions ; Mutagens/metabolism/toxicity ; Polyketides/metabolism/toxicity ; }, abstract = {The human intestinal tract is densely colonized by a microbial community that is subject to intense competition. Bacteria in this complex habitat seek to outcompete their neighbors for nutrients and eliminate competitors with antibacterial toxins. Antagonism can be mediated by diverse effectors including toxic proteins and small molecule inhibitors that are released extracellularly or delivered by specialized secretion systems to targeted cells. Two prototypical microbiota-derived enterotoxins, colibactin and tilimycin, and the newly discovered family of indolimines represent an expanding group of non-proteinaceous small molecules which specifically target DNA. In addition to cell killing, they generate mutations and genome instability in intoxicated microbes and host cells alike. They have been studied in detail because of their direct toxicity to human cells and important etiological roles in intestinal pathologies. Increasing evidence, however, reveals that these commensal genotoxins are also mediators of interbacterial antagonism, which impacts gut microbial ecology. In this review, we illustrate the functional versatility of commensal genotoxins in the gut ecosystem.}, }
@article {pmid39557685, year = {2024}, author = {Mai, N and Foysal, MJ and Timms, VJ and Pearson, LA and Romanis, CS and Mills, TJT and Powell, JR and Neilan, BA}, title = {Seasonal and Spatial Dynamics of Fungal Leaf Endophytes in Eucalyptus crebra (Narrow-Leaved Ironbark).}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {142}, pmid = {39557685}, issn = {1432-184X}, support = {CE200100029//Australian Research Council/ ; CE200100029//Australian Research Council/ ; CE200100029//Australian Research Council/ ; CE200100029//Australian Research Council/ ; FF0883440//Australian Research Council/ ; }, mesh = {*Eucalyptus/microbiology ; *Seasons ; *Endophytes/isolation &amp; purification/classification/genetics ; *Plant Leaves/microbiology ; *Fungi/classification/isolation &amp; purification/genetics ; Biodiversity ; Ascomycota/genetics/isolation &amp; purification ; Basidiomycota/isolation &amp; purification/genetics/classification ; }, abstract = {Fungal endophytes play an important role in improving the health and productivity of native and cultivated plant species. Despite their ecological and industrial importance, few eucalypt species have been studied in terms of their endophyte communities. We examined the seasonal and spatial dynamics of fungal leaf endophytes in the model species, Eucalyptus crebra (narrow-leaved ironbark), using ITS-based amplicon sequencing. Alpha and beta diversity analyses revealed significantly higher species richness in summer compared to autumn and spring. Similarly, two-way ANOVA analysis showed significantly higher species diversity in summer compared to autumn (observed p < 0.001, Chao1 p < 0.005) and spring (observed p < 0.005, Chao1 p < 0.005). No difference in Shannon index was observed among different canopy levels across the season. Beta-diversity showed differences in fungal composition across the seasons and at various canopy levels based on unweighted UniFrac distance metric (PERMANOVA season p < 0.001, canopy p < 0.05), signifying distinct separation of fungi based on presence-absence. Ascomycota was the most abundant and diverse phylum and was present throughout the year. In contrast, Basidiomycota was only observed during cooler and drier seasons. Neofusicoccum was the most abundant genus, but distribution fluctuated significantly across the seasons. Pestalotiopsis and Neopestalotiopsis were most abundant in the low leaf canopy, whereas Pseudosydowia was most abundant in the high canopy. This study indicates that the diversity and abundance of endophytic fungi in the leaves of healthy E. crebra trees fluctuate seasonally and across canopy levels. The data generated can be used as a baseline for assessing and potentially modulating the health of E. crebra and other important Eucalyptus spp.}, }
@article {pmid39551884, year = {2024}, author = {Mamo, Z and Abera, S and Tafesse, M}, title = {Taxonomic and functional profiling of microbial community in municipal solid waste dumpsite.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {40}, number = {12}, pages = {384}, pmid = {39551884}, issn = {1573-0972}, support = {EN-1/17-1/18//Addis Ababa Science and Technology University/ ; }, mesh = {*Solid Waste ; *Bacteria/classification/genetics/metabolism ; *Waste Disposal Facilities ; *Microbiota ; *Metagenomics ; Phylogeny ; Refuse Disposal ; Biodegradation, Environmental ; Drug Resistance, Microbial/genetics ; Soil Microbiology ; }, abstract = {Understanding the microbial ecology of landfills is crucial for improving waste management strategies and utilizing the potential of these microbial communities for biotechnological applications. This study aimed to conduct a comprehensive taxonomic and functional profiling of the microbial community present in the Addis Ababa municipal solid waste dumpsite using a shotgun metagenomics sequencing approach. The taxonomic analysis of the sample revealed the significant presence of bacteria, with the Actinomycetota (56%), Pseudomonadota (23%), Bacillota (3%), and Chloroflexota (3%) phyla being particularly abundant. The most abundant KEGG categories were carbohydrates metabolism, membrane transport, signal transduction, and amino acid metabolism. The biodegradation and metabolism of xenobiotics, as well as terpenoids and polyketides, were also prevalent. Moreover, the Comprehensive Antibiotic Resistance Database (CARD) identified 52 antibiotic resistance gene (ARG) subtypes belonging to 14 different drug classes, with the highest abundances observed for glycopeptide, phosphonic acid, and multidrug resistance genes. Actinomycetota was the dominant phylum harboring ARGs, followed by Pseudomonadota and Chloroflexota. This study offers valuable insights into the taxonomic and functional diversity of the microbial community in the Addis Ababa municipal solid waste dumpsite. It sheds light on the widespread presence of metabolically versatile microbes, antibiotic resistance genes, mobile genetic elements, and pathogenic bacteria. This understanding can contribute to the creation of efficient waste management strategies and the investigation of possible biotechnological uses for these microbial communities.}, }
@article {pmid39551202, year = {2024}, author = {Duran, C and Bouchard, A and Agogué, H and Dupuy, C and Duran, R and Cravo-Laureau, C}, title = {Importance of eukaryotes in shaping microbial benthic communities in Charente-maritime marshes, France.}, journal = {The Science of the total environment}, volume = {957}, number = {}, pages = {177523}, doi = {10.1016/j.scitotenv.2024.177523}, pmid = {39551202}, issn = {1879-1026}, mesh = {*Eukaryota ; France ; *Microbiota ; *Wetlands ; Animals ; Bacteria/classification ; Salinity ; Archaea ; Seasons ; Environmental Monitoring ; }, abstract = {Marshes are wetlands known for providing major ecosystem services in terms of water quality and human activities. These ecosystem services are mainly provided by marshes' benthic community, composed of prokaryotes (bacteria and archaea) but also of eukaryotes (micro-eukaryotes and meiofauna). The aim of this study is to (1) assess the environmental parameters affecting benthic community composition in marshes, (2) highlight the associations between organisms from the three domains of life, and (3) determine the parameters controlling these associations. Hence, benthic communities of eight different marshes from three typologies (salted, brackish and freshwater) and four seasons (autumn 2020, spring 2021, summer 2021 and autumn 2021) were assessed. This study revealed three main drivers of community composition. First, salinity drives the community composition illustrated by the differences observed between the three typologies of marshes. Relative abundance of Nitrososphaeria, Halobacteria, Bacillariophyceae, Conoidasida and nematodes increased with salinity while methanogenic archaea, Chlorophyceae and copepod's relative abundance decreased. The second driver is the physical-chemistry of the site, particularly nutrients. The season is the last driver of community composition, seasonal pattern varying for each site within a typology. LEfSe analyses defined biomarkers of typology and season, among which many prokaryotes involved in the nitrogen cycle and photosynthetic micro-eukaryotes where present in different co-occurrence networks, highlighting the importance of nitrogen cycle in marshes. Co-occurrence networks revealed several connections between organisms of the three domains of life, particularly between prokaryotes and photosynthetic eukaryotes. This study illustrates thus the importance of holistic approaches in microbial ecology for revealing a comprehensive view of the whole microbial interactions occurring in complex ecosystems.}, }
@article {pmid39549623, year = {2025}, author = {White, CA and Antell, EH and Schwartz, SL and Lawrence, JE and Keren, R and Zhou, L and Yu, K and Zhuang, WQ and Alvarez-Cohen, L}, title = {Life history strategies determine response to SRT driven crash in anammox bioreactors.}, journal = {Water research}, volume = {268}, number = {Pt B}, pages = {122727}, doi = {10.1016/j.watres.2024.122727}, pmid = {39549623}, issn = {1879-2448}, mesh = {*Bioreactors/microbiology ; Anaerobiosis ; *RNA, Ribosomal, 16S/genetics ; Oxidation-Reduction ; Ammonium Compounds/metabolism ; Waste Disposal, Fluid/methods ; Bacteria/metabolism/genetics ; }, abstract = {Anaerobic ammonium oxidation (anammox) is a biological process often applied in wastewater treatment plants for nitrogen removal from highly concentrated side-stream effluents from anaerobic digesters. However, they are vulnerable to process instability prompted by operational shocks and microbial community imbalances, resulting in lengthy recovery times. These issues are further compounded by a lack of understanding of how sustained press disturbances influence the microbial ecology of the system. Here we investigate the response and recovery of an anammox membrane bioreactor to a solids retention time (SRT)-induced reactor crash using 16S rRNA gene and shotgun metagenomic sequencing. We observed a strong selection of bacterial groups based on reproduction strategies, with the Orders Rhodospirillales and Sphingobacteriales increasing from 1.0 % and 11.9 % prior to the crash to 31.9 % and 18.1 % during the crash respectively. The Orders Brocadiales and Anaerolineales decreased from 17.3 % and 28.3 % to 7.3 % and 1.4 % over the same time period, respectively. Metagenomic and metatranscriptomic analyses revealed differential crash responses in metabolically distinct groups of bacteria, with increased expression of genes for extracellular carbohydrate active enzymes, peptidases and membrane transporters. Following the crash, the reactor recovered to its prior state of nitrogen removal performance and pathway analysis demonstrated increased expression of genes related to exopolysaccharide biosynthesis and quorum sensing during the reactor recovery period. This study highlights the effects of reactor perturbations on microbial community dynamics in anammox bioreactors and provides insight into potential recovery mechanisms from severe disturbance.}, }
@article {pmid39549075, year = {2024}, author = {de la Sovera, V and Bovio-Winkler, P and Zinola, G and Etchebehere, C}, title = {Microbial community evolution in a lab-scale reactor operated to obtain biomass for biochemical methane potential assays.}, journal = {Applied microbiology and biotechnology}, volume = {108}, number = {1}, pages = {519}, pmid = {39549075}, issn = {1432-0614}, support = {SNI//ANII/ ; SNI//ANII/ ; SNI//ANII/ ; (II/FVF/2019/121).//Carlos Vaz Ferreira/ ; }, mesh = {*Methane/metabolism ; *Biomass ; *Bioreactors/microbiology ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; *Archaea/genetics/metabolism/classification ; Anaerobiosis ; *RNA, Ribosomal, 16S/genetics ; *Sewage/microbiology ; Microbiota ; Biodegradation, Environmental ; }, abstract = {Biochemical methane potential (BMP) test is an important tool to evaluate the methane production biodegradability and toxicity of different wastes or wastewaters. This is a key parameter for assessing design and feasibility issues in the full-scale implementation of anaerobic digestion processes. A standardized and storable inoculum is the key to obtain reproducible results. In Uruguay, a local enterprise dedicated to design and install anaerobic digesters operated a lab-scale bioreactor as a source of biomass for BMP tests, using a protocol previously described. This reactor was controlled and fed with a mixture of varied organic compounds (lipids, cellulolytic wastes, proteins). Biomass was reintroduced into the reactor after BMP assays to maintain a constant volume and biomass concentration. The aim of this work was to evaluate how the microbial community evolved during this operation and the effect of storing biomass in the refrigerator. The composition of the microbial communities was analyzed by 16S rRNA amplicon sequencing using primers for Bacteria and Archaea. The methanogenic activity was determined, and the methanogens were quantified by mcrA qPCR. One sample was stored for a 5-month period in the refrigerator (4 °C); the activity and the microbial community composition were analyzed before and after storage. Results showed that applying the reported methodology, a reliable methanogenic sludge with an acceptable SMA was obtained even though the reactor suffered biomass alterations along the evaluated period. Refrigerating the acclimatized biomass for 5 months did not affect its activity nor its microbial composition according to the 16S rRNA gene sequence analysis, even though changes in the mcrA abundance were observed. KEY POINTS: • The applied methodology was successful to obtain biomass suitable to perform BMP assays. • The microbial community was resilient to external biomass addition. • Biomass storage at 4 °C for 5 months did not alter the methanogenic activity.}, }
@article {pmid39546027, year = {2024}, author = {Khamespanah, E and Asad, S and Vanak, Z and Mehrshad, M}, title = {Niche-Aware Metagenomic Screening for Enzyme Methioninase Illuminates Its Contribution to Metabolic Syntrophy.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {141}, pmid = {39546027}, issn = {1432-184X}, mesh = {*Carbon-Sulfur Lyases/genetics/metabolism ; *Metagenomics ; *Phylogeny ; *Bacteria/genetics/classification/enzymology/isolation &amp; purification/metabolism ; Archaea/genetics/enzymology/classification ; Groundwater/microbiology ; Metagenome ; Seawater/microbiology ; }, abstract = {The single-step methioninase-mediated degradation of methionine (as a sulfur containing amino acid) is a reaction at the interface of carbon, nitrogen, sulfur, and methane metabolism in microbes. This enzyme also has therapeutic application due to its role in starving auxotrophic cancer cells. Applying our refined in silico screening pipeline on 33,469 publicly available genome assemblies and 1878 metagenome assembled genomes/single-cell amplified genomes from brackish waters of the Caspian Sea and the Fennoscandian Shield deep groundwater resulted in recovering 1845 methioninases. The majority of recovered methioninases belong to representatives of phyla Proteobacteria (50%), Firmicutes (29%), and Firmicutes_A (13%). Prevalence of methioninase among anaerobic microbes and in the anoxic deep groundwater together with the relevance of its products for energy conservation in anaerobic metabolism highlights such environments as desirable targets for screening novel methioninases and resolving its contribution to microbial metabolism and interactions. Among archaea, majority of detected methioninases are from representatives of Methanosarcina that are able to use methanethiol, the sulfur containing product from methionine degradation, as a precursor for methanogenesis. Branching just outside these archaeal methioninases in the phylogenetic tree, we recovered three methioninases belonging to representatives of Patescibacteria reconstructed from deep groundwater metagenomes. We hypothesize that methioninase in Patescibacteria could contribute to their syntrophic interactions where their methanogenic partners/hosts benefit from the produced 2-oxobutyrate and methanethiol. Our results underscore the significance of accounting for specific ecological niche in screening for enzyme variates with desired characteristics. Finally, complementing of our findings with experimental validation of methioninase activity confirms the potential of our in silico screening in clarifying the peculiar ecological role of methioninase in anoxic environments.}, }
@article {pmid39545996, year = {2024}, author = {Scheelings, TF and Van, TTH and Moore, RJ and Skerratt, LF}, title = {Location Matters: Variations in Cloacal Microbiota Composition of Spatially Separated Freshwater Turtles.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {140}, pmid = {39545996}, issn = {1432-184X}, mesh = {Animals ; *Turtles/microbiology ; *Cloaca/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; *Fresh Water/microbiology ; Australia ; Gastrointestinal Microbiome ; Biodiversity ; }, abstract = {The gut microbiota of vertebrates is malleable and may be shaped by both intrinsic and extrinsic factors. Here, the effect that geography has on the cloacal microbiota of two species of Australian freshwater chelonians, eastern longneck turtle (Chelodina longicollis) and Macquarie River turtle (Emydura macquarii), captured from waterbodies with different levels of anthropogenic pressure was investigated. We analysed the microbiota composition, structure and diversity through 16S rRNA gene amplicon sequencing. It was hypothesised that animals from less disturbed environments would harbour a more diverse cloacal microbial population. The cloacal microbiotas from 93 turtles (C. longicollis n = 78; E. macquarii n = 15), from five locations, were analysed. For both species, the most predominant phylum was Proteobacteria. Cloacal microbiota alpha diversity varied significantly between the C. longicollis from all locations, but no differences were found for E. macquarii. In C. longicollis, turtles from wetlands within the centre of Melbourne had the lowest alpha diversity metrics, while the highest alpha diversity values were seen in turtles captured from an undisturbed rural waterbody. Beta diversity, obtained by weighted UniFrac distance, showed significant differences between locations of capture for both species of turtles in this investigation. For C. longicollis, 87 biomarkers were identified responsible for explaining differences between locations, and in E. macquarii, 42 biomarkers were found. This is the first study to explore the cloacal microbiota composition of the eastern longneck turtle and gives greater insight into microbial community structures in Macquarie River turtles. Our study demonstrated that cloacal microbiota composition of freshwater turtles was significantly influenced by locality and that disrupted environments may reduce microbial diversity in C. longicollis. Interestingly, we discovered that the effects of location contrasted significantly between species for alpha diversity with differences discovered for C. longicollis but not E. macquarii. However, for both species, beta diversity was notably influenced by habitat type. These results highlight the need to interpret chelonian microbiota data in the context of geography and human disturbance of the environment.}, }
@article {pmid39544963, year = {2024}, author = {Wong, HL and Bulzu, PA and Ghai, R and Chiriac, MC and Salcher, MM}, title = {Ubiquitous genome streamlined Acidobacteriota in freshwater environments.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae124}, pmid = {39544963}, issn = {2730-6151}, abstract = {Acidobacteriota are abundant in soil, peatlands, and sediments, but their ecology in freshwater environments remains understudied. UBA12189, an Acidobacteriota genus, is an uncultivated, genome-streamlined lineage with a small genome size found in aquatic environments where detailed genomic analyses are lacking. Here, we analyzed 66 MAGs of UBA12189 (including one complete genome) from freshwater lakes and rivers in Europe, North America, and Asia. UBA12189 has small genome sizes (<1.4 Mbp), low GC content, and a highly diverse pangenome. In freshwater lakes, this bacterial lineage is abundant from the surface waters (epilimnion) down to a 300-m depth (hypolimnion). UBA12189 appears to be free-living from CARD-FISH analysis. When compared to other genome-streamlined bacteria such as Nanopelagicales and Methylopumilus, genome reduction has caused UBA12189 to have a more limited metabolic repertoire in carbon, sulfur, and nitrogen metabolisms, limited numbers of membrane transporters, as well as a higher degree of auxotrophy for various amino acids, vitamins, and reduced sulfur. Despite having reduced genomes, UBA12189 encodes proteorhodopsin, complete biosynthesis pathways for heme and vitamin K2, cbb3-type cytochrome c oxidases, and heme-requiring enzymes. These genes may give a selective advantage during the genome streamlining process. We propose the new genus Acidiparvus, with two new species named "A. lacustris" and "A. fluvialis". Acidiparvus is the first described genome-streamlined lineage under the phylum Acidobacteriota, which is a free-living, slow-growing scavenger in freshwater environments.}, }
@article {pmid39543974, year = {2024}, author = {Gonsiorczyk, T and Hupfer, M and Hilt, S and Gessner, MO}, title = {Rapid Eutrophication of a Clearwater Lake: Trends and Potential Causes Inferred From Phosphorus Mass Balance Analyses.}, journal = {Global change biology}, volume = {30}, number = {11}, pages = {e17575}, doi = {10.1111/gcb.17575}, pmid = {39543974}, issn = {1365-2486}, mesh = {*Eutrophication ; *Lakes/chemistry ; *Phosphorus/analysis ; *Geologic Sediments/analysis/chemistry ; *Seasons ; Environmental Monitoring/methods ; }, abstract = {Many clearwater lakes increasingly show symptoms of eutrophication, but the underlying causes are largely unknown. We combined long-term water chemistry data, multi-year sediment trap measurements, sediment analyses and simple mass balance models to elucidate potential causes of eutrophication of a deep temperate clearwater lake, where total phosphorus (TP) concentrations quadrupled within a decade, accompanied by expanding hypolimnetic anoxia. Discrepancies between modeled and empirically determined P inputs suggest that the observed sharp rise in TP was driven by internal processes. The magnitude of seasonal variation in TP greatly increased at the same time, both in surface and deep water, partly decoupled from deep water oxygen conditions. A positive correlation between annual P loss from the upper water column and hypolimnetic P accumulation could hint at a short-circuited P cycle involving lateral TP transport from shallow-water zones and deposition and release from sediments in deep water. This hypothesis is also supported by P budgets for the upper 20 m during stable summer stratification, suggesting that sediments in shallow lake areas acted as a P net source until 2018. These changes are potentially related to shifts in submerged macrophytes from wintergreen charophyte meadows (Nitellopsis obtusa) to annual free-floating hornwort (Ceratophyllum demersum) and to increased sulfide formation, promoting iron fixation in the sediments. Iron bound to sulfur is unavailable for binding P, resulting in a positive feedback between P release in shallow lake areas, primary productivity, macrophyte community structure and redox-dependent sediment biogeochemistry. Overall, our results suggest that relationships more complex than the commonly invoked increase in internal P release under increasingly anoxic conditions can drive rapid lake eutrophication. Since the proportion of littoral areas is typically large even in deep stratified lakes, littoral processes may contribute more frequently to the rapid lake eutrophication trends observed around the world than is currently recognized.}, }
@article {pmid39541983, year = {2024}, author = {Urtecho, G and Moody, T and Huang, Y and Sheth, RU and Richardson, M and Descamps, HC and Kaufman, A and Lekan, O and Zhang, Z and Velez-Cortes, F and Qu, Y and Cohen, L and Ricaurte, D and Gibson, TE and Gerber, GK and Thaiss, CA and Wang, HH}, title = {Spatiotemporal dynamics during niche remodeling by super-colonizing microbiota in the mammalian gut.}, journal = {Cell systems}, volume = {15}, number = {11}, pages = {1002-1017.e4}, pmid = {39541983}, issn = {2405-4720}, support = {R35 GM143056/GM/NIGMS NIH HHS/United States ; T32 GM007367/GM/NIGMS NIH HHS/United States ; R01 GM130777/GM/NIGMS NIH HHS/United States ; P30 DK132710/DK/NIDDK NIH HHS/United States ; U54 CA272220/CA/NCI NIH HHS/United States ; R21 AI146817/AI/NIAID NIH HHS/United States ; R01 DK118044/DK/NIDDK NIH HHS/United States ; R01 AI132403/AI/NIAID NIH HHS/United States ; R01 EB031935/EB/NIBIB NIH HHS/United States ; }, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Mice ; *Fecal Microbiota Transplantation/methods ; Mice, Inbred C57BL ; Gastrointestinal Tract/microbiology ; Dysbiosis/microbiology ; Mammals/microbiology ; Feces/microbiology ; }, abstract = {While fecal microbiota transplantation (FMT) has been shown to be effective in reversing gut dysbiosis, we lack an understanding of the fundamental processes underlying microbial engraftment in the mammalian gut. Here, we explored a murine gut colonization model leveraging natural inter-individual variations in gut microbiomes to elucidate the spatiotemporal dynamics of FMT. We identified a natural "super-donor" consortium that robustly engrafts into diverse recipients and resists reciprocal colonization. Temporal profiling of the gut microbiome showed an ordered succession of rapid engraftment by early colonizers within 72 h, followed by a slower emergence of late colonizers over 15-30 days. Moreover, engraftment was localized to distinct compartments of the gastrointestinal tract in a species-specific manner. Spatial metagenomic characterization suggested engraftment was mediated by simultaneous transfer of spatially co-localizing species from the super-donor consortia. These results offer a mechanism of super-donor colonization by which nutritional niches are expanded in a spatiotemporally dependent manner. A record of this paper's transparent peer review process is included in the supplemental information.}, }
@article {pmid39541852, year = {2025}, author = {Wang, Q and Wang, M and Yang, Q and Feng, L and Zhang, H and Wang, R and Wang, R}, title = {The role of bacteriophages in facilitating the horizontal transfer of antibiotic resistance genes in municipal wastewater treatment plants.}, journal = {Water research}, volume = {268}, number = {Pt B}, pages = {122776}, doi = {10.1016/j.watres.2024.122776}, pmid = {39541852}, issn = {1879-2448}, mesh = {*Bacteriophages/genetics ; *Gene Transfer, Horizontal ; *Wastewater ; Drug Resistance, Microbial/genetics ; Waste Disposal, Fluid ; Plasmids/genetics ; Bacteria/virology/genetics ; }, abstract = {Bacteriophages play integral roles in the ecosystem; however, their precise involvement in horizontal gene transfer and the spread of antibiotic resistance genes (ARGs) are not fully understood. In this study, a coculture system involving consortia of bacteriophages and multidrug-resistant bacteria from an aerobic tank in a municipal wastewater treatment plant (WWTP) was established to investigate the functions of bacteriophages in ARG transfer and spread. The results of the cocultivation of the MRB and bacteriophage consortia indicated that the bacterial community remained stable throughout the whole process, but the addition of bacteriophages significantly increased ARG abundance, especially in bacteriophage DNA. Nine out of the 11 identified ARGs significantly increased, indicating that more bacteriophage particles carried ARGs in the system after cocultivation. In addition, 686 plasmids were detected during cocultivation, of which only 3.36 % were identified as conjugative plasmids, which is significantly lower than the proportion found among previously published plasmids (25.2 %, totaling 14,029 plasmids). Our findings revealed that bacteriophages may play important roles in the horizontal transfer of ARGs through both bacteriophage-mediated conduction and an increase in extracellular ARGs; however, conjugative transfer may not be the main mechanism by which multidrug-resistant bacteria acquire and spread ARGs. Unlike in most previous reports, a coculture system of diverse bacteria and bacteriophages was established in this study to assess bacteriophage functions in ARG transfer and dissemination in the environment, overcoming the limitations associated with the isolation of bacteria and bacteriophages, as well as the specificity of bacteriophage hosts.}, }
@article {pmid39540979, year = {2024}, author = {Frew, A and Aguilar-Trigueros, CA}, title = {Increasing Phylogenetic Clustering of Arbuscular Mycorrhizal Fungal Communities in Roots Explains Enhanced Plant Growth and Phosphorus Uptake.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {139}, pmid = {39540979}, issn = {1432-184X}, support = {DE220100479//Australian Research Council/ ; }, mesh = {*Mycorrhizae/genetics/physiology ; *Phosphorus/metabolism ; *Plant Roots/microbiology/growth &amp; development ; *Phylogeny ; *Symbiosis ; *Sorghum/microbiology/growth &amp; development ; Soil Microbiology ; Mycobiome ; Biomass ; Plant Development ; }, abstract = {Temporal variation during the assembly of arbuscular mycorrhizal (AM) fungal communities within plant roots have been posited as critical drivers of the plant-fungal symbiotic outcomes. However, functional implications of these dynamics for the host plant remain poorly understood. We conducted a controlled pot experiment with Sorghum bicolor to investigate how temporal shifts in AM fungal community composition and phylogenetic diversity influence plant growth and phosphorus responses to the symbiosis. We characterised the root-colonising AM fungal communities across three time points and explored their community assembly processes by analysing their phylogenetic diversity and employing joint species distribution modelling with the Hierarchical Modelling of Species Communities (HMSC) framework. We found strong AM fungal turnover through time with a high phylogenetic signal, indicating recruitment of phylogenetically clustered AM fungal species in the host. This temporal phylogenetic clustering of communities coincided with marked increases in plant biomass and phosphorus responses to the AM fungal symbiosis, suggesting that host selection for specific fungi may be a key determinant of these benefits.}, }
@article {pmid39537004, year = {2025}, author = {Bernetti, A and Barili, S and Sannino, C and Mugnai, G and Borruso, L and Pinchuk, I and Pezzolla, D and Turchetti, B and Gigliotti, G and Buzzini, P}, title = {Selective response of soil bacterial and fungal taxa to biodegradable polymers.}, journal = {Environmental research}, volume = {264}, number = {Pt 1}, pages = {120344}, doi = {10.1016/j.envres.2024.120344}, pmid = {39537004}, issn = {1096-0953}, mesh = {*Fungi/metabolism/classification ; *Soil Microbiology ; *Bacteria/classification/metabolism/drug effects ; *Biodegradation, Environmental ; Polymers ; Soil/chemistry ; }, abstract = {Biodegradable mulching films offer an eco-friendly alternative to petroleum-based plastics in agriculture, but their effects on soil parameters are not well understood. A microcosm experiment (20 °C, 75% field capacity) investigated the impact of two doses (0.021% and 1% w/w) of a biodegradable polymer on soil chemical and microbiological properties over a year. The 1% dose significantly (p < 0.05) increased CO2 emissions, water-extractable organic C, and hydrolytic activity. A significant (p < 0.05) effect on microbial alpha- and beta-diversity was noted only during short- and medium-term incubations. In contrast, a taxon-related response was found for both bacterial and fungal taxa affecting the abundance of the genera Aquicella, Cellvibrio, Bacillus, Ramlibacter, and Saccharibacteria genera incertae sedis among bacteria, and Malassezia, Orbilia, and Rhodotorula among fungi (including both yeast and filamentous lifestyles). Microbial functions revealed a greater impact on fungal communities compared to bacterial ones. However, after one year of exposition, only a marginal effect on the abundance of both bacterial and fungal functional groups was found in the microcosms. A significantly higher concentration of tightly bound exopolysaccharides in the presence of 1% biodegradable polymer at the start of the experiment suggested their key role in microbial degradation of bioplastics via biofilm formation.}, }
@article {pmid39536049, year = {2024}, author = {Zhao, Y and Cordero, OX and Tikhonov, M}, title = {Linear-regression-based algorithms can succeed at identifying microbial functional groups despite the nonlinearity of ecological function.}, journal = {PLoS computational biology}, volume = {20}, number = {11}, pages = {e1012590}, pmid = {39536049}, issn = {1553-7358}, mesh = {*Algorithms ; Linear Models ; *Ecosystem ; *Computational Biology/methods ; Models, Biological ; Microbiota/physiology ; Nonlinear Dynamics ; }, abstract = {Microbial communities play key roles across diverse environments. Predicting their function and dynamics is a key goal of microbial ecology, but detailed microscopic descriptions of these systems can be prohibitively complex. One approach to deal with this complexity is to resort to coarser representations. Several approaches have sought to identify useful groupings of microbial species in a data-driven way. Of these, recent work has claimed some empirical success at de novo discovery of coarse representations predictive of a given function using methods as simple as a linear regression, against multiple groups of species or even a single such group (the ensemble quotient optimization (EQO) approach). Modeling community function as a linear combination of individual species' contributions appears simplistic. However, the task of identifying a predictive coarsening of an ecosystem is distinct from the task of predicting the function well, and it is conceivable that the former could be accomplished by a simpler methodology than the latter. Here, we use the resource competition framework to design a model where the "correct" grouping to be discovered is well-defined, and use synthetic data to evaluate and compare three regression-based methods, namely, two proposed previously and one we introduce. We find that regression-based methods can recover the groupings even when the function is manifestly nonlinear; that multi-group methods offer an advantage over a single-group EQO; and crucially, that simpler (linear) methods can outperform more complex ones.}, }
@article {pmid39524341, year = {2024}, author = {Dzialo, MC and Arumugam, S and Piampongsant, S and Cool, L and Vanderaa, C and Herrera-Malaver, B and Opsomer, T and Dehaen, W and Wenseleers, T and Roncoroni, M and Alawamleh, A and Wäckers, F and Lievens, B and Hansson, BS and Voordeckers, K and Sachse, S and Verstrepen, KJ}, title = {Drosophila suzukii and Drosophila melanogaster prefer distinct microbial and plant aroma compounds in a complex fermented matrix.}, journal = {iScience}, volume = {27}, number = {11}, pages = {111141}, pmid = {39524341}, issn = {2589-0042}, abstract = {Volatile aroma compounds are important chemical cues for insects. Behavioral responses to specific odors differ strongly between insect species, and the exact causative molecules are often unknown. Beer is frequently used in insect traps because it combines hundreds of plant and microbial aromas that attract many insects. Here, we analyzed responses of the pest fruit fly Drosophila suzukii and benign Drosophila melanogaster to beers with different chemical compositions. Using extensive chemical and behavioral assays, we identified ecologically relevant chemicals that influence drosophilid behavior and that induce different odor-evoked activity patterns in the antennal lobe of the two species obtained by functional imaging. Specific mixes of compounds increased the species-specificity and sex-specificity of lures in both laboratory and greenhouse settings. Together, our study shows how examining insect responses to highly complex natural mixtures of aroma compounds provides insight into insect-specific behavioral responses and also opens avenues for improved pest control.}, }
@article {pmid39535358, year = {2024}, author = {Tidimalo, C and Maximiliano, O and Karen, J and Lebre, PH and Bernard, O and Michelle, G and Oagile, D and Cowan, DA}, title = {Microbial diversity in the arid and semi-arid soils of Botswana.}, journal = {Environmental microbiology reports}, volume = {16}, number = {6}, pages = {e70044}, pmid = {39535358}, issn = {1758-2229}, support = {//PhD bursary for Tidimalo Coetzee from the University of Botswana/ ; //Oppenheimer Foundation/ ; 674-AA-2010-A1//United States Agency for International Development/ ; //University of Pretoria for postdoctoral support/ ; }, mesh = {*Soil Microbiology ; Botswana ; *Bacteria/classification/genetics/isolation &amp; purification ; *Fungi/classification/genetics/isolation &amp; purification ; *RNA, Ribosomal, 16S/genetics ; *Soil/chemistry ; *Biodiversity ; Microbiota/genetics ; Phylogeny ; Hydrogen-Ion Concentration ; DNA, Bacterial/genetics ; }, abstract = {To date, little research has been conducted on the landscape-scale distribution of soil microbial communities and the factors driving their community structures in the drylands of Africa. We investigated the influence of landscape-scale variables on microbial community structure and diversity across different ecological zones in Botswana. We used amplicon sequencing of bacterial 16S rRNA gene and fungal internal transcribed spacers (ITS) and a suite of environmental parameters to determine drivers of microbial community structure. Bacterial communities were dominated by Actinomycetota (21.1%), Pseudomonadota (15.9%), and Acidobacteriota (10.9%). The dominant fungal communities were Ascomycota (57.3%) and Basidiomycota (7.5%). Soil pH, mean annual precipitation, total organic carbon, and soil ions (calcium and magnesium) were the major predictors of microbial community diversity and structure. The co-occurrence patterns of bacterial and fungal communities were influenced by soil pH, with network-specific fungi-bacteria interactions observed. Potential keystone taxa were identified for communities in the different networks. Most of these interactions were between microbial families potentially involved in carbon cycling, suggesting functional redundancy in these soils. Our findings highlight the significance of soil pH in determining the landscape-scale structure of microbial communities in Botswana's dryland soils.}, }
@article {pmid39532738, year = {2024}, author = {Fu, M and Liu, Y and Li, S and Yan, D and Liu, P and Liu, Y and Ji, M}, title = {The Spatial Dynamics of Diazotrophs in the Forefield of Three Tibetan Glaciers.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {138}, pmid = {39532738}, issn = {1432-184X}, support = {42171138//National Natural Science Foundation of China/ ; 32161123004//National Natural Science Foundation of China/ ; 32161123004//National Natural Science Foundation of China/ ; 42171138//National Natural Science Foundation of China/ ; 42171138//National Natural Science Foundation of China/ ; 42171138//National Natural Science Foundation of China/ ; 32161123004//National Natural Science Foundation of China/ ; }, mesh = {*Ice Cover/microbiology ; Tibet ; *Soil Microbiology ; *Nitrogen Fixation ; Soil/chemistry ; Nitrogen/metabolism ; Ecosystem ; Bacteria/classification/metabolism/genetics/isolation &amp; purification/enzymology ; Nitrogen-Fixing Bacteria/metabolism/classification/isolation &amp; purification/genetics ; Phylogeny ; Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Nitrogen is often a limiting nutrient for microbial communities and plants in glacier forefields. Nitrogen-fixing microorganisms (diazotrophs) play an important role in providing bioavailable nitrogen, with their composition determining the nitrogen-fixating capacities. This study investigates the spatial and temporal dynamics of diazotrophs in the forefields of three Tibetan glaciers: Qiangyong, Kuoqionggangri, and Longxiazailongba. We collected soil samples from recently deglaciated barren grounds, and also along an ecosystem succession transect at Kuoqionggangri glacier, encompassing barren ground, herb steppe, legume steppe, and alpine meadow ecosystems. Our finding revealed abundant and diverse diazotrophs in the recently deglaciated barren ground. They are taxonomically affiliated with anaerobic Bradyrhizobium, Desulfobulbus, and Pelobacter, which may be relics from subglacial sediments. The vegetated soils (herb steppe, legume steppe, and alpine meadow) were dominated by phototrophic Nostoc and Anabaena, as well as symbiotic Sinorhizobium. Soil physicochemical parameters, such as soil organic carbon, pH, and nitrate ion, significantly influenced diazotroph community structure. This study highlights the critical role of diazotrophs in mitigating nitrogen limitation during early ecosystem development in glacier forefields. Understanding the distribution and ecological drivers of diazotrophs in these rapidly changing environments provides insights into biogeochemical cycling and ecosystem resilience under climate change.}, }
@article {pmid39528791, year = {2025}, author = {Peixoto, R and Voolstra, CR and Stein, LY and Hugenholtz, P and Salles, JF and Amin, SA and Häggblom, M and Gregory, A and Makhalanyane, TP and Wang, F and Agbodjato, NA and Wang, Y and Jiao, N and Lennon, JT and Ventosa, A and Bavoil, PM and Miller, V and Gilbert, JA}, title = {Microbial solutions must be deployed against climate catastrophe.}, journal = {Nature reviews. Microbiology}, volume = {23}, number = {1}, pages = {1-2}, pmid = {39528791}, issn = {1740-1534}, support = {BAS/1/1095-01-01//King Abdullah University of Science and Technology (KAUST)/ ; }, }
@article {pmid39528727, year = {2024}, author = {Peixoto, R and Voolstra, CR and Stein, LY and Hugenholtz, P and Salles, JF and Amin, SA and Häggblom, M and Gregory, A and Makhalanyane, TP and Wang, F and Agbodjato, NA and Wang, Y and Jiao, N and Lennon, JT and Ventosa, A and Bavoil, PM and Miller, V and Gilbert, JA}, title = {Microbial solutions must be deployed against climate catastrophe.}, journal = {Nature microbiology}, volume = {9}, number = {12}, pages = {3084-3085}, pmid = {39528727}, issn = {2058-5276}, support = {BAS/1/1095-01-01//King Abdullah University of Science and Technology (KAUST)/ ; }, }
@article {pmid39528652, year = {2024}, author = {Peixoto, R and Voolstra, CR and Stein, LY and Hugenholtz, P and Salles, JF and Amin, SA and Häggblom, M and Gregory, A and Makhalanyane, TP and Wang, F and Agbodjato, NA and Wang, Y and Jiao, N and Lennon, JT and Ventosa, A and Bavoil, PM and Miller, V and Gilbert, JA}, title = {Microbial solutions must be deployed against climate catastrophe.}, journal = {npj biodiversity}, volume = {3}, number = {1}, pages = {34}, pmid = {39528652}, issn = {2731-4243}, support = {BAS/1/1095-01-01//King Abdullah University of Science and Technology (KAUST)/ ; }, abstract = {This paper is a call to action. By publishing concurrently across journals like an emergency bulletin, we are not merely making a plea for awareness about climate change. Instead, we are demanding immediate, tangible steps that harness the power of microbiology and the expertise of researchers and policymakers to safeguard the planet for future generations.}, }
@article {pmid39528617, year = {2024}, author = {Peixoto, R and Voolstra, CR and Stein, LY and Hugenholtz, P and Salles, JF and Amin, SA and Häggblom, M and Gregory, A and Makhalanyane, TP and Wang, F and Agbodjato, NA and Wang, Y and Jiao, N and Lennon, JT and Ventosa, A and Bavoil, PM and Miller, V and Gilbert, JA}, title = {Microbial solutions must be deployed against climate catastrophe.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {1466}, pmid = {39528617}, issn = {2399-3642}, support = {BAS/1/1095-01-01//King Abdullah University of Science and Technology (KAUST)/ ; }, abstract = {This paper is a call to action. By publishing concurrently across journals like an emergency bulletin, we are not merely making a plea for awareness about climate change. Instead, we are demanding immediate, tangible steps that harness the power of microbiology and the expertise of researchers and policymakers to safeguard the planet for future generations.}, }
@article {pmid39528577, year = {2024}, author = {Peixoto, R and Voolstra, CR and Stein, LY and Hugenholtz, P and Salles, JF and Amin, SA and Häggblom, M and Gregory, A and Makhalanyane, TP and Wang, F and Agbodjato, NA and Wang, Y and Jiao, N and Lennon, JT and Ventosa, A and Bavoil, PM and Miller, V and Gilbert, JA}, title = {Microbial solutions must be deployed against climate catastrophe.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {122}, pmid = {39528577}, issn = {2055-5008}, support = {BAS/1/1095-01-01//King Abdullah University of Science and Technology (KAUST)/ ; }, abstract = {This paper is a call to action. By publishing concurrently across journals like an emergency bulletin, we are not merely making a plea for awareness about climate change. Instead, we are demanding immediate, tangible steps that harness the power of microbiology and the expertise of researchers and policymakers to safeguard the planet for future generations.}, }
@article {pmid39528441, year = {2024}, author = {Peixoto, R and Voolstra, CR and Stein, LY and Hugenholtz, P and Salles, JF and Amin, SA and Häggblom, M and Gregory, A and Makhalanyane, TP and Wang, F and Agbodjato, NA and Wang, Y and Jiao, N and Lennon, JT and Ventosa, A and Bavoil, PM and Miller, V and Gilbert, JA}, title = {Microbial solutions must be deployed against climate catastrophe.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {9637}, pmid = {39528441}, issn = {2041-1723}, support = {BAS/1/1095-01-01//King Abdullah University of Science and Technology (KAUST)/ ; }, abstract = {This paper is a call to action. By publishing concurrently across journals like an emergency bulletin, we are not merely making a plea for awareness about climate change. Instead, we are demanding immediate, tangible steps that harness the power of microbiology and the expertise of researchers and policymakers to safeguard the planet for future generations.}, }
@article {pmid39528211, year = {2024}, author = {Jang, J and Park, J and Hwang, CY and Gim, Y and Park, KT and Yoon, YJ and Seo, M and Lee, BY}, title = {Selective transmission of airborne bacterial communities from the ocean to the atmosphere over the Northern Pacific Ocean.}, journal = {The Science of the total environment}, volume = {957}, number = {}, pages = {177462}, doi = {10.1016/j.scitotenv.2024.177462}, pmid = {39528211}, issn = {1879-1026}, mesh = {Pacific Ocean ; *Air Microbiology ; *Seawater/microbiology ; *Bacteria/classification ; Environmental Monitoring ; Atmosphere/chemistry ; Aerosols/analysis ; }, abstract = {This study simultaneously measured the taxonomic diversity of bacterial communities in both seawater and PM2.5 aerosol samples collected from the Northern Pacific Ocean during a cruise covering 7724 km between 37°N 126°E and 58°N 179°E. The relative abundance of Proteobacteria, Cyanobacteria, and Firmicutes were found to be more prevalent in aerosol samples (39 ± 16 %, 5.1 ± 1.9 %, and 3.2 ± 1.7 %, respectively) than in seawater samples (26 ± 9 %, 3.8 ± 1.7 %, and 0.02 ± 0.09 %, respectively). The preferential aerosolization of bacterial communities such as Proteobacteria and Firmicutes was likely to be accompanied by a terrestrial origin and high hydrophobicity. Cyanobacteria could undergo increased aerosolization, possibly because of their smaller size in the significantly higher salinity open ocean (32.8 ± 0.14 PSU) compared to those in lower salinity coastal areas (31.3 ± 1.4 PSU). The results of this study indicated that bacterial properties substantially affect their transfer from the ocean to the atmosphere, possibly influencing climate change and public health.}, }
@article {pmid39527614, year = {2024}, author = {Peixoto, R and Voolstra, CR and Stein, LY and Hugenholtz, P and Salles, JF and Amin, SA and Häggblom, M and Gregory, A and Makhalanyane, TP and Wang, F and Agbodjato, NA and Wang, Y and Jiao, N and Lennon, JT and Ventosa, A and Bavoil, PM and Miller, V and Gilbert, JA}, title = {Microbial solutions must be deployed against climate catastrophe.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39527614}, issn = {1751-7370}, }
@article {pmid39527081, year = {2024}, author = {Peixoto, R and Voolstra, CR and Stein, LY and Hugenholtz, P and Falcao Salles, J and Amin, SA and Häggblom, M and Gregory, A and Makhalanyane, TP and Wang, F and Adoukè Agbodjato, N and Wang, Y and Jiao, N and Lennon, JT and Ventosa, A and Bavoil, PM and Miller, V and Gilbert, JA}, title = {Microbial solutions must be deployed against climate catastrophe.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {11}, pages = {}, pmid = {39527081}, issn = {1574-6941}, abstract = {Injecting H2 in deep underground to store this energy carrier will produce artificial subsurface lithoautotrophic microbial ecosystems that modify the taxonomic diversity of indigenous microbial communities and their metabolic activities.}, }
@article {pmid39526991, year = {2025}, author = {Peixoto, R and Voolstra, CR and Stein, LY and Hugenholtz, P and Falcao Salles, J and Amin, SA and Häggblom, M and Gregory, A and Makhalanyane, TP and Wang, F and Agbodjato, NA and Wang, Y and Jiao, N and Lennon, JT and Ventosa, A and Bavoil, PM and Miller, V and Gilbert, JA}, title = {Microbial solutions must be deployed against climate catastrophe.}, journal = {mSystems}, volume = {10}, number = {1}, pages = {e0141624}, pmid = {39526991}, issn = {2379-5077}, }
@article {pmid39526896, year = {2024}, author = {Wei, F and Jiang, H and Zhu, C and Zhong, L and Lin, Z and Wu, Y and Song, L}, title = {The co-fermentation of whole-grain black barley and quinoa improves murine cognitive impairment induced by a high-fat diet via altering gut microbial ecology and suppressing neuroinflammation.}, journal = {Food &amp; function}, volume = {15}, number = {23}, pages = {11667-11685}, doi = {10.1039/d4fo02704c}, pmid = {39526896}, issn = {2042-650X}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Diet, High-Fat/adverse effects ; *Cognitive Dysfunction ; *Mice, Inbred C57BL ; *Chenopodium quinoa/chemistry ; Male ; *Hordeum/chemistry ; *Fermentation ; Neuroinflammatory Diseases/metabolism ; Lactobacillus ; Hippocampus/metabolism ; Brain-Gut Axis ; Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {A high-fat diet (HFD) is associated with various adverse health outcomes, including cognitive impairment and an elevated risk of neurodegenerative conditions. This relationship is partially attributed to the influence of an HFD on the gut microbiota. The objective of this research was to evaluate the neuroprotective benefits of co-fermented black barley and quinoa with Lactobacillus (FG) against cognitive impairments triggered by an HFD and to investigate the microbiota-gut-brain axis mechanisms involved. C57BL/6J mice were randomized into four groups: the normal control group (NC, n = 10), the high-fat diet group (HFD, n = 10), the high-fat diet group supplemented with FG (HFG, 10 mL per kg BW, n = 10), and the high-fat diet group supplemented with Lactobacillus (HFL, 10 mL per kg BW, n = 10). Our results showed that the FG intervention enhanced the behavioral and locomotor skills of the mice, elevated the levels of dopamine (DA) and norepinephrine (NPI) in brain tissues, and alleviated synaptic ultrastructural damage in the hippocampus. Furthermore, FG intervention was observed to exert a protective effect on both the blood-brain barrier and the colonic barrier, as evidenced by an increase in the mRNA levels of Zona occludens-1 (ZO-1), Claudin-4, and Occludin in the hippocampus and colon. These beneficial effects may be attributed to FG's regulation of gut microbiota dysbiosis, which involves the restoration of intestinal flora diversity, reduction of the Firmicutes/Bacteroidetes (F/B) ratio, and a decrease in the levels of pro-inflammatory bacteria such as s_Escherichia coli E and g_Escherichia; moreover, there was an increase in the abundances of anti-inflammatory bacteria, such as s_Bacteroides thetaiotaomicron and s_Parabacteroides goldsteinii. Metagenomic analysis revealed that the FG treatment downregulated the lipopolysaccharide (LPS) pathway and upregulated neurotransmitter biosynthetic pathways. These probiotic effects of FG resulted in reduced production and "leakage" of LPS and decreased mRNA expression of Toll-like receptor 4 (Tlr4), cluster of differentiation 14 (CD14), and myeloid differentiation factor 88 (Myd88) in hippocampal and colon tissues. Consequently, a reduction was observed in the levels of inflammatory cytokines in the serum, hippocampus, and colon, along with suppression of the immunoreactivity of microglia and astrocytes. Our results suggest that FG may serve as an intervention strategy for preventing cognitive impairments caused by an HFD.}, }
@article {pmid39526802, year = {2024}, author = {Schiml, VC and Walter, JM and Hagen, LH and Varnai, A and Bergaust, LL and De Leon, AVP and Elsgaard, L and Bakken, LR and Arntzen, M&#xd8;}, title = {Microbial consortia driving (ligno)cellulose transformation in agricultural woodchip bioreactors.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {12}, pages = {e0174224}, pmid = {39526802}, issn = {1098-5336}, support = {295910//Norges Forskningsr&#xe5;d (Forskningsr&#xe5;det)/ ; NNF20OC0061313//Novo Nordisk Fonden (NNF)/ ; }, mesh = {*Bioreactors/microbiology ; *Lignin/metabolism ; *Microbial Consortia ; Bacteria/metabolism/classification/genetics/isolation &amp; purification ; Denitrification ; Agriculture ; RNA, Ribosomal, 16S/genetics ; Cellulose/metabolism ; Wood/metabolism/microbiology ; }, abstract = {UNLABELLED: Freshwater ecosystems can be largely affected by neighboring agriculture fields where potential fertilizer nitrate run-off may leach into surrounding water bodies. To counteract this eutrophic driver, farmers in certain areas are utilizing denitrifying woodchip bioreactors (WBRs) in which a consortium of microorganisms convert the nitrate into nitrogen gases in anoxia, fueled by the degradation of lignocellulose. Polysaccharide-degrading strategies have been well described for various aerobic and anaerobic systems, including the use of carbohydrate-active enzymes, utilization of lytic polysaccharide monooxygenases (LPMOs) and other redox enzymes, as well as the use of cellulosomes and polysaccharide utilization loci (PULs). However, for denitrifying microorganisms, the lignocellulose-degrading strategies remain largely unknown. Here, we have applied a combination of enrichment techniques, gas measurements, multi-omics approaches, and amplicon sequencing of fungal ITS and procaryotic 16S rRNA genes to identify microbial drivers for lignocellulose transformation in woodchip bioreactors and their active enzymes. Our findings highlight a microbial community enriched for (ligno)cellulose-degrading denitrifiers with key players from the taxa Giesbergeria, Cellulomonas, Azonexus, and UBA5070 (Fibrobacterota). A wide substrate specificity is observed among the many expressed carbohydrate-active enzymes (CAZymes) including PULs from Bacteroidetes. This suggests a broad degradation of lignocellulose subfractions, including enzymes with auxiliary activities whose functionality is still puzzling under strict anaerobic conditions.<br><br>IMPORTANCE: Freshwater ecosystems face significant threats from agricultural runoff, which can lead to eutrophication and subsequent degradation of water quality. One solution to mitigate this issue is using denitrifying woodchip bioreactors (WBRs), where microorganisms convert nitrate into nitrogen gases utilizing lignocellulose as a carbon source. Despite the well-documented polysaccharide-degrading strategies in various systems, the mechanisms employed by denitrifying microorganisms in WBRs remain largely unexplored. This study fills a critical knowledge gap by revealing the degrading strategies of denitrifying microbial communities in WBRs. By integrating state-of-the-art techniques, we have identified key microbial drivers including Giesbergeria, Cellulomonas, Azonexus, and UBA5070 (Fibrobacterota) playing significant roles in lignocellulose transformation and showcasing a broad substrate specificity and complex metabolic capability. Our findings advance the understanding of microbial ecology in WBRs and by revealing the enzymatic activities, this research may inform efforts to improve water quality, protect aquatic ecosystems, and reduce greenhouse gas emissions from WBRs.}, }
@article {pmid39520764, year = {2025}, author = {Rodriguez-Caturla, MY and Margalho, LP and Graça, JS and Pia, AKR and Xavier, VL and Noronha, MF and Cabral, L and Lemos-Junior, WJF and Castillo, CJC and SantˈAna, AS}, title = {Bacterial dynamics and volatile metabolome changes of vacuum-packaged beef with different pH during chilled storage.}, journal = {International journal of food microbiology}, volume = {427}, number = {}, pages = {110955}, doi = {10.1016/j.ijfoodmicro.2024.110955}, pmid = {39520764}, issn = {1879-3460}, mesh = {*Volatile Organic Compounds/analysis/metabolism ; Hydrogen-Ion Concentration ; Vacuum ; Cattle ; Animals ; *Red Meat/microbiology ; *Food Packaging/methods ; *Food Microbiology ; *Food Storage ; Bacteria/metabolism/growth &amp; development/classification/genetics/isolation &amp; purification ; Metabolome ; Brazil ; RNA, Ribosomal, 16S/genetics ; }, abstract = {This study aimed to assess the growth of spoilage bacteria in Brazilian vacuum-packed beef across different pH ranges (5.4-5.8, 5.8-6.1, ≥6.1) stored at temperatures of 0 °C, 4 °C, and 7 °C. Additionally, the research sought to identify predominant spoilage bacteria at the genus level using 16S rDNA gene sequencing and analyze the principal volatile organic compounds (VOCs) produced by this microbiota through HS-SPME/GC-MS. Lactic acid bacteria (LAB) consistently exhibited counts exceeding 6.0 Log CFU/g, regardless of temperature and pH conditions. The bacterial diversity in the meat samples reflected the influence of slaughterhouse environments, with Pseudomonas and Serratia remaining dominant across different cuts and pH levels. Post-storage, variations in pH and temperature modulated the initial bacterial diversity, leading to a reduction in diversity and an increase in LAB such as Lactobacillus, Lactococcus, Leuconostoc, and Carnobacterium. Notably, these changes were observed within pH ranges of 5.4-5.8 and 5.8-6.1, irrespective of beef cuts and storage temperatures. Based on high throughput sequencing and VOCS, correlation analysis revealed a relationship between the growth of specific spoilage microorganisms under vacuum conditions and the presence of VOCs such as alcohols (e.g., 1-propanol, 2-methyl-) and ketones (e.g., 2-nonanone, 2-octanone, 2-heptanone), identifying them as potential indicators of spoilage bacteria growth.}, }
@article {pmid39520558, year = {2024}, author = {Boadella, J and Butturini, A and Doménech-Pascual, A and Freixinos, Z and Perujo, N and Urmeneta, J and Vidal, A and Romaní, AM}, title = {Microbial Life in Playa-Lake Sediments: Adapted Structure, Plastic Function to Extreme Water Activity Variations.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {137}, pmid = {39520558}, issn = {1432-184X}, support = {PID2021-123735OB-C21//Spanish Ministry of Science, Innovation and Universities/ ; PID2021-123735OB-C21//Spanish Ministry of Science, Innovation and Universities/ ; PID2021-123735OB-C21//Spanish Ministry of Science, Innovation and Universities/ ; PID2021-123735OB-C21//Spanish Ministry of Science, Innovation and Universities/ ; 2020 FISDU 00465//Catalan Government Ministry of Business and Knowledge, Area of Universities and Research/ ; }, mesh = {*Lakes/microbiology/chemistry ; *Geologic Sediments/microbiology/chemistry ; *Biofilms/growth &amp; development ; *Salinity ; *Bacteria/classification/genetics/metabolism ; Biomass ; Droughts ; Water ; }, abstract = {Saline shallow lakes in arid and semi-arid regions frequently undergo drying episodes, leading to significant variations in salinity and water availability. Research on the impacts of salinity and drought on the structure and function of biofilms in hypersaline shallow lakes is limited. This study aimed to understand the potential changes of biofilms in playa-lake sediments during the drying process. Sediments were sampled at different depths (surface, subsurface) and hydrological periods (wet, retraction, and dry), which included a decrease in water activity (aw, the availability of water for microbial use) from 0.99 to 0.72. aw reduction caused a greater effect on functional variables compared to structural variables, indicating the high resistance of the studied biofilms to changes in salinity and water availability. Respiration and hydrolytic extracellular enzyme activities exhibited higher values under high aw, while phenol oxidase activity and prokaryote biomass increased at lower aw. This shift occurred at both depths but was more pronounced at the surface, possibly due to the more extreme conditions (up to 0.7 aw). The increased levels of extracellular polymeric substances and carotenoids developed at low aw may help protect microorganisms in high salinity and drought environments. However, these harsh conditions may interfere with the activity of hydrolytic enzymes and their producers, while promoting the growth of resistant prokaryotes and their capacity to obtain C and N sources from recalcitrant compounds. The resilience of biofilms in hypersaline lakes under extreme conditions is given by their resistant biochemichal structure and the adaptability of their microbial functioning.}, }
@article {pmid39516195, year = {2024}, author = {Speth, DR and Zeller, LM and Graf, JS and Overholt, WA and Küsel, K and Milucka, J}, title = {Genetic potential for aerobic respiration and denitrification in globally distributed respiratory endosymbionts.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {9682}, pmid = {39516195}, issn = {2041-1723}, mesh = {*Symbiosis ; *Phylogeny ; *Denitrification ; Metagenome ; Aerobiosis ; Ciliophora/genetics/metabolism ; Groundwater/microbiology ; Gammaproteobacteria/genetics/metabolism ; Germany ; Electron Transport Complex IV/genetics/metabolism ; California ; Genome, Bacterial ; }, abstract = {The endosymbiont Candidatus Azoamicus ciliaticola was proposed to generate ATP for its eukaryotic host, an anaerobic ciliate of the Plagiopylea class, fulfilling a function analogous to mitochondria in other eukaryotic cells. The discovery of this respiratory endosymbiosis has major implications for both evolutionary history and ecology of microbial eukaryotes. However, with only a single species described, knowledge of its environmental distribution and diversity is limited. Here we report four complete, circular metagenome assembled genomes (cMAGs) representing respiratory endosymbionts inhabiting groundwater in California, Ohio, and Germany. These cMAGs form two lineages comprising a monophyletic clade within the uncharacterized gammaproteobacterial order UBA6186, enabling evolutionary analysis of their key protein complexes. Strikingly, all four cMAGs encode a cytochrome cbb3 oxidase, which indicates that these endosymbionts have the capacity for aerobic respiration. Accordingly, we detect these respiratory endosymbionts in diverse habitats worldwide, thus further expanding the ecological scope of this respiratory symbiosis.}, }
@article {pmid39513042, year = {2024}, author = {Park, KJ and Gao, Y}, title = {Gut-brain axis and neurodegeneration: mechanisms and therapeutic potentials.}, journal = {Frontiers in neuroscience}, volume = {18}, number = {}, pages = {1481390}, pmid = {39513042}, issn = {1662-4548}, abstract = {This paper reviews the effects of gut microbiota in regulating neurodegenerative diseases through controlling gut-brain axis. Specific microbial populations and their metabolites (short-chain fatty acids and tryptophan derivatives) regulate neuroinflammation, neurogenesis and neural barrier integrity. We then discuss ways by which these insights lead to possible interventions - probiotics, prebiotics, dietary modification, and fecal microbiota transplantation (FMT). We also describe what epidemiological and clinical studies have related certain microbiota profiles with the courses of neurodegenerative diseases and how these impact the establishment of microbiome-based diagnostics and individualized treatment options. We aim to guide microbial ecology research on this key link to neurodegenerative disorders and also to highlight collaborative approaches to manage neurological health by targeting microbiome-related factors.}, }
@article {pmid39511174, year = {2024}, author = {Chen, SC and Chen, S and Musat, N and Kümmel, S and Ji, J and Lund, MB and Gilbert, A and Lechtenfeld, OJ and Richnow, HH and Musat, F}, title = {Back flux during anaerobic oxidation of butane support archaea-mediated alkanogenesis.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {9628}, pmid = {39511174}, issn = {2041-1723}, support = {NNF22OC0071609//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; ERC-RA-0020//Helmholtz Association/ ; 101059607//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Sk&#x142;odowska-Curie Actions (H2020 Excellent Science - Marie Sk&#x142;odowska-Curie Actions)/ ; 12471341//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Oxidation-Reduction ; Anaerobiosis ; *Archaea/metabolism/genetics ; *Butanes/metabolism ; *Carbon Dioxide/metabolism ; Oxidoreductases/metabolism/genetics ; Kinetics ; Alkanes/metabolism ; Thermodynamics ; }, abstract = {Microbial formation and oxidation of volatile alkanes in anoxic environments significantly impacts biogeochemical cycles on Earth. The discovery of archaea oxidizing volatile alkanes via deeply branching methyl-coenzyme M reductase variants, dubbed alkyl-CoM reductases (ACR), prompted the hypothesis of archaea-catalysed alkane formation in nature (alkanogenesis). A combination of metabolic modelling, anaerobic physiology assays, and isotope labeling of Candidatus Syntrophoarchaeum archaea catalyzing the anaerobic oxidation of butane (AOB) show a back flux of CO2 to butane, demonstrating reversibility of the entire AOB pathway. Back fluxes correlate with thermodynamics and kinetics of the archaeal catabolic system. AOB reversibility supports a biological formation of butane, and generally of higher volatile alkanes, helping to explain the presence of isotopically light alkanes and deeply branching ACR genes in sedimentary basins isolated from gas reservoirs.}, }
@article {pmid39509969, year = {2024}, author = {Aparicio, S and Ríos-Mejía, A and Gallardo-Mejías, JP and Robles, &#xc1; and Borrás, L}, title = {Microalgae-bacteria consortia dynamics in a long term operated membrane-coupled high-rate algal pond (MHRAP).}, journal = {Journal of environmental management}, volume = {371}, number = {}, pages = {123186}, doi = {10.1016/j.jenvman.2024.123186}, pmid = {39509969}, issn = {1095-8630}, mesh = {*Microalgae ; *Wastewater/microbiology ; *Bacteria/metabolism/classification ; Ponds/microbiology ; Waste Disposal, Fluid/methods ; Biomass ; }, abstract = {Traditional activated sludge-based technologies have significant drawbacks, including high energy requirements and greenhouse gas emissions. Microalgae-based processes offer a promising, low-cost, and environmentally friendly alternative. However, the knowledge of treatment systems based on microalgae-bacteria consortia is limited, and even more so is their microbial composition and its relationship with operational parameters. Thus, this study explores the dynamics of microalgae-bacteria consortia in a long-term operated membrane-coupled high-rate algal pond (MHRAP) for wastewater treatment. For this, a pilot-scale MHRAP plant, located in a wastewater treatment plant in Valencia (Spain), was monitored under various hydraulic retention times (HRT) and wastewater influents: i) effluent from a primary settler and ii) effluent form pre-treatment. The biomass retention time was kept constant at 6 days. The composition of the bacterial community was studied through 16S rDNA sequencing, while 18S rDNA sequencing was used to study the microalgae. The results indicate that shorter HRTs significantly increased bacterial diversity, but not eukarya. Principal Co-ordinates Analysis (PCoA) revealed that the HRT and the incoming wastewater quality control the type of the bacterial populations. However, this effect was not observed in eukaryotic organisms. The dominant microalgae genera identified were Desmodesmus and Coelastrella, with Coelastrella becoming more prevalent at shorter HRTs. For bacteria, Verrumicrobiota dominated (18-56%) at high HRT while Proteobacteria was dominant (28-44%) at HRTs below 6 days. The changes observed in the bacterial composition, including the ammonia oxidizing bacteria (AOB) community (mainly Nitrosomonas), suggest that photo-inhibition could be taking place. The nitrite oxidizing bacteria (NOB) community was dominated by Nitrospira and Candidatus Nitrotoga. Operational parameters such as light intensity, pH, and nitrite concentration were found to significantly influence the microbial community structure. Higher light intensity and alkaline pH favored the growth of Desmodesmus, while Coelastrella thrived under lower HRTs. Bacterial diversity plays a crucial role in the treatment process, while microalgae primarily support aerobic bacterial processes by providing oxygen. These findings contribute to a deeper understanding of the complex biological processes in microalgae-bacteria consortia and offer insights into improving wastewater treatment technologies.}, }
@article {pmid39508609, year = {2024}, author = {Xue, S-J and Liu, J and Zhao, F-Y and Zhang, X-T and Zhu, Z-Q and Zhang, J-Y}, title = {Spatio-temporal distribution and biotechnological potential of culturable yeasts in the intertidal sediments and seawater of Aoshan Bay, China.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {12}, pages = {e0157024}, pmid = {39508609}, issn = {1098-5336}, support = {1120015//the Advanced Talents Foundation of Qingdao Agricultural University/ ; tsqn201909133//the Young experts of Taishan Scholars in Shandong Province/ ; 1120011//the Initiative grant for high-level personnel recruitment in Qingdao Agricultural University/ ; CARS-47//the earmarked fund/ ; }, mesh = {*Geologic Sediments/microbiology ; China ; *Seawater/microbiology ; *Yeasts/genetics/classification/isolation &amp; purification/metabolism ; *Bays/microbiology ; Biodiversity ; Biotechnology ; Spatio-Temporal Analysis ; Ecosystem ; Microbiota ; }, abstract = {Marine yeasts play a crucial role in marine microbial ecology, facilitating the biogeochemical cycling of carbon and nitrogen in marine ecosystems, while also serving as important reservoirs of bioactive compounds with extensive applications in pharmaceuticals, agriculture, and various industries. Intertidal flats, characterized by their complex ecological dynamics, are postulated to harbor a wealth of yeast resources. This study employed a culture-dependent approach to assess the diversity, spatio-temporal distribution, and biotechnological potential of yeast communities residing within the intertidal sediments and seawater of Aoshan Bay. A total of 392 yeast strains were identified from 20 distinct genera, encompassing 43 recognized species and four candidate novel species. Notably, 17 of these species were identified as novel occurrences in marine environments, underscoring the rich yeast biodiversity of the Aoshan Bay ecosystem, with Candida emerging as the dominant genus in both sedimentary and aqueous habitats. Yeast community composition exhibited significant spatial and temporal variation, with peak diversity and abundance observed in autumn, the subtidal zone, and the surface soil layer. No clear pattern, however, emerged linking these shifts to specific changes in community composition, highlighting the complex interactions between microbial communities, environmental variables, and anthropogenic disturbance. Although several yeast species isolated here have been previously recognized for their biotechnological potential, their diverse and abundant extracellular enzyme profiles were characterized, further highlighting their crucial role in organic matter decomposition and nutrient cycling within the tidal ecosystem, as well as their potential applicability in the food, fine chemical, textile, and pharmaceutical industries.IMPORTANCEThis study presents groundbreaking insights into the yeast diversity of Aoshan Bay, offering invaluable information on their spatial and temporal distribution patterns, as well as their biotechnological potential in the tidal environment. The findings reveal that the eutrophic intertidal flat is a rich repository of yeasts with abundant extracellular enzymatic activity and an important role in nutrient cycling and decomposition processes. Also, these yeasts serve as crucial indicators of ecosystem health and function and are excellent candidates for biotechnological and industrial applications. Collectively, this study not only expands our knowledge of the diversity and distribution of intertidal yeasts but also highlights their promising potential for biotechnological applications.}, }
@article {pmid39505133, year = {2025}, author = {Hu, Y and Song, Y and Cai, J and Chao, J and Gong, Y and Jiang, X and Shao, K and Tang, X and Gao, G}, title = {Stronger biogeographical pattern of bacterioplankton communities than biofilm communities along a riverine ecosystem: A local scale study of the Kaidu river in the arid and semi-arid northwest of China.}, journal = {Environmental research}, volume = {264}, number = {Pt 1}, pages = {120294}, doi = {10.1016/j.envres.2024.120294}, pmid = {39505133}, issn = {1096-0953}, mesh = {China ; *Biofilms/growth &amp; development ; *Rivers/microbiology ; *Plankton ; *Bacteria/classification/genetics ; Ecosystem ; }, abstract = {Although the biogeographical pattern and mechanisms underlying microbial assembly have been well-explored in lentic ecosystems, the relevant scenarios in lotic ecosystems remain poorly understood. By sequencing the bacterial communities in bacterioplankton and biofilm, our study detected their distance-decay relationship (DDR), and the balance between deterministic and stochastic processes, along the Kaidu river in an arid and semi-arid region of northwest China. Our results revealed that bacterioplankton and biofilm had significantly contrasting community structures. The bacterioplankton communities showed a gradually decreasing trend in alpha-diversity from the headwater to the river mouth, contrasting with the alpha-diversity of biofilm communities which was constant along the river length. Both bacterioplankton and biofilm showed significant DDRs along the 500-km river corridor with the slope of the bacterioplankton DDR being steeper than that of the biofilm DDR, which implies a stronger biogeography of bacterioplankton than biofilm. Relative to biofilm communities, the species interactions formed a denser and more complex network in the bacterioplankton communities than in the biofilm communities. Our results also revealed that there was a transition of community assembly from deterministic to stochastic processes upstream to downstream, although both the bacterioplankton and biofilm communities were mainly regulated by deterministic processes within the entire river. All these empirical results expand our knowledge of microbial ecology in an arid and semi-arid lotic ecosystem.}, }
@article {pmid39503489, year = {2024}, author = {Teixeira, GM and Cordeiro Montanari, GC and Nicoletto, MLA and da Silva, DV and Noriler, SA and de Oliveira, JP and da Silva Rodrigues, MV and Sipoli Sanches, D and de Padua Pereira, U and Nunes da Rocha, U and Oliveira, AGd}, title = {Draft genome of Bacillus velezensis CMRP6330, a suitable biocontrol agent for disease management in crops.}, journal = {Microbiology resource announcements}, volume = {13}, number = {12}, pages = {e0065724}, pmid = {39503489}, issn = {2576-098X}, support = {305899/2021-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; 465133/2014-4//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; 460129525//Deutsche Forschungsgemeinschaft (DFG)/ ; }, abstract = {As a biological alternative to managing diseases in crop production, we highlight the Bacillus velezensis strain LABIM41 (CMRP6330). Its genome, composed of 3,970,959 bp, possesses a rich metabolic machinery and a wide range of molecules with different biological activities and roles in its symbiotic relationship with its plant hosts.}, }
@article {pmid39502209, year = {2024}, author = {Kipkoech, R and Takase, M and Ahogle, AMA and Ocholla, G}, title = {Analysis of properties of biodiesel and its development and promotion in Ghana.}, journal = {Heliyon}, volume = {10}, number = {20}, pages = {e39078}, pmid = {39502209}, issn = {2405-8440}, abstract = {The increasing global population and the challenges associated with fossil fuel has led to a surge in energy demand, necessitating research on renewable and environmentally friendly energy sources. Biodiesel, is produced from biomass materials like vegetable oil and fats, is a promising alternative. Transesterification is a principal method used in biodiesel production, as it is simple, versatile, and efficient. Biodiesel offers several advantages, including emissions, lubricity, and safety, making it a sustainable fuel option and its properties conforms to the international standards. However, it has lower energy content, cold weather performance issues, and slightly reduced engine power compared to petroleum diesel. The choice of biodiesel feedstock depends on its properties, with jatropha oil and other feedstocks being potential in Ghana. Research on biodiesel in Ghana is still in early stages and the Ghanaian government's policy aims to replace 10 % of petroleum fuel with biofuel by 2020 and 20 % by 2030, but these goals have not been achieved due to barriers. Despite these challenges, the government and stakeholders in the biofuel industry are working to optimize the biodiesel sector for sustainability, efficiency, and scalability. Innovative cultivation techniques and low-cost oil extraction methods are required, necessitating interdisciplinary research collaborations. By capitalizing on these opportunities and implementing targeted interventions, Ghana can become a regional leader in sustainable biodiesel production.}, }
@article {pmid39501667, year = {2025}, author = {You, Z and Zhang, X and Huang, S and Chen, D and Zhu, Y and Li, G and Chen, X}, title = {The influence of skin microbial ecology on γδ T-cell immune pathways in allergic dermatitis models in mice.}, journal = {Journal of leukocyte biology}, volume = {117}, number = {5}, pages = {}, doi = {10.1093/jleuko/qiae244}, pmid = {39501667}, issn = {1938-3673}, mesh = {Animals ; *Dermatitis, Atopic/immunology/microbiology/pathology ; *Skin/microbiology/immunology/pathology ; *Microbiota/immunology ; Disease Models, Animal ; Mice ; *Receptors, Antigen, T-Cell, gamma-delta/immunology/metabolism ; RNA, Ribosomal, 16S/genetics ; Cytokines/metabolism ; Immunoglobulin E/blood ; Female ; *Intraepithelial Lymphocytes/immunology ; }, abstract = {Atopic dermatitis is a complex disease influenced by alterations in the skin microbiome and immune dysregulation. Despite the recognized role of these factors, the specific pathways by which distinct microbial populations affect skin immunity remain insufficiently understood. On a molecular level, the pathogenesis of atopic dermatitis involves critical cytokines such as IL-4, IL-17, interferon-γ, and IL-10, which contribute to the imbalance in T helper cell responses. Importantly, gamma-delta (γδ) T cells, which produce these cytokines and infiltrate affected epithelial cells in atopic dermatitis, have been underexplored. This study seeks to alleviate atopic dermatitis symptoms in mice by adjusting both peripheral and local immune environments through the transplantation of skin microbiota. By employing 16S rRNA sequencing, we characterized the skin microbiome of the mouse model. Our results demonstrate that microbiota intervention significantly reduces skin thickening and serum IgE levels in DNCB-induced atopic dermatitis mice. Additionally, changes in skin microbiota modulated immune cell dynamics, restoring the T helper 1 / T helper 2 balance and leading to clinical improvement. These findings highlight the critical role of skin microbiota in shaping immune responses, positioning microbiota-based therapies as a potential treatment for atopic dermatitis.}, }
@article {pmid39501615, year = {2025}, author = {Prost-Boxoen, L and Bafort, Q and Van de Vloet, A and Almeida-Silva, F and Paing, YT and Casteleyn, G and D'hondt, S and De Clerck, O and Van de Peer, Y}, title = {Asymmetric genome merging leads to gene expression novelty through nucleo-cytoplasmic disruptions and transcriptomic shock in Chlamydomonas triploids.}, journal = {The New phytologist}, volume = {245}, number = {2}, pages = {869-884}, pmid = {39501615}, issn = {1469-8137}, support = {833522//H2020 European Research Council/ ; I001621N//European Marine Biological Resource Centre Belgium/ ; 11H0426N//Fonds Wetenschappelijk Onderzoek/ ; G0C0116N//Fonds Wetenschappelijk Onderzoek/ ; 833522/ERC_/European Research Council/International ; BOF.MET.2021.0005.01//Bijzonder Onderzoeksfonds UGent/ ; 1168420N//Fonds Wetenschappelijk Onderzoek/ ; }, mesh = {*Genome, Plant ; *Transcriptome/genetics ; *Chlamydomonas reinhardtii/genetics ; *Cell Nucleus/metabolism/genetics ; *Cytoplasm/metabolism/genetics ; Triploidy ; Gene Expression Regulation, Plant ; Genetic Fitness ; }, abstract = {Genome merging is a common phenomenon causing a wide range of consequences on phenotype, adaptation, and gene expression, yet its broader implications are not well-understood. Two consequences of genome merging on gene expression remain particularly poorly understood: dosage effects and evolution of expression. We employed Chlamydomonas reinhardtii as a model to investigate the effects of asymmetric genome merging by crossing a diploid with a haploid strain to create a novel triploid line. Five independent clonal lineages derived from this triploid line were evolved for 425 asexual generations in a laboratory natural selection experiment. Utilizing fitness assays, flow cytometry, and RNA-Seq, we assessed the immediate consequences of genome merging and subsequent evolution. Our findings reveal substantial alterations in genome size, gene expression, protein homeostasis, and cytonuclear stoichiometry. Gene expression exhibited expression-level dominance and transgressivity (i.e. expression level higher or lower than either parent). Ongoing expression-level dominance and a pattern of 'functional dominance' from the haploid parent was observed. Despite major genomic and nucleo-cytoplasmic disruptions, enhanced fitness was detected in the triploid strain. By comparing gene expression across generations, our results indicate that proteostasis restoration is a critical component of rapid adaptation following genome merging in Chlamydomonas reinhardtii and possibly other systems.}, }
@article {pmid39500284, year = {2024}, author = {Arrigan, D and Kothe, CI and Oliverio, A and Evans, JD and Wolfe, BE}, title = {Novel fermentations integrate traditional practice and rational design of fermented-food microbiomes.}, journal = {Current biology : CB}, volume = {34}, number = {21}, pages = {R1094-R1108}, doi = {10.1016/j.cub.2024.09.047}, pmid = {39500284}, issn = {1879-0445}, mesh = {*Fermented Foods/microbiology ; *Fermentation ; *Microbiota ; *Food Microbiology/methods ; Humans ; }, abstract = {Fermented foods and beverages have been produced around the world for millennia, providing humans with a range of gastronomic, cultural, health, and scientific benefits. Building on these traditional forms, a convergence of factors, including culinary innovation, globalization, shifts in consumer preferences, and advances in microbiome sciences, has led to the emergence of so-called 'novel fermentations'. In this review, we define novel fermentation as the confluence of traditional food practices and rational microbiome design. Using principles of microbial ecology and evolution, we develop a microbiological framework that outlines several strategies for producing and characterizing novel fermentations, including switching substrates, engrafting target species, assembling whole-community chimeras, and generating novel phenotypes. A subsequent analysis of existing traditional ferments points to gaps in 'fermentation space' where novel ferments could potentially be produced using new combinations of microbes and food substrates. We highlight some important safety and sociocultural issues presented by the repurposing and modification of microbes from traditional ferments that fermented-food producers and microbiologists need to address.}, }
@article {pmid39499580, year = {2024}, author = {Zhang, X and Zhang, XX and Ma, L}, title = {New Horizons in Micro/Nanoplastic-Induced Oxidative Stress: Overlooked Free Radical Contributions and Microbial Metabolic Dysregulations in Anaerobic Digestion.}, journal = {Environmental science &amp; technology}, volume = {58}, number = {48}, pages = {21251-21264}, doi = {10.1021/acs.est.4c08865}, pmid = {39499580}, issn = {1520-5851}, mesh = {*Oxidative Stress ; Anaerobiosis ; Free Radicals/metabolism ; *Reactive Oxygen Species/metabolism ; }, abstract = {Excessive production of reactive oxygen species (ROS) induced by micro/nanoplastics (MPs/NPs) is highly toxic to microbes. However, the mechanisms underlying ROS generation and metabolic regulation within anaerobic guilds remain poorly understood. In this study, we investigated the effects of environmentally relevant levels of polypropylene (PP)-MPs/NPs on oxidative stress and microbial ecology during anaerobic digestion (AD). Electron paramagnetic resonance spectroscopy revealed that PP-MPs/NPs elevated the concentrations of environmentally persistent free radicals (EPFRs) and derived hydroxyl radicals ([•]OH). EPFRs were identified as the primary contributors to [•]OH generation, as evidenced by a high Spearman correlation coefficient (r = 0.884, p < 0.001) and free radical-quenching studies. The formation of [•]OH enhanced ROS production by 86.2-100.9%, resulting in decreased cellular viability and methane production (by 37.5-50.5%) at 100 mg/g TS PP-MPs/NPs. Genome-centric metagenomic and metatranscriptomic analyses suggested that PP-MPs/NPs induced the reassembly of community structures, re-evolution of functional traits, and remodeling of interspecies interactions. Specifically, PP-MPs/NPs induced a shift in methanogen consortia from hydrogenotrophic Methanofollis sp. to acetoclastic and hydrogenotrophic Methanothrix soehngenii, primarily because of the latter's diverse ingestion patterns, electron bifurcation complexes, and ROS-scavenging abilities. Downregulation of genes associated with antioxidative defense systems (i.e., sodN, katA, and osmC) and ROS-driven redox signal transduction pathways (c-di-AMP and phosphorylation signaling pathways) provided insights into the mechanisms underlying ROS-induced microbial metabolic dysregulation. Our findings enhance the understanding of microbial ecological and metabolic traits under MPs/NPs stressors, facilitating the control of MPs/NPs toxicity and the stabilization of AD processes.}, }
@article {pmid39498487, year = {2024}, author = {Dooley, KD and Henry, LP and Bergelson, J}, title = {Impact of timing on the invasion of synthetic bacterial communities.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39498487}, issn = {1751-7370}, support = {//Hutchinson Fund at The University of Chicago/ ; //The Simons Foundation/ ; 951444//ERC Synergy/ ; }, mesh = {*Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; Biodiversity ; Introduced Species ; Time Factors ; }, abstract = {Microbial communities regularly experience ecological invasions that can lead to changes in composition and function. Factors thought to impact susceptibility to invasions, such as diversity and resource use, vary over the course of community assembly. We used synthetic bacterial communities to evaluate the success and impact of invasions occurring at different times during the community assembly process. Fifteen distinct communities were subjected to each of three bacterial invaders at the initial assembly of the community ("initial invasion"), 24 h into community assembly ("early invasion"), when the community was still undergoing transient dynamics, and 7 days into community assembly ("late invasion"), once the community had settled into its final composition. Communities were passaged daily and characterized through sequencing after reaching a stable composition. Invasions often failed to persist over time, particularly in higher richness communities. However, invasions had their largest effect on composition when they occurred before a community had settled into a stable composition. We found instances where an invader was ultimately excluded yet had profound and long-lasting effects on invaded communities. Invasion outcome was positively associated with lower community richness and resource use efficiency by the community, which varied throughout assembly. Our results demonstrate that microbial communities experiencing transient community dynamics are more affected by, and in some instances prone to, invasion, a finding relevant to efforts to modify the composition of microbial communities.}, }
@article {pmid39498135, year = {2024}, author = {Gu, Y and Meng, D and Liu, Z and Zhang, M and Yang, Z and Yin, H and Liang, Y and Xiao, N}, title = {Biotic and abiotic properties mediating sediment microbial diversity and function in a river-lake continuum.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1479670}, pmid = {39498135}, issn = {1664-302X}, abstract = {A river-lake system plays an important role in water management by providing long-term and frequent water diversions. However, hydrological connectivity in the system can have a profound effect on sediment microbial communities through pH, nutrient concentrations, and benthos invertebrates. Consequently, identifying the key environmental factors and their driving mechanisms is vital for microbial adaptation strategies to extreme environments. In this study, we analyzed the significant difference in sediment bacterial and fungal community structures and diversity indices among Dongting Lake and its tributary rivers, which worked as a typical river-connected lake ecosystem. There were significant differences in biotic and abiotic environments in the sediment habitats of Dongting Lake and its tributary rivers. Random forest analysis revealed that pH and Mollusca were found to be the most important abiotic and biotic variables for predicting both bacterial and fungal community structures, respectively. The beta diversity decomposition analyses showed that the bacterial and fungal community compositional dissimilarities among different sections were dominated by species replacement processes, with more than half of the OTUs in each section being unique. Notably, both biotic and abiotic factors affected the number and the relative abundance of these bacterial and fungal unique OTUs, leading to changes in community composition. Mollusca, pH, TP, NO3-N, and NH4-N were negatively related to the relative abundance of Actinobacteria, Acidobacteria, Gemmatimonadetes, Planctomycetes, and Ascomycota, while Annelida and ORP were positively related to the relative abundance of Actinobacteria and Gemmatimonadetes. Additionally, PICRUSt analysis revealed that the functional dissimilarity among lakes and rivers was strengthened in unique species compared to all species in bacterial and fungal communities, and the changes of functional types helped to improve the habitat environment in the main Dongting Lake and promote the process of microbial growth. From our results, the role of macrozoobenthos and physicochemical characteristics in driving the sediment microbial community spatial variations became clear, which contributed to further understanding of the river-lake ecosystem.}, }
@article {pmid39497067, year = {2024}, author = {Moeller, AH and Dillard, BA and Goldman, SL and Real, MVF and Sprockett, DD}, title = {Removal of sequencing adapter contamination improves microbial genome databases.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {1033}, pmid = {39497067}, issn = {1471-2164}, support = {R01 DK139214/DK/NIDDK NIH HHS/United States ; R35 GM138284/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Databases, Genetic ; DNA Contamination ; Genome, Microbial ; Humans ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; Cattle ; Mice ; Swine ; }, abstract = {Advances in assembling microbial genomes have led to growth of reference genome databases, which have been transformative for applied and basic microbiome research. Here we show that published microbial genome databases from humans, mice, cows, pigs, fish, honeybees, and marine environments contain significant sequencing-adapter contamination that systematically reduces assembly accuracy and contiguousness. By removing the adapter-contaminated ends of contiguous sequences and reassembling MGnify reference genomes, we improve the quality of assemblies in these databases.}, }
@article {pmid39496952, year = {2024}, author = {Djotan, AKG and Matsushita, N and Fukuda, K}, title = {Within-Site Variations in Soil Physicochemical Properties Explained the Spatiality and Cohabitation of Arbuscular Mycorrhizal Fungi in the Roots of Cryptomeria Japonica.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {136}, pmid = {39496952}, issn = {1432-184X}, support = {JP22H02382//Japan Society for the Promotion of Science/ ; }, mesh = {*Mycorrhizae/classification ; *Soil/chemistry ; *Soil Microbiology ; *Cryptomeria/microbiology ; *Plant Roots/microbiology ; Japan ; Phosphorus/analysis ; Forests ; Hydrogen-Ion Concentration ; Nitrogen/analysis/metabolism ; Carbon/analysis/metabolism ; }, abstract = {Arbuscular mycorrhizal fungi (AMF) live in a community in the roots of host plants. Still, the patterns and factors that drive their spatiality and cohabitation remain uncovered, particularly that of trees in planted forests, which we aimed to clarify in Cryptomeria japonica, a major plantation tree in Japan. We analyzed 65 paired root and soil samples of Cryptomeria japonica trees collected from 11 microsite (MS) plots at two environmentally different forest sites in central Japan and measured soil pH, total phosphorus (TP), C, N, and the carbon-to-nitrogen ratio. Root AMF communities were recovered using Illumina's next-generation amplicon sequencing targeting the small subunit of ribosomal DNA. We detected more than 500 AMF OTUs at each site but only three belonging to Dominikia, Rhizophagus, and Sclerocystis were dominant in the roots of C. japonica, detected each at an average relative abundance higher than 20%. Two showed negatively correlated spatial distributions and different associations with soil pH. Similarly, the physicochemical properties at MSs significantly determined the AMF assemblages in the roots of C. japonica. Dominikia, Rhizophagus, and Sclerocystis coexist in the roots of C. japonica where soil physicochemical properties, particularly pH, determine their spatial dynamic, turnovers, and cohabitation patterns. These findings highlight the importance of simultaneous colonization of plants by multiple AMF.}, }
@article {pmid39496518, year = {2024}, author = {Khaleque, HN and Fathollahzadeh, H and Kaksonen, AH and Valdés, J and Vergara, E and Holmes, DS and Watkin, ELJ}, title = {Genomic insights into key mechanisms for carbon, nitrogen, and phosphate assimilation by the acidophilic, halotolerant genus Acidihalobacter members.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {12}, pages = {}, pmid = {39496518}, issn = {1574-6941}, support = {//Curtin University/ ; //CSIRO/ ; }, mesh = {*Phosphates/metabolism ; *Carbon/metabolism ; *Nitrogen/metabolism ; *Genome, Bacterial ; Citric Acid Cycle/genetics ; Genomics ; Phylogeny ; Bacterial Proteins/genetics/metabolism ; }, abstract = {In-depth comparative genomic analysis was conducted to predict carbon, nitrogen, and phosphate assimilation pathways in the halotolerant, acidophilic genus Acidihalobacter. The study primarily aimed to understand how the metabolic capabilities of each species can determine their roles and effects on the microbial ecology of their unique saline and acidic environments, as well as in their potential application to saline water bioleaching systems. All four genomes encoded the genes for the complete tricarboxylic acid cycle, including 2-oxoglutarate dehydrogenase, a key enzyme absent in obligate chemolithotrophic acidophiles. Genes for a unique carboxysome shell protein, csoS1D, typically found in halotolerant bacteria but not in acidophiles, were identified. All genomes contained lactate and malate utilization genes, but only A. ferrooxydans DSM 14175T contained genes for the metabolism of propionate. Genes for phosphate assimilation were present, though organized differently across species. Only A. prosperus DSM 5130T and A. aeolianus DSM 14174T genomes contained nitrogen fixation genes, while A. ferrooxydans DSM 14175T and A. yilgarnensis DSM 105917T possessed genes for urease transporters and respiratory nitrate reductases, respectively. The findings suggest that all species can fix carbon dioxide but can also potentially utilize exogenous carbon sources and that the non-nitrogen-fixing species rely on alternative nitrogen assimilation mechanisms.}, }
@article {pmid39494810, year = {2024}, author = {Malik, M and Das, S and Paul, P and Chakraborty, P and Roy, R and Maity, A and Das, A and Dasgupta, M and Trivedi, S and Tribedi, P}, title = {Cuminaldehyde in combination with tetracycline shows promising antibiofilm activity against drug-resistant Pseudomonas aeruginosa.}, journal = {Biofouling}, volume = {40}, number = {10}, pages = {862-881}, doi = {10.1080/08927014.2024.2422874}, pmid = {39494810}, issn = {1029-2454}, mesh = {*Biofilms/drug effects ; *Pseudomonas aeruginosa/drug effects/physiology ; *Anti-Bacterial Agents/pharmacology ; *Tetracycline/pharmacology ; *Microbial Sensitivity Tests ; *Benzaldehydes/pharmacology ; *Cymenes/pharmacology ; Drug Synergism ; Reactive Oxygen Species/metabolism ; Drug Resistance, Bacterial/drug effects ; Virulence Factors ; }, abstract = {Pseudomonas aeruginosa, an opportunistic pathogen often causes biofilm-linked infections. A combinatorial approach involving tetracycline (antibiotic) and cuminaldehyde (phytochemical) was explored to combat this infectious pathogen. The results showed that both tetracycline and cuminaldehyde individually demonstrated antibacterial effects. However, when the compounds were applied together, there was a significant increase in their antimicrobial potential. The determined fractional inhibitory concentration index of 0.43 indicated a synergistic interaction between the two compounds. Furthermore, a series of experiments demonstrated that the combined application of cuminaldehyde and tetracycline could lead to a significant enhancement of their antibiofilm potential. This enhanced antibiofilm potential was attributed to the accumulation of reactive oxygen species and increased cell membrane permeability. Besides, this combinatorial application reduced the secretion of various virulence factors from P. aeruginosa. Therefore, this combined approach holds promise for effectively treating P. aeruginosa biofilms.}, }
@article {pmid39493671, year = {2024}, author = {Kleikamp, HBC and van der Zwaan, R and van Valderen, R and van Ede, JM and Pronk, M and Schaasberg, P and Allaart, MT and van Loosdrecht, MCM and Pabst, M}, title = {NovoLign: metaproteomics by sequence alignment.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae121}, pmid = {39493671}, issn = {2730-6151}, abstract = {Tremendous advances in mass spectrometric and bioinformatic approaches have expanded proteomics into the field of microbial ecology. The commonly used spectral annotation method for metaproteomics data relies on database searching, which requires sample-specific databases obtained from whole metagenome sequencing experiments. However, creating these databases is complex, time-consuming, and prone to errors, potentially biasing experimental outcomes and conclusions. This asks for alternative approaches that can provide rapid and orthogonal insights into metaproteomics data. Here, we present NovoLign, a de novo metaproteomics pipeline that performs sequence alignment of de novo sequences from complete metaproteomics experiments. The pipeline enables rapid taxonomic profiling of complex communities and evaluates the taxonomic coverage of metaproteomics outcomes obtained from database searches. Furthermore, the NovoLign pipeline supports the creation of reference sequence databases for database searching to ensure comprehensive coverage. We assessed the NovoLign pipeline for taxonomic coverage and false positive annotations using a wide range of in silico and experimental data, including pure reference strains, laboratory enrichment cultures, synthetic communities, and environmental microbial communities. In summary, we present NovoLign, a de novo metaproteomics pipeline that employs large-scale sequence alignment to enable rapid taxonomic profiling, evaluation of database searching outcomes, and the creation of reference sequence databases. The NovoLign pipeline is publicly available via: https://github.com/hbckleikamp/NovoLign.}, }
@article {pmid39491387, year = {2023}, author = {González-Alonso, V and Pradal, I and Wardhana, YR and Cnockaert, M and Wieme, AD and Vandamme, P and De Vuyst, L}, title = {Microbial ecology and metabolite dynamics of backslopped triticale sourdough productions and the impact of scale.}, journal = {International journal of food microbiology}, volume = {408}, number = {}, pages = {110445}, doi = {10.1016/j.ijfoodmicro.2023.110445}, pmid = {39491387}, issn = {1879-3460}, abstract = {Triticale (X Triticosecale Wittmack) is a hybrid of wheat (Triticum aestivum L.) and rye (Secale cereale L.), combining the positive attributes of both cereals. However, it has not been exploited for sourdough production yet. Further, the effect of scale on sourdough production has not been investigated systematically up to now. The aims of the present study were to assess the microbial ecology and metabolomic output of eleven spontaneously fermented, backslopped sourdough productions made with triticale flour on a scale of 100, 200, 500, and 1000 g. The acidification profile [pH and total titratable acidity (TTA)], microbial diversity (culture-dependent and culture-independent), metabolite dynamics, and appropriate correlations were determined. After ten fermentation steps, different species of Lactobacillaceae were prevalent in the mature sourdoughs, in particular Latilactobacillus curvatus, Limosilactobacillus fermentum, and Pediococcus pentosaceus. The microbial diversity could be traced back to the grains and was also present in the milling fractions (flour, bran, and shorts). Furthermore, thanks to the use of Illumina-based high-throughput sequencing and an amplicon sequence variant (ASV) approach, the presence of undesirable bacterial groups (bacilli, clostridia, and enterobacteria) during the initial steps of the backslopping cycle was revealed, as well as a finetuned taxonomic diversity of the LAB genera involved. Small sourdough productions (100 and 200 g) selected for a lower species diversity and reached a stable consortium faster than large ones (500 and 1000 g). Although a comparable final pH of 3.6-4.0 was obtained, the TTA of small sourdoughs was lower than that of large ones. Regarding the metabolic output, the simultaneous production of mannitol and erythritol, beyond ethanol and glycerol, could be linked to sourdoughs in which Liml. fermentum was the sole LAB species present. Further, the use of the arginine deiminase pathway by P. pentosaceus and Liml. fermentum was obvious. An appropriate extraction method followed by liquid injection gas chromatography coupled to triple quadrupole tandem mass spectrometry allowed the quantification of interesting volatile organic compounds, such as ethyl lactate. These findings support the inclusion of triticale as a viable alternative to wheat or rye for the production of sourdoughs that can be integrated into bread-making production schemes.}, }
@article {pmid39482450, year = {2024}, author = {Gao, L and Rao, MPN and Liu, YH and Wang, PD and Lian, ZH and Abdugheni, R and Jiang, HC and Jiao, JY and Shurigin, V and Fang, BZ and Li, WJ}, title = {SALINITY-Induced Changes in Diversity, Stability, and Functional Profiles of Microbial Communities in Different Saline Lakes in Arid Areas.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {135}, pmid = {39482450}, issn = {1432-184X}, support = {2021FY100900//National Science and Technology Fundamental Resources Investigation Program of China/ ; 2022D01A154//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022B0202110001//Key-Area Research and Development Programof Guangdong Province/ ; }, mesh = {*Lakes/microbiology/chemistry ; *Salinity ; *Archaea/genetics/classification/isolation &amp; purification ; *Bacteria/genetics/classification/isolation &amp; purification ; *Microbiota ; *RNA, Ribosomal, 16S/genetics ; *Biodiversity ; Geologic Sediments/microbiology ; Phylogeny ; Desert Climate ; Ecosystem ; }, abstract = {Saline lakes, characterized by high salinity and limited nutrient availability, provide an ideal environment for studying extreme halophiles and their biogeochemical processes. The present study examined prokaryotic microbial communities and their ecological functions in lentic sediments (with the salinity gradient and time series) using 16S rRNA amplicon sequencing and a metagenomic approach. Our findings revealed a negative correlation between microbial diversity and salinity. The notable predominance of Archaea in high-salinity lakes signified a considerable alteration in the composition of the microbial community. The results indicate that elevated salinity promotes homogeneous selection pressures, causing substantial alterations in microbial diversity and community structure, and simultaneously hindering interactions among microorganisms. This results in a notable decrease in the complexity of microbial ecological networks, ultimately influencing the overall ecological functional responses of microbial communities such as carbon fixation, sulfur, and nitrogen metabolism. Overall, our findings reveal salinity drives a notable predominance of Archaea, selects for species adapted to extreme conditions, and decreases microbial community complexity within saline lake ecosystems.}, }
@article {pmid39480531, year = {2024}, author = {Dobrzyński, J and Naziębło, A}, title = {Paenibacillus as a Biocontrol Agent for Fungal Phytopathogens: Is P. polymyxa the Only One Worth Attention?.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {134}, pmid = {39480531}, issn = {1432-184X}, mesh = {*Plant Diseases/microbiology/prevention &amp; control ; *Paenibacillus/physiology/metabolism ; *Paenibacillus polymyxa/physiology ; Biological Control Agents ; Fusarium/physiology ; Colletotrichum/physiology/growth &amp; development ; Pest Control, Biological ; Rhizoctonia/physiology/growth &amp; development ; Botrytis/growth &amp; development/physiology ; Fungi/physiology ; }, abstract = {Control of fungal phytopathogens is a significant challenge in modern agriculture. The widespread use of chemical fungicides to control these pathogens often leads to environmental and food contamination. An eco-friendly alternative that can help reduce reliance on these chemicals is plant growth-promoting bacteria (PGPB), particularly those of the genus Paenibacillus, which appear to be highly effective. The review aims to summarize the existing knowledge on the potential of Paenibacillus spp. as fungal biocontrol agents, identify knowledge gaps, and answer whether other species of the genus Paenibacillus, in addition to Paenibacillus polymyxa, can also be effective biocontrol agents. Paenibacillus spp. can combat plant phytopathogens through various mechanisms, including the production of lipopeptides (such as fusaricidin, paenimyxin, and pelgipeptin), the induction of systemic resistance (ISR), hydrolytic enzymes (chitinase, cellulase, and glucanase), and volatile organic compounds. These properties enable Paenibacillus strains to suppress the growth of fungi such as Fusarium oxysporum, F. solani, Rhizoctonia solani, Botrytis cinerea, or Colletotrichum gloeosporioides. Notably, several strains of Paenibacillus, including P. polymyxa, P. illinoisensis KJA-424, P. lentimorbus B-30488, and P. elgii JCK1400, have demonstrated efficacy in controlling fungal diseases in plants. Importantly, many formulations with Paenibacillus strains have already been patented, and some are commercially available, but most of them contain only P. polymyxa. Nevertheless, considering the data presented in this review, we believe that other strains from the Paenibacillus genus (besides P. polymyxa) will also be commercialized and used in plant protection in the future. Importantly, there is still limited information regarding their impact on the native microbiota, particularly from the metataxonomic and metagenomic perspectives. Expanding knowledge in this area could enhance the effectiveness of biocontrol agents containing Paenibacillus spp., ensuring safe and sustainable use of biological fungicides.}, }
@article {pmid39488271, year = {2024}, author = {Allen, J and Sire, M and Belouard, N and Gorzerino, C and Coutellec, MA and Mony, C and Pannard, A and Piscart, C}, title = {Could landscape ecology principles apply at the microscale? A metabarcoding approach on Trichoptera larvae-associated microbial diversity.}, journal = {The Science of the total environment}, volume = {955}, number = {}, pages = {177304}, doi = {10.1016/j.scitotenv.2024.177304}, pmid = {39488271}, issn = {1879-1026}, mesh = {Animals ; *Larva ; *Microbiota ; *Insecta ; *DNA Barcoding, Taxonomic ; *Bacteria/classification/genetics ; Fungi ; Biodiversity ; Ecology ; Diatoms ; Ecosystem ; Environmental Monitoring/methods ; }, abstract = {Landscape heterogeneity is known as a major factor of community structure and composition. Whether this effect of the landscape extends at different scales and particularly at the relevant scale for microorganisms remained to be determined. We used the cases produced by aquatic larvae of Trichoptera, which assemble organic or mineral particles, as naturally replicated experimental systems representing structured substrates to determine the effect of landscape structuration on microbial communities. A metabarcoding approach was used to characterise fungal, bacterial and diatom communities on cases produced by six Trichoptera species and related unstructured organic and mineral substrates. The structuration of the particles constituting the cases was also determined as a measure of microscale landscape. Structured substrates harboured communities of diatoms, fungi and bacteria that differed from those found on unstructured substrates. Microbial communities also differed between organic and mineral substrates. We found a higher microbial diversity on structured substrates than on unstructured substrates. The heterogeneity of the microscale landscape also affected bacterial and fungal communities within cases. These results highlight the importance of microscale landscape structuration for microbial diversity and demonstrate that approaches of landscape ecology could be downscaled to the microscale.}, }
@article {pmid39488149, year = {2024}, author = {Németh, Z and Svigruha, R and Ács, A and Farkas, A and Tapolczai, K and Elekes, K and Fodor, I and Pirger, Z}, title = {Developmental, behavioral, and biochemical effects of chronic exposure to sublethal concentrations of organic UV-filter compounds on a freshwater model species.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {277}, number = {}, pages = {107134}, doi = {10.1016/j.aquatox.2024.107134}, pmid = {39488149}, issn = {1879-1514}, mesh = {Animals ; *Water Pollutants, Chemical/toxicity ; *Sunscreening Agents/toxicity ; *Daphnia/drug effects ; Reproduction/drug effects ; Ultraviolet Rays ; Heart Rate/drug effects ; Fresh Water/chemistry ; Catalase/metabolism ; Swimming ; Behavior, Animal/drug effects/radiation effects ; Superoxide Dismutase/metabolism ; Glutathione Transferase/metabolism ; Acrylates ; }, abstract = {The prevalence of organic/chemical UV-filter compounds in aquatic ecosystems represents a growing environmental issue. The long-term toxicity risks of many UV-filters at environmentally relevant concentrations to aquatic biota are still less studied, especially in the case of invertebrates. This study was designed to evaluate the chronic toxicity of avobenzone (AVO), octocrylene (OCTO), and octinoxate (OCTI), three UV-filters which frequently occur in the aquatic environment, to the water flea (Daphnia magna) at an environmentally relevant concentration of 200 ng l[-1] in a 21-day exposure. Potential alterations in the growth, reproduction, and heart rate were continuously monitored during the treatments. Filtration rate, swimming, and the state of the antioxidant- and metabolic functions were evaluated at the end of exposures. Avobenzone significantly increased the reproductive output, heart rate, and filtration rate, while evoked a significant decrease of swimming behavior, and inhibited the activity of catalase (CAT) and glutathione S-transferase (GST) enzymes. The body size, reproduction, heart rate, and superoxide dismutase (SOD) activity were significantly increased whereas the activity of GST and CAT was significantly reduced by OCTO. OCTI significantly increased reproduction, heart rate, CAT and SOD activity but significantly decreased the swimming behavior. Our results confirmed that chronic exposure to organic UV-filters even at environmentally relevant concentrations affect basic physiological traits and cellular defense pathways in D. magna. Highlighting, our observations revealed previously unknown physiological changes (e.g., altered heart rate, filtration rate, SOD activity) caused by the investigated UV-filter compounds. Future research is to be aimed at investigating the mixture effects of these compounds and at the understanding of the potential cellular and molecular mechanisms underlying the changes induced.}, }
@article {pmid39485000, year = {2024}, author = {Kortekaas Krohn, I and Callewaert, C and Belasri, H and De Pessemier, B and Diez Lopez, C and Mortz, CG and O'Mahony, L and Pérez-Gordo, M and Sokolowska, M and Unger, Z and Untersmayr, E and Homey, B and Gomez-Casado, C}, title = {The influence of lifestyle and environmental factors on host resilience through a homeostatic skin microbiota: An EAACI Task Force Report.}, journal = {Allergy}, volume = {79}, number = {12}, pages = {3269-3284}, pmid = {39485000}, issn = {1398-9995}, support = {//European Academy of Allergy and Clinical Immunology/ ; }, mesh = {Humans ; *Microbiota/immunology ; *Skin/microbiology/immunology ; *Homeostasis ; *Life Style ; Skin Diseases/etiology/immunology/microbiology ; Environment ; }, abstract = {Human skin is colonized with skin microbiota that includes commensal bacteria, fungi, arthropods, archaea and viruses. The composition of the microbiota varies at different anatomical locations according to changes in body temperature, pH, humidity/hydration or sebum content. A homeostatic skin microbiota is crucial to maintain epithelial barrier functions, to protect from invading pathogens and to interact with the immune system. Therefore, maintaining homeostasis holds promise to be an achievable goal for microbiome-directed treatment strategies as well as a prophylactic strategy to prevent the development of skin diseases, as dysbiosis or disruption of homeostatic skin microbiota is associated with skin inflammation. A healthy skin microbiome is likely modulated by genetic as well as environmental and lifestyle factors. In this review, we aim to provide a complete overview of the lifestyle and environmental factors that can contribute to maintaining the skin microbiome healthy. Awareness of these factors could be the basis for a prophylactic strategy to prevent the development of skin diseases or to be used as a therapeutic approach.}, }
@article {pmid39482383, year = {2024}, author = {Gaborieau, B and Vaysset, H and Tesson, F and Charachon, I and Dib, N and Bernier, J and Dequidt, T and Georjon, H and Clermont, O and Hersen, P and Debarbieux, L and Ricard, JD and Denamur, E and Bernheim, A}, title = {Prediction of strain level phage-host interactions across the Escherichia genus using only genomic information.}, journal = {Nature microbiology}, volume = {9}, number = {11}, pages = {2847-2861}, pmid = {39482383}, issn = {2058-5276}, support = {R21042KS/RSE22002KSA//Institut National de la Sant&#xe9; et de la Recherche M&#xe9;dicale (National Institute of Health and Medical Research)/ ; R21042KS/RSE22002KSA//Institut National de la Sant&#xe9; et de la Recherche M&#xe9;dicale (National Institute of Health and Medical Research)/ ; R21042KS/RSE22002KSA//Institut National de la Sant&#xe9; et de la Recherche M&#xe9;dicale (National Institute of Health and Medical Research)/ ; R21042KS/RSE22002KSA//Institut National de la Sant&#xe9; et de la Recherche M&#xe9;dicale (National Institute of Health and Medical Research)/ ; R21042KS/RSE22002KSA//Institut National de la Sant&#xe9; et de la Recherche M&#xe9;dicale (National Institute of Health and Medical Research)/ ; R21042KS/RSE22002KSA//Institut National de la Sant&#xe9; et de la Recherche M&#xe9;dicale (National Institute of Health and Medical Research)/ ; PECAN 101040529//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; PECAN 101040529//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; PECAN 101040529//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; PECAN 101040529//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; PECAN 101040529//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; PECAN 101040529//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; ANR-19-AMRB-0002//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-19-AMRB-0002//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-20-CE92-0048//Agence Nationale de la Recherche (French National Research Agency)/ ; DEQ20161136698//Fondation pour la Recherche M&#xe9;dicale (Foundation for Medical Research in France)/ ; }, mesh = {*Host Specificity ; *Bacteriophages/genetics/physiology/classification ; *Genomics/methods ; Algorithms ; Escherichia coli/virology/genetics ; Phage Therapy ; Escherichia/genetics/virology ; Genome, Bacterial/genetics ; Genome, Viral/genetics ; Host-Pathogen Interactions ; ROC Curve ; Host Microbial Interactions ; }, abstract = {Predicting bacteriophage infection of specific bacterial strains promises advancements in phage therapy and microbial ecology. Whether the dynamics of well-established phage-host model systems generalize to the wide diversity of microbes is currently unknown. Here we show that we could accurately predict the outcomes of phage-bacteria interactions at the strain level in natural isolates from the genus Escherichia using only genomic data (area under the receiver operating characteristic curve (AUROC) of 86%). We experimentally established a dataset of interactions between 403 diverse Escherichia strains and 96 phages. Most interactions are explained by adsorption factors as opposed to antiphage systems which play a marginal role. We trained predictive algorithms and pinpoint poorly predicted interactions to direct future research efforts. Finally, we established a pipeline to recommend tailored phage cocktails, demonstrating efficiency on 100 pathogenic E. coli isolates. This work provides quantitative insights into phage-host specificity and supports the use of predictive algorithms in phage therapy.}, }
@article {pmid39481794, year = {2024}, author = {Li, X and Li, Y and Wang, Y and Liu, Y and Riaz, L and Wang, Q and Zeng, X and Qin, Z and Irfan, M and Yang, Q}, title = {Methodology comparison of environmental sediment fungal community analysis.}, journal = {Environmental research}, volume = {263}, number = {Pt 3}, pages = {120260}, doi = {10.1016/j.envres.2024.120260}, pmid = {39481794}, issn = {1096-0953}, mesh = {*Geologic Sediments/microbiology ; *Fungi/genetics/isolation &amp; purification/classification ; *RNA, Ribosomal, 18S/genetics ; *High-Throughput Nucleotide Sequencing ; DNA, Fungal/analysis ; DNA, Ribosomal Spacer/genetics ; Mycobiome ; Rivers/microbiology ; }, abstract = {Fungi play important roles in ecosystems. Analyzing fungal communities in environments has long been a challenge due to the large difference in compositions retrieved using different methods or sequencing regions, obscuring the true abundance and species information. Our study aimed to compare and determine more accurate approach for evaluating fungal populations in river sediment. To achieve this, different primer sets in the internal transcribed spacer (ITS) (ITS5/ITS1R, ITS1F/ITS2), 18S rRNA gene (0817F/1196R) for High-throughput sequencing (HTS), metagenomic shotgun sequencing (MS) directly from environmental samples, and HTS using ITS primers for the fungal samples collected from plate cultivation were used to characterize the fungal communities. We calculated diversity index and used FungalTraits to analyze methods preferences for fungal species. The study revealed that when analyzing the fungal species directly from environmental samples, amplification and sequencing of ITS region demonstrated more accuracy than MS and 18S rRNA gene sequencing methods, but displayed significant primer preference. Over 30 % fungal species from HTS after plate cultivation were not present in HTS from the environmental samples. NMDS analysis demonstrated significant disparities in species diversity among different methods, suggesting potential complementarity between them. Over 85% species identified by HTS using ITS primers belonged to filamentous fungi, while the MS mostly identified yeast (62%). Therefore, to get more accurate fungal community information in sediment, multiple methods were recommended by using cultivation, molecular biological methods dependent on PCR techniques like ITS1F/ITS2 primer for HTS and PCR independent method such as metagenomic shotgun sequencing techniques.}, }
@article {pmid39476778, year = {2025}, author = {Li, J and Sun, Y and Zhang, Q and Liu, S and Liu, P and Zhang, XX}, title = {Unveiling the potential role of virus-encoded polyphosphate kinases in enhancing phosphorus removal in activated sludge systems.}, journal = {Water research}, volume = {268}, number = {Pt A}, pages = {122678}, doi = {10.1016/j.watres.2024.122678}, pmid = {39476778}, issn = {1879-2448}, mesh = {*Viral Proteins/genetics/metabolism ; Phylogeny ; *Viruses/classification/enzymology/genetics ; Bacteria/classification/enzymology/genetics ; Water Purification ; Genetic Variation ; *Phosphotransferases (Phosphate Group Acceptor)/chemistry/genetics/metabolism ; Models, Molecular ; Protein Structure, Tertiary ; Sequence Analysis, Protein ; Sewage/virology ; }, abstract = {While microbial phosphate removal in activated sludge (AS) systems has been extensively studied, the role of viruses in this process remains largely unexplored. In this study, we identified 149 viral auxiliary metabolic genes associated with phosphorus cycling from 2,510 viral contigs (VCs) derived from AS systems. Notably, polyphosphate kinase 1 (ppk1) and polyphosphate kinase 2 (ppk2) genes, which are primarily responsible for phosphate removal, were found in five unclassified VCs. These genes exhibited conserved protein structures and active catalytic sites, indicating a pivotal role of viruses in enhancing phosphorus removal. Phylogenetic analysis demonstrated a close relationship between viral ppk genes and their bacterial counterparts, suggesting the occurrence of horizontal gene transfer. Furthermore, experimental assays validated that viral ppk genes enhanced host phosphate removal capabilities. VCs carrying ppk genes were observed across diverse ecological and geographical contexts, suggesting their potential to bolster host functions in varied environmental and nutrient settings, spanning natural and engineered systems. These findings uncover a previously underappreciated mechanism by which viruses enhance phosphate removal in wastewater treatment plants. Overall, our study highlights the potential for leveraging virus-encoded genes to improve the efficiency of biological phosphorus removal processes, offering new insights into the microbial ecology of AS systems and the role of viruses in biogeochemical cycling.}, }
@article {pmid39472801, year = {2024}, author = {Valiei, A and Dickson, AM and Aminian-Dehkordi, J and Mofrad, MRK}, title = {Bacterial community dynamics as a result of growth-yield trade-off and multispecies metabolic interactions toward understanding the gut biofilm niche.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {441}, pmid = {39472801}, issn = {1471-2180}, mesh = {*Bacteria/metabolism/classification/growth &amp; development/genetics ; *Biofilms/growth &amp; development ; Humans ; *Gastrointestinal Microbiome ; Microbial Interactions ; Bacterial Physiological Phenomena ; Models, Biological ; Kinetics ; Symbiosis ; Ecosystem ; Nutrients/metabolism ; }, abstract = {Bacterial communities are ubiquitous, found in natural ecosystems, such as soil, and within living organisms, like the human microbiome. The dynamics of these communities in diverse environments depend on factors such as spatial features of the microbial niche, biochemical kinetics, and interactions among bacteria. Moreover, in many systems, bacterial communities are influenced by multiple physical mechanisms, such as mass transport and detachment forces. One example is gut mucosal communities, where dense, closely packed communities develop under the concurrent influence of nutrient transport from the lumen and fluid-mediated detachment of bacteria. In this study, we model a mucosal niche through a coupled agent-based and finite-volume modeling approach. This methodology enables us to model bacterial interactions affected by nutrient release from various sources while adjusting individual bacterial kinetics. We explored how the dispersion and abundance of bacteria are influenced by biochemical kinetics in different types of metabolic interactions, with a particular focus on the trade-off between growth rate and yield. Our findings demonstrate that in competitive scenarios, higher growth rates result in a larger share of the niche space. In contrast, growth yield plays a critical role in neutralism, commensalism, and mutualism interactions. When bacteria are introduced sequentially, they cause distinct spatiotemporal effects, such as deeper niche colonization in commensalism and mutualism scenarios driven by species intermixing effects, which are enhanced by high growth yields. Moreover, sub-ecosystem interactions dictate the dynamics of three-species communities, sometimes yielding unexpected outcomes. Competitive, fast-growing bacteria demonstrate robust colonization abilities, yet they face challenges in displacing established mutualistic systems. Bacteria that develop a cooperative relationship with existing species typically obtain niche residence, regardless of their growth rates, although higher growth yields significantly enhance their abundance. Our results underscore the importance of bacterial niche dynamics in shaping community properties and succession, highlighting a new approach to manipulating microbial systems.}, }
@article {pmid39470240, year = {2024}, author = {Dumann, G and Rohland, O and Abdel-Glil, MY and Allen, RJ and Bauer, M and Busch, A}, title = {Draft genomes of the bile duct microbiome strains Klebsiella pneumoniae and Enterococcus lactis isolated from bilioenteric drainages with biofilm-forming abilities.}, journal = {Microbiology resource announcements}, volume = {13}, number = {12}, pages = {e0020224}, pmid = {39470240}, issn = {2576-098X}, support = {EXC 2051 - Project-ID 390713860//Deutsche Forschungsgemeinschaft (DFG)/ ; }, abstract = {We describe the genetic properties of two strains isolated from the elusive bile duct microbiome from solid organ transplant patients. Bacterial strains Enterococcus lactis (MS-STENT-08-E-001) and Klebsiella pneumoniae (MS-STENT-01-M-001) were isolated from the biofilms of bile duct catheters.}, }
@article {pmid39468827, year = {2024}, author = {Flores, JN and Lubin, JB and Silverman, MA}, title = {The case for microbial intervention at weaning.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2414798}, pmid = {39468827}, issn = {1949-0984}, support = {R01 DK133453/DK/NIDDK NIH HHS/United States ; T32 GM008562/GM/NIGMS NIH HHS/United States ; }, mesh = {*Weaning ; *Gastrointestinal Microbiome ; Humans ; Animals ; *Probiotics/administration &amp; dosage ; Host Microbial Interactions ; Diet ; Bacteria/classification/isolation &amp; purification/genetics/metabolism ; Intestines/microbiology/immunology ; }, abstract = {Weaning, the transition from a milk-based diet to solid food, coincides with the most significant shift in gut microbiome composition in the lifetime of most mammals. Notably, this period also marks a "window of opportunity" where key components of the immune system develop, and host-microbe interactions shape long-term immune homeostasis thereby influencing the risk of autoimmune and inflammatory diseases. This review provides a comprehensive analysis of the changes in nutrition, microbiota, and host physiology that occur during weaning. We explore how these weaning-associated processes differ across species, lifestyles, and regions of the intestine. Using prinicples of microbial ecology, we propose that the weaning transition is an optimal period for microbiome-targeted therapeutic interventions. Additionally, we suggest that replicating features of the weaning microbiome in adults could promote the successful engraftment of probiotics. Finally, we highlight key research areas that could deepen our understanding of the complex relationships between diet, commensal microbes, and the host, informing the development of more effective microbial therapies.}, }
@article {pmid39468208, year = {2024}, author = {Ilicic, D and Woodhouse, J and Karsten, U and Schimani, K and Zimmermann, J and Grossart, HP}, title = {Chytrid fungi infecting Arctic microphytobenthic communities under varying salinity conditions.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {25821}, pmid = {39468208}, issn = {2045-2322}, mesh = {Arctic Regions ; *Salinity ; *Chytridiomycota/genetics/isolation &amp; purification ; Diatoms/microbiology/genetics ; Mycobiome ; Ecosystem ; Biodiversity ; Food Chain ; }, abstract = {This study aimed to investigate the presence and diversity of fungal parasites in Arctic coastal microphytobenthic communities. These communities represent a key component in the functioning of Arctic trophic food webs. Fungal parasites, particularly Chytridiomycota (chytrids), play significant roles by controlling microalgal bloom events, impacting genetic diversity, modifying microbial interactions, and accelerating nutrient and energy transfer to higher trophic levels. In the context of rapid Arctic warming and increased glacier meltwater, which significantly affects these communities, we used high-throughput sequencing to explore fungal community composition. Our results show that chytrids dominate fungal communities in Arctic benthic habitats and that the overall fungal diversity is primarily influenced by the salinity gradient. Chytrid representation is positively correlated with the presence of potential benthic diatom (Surirella, Nitzschia, Navicula) and green algae (Ulvophyceae) hosts, while microscopic observations provide further evidence for the presence of active chytrid infections.}, }
@article {pmid39467902, year = {2024}, author = {Awais, M and Xiang, Y and Shah, N and Bilal, H and Yang, D and Hu, H and Li, T and Ji, X and Li, H}, title = {Unraveling the Role of Contaminants Reshaping the Microflora in Zea mays Seeds from Heavy Metal-Contaminated and Pristine Environment.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {133}, pmid = {39467902}, issn = {1432-184X}, support = {KUST-AN2023006Y//Kunming University of Science and Technology Plan Project/ ; KUST-AN2023006Y//Kunming University of Science and Technology Plan Project/ ; 42267059//National Natural Science Foundation of China/ ; SKLEG2023216//State Key Laboratory of Environmental Geochemistry, Chinese Academy of Sciences/ ; }, mesh = {*Zea mays/microbiology ; *Metals, Heavy/analysis ; *Seeds/microbiology ; *Bacteria/genetics/classification/isolation &amp; purification/drug effects ; China ; *Soil Pollutants/analysis ; *Fungi/genetics/classification/isolation &amp; purification/drug effects ; *Microbiota/drug effects ; Soil Microbiology ; High-Throughput Nucleotide Sequencing ; }, abstract = {Heavy metal (HM) contaminants are the emerging driving force for reshaping the microflora of plants by eradicating the non-tolerance and non-resistant microbes via their lethal effects. Seeds served as a prime source of ancestral microbial diversity hereditary transfer from generation to generation. However, the problem arises when they got exposed to metal contamination, does metal pollutant disrupt the delicate balance of microbial communities within seeds and lead to shifts in their microflora across generations. In this study, the endophytic community within Zea mays seeds was compared across three distinct regions in Yunnan province, China: a HM-contaminated site Ayika (AK), less-contaminated site Sanduoduo (SD), and a non-contaminated Site Dali (DL). High-throughput sequencing techniques were employed to analyze the microbial communities. A total of 492,177 high-quality reads for bacterial communities and 1,001,229 optimized sequences for fungal communities were obtained. These sequences were assigned to 502 and 239 operational taxonomic units (OTUs) for bacteria and fungi, respectively. A higher diversity was recorded in AK samples than in SD and DL. Microbial community structure analysis showed higher diversity and significant fluctuation in specific taxa abundance in the metal-polluted samples exhibiting higher response of microbial flora to HM. In AK samples, bacterial genera such as Gordonia and Burkholderia-Caballeronia-Paraburkholderia were dominant, while in SD Pseudomonas and Streptomyces were dominant. Among the fungal taxa, Fusarium, Saccharomycopsis, and Lecanicillium were prevalent in HM-contaminated sites. Our finding revealed the influential effect of HM contaminants on reshaping the seed microbiome of the Zea mays, showing both the resilience of certain important microbial taxa as well the shifts in the diversity in the contaminated and pristine conditions. The knowledge will benefit to develop effective soil remediation, reclamation, and crop management techniques, and eventually assisting in the extenuation of metal pollution's adverse effects on plant health and agricultural productivity.}, }
@article {pmid40809489, year = {2023}, author = {Laforge, P and Vincent, AT and Duchaine, C and Feutry, P and Dion-Fortier, A and Plante, PL and Pouliot, &#xc9; and Fournaise, S and Saucier, L}, title = {Contribution of farms to the microbiota in the swine value chain.}, journal = {Frontiers in systems biology}, volume = {3}, number = {}, pages = {1183868}, pmid = {40809489}, issn = {2674-0702}, abstract = {Introduction: A thorough understanding of the microbial ecology within the swine value chain is essential to develop new strategies to optimize the microbiological quality of pork products. To our knowledge, no study to date has followed the microbiota through the value chain from live farm animals to the cuts of meat obtained for market. The objective of this study is to evaluate how the microbiota of pigs and their environment influence the microbial composition of samples collected throughout the value chain, including the meat plant and meat cuts. Method and results: Results from 16S rDNA sequencing, short-chain fatty acid concentrations and metabolomic analysis of pig feces revealed that the microbiota from two farms with differing sanitary statuses were distinctive. The total aerobic mesophilic bacteria and Enterobacteriaceae counts from samples collected at the meat plant after the pre-operation cleaning and disinfection steps were at or around the detection limit and the pigs from the selected farms were the first to be slaughtered on each shipment days. The bacterial counts of individual samples collected at the meat plant did not vary significantly between the farms. Alpha diversity results indicate that as we move through the steps in the value chain, there is a clear reduction in the diversity of the microbiota. A beta diversity analysis revealed a more distinct microbiota at the farms compared to the meat plant which change and became more uniform as samples were taken towards the end of the value chain. The source tracker analysis showed that only 12.92% of the microbiota in shoulder samples originated from the farms and 81% of the bacteria detected on the dressed carcasses were of unknown origin. Discussion: Overall, the results suggest that with the current level of microbial control at farms, it is possible to obtain pork products with similar microbiological quality from different farms. However, broader studies are required to determine the impact of the sanitary status of the herd on the final products.}, }
@article {pmid39460615, year = {2024}, author = {Wen, J and Zhang, H and Chu, D and Chen, X and Feng, J and Wang, Y and Liu, G and Zhang, Y and Li, Y and Ning, K}, title = {Deep learning revealed the distribution and evolution patterns for invertible promoters across bacterial lineages.}, journal = {Nucleic acids research}, volume = {52}, number = {21}, pages = {12817-12830}, pmid = {39460615}, issn = {1362-4962}, support = {32071465//National Natural Science Foundation of China/ ; 2023YFA1800900//National Key Research and Development Program of China/ ; }, mesh = {*Promoter Regions, Genetic ; *Deep Learning ; *Bacteria/genetics/classification ; *Genome, Bacterial ; *Phylogeny ; *Evolution, Molecular ; Gene Expression Regulation, Bacterial ; Metagenome/genetics ; Biofilms ; }, abstract = {Invertible promoters (invertons) are crucial regulatory elements in bacteria, facilitating gene expression changes under stress. Despite their importance, their prevalence and the range of regulated gene functions are largely unknown. We introduced DeepInverton, a deep learning model that identifies invertons across a broad phylogenetic spectrum without using sequencing reads. By analyzing 68 733 bacterial genomes and 9382 metagenomes, we have uncovered over 200 000 nonredundant invertons and have also highlighted their abundance in pathogens. Additionally, we identified a post-Cambrian Explosion increase of invertons, paralleling species diversification. Furthermore, we revealed that invertons regulate diverse functions, including antimicrobial resistance and biofilm formation, underscoring their role in environmental adaptation. Notably, the majority of inverton identifications by DeepInverton have been confirmed by the in vitro experiments. The comprehensive inverton profiles have deepened our understanding of invertons at pan-genome and pan-metagenome scales, enabling a broad spectrum of applications in microbial ecology and synthetic biology.}, }
@article {pmid39454273, year = {2025}, author = {Xun, F and Feng, M and Zhao, C and Luo, W and Han, X and Ci, Z and Yin, Y and Wang, R and Wu, QL and Grossart, HP and Xing, P}, title = {Epilimnetic oligotrophication increases contribution of oxic methane production to atmospheric methane flux from stratified lakes.}, journal = {Water research}, volume = {268}, number = {Pt A}, pages = {122602}, doi = {10.1016/j.watres.2024.122602}, pmid = {39454273}, issn = {1879-2448}, mesh = {*Methane/metabolism ; *Lakes/microbiology ; Atmosphere ; Phosphorus/metabolism ; }, abstract = {Although considerable attention has been paid to the effects of eutrophication on aquatic methane (CH4) emissions to the atmosphere, the ecosystem-level effects of oligotrophication/re-oligotrophication on aquatic CH4 production and subsequent ecological responses remain to be elucidated. It has been hypothesized that dissolved inorganic phosphorus (DIP)-deficient conditions drive the ecosystem to utilize poorly bioavailable organic phosphorus for biomass formation, thereby generating CH4 as a by-product. To test this hypothesis, a mass balance approach was used to estimate in situ oxic methane production (OMP) in an oligotrophic, deep Lake Fuxian. The isotopic signature of dissolved [13]C-CH4, the potential substrates for OMP, and the phnJ/phnD genes associated with microbial demethylation of organic phosphorus compounds were analyzed. Our results indicate that CH4 accumulation was maximal in the surface mixed layer (SML, i.e., Epilimnion) during lake stratification, and ∼ 86 % of the total CH4 flux to the atmosphere was due to OMP. Decomposition of methylphosphonate (MPn) by Alphaproteobacteria (genera Sphingomonas and Mesorhizobium) contributed significantly to OMP. Furthermore, water temperature (Temp), chlorophyll a (Chla), and DIP were the most critical predictors of water OMP potential. Meta-analysis of currently available global data showed that OMP had a negative exponential distribution with DIP (OMP = 2.0 e[-0.71DIP], R[2] = 0.57, p < 0.05). DIP concentrations below a threshold of 3.40 ∼ 9.35 μg P L[-1] triggered OMP processes and increased the atmospheric CH4 emissions. Under future warming scenarios, stratification and catchment management induced oligotrophication or re-oligotrophication may systematically affect the biogeochemical cycling of phosphorus and the OMP contribution to CH4 emission in stratified lakes.}, }
@article {pmid39452361, year = {2024}, author = {Kiewra, D and Dyczko, D and Žákovská, A and Nejezchlebova, H}, title = {Prevalence of Borrelia and Rickettsia in Ixodes ricinus from Chosen Urban and Protected Areas in Poland and the Czech Republic.}, journal = {Insects}, volume = {15}, number = {10}, pages = {}, pmid = {39452361}, issn = {2075-4450}, abstract = {(1) Background: Ixodes ricinus is responsible for the spreading of medically important pathogens. Monitoring the level of tick infection in various areas is essential for determining the potential tick-born risk. This study aimed to detect Borrelia spp. and Rickettsia spp. in I. ricinus ticks collected in urban and protected areas both in Poland and the Czech Republic. (2) Methods: Ticks were collected by flagging in the years 2016-2017. Borrelia spp. was detected using nested PCR targeting the flaB gene and Rickettsia spp. using nested PCR targeting gltA. (3) Results: In total, DNA of Borrelia spp. was detected in 25.9% of samples. Ticks collected in Poland were more infected compared to the Czech Republic and ticks collected in protected areas were more infected with Borrelia spp. than ticks collected in urban areas. The RFLP analysis showed the occurrence of B. afzelii and B. garinii in both countries, and additionally B. valaisiana, B. burgdorferi s.s., and B. miyamotoi in Poland. Rickettsia spp. was detected in 17.4% of I. ricinus, with comparable infection level in both countries; however, regional differences were observed. (4) Conclusion: The regional differences in Borrelia spp. and Rickettsia spp. prevalence in I. ricinus indicate the complexity of factors influencing the level of infection and underline the need for adaptation public health surveillance strategies in each region.}, }
@article {pmid39450335, year = {2024}, author = {Hodžić, A and Veinović, G and Alić, A and Seki, D and Kunert, M and Nikolov, G and Sukara, R and Šupić, J and Tomanović, S and Berry, D}, title = {A metalloprotease secreted by an environmentally acquired gut bacterium hinders Borrelia afzelii colonization in Ixodes ricinus.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1476266}, pmid = {39450335}, issn = {2235-2988}, mesh = {*Ixodes/microbiology ; Animals ; *Borrelia burgdorferi Group/genetics/metabolism ; *Gastrointestinal Microbiome ; *Metalloproteases/metabolism ; Bacillus cereus/enzymology/metabolism/genetics ; Lyme Disease/microbiology ; Bacterial Proteins/metabolism/genetics ; }, abstract = {Although the importance of the microbiome in the context of tick biology and vector competence has recently come into a broader research focus, the field is still in its infancy and the complex ecological interactions between the tick residential bacteria and pathogens are obscure. Here, we show that an environmentally acquired gut bacterium has the potential to impair Borrelia afzelii colonization within the tick vector through a secreted metalloprotease. Oral introduction of either Bacillus cereus LTG-1 isolate or its purified enhancin (BcEnhancin) protein significantly reduces B. afzelii burden in the guts of Ixodes ricinus ticks. This effect is attributed to the ability of BcEnhancin to degrade a glycan-rich peritrophic matrix (PM), which is a gut protective barrier essential for Borrelia survival. Our study highlights the importance of the gut microbiome in determining tick vector competence and provides a deeper mechanistic insight into the complex network of interactions between Borrelia, the tick, and the tick microbiome.}, }
@article {pmid39450162, year = {2024}, author = {Nenciarini, S and Rivero, D and Ciccione, A and Amoriello, R and Cerasuolo, B and Pallecchi, M and Bartolucci, GL and Ballerini, C and Cavalieri, D}, title = {Impact of cooperative or competitive dynamics between the yeast Saccharomyces cerevisiae and lactobacilli on the immune response of the host.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1399842}, pmid = {39450162}, issn = {1664-3224}, mesh = {Humans ; *Saccharomyces cerevisiae/immunology ; *Gastrointestinal Microbiome/immunology ; *Lactobacillus/immunology ; Probiotics ; Animals ; Microbial Interactions/immunology ; Dysbiosis/immunology ; }, abstract = {Fungi and bacteria can be found coexisting in a wide variety of environments. The combination of their physical and molecular interactions can result in a broad range of outcomes for each partner, from competition to cooperative relationships. Most of these interactions can also be found in the human gastrointestinal tract. The gut microbiota is essential for humans, helping the assimilation of food components as well as the prevention of pathogen invasions through host immune system modulation and the production of beneficial metabolites such as short-chain fatty acids (SCFAs). Several factors, including changes in diet habits due to the progressive Westernization of the lifestyle, are linked to the onset of dysbiosis statuses that impair the correct balance of the gut environment. It is therefore crucial to explore the interactions between commensal and diet-derived microorganisms and their influence on host health. Investigating these interactions through co-cultures between human- and fermented food-derived lactobacilli and yeasts led us to understand how the strains' growth yield and their metabolic products rely on the nature and concentration of the species involved, producing either cooperative or competitive dynamics. Moreover, single cultures of yeasts and lactobacilli proved to be ideal candidates for developing immune-enhancing products, given their ability to induce trained immunity in blood-derived human monocytes in vitro. Conversely, co-cultures as well as mixtures of yeasts and lactobacilli have been shown to induce an anti-inflammatory response on the same immune cells in terms of cytokine profiles and activation surface markers, opening new possibilities in the design of probiotic and dietary therapies.}, }
@article {pmid39449043, year = {2024}, author = {Zhai, X and Gobbi, A and Kot, W and Krych, L and Nielsen, DS and Deng, L}, title = {A single-stranded based library preparation method for virome characterization.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {219}, pmid = {39449043}, issn = {2049-2618}, mesh = {*Virome/genetics ; *Genome, Viral/genetics ; *Gastrointestinal Microbiome/genetics ; *Gene Library ; Humans ; DNA, Viral/genetics ; DNA, Single-Stranded/genetics ; High-Throughput Nucleotide Sequencing/methods ; Reproducibility of Results ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: The gut virome is an integral component of the gut microbiome, playing a crucial role in maintaining gut health. However, accurately depicting the entire gut virome is challenging due to the inherent diversity of genome types (dsDNA, ssDNA, dsRNA, and ssRNA) and topologies (linear, circular, or fragments), with subsequently biases associated with current sequencing library preparation methods. To overcome these problems and improve reproducibility and comparability across studies, universal or standardized virome sequencing library construction methods are highly needed in the gut virome study.<br><br>RESULTS: We repurposed the ligation-based single-stranded library (SSLR) preparation method for virome studies. We demonstrate that the SSLR method exhibits exceptional efficiency in quantifying viral DNA genomes (both dsDNA and ssDNA) and outperforms existing double-stranded (Nextera) and single-stranded (xGen, MDA&#x2009;+&#x2009;Nextera) library preparation approaches in terms of minimal amplification bias, evenness of coverage, and integrity of assembling viral genomes. The SSLR method can be utilized for the simultaneous library preparation of both DNA and RNA viral genomes. Furthermore, the SSLR method showed its ability to capture highly modified phage genomes, which were often lost using other library preparation approaches.<br><br>CONCLUSION: We introduce and improve a fast, simple, and efficient ligation-based single-stranded DNA library preparation for gut virome study. This method is compatible with Illumina sequencing platforms and only requires ligation reagents within 3-h library preparation, which is similar or even better than the advanced library preparation method (xGen). We hope this method can be further optimized, validated, and widely used to make gut virome study more comparable and reproducible. Video Abstract.}, }
@article {pmid39448159, year = {2025}, author = {Diaz, M and Aird, H and Le Viet, T and Gutiérrez, AV and Larke-Mejia, N and Omelchenko, O and Moragues-Solanas, L and Fritscher, J and Som, N and McLauchlin, J and Hildebrand, F and Jørgensen, F and Gilmour, M}, title = {Microbial composition and dynamics in environmental samples from a ready-to-eat food production facility with a long-term colonization of Listeria monocytogenes.}, journal = {Food microbiology}, volume = {125}, number = {}, pages = {104649}, doi = {10.1016/j.fm.2024.104649}, pmid = {39448159}, issn = {1095-9998}, mesh = {*Listeria monocytogenes/genetics/isolation &amp; purification/growth &amp; development/classification ; *Fast Foods/microbiology ; Food Microbiology ; Microbiota ; Bacteria/genetics/classification/isolation &amp; purification/growth &amp; development ; Environmental Microbiology ; Metagenomics ; Pseudomonas fluorescens/genetics/isolation &amp; purification/growth &amp; development/classification ; Food Contamination/analysis ; }, abstract = {Listeria monocytogenes is a foodborne pathogen of significant concern for the food industry due to its remarkable ability to persist through safety control efforts, posing a subsequent health threat to consumers. Understanding the microbial communities coexisting with L. monocytogenes in food processing environments provides insights into its persistence mechanisms. We investigated the microbial communities on non-food contact surfaces in a facility producing ready-to-eat foods, known to harbour a ST121 L. monocytogenes strain over multiple years. A 10-week sampling period was coordinated with the company and public health authorities. Metagenomic analysis revealed a stable microbial composition dominated by Pseudomonas fluorescens. While highly related populations were present in high-care production zones, distinctive taxa characteristic of specific areas were observed (e.g., Sphingomonas aerolata). Although Listeria spp. were not detected in metagenomes, they were detected in cultured samples, suggesting low relative abundance in factory settings. The findings suggest that a stable resident microbiota, with distinct adaptations to different areas within the factory, was selected for by their collective ability to survive control efforts in this environment. Listeria spp. was a member of this microbial community, albeit at low abundance, and may likewise benefit from the mutualism of the overall microbial community.}, }
@article {pmid39446706, year = {2024}, author = {Shinfuku, MS and Domeignoz-Horta, LA and Choudoir, MJ and Frey, SD and Mitchell, MF and Ranjan, R and DeAngelis, KM}, title = {Seasonal effects of long-term warming on ecosystem function and bacterial diversity.}, journal = {PloS one}, volume = {19}, number = {10}, pages = {e0311364}, pmid = {39446706}, issn = {1932-6203}, mesh = {*Seasons ; *Soil Microbiology ; *Biodiversity ; *Bacteria/classification/genetics ; *Ecosystem ; *Climate Change ; Soil/chemistry ; Global Warming ; }, abstract = {Across biomes, soil biodiversity promotes ecosystem functions. However, whether this relationship will be maintained within ecosystems under climate change is uncertain. Here, using two long-term soil warming experiments, we investigated how warming affects the relationship between ecosystem functions and bacterial diversity across seasons, soil horizons, and warming duration. Soils were sampled from these warming experiments located at the Harvard Forest Long-Term Ecological Research (LTER) site, where soils had been heated +5°C above ambient for 13 or 28 years at the time of sampling. We assessed seven measurements representative of different ecosystem functions and nutrient pools. We also surveyed bacterial community diversity. We found that ecosystem function was significantly affected by season, with autumn samples having a higher intercept than summer samples in our model, suggesting a higher overall baseline of ecosystem function in the fall. The effect of warming on bacterial diversity was similarly affected by season, where warming in the summer was associated with decreased bacterial evenness in the organic horizon. Despite the decreased bacterial evenness in the warmed plots, we found that the relationship between ecosystem function and bacterial diversity was unaffected by warming or warming duration. Our findings highlight that season is a consistent driver of ecosystem function as well as a modulator of climate change effects on bacterial community evenness.}, }
@article {pmid39445507, year = {2024}, author = {Liu, L and Zhang, X and Schorn, S and Doda, T and Kang, M and Bouffard, D and Kirillin, G and Milucka, J and Shi, X and Grossart, HP}, title = {Strong Subseasonal Variability of Oxic Methane Production Challenges Methane Budgeting in Freshwater Lakes.}, journal = {Environmental science &amp; technology}, volume = {58}, number = {44}, pages = {19690-19701}, doi = {10.1021/acs.est.4c07413}, pmid = {39445507}, issn = {1520-5851}, mesh = {*Methane ; *Lakes ; Seasons ; Environmental Monitoring ; Fresh Water ; }, abstract = {Methane (CH4) accumulation in the well-oxygenated lake epilimnion enhances the diffusive atmospheric CH4 emission. Both lateral transport and in situ oxic methane production (OMP) have been suggested as potential sources. While the latter has been recently supported by increasing evidence, quantifying the exact contribution of OMP to atmospheric emissions remains challenging. Based on a large high-resolution field data set collected during 2019-2020 in the deep stratified Lake Stechlin and on three-dimensional hydrodynamic modeling, we improved existing CH4 budgets by resolving each component of the mass balance model at a seasonal scale and therefore better constrained the residual OMP. All terms in our model showed a large temporal variability at scales from intraday to seasonal, and the modeled OMP was most sensitive to the surface CH4 flux estimates. Future efforts are needed to reduce the uncertainties in estimating OMP rates using the mass balance approach by increasing the frequency of atmospheric CH4 flux measurements.}, }
@article {pmid39442306, year = {2024}, author = {Wen, X and Xiang, L and Harindintwali, JD and Wang, Y and He, C and Fu, Y and Wei, S and Hashsham, SA and Jiang, J and Jiang, X and Wang, F}, title = {Mitigating risks from atrazine drift to soybeans through foliar pre-spraying with a degrading bacterium.}, journal = {Journal of hazardous materials}, volume = {480}, number = {}, pages = {136224}, doi = {10.1016/j.jhazmat.2024.136224}, pmid = {39442306}, issn = {1873-3336}, mesh = {*Atrazine/toxicity/metabolism ; *Glycine max/metabolism/drug effects/growth &amp; development/microbiology ; *Herbicides/toxicity/metabolism ; *Plant Leaves/metabolism/drug effects ; *Biodegradation, Environmental ; Soil Pollutants/toxicity/metabolism ; Chlorophyll/metabolism ; }, abstract = {Herbicides play a crucial role in managing weeds in agriculture, ensuring the productivity and quality of crops. However, herbicide drift poses a significant threat to sensitive plants, necessitating the consideration of ecosystem-based solutions to address this issue. In this study, foliar pre-spraying of atrazine-degrading Paenarthrobacter sp. AT5 was proposed as a new approach to mitigate the risks associated with atrazine drift on soybeans. Exposure to atrazine reduced chlorophyll levels and disturbed the antioxidant system and metabolic processes in soybean leaves, ultimately causing leaves to turn yellow. However, by pre-spraying, strain AT5 successfully colonized the surface of soybean leaves and mitigated the harmful effects of atrazine. This was achieved by slowing down atrazine absorption, expediting its reduction (half-life decreased from 2.22 d to 0.86 d), altering its degradation pathway (enhancing hydroxylation while weakening alkylation), and enhancing the interaction within phyllosphere bacteria communities. This study introduces a new approach that is both eco-friendly and user-friendly for reducing the risks of herbicide drift to sensitive crops, hence promoting the development of mixed cropping.}, }
@article {pmid39440978, year = {2024}, author = {Soto Ocaña, J and Friedman, ES and Keenan, O and Bayard, NU and Ford, E and Tanes, C and Munneke, MJ and Beavers, WN and Skaar, EP and Bittinger, K and Zemel, BS and Wu, GD and Zackular, JP}, title = {Metal availability shapes early life microbial ecology and community succession.}, journal = {mBio}, volume = {15}, number = {11}, pages = {e0153424}, pmid = {39440978}, issn = {2150-7511}, support = {R01DK107565, P30DK050306//HHS | National Institutes of Health (NIH)/ ; R35GM138369//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; UL1 TR001878/TR/NCATS NIH HHS/United States ; R01DK107565//HHS | National Institutes of Health (NIH)/ ; P30 DK050306/DK/NIDDK NIH HHS/United States ; P30 DK058404/DK/NIDDK NIH HHS/United States ; R01 DK107565/DK/NIDDK NIH HHS/United States ; R35 GM138369/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Infant ; *Metals/metabolism ; *Leukocyte L1 Antigen Complex/metabolism/analysis ; Bacteria/metabolism/classification/genetics ; Breast Feeding ; Feces/microbiology ; Gastrointestinal Tract/microbiology ; Infant, Newborn ; Microbiota ; Infant Formula ; }, abstract = {The gut microbiota plays a critical role in human health and disease. Microbial community assembly and succession early in life are influenced by numerous factors. In turn, assembly of this microbial community is known to influence the host, including immune system development, and has been linked to outcomes later in life. To date, the role of host-mediated nutritional immunity and metal availability in shaping microbial community assembly and succession early in life has not been explored in depth. Using a human infant cohort, we show that the metal-chelating protein calprotectin is highly abundant in infants. Taxa previously shown to be successful early colonizers of the infant gut, such as Enterococcus, Enterobacteriaceae, and Bacteroides, are highly resistant to experimental metal starvation in culture. Lactobacillus, meanwhile, is highly susceptible to metal restriction, pointing to a possible mechanism by which host-mediated metal limitation shapes the fitness of early colonizing taxa in the infant gut. We further demonstrate that formula-fed infants harbor markedly higher levels of metals in their gastrointestinal tract compared to breastfed infants. Formula-fed infants with high levels of metals harbor distinct microbial communities compared to breastfed infants, with higher levels of Enterococcus, Enterobacter, and Klebsiella, taxa which show increased resistance to the toxic effects of high metal concentrations. These data highlight a new paradigm in microbial community assembly and suggest an unappreciated role for nutritional immunity and dietary metals in shaping the earliest colonization events of the microbiota.IMPORTANCEEarly life represents a critical window for microbial colonization of the human gastrointestinal tract. Surprisingly, we still know little about the rules that govern the successful colonization of infants and the factors that shape the success of early life microbial colonizers. In this study, we report that metal availability is an important factor in the assembly and succession of the early life microbiota. We show that the host-derived metal-chelating protein, calprotectin, is highly abundant in infants and successful early life colonizers can overcome metal restriction. We further demonstrate that feeding modality (breastmilk vs formula) markedly impacts metal levels in the gut, potentially influencing microbial community succession. Our work suggests that metals, a previously unexplored aspect of early life ecology, may play a critical role in shaping the early events of microbiota assembly in infants.}, }
@article {pmid39440963, year = {2024}, author = {Wang, Y and Sun, Y and Huang, K and Gao, Y and Lin, Y and Yuan, B and Wang, X and Xu, G and Nussio, LG and Yang, F and Ni, K}, title = {Multi-omics analysis reveals the core microbiome and biomarker for nutrition degradation in alfalfa silage fermentation.}, journal = {mSystems}, volume = {9}, number = {11}, pages = {e0068224}, pmid = {39440963}, issn = {2379-5077}, support = {32171686//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {*Medicago sativa/microbiology/metabolism ; *Silage/microbiology ; *Fermentation ; *Microbiota/genetics ; Animals ; Biomarkers/metabolism ; Bacteria/genetics/metabolism/classification/isolation &amp; purification ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing ; Cattle ; Multiomics ; }, abstract = {UNLABELLED: Alfalfa (Medicago sativa L.) is one of the most extensively cultivated forage crops globally, and its nutritional quality critically influences the productivity of dairy cows. Silage fermentation is recognized as a crucial technique for the preservation of fresh forage, ensuring the retention of its vital nutrients. However, the detailed microbial components and their functions in silage fermentation are not fully understood. This study integrated large-scale microbial culturing with high-throughput sequencing to thoroughly examine the microbial community structure in alfalfa silage and explored the potential pathways of nutritional degradation via metagenomic analysis. The findings revealed an enriched microbial diversity in silage, indicated by the identification of amplicon sequence variants. Significantly, the large-scale culturing approach recovered a considerable number of unique microbes undetectable by high-throughput sequencing. Predominant genera, such as Lactiplantibacillus, Leuconostoc, Lentilactobacillus, Weissella, and Liquorilactobacillus, were identified based on their abundance and prevalence. Additionally, genes associated with Enterobacteriaceae were discovered, which might be involved in pathways leading to the production of ammonia-N and butyric acid. Overall, this study offers a comprehensive insight into the microbial ecology of silage fermentation and provides valuable information for leveraging microbial consortia to enhance fermentation quality.<br><br>IMPORTANCE: Silage fermentation is a microbial-driven anaerobic process that efficiently converts various substrates into nutrients readily absorbable and metabolizable by ruminant animals. This study, integrating culturomics and metagenomics, has successfully identified core microorganisms involved in silage fermentation, including those at low abundance. This discovery is crucial for the targeted cultivation of specific microorganisms to optimize fermentation processes. Furthermore, our research has uncovered signature microorganisms that play pivotal roles in nutrient metabolism, significantly advancing our understanding of the intricate relationships between microbial communities and nutrient degradation during silage fermentation.}, }
@article {pmid39437908, year = {2024}, author = {Yang, X and Chen, N and Yu, H and Liu, X and Feng, Y and Xing, D and Tian, Y}, title = {Applying machine learning and genetic algorithms accelerated for optimizing ethanol production.}, journal = {The Science of the total environment}, volume = {955}, number = {}, pages = {177027}, doi = {10.1016/j.scitotenv.2024.177027}, pmid = {39437908}, issn = {1879-1026}, mesh = {*Ethanol/metabolism ; *Machine Learning ; *Algorithms ; Zea mays ; Fermentation ; Neural Networks, Computer ; Biofuels ; }, abstract = {Corn straws can produce bioethanol via simultaneous saccharification and co-fermentation (SSCF). However, identifying optimal combinations of operating parameters from numerous possibilities through a cost-effective strategy to improve SSCF efficiency and yield remains challenging. The eXtreme Gradient Boost (XGB) and deep neural network (DNN) models were constructed to accurately predict ethanol yield from only five input variables, achieving >83 % accuracy. Subsequently, the XGB and the DNN models were merged with the genetic algorithm (GA) as the new optimization strategies. Experimental validation showed that the new strategy optimize the efficiency and yield of the SSCF ethanol production system quickly and accurately. Moreover, the potential optimization mechanism was investigated through the comprehensive interpretability analysis for XGB and the microbial ecology analysis. Enzyme Solution Volume (61.7 %) dominated, followed by time (12.9 %), substrate concentration (10.4 %), temperature (7.7 %), and inoculum volume (7.3 %). This efficient and accurate algorithm design strategy can significantly reduce the time required to optimize biochemical systems.}, }
@article {pmid39436938, year = {2024}, author = {Rocha, U and Kasmanas, JC and Toscan, R and Sanches, DS and Magnusdottir, S and Saraiva, JP}, title = {Simulation of 69 microbial communities indicates sequencing depth and false positives are major drivers of bias in prokaryotic metagenome-assembled genome recovery.}, journal = {PLoS computational biology}, volume = {20}, number = {10}, pages = {e1012530}, pmid = {39436938}, issn = {1553-7358}, mesh = {*Metagenome/genetics ; *Microbiota/genetics ; *Computer Simulation ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; Bacteria/genetics/classification ; Genome, Bacterial/genetics ; }, abstract = {We hypothesize that sample species abundance, sequencing depth, and taxonomic relatedness influence the recovery of metagenome-assembled genomes (MAGs). To test this hypothesis, we assessed MAG recovery in three in silico microbial communities composed of 42 species with the same richness but different sample species abundance, sequencing depth, and taxonomic distribution profiles using three different pipelines for MAG recovery. The pipeline developed by Parks and colleagues (8K) generated the highest number of MAGs and the lowest number of true positives per community profile. The pipeline by Karst and colleagues (DT) showed the most accurate results (~ 92%), outperforming the 8K and Multi-Metagenome pipeline (MM) developed by Albertsen and collaborators. Sequencing depth influenced the accurate recovery of genomes when using the 8K and MM, even with contrasting patterns: the MM pipeline recovered more MAGs found in the original communities when employing sequencing depths up to 60 million reads, while the 8K recovered more true positives in communities sequenced above 60 million reads. DT showed the best species recovery from the same genus, even though close-related species have a low recovery rate in all pipelines. Our results highlight that more bins do not translate to the actual community composition and that sequencing depth plays a role in MAG recovery and increased community resolution. Even low MAG recovery error rates can significantly impact biological inferences. Our data indicates that the scientific community should curate their findings from MAG recovery, especially when asserting novel species or metabolic traits.}, }
@article {pmid39436933, year = {2024}, author = {Di Nezio, F and Ong, ILH and Riedel, R and Goshal, A and Dhar, J and Roman, S and Storelli, N and Sengupta, A}, title = {Synergistic phenotypic adaptations of motile purple sulphur bacteria Chromatium okenii during lake-to-laboratory domestication.}, journal = {PloS one}, volume = {19}, number = {10}, pages = {e0310265}, pmid = {39436933}, issn = {1932-6203}, mesh = {*Lakes/microbiology ; *Phenotype ; *Adaptation, Physiological ; Chromatiaceae/physiology ; Microscopy, Atomic Force ; }, abstract = {Isolating microorganisms from natural environments for cultivation under optimized laboratory settings has markedly improved our understanding of microbial ecology. Artificial growth conditions often diverge from those in natural ecosystems, forcing wild isolates into distinct selective pressures, resulting in diverse eco-physiological adaptations mediated by modification of key phenotypic traits. For motile microorganisms we still lack a biophysical understanding of the relevant traits emerging during domestication and their mechanistic interplay driving short-to-long-term microbial adaptation under laboratory conditions. Using microfluidics, atomic force microscopy, quantitative imaging, and mathematical modeling, we study phenotypic adaptation of Chromatium okenii, a motile phototrophic purple sulfur bacterium from meromictic Lake Cadagno, grown under laboratory conditions over multiple generations. Our results indicate that naturally planktonic C. okenii leverage shifts in cell-surface adhesive interactions, synergistically with changes in cell morphology, mass density, and distribution of intracellular sulfur globules, to suppress their swimming traits, ultimately switching to a sessile lifeform. A computational model of cell mechanics confirms the role of such phenotypic shifts in suppressing the planktonic lifeform. By investigating key phenotypic traits across different physiological stages of lab-grown C. okenii, we uncover a progressive loss of motility during the early stages of domestication, followed by concomitant deflagellation and enhanced surface attachment, ultimately driving the transition of motile sulfur bacteria to a sessile state. Our results establish a mechanistic link between suppression of motility and surface attachment via phenotypic changes, underscoring the emergence of adaptive fitness under laboratory conditions at the expense of traits tailored for natural environments.}, }
@article {pmid39436423, year = {2024}, author = {Hirota, A and Kouduka, M and Fukuda, A and Miyakawa, K and Sakuma, K and Ozaki, Y and Ishii, E and Suzuki, Y}, title = {Biofilm Formation on Excavation Damaged Zone Fractures in Deep Neogene Sedimentary Rock.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {132}, pmid = {39436423}, issn = {1432-184X}, mesh = {*Biofilms/growth &amp; development ; *RNA, Ribosomal, 16S/genetics ; *Geologic Sediments/microbiology ; Phylogeny ; Groundwater/microbiology ; Bacteria/genetics/classification/isolation &amp; purification/metabolism ; Gammaproteobacteria/genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; }, abstract = {Deep underground galleries are used to access the deep biosphere in addition to mining and other engineering applications, such as geological disposal of radioactive waste. Fracture networks developed in the excavation damaged zone (EDZ) are concerned with accelerating mass transport, where microbial colonization might be possible due to the availability of space and nutrients. In this study, microbial biofilms at EDZ fractures were investigated by drilling from a 350-m-deep gallery and subsequent borehole logging at the Horonobe Underground Research Laboratory (URL). By using microscopic and spectroscopic techniques, the dense colonization of microbial cells was demonstrated at the surfaces of the EDZ fractures with high hydraulic conductivity. 16S rRNA gene sequence analysis revealed the dominance of gammaproteobacterial lineages, the cultivated members of which are aerobic methanotrophs. The near-complete genomes from Horonobe groundwater, affiliated with the methanotrophic lineages, were fully equipped with genes involved in aerobic methanotrophy. Although the mediation of aerobic methanotrophy remains to be demonstrated, microbial O2 production was supported by the presence of genes in the near-complete genomes, such as catalase and superoxide dismutase that produce O2 from reactive oxygen species and a nitric oxide reductase gene with the substitutions of amino acids in motifs. It is concluded that the EDZ fractures provide energetically favorable subsurface habitats for microorganisms.}, }
@article {pmid39435521, year = {2024}, author = {Muratore, TJ and Knorr, MA and Simpson, MJ and Stephens, RB and Phillips, RP and Frey, SD}, title = {Response of Root Respiration to Warming and Nitrogen Addition Depends on Tree Species.}, journal = {Global change biology}, volume = {30}, number = {10}, pages = {e17530}, doi = {10.1111/gcb.17530}, pmid = {39435521}, issn = {1365-2486}, support = {DEB-1456610//National Science Foundation/ ; DEB-1832110//National Science Foundation/ ; 2106096//National Science Foundation/ ; Hatch NH-00701//New Hampshire Agricultural Experiment Station/ ; //Natural Sciences and Engineering Research Council (NSERC) of Canada/ ; }, mesh = {*Plant Roots/metabolism/growth &amp; development ; *Nitrogen/metabolism ; *Acer/physiology/metabolism/growth &amp; development ; *Quercus/physiology/metabolism ; Soil/chemistry ; Global Warming ; Biomass ; Carbon Dioxide/metabolism ; Trees/growth &amp; development/metabolism/physiology ; }, abstract = {Roots contribute a large fraction of CO2 efflux from soils, yet the extent to which global change factors affect root-derived fluxes is poorly understood. We investigated how red maple (Acer rubrum) and red oak (Quercus rubra) root biomass and respiration respond to long-term (15 years) soil warming, nitrogen addition, or their combination in a temperate forest. We found that ecosystem root respiration was decreased by 40% under both single-factor treatments (nitrogen addition or warming) but not under their combination (heated × nitrogen). This response was driven by the reduction of mass-specific root respiration under warming and a reduction in maple root biomass in both single-factor treatments. Mass-specific root respiration rates for both species acclimated to soil warming, resulting in a 43% reduction, but were not affected by N addition or the combined heated × N treatment. Notably, the addition of nitrogen to warmed soils alleviated thermal acclimation and returned mass-specific respiration rates to control levels. Oak roots contributed disproportionately to ecosystem root respiration despite the decrease in respiration rates as their biomass was maintained or enhanced under warming and nitrogen addition. In contrast, maple root respiration rates were consistently higher than oak, and this difference became critical in the heated × nitrogen treatment, where maple root biomass increased, contributing significantly more CO2 relative to single-factor treatments. Our findings highlight the importance of accounting for the root component of respiration when assessing soil carbon loss in response to global change and demonstrate that combining warming and N addition produces effects that cannot be predicted by studying these factors in isolation.}, }
@article {pmid39435438, year = {2024}, author = {Michalska-Smith, M and Schlatter, DC and Pombubpa, N and Castle, SC and Grandy, AS and Borer, ET and Seabloom, EW and Kinkel, LL}, title = {Plant community richness and foliar fungicides impact soil Streptomyces inhibition, resistance, and resource use phenotypes.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1452534}, pmid = {39435438}, issn = {1664-302X}, abstract = {Plants serve as critical links between above- and below-ground microbial communitites, both influencing and being influenced by microbes in these two realms. Below-ground microbial communities are expected to respond to soil resource environments, which are mediated by the roots of plants that can, in turn, be influenced by the above-ground community of foliar endophytes. For instance, diverse plant communities deposit more, and more diverse, nutrients into the soil, and this deposition is often increased when foliar pathogens are removed. Differences in soil resources can alter soil microbial composition and phenotypes, including inhibitory capacity, resource use, and antibiotic resistance. In this work, we consider plots differing in plant richness and application of foliar fungicide, evaluating consequences on soil resource levels and root-associated Streptomyces phenotypes. Soil carbon, nitrogen, phosphorus, potassium, and organic matter were greater in samples from polyculture than monoculture, yet this increase was surprisingly offset when foliar fungal communities were disrupted. We find that Streptomyces phenotypes varied more between richness plots-with the Streptomyces from polyculture showing lower inhibitory capacity, altered resource-use profiles, and greater antibiotic resistance-than between subplots with/without foliar fungicide. Where foliar fungicide affected phenotypes, it did so differently in polyculture than in monoculture, for instance decreasing niche width and overlap in monoculture while increasing them in polyculture. No differences in phenotype were correlated with soil nutrient levels, suggesting the need for further research looking more closely at soil resource diversity and particular compounds that were found to differ between treatments.}, }
@article {pmid39435044, year = {2024}, author = {Gruseck, R and Palatinszky, M and Wagner, M and Hofmann, T and Zumstein, M}, title = {Quantification of guanidine in environmental samples using benzoin derivatization and LC-MS analysis.}, journal = {MethodsX}, volume = {13}, number = {}, pages = {102972}, pmid = {39435044}, issn = {2215-0161}, abstract = {The recent discovery of guanidine-dependent riboswitches in many microbes raised interest in the biological function and metabolism of this nitrogen-rich compound. However, very little is known about the concentrations of guanidine in the environment. Several methods have been published for quantifying guanidine and guanidino compounds in human urine and blood, often relying on derivatization followed by fluorescence detection. We adapted this analytical approach using benzoin as the derivatization agent to sensitively and selectively quantify guanidine in environmental samples, thereby facilitating future research on the biological and environmental roles of guanidine. This adapted method was applied to human urine, raw wastewater, and biological growth media as relevant matrices. Our liquid chromatography-tandem mass spectrometry analyses of the derivatized solutions identified a different major derivatization product than previously reported. This product was consistently observed across various substrates (guanidine, methylguanidine, and arginine) and derivatization agents (benzoin and anisoin). We observed a constant background signal, restricting our analyses to a lower limit of quantification of 50 nM. Despite this limitation, our method allowed for the quantification of guanidine concentrations significantly lower than those reported in previous derivatization-based studies.•Selective and sensitive detection of guanidine by LC-MS.•Method development and validation for robust detection of guanidine in environmental samples.•Reduction of sample preparation steps and reduced usage of toxic chemicals compared to previous methods.}, }
@article {pmid39432984, year = {2024}, author = {Sun, Y and Wang, N and Zhong, X and Xu, G}, title = {Can microplastics variability drive the colonization dynamics of periphytic protozoan fauna in marine environments?.}, journal = {Marine pollution bulletin}, volume = {209}, number = {Pt A}, pages = {117148}, doi = {10.1016/j.marpolbul.2024.117148}, pmid = {39432984}, issn = {1879-3363}, mesh = {*Microplastics ; *Water Pollutants, Chemical/analysis ; *Environmental Monitoring ; Biodiversity ; Animals ; Aquatic Organisms ; }, abstract = {In recent years, microplastics have become a global environmental hot topic of concern. To explore the effects of different concentrations of microplastics on colonization dynamics of periphytic protozoan fauna, a 21-day study was conducted in temperature-controlled circulation systems. Periphytic protozoan communities were used as test organisms and exposed to five concentrations of MPs: 0, 1, 5, 25, and 125 mg l[-1], identification and enumeration were conducted on days 3, 5, 7, 10, 14 and 21. The results showed that the colonization dynamics were driven by MPs and significantly shifted at concentrations over 5 mg l[-1]. However, a notable decline in maximum species richness and abundance was observed in the high concentrations of microplastic, along with significant deviations in colonization patterns from the control group (0 mg l[-1]). Therefore, it is suggested that the colonization dynamics of periphytic protozoa can serve as a bioindicator for assessing microplastic concentrations in marine environments.}, }
@article {pmid39432094, year = {2024}, author = {Shafana Farveen, M and Narayanan, R}, title = {Omic-driven strategies to unveil microbiome potential for biodegradation of plastics: a review.}, journal = {Archives of microbiology}, volume = {206}, number = {11}, pages = {441}, pmid = {39432094}, issn = {1432-072X}, mesh = {*Biodegradation, Environmental ; *Plastics/metabolism ; *Microbiota ; Bacteria/metabolism/genetics/classification ; Proteomics ; Genomics ; Microbial Consortia ; }, abstract = {Plastic waste accumulation has lately been identified as the leading and pervasive environmental concern, harming all living beings, natural habitats, and the global market. Given this issue, developing ecologically friendly solutions, such as biodegradation instead of standard disposal, is critical. To effectively address and develop better strategies, it is critical to understand the inter-relationship between microorganisms and plastic, the role of genes and enzymes involved in this process. However, the complex nature of microbial communities and the diverse mechanisms involved in plastic biodegradation have hindered the development of efficient plastic waste degradation strategies. Omics-driven approaches, encompassing genomics, transcriptomics and proteomics have revolutionized our understanding of microbial ecology and biotechnology. Therefore, this review explores the application of omics technologies in plastic degradation studies and discusses the key findings, challenges, and future prospects of omics-based approaches in identifying novel plastic-degrading microorganisms, enzymes, and metabolic pathways. The integration of omics technologies with advanced molecular technologies such as the recombinant DNA technology and synthetic biology would guide in the optimization of microbial consortia and engineering the microbial systems for enhanced plastic biodegradation under various environmental conditions.}, }
@article {pmid39431865, year = {2024}, author = {Daly, SE and Feng, J and Daeschel, D and Kovac, J and Snyder, AB}, title = {The choice of 16S rRNA gene sequence analysis impacted characterization of highly variable surface microbiota in dairy processing environments.}, journal = {mSystems}, volume = {9}, number = {11}, pages = {e0062024}, pmid = {39431865}, issn = {2379-5077}, support = {2022-67017-36289//U.S. Department of Agriculture (USDA)/ ; }, mesh = {*RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Bacteria/genetics/classification ; Food Microbiology ; Food Handling ; Dairying ; Dairy Products/microbiology ; }, abstract = {Accurate knowledge of the microbiota collected from surfaces in food processing environments is important for food quality and safety. This study assessed discrepancies in taxonomic composition and alpha and beta diversity values generated from eight different bioinformatic workflows for the analysis of 16S rRNA gene sequences extracted from the microbiota collected from surfaces in dairy processing environments. We found that the microbiota collected from environmental surfaces varied widely in density (0-9.09 log10 CFU/cm[2]) and Shannon alpha diversity (0.01-3.40). Consequently, depending on the sequence analysis method used, characterization of low-abundance genera (i.e., below 1% relative abundance) and the number of genera identified (114-173 genera) varied considerably. Some low-abundance genera, including Listeria, varied between the amplicon sequence variant (ASV) and operational taxonomic unit (OTU) methods. Centered log-ratio transformation inflated alpha and beta diversity values compared to rarefaction. Furthermore, the ASV method also inflated alpha and beta diversity values compared to the OTU method (P < 0.05). Therefore, for sparse, uneven, low-density data sets, the OTU method and rarefaction are better for taxonomic and ecological characterization of surface microbiota.IMPORTANCECulture-dependent environmental monitoring programs are used by the food industry to identify foodborne pathogens and spoilage biota on surfaces in food processing environments. The use of culture-independent 16S rRNA amplicon sequencing to characterize this surface microbiota has been proposed as a tool to enhance environmental monitoring. However, there is no consensus on the most suitable bioinformatic analyses to accurately capture the diverse levels and types of bacteria on surfaces in food processing environments. Here, we quantify the impact of different bioinformatic analyses on the results and interpretation of 16S rRNA amplicon sequences collected from three cultured dairy facilities in New York State. This study provides guidance for the selection of appropriate 16S rRNA analysis procedures for studying environmental microbiota in dairy processing environments.}, }
@article {pmid39430784, year = {2024}, author = {Li, X and Wang, Q and Wu, F and Ye, Z and Li, Y}, title = {Association between advanced lung cancer inflammation index and chronic kidney disease: a cross-sectional study.}, journal = {Frontiers in nutrition}, volume = {11}, number = {}, pages = {1430471}, pmid = {39430784}, issn = {2296-861X}, abstract = {BACKGROUND: Chronic kidney disease (CKD) is one of the common chronic diseases, and malnutrition and inflammation play a key role in the development of CKD. The advanced lung cancer inflammation index (ALI) is a novel index of nutrition and inflammation, and its association with CKD has not yet been clarified. The aim of this study was to explore the potential association between ALI and CKD.<br><br>METHODS: We conducted a cross-sectional survey using data extracted from the National Health and Nutrition Examination Survey (NHANES, 2003-2018). Weighted multivariate logistic regression was used to assess the association between ALI and CKD, and smoothed curve fitting and threshold effect analyses were used to describe the nonlinear association between ALI and CKD. Subgroup analyses were performed to further assess the influence of other covariates on the relationship between ALI and CKD.<br><br>RESULTS: A total of 39,469 adult participants were included in the study, of whom 7,204 (18.25%) were diagnosed with CKD. After adjusting for multiple confounders, we found a significant negative correlation between ALI and CKD (OR&#x2009;=&#x2009;0.93; 95%CI, 0.91-0.95; p&#x2009;<&#x2009;0.0001). The risk of CKD tended to decrease with increasing quartiles of ALI. Smoothed curve fitting showed an L-shaped negative correlation between ALI and CKD. Threshold analysis showed a saturation effect of ALI at the inflection point of 55.09. Subgroup analyses and interaction tests showed that this negative association was maintained across age, sex, race, BMI, diabetes, hypertension, cardiovascular disease, and cancer subgroups (P for interaction >0.05).<br><br>CONCLUSION: Our findings suggest a significant correlation between ALI and CKD in the US adult population. However, more large-scale prospective studies are still needed to further confirm our findings.}, }
@article {pmid39430052, year = {2025}, author = {Qin, K and Wang, Q and Qing, J and Li, Y and Gong, H and Zha, Z and Zhou, B and Li, Y}, title = {Analysis of mutations in Chinese patients with polycystic kidney disease by targeted exome sequencing.}, journal = {Genes &amp; diseases}, volume = {12}, number = {1}, pages = {101246}, pmid = {39430052}, issn = {2352-3042}, }
@article {pmid39425011, year = {2024}, author = {Sánchez, V and Baumann, A and Kromm, F and Yergaliyev, T and Brandt, A and Scholda, J and Kopp, F and Camarinha-Silva, A and Bergheim, I}, title = {Oral supplementation of choline attenuates the development of alcohol-related liver disease (ALD).}, journal = {Molecular medicine (Cambridge, Mass.)}, volume = {30}, number = {1}, pages = {181}, pmid = {39425011}, issn = {1528-3658}, mesh = {Animals ; *Choline/administration &amp; dosage/metabolism ; *Liver Diseases, Alcoholic/metabolism/etiology/prevention &amp; control/pathology/drug therapy ; *Dietary Supplements ; Mice ; Female ; *Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; Liver/metabolism/drug effects/pathology ; Administration, Oral ; Permeability ; Ethanol/adverse effects ; Disease Models, Animal ; }, abstract = {BACKGROUND: Chronic alcohol intake is associated with alterations of choline metabolism in various tissues. Here, we assessed if an oral choline supplementation attenuated the development of alcohol-related liver disease (ALD) in mice.<br><br>METHODS: Female C57BL/6&#xa0;J mice (n&#x2009;=&#x2009;8/group) were either pair-fed a liquid control diet, or a Lieber DeCarli liquid diet (5% ethanol)&#x2009;&#xb1;&#x2009;2.7&#xa0;g choline/kg diet for 29&#xa0;days. Liver damage, markers of intestinal permeability and intestinal microbiota composition were determined. Moreover, the effects of choline on ethanol-induced intestinal permeability were assessed in an ex vivo model.<br><br>RESULTS: ALD development as determined by liver histology and assessing markers of inflammation (e.g., nitric oxide, interleukin 6 and 4-hydroxynonenal protein adducts) was attenuated by the supplementation of choline. Intestinal permeability in small intestine being significantly higher in ethanol-fed mice was at the level of controls in ethanol-fed mice receiving choline. In contrast, no effects of the choline supplementation were found on intestinal microbiota composition. Choline also significantly attenuated the ethanol-induced intestinal barrier dysfunction in small intestinal tissue ex vivo, an effect almost entirely abolished by the choline oxidase inhibitor dimbunol.<br><br>CONCLUSION: Our results suggest that an oral choline supplementation attenuates the development of ALD in mice and is related to a protection from intestinal barrier dysfunction.}, }
@article {pmid39423562, year = {2024}, author = {Dal Bello, M and Abreu, CI}, title = {Temperature structuring of microbial communities on a global scale.}, journal = {Current opinion in microbiology}, volume = {82}, number = {}, pages = {102558}, pmid = {39423562}, issn = {1879-0364}, support = {F32 GM145148/GM/NIGMS NIH HHS/United States ; }, mesh = {*Temperature ; *Microbiota ; *Bacteria/metabolism/genetics/classification/growth &amp; development ; Bacterial Physiological Phenomena ; Ecosystem ; }, abstract = {Temperature is a fundamental physical constraint regulating key aspects of microbial life. Protein binding, membrane fluidity, central dogma processes, and metabolism are all tightly controlled by temperature, such that growth rate profiles across taxa and environments follow the same general curve. An open question in microbial ecology is how the effects of temperature on individual traits scale up to determine community structure and function at planetary scales. Here, we review recent theoretical and experimental efforts to connect physiological responses to the outcome of species interactions, the assembly of microbial communities, and their function as temperature changes. We identify open questions in the field and define a roadmap for future studies.}, }
@article {pmid39423289, year = {2024}, author = {Steensen, K and Séneca, J and Bartlau, N and Yu, XA and Hussain, FA and Polz, MF}, title = {Tailless and filamentous prophages are predominant in marine Vibrio.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39423289}, issn = {1751-7370}, support = {//Life Science Compute Cluster of the University of Vienna/ ; 572792//Simons Foundation/ ; //Austrian Science Fund/ ; }, mesh = {*Prophages/genetics/isolation &amp; purification ; *Vibrio/virology/genetics ; *Genome, Viral ; Phylogeny ; Genomics ; }, abstract = {Although tailed bacteriophages (phages) of the class Caudoviricetes are thought to constitute the most abundant and ecologically relevant group of phages that can integrate their genome into the host chromosome, it is becoming increasingly clear that other prophages are widespread. Here, we show that prophages derived from filamentous and tailless phages with genome sizes below 16 kb make up the majority of prophages in marine bacteria of the genus Vibrio. To estimate prophage prevalence unaffected by database biases, we combined comparative genomics and chemical induction of 58 diverse Vibrio cyclitrophicus isolates, resulting in 107 well-curated prophages. Complemented with computationally predicted prophages, we obtained 1158 prophages from 931 naturally co-existing strains of the family Vibrionaceae. Prophages resembling tailless and filamentous phages predominated, accounting for 80% of all prophages in V. cyclitrophicus and 60% across the Vibrionaceae. In our experimental model, prophages of all three viral realms actively replicated upon induction indicating their ability to transfer to new hosts. Indeed, prophages were rapidly gained and lost, as suggested by variable prophage content between closely related V. cyclitrophicus. Prophages related to filamentous and tailless phages were integrated into only three genomic locations and restored the function of their integration site. Despite their small size, they contained highly diverse accessory genes that may contribute to host fitness, such as phage defense systems. We propose that, like their well-studied tailed equivalent, tailless and filamentous temperate phages are active and highly abundant drivers of host ecology and evolution in marine Vibrio, which have been largely overlooked.}, }
@article {pmid39419992, year = {2024}, author = {Mei, S and Wang, M and Salles, JF and Hackl, T}, title = {Diverse rhizosphere-associated Pseudomonas genomes from along a Wadden Island salt marsh transition zone.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {1140}, pmid = {39419992}, issn = {2052-4463}, support = {[2020]596//China Scholarship Council (CSC)/ ; }, mesh = {*Rhizosphere ; *Pseudomonas/genetics ; *Soil Microbiology ; *Wetlands ; *Genome, Bacterial ; Artemisia/genetics/microbiology ; Biodiversity ; }, abstract = {Soil microbes are key drivers of ecosystem processes promoting nutrient cycling, system productivity, and resilience. While much is known about the roles of microbes in established systems, their impact on soil development and the successional transformation over time remains poorly understood. Here, we provide 67 diverse, rhizosphere-associated Pseudomonas draft genomes from an undisturbed salt march primary succession spanning >100 years of soil development. Pseudomonas are cosmopolitan bacteria with a significant role in plant establishment and growth. We obtained isolates associated with Limonium vulgare and Artemisia maritima, two typical salt marsh perennial plants with roles in soil stabilization, salinity regulation, and biodiversity support. We anticipate that our data, in combination with the provided physiochemical measurements, will help identify genomic signatures associated with the different selective regimes along the successional stages, such as varying soil complexity, texture, and nutrient availability. Such findings would advance our understanding of Pseudomonas' role in natural soil ecosystems and provide the basis for a better understanding of the roles of microbes throughout ecosystem transformations.}, }
@article {pmid39419884, year = {2024}, author = {Mohammed, FA and Abu-Hussien, SH and Dougdoug, NKE and Koutb, N and Korayem, AS}, title = {Streptomyces fradiae Mitigates the Impact of Potato Virus Y by Inducing Systemic Resistance in Two Egyptian Potato (Solanum tuberosum L.) Cultivars.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {131}, pmid = {39419884}, issn = {1432-184X}, mesh = {*Solanum tuberosum/virology/microbiology ; *Streptomyces/isolation &amp; purification/physiology/genetics ; *Potyvirus/physiology ; *Plant Diseases/virology/microbiology ; *Disease Resistance ; RNA, Ribosomal, 16S/genetics ; }, abstract = {In this study, the impact of culture media filtrate of QD3 actinobacterial isolate on two potato cultivars, Spunta and Diamond, infected with potato virus Y (PVY) was investigated. Various parameters, including infection percentage, PVY virus infectivity, disease severity scoring, PVY optical density, photosynthetic and defense-related biochemical markers, enzymatic profiling, phenolic compounds, proline content, salicylic acid levels, and growth and yield parameters, were assessed to elucidate the potential of the QD3 actinobacterial isolate culture filtrate in mitigating PVY-induced damage. The physiological and biochemical characteristics of the QD3 actinobacterial isolate, including its salinity tolerance, pH preferences, and metabolic traits, were investigated. Molecular identification via 16S rRNA gene sequencing confirmed its classification as Streptomyces fradiae QD3, and it was deposited in GenBank with the gene accession number MN160630. Distinct responses between Spunta and Diamond cultivars, with Spunta displaying greater resistance to PVY infection. Notably, pre-infection foliar application of the QD3 filtrate significantly reduced disease symptoms and virus infection in both cultivars. For post-PVY infection, the QD3 filtrate effectively mitigated disease severity and the PVY optical density. Furthermore, the QD3 filtrate positively influenced photosynthetic pigments, enzymatic antioxidant activities, and key biochemical components associated with plant defense mechanisms. Gas chromatography‒mass spectrometry (GC‒MS) analysis revealed palmitic acid (hexadecanoic acid, methyl ester) and oleic acid (9-octadecanoic acid, methyl ester) as the most prominent compounds, with retention times of 23.23 min and 26.41 min, representing 53.27% and 23.25%, respectively, of the total peak area as primary unsaturated fatty acids and demonstrating antiviral effects against plant viruses. Cytotoxicity assays on normal human skin fibroblasts (HSFs) revealed the safety of QD3 metabolites, with low discernible toxicity at high concentrations, reinforcing their potential as safe and effective interventions. The phytotoxicity results indicate that all the seeds presented high germination rates of approximately 95-98%, suggesting that the treatment conditions had no phytotoxic effect on the Brassica oleracea (broccoli) seeds, Lactuca sativa (lettuce) seeds, and Eruca sativa (arugula or rocket) seeds. Overall, the results of this study suggest that the S. fradiae filtrate has promising anti-PVY properties, influencing various physiological, biochemical, and molecular aspects in potato cultivars. These findings provide valuable insights into potential strategies for managing PVY infections in potato crops, emphasizing the importance of Streptomyces-derived interventions in enhancing plant health and crop protection.}, }
@article {pmid39419230, year = {2024}, author = {Siebert, C and Ionescu, D and Mallast, U and Merchel, S and Merkel, B and Möller, P and Pavetich, S and Pohl, T and Rödiger, T and Yechieli, Y}, title = {A new type of submarine chimneys built of halite.}, journal = {The Science of the total environment}, volume = {955}, number = {}, pages = {176752}, doi = {10.1016/j.scitotenv.2024.176752}, pmid = {39419230}, issn = {1879-1026}, abstract = {In contrast to the subaquatic sulphide and carbonate chimneys, which are known from Mid Ocean Ridges and abyssal submarine volcanoes, chimneys built of salts have not been described yet. Here we present such halite chimneys as a new form of cold-water smokers in hypersaline environments. The here described structures rise up from the bottom of the Dead Sea and result from the submarine discharge of saturated halite-dissolution brines into the salt lake, which is at halite saturation and holds remarkable chloride excess. At the interface with the lake brine, halite precipitates instantaneously, forming chimneys up to several meters in height. The brines leading to the formation of these chimneys vary in composition, while their generation processes are similar. Fresh groundwater from surrounding aquifers enters the saline lake sediments and considerably leaches halite in the adjacencies of the lake. Simultaneously, it mixes with ancient brines before it emerges from the lake floor. The distinct differences in composition between the Dead Sea and the emerging chimney brines lead to the instantaneous crystallisation of halite and few other mineral phases. The chimney structure result from the buoyancy flow of the chimney brines, which are less dense then the ambient Dead Sea. The chimneys indicate intense cavitation of massive halite bodies in the subsurface of the Dead Sea environment, a process that leads to increasing formation of hazardous sinkholes. Since chimneys are proven in shallow water but may be expected in deeper parts too, they are comfortably mappable by echo-sounding or aerial imaging. They thus provide in the Dead Sea as in any likewise setting a potent predictive tool to locate dangerous subsurface cavitation and hence areas that are at risk of collapse in the near future.}, }
@article {pmid39419211, year = {2024}, author = {Santos-Silva, L and Roque, WF and de Moura, JM and Mello, IS and de Carvalho, LAL and Pinheiro, DG and Bouzan, RS and Brescovit, AD and de Andrade, RLT and da Silva, GF and Battirola, LD and Soares, MA}, title = {Toxic metals in Amazonian soil modify the bacterial community associated with Diplopoda.}, journal = {The Science of the total environment}, volume = {955}, number = {}, pages = {176915}, doi = {10.1016/j.scitotenv.2024.176915}, pmid = {39419211}, issn = {1879-1026}, mesh = {*Soil Pollutants/toxicity ; Animals ; *Bacteria/drug effects/classification ; *Microbiota/drug effects ; Arthropods/drug effects ; Soil Microbiology ; Cadmium/toxicity ; Brazil ; Mercury/toxicity/metabolism ; Soil/chemistry ; Environmental Monitoring ; Rainforest ; }, abstract = {Toxic metal pollution in the Amazon is a serious problem that reduces the quality of water, soil, air, and consequently alters communities of fauna, flora, and microbiota, harming human health and well-being. Our aim was to determine the impact of toxic metals on the structure of the bacterial community associated with Diplopoda in the Amazon rainforest. Animals were kept in microcosms contaminated with cadmium (50 mg.kg[-1]), mercury (35 mg.kg[-1]) and no toxic metal (control). The intestinal and molting chamber microbiota were accessed by culture-dependent and culture-independent methods (16S metabarcoding). The cultivated strains were identified, and their functional traits evaluated: secretion of enzymes, growth at different pH, resistance to metals and antibiotics, and ability to reduce toxic effects of metals on plants. Our research described Brachyurodesmus albus, a new species of Diplopoda. We obtained 177 isolates distributed in 35 genera and 61 species of bacteria (Pseudomonadota, Bacillota, Bacteroidota and Actinomycetota) associated with the gut and molting chamber of B. albus. Metabarcoding data provided a more robust access to the bacterial community, resulting in 24 phyla, 561 genera and 6792 ASVs. The presence of metal Cd and Hg alters the composition and abundance of bacteria associated with B. albus (PERMANOVA p < 0.05). The microhabitat (gut and molting chamber) harbours bacterial communities that differ in composition and abundance (PERMANOVA p < 0.05). The presence of Cd and Hg alters important metabolic pathways related to the prokaryotic defense system; antimicrobial resistance genes, endocytosis and secretion system, estimated by PICRUSt. Bacteria selected with high resistance to Cd and Hg buffer the toxic effect of metals on tomato seedlings. This work describes B. albus and concludes that its diverse bacterial microbiota is altered by soil contamination by toxic metals, as well as being an important repository for prospecting strains to be applied in bioremediation programs.}, }
@article {pmid39419002, year = {2024}, author = {Meroz, N and Livny, T and Toledano, G and Sorokin, Y and Tovi, N and Friedman, J}, title = {Evolution in microbial microcosms is highly parallel, regardless of the presence of interacting species.}, journal = {Cell systems}, volume = {15}, number = {10}, pages = {930-940.e5}, doi = {10.1016/j.cels.2024.09.007}, pmid = {39419002}, issn = {2405-4720}, mesh = {*Biological Evolution ; Microbial Interactions/physiology ; Adaptation, Physiological ; Mutation ; Bacteria/genetics/metabolism ; Evolution, Molecular ; }, abstract = {Evolution often follows similar trajectories in replicate populations, suggesting that it may be predictable. However, populations are naturally embedded in multispecies communities, and the extent to which evolution is contingent on the specific species interacting with the focal population is still largely unexplored. Here, we study adaptations in strains of 11 different species, experimentally evolved both in isolation and in various pairwise co-cultures. Although partner-specific effects are detectable, evolution was mostly shared between strains evolved with different partners; similar changes occurred in strains' growth abilities, in community properties, and in about half of the repeatedly mutated genes. This pattern persisted even in species pre-adapted to the abiotic conditions. These findings indicate that evolution may not always depend strongly on the biotic environment, making predictions regarding coevolutionary dynamics less challenging than previously thought. A record of this paper's transparent peer review process is included in the supplemental information.}, }
@article {pmid39418776, year = {2024}, author = {Xie, Q and Sun, J and Sun, M and Wang, Q and Wang, M}, title = {Perturbed microbial ecology in neuromyelitis optica spectrum disorder: Evidence from the gut microbiome and fecal metabolome.}, journal = {Multiple sclerosis and related disorders}, volume = {92}, number = {}, pages = {105936}, doi = {10.1016/j.msard.2024.105936}, pmid = {39418776}, issn = {2211-0356}, mesh = {*Neuromyelitis Optica/microbiology/immunology ; Humans ; *Gastrointestinal Microbiome/physiology ; *Feces/microbiology ; Animals ; Female ; Adult ; *Fecal Microbiota Transplantation ; Mice ; Male ; Metabolome/physiology ; Middle Aged ; }, abstract = {BACKGROUND: Neuromyelitis optica spectrum disorder (NMOSD) is a central nervous system inflammatory demyelinating immune-mediated ailment, which is influenced by genetic, epigenetic, and environmental elements. The escalating incidence of NMOSD in recent years implies alterations in environmental risk factors. Recent research has established a correlation between gut microbiomes and the development of NMOSD.<br><br>METHODS: Metagenomic shotgun sequencing and gas chromatography-mass spectrometry (GC-MS) were employed to assess alterations of the structure and function in the fecal microbiome, as well as levels of short-chain fatty acids (SCFAs) in fecal and blood samples, among individuals with neuromyelitis optica spectrum disorder (NMOSD) during the acute phase (n = 25), the remission phase (n = 11), and a group of healthy controls (HCs) (n = 24). We further explored the correlation between gut microbiota and the pathogenesis of NMOSD through fecal microbiota transplantation (FMT). The gut microbiome from human donors diagnosed with NMOSD or HCs was transplanted into germ-free mice, followed by an analysis of the alterations in the structure and functionality of the transplanted mice's gut microbiome. Additionally, the impact of microbiome transfer on the immunity and spinal cord of germ-free mice was assessed through various techniques, including ELISA, flow cytometry, western blot, histopathology, and transcriptome sequencing.<br><br>RESULTS: (1) At the taxonomic levels of genus and species, there were significant differences in the &#x3b1;-diversity of the microbiome between HCs and NMOSD patients in the acute phase, with NMOSD patients having higher species diversity. (2) In the acute phase, the gut microbiota of NMOSD patients was characterized by Ruminococcaceae_unclassified, Campylobacter, Parabacteroides, Lactobacillus, Akkermansia, Streptococcus oralis, Clostridium leptum, Clostridium asparagiforme, Firmicutes bacterium CAG 238, and Lactobacillus fermentum. (3) The relative abundances of Coprobacter, Turicimonas, Gemmiger, Enterobacter, Roseburia sp.CAG 471, Veillonella tobetsuensis, Proteobacteria bacterium CAG 139, Ruminococcus bicirculans, Lactococcus lactis, Flavonifractor plautii, and Streptococcus cristatus were notably lower in patients experiencing remission compared to NMOSD patients in the acute phase, On the other hand, the relative abundances of Flavonifractor (P = 0.049) and Clostridium aldenense (P = 0.049) were significantly higher. Following medication, the gut microbiome distribution in NMOSD patients during remission closely resembled that of healthy controls (HCs). (4) Compared with HCs, acetate levels in the feces of patients with NMOSD in the acute phase were significantly lower. (5) In addition, we transplanted feces from NMOSD patients into germ-free mice and revealed a significant increase in the levels of IL-6, IL-17A, and IL-23 in the blood of mice belonging to the NMOSD fecal transplantation (NFMT) group. Additionally, the IL-10 level exhibited a significant reduction. Moreover, the proportion of Th17 cells displayed a significant increase, while the proportion of Treg cells exhibited a significant decrease in the spleens of NFMT mice.<br><br>CONCLUSION: Patients in the acute phase of neuromyelitis optica spectrum disorder (NMOSD) exhibited imbalances in their gut microbiota and a deficiency in short-chain fatty acids (SCFAs). Following drug treatment, the composition of intestinal microbes in NMOSD patients during the remission phase closely resembled that of the healthy control population. The FMT experiment provided evidence of the significant association between intestinal flora and the pathogenesis of NMOSD. Consequently, investigating gut microbiota and identifying novel microbial markers hold promise for the diagnosis and treatment of NMOSD patients.}, }
@article {pmid39418385, year = {2024}, author = {Lien, YW and Amendola, D and Lee, KS and Bartlau, N and Xu, J and Furusawa, G and Polz, MF and Stocker, R and Weiss, GL and Pilhofer, M}, title = {Mechanism of bacterial predation via ixotrophy.}, journal = {Science (New York, N.Y.)}, volume = {386}, number = {6719}, pages = {eadp0614}, doi = {10.1126/science.adp0614}, pmid = {39418385}, issn = {1095-9203}, mesh = {*Bacterial Adhesion ; *Bacteroidetes/physiology/ultrastructure ; Cryoelectron Microscopy ; Single-Cell Analysis ; *Type VI Secretion Systems/metabolism/ultrastructure ; *Vibrio/physiology/ultrastructure ; *Flagella/ultrastructure ; }, abstract = {Ixotrophy is a contact-dependent predatory strategy of filamentous bacteria in aquatic environments for which the molecular mechanism remains unknown. We show that predator-prey contact can be established by gliding motility or extracellular assemblages we call "grappling hooks." Cryo-electron microscopy identified the grappling hooks as heptamers of a type IX secretion system substrate. After close predator-prey contact is established, cryo-electron tomography and functional assays showed that puncturing by a type VI secretion system mediated killing. Single-cell analyses with stable isotope-labeled prey revealed that prey components are taken up by the attacker. Depending on nutrient availability, insertion sequence elements toggle the activity of ixotrophy. A marine metagenomic time series shows coupled dynamics of ixotrophic bacteria and prey. We found that the mechanism of ixotrophy involves multiple cellular machineries, is conserved, and may shape microbial populations in the environment.}, }
@article {pmid39417884, year = {2024}, author = {Mircea, C and Rusu, I and Levei, EA and Cristea, A and Gridan, IM and Zety, AV and Banciu, HL}, title = {The Fungal Side of the Story: Saprotrophic- vs. Symbiotrophic-Predicted Ecological Roles of Fungal Communities in Two Meromictic Hypersaline Lakes from Romania.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {130}, pmid = {39417884}, issn = {1432-184X}, support = {PN-III-P4-ID-PCE-2020-1559//Unitatea Executiva pentru Finantarea Invatamantului Superior, a Cercetarii, Dezvoltarii si Inovarii/ ; PN-III-P1-1.1-PD-2021-0634//Unitatea Executiva pentru Finantarea Invatamantului Superior, a Cercetarii, Dezvoltarii si Inovarii/ ; PN-III-P4-ID-PCE-2020-1559//Unitatea Executiva pentru Finantarea Invatamantului Superior, a Cercetarii, Dezvoltarii si Inovarii/ ; PN-III-P4-ID-PCE-2020-1559//Unitatea Executiva pentru Finantarea Invatamantului Superior, a Cercetarii, Dezvoltarii si Inovarii/ ; PN-III-P4-ID-PCE-2020-1559//Unitatea Executiva pentru Finantarea Invatamantului Superior, a Cercetarii, Dezvoltarii si Inovarii/ ; PN-III-P4-ID-PCE-2020-1559//Unitatea Executiva pentru Finantarea Invatamantului Superior, a Cercetarii, Dezvoltarii si Inovarii/ ; }, mesh = {*Lakes/microbiology ; Romania ; *Fungi/genetics/classification/isolation &amp; purification/physiology ; *Salinity ; *Mycobiome ; RNA, Ribosomal, 18S/genetics ; Biodiversity ; Geologic Sediments/microbiology ; Soil Microbiology ; DNA, Fungal/genetics ; Phylogeny ; }, abstract = {Over three-quarters of Earth's surface exhibits extreme environments where life thrives under harsh physicochemical conditions. While prokaryotes have often been investigated in these environments, only recent studies have revealed the remarkable adaptability of eukaryotes, in particular fungi. This study explored the mycobiota of two meromictic hypersaline lakes, Ursu and Fără Fund, in Transylvania (Romania). The intrinsic and extrinsic fungal diversity was assessed using amplicon sequencing of environmental DNA samples from sediments, water columns, surrounding soils, and an associated rivulet. The fungal communities, illustrated by the 18S rRNA gene and ITS2 region, exhibited contrasting patterns between the lakes. The ITS2 region assessed better than the 18S rRNA gene the fungal diversity. The ITS2 data showed that Ascomycota was the most abundant fungal group identified in both lakes, followed by Aphelidiomycota, Chytridiomycota, and Basidiomycota. Despite similar α-diversity levels, significant differences in fungal community structure were observed between the lakes, correlated with salinity, total organic carbon, total nitrogen, and ammonium. Taxonomic profiling revealed depth-specific variations, with Saccharomycetes prevalent in Ursu Lake's deeper layers and Lecanoromycetes prevalent in the Fără Fund Lake. The functional annotation using FungalTraits revealed diverse ecological roles within the fungal communities. Lichenized fungi were dominant in Fără Fund Lake, while saprotrophs were abundant in Ursu Lake. Additionally, wood and soil saprotrophs, along with plant pathogens, were more prevalent in the surrounding soils, rivulet, and surface water layers. A global overview of the trophic relations in each studied niche was impossible to establish due to the unconnected graphs corresponding to the trophic interactions of the analyzed fungi. Plotting the unweighted connected subgraphs at the genus level suggests that salinity made the studied niches similar for the identified taxa. This study shed light on the understudied fungal diversity, distribution, and ecological functions in hypersaline environments.}, }
@article {pmid39415203, year = {2024}, author = {Tong, X and Luo, D and Leung, MHY and Lee, JYY and Shen, Z and Jiang, W and Mason, CE and Lee, PKH}, title = {Diverse and specialized metabolic capabilities of microbes in oligotrophic built environments.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {198}, pmid = {39415203}, issn = {2049-2618}, support = {BK20230230//Jiangsu Science and Technology Programme/ ; 11214721//Hong Kong Research Grants Council, General Research Fund/ ; R1016-20F//Hong Kong Research Grants Council, Research Impact Fund/ ; }, mesh = {Humans ; Hong Kong ; *Microbiota ; *Built Environment ; *Metagenome ; *Phylogeny ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Skin/microbiology ; Micrococcus luteus/genetics/metabolism ; Genome, Bacterial ; }, abstract = {BACKGROUND: Built environments (BEs) are typically considered to be oligotrophic and harsh environments for microbial communities under normal, non-damp conditions. However, the metabolic functions of microbial inhabitants in BEs remain poorly understood. This study aimed to shed light on the functional capabilities of microbes in BEs by analyzing 860 representative metagenome-assembled genomes (rMAGs) reconstructed from 738 samples collected from BEs across the city of Hong Kong and from the skin surfaces of human occupants. The study specifically focused on the metabolic functions of rMAGs that are either phylogenetically novel or prevalent in BEs.<br><br>RESULTS: The diversity and composition of BE microbiomes were primarily shaped by the sample type, with Micrococcus luteus and Cutibacterium acnes being prevalent. The metabolic functions of rMAGs varied significantly based on taxonomy, even at the strain level. A novel strain affiliated with the Candidatus class Xenobia in the Candidatus phylum Eremiobacterota and two novel strains affiliated with the superphylum Patescibacteria exhibited unique functions compared with their close relatives, potentially aiding their survival in BEs and on human skins. The novel strains in the class Xenobia possessed genes for transporting nitrate and nitrite as nitrogen sources and nitrosative stress mitigation induced by nitric oxide during denitrification. The two novel Patescibacteria strains both possessed a broad array of genes for amino acid and trace element transport, while one of them carried genes for carotenoid and ubiquinone biosynthesis. The globally prevalent M. luteus in BEs displayed a large and open pangenome, with high infraspecific genomic diversity contributed by 11 conspecific strains recovered from BEs in a single geographic region. The versatile metabolic functions encoded in the large accessory genomes of M. luteus may contribute to its global ubiquity and specialization in BEs.<br><br>CONCLUSIONS: This study illustrates that the microbial inhabitants of BEs possess metabolic potentials that enable them to tolerate and counter different biotic and abiotic conditions. Additionally, these microbes can efficiently utilize various limited residual resources from occupant activities, potentially enhancing their survival and persistence within BEs. A better understanding of the metabolic functions of BE microbes will ultimately facilitate the development of strategies to create a healthy indoor microbiome. Video Abstract.}, }
@article {pmid39414684, year = {2024}, author = {Siqueira, JS and de Carvalho, LAL and Santos, CHB and Frezarin, ET and Pinheiro, DG and Nicodemo, D and Desoignies, N and Rigobelo, EC}, title = {Influence of Growth Support on the Diversity, Composition, and Functionality of Microbial Communities Associated with Tillandsia recurvata.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {129}, pmid = {39414684}, issn = {1432-184X}, mesh = {*Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; *Plant Roots/microbiology ; *Plant Leaves/microbiology ; Fungi/classification/genetics/isolation &amp; purification/physiology ; Biodiversity ; Trees/microbiology ; Soil Microbiology ; }, abstract = {Tillandsia recurvata is an epiphytic plant commonly found in tropical regions and colonizes tree trunks, fences, and power wires. This plant plays an important role in interacting with trees, sharing microorganisms, and performing specific functions in the process of tree colonization. The objective of this study was to evaluate and compare the microbiomes of T. recurvata collected from two different locations (trees and fences) and two plant tissues (leaves and roots). The hypothesis of this study was that the microbiome of T. recurvata is composed of microorganisms that would provide nutritional support to compensate for the lack of nutrients in a particular growth support. The results showed significant differences in microbial diversity between trees and fences, with trees exhibiting higher richness and more complex microbial networks. Proteobacteria was the most prevalent bacterial phylum, with Actinobacteria and Sphingomonas also playing key roles in nitrogen fixation and plant growth. Fungal communities were similar across locations, with Ascomycota and Basidiomycota being predominant, but Paraconiothyrium and Nigrospora showed significant differences in abundance between trees and fences. Functional analysis indicated similar metabolic profiles across leaf and root samples, with key functions for T. recurvata including carbohydrate and amino acid metabolism, stress control, and biofertilization.}, }
@article {pmid39411441, year = {2024}, author = {Pardo-Esté, C and Cortés, J and Castro-Severyn, J and Pérez, V and Henriquez-Aedo, K and Cuadros, F and Yañez, C and Cuadros-Orellana, S and Dorador, C and Molina, V and Eissler, Y and Paquis, P and Jeffrey, WH and Pozo, P and Pérez, PA and Hengst, MB}, title = {Secondary metabolites with antimicrobial activity produced by thermophilic bacteria from a high-altitude hydrothermal system.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1477458}, pmid = {39411441}, issn = {1664-302X}, abstract = {Thermophilic microorganisms possess several adaptations to thrive in high temperature, which is reflected as biosynthesis of proteins and thermostable molecules, isolation and culture represent a great methodological challenge, therefore High throughput sequencing enables screening of the whole bacterial genome for functional potential, providing rapid and cost-effective information to guide targeted cultures for the identification and characterization of novel natural products. In this study, we isolated two thermophilic bacterial strains corresponding to Bacillus LB7 and Streptomyces LB8, from the microbial mats in the Atacama Desert. By combining genome mining, targeted cultures and biochemical characterization, we aimed to identify their capacity to synthesize bioactive compounds with antimicrobial properties. Additionally, we determined the capability to produce bioactive compounds under controlled in vitro assays and detected by determining their masses by Thin-Layer Chromatography/Mass Spectrometry (TLC/MS). Overall, both isolates can produce antimicrobial (e.g., Myxalamide C by-product) and antioxidants (e.g. Dihydroxymandelic Acid, Amide biotine and Flavone by-products) compounds. Bacillus LB7 strain possesses a more diverse repertoire with 51.95% of total metabolites unmatched, while Streptomyces LB8 favors mainly antioxidants, but has over 70% of unclassified compounds, highlighting the necessity to study and elucidate the structure of novel compounds. Based on these results, we postulate that the uncultured or rare cultured thermophiles inhabiting high-altitude hydrothermal ecosystems in the Atacama Desert offer a promising opportunity to the study of novel microbial bioactive compounds.}, }
@article {pmid39411429, year = {2024}, author = {Xiao, P and Wu, Y and Zuo, J and Grossart, HP and Sun, R and Li, G and Jiang, H and Cheng, Y and Wang, Z and Geng, R and Zhang, H and Ma, Z and Yan, A and Li, R}, title = {Differential microbiome features in lake-river systems of Taihu basin in response to water flow disturbance.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1479158}, pmid = {39411429}, issn = {1664-302X}, abstract = {INTRODUCTION: In riverine ecosystems, dynamic interplay between hydrological conditions, such as flow rate, water level, and rainfall, significantly shape the structure and function of bacterial and microeukaryotic communities, with consequences for biogeochemical cycles and ecological stability. Lake Taihu, one of China's largest freshwater lakes, frequently experiences cyanobacterial blooms primarily driven by nutrient over-enrichment and hydrological changes, posing severe threats to water quality, aquatic life, and surrounding human populations. This study explored how varying water flow disturbances influence microbial diversity and community assembly within the interconnected river-lake systems of the East and South of Lake Taihu (ET&amp;ST). The Taipu River in the ET region accounts for nearly one-third of Lake Taihu's outflow, while the ST region includes the Changdougang and Xiaomeigang rivers, which act as inflow rivers. These two rivers not only channel water into Lake Taihu but can also cause the backflow of lake water into the rivers, creating distinct river-lake systems subjected to different intensities of water flow disturbances.<br><br>METHODS: Utilizing high-throughput sequencing, we selected 22 sampling sites in the ET and ST interconnected river-lake systems and conducted seasonally assessments of bacterial and microeukaryotic community dynamics. We then compared differences in microbial diversity, community assembly, and co-occurrence networks between the two regions under varying hydrological regimes.<br><br>RESULTS AND DISCUSSION: This study demonstrated that water flow intensity and temperature disturbances significantly influenced diversity, community structure, community assembly, ecological niches, and coexistence networks of bacterial and eukaryotic microbes. In the ET region, where water flow disturbances were stronger, microbial richness significantly increased, and phylogenetic relationships were closer, yet variations in community structure were greater than in the ST region, which experienced milder water flow disturbances. Additionally, migration and dispersal rates of microbes in the ET region, along with the impact of dispersal limitations, were significantly higher than in the ST region. High flow disturbances notably reduced microbial niche width and overlap, decreasing the complexity and stability of microbial coexistence networks. Moreover, path analysis indicated that microeukaryotic communities exhibited a stronger response to water flow disturbances than bacterial communities. Our findings underscore the critical need to consider the effects of hydrological disturbance on microbial diversity, community assembly, and coexistence networks when developing strategies to manage and protect river-lake ecosystems, particularly in efforts to control cyanobacterial blooms in Lake Taihu.}, }
@article {pmid39409485, year = {2024}, author = {Jechow, A and Bumberger, J and Palm, B and Remmler, P and Schreck, G and Ogashawara, I and Kiel, C and Kohnert, K and Grossart, HP and Singer, GA and Nejstgaard, JC and Wollrab, S and Berger, SA and Hölker, F}, title = {Characterizing and Implementing the Hamamatsu C12880MA Mini-Spectrometer for Near-Surface Reflectance Measurements of Inland Waters.}, journal = {Sensors (Basel, Switzerland)}, volume = {24}, number = {19}, pages = {}, pmid = {39409485}, issn = {1424-8220}, support = {Leibniz Competition No. K45/2017 (CONNECT-Connectivity and synchronization of lake ecosystems in space and time)//Leibniz Association/ ; IGB Frontiers project (2017)//Leibniz Institute of Freshwater Ecology and Inland Fisheries/ ; }, abstract = {In recent decades, inland water remote sensing has seen growing interest and very strong development. This includes improved spatial resolution, increased revisiting times, advanced multispectral sensors and recently even hyperspectral sensors. However, inland waters are more challenging than oceanic waters due to their higher complexity of optically active constituents and stronger adjacency effects due to their small size and nearby vegetation and built structures. Thus, bio-optical modeling of inland waters requires higher ground-truthing efforts. Large-scale ground-based sensor networks that are robust, self-sufficient, non-maintenance-intensive and low-cost could assist this otherwise labor-intensive task. Furthermore, most existing sensor systems are rather expensive, precluding their employability. Recently, low-cost mini-spectrometers have become widely available, which could potentially solve this issue. In this study, we analyze the characteristics of such a mini-spectrometer, the Hamamatsu C12880MA, and test it regarding its application in measuring water-leaving radiance near the surface. Overall, the measurements performed in the laboratory and in the field show that the system is very suitable for the targeted application.}, }
@article {pmid39406893, year = {2025}, author = {Ioannou, A and Berkhout, MD and Geerlings, SY and Belzer, C}, title = {Akkermansia muciniphila: biology, microbial ecology, host interactions and therapeutic potential.}, journal = {Nature reviews. Microbiology}, volume = {23}, number = {3}, pages = {162-177}, pmid = {39406893}, issn = {1740-1534}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Akkermansia/physiology/genetics/classification ; Probiotics/therapeutic use ; *Host Microbial Interactions ; *Verrucomicrobia/physiology/genetics/classification ; Animals ; Intestinal Mucosa/microbiology ; Phylogeny ; Mucins/metabolism ; }, abstract = {Akkermansia muciniphila is a gut bacterium that colonizes the gut mucosa, has a role in maintaining gut health and shows promise for potential therapeutic applications. The discovery of A. muciniphila as an important member of our gut microbiome, occupying an extraordinary niche in the human gut, has led to new hypotheses on gut health, beneficial microorganisms and host-microbiota interactions. This microorganism has established a unique position in human microbiome research, similar to its role in the gut ecosystem. Its unique traits in using mucin sugars and mechanisms of action that can modify host health have made A. muciniphila a subject of enormous attention from multiple research fields. A. muciniphila is becoming a model organism studied for its ability to modulate human health and gut microbiome structure, leading to commercial products, a genetic model and possible probiotic formulations. This Review provides an overview of A. muciniphila and Akkermansia genus phylogeny, ecophysiology and diversity. Furthermore, the Review discusses perspectives on ecology, strategies for harnessing beneficial effects of A. muciniphila for human mucosal metabolic and gut health, and its potential as a biomarker for diagnostics and prognostics.}, }
@article {pmid39406702, year = {2024}, author = {Wegner, H and Roitman, S and Kupczok, A and Braun, V and Woodhouse, JN and Grossart, HP and Zehner, S and Béjà, O and Frankenberg-Dinkel, N}, title = {Identification of Shemin pathway genes for tetrapyrrole biosynthesis in bacteriophage sequences from aquatic environments.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {8783}, pmid = {39406702}, issn = {2041-1723}, support = {FR1487/16-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 143/18//Israel Science Foundation (ISF)/ ; }, mesh = {*Tetrapyrroles/biosynthesis/metabolism ; *Bacteriophages/genetics/metabolism ; Escherichia coli/genetics/virology/metabolism ; 5-Aminolevulinate Synthetase/genetics/metabolism ; Amino Acid Sequence ; Heme/metabolism/biosynthesis ; Aminolevulinic Acid/metabolism ; Phylogeny ; Fresh Water/virology ; Biosynthetic Pathways/genetics ; }, abstract = {Tetrapyrroles such as heme, chlorophyll, and vitamin B12 are essential for various metabolic pathways. They derive from 5-aminolevulinic acid (5-ALA), which can be synthesized by a single enzyme (5-ALA synthase or AlaS, Shemin pathway) or by a two-enzyme pathway. The genomes of some bacteriophages from aquatic environments carry various tetrapyrrole biosynthesis genes. Here, we analyze available metagenomic datasets and identify alaS homologs (viral alaS, or valaS) in sequences corresponding to marine and freshwater phages. The genes are found individually or as part of complete or truncated three-gene loci encoding heme-catabolizing enzymes. Amino-acid sequence alignments and three-dimensional structure prediction support that the valaS sequences likely encode functional enzymes. Indeed, we demonstrate that is the case for a freshwater phage valaS sequence, as it can complement an Escherichia coli 5-ALA auxotroph, and an E. coli strain overexpressing the gene converts the typical AlaS substrates glycine and succinyl-CoA into 5-ALA. Thus, our work identifies valaS as an auxiliary metabolic gene in phage sequences from aquatic environments, further supporting the importance of tetrapyrrole metabolism in bacteriophage biology.}, }
@article {pmid39404095, year = {2024}, author = {Leleiwi, I and Kokkinias, K and Kim, Y and Baniasad, M and Shaffer, M and Sabag-Daigle, A and Daly, RA and Flynn, RM and Wysocki, VH and Ahmer, BMM and Borton, MA and Wrighton, KC}, title = {Gut microbiota carbon and sulfur metabolisms support Salmonella infections.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39404095}, issn = {1751-7370}, support = {T32 AI162691/AI/NIAID NIH HHS/United States ; T32GM132057//NIH Predoctoral Training/ ; DE-SC0021350//DOE/ ; R01AI143288//NIH NIAID/ ; R01 AI143288/AI/NIAID NIH HHS/United States ; T32 GM132057/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; *Sulfur/metabolism ; *Carbon/metabolism ; *Salmonella typhimurium/genetics ; Feces/microbiology ; Mice, Inbred C57BL ; Salmonella Infections/microbiology ; Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Salmonella Infections, Animal/microbiology ; Female ; }, abstract = {Salmonella enterica serovar Typhimurium is a pervasive enteric pathogen and ongoing global threat to public health. Ecological studies in the Salmonella impacted gut remain underrepresented in the literature, discounting microbiome mediated interactions that may inform Salmonella physiology during colonization and infection. To understand the microbial ecology of Salmonella remodeling of the gut microbiome, we performed multi-omics on fecal microbial communities from untreated and Salmonella-infected mice. Reconstructed genomes recruited metatranscriptomic and metabolomic data providing a strain-resolved view of the expressed metabolisms of the microbiome during Salmonella infection. These data informed possible Salmonella interactions with members of the gut microbiome that were previously uncharacterized. Salmonella-induced inflammation significantly reduced the diversity of genomes that recruited transcripts in the gut microbiome, yet increased transcript mapping was observed for seven members, among which Luxibacter and Ligilactobacillus transcript read recruitment was most prevalent. Metatranscriptomic insights from Salmonella and other persistent taxa in the inflamed microbiome further expounded the necessity for oxidative tolerance mechanisms to endure the host inflammatory responses to infection. In the inflamed gut lactate was a key metabolite, with microbiota production and consumption reported amongst members with detected transcript recruitment. We also showed that organic sulfur sources could be converted by gut microbiota to yield inorganic sulfur pools that become oxidized in the inflamed gut, resulting in thiosulfate and tetrathionate that support Salmonella respiration. This research advances physiological microbiome insights beyond prior amplicon-based approaches, with the transcriptionally active organismal and metabolic pathways outlined here offering intriguing intervention targets in the Salmonella-infected intestine.}, }
@article {pmid39404077, year = {2024}, author = {Ellington, AJ and Walters, K and Christner, BC and Fox, S and Bonfantine, K and Walker, C and Lampman, P and Vuono, DC and Strickland, M and Lambert, K and Kobziar, LN}, title = {Dispersal of microbes from grassland fire smoke to soils.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39404077}, issn = {1751-7370}, support = {P20 GM103408/GM/NIGMS NIH HHS/United States ; 2039531//National Science Foundation/ ; P20GM103408//National Institute of General Medical Sciences of the National Institutes of Health/ ; }, mesh = {*Soil Microbiology ; *Smoke ; *Grassland ; *Soil/chemistry ; Bacteria/classification/isolation &amp; purification/radiation effects ; Microbiota ; Wildfires ; Fires ; Biomass ; Poaceae/microbiology ; Carbon/analysis/metabolism ; }, abstract = {Wildland fire is increasingly recognized as a driver of bioaerosol emissions, but the effects that smoke-emitted microbes have on the diversity and community assembly patterns of the habitats where they are deposited remain unknown. In this study, we examined whether microbes aerosolized by biomass burning smoke detectably impact the composition and function of soil sinks using lab-based mesocosm experiments. Soils either containing the native microbial community or presterilized by γ-irradiation were inundated with various doses of smoke from native tallgrass prairie grasses. Smoke-inundated, γ-irradiated soils exhibited significantly higher respiration rates than both smoke-inundated, native soils and γ-irradiated soils exposed to ambient air only. Microbial communities in γ-irradiated soils were significantly different between smoke-treated and control soils, which supports the hypothesis that wildland fire smoke can act as a dispersal agent. Community compositions differed based on smoke dose, incubation time, and soil type. Concentrations of phosphate and microbial biomass carbon and nitrogen together with pH were significant predictors of community composition. Source tracking analysis attributed smoke as contributing nearly 30% of the taxa found in smoke-inundated, γ-irradiated soils, suggesting smoke may play a role in the recovery of microbial communities in similar damaged soils. Our findings demonstrate that short-distance microbial dispersal by biomass burning smoke can influence the assembly processes of microbial communities in soils and has implications for a broad range of subjects including agriculture, restoration, plant disease, and biodiversity.}, }
@article {pmid39402079, year = {2024}, author = {Ashraf, H and Dikarlo, P and Masia, A and Zarbo, IR and Solla, P and Ijaz, UZ and Sechi, LA}, title = {Mycobacterium avium subspecies paratuberculosis (MAP) infection, and its impact on gut microbiome of individuals with multiple sclerosis.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {24027}, pmid = {39402079}, issn = {2045-2322}, support = {EP/V030515/1//Engineering and Physical Sciences Research Council/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Mycobacterium avium subsp. paratuberculosis/isolation &amp; purification ; *Paratuberculosis/microbiology ; *Multiple Sclerosis/microbiology ; Female ; Male ; *RNA, Ribosomal, 16S/genetics ; Adult ; Feces/microbiology ; Middle Aged ; }, abstract = {The microbial ecology of Mycobacterium avium subspecies paratuberculosis infections (MAP) within the context of Multiple Sclerosis (MS) is largely an unexplored topic in the literature. Thus, we have characterized the compositional and predicted functional differences of the gut microbiome between MS patients with MAP (MAP+) and without (MAP-) infection. This was done in the context of exposome differences (through self-reported filled questionnaires), principally in anthropometric and sociodemographic patterns to gain an understanding of the gut microbiome dynamics. 16S rRNA microbiome profiling of faecal samples (n = 69) was performed for four groups, which differed by disease and MAP infection: healthy cohort (HC) MAP-; HC MAP+ ; MS MAP-; and MS MAP+ . Using a dynamic strategy, with MAP infection and time of sampling as occupancy models, we have recovered the core microbiome for both HC and MS individuals. Additional application of neutral modeling suggests key genera that are under selection pressure by the hosts. These include members of the phyla Actinobacteriota, Bacteroidota, and Firmicutes. As several subjects provided multiple samples, a Quasi Conditional Association Test that incorporates paired-nature of samples found major differences in Archaea. To consolidate treatment groups, confounders, microbiome, and the disease outcome parameters, a mediation analysis is performed for MS cohort. This highlighted certain genera i.e., Sutterella, Akkermansia, Bacteriodes, Gastranaerophilales, Alistipes, Balutia, Faecalibacterium, Lachnospiraceae, Anaerostipes, Ruminococcaceae, Eggerthellaceae and Clostridia-UCG-014 having mediatory effect using disease duration as an outcome and MAP infection as a treatment group. Our analyses indicate that the gut microbiome may be an important target for dietary and lifestyle intervention in MS patients with and without MAP infection.}, }
@article {pmid39401449, year = {2024}, author = {Ahmerkamp, S and Pacherres, CO and Mosshammer, M and Godefroid, M and Wind-Hansen, M and Kuypers, M and Behrendt, L and Koren, K and Kühl, M}, title = {Novel Approach for Lifetime-Proportional Luminescence Imaging Using Frame Straddling.}, journal = {ACS sensors}, volume = {9}, number = {10}, pages = {5531-5540}, pmid = {39401449}, issn = {2379-3694}, mesh = {*Luminescent Measurements/methods ; Luminescence ; Oxygen/chemistry ; }, abstract = {Optode-based chemical imaging is a rapidly evolving field that has substantially enhanced our understanding of the role of microenvironments and chemical gradients in biogeochemistry, microbial ecology, and biomedical sciences. Progress in sensor chemistry has resulted in a broadened spectrum of analytes, alongside enhancements in sensor performance (e.g., sensitivity, brightness, and photostability). However, existing imaging techniques are often costly, challenging to implement, and limited in their recording speed. Here we use the "frame-straddling" technique, originally developed for particle image velocimetry for imaging the O2-dependent, integrated luminescence decay of optical O2 sensor materials. The method synchronizes short excitation pulses and camera exposures to capture two frames at varying brightness, where the first excitation pulse occurs at the end of the exposure of the first frame and the second excitation pulse at the beginning of the second frame. Here the first frame truncates the luminescence decay, whereas the second frame fully captures it. The difference between the frames quantifies the integral of the luminescence decay curve, which is proportional to the luminescence lifetime, at time scales below one millisecond. Short excitation pulses avoid depopulation of the ground state of luminophores, resulting in a linear Stern-Volmer response with increasing concentrations of the quencher (O2), which can be predicted through a simple model. This methodology is compatible with a wide range of camera systems, making it a versatile tool for various optode based chemical imaging applications. We showcase the utility of frame straddling in measuring O2 dynamics around algae and by observing O2 scavenging sodium dithionite particles sinking through oxygenated water.}, }
@article {pmid39399973, year = {2024}, author = {Simpson, A and Wood-Charlson, EM and Smith, M and Koch, BJ and Beilsmith, K and Kimbrel, JA and Kellom, M and Hunter, CI and Walls, RL and Schriml, LM and Wilhelm, RC}, title = {MISIP: a data standard for the reuse and reproducibility of any stable isotope probing-derived nucleic acid sequence and experiment.}, journal = {GigaScience}, volume = {13}, number = {}, pages = {}, pmid = {39399973}, issn = {2047-217X}, support = {IND90024429//USDA/ ; //Purdue University/ ; //Lawrence Berkeley National Laboratory/ ; }, mesh = {*Isotope Labeling/methods ; Reproducibility of Results ; Microbiota/genetics ; Metadata ; Metagenomics/methods ; Sequence Analysis, DNA/methods ; Metagenome ; }, abstract = {DNA/RNA-stable isotope probing (SIP) is a powerful tool to link in situ microbial activity to sequencing data. Every SIP dataset captures distinct information about microbial community metabolism, process rates, and population dynamics, offering valuable insights for a wide range of research questions. Data reuse maximizes the information derived from the labor and resource-intensive SIP approaches. Yet, a review of publicly available SIP sequencing metadata showed that critical information necessary for reproducibility and reuse was often missing. Here, we outline the Minimum Information for any Stable Isotope Probing Sequence (MISIP) according to the Minimum Information for any (x) Sequence (MIxS) framework and include examples of MISIP reporting for common SIP experiments. Our objectives are to expand the capacity of MIxS to accommodate SIP-specific metadata and guide SIP users in metadata collection when planning and reporting an experiment. The MISIP standard requires 5 metadata fields-isotope, isotopolog, isotopolog label, labeling approach, and gradient position-and recommends several fields that represent best practices in acquiring and reporting SIP sequencing data (e.g., gradient density and nucleic acid amount). The standard is intended to be used in concert with other MIxS checklists to comprehensively describe the origin of sequence data, such as for marker genes (MISIP-MIMARKS) or metagenomes (MISIP-MIMS), in combination with metadata required by an environmental extension (e.g., soil). The adoption of the proposed data standard will improve the reuse of any sequence derived from a SIP experiment and, by extension, deepen understanding of in situ biogeochemical processes and microbial ecology.}, }
@article {pmid39398475, year = {2024}, author = {Kumar, G and Bhadury, P}, title = {Dataset of metagenomic profiles of human gut microbiome from frozen fecal samples sequenced using Illumina and ONT chemistries.}, journal = {Data in brief}, volume = {57}, number = {}, pages = {110961}, pmid = {39398475}, issn = {2352-3409}, abstract = {The data presented in this study are metagenomic profiles of human gut microbiome deduced from frozen fecal samples using two different sequencing chemistries namely, Illumina and Oxford Nanopore Technologies (ONT). The generated data is obtained from genomic DNA extracted from frozen fecal samples collected from a healthy individual on Day 3, Day 5, Day 9, Day 12, and Day 30, in addition to Day 1 (unfrozen). The metagenomic sequence data have been deposited at NCBI SRA as BioProject PRJNA827663. The taxonomic annotation undertaken using MG-RAST showed relative abundance of bacteria represented by different taxonomic levels varied significantly based on two sequencing chemistries. There was distinct temporal variation in the relative abundance of bacteria at different taxonomic levels based on the day of extraction of genomic DNA. This dataset can be used to study differences in functional profiles of human gut microbiome using different sequencing technologies. Moreover, generated data can aid in selection of most appropriate sequencing chemistry to study future human gut microbiome studies based on the appropriate preservation method of fecal samples.}, }
@article {pmid39397203, year = {2024}, author = {Liu, K and Yan, Q and Guo, X and Wang, W and Zhang, Z and Ji, M and Wang, F and Liu, Y}, title = {Glacier Retreat Induces Contrasting Shifts in Bacterial Biodiversity Patterns in Glacial Lake Water and Sediment : Bacterial Communities in Glacial Lakes.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {128}, pmid = {39397203}, issn = {1432-184X}, support = {ANSO-CR-KP-2021-04//the Key Collaborative Research Program of the Alliance of International Science Organizations/ ; 42330410//National Natural Science Foundation of China/ ; 2019QZKK0503//the Second Tibetan Plateau Scientific Expedition and Research Program (STEP)/ ; }, mesh = {*Lakes/microbiology ; *Geologic Sediments/microbiology ; *Ice Cover/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Biodiversity ; Microbiota ; Ecosystem ; Tibet ; RNA, Ribosomal, 16S/genetics ; Water Microbiology ; }, abstract = {Glacial lake ecosystems are experiencing rapid changes due to accelerated glacier retreat. As glaciers recede, their influence on downstream habitats diminishes, potentially affecting the biodiversity of glacial lake microbial communities. However, there remains a knowledge gap regarding how bacterial biodiversity patterns in glacial lakes are altered by diminishing glacial influence. Here, we investigated shifts in bacterial communities in paired water and sediment samples collected from seven glacial lakes on the Tibetan Plateau, using a space-for-time substitution approach to understand the consequences of glacier retreat. Our findings reveal that bacterial diversity in lake water increases significantly with a higher glacier index (GI), whereas sediment bacterial diversity exhibits a negative correlation with GI. Both the water and sediment bacterial communities display significant structural shifts along the GI gradient. Notably, reduced glacial influence decreases the complexity of bacterial co-occurrence networks in lake water but enhances the network complexity in sediment. This divergence in diversity and co-occurrence patterns highlights that water and sediment bacterial communities respond differently to changes in glacial influence in these lake ecosystems. This study provides insights into how diminishing glacial influence impacts the bacterial biodiversity in glacial lake water and sediments, revealing contrasting patterns between the two habitats. These findings emphasize the need for comprehensive monitoring to understand the implications of glacier retreat on these fragile ecosystems.}, }
@article {pmid39388223, year = {2024}, author = {Alcaraz, CM and Séneca, J and Kunert, M and Pree, C and Sudo, M and Petersen, JM}, title = {Sulfur-oxidizing symbionts colonize the digestive tract of their lucinid hosts.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39388223}, issn = {1751-7370}, support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; *Symbiosis ; *Bivalvia/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Tract/microbiology ; *Gills/microbiology ; *Sulfur/metabolism ; *In Situ Hybridization, Fluorescence ; Oxidation-Reduction ; Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Phylogeny ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; }, abstract = {Like many marine invertebrates, marine lucinid clams have an intimate relationship with beneficial sulfur-oxidizing bacteria located within specialized gill cells known as bacteriocytes. Most previous research has focused on the symbionts in the gills of these (and other) symbiotic bivalves, often assuming that the symbionts only persistently colonize the gills, at least in the adult stage. We used 16S rRNA gene sequencing and digital polymerase chain reaction with symbiont-specific primers targeting the soxB gene on the foot, mantle, visceral mass, and gills of the lucinid clam Loripes orbiculatus. We also used fluorescence in situ hybridization with symbiont-specific probes to examine symbiont distribution at the level of the whole holobiont. Despite 40 years of research on these symbioses, we detected previously unknown populations of symbiont cells in several organs, including the digestive tract. As in the well-studied gills, symbionts in the digestive tract may be housed within host cells. A 14-month starvation experiment without hydrogen sulfide to power symbiont metabolism caused a larger reduction in symbiont numbers in the gills compared to the visceral mass, raising the possibility that symbionts in the digestive tract are persistent and may have a distinct physiology and role in the symbiosis compared with the gill symbionts. Our results highlight the unexpectedly complex relationships between marine lucinid clams and their symbionts and challenge the view that chemosynthetic symbionts are restricted to the gills of these hosts.}, }
@article {pmid39387587, year = {2024}, author = {Akob, DM and Oates, AE and Girguis, PR and Badgley, BD and Cooper, VS and Poretsky, RS and Tierney, BT and Litchman, E and Whitaker, RJ and Whiteson, KL and Metcalf, CJE and , }, title = {Perspectives on the future of ecology, evolution, and biodiversity from the Council on Microbial Sciences of the American Society for Microbiology.}, journal = {mSphere}, volume = {9}, number = {11}, pages = {e0030724}, pmid = {39387587}, issn = {2379-5042}, mesh = {*Biodiversity ; *Ecology ; *Microbiology ; *Societies, Scientific ; United States ; Biological Evolution ; Humans ; Microbiota ; }, abstract = {The field of microbial ecology, evolution, and biodiversity (EEB) is at the leading edge of understanding how microbes shape our biosphere and influence the well-being of humankind and Earth. To that end, EEB is developing new transdisciplinary tools to analyze these ecologically critical, complex microbial communities. The American Society for Microbiology's Council on Microbial Sciences hosted a virtual retreat in 2023 to discuss the trajectory of EEB both within the Society and microbiology writ large. The retreat emphasized the interconnectedness of microbes and their outsized global influence on environmental and host health. The maximal potential impact of EEB will not be achieved without contributions from disparate fields that unite diverse technologies and data sets. In turn, this level of transdisciplinary efforts requires actively encouraging "broad" research, spanning inclusive global collaborations that incorporate both scientists and the public. Together, the American Society for Microbiology and EEB are poised to lead a paradigm shift that will result in a new era of collaboration, innovation, and societal relevance for microbiology.}, }
@article {pmid39387577, year = {2024}, author = {Beck, KL and Haiminen, N and Agarwal, A and Carrieri, AP and Madgwick, M and Kelly, J and Pylro, V and Kawas, B and Wiedmann, M and Ganda, E}, title = {Development and evaluation of statistical and artificial intelligence approaches with microbial shotgun metagenomics data as an untargeted screening tool for use in food production.}, journal = {mSystems}, volume = {9}, number = {11}, pages = {e0084024}, pmid = {39387577}, issn = {2379-5077}, support = {#PEN04752, #PEN04731//U.S. Department of Agriculture (USDA)/ ; }, mesh = {*Metagenomics/methods ; *Artificial Intelligence ; *Milk/microbiology/chemistry ; Animals ; Food Microbiology/methods ; Microbiota/genetics ; Algorithms ; Principal Component Analysis ; Machine Learning ; }, abstract = {UNLABELLED: The increasing knowledge of microbial ecology in food products relating to quality and safety and the established usefulness of machine learning algorithms for anomaly detection in multiple scenarios suggests that the application of microbiome data in food production systems for anomaly detection could be a valuable approach to be used in food systems. These methods could be used to identify ingredients that deviate from their typical microbial composition, which could indicate food fraud or safety issues. The objective of this study was to assess the feasibility of using shotgun sequencing data as input into anomaly detection algorithms using fluid milk as a model system. Contrastive principal component analysis (PCA), cluster-based methods, and explainable artificial intelligence (AI) were evaluated for the detection of two anomalous sample classes using longitudinal metagenomic profiling of fluid milk compared to baseline (BL) samples collected under comparable circumstances. Traditional methods (alpha and beta diversity, clustering-based contrastive PCA, multidimensional scaling, and dendrograms) failed to differentiate anomalous sample classes; however, explainable AI was able to classify anomalous vs baseline samples and indicate microbial drivers in association with antibiotic use. We validated the potential for explainable AI to classify different milk sources using larger publicly available fluid milk 16S rDNA sequencing data sets and demonstrated that explainable AI is able to differentiate between milk storage methods, processing stages, and seasons. Our results indicate that the application of artificial intelligence continues to hold promise in the realm of microbiome data analysis and could present further opportunities for downstream analytic automation to aid in food safety and quality.<br><br>IMPORTANCE: We evaluated the feasibility of using untargeted metagenomic sequencing of raw milk for detecting anomalous food ingredient content with artificial intelligence methods in a study specifically designed to test this hypothesis. We also show through analysis of publicly available fluid milk microbial data that our artificial intelligence approach is able to successfully predict milk in different stages of processing. The approach could potentially be applied in the food industry for safety and quality control.}, }
@article {pmid39387551, year = {2024}, author = {Halbrook, S and Wilber, W and Barrow, ME and Farrer, EC}, title = {Bacterial community response to novel and repeated disturbances.}, journal = {Environmental microbiology reports}, volume = {16}, number = {5}, pages = {e70022}, pmid = {39387551}, issn = {1758-2229}, support = {LEQSF(2017-20)-RD-A-14//Louisiana Board of Regents/ ; //Tulane University/ ; DEB-2141922//National Science Foundation/ ; }, mesh = {*Bacteria/genetics/classification/isolation &amp; purification ; Salinity ; Microbiota ; Ecosystem ; Biodiversity ; }, abstract = {Disturbance response and recovery are increasingly important in microbial ecology, as microbes may recover from disturbances differently than macro communities. Past disturbances can alter microbial community structure and their response to subsequent disturbance events, but it remains unclear if the same recovery patterns persist after long-term exposure to stress. Here, we compare bacterial community composition in a community that experienced 2 years of monthly salinity addition disturbances with a community that has not experienced salinity additions. We then track the response and recovery to an additional salinity addition based on past disturbance exposure. We tested the following hypotheses: first, communities with a repeated disturbance history will have a different community composition than communities without a disturbance history; second, communities exposed to repeated disturbances will undergo a different recovery trajectory than communities experiencing a novel disturbance. We find that repeated disturbances alter community composition and affect community response and recovery to a subsequent disturbance after 2 years, primarily through increased resistance. This work enhances our understanding of microbial temporal dynamics and suggests that novel disturbances may pose a threat to microbial community structure and function.}, }
@article {pmid39392836, year = {2024}, author = {Daisley, BA and Allen-Vercoe, E}, title = {Microbes as medicine.}, journal = {Annals of the New York Academy of Sciences}, volume = {1541}, number = {1}, pages = {63-82}, pmid = {39392836}, issn = {1749-6632}, support = {950-232131//Canada Research Chairs/ ; PDF-402947//Natural Sciences and Engineering Research Council of Canada/ ; //Natural Sciences and Engineering Research Council of Canada/ ; 2023//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Humans ; *Probiotics/therapeutic use ; *Microbiota/drug effects/physiology ; Anti-Bacterial Agents/therapeutic use/pharmacology ; Precision Medicine/methods ; Animals ; }, abstract = {Over the last two decades, advancements in sequencing technologies have significantly deepened our understanding of the human microbiome's complexity, leading to increased concerns about the detrimental effects of antibiotics on these intricate microbial ecosystems. Concurrently, the rise in antimicrobial resistance has intensified the focus on how beneficial microbes can be harnessed to treat diseases and improve health and offer potentially promising alternatives to traditional antibiotic treatments. Here, we provide a comprehensive overview of both established and emerging microbe-centric therapies, from probiotics to advanced microbial ecosystem therapeutics, examine the sophisticated ways in which microbes are used medicinally, and consider their impacts on microbiome homeostasis and health outcomes through a microbial ecology lens. In addition, we explore the concept of rewilding the human microbiome by reintroducing "missing microbes" from nonindustrialized societies and personalizing microbiome modulation to fit individual microbial profiles-highlighting several promising directions for future research. Ultimately, the advancements in sequencing technologies combined with innovative microbial therapies and personalized approaches herald a new era in medicine poised to address antibiotic resistance and improve health outcomes through targeted microbiome management.}, }
@article {pmid39392487, year = {2024}, author = {Legeay, J and Basiru, S and Ziami, A and Errafii, K and Hijri, M}, title = {Response of Alternaria and Fusarium Species to Low Precipitation in a Drought-Tolerant Plant in Morocco.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {127}, pmid = {39392487}, issn = {1432-184X}, support = {Project AS-85//OPC Africa and OCP Innovation/ ; }, mesh = {Morocco ; *Fusarium/physiology/isolation &amp; purification/classification ; *Droughts ; *Alternaria/physiology/classification ; *Plant Roots/microbiology ; *Rain ; Soil Microbiology ; Mycobiome ; Rhizosphere ; }, abstract = {The plant mycobiome plays a crucial role in the host life cycle, influencing both healthy and diseased states, and is essential for plant tolerance to drought. In this study, we used ITS metabarcoding to investigate the fungal community of the drought-resistant plant Malva sylvestris L. in Morocco along a gradient of precipitation, encompassing subhumid and semi-arid environments. We sampled three biotopes: rhizosphere, bulk soil, and root endosphere. Our findings revealed an absence of beta-diversity differences between bulk soil and rhizosphere, indicating that the plant does not selectively influence its rhizosphere mycobiome. Additionally, ASVs belonging to the genus Alternaria represented up to 30% of reads in the plant's roots and correlated with drought (p = 0.006), indicating a potential role for this fungal genus in mitigating drought, possibly as part of the dark septate endophyte group. Root staining and microscopic observation revealed extensive colonization by fungal hyphae and microsclerotia-like structures. Furthermore, ASVs identified as Fusarium equiseti were also correlated with low precipitation and recognized as a hub taxon in the roots. However, it remains uncertain whether this species is pathogenic or beneficial to the plant. These insights contribute to our understanding of the plant mycobiome's role in drought tolerance and highlight the importance of specific fungal taxa in supporting plant health under varying environmental conditions. Future research should focus on characterizing these taxa's functional roles and their interactions with the host plant to further elucidate their contributions to drought resistance.}, }
@article {pmid39390291, year = {2025}, author = {Delzenne, NM and Bindels, LB and Neyrinck, AM and Walter, J}, title = {The gut microbiome and dietary fibres: implications in obesity, cardiometabolic diseases and cancer.}, journal = {Nature reviews. Microbiology}, volume = {23}, number = {4}, pages = {225-238}, pmid = {39390291}, issn = {1740-1534}, mesh = {*Dietary Fiber/metabolism ; Humans ; *Gastrointestinal Microbiome/physiology ; *Obesity/microbiology ; *Neoplasms/microbiology/prevention &amp; control ; *Cardiovascular Diseases/microbiology/prevention &amp; control ; *Metabolic Diseases/microbiology ; Animals ; Bacteria/classification/metabolism/genetics ; }, abstract = {Dietary fibres constitute a heterogeneous class of nutrients that are key in the prevention of various chronic diseases. Most dietary fibres are fermented by the gut microbiome and may, thereby, modulate the gut microbial ecology and metabolism, impacting human health. Dietary fibres may influence the occurrence of specific bacterial taxa, with this effect varying between individuals. The effect of dietary fibres on microbial diversity is a matter of debate. Most intervention studies with dietary fibres in the context of obesity and related metabolic disorders reveal the need for an accurate assessment of the microbiome to better understand the variable response to dietary fibres. Epidemiological studies confirm that a high dietary fibre intake is strongly associated with a reduced occurrence of many types of cancer. However, there is a need to determine the impact of intervention with specific dietary fibres on cancer risk, therapy efficacy and toxicity, as well as in cancer cachexia. In this Review, we summarize the mechanisms by which the gut microbiome can mediate the physiological benefits of dietary fibres in the contexts of obesity, cardiometabolic diseases and cancer, their incidence being clearly linked to low dietary fibre intake.}, }
@article {pmid39389280, year = {2024}, author = {Lima, M and Muddana, C and Xiao, Z and Bandyopadhyay, A and Wangikar, PP and Pakrasi, HB and Tang, YJ}, title = {The new chassis in the flask: Advances in Vibrio natriegens biotechnology research.}, journal = {Biotechnology advances}, volume = {77}, number = {}, pages = {108464}, doi = {10.1016/j.biotechadv.2024.108464}, pmid = {39389280}, issn = {1873-1899}, mesh = {*Vibrio/genetics ; *Biotechnology/methods ; *Metabolic Engineering/methods ; *Synthetic Biology/methods ; Systems Biology/trends ; }, abstract = {Biotechnology has been built on the foundation of a small handful of well characterized and well-engineered organisms. Recent years have seen a breakout performer gain attention as a new entrant into the bioengineering toolbox: Vibrio natriegens. This review covers recent research efforts into making V. natriegens a biotechnology platform, using a large language model (LLM) and knowledge graph to expedite the literature survey process. Scientists have made advancements in research pertaining to the fundamental metabolic characteristics of V. natriegens, development and characterization of synthetic biology tools, systems biology analysis and metabolic modeling, bioproduction and metabolic engineering, and microbial ecology. Each of these subcategories has relevance to the future of V. natriegens for bioengineering applications. In this review, we cover these recent advancements and offer context for the impact they may have on the field, highlighting benefits and drawbacks of using this organism. From examining the recent bioengineering research, it appears that V. natriegens is on the precipice of becoming a platform bacterium for the future of biotechnology.}, }
@article {pmid39386005, year = {2024}, author = {Lin, X and Waring, K and Ghezzi, H and Tropini, C and Tyson, J and Ziels, RM}, title = {High accuracy meets high throughput for near full-length 16S ribosomal RNA amplicon sequencing on the Nanopore platform.}, journal = {PNAS nexus}, volume = {3}, number = {10}, pages = {pgae411}, pmid = {39386005}, issn = {2752-6542}, abstract = {Small subunit (SSU) ribosomal RNA (rRNA) gene amplicon sequencing is a foundational method in microbial ecology. Currently, short-read platforms are commonly employed for high-throughput applications of SSU rRNA amplicon sequencing, but at the cost of poor taxonomic classification due to limited fragment lengths. The Oxford Nanopore Technologies (ONT) platform can sequence full-length SSU rRNA genes, but its lower raw-read accuracy has so-far limited accurate taxonomic classification and de novo feature generation. Here, we present a sequencing workflow, termed ssUMI, that combines unique molecular identifier (UMI)-based error correction with newer (R10.4+) ONT chemistry and sample barcoding to enable high throughput near full-length SSU rRNA (e.g. 16S rRNA) amplicon sequencing. The ssUMI workflow generated near full-length 16S rRNA consensus sequences with 99.99% mean accuracy using a minimum subread coverage of 3×, surpassing the accuracy of Illumina short reads. The consensus sequences generated with ssUMI were used to produce error-free de novo sequence features with no false positives with two microbial community standards. In contrast, Nanopore raw reads produced erroneous de novo sequence features, indicating that UMI-based error correction is currently necessary for high-accuracy microbial profiling with R10.4+ ONT sequencing chemistries. We showcase the cost-competitive scalability of the ssUMI workflow by sequencing 87 time-series wastewater samples and 27 human gut samples, obtaining quantitative ecological insights that were missed by short-read amplicon sequencing. ssUMI, therefore, enables accurate and low-cost full-length 16S rRNA amplicon sequencing on Nanopore, improving accessibility to high-resolution microbiome science.}, }
@article {pmid39383960, year = {2024}, author = {Goswami, V and Deepika, S and Sharma, P and Kothamasi, D}, title = {Recycling steel slag as fertiliser proxy in agriculture is good circular economy but disrupts plant microbial symbioses in the soil.}, journal = {The Science of the total environment}, volume = {954}, number = {}, pages = {176750}, doi = {10.1016/j.scitotenv.2024.176750}, pmid = {39383960}, issn = {1879-1026}, mesh = {*Agriculture/methods ; *Fertilizers ; *Mycorrhizae/physiology ; *Soil Microbiology ; *Symbiosis ; Steel ; Hordeum/microbiology ; Recycling ; Soil/chemistry ; }, abstract = {Modern agriculture depends on synthetic fertilisers to ensure food security but their manufacture and use accounts for ~5 % of the global greenhouse gas emissions. Achieving climate change targets therefore requires alternatives, that while maintaining crop productivity, reduce emissions across the lifecycle of fertiliser utilisation. Steel slag, a nutrient-rich by-product of steel manufacture, offers a viable alternative. Being substantially cheaper than fertilisers, it is economically attractive for farmers, particularly in low-middle income countries of the Global South. However, slag application in agriculture poses risk of pollutant transfer to the human food chain and disruption of key plant-microbe symbioses like the arbuscular mycorrhizal fungi (AMF). Here, using barley as a model crop, we tested the suitability of slag as a fertiliser proxy. Mycorrhizal and non-mycorrhizal barley were grown in soils ameliorated with slag in concentrations of 0, 2, 5 and 10 t ha[-1]. We analysed slag-mycorrhiza interaction and their combined effects on crop yield and risks to human nourishment. Slag increased grain yield by respective 32 and 21 % in mycorrhizal and non-mycorrhizal barley. Grain concentration of metal pollutants in mycorrhizal and non-mycorrhizal barley fertilised with slag were within the WHO recommended limits. But slag reduced mycorrhizal colonisation in barley roots and extraradical hyphal spread in the soil. The consequent decline in symbiont function lowered AMF-mediated plant nutrient uptake and increased mineral losses in leachates. AMF are keystone species of the soil microbiome. Loss of AMF function presents long-term ecological consequences for agriculture and necessitates a careful evaluation of slag application to soil.}, }
@article {pmid39382725, year = {2024}, author = {Wang, L and Liu, Z and Bres, C and Jin, G and Fanin, N}, title = {Coniferous Tree Species Identity and Leaf Aging Alter the Composition of Phyllosphere Communities Through Changes in Leaf Traits.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {126}, pmid = {39382725}, issn = {1432-184X}, support = {2572021AW30//Fundamental Research Funds for the Central Universities/ ; 2022YFD2201100//National Key R &amp; D Program of China/ ; 2572022DS13//the Fundamental Research Funds for the Central Universities/ ; }, mesh = {*Plant Leaves/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; *Trees/microbiology/growth &amp; development ; Fungi/classification/genetics/physiology/isolation &amp; purification ; Pinus/microbiology/growth &amp; development ; Abies/microbiology ; Picea/microbiology/growth &amp; development ; Biodiversity ; Tracheophyta/microbiology ; }, abstract = {Phyllosphere microorganisms are essential for plant growth and health. Although there are an increasing number of studies showing that the composition of phyllosphere communities varies among different plant species, it remains unclear whether and how their bacterial and fungal community composition predictably varies with plant traits and leaf age. In this study, we used high-throughput sequencing to explore the diversity and composition of phyllosphere communities in needles of different ages (originating from different cohorts) for three evergreen coniferous species (Pinus koraiensis, Picea koraiensis, and Abies nephrolepis). Our results indicated that Gammaproteobacteria (bacteria) and Dothideomycetes (fungi) were dominant in newly formed needles, whereas Actinobacteria (bacteria) and Eurotiomycetes (fungi) were dominant in perennial needles. Tree species identity and needle age were the main factors explaining the variations of the α diversity (species richness of phyllosphere communities) and β diversity (dissimilarity among phyllosphere communities). In particular, we found that leaf dry matter content, leaf mass per area, and total phosphorus content emerged as key predictors of composition and diversity of phyllosphere microbial communities, underscoring the major influence of tree species identity and needle age on phyllosphere communities through changes in plant functional traits. Finally, we found that the interaction between tree species identity and needle age also contributed significantly to explaining the diversity and composition of phyllosphere communities, probably because differences in plant functional traits or environmental conditions between new and perennial needles depend on tree growth rates and resource acquisition strategies. These findings provide new insights into the mechanisms of community assembly among different evergreen tree species and offer a better understanding of the interactions between plant traits and phyllosphere microorganisms during needle aging.}, }
@article {pmid39382674, year = {2024}, author = {Murray, MLH and Dopheide, A and Leonard, J and Padamsee, M and Schwendenmann, L}, title = {Phyllosphere of Agathis australis Leaves and the Impact of the Soil-Borne Pathogen Phytophthora agathidicida.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {125}, pmid = {39382674}, issn = {1432-184X}, mesh = {*Plant Leaves/microbiology ; *Phytophthora/isolation &amp; purification/genetics ; *Soil Microbiology ; *Plant Diseases/microbiology ; *Microbiota ; New Zealand ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation &amp; purification ; Soil/chemistry ; Combretaceae/microbiology ; }, abstract = {Leaf surface microbial communities play an important role in forest ecosystems and are known to be affected by environmental and host conditions, including diseases impacting the host. Phytophthora agathidicida is a soil-borne pathogen that causes severe disease (kauri dieback) in one of New Zealand's endemic trees, Agathis australis (kauri). This research characterised the microbial communities of the A. australis phyllosphere (i.e. leaf surface) using modern molecular techniques and explored the effects of P. agathidicida on those communities. Fresh leaves were collected from trees where P. agathidicida was and was not detected in the soil and characterisation of the leaf surface microbial community was carried out via high-throughput amplicon sequencing of the internal transcribed spacer (ITS) and 16S ribosomal RNA regions. Nutrients in leaf leachates were also measured to identify other possible drivers of microbial diversity. The dominant phyllosphere microbial phylum was Proteobacteria followed by Acidobacteria. The phyllosphere microbial richness of A. agathis associated with P. agathidicida-infected soils was found to be generally lower than where the pathogen was not detected for both prokaryote (bacterial) and fungal phyla. Leaf leachate pH as well as boron and silicon had significant associations with bacterial and fungal community structure. These findings contribute to the development of a comprehensive understanding of A. australis leaf surface microbial communities and the effects of the soil pathogen P. agathidicida on those communities.}, }
@article {pmid39382297, year = {2024}, author = {Eigemann, F and Hoffmann, J and Schampera, C and Liu, S and Bolaños, LM and Heemeyer, M and Carlson, CA and Giovannoni, S and Hellweger, FL}, title = {Emergent ecology in a microscale model of the surface ocean.}, journal = {mBio}, volume = {15}, number = {11}, pages = {e0237224}, pmid = {39382297}, issn = {2150-7511}, support = {BIOS-SCOPE//Simons Foundation (SF)/ ; //North-German Supercomputing Alliance/ ; }, mesh = {*Phytoplankton/metabolism/physiology ; *Oceans and Seas ; *Ecosystem ; *Seawater/microbiology/chemistry ; Bacteria/metabolism/genetics ; Models, Biological ; Chemotaxis ; Bacterial Physiological Phenomena ; Carbon/metabolism ; Cyanobacteria/metabolism/physiology/growth &amp; development ; Ecology ; }, abstract = {Microbial processes operate at the microscale, which is not resolved by existing ecosystem models. Here, we present a novel model that simulates a 1 mL three-dimensional cube using a hybrid Lagrangian-Eulerian approach, at ecologically relevant timescales. The model simulates individual microbes, including three phytoplankton size classes with healthy, senescent, and dead lifecycle stages; copiotrophic and oligotrophic heterotrophic bacteria; and dissolved organic matter at 50 µm resolution. Diffusion, shear, sedimentation, chemotaxis, and attachment processes are explicitly resolved. The emerging quantitative representation of the ecosystem shows that (1) copiotrophs grow mostly attached to eukaryotic phytoplankters and get almost all of their carbon from them vs. oligotrophs that grow on exudates and lysates of cyanobacteria; (2) contrasting diel patterns in substrate appearance in the phycosphere vs. ambient water and growth of particle-associated copiotrophs vs. free-living oligotrophs; (3) attached bacteria reduce carbon flux from the phycosphere, lowering chemotactic efficiency toward eukaryotes below that toward cyanobacteria; (4) shear reduces chemotactic efficiency and fitness of the copiotroph; and (5) the main benefit of chemotaxis is to locate attachment partners. These patterns are consistent with available observations. Our study provides insights into the microscale ecology of marine bacteria, and the open-source code is a tool for further research in this area.IMPORTANCEA large amount of global CO2 fixation is performed by marine phytoplankton, and a substantial fraction of that is released as dissolved organic carbon and further processed by heterotrophic bacteria. The interaction between phytoplankton and bacteria, i.e., the carbon flux between them, is therefore an important process in the global carbon and climate system. Some bacteria have developed specialized behavioral traits, like swimming and attachment, to increase their carbon acquisition. These interactions occur at the micrometer scale, for example, the immediate vicinity of phytoplankters (the phycosphere), but existing biogeochemical models typically only simulate down to the 1 meter vertical or ~100 kilometer horizontal scale. We present a new microscale model and use it to predict fluxes and other features in the surface ocean. The model makes important predictions about the fluxes between various types of phytoplankton and bacteria and the role of behavioral traits, and it provides a basis and tool for further research in this area.}, }
@article {pmid39381885, year = {2024}, author = {Witzgall, K and Hesse, BD and Pacay-Barrientos, NL and Jansa, J and Seguel, O and Oses, R and Buegger, F and Guigue, J and Rojas, C and Rousk, K and Grams, TEE and Pietrasiak, N and Mueller, CW}, title = {Soil carbon and nitrogen cycling at the atmosphere-soil interface: Quantifying the responses of biocrust-soil interactions to global change.}, journal = {Global change biology}, volume = {30}, number = {10}, pages = {e17519}, doi = {10.1111/gcb.17519}, pmid = {39381885}, issn = {1365-2486}, support = {MU3021/6-2//Deutsche Forschungsgemeinschaft/ ; EAR-2012475//National Science Foundation (NSF)/ ; }, mesh = {*Soil/chemistry ; *Climate Change ; *Nitrogen Cycle ; *Soil Microbiology ; *Carbon Cycle ; *Droughts ; *Atmosphere/chemistry ; Carbon/metabolism/analysis ; Carbon Dioxide/metabolism/analysis ; Nitrogen/metabolism/analysis ; Ecosystem ; }, abstract = {In drylands, where water scarcity limits vascular plant growth, much of the primary production occurs at the soil surface. This is where complex macro- and microbial communities, in an intricate bond with soil particles, form biological soil crusts (biocrusts). Despite their critical role in regulating C and N cycling in dryland ecosystems, there is limited understanding of the fate of biologically fixed C and N from biocrusts into the mineral soil, or how climate change will affect C and N fluxes between the atmosphere, biocrusts, and subsurface soils. To address these gaps, we subjected biocrust-soil systems to experimental warming and drought under controlled laboratory conditions, monitored CO2 fluxes, and applied dual isotopic labeling pulses ([13]CO2 and [15]N2). This allowed detailed quantification of elemental pathways into specific organic matter (OM) pools and microbial biomass via density fractionation and phospholipid fatty acid analyses. While biocrusts modulated CO2 fluxes regardless of the temperature regime, drought severely limited their photosynthetic C uptake to the extent that the systems no longer sustained net C uptake. Furthermore, the effect of biocrusts extended into the underlying 1 cm of mineral soil, where C and N accumulated as mineral-associated OM (MAOM<63μm). This was strongly associated with increased relative dominance of fungi, suggesting that fungal hyphae facilitate the downward C and N translocation and subsequent MAOM formation. Most strikingly, however, these pathways were disrupted in systems exposed to warming, where no effects of biocrusts on the elemental composition of the underlying soil nor on MAOM were determined. This was further associated with reduced net biological N fixation under combined warming and drought, highlighting how changing climatic conditions diminish some of the most fundamental ecosystem functions of biocrusts, with detrimental repercussions for C and N cycling and the persistence of soil organic matter pools in dryland ecosystems.}, }
@article {pmid39380680, year = {2024}, author = {Karavaeva, V and Sousa, FL}, title = {Navigating the archaeal frontier: insights and projections from bioinformatic pipelines.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1433224}, pmid = {39380680}, issn = {1664-302X}, abstract = {Archaea continues to be one of the least investigated domains of life, and in recent years, the advent of metagenomics has led to the discovery of many new lineages at the phylum level. For the majority, only automatic genomic annotations can provide information regarding their metabolic potential and role in the environment. Here, genomic data from 2,978 archaeal genomes was used to perform automatic annotations using bioinformatics tools, alongside synteny analysis. These automatic classifications were done to assess how good these different tools perform in relation to archaeal data. Our study revealed that even with lowered cutoffs, several functional models do not capture the recently discovered archaeal diversity. Moreover, our investigation revealed that a significant portion of archaeal genomes, approximately 42%, remain uncharacterized. In comparison, within 3,235 bacterial genomes, a diverse range of unclassified proteins is obtained, with well-studied organisms like Escherichia coli having a substantially lower proportion of uncharacterized regions, ranging from <5 to 25%, and less studied lineages being comparable to archaea with the range of 35-40% of unclassified regions. Leveraging this analysis, we were able to identify metabolic protein markers, thereby providing insights into the metabolism of the archaea in our dataset. Our findings underscore a substantial gap between automatic classification tools and the comprehensive mapping of archaeal metabolism. Despite advances in computational approaches, a significant portion of archaeal genomes remains unexplored, highlighting the need for extensive experimental validation in this domain, as well as more refined annotation methods. This study contributes to a better understanding of archaeal metabolism and underscores the importance of further research in elucidating the functional potential of archaeal genomes.}, }
@article {pmid39379763, year = {2024}, author = {Peng, Z and Xu, Z and Tong, H and Xing, Y and Luo, Z and Wu, Y and Yu, Z}, title = {Leaf Rust Pathogens on Hypericum pseudohenryi: Describing Melampsora danbaensis sp. nov. and M. hyperici-pseudohenryi sp. nov. from China.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {122}, pmid = {39379763}, issn = {1432-184X}, support = {2023YFC2604800-03//National Key Research and Development Program of China/ ; }, mesh = {China ; *Hypericum/microbiology/classification ; *Phylogeny ; *Plant Diseases/microbiology ; *Plant Leaves/microbiology ; *Basidiomycota/classification/genetics/isolation &amp; purification ; DNA, Fungal/genetics ; Spores, Fungal ; }, abstract = {Based on morphological and phylogenetic evidence, two novel species of Melampsora were discovered on Hypericum pseudohenryi in China and have been thoroughly characterized. One of these species, designated as M. danbaensis, exhibits distinct features such as aecia of Uredo-type, typically appearing in gregarious or grouped arrangements, and presenting a shallowly pulvinate structure. Aeciospores exhibit tremendous variations in size, ranging in shape from globose to ellipsoidal and bearing pronounced verrucose texture. Telia resemble crusts one-spore deep, covering nearly the entire abaxial leaf surface, with sessile teliospores reaching sizes of up to 65.8 µm, and exhibiting a clavate to cylindrical shape. Another species, designated as M. hyperici-pseudohenryi, is distinguished by Uredo-type uredinia, which are hypophyllous, scattered or grouped, and interspersed with numerous paraphyses. Its urediniospores tend to be globose, ellipsoidal or obovoid, echinulate, and are accompanied by clavate to capitate paraphyses reaching lengths up to 77.6 µm. Phylogenetically, both species form a novel monophyletic clade within the Melampsora genus, with robust support demonstrated by a high Maximum likelihood bootstrap support (MLBS) value of 100% and a Bayesian posterior probability (BPP) of 1. This study enriches our understanding of the diversity and geographical distribution of Melampsora species that infect Hypericum plants in China.}, }
@article {pmid39379709, year = {2024}, author = {Larrouy, JL and Ridgway, HJ and Dhami, MK and Jones, EE}, title = {Improvement in Microbiota Recovery Using Cas-9 Digestion of Mānuka Plastid and Mitochondrial DNA.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {124}, pmid = {39379709}, issn = {1432-184X}, support = {C11X1803//Ministry of Business, Innovation and Employment/ ; C11X1803//Ministry of Business, Innovation and Employment/ ; C11X1803//Ministry of Business, Innovation and Employment/ ; C11X1803//Ministry of Business, Innovation and Employment/ ; }, mesh = {*RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Plastids/genetics ; *DNA, Mitochondrial/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; Lamiales/microbiology/genetics ; CRISPR-Cas Systems ; DNA, Bacterial/genetics ; RNA, Guide, CRISPR-Cas Systems/genetics ; Sequence Analysis, DNA ; }, abstract = {Understanding host-microbe interactions in planta is an expanding area of research. Amplicon sequencing of the 16S rRNA gene is a powerful and common method to study bacterial communities associated with plants. However, the co-amplification of mitochondrial and plastid 16S rRNA genes by universal primers impairs the sensitivity and performance of 16S rRNA sequencing. In 2020, a new method, Cas-16S-seq, was reported in the literature to remove host contamination for profiling the microbiota in rice, a well-studied domestic plant, by engineering RNA-programmable Cas9 nuclease in 16S rRNA sequencing. For the first time, we tested the efficiency and applicability of the Cas-16S-seq method on foliage, flowers, and seed of a non-domesticated wild plant for which there is limited genomic information, Leptospermum scoparium (mānuka). Our study demonstrated the efficiency of the Cas-16S-seq method for L. scoparium in removing host contamination in V4-16S amplicons. An increase of 46% in bacterial sequences was found using six guide RNAs (gRNAs), three gRNAs targeting the mitochondrial sequence, and three gRNAs targeting the chloroplast sequence of L. scoparium in the same reaction. An increase of 72% in bacterial sequences was obtained by targeting the mitochondrial and chloroplast sequences of L. scoparium in the same sample at two different steps of the library preparation (DNA and 1st step PCR). The number of OTUs (operational taxonomic units) retrieved from soil samples was consistent when using the different methods (Cas-16S-seq and 16S-seq) indicating that the Cas-16S-seq implemented for L. scoparium did not introduce bias to microbiota profiling. Our findings provide a valuable tool for future studies investigating the bacterial microbiota of L. scoparium in addition to evaluating an important tool in the plant microbiota research on other non-domesticated wild species.}, }
@article {pmid39379544, year = {2024}, author = {Bastidas Navarro, M and Balseiro, E and Modenutti, B}, title = {Lake Bacterial Communities in North Patagonian Andes: The Effect of the Nothofagus pumilio Treeline.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {123}, pmid = {39379544}, issn = {1432-184X}, support = {PICT 2015-2138//Fondo para la Investigaci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; PICT 2017-1940//Fondo para la Investigaci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; PICT 2018-1563//Fondo para la Investigaci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; }, mesh = {*Lakes/microbiology/chemistry ; *Bacteria/classification/genetics/isolation &amp; purification ; *Phylogeny ; Cyanobacteria/genetics/classification ; Microbiota ; Nitrogen/analysis ; Carbon/analysis/metabolism ; Phosphorus/analysis ; Biodiversity ; Altitude ; Trees/microbiology ; Argentina ; }, abstract = {One of the most noticeable environmental discontinuities in mountains is the transition that exists in vegetation below and above the treeline. In the North Patagonian Andean lakes (between 900 and 1950 m a.s.l.), we analyzed the bacterial community composition of lakes in relation to surrounding vegetation (erected trees, krummholz belt, and bare rocks), dissolved organic carbon (DOC), and total dissolved nutrients (nitrogen, TDN and phosphorus, TDP). We observed a decrease in DOC, TDP, and TDN concentrations with altitude, reflecting shifts in the source inputs entering the lakes by runoff. Cluster analysis based on bacterial community composition showed a segregation of the lakes below treeline, from those located above. This first cluster was characterized by the cyanobacteria Cyanobium PCC-6307, while in the krummholz belt and bare rocks, bacterial communities were dominated by Actinobacteria hgcl-clade and Proteobacteria (Sandarakinorhabdus and Rhodovarius), with the presence of pigments such as actinorhodopsin, carotenoids, and bacteriochlorophyll a. The net relatedness index (NRI), which considers the community phylogenetic dispersion, showed that lakes located on bare rocks were structured by environmental filtering, while communities of lakes below treeline were structured by species interactions such as competition. Beta-diversity was higher among lakes below than among lakes located above the treeline. The contribution of species turnover was more important than nestedness. Our study brings light on how bacterial communities may respond to changes in the surrounding vegetation, highlighting the importance of evaluating different aspects of community structure to understand metacommunity organization.}, }
@article {pmid39378744, year = {2025}, author = {Zhu, T and Li, S and Tao, C and Chen, W and Chen, M and Zong, Z and Wang, Y and Li, Y and Yan, B}, title = {Understanding the mechanism of microplastic-associated antibiotic resistance genes in aquatic ecosystems: Insights from metagenomic analyses and machine learning.}, journal = {Water research}, volume = {268}, number = {Pt A}, pages = {122570}, doi = {10.1016/j.watres.2024.122570}, pmid = {39378744}, issn = {1879-2448}, mesh = {*Machine Learning ; *Microplastics/toxicity ; *Drug Resistance, Microbial/genetics ; *Metagenomics ; *Ecosystem ; Water Pollutants, Chemical/toxicity ; }, abstract = {The pervasive presence of microplastics (MPs) in aquatic systems facilitates the transmission of antibiotic resistance genes (ARGs), thereby posing risks to ecosystems and human well-being. However, owing to variations in environmental backgrounds and the limited scope of research subjects, studies on ARGs in MPs lack unified conclusions, particularly regarding whether different types of MPs selectively promote ARG enrichment. Analysing large-scale datasets can better encompass broad spatiotemporal scales and diverse samples, facilitating a more extensive exploration of the complex ecological relationships between MPs and ARGs. The present study integrated existing metagenomic datasets to conduct a comprehensive risk assessment and comparative analysis of resistance groups across various MPs. In addition, we endeavoured to elucidate potential associations between ARGs and bacterial taxa, as well as MP structural features, using machine learning (ML) methods. The findings of our research highlight the pivotal role of MP type in shaping plastispheres, accounting for 9.56 % of the biotic variation (Adonis index) and explaining 18.59 % of the ARG variance. Compared to conventional MPs, biodegradable MPs, such as polyhydroxyalkanoates (PHA) and polylactic acid (PLA), exhibit lower species uniformity and diversity but pose a higher risk of ARG occurrence. These ML approaches effectively forecasted ARG abundance by using the bacterial taxa and molecular structure descriptors (MDs) of MPs (average R[2]tra = 0.882, R[2]test = 0.759). Feature analysis showed that MDs associated with lipophilicity, solubility, toxicity, and surface potential significantly influenced the relative abundance of ARGs in the plastispheres. The interpretable multiple linear regression (MLR) model, particularly notable, elucidated a linear relationship between bacterial genera and ARGs, offering promise for identifying potential ARG hosts. This study offers novel insights into ARG dynamics and ecological risks within aquatic plastispheres, highlighting the importance of comprehensive MP monitoring initiatives.}, }
@article {pmid39377576, year = {2024}, author = {Woldetsadik, YA and Lazinski, DW and Camilli, A}, title = {A Vibrio cholerae anti-phage system depletes nicotinamide adenine dinucleotide to restrict virulent bacteriophages.}, journal = {mBio}, volume = {15}, number = {11}, pages = {e0245724}, pmid = {39377576}, issn = {2150-7511}, support = {AI055058//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; GM139772//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R37 AI055058/AI/NIAID NIH HHS/United States ; R01 AI055058/AI/NIAID NIH HHS/United States ; R21 AI147658/AI/NIAID NIH HHS/United States ; T32 GM139772/GM/NIGMS NIH HHS/United States ; AI147658//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; }, mesh = {*NAD/metabolism ; *Bacteriophages/genetics/physiology ; *Vibrio cholerae/virology/genetics ; Virulence ; Bacterial Proteins/genetics/metabolism ; Genomic Islands ; Virus Replication ; }, abstract = {Bacteria and their predatory viruses (bacteriophages or phages) are in a perpetual molecular arms race. This has led to the evolution of numerous phage defensive systems in bacteria that are still being discovered, as well as numerous ways of interference or circumvention on the part of phages. Here, we identify a unique molecular battle between the classical biotype of Vibrio cholerae and virulent phages ICP1, ICP2, and ICP3. We show that classical biotype strains resist almost all isolates of these phages due to a 25-kb genomic island harboring several putative anti-phage systems. We observed that one of these systems, Nezha, encoding SIR2-like and helicase proteins, inhibited the replication of all three phages. Bacterial SIR2-like enzymes degrade the essential metabolic coenzyme nicotinamide adenine dinucleotide (NAD[+]), thereby preventing replication of the invading phage. In support of this mechanism, we identified one phage isolate, ICP1_2001, which circumvents Nezha by encoding two putative NAD[+] regeneration enzymes. By restoring the NAD[+] pool, we hypothesize that this system antagonizes Nezha without directly interacting with its proteins and should be able to antagonize other anti-phage systems that deplete NAD[+].IMPORTANCEBacteria and phages are in a perpetual molecular arms race, with bacteria evolving an extensive arsenal of anti-phage systems and phages evolving mechanisms to overcome these systems. This study identifies a previously uncharacterized facet of the arms race between Vibrio cholerae and its phages. We identify an NAD[+]-depleting anti-phage defensive system called Nezha, potent against three virulent phages. Remarkably, one phage encodes proteins that regenerate NAD[+] to counter the effects of Nezha. Without Nezha, the NAD[+] regeneration genes are detrimental to the phage. Our study provides new insight into the co-evolutionary dynamics between bacteria and phages and informs the microbial ecology and phage therapy fields.}, }
@article {pmid39376571, year = {2024}, author = {Qian, C and Hui, J and Peng, Z and Sun, X and Zhang, J}, title = {Mucosal microbiota characterization in gastric cancer identifies immune-activated-related transcripts relevant gastric microbiome signatures.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1435334}, pmid = {39376571}, issn = {1664-3224}, mesh = {Humans ; *Stomach Neoplasms/immunology/microbiology/genetics/mortality ; *Gastric Mucosa/microbiology/immunology/metabolism ; Female ; *Tumor Microenvironment/immunology ; Male ; Middle Aged ; *Gastrointestinal Microbiome/immunology/genetics ; Aged ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/immunology/genetics ; Adult ; }, abstract = {Tumor microenvironment (TME) immune cells and gastric mucosal microbiome constitute two vital elements of tumor tissue. Increasing evidence has elucidated their clinicopathological significance in predicting outcomes and therapeutic efficacy. However, comprehensive characterization of immune cell-associated microbiome signatures in the TME is still in the early stages of development. Here, we characterized the gastric mucosa microbiome and its associations with immune-activated related transcripts (IATs) in 170 GC tumor tissues and matched non-tumor tissues using 16s rRNA gene sequencing and quantitative reverse transcription-PCR. Microbial diversity and richness were significantly higher in GC tumor tissues than in non-tumor tissues. Differences in microbial composition between the groups were evident, with Firmicutes, Proteobacteria, Bacteroidota, Campilobacterota, Actinobacteria, Fusobacteriota, Verrucomicrobiota, Acidobacteriota, and Cyanobacteria being the dominant phyla in the gastric mucosal microbiota. Microbial interaction network analysis revealed distinctive centralities of oral bacteria (such as Fusobacterium, Porphyromonas, Prevotella, etc.) in both tumor and normal mucosae networks, suggesting their significant influence on GC microbial ecology. Furthermore, we analyzed the expression of IATs (CXCL9, CXCL10, GZMA, GZMB, PRF1, CD8A, IFNG, TBX2, and TNF) and characterized IAT-relevant gastric microbiome signatures in GC patients. Our results showed that the expression of CXCL9, CXCL10, GZMA, GZMB, PRF1 and IFNG was significantly higher in tumor tissues than in adjacent normal tissues in GC patients. Notably, high expression of IATs in tumor tissues was associated with improved survival in GC patients and could serve as a powerful predictor for disease-free survival. Additionally, analysis of IAT levels and mucosal microbiota diversity revealed a correlation between higher IAT expression and increased microbiota richness and evenness in the IATs [high] group, suggesting potential interactions between mucosal microbiota and tumor immunopathology. Spearman correlation analysis showed positive associations between IAT expression and specific mucosal bacterial species. Notably, Akkermansia muciniphila demonstrated potential involvement in modulating GZMB expression in the GC mucosal microenvironment. These findings underscore the importance of mucosal microbiota alterations in GC and suggest potential therapeutic targets focusing on modulating the tumor microbiota for improved clinical outcomes. The detailed characterization of these elements has profound implications for both treatment and survival prediction in GC. We observed that microbial diversity and richness were significantly higher in GC tumor tissues compared to non-tumor tissues. These differences highlight the unique microbial landscape of GC tumors and suggest that the microbiome could influence tumor development and progression. Importantly, our study demonstrated that high expression levels of IATs in GC tumor tissues were associated with improved patient survival. This suggests that IATs not only reflect immune activation but also serve as valuable biomarkers for predicting disease-free survival. The potential of IATs as predictive markers underscores their utility in guiding therapeutic strategies and personalizing treatment approaches. Moreover, the correlation between higher IAT expression and increased microbiota richness and evenness suggests that a diverse and balanced microbiome may enhance immune responses and contribute to better clinical outcomes. These findings highlight the critical need to consider mucosal microbiota alterations in GC management. Targeting the tumor microbiota could emerge as a promising therapeutic strategy, potentially leading to more effective treatments and improved patient outcomes. Understanding and modulating the microbiome's role in GC opens new avenues for innovative therapeutic interventions and personalized medicine.}, }
@article {pmid39375832, year = {2024}, author = {Obiol, A and Del Campo, J and de Vargas, C and Mahé, F and Massana, R}, title = {How marine are Marine Stramenopiles (MAST)? A cross-system evaluation.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {11}, pages = {}, pmid = {39375832}, issn = {1574-6941}, support = {PID2019-108457RB-I00//Spanish Ministry of Science and Innovation/ ; EUR2022-134047//GENEXLAB/ ; PID2022-137508NB-I00//EPIC/ ; CEX2019-000928-S//Severo Ochoa Centre of Excellence/ ; }, mesh = {*Phylogeny ; *Seawater/microbiology ; *Stramenopiles/genetics/classification ; Aquatic Organisms/genetics ; Biodiversity ; Ecosystem ; Sequence Analysis, DNA ; Genes, rRNA ; }, abstract = {Marine Stramenopiles (MAST) were first described two decades ago through ribosomal RNA gene (rRNA gene) sequences from marine surveys of microbial eukaryotes. MAST comprise several independent lineages at the base of the Stramenopiles. Despite their prevalence in the ocean, the majority of MAST diversity remains uncultured. Previous studies, mainly in marine environments, have explored MAST's cell morphology, distribution, trophic strategies, and genomics using culturing-independent methods. In comparison, less is known about their presence outside marine habitats. Here, we analyse the extensive EukBank dataset to assess the extent to which MAST can be considered marine protists. Additionally, by incorporating newly available rRNA gene sequences, we update Stramenopiles phylogeny, identifying three novel MAST lineages. Our results indicate that MAST are primarily marine with notable exceptions within MAST-2 and MAST-12, where certain subclades are prevalent in freshwater and soil habitats. In the marine water column, only a few MAST species, particularly within clades -1, -3, -4, and -7, dominate and exhibit clear latitudinal distribution patterns. Overall, the massive sequencing dataset analysed in our study confirms and partially expands the previously described diversity of MASTs groups and underscores the predominantly marine nature of most of these uncultured lineages.}, }
@article {pmid39366327, year = {2024}, author = {Xu, J and Li, X and Xi, C and Weir, MH}, title = {Development of a machine learning model to support low cost real-time Legionella monitoring in premise plumbing systems.}, journal = {Water research}, volume = {267}, number = {}, pages = {122510}, doi = {10.1016/j.watres.2024.122510}, pmid = {39366327}, issn = {1879-2448}, mesh = {*Machine Learning ; *Water Microbiology ; *Legionella pneumophila ; Legionella ; Water Quality ; Environmental Monitoring/methods ; Water Supply ; Amoeba ; }, abstract = {Legionella pneumophila (L. pneumophila) is a pathogenic bacterium primarily known for causing Legionnaires' Disease which is known for high mortality rates, particularly in the elderly. With caseloads continuing to increase, further research is needed to improve our understanding of optimized sampling schema and safe limits of L. pneumophila, in part to target improved treatment options and realistic population-level risk modeling. Particularly in healthcare and other high-risk locations these become crucial and time sensitive needs. Therefore, we conceptualized this research as a means of incorporating easily measured physiochemical water quality parameters and generalization of the unique ecology of building water systems to build a computational model that can allow for more rapid and accurate decision making. This research uses the specific machine learning (ML) method called statistical learning theory to incorporate concentration of host cells, such as native amoeba, and physiochemical water quality parameters to estimate the probability of observing ranges of Legionella gene copy concentrations. Using data from previously published research on Legionella prevalence in a large building, our ML method trains the model on the relative impacts of physiochemical parameters on likely amoeba host cell occurrences. The model is expanded to estimate host cell concentrations using correlations and regressions operated through LASSO algorithms. After categorization variables from these results are then used to inform a logistic regression to provide an estimate of the probability of Legionella gene copy concentration ranges. In summary, conventional results generated by logistic regression and multiple linear regression quantified the associations among ecological conditions in the water and ability to predict a likely range of Legionella concentration in a management focused way. Further, two ML methods, PCA and LASSO, demonstrated feasibility in accurate real-time monitoring of Legionella through physiochemical indicators as evidenced with good accuracy of predictions based for validation results. Furthermore results demonstrate the vital need to account for the impact of water quality on building on host cells, and via their quantified water microbial ecology, not just Legionella concentrations.}, }
@article {pmid39365014, year = {2024}, author = {Arnold, ND and Paper, M and Fuchs, T and Ahmad, N and Jung, P and Lakatos, M and Rodewald, K and Rieger, B and Qoura, F and Kandawa-Schulz, M and Mehlmer, N and Brück, TB}, title = {High-quality genome of a novel Thermosynechococcaceae species from Namibia and characterization of its protein expression patterns at elevated temperatures.}, journal = {MicrobiologyOpen}, volume = {13}, number = {5}, pages = {e70000}, pmid = {39365014}, issn = {2045-8827}, support = {031B0838B//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 031A305A//Bundesministerium f&#xfc;r Wirtschaft und Energie/ ; //Bayerisches Staatsministerium f&#xfc;r Umwelt und Verbraucherschutz/ ; }, mesh = {Namibia ; *Cyanobacteria/genetics/classification/metabolism ; *Genome, Bacterial ; *Phylogeny ; *Hot Springs/microbiology ; *RNA, Ribosomal, 16S/genetics ; Bacterial Proteins/genetics/metabolism ; Hot Temperature ; Sequence Analysis, DNA ; Proteome/analysis ; DNA, Bacterial/genetics ; }, abstract = {Thermophilic cyanobacteria thrive in extreme environments, making their thermoresistant enzymes valuable for industrial applications. Common habitats include hot springs, which act as evolutionary accelerators for speciation due to geographical isolation. The family Thermosynechococcaceae comprises thermophilic cyanobacteria known for their ability to thrive in high-temperature environments. These bacteria are notable for their photosynthetic capabilities, significantly contributing to primary production in extreme habitats. Members of Thermosynechococcaceae exhibit unique adaptations that allow them to perform photosynthesis efficiently at elevated temperatures, making them subjects of interest for studies on microbial ecology, evolution, and potential biotechnological applications. In this study, the genome of a thermophilic cyanobacterium, isolated from a hot spring near Okahandja in Namibia, was sequenced using a PacBio Sequel IIe long-read platform. Cultivations were performed at elevated temperatures of 40, 50, and 55°C, followed by proteome analyses based on the annotated genome. Phylogenetic investigations, informed by the 16S rRNA gene and aligned nucleotide identity (ANI), suggest that the novel cyanobacterium is a member of the family Thermosynechococcaceae. Furthermore, the new species was assigned to a separate branch, potentially representing a novel genus. Whole-genome alignments supported this finding, revealing few conserved regions and multiple genetic rearrangement events. Additionally, 129 proteins were identified as differentially expressed in a temperature-dependent manner. The results of this study broaden our understanding of cyanobacterial adaptation to extreme environments, providing a novel high-quality genome of Thermosynechococcaceae cyanobacterium sp. Okahandja and several promising candidate proteins for expression and characterization studies.}, }
@article {pmid39364584, year = {2025}, author = {Buchner, D and Sinclair, JS and Ayasse, M and Beermann, AJ and Buse, J and Dziock, F and Enss, J and Frenzel, M and Hörren, T and Li, Y and Monaghan, MT and Morkel, C and Müller, J and Pauls, SU and Richter, R and Scharnweber, T and Sorg, M and Stoll, S and Twietmeyer, S and Weisser, WW and Wiggering, B and Wilmking, M and Zotz, G and Gessner, MO and Haase, P and Leese, F}, title = {Upscaling biodiversity monitoring: Metabarcoding estimates 31,846 insect species from Malaise traps across Germany.}, journal = {Molecular ecology resources}, volume = {25}, number = {1}, pages = {e14023}, pmid = {39364584}, issn = {1755-0998}, support = {//Hessisches Landesamt f&#xfc;r Naturschutz, Umwelt und Geologie/ ; 871128//EU Horizon 2020 project eLTER PLUS/ ; //Landes-Offensive zur Entwicklung Wissenschaftlich-&#xf6;konomischer Exzellenz of the German federal State of Hesse/ ; }, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; Germany ; *Biodiversity ; *Insecta/classification/genetics/physiology ; }, abstract = {Mitigating ongoing losses of insects and their key functions (e.g. pollination) requires tracking large-scale and long-term community changes. However, doing so has been hindered by the high diversity of insect species that requires prohibitively high investments of time, funding and taxonomic expertise when addressed with conventional tools. Here, we show that these concerns can be addressed through a comprehensive, scalable and cost-efficient DNA metabarcoding workflow. We use 1815 samples from 75 Malaise traps across Germany from 2019 and 2020 to demonstrate how metabarcoding can be incorporated into large-scale insect monitoring networks for less than 50 € per sample, including supplies, labour and maintenance. We validated the detected species using two publicly available databases (GBOL and GBIF) and the judgement of taxonomic experts. With an average of 1.4 M sequence reads per sample we uncovered 10,803 validated insect species, of which 83.9% were represented by a single Operational Taxonomic Unit (OTU). We estimated another 21,043 plausible species, which we argue either lack a reference barcode or are undescribed. The total of 31,846 species is similar to the number of insect species known for Germany (~35,500). Because Malaise traps capture only a subset of insects, our approach identified many species likely unknown from Germany or new to science. Our reproducible workflow (~80% OTU-similarity among years) provides a blueprint for large-scale biodiversity monitoring of insects and other biodiversity components in near real time.}, }
@article {pmid39361898, year = {2024}, author = {Ramoneda, J and Hoffert, M and Stallard-Olivera, E and Casamayor, EO and Fierer, N}, title = {Leveraging genomic information to predict environmental preferences of bacteria.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39361898}, issn = {1751-7370}, support = {OPP 2133684//US National Science Foundation/ ; AEROSMIC PID2021-127701NB-I00//European Regional Development Fund/ ; //Spanish Agency of Research/ ; PID2023-151209NA-I00//Spanish Agency of Research/ ; 2022-BP-00050//Generalitat de Catalunya/ ; P2EZP3_199849/SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {*Bacteria/genetics/classification ; Genome, Bacterial ; Genomics ; Environment ; Bacterial Physiological Phenomena ; }, abstract = {Genomic information is now available for a broad diversity of bacteria, including uncultivated taxa. However, we have corresponding knowledge on environmental preferences (i.e. bacterial growth responses across gradients in oxygen, pH, temperature, salinity, and other environmental conditions) for a relatively narrow swath of bacterial diversity. These limits to our understanding of bacterial ecologies constrain our ability to predict how assemblages will shift in response to global change factors, design effective probiotics, or guide cultivation efforts. We need innovative approaches that take advantage of expanding genome databases to accurately infer the environmental preferences of bacteria and validate the accuracy of these inferences. By doing so, we can broaden our quantitative understanding of the environmental preferences of the majority of bacterial taxa that remain uncharacterized. With this perspective, we highlight why it is important to infer environmental preferences from genomic information and discuss the range of potential strategies for doing so. In particular, we highlight concrete examples of how both cultivation-independent and cultivation-dependent approaches can be integrated with genomic data to develop predictive models. We also emphasize the limitations and pitfalls of these approaches and the specific knowledge gaps that need to be addressed to successfully expand our understanding of the environmental preferences of bacteria.}, }
@article {pmid39360821, year = {2024}, author = {Han, S and Kim, S and Sedlacek, CJ and Farooq, A and Song, C and Lee, S and Liu, S and Brüggemann, N and Rohe, L and Kwon, M and Rhee, S-K and Jung, M-Y}, title = {Adaptive traits of Nitrosocosmicus clade ammonia-oxidizing archaea.}, journal = {mBio}, volume = {15}, number = {11}, pages = {e0216924}, pmid = {39360821}, issn = {2150-7511}, support = {2019R1A6A1A10072987//National Research Foundation of Korea (NRF)/ ; 2021R1C1C1008303//National Research Foundation of Korea (NRF)/ ; 2022R1A4A503144711//National Research Foundation of Korea (NRF)/ ; ZK74//Austrian Science Fund (FWF)/ ; 2023RIS-009//Regional Innovation Strategy (RIS)/ ; }, mesh = {*Ammonia/metabolism ; *Oxidation-Reduction ; *Archaea/genetics/metabolism/classification ; *Nitrification ; *Phylogeny ; Genome, Archaeal ; Adaptation, Physiological ; Genomics ; }, abstract = {UNLABELLED: Nitrification is a core process in the global nitrogen (N) cycle mediated by ammonia-oxidizing microorganisms, including ammonia-oxidizing archaea (AOA) as a key player. Although much is known about AOA abundance and diversity across environments, the genetic drivers of the ecophysiological adaptations of the AOA are often less clearly defined. This is especially true for AOA within the genus Nitrosocosmicus, which have several unique physiological traits (e.g., high substrate tolerance, low substrate affinity, and large cell size). To better understand what separates the physiology of Nitrosocosmicus AOA, we performed comparative genomics with genomes from 39 cultured AOA, including five Nitrosocosmicus AOA. The absence of a canonical high-affinity type ammonium transporter and typical S-layer structural genes was found to be conserved across all Nitrosocosmicus AOA. In agreement, cryo-electron tomography confirmed the absence of a visible outermost S-layer structure, which has been observed in other AOA. In contrast to other AOA, the cryo-electron tomography highlighted the possibility that Nitrosocosmicus AOA may possess a glycoprotein or glycolipid-based glycocalyx cell covering outer layer. Together, the genomic, physiological, and metabolic properties revealed in this study provide insight into niche adaptation mechanisms and the overall ecophysiology of members of the Nitrosocosmicus clade in various terrestrial ecosystems.<br><br>IMPORTANCE: Nitrification is a vital process within the global biogeochemical nitrogen cycle but plays a significant role in the eutrophication of aquatic ecosystems and the production of the greenhouse gas nitrous oxide (N2O) from industrial agriculture ecosystems. While various types of ammonia-oxidizing microorganisms play a critical role in the N cycle, ammonia-oxidizing archaea (AOA) are often the most abundant nitrifiers in natural environments. Members of the genus Nitrosocosmicus are one of the prevalent AOA groups detected in undisturbed terrestrial ecosystems and have previously been reported to possess a range of physiological characteristics that set their physiology apart from other AOA species. This study provides significant progress in understanding these unique physiological traits and their genetic drivers. Our results highlight how physiological studies based on comparative genomics-driven hypotheses can contribute to understanding the unique niche of Nitrosocosmicus AOA.}, }
@article {pmid39360459, year = {2024}, author = {Li, X and Leizeaga, A and Rousk, J and Zhou, S and Hugelius, G and Manzoni, S}, title = {Recovery of Soil Microbial Metabolism After Rewetting Depends on Interacting Environmental Conditions and Changes in Functional Groups and Life History Strategies.}, journal = {Global change biology}, volume = {30}, number = {10}, pages = {e17522}, doi = {10.1111/gcb.17522}, pmid = {39360459}, issn = {1365-2486}, support = {101001608//H2020 European Research Council/ ; KAW 2017.0171//Knut och Alice Wallenbergs Stiftelse/ ; KAW 2022.0175//Knut och Alice Wallenbergs Stiftelse/ ; //Schmidt Sciences, LLC/ ; }, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Carbon/metabolism ; *Fungi/physiology/metabolism ; *Climate Change ; Bacteria/metabolism/growth &amp; development ; Microbiota ; Hydrogen-Ion Concentration ; }, abstract = {Climate change is causing an intensification of soil drying and rewetting events, altering microbial functioning and potentially destabilizing soil organic carbon. After rewetting, changes in microbial community carbon use efficiency (CUE), investment in life history strategies, and fungal to bacterial dominance co-occur. Still, we have yet to generalize what drives these dynamic responses. Here, we collated 123 time series of microbial community growth (G, sum of fungal and bacterial growth, evaluated by leucine and acetate incorporation, respectively) and respiration (R) after rewetting and calculated CUE = G/(G + R). First, we characterized CUE recovery by two metrics: maximum CUE and time to maximum CUE. Second, we translated microbial growth and respiration data into microbial investments in life history strategies (high yield (Y), resource acquisition (A), and stress tolerance (S)). Third, we characterized the temporal change in fungal to bacterial dominance. Finally, the metrics describing the CUE recovery, investment in life history strategies, and fungal to bacterial dominance after rewetting were explained by environmental factors and microbial properties. CUE increased after rewetting as fungal dominance declined, but the maximum CUE was explained by the CUE under moist conditions, rather than specific environmental factors. In contrast, higher soil pH and carbon availability accelerated the decline of microbial investment in stress tolerance and fungal dominance. We conclude that microbial CUE recovery is mostly driven by the shifting microbial community composition and the metabolic capacity of the community, whereas changes in microbial investment in life history strategies and fungal versus bacterial dominance depend on soil pH and carbon availability.}, }
@article {pmid39360321, year = {2024}, author = {MacGregor, H and Fukai, I and Ash, K and Arkin, AP and Hazen, TC}, title = {Potential applications of microbial genomics in nuclear non-proliferation.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1410820}, pmid = {39360321}, issn = {1664-302X}, abstract = {As nuclear technology evolves in response to increased demand for diversification and decarbonization of the energy sector, new and innovative approaches are needed to effectively identify and deter the proliferation of nuclear arms, while ensuring safe development of global nuclear energy resources. Preventing the use of nuclear material and technology for unsanctioned development of nuclear weapons has been a long-standing challenge for the International Atomic Energy Agency and signatories of the Treaty on the Non-Proliferation of Nuclear Weapons. Environmental swipe sampling has proven to be an effective technique for characterizing clandestine proliferation activities within and around known locations of nuclear facilities and sites. However, limited tools and techniques exist for detecting nuclear proliferation in unknown locations beyond the boundaries of declared nuclear fuel cycle facilities, representing a critical gap in non-proliferation safeguards. Microbiomes, defined as "characteristic communities of microorganisms" found in specific habitats with distinct physical and chemical properties, can provide valuable information about the conditions and activities occurring in the surrounding environment. Microorganisms are known to inhabit radionuclide-contaminated sites, spent nuclear fuel storage pools, and cooling systems of water-cooled nuclear reactors, where they can cause radionuclide migration and corrosion of critical structures. Microbial transformation of radionuclides is a well-established process that has been documented in numerous field and laboratory studies. These studies helped to identify key bacterial taxa and microbially-mediated processes that directly and indirectly control the transformation, mobility, and fate of radionuclides in the environment. Expanding on this work, other studies have used microbial genomics integrated with machine learning models to successfully monitor and predict the occurrence of heavy metals, radionuclides, and other process wastes in the environment, indicating the potential role of nuclear activities in shaping microbial community structure and function. Results of this previous body of work suggest fundamental geochemical-microbial interactions occurring at nuclear fuel cycle facilities could give rise to microbiomes that are characteristic of nuclear activities. These microbiomes could provide valuable information for monitoring nuclear fuel cycle facilities, planning environmental sampling campaigns, and developing biosensor technology for the detection of undisclosed fuel cycle activities and proliferation concerns.}, }
@article {pmid39359935, year = {2024}, author = {Li, Y and Li, Z and Zheng, S and Xu, X}, title = {Probiotics in the management of radiation-induced oral mucositis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1477143}, pmid = {39359935}, issn = {2235-2988}, mesh = {*Probiotics/therapeutic use ; Humans ; *Stomatitis/etiology/microbiology/therapy/prevention &amp; control ; *Radiation Injuries/therapy ; *Dysbiosis ; Microbiota ; Head and Neck Neoplasms/radiotherapy ; Radiotherapy/adverse effects ; Mouth/microbiology ; Quality of Life ; }, abstract = {Oral mucositis is a common and debilitating oral complication in head and neck cancer patients undergoing radiotherapy, resulting in diminished quality of life and potential treatment disruptions. Oral microbiota has long been recognized as a contributing factor in the initiation and progression of radiation-induced oral mucositis (RIOM). Numerous studies have indicated that the radiation-induced oral microbial dysbiosis promotes the occurrence and severity of oral mucositis. Therefore, approaches that modulate oral microbial ecology are promising for the management of RIOM. Probiotics as a relatively predicable and safe measure that modulates microecology have garnered significant interest. In this review, we discussed the correlation between RIOM and oral microbiota, with a particular focus on the efficacy of probiotics in the control of RIOM, in order to provide novel paradigm for the management of this disease.}, }
@article {pmid39358950, year = {2024}, author = {Zhang, J and Qin, L and Chang, Y and He, Y and Zhao, W and Zhao, Y and Ding, Y and Gao, J and Zhao, X}, title = {One-Pot Assay for Rapid Detection of Stenotrophomonas maltophilia by RPA-CRISPR/Cas12a.}, journal = {ACS synthetic biology}, volume = {13}, number = {10}, pages = {3400-3412}, doi = {10.1021/acssynbio.4c00481}, pmid = {39358950}, issn = {2161-5063}, mesh = {*Stenotrophomonas maltophilia/genetics ; *CRISPR-Cas Systems/genetics ; Nucleic Acid Amplification Techniques/methods ; Recombinases/metabolism/genetics ; DNA, Bacterial/genetics ; CRISPR-Associated Proteins/genetics ; Endodeoxyribonucleases/genetics ; Bacterial Proteins ; }, abstract = {Stenotrophomonas maltophilia (S. maltophilia, SMA) is a common opportunistic pathogen that poses a serious threat to the food industry and human health. Traditional detection methods for SMA are time-consuming, have low detection rates, require complex and expensive equipment and professional technical personnel for operation, and are unsuitable for on-site detection. Therefore, establishing an efficient on-site detection method has great significance in formulating appropriate treatment strategies and ensuring food safety. In the present study, a rapid one-pot detection method was established for SMA using a combination of Recombinase Polymerase Amplification (RPA) and CRISPR/Cas12a, referred to as ORCas12a-SMA (one-pot RPA-CRISPR/Cas12a platform). In the ORCas12a-SMA detection method, all components were added into a single tube simultaneously to achieve one-pot detection and address the problems of nucleic acid cross-contamination and reduced sensitivity caused by frequent cap opening during stepwise detection. The ORCas12a-SMA method could detect at least 3 × 10° copies·μL[-1] of SMA genomic DNA within 30 min at 37 °C. Additionally, this method exhibited sensitivity compared to the typical two-step RPA-CRISPR/Cas12a method. Overall, the ORCas12a-SMA detection offered the advantages of rapidity, simplicity, high sensitivity and specificity, and decreased need for complex large-scale instrumentation. This assay is the first application of the one-pot platform based on the combination of RPA and CRISPR/Cas12a in SMA detection and is highly suitable for point-of-care testing. It helps reduce losses in the food industry and provides assistance in formulating timely and appropriate antimicrobial treatment plans.}, }
@article {pmid39358586, year = {2025}, author = {de Lorenzo, V and Baquero, F and Aguilar, A}, title = {Carlos Asensio and the dawn of molecular microbial ecology.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {28}, number = {5}, pages = {897-908}, pmid = {39358586}, issn = {1618-1905}, support = {CL6-2021-UE 101060625//Horizon 2020 Framework Programme/ ; Y2020/TCS- 6555//Comunidad de Madrid/ ; }, mesh = {History, 20th Century ; Spain ; Humans ; Gastrointestinal Microbiome ; *Microbiology/history ; }, abstract = {At near 50 years of the discovery of microcins, this article highlights the pivotal-but under-recognised-influence of Spanish biochemist Carlos Asensio (1925-1982) in contemporary microbiology, featuring the epistemological, sociological, and cultural impact of his scientific achievements. At a time when the intestinal microbiome is central to current biomedical research, it is due to emphasise his role in the establishment of new scientific fields that are now considered fundamental. Despite his premature death at the peak of his conceptual and experimental creativity, many of his ideas about microbial communication in complex communities inspired a generation of researchers and opened new topics reach to this day. Asensio was also a trailblazer in Spain, advocating for fundamental research within the socio-economic context of his time. He foresaw the shift towards what is now termed the knowledge-based bioeconomy, recognised the need for multidisciplinary research teams, and advocated integration science into societal and political agendas. These facets became evident during his research on microcins, low molecular weight bioactive compounds produced by enterobacteria. These molecules were hypothesised as mediators of microbial interactions in the human gut and were considered potential new antibiotics and even antitumoral agents. His research mobilised young talent and attracted unprecedented resources in Spain during the late 1970s-early 1980s. It underscored the medical value of microbial ecology and exemplified the benefits of collaboration between academia and industry. Asensio played a pivotal role in the emergence of molecular microbial ecology as a research discipline and its foundational and applied significance in biotechnology.}, }
@article {pmid39358432, year = {2024}, author = {Zhi, W and Li, A and Wang, Q and Yuan, X and Qing, J and Zhang, C and Wang, Y and Li, Y}, title = {Safety and efficacy assessment of fecal microbiota transplantation as an adjunctive treatment for IgA nephropathy: an exploratory clinical trial.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {22935}, pmid = {39358432}, issn = {2045-2322}, support = {82170716//National Science Foundation of China/ ; }, mesh = {Humans ; *Glomerulonephritis, IGA/therapy ; Male ; Female ; Adult ; *Fecal Microbiota Transplantation/methods/adverse effects ; *Gastrointestinal Microbiome ; Middle Aged ; Treatment Outcome ; Cytokines/blood/metabolism ; }, abstract = {To assess the safety and efficacy of fecal microbiota transplantation (FMT) as an adjunctive therapeutic intervention for IgA nephropathy (IgAN). Fifteen patients with IgA nephropathy were recruited based on inclusion and exclusion criteria and underwent FMT using enteric microbial capsules. Clinical indicators, intestinal microbiota and metabolomic profiles, as well as changes in serum immune cells and cytokines, were monitored before and after FMT. No severe adverse reactions were observed in the subjects. After FMT, there was a reduction in the 24-h urinary protein quantification in subjects. The relative abundances of Phocaeicola_vulgatus, Bacteroides_uniformis, Prevotella_copri, Phocaeicola_dorei, Bacteroides_ovatus, Bacteroides_xylanisolvens, Parabacteroides _distasonis, Bifidobacterium_pseudocatenulatum, Bacteroides_sp._HF-162, and Bifidobacterium_longum changed after FMT. In terms of intestinal metabolites, the levels of acylcarnitine18:0 (ACar.18:0), cotinine, N-arachidonoyl-L-serine, phosphatidylcholine (PC. (18:3e/22:6)), serotonin, and fumagillin showed significant changes. Flow cytometry analysis showed the absolute count of plasma B cells decreased in subjects, and this change correlated with alterations in the intestinal microbiota and metabolites. This study preliminarily evaluates the safety and efficacy of FMT in patients with IgAN. No significant adverse reactions were observed, and the administration of FMT alongside ACEI/ARB therapy was effective in reducing urinary protein levels in patients with IgAN, a process that may be associated with B-cell immunity.}, }
@article {pmid39357457, year = {2024}, author = {Olavarria, K and Sousa, DZ}, title = {Thermodynamic tools for more efficient biotechnological processes: an example in poly-(3-hydroxybutyrate) production from carbon monoxide.}, journal = {Current opinion in biotechnology}, volume = {90}, number = {}, pages = {103212}, doi = {10.1016/j.copbio.2024.103212}, pmid = {39357457}, issn = {1879-0429}, mesh = {*Carbon Monoxide/metabolism ; *Hydroxybutyrates/metabolism ; *Thermodynamics ; *Polyesters/metabolism/chemistry ; *Biotechnology/methods ; Metabolic Engineering/methods ; Polyhydroxybutyrates ; }, abstract = {Modern biotechnology requires the integration of several disciplines, with thermodynamics being a crucial one. Experimental approaches frequently used in biotechnology, such as rewiring of metabolic networks or culturing of micro-organisms in engineered environments, can benefit from the application of thermodynamic tools. In this paper, we provide an overview of several thermodynamic tools that are useful for the design and optimization of biotechnological processes, and we demonstrate their potential application in the production of poly-(3-hydroxybutyrate) (PHB) from carbon monoxide (CO). We discuss how these tools can aid in the design of metabolic engineering strategies, the calculation of expected yields, the assessment of the thermodynamic feasibility of the targeted conversions, the identification of potential thermodynamic bottlenecks, and the selection of genetic engineering targets. Although we illustrate these tools using the specific example of PHB production from CO, they can be applied to other substrates and products.}, }
@article {pmid39357161, year = {2024}, author = {Wan, W and Grossart, HP and Zhang, W and Xiong, X and Yuan, W and Liu, W and Yang, Y}, title = {Lake ecological restoration of vegetation removal mitigates algal blooms and alters landscape patterns of water and sediment bacteria.}, journal = {Water research}, volume = {267}, number = {}, pages = {122516}, doi = {10.1016/j.watres.2024.122516}, pmid = {39357161}, issn = {1879-2448}, mesh = {*Lakes/microbiology ; *Geologic Sediments/microbiology ; *Bacteria ; *Eutrophication ; Nitrogen ; Phosphorus ; Ecosystem ; Phylogeny ; }, abstract = {Elucidating the influences of ecological restoration measure of lakeshore vegetation removal on water quality and biological community is an important but underestimated subject. We adopted molecular and statistical tools to estimate ecological restoration performance in a plateau lake receiving vegetation removal and simultaneously investigated variabilities of bacterial communities in water and sediment. Significant decreases in lake trophic level and algal bloom degree followed notable decreases in water total nitrogen and total phosphorus after vegetation removal. Non-significant changes in sediment nutrients accompanied remarkable variabilities of abundance and composition of nutrient-cycling functional genes (NCFGs) of sediment bacteria. Taxonomic and phylogenetic α-diversities, functional redundancies, and dispersal potentials of bacteria in water and sediment decreased after vegetation removal, and community successions of water and sediment bacteria were separately significant and non-significant. There were opposite changes in ecological attributes of bacteria in water and sediment in response to vegetation removal, including niche breadth, species replacement, richness difference, community complexity, and community stability. Species replacement rather than richness difference affected more on taxonomic β-diversities of bacteria in water and sediment before and after vegetation removal, and determinism rather than stochasticity dominated bacterial community assemblage. Our results highlighted vegetation removal mitigated algal bloom and affected differently on landscapes of water and sediment bacteria. These findings point to dominant ecological mechanisms underlying landscape shifts in water and sediment bacteria in a disturbed lake receiving vegetation removal and have the potential to guide lake ecological restoration.}, }
@article {pmid39353102, year = {2024}, author = {He, J and Castilla-Alcantara, JC and Ortega-Calvo, JJ and Harms, H and Wick, LY}, title = {DC Electric Fields Promote Biodegradation of Waterborne Naphthalene in Biofilter Systems.}, journal = {Environmental science &amp; technology}, volume = {58}, number = {41}, pages = {18234-18243}, pmid = {39353102}, issn = {1520-5851}, mesh = {*Biodegradation, Environmental ; Filtration ; Electricity ; Water Pollutants, Chemical/metabolism ; Naphthalenes/metabolism ; }, abstract = {Biofiltration is a simple and low-cost method for the cleanup of contaminated water. However, the reduced availability of dissolved chemicals to surface-attached degrader bacteria may limit its efficient use at certain hydraulic loadings. When a direct current (DC) electric field is applied to an immersed packed bed, it invokes electrokinetic processes, such as electroosmotic water flow (EOF). EOF is a surface-charge-induced plug-flow-shaped movement of pore fluids. It acts at a nanometer distance above surfaces and allows the change of microscale pressure-driven flow profiles and, hence, the availability of dissolved contaminants to microbial degraders. In laboratory percolation columns, we assessed the effects of a weak DC electric field (E = 0.5 V·cm[-1]) on the biodegradation of waterborne naphthalene (NAH) by surface-attached Pseudomonas fluorescens LP6a. To vary NAH bioavailability, we used different NAH concentrations (C0 = 2.7, 5.1, or 7.8 × 10[-5] mol·L[-1]) and Darcy velocities typical for biofiltration (U¯ = 0.2-1.2 × 10[-4] m·s[-1]). In DC-free controls, we observed higher specific degradation rates (qc) at higher NAH concentrations. The qc depended on U¯, suggesting bioavailability restrictions depending on the hydraulic residence times. DC fields consistently increased qc and resulted in linearly increasing benefits up to 55% with rising hydraulic loadings relative to controls. We explain these biodegradation benefits by EOF-altered microscale flow profiles allowing for better NAH provision to bacteria attached to the collectors even though the EOF was calculated to be 100-800 times smaller than bulk water flow. Our data suggest that electrokinetic approaches may give rise to future technical applications that allow regulating biodegradation, for example, in response to fluctuating hydraulic loadings.}, }
@article {pmid39354222, year = {2024}, author = {Suzuki, Y and Webb, SJ and Kouduka, M and Kobayashi, H and Castillo, J and Kallmeyer, J and Moganedi, K and Allwright, AJ and Klemd, R and Roelofse, F and Mapiloko, M and Hill, SJ and Ashwal, LD and Trumbull, RB}, title = {Subsurface Microbial Colonization at Mineral-Filled Veins in 2-Billion-Year-Old Mafic Rock from the Bushveld Igneous Complex, South Africa.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {116}, pmid = {39354222}, issn = {1432-184X}, support = {AB0502//Astrobiology Center Program of National Institutes of Natural Sciences (NINS)/ ; }, mesh = {South Africa ; *Bacteria/isolation &amp; purification/classification ; Geologic Sediments/microbiology ; Minerals/analysis/metabolism ; Clay/chemistry ; Soil Microbiology ; }, abstract = {Recent advances in subsurface microbiology have demonstrated the habitability of multi-million-year-old igneous rocks, despite the scarce energy supply from rock-water interactions. Given the minimal evolution coupled with exceedingly slow metabolic rates in subsurface ecosystems, spatiotemporally stable igneous rocks can sustain microbes over geological time scales. This study investigated a 2-billion-year-old mafic rock in the Bushveld Igneous Complex, South Africa, where ultradeep drilling is being executed by the International Continental Scientific Drilling Program (ICDP). New procedures were successfully developed to simultaneously detect indigenous and contaminant microbial cells in a drill core sample. Precision rock sectioning coupled with infrared, fluorescence, and electron microscopy imaging of the rock section with submicron resolution revealed microbial colonization in veins filled with clay minerals. The entry and exit of microbial cells in the veins are severely limited by tight packing with clay minerals, the formation of which supplies energy sources for long-term habitability. Further microbiological characterization of drilled rock cores from the Bushveld Igneous Complex will expand the understanding of microbial evolution in deep igneous rocks over 2 billion years.}, }
@article {pmid39354152, year = {2024}, author = {Freire-Zapata, V and Holland-Moritz, H and Cronin, DR and Aroney, S and Smith, DA and Wilson, RM and Ernakovich, JG and Woodcroft, BJ and Bagby, SC and ,  and ,  and Rich, VI and Sullivan, MB and Stegen, JC and Tfaily, MM}, title = {Microbiome-metabolite linkages drive greenhouse gas dynamics over a permafrost thaw gradient.}, journal = {Nature microbiology}, volume = {9}, number = {11}, pages = {2892-2908}, pmid = {39354152}, issn = {2058-5276}, support = {DE-SC0021349//DOE | SC | Biological and Environmental Research (BER)/ ; 2022070//NSF | Directorate for Biological Sciences (BIO)/ ; }, mesh = {*Permafrost/microbiology ; *Greenhouse Gases/metabolism/analysis ; *Microbiota ; *Methane/metabolism ; *Metagenomics ; *Carbon Dioxide/metabolism ; *Bacteria/metabolism/genetics/classification ; Sweden ; Ecosystem ; Soil Microbiology ; }, abstract = {Interactions between microbiomes and metabolites play crucial roles in the environment, yet how these interactions drive greenhouse gas emissions during ecosystem changes remains unclear. Here we analysed microbial and metabolite composition across a permafrost thaw gradient in Stordalen Mire, Sweden, using paired genome-resolved metagenomics and high-resolution Fourier transform ion cyclotron resonance mass spectrometry guided by principles from community assembly theory to test whether microorganisms and metabolites show concordant responses to changing drivers. Our analysis revealed divergence between the inferred microbial versus metabolite assembly processes, suggesting distinct responses to the same selective pressures. This contradicts common assumptions in trait-based microbial models and highlights the limitations of measuring microbial community-level data alone. Furthermore, feature-scale analysis revealed connections between microbial taxa, metabolites and observed CO2 and CH4 porewater variations. Our study showcases insights gained by using feature-level data and microorganism-metabolite interactions to better understand metabolic processes that drive greenhouse gas emissions during ecosystem changes.}, }
@article {pmid39350412, year = {2024}, author = {Khan, A and Abass, S and Nizami, SAI and Shariq, M and Zahiruddin, S and Parveen, B and Parveen, R}, title = {The Gut Health Revolution: Herbs and Dietary Phytochemicals in Balancing Gut Microbiota for Optimal Human Health.}, journal = {Current pharmaceutical biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.2174/0113892010313921240923125946}, pmid = {39350412}, issn = {1873-4316}, abstract = {The gut microbiota is a varied population of microorganisms that live in the human gastrointestinal system. Emerging research emphasizes the importance of this microbial ecology in general health and its influence on a variety of disorders. The review explores the synergy between herbal treatment and traditional medicine, emphasizing their cultural significance and therapeutic benefits. It delves into the intricate relationship between herbal remedies, traditional healing practices, and their sustained usage over centuries. The review highlights the pivotal role of the gut microbiota in herbal medicine, elucidating how treatments influence the gastrointestinal microorganisms, impacting overall health. Dietary phytochemicals are underscored for their significance in herbal medicine and nutritional well-being, along with the interdependence of plant extracts and botanicals. The investigation explores the molecular connections between phytoconstituents and gut microbiota, aiming to deepen the understanding of herbal medicine's tailored approach to specific health challenges. The summary concludes by emphasizing herbal treatments' unique ability to regulate gut flora, contributing to overall gastrointestinal wellbeing. In closing, the review provides a concise overview, serving as a valuable resource for integrative medicine research, with recommendations for future exploration of herbal medicine's potential in healthcare.}, }
@article {pmid39349736, year = {2024}, author = {Karačić, S and Suarez, C and Hagelia, P and Persson, F and Modin, O and Martins, PD and Wilén, BM}, title = {Microbial acidification by N, S, Fe and Mn oxidation as a key mechanism for deterioration of subsea tunnel sprayed concrete.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {22742}, pmid = {39349736}, issn = {2045-2322}, mesh = {*Oxidation-Reduction ; *Manganese/metabolism ; *Iron/metabolism ; *Construction Materials/microbiology ; Corrosion ; *Biofilms/growth &amp; development ; Nitrogen/metabolism ; Sulfur/metabolism ; Steel/chemistry ; Bacteria/metabolism/genetics ; Hydrogen-Ion Concentration ; }, abstract = {The deterioration of fibre-reinforced sprayed concrete was studied in the Oslofjord subsea tunnel (Norway). At sites with intrusion of saline groundwater resulting in biofilm growth, the concrete exhibited significant concrete deterioration and steel fibre corrosion. Using amplicon sequencing and shotgun metagenomics, the microbial taxa and surveyed potential microbial mechanisms of concrete degradation at two sites over five years were identified. The concrete beneath the biofilm was investigated with polarised light microscopy, scanning electron microscopy and X-ray diffraction. The oxic environment in the tunnel favoured aerobic oxidation processes in nitrogen, sulfur and metal biogeochemical cycling as evidenced by large abundances of metagenome-assembled genomes (MAGs) with potential for oxidation of nitrogen, sulfur, manganese and iron, observed mild acidification of the concrete, and the presence of manganese- and iron oxides. These results suggest that autotrophic microbial populations involved in the cycling of several elements contributed to the corrosion of steel fibres and acidification causing concrete deterioration.}, }
@article {pmid39349195, year = {2024}, author = {Cheng, X and Zhao, R and Bodelier, PLE and Song, Y and Yang, K and Tuovinen, OH and Wang, H}, title = {Differential response of subterranean microbiome to exogenous organic matter input in a cave ecosystem.}, journal = {The Science of the total environment}, volume = {954}, number = {}, pages = {176584}, doi = {10.1016/j.scitotenv.2024.176584}, pmid = {39349195}, issn = {1879-1026}, mesh = {*Microbiota ; *Caves/microbiology ; Soil Microbiology ; Bacteria/metabolism ; Fungi ; Ecosystem ; Climate Change ; }, abstract = {As a recurrent climatic phenomenon in the context of climate change, extreme rainstorms induce vertical translocation of organic matter and increase moisture content in terrestrial ecosystems. However, it remains unclear whether heavy rainstorms can impact microbial communities in the deep biosphere by modulating organic matter input. In this study, we present findings on the different responses of bacterial and fungal communities in a subsurface cave to rainstorms and moisture variations through field surveys and microcosm experiments. During periods of rainstorms, the influx of dissolved organic matter (DOM) from soil overlying the cave into cave sediments significantly enhanced the correlation between core bacteria and environmental factors, particularly fluorescence spectral indices. The resource utilization of core bacteria was diminished, while the functional diversity of core fungi remained relatively unaltered. We also performed simulated experiments with restricted external DOM inputs, in which DOM content was observed to decrease and microbial diversity increase in response to artificially increased moisture content (MC). The niche breadth of core bacteria decreased and became more closely associated with DOM as the MC increased, while the niche breadth of core fungi remained predominantly unchanged. Compared to fungi, cave bacteria exhibited higher sensitivity towards variations in DOM. The core microbiome can efficiently utilize the available organic matter and participate in nitrogen- and sulfur-related metabolic processes. The study systematically revealed distinct microbial responses to rainstorm events, thereby providing valuable insights for future investigations into energy utilization within deep biospheres.}, }
@article {pmid39349071, year = {2024}, author = {Toporowska, M and Żebracki, K and Mazur, A and Mazur-Marzec, H and Šulčius, S and Alzbutas, G and Lukashevich, V and Dziga, D and Mieczan, T}, title = {Biodegradation of microcystins by microbiota of duckweed Spirodelapolyrhiza.}, journal = {Chemosphere}, volume = {366}, number = {}, pages = {143436}, doi = {10.1016/j.chemosphere.2024.143436}, pmid = {39349071}, issn = {1879-1298}, mesh = {*Microcystins/metabolism ; *Biodegradation, Environmental ; *Microbiota ; *Araceae/metabolism ; Tandem Mass Spectrometry ; Cyanobacteria/metabolism/genetics ; Bacteria/metabolism/genetics/classification ; }, abstract = {Cyanobacteria-produced allelochemicals, including hepatotoxic microcystins (MCs), exert an inhibitory effect on macrophyte growth. However, the role of macrophyte-associated bacteria and algae (macrophyte microbiota) in mitigating these immediate negative effects of cyanotoxins remains poorly understood. In this paper, we analyzed the biodegradation of microcystin-RR, MC-LR, and MC-LF by microbiota of the macrophyte Spirodela polyrhiza. The biodegradation of two MC variants was observed and LC-MS/MS analysis allowed identifying the degradation products of MC-RR (m/z 1011, 984, 969, 877, 862, 820, and 615) and MC-LR (m/z 968 and 953), including eight previously unreported products. No degradation products of MC-LF were detected, suggesting its stability and resistance under experimental conditions. NGS-based profiling of microbial consortia revealed no major differences in bacterial community composition across experimental treatments. Taxa previously reported as capable of MC degradation have been found in S. polyrhiza microbiota. Furthermore, the presence of genes encoding putative microcystinase homologues and the formation of new linear intermediates suggest a biochemical pathway that is similar, but not identical to previously reported. The ability of aquatic plant microbiota to biodegrade MCs holds environmental significance, and further studies in this field are required.}, }
@article {pmid39348267, year = {2024}, author = {Clegg, T and Pawar, S}, title = {Variation in thermal physiology can drive the temperature-dependence of microbial community richness.}, journal = {eLife}, volume = {13}, number = {}, pages = {}, pmid = {39348267}, issn = {2050-084X}, support = {NERC QMEE Centre for Doctoral Training NE/P012345/1//Natural Environment Research Council/ ; RF-2020-653\2//Leverhulme Trust/ ; NE/M020843/1//NERC Natural Environment Research Council/ ; NE/S000348/1//NERC Natural Environment Research Council/ ; }, mesh = {*Temperature ; *Microbiota/physiology ; Bacteria/classification/genetics/metabolism ; Biodiversity ; Bacterial Physiological Phenomena ; }, abstract = {Predicting how species diversity changes along environmental gradients is an enduring problem in ecology. In microbes, current theories tend to invoke energy availability and enzyme kinetics as the main drivers of temperature-richness relationships. Here, we derive a general empirically-grounded theory that can explain this phenomenon by linking microbial species richness in competitive communities to variation in the temperature-dependence of their interaction and growth rates. Specifically, the shape of the microbial community temperature-richness relationship depends on how rapidly the strength of effective competition between species pairs changes with temperature relative to the variance of their growth rates. Furthermore, it predicts that a thermal specialist-generalist tradeoff in growth rates alters coexistence by shifting this balance, causing richness to peak at relatively higher temperatures. Finally, we show that the observed patterns of variation in thermal performance curves of metabolic traits across extant bacterial taxa is indeed sufficient to generate the variety of community-level temperature-richness responses observed in the real world. Our results provide a new and general mechanism that can help explain temperature-diversity gradients in microbial communities, and provide a quantitative framework for interlinking variation in the thermal physiology of microbial species to their community-level diversity.}, }
@article {pmid39346682, year = {2024}, author = {Child, HT and Wierzbicki, L and Joslin, GR and Tennant, RK}, title = {Comparative evaluation of soil DNA extraction kits for long read metagenomic sequencing.}, journal = {Access microbiology}, volume = {6}, number = {9}, pages = {}, pmid = {39346682}, issn = {2516-8290}, abstract = {Metagenomics has been transformative in our understanding of the diversity and function of soil microbial communities. Applying long read sequencing to whole genome shotgun metagenomics has the potential to revolutionise soil microbial ecology through improved taxonomic classification, functional characterisation and metagenome assembly. However, optimisation of robust methods for long read metagenomics of environmental samples remains undeveloped. In this study, Oxford Nanopore sequencing using samples from five commercially available soil DNA extraction kits was compared across four soil types, in order to optimise read length and reproducibility for comparative long read soil metagenomics. Average extracted DNA lengths varied considerably between kits, but longer DNA fragments did not translate consistently into read lengths. Highly variable decreases in the length of resulting reads from some kits were associated with poor classification rate and low reproducibility in microbial communities identified between technical repeats. Replicate samples from other kits showed more consistent conversion of extracted DNA fragment size into read length and resulted in more congruous microbial community representation. Furthermore, extraction kits showed significant differences in the community representation and structure they identified across all soil types. Overall, the QIAGEN DNeasy PowerSoil Pro Kit displayed the best suitability for reproducible long-read WGS metagenomic sequencing, although further optimisation of DNA purification and library preparation may enable translation of higher molecular weight DNA from other kits into longer read lengths. These findings provide a novel insight into the importance of optimising DNA extraction for achieving replicable results from long read metagenomic sequencing of environmental samples.}, }
@article {pmid39346007, year = {2024}, author = {Eisenhofer, R and Alberdi, A and Woodcroft, BJ}, title = {Quantifying microbial DNA in metagenomes improves microbial trait estimation.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae111}, pmid = {39346007}, issn = {2730-6151}, abstract = {Shotgun metagenomics is a powerful tool for studying the genomic traits of microbial community members, such as genome size, gene content, etc. While such traits can be used to better understand the ecology and evolution of microbial communities, the accuracy of their estimations can be critically influenced by both known and unknown factors. One factor that can bias trait estimations is the proportion of eukaryotic and viral DNA in a metagenome, as some bioinformatic tools assume that all DNA reads in a metagenome are bacterial or archaeal. Here, we add to a recent debate about the influence of eukaryotic DNA in the estimation of average genome size from a global soil sample dataset using a new bioinformatic tool. Contrary to what was assumed, our reanalysis of this dataset revealed that soil samples can contain a substantial proportion of non-microbial DNA, which severely inflated the original estimates of average genome size. Correcting for this bias significantly improves the statistical support for the negative relationship between average bacterial genome size and soil pH. These results highlight that metagenomes can contain large quantities of non-microbial DNA and that new methods that correct for this can improve microbial trait estimation.}, }
@article {pmid39340684, year = {2024}, author = {Vinothini, K and Nakkeeran, S and Saranya, N and Jothi, P and Richard, JI and Perveen, K and Bukhari, NA and Glick, BR and Sayyed, RZ and Mastinu, A}, title = {Rhizosphere Engineering of Biocontrol Agents Enriches Soil Microbial Diversity and Effectively Controls Root-Knot Nematodes.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {120}, pmid = {39340684}, issn = {1432-184X}, mesh = {Animals ; *Solanum lycopersicum/microbiology/parasitology ; *Soil Microbiology ; *Rhizosphere ; *Bacillus/genetics/physiology ; *Plant Roots/microbiology/parasitology ; *Pest Control, Biological ; Plant Diseases/parasitology/prevention &amp; control/microbiology ; Trichoderma/physiology/genetics ; Tylenchoidea/physiology ; Microbiota ; Antinematodal Agents/pharmacology ; Biological Control Agents/pharmacology ; Bacteria/genetics/classification ; }, abstract = {The root-knot nematode (RKN) causes significant yield loss in tomatoes. Understanding the interaction of biocontrol agents (BCAs)-nematicides-soil microbiomes and RKNs is essential for enhancing the efficacy of biocontrol agents and nematicides to curb RKN damage to crops. The present study aimed to evaluate the in vitro effectiveness of BACa and nematicide against RKN and to apply the amplicon sequencing to assess the interaction of Bacillus velezensis (VB7) and Trichoderma koningiopsis (TK) against RKNs. Metagenomic analysis revealed the relative abundance of three phyla such as Proteobacteria (42.16%), Firmicutes (19.57%), and Actinobacteria (17.69%) in tomato rhizospheres. Those tomato rhizospheres treated with the combined application of B. velezensis VB7 + T. koningiopsis TK and RKN had a greater frequency of diversity and richness than the control. RKN-infested tomato rhizosphere drenched with bacterial and fungal antagonists had the maximum diversity index of bacterial communities. A strong correlation with a maximum number of interconnection edges in the phyla Proteobacteria, Firmicutes, and Actinobacteria was evident in soils treated with both B. velezensis VB7 and T. koningiopsis TK challenged against RKN in infected soil. The present study determined a much greater diversity of bacterial taxa observed in tomato rhizosphere soils treated with B. velezensis VB7 and T. koningiopsis TK than in untreated soil. It is suggested that the increased diversity and abundance of bacterial communities might be responsible for increased nematicidal properties in tomato plants. Hence, the combined applications of B. velezensis VB7 and T. koningiopsis TK can enhance the nematicidal action to curb RKN infecting tomatoes.}, }
@article {pmid39340560, year = {2024}, author = {Charalampous, G and Kormas, KA and Antoniou, E and Kalogerakis, N and Gontikaki, E}, title = {Distinct Communities of Bacteria and Unicellular Eukaryotes in the Different Water Masses of Cretan Passage Water Column (Eastern Mediterranean Sea).}, journal = {Current microbiology}, volume = {81}, number = {11}, pages = {381}, pmid = {39340560}, issn = {1432-0991}, support = {1874//Hellenic Foundation for Research and Innovation/ ; 1510//Hellenic Foundation for Research and Innovation/ ; }, mesh = {Mediterranean Sea ; *Bacteria/classification/genetics/isolation &amp; purification ; *Eukaryota/classification/genetics/isolation &amp; purification ; *Seawater/microbiology ; *Microbiota ; *RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; Phylogeny ; Ecosystem ; }, abstract = {Elucidating marine microbiota diversity and dynamics holds significant importance due to their role in maintaining vital ecosystem functions and services including climate regulation. This work aims to contribute in the understanding of microbial ecology and networking in one of the world's most understudied marine regions, the Eastern Mediterranean Sea. High-throughput 16S and 18S rRNA gene sequencing analysis was applied to study the diversity of bacteria and unicellular eukaryotes in the different water masses of the Cretan Passage during two seasonally-different sampling expeditions. We assumed that microbial associations differ between the surface and deepwater masses and created co-occurrence networks to evaluate this hypothesis. Our results unveiled vertical variations in both bacterial and unicellular eukaryotic diversity with species fluctuations indicative of seasonality being recorded in the surface water mass. Heterotrophic taxa and grazers related to organic matter degradation and nutrient cycling were enriched in the deepest water layers. Moreover, surface waters presented a higher number of microbial associations indicating abundant ecological niches compared to the deepest layer, possibly related to the lack of bottom-up resources in the oligotrophic deep ocean. Overall, our data provide insight in a heavily stressed, yet underexplored, marine area that requires further research to unravel the ecological roles of marine microbes. To our knowledge, this is the first study that combines molecular biology tools to provide data on both planktic prokaryotes and unicellular eukaryotes across the different water masses in this marine region of the Eastern Mediterranean basin.}, }
@article {pmid39340556, year = {2024}, author = {Fernandez de Landa, G and Alberoni, D and Braglia, C and Baffoni, L and Fernandez de Landa, M and Revainera, PD and Quintana, S and Zumpano, F and Maggi, MD and Di Gioia, D}, title = {The Gut Microbiome of Two Wild Bumble Bee Species Native of South America: Bombus pauloensis and Bombus bellicosus.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {121}, pmid = {39340556}, issn = {1432-184X}, support = {777760//European Commission/ ; 777760//European Commission/ ; 777760//European Commission/ ; 777760//European Commission/ ; }, mesh = {Animals ; Bees/microbiology ; *Gastrointestinal Microbiome ; *Nosema/physiology/isolation &amp; purification/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; Biodiversity ; South America ; }, abstract = {South America is populated by a wide range of bumble bee species that represent an important source of biodiversity, supporting pollination services in natural and agricultural ecosystems. These pollinators provide unique specific microbial niches, populated by a wide number of microorganisms such as symbionts, environmental opportunistic bacteria, and pathogens. Recently, it was demonstrated how microbial populations are shaped by trophic resources and environmental conditions but also by anthropogenic pressure, which strongly affects microbes' functionality. This study is focused on the impact of different land uses (natural reserve, agroecosystem, and suburban) on the gut microbiome composition of two South American bumble bees, Bombus pauloensis and Bombus bellicosus. Gut microbial DNA extracted from collected bumble bees was sequenced on the Illumina MiSeq platform and correlated with land use. Nosema ceranae load was analyzed with qPCR and correlated with microbiome data. Significant differences in gut microbiome composition between the two wild bumble bee species were highlighted, with notable variations in α- and β-diversity across study sites. Bombus bellicosus showed a high abundance of Pseudomonas, a genus that includes environmental saprobes, and was found to be the second major taxa populating the gut microbiome, probably indicating the vulnerability of this host to environmental pollution. Pathogen analysis unveils a high prevalence of N. ceranae, with B. bellicosus showing higher susceptibility. Finally, Gilliamella exhibited a negative correlation with N. ceranae, suggesting a potential protective role of this commensal taxon. Our findings underscore the importance of considering microbial dynamics in pollinator conservation strategies, highlighting potential interactions between gut bacteria and pathogens in shaping bumble bee health.}, }
@article {pmid39340548, year = {2024}, author = {Radouane, N and Errafii, K and Mouhib, S and Mhand, KA and Legeay, J and Hijri, M}, title = {Potential Plant-To-Plant Transmission: Shared Endophytic Bacterial Community Between Ziziphus lotus and Its Parasite Cuscuta epithymum.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {119}, pmid = {39340548}, issn = {1432-184X}, support = {Projects AS-77 and AS-85//OCP Group/ ; }, mesh = {*Cuscuta/physiology/microbiology/genetics ; *Ziziphus/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Endophytes/genetics/physiology/classification/isolation &amp; purification ; *Bacteria/genetics/classification/isolation &amp; purification ; Host-Parasite Interactions ; DNA, Bacterial/genetics ; }, abstract = {Microbiota associated with host-parasite relationships offer an opportunity to explore interactions among plants, parasites, and microbes, thereby contributing to the overall complexity of community structures. The dynamics of ecological interactions between parasitic plants and their hosts in arid environments remain largely understudied, especially in Africa. This study aimed to examine the bacterial communities of Cuscuta epithymum L. (clover dodder), an epiphytic parasitic plant, and its host, Ziziphus lotus L. (jujuba), in an arid environment. Our goal was to uncover the ecological complexities of microbial communities within the framework of plant-plant interactions. We conducted a comprehensive analysis of the bacterial composition and diversity within populations of the C. epithymum parasite, the infected- and non-infected jujuba host, and their interface at the shoots of the host. This involved amplicon sequencing, targeting the V5-V6 regions of the 16S rRNA gene. A total of 5680 amplicon sequence variants (ASVs) were identified, with Pseudomonadota, Bacillota, and Actinobacteriota being prevalent phyla. Among the bacterial communities, three genera were dominant: Cutibacterium, Staphylococcus, and Acinetobacter. Interestingly, analyses of alpha-diversity (p = 0.3 for Shannon index and p = 0.5 for Simplon index) and beta-diversity (PERMANOVA, with p-values of 0.6 and 0.3) revealed no significant differences between Cuscuta-infected and non-infected jujube shrubs, suggesting a shared shoot endophytic bacteriome. This finding advances our comprehension of microbial communities linked to plant-parasite interactions in the arid environments of Africa. Further research on various hosts is required to confirm plant-to-plant bacterial transmission through Cuscuta infection. Additionally, studies on functional diversity, cytology, ecophysiology and the mechanisms by which bacterial communities transferred between host and parasite are necessary.}, }
@article {pmid39338505, year = {2024}, author = {Shah, H and Trivedi, M and Gurjar, T and Sahoo, DK and Jergens, AE and Yadav, VK and Patel, A and Pandya, P}, title = {Decoding the Gut Microbiome in Companion Animals: Impacts and Innovations.}, journal = {Microorganisms}, volume = {12}, number = {9}, pages = {}, pmid = {39338505}, issn = {2076-2607}, abstract = {The changing notion of "companion animals" and their increasing global status as family members underscores the dynamic interaction between gut microbiota and host health. This review provides a comprehensive understanding of the intricate microbial ecology within companion animals required to maintain overall health and prevent disease. Exploration of specific diseases and syndromes linked to gut microbiome alterations (dysbiosis), such as inflammatory bowel disease, obesity, and neurological conditions like epilepsy, are highlighted. In addition, this review provides an analysis of the various factors that impact the abundance of the gut microbiome like age, breed, habitual diet, and microbe-targeted interventions, such as probiotics. Detection methods including PCR-based algorithms, fluorescence in situ hybridisation, and 16S rRNA gene sequencing are reviewed, along with their limitations and the need for future advancements. Prospects for longitudinal investigations, functional dynamics exploration, and accurate identification of microbial signatures associated with specific health problems offer promising directions for future research. In summary, it is an attempt to provide a deeper insight into the orchestration of multiple microbial species shaping the health of companion animals and possible species-specific differences.}, }
@article {pmid39338496, year = {2024}, author = {Denux, M and Armenteros, M and Weber, L and Miller, CA and Sántha, K and Apprill, A}, title = {Coral Reef Water Microbial Communities of Jardines de la Reina, Cuba.}, journal = {Microorganisms}, volume = {12}, number = {9}, pages = {}, pmid = {39338496}, issn = {2076-2607}, abstract = {Globally, coral reef ecosystems are undergoing significant change related to climate change and anthropogenic activities. Yet, the Cuban archipelago of Jardines de la Reina (JR) has experienced fewer stressors due to its geographical remoteness and high level of conservation. This study examines the surface and benthic reef water microbial communities associated with 32 reef sites along the JR archipelago and explores the relationship between the community composition of reef microorganisms examined using bacterial and archaeal small subunit ribosomal RNA gene (16S rRNA gene) sequencing compared to geographic, conservation/protection level, environmental, physicochemical, and reef benthic and pelagic community features. Reef nutrient concentrations were low and microbial communities dominated by picocyanobacteria and SAR11 and SAR86 clade bacteria, characteristic of an oligotrophic system. Reef water microbial community alpha and beta diversity both varied throughout the archipelago and were strongly related to geography. Three sites in the western archipelago showed unique microbial communities, which may be related to the hydrogeography and influences of the channels linking the Ana Maria gulf with the Caribbean Sea. Overall, this work provides the first extensive description of the reef microbial ecology of the Caribbean's 'Crown Jewel' reef system and a framework to evaluate the influence of ongoing stressors on the reef microorganisms.}, }
@article {pmid39338466, year = {2024}, author = {Lauzon, J and Caron, D and Lazar, CS}, title = {The Saint-Leonard Urban Glaciotectonic Cave Harbors Rich and Diverse Planktonic and Sedimentary Microbial Communities.}, journal = {Microorganisms}, volume = {12}, number = {9}, pages = {}, pmid = {39338466}, issn = {2076-2607}, support = {RGPIN-2019-06670//Natural Sciences and Engineering Research Council/ ; }, abstract = {The terrestrial subsurface harbors unique microbial communities that play important biogeochemical roles and allow for studying a yet unknown fraction of the Earth's biodiversity. The Saint-Leonard cave in Montreal City (Canada) is of glaciotectonic origin. Its speleogenesis traces back to the withdrawal of the Laurentide Ice Sheet 13,000 years ago, during which the moving glacier dislocated the sedimentary rock layers. Our study is the first to investigate the microbial communities of the Saint-Leonard cave. By using amplicon sequencing, we analyzed the taxonomic diversity and composition of bacterial, archaeal and eukaryote communities living in the groundwater (0.1 µm- and 0.2 µm-filtered water), in the sediments and in surface soils. We identified a microbial biodiversity typical of cave ecosystems. Communities were mainly shaped by habitat type and harbored taxa associated with a wide variety of lifestyles and metabolic capacities. Although we found evidence of a geochemical connection between the above soils and the cave's galleries, our results suggest that the community assembly dynamics are driven by habitat selection rather than dispersal. Furthermore, we found that the cave's groundwater, in addition to being generally richer in microbial taxa than sediments, contained a considerable diversity of ultra-small bacteria and archaea.}, }
@article {pmid39338465, year = {2024}, author = {Cruz, LG and Shen, FT and Chen, CP and Chen, WC}, title = {Dose Effect of Polyethylene Microplastics Derived from Commercial Resins on Soil Properties, Bacterial Communities, and Enzymatic Activity.}, journal = {Microorganisms}, volume = {12}, number = {9}, pages = {}, pmid = {39338465}, issn = {2076-2607}, support = {MOST 110-2313-B-005-015-//National Science and Technology Council/ ; }, abstract = {Soils are the largest reservoir of microplastics (MPs) on earth. Since MPs can remain in soils for a very long time, their effects are magnified. In this study, different concentrations of polyethylene (PE) MPs derived from commercial resins (0%, 1%, 7%, and 14%, represented as MP_0, MP_1, MP_7, and MP_14) were added to soils to assess the changes in the soils' chemical properties, enzyme activities, and bacterial communities during a 70-day incubation period. The results show that PE MP treatments with low concentrations differed from other treatments in terms of exchangeable Ca and Mg, whereas at high concentrations, the pH and availability of phosphate ions differed. Fluorescein diacetate (FDA), acid phosphatase (ACP), and N-acetyl-β-d-glucosaminidase (NAG) enzyme activities exhibited a dose-related trend with the addition of the PE MPs; however, the average FDA and ACP activities were significantly affected only by MP_14. Changes in the microbial communities were observed at both the phylum and family levels with all PE MP treatments. It was revealed that even a low dosage of PE MPs in soils can affect the functional microbes, and a greater impact is observed on those that can survive in polluted environments with limited resources.}, }
@article {pmid39338425, year = {2024}, author = {Lyu, G and Hu, J and Ma, J}, title = {Variation in Bacterial and Fungal Communities in Soils from Three Major Apple Pear (Pyrus bretschneideri Rehd.) Orchards.}, journal = {Microorganisms}, volume = {12}, number = {9}, pages = {}, pmid = {39338425}, issn = {2076-2607}, support = {41571304//National Natural Science Foundation of China/ ; }, abstract = {Microbial communities are closely related to the overall health and quality of soil, but studies on microbial ecology in apple pear orchard soils are limited. In the current study, 28 soil samples were collected from three apple pear orchards, and the composition and structure of fungal and bacterial communities were investigated by high-throughput sequencing. The molecular ecological network showed that the keystone taxa of bacterial communities were Actinobacteria, Proteobacteria, Gemmatimonadetes, Acidobacteria, Nitrospirae, and Chloroflexi, and the keystone taxon of fungal communities was Ascomycota. Mantel tests showed that soil texture and pH were important factors shaping soil bacterial and fungal communities, and soil water soluble organic carbon (WSOC) and nitrate nitrogen (NO3[-]-N) were also closely related to soil bacterial communities. Canonical correspondence analysis (CCA) and variation partition analysis (VPA) revealed that geographic distance, soil texture, pH, and other soil properties could explain 10.55%, 13.5%, and 19.03% of the overall variation in bacterial communities, and 11.61%, 13.03%, and 20.26% of the overall variation in fungal communities, respectively. The keystone taxa of bacterial and fungal communities in apple pear orchard soils and their strong correlation with soil properties could provide useful clues toward sustainable management of orchards.}, }
@article {pmid39338386, year = {2024}, author = {Galinytė, D and Bernatoniene, J and Žilius, M and Rysevaitė-Kyguolienė, K and Savickas, A and Karosienė, J and Briedis, V and Pauža, DH and Savickienė, N}, title = {In Vitro Study of Cyano-Phycocyanin Release from Hydrogels and Ex Vivo Study of Skin Penetration.}, journal = {Pharmaceuticals (Basel, Switzerland)}, volume = {17}, number = {9}, pages = {}, pmid = {39338386}, issn = {1424-8247}, abstract = {BACKGROUND: This study explored the most suitable materials for incorporating cyano-phycocyanin (C-PC) into hydrogels, focusing on maintaining the C-PC's long-term structural integrity and stabilityNext, the release of C-PC from the hydrogels and its skin penetration were investigated.<br><br>METHODS: A series of 1% (w/w) C-PC hydrogels was prepared using various gelling agents and preservatives. Spectrophotometric measurements compared the amount of C-PC in the hydrogels to the initially added amount. After selecting the most suitable gelling agent and preservative, two C-PC hydrogels, with and without propylene glycol (PG) (Sigma-Aldrich, St. Louis, MO, USA), were produced for further testing. In vitro release studies utilized modified Franz-type diffusion cells, while ex vivo skin-permeation studies employed Bronaugh-type cells and human skin. Confocal laser scanning microscopy analyzed C-PC accumulation in the skin.<br><br>RESULTS: The findings demonstrated that sodium alginate (Sigma-Aldrich, St. Louis, MO, USA), hydroxyethyl cellulose (HEC) (Sigma-Aldrich, St. Louis, MO, USA), and Soligel[TM] (Givaudan, Vernier, Switzerland) are effective biopolymers for formulating hydrogels while maintaining C-PC stability. After 6 h, C-PC release from the hydrogel containing PG was approximately 10% or 728.07 (&#xb1;19.35) &#x3bc;g/cm[2], significantly higher than the nearly 7% or 531.44 (&#xb1;26.81) &#x3bc;g/cm[2] release from the hydrogel without PG (p < 0.05). The ex vivo qualitative skin-permeation study indicated that PG enhances C-PC penetration into the outermost skin layer.<br><br>CONCLUSION: PG's ability to enhance the release of C-PC from the hydrogel, coupled with its capacity to modify the skin barrier ex vivo, facilitates the penetration of C-PC into the stratum corneum.}, }
@article {pmid39335049, year = {2024}, author = {Afonso, L and Grzegorczyk, KG and Salomão, JM and Basso, KR and Alves, LC and Silva, MCD and Chryssafidis, AL and Gionco-Cano, B and Yamada-Ogatta, SF and Andrade, G}, title = {Fluopsin C Promotes Biofilm Removal of XDR Acinetobacter baumannii and Presents an Additive Effect with Polymyxin B on Planktonic Cells.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {9}, pages = {}, pmid = {39335049}, issn = {2079-6382}, support = {439754/2018-6//National Council for Scientific and Technological Development/ ; 406016/2022-4//National Council for Scientific and Technological Development/ ; }, abstract = {Acinetobacter baumannii emerged as one of the most important pathogens for the development of new antimicrobials due to the worldwide detection of isolates resistant to all commercial antibiotics, especially in nosocomial infections. Biofilm formation enhances A. baumannii survival by impairing antimicrobial action, being an important target for new antimicrobials. Fluopsin C (FlpC) is an organocupric secondary metabolite with broad-spectrum antimicrobial activity. This study aimed to evaluate the antibiofilm activity of FlpC in established biofilms of extensively drug-resistant A. baumannii (XDRAb) and the effects of its combination with polymyxin B (PolB) on planktonic cells. XDRAb susceptibility profiles were determined by Vitek 2 Compact, disk diffusion, and broth microdilution. FlpC and PolB interaction was assessed using the microdilution checkerboard method and time-kill kinetics. Biofilms of XDRAb characterization and removal by FlpC exposure were assessed by biomass staining with crystal violet. Confocal Laser Scanning Microscopy was used to determine the temporal removal of the biofilms using DAPI, and cell viability using live/dead staining. The minimum inhibitory concentration (MIC) of FlpC on XDRAb was 3.5 µg mL[-1]. Combining FlpC + PolB culminated in an additive effect, increasing bacterial susceptibility to both antibiotics. FlpC-treated 24 h biofilms reached a major biomass removal of 92.40 ± 3.38% (isolate 230) using 7.0 µg mL[-1] FlpC. Biomass removal occurred significantly over time through the dispersion of the extracellular matrix and decreasing cell number and viability. This is the first report of FlpC's activity on XDRAb and the compound showed a promissory response on planktonic and sessile cells, making it a candidate for the development of a new antimicrobial product.}, }
@article {pmid39332295, year = {2024}, author = {Tapia, N and Gallardo-Bustos, C and Rojas, C and Vargas, IT}, title = {Long-term evaluation of soil-based bioelectrochemical green roof systems for greywater treatment.}, journal = {Journal of environmental management}, volume = {370}, number = {}, pages = {122643}, doi = {10.1016/j.jenvman.2024.122643}, pmid = {39332295}, issn = {1095-8630}, mesh = {*Soil/chemistry ; *Bioelectric Energy Sources ; Water Purification/methods ; Waste Disposal, Fluid/methods ; Biological Oxygen Demand Analysis ; }, abstract = {Water scarcity has generated the need to identify new sources. Due to its low organic contaminant load, greywater reuse has emerged as a potential alternative. Moreover, the search for decentralized treatment systems in urban areas has prompted research on using green roofs for greywater treatment. However, the performance of organic matter removal is limited by the type of substrate and height of the growing media. Bioelectrochemical systems (BESs) improve treatment performance by providing an additional electron acceptor (the electrode). In this study, nine reactors under three different conditions, i.e., open circuit (OC), microbial fuel cell (MFC), and microbial electrolysis cell (MEC), were built to evaluate the treatment of synthetic greywater in a substrate-growing medium composed of perlite and coconut fiber and operated in batch-cycle mode for 397 days. The results suggested that using BESs enables greywater treatment and the removal of pollutants to levels that allow their reuse for irrigation. Furthermore, electrical conductivity was reduced from 732.4 ± 41.2 μS/cm[2] in OC to 637.32 ± 22.73 μS/cm[2] and 543.15 ± 19.69 μS/cm[2] in MEC and MFC, respectively. The soluble chemical oxygen demand in the latter treatments reached 76% removal, compared to levels above the OC, which only reached approximately 67%. Microbial community analysis revealed differences, mainly in the cathodes, showing a higher development of Flavobacterium, Azospirillum, and Zoogloea in MFCs, which could explain the higher levels of organic matter removal in the other conditions, suggesting that the BES could produce an enrichment of beneficial bacterial groups for treatment. Therefore, implementing BESs in green roofs enables sustainable long-term greywater treatment.}, }
@article {pmid39331293, year = {2024}, author = {Bianchelli, J and Sagua, MI and Quiroga, MP and Nuozzi, G and Fernández, J and Schiaffino, MR}, title = {Temporal dynamics of Legionella (Proteobacteria, Legionellaceae) in two Pampean shallow lakes from Argentina.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {49}, pages = {59058-59070}, pmid = {39331293}, issn = {1614-7499}, support = {PICT 0891-2017//Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; PICTO 00006-2019//Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; SIB 2053-2022//Universidad Nacional del Noroeste de la Provincia de Buenos Aires/ ; }, mesh = {Argentina ; *Lakes/microbiology ; *Legionella/genetics ; Water Microbiology ; Real-Time Polymerase Chain Reaction ; }, abstract = {Aquatic systems have traditionally played a key role in the development of human life, providing multiple ecosystem services to society and being a reservoir for a wide biodiversity of organisms. Among them, bacteria belonging to Legionella stand out, mainly because they are of great interest both in the field of microbial ecology and public health, since some of them turn out to be pathogenic for humans. The aim of this work was to study the monthly temporal dynamics of Legionella spp. and its relationship with the environmental variables measured in two Pampean shallow lakes (Gómez and Carpincho, Buenos Aires Province, Argentina). The analysis was carried out using a quantitative approach by real-time polymerase chain reaction (qPCR) and a non-quantitative approach using bacterial diversity data obtained by next-generation sequencing (NGS), using the Illumina MiSeq platform. Our results showed that the overall Legionella abundance was very high in the studied Pampean shallow lakes. Notably, fluctuations in dissolved organic carbon and temperature influenced the dynamics shifts in Legionella abundances. Correlation analyses between Legionella reads from NGS and copy numbers obtained through qPCR revealed positive relationships, unveiling distinctions attributable to the diverse sequence processing algorithms employed in the analysis of NGS data.}, }
@article {pmid39330355, year = {2024}, author = {Abbà, S and Valentini, B and Stefanini, I}, title = {Fungal Identifier (FId): An Updated Polymerase Chain Reaction-Restriction Fragment Length Polymorphism Approach to Ease Ascomycetous Yeast Isolates' Identification in Ecological Studies.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {10}, number = {9}, pages = {}, pmid = {39330355}, issn = {2309-608X}, support = {RGP0060/2021//HFSP/ ; 20225SXSHY//PRIN 2022/ ; }, abstract = {Culturomics has been temporarily exceeded by the advent of omics approaches such as metabarcoding and metagenomics. However, despite improving our knowledge of microbial population composition, both metabarcoding and metagenomics are not suitable for investigating and experimental testing inferences about microbial ecological roles and evolution. This leads to a recent revival of culturomics approaches, which should be supported by improvements in the available tools for high-throughput microbial identification. This study aimed to update the classical PCR-RFLP approach in light of the currently available knowledge on yeast genomics. We generated and analyzed a database including more than 1400 ascomycetous yeast species, each characterized by PCR-RFLP profiles obtained with 143 different endonucleases. The results allowed for the in silico evaluation of the performance of the tested endonucleases in the yeast species' identification and the generation of FId (Fungal Identifier), an online freely accessible tool for the identification of yeast species according to experimentally obtained PCR-RFLP profiles.}, }
@article {pmid39328926, year = {2024}, author = {Duque-Granda, D and Vivero-Gómez, RJ and Junca, H and Cadavid-Restrepo, G and Moreno-Herrera, CX}, title = {Interaction and effects of temperature preference under a controlled environment on the diversity and abundance of the microbiome in Lutzomyia longipalpis (Diptera: Psychodidae).}, journal = {Biotechnology reports (Amsterdam, Netherlands)}, volume = {44}, number = {}, pages = {e00857}, pmid = {39328926}, issn = {2215-017X}, abstract = {Characterization of the temperature effects on the abundance and richness of the microbiota of Lutzomyia longipalpis, insect vector of Leishmania infantum in America, is an aspect of pivotal importance to understand the interactions between temperature, bacteria, and Leishmania infection. We developed and used a customized device with a temperature gradient (21-34 °C) to assess the temperature preferences of wild females of Lu. longipalpis collected in a rural area (Ricaurte, Cundinamarca, Colombia). Each replicate consisted of 50 females exposed to the gradient for an hour. At the end of the exposure time, insects were collected and separated by the temperature ranges selected varying from 21 °C to 34 °C. They were organized in 17 pools from which total DNA extracts were obtained, and samples were subjected to 16S rRNA amplicon sequencing analyzes. The most abundant phyla across the different temperature ranges were Proteobacteria (17.22-90.73 %), Firmicutes (5.99-77.21 %) and Actinobacteria (1.56-59.85 %). Results also showed an abundance (30 % to 57.36 %) of Pseudomonas (mainly at temperatures of 21-29 °C and 34 °C) that decreased to 6.55 %-13.20 % at temperatures of 31-33 °C, while Bacillus increase its abundance to 67.24 % at 29-33 °C. Serratia also had a greater representation (49.79 %), specifically in sand flies recovered at 25-27 °C. No significant differences were found at α-diversity level when comparing richness using the Shannon-Wiener, Simpson, and Chao1 indices, while β-diversity differences were found using the Bray-Curtis index (F-value of 3.5073, p-value < 0.013, R-squared of 0,4889), especially in the groups of Lu. longipalpis associated at higher temperatures (29-33 °C). It was also possible to detect the presence of endosymbionts such as Spiroplasma and Arsenophonus in the range of 29-33 °C. Rickettsia was only detected in Lu. longipalpis sand flies recovered between 25-27 °C. It was possible to characterize Lu. longipalpis microbiota in response to intraspecific temperature preferences and observe changes in bacterial communities and endosymbionts at different ranges of said environmental variable, which may be important in its vector competence and environmental plasticity to adapt to new climate change scenarios.}, }
@article {pmid39327479, year = {2024}, author = {Tavaddod, S and Dawson, A and Allen, RJ}, title = {Bacterial aggregation triggered by low-level antibiotic-mediated lysis.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {90}, pmid = {39327479}, issn = {2055-5008}, support = {682237//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; BB/R012415/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; 390713860//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 682237//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Euratom (H2020 Euratom Research and Training Programme 2014-2018)/ ; 682237//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Euratom (H2020 Euratom Research and Training Programme 2014-2018)/ ; }, mesh = {*Anti-Bacterial Agents/pharmacology ; *Escherichia coli/drug effects/genetics ; *Bacteriolysis/drug effects ; Biofilms/drug effects/growth &amp; development ; Microbial Sensitivity Tests ; }, abstract = {Suspended bacterial aggregates play a central role in ocean biogeochemistry, industrial processes and probably many clinical infections - yet the factors that trigger aggregation remain poorly understood, as does the relationship between suspended aggregates and surface-attached biofilms. Here we show that very low doses of cell-wall targeting antibiotic, far below the minimal inhibitory concentration, can trigger aggregation of Escherichia coli cells. This occurs when a few cells lyse, releasing extracellular DNA - thus, cell-to-cell variability in antibiotic response leads to population-level aggregation. Although lysis-triggered aggregation echoes known trigger mechanisms for surface-attached biofilms, these aggregates may have different ecological implications since they do not show increased biofilm-forming potential or increased antibiotic resistance. Our work contributes to understanding the nature of bacterial aggregates and the factors that trigger their formation, and the possible consequences of widespread low-dose antibiotic exposure in the environment and in the body.}, }
@article {pmid39327101, year = {2024}, author = {Goldman, AD and Fournier, GP}, title = {The very early evolution of biological complexity.}, journal = {Trends in genetics : TIG}, volume = {40}, number = {11}, pages = {912-913}, doi = {10.1016/j.tig.2024.09.001}, pmid = {39327101}, issn = {0168-9525}, mesh = {*Biological Evolution ; Phylogeny ; Evolution, Molecular ; }, abstract = {All extant life is descended from a common ancestor, which, despite being very ancient, appears to have been a complex cellular organism. A new study by Moody et al. shows that this ancestor was not only a complex cell, but also lived within a microbial ecology likely inhabited by other complex cells.}, }
@article {pmid39326062, year = {2024}, author = {Sun, X and Favier, A and Folmar, J and Pyenson, NC and Sanchez, A and Rebolleda-Gómez, M}, title = {Metabolic Plasticity Shapes Microbial Communities across a Temperature Gradient.}, journal = {The American naturalist}, volume = {204}, number = {4}, pages = {381-399}, doi = {10.1086/731997}, pmid = {39326062}, issn = {1537-5323}, mesh = {*Temperature ; *Microbiota ; Bacteria/metabolism ; Fermentation ; Carbon/metabolism ; Ecosystem ; }, abstract = {AbstractA central challenge in community ecology is understanding and predicting the effects of abiotic factors on community assembly. In particular, microbial communities play a central role in the ecosystem, but we do not understand how changing factors like temperature are going to affect community composition or function. In this article, we studied the self-assembly of multiple communities in synthetic environments to understand changes in microbial community composition based on metabolic responses of different functional groups along a temperature gradient. In many microbial communities, different microbial functional groups coexist through the partitioning of carbon sources in an emergent trophic structure (cross-feeding). In this system, respirofermentative bacteria display a preference for the sugars supplied as the only carbon source but secrete secondary carbon sources (organic acids) that are more efficiently consumed by obligate respirators. As a consequence of this trophic structure, the metabolic plasticity of the respirofermenters has downstream consequences for the relative abundance of respirators across temperatures. We found that the effects of different temperatures on microbial composition can largely be described by an increase in fermentation by-products with increasing temperatures from the respirofermentative bacteria. This research highlights the importance of metabolic plasticity and metabolic trade-offs in predicting species interactions and community dynamics across abiotic gradients.}, }
@article {pmid39321934, year = {2024}, author = {Liu, YC and Ramiro-Garcia, J and O'Connor, S and Paulo, LM and Maria Braguglia, C and Cristina Gagliano, M and O'Flaherty, V}, title = {Microbial community response to temperature reduction during anaerobic treatment of long chain fatty acids-containing wastewater.}, journal = {Bioresource technology}, volume = {413}, number = {}, pages = {131529}, doi = {10.1016/j.biortech.2024.131529}, pmid = {39321934}, issn = {1873-2976}, mesh = {*Wastewater/microbiology/chemistry ; Anaerobiosis ; *Fatty Acids/metabolism ; *Bioreactors ; *Temperature ; Bacteria/metabolism ; Water Purification/methods ; Biomass ; Microbiota/physiology ; }, abstract = {Acclimating mesophilic biomass to low temperatures have been used to start-up psychrophilic anaerobic reactors, but limited microbial information is available during the acclimation. To investigate microbial responses to temperature reductions, duplicate lab-scale anaerobic digestion (AD) reactors were operated for 166 days, with the temperature being reduced from 37°C to 15°C, using synthetic long chain fatty acid (LCFA)-containing wastewater as the feedstock. The acclimated biomass at 15°C exhibited efficient removal of organic matter (total COD>75%, soluble COD>88%, and LCFA>99%). Temperature reductions lead to significant reductions in microbiome diversity. Fermentative bacteria were highly dynamic and functional redundant during temperature reductions. Smithella was the dominant syntrophic bacteria involved in LCFA degradation coupled with Methanothrix and Methanocorpusculum at 15°C. Membrane modifications and compatible cellular solutes production were triggered by temperature reductions as microbial response to cold stress. This study provided molecular insights in microbial acclimation to low temperatures for psychrophilic AD.}, }
@article {pmid39319483, year = {2024}, author = {Rasmussen, KL and Thieringer, PH and Nevadomski, S and Martinez, AM and Dawson, KS and Corsetti, FA and Zheng, XY and Lv, Y and Chen, X and Celestian, AJ and Berelson, WM and Rollins, NE and Spear, JR}, title = {Living to Lithified: Construction and Preservation of Silicified Biomarkers.}, journal = {Geobiology}, volume = {22}, number = {5}, pages = {1-30}, doi = {10.1111/gbi.12620}, pmid = {39319483}, issn = {1472-4669}, support = {/NASA/NASA/United States ; //Geological Society of America/ ; }, mesh = {*Biomarkers/analysis ; Cyanobacteria/metabolism ; Geologic Sediments/microbiology/chemistry ; Bacteria/metabolism ; Hot Springs/microbiology/chemistry ; }, abstract = {Whole microorganisms are rarely preserved in the fossil record but actively silicifying environments like hot springs provide an opportunity for microbial preservation, making silicifying environments critical for the study of microbial life through time on Earth and possibly other planetary bodies. Yet, the changes that biosignatures may undergo through lithification and burial remain unconstrained. At Steep Cone Geyser in Yellowstone National Park, we collected microbial material from (1) the living system across the active outflows, (2) the silicified areas adjacent to flows, and (3) lithified and buried material to assess the preservation of biosignatures and their changes across the lithification transect. Five biofabrics, built predominantly by Cyanobacteria Geitlerinema, Pseudanabaenaceae, and Leptolyngbya with some filamentous anoxygenic phototrophs contributions, were identified and tracked from the living system through the process of silicification/lithification. In the living systems, δ[30]Si values decrease from +0.13‰ in surficial waters to -2‰ in biomat samples, indicating a kinetic isotope effect potentially induced by increased association with actively growing biofabrics. The fatty acids C16:1 and iso-C14:0 and the hydrocarbon C17:0 were disentangled from confounding signals and determined to be reliable lipid biosignatures for living biofabric builders and tenant microorganisms. Builder and tenant microbial biosignatures were linked to specific Cyanobacteria, anoxygenic phototrophs, and heterotrophs, which are prominent members of the living communities. Upon lithification and burial, silicon isotopes of silicified biomass began to re-equilibrate, increasing from δ[30]Si -2‰ in living biomats to -0.55‰ in lithified samples. Active endolithic microbial communities were identified in lithified samples and were dominated by Cyanobacteria, heterotrophic bacteria, and fungi. Results indicate that distinct microbial communities build and inhabit silicified biofabrics through time and that microbial biosignatures shift over the course of lithification. These findings improve our understanding of how microbial communities silicify, the biomarkers they retain, and transitionary impacts that may occur through lithification and burial.}, }
@article {pmid39317790, year = {2024}, author = {Knorr, MA and Contosta, AR and Morrison, EW and Muratore, TJ and Anthony, MA and Stoica, I and Geyer, KM and Simpson, MJ and Frey, SD}, title = {Unexpected sustained soil carbon flux in response to simultaneous warming and nitrogen enrichment compared with single factors alone.}, journal = {Nature ecology &amp; evolution}, volume = {8}, number = {12}, pages = {2277-2285}, pmid = {39317790}, issn = {2397-334X}, mesh = {*Soil/chemistry ; *Nitrogen/analysis/metabolism ; *Carbon Cycle ; *Carbon/analysis/metabolism ; Global Warming ; Forests ; Climate Change ; }, abstract = {Recent observations document that long-term soil warming in a temperate deciduous forest leads to significant soil carbon loss, whereas chronic soil nitrogen enrichment leads to significant soil carbon gain. Most global change experiments like these are single factor, investigating the impacts of one stressor in isolation of others. Because warming and ecosystem nitrogen enrichment are happening concurrently in many parts of the world, we designed a field experiment to test how these two factors, alone and in combination, impact soil carbon cycling. Here, we show that long-term continuous soil warming or nitrogen enrichment when applied alone followed the predicted response, with warming resulting in significant soil carbon loss and nitrogen fertilization tending towards soil carbon gain. The combination treatment showed an unanticipated response, whereby soil respiratory carbon loss was significantly higher than either single factor alone, but without a concomitant decline in soil carbon storage. Observations suggest that when soils are exposed to both factors simultaneously, plant carbon inputs to the soil are enhanced, counterbalancing soil carbon loss and helping maintain soil carbon stocks near control levels. This has implications for both atmospheric CO2 emissions and soil fertility and shows that coupling two important global change drivers results in a distinctive response that was not predicted by the behaviour of the single factors in isolation.}, }
@article {pmid39311575, year = {2024}, author = {Han, C-J and Huang, J-P and Chiang, M-R and Jean, OSM and Nand, N and Etebari, K and Shelomi, M}, title = {The hindgut microbiota of coconut rhinoceros beetles (Oryctes rhinoceros) in relation to their geographical populations.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {10}, pages = {e0098724}, pmid = {39311575}, issn = {1098-5336}, support = {MOST-109-2311-B-002-016-MY3//National Science and Technology Council (NSTC)/ ; 111L7822,112L7814,113L7801//Ministry of Education, Taiwan/ ; }, mesh = {Animals ; *Coleoptera/microbiology ; *Gastrointestinal Microbiome ; *Symbiosis ; Bacteria/classification/genetics/isolation &amp; purification ; Cocos/microbiology ; Genetic Variation ; }, abstract = {The coconut rhinoceros beetle (CRB, Oryctes rhinoceros) is a palm tree pest capable of rapidly expanding its population in new territories. Previous studies identified a digestive symbiosis between CRB and its gut microbes. However, no research compared the genetic variation of CRBs with their hindgut microbiota on a global scale. This study aims to investigate the genetic divergence of CRB and the compositional variation of CRB's microbiota across different geographical locations, and explore the association between them and their predicted functional profiles and environmental data. The research reveals a distinct and consistent microbial community within local populations, but it varies across different geographical populations. The microbial functional profiles linked to the production of digestive enzymes, including cellulases and ligninases, are nonetheless globally conserved. This suggests that CRBs employ specific mechanisms to select and maintain microbes with functional benefits, contributing to host adaptability, stress tolerance, and fitness. The CRB microbial communities did not appear to recapitulate the genetic variation of their hosts. Rather than depend on obligate symbionts, CRBs seem to establish similar digestive associations with whatever environmentally acquired microbes are available wherever they are, aiding them in successfully establishing after invading a new location.IMPORTANCECoconut rhinoceros beetles (CRBs) are notorious pests on Arecaceae plants, posing destructive threats to countries highly reliant on coconut, oil palm, and date palm as economic crops. In the last century, CRBs have rapidly expanded their presence to territories that were once free of these beetles. The United States, for instance, has officially designated CRBs as invasive and alien pests. Given their remarkable ability to swiftly adapt to new environments, their gut microbes may play a crucial role in this process. While the microbiota of CRBs vary depending on geographical location, these beetles consistently exhibit a functionally identical digestive association with locally acquired microbes. This underscores the significance of CRB-microbe association in shaping the adaptive strategies of this agricultural pest.}, }
@article {pmid39311333, year = {2025}, author = {Deo, R and Lakra, U and Ojha, M and Nigam, VK and Sharma, SR}, title = {Exopolysaccharides in microbial interactions: signalling, quorum sensing, and community dynamics.}, journal = {Natural product research}, volume = {39}, number = {11}, pages = {3224-3239}, doi = {10.1080/14786419.2024.2405867}, pmid = {39311333}, issn = {1478-6427}, mesh = {*Quorum Sensing/physiology ; *Microbial Interactions ; *Polysaccharides, Bacterial/metabolism ; Ecosystem ; Signal Transduction ; }, abstract = {Microbial interactions within diverse ecosystems are intricately governed by the dynamic interplay of exopolysaccharides (EPSs) produced by microorganisms. This review delves into the multifaceted roles of EPS in microbial signalling, quorum sensing (QS), and community dynamics, highlighting their significance in orchestrating cooperative behaviours and shaping community structures. EPSs serve as pivotal signalling molecules, influencing chemical communication and promoting intricate interactions among microorganisms. The integration of EPS into QS mechanisms adds an additional layer of complexity, allowing microorganisms to assess population density and synchronise communal responses. Furthermore, EPSs actively contribute to community dynamics by influencing spatial organisation, adhesion, and resistance to environmental stressors. By providing comprehensive knowledge of EPS dynamics, this review offers valuable insights into microbial ecology, serving as a foundational resource for future research. It will benefit the research community by advancing our understanding of microbial ecosystems, with broad applications in biotechnology, environmental science, and beyond.}, }
@article {pmid39297874, year = {2024}, author = {Castledine, M and Pennycook, J and Newbury, A and Lear, L and Erdos, Z and Lewis, R and Kay, S and Sanders, D and Sünderhauf, D and Buckling, A and Hesse, E and Padfield, D}, title = {Characterizing a stable five-species microbial community for use in experimental evolution and ecology.}, journal = {Microbiology (Reading, England)}, volume = {170}, number = {9}, pages = {}, pmid = {39297874}, issn = {1465-2080}, mesh = {*Soil Microbiology ; *Microbiota ; *Bacteria/genetics/classification/isolation &amp; purification ; Ecology ; Biological Evolution ; Microbial Interactions ; }, abstract = {Model microbial communities are regularly used to test ecological and evolutionary theory as they are easy to manipulate and have fast generation times, allowing for large-scale, high-throughput experiments. A key assumption for most model microbial communities is that they stably coexist, but this is rarely tested experimentally. Here we report the (dis)assembly of a five-species microbial community from a metacommunity of soil microbes that can be used for future experiments. Using reciprocal invasion-from-rare experiments we show that all species can coexist and we demonstrate that the community is stable for a long time (~600 generations). Crucially for future work, we show that each species can be identified by their plate morphologies, even after >1 year in co-culture. We characterise pairwise species interactions and produce high-quality reference genomes for each species. This stable five-species community can be used to test key questions in microbial ecology and evolution.}, }
@article {pmid39303870, year = {2024}, author = {McDonagh, F and Tumeo, A and Murray, EK and Hallahan, B and Miliotis, G}, title = {Complete genome of Escherichia coli sequence type 73 with acquired blaTEM-1 and high genotypic virulence load identified in human saliva.}, journal = {Journal of global antimicrobial resistance}, volume = {39}, number = {}, pages = {149-152}, doi = {10.1016/j.jgar.2024.08.011}, pmid = {39303870}, issn = {2213-7173}, mesh = {Humans ; *Escherichia coli/genetics/drug effects/pathogenicity/isolation &amp; purification ; *Genome, Bacterial ; *Virulence Factors/genetics ; *Phylogeny ; *Escherichia coli Infections/microbiology ; *Saliva/microbiology ; Virulence/genetics ; Genotype ; beta-Lactamases/genetics ; Whole Genome Sequencing ; Schizophrenia/genetics/microbiology ; Anti-Bacterial Agents/pharmacology ; }, abstract = {OBJECTIVES: Escherichia coli sequence type (ST) 73 is a pandemic lineage of the ExPEC (Extraintestinal Pathogenic E. coli) family associated with conserved virulence. We report the complete genome of a genomically hypervirulent E. coli ST73 strain isolated from the oral cavity of a patient with a diagnosis of treatment resistant schizophrenia and receiving clozapine treatment.<br><br>METHODS: E. coli strain GABEEC132 underwent second and third generation sequencing with Illumina and Oxford-Nanopore-Technologies (ONT) platforms. Antibiotic resistance genes (ARGs) and virulence factors (VFs) were bioinformatically identified using the NCBI-AMR-Finder-Plus database and Virulence-Factors-database (VFDB), respectively. To contextualize the genome within a broader epidemiological framework, phylogenetic analysis was conducted using representative genomes of E. coli ST73 O6:H1 (n = 55).<br><br>RESULTS: E. coli strain GABEEC132 was identified as possessing the O6:H1 serotype and classified within the B2 phylogroup. The strain exhibited a high genomic virulence load, encoding for 194 VFs. Additionally, it encoded three ARGs, including an acquired blaTEM-1 located on a rep_cluster_2350 8 237 Kb mobilisable plasmid, presenting phenotypic resistance to ampicillin and piperacillin.<br><br>CONCLUSION: This report provides novel insights into the oral prevalence of genotypically hypervirulent and drug-resistant E. coli ST73, a pandemic lineage.}, }
@article {pmid39301056, year = {2024}, author = {Smith, L and Fullerton, H and Moyer, CL}, title = {Complex hydrothermal vent microbial mat communities used to assess primer selection for targeted amplicon surveys from Kama'ehuakanaloa Seamount.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e18099}, pmid = {39301056}, issn = {2167-8359}, mesh = {*Hydrothermal Vents/microbiology ; *Archaea/genetics/isolation &amp; purification ; *Microbiota/genetics ; *Bacteria/genetics/isolation &amp; purification/classification ; DNA Primers/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The microbiota of hydrothermal vents has been widely implicated in the dynamics of oceanic biogeochemical cycling. Lithotrophic organisms utilize reduced chemicals in the vent effluent for energy, which fuels carbon fixation, and their metabolic byproducts can then support higher trophic levels and high-biomass ecosystems. However, despite the important role these microorganisms play in our oceans, they are difficult to study. Most are resistant to culturing in a lab setting, so culture-independent methods are necessary to examine community composition. Targeted amplicon surveying has become the standard practice for assessing the structure and diversity of hydrothermal vent microbial communities. Here, the performance of primer pairs targeting the V3V4 and V4V5 variable regions of the SSU rRNA gene was assessed for use on environmental samples from microbial mats surrounding Kama'ehuakanaloa Seamount, an iron-dominated hydrothermal vent system. Using the amplicon sequence variant (ASV) approach to taxonomic identification, the structure and diversity of microbial communities were elucidated, and both primer pairs generated robust data and comparable alpha diversity profiles. However, several distinct differences in community composition were identified between primer sets, including differential relative abundances of both bacterial and archaeal phyla. The primer choice was determined to be a significant driver of variation among the taxonomic profiles generated. Based on the higher quality of the raw sequences generated and on the breadth of abundant taxa found using the V4V5 primer set, it is determined as the most efficacious primer pair for whole-community surveys of microbial mats at Kama'ehuakanaloa Seamount.}, }
@article {pmid39303138, year = {2024}, author = {Boukheloua, R and Mukherjee, I and Park, H and Šimek, K and Kasalický, V and Ngochera, M and Grossart, HP and Picazo-Mozo, A and Camacho, A and Cabello-Yeves, PJ and Rodriguez-Valera, F and Callieri, C and Andrei, AS and Pernthaler, J and Posch, T and Alfreider, A and Sommaruga, R and Hahn, MW and Sonntag, B and López-García, P and Moreira, D and Jardillier, L and Lepère, C and Biderre-Petit, C and Bednarska, A and Ślusarczyk, M and Tóth, VR and Banciu, HL and Kormas, K and Orlić, S and Šantić, D and Muyzer, G and Herlemann, DPR and Tammert, H and Bertilsson, S and Langenheder, S and Zechmeister, T and Salmaso, N and Storelli, N and Capelli, C and Lepori, F and Lanta, V and Vieira, HH and Kostanjšek, F and Kabeláčová, K and Chiriac, MC and Haber, M and Shabarova, T and Fernandes, C and Rychtecký, P and Znachor, P and Szőke-Nagy, T and Layoun, P and Wong, HL and Kavagutti, VS and Bulzu, PA and Salcher, MM and Piwosz, K and Ghai, R}, title = {Global freshwater distribution of Telonemia protists.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39303138}, issn = {1751-7370}, support = {20-12496X//Grant Agency of the Czech Republic/ ; 017/2022/P//GAJU/ ; 2021/03/Y/NZ8/00076//National Science Centre/ ; }, mesh = {*Fresh Water/microbiology/parasitology ; *Phylogeny ; *RNA, Ribosomal, 18S/genetics ; *In Situ Hybridization, Fluorescence ; Metagenome ; Lakes/microbiology/parasitology ; Biodiversity ; Metagenomics ; }, abstract = {Telonemia are one of the oldest identified marine protists that for most part of their history have been recognized as a distinct incertae sedis lineage. Today, their evolutionary proximity to the SAR supergroup (Stramenopiles, Alveolates, and Rhizaria) is firmly established. However, their ecological distribution and importance as a natural predatory flagellate, especially in freshwater food webs, still remain unclear. To unravel the distribution and diversity of the phylum Telonemia in freshwater habitats, we examined over a thousand freshwater metagenomes from all over the world. In addition, to directly quantify absolute abundances, we analyzed 407 samples from 97 lakes and reservoirs using Catalyzed Reporter Deposition-Fluorescence in situ Hybridization (CARD-FISH). We recovered Telonemia 18S rRNA gene sequences from hundreds of metagenomic samples from a wide variety of habitats, indicating a global distribution of this phylum. However, even after this extensive sampling, our phylogenetic analysis did not reveal any new major clades, suggesting current molecular surveys are near to capturing the full diversity within this group. We observed excellent concordance between CARD-FISH analyses and estimates of abundances from metagenomes. Both approaches suggest that Telonemia are largely absent from shallow lakes and prefer to inhabit the colder hypolimnion of lakes and reservoirs in the Northern Hemisphere, where they frequently bloom, reaching 10%-20% of the total heterotrophic flagellate population, making them important predatory flagellates in the freshwater food web.}, }
@article {pmid39302483, year = {2024}, author = {Nelson, K and Schloter, M}, title = {Special Collection on Pollution, Bioremediation, and the Environment.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {118}, pmid = {39302483}, issn = {1432-184X}, mesh = {*Biodegradation, Environmental ; *Environmental Pollution ; }, }
@article {pmid39299325, year = {2024}, author = {Ren, W and Ren, G and Kuramae, EE and Bodelier, PLE and Chen, S and Teng, Y and Luo, Y}, title = {Mode of application of sulfonated graphene modulated bioavailable heavy metal contents and microbial community composition in long-term heavy metal contaminated soil.}, journal = {The Science of the total environment}, volume = {954}, number = {}, pages = {176295}, doi = {10.1016/j.scitotenv.2024.176295}, pmid = {39299325}, issn = {1879-1026}, mesh = {*Soil Microbiology ; *Soil Pollutants/metabolism/analysis ; *Graphite ; *Metals, Heavy/analysis/metabolism ; *Microbiota/drug effects ; *Biodegradation, Environmental ; Soil/chemistry ; Bacteria/metabolism ; Cadmium/metabolism/analysis ; }, abstract = {Nanomaterials are increasingly recognized for their potential in soil remediation. However, their impact on soil microbial communities in contaminated soil remains poorly understood. In this study, we investigated the dynamic effects of sulfonated graphene (SG) following one-time or repeated applications on heavy metal availability and soil microbial communities in long-term heavy metal-contaminated soil over 180 days. Our findings revealed that one-time SG application at 30 mg kg[-1] significantly increased the bioavailable cadmium (Cd) and copper (Cu) contents by approximately 30 %-40 % after 2 and 180 days. Repeated SG applications, however, displayed no significant influence on heavy metal availability. One-time SG application, coupled with the increased available Cd, induced significant enrichment of some specific functional bacterial genera involved in glycan biosynthesis metabolism and biosynthesis of other secondary metabolites, thereby decreasing the available contents of heavy metals after 90 days. However, the shifts in bacterial community structure and function were subsequently partially recovered after 180 days. Conversely, repeated SG treatments led to minimal alterations after 90 days while leading to similar shifts in the bacterial community at 60 mg kg[-1] after 180 days. The fungal community structure remained largely unaltered across all SG treatments. Intriguingly, SG treatments substantially stimulated fungal biomass, with the stimulation degree dependent on SG dosage. These results provide valuable insights for developing phytoremediation strategies, suggesting tailored SG applications during specific growth phases to optimize remediation efficiency.}, }
@article {pmid39296299, year = {2024}, author = {Wang, X and Li, H and Yang, Y and Wu, Z and Wang, Z and Li, D and Xia, W and Zou, S and Liu, Y and Wang, F}, title = {Geographic and environmental impacts on gut microbiome in Himalayan langurs (Semnopithecus schistaceus) and Xizang macaques (Macaca mulatta vestita).}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1452101}, pmid = {39296299}, issn = {1664-302X}, abstract = {INTRODUCTION: Gut microbiome plays a crucial role in the health of wild animals. Their structural and functional properties not only reflect the host's dietary habits and habitat conditions but also provide essential support for ecological adaptation in various environments.<br><br>METHODS: This study investigated the gut microbiome of Himalayan langurs (Semnopithecus schistaceus) and Xizang macaques (Macaca mulatta vestita) across different geographic regions using 16S rRNA gene and metagenomic sequencing.<br><br>RESULTS: Results showed distinct clustering patterns in gut microbiota based on geographic location. Soil had an insignificant impact on host gut microbiome. Himalayan langurs from mid-altitude regions exhibited higher levels of antibiotic resistance genes associated with multidrug resistance, while Xizang macaques from high-altitude regions showed a broader range of resistance genes. Variations in carbohydrate-active enzymes and KEGG pathways indicated unique metabolic adaptations to different environments.<br><br>DISCUSSION: These findings provide valuable insights into the health and conservation of these primates and the broader implications of microbial ecology and functional adaptations in extreme conditions.}, }
@article {pmid39296290, year = {2024}, author = {Wang, Z and Gao, Z and Yu, Y and Li, H and Luo, W and Ji, Z and Ding, H}, title = {New insights into the structure and function of microbial communities in Maxwell Bay, Antarctica.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1463144}, pmid = {39296290}, issn = {1664-302X}, abstract = {The microbial communities inhabiting polar ecosystems, particularly in Maxwell Bay, Antarctica, play a pivotal role in nutrient cycling and ecosystem dynamics. However, the diversity of these microbial communities remains underexplored. In this study, we aim to address this gap by investigating the distribution, environmental drivers, and metabolic potential of microorganisms in Maxwell Bay. We analyzed the prokaryotic and eukaryotic microbiota at 11 stations, revealing distinctive community structures and diverse phylum dominance by using high-throughput sequencing. Spatial analysis revealed a significant impact of longitude on microbial communities, with microeukaryotes exhibiting greater sensitivity to spatial factors than microprokaryotes. We constructed co-occurrence networks to explore the stability of microbial communities, indicating the complexity and stability of microprokaryotic communities compared with those of microeukaryotes. Our findings suggest that the microeukaryotic communities in Maxwell Bay are more susceptible to disturbances. Additionally, this study revealed the spatial correlations between microbial communities, diversity, and environmental variables. Redundancy analysis highlighted the significance of pH and dissolved oxygen in shaping microprokaryotic and microeukaryotic communities, indicating the anthropogenic influence near the scientific research stations. Functional predictions using Tax4Fun2 and FUNGuild revealed the metabolic potential and trophic modes of the microprokaryotic and microeukaryotic communities, respectively. Finally, this study provides novel insights into the microbial ecology of Maxwell Bay, expanding the understanding of polar microbiomes and their responses to environmental factors.}, }
@article {pmid39294302, year = {2024}, author = {Sousa, LGV and Novak, J and França, A and Muzny, CA and Cerca, N}, title = {Gardnerella vaginalis, Fannyhessea vaginae, and Prevotella bivia Strongly Influence Each Other's Transcriptome in Triple-Species Biofilms.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {117}, pmid = {39294302}, issn = {1432-184X}, support = {R01AI146065-01A1//National Institute of Allergy and Infectious Diseases/ ; UIDB/04469/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2020.04912.BD//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; DL57/2016/CP1377/CT0032//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; R01 AI146065/AI/NIAID NIH HHS/United States ; }, mesh = {*Biofilms/growth &amp; development ; *Gardnerella vaginalis/genetics ; *Transcriptome ; *Prevotella/genetics/physiology ; Female ; Humans ; Vaginosis, Bacterial/microbiology ; Vagina/microbiology ; }, abstract = {Bacterial vaginosis (BV), the most common vaginal infection worldwide, is characterized by the development of a polymicrobial biofilm on the vaginal epithelium. While Gardnerella spp. have been shown to have a prominent role in BV, little is known regarding how other species can influence BV development. Thus, we aimed to study the transcriptome of Gardnerella vaginalis, Fannyhessea vaginae, and Prevotella bivia, when growing in triple-species biofilms. Single and triple-species biofilms were formed in vitro, and RNA was extracted and sent for sequencing. cDNA libraries were prepared and sequenced. Quantitative PCR analysis (qPCR) was performed on the triple-species biofilms to evaluate the biofilm composition. The qPCR results revealed that the triple-species biofilms were mainly composed by G. vaginalis and P. bivia was the species with the lowest percentage. The RNA-sequencing analysis revealed a total of 432, 126, and 39 differentially expressed genes for G. vaginalis, F. vaginae, and P. bivia, respectively, when growing together. Gene ontology enrichment of G. vaginalis downregulated genes revealed several functions associated with metabolism, indicating a low metabolic activity of G. vaginalis when growing in polymicrobial biofilms. This work highlighted that the presence of 3 different BV-associated bacteria in the biofilm influenced each other's transcriptome and provided insight into the molecular mechanisms that enhanced the virulence potential of polymicrobial consortia. These findings will contribute to understand the development of incident BV and the interactions occurring within the biofilm.}, }
@article {pmid39290267, year = {2024}, author = {Zhang, K and Zhang, Q and Qiu, H and Ma, Y and Hou, N and Zhang, J and Kan, C and Han, F and Sun, X and Shi, J}, title = {The complex link between the gut microbiome and obesity-associated metabolic disorders: Mechanisms and therapeutic opportunities.}, journal = {Heliyon}, volume = {10}, number = {17}, pages = {e37609}, pmid = {39290267}, issn = {2405-8440}, abstract = {Microbial interactions are widespread and important processes that support the link between disease and microbial ecology. The gut microbiota is a major source of microbial stimuli that can have detrimental or beneficial effects on human health. It is also an endocrine organ that maintains energy homeostasis and host immunity. Obesity is a highly and increasingly prevalent metabolic disease and the leading cause of preventable death worldwide. An imbalance in the gut microbiome is associated with several diseases including obesity-related metabolic disorders. This review summarizes the complex association between the gut microbiome and obesity-associated metabolic diseases and validates the role and mechanisms of ecological dysregulation in the gut in obesity-associated metabolic disorders. Therapies that could potentially alleviate obesity-associated metabolic diseases by modulating the gut microbiota are discussed.}, }
@article {pmid39288091, year = {2024}, author = {Liu, X and Salles, JF}, title = {Drivers and consequences of microbial community coalescence.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39288091}, issn = {1751-7370}, support = {//China Scholarship Council and the European Research Council/ ; }, mesh = {*Microbiota ; *Ecosystem ; Bacteria/genetics/classification/isolation &amp; purification ; }, abstract = {Microbial communities are undergoing unprecedented dispersion and amalgamation across diverse ecosystems, thereby exerting profound and pervasive influences on microbial assemblages and ecosystem dynamics. This review delves into the phenomenon of community coalescence, offering an ecological overview that outlines its four-step process and elucidates the intrinsic interconnections in the context of community assembly. We examine pivotal mechanisms driving community coalescence, with a particular emphasis on elucidating the fates of both source and resident microbial communities and the consequential impacts on the ecosystem. Finally, we proffer recommendations to guide researchers in this rapidly evolving domain, facilitating deeper insights into the ecological ramifications of microbial community coalescence.}, }
@article {pmid39287748, year = {2024}, author = {Kujawska, M and Neuhaus, K and Huptas, C and Jiménez, E and Arboleya, S and Schaubeck, M and Hall, LJ}, title = {Exploring the Potential Probiotic Properties of Bifidobacterium breve DSM 32583-A Novel Strain Isolated from Human Milk.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {39287748}, issn = {1867-1314}, abstract = {Human milk is the best nutrition for infants, providing optimal support for the developing immune system and gut microbiota. Hence, it has been used as source for probiotic strain isolation, including members of the genus Bifidobacterium, in an effort to provide beneficial effects to infants who cannot be exclusively breastfed. However, not all supplemented bifidobacteria can effectively colonise the infant gut, nor confer health benefits to the individual infant host; therefore, new isolates are needed to develop a range of dietary products for this specific age group. Here, we investigated the beneficial potential of Bifidobacterium breve DSM 32583 isolated from human milk. We show that in vitro B. breve DSM 32583 exhibited several characteristics considered fundamental for beneficial bacteria, including survival in conditions simulating those present in the digestive tract, adherence to human epithelial cell lines, and inhibition of growth of potentially pathogenic microorganisms. Its antibiotic resistance patterns were comparable to those of known beneficial bifidobacterial strains, and its genome did not contain plasmids nor virulence-associated genes. These results suggest that B. breve DSM 32583 is a potential probiotic candidate.}, }
@article {pmid39287688, year = {2024}, author = {Demin, K and Prazdnova, E and Kulikov, M and Mazanko, M and Gorovtsov, A}, title = {Alternative agar substitutes for culturing unculturable microorganisms.}, journal = {Archives of microbiology}, volume = {206}, number = {10}, pages = {405}, pmid = {39287688}, issn = {1432-072X}, support = {SP-12-23-04//Strategic Academic Leadership Program of the Southern Federal University "Priority 2030"/ ; SP-12-23-04//Strategic Academic Leadership Program of the Southern Federal University "Priority 2030"/ ; SP-12-23-04//Strategic Academic Leadership Program of the Southern Federal University "Priority 2030"/ ; }, mesh = {*Agar/chemistry ; *Culture Media/chemistry ; *Polysaccharides, Bacterial/metabolism ; *Bacteria/growth &amp; development/metabolism/drug effects ; Gels/chemistry ; }, abstract = {Gelling agents are necessary for the preparation of solid or semisolid media. For more than a hundred years, agar has been the primary gelling agent. However, a substantial body of evidence has accumulated suggesting that agar-based media inhibit the growth of many microbial species through the generation of reactive oxygen species (ROS), toxic organic contaminants, or competitive exclusion effects. In this review we have compiled the largest amount of data to date on the use of various gelling agents in microbial isolation and cultivation, with the particular emphasis on rare microbe isolation cases. Our analysis suggested that microbial-derived compounds (especially gellan gum), as gelling agents, are superior to agar in their ability to isolate and maintain either new or known microbial species. We analyzed the reasons behind this success and concluded that there are phylum-level differences in microbial responses to the changes in conditions from natural to the laboratory conditions (with respect to gelling agent usage). Consequently, we hypothesize that at least partial success of microbial-derived gelling agents lies in the recreation of the natural microenvironment conditions (which we address as the "familiarity of conditions" hypothesis). Finally, we present a list of recommendations and suggestions for further microbial ecology studies.}, }
@article {pmid39287374, year = {2024}, author = {Vinogradova, E and Mukhanbetzhanov, N and Nurgaziyev, M and Jarmukhanov, Z and Aipova, R and Sailybayeva, A and Bekbossynova, M and Kozhakhmetov, S and Kushugulova, A}, title = {Impact of urbanization on gut microbiome mosaics across geographic and dietary contexts.}, journal = {mSystems}, volume = {9}, number = {10}, pages = {e0058524}, pmid = {39287374}, issn = {2379-5077}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Urbanization ; Male ; Female ; Kazakhstan/epidemiology ; *Diet ; Adult ; Rural Population/statistics &amp; numerical data ; Middle Aged ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Urban Population/statistics &amp; numerical data ; Bacteria/genetics/classification/isolation &amp; purification ; Feces/microbiology ; Young Adult ; }, abstract = {UNLABELLED: This study provides a comprehensive assessment of how urban-rural divides influence gut microbial diversity and composition across the distinct geographical landscapes of Kazakhstan, elucidating the intricate interplay between lifestyle, environment, and gut microbiome. In this prospective cohort study, we enrolled 651 participants from urban centers and rural settlements across Kazakhstan, following ethical approval and informed consent. Comprehensive demographic, dietary, and stool sample data were collected. 16S rRNA gene sequencing and shotgun metagenomics techniques were employed to delineate the intricate patterns of the gut microbiome. A rigorous statistical framework dissected the interplay between urbanization gradients, geography, dietary lifestyles, and microbial dynamics. Our findings demonstrate a stark microbial divide between urban and rural gut ecosystems. The study found significant differences in gut microbiome diversity and composition between urban and rural populations in Kazakhstan. Urban microbiomes exhibited reduced diversity, higher Firmicutes/Bacteroidetes ratios, and increased prevalence of genera Coprococcus and Parasutterella. In contrast, rural populations had greater microbial diversity and abundance of Ligilactobacillus, Sutterella, and Paraprevotella. Urbanization also influenced dietary patterns, with urban areas consuming more salt, cholesterol, and protein, while rural areas had diets richer in carbohydrates and fiber. The study also identified distinct patterns in the prevalence of antibiotic resistance genes and virulence factors between urban and rural gut microbiomes. This study sheds light on how urbanization may be deeply involved in shaping the intricate mosaic of the gut microbiome across Kazakhstan's diverse geographical and dietary landscapes, underscoring the complex interplay between environmental exposures, dietary lifestyles, and the microbial residents inhabiting our intestines.<br><br>IMPORTANCE: The study examined gut microbiome composition across diverse geographical locations in Kazakhstan, spanning urban centers and rural settlements. This allows for thoroughly investigating how urbanization gradients and geographic factors shape the gut microbiome. The study's examination of the gut resistome and prevalence of virulence-associated genes provide essential insights into the public health implications of urbanization-driven microbiome alterations. Collecting comprehensive demographic, dietary, and stool sample data enables the researchers to better understand the relationships between urbanization, nutritional patterns, and gut microbiome composition. The findings have important implications for understanding how urbanization-driven microbiome changes may impact human health and well-being, paving the way for tailored interventions to restore a balanced gut microbial ecology.}, }
@article {pmid39283121, year = {2024}, author = {Machado, DT and Dias, BdC and Cayô, R and Gales, AC and Marques de Carvalho, F and Vasconcelos, ATR}, title = {Uncovering new Firmicutes species in vertebrate hosts through metagenome-assembled genomes with potential for sporulation.}, journal = {Microbiology spectrum}, volume = {12}, number = {11}, pages = {e0211324}, pmid = {39283121}, issn = {2165-0497}, support = {E-26/210.012/2020//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro (FAPERJ)/ ; 88887.677436/2022-00//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior (CAPES)/ ; 402659/2018-0,443805/2018-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; OPP1193112//Bill and Melinda Gates Foundation (GF)/ ; 88887.508687/2020-00//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior (CAPES)/ ; 302023/2024-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; 307915/2022-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; 312066/2019-8//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; 307145/2021-2//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; E-26/201.046/2022//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro (FAPERJ)/ ; }, mesh = {Animals ; *Spores, Bacterial/genetics/growth &amp; development ; *Phylogeny ; *Metagenome ; *Genome, Bacterial/genetics ; *Firmicutes/genetics/classification ; Humans ; Cattle ; Swine ; Gastrointestinal Microbiome/genetics ; Vertebrates/microbiology ; Poultry/microbiology ; }, abstract = {Metagenome-assembled genomes (MAGs) have contributed to identifying non-culturable microorganisms and understanding their ecological functions. MAGs offer an advantage in investigating sporulation-associated genes, especially given the difficulty of isolating many species residing in the gut microbiota of multiple hosts. Bacterial sporulation is a key survival mechanism with implications for pathogenicity and biotechnology. Here, we investigate MAGs from vertebrate hosts, emphasizing taxonomic identification and identifying sporulation-associated genes in potential novel species within the Firmicutes phylum. We identified potential new species in the classes Clostridia (Borkfalkiaceae, Lachnospiraceae, Monoglobaceae, and Oscillospiraceae families) and Bacilli (Bacillaceae and Erysipelotrichaceae families) through phylogenetic and functional pathway analyses, highlighting their sporulation potential. Our study covers 146 MAGs, 124 of them without refined taxonomic assignments at the family level. We found that Clostridia and Bacilli have unique sporulation gene profiles in the refined family MAGs for cattle, swine, poultry, and human hosts. The presence of genes related to Spo0A regulon, engulfment, and spore cortex in MAGs underscores fundamental mechanisms in sporulation processes in currently uncharacterized species with sporulation potential from metagenomic dark matter. Furthermore, genomic analyses predict sporulation potential based on gene presence, genome size, and metabolic pathways involved in spore formation. We emphasize MAGs covering families not yet characterized through the phylogenetic analysis, and with extensive potential for spore-forming bacteria within Clostridia, Bacilli, UBA4882, and UBA994 classes. These findings contribute to exploring spore-forming bacteria, which provides evidence for novel species diversity in multiple hosts, their adaptive strategies, and potential applications in biotechnology and host health.IMPORTANCESpores are essential for bacterial survival in harsh environments, facilitating their persistence and adaptation. Exploring sporulation-associated genes in metagenome-assembled genomes (MAGs) from different hosts contributes to clinical and biotechnological domains. Our study investigated the extent of genes associated with bacterial sporulation in MAGs from poultry, swine, cattle, and humans, revealing these genes in uncultivated bacteria. We identified potential novel Firmicutes species with sporulation capabilities through phylogenetic and functional analyses. Notably, MAGs belonging to Clostridia, Bacilli, and unknown classes, namely UBA4882 and UBA994, remained uncharacterized at the family level, which raises the hypothesis that sporulation would also be present in these genomes. These findings contribute to our understanding of microbial adaptation and have implications for microbial ecology, underlining the importance of sporulation in Firmicutes across different hosts. Further studies into novel species and their sporulation capability can contribute to bacterial maintenance mechanisms in various organisms and their applications in biotechnology studies.}, }
@article {pmid39282566, year = {2024}, author = {Abdelshafy Mohamad, OA and Liu, YH and Huang, Y and Kuchkarova, N and Dong, L and Jiao, JY and Fang, BZ and Ma, JB and Hatab, S and Li, WJ}, title = {Metabonomic analysis to identify exometabolome changes underlying antifungal and growth promotion mechanisms of endophytic Actinobacterium Streptomyces albidoflavus for sustainable agriculture practice.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1439798}, pmid = {39282566}, issn = {1664-302X}, abstract = {In recent years, there has been an increasing focus on microbial ecology and its possible impact on agricultural production, owing to its eco-friendly nature and sustainable use. The current study employs metabolomics technologies and bioinformatics approaches to identify changes in the exometabolome of Streptomyces albidoflavus B24. This research aims to shed light on the mechanisms and metabolites responsible for the antifungal and growth promotion strategies, with potential applications in sustainable agriculture. Metabolomic analysis was conducted using Q Exactive UPLC-MS/MS. Our findings indicate that a total of 3,840 metabolites were identified, with 137 metabolites exhibiting significant differences divided into 61 up and 75 downregulated metabolites based on VIP >1, |FC| >1, and p < 0.01. The interaction of S. albidoflavus B24 monoculture with the co-culture demonstrated a stronger correlation coefficient. The Principal Component Analysis (PCA) demonstrates that PCA1 accounted for 23.36%, while PCA2 accounted for 20.28% distinction. OPLS-DA score plots indicate significant separation among different groups representing (t1) 24% as the predicted component (to1) depicts 14% as the orthogonal component. According to the findings of this comprehensive study, crude extracts from S. albidoflavus demonstrated varying abilities to impede phytopathogen growth and enhance root and shoot length in tested plants. Through untargeted metabolomics, we discovered numerous potential molecules with antagonistic activity against fungal phytopathogens among the top 10 significant metabolites with the highest absolute log2FC values. These include Tetrangulol, 4-Hydroxybenzaldehyde, and Cyclohexane. Additionally, we identified plant growth-regulating metabolites such as N-Succinyl-L-glutamate, Nicotinic acid, L-Aspartate, and Indole-3-acetamide. The KEGG pathway analysis has highlighted these compounds as potential sources of antimicrobial properties. The inhibitory effect of S. albidoflavus crude extracts on pathogen growth is primarily attributed to the presence of specific gene clusters responsible for producing cyclic peptides such as ansamycins, porphyrin, alkaloid derivatives, and neomycin. Overall, it is apparent that crude extracts from S. albidoflavus exhibited varying abilities to inhibit the growth of three phytopathogens and enhancement in both root and shoot length of tested plants. This research enhances our understanding of how secondary metabolites contribute to growth promotion and biocontrol, supporting ecosystem sustainability and resilience while boosting productivity in sustainable agriculture.}, }
@article {pmid39282232, year = {2024}, author = {Taylor, T and Daksa, J and Shimels, MZ and Etalo, DW and Thiombiano, B and Walmsey, A and Chen, AJ and Bouwmeester, HJ and Raaijmakers, JM and Brady, SM and Kawa, D}, title = {Evaluating Mechanisms of Soil Microbiome Suppression of Striga Infection in Sorghum.}, journal = {Bio-protocol}, volume = {14}, number = {17}, pages = {e5058}, pmid = {39282232}, issn = {2331-8325}, abstract = {The root parasitic weed Striga hermonthica has a devastating effect on sorghum and other cereal crops in Sub-Saharan Africa. Available Striga management strategies are rarely sufficient or not widely accessible or affordable. Identification of soil- or plant-associated microorganisms that interfere in the Striga infection cycle holds potential for development of complementary biological control measures. Such inoculants should be preferably based on microbes native to the regions of their application. We developed a method to assess microbiome-based soil suppressiveness to Striga with a minimal amount of field-collected soil. We previously used this method to identify the mechanisms of microbe-mediated suppression of Striga infection and to test individual microbial strains. Here, we present protocols to assess the functional potential of the soil microbiome and individual bacterial taxa that adversely affect Striga parasitism in sorghum via three major known suppression mechanisms. These methods can be further extended to other Striga hosts and other root parasitic weeds. Key features • This protocol provides a detailed description of the methods used in Kawa et al. [1]. • This protocol is optimized to assess soil suppressiveness to Striga infection by using natural field-collected soil and the same soil sterilized by gamma-radiation. • This protocol is optimized to test bacterial (and not fungal) isolates. • This protocol can be easily extended to other host-parasite-microbiome systems.}, }
@article {pmid39277779, year = {2024}, author = {Boltz, JP and Rittmann, BE}, title = {Microbial ecology of nitrate-, selenate-, selenite-, and sulfate-reducing bacteria in a H2-driven bioprocess.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {11}, pages = {}, pmid = {39277779}, issn = {1574-6941}, mesh = {*Nitrates/metabolism ; *Sulfates/metabolism ; *Bioreactors/microbiology ; *Selenic Acid/metabolism ; *Hydrogen/metabolism ; *Bacteria/metabolism/genetics/growth &amp; development/classification ; *Selenious Acid/metabolism ; *Oxidation-Reduction ; Wastewater/microbiology ; Selenium Compounds/metabolism ; Biofilms/growth &amp; development ; Autotrophic Processes ; }, abstract = {A hydrogen (H2)-based membrane biofilm reactor (H2-MBfR) can reduce electron acceptors nitrate (NO3-), selenate (SeO42-), selenite (HSeO3-), and sulfate (SO42-), which are in wastewaters from coal mining and combustion. This work presents a model to describe a H2-driven microbial community comprised of hydrogenotrophic and heterotrophic bacteria that respire NO3-, SeO42-, HSeO3-, and SO42-. The model provides mechanistic insights into the interactions between autotrophic and heterotrophic bacteria in a microbial community that is founded on H2-based autotrophy. Simulations were carried out for a range of relevant solids retention times (SRT; 0.1-20 days) and with adequate H2-delivery capacity to reduce all electron acceptors. Bacterial activity began at an ∼0.6-day SRT, when hydrogenotrophic denitrifiers began to accumulate. Selenate-reducing and selenite-reducing hydrogenotrophs became established next, at SRTs of ∼1.2 and 2 days, respectively. Full NO3-, SeO42-, and HSeO3- reductions were complete by an SRT of ∼5 days. SO42- reduction began at an SRT of ∼10 days and was complete by ∼15 days. The desired goal of reducing NO3-, SeO42-, and HSeO3-, but not SO42-, was achievable within an SRT window of 5-10 days. Autotrophic hydrogenotrophs dominated the active biomass, but nonactive solids were a major portion of the solids, especially for an SRT ≥ 5 days.}, }
@article {pmid39267336, year = {2024}, author = {Du, X and Guo, Y and Zhao, X and Zhang, L and Fan, R and Li, Y}, title = {METTL3-mediated TIM1 promotes macrophage M1 polarization and inflammation through IGF2BP2-dependent manner.}, journal = {Journal of biochemical and molecular toxicology}, volume = {38}, number = {10}, pages = {e23845}, doi = {10.1002/jbt.23845}, pmid = {39267336}, issn = {1099-0461}, support = {20210302124578//This study was supported by the Shanxi Province Basic Research Program Project/ ; }, mesh = {Humans ; *Macrophages/metabolism ; *Inflammation/metabolism/pathology/genetics ; *Hepatitis A Virus Cellular Receptor 1/metabolism/genetics ; *Methyltransferases/metabolism/genetics ; *RNA-Binding Proteins/metabolism/genetics ; THP-1 Cells ; Lipopolysaccharides/pharmacology ; }, abstract = {Macrophage polarization and inflammation may play an important role in the development of sepsis. T-cell immunoglobulin mucin 1 (TIM1) has been demonstrated to promote macrophage inflammatory responses. However, whether TIM1 regulates macrophage polarization and inflammation to affect sepsis development remains unclear. Human monocytic leukemia cell line was induced into macrophages, followed by stimulated with LPS and IL-4 to induce M1 polarization and M2 polarization. The expression levels of TIM1, methyltransferase 3 (METTL3), and insulin like growth factor 2 mRNA binding protein 2 (IGF2BP2) were examined by qRT-PCR and western blot. IL-6, IL-1β, and TNF-α levels were tested by ELISA. CD86[+]cell rate was analyzed by flow cytometry. The m[6]A methylation level of TIM1 was assessed by MeRIP assay. The interaction of between TIM1 and METTL3 or IGF2BP2 was assessed by dual-luciferase reporter assay and RIP assay. TIM1 knockdown repressed LPS-induced macrophage M1 polarization and inflammation. In terms of mechanism, METTL3 promoted TIM1 expression through m[6]A modification, and this modification could be recognized by IGF2BP2. Besides, knockdown of METTL3/IGF2BP2 suppressed LPS-induced macrophage M1 polarization and inflammation, while this effect could be eliminated by TIM1 overexpression. METTL3/IGF2BP2/TIM1 axis promoted macrophage M1 polarization and inflammation, which might provide potential target for sepsis treatment.}, }
@article {pmid39273112, year = {2024}, author = {Druker, S and Sicsic, R and Ravid, S and Scheinin, S and Raz, T}, title = {Reproductive Tract Microbial Transitions from Late Gestation to Early Postpartum Using 16S rRNA Metagenetic Profiling in First-Pregnancy Heifers.}, journal = {International journal of molecular sciences}, volume = {25}, number = {17}, pages = {}, pmid = {39273112}, issn = {1422-0067}, mesh = {Female ; Animals ; Pregnancy ; *RNA, Ribosomal, 16S/genetics ; Cattle ; *Postpartum Period ; *Vagina/microbiology ; *Microbiota/genetics ; *Uterus/microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; Metagenomics/methods ; Metagenome ; }, abstract = {Studies in recent years indicate that reproductive tract microbial communities are crucial for shaping mammals' health and reproductive outcomes. Following parturition, uterine bacterial contamination often occurs due to the open cervix, which may lead to postpartum uterine inflammatory diseases, especially in primiparous individuals. However, investigations into spatio-temporal microbial transitions in the reproductive tract of primigravid females remain limited. Our objective was to describe and compare the microbial community compositions in the vagina at late gestation and in the vagina and uterus at early postpartum in first-pregnancy heifers. Three swab samples were collected from 33 first-pregnancy Holstein Friesian heifers: one vaginal sample at gestation day 258 ± 4, and vaginal and uterine samples at postpartum day 7 ± 2. Each sample underwent 16S rRNA V4 region metagenetic analysis via Illumina MiSeq, with bioinformatics following Mothur MiSeq SOP. The reproductive tract bacterial communities were assigned to 1255 genus-level OTUs across 30 phyla. Dominant phyla, accounting for approximately 90% of the communities, included Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, and Fusobacteria. However, the results revealed distinct shifts in microbial composition between the prepartum vagina (Vag-pre), postpartum vagina (Vag-post), and postpartum uterus (Utr-post). The Vag-pre and Utr-post microbial profiles were the most distinct. The Utr-post group had lower relative abundances of Proteobacteria but higher abundances of Bacteroidetes, Fusobacteria, and Tenericutes compared to Vag-pre, while Vag-post displayed intermediate values for these phyla, suggesting a transitional profile. Additionally, the Utr-post group exhibited lower bacterial richness and diversity compared to both Vag-pre and Vag-post. The unsupervised probabilistic Dirichlet Multinomial Mixtures model identified two distinct community types: most Vag-pre samples clustered into one type and Utr-post samples into another, while Vag-post samples were distributed evenly between the two. LEfSe analysis revealed distinct microbial profiles at the genus level. Overall, specific microbial markers were associated with anatomical and temporal transitions, revealing a dynamic microbial landscape during the first pregnancy and parturition. These differences highlight the complexity of these ecosystems and open new avenues for research in reproductive biology and microbial ecology.}, }
@article {pmid39272492, year = {2024}, author = {Nerini, M and Russo, A and Decorosi, F and Meriggi, N and Viti, C and Cavalieri, D and Marvasi, M}, title = {A Microbial Phenomics Approach to Determine Metabolic Signatures to Enhance Seabream Sparus aurata Traceability, Differentiating between Wild-Caught and Farmed.}, journal = {Foods (Basel, Switzerland)}, volume = {13}, number = {17}, pages = {}, pmid = {39272492}, issn = {2304-8158}, support = {2/SSL/16/TO-1/ICR/21/TO//Regione Toscana with the project PO FEAMP 2014-2020 - Misura 1.39 SSL FLAG Costa degli Etrusch/ ; }, abstract = {BACKGROUND: The need for efficient and simplified techniques for seafood traceability is growing. This study proposes the Biolog EcoPlate assay as an innovative method for assessing wild and farmed Sparus aurata traceability, offering advantages over other molecular techniques in terms of technical simplicity.<br><br>METHODS: The Biolog EcoPlate assay, known for its high-throughput capabilities in microbial ecology, was utilized to evaluate the functional diversity of microbial communities from various organs of S. aurata (seabream) from the Mediterranean area. Samples were taken from the anterior and posterior gut, cloaca swabs and gills to distinguish between farmed and wild-caught individuals. The analysis focused on color development in OmniLog Units for specific carbon sources at 48 h.<br><br>RESULTS: Gills provided the most accurate clusterization of sample origin. The assay monitored the development of color for carbon sources such as &#x3b1;-cyclodextrin, D-cellobiose, glycogen, &#x3b1;-D-lactose, L-threonine and L-phenylalanine. A mock experiment using principal component analysis (PCA) successfully identified the origin of a blind sample. Shannon and Simpson indexes were used to statistically assess the diversity, reflecting the clusterization of different organ samples; Conclusions: The Biolog EcoPlate assay proves to be a quick, cost-effective method for discriminate S. aurata traceability (wild vs. farmed), demonstrating reliable reproducibility and effective differentiation between farmed and wild-caught seabream.}, }
@article {pmid39268533, year = {2024}, author = {Wilson, T and Siddiqi, M and Xi, Y and LaPointe, G}, title = {Tracking the microbial communities from the farm to the processing facility of a washed-rind cheese operation.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1404795}, pmid = {39268533}, issn = {1664-302X}, abstract = {Milk residue and the accompanying biofilm accumulation in milking systems can compromise the microbial quality of milk and the downstream processes of cheese production. Over a six-month study, the microbial ecosystems of milk (n = 24), tap water (n = 24) and environmental swabs (n = 384) were cultured by plating decimal dilutions to obtain viable counts of total aerobic mesophilic lactose-utilizing bacteria (lactose-M17), lactic acid bacteria (MRS), yeasts and molds (Yeast, Glucose, Chloramphenicol (YGC) medium). Viable aerobic lactose-M17 plate counts of milk remained well below 4.7 log CFU/ml over five of the months, except for 1 week in November where milk at the facility exceeded 5 log CFU/ml. Swab samples of the farm milking equipment showed consistent viable counts after sanitation, while the bulk tank swabs contained the lowest counts. Viable counts from swabs of the facility were generally below the detection limit in the majority of samples with occasional residual contamination on some food contact surfaces. Extracted DNA was amplified using primers targeting the V3-V4 region of the 16S rRNA gene, and the amplicons were sequenced by MiSeq to determine the shared microbiota between the farm and the processing facility (8 genera). Culture independent analysis of bacterial taxa in milk, water and residual contamination after sanitation with swab samples revealed the shared and distinct microbiota between the sample types of both facilities. Amplicon sequence variants (ASVs) of the V3-V4 region of the 16S rRNA gene revealed that the microbiota of milk samples had lower diversity than water or environmental swabs (279 ASVs compared to 3,444 in water and 8,747 in environmental swabs). Brevibacterium and Yaniella (both Actinomycetota) were observed in all sampling types. Further studies will include whole genome sequencing of Brevibacterium spp. isolates to determine their functionality and diversity within the system.}, }
@article {pmid39266780, year = {2024}, author = {Cao, X and Li, M and Wu, X and Fan, S and Lin, L and Xu, L and Zhang, X and Zhou, F}, title = {Gut fungal diversity across different life stages of the onion fly Delia antiqua.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {115}, pmid = {39266780}, issn = {1432-184X}, mesh = {Animals ; *Diptera/microbiology/growth &amp; development ; *Fungi/classification/isolation &amp; purification/genetics ; *Gastrointestinal Microbiome ; *Larva/microbiology/growth &amp; development ; Male ; Female ; Pupa/microbiology/growth &amp; development ; Biodiversity ; Life Cycle Stages ; Mycobiome ; }, abstract = {A significant number of microorganisms inhabit the intestinal tract or the body surface of insects. While the majority of research on insect microbiome interaction has mainly focused on bacteria, of late multiple studies have been acknowledging the importance of fungi and have started reporting the fungal communities as well. In this study, high-throughput sequencing was used to compare the diversity of intestinal fungi in Delia antiqua (Diptera: Anthomyiidae) at different growth stages, and effect of differential fungi between adjacent life stages on the growth and development of D. antiqua was investigated. The results showed that there were significant differences in the α and β diversity of gut fungal communities between two adjacent growth stages. Among the dominant fungi, genera Penicillium and Meyerozyma and family Cordycipitaceae had higher abundances. Cordycipitaceae was mainly enriched in the pupal and adult (male and female) stages, Penicillium was mainly enriched in the pupal, 2nd instar and 3rd instar larval stages, and Meyerozyma was enriched in the pupal stage. Only three fungal species were found to differ between two adjacent growth stages. These three fungal species including Fusarium oxysporum, Meyerozyma guilliermondii and Penicillium roqueforti generally inhibited the growth and development of D. antiqua, with only P. roqueforti promoting the growth and development of female insects. This study will provide theoretical support for the search for new pathogenic microorganisms for other fly pests control and the development of new biological control strategies for fly pests.}, }
@article {pmid39264951, year = {2024}, author = {Pfennig, T and Kullmann, E and Zavřel, T and Nakielski, A and Ebenhöh, O and Červený, J and Bernát, G and Matuszyńska, AB}, title = {Shedding light on blue-green photosynthesis: A wavelength-dependent mathematical model of photosynthesis in Synechocystis sp. PCC 6803.}, journal = {PLoS computational biology}, volume = {20}, number = {9}, pages = {e1012445}, pmid = {39264951}, issn = {1553-7358}, mesh = {*Photosynthesis/physiology ; *Synechocystis/metabolism/physiology ; *Light ; *Models, Biological ; Computational Biology ; Carbon Dioxide/metabolism ; Carbon Cycle/physiology ; Phycobilisomes/metabolism ; Computer Simulation ; }, abstract = {Cyanobacteria hold great potential to revolutionize conventional industries and farming practices with their light-driven chemical production. To fully exploit their photosynthetic capacity and enhance product yield, it is crucial to investigate their intricate interplay with the environment including the light intensity and spectrum. Mathematical models provide valuable insights for optimizing strategies in this pursuit. In this study, we present an ordinary differential equation-based model for the cyanobacterium Synechocystis sp. PCC 6803 to assess its performance under various light sources, including monochromatic light. Our model can reproduce a variety of physiologically measured quantities, e.g. experimentally reported partitioning of electrons through four main pathways, O2 evolution, and the rate of carbon fixation for ambient and saturated CO2. By capturing the interactions between different components of a photosynthetic system, our model helps in understanding the underlying mechanisms driving system behavior. Our model qualitatively reproduces fluorescence emitted under various light regimes, replicating Pulse-amplitude modulation (PAM) fluorometry experiments with saturating pulses. Using our model, we test four hypothesized mechanisms of cyanobacterial state transitions for ensemble of parameter sets and found no physiological benefit of a model assuming phycobilisome detachment. Moreover, we evaluate metabolic control for biotechnological production under diverse light colors and irradiances. We suggest gene targets for overexpression under different illuminations to increase the yield. By offering a comprehensive computational model of cyanobacterial photosynthesis, our work enhances the basic understanding of light-dependent cyanobacterial behavior and sets the first wavelength-dependent framework to systematically test their producing capacity for biocatalysis.}, }
@article {pmid39264809, year = {2024}, author = {Boverhoff, D and Kool, J and Pijnacker, R and Ducarmon, QR and Zeller, G and Shetty, S and Sie, S and Mulder, AC and van der Klis, F and Franz, E and Mughini-Gras, L and van Baarle, D and Fuentes, S}, title = {Profiling the fecal microbiome and its modulators across the lifespan in the Netherlands.}, journal = {Cell reports}, volume = {43}, number = {9}, pages = {114729}, doi = {10.1016/j.celrep.2024.114729}, pmid = {39264809}, issn = {2211-1247}, mesh = {Netherlands ; Humans ; *Feces/microbiology ; Adult ; Aged ; Middle Aged ; Adolescent ; Child, Preschool ; Aged, 80 and over ; Child ; Infant ; Male ; Female ; Young Adult ; Infant, Newborn ; Longevity ; Gastrointestinal Microbiome/genetics ; Microbiota ; }, abstract = {Defining what constitutes a healthy microbiome throughout our lives remains an ongoing challenge. Understanding to what extent host and environmental factors can influence it has been the primary motivation for large population studies worldwide. Here, we describe the fecal microbiome of 3,746 individuals (0-87 years of age) in a nationwide study in the Netherlands, in association with extensive questionnaires. We validate previous findings, such as infant-adult trajectories, and explore the collective impact of our variables, which explain over 40% of the variation in microbiome composition. We identify associations with less explored factors, particularly those ethnic related, which show the largest impact on the adult microbiome composition, diversity, metabolic profiles, and CAZy (carbohydrate-active enzyme) repertoires. Understanding the sources of microbiome variability is crucial, given its potential as a modifiable target with therapeutic possibilities. With this work, we aim to serve as a foundational element for the design of health interventions and fundamental research.}, }
@article {pmid39264366, year = {2024}, author = {Yüksel, E and Voragen, AGJ and Kort, R}, title = {The pectin metabolizing capacity of the human gut microbiota.}, journal = {Critical reviews in food science and nutrition}, volume = {}, number = {}, pages = {1-23}, doi = {10.1080/10408398.2024.2400235}, pmid = {39264366}, issn = {1549-7852}, abstract = {The human gastrointestinal microbiota, densely populated with a diverse array of microorganisms primarily from the bacterial phyla Bacteroidota, Bacillota, and Actinomycetota, is crucial for maintaining health and physiological functions. Dietary fibers, particularly pectin, significantly influence the composition and metabolic activity of the gut microbiome. Pectin is fermented by gut bacteria using carbohydrate-active enzymes (CAZymes), resulting in the production of short-chain fatty acids (SCFAs) such as acetate, propionate, and butyrate, which provide various health benefits. The gastrointestinal microbiota has evolved to produce CAZymes that target different pectin components, facilitating cross-feeding within the microbial community. This review explores the fermentation of pectin by various gut bacteria, focusing on the involved transport systems, CAZyme families, SCFA synthesis capacity, and effects on microbial ecology in the gut. It addresses the complexities of the gut microbiome's response to pectin and highlights the importance of microbial cross-feeding in maintaining a balanced and diverse gut ecosystem. Through a systematic analysis of pectinolytic CAZyme production, this review provides insights into the enzymatic mechanisms underlying pectin degradation and their broader implications for human health, paving the way for more targeted and personalized dietary strategies.}, }
@article {pmid39264291, year = {2024}, author = {Jones, BS and DeWitt, ME and Wenner, JJ and Sanders, JW}, title = {Lyme Disease Under-Ascertainment During the COVID-19 Pandemic in the United States: Retrospective Study.}, journal = {JMIR public health and surveillance}, volume = {10}, number = {}, pages = {e56571}, pmid = {39264291}, issn = {2369-2960}, mesh = {Humans ; *Lyme Disease/epidemiology ; *COVID-19/epidemiology ; United States/epidemiology ; North Carolina/epidemiology ; Retrospective Studies ; Pandemics ; Bayes Theorem ; }, abstract = {BACKGROUND: The COVID-19 pandemic resulted in a massive disruption in access to care and thus passive, hospital- and clinic-based surveillance programs. In 2020, the reported cases of Lyme disease were the lowest both across the United States and North Carolina in recent years. During this period, human contact patterns began to shift with higher rates of greenspace utilization and outdoor activities, putting more people into contact with potential vectors and associated vector-borne diseases. Lyme disease reporting relies on passive surveillance systems, which were likely disrupted by changes in health care-seeking behavior during the pandemic.<br><br>OBJECTIVE: This study aimed to quantify the likely under-ascertainment of cases of Lyme disease during the COVID-19 pandemic in the United States and North Carolina.<br><br>METHODS: We fitted publicly available, reported Lyme disease cases for both the United States and North Carolina prior to the year 2020 to predict the number of anticipated Lyme disease cases in the absence of the pandemic using a Bayesian modeling approach. We then compared the ratio of reported cases divided by the predicted cases to quantify the number of likely under-ascertained cases. We then fitted geospatial models to further quantify the spatial distribution of the likely under-ascertained cases and characterize spatial dynamics at local scales.<br><br>RESULTS: Reported cases of Lyme Disease were lower in 2020 in both the United States and North Carolina than prior years. Our findings suggest that roughly 14,200 cases may have gone undetected given historical trends prior to the pandemic. Furthermore, we estimate that only 40% to 80% of Lyme diseases cases were detected in North Carolina between August 2020 and February 2021, the peak months of the COVID-19 pandemic in both the United States and North Carolina, with prior ascertainment rates returning to normal levels after this period. Our models suggest both strong temporal effects with higher numbers of cases reported in the summer months as well as strong geographic effects.<br><br>CONCLUSIONS: Ascertainment rates of Lyme disease were highly variable during the pandemic period both at national and subnational scales. Our findings suggest that there may have been a substantial number of unreported Lyme disease cases despite an apparent increase in greenspace utilization. The use of counterfactual modeling using spatial and historical trends can provide insight into the likely numbers of missed cases. Variable ascertainment of cases has implications for passive surveillance programs, especially in the trending of disease morbidity and outbreak detection, suggesting that other methods may be appropriate for outbreak detection during disturbances to these passive surveillance systems.}, }
@article {pmid39260494, year = {2024}, author = {Ejaz, MR and Badr, K and Hassan, ZU and Al-Thani, R and Jaoua, S}, title = {Metagenomic approaches and opportunities in arid soil research.}, journal = {The Science of the total environment}, volume = {953}, number = {}, pages = {176173}, doi = {10.1016/j.scitotenv.2024.176173}, pmid = {39260494}, issn = {1879-1026}, mesh = {*Soil Microbiology ; *Metagenomics ; *Soil/chemistry ; Desert Climate ; Microbiota ; }, abstract = {Arid soils present unique challenges and opportunities for studying microbial diversity and bioactive potential due to the extreme environmental conditions they bear. This review article investigates soil metagenomics as an emerging tool to explore complex microbial dynamics and unexplored bioactive potential in harsh environments. Utilizing advanced metagenomic techniques, diverse microbial populations that grow under extreme conditions such as high temperatures, salinity, high pH levels, and exposure to metals and radiation can be studied. The use of extremophiles to discover novel natural products and biocatalysts emphasizes the role of functional metagenomics in identifying enzymes and secondary metabolites for industrial and pharmaceutical purposes. Metagenomic sequencing uncovers a complex network of microbial diversity, offering significant potential for discovering new bioactive compounds. Functional metagenomics, connecting taxonomic diversity to genetic capabilities, provides a pathway to identify microbes' mechanisms to synthesize valuable secondary metabolites and other bioactive substances. Contrary to the common perception of desert soil as barren land, the metagenomic analysis reveals a rich diversity of life forms adept at extreme survival. It provides valuable findings into their resilience and potential applications in biotechnology. Moreover, the challenges associated with metagenomics in arid soils, such as low microbial biomass, high DNA degradation rates, and DNA extraction inhibitors and strategies to overcome these issues, outline the latest advancements in extraction methods, high-throughput sequencing, and bioinformatics. The importance of metagenomics for investigating diverse environments opens the way for future research to develop sustainable solutions in agriculture, industry, and medicine. Extensive studies are necessary to utilize the full potential of these powerful microbial communities. This research will significantly improve our understanding of microbial ecology and biotechnology in arid environments.}, }
@article {pmid39259499, year = {2024}, author = {Schwab, ST and Bühler, LY and Schleheck, D and Nelson, TF and Mecking, S}, title = {Correlation of Enzymatic Depolymerization Rates with the Structure of Polyethylene-Like Long-Chain Aliphatic Polyesters.}, journal = {ACS macro letters}, volume = {13}, number = {10}, pages = {1245-1250}, pmid = {39259499}, issn = {2161-1653}, abstract = {Long-chain aliphatic polyesters are emerging sustainable materials that exhibit polyethylene-like properties while being amenable to chemical recycling and biodegradation. However, varying polyester chemical structures results in markedly different degradation rates, which cannot be predicted from commonly correlated bulk polyester properties, such as polymer melting temperature. To elucidate these structure-degradability relationships, long-chain polyesters varying in their monomer composition and crystallinity were subjected to enzymatic hydrolysis, the rates of which were quantified via detection of formed monomers. Copolymers with poorly water-soluble, long-chain diol monomers (e.g., 1,18-octadecanediol) demonstrated strongly reduced depolymerization rates compared to copolymers with shorter chain length diol monomers. This was illustrated by, e.g., the 20× faster hydrolysis of PE-4,18, consisting of 1,4-butanediol and 1,18-octadecanedicarboxylic acid monomers, relative to PE-18,4. The insoluble long-chain diol monomer released upon hydrolysis was proposed to remain attached to the bulk polymer surface, decreasing the accessibility of the remaining ester bonds to enzymes for further hydrolysis. Tuning of polyester crystallinity via the introduction of branched monomers led to variable hydrolysis rates, which increased by an order of magnitude when crystallinity decreased from 72% to 45%. The results reported enables the informed design of polyester structures with balanced material properties and amenability to depolymerization.}, }
@article {pmid39259393, year = {2024}, author = {Berlow, M and Mesa, M and Creek, M and Duarte, JG and Carpenter, E and Phinizy, B and Andonian, K and Dlugosch, KM}, title = {Plant G × Microbial E: Plant Genotype Interaction with Soil Bacterial Community Shapes Rhizosphere Composition During Invasion.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {113}, pmid = {39259393}, issn = {1432-184X}, support = {1750280//NSF/ ; 1750280//NSF/ ; 1750280//NSF/ ; 1750280//NSF/ ; 1750280//NSF/ ; 1750280//NSF/ ; 1750280//NSF/ ; 1750280//NSF/ ; 2023-67012-40306//USDA/ ; 2023-67013-40169//USDA/ ; 2023-67013-40169//USDA/ ; }, mesh = {*Soil Microbiology ; *Rhizosphere ; *Introduced Species ; *Genotype ; *Microbiota ; *Bacteria/genetics/classification/isolation &amp; purification ; Centaurea/microbiology/genetics ; Plant Roots/microbiology ; California ; Soil/chemistry ; }, abstract = {It is increasingly recognized that different genetic variants of hosts can uniquely shape their microbiomes. Invasive species often evolve in their introduced ranges, but little is known about the potential for their microbial associations to change during invasion as a result. We asked whether host genotype (G), microbial environment (E), or their interaction (G × E) affected the composition and diversity of host-associated microbiomes in Centaurea solstitialis (yellow starthistle), a Eurasian plant that is known to have evolved novel genotypes and phenotypes and to have altered microbial interactions, in its severe invasion of CA, USA. We conducted an experiment in which native and invading plant genotypes were inoculated with native and invaded range soil microbial communities. We used amplicon sequencing to characterize rhizosphere bacteria in both the experiment and the field soils from which they were derived. We found that native and invading plant genotypes accumulated different microbial associations at the family level in each soil community, often counter to differences in family abundance between soil communities. Root associations with potentially beneficial Streptomycetaceae were particularly interesting, as these were more abundant in the invaded range field soil and accumulated on invading genotypes. We also found that bacterial diversity is higher in invaded soils, but that invading genotypes accumulated a lower diversity of bacteria and unique microbial composition in experimental inoculations, relative to native genotypes. Thus variation in microbial associations of invaders was driven by the interaction of plant G and microbial E, and rhizosphere microbial communities appear to change in composition in response to host evolution during invasion.}, }
@article {pmid39259373, year = {2024}, author = {Zhang, K and Tan, X and Zhang, Q}, title = {Nutritional Quality of Basal Resource in Stream Food Webs Increased with Light Reduction-Implications for Riparian Revegetation.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {114}, pmid = {39259373}, issn = {1432-184X}, support = {Nos. 32271665, 32030069//National Natural Science Foundation of China/ ; Nos. 32271665, 32030069//National Natural Science Foundation of China/ ; Nos. 32271665, 32030069//National Natural Science Foundation of China/ ; }, mesh = {*Rivers/microbiology/chemistry ; *Food Chain ; *Fatty Acids, Unsaturated/analysis/metabolism ; *Light ; Cyanobacteria/metabolism/growth &amp; development ; Chlorophyta/metabolism/growth &amp; development ; Diatoms/metabolism/growth &amp; development ; Nutritive Value ; }, abstract = {Biofilms are considered a basal resource with high nutritional quality in stream food webs, as periphytic algae are abundant of polyunsaturated fatty acids (PUFAs). PUFAs are essential for growth and reproduction of consumers who cannot or have very limited capacity to biosynthesize. Yet, how the nutritional quality based on PUFA of basal food sources changes with light intensity remains unclear. We conducted a manipulative experiment in mesocosms to explore the response and mechanisms of nutritional quality to shading, simulating riparian restoration. We found a significant increase in PUFA% (including arachidonic acid, ARA) under shading conditions. The increased PUFA is caused by the algal community succession from Cyanobacteria and Chlorophyta to Bacillariophyta which is abundant of PUFA (especially eicosapentaenoic acid, EPA; docosahexaenoic acid, DHA). On the other hand, shading increased PUFA via upregulating enzymes such as Δ12 desaturase (FAD2, EC:1.14.19.6) and 3-ketoacyl-CoA synthase (KCS, EC:2.3.1.199) in the biosynthesis of unsaturated fatty acid elongation pathways. Our findings imply that riparian reforestation by decreasing light intensity increases the nutritional quality of basal resources in streams, which may enhance transfer of good quality carbon to consumers in higher trophic levels through bottom-up effects.}, }
@article {pmid39258201, year = {2024}, author = {Iliopoulou, S and Kourteli, M and Damialis, A and Kapsanaki-Gotsi, E and Pyrri, I}, title = {Air mycobiome in the National Library of Greece following relocation to novel premises.}, journal = {Heliyon}, volume = {10}, number = {16}, pages = {e36362}, pmid = {39258201}, issn = {2405-8440}, abstract = {The aim of this work was to study the diversity and spatiotemporal fluctuations of airborne fungi in the National Library of Greece after its relocation from the Vallianeio historic building in the center of Athens to entirely new premises at the Stavros Niarchos Foundation Cultural Center, and also to compare the fungal aerosol in between the two sites. The air mycobiota were studied by a volumetric culture-based method, during the year 2019 in order to assess their diversity and abundance and to compare with those previously reported in the historic building. Twenty-eight genera of filamentous fungi were recovered indoors and 17 outdoors, in addition to yeasts registered as a group. The number of fungal genera recovered was almost similar in both premises, whereas seventeen genera indoors were identical, dominated by Penicillium, Cladosporium and Aspergillus. The mean daily fungal concentration was found to be 66 CFU m[-3] indoors and 927 CFU m[-3] outdoors in the new location vs 293 and 428 CFU m[-] [3] indoors and 707 and 648 CFU m[-] [3] outdoors in the previous one. The mean daily concentration indoors was consistently and significantly lower (P < 0.05) in the new building than in the historic one, although it was higher outdoors. The indoor/outdoor ratio for the total fungi was 0.07 in the new vs 0.41 and 0.66 in the previous one and reveals a superior indoor air quality in the new site. Air temperature and occupancy had a statistically significant impact on the concentration of indoor fungi. The remarkably reduced concentration of the mycobiota in the new premises indicated a considerable decline in fungal burden, mainly due to technological excellency of the facility and continuous preventive measures to ensure an enhanced indoor air quality in the National Library of Greece. This case study provides a paradigm about upgrading of indoor air after re-establishment of a facility in another setting.}, }
@article {pmid39256405, year = {2024}, author = {Gan, L and Zheng, J and Xu, WH and Lin, J and Liu, J and Zhang, Y and Wu, Z and Lv, Z and Jia, Y and Guo, Q and Chen, S and Liu, C and Defoirdt, T and Qin, Q and Liu, Y}, title = {Author Correction: Deciphering the virulent Vibrio harveyi causing spoilage in muscle of aquatic crustacean Litopenaeus vannamei.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {21131}, doi = {10.1038/s41598-024-71652-4}, pmid = {39256405}, issn = {2045-2322}, }
@article {pmid39256399, year = {2024}, author = {Huang, WRH and Braam, C and Kretschmer, C and Villanueva, SL and Liu, H and Ferik, F and van der Burgh, AM and Boeren, S and Wu, J and Zhang, L and Nürnberger, T and Wang, Y and Seidl, MF and Evangelisti, E and Stuttmann, J and Joosten, MHAJ}, title = {Author Correction: Receptor-like cytoplasmic kinases of different subfamilies differentially regulate SOBIR1/BAK1-mediated immune responses in Nicotiana benthamiana.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {7910}, doi = {10.1038/s41467-024-52322-5}, pmid = {39256399}, issn = {2041-1723}, }
@article {pmid39255667, year = {2024}, author = {Mei, Z and Wang, F and Fu, Y and Liu, Y and Hashsham, SA and Wang, Y and Harindintwali, JD and Dou, Q and Virta, M and Jiang, X and Deng, Y and Zhang, T and Tiedje, JM}, title = {Biofilm enhanced the mitigations of antibiotics and resistome in sulfadiazine and trimethoprim co-contaminated soils.}, journal = {Journal of hazardous materials}, volume = {479}, number = {}, pages = {135721}, pmid = {39255667}, issn = {1873-3336}, support = {P42 ES004911/ES/NIEHS NIH HHS/United States ; }, mesh = {*Sulfadiazine/pharmacology ; *Biofilms/drug effects ; *Trimethoprim/pharmacology ; *Soil Pollutants/toxicity ; *Anti-Bacterial Agents/pharmacology ; *Soil Microbiology ; *Manure/microbiology ; Arthrobacter/genetics/drug effects/metabolism ; Charcoal ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; }, abstract = {Reducing antibiotic levels in soil ecosystems is vital to curb the dissemination of antimicrobial resistance genes (ARGs) and mitigate global health threats. However, gaps persist in understanding how antibiotic resistome can be suppressed during antibiotic degradation. Herein, we investigate the efficacy of a biochar biofilm incorporating antibiotics-degrading bacterial strain (Arthrobacter sp. D2) to mitigate antibiotic resistome in non-manured and manure-amended soils with sulfadiazine (SDZ) and trimethoprim (TMP) contamination. Results show that biofilm enhanced SDZ degradation by 83.0% within three days and increased TMP attenuation by 55.4% over 60 days in non-manured soils. In the non-manured black soil, the relative abundance of ARGs increased initially after biofilm inoculation. However, by day 30, it decreased by 20.5% compared to the controls. Moreover, after 7 days, biofilm reduced TMP by 38.5% in manured soils and decreased the total ARG abundance by 19.0%. Thus, while SDZ degradation did not increase sulfonamide resistance genes, TMP dissipation led to a proliferation of insertion sequences and related TMP resistance genes. This study underscores the importance of antibiotic degradation in reducing related ARGs while cautioning against the potential proliferation and various ARGs transfer by resistant microorganisms.}, }
@article {pmid39254334, year = {2024}, author = {Lyng, M and Þórisdóttir, B and Sveinsdóttir, SH and Hansen, ML and Jelsbak, L and Maróti, G and Kovács, &#xc1;T}, title = {Taxonomy of Pseudomonas spp. determines interactions with Bacillus subtilis.}, journal = {mSystems}, volume = {9}, number = {10}, pages = {e0021224}, pmid = {39254334}, issn = {2379-5077}, support = {DNRF137//Danmarks Grundforskningsfond (DNRF)/ ; NNF19SA0059360//Novo Nordisk Fonden (NNF)/ ; NNF19OC0055625//Novo Nordisk Fonden (NNF)/ ; PhD fellowship//Technical University of Denmark/ ; }, mesh = {*Pseudomonas/physiology ; *Bacillus subtilis/physiology ; *Soil Microbiology ; *Microbial Interactions/physiology ; Rhizosphere ; }, abstract = {UNLABELLED: Bacilli and pseudomonads are among the most well-studied microorganisms commonly found in soil and frequently co-isolated. Isolates from these two genera are frequently used as plant beneficial microorganisms; therefore, their interaction in the plant rhizosphere is relevant for agricultural applications. Despite this, no systematic approach has been employed to assess the coexistence of members from these genera. Here, we screened 720 fluorescent soil isolates for their effects on Bacillus subtilis pellicle formation in two types of media and found a predictor for interaction outcome in Pseudomonas taxonomy. Interactions were context-dependent, and both medium composition and culture conditions strongly influenced interactions. Negative interactions were associated with Pseudomonas capeferrum, Pseudomonas entomophila, and Pseudomonas protegens, and 2,4-diacetylphloroglucinol was confirmed as a strong (but not exclusive) inhibitor of B. subtilis. Non-inhibiting strains were closely related to Pseudomonas trivialis and Pseudomonas lini. Using such a non-inhibiting isolate, Pseudomonas P9_31, which increased B. subtilis pellicle formation demonstrated that the two species were spatially segregated in cocultures. Our study is the first one to propose an overall negative outcome from pairwise interactions between B. subtilis and fluorescent pseudomonads; hence, cocultures comprising members from these groups are likely to require additional microorganisms for coexistence.<br><br>IMPORTANCE: There is a strong interest in the microbial ecology field to predict interaction among microorganisms, whether two microbial isolates will promote each other's growth or compete for resources. Numerous studies have been performed based on surveying the available literature or testing phylogenetically diverse sets of species in synthetic communities. Here, a high throughput screening has been performed using 720 Pseudomonas isolates, and their impact on the biofilm formation of Bacillus subtilis was tested. The aim was to determine whether a majority of Pseudomonas will promote or inhibit the biofilms of B. subtilis in the co-cultures. This study reports that Pseudomonas taxonomy is a good predictor of interaction outcome, and only a minority of Pseudomonas isolates promote Bacillus biofilm establishment.}, }
@article {pmid39252061, year = {2024}, author = {Trego, A and O'Sullivan, S and O'Flaherty, V and Collins, G and Ijaz, UZ}, title = {Individual methanogenic granules are whole-ecosystem replicates with reproducible responses to environmental cues.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {68}, pmid = {39252061}, issn = {2524-6372}, support = {3C-BIOTECH 261330/ERC_/European Research Council/International ; 3C-BIOTECH 261330/ERC_/European Research Council/International ; 3C-BIOTECH 261330/ERC_/European Research Council/International ; TC/2014/0016//Enterprise Ireland/ ; 14/IA/2371/SFI_/Science Foundation Ireland/Ireland ; 17/CDA/4658/SFI_/Science Foundation Ireland/Ireland ; NE/L011956/1//Natural Environment Research Council/ ; }, abstract = {BACKGROUND: In this study, individual methanogenic (anaerobic), granular biofilms were used as true community replicates to assess whole-microbial-community responses to environmental cues. The aggregates were sourced from a lab-scale, engineered, biological wastewater treatment system, were size-separated, and the largest granules were individually subjected to controlled environmental cues in micro-batch reactors (μBRs).<br><br>RESULTS: Individual granules were identical with respect to the structure of the active community based on cDNA analysis. Additionally, it was observed that the active microbial community of individual granules, at the depth of 16S rRNA gene sequencing, produced reproducible responses to environmental changes in pH, temperature, substrate, and trace-metal supplementation. We identified resilient and susceptible taxa associated with each environmental condition tested, as well as selected specialists, whose niche preferences span the entire trophic chain required for the complete anaerobic degradation of organic matter.<br><br>CONCLUSIONS: We found that single anaerobic granules can be considered highly-replicated whole-ecosystems with potential usefulness for the field of microbial ecology. Additionally, they act as the smallest whole-community unit within the meta-community of an engineered bioreactor. When subjected to various environmental cues, anaerobic granules responded reproducibly allowing for rare or unique opportunities for high-throughput studies testing whole-community responses to a wide range of environmental conditions.}, }
@article {pmid39250422, year = {2024}, author = {Vijay, S and Bao, NLH and Vinh, DN and Nhat, LTH and Thu, DDA and Quang, NL and Trieu, LPT and Nhung, HN and Ha, VTN and Thai, PVK and Ha, DTM and Lan, NH and Caws, M and Thwaites, GE and Javid, B and Thuong, NT}, title = {Rifampicin tolerance and growth fitness among isoniazid-resistant clinical Mycobacterium tuberculosis isolates from a longitudinal study.}, journal = {eLife}, volume = {13}, number = {}, pages = {}, pmid = {39250422}, issn = {2050-084X}, support = {10.35802/207487/WT_/Wellcome Trust/United Kingdom ; R21 AI169005/AI/NIAID NIH HHS/United States ; R21AI169005//National Institute of Allergy and Infectious Diseases/ ; 10.35802/106680/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; 10.35802/206724/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Rifampin/pharmacology ; *Mycobacterium tuberculosis/drug effects/genetics ; *Isoniazid/pharmacology ; Longitudinal Studies ; *Microbial Sensitivity Tests ; Humans ; *Antitubercular Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Tuberculosis, Multidrug-Resistant/microbiology/drug therapy ; Tuberculosis/microbiology/drug therapy ; }, abstract = {Antibiotic tolerance in Mycobacterium tuberculosis reduces bacterial killing, worsens treatment outcomes, and contributes to resistance. We studied rifampicin tolerance in isolates with or without isoniazid resistance (IR). Using a minimum duration of killing assay, we measured rifampicin survival in isoniazid-susceptible (IS, n=119) and resistant (IR, n=84) isolates, correlating tolerance with bacterial growth, rifampicin minimum inhibitory concentrations (MICs), and isoniazid-resistant mutations. Longitudinal IR isolates were analyzed for changes in rifampicin tolerance and genetic variant emergence. The median time for rifampicin to reduce the bacterial population by 90% (MDK90) increased from 1.23 days (IS) and 1.31 days (IR) to 2.55 days (IS) and 1.98 days (IR) over 15-60 days of incubation, indicating fast and slow-growing tolerant sub-populations. A 6 log10-fold survival fraction classified tolerance as low, medium, or high, showing that IR is linked to increased tolerance and faster growth (OR = 2.68 for low vs. medium, OR = 4.42 for low vs. high, p-trend = 0.0003). High tolerance in IR isolates was associated with rifampicin treatment in patients and genetic microvariants. These findings suggest that IR tuberculosis should be assessed for high rifampicin tolerance to optimize treatment and prevent the development of multi-drug-resistant tuberculosis.}, }
@article {pmid39249553, year = {2024}, author = {Morimura, H and Ishigami, K and Sato, T and Sone, T and Kikuchi, Y}, title = {Geographical, Seasonal, and Growth-Related Dynamics of Gut Microbiota in a Grapevine Pest, Apolygus spinolae (Heteroptera: Miridae).}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {112}, pmid = {39249553}, issn = {1432-184X}, support = {22KJ0057//Japan Society for the Promotion of Science/ ; 21K20579//Japan Society for the Promotion of Science/ ; S-3-7//Northern Advancement Center for Science and Technology/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Vitis/microbiology ; *Heteroptera/microbiology/growth &amp; development ; *Seasons ; *Bacteria/classification/genetics/isolation &amp; purification ; *Symbiosis ; Japan ; Nymph/microbiology/growth &amp; development ; }, abstract = {A number of insects are associated with gut symbiotic microorganisms, wherein symbiotic partners play pivotal metabolic roles for each other such as nutrient supplementation, diet degradation, and pesticide detoxification. Despite the ecological and evolutionary importance of gut microbial communities in insects, their diversity and dynamics remain unclear in many species. The green plant bug Apolygus spinolae, a notorious grapevine pest in Japan, damages grape shoots and severely reduces grape berry yield and quality. The plant bug possesses a simple tubular gut housing ~ 10[4] bacteria. Here, we investigated geographic, seasonal, and growth-related dynamics of gut microbiota by high-throughput sequencing in 82 individuals (11 nymphs and 71 adults) from five locations in Hokkaido, Japan. In plant bugs, gut microbiota changed dynamically depending on region, season, and developmental stage. Among the gut bacteria, Serratia was consistently and abundantly detected and was significantly affected by seasonal changes. In addition, Caballeronia, known as a specific symbiont in some stinkbug species, was abundantly detected, especially in insects collected in late summer despite A. spinolae complete lack of midgut crypts known as symbiotic organ harboring Caballeronia in other stinkbug species. Considering their prevalence among host bug populations, it is possible these gut microorganisms play a pivotal role in the adaptation of the green plant bug to grapevine fields, although further confirmation through rearing experiments is needed.}, }
@article {pmid39248572, year = {2024}, author = {Sivaloganathan, DM and Wan, X and Leon, G and Brynildsen, MP}, title = {Loss of Gre factors leads to phenotypic heterogeneity and cheating in Escherichia coli populations under nitric oxide stress.}, journal = {mBio}, volume = {15}, number = {10}, pages = {e0222924}, pmid = {39248572}, issn = {2150-7511}, support = {CBET-1453325//National Science Foundation (NSF)/ ; PGSD3 - 516782 - 2018//Canadian Government | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; Focused Research Team award on Precision Antibiotics//Princeton University (PU)/ ; }, mesh = {*Escherichia coli/genetics/metabolism/drug effects ; *Escherichia coli Proteins/genetics/metabolism ; *Gene Expression Regulation, Bacterial ; Hydrogen Peroxide/pharmacology/metabolism/toxicity ; *Nitric Oxide/metabolism ; Phenotype ; Stress, Physiological ; Transcription Factors/genetics/metabolism ; Transcriptional Elongation Factors/metabolism/genetics ; }, abstract = {Nitric oxide (·NO) is one of the toxic metabolites that bacteria can be exposed to within phagosomes. Gre factors, which are also known as transcript cleavage factors or transcription elongation factors, relieve back-tracked transcription elongation complexes by cleaving nascent RNAs, which allows transcription to resume after stalling. Here we discovered that loss of both Gre factors in Escherichia coli, GreA and GreB, significantly compromised ·NO detoxification due to ·NO-induced phenotypic heterogeneity in ΔgreAΔgreB populations, which did not occur in wild-type cultures. Under normal culturing conditions, both wild-type and ΔgreAΔgreB synthesized transcripts uniformly, whereas treatment with ·NO led to bimodal transcript levels in ΔgreAΔgreB that were unimodal in wild-type. Interestingly, exposure to another toxic metabolite of phagosomes, hydrogen peroxide (H2O2), produced analogous results. Furthermore, we showed that loss of Gre factors led to cheating under ·NO stress where transcriptionally deficient cells benefited from the detoxification activities of the transcriptionally proficient subpopulation. Collectively, these results show that loss of Gre factor activities produces phenotypic heterogeneity under ·NO and H2O2 stress that can yield cheating between subpopulations.IMPORTANCEToxic metabolite stress occurs in a broad range of contexts that are important to human health, microbial ecology, and biotechnology, whereas Gre factors are highly conserved throughout the bacterial kingdom. Here we discovered that loss of Gre factors in E. coli leads to phenotypic heterogeneity under ·NO and H2O2 stress, which we further show with ·NO results in cheating between subpopulations. Collectively, these data suggest that Gre factors play a role in coping with toxic metabolite stress, and that loss of Gre factors can produce cheating between neighbors.}, }
@article {pmid39248476, year = {2024}, author = {Maitra, P and Hrynkiewicz, K and Szuba, A and Niestrawska, A and Mucha, J}, title = {The effects of Pinus sylvestris L. geographical origin on the community and co-occurrence of fungal and bacterial endophytes in a common garden experiment.}, journal = {Microbiology spectrum}, volume = {12}, number = {10}, pages = {e0080724}, pmid = {39248476}, issn = {2165-0497}, mesh = {*Pinus sylvestris/microbiology ; *Endophytes/classification/isolation &amp; purification/genetics/physiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Fungi/classification/isolation &amp; purification/genetics/physiology ; *Plant Roots/microbiology ; *Microbiota ; Seasons ; Phylogeny ; Biodiversity ; }, abstract = {UNLABELLED: Below-ground microorganisms, particularly endophytes, are pivotal for plant establishment and functioning through nutrient acquisition and enhancing resistance to abiotic and biotic stresses. The impact of host plant origin within a species on the composition and interaction networks of root endophytic fungi and bacteria has been less explored compared with plant phylogeny and biological distance. This study investigates the effect of geographic origin on the fungal and bacterial microbiomes of Pinus sylvestris L. root endophytes. Roots from plants grown in a common garden, originating from six locations, were harvested in two distinct seasons. Fungal and bacterial microbiomes were analyzed using Illumina MiSeq sequencing. The operational taxonomic unit (OTU) richness of endophytic fungi and bacteria showed no significant variation due to tree origin or season. However, the Shannon diversity index for endophytic fungi was seasonally influenced. The composition of endophytic fungal and bacterial communities was affected by both tree origin and season, correlating with host root biochemical parameters, such as starch, total non-structural carbohydrates, carbon, nitrogen, and climatic factors, such as mean annual precipitation and temperature. Moreover, the abundance of specific endophytic fungi and bacteria varied across different P. sylvestris origins, depending on the season. The complexity of the co-occurrence networks of fungal and bacterial endophytes within P. sylvestris also differed by geographical origin and season. This study highlights the significant role of biochemical and climatic factors associated with tree origin in shaping interactions with endophytic communities, potentially affecting plant health and adaptability across diverse environments.<br><br>IMPORTANCE: This study advances our understanding of how plant ecotype and seasonal changes influence root endophytic communities in Scots pine (Pinus sylvestris). By examining trees from various origins grown in a common garden, it highlights the role of tree origin and season in shaping fungal and bacterial community and co-occurrence networks. Importantly, this research demonstrates that tree origin impacts the composition and interaction networks of root endophytes and depends on the season. The study's findings suggest that root biochemical traits and climatic conditions (e.g., temperature, precipitation) associated with tree origin are crucial in determining the assembly of endophytic communities. This understanding could lead to innovative strategies for enhancing plant health and adaptability across different environments, contributing to forestry and conservation efforts. The research underscores the complexity of plant-microbe interactions and the need for a comprehensive approach to studying them, highlighting the interplay between tree origin and microbial ecology in forest ecosystems.}, }
@article {pmid39248406, year = {2024}, author = {Yuan, X and Qing, J and Zhi, W and Wu, F and Yan, Y and Li, Y}, title = {Gut and respiratory microbiota landscapes in IgA nephropathy: a cross-sectional study.}, journal = {Renal failure}, volume = {46}, number = {2}, pages = {2399749}, pmid = {39248406}, issn = {1525-6049}, mesh = {Humans ; *Glomerulonephritis, IGA/microbiology ; Cross-Sectional Studies ; Male ; Female ; Adult ; *Gastrointestinal Microbiome ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Machine Learning ; Case-Control Studies ; Bacteria/isolation &amp; purification/classification/genetics ; Microbiota ; Young Adult ; }, abstract = {BACKGROUND: IgA nephropathy (IgAN) is intimately linked to mucosal immune responses, with nasopharyngeal and intestinal lymphoid tissues being crucial for its abnormal mucosal immunity. The specific pathogenic bacteria in these sites associated with IgAN, however, remain elusive. Our study employs 16S rRNA sequencing and machine learning (ML) approaches to identify specific pathogenic bacteria in these locations and to investigate common pathogens that may exacerbate IgAN.<br><br>METHODS: In this cross-sectional analysis, we collected pharyngeal swabs and stool specimens from IgAN patients and healthy controls. We applied 16SrRNA sequencing to identify differential microbial populations. ML algorithms were then used to classify IgAN based on these microbial differences. Spearman correlation analysis was employed to link key bacteria with clinical parameters.<br><br>RESULTS: We observed a reduced microbial diversity in IgAN patients compared to healthy controls. In the gut microbiota of IgAN patients, increases in Bacteroides, Escherichia-Shigella, and Parabacteroides, and decreases in Parasutterella, Dialister, Faecalibacterium, and Subdoligranulum were notable. In the respiratory microbiota, increases in Neisseria, Streptococcus, Fusobacterium, Porphyromonas, and Ralstonia, and decreases in Prevotella, Leptotrichia, and Veillonella were observed. Post-immunosuppressive therapy, Oxalobacter and Butyricoccus levels were significantly reduced in the gut, while Neisseria and Actinobacillus levels decreased in the respiratory tract. Veillonella and Fusobacterium appeared to influence IgAN through dual immune loci, with Fusobacterium abundance correlating with IgAN severity.<br><br>CONCLUSIONS: This study revealing that changes in flora structure could provide important pathological insights for identifying therapeutic targets, and ML could facilitate noninvasive diagnostic methods for IgAN.}, }
@article {pmid39247694, year = {2024}, author = {Nasher, F and Wren, BW}, title = {Unravelling mechanisms of bacterial recognition by Acanthamoeba: insights into microbial ecology and immune responses.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1405133}, pmid = {39247694}, issn = {1664-302X}, abstract = {Acanthamoeba, are ubiquitous eukaryotic microorganisms, that play a pivotal role in recognizing and engulfing various microbes during predation, offering insights into microbial dynamics and immune responses. An intriguing observation lies in the apparent preference of Acanthamoeba for Gram-negative over Gram-positive bacteria, suggesting potential differences in the recognition and response mechanisms to bacterial prey. Here, we comprehensively review pattern recognition receptors (PRRs) and microbe associated molecular patterns (MAMPs) that influence Acanthamoeba interactions with bacteria. We analyze the molecular mechanisms underlying these interactions, and the key finding of this review is that Acanthamoeba exhibits an affinity for bacterial cell surface appendages that are decorated with carbohydrates. Notably, this parallels warm-blooded immune cells, underscoring a conserved evolutionary strategy in microbial recognition. This review aims to serve as a foundation for exploring PRRs and MAMPs. These insights enhance our understanding of ecological and evolutionary dynamics in microbial interactions and shed light on fundamental principles governing immune responses. Leveraging Acanthamoeba as a model organism, provides a bridge between ecological interactions and immunology, offering valuable perspectives for future research.}, }
@article {pmid39247294, year = {2024}, author = {Grimm, H and Drabesch, S and Nicol, A and Straub, D and Joshi, P and Zarfl, C and Planer-Friedrich, B and Muehe, EM and Kappler, A}, title = {Arsenic immobilization and greenhouse gas emission depend on quantity and frequency of nitrogen fertilization in paddy soil.}, journal = {Heliyon}, volume = {10}, number = {16}, pages = {e35706}, pmid = {39247294}, issn = {2405-8440}, abstract = {Nitrogen (N) fertilization in paddy soils decreases arsenic mobility and methane emissions. However, it is unknown how quantity and frequency of N fertilization affects the interlinked redox reactions of iron(II)-driven denitrification, iron mineral (trans-)formation with subsequent arsenic (im-)mobilization, methane and nitrous oxide emissions, and how this links to microbiome composition. Thus, we incubated paddy soil from Vercelli, Italy, over 129 days and applied nitrate fertilizer at different concentrations (control: 0, low: ∼35, medium: ∼100, high: ∼200 mg N kg[-1] soil[-1]) once at the beginning and after 49 days. In the high N treatment, nitrate reduction was coupled to oxidation of dissolved and solid-phase iron(II), while naturally occurring arsenic was retained on iron minerals due to suppression of reductive iron(III) mineral dissolution. In the low N treatment, 40 μg L[-1] of arsenic was mobilized into solution after nitrate depletion, with 69 % being immobilized after a second nitrate application. In the non-fertilized control, concentrations of dissolved arsenic were as high as 76 μg L[-1], driven by mobilization of 36 % of the initial mineral-bound arsenic. Generally, N fertilization led to 1.5-fold higher total GHG emissions (sum of CO2, CH4 and N2O as CO2 equivalents), 158-fold higher N2O, and 7.5-fold lower CH4 emissions compared to non-fertilization. On day 37, Gallionellaceae, Comamonadaceae and Rhodospirillales were more abundant in the high N treatment compared to the non-fertilized control, indicating their potential role as key players in nitrate reduction coupled to iron(II) oxidation. The findings underscore the dual effect of N fertilization, immobilizing arsenic in the short-term (low/medium N) or long-term (high N), while simultaneously increasing N2O and lowering CH4 emissions. This highlights the significance of both the quantity and frequency of N fertilizer application in paddy soils.}, }
@article {pmid39244747, year = {2024}, author = {Bayer, B and Liu, S and Louie, K and Northen, TR and Wagner, M and Daims, H and Carlson, CA and Santoro, AE}, title = {Metabolite release by nitrifiers facilitates metabolic interactions in the ocean.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39244747}, issn = {1751-7370}, support = {J 4426/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {*Seawater/microbiology ; *Nitrification ; Oceans and Seas ; Nitrites/metabolism ; Heterotrophic Processes ; Microbial Interactions ; Metabolome ; Coculture Techniques ; Ammonia/metabolism ; }, abstract = {Microbial chemoautotroph-heterotroph interactions may play a pivotal role in the cycling of carbon in the deep ocean, reminiscent of phytoplankton-heterotroph associations in surface waters. Nitrifiers are the most abundant chemoautotrophs in the global ocean, yet very little is known about nitrifier metabolite production, release, and transfer to heterotrophic microbial communities. To elucidate which organic compounds are released by nitrifiers and potentially available to heterotrophs, we characterized the exo- and endometabolomes of the ammonia-oxidizing archaeon Nitrosopumilus adriaticus CCS1 and the nitrite-oxidizing bacterium Nitrospina gracilis Nb-211. Nitrifier endometabolome composition was not a good predictor of exometabolite availability, indicating that metabolites were predominately released by mechanisms other than cell death/lysis. Although both nitrifiers released labile organic compounds, N. adriaticus preferentially released amino acids, particularly glycine, suggesting that its cell membranes might be more permeable to small, hydrophobic amino acids. We further initiated co-culture systems between each nitrifier and a heterotrophic alphaproteobacterium, and compared exometabolite and transcript patterns of nitrifiers grown axenically to those in co-culture. In particular, B vitamins exhibited dynamic production and consumption patterns in nitrifier-heterotroph co-cultures. We observed an increased production of vitamin B2 and the vitamin B12 lower ligand dimethylbenzimidazole by N. adriaticus and N. gracilis, respectively. In contrast, the heterotroph likely produced vitamin B5 in co-culture with both nitrifiers and consumed the vitamin B7 precursor dethiobiotin when grown with N. gracilis. Our results indicate that B vitamins and their precursors could play a particularly important role in governing specific metabolic interactions between nitrifiers and heterotrophic microbes in the ocean.}, }
@article {pmid39244369, year = {2024}, author = {Baptista, RC and Ferrocino, I and Pavani, M and Guerreiro, TM and Câmara, AA and Lang, &#xc9; and Dos Santos, JLP and Catharino, RR and Alves Filho, EG and Rodrigues, S and de Brito, ES and Caturla, MYR and Sant'Ana, AS and Cocolin, L}, title = {Microbiota diversity of three Brazilian native fishes during ice and frozen storage.}, journal = {Food microbiology}, volume = {124}, number = {}, pages = {104617}, doi = {10.1016/j.fm.2024.104617}, pmid = {39244369}, issn = {1095-9998}, mesh = {Animals ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Volatile Organic Compounds/analysis/metabolism ; *Food Storage ; *Fishes/microbiology ; Brazil ; *Seafood/microbiology/analysis ; *RNA, Ribosomal, 16S/genetics ; *Freezing ; Ice ; Food Microbiology ; Biodiversity ; Female ; }, abstract = {This study aimed to assess the bacterial microbiota involved in the spoilage of pacu (Piaractus mesopotamics), patinga (female Piaractus mesopotamics x male Piaractus brachypomus), and tambacu (female Colossoma macropomum × male Piaractus mesopotamics) during ice and frozen storage. Changes in the microbiota of three fish species (N = 22) during storage were studied through 16S rRNA amplicon-based sequencing and correlated with volatile organic compounds (VOCs) and metabolites assessed by nuclear magnetic resonance (NMR). Storage conditions (time and temperature) affected the microbiota diversity in all fish samples. Fish microbiota comprised mainly of Pseudomonas sp., Brochothrix sp., Acinetobacter sp., Bacillus sp., Lactiplantibacillus sp., Kocuria sp., and Enterococcus sp. The relative abundance of Kocuria, P. fragi, L. plantarum, Enterococcus, and Acinetobacter was positively correlated with the metabolic pathways of ether lipid metabolism while B. thermosphacta and P. fragi were correlated with metabolic pathways involved in amino acid metabolism. P. fragi was the most prevalent spoilage bacteria in both storage conditions (ice and frozen), followed by B. thermosphacta. Moreover, the relative abundance of identified Bacillus strains in fish samples stored in ice was positively correlated with the production of VOCs (1-hexanol, nonanal, octenol, and 2-ethyl-1-hexanol) associated with off-flavors. [1]H NMR analysis confirmed that amino acids, acetic acid, and ATP degradation products increase over (ice) storage, and therefore considered chemical spoilage index of fish fillets.}, }
@article {pmid39243903, year = {2024}, author = {Macedo Silva, JR and Petra de Oliveira Barros, V and Terceiro, PS and Nunes de Oliveira, &#xcd; and Francisco da Silva Moura, O and Duarte de Freitas, J and Crispim, AC and Maciel Melo, VM and Thompson, FL and Maraschin, M and Landell, MF}, title = {Brazilian mangrove sediments as a source of biosurfactant-producing yeast Pichia pseudolambica for bioremediation.}, journal = {Chemosphere}, volume = {365}, number = {}, pages = {143285}, doi = {10.1016/j.chemosphere.2024.143285}, pmid = {39243903}, issn = {1879-1298}, mesh = {*Surface-Active Agents/metabolism ; *Biodegradation, Environmental ; Brazil ; *Pichia/metabolism ; *Geologic Sediments/microbiology/chemistry ; Surface Tension ; Wetlands ; Hydrocarbons/metabolism ; }, abstract = {This work highlights the biosurfactant production potential of yeasts from mangroves in northeastern Brazil. The biosurfactants were evaluated by their emulsifying capacity (EI24), with 6 isolates showing values between 50% and 62%. Surfactant properties from crude extract were measured using drop collapse, oil displacement, Parafilm® M, surface tension and critical micellar concentration tests. The effects of temperature, salinity, pH, and the ability to emulsify different hydrocarbons were analyzed, showing a promising potential of the yeast species investigated to tolerance to high temperatures and acidic pH, in addition to emulsifying different sources of hydrocarbons with environmental impact. It is important to note that the Pichia pseudolambica isolates showed a remarkable ability to reduce the surface tension of water, from 70.82 mN/m to 36.47 mN/m. In addition, the critical micellar concentration (CMC) values ranged from 7 to 16 mg/mL, highlighting the promising surfactant activity of these isolates for future applications. It was identified that the biosurfactant adhered to the yeast cell wall, and FTIR and 1H NMR spectroscopy analysis was carried out on the yeast biomass and its post-sonication supernatant. The results indicate the presence of characteristic functional groups and peaks found in biosurfactants of a glycolipid nature. Taking together the results reveals the promising potential of biosurfactant biosynthesis of P. pseudolambica yeast, a trait not reported in the literature so far for this species. P. pseudolambica presents a relevant metabolic potential for alternative substrate use and resilience to adverse conditions that could enable it to produce biosurfactants for the biotechnological remediation of areas contaminated by oil derivatives. The metabolic properties herein investigated, together with their presence in Brazilian mangroves, make P. pseudolambica an emerging candidate for developing industrial processes and sustainable strategies for the recovery of ecosystems impacted by oil spills, being positioned as a sustainable alternative to conventional surfactants.}, }
@article {pmid39243542, year = {2024}, author = {Song, Y and Zhang, Z and Liu, Y and Peng, F and Feng, Y}, title = {Enhancement of anaerobic treatment of antibiotic pharmaceutical wastewater through the development of iron-based and carbon-based materials: A critical review.}, journal = {Journal of hazardous materials}, volume = {479}, number = {}, pages = {135514}, doi = {10.1016/j.jhazmat.2024.135514}, pmid = {39243542}, issn = {1873-3336}, mesh = {*Anti-Bacterial Agents/chemistry ; *Wastewater/chemistry ; Anaerobiosis ; *Iron/chemistry ; *Water Pollutants, Chemical/chemistry ; Carbon/chemistry ; Waste Disposal, Fluid/methods ; Biodegradation, Environmental ; Water Purification/methods ; }, abstract = {The extensive use of antibiotics has created an urgent need to address antibiotic wastewater treatment, posing significant challenges for environmental protection and public health. Recent advances in the efficacy and mechanisms of conductive materials (CMs) for enhancing the anaerobic biological treatment of antibiotic pharmaceutical wastewater are reviewed. For the first time, the focus is on the various application forms of iron-based and carbon-based CMs in strengthening the anaerobic methanogenic system. This includes the use of single CMs such as zero-valent iron (ZVI), magnetite, biochar (BC), activated carbon (AC), and graphene (GP), as well as iron-based and carbon-based composite CMs with diverse structures. These structures include mixed, surface-loaded, and core-shell combinations, reflecting the development of CMs. Iron-based and carbon-based CMs promote the rapid removal of antibiotics through adsorption and enhanced biodegradation. They also mitigate the inhibitory effects of toxic pollutants on microbial activity and reduce the expression of antibiotic resistance genes (ARGs). Additionally, as effective electron carriers, these CMs enrich microorganisms with direct interspecies electron transfer (DIET) functions, accelerate interspecies electron transfer, and facilitate the conversion of organic matter into methane. Finally, this review proposes the use of advanced molecular detection technologies to clarify microbial ecology and metabolic mechanisms, along with microscopic characterization techniques for the modification of CMs. These methods can provide more direct evidence to analyze the mechanisms underlying the cooperative anaerobic treatment of refractory organic wastewater by CMs and microorganisms.}, }
@article {pmid39239791, year = {2024}, author = {Fouad, AM and Abo-Al-Ela, HG and Negm, EA and Abdelhaseib, M and Alian, A and Abdelsater, N and Said, REM and Anwar, FAS and Assar, DH and Mohamed, SA}, title = {Impact of Polyonchobothrium magnum on health and gut microbial ecology of African catfish (Clarias gariepinus): Insights from morphological, molecular, and microbiological analyses.}, journal = {Journal of fish diseases}, volume = {}, number = {}, pages = {e14013}, doi = {10.1111/jfd.14013}, pmid = {39239791}, issn = {1365-2761}, abstract = {Parasites pose significant challenges to aquaculture and fisheries industries. Our study focuses on the Polyonchobothrium magnum and African catfish to address a potential health issue in aquaculture, explore host-parasite interactions that can help develop effective management practices to ensure fish health and industry sustainability. P. magnum was isolated from the stomach of African catfish (Clarias gariepinus) as the primary site of infection, with a prevalence of 10%. Most affected fish were heavily infected (8 out of 10). Infection was confirmed by sequencing the PCR-targeted region of the nicotinamide adenine dinucleotide dehydrogenase subunit 1 (ND1) gene, along with light and scanning electron microscopes. The parasite had an elongated scolex with deep bothria, a prominent apical disc wider than the scolex itself, and a four-lobed appearance. The scolex contained a central rostellum divided into two semicircles, bearing 26-30 hooks, with an average of 28. The apical disc had large hooks arranged in four quadrants, with 6-8 hooks each, averaging 7 per quadrant. No neck was observed. Phylogenetic analysis of our sequence showed a 100% match with isolates from Guangzhou, China. In infected fish, the anterior kidney showed increased expression levels of nuclear factor kappa B and lysozyme, but decreased levels of in major histocompatibility complex antigen II. Plasma analysis revealed a significant drop in superoxide dismutase, a rise in interleukin-1 beta, and lower IgM levels compared to non-infected controls. Non-infected fish displayed greater gut microbiota diversity, with dominant families including Moraxellaceae, Enterobacteriaceae, Fusobacteriaceae, and Caulobacteraceae, and prevalent genera such as Acinetobacter, Cetobacterium, and Brevundimonas. In contrast, infected fish exhibited very low diversity, with significantly higher proportions of Enterobacteriaceae (45.99%) and Aeromonadaceae (41.79%) compared to non-infected fish, which had 13.76% and 3.64% respectively. Cetobacterium somerae was prevalent in non-infected fish, while infected fish harboured Aeromonas fluvialis, Plesiomonas shigelloides, and Gallaecimonas xiamenensis. Overall, P. magnum disrupted the immune status and gut microbiota of the host, thereby impacting its health.}, }
@article {pmid39236824, year = {2024}, author = {Guo, Q and Xiao, Y and Zhu, Y and Korpelainen, H and Li, C}, title = {Selenium availability in tea: Unraveling the role of microbiota assembly and functions.}, journal = {The Science of the total environment}, volume = {952}, number = {}, pages = {175995}, doi = {10.1016/j.scitotenv.2024.175995}, pmid = {39236824}, issn = {1879-1026}, mesh = {*Selenium/metabolism/analysis ; *Microbiota ; *Camellia sinensis/metabolism ; *Soil Microbiology ; Tea ; Soil/chemistry ; Soil Pollutants/metabolism/analysis ; Bacteria/metabolism ; }, abstract = {Tea (Camellia sinensis (L.) O. Kuntze) plants have a strong ability to accumulate selenium (Se). However, the question of how tea plants affect Se availability has received little attention. In this study, five tea cultivars, including Soubei (SB), Aolǜ (AL), Longjing43 (LJ), Zhaori (ZR) and Fenglǜ (FL), were chosen for the study. Quantitative Microbial Ecology Chip and high-throughput sequencing were used to explore the effects of five tea cultivars on soil functions, microbial community structures and Se availability. The results showed that the total soil Se content in the FL garden was lower compared to LJ and SB gardens, whereas available Se was highest in the FL garden. Based on the Bray-Curtis distances, tea cultivar was the main factor affecting bacterial and fungal community structures. The abundance of functional genes concerning carbon, nitrogen, phosphorus and sulfur cycling processes varied among tea gardens. The higher soil NH4[+] and NO3[-] contents, and higher abundance of functional genes like nifH, amoA1 and narG, whereas lower total nitrogen in the FL garden than in the AL and LJ tea gardens demonstrated that the FL tea plants induced microbes to accelerate soil nitrogen cycling processes. Dominant microbes that positively related with functional genes like nifH, narG, and amoA1 were also positively related with the available Se content. In conclusion, tea cultivars could regulate soil functions through affecting microbial community structures and then affecting the soil Se availability. The soil nitrogen cycle processes are suggested to be closely related with Se transformation in tea gardens.}, }
@article {pmid39236233, year = {2024}, author = {Richards, L and Cremin, K and Coates, M and Vigor, F and Schäfer, P and Soyer, OS}, title = {Ammonia leakage can underpin nitrogen-sharing among soil microorganisms.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39236233}, issn = {1751-7370}, support = {//Gordon and Betty Moore Foundation/ ; //Midlands Integrative Biosciences Training Partnership/ ; P3141153//Baden-W&#xfc;rttemberg Stiftung/ ; }, mesh = {*Ammonia/metabolism ; *Soil Microbiology ; *Nitrogen/metabolism ; *Nitrates/metabolism ; *Bacillus subtilis/metabolism/growth &amp; development/genetics ; Soil/chemistry ; Microbial Interactions ; Hydrogen-Ion Concentration ; Ammonium Compounds/metabolism ; }, abstract = {Soil microbial communities host a large number of microbial species that support important ecological functions such as biogeochemical cycling and plant nutrition. The extent and stability of these functions are affected by inter-species interactions among soil microorganisms, yet the different mechanisms underpinning microbial interactions in the soil are not fully understood. Here, we study the extent of nutrient-based interactions among two model, plant-supporting soil microorganisms, the fungi Serendipita indica, and the bacteria Bacillus subtilis. We found that S. indica is unable to grow with nitrate - a common nitrogen source in the soil - but this inability could be rescued, and growth restored in the presence of B. subtilis. We demonstrate that this effect is due to B. subtilis utilising nitrate and releasing ammonia, which can be used by S. indica. We refer to this type of mechanism as ammonia mediated nitrogen sharing (N-sharing). Using a mathematical model, we demonstrated that the pH dependent equilibrium between ammonia (NH3) and ammonium (NH+4) results in an inherent cellular leakiness, and that reduced amonnium uptake or assimilation rates could result in higher levels of leaked ammonia. In line with this model, a mutant B. subtilis - devoid of ammonia uptake - showed higher S. indica growth support in nitrate media. These findings highlight that ammonia based N-sharing can be a previously under-appreciated mechanism underpinning interaction among soil microorganisms and could be influenced by microbial or abiotic alteration of pH in microenvironments.}, }
@article {pmid39235751, year = {2025}, author = {Lemée, P and Bridier, A}, title = {Bioinformatic Pipeline for Profiling Foodborne Bacterial Ecology and Resistome from Short-Read Metagenomics.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2852}, number = {}, pages = {289-309}, pmid = {39235751}, issn = {1940-6029}, mesh = {*Metagenomics/methods ; *Computational Biology/methods ; *Food Microbiology/methods ; *Bacteria/genetics ; *High-Throughput Nucleotide Sequencing/methods ; Metagenome ; Microbiota/genetics ; }, abstract = {Next-generation sequencing revolutionized food safety management these last years providing access to a huge quantity of valuable data to identify, characterize, and monitor bacterial pathogens on the food chain. Shotgun metagenomics emerged as a particularly promising approach as it enables in-depth taxonomic profiling and functional investigation of food microbial communities. In this chapter, we provide a comprehensive step-by-step bioinformatical workflow to characterize bacterial ecology and resistome composition from metagenomic short-reads obtained by shotgun sequencing.}, }
@article {pmid39235736, year = {2025}, author = {Islam, DT and Mobasser, S and Kotaru, S and Telli, AE and Telli, N and Cupples, AM and Hashsham, SA}, title = {Electrochemical Detection of Nucleic Acids Using Three-Dimensional Graphene Screen-Printed Electrodes.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2852}, number = {}, pages = {47-64}, pmid = {39235736}, issn = {1940-6029}, mesh = {*Graphite/chemistry ; *Electrodes ; *Electrochemical Techniques/methods/instrumentation ; *Biosensing Techniques/methods/instrumentation ; Nucleic Acids/analysis ; Humans ; DNA/analysis ; }, abstract = {Electrochemical approaches, along with miniaturization of electrodes, are increasingly being employed to detect and quantify nucleic acid biomarkers. Miniaturization of the electrodes is achieved through the use of screen-printed electrodes (SPEs), which consist of one to a few dozen sets of electrodes, or by utilizing printed circuit boards. Electrode materials used in SPEs include glassy carbon (Chiang H-C, Wang Y, Zhang Q, Levon K, Biosensors (Basel) 9:2-11, 2019), platinum, carbon, and graphene (Cheng FF, He TT, Miao HT, Shi JJ, Jiang LP, Zhu JJ, ACS Appl Mater Interfaces 7:2979-2985, 2015). There are numerous modifications to the electrode surfaces as well (Cheng FF, He TT, Miao HT, Shi JJ, Jiang LP, Zhu JJ, ACS Appl Mater Interfaces 7:2979-2985, 2015). These approaches offer distinct advantages, primarily due to their demonstrated superior limit of detection without amplification. Using the SPEs and potentiostats, we can detect cells, proteins, DNA, and RNA concentrations in the nanomolar (nM) to attomolar (aM) range. The focus of this chapter is to describe the basic approach adopted for the use of SPEs for nucleic acid measurement.}, }
@article {pmid39235733, year = {2025}, author = {Williams, MR and Telli, AE and Telli, N and Islam, DT and Hashsham, SA}, title = {Direct or DNA Extraction-Free Amplification and Quantification of Foodborne Pathogens.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2852}, number = {}, pages = {3-17}, pmid = {39235733}, issn = {1940-6029}, mesh = {*Nucleic Acid Amplification Techniques/methods ; *Food Microbiology/methods ; Animals ; *Milk/microbiology ; *Salmonella/genetics/isolation &amp; purification ; *DNA, Bacterial/genetics/isolation &amp; purification ; *Polymerase Chain Reaction/methods ; Foodborne Diseases/microbiology ; Escherichia coli/genetics/isolation &amp; purification ; Molecular Diagnostic Techniques/methods ; Swine ; }, abstract = {The use of direct nucleic acid amplification of pathogens from food matrices has the potential to reduce time to results over DNA extraction-based approaches as well as traditional culture-based approaches. Here we describe protocols for assay design and experiments for direct amplification of foodborne pathogens in food sample matrices using loop-mediated isothermal amplification (LAMP) and polymerase chain reaction (PCR). The examples provided include the detection of Escherichia coli in milk samples and Salmonella in pork meat samples. This protocol includes relevant reagents and methods including obtaining target sequences, assay design, sample processing, and amplification. These methods, though used for specific example matrices, could be applied to many other foodborne pathogens and sample types.}, }
@article {pmid39234658, year = {2024}, author = {King, WL and Hayward, RJ and Goebel, M and Fleishman, SM and Bauerle, TL and Bell, TH}, title = {Getting to the root of root-microbe interactions.}, journal = {Science progress}, volume = {107}, number = {3}, pages = {368504241278783}, pmid = {39234658}, issn = {2047-7163}, mesh = {Ecosystem ; Microbiota/physiology ; *Plant Roots/microbiology/metabolism ; Plants/microbiology/metabolism ; *Soil Microbiology ; }, abstract = {Microbial relationships with roots influence many ecosystem functions and nutrient fluxes, including their sometimes-profound effects on plant health and productivity. Fine roots were often classified with a diameter less than 2 mm, but fine roots under that size perform distinct functional roles in the environment. Importantly, two broad functional categories of fine roots are absorptive and transportive, with absorptive fine roots acting as metabolic hotspots for root activity. In two of our recent studies, we have shown that several microbial community characteristics differ between absorptive and transportive fine roots, including composition, abundance, and function, as well as the root metabolome. This highlights a growing recognition within microbial ecology that we must consider fine-scale environmental variability, such as root physiology and morphology, when interpreting microbial patterns. In this commentary, we summarize the findings of our latest article, further speculate on some of these patterns, and suggest future studies for examining decomposition and applying cutting-edge single-cell sequencing techniques.}, }
@article {pmid39234547, year = {2024}, author = {Marshall, IPG}, title = {Electromicrobiological concentration cells are an overlooked potential energy conservation mechanism for subsurface microorganisms.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1407868}, pmid = {39234547}, issn = {1664-302X}, abstract = {Thermodynamics has predicted many different kinds of microbial metabolism by determining which pairs of electron acceptors and donors will react to produce an exergonic reaction (a negative net change in Gibbs free energy). In energy-limited environments, such as the deep subsurface, such an approach can reveal the potential for unexpected or counter-intuitive energy sources for microbial metabolism. Up until recently, these thermodynamic calculations have been carried out with the assumption that chemical species appearing on the reactant and product side of a reaction formula have a constant concentration, and thus do not count towards net concentration changes and the overall direction of the reaction. This assumption is reasonable considering microorganisms are too small (~1 μm) for any significant differences in concentration to overcome diffusion. However, recent discoveries have demonstrated that the reductive and oxidative halves of reactions can be separated by much larger distances, from millimetres to centimetres via conductive filamentous bacteria, mineral conductivity, and biofilm conductivity. This means that the concentrations of reactants and products can indeed be different, and that concentration differences can contribute to the net negative change in Gibbs free energy. It even means that the same redox reaction, simultaneously running in forward and reverse, can drive energy conservation, in an ElectroMicrobiological Concentration Cell (EMCC). This paper presents a model to investigate this phenomenon and predict under which circumstances such concentration-driven metabolism might take place. The specific cases of oxygen concentration cells, sulfide concentration cells, and hydrogen concentration cells are examined in more detail.}, }
@article {pmid39233440, year = {2024}, author = {Hosseiniyan Khatibi, SM and Dimaano, NG and Veliz, E and Sundaresan, V and Ali, J}, title = {Exploring and exploiting the rice phytobiome to tackle climate change challenges.}, journal = {Plant communications}, volume = {5}, number = {12}, pages = {101078}, pmid = {39233440}, issn = {2590-3462}, mesh = {*Climate Change ; *Oryza/microbiology/growth &amp; development ; *Microbiota ; Crops, Agricultural/growth &amp; development/genetics ; Agriculture/methods ; }, abstract = {The future of agriculture is uncertain under the current climate change scenario. Climate change directly and indirectly affects the biotic and abiotic elements that control agroecosystems, jeopardizing the safety of the world's food supply. A new area that focuses on characterizing the phytobiome is emerging. The phytobiome comprises plants and their immediate surroundings, involving numerous interdependent microscopic and macroscopic organisms that affect the health and productivity of plants. Phytobiome studies primarily focus on the microbial communities associated with plants, which are referred to as the plant microbiome. The development of high-throughput sequencing technologies over the past 10 years has dramatically advanced our understanding of the structure, functionality, and dynamics of the phytobiome; however, comprehensive methods for using this knowledge are lacking, particularly for major crops such as rice. Considering the impact of rice production on world food security, gaining fresh perspectives on the interdependent and interrelated components of the rice phytobiome could enhance rice production and crop health, sustain rice ecosystem function, and combat the effects of climate change. Our review re-conceptualizes the complex dynamics of the microscopic and macroscopic components in the rice phytobiome as influenced by human interventions and changing environmental conditions driven by climate change. We also discuss interdisciplinary and systematic approaches to decipher and reprogram the sophisticated interactions in the rice phytobiome using novel strategies and cutting-edge technology. Merging the gigantic datasets and complex information on the rice phytobiome and their application in the context of regenerative agriculture could lead to sustainable rice farming practices that are resilient to the impacts of climate change.}, }
@article {pmid39233079, year = {2024}, author = {Zhang, G and Guo, Z and Ke, Y and Li, H and Xiao, X and Lin, D and Lin, L and Wang, Y and Liu, J and Lu, H and Hong, H and Yan, C}, title = {Comparative analysis of size-fractional eukaryotic microbes in subtropical riverine systems inferred from 18S rRNA gene V4 and V9 regions.}, journal = {The Science of the total environment}, volume = {953}, number = {}, pages = {175972}, doi = {10.1016/j.scitotenv.2024.175972}, pmid = {39233079}, issn = {1879-1026}, mesh = {*RNA, Ribosomal, 18S/genetics ; *Rivers/microbiology ; *Eukaryota/genetics ; Microbiota/genetics ; Ecosystem ; Environmental Monitoring/methods ; }, abstract = {Eukaryotic microbes play key ecological roles in riverine ecosystems. Amplicon sequencing has greatly facilitated the identification and characterization of eukaryotic microbial communities. Currently, 18S rRNA gene V4 and V9 hypervariable regions are widely used for sequencing eukaryotic microbes. Identifying optimal regions for the profiling of size-fractional eukaryotic microbial communities is critical for microbial ecological studies. In this study, we spanned three rivers with typical natural-human influenced transition gradients to evaluate the performance of the 18S rRNA gene V4 and V9 hypervariable regions for sequencing size-fractional eukaryotic microbes (>180 μm, 20-180 μm, 5-20 μm, 3-5 μm, 0.8-3 μm). Our comparative analysis revealed that amplicon results depend on the specific species and microbial size. The V9 region was most effective for detecting a broad taxonomic range of species. The V4 region was superior to the V9 region for the identification of microbes in the minor 3 μm and at the family and genus levels, especially for specific microbial groups, such as Labyrinthulomycetes. However, the V9 region was more effective for studies of diverse eukaryotic groups, including Archamoebae, Heterolobosea, and Microsporidia, and various algae, such as Haptophyta, Florideophycidae, and Bangiales. Our results highlight the importance of accounting for potential misclassifications when employing both V4 and V9 regions for the identification of microbial sequences. The use of optimal regions for amplification could enhance the utility of amplicon sequencing in environmental studies. The insights gained from this work will aid future studies that employ amplicon-based identification approaches for the characterization of eukaryotic microbial communities and contribute to our understanding of microbial ecology within aquatic systems.}, }
@article {pmid39231820, year = {2024}, author = {Song, X and Li, J and Xiong, Z and Sha, H and Wang, G and Liu, Q and Zeng, T}, title = {Effects of Detoxifying Substances on Uranium Removal by Bacteria Isolated from Mine Soils: Performance, Mechanisms, and Bacterial Communities.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {111}, pmid = {39231820}, issn = {1432-184X}, support = {52170164//National Natural Science Foundation of China/ ; 2022RC1184//Science and Technology Innovation Program of Hunan Province of China/ ; }, mesh = {*Uranium/metabolism ; *Soil Microbiology ; *Bacteria/metabolism/genetics/isolation &amp; purification/classification ; *Mining ; *Biodegradation, Environmental ; Acyl-Butyrolactones/metabolism ; Glutathione/metabolism ; Soil Pollutants, Radioactive/metabolism ; }, abstract = {In this study, we investigated the effect of detoxifying substances on U(VI) removal by bacteria isolated from mine soil. The results demonstrated that the highest U(VI) removal efficiency (85.6%) was achieved at pH 6.0 and a temperature of 35 °C, with an initial U(VI) concentration of 10 mg/L. For detoxifying substances, signaling molecules acyl homoserine lactone (AHLs, 0.1 µmol/L), anthraquinone-2, 6-disulfonic acid (AQDS, 1 mmol/L), reduced glutathione (GSH, 0.1 mmol/L), selenium (Se, 1 mg/L), montmorillonite (MT, 1 g/L), and ethylenediaminetetraacetic acid (EDTA, 0.1 mmol/L) substantially enhanced the bacterial U(VI) removal by 34.9%, 37.4%, 54.5%, 35.1%, 32.8%, and 47.8% after 12 h, respectively. This was due to the alleviation of U(VI) toxicity in bacteria through detoxifying substances, as evidenced by lower malondialdehyde (MDA) content and higher superoxide dismutase (SOD) and catalase (CAT) activities for bacteria exposed to U(VI) and detoxifying substances, compared to those exposed to U(VI) alone. FTIR results showed that hydroxyl, carboxyl, phosphorus, and amide groups participated in the U(VI) removal. After exposure to U(VI), the relative abundances of Chryseobacterium and Stenotrophomonas increased by 48.5% and 12.5%, respectively, suggesting their tolerance ability to U(VI). Gene function prediction further demonstrated that the detoxifying substances AHLs alleviate U(VI) toxicity by influencing bacterial metabolism. This study suggests the potential application of detoxifying substances in the U(VI)-containing wastewater treatment through bioremediation.}, }
@article {pmid39230264, year = {2024}, author = {Rodriguez-Gonzalez, RA and Balacheff, Q and Debarbieux, L and Marchi, J and Weitz, JS}, title = {Metapopulation model of phage therapy of an acute Pseudomonas aeruginosa lung infection.}, journal = {mSystems}, volume = {9}, number = {10}, pages = {e0017124}, pmid = {39230264}, issn = {2379-5077}, support = {R01 AI146592/AI/NIAID NIH HHS/United States ; //Consejo Nacional de Ciencia y Tecnolog&#xed;a (CONACYT)/ ; }, mesh = {*Pseudomonas aeruginosa/virology ; *Phage Therapy/methods ; *Pseudomonas Infections/therapy/immunology ; Animals ; Mice ; Bacteriophages/physiology ; Lung/microbiology/immunology/virology ; Models, Biological ; Mice, Inbred C57BL ; Humans ; Drug Resistance, Multiple, Bacterial ; }, abstract = {UNLABELLED: Infections caused by multidrug resistant (MDR) pathogenic bacteria are a global health threat. Bacteriophages ("phage") are increasingly used as alternative or last-resort therapeutics to treat patients infected by MDR bacteria. However, the therapeutic outcomes of phage therapy may be limited by the emergence of phage resistance during treatment and/or by physical constraints that impede phage-bacteria interactions in vivo. In this work, we evaluate the role of lung spatial structure on the efficacy of phage therapy for Pseudomonas aeruginosa infections. To do so, we developed a spatially structured metapopulation network model based on the geometry of the bronchial tree, including host innate immune responses and the emergence of phage-resistant bacterial mutants. We model the ecological interactions between bacteria, phage, and the host innate immune system at the airway (node) level. The model predicts the synergistic elimination of a P. aeruginosa infection due to the combined effects of phage and neutrophils, given the sufficient innate immune activity and efficient phage-induced lysis. The metapopulation model simulations also predict that MDR bacteria are cleared faster at distal nodes of the bronchial tree. Notably, image analysis of lung tissue time series from wild-type and lymphocyte-depleted mice revealed a concordant, statistically significant pattern: infection intensity cleared in the bottom before the top of the lungs. Overall, the combined use of simulations and image analysis of in vivo experiments further supports the use of phage therapy for treating acute lung infections caused by P. aeruginosa, while highlighting potential limits to therapy in a spatially structured environment given impaired innate immune responses and/or inefficient phage-induced lysis.<br><br>IMPORTANCE: Phage therapy is increasingly employed as a compassionate treatment for severe infections caused by multidrug-resistant (MDR) bacteria. However, the mixed outcomes observed in larger clinical studies highlight a gap in understanding when phage therapy succeeds or fails. Previous research from our team, using in vivo experiments and single-compartment mathematical models, demonstrated the synergistic clearance of acute P. aeruginosa pneumonia by phage and neutrophils despite the emergence of phage-resistant bacteria. In fact, the lung environment is highly structured, prompting the question of whether immunophage synergy explains the curative treatment of P. aeruginosa when incorporating realistic physical connectivity. To address this, we developed a metapopulation network model mimicking the lung branching structure to assess phage therapy efficacy for MDR P. aeruginosa pneumonia. The model predicts the synergistic elimination of P. aeruginosa by phage and neutrophils but emphasizes potential challenges in spatially structured environments, suggesting that higher innate immune levels may be required for successful bacterial clearance. Model simulations reveal a spatial pattern in pathogen clearance where P. aeruginosa are cleared faster at distal nodes of the bronchial tree than in primary nodes. Interestingly, image analysis of infected mice reveals a concordant and statistically significant pattern: infection intensity clears in the bottom before the top of the lungs. The combined use of modeling and image analysis supports the application of phage therapy for acute P. aeruginosa pneumonia while emphasizing potential challenges to curative success in spatially structured in vivo environments, including impaired innate immune responses and reduced phage efficacy.}, }
@article {pmid39229495, year = {2024}, author = {Li, L and Chen, S and Xue, X and Chen, J and Tian, J and Huo, L and Zhang, T and Zeng, X and Su, S}, title = {Purifying selection drives distinctive arsenic metabolism pathways in prokaryotic and eukaryotic microbes.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae106}, pmid = {39229495}, issn = {2730-6151}, abstract = {Microbes play a crucial role in the arsenic biogeochemical cycle through specific metabolic pathways to adapt to arsenic toxicity. However, the different arsenic-detoxification strategies between prokaryotic and eukaryotic microbes are poorly understood. This hampers our comprehension of how microbe-arsenic interactions drive the arsenic cycle and the development of microbial methods for remediation. In this study, we utilized conserved protein domains from 16 arsenic biotransformation genes (ABGs) to search for homologous proteins in 670 microbial genomes. Prokaryotes exhibited a wider species distribution of arsenic reduction- and arsenic efflux-related genes than fungi, whereas arsenic oxidation-related genes were more prevalent in fungi than in prokaryotes. This was supported by significantly higher acr3 (arsenite efflux permease) expression in bacteria (upregulated 3.72-fold) than in fungi (upregulated 1.54-fold) and higher aoxA (arsenite oxidase) expression in fungi (upregulated 5.11-fold) than in bacteria (upregulated 2.05-fold) under arsenite stress. The average values of nonsynonymous substitutions per nonsynonymous site to synonymous substitutions per synonymous site (dN/dS) of homologous ABGs were higher in archaea (0.098) and bacteria (0.124) than in fungi (0.051). Significant negative correlations between the dN/dS of ABGs and species distribution breadth and gene expression levels in archaea, bacteria, and fungi indicated that microbes establish the distinct strength of purifying selection for homologous ABGs. These differences contribute to the distinct arsenic metabolism pathways in prokaryotic and eukaryotic microbes. These observations facilitate a significant shift from studying individual or several ABGs to characterizing the comprehensive microbial strategies of arsenic detoxification.}, }
@article {pmid39226184, year = {2024}, author = {Zhai, Z and Yang, Y and Chen, S and Wu, Z}, title = {Long-Term Exposure to Polystyrene Microspheres and High-Fat Diet-Induced Obesity in Mice: Evaluating a Role for Microbiota Dysbiosis.}, journal = {Environmental health perspectives}, volume = {132}, number = {9}, pages = {97002}, pmid = {39226184}, issn = {1552-9924}, mesh = {Animals ; *Dysbiosis/microbiology ; Mice ; *Obesity/microbiology ; *Diet, High-Fat ; *Mice, Inbred C57BL ; *Microspheres ; *Polystyrenes/toxicity ; *Gastrointestinal Microbiome/drug effects ; Male ; Microplastics/toxicity ; RNA, Ribosomal, 16S ; }, abstract = {BACKGROUND: Microplastics (MPs) have become a global environmental problem, emerging as contaminants with potentially alarming consequences. However, long-term exposure to polystyrene microspheres (PS-MS) and its effects on diet-induced obesity are not yet fully understood.<br><br>OBJECTIVES: We aimed to investigate the effect of PS-MS exposure on high-fat diet (HFD)-induced obesity and underlying mechanisms.<br><br>METHODS: In the present study, C57BL/6J mice were fed a normal diet (ND) or a HFD in the absence or presence of PS-MS via oral administration for 8 wk. Antibiotic depletion of the microbiota and fecal microbiota transplantation (FMT) were performed to assess the influence of PS-MS on intestinal microbial ecology. We performed 16S rRNA sequencing to dissect microbial discrepancies and investigated the dysbiosis-associated intestinal integrity and inflammation in serum.<br><br>RESULTS: Compared with HFD mice, mice fed the HFD with PS-MS exhibited higher body weight, liver weight, metabolic dysfunction-associated steatotic liver disease (MASLD) activity scores, and mass of white adipose tissue, as well as higher blood glucose and serum lipid concentrations. Furthermore, 16S rRNA sequencing of the fecal microbiota revealed that mice fed the HFD with PS-MS had greater &#x3b1;-diversity and greater relative abundances of Lachnospiraceae, Oscillospiraceae, Bacteroidaceae, Akkermansiaceae, Marinifilaceae, Deferribacteres, and Desulfovibrio, but lower relative abundances of Atopobiaceae, Bifidobacterium, and Parabacteroides. Mice fed the HFD with PS-MS exhibited lower expression of MUC2 mucin and higher levels of lipopolysaccharide and inflammatory cytokines [tumor necrosis factor-&#x3b1; (TNF-&#x3b1;), interleukin-6 (IL-6), IL-1&#x3b2;, and IL-17A] in serum. Correlation analyses revealed that differences in the microbial flora of mice exposed to PS-MS were associated with obesity. Interestingly, microbiota-depleted mice did not show the same PS-MS-associated differences in Muc2 and Tjp1 expression in the distal colon, expression of inflammatory cytokines in serum, or obesity outcomes between HFD and HFD + PS-MS. Importantly, transplantation of feces from HFD + PS-MS mice to microbiota-depleted HFD-fed mice resulted in a lower expression of mucus proteins, higher expression of inflammatory cytokines, and obesity outcomes, similar to the findings in HFD + PS-MS mice.<br><br>CONCLUSIONS: Our findings provide a new gut microbiota-driven mechanism for PS-MS-induced obesity in HFD-fed mice, suggesting the need to reevaluate the adverse health effects of MPs commonly found in daily life, particularly in susceptible populations. https://doi.org/10.1289/EHP13913.}, }
@article {pmid39224076, year = {2024}, author = {McMillan, AS and Theriot, CM}, title = {Bile acids impact the microbiota, host, and C. difficile dynamics providing insight into mechanisms of efficacy of FMTs and microbiota-focused therapeutics.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2393766}, pmid = {39224076}, issn = {1949-0984}, support = {R35 GM149222/GM/NIGMS NIH HHS/United States ; T32 GM133366/GM/NIGMS NIH HHS/United States ; }, mesh = {*Bile Acids and Salts/metabolism ; Humans ; *Fecal Microbiota Transplantation ; *Clostridioides difficile/physiology ; *Gastrointestinal Microbiome ; *Clostridium Infections/therapy/microbiology ; Animals ; }, abstract = {Clostridioides difficile is a major nosocomial pathogen, causing significant morbidity and mortality worldwide. Antibiotic usage, a major risk factor for Clostridioides difficile infection (CDI), disrupts the gut microbiota, allowing C. difficile to proliferate and cause infection, and can often lead to recurrent CDI (rCDI). Fecal microbiota transplantation (FMT) and live biotherapeutic products (LBPs) have emerged as effective treatments for rCDI and aim to restore colonization resistance provided by a healthy gut microbiota. However, much is still unknown about the mechanisms mediating their success. Bile acids, extensively modified by gut microbes, affect C. difficile's germination, growth, and toxin production while also shaping the gut microbiota and influencing host immune responses. Additionally, microbial interactions, such as nutrient competition and cross-feeding, contribute to colonization resistance against C. difficile and may contribute to the success of microbiota-focused therapeutics. Bile acids as well as other microbial mediated interactions could have implications for other diseases being treated with microbiota-focused therapeutics. This review focuses on the intricate interplay between bile acid modifications, microbial ecology, and host responses with a focus on C. difficile, hoping to shed light on how to move forward with the development of new microbiota mediated therapeutic strategies to combat rCDI and other intestinal diseases.}, }
@article {pmid39222062, year = {2024}, author = {Acheampong, DA and Jenjaroenpun, P and Wongsurawat, T and Kurilung, A and Pomyen, Y and Kandel, S and Kunadirek, P and Chuaypen, N and Kusonmano, K and Nookaew, I}, title = {CAIM: coverage-based analysis for identification of microbiome.}, journal = {Briefings in bioinformatics}, volume = {25}, number = {5}, pages = {}, pmid = {39222062}, issn = {1477-4054}, support = {P20 GM125503/GM/NIGMS NIH HHS/United States ; R01 CA143130/CA/NCI NIH HHS/United States ; P20GM125503//National Institute of General Medical Sciences of the National Institutes of Health/ ; R01CA143130/NH/NIH HHS/United States ; }, mesh = {Humans ; *Microbiota/genetics ; *Metagenomics/methods ; Computational Biology/methods ; Metagenome ; High-Throughput Nucleotide Sequencing/methods ; Software ; Algorithms ; Sequence Analysis, DNA/methods ; }, abstract = {Accurate taxonomic profiling of microbial taxa in a metagenomic sample is vital to gain insights into microbial ecology. Recent advancements in sequencing technologies have contributed tremendously toward understanding these microbes at species resolution through a whole shotgun metagenomic approach. In this study, we developed a new bioinformatics tool, coverage-based analysis for identification of microbiome (CAIM), for accurate taxonomic classification and quantification within both long- and short-read metagenomic samples using an alignment-based method. CAIM depends on two different containment techniques to identify species in metagenomic samples using their genome coverage information to filter out false positives rather than the traditional approach of relative abundance. In addition, we propose a nucleotide-count-based abundance estimation, which yield lesser root mean square error than the traditional read-count approach. We evaluated the performance of CAIM on 28 metagenomic mock communities and 2 synthetic datasets by comparing it with other top-performing tools. CAIM maintained a consistently good performance across datasets in identifying microbial taxa and in estimating relative abundances than other tools. CAIM was then applied to a real dataset sequenced on both Nanopore (with and without amplification) and Illumina sequencing platforms and found high similarity of taxonomic profiles between the sequencing platforms. Lastly, CAIM was applied to fecal shotgun metagenomic datasets of 232 colorectal cancer patients and 229 controls obtained from 4 different countries and 44 primary liver cancer patients and 76 controls. The predictive performance of models using the genome-coverage cutoff was better than those using the relative-abundance cutoffs in discriminating colorectal cancer and primary liver cancer patients from healthy controls with a highly confident species markers.}, }
@article {pmid39221110, year = {2024}, author = {Mohr, AE and Jasbi, P and van Woerden, I and Chi, J and Gu, H and Bruening, M and Whisner, CM}, title = {Microbial Ecology and Metabolism of Emerging Adulthood: Gut Microbiome Insights from a College Freshman Cohort.}, journal = {Gut microbes reports}, volume = {1}, number = {1}, pages = {1-23}, pmid = {39221110}, issn = {2993-3935}, support = {DP5 OD017910/OD/NIH HHS/United States ; T32 DK137525/DK/NIDDK NIH HHS/United States ; }, abstract = {The human gut microbiome (GM) undergoes dynamic changes throughout life, transitioning from infancy to adulthood. Despite improved understanding over the past years about how genetics, lifestyle, and the external environment impact the GM, limited research has explored the GM's evolution during late-stage adolescence, especially among college students. This study addresses this gap by investigating the longitudinal dynamics of fecal microbial, functional, and metabolomic signatures in a diverse group of first-year, dormitory-housed college students. A total of 485 stool samples from 246 participants were analyzed, identifying four primary GM community types, predominantly led by Bacteroides (66.8% of samples), as well as Blautia and Prevotella. The Prevotella/Bacteroides (P/B) ratio emerged as a robust GM composition indicator, predictively associated with 15 metabolites. Notably, higher P/B ratios correlated negatively with p-cresol sulfate and cholesterol sulfate, implying potential health implications, while positively correlating with kynurenic acid. Distinct GM transition and stability patterns were found from a detailed longitudinal subset of 93 participants over an academic year. Parasutterella and the Ruminococcus gnavus group exhibited positive associations with compositional variability, whereas Faecalibacterium and Eubacterium ventriosum group displayed negative associations, the latter suggesting stabilizing roles in the GM. Most notably, nearly half of the longitudinal cohort experienced GM community shifts, emphasizing long-term GM adaptability. Comparing individuals with stable community types to those undergoing transitions, we observed significant differences in microbial composition and diversity, signifying substantial shifts in the microbiota during transitions. Although diet-related variables contributed to some observed variance, diet did not independently predict the probability of switching between community types within the study's timeframe via multi-state Markov modeling. Furthermore, exploration of stability within dynamic microbiomes among the longitudinal cohort experiencing shifts in community types revealed that microbiome taxa at the genus level exhibited significantly higher total variance than estimated functional and fecal metabolomic features. This suggests tight control of function and metabolism, despite community shifting. Overall, this study highlights the dynamic nature of the late-stage adolescent GM, the role of core taxa, metabolic pathways, the fecal metabolome, and lifestyle and dietary factors, contributing to our understanding of GM assembly and potential health implications during this life phase.}, }
@article {pmid39218095, year = {2024}, author = {Anedda, E and Alexa, EA and Farrell, ML and Croffie, M and Madigan, G and Morris, D and Burgess, CM}, title = {Comparison of antimicrobial resistant Enterobacterales isolates from the dairy production environment in low and high zinc containing regions.}, journal = {The Science of the total environment}, volume = {953}, number = {}, pages = {175905}, doi = {10.1016/j.scitotenv.2024.175905}, pmid = {39218095}, issn = {1879-1026}, mesh = {*Zinc/analysis ; *Enterobacteriaceae/drug effects ; *Soil Microbiology ; Anti-Bacterial Agents/pharmacology ; Dairying ; Drug Resistance, Bacterial/genetics ; Ireland ; Animals ; Milk/microbiology ; Cattle ; Soil Pollutants/analysis ; }, abstract = {Heavy metals occur naturally in the environment, and their concentration varies in soil across different regions. However, the presence of heavy metals may influence the antimicrobial resistance (AMR) in bacterial populations. Therefore, the objective of this study was to investigate and characterise the antimicrobial resistance profiles of Enterobacterales in soil and bovine milk filters from high and low zinc-containing regions in Ireland. In total, 50 soil samples and 29 milk filters were collected from two geographic locations with varying soil zinc concentrations. Samples were cultured for the enumeration and detection of Enterobacterales. Specifically, extended-spectrum beta-lactamase-producing Enterobacterales, carbapenem-resistant Enterobacterales and ciprofloxacin-resistant Enterobacterales were isolated using selective media. Species identification was performed using MALDI-TOF. The phenotypic resistance profiles of selected Enterobacterales were determined by disk diffusion testing, following EUCAST and CLSI criteria; while, the genotypic resistance profiles of the same isolates were determined by whole genome sequencing (WGS). Heavy metal concentrations were also measured for all soil samples. A total of 40 antimicrobial resistant Enterobacterales were identified in soil (n = 31) and milk filters (n = 9). The predominant species detected in the high zinc-containing region was Escherichia coli in both sample types (soil n = 10, milk filters n = 2), while in the low zinc-containing region Serratia fonticola was predominant in soil samples (n = 8) and E. coli in milk filters (n = 4). Ten E. coli isolates identified from soil samples in the high zinc-containing region were multidrug resistant, showing resistance to all the antimicrobials tested, except for carbapenems. The WGS findings confirmed the phenotypic resistance results. Moreover, zinc resistance-associated genes and genes encoding for efflux pumps were identified. The current study revealed distinct phenotypic resistance profiles of Enterobacterales in low and high zinc-containing regions, and highlighted the benefit of utilising milk filters for AMR surveillance in dairy production.}, }
@article {pmid39216241, year = {2024}, author = {Liao, X and Hou, L and Zhang, L and Grossart, HP and Liu, K and Liu, J and Chen, Y and Liu, Y and Hu, A}, title = {Distinct influences of altitude on microbiome and antibiotic resistome assembly in a glacial river ecosystem of Mount Everest.}, journal = {Journal of hazardous materials}, volume = {479}, number = {}, pages = {135675}, doi = {10.1016/j.jhazmat.2024.135675}, pmid = {39216241}, issn = {1873-3336}, mesh = {*Rivers/microbiology ; *Altitude ; *Microbiota/drug effects ; *Drug Resistance, Microbial/genetics ; Ecosystem ; Bacteria/genetics/drug effects/classification ; Geologic Sediments/microbiology ; Viruses/drug effects/genetics ; Anti-Bacterial Agents/pharmacology ; Ice Cover/microbiology ; China ; }, abstract = {The profound influences of altitude on aquatic microbiome were well documented. However, differences in the responses of different life domains (bacteria, microeukaryotes, viruses) and antibiotics resistance genes (ARGs) in glacier river ecosystems to altitude remain unknown. Here, we employed shotgun metagenomic and amplicon sequencing to characterize the altitudinal variations of microbiome and ARGs in the Rongbu River, Mount Everest. Our results indicated the relative influences of stochastic processes on microbiome and ARGs assembly in water and sediment were in the following order: microeukaryotes < ARGs < viruses < bacteria. Moreover, distinct assembly patterns of the microbiome and ARGs were found in response to differences in altitude, the latter of which shift from deterministic to stochastic processes with increasing differences in altitude. Partial least squares path modeling revealed that mobile genetic elements (MGEs) and viral β-diversity were the major factors influencing the ARG abundances. Taken together, our work revealed that altitude-caused environmental changes led to significant changes in the composition and assembly processes of the microbiome and ARGs, while ARGs had a unique response pattern to altitude. Our findings provide novel insights into the impacts of altitude on the biogeographic distribution of microbiome and ARGs, and the associated driving forces in glacier river ecosystems.}, }
@article {pmid39215820, year = {2024}, author = {Thompson, C and Silva, R and Gibran, FZ and Bacha, L and de Freitas, MAM and Thompson, M and Landuci, F and Tschoeke, D and Zhang, XH and Wang, X and Zhao, W and Gatts, PV and de Almeida, MG and de Rezende, CE and Thompson, F}, title = {The Abrolhos Nominally Herbivorous Coral Reef Fish Acanthurus chirurgus, Kyphosus sp., Scarus trispinosus, and Sparisoma axillare Have Similarities in Feeding But Species-Specific Microbiomes.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {110}, pmid = {39215820}, issn = {1432-184X}, mesh = {Animals ; *Coral Reefs ; *RNA, Ribosomal, 16S/genetics ; *Fishes/microbiology ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation &amp; purification ; Herbivory ; Species Specificity ; Carbon Isotopes/analysis ; Nitrogen Isotopes/analysis ; Perciformes/microbiology ; Diet/veterinary ; }, abstract = {Coral reefs rely heavily on reef fish for their health, yet overfishing has resulted in their decline, leading to an increase in fast-growing algae and changes in reef ecosystems, a phenomenon described as the phase-shift. A clearer understanding of the intricate interplay between herbivorous, their food, and their gut microbiomes could enhance reef health. This study examines the gut microbiome and isotopic markers (δ[13]C and δ[15]N) of four key nominally herbivorous reef fish species (Acanthurus chirurgus, Kyphosus sp., Scarus trispinosus, and Sparisoma axillare) in the Southwestern Atlantic's Abrolhos Reef systems. Approximately 16.8 million 16S rRNA sequences were produced for the four fish species, with an average of 317,047 ± 57,007 per species. Bacteria such as Proteobacteria, Firmicutes, and Cyanobacteria were prevalent in their microbiomes. These fish show unique microbiomes that result from co-diversification, diet, and restricted movement. Coral-associated bacteria (Endozoicomonas, Rhizobia, and Ruegeria) were found in abundance in the gut contents of the parrotfish species Sc. trispinosus and Sp. axillare. These parrotfishes could aid coral health by disseminating such beneficial bacteria across the reef. Meanwhile, Kyphosus sp. predominantly had Pirellulaceae and Rhodobacteraceae. Four fish species had a diet composed of turf components (filamentous Cyanobacteria) and brown algae (Dictyopteris). They also had similar isotopic niches, suggesting they shared food sources. A significant difference was observed between the isotopic signature of fish muscular gut tissue and gut contents, pointing to the role that host genetics and gut microbes play in differentiating fish tissues.}, }
@article {pmid39215735, year = {2024}, author = {Paulo, LM and Liu, YC and Castilla-Archilla, J and Ramiro-Garcia, J and Hughes, D and Mahony, T and Holohan, BC and Wilmes, P and O'Flaherty, V}, title = {Full-scale study on high-rate low-temperature anaerobic digestion of agro-food wastewater: process performances and microbial community.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {90}, number = {4}, pages = {1239-1249}, pmid = {39215735}, issn = {0273-1223}, support = {14/IA/2371/SFI_/Science Foundation Ireland/Ireland ; TC/2014/0016//Enterprise Ireland/ ; }, mesh = {*Bioreactors ; Anaerobiosis ; *Wastewater ; *Waste Disposal, Fluid/methods ; Temperature ; Biological Oxygen Demand Analysis ; Bacteria/metabolism/classification ; Biofuels ; Industrial Waste ; }, abstract = {The fast-growing global population has led to a substantial increase in food production, which generates large volumes of wastewater during the process. Despite most industrial wastewater being discharged at lower ambient temperatures (<20 °C), majority of the high-rate anaerobic reactors are operated at mesophilic temperatures (>30 °C). High-rate low-temperature anaerobic digestion (LtAD) has proven successful in treating industrial wastewater both at laboratory and pilot scales, boasting efficient organic removal and biogas production. In this study, we demonstrated the feasibility of two full-scale high-rate LtAD bioreactors treating meat processing and dairy wastewater, and the microbial communities in both reactors were examined. Both reactors exhibited rapid start-up, achieving considerable chemical oxygen demand (COD) removal efficiencies (total COD removal >80%) and generating high-quality biogas (CH4% in biogas >75%). Long-term operations (6-12 months) underscored the robustness of LtAD bioreactors even during winter periods (average temperature <12 °C), as evidenced by sustained high COD removal rates (total COD removal >80%). The stable performance was underpinned by a resilient microbial community comprising active acetoclastic methanogens, hydrolytic, and fermentative bacteria. These findings underscore the feasibility of high-rate low-temperature anaerobic wastewater treatment, offering promising solutions to the zero-emission wastewater treatment challenge.}, }
@article {pmid39212186, year = {2024}, author = {Junker Mentzel, CM and Hui, Y and Hammerich, TMS and Klug-Dambmann, M and Liu, Y and Zachariassen, LF and Hansen, LH and Aslampaloglou, A and Kiersgaard, M and Nielsen, DS and Hansen, AK and Krych, L}, title = {Low-gainer diet-induced obese microbiota transplanted mice exhibit increased fighting.}, journal = {Clinical and translational science}, volume = {17}, number = {9}, pages = {e13906}, pmid = {39212186}, issn = {1752-8062}, support = {//LIFEPHARM/ ; //Novo Nordisk A/S/ ; //Center for Applied Laboratory Animal Research/ ; }, mesh = {Animals ; Male ; *Obesity/microbiology/etiology ; *Gastrointestinal Microbiome/physiology ; *Fecal Microbiota Transplantation ; *Mice, Inbred C57BL ; *Diet, High-Fat/adverse effects ; *Weight Gain ; Mice ; Disease Models, Animal ; Leptin/blood/metabolism ; Feces/microbiology ; }, abstract = {Weight gain variation is a great challenge in diet-induced obesity studies since low-gainer animals are of limited experimental value. The inbred C57BL/6 (B6) mice are frequently used models due to their genetic homogeneity and susceptibility to diet-induced obesity (DIO). The aim of this study is to investigate if the gut microbiota (GM) influences the fraction of low weight gainers in DIO studies. A total of 100 male B6 mice (donor population) were fed a high-fat diet for 14 weeks and divided into the study groups high gainer (HG) and low gainer (LG) based on their weight gain. Subsequently, fecal matter transplantation (FMT) was done on germ-free B6 mice with GM from HG and LG donors (FMT population). LG (13.35 ± 2.5 g) and HG (25.52 ± 2.0 g) animals were identified by the weight gain from week 1 to week 12. Interestingly, the start weight of the LG (20.36 ± 1.4 g) and HG (21.59 ± 0.7 g) groups differed significantly. Transplanting LG or HG fecal matter to germ-free mice resulted in significant differences in weight gain between HG and LG, as well as differences in serum leptin levels and epididymal fat pad weight. A clear LG-specific GM composition could not be distinguished by 16S rRNA gene amplicon sequencing. Surprisingly, significantly more fighting was recorded in LG groups of both donor populations and when transplanted to germ-free mice. The HG and LG phenotypes could be transferred to germ-free mice. The increased fighting in the LG group in both studies suggests not only that the tendency to fight can be transferred by FMT in these mice, but also that fighting should be prevented in DIO studies to minimize the number of LG animals.}, }
@article {pmid39214074, year = {2024}, author = {Letourneau, J and Carrion, VM and Zeng, J and Jiang, S and Osborne, OW and Holmes, ZC and Fox, A and Epstein, P and Tan, CY and Kirtley, M and Surana, NK and David, LA}, title = {Interplay between particle size and microbial ecology in the gut microbiome.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39214074}, issn = {1751-7370}, support = {R01 DK116187/DK/NIDDK NIH HHS/United States ; 2016-IDG-1013//North Carolina Biotechnology Center/ ; N00014-18-1-2616//Office of Naval Research/ ; 1R01DK116187/NH/NIH HHS/United States ; }, mesh = {*Gastrointestinal Microbiome ; Humans ; Animals ; *Feces/microbiology ; Mice ; *Particle Size ; Adult ; Male ; Female ; Bacteria/classification/genetics/isolation &amp; purification ; Diet ; Young Adult ; Mice, Inbred C57BL ; Mastication ; Middle Aged ; }, abstract = {Physical particles can serve as critical abiotic factors that structure the ecology of microbial communities. For non-human vertebrate gut microbiomes, fecal particle size (FPS) has been known to be shaped by chewing efficiency and diet. However, little is known about what drives FPS in the human gut. Here, we analyzed FPS by laser diffraction across a total of 76 individuals and found FPS to be strongly individualized. Contrary to our initial hypothesis, a behavioral intervention with 41 volunteers designed to increase chewing efficiency did not impact FPS. Dietary patterns could also not be associated with FPS. Instead, we found evidence that human and mouse gut microbiomes shaped FPS. Fecal samples from germ-free and antibiotic-treated mice exhibited increased FPS relative to colonized mice. In humans, markers of longer transit time were correlated with smaller FPS. Gut microbiota diversity and composition were also associated with FPS. Finally, ex vivo culture experiments using human fecal microbiota from distinct donors showed that differences in microbiota community composition can drive variation in particle size. Together, our results support an ecological model in which the human gut microbiome plays a key role in reducing the size of food particles during digestion. This finding has important implications for our understanding of energy extraction and subsequent uptake in gastrointestinal tract. FPS may therefore be viewed as an informative functional readout, providing new insights into the metabolic state of the gut microbiome.}, }
@article {pmid39211880, year = {2024}, author = {Schluter, J and Matheis, F and Ebina, W and Jogia, W and Sullivan, AP and Gordon, K and Fanega de la Cruz, E and Victory-Hays, ME and Heinly, MJ and Diefenbach, CS and Peled, JU and Foster, KR and Levitt, A and McLaughlin, E}, title = {A randomized controlled trial of postbiotic administration during antibiotic treatment increases microbiome diversity and enriches health associated taxa.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.07.25.24311015}, pmid = {39211880}, support = {DP2 AI164318/AI/NIAID NIH HHS/United States ; }, abstract = {Antibiotic-induced microbiome injury, defined as a reduction of ecological diversity and obligate anaerobe taxa, is associated with negative health outcomes in hospitalized patients, and healthy individuals who received antibiotics in the past are at higher risk for autoimmune diseases. No interventions are currently available that effectively target the microbial ecosystem in the gut to prevent this negative collateral damage of antibiotics. Here, we present the results from a single-center, randomized placebo-controlled trial involving 32 patients who received an oral, fermentation-derived postbiotic alongside oral antibiotic therapy for gastrointestinal (GI)-unrelated infections. Postbiotics comprise complex mixtures of metabolites produced by bacteria during fermentation and other processes, which can mediate microbial ecology. Bacterial ecosystem alpha diversity, quantified by the inverse Simpson index, during the end of the antibiotic course was significantly higher (+40%) across the 16 postbiotic-treated patients compared with the 16 patients who received a placebo, and the postbiotic was well-tolerated. Secondary analyses of 157 stool samples collected longitudinally revealed that the increased diversity was driven by enrichment in health-associated microbial genera: obligate anaerobe Firmicutes, in particular taxa belonging to the Lachnospiraceae family, were higher in treated patients; conversely, Escherichia/Shigella abundances, which comprise pathobionts and antimicrobial-resistant strains, were reduced in postbiotic-treated patients at the end of their antibiotic course and up to 10 days later. Taken together, these results indicate that postbiotic co-administration during antibiotic therapy could support a health-associated gut microbiome community and may reduce antibiotic-induced microbiome injury.}, }
@article {pmid39204682, year = {2024}, author = {Andreata, MFL and Afonso, L and Niekawa, ETG and Salomão, JM and Basso, KR and Silva, MCD and Alves, LC and Alarcon, SF and Parra, MEA and Grzegorczyk, KG and Chryssafidis, AL and Andrade, G}, title = {Microbial Fertilizers: A Study on the Current Scenario of Brazilian Inoculants and Future Perspectives.}, journal = {Plants (Basel, Switzerland)}, volume = {13}, number = {16}, pages = {}, pmid = {39204682}, issn = {2223-7747}, abstract = {The increasing need for sustainable agricultural practices, combined with the demand for enhanced crop productivity, has led to a growing interest in utilizing microorganisms for biocontrol of diseases and pests, as well as for growth promotion. In Brazilian agriculture, the use of plant growth-promoting rhizobacteria (PGPR) and plant growth-promoting fungi (PGPF) has become increasingly prevalent, with a corresponding rise in the number of registered microbial inoculants each year. PGPR and PGPF occupy diverse niches within the rhizosphere, playing a crucial role in soil nutrient cycling and influencing a wide range of plant physiological processes. This review examines the primary mechanisms employed by these microbial agents to promote growth, as well as the strategy of co-inoculation to enhance product efficacy. Furthermore, we provide a comprehensive analysis of the microbial inoculants currently available in Brazil, detailing the microorganisms accessible for major crops, and discuss the market's prospects for the research and development of novel products in light of current challenges faced in the coming years.}, }
@article {pmid39203927, year = {2024}, author = {Govaert, M and Rotsaert, C and Vannieuwenhuyse, C and Duysburgh, C and Medlin, S and Marzorati, M and Jarrett, H}, title = {Survival of Probiotic Bacterial Cells in the Upper Gastrointestinal Tract and the Effect of the Surviving Population on the Colonic Microbial Community Activity and Composition.}, journal = {Nutrients}, volume = {16}, number = {16}, pages = {}, pmid = {39203927}, issn = {2072-6643}, support = {Not applicable//Heights/ ; }, mesh = {*Probiotics ; Humans ; *Gastrointestinal Microbiome ; *Colon/microbiology ; *Upper Gastrointestinal Tract/microbiology ; Microbial Viability ; Bacteria/growth &amp; development ; Fatty Acids, Volatile/metabolism ; }, abstract = {Many health-promoting effects have been attributed to the intake of probiotic cells. However, it is important that probiotic cells arrive at the site of their activity in a viable state in order to exert their beneficial effects. Careful selection of the appropriate probiotic formulation is therefore required as mainly the type of probiotic species/strain and the administration strategy may affect survival of the probiotic cells during the upper gastrointestinal (GIT) passage. Therefore, the current study implemented Simulator of the Human Microbial Ecosystem (SHIME[®]) technology to investigate the efficacy of different commercially available probiotic formulations on the survival and culturability of probiotic bacteria during upper GIT passage. Moreover, Colon-on-a-Plate (CoaP™) technology was applied to assess the effect of the surviving probiotic bacteria on the gut microbial community (activity and composition) of three human donors. Significantly greater survival and culturability rates were reported for the delayed-release capsule formulation (>50%) as compared to the powder, liquid, and standard capsule formulations (<1%) (p < 0.05), indicating that the delayed-release capsule was most efficacious in delivering live bacteria cells. Indeed, administration of the delayed-release capsule probiotic digest resulted in enhanced production of SCFAs and shifted gut microbial community composition towards beneficial bacterial species. These results thus indicate that careful selection of the appropriate probiotic formulation and administration strategy is crucial to deliver probiotic cells in a viable state at the site of their activity (distal ileum and colon).}, }
@article {pmid39203578, year = {2024}, author = {Yan, Y and Shi, Z and Wang, C and Jin, Z and Yin, J and Zhu, G}, title = {Viral Diversity and Ecological Impact of DNA Viruses in Dominant Tick Species in China.}, journal = {Microorganisms}, volume = {12}, number = {8}, pages = {}, pmid = {39203578}, issn = {2076-2607}, support = {RCYJ2012//Basic Scientific Research Funds of Hangzhou Medical College/ ; }, abstract = {Ticks are blood-feeding ectoparasites that also transmit various pathogens, posing severe risks to human and animal health. DNA viruses play a crucial role in the microbial ecology of ticks, but their distribution and ecological significance remain largely undetermined. Here, we assembled an extensive catalog encompassing 4320 viral operational taxonomic units (vOTUs) from six main dominant tick species in China, of which 94.8% have not been found in any other environment. To bridge the knowledge gap in tick DNA virus research and provide a crucial resource platform, we developed the Tick DNA Virus Database. This database includes the vOTUs that are known to cause diseases. Most of the predicted vOTUs are associated with dominant bacterial and archaeal phyla. We identified 105 virus-encoded putative auxiliary metabolic genes (AMGs) that are involved in host metabolism and environmental adaptation, potentially influencing ticks through both top-down and bottom-up mechanisms. The identification of microbial communities and antibiotic resistance in wild tick species suggests that wild ticks are reservoirs of antibiotic resistance and potential spreaders of antibiotic resistance. These findings reveal the potential role of tick viruses in ecosystems, highlighting the importance of monitoring tick microbiomes to address global public health challenges.}, }
@article {pmid39203418, year = {2024}, author = {Barazetti, AR and Dealis, ML and Basso, KR and Silva, MCD and Alves, LDC and Parra, MEA and Simionato, AS and Cely, MVT and Macedo, AL and Silva, DB and Andrade, G}, title = {Evaluation of Resistance Induction Promoted by Bioactive Compounds of Pseudomonas aeruginosa LV Strain against Asian Soybean Rust.}, journal = {Microorganisms}, volume = {12}, number = {8}, pages = {}, pmid = {39203418}, issn = {2076-2607}, abstract = {Pseudomonas are known as higher producers of secondary metabolites with antimicrobial properties and plant growth promoters, including resistance induction. These mechanisms should be an alternative to pesticide use in crop production. Phakopsora pachyrhizi causes Asian soybean rust, representing a high loss of yield around the world. The objective of this paper was to evaluate the application of secondary metabolites produced by Pseudomonas aeruginosa LV strain from the semi-purified fraction F4A in soybean plants to induce plant resistance against P. pachyrhizi in field conditions. The experimental design was performed in randomized blocks with three replicates using two F4A doses (1 and 10 μg mL[-1]) combined or not with fungicides (Unizeb Gold[®] or Sphere Max[®]). The control treatment, with Uni + Sph, saponins, flavonoids, and sphingolipids, showed higher intensities in the plants. In contrast, plants treated with the F4A fraction mainly exhibited fatty acid derivatives and some non-identified compounds with nitrogen. Plants treated with Sphere Max[®], with or without F4A10, showed higher intensities of glycosylated flavonoids, such as kaempferol, luteolin, narigenin, and apigenin. Plants treated with F4A showed higher intensities of genistein and fatty acid derivatives. These increases in flavonoid compound biosynthesis and antioxidant properties probably contribute to the protection against reactive oxygen species (ROS).}, }
@article {pmid39203403, year = {2024}, author = {Al-Tarshi, M and Dobretsov, S and Al-Belushi, M}, title = {Bacterial Communities across Multiple Ecological Niches (Water, Sediment, Plastic, and Snail Gut) in Mangrove Habitats.}, journal = {Microorganisms}, volume = {12}, number = {8}, pages = {}, pmid = {39203403}, issn = {2076-2607}, support = {RC/GRG-AGR/FISH/22/01//Ministry of Higher Education, Research and Innovation/ ; RC/GRG-AGR/FISH/22/01//Sultan Qaboos University/ ; }, abstract = {Microbial composition across substrates in mangroves, particularly in the Middle East, remains unclear. This study characterized bacterial communities in sediment, water, Terebralia palustris snail guts, and plastic associated with Avicennia marina mangrove forests in two coastal lagoons in the Sea of Oman using 16S rDNA gene MiSeq sequencing. The genus Vibrio dominated all substrates except water. In the gut of snails, Vibrio is composed of 80-99% of all bacterial genera. The water samples showed a different pattern, with the genus Sunxiuqinia being dominant in both Sawadi (50.80%) and Qurum (49.29%) lagoons. There were significant differences in bacterial communities on different substrata, in particular plastic. Snail guts harbored the highest number of unique Operational Taxonomic Units (OTUs) in both lagoons, accounting for 30.97% OTUs in Sawadi and 28.91% OTUs in Qurum, compared to other substrates. Plastic in the polluted Sawadi lagoon with low salinity harbored distinct genera such as Vibrio, Aestuariibacter, Zunongwangia, and Jeotgalibacillus, which were absent in the Qurum lagoon with higher salinity and lower pollution. Sawadi lagoon exhibited higher species diversity in sediment and plastic substrates, while Qurum lagoon demonstrated lower species diversity. The principal component analysis (PCA) indicates that environmental factors such as salinity, pH, and nutrient levels significantly influence bacterial community composition across substrates. Variations in organic matter and potential anthropogenic influences, particularly from plastics, further shape bacterial communities. This study highlights the complex microbial communities in mangrove ecosystems, emphasizing the importance of considering multiple substrates in mangrove microbial ecology studies. The understanding of microbial dynamics and anthropogenic impacts is crucial for shaping effective conservation and management strategies in mangrove ecosystems, particularly in the face of environmental changes.}, }
@article {pmid39200461, year = {2024}, author = {Han, D and Yang, Y and Guo, Z and Dai, S and Jiang, M and Zhu, Y and Wang, Y and Yu, Z and Wang, K and Rong, C and Yu, Y}, title = {A Review on the Interaction of Acetic Acid Bacteria and Microbes in Food Fermentation: A Microbial Ecology Perspective.}, journal = {Foods (Basel, Switzerland)}, volume = {13}, number = {16}, pages = {}, pmid = {39200461}, issn = {2304-8158}, support = {32200012//National Natural Science Foundation of China/ ; 22KJB180016//Basic Science Research Program for Higher Education Institutions in Jiangsu Province (Natural Science)/ ; }, abstract = {In fermented foods, acetic acid bacteria (AAB), kinds of bacteria with a long history of utilization, contribute to safety, nutritional, and sensory properties primarily through acetic acid fermentation. AAB are commonly found in various fermented foods such as vinegar, sour beer, fermented cocoa and coffee beans, kefir beverages, kombucha, and sourdough. They interact and cooperate with a variety of microorganisms, resulting in the formation of diverse metabolites and the production of fermented foods with distinct flavors. Understanding the interactions between AAB and other microbes is crucial for effectively controlling and utilizing AAB in fermentation processes. However, these microbial interactions are influenced by factors such as strain type, nutritional conditions, ecological niches, and fermentation duration. In this review, we examine the relationships and research methodologies of microbial interactions and interaction studies between AAB and yeasts, lactic acid bacteria (LAB), and bacilli in different food fermentation processes involving these microorganisms. The objective of this review is to identify key interaction models involving AAB and other microorganisms. The insights gained will provide scientific guidance for the effective utilization of AAB as functional microorganisms in food fermentation processes.}, }
@article {pmid39198281, year = {2024}, author = {He, Z and Smets, BF and Dechesne, A}, title = {Mating Assay: Plating Below a Cell Density Threshold is Required for Unbiased Estimation of Plasmid Conjugation Frequency of RP4 Transfer Between E. coli Strains.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {109}, pmid = {39198281}, issn = {1432-184X}, support = {0236-00022B//Innovationsfonden/ ; 0236-00022B//Innovationsfonden/ ; 0236-00022B//Innovationsfonden/ ; PhD Scholarship//Sino-Danish Center/ ; PhD Scholarship//Sino-Danish Center/ ; }, mesh = {*Escherichia coli/genetics ; *Conjugation, Genetic ; *Plasmids/genetics ; Gene Transfer, Horizontal ; }, abstract = {Mating assays are common laboratory experiments for measuring the conjugation frequency, i.e. efficiency at which a plasmid transfers from a population of donor cells to a population of recipient cells. Selective plating remains a widely used quantification method to enumerate transconjugants at the end of such assays. However, conjugation frequencies may be inaccurately estimated because plasmid transfer can occur on transconjugant-selective plates rather than only during the intended mating duration. We investigated the influence of cell density on this phenomenon. We conducted mating experiments with IncPα plasmid RP4 harbored in Escherichia coli at a fixed cell density and mating conditions, inoculated a serial dilution of the mating mixture on transconjugant-selective plates or in transconjugant-selective broth, and compared the results to a model of cell-to-cell distance distribution. Our findings suggest that irrespective of the mating mode (liquid vs solid), the enumeration of transconjugants becomes significantly biased if the plated cell density exceeds 28 Colony Forming Unit (CFU)/mm[2] (or 1.68•10[5] CFU/standard 9 cm Petri dish). This threshold is determined with a 95% confidence interval of ± 4 CFU/mm[2] (± 2.46•10[4] CFU/standard 9 cm Petri dish). Liquid mating assays were more sensitive to this bias because the conjugation frequency of RP4 is several orders of magnitude lower in suspension compared to surface mating. Therefore, if selective plating is used, we recommend to plate at this density threshold and that negative controls are performed where donors and recipients are briefly mixed before plating at the same dilutions as for the actual mating assay. As an alternative, a liquid enumeration method can be utilized to increase the signal-to-noise ratio and allow for more accurate enumeration of transconjugants.}, }
@article {pmid39197278, year = {2024}, author = {Peng, C and Wang, Y and Sha, X and Li, M and Wang, X and Wang, J and Wang, Y and Liu, C and Wang, L}, title = {Adverse effect of TWPs on soil fungi and the contribution of benzothiazole rubber additives.}, journal = {Journal of hazardous materials}, volume = {479}, number = {}, pages = {135574}, doi = {10.1016/j.jhazmat.2024.135574}, pmid = {39197278}, issn = {1873-3336}, mesh = {*Benzothiazoles ; *Soil Microbiology ; *Fungi/drug effects ; *Rubber ; *Soil Pollutants/toxicity/analysis ; Biomass ; }, abstract = {Tire wear particles (TWPs) pollution is widely present in soil, especially in areas severely affected by traffic. Herein, regular variation of fungal biomass with TWPs was found in soils with different distances from the highway. In addition, the concentrations of benzothiazole compounds (BTHs), an important class of rubber vulcanization accelerators, were found to be positively correlated to the TWPs abundance. Sixty days' soil microcosm experiments were conducted to further confirm the adverse effect of TWPs and BTHs on soil fungi. TWPs spiking at 1000 mg/kg, a detectable level in the roadside, resulted in significant reduction of biomass and significant changes of soil fungal community structure, with Eurotium and Polyporales being the sensitive species. BTH+ 2-hydroxybenzothiazole (OHBT) (the dominant BTHs in soil) spiking at 200 ng/kg, the dose equivalent to 1000 mg/kg TWPs pollution, also caused a similar magnitude of soil fungal biomass reduction. Adonis demonstrated no significant difference of fungal community structure between TWPs and BTH+OHBT spiked soil, suggesting the adverse effect of TWPs on soil fungi may be explained by the act of BTHs. Pure culture using the representative soil fungi Eurotium and Polyporales also confirmed that BTHs were the main contributors to the adverse effect of TWPs on soil fungi.}, }
@article {pmid39196435, year = {2024}, author = {Tenore, A and Russo, F and Jacob, J and Grattepanche, JD and Buttaro, B and Klapper, I}, title = {A Mathematical Model of Diel Activity and Long Time Survival in Phototrophic Mixed-Species Subaerial Biofilms.}, journal = {Bulletin of mathematical biology}, volume = {86}, number = {10}, pages = {123}, pmid = {39196435}, issn = {1522-9602}, support = {1951532//National Science Foundation/ ; 2325170//National Science Foundation/ ; }, mesh = {*Biofilms/growth &amp; development ; *Models, Biological ; *Mathematical Concepts ; *Phototrophic Processes/physiology ; *Cyanobacteria/physiology/metabolism ; *Computer Simulation ; Biomass ; Heterotrophic Processes/physiology ; Microbial Interactions/physiology ; Bacterial Physiological Phenomena ; }, abstract = {Subaerial biofilms (SAB) are intricate microbial communities living on terrestrial surfaces, of interest in a variety of contexts including cultural heritage preservation, microbial ecology, biogeochemical cycling, and biotechnology. Here we propose a mathematical model aimed at better understanding the interplay between cyanobacteria and heterotrophic bacteria, common microbial SAB constituents, and their mutual dependence on local environmental conditions. SABs are modeled as thin mixed biofilm-liquid water layers sitting on stone. A system of ordinary differential equations regulates the dynamics of key SAB components: cyanobacteria, heterotrophs, polysaccharides and decayed biomass, as well as cellular levels of organic carbon, nitrogen and energy. These components are interconnected through a network of energetically dominant metabolic pathways, modeled with limitation terms reflecting the impact of biotic and abiotic factors. Daily cylces of temperature, humidity, and light intensity are considered as input model variables that regulate microbial activity by influencing water availability and metabolic kinetics. Relevant physico-chemical processes, including pH regulation, further contribute to a description of the SAB ecology. Numerical simulations explore the dynamics of SABs in a real-world context, revealing distinct daily activity periods shaped by water activity and light availability, as well as longer time scale survivability conditions. Results also suggest that heterotrophs could play a substantial role in decomposing non-volatile carbon compounds and regulating pH, thus influencing the overall composition and stability of the biofilm.}, }
@article {pmid39196422, year = {2024}, author = {Toloza-Moreno, DL and Yockteng, R and Pérez-Zuñiga, JI and Salinas-Castillo, C and Caro-Quintero, A}, title = {Implications of Domestication in Theobroma cacao L. Seed-Borne Microbial Endophytes Diversity.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {108}, pmid = {39196422}, issn = {1432-184X}, mesh = {*Cacao/microbiology ; *Endophytes/genetics/classification/isolation &amp; purification/physiology ; *Seeds/microbiology/growth &amp; development ; *Bacteria/classification/genetics/isolation &amp; purification ; *Domestication ; Microbiota ; Fungi/genetics/classification/isolation &amp; purification ; Genotype ; Biodiversity ; }, abstract = {The study of plant-microbe interactions is a rapidly growing research field, with increasing attention to the role of seed-borne microbial endophytes in protecting the plant during its development from abiotic and biotic stresses. Recent evidence suggests that seed microbiota is crucial in establishing the plant microbial community, affecting its composition and structure, and influencing plant physiology and ecology. For Theobroma cacao L., the diversity and composition of vertically transmitted microbes have yet to be addressed in detail. We explored the composition and diversity of seed-borne endophytes in cacao pods of commercial genotypes (ICS95, IMC67), recently liberated genotypes from AGROSAVIA (TCS01, TCS19), and landraces from Tumaco (Colombia) (AC9, ROS1, ROS2), to evaluate microbial vertical transmission and establishment in various tissues during plant development. We observed a higher abundance of Pseudomonas and Pantoea genera in the landraces and AGROSAVIA genotypes, while the commercial genotypes presented a higher number of bacteria species but in low abundance. In addition, all the genotypes and plant tissues showed a high percentage of fungi of the genus Penicillium. These results indicate that domestication in cacao has increased bacterial endophyte diversity but has reduced their abundance. We isolated some of these seed-borne endophytes to evaluate their potential as growth promoters and found that Bacillus, Pantoea, and Pseudomonas strains presented high production of indole acetic acid and ACC deaminase activity. Our results suggest that cacao domestication could lead to the loss of essential bacteria for seedling establishment and development. This study improves our understanding of the relationship and interaction between perennial plants and seed-borne microbiota.}, }
@article {pmid39193431, year = {2024}, author = {Ding, J and Cui, X and Wang, X and Zhai, F and Wang, L and Zhu, L}, title = {Multi-omics analysis of gut microbiota and metabolites reveals contrasting profiles in domestic pigs and wild boars across urban environments.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1450306}, pmid = {39193431}, issn = {1664-302X}, abstract = {The gut microbiota plays a crucial role in host health and metabolism. This study explores the differences in gut microbiota and metabolites between domestic pigs (DP) and wild boars (WB) in urban environments. We analyzed gut microbial composition, metabolic profiles, virome composition, antibiotic resistance genes (ARGs), and human pathogenic bacteria (HPB) in both DP and WB. Our results revealed that DP exhibited a higher Firmicutes/Bacteroidetes ratio and were enriched in bacterial genera associated with domestication and modern feeding practices. Metabolomic analysis showed distinct profiles, with WB significantly enriched in the Pantothenate and CoA biosynthesis pathway, highlighting dietary and environmental influences on host metabolism. Additionally, DP had a distinct gut virome composition, particularly enriched in lytic phages of the Chaseviridae family. ARG analysis indicated a higher abundance of tetracycline resistance genes in DP, likely due to antibiotic use in pig farms. Furthermore, variations in HPB composition underscored potential health risks associated with contact with pig feces. These findings provide valuable insights into the microbial ecology of domestic pigs and wild boars, emphasizing the importance of these comparisons in identifying zoonotic pathogen transmission pathways and managing antibiotic resistance. Continued research in this area is essential for developing effective strategies to mitigate public health risks and promote sustainable livestock management practices.}, }
@article {pmid39191402, year = {2024}, author = {Aoun, N and Georgoulis, SJ and Avalos, JK and Grulla, KJ and Miqueo, K and Tom, C and Lowe-Power, TM}, title = {A pangenomic atlas reveals eco-evolutionary dynamics that shape type VI secretion systems in plant-pathogenic Ralstonia.}, journal = {mBio}, volume = {15}, number = {10}, pages = {e0032324}, pmid = {39191402}, issn = {2150-7511}, support = {Hatch #1023861,Award# 1030618//USDA | National Institute of Food and Agriculture (NIFA)/ ; //Hellman Foundation (The Hellman Foundation)/ ; }, mesh = {*Type VI Secretion Systems/genetics/metabolism ; *Phylogeny ; *Genome, Bacterial ; *Ralstonia solanacearum/genetics/metabolism ; *Evolution, Molecular ; Plant Diseases/microbiology ; Bacterial Toxins/genetics/metabolism ; Burkholderiaceae/genetics/metabolism/classification ; Multigene Family ; Ralstonia/genetics/metabolism ; Genomics ; Gene Transfer, Horizontal ; }, abstract = {Soilborne Ralstonia solanacearum species complex (RSSC) pathogens disrupt microbial communities as they invade roots and fatally wilt plants. RSSC pathogens secrete antimicrobial toxins using a type VI secretion system (T6SS). To investigate how evolution and ecology have shaped the T6SS of these bacterial pathogens, we analyzed the T6SS gene content and architecture across the RSSC and their evolutionary relatives. Our analysis reveals that two ecologically similar Burkholderiaceae taxa, xylem-pathogenic RSSC and Paracidovorax, have convergently evolved to wield large arsenals of T6SS toxins. To understand the mechanisms underlying genomic enrichment of T6SS toxins, we compiled an atlas of 1,066 auxiliary T6SS toxin clusters ("aux" clusters) across 99 high-quality RSSC genomes. We classified 25 types of aux clusters with toxins that predominantly target lipids, nucleic acids, or unknown cellular substrates. The aux clusters were located in diverse genetic neighborhoods and had complex phylogenetic distributions, suggesting frequent horizontal gene flow. Phages and other mobile genetic elements account for most of the aux cluster acquisition on the chromosome but very little on the megaplasmid. Nevertheless, RSSC genomes were more enriched in aux clusters on the megaplasmid. Although the single, ancestral T6SS was broadly conserved in the RSSC, the T6SS has been convergently lost in atypical, non-soilborne lineages. Overall, our data suggest dynamic interplay between the lifestyle of RSSC lineages and the evolution of T6SSes with robust arsenals of toxins. This pangenomic atlas poises the RSSC as an emerging, tractable model to understand the role of the T6SS in shaping pathogen populations.IMPORTANCEWe explored the eco-evolutionary dynamics that shape the inter-microbial warfare mechanisms of a globally significant plant pathogen, the Ralstonia solanacearum species complex. We discovered that most Ralstonia wilt pathogens have evolved extensive and diverse repertoires of type VI secretion system-associated antimicrobial toxins. These expansive toxin arsenals potentially enhance the ability of Ralstonia pathogens to invade plant microbiomes, enabling them to rapidly colonize and kill their host plants. We devised a classification system to categorize the Ralstonia toxins. Interestingly, many of the toxin gene clusters are encoded on mobile genetic elements, including prophages, which may be mutualistic symbionts that enhance the inter-microbial competitiveness of Ralstonia wilt pathogens. Moreover, our findings suggest that the convergent loss of this multi-gene trait contributes to genome reduction in two vector-transmitted lineages of Ralstonia pathogens. Our findings demonstrate that the interplay between microbial ecology and pathogen lifestyle shapes the evolution of a genetically complex antimicrobial weapon.}, }
@article {pmid39190978, year = {2024}, author = {Xu, M and Wang, F and Stedtfeld, RD and Fu, Y and Xiang, L and Sheng, H and Li, Z and Hashsham, SA and Jiang, X and Tiedje, JM}, title = {Transfer of antibiotic resistance genes from soil to rice in paddy field.}, journal = {Environment international}, volume = {191}, number = {}, pages = {108956}, doi = {10.1016/j.envint.2024.108956}, pmid = {39190978}, issn = {1873-6750}, mesh = {*Oryza/genetics ; *Soil Microbiology ; *Fertilizers ; *Soil/chemistry ; *Drug Resistance, Microbial/genetics ; Animals ; Agriculture ; Swine ; Composting ; Genes, Bacterial ; }, abstract = {The global spread and distribution of antibiotic resistance genes (ARGs) has received much attention whereas knowledge about the transmission of ARGs from one matrix to another is still insufficient. In this study, the paddy fields fertilized with chemical fertilizer, swine compost, and no fertilizer were investigated to assess the transfer of ARGs from soil to rice. Soil and plant samples were collected at day 0, 7, 30 and 79 representing various stages of paddy growth. High throughput qPCR was applied to quantify ARGs using a set of 144 primers. Gene copy number of ARGs measured in soil initially decreased and then increased in soil with no fertilizer and chemical fertilizer, indicating that crop planting and flooding conditions did influence the ARGs profiles in soil. Application of swine compost significantly enhanced the relative abundance and gene copy number of ARGs in paddy soil. Rice seedlings contained substantial amount of ARGs and their relative abundance continually decreased after transplant. Compared with initial stage, detection frequencies of ARGs increased in soil without swine compost at harvest time (day 79), indicating the transmission of ARGs from irrigation water to soil. Detection frequencies of ARGs increased in soil and rice root with swine compost at harvest time, indicating the transfer of ARGs from swine compost to soil and rice root. There was no significant difference in abundance and diversity of ARGs in rice grains with these three different fertilizations. The source of the ARGs in rice grain still needs further exploration.}, }
@article {pmid39189736, year = {2024}, author = {Wang, L and Ducoste, JJ and de Los Reyes, FL}, title = {Perturbations to common gardens of anaerobic co-digesters reveal relationships between functional resilience and microbial community composition.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {9}, pages = {e0029824}, pmid = {39189736}, issn = {1098-5336}, support = {15-05-U//North Carolina Water Resources Research Institute/ ; CBET 1805666//National Science Foundation (NSF)/ ; }, mesh = {*Microbiota/physiology ; *Bioreactors/microbiology ; Anaerobiosis ; *Methane/metabolism ; Bacteria/metabolism/classification/genetics ; }, abstract = {We report the relationship between enrichment of adapted populations and enhancement of community functional resilience in methanogenic bioreactors. Although previous studies have shown the positive effects of acclimation, this work directly investigated the relationships between microbiome dynamics and performance of anaerobic co-digesting reactors in response to different levels of an environmental perturbation (loading of grease interceptor waste [GIW]). Using the methanogenic microbiome from a full-scale digester, we developed eight sets of microbial communities in triplicate using different feed sources. These substrate-specific microbiomes were then exposed to three independent disturbance events of low-, mid- and high-GIW loading rates. This approach allowed us to directly attribute differences in community responses to differences in community composition. Despite identical inocula, environment (digester operation, substrate loading rate, and feeding patterns) and general whole-community function (methane production and effluent quality) during the cultivation period, different substrates led to different microbial community assemblies. Lipid pre-acclimation led to enrichment of a pool of specialized populations, along with thriving of sub-dominant communities. The enrichment of these populations improved functional resilience and process performance when exposed to a low level of lipid-rich perturbation compared with less-acclimated communities. At higher levels of perturbation, the communities were not able to recover methanogenesis, indicating a loading limit to the resilience response. This study extends our current understanding of environmental perturbations, feed-specific adaptation, and functional resilience in methanogenic bioreactors.IMPORTANCEThis study demonstrates, for the first time for GIW co-digestion, how applying similar perturbations to different microbial communities was used to directly identify the causal relationships between microbial community, function, and environment in triplicate anaerobic microbiomes. We evaluated the impact of feed-specific adaptation on methanogenic microbiomes and demonstrated how microbiomes can be influenced to improve their functional (methanogenic) resilience to GIW inhibition. These findings demonstrate how an ecological framework can help improve a biological engineering application, and more specifically, increase the potential of anaerobic co-digestion for converting wastes to energy.}, }
@article {pmid39188310, year = {2024}, author = {Berrios, L and Venturini, AM and Ansell, TB and Tok, E and Johnson, W and Willing, CE and Peay, KG}, title = {Co-inoculations of bacteria and mycorrhizal fungi often drive additive plant growth responses.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae104}, pmid = {39188310}, issn = {2730-6151}, abstract = {Controlled greenhouse studies have shown the numerous ways that soil microbes can impact plant growth and development. However, natural soil communities are highly complex, and plants interact with many bacterial and fungal taxa simultaneously. Due to logistical challenges associated with manipulating more complex microbiome communities, how microbial communities impact emergent patterns of plant growth therefore remains poorly understood. For instance, do the interactions between bacteria and fungi generally yield additive (i.e. sum of their parts) or nonadditive, higher order plant growth responses? Without this information, our ability to accurately predict plant responses to microbial inoculants is weakened. To address these issues, we conducted a meta-analysis to determine the type (additive or higher-order, nonadditive interactions), frequency, direction (positive or negative), and strength that bacteria and mycorrhizal fungi (arbuscular and ectomycorrhizal) have on six phenotypic plant growth responses. Our results demonstrate that co-inoculations of bacteria and mycorrhizal fungi tend to have positive additive effects on many commonly reported plant responses. However, ectomycorrhizal plant shoot height responds positively and nonadditively to co-inoculations of bacteria and ectomycorrhizal fungi, and the strength of additive effects also differs between mycorrhizae type. These findings suggest that inferences from greenhouse studies likely scale to more complex field settings and that inoculating plants with diverse, beneficial microbes is a sound strategy to support plant growth.}, }
@article {pmid39187952, year = {2024}, author = {Stryker, J and White, E and Díaz-Almeyda, E and Sidoti, B and Oberle, B}, title = {Tank formation transforms nitrogen metabolism of an epiphytic bromeliad and its phyllosphere bacteria.}, journal = {American journal of botany}, volume = {111}, number = {12}, pages = {e16396}, doi = {10.1002/ajb2.16396}, pmid = {39187952}, issn = {1537-2197}, mesh = {*Nitrogen/metabolism ; *Plant Leaves/microbiology/metabolism ; *Bacteria/metabolism/classification ; Tillandsia/metabolism/physiology ; Microbiota ; Bromeliaceae/metabolism/microbiology/physiology ; }, abstract = {PREMISE: Up to half of tropical forest plant species grow on other plants. Lacking access to soils, vascular epiphytes have unique adaptations for mineral nutrition. Among the most distinctive is the tank growth form of certain large bromeliads, which absorb nutrients that are cycled by complex microbial communities in water trapped among their overlapping leaf bases. However, tanks form only after years of growth by juvenile plants, which must acquire nutrients differently. Understanding how nutrient dynamics change during tank bromeliad development can provide key insights into the role of microorganisms in the maintenance of tropical forest biodiversity.<br><br>METHODS: We evaluated variations in plant morphology, growth, foliar nitrogen physiology, and phyllosphere bacterial communities along a size gradient spanning the transition to tank formation in the threatened species Tillandsia utriculata.<br><br>RESULTS: Sequential morphological and growth phases coincided with the transition to tank formation when the longest leaf on plants was between 14 and 19&#x2009;cm. Before this point, foliar ammonium concentrations were very high, but after, leaf segments absorbed significantly more nitrate. Leaf-surface bacterial communities tracked ontogenetic changes in plant morphology and nitrogen metabolism, with less-diverse communities in tankless plants distinguished by a high proportion of taxa implicated in ureolysis, nitrogen fixation, and methanotrophy, whereas nitrate reduction characterized communities on individuals that could form a tank.<br><br>CONCLUSIONS: Coupled changes in plant morphology, physiology, and microbiome function facilitate the transition between alternative nutritional modes in tank bromeliads. Comparing bromeliads across life stages and habitats may illuminate how nitrogen-use varies across scales.}, }
@article {pmid39182301, year = {2024}, author = {Peruzzo, A and Petrin, S and Boscolo Anzoletti, A and Mancin, M and Di Cesare, A and Sabatino, R and Lavagnolo, MC and Beggio, G and Baggio, G and Danesi, P and Barco, L and Losasso, C}, title = {The integration of omics and cultivation-dependent methods could effectively determine the biological risks associated with the utilization of soil conditioners in agriculture.}, journal = {Journal of hazardous materials}, volume = {478}, number = {}, pages = {135567}, doi = {10.1016/j.jhazmat.2024.135567}, pmid = {39182301}, issn = {1873-3336}, mesh = {*Agriculture ; *Soil Microbiology ; *Sewage/microbiology ; *Bacteria/genetics ; Soil/chemistry ; Composting ; Metagenomics ; Fertilizers ; }, abstract = {In the circular economy, reusing agricultural residues, treated biowaste, and sewage sludges-commonly referred to as soil conditioners-in agriculture is essential for converting waste into valuable resources. However, these materials can also contribute to the spread of antimicrobial-resistant pathogens in treated soils. In this study, we analyzed different soil conditioners categorized into five groups: compost from source-separated biowaste and green waste, agro-industrial digestate, digestate from anaerobic digestion of source-separated biowaste, compost from biowaste digestate, and sludges from wastewater treatment plants. Under Italian law, only the first two categories are approved for agricultural use, despite Regulation 1009/2019/EU allowing the use of digestate from anaerobic digestion of source-separated biowaste in CE-marked fertilizers. We examined the bacterial community and associated resistome of each sample using metagenomic approaches. Additionally, we detected and isolated various pathogens to provide a comprehensive understanding of the potential risks associated with sludge application in agriculture. The compost samples exhibited higher bacterial diversity and a greater abundance of potentially pathogenic bacteria compared to other samples, except for wastewater treatment plant sludges, which had the highest frequency of Salmonella isolation and resistome diversity. Our findings suggest integrating omics and cultivation-dependent methods to accurately assess the biological risks of using sludge in agriculture.}, }
@article {pmid39180136, year = {2024}, author = {Khadem, S and Berry, D and Al-Khlifeh, E}, title = {Climate influences the gut eukaryome of wild rodents in the Great Rift Valley of Jordan.}, journal = {Parasites &amp; vectors}, volume = {17}, number = {1}, pages = {358}, pmid = {39180136}, issn = {1756-3305}, mesh = {Jordan ; Animals ; Mice ; Rats ; *Eukaryota/classification/genetics/growth &amp; development ; *Climate ; *Gastrointestinal Microbiome/genetics ; *Rodentia/parasitology ; *Animals, Wild/parasitology ; High-Throughput Nucleotide Sequencing ; RNA, Ribosomal, 18S ; Feces/parasitology ; }, abstract = {BACKGROUND: The mammalian gut microbiome includes a community of eukaryotes with significant taxonomic and functional diversity termed the eukaryome. The molecular analysis of eukaryotic diversity in microbiomes of wild mammals is still in its early stages due to the recent emergence of interest in this field. This study aimed to fill this knowledge gap by collecting data on eukaryotic species found in the intestines of wild rodents. Because little is known about the influence of climate on the gut eukaryome, we compared the composition of the gut eukaryotes in two rodent species, Mus musculus domesticus and Acomys cahirinus, which inhabit a transect crossing a temperate and tropical zone on the Jordanian side of the Great Rift Valley (GRV).<br><br>METHODS: We used high-throughput amplicon sequencing targeting the 18S rRNA gene in fecal samples from rodents to identify eukaryotic organisms, their relative abundance, and their potential for pathogenicity.<br><br>RESULTS: Nematodes and protozoa were the most prevalent species in the eukaryome communities, whereas fungi made up 6.5% of the total. Sixty percent of the eukaryotic ASVs belonged to taxa that included known pathogens. Eighty percent of the rodents were infected with pinworms, specifically Syphacia obvelata. Eukaryotic species diversity differed significantly between bioclimatic zones (p&#x2009;=&#x2009;0.001). Nippostrongylus brasiliensis and Aspiculuris tetraptera were found to be present exclusively in the Sudanian zone rodents. This area has not reported any cases of Trichuris infections. Yet, Capillaria infestations were unique to the Mediterranean region, while Trichuris vulpis infestations were also prevalent in the Mediterranean and Irano-Turanian regions.<br><br>CONCLUSIONS: This study highlights the importance of considering host species diversity and environmental factors when studying eukaryome composition in wild mammals. These data will be valuable as a reference to eukaryome study.}, }
@article {pmid39178936, year = {2024}, author = {Anedda, E and Ekhlas, D and Alexa, E and Farrell, ML and Gaffney, MT and Madigan, G and Morris, D and Burgess, CM}, title = {Characterization of antimicrobial resistant Enterobacterales isolated from spinach and soil following zinc amendment.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {361}, number = {}, pages = {124774}, doi = {10.1016/j.envpol.2024.124774}, pmid = {39178936}, issn = {1873-6424}, mesh = {*Spinacia oleracea/microbiology ; *Soil Microbiology ; *Zinc/pharmacology ; *Enterobacteriaceae/drug effects/genetics ; *Anti-Bacterial Agents/pharmacology ; *Soil Pollutants ; Soil/chemistry ; Microbial Sensitivity Tests ; Drug Resistance, Bacterial/genetics ; }, abstract = {Antimicrobial resistant bacteria can occur in the primary food production environment. The emergence and dissemination of antimicrobial resistance (AMR) in the environment can be influenced by several factors, including the presence of heavy metals. The aim of this study was to examine the presence and characteristics of antimicrobial resistant Enterobacterales in soils and spinach grown in soils with and without zinc amendment. A total of 160 samples (92 soil and 68 spinach) were collected from two locations, in which some plots had been amended with zinc. Samples were cultured on selective agars for detection of extended-spectrum beta-lactamase-producing Enterobacterales (ESBL), carbapenem-resistant Enterobacterales and ciprofloxacin-resistant Enterobacterales. Samples were also cultured for enumeration of total Enterobacterales. Isolates were identified by MALDI-TOF. Antimicrobial susceptibility testing was carried out in accordance with EUCAST and CLSI criteria. The whole genome sequence (WGS) of selected isolates was determined. Inductively coupled plasma atomic emission spectrometry was also performed on soil samples in order to measure the concentration of zinc. In total 20 antimicrobial resistant Enterobacterales were isolated from the soil (n = 8) and spinach samples (n = 12). In both sample types, Serratia fonticola (n = 16) was the dominant species, followed by Escherichia coli (n = 1), Citrobacter freundii (n = 1) and Morganella morganii (n = 1) detected in spinach samples, and Enterobacter cloacae (n = 1) detected in a soil sample. The WGS identified genes conferring resistance to different antimicrobials in agreement with the phenotypic results; 14 S. fonticola isolates were confirmed as ESBL producers and harboured the blaFONA gene. Genes that encoded for zinc resistance and multidrug efflux pumps, transporters that can target both antimicrobials and heavy metals, were also identified. Overall, the findings of this study suggest the presence of zinc did not influence the AMR Enterobacterales in soil or spinach samples.}, }
@article {pmid39178591, year = {2024}, author = {Gao, FZ and Hu, LX and Liu, YS and Qiao, LK and Chen, ZY and Su, JQ and He, LY and Bai, H and Zhu, YG and Ying, GG}, title = {Unveiling the overlooked small-sized microbiome in river ecosystems.}, journal = {Water research}, volume = {265}, number = {}, pages = {122302}, doi = {10.1016/j.watres.2024.122302}, pmid = {39178591}, issn = {1879-2448}, mesh = {*Rivers/microbiology ; *Microbiota ; *Ecosystem ; Metagenomics ; Bacteria/genetics ; }, abstract = {Enriching microorganisms using a 0.22-μm pore size is a general pretreatment procedure in river microbiome research. However, it remains unclear the extent to which this method loses microbiome information. Here, we conducted a comparative metagenomics-based study on microbiomes with sizes over 0.22 μm (large-sized) and between 0.22 μm and 0.1 μm (small-sized) in a subtropical river. Although the absolute concentration of small-sized microbiome was about two orders of magnitude lower than that of large-sized microbiome, sequencing only large-sized microbiome resulted in a significant loss of microbiome diversity. Specifically, the microbial community was different between two sizes, and 347 genera were only detected in small-sized microbiome. Small-sized microbiome had much more diverse viral community than large-sized fraction. The viruses had abundant ecological functions and were hosted by 825 species of 169 families, including pathogen-related families. Small-sized microbiome had distinct antimicrobial resistance risks from large-sized microbiome, showing an enrichment of eight antibiotic resistance gene (ARG) types as well as the detection of 140 unique ARG subtypes and five enriched risk rank I ARGs. Draft genomes of five major resistant pathogens having diverse ecological and pollutant-degrading functions were only assembled in small-sized microbiome. These findings provide novel insights into river ecosystems, and highlight the overlooked small-sized microbiome in the environment.}, }
@article {pmid39175749, year = {2024}, author = {Peña-Salinas, ME and Speth, DR and Utter, DR and Spelz, RM and Lim, S and Zierenberg, R and Caress, DW and Núñez, PG and Vázquez, R and Orphan, VJ}, title = {Thermotogota diversity and distribution patterns revealed in Auka and JaichMaa 'ja 'ag hydrothermal vent fields in the Pescadero Basin, Gulf of California.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e17724}, pmid = {39175749}, issn = {2167-8359}, mesh = {*Hydrothermal Vents/microbiology ; *Geologic Sediments/microbiology/chemistry ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; Seawater/microbiology/chemistry ; California ; Bacteria/genetics/classification ; }, abstract = {Discovering new deep hydrothermal vent systems is one of the biggest challenges in ocean exploration. They are a unique window to elucidate the physical, geochemical, and biological processes that occur on the seafloor and are involved in the evolution of life on Earth. In this study, we present a molecular analysis of the microbial composition within the newly discovered hydrothermal vent field, JaichMaa 'ja 'ag, situated in the Southern Pescadero Basin within the Gulf of California. During the cruise expedition FK181031 in 2018, 33 sediment cores were collected from various sites within the Pescadero vent fields and processed for 16S rRNA amplicon sequence variants (ASVs) and geochemical analysis. Correlative analysis of the chemical composition of hydrothermal pore fluids and microbial abundances identified several sediment-associated phyla, including Thermotogota, that appear to be enriched in sediment horizons impacted by hydrothermal fluid flow. Comparative analysis of Thermotogota with the previously explored Auka hydrothermal vent field situated 2 km away displayed broad similarity between the two locations, although at finer scales (e.g., ASV level), there were notable differences that point to core-to-core and site-level factors revealing distinct patterns of distribution and abundance within these two sediment-hosted hydrothermal vent fields. These patterns are intricately linked to the specific physical and geochemical conditions defining each vent, illuminating the complexity of this unique deep ocean chemosynthetic ecosystem.}, }
@article {pmid39175056, year = {2024}, author = {Sbardellati, DL and Vannette, RL}, title = {Targeted viromes and total metagenomes capture distinct components of bee gut phage communities.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {155}, pmid = {39175056}, issn = {2049-2618}, support = {2023-67011-40501//U.S. Department of Agriculture/ ; 1929516//National Science Foundation/ ; }, mesh = {Bees/virology/microbiology ; Animals ; *Bacteriophages/genetics/isolation &amp; purification/classification ; *Virome ; *Metagenome ; Gastrointestinal Microbiome/genetics ; Metagenomics/methods ; Gastrointestinal Tract/microbiology/virology ; }, abstract = {BACKGROUND: Despite being among the most abundant biological entities on earth, bacteriophage (phage) remain an understudied component of host-associated systems. One limitation to studying host-associated phage is the lack of consensus on methods for sampling phage communities. Here, we compare paired total metagenomes and viral size fraction metagenomes (viromes) as methods for investigating the dsDNA viral communities associated with the GI tract of two bee species: the European honey bee Apis mellifera and the eastern bumble bee Bombus impatiens.<br><br>RESULTS: We find that viromes successfully enriched for phage, thereby increasing phage recovery, but only in honey bees. In contrast, for bumble bees, total metagenomes recovered greater phage diversity. Across both bee species, viromes better sampled low occupancy phage, while total metagenomes were biased towards sampling temperate phage. Additionally, many of the phage captured by total metagenomes were absent altogether from viromes. Comparing between bees, we show that phage communities in commercially reared bumble bees are significantly reduced in diversity compared to honey bees, likely reflecting differences in bacterial titer and diversity. In a broader context, these results highlight the complementary nature of total metagenomes and targeted viromes, especially when applied to host-associated environments.<br><br>CONCLUSIONS: Overall, we suggest that studies interested in assessing total communities of host-associated phage should consider using both approaches. However, given the constraints of virome sampling, total metagenomes may serve to sample phage communities with the understanding that they will preferentially sample dominant and temperate phage. Video Abstract.}, }
@article {pmid39174521, year = {2024}, author = {Foulquier, A and Datry, T and Corti, R and von Schiller, D and Tockner, K and Stubbington, R and Gessner, MO and Boyer, F and Ohlmann, M and Thuiller, W and Rioux, D and Miquel, C and Albariño, R and Allen, DC and Altermatt, F and Arce, MI and Arnon, S and Banas, D and Banegas-Medina, A and Beller, E and Blanchette, ML and Blessing, J and Boëchat, IG and Boersma, K and Bogan, M and Bonada, N and Bond, N and Brintrup, K and Bruder, A and Burrows, R and Cancellario, T and Canhoto, C and Carlson, S and Cid, N and Cornut, J and Danger, M and de Freitas Terra, B and De Girolamo, AM and Del Campo, R and Díaz Villanueva, V and Dyer, F and Elosegi, A and Febria, C and Figueroa Jara, R and Four, B and Gafny, S and Gómez, R and Gómez-Gener, L and Guareschi, S and Gücker, B and Hwan, J and Jones, JI and Kubheka, PS and Laini, A and Langhans, SD and Launay, B and Le Goff, G and Leigh, C and Little, C and Lorenz, S and Marshall, J and Martin Sanz, EJ and McIntosh, A and Mendoza-Lera, C and Meyer, EI and Miliša, M and Mlambo, MC and Morais, M and Moya, N and Negus, P and Niyogi, D and Pagán, I and Papatheodoulou, A and Pappagallo, G and Pardo, I and Pařil, P and Pauls, SU and Polášek, M and Rodríguez-Lozano, P and Rolls, RJ and Sánchez-Montoya, MM and Savić, A and Shumilova, O and Sridhar, KR and Steward, A and Taleb, A and Uzan, A and Valladares, Y and Vander Vorste, R and Waltham, NJ and Zak, DH and Zoppini, A}, title = {Unravelling large-scale patterns and drivers of biodiversity in dry rivers.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {7233}, pmid = {39174521}, issn = {2041-1723}, support = {869226 (DRYvER)//EC | EU Framework Programme for Research and Innovation H2020 | H2020 European Institute of Innovation and Technology (H2020 The European Institute of Innovation and Technology)/ ; }, mesh = {*Biodiversity ; *Rivers/microbiology ; Animals ; Fungi/classification/genetics ; Geologic Sediments/microbiology ; Bacteria/classification/genetics ; Invertebrates/classification ; DNA Barcoding, Taxonomic ; Plants/classification ; Archaea/classification/genetics ; }, abstract = {More than half of the world's rivers dry up periodically, but our understanding of the biological communities in dry riverbeds remains limited. Specifically, the roles of dispersal, environmental filtering and biotic interactions in driving biodiversity in dry rivers are poorly understood. Here, we conduct a large-scale coordinated survey of patterns and drivers of biodiversity in dry riverbeds. We focus on eight major taxa, including microorganisms, invertebrates and plants: Algae, Archaea, Bacteria, Fungi, Protozoa, Arthropods, Nematodes and Streptophyta. We use environmental DNA metabarcoding to assess biodiversity in dry sediments collected over a 1-year period from 84 non-perennial rivers across 19 countries on four continents. Both direct factors, such as nutrient and carbon availability, and indirect factors such as climate influence the local biodiversity of most taxa. Limited resource availability and prolonged dry phases favor oligotrophic microbial taxa. Co-variation among taxa, particularly Bacteria, Fungi, Algae and Protozoa, explain more spatial variation in community composition than dispersal or environmental gradients. This finding suggests that biotic interactions or unmeasured ecological and evolutionary factors may strongly influence communities during dry phases, altering biodiversity responses to global changes.}, }
@article {pmid39172818, year = {2024}, author = {Frazier, AN and Belk, AD and Beck, MR and Koziel, JA}, title = {Impact of methane mitigation strategies on the native ruminant microbiome: A protocol for a systematic review and meta-analysis.}, journal = {PloS one}, volume = {19}, number = {8}, pages = {e0308914}, pmid = {39172818}, issn = {1932-6203}, mesh = {*Methane/metabolism ; *Ruminants/microbiology ; Animals ; *Microbiota ; *Systematic Reviews as Topic ; *RNA, Ribosomal, 16S/genetics ; *Meta-Analysis as Topic ; }, abstract = {Recently, research has investigated the role of the ruminant native microbiome, and the role microbes play in methane (CH4) production and mitigation. However, the variation across microbiome studies makes implementing impactful strategies difficult. The first objective of this study is to identify, summarize, compile, and discuss the current literature on CH4 mitigation strategies and how they interact with the native ruminant microbiome. The second objective is to perform a meta-analysis on the identified16S rRNA sequencing data. A literature search using Web of Science, Scopus, AGRIS, and Google Scholar will be implemented. Eligible criteria will be defined using PICO (population, intervention, comparator, and outcomes) elements. Two independent reviewers will be utilized for both the literature search and data compilation. Risk of bias will be assessed using the Cochrane Risk Bias 2.0 tool. Publicly available 16S rRNA amplicon gene sequencing data will be downloaded from NCBI Sequence Read Archive, European Nucleotide Archive or similar database using appropriate extraction methods. Data processing will be performed using QIIME2 following a standardized protocol. Meta-analyses will be performed on both alpha and beta diversity as well as taxonomic analyses. Alpha diversity metrics will be tested using a Kruskal-Wallis test with a Benjamini-Hochberg multiple testing correction. Beta diversity will be statistically tested using PERMANOVA testing with multiple test corrections. Hedge's g standardized mean difference statistic will be used to calculate fixed and random effects model estimates using a 95% confidence interval. Heterogeneity between studies will be assessed using the I2 statistic. Potential publication bias will be further assessed using Begg's correlation test and Egger's regression test. The GRADE approach will be used to assess the certainty of evidence. The following protocol will be used to guide future research and meta-analyses for investigating CH4 mitigation strategies and ruminant microbial ecology. The future work could be used to enhance livestock management techniques for GHG control. This protocol is registered in Open Science Framework (https://osf.io/vt56c) and available in the Systematic Reviews for Animals and Food (https://www.syreaf.org/contact).}, }
@article {pmid39171106, year = {2024}, author = {Pi, X and Du, Z and Teng, W and Fu, H and Hu, L and Li, J and Ding, J and Yang, X and Zhang, Y}, title = {Characteristics of stachyose-induced effects on gut microbiota and microbial metabolites in vitro associated with obesity in children.}, journal = {Frontiers in nutrition}, volume = {11}, number = {}, pages = {1411374}, pmid = {39171106}, issn = {2296-861X}, abstract = {Childhood obesity presents a serious health concern associated with gut microbiota alterations. Dietary interventions targeting the gut microbiota have emerged as promising strategies for managing obesity in children. This study aimed to elucidate the impact of stachyose (STS) supplementation on the gut microbiota composition and metabolic processes in obese children. Fecal samples were collected from 40 obese children (20 boys and 20 girls) aged between 6 and 15 and in vitro fermentation was conducted with or without the addition of STS, respectively, followed by 16S rRNA amplicon sequencing and analysis of short-chain fatty acids (SCFAs) and gases. Notably, our results revealed that STS supplementation led to significant alterations in gut microbiota composition, including an increase in the abundance of beneficial bacteria such as Bifidobacterium and Faecalibacterium, and a decrease in harmful bacteria including Escherichia-Shigella, Parabacteroides, Eggerthella, and Flavonifractor. Moreover, STS supplementation resulted in changes in SCFAs production, with significant increases in acetate levels and reductions in propionate and propionate, while simultaneously reducing the generation of gases such as H2S, H2, and NH3. The Area Under the Curve (AUC)-Random Forest algorithm and PICRUSt 2 were employed to identify valuable biomarkers and predict associations between the gut microbiota, metabolites, and metabolic pathways. The results not only contribute to the elucidation of STS's modulatory effects on gut microbiota but also underscore its potential in shaping metabolic activities within the gastrointestinal environment. Furthermore, our study underscores the significance of personalized nutrition interventions, particularly utilizing STS supplementation, in the management of childhood obesity through targeted modulation of gut microbial ecology and metabolic function.}, }
@article {pmid39168311, year = {2025}, author = {MacGibeny, MA and Adjei, S and Pyle, H and Bunick, CG and Ghannoum, M and Grada, A and Harris-Tryon, T and Tyring, SK and Kong, HH}, title = {The human skin microbiome in health.}, journal = {Journal of the American Academy of Dermatology}, volume = {93}, number = {2}, pages = {329-336}, pmid = {39168311}, issn = {1097-6787}, support = {Z99 AR999999/ImNIH/Intramural NIH HHS/United States ; ZIA AR041217/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Humans ; *Microbiota/physiology/drug effects ; *Skin/microbiology/immunology ; *Skin Diseases/microbiology ; Host Microbial Interactions ; Skin Microbiome ; }, abstract = {Human skin is home to a myriad of microorganisms, including bacteria, viruses, fungi, and mites, many of which are considered commensal microbes that aid in maintaining the overall homeostasis or steady-state condition of the skin and contribute to skin health. Our understanding of the complexities of the skin's interaction with its microorganisms is evolving. This knowledge is based primarily on in vitro and animal studies, and more work is needed to understand how this knowledge relates to humans. Here, we introduce the concept of the skin microbiome and discuss skin microbial ecology, some intrinsic factors with potential influence on the human skin microbiome, and possible microbiome-host interactions. The second article of this two-part CME series describes how microbiome alterations may be associated with skin disease, how medications can affect the microbiome, and what microbiome-based therapies are under investigation.}, }
@article {pmid39165397, year = {2024}, author = {Jacob, M and Thomas, PK and Giebel, HA and Billerbeck, S and Simon, M and Striebel, M and Dlugosch, L}, title = {Cross-domain diversity effects: linking diatom species richness, intraspecific richness, and biomass production to host-associated bacterial diversity.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae046}, pmid = {39165397}, issn = {2730-6151}, abstract = {Interactions between bacteria and microalgae are important for the functioning of aquatic ecosystems, yet interactions based on the biodiversity of these two taxonomic domains have been scarcely studied. Specifically, it is unclear whether a positive biodiversity-productivity relationship in phytoplankton is largely facilitated by niche partitioning among the phytoplankton organisms themselves or whether associated bacterial communities play an additional role in modifying these diversity effects. Moreover, the effects of intraspecific diversity in phytoplankton communities on bacterial community diversity have not been tested. To address these points, we factorially manipulated both species and intraspecific richness of three diatoms to test the effects of diatom species/strain diversity on biomass production and bacterial diversity in algae-bacteria communities. The results show that diatom intraspecific diversity has significant positive effects on culture biomass and the diversity of the associated free-living bacterial community (0.2-3 μm size fraction), which are comparable in magnitude to species diversity effects. However, there were little to no effects of diatom diversity on host-associated bacterial diversity (>3 μm size fraction), or of bacterial diversity on biomass production. These results suggest a decoupling of bacterial diversity from the diatom diversity-productivity relationship and provide early insights regarding the relations between diversity across domains in aquatic ecosystems.}, }
@article {pmid39165109, year = {2024}, author = {Gloder, G and Bourne, ME and Cuny, MAC and Verreth, C and Crauwels, S and Dicke, M and Poelman, EH and Jacquemyn, H and Lievens, B}, title = {Caterpillar-parasitoid interactions: species-specific influences on host microbiome composition.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {10}, pages = {}, pmid = {39165109}, issn = {1574-6941}, support = {G.0961.19//Flemish Fund for Scientific Research/ ; }, mesh = {Animals ; *Larva/microbiology ; *Microbiota ; *Butterflies/microbiology/parasitology ; *Host-Parasite Interactions ; Wolbachia/genetics ; Species Specificity ; Nosema/pathogenicity ; Wasps/microbiology ; Bacteria/classification/genetics/growth &amp; development ; }, abstract = {There is increasing evidence that host-parasitoid interactions can have a pronounced impact on the microbiome of host insects, but it is unclear to what extent this is caused by the host and/or parasitoid. Here, we compared the internal and external microbiome of caterpillars of Pieris brassicae and Pieris rapae parasitized by Cotesia glomerata or Cotesia rubecula with nonparasitized caterpillars. Additionally, we investigated the internal and external microbiome of the parasitoid larvae. Both internal and external bacterial densities were significantly higher for P. brassicae than P. rapae, while no differences were found between parasitized and nonparasitized caterpillars. In contrast, parasitism significantly affected the composition of the internal and external microbiome of the caterpillars and the parasitoid larvae, but the effects were dependent on the host and parasitoid species. Irrespective of host species, a Wolbachia species was exclusively found inside caterpillars parasitized by C. glomerata, as well as in the corresponding developing parasitoid larvae. Similarly, a Nosema species was abundantly present inside parasitized caterpillars and the parasitoid larvae, but this was independent of the host and the parasitoid species. We conclude that parasitism has pronounced effects on host microbiomes, but the effects depend on both the host and parasitoid species.}, }
@article {pmid39163484, year = {2024}, author = {Dede, B and Reeves, EP and Walter, M and Bach, W and Amann, R and Meyerdierks, A}, title = {Bacterial chemolithoautotrophy in ultramafic plumes along the Mid-Atlantic Ridge.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39163484}, issn = {1751-7370}, support = {EXC-309-49926684//Deutsche Forschungsgemeinschaft/ ; //Norwegian Research Council/ ; 179560//University of Bergen Centre for Geobiology/ ; //Max Planck Society/ ; }, mesh = {*Hydrothermal Vents/microbiology ; Atlantic Ocean ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; *Chemoautotrophic Growth ; *Seawater/microbiology ; Microbiota ; Hydrogen/metabolism ; Phylogeny ; Sulfur/metabolism ; Oxidation-Reduction ; In Situ Hybridization, Fluorescence ; Carbon Dioxide/metabolism ; }, abstract = {Hydrothermal vent systems release reduced chemical compounds that act as an important energy source in the deep sea. Chemolithoautotrophic microbes inhabiting hydrothermal plumes oxidize these compounds, in particular, hydrogen and reduced sulfur, to obtain the energy required for CO2 fixation. Here, we analysed the planktonic communities of four hydrothermal systems located along the Mid-Atlantic Ridge: Irinovskoe, Semenov-2, Logatchev-1, and Ashadze-2, by combining long-read 16S rRNA gene analysis, fluorescence in situ hybridization, meta-omics, and thermodynamic calculations. Sulfurimonas and SUP05 dominated the microbial communities in these hydrothermal plumes. Investigation of Sulfurimonas and SUP05 MAGs, and their gene transcription in plumes indicated a niche partitioning driven by hydrogen and sulfur. In addition to sulfur and hydrogen oxidation, a novel SAR202 clade inhabiting the plume, here referred to as genus Carboxydicoccus, harbours the capability for CO oxidation and CO2 fixation via reverse TCA cycle. Both pathways were also highly transcribed in other hydrogen-rich plumes, including the Von Damm vent field. Carboxydicoccus profundi reached up to 4% relative abundance (1.0 x 103 cell ml- 1) in Irinovskoe non-buoyant plume and was also abundant in non-hydrothermally influenced deep-sea metagenomes (up to 5 RPKM). Therefore, CO, which is probably not sourced from the hydrothermal fluids (1.9-5.8 μM), but rather from biological activities within the rising fluid, may serve as a significant energy source in hydrothermal plumes. Taken together, this study sheds light on the chemolithoautotrophic potential of the bacterial community in Mid-Atlantic Ridge plumes.}, }
@article {pmid39162854, year = {2024}, author = {Joshi, S and Pham, K and Moe, L and McNees, R}, title = {Exploring the Microbial Diversity and Composition of Three Cigar Product Categories.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {107}, pmid = {39162854}, issn = {1432-184X}, support = {UC2 FD006890/FD/FDA HHS/United States ; }, mesh = {*Tobacco Products ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; *Biodiversity ; Phylogeny ; High-Throughput Nucleotide Sequencing ; DNA, Bacterial/genetics ; }, abstract = {Cigars and cigarillos are emerging as popular tobacco alternatives to cigarettes. However, these products may be equally harmful to human health than cigarettes and are associated with similar adverse health effects. We used 16S rRNA gene amplicon sequencing to extensively characterize the microbial diversity and investigate differences in microbial composition across 23 different products representing three different cigar product categories: filtered cigar, cigarillo, and large cigar. High throughput sequencing of the V4 hypervariable region of the 16 s rRNA gene revealed 2124 Operational Taxonomic Units (OTUs). Our findings showed that the three categories of cigars differed significantly in observed richness and Shannon diversity, with filtered cigars exhibiting lower diversity compared to large cigars and cigarillos. We also found a shared and unique microbiota among different product types. Firmicutes was the most abundant phylum in all product categories, followed by Actinobacteria. Among the 16 genera shared across all product types were Bacillus, Staphylococcus, Pseudomonas, and Pantoea. Nine genera were exclusively shared by large cigars and cigarillos and an additional thirteen genera were exclusive to filtered cigars. Analysis of individual cigar products showed consistent microbial composition across replicates for most large cigars and cigarillos while filtered cigars showed more inter-product variability. These findings provide important insights into the microbial diversity of the different cigar product types.}, }
@article {pmid39162497, year = {2024}, author = {Chatzigiannidou, I and Heyse, J and Props, R and Rubbens, P and Mermans, F and Teughels, W and Van de Wiele, T and Boon, N}, title = {Real-time flow cytometry to assess qualitative and quantitative responses of oral pathobionts during exposure to antiseptics.}, journal = {Microbiology spectrum}, volume = {12}, number = {10}, pages = {e0095524}, pmid = {39162497}, issn = {2165-0497}, support = {G0B2719N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; 1221020N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; 3G020119//Fonds Wetenschappelijk Onderzoek (FWO)/ ; }, mesh = {*Flow Cytometry/methods ; *Anti-Infective Agents, Local/pharmacology ; *Chlorhexidine/pharmacology ; Humans ; *Bacteria/drug effects ; *Triclosan/pharmacology ; Cetylpyridinium/pharmacology ; Microbial Sensitivity Tests/methods ; Mouth/microbiology ; Periodontitis/microbiology ; }, abstract = {UNLABELLED: Antiseptics are widely used in oral healthcare to prevent or treat oral diseases, such as gingivitis and periodontitis. However, the incidence of bacteria being tolerant to standard antiseptics has sharply increased over the last few years. This stresses the urgency for surveillance against tolerant organisms, as well as the discovery of novel antimicrobials. Traditionally, susceptibility to antimicrobials is assessed by broth micro-dilution or disk diffusion assays, both of which are time-consuming, labor-intensive, and provide limited information on the mode of action of the antimicrobials. The abovementioned limitations highlight the need for the development of new methods to monitor and further understand antimicrobial susceptibility. In this study, we used real-time flow cytometry, combined with membrane permeability staining, as a quick and sensitive technology to study the quantitative and qualitative responses of two oral pathobionts to different concentrations of chlorhexidine (CHX), cetylpyridinium chloride (CPC), or triclosan. Apart from the real-time monitoring of cell damage, we further applied a phenotypic fingerprinting method to differentiate between the bacterial subpopulations that arose due to treatment. We quantified the pathobiont damage rate of different antiseptics at different concentrations within 15 minutes of exposure and identified the conditions under which the bacteria were most susceptible. Moreover, we detected species-specific and treatment-specific phenotypic subpopulations. This proves that real-time flow cytometry can provide information on the susceptibility of different microorganisms in a short time frame while differentiating between antiseptics and thus could be a valuable tool in the discovery of novel antimicrobial compound, while at the same time deciphering their mode of action.<br><br>IMPORTANCE: With increasing evidence that microorganisms are becoming more tolerant to standard antimicrobials, faster and more accessible antimicrobial susceptibility testing methods are needed. However, traditional susceptibility assays are laborious and time-consuming. To overcome the abovementioned limitations, we introduce a novel approach to define antimicrobial susceptibility in a much shorter time frame with the use of real-time flow cytometry. Furthermore, phenotypic fingerprinting analysis can be applied on the data to study the way antiseptics affect the bacterial cell morphology over time and, thus, gain information on the mode of action of a certain compound.}, }
@article {pmid39162262, year = {2024}, author = {Liu, M and Li, Q and Xu, W and Wang, L and Wu, F and Tan, L and Li, L and Zhang, G}, title = {Characterization of water microbiota and their relationship with resident oysters during an oyster mortality event.}, journal = {Microbiology spectrum}, volume = {12}, number = {10}, pages = {e0288123}, pmid = {39162262}, issn = {2165-0497}, support = {2022YFD2400304//National Key R&amp;D Program of China/ ; 2022LZGC015//Key Research and Development Program of Shandong/ ; ZFJH202309//Key Research and Development Program of Shandong/ ; CARS-49//Earmarked Fund for CARS/ ; }, mesh = {Animals ; *Microbiota/physiology ; *Ostreidae/microbiology ; *Water Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Seawater/microbiology ; Cyanobacteria/genetics/physiology/growth &amp; development ; Temperature ; }, abstract = {Microorganisms are vital for the health of marine invertebrates, and their assembly is driven by both deterministic and stochastic factors that regulate residents (innate to the host) and transients (from ambient water). However, the role of water microbiota and the significance of deterministic and stochastic processes in aquatic hosts facing mortality threats are largely unknown. This study examines the shifts in water microbiota during an oyster mortality event using amplicon sequencing and compared with those of resident oysters to disentangle the balance of the deterministic and stochastic factors involved. Water temperature and dissolved oxygen significantly shape the microbial community with a distinct monthly pattern, and Cyanobacteria blooms might exacerbate oyster mortality. The comparative analysis of microbial communities in oysters and water revealed that ≤ 21% of the genera were shared between oysters and water, implying that water microbiota cannot easily transfer into oysters. Furthermore, these shared genera had different functions, with oysters more involved in promoting host digestion and nutrient acquisition and water bacteria enriched more in functions promoting their own growth and survival. These findings illustrate that oysters may possess specific selection or barrier mechanisms that permit a small percentage of transients, controlled by stochastic factors and having a minimal effect on oyster mortality, to enter, whereas the majority of oyster microbiota are residents governed by deterministic factors. Consequently, oysters exhibit some plasticity in their symbiotic microbiota, enabling them to maintain microbial homeostasis and adapt to complex microbial surroundings. This may be a shared mechanism among marine invertebrates for survival in complex marine environments.IMPORTANCEPacific oysters are widely cultured and play vital ecological roles. However, the summer mortality hinders sustainable oyster farming. Untangling causative mechanisms of oyster mortality is a complex task due to the intricate "interactome" involving environmental factors, hosts, and pathogens. Interactions between hosts and microorganisms offer an ideal avenue for investigating the truth. We systematically investigated the microbial community in water and resident oysters during a summer mortality event and proposed that the assembly of oyster microbiota is primarily governed by deterministic processes independent of mortality. Pathogens mainly originate from resident members of the oyster microbiota, with a limited influence from the microbial community in the water. Additionally, environmental degraders, such as Cyanobacteria blooms, cannot be overlooked as a contributing factor of oyster mortality. This study evaluated the weight of deterministic and stochastic factors in microbial assembly during an oyster mortality event and greatly broadened our understanding of the "interactome" through the interaction between oysters and water in microbiota.}, }
@article {pmid39161630, year = {2024}, author = {Blázquez, M and Pérez-Vargas, I and Garrido-Benavent, I and Villar-dePablo, M and Turégano, Y and Frías-López, C and Sánchez-Gracia, A and de Los Ríos, A and Gasulla, F and Pérez-Ortega, S}, title = {Endless forms most frustrating: disentangling species boundaries in the Ramalina decipiens group (Lecanoromycetes, Ascomycota), with the description of six new species and a key to the group.}, journal = {Persoonia}, volume = {52}, number = {}, pages = {44-93}, pmid = {39161630}, issn = {0031-5850}, abstract = {Oceanic islands have been recognized as natural laboratories in which to study a great variety of evolutionary processes. One such process is evolutionary radiations, the diversification of a single ancestor into a number of species that inhabit different environments and differ in the traits that allow them to exploit those environments. The factors that drive evolutionary radiations have been studied for decades in charismatic organisms such as birds or lizards, but are lacking in lichen-forming fungi, despite recent reports of some lineages showing diversification patterns congruent with radiation. Here we propose the Ramalina decipiens group as a model system in which to carry out such studies. This group is currently thought to be comprised of five saxicolous species, all of them endemic to the Macaronesian region (the Azores, Madeira, Selvagens, Canary and Cape Verde islands). Three species are single-island endemics (a rare geographic distribution pattern in lichens), whereas two are widespread and show extreme morphological variation. The latter are suspected to harbor unrecognized species-level lineages. In order to use the Ramalina decipiens group as a model system it is necessary to resolve the group's phylogeny and to clarify its species boundaries. In this study we attempt to do so following an integrative taxonomy approach. We constructed a phylogenetic tree based on six molecular markers, four of which are newly developed and generated competing species hypotheses based on molecular (species discovery strategies based on both single locus and multilocus datasets) and phenotypic data (unsupervised clustering algorithms based on morphology, secondary chemistry and geographic origin). We found that taxonomic diversity in the Ramalina decipiens group has been highly underestimated in previous studies. In consequence, we describe six new species, most of them single-island endemics and provide a key to the group. Phylogenetic relationships among species have been reconstructed with almost full support which, coupled with the endemic character of the group, makes it an excellent system for the study of island radiations in lichen-forming fungi. Citation: Blázquez M, Pérez-Vargas I, Garrido-Benavent I, et al. 2024. Endless forms most frustrating: disentangling species boundaries in the Ramalina decipiens group (Lecanoromycetes, Ascomycota), with the description of six new species and a key to the group. Persoonia 52: 44-93. https://doi.org/10.3767/persoonia.2024.52.03 .}, }
@article {pmid39160591, year = {2024}, author = {Lee, H and Hwang, K and Cho, A and Kim, S and Kim, M and Morgan-Kiss, R and Priscu, JC and Kim, KM and Kim, OS}, title = {Microbial assemblages and associated biogeochemical processes in Lake Bonney, a permanently ice-covered lake in the McMurdo Dry Valleys, Antarctica.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {60}, pmid = {39160591}, issn = {2524-6372}, support = {PE23130//Korea Polar Research Institute/ ; PE23130//Korea Polar Research Institute/ ; PE23130//Korea Polar Research Institute/ ; PE23130//Korea Polar Research Institute/ ; PE23130//Korea Polar Research Institute/ ; PE23130//Korea Polar Research Institute/ ; PE23130//Korea Polar Research Institute/ ; OPP 1637708//National Science Foundation/ ; OPP 1637708//National Science Foundation/ ; }, abstract = {BACKGROUND: Lake Bonney, which is divided into a west lobe (WLB) and an east lobe (ELB), is a perennially ice-covered lake located in the McMurdo Dry Valleys of Antarctica. Despite previous reports on the microbial community dynamics of ice-covered lakes in this region, there is a paucity of information on the relationship between microbial genomic diversity and associated nutrient cycling. Here, we applied gene- and genome-centric approaches to investigate the microbial ecology and reconstruct microbial metabolic potential along the depth gradient in Lake Bonney.<br><br>RESULTS: Lake Bonney is strongly chemically stratified with three distinct redox zones, yielding different microbial niches. Our genome enabled approach revealed that in the sunlit and relatively freshwater epilimnion, oxygenic photosynthetic production by the cyanobacterium Pseudanabaena and a diversity of protists and microalgae may provide new organic carbon to the environment. CO-oxidizing bacteria, such as Acidimicrobiales, Nanopelagicales, and Burkholderiaceae were also prominent in the epilimnion and their ability to oxidize carbon monoxide to carbon dioxide may serve as a supplementary energy conservation strategy. In the more saline metalimnion of ELB, an accumulation of inorganic nitrogen and phosphorus supports photosynthesis despite relatively low light levels. Conversely, in WLB the release of organic rich subglacial discharge from Taylor Glacier into WLB would be implicated in the possible high abundance of heterotrophs supported by increased potential for glycolysis, beta-oxidation, and glycoside hydrolase and may contribute to the growth of iron reducers in the dark and extremely saline hypolimnion of WLB. The suboxic and subzero temperature zones beneath the metalimnia in both lobes supported microorganisms capable of utilizing reduced nitrogens and sulfurs as electron donors. Heterotrophs, including nitrate reducing sulfur oxidizing bacteria, such as Acidimicrobiales (MAG72) and Salinisphaeraceae (MAG109), and denitrifying bacteria, such as Gracilimonas (MAG7), Acidimicrobiales (MAG72) and Salinisphaeraceae (MAG109), dominated the hypolimnion of WLB, whereas the environmental harshness of the hypolimnion of ELB was supported by the relatively low in metabolic potential, as well as the abundance of halophile Halomonas and endospore-forming Virgibacillus.<br><br>CONCLUSIONS: The vertical distribution of microbially driven C, N and S cycling genes/pathways in Lake Bonney reveals the importance of geochemical gradients to microbial diversity and biogeochemical cycles with the vertical water column.}, }
@article {pmid39159439, year = {2024}, author = {Dos Santos, A and Schultz, J and Almeida Trapp, M and Modolon, F and Romanenko, A and Kumar Jaiswal, A and Gomes, L and Rodrigues-Filho, E and Rosado, AS}, title = {Investigating Polyextremophilic Bacteria in Al Wahbah Crater, Saudi Arabia: A Terrestrial Model for Life on Saturn's Moon Enceladus.}, journal = {Astrobiology}, volume = {24}, number = {8}, pages = {824-838}, doi = {10.1089/ast.2024.0017}, pmid = {39159439}, issn = {1557-8070}, mesh = {Saudi Arabia ; *Exobiology/methods ; *Extraterrestrial Environment ; Genome, Bacterial/genetics ; Mars ; Bacteria/genetics/isolation &amp; purification ; Phylogeny ; }, abstract = {The study of extremophilic microorganisms has sparked interest in understanding extraterrestrial microbial life. Such organisms are fundamental for investigating life forms on Saturn's icy moons, such as Enceladus, which is characterized by potentially habitable saline and alkaline niches. Our study focused on the salt-alkaline soil of the Al Wahbah crater in Saudi Arabia, where we identified microorganisms that could be used as biological models to understand potential life on Enceladus. The search involved isolating 48 bacterial strains, sequencing the genomes of two thermo-haloalkaliphilic strains, and characterizing them for astrobiological application. A deeper understanding of the genetic composition and functional capabilities of the two novel strains of Halalkalibacterium halodurans provided valuable insights into their survival strategies and the presence of coding genes and pathways related to adaptations to environmental stressors. We also used mass spectrometry with a molecular network approach, highlighting various classes of molecules, such as phospholipids and nonproteinogenic amino acids, as potential biosignatures. These are essential features for understanding life's adaptability under extreme conditions and could be used as targets for biosignatures in upcoming missions exploring Enceladus' orbit. Furthermore, our study reinforces the need to look at new extreme environments on Earth that might contribute to the astrobiology field.}, }
@article {pmid39158314, year = {2024}, author = {Guéneau, V and Jiménez, G and Castex, M and Briandet, R}, title = {Insights into the genomic and phenotypic characteristics of Bacillus spp. strains isolated from biofilms in broiler farms.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {9}, pages = {e0066324}, pmid = {39158314}, issn = {1098-5336}, support = {2020/0548//Association Nationale de la Recherche et de la Technologie (ANRT)/ ; }, mesh = {*Genome, Bacterial ; *Phenotype ; *Bacillus/genetics/isolation &amp; purification ; *Biofilms ; *Chickens/microbiology ; Animals ; *Farms ; Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Biosynthetic Pathways/genetics ; Multigene Family ; Phylogeny ; Livestock/microbiology ; DNA, Bacterial/genetics ; Deoxyribonuclease I/metabolism ; }, abstract = {The characterization of surface microbiota living in biofilms within livestock buildings has been relatively unexplored, despite its potential impact on animal health. To enhance our understanding of these microbial communities, we characterized 11 spore-forming strains isolated from two commercial broiler chicken farms. Sequencing of the strains revealed them to belong to three species Bacillus velezensis, Bacillus subtilis, and Bacillus licheniformis. Genomic analysis revealed the presence of antimicrobial resistance genes and genes associated with antimicrobial secretion specific to each species. We conducted a comprehensive characterization of the biofilm formed by these strains under various conditions, and we revealed significant structural heterogeneity across the different strains. A macro-colony interaction model was employed to assess the compatibility of these strains to coexist in mixed biofilms. We identified highly competitive B. velezensis strains, which cannot coexist with other Bacillus spp. Using confocal laser scanning microscopy along with a specific dye for extracellular DNA, we uncovered the importance of extracellular DNA for the formation of B. licheniformis biofilms. Altogether, the results highlight the heterogeneity in both genome and biofilm structure among Bacillus spp. isolated from biofilms present within livestock buildings.IMPORTANCELittle is known about the microbial communities that develop on farms in direct contact with animals. Nonpathogenic strains of Bacillus velezensis, Bacillus subtilis, and Bacillus licheniformis were found in biofilm samples collected from surfaces in contact with animals. Significant genetic and phenotypic diversity was described among these Bacillus strains. The strains do not possess mobile antibiotic resistance genes in their genomes and have a strong capacity to form structured biofilms. Among these species, B. velezensis was noted for its high competitiveness compared with the other Bacillus spp. Additionally, the importance of extracellular DNA in the formation of B. licheniformis biofilms was observed. These findings provide insights for the management of these surface microbiota that can influence animal health, such as the use of competitive strains to minimize the establishment of undesirable bacteria or enzymes capable of specifically deconstructing biofilms.}, }
@article {pmid39157765, year = {2024}, author = {de Santana, CO and Spealman, P and Oliveira, E and Gresham, D and de Jesus, T and Chinalia, F}, title = {Prokaryote communities along a source-to-estuary river continuum in the Brazilian Atlantic Forest.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e17900}, pmid = {39157765}, issn = {2167-8359}, mesh = {Brazil ; *Rivers/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Geologic Sediments/microbiology ; Bacteria/genetics/classification/isolation &amp; purification ; Forests ; Estuaries ; Biodiversity ; Archaea/genetics/classification/isolation &amp; purification ; Microbiota ; }, abstract = {The activities of microbiomes in river sediments play an important role in sustaining ecosystem functions by driving many biogeochemical cycles. However, river ecosystems are frequently affected by anthropogenic activities, which may lead to microbial biodiversity loss and/or changes in ecosystem functions and related services. While parts of the Atlantic Forest biome stretching along much of the eastern coast of South America are protected by governmental conservation efforts, an estimated 89% of these areas in Brazil are under threat. This adds urgency to the characterization of prokaryotic communities in this vast and highly diverse biome. Here, we present prokaryotic sediment communities in the tropical Juliana River system at three sites, an upstream site near the river source in the mountains (Source) to a site in the middle reaches (Valley) and an estuarine site near the urban center of Ituberá (Mangrove). The diversity and composition of the communities were compared at these sites, along with environmental conditions, the former by using qualitative and quantitative analyses of 16S rRNA gene amplicons. While the communities included distinct populations at each site, a suite of core taxa accounted for the majority of the populations at all sites. Prokaryote diversity was highest in the sediments of the Mangrove site and lowest at the Valley site. The highest number of genera exclusive to a given site was found at the Source site, followed by the Mangrove site, which contained some archaeal genera not present at the freshwater sites. Copper (Cu) concentrations were related to differences in communities among sites, but none of the other environmental factors we determined was found to have a significant influence. This may be partly due to an urban imprint on the Mangrove site by providing organic carbon and nutrients via domestic effluents.}, }
@article {pmid39155010, year = {2024}, author = {Wong, LC and Rodenburg, U and Leite, RR and Korthals, GW and Pover, J and Koerten, H and Kuramae, EE and Bodelier, PLE}, title = {Exploring microbial diversity and interactions for asbestos modifying properties.}, journal = {The Science of the total environment}, volume = {951}, number = {}, pages = {175577}, doi = {10.1016/j.scitotenv.2024.175577}, pmid = {39155010}, issn = {1879-1026}, mesh = {*Biodegradation, Environmental ; *Bacteria/metabolism/classification ; Fungi/metabolism ; Asbestos ; Soil Microbiology ; Iron/metabolism ; Asbestos, Serpentine ; }, abstract = {Asbestos poses a substantial environmental health risk, and biological treatment offers a promising approach to mitigate its impact by altering its chemical composition. However, the dynamics of microbial co-inoculation in asbestos bioremediation remain poorly understood. This study investigates the effect of microbial single cultures and co-cultures on modifying crocidolite and chrysotile fibers, focusing on the extraction of iron and magnesium. Seventy bacterial and eighty-three fungal strains were isolated from five diverse sites, characterized phylogenetically using the 16S rRNA gene and ITS region, respectively, and assessed for siderophore and organic acid production. Most bacterial strains were identified as Pseudomonas, while Penicillium predominated among fungal strains. Ten bacterial and 25 fungal strains were found to produce both organic compounds. Four microbial co-cultures (one bacterium-bacterium, two fungus-bacterium, and one fungus-fungus) exhibiting synergistic effects in plate assays, alongside their respective single cultures, were incubated with crocidolite and chrysotile. ICP-OES analysis revealed that in crocidolite, the co-culture HRF19-HRB12 removed more iron than their single cultures, while Penicillium TPF36 showed the highest iron removal. The co-culture of two Pseudomonas strains (HRB12-RB5) exhibited the highest magnesium concentration in the supernatant. In chrysotile, the co-culture HRB12-RB5 removed more iron than their individual cultures, with Penicillium TFSF27 exhibiting the highest iron concentration in the solution. Penicillium TFSF27 and the co-culture TFSF27-TPF36 demonstrated the highest magnesium removal. SEM-XRMA analysis showed a significant reduction in iron and magnesium content, confirming elemental extraction from the fibers' structure. This study significantly broadens the range of microbial strains capable of modifying asbestos fibers and underscores the potential of microbial co-cultures in asbestos remediation.}, }
@article {pmid39150265, year = {2024}, author = {Longhi, G and Lugli, GA and Tarracchini, C and Fontana, F and Bianchi, MG and Carli, E and Bussolati, O and van Sinderen, D and Turroni, F and Ventura, M}, title = {From raw milk cheese to the gut: investigating the colonization strategies of Bifidobacterium mongoliense.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {9}, pages = {e0124424}, pmid = {39150265}, issn = {1098-5336}, support = {PE00000003//National Recovery and Resilience Plan (NRRP)/ ; SFI/12/RC/2273a//Irish Government's National Development Plan/ ; SFI/12/RC/2273b//Irish Government's National Development Plan/ ; }, mesh = {*Cheese/microbiology ; *Bifidobacterium/genetics/metabolism/growth &amp; development ; Humans ; *Milk/microbiology ; *Gastrointestinal Microbiome ; Animals ; Italy ; }, abstract = {The microbial ecology of raw milk cheeses is determined by bacteria originating from milk and milk-producing animals. Recently, it has been shown that members of the Bifidobacterium mongoliense species may become transmitted along the Parmigiano Reggiano cheese production chain and ultimately may colonize the consumer intestine. However, there is a lack of knowledge regarding the molecular mechanisms that mediate the interaction between B. mongoliense and the human gut. Based on 128 raw milk cheeses collected from different Italian regions, we isolated and characterized 10 B. mongoliense strains. Comparative genomics allowed us to unveil the presence of enzymes required for the degradation of sialylated host-glycans in B. mongoliense, corroborating the appreciable growth on de Man-Rogosa-Sharpe (MRS) medium supplemented with 3'-sialyllactose (3'-SL) or 6'-sialyllactose (6'-SL). The B. mongoliense BMONG18 was chosen, due to its superior ability to utilize 3'-SL and mucin as representative strain, to investigate its behavior when co-inoculated with other bifidobacterial species. Conversely, members of other bifidobacterial species did not appear to benefit from the presence of BMONG18, highlighting a competitive scenario for nutrient acquisition. Transcriptomic data of BMONG18 reveal no significant differences in gene expression when cultivated in a gut simulating medium (GSM), regardless of whether cheese was included or not. Furthermore, BMONG18 was shown to exhibit high adhesion capabilities to HT29-MTX human cells, in line with its colonization ability of a human host.IMPORTANCEFermented foods are nourishments produced through controlled microbial growth that play an essential role in worldwide human nutrition. Research interest in fermented foods has increased since the 80s, driven by growing awareness of their potential health benefits beyond mere nutritional content. Bifidobacterium mongoliense, previously identified throughout the production process of Parmigiano Reggiano cheese, was found to be capable of establishing itself in the intestines of its consumers. Our study underscores molecular mechanisms through which this bifidobacterial species, derived from food, interacts with the host and other gut microbiota members.}, }
@article {pmid39150230, year = {2024}, author = {Li, J and Yang, X and Zhang, X and Zhang, L}, title = {Effects and mechanisms of microbial ecology and diversity on phytoremediation of cadmium-contaminated soil under the influence of biodegradable organic acids.}, journal = {International journal of phytoremediation}, volume = {26}, number = {14}, pages = {2392-2403}, doi = {10.1080/15226514.2024.2391025}, pmid = {39150230}, issn = {1549-7879}, mesh = {*Biodegradation, Environmental ; *Soil Pollutants/metabolism ; *Cadmium/metabolism ; *Bacillus megaterium/metabolism ; *Soil Microbiology ; *Lolium/metabolism ; Rhizosphere ; Citric Acid/metabolism ; Bacteria/metabolism ; }, abstract = {In recent years, heavy metal pollution has become a global environmental problem and poses a great threat to the health of people and ecosystems. Therefore, strategies for the effective remediation of Cd from contaminated soil are urgently needed. In this study, ryegrass was utilized as a remediation plant, and its remediation potential was enhanced through the application of Citric Acid (CA) in conjunction with Bacillus megaterium (B. megaterium). The P3 treatment (CA + Bacillus megaterium) exhibited a significantly higher efficiency in promoting cadmium extraction by ryegrass, resulting in a 1.79-fold increase in shoot cadmium accumulation compared to the control group (CK) with no Bacillus megaterium or CA. Moreover, the P3 treatment led to an increased abundance of Actinobacteriota, Acidobacteriota, and Patescibacteria in the rhizosphere. The concentration of amino derivatives (such as betaine, sulfolithocholylglycine, N-alpha-acetyl-lysine, glycocholic acid, arginyl-threonine) showed significant upregulation following the P3 treatment. In summary, this study proposes a viable approach for phytoremediation of soil contaminated with cadmium by harnessing the mobilizing abilities of soil bacteria.}, }
@article {pmid39148674, year = {2024}, author = {Dyczko, D and Błażej, P and Kiewra, D}, title = {The influence of forest habitat type on Ixodes ricinus infections with Rickettsia spp. in south-western Poland.}, journal = {Current research in parasitology &amp; vector-borne diseases}, volume = {6}, number = {}, pages = {100200}, pmid = {39148674}, issn = {2667-114X}, abstract = {This study investigates the prevalence of Rickettsia spp. in Ixodes ricinus tick populations in different forest habitat types (broadleaf forest, mixed broadleaf and coniferous forest, and coniferous forest) in south-western Poland. During the survey periods from April to June 2018 and 2019 a total of 494 I. ricinus ticks, including 374 nymphs, 60 females and 60 males, were tested for Rickettsia infections by nested PCR targeting the gltA gene. The overall infection rate was 42.3%; however, we observed statistically significant year-to-year variation. Infection rates varied between tick developmental stages and were significantly influenced by forest habitat type. As assessed by a generalized linear mixed model (GLMM), the highest infection rates were observed in mixed broadleaf and coniferous forests, while coniferous forests had a significant negative effect on infection prevalence. DNA sequencing of selected samples confirmed the predominance of Rickettsia helvetica (91.2%) and less frequent Rickettsia monacensis (8.8%). This study suggests that the forest habitat types can influence Rickettsia spp. infection in tick populations; however, a comprehensive understanding of all factors influencing the level of infection requires future study.}, }
@article {pmid39143010, year = {2024}, author = {Ozbayram, EG and Kleinsteuber, S and Sträuber, H and Schroeder, BG and da Rocha, UN and Corrêa, FB and Harms, H and Nikolausz, M}, title = {Three-domain microbial communities in the gut of Pachnoda marginata larvae: A comparative study revealing opposing trends in gut compartments.}, journal = {Environmental microbiology reports}, volume = {16}, number = {4}, pages = {e13324}, pmid = {39143010}, issn = {1758-2229}, mesh = {Animals ; *Larva/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Archaea/classification/genetics/isolation &amp; purification ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Eukaryota/classification/genetics/isolation &amp; purification ; Phylogeny ; Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {This study aimed to examine the bacterial, methanogenic archaeal, and eukaryotic community structure in both the midgut and hindgut of Pachnoda marginata larvae using an amplicon sequencing approach. The goal was to investigate how various diets and the soil affect the composition of these three-domain microbial communities within the gut of insect larvae. The results indicated a notable variation in the microbial community composition among the gut compartments. The majority of the bacterial community in the hindgut was composed of Ruminococcaceae and Christensenellaceae. Nocardiaceae, Microbacteriaceae, and Lachnospiraceae were detected in midgut samples from larvae feeding on the leaf diet, whereas Sphingomonadaceae, Rhodobacteraceae, and Promicromonasporaceae dominated the bacterial community of midgut of larvae feeding on the straw diet. The diet was a significant factor that influenced the methanogenic archaeal and eukaryotic community patterns. The methanogenic communities in the two gut compartments significantly differed from each other, with the midgut communities being more similar to those in the soil. A higher diversity of methanogens was observed in the midgut samples of both diets compared to the hindgut. Overall, the microbiota of the hindgut was more host-specific, while the assembly of the midgut was more influenced by the environmental microorganisms.}, }
@article {pmid39142044, year = {2024}, author = {Battulga, B and Nakayama, M and Matsuoka, S and Kondo, T and Atarashi-Andoh, M and Koarashi, J}, title = {Dynamics and functions of microbial communities in the plastisphere in temperate coastal environments.}, journal = {Water research}, volume = {264}, number = {}, pages = {122207}, doi = {10.1016/j.watres.2024.122207}, pmid = {39142044}, issn = {1879-2448}, mesh = {*Biofilms ; *Bacteria/genetics/classification ; Fungi/genetics ; Microbiota ; Microplastics ; Japan ; Geologic Sediments/microbiology ; Seawater/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Microbial attachment and biofilm formation on microplastics (MPs <5 mm in size) in the environment have received growing attention. However, there is limited knowledge of microbial function and their effect on the properties and behavior of MPs in the environment. In this study, microbial communities in the plastisphere were explored to understand microbial ecology as well as their impact on aquatic ecosystems. Using the amplicon sequencing of 16S and internal transcribed spacer (ITS) genes, we uncovered the composition and diversity of bacterial and fungal communities in samples of MPs (fiber, film, foam, and fragment), surface water, bottom sediment, and coastal sand in two contrasting coastal areas of Japan. Differences in microbial diversity and taxonomic composition were detected depending on sample type (MPs, water, sediment, and sand) and the research site. Although relatively higher bacterial and fungal gene counts were determined in MP fragments and foams from the research sites, there were no significant differences in microbial community composition depending on the morphotypes of MPs. Given the colonization by hydrocarbon-degrading communities and the presence of pathogens on MPs, the complex processes of microbial taxa influence the characteristics of MP-associated biofilms, and thus, the properties of MPs. This study highlights the metabolic functions of microbes in MP-associated biofilms, which could be key to uncovering the true impact of plastic debris on the global ecosystem.}, }
@article {pmid39141295, year = {2024}, author = {Turbant, F and Blache, A and Węgrzyn, G and Achouak, W and Wien, F and Arluison, V}, title = {Use of Synchrotron Radiation Circular Dichroism to Analyze the Interaction and Insertion of Proteins into Bacterial Outer Membrane Vesicles.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2843}, number = {}, pages = {73-94}, pmid = {39141295}, issn = {1940-6029}, mesh = {*Circular Dichroism/methods ; *Synchrotrons ; *Bacterial Outer Membrane Proteins/chemistry/metabolism ; Bacterial Outer Membrane/metabolism/chemistry ; Protein Structure, Secondary ; Lipid Bilayers/metabolism/chemistry ; }, abstract = {Circular dichroism (CD) is a spectroscopic technique commonly used for the analysis of proteins. Particularly, it allows the determination of protein secondary structure content in various media, including the membrane environment. In this chapter, we present how CD applications can be used to analyze the interaction of proteins with bacterial outer membrane vesicles (OMVs). Most CD studies characterizing the structure of proteins inserted into membranes rely on artificial lipid bilayers, mimicking natural membranes. Nevertheless, these artificial models lack the important features of the true membrane, especially for the outer membrane of Gram-negative bacteria. These features include lipid diversity, glycosylation, and asymmetry. Here, we show how to analyze the interactions of proteins, either integral or peripheral, with OMVs in solution and with supported membranes of OMVs, using conventional CD and orientated circular dichroism (OCD). We explain how to decipher the spectroscopic signals to obtain information on the molecular structure of the protein upon its interaction with an OMV and through its potential insertion into an OMV membrane.}, }
@article {pmid39141097, year = {2024}, author = {Papazachariou, V and Fernández-Juárez, V and Parfrey, LW and Riemann, L}, title = {Nitrogen Fixation and Microbial Communities Associated with Decomposing Seagrass Leaves in Temperate Coastal Waters.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {106}, pmid = {39141097}, issn = {1432-184X}, mesh = {*Nitrogen Fixation ; *Plant Leaves/microbiology ; *Seawater/microbiology/chemistry ; *Microbiota ; *Zosteraceae/microbiology/metabolism ; Nitrogen/metabolism/analysis ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Denmark ; Cyanobacteria/metabolism/genetics/classification/isolation &amp; purification ; }, abstract = {Seagrass meadows play pivotal roles in coastal biochemical cycles, with nitrogen fixation being a well-established process associated with living seagrass. Here, we tested the hypothesis that nitrogen fixation is also associated with seagrass debris in Danish coastal waters. We conducted a 52-day in situ experiment to investigate nitrogen fixation (proxied by acetylene reduction) and dynamics of the microbial community (16S rRNA gene amplicon sequencing) and the nitrogen fixing community (nifH DNA/RNA amplicon sequencing) associated with decomposing Zostera marina leaves. The leaves harboured distinct microbial communities, including distinct nitrogen fixers, relative to the surrounding seawater and sediment throughout the experiment. Nitrogen fixation rates were measurable on most days, but highest on days 3 (dark, 334.8 nmol N g[-1] dw h[-1]) and 15 (light, 194.6 nmol N g[-1] dw h[-1]). Nitrogen fixation rates were not correlated with the concentration of inorganic nutrients in the surrounding seawater or with carbon:nitrogen ratios in the leaves. The composition of nitrogen fixers shifted from cyanobacterial Sphaerospermopsis to heterotrophic genera like Desulfopila over the decomposition period. On the days with highest fixation, nifH RNA gene transcripts were mainly accounted for by cyanobacteria, in particular by Sphaerospermopsis and an unknown taxon (order Nostocales), alongside Proteobacteria. Our study shows that seagrass debris in temperate coastal waters harbours substantial nitrogen fixation carried out by cyanobacteria and heterotrophic bacteria that are distinct relative to the surrounding seawater and sediments. This suggests that seagrass debris constitutes a selective environment where degradation is affected by the import of nitrogen via nitrogen fixation.}, }
@article {pmid39140100, year = {2024}, author = {Crous, PW and Jurjević, &#x17d; and Balashov, S and De la Peña-Lastra, S and Mateos, A and Pinruan, U and Rigueiro-Rodríguez, A and Osieck, ER and Altés, A and Czachura, P and Esteve-Raventós, F and Gunaseelan, S and Kaliyaperumal, M and Larsson, E and Luangsa-Ard, JJ and Moreno, G and Pancorbo, F and Piątek, M and Sommai, S and Somrithipol, S and Asif, M and Delgado, G and Flakus, A and Illescas, T and Kezo, K and Khamsuntorn, P and Kubátová, A and Labuda, R and Lavoise, C and Lebel, T and Lueangjaroenkit, P and Maciá-Vicente, JG and Paz, A and Saba, M and Shivas, RG and Tan, YP and Wingfield, MJ and Aas, T and Abramczyk, B and Ainsworth, AM and Akulov, A and Alvarado, P and Armada, F and Assyov, B and Avchar, R and Avesani, M and Bezerra, JL and Bhat, JD and Bilański, P and Bily, DS and Boccardo, F and Bozok, F and Campos, JC and Chaimongkol, S and Chellappan, N and Costa, MM and Dalecká, M and Darmostuk, V and Daskalopoulos, V and Dearnaley, J and Dentinger, BTM and De Silva, NI and Dhotre, D and Carlavilla, JR and Doungsa-Ard, C and Dovana, F and Erhard, A and Ferro, LO and Gallegos, SC and Giles, CE and Gore, G and Gorfer, M and Guard, FE and Hanson, S&#xc5; and Haridev, P and Jankowiak, R and Jeffers, SN and Kandemir, H and Karich, A and Kisło, K and Kiss, L and Krisai-Greilhuber, I and Latha, KPD and Lorenzini, M and Lumyong, S and Manimohan, P and Manjón, JL and Maula, F and Mazur, E and Mesquita, NLS and Młynek, K and Mongkolsamrit, S and Morán, P and Murugadoss, R and Nagarajan, M and Nalumpang, S and Noisripoom, W and Nosalj, S and Novaes, QS and Nowak, M and Pawłowska, J and Peiger, M and Pereira, OL and Pinto, A and Plaza, M and Polemis, E and Polhorský, A and Ramos, DO and Raza, M and Rivas-Ferreiro, M and Rodriguez-Flakus, P and Ruszkiewicz-Michalska, M and Sánchez, A and Santos, A and Schüller, A and Scott, PA and Şen, I and Shelke, D and Śliwa, L and Solheim, H and Sonawane, H and Strašiftáková, D and Stryjak-Bogacka, M and Sudsanguan, M and Suwannarach, N and Suz, LM and Syme, K and Taşkın, H and Tennakoon, DS and Tomka, P and Vaghefi, N and Vasan, V and Vauras, J and Wiktorowicz, D and Villarreal, M and Vizzini, A and Wrzosek, M and Yang, X and Yingkunchao, W and Zapparoli, G and Zervakis, GI and Groenewald, JZ}, title = {Fungal Planet description sheets: 1614-1696.}, journal = {Fungal systematics and evolution}, volume = {13}, number = {}, pages = {183-440}, pmid = {39140100}, issn = {2589-3831}, abstract = {Novel species of fungi described in this study include those from various countries as follows: Australia, Baobabopsis sabindy in leaves of Eragrostis spartinoides, Cortinarius magentiguttatus among deep leaf litter, Laurobasidium azarandamiae from uredinium of Puccinia alyxiae on Alyxia buxifolia, Marasmius pseudoelegans on well-rotted twigs and litter in mixed wet sclerophyll and subtropical rainforest. Bolivia, Favolaschia luminosa on twigs of Byttneria hirsuta, Lecanora thorstenii on bark, in savannas with shrubs and trees. Brazil, Asterina costamaiae on leaves of Rourea bahiensis, Purimyces orchidacearum (incl. Purimyces gen. nov.) as root endophyte on Cattleya locatellii. Bulgaria, Monosporascus bulgaricus and Monosporascus europaeus isolated from surface-sterilised, asymptomatic roots of Microthlaspi perfoliatum. Finland, Inocybe undatolacera on a lawn, near Betula pendula. France, Inocybe querciphila in humus of mixed forest. Germany, Arrhenia oblongispora on bare soil attached to debris of herbaceous plants and grasses. Greece, Tuber aereum under Quercus coccifera and Acer sempervirens. India, Alfoldia lenyadriensis from the gut of a Platynotus sp. beetle, Fulvifomes subramanianii on living Albizzia amara, Inosperma pavithrum on soil, Phylloporia parvateya on living Lonicera sp., Tropicoporus maritimus on living Peltophorum pterocarpum. Indonesia, Elsinoe atypica on leaf of Eucalyptus pellita. Italy, Apiotrichum vineum from grape wine, Cuphopyllus praecox among grass. Madagascar, Pisolithus madagascariensis on soil under Intsia bijuga. Netherlands, Cytosporella calamagrostidis and Periconia calamagrostidicola on old leaves of Calamagrostis arenaria, Hyaloscypha caricicola on leaves of Carex sp., Neoniesslia phragmiticola (incl. Neoniesslia gen. nov.) on leaf sheaths of standing dead culms of Phragmites australis, Neptunomyces juncicola on culms of Juncus maritimus, Zenophaeosphaeria calamagrostidis (incl. Zenophaeosphaeria gen. nov.) on culms of Calamagrostis arenaria. Norway, Hausneria geniculata (incl. Hausneria gen. nov.) from a gallery of Dryocoetes alni on Alnus incana. Pakistan, Agrocybe auriolus on leaf litter of Eucalyptus camaldulensis, Rhodophana rubrodisca in nutrient-rich loamy soil with Morus alba. Poland, Cladosporium nubilum from hypersaline brine, Entomortierella ferrotolerans from soil at mines and postmining sites, Pseudopezicula epiphylla from sooty mould community on Quercus robur, Quixadomyces sanctacrucensis from resin of Pinus sylvestris, Szafranskia beskidensis (incl. Szafranskia gen. nov.) from resin of Abies alba. Portugal, Ascocoryne laurisilvae on degraded wood of Laurus nobilis, Hygrocybe madeirensis in laurel forests, Hygrocybula terracocta (incl. Hygrocybula gen. nov.) on mossy areas of laurel forests planted with Cryptomeria japonica. Republic of Kenya, Penicillium gorferi from a sterile chicken feather embedded in a soil sample. Slovakia, Cerinomyces tatrensis on bark of Pinus mugo, Metapochonia simonovicovae from soil. South Africa, Acremonium agapanthi on culms of Agapanthus praecox, Alfaria elegiae on culms of Elegia ebracteata, Beaucarneamyces stellenboschensis (incl. Beaucarneamyces gen. nov.) on dead leaves of Beaucarnea stricta, Gardeniomyces kirstenboschensis (incl. Gardeniomyces gen. nov.) rotting fruit of Gardenia thunbergia, Knufia dianellae on dead leaves of Dianella caerulea, Lomaantha quercina on twigs of Quercus suber. Melanina restionis on dead leaves of Restio duthieae, Microdochium buffelskloofinum on seeds of Eragrostis cf. racemosa, Thamnochortomyces kirstenboschensis (incl. Thamnochortomyces gen. nov.) on culms of Thamnochortus fraternus, Tubeufia hagahagana on leaves of Hypoxis angustifolia, Wingfieldomyces cypericola on dead leaves of Cyperus papyrus. Spain, Geastrum federeri in soil under Quercus suber and Q. canariensis, Geastrum nadalii in calcareous soil under Juniperus, Quercus, Cupressus, Pinus and Robinia, Hygrocybe garajonayensis in laurel forests, Inocybe cistophila on acidic soil under Cistus ladanifer, Inocybe sabuligena in a mixed Quercus ilex subsp. ballota/Juniperus thurifera open forest, Mycena calongei on mossy bark base of Juniperus oxycedrus, Rhodophana ulmaria on soil in Ulmus minor forest, Tuber arriacaense in soil under Populus pyramidalis, Volvariella latispora on grassy soils in a Quercus ilex ssp. rotundifolia stand. Sweden, Inocybe iota in alpine heath on calcareous soil. Thailand, Craterellus maerimensis and Craterellus sanbuakwaiensis on laterite and sandy soil, Helicocollum samlanense on scale insects, Leptosporella cassiae on dead twigs of Cassia fistula, Oxydothis coperniciae on dead leaf of Copernicia alba, Russula mukdahanensis on soil, Trechispora sangria on soil, Trechispora sanpatongensis on soil. Türkiye, Amanita corylophila in a plantation of Corylus avellana. Ukraine, Pararthrophiala adonis (incl. Pararthrophiala gen. nov.) on dead stems of Adonis vernalis. USA, Cladorrhinum carnegieae from Carnegiea gigantea, Dematipyriformia americana on swab from basement wall, Dothiora americana from outside air, Dwiroopa aeria from bedroom air, Lithohypha cladosporioides from hospital swab, Macroconia verruculosa on twig of Ilex montana, associated with black destroyed ascomycetous fungus and Biatora sp., Periconia floridana from outside air, Phytophthora fagacearum from necrotic leaves and shoots of Fagus grandifolia, Queenslandipenidiella californica on wood in crawlspace. Morphological and culture characteristics are supported by DNA barcodes. Citation: Crous PW, Jurjević Z, Balashov S, De la Peña-Lastra S, Mateos A, Pinruan U, Rigueiro-Rodríguez A, Osieck ER, Altés A, Czachura P, Esteve-Raventós F, Gunaseelan S, Kaliyaperumal M, Larsson E, Luangsa-ard JJ, Moreno G, Pancorbo F, Piątek M, Sommai S, Somrithipol S, Asif M, Delgado G, Flakus A, Illescas T, Kezo K, Khamsuntorn P, Kubátová A, Labuda R, Lavoise C, Lebel T, Lueangjaroenkit P, Maciá-Vicente JG, Paz A, Saba M, Shivas RG, Tan YP, Wingfield MJ, Aas T, Abramczyk B, Ainsworth AM, Akulov A, Alvarado P, Armada F, Assyov B, Avchar R, Avesani M, Bezerra JL, Bhat JD, Bilański P, Bily DS, Boccardo F, Bozok F, Campos JC, Chaimongkol S, Chellappan N, Costa MM, Dalecká M, Darmostuk V, Daskalopoulos V, Dearnaley J, Dentinger BTM, De Silva NI, Dhotre D, Carlavilla JR, Doungsa-ard C, Dovana F, Erhard A, Ferro LO, Gallegos SC, Giles CE, Gore G, Gorfer M, Guard FE, Hanson S-A, Haridev P, Jankowiak R, Jeffers SN, Kandemir H, Karich A, Kisło K, Kiss L, Krisai-Greilhuber I, Latha KPD, Lorenzini M, Lumyong S, Manimohan P, Manjón JL, Maula F, Mazur E, Mesquita NLS, Młynek K, Mongkolsamrit S, Morán P, Murugadoss R, Nagarajan M, Nalumpang S, Noisripoom W, Nosalj S, Novaes QS, Nowak M, Pawłowska J, Peiger M, Pereira OL, Pinto A, Plaza M, Polemis E, Polhorský A, Ramos DO, Raza M, Rivas-Ferreiro M, Rodriguez-Flakus P, Ruszkiewicz-Michalska M, Sánchez A, Santos A, Schüller A, Scott PA, Şen İ, Shelke D, Śliwa L, Solheim H, Sonawane H, Strašiftáková D, Stryjak-Bogacka M, Sudsanguan M, Suwannarach N, Suz LM, Syme K, Taşkın H, Tennakoon DS, Tomka P, Vaghefi N, Vasan V, Vauras J, Wiktorowicz D, Villarreal M, Vizzini A, Wrzosek M, Yang X, Yingkunchao W, Zapparoli G, Zervakis GI, Groenewald JZ (2024). Fungal Planet description sheets: 1614-1696. Fungal Systematics and Evolution 13: 183-440. doi: 10.3114/fuse.2024.13.11.}, }
@article {pmid39136489, year = {2024}, author = {Brar, G and Floden, M and McFrederick, Q and Rajamohan, A and Yocum, G and Bowsher, J}, title = {Environmentally acquired gut-associated bacteria are not critical for growth and survival in a solitary bee, Megachile rotundata.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {9}, pages = {e0207623}, pmid = {39136489}, issn = {1098-5336}, support = {RII Track-2 FEC18268341826834//National Science Foundation (NSF)/ ; IOS-1557940//National Science Foundation (NSF)/ ; ARS 3060-21220-032-00D//U.S. Department of Agriculture (USDA)/ ; ARS 3060-21220-032-00D//U.S. Department of Agriculture (USDA)/ ; }, mesh = {Animals ; Bees/microbiology/growth &amp; development ; *Gastrointestinal Microbiome ; *Larva/microbiology/growth &amp; development ; *Pollen/microbiology ; Female ; Bacteria/classification/genetics/isolation &amp; purification/growth &amp; development ; Lactobacillaceae/genetics/growth &amp; development/physiology/isolation &amp; purification ; }, abstract = {Social bees have been extensively studied for their gut microbial functions, but the significance of the gut microbiota in solitary bees remains less explored. Solitary bee, Megachile rotundata females provision their offspring with pollen from various plant species, harboring a diverse microbial community that colonizes larvae guts. The Apilactobacillus is the most abundant microbe, but evidence concerning the effects of Apilactobacillus and other provision microbes on growth and survival are lacking. We hypothesized that the presence of Apilactobacillus in abundance would enhance larval and prepupal development, weight, and survival, while the absence of intact microbial communities was expected to have a negative impact on bee fitness. We reared larvae on pollen provisions with naturally collected microbial communities (Natural pollen) or devoid of microbial communities (Sterile pollen). We also assessed the impact of introducing Apilactobacillus micheneri by adding it to both types of pollen provisions. Feeding larvae with sterile pollen + A. micheneri led to the highest mortality rate, followed by natural pollen + A. micheneri, and sterile pollen. Larval development was significantly delayed in groups fed with sterile pollen. Interestingly, larval and prepupal weights did not significantly differ across treatments compared to natural pollen-fed larvae. 16S rRNA gene sequencing found a dominance of Sodalis, when A. micheneri was introduced to natural pollen. The presence of Sodalis with abundant A. micheneri suggests potential crosstalk between both, shaping bee nutrition and health. Hence, this study highlights that the reliance on nonhost-specific environmental bacteria may not impact fitness of M. rotundata.IMPORTANCEThis study investigates the impact of environmentally acquired gut microbes of solitary bee fitness with insights into the microbial ecology of bee and their health. While the symbiotic microbiome is well-studied in social bees, the role of environmental acquired microbiota in solitary bees remains unclear. Assessing this relationship in a solitary pollinator, the leaf-cutting bee, Megachile rotundata, we discovered that this bee species does not depend on the diverse environmental bacteria found in pollen for either its larval growth or survival. Surprisingly, high concentrations of the most abundant pollen bacteria, Apilactobacillus micheneri did not consistently benefit bee fitness, but caused larval mortality. Our findings also suggest an interaction between Apilactobacillus and the Sodalis and perhaps their role in bee nutrition. Hence, this study provides significant insights that contribute to understanding the fitness, conservation, and pollination ecology of other solitary bee species in the future.}, }
@article {pmid39133233, year = {2024}, author = {Kwiatkowska, K and Ormaniec, P}, title = {Microbial Succession on Microplastics in Wastewater Treatment Plants: Exploring the Complexities of Microplastic-Microbiome Interactions.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {105}, pmid = {39133233}, issn = {1432-184X}, mesh = {*Microplastics/analysis ; *Wastewater/microbiology/chemistry ; *Biofilms ; *Microbiota ; *Sewage/microbiology/chemistry ; Waste Disposal, Fluid ; Water Pollutants, Chemical/analysis ; Bacteria/classification/metabolism ; Plastics/chemistry ; }, abstract = {Despite some effectiveness of wastewater treatment processes, microplastics accumulate in sewage sludge and their further use may contribute to the release of plastic microplastics into the environment. There is an urgent need to reduce the amount of microplastics in sewage sludge. Plastic particles serve as solid substrates for various microorganisms, promoting the formation of microbial biofilms with different metabolic activities. The biofilm environment associated with microplastics will determine the efficiency of treatment processes, especially biological methods, and the mechanisms of organic compound conversion. A significant source of microplastics is the land application of sewage sludge from wastewater treatment plants. The detrimental impact of microplastics affects soil enzymatic activity, soil microorganisms, flora, fauna, and plant production. This review article summarizes the development of research related to microplastics and discusses the issue of microplastic introduction from sewage sludge. Given that microplastics can contain complex composite polymers and form a plastisphere, further research is needed to understand their potential environmental impact, pathogenicity, and the characteristics of biofilms in wastewater treatment systems. The article also discusses the physicochemical properties of microplastics in wastewater treatment plants and their role in biofilm formation. Then, the article explained the impact of these properties on the possibility of the formation of biofilms on their surface due to the peculiar structure of microorganisms and also characterized what factors enable the formation of specific plastisphere in wastewater treatment plants. It highlights the urgent need to understand the basic information about microplastics to assess environmental toxicity more rationally, enabling better pollution control and the development of regulatory standards to manage microplastics entering the environment.}, }
@article {pmid39132685, year = {2025}, author = {Ye, D and Liu, Y and Li, J and Zhou, J and Cao, J and Wu, Y and Wang, X and Fang, Y and Ye, X and Zou, J and Ma, Q}, title = {Competitive dynamics and balance between Streptococcus mutans and commensal streptococci in oral microecology.}, journal = {Critical reviews in microbiology}, volume = {51}, number = {3}, pages = {532-543}, doi = {10.1080/1040841X.2024.2389386}, pmid = {39132685}, issn = {1549-7828}, mesh = {*Mouth/microbiology ; Humans ; Biofilms/growth &amp; development ; *Dental Caries/microbiology ; *Streptococcus mutans/physiology/growth &amp; development ; *Streptococcus/physiology/growth &amp; development ; Microbiota ; }, abstract = {Dental caries, as a biofilm-related disease, is closely linked to dysbiosis in microbial ecology within dental biofilms. Beyond its impact on oral health, bacteria within the oral cavity pose systemic health risks by potentially entering the bloodstream, thereby increasing susceptibility to bacterial endocarditis, among other related diseases. Streptococcus mutans, a principal cariogenic bacterium, possesses virulence factors crucial to the pathogenesis of dental caries. Its ability to adhere to tooth surfaces, produce glucans for biofilm formation, and metabolize sugars into lactic acid contributes to enamel demineralization and the initiation of carious lesions. Its aciduricity and ability to produce bacteriocins enable a competitive advantage, allowing it to thrive in acidic environments and dominate in changing oral microenvironments. In contrast, commensal streptococci, such as Streptococcus sanguinis, Streptococcus gordonii, and Streptococcus salivarius, act as primary colonizers and compete with S. mutans for adherence sites and nutrients during biofilm formation. This competition involves the production of alkali, peroxides, and antibacterial substances, thereby inhibiting S. mutans growth and maintaining microbial balance. This dynamic interaction influences the balance of oral microbiota, with disruptions leading to shifts in microbial composition that are marked by rapid increases in S. mutans abundance, contributing to the onset of dental caries. Thus, understanding the dynamic interactions between commensal and pathogenic bacteria in oral microecology is important for developing effective strategies to promote oral health and prevent dental caries. This review highlights the roles and competitive interactions of commensal bacteria and S. mutans in oral microecology, emphasizing the importance of maintaining oral microbial balance for health, and discusses the pathological implications of perturbations in this balance.}, }
@article {pmid39128495, year = {2025}, author = {De Pessemier, B and López, CD and Taelman, S and Verdonck, M and Chen, Y and Stockman, A and Lambert, J and Van de Wiele, T and Callewaert, C}, title = {Comparative Whole Metagenome Analysis in Lesional and Nonlesional Scalp Areas of Patients with Psoriasis Capitis and Healthy Individuals.}, journal = {The Journal of investigative dermatology}, volume = {145}, number = {3}, pages = {605-617.e14}, doi = {10.1016/j.jid.2024.07.020}, pmid = {39128495}, issn = {1523-1747}, mesh = {Humans ; *Psoriasis/microbiology/pathology ; *Metagenome ; Male ; Female ; *Scalp/microbiology/pathology ; Adult ; Middle Aged ; *Microbiota/genetics ; Metagenomics ; Staphylococcus aureus/isolation &amp; purification/genetics ; Case-Control Studies ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Psoriasis is an immune-mediated inflammatory disorder, where the majority of the patients suffer from psoriasis capitis or scalp psoriasis. Current therapeutics remain ineffective to treat scalp lesions. In this study, we present a whole-metagenome characterization of the scalp microbiome in psoriasis capitis. We investigated how changes in the homeostatic cutaneous microbiome correlate with the condition and identified metagenomic biomarkers (taxonomic, functional, virulence factors, antimicrobial resistance genes) that could partly explain its emergence. Within this study, 83 top and back scalp samples from healthy individuals and 64 lesional and nonlesional scalp samples from subjects with untreated psoriasis capitis were analyzed. Using qPCR targeting the 16S and 18S ribosomal RNA genes, we found a significant decrease in microbial load within scalp regions affected by psoriasis compared with that in their nonlesional counterparts. Metagenomic analysis revealed that psoriatic lesions displayed significant lower Cutibacterium species (including C. modestum, C. namnetense, C. granulosum, C. porci), along with an elevation in Staphylococcus aureus. A heightened relative presence of efflux pump protein-encoding genes was detected, suggesting potential antimicrobial resistance mechanisms. These mechanisms are known to specifically target human antimicrobial peptides (including cathelicidin LL-37), which are frequently encountered within psoriasis lesions. These shifts in microbial community dynamics may contribute to psoriasis disease pathogenesis.}, }
@article {pmid39126446, year = {2025}, author = {Izumi, H}, title = {Abundances of ectomycorrhizal exploration types show the type-dependent temporal dynamics over the seasons-a controlled growth container experiment.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {28}, number = {4}, pages = {633-641}, pmid = {39126446}, issn = {1618-1905}, mesh = {*Mycorrhizae/classification/growth &amp; development/physiology/isolation &amp; purification ; Seasons ; *Quercus/microbiology/growth &amp; development ; Soil Microbiology ; Symbiosis ; Forests ; Trees/microbiology ; }, abstract = {Ectomycorrhizas are ubiquitous symbiotic associations between host trees and soil fungi. While the seasonal changes of the taxonomic community structure of ectomycorrhizal fungi have been studied extensively, the temporal dynamics of ectomycorrhizal exploration types which have been proposed for elucidating the functional roles of ectomycorrhizas have not been fully examined. The purpose of the study is to test the hypothesis of whether the abundance of the exploration types in the hosts with different phenology shows different temporal patterns over the seasons. Two host species, deciduous Quercus acutissima and evergreen Q. glauca, were planted in growth containers with natural forest soils and were grown in single or combined species treatment, under similar environmental conditions and in shared soil spore banks of the ectomycorrhizal fungi. The ectomycorrhizal exploration types that occurred on these two host species in two different treatments were observed for two growing seasons. The observed exploration types, namely contact, short-distance, and long-distance type as well as the overall abundance of the ectomycorrhizas showed distinct temporal patterns although no specific response to the host seasonal phenology was found. The abundances of the contact type showed no relation to the seasons whereas those of the short- and the long-distance type increased with time. The formation of the long-distance type was strongly influenced by the host species treatments while that of the other two types was not so. Therefore, the different exploration types demonstrate distinct temporal patterns depending on the types but no specific seasonal responses.}, }
@article {pmid39123264, year = {2024}, author = {Rothrock, MJ and Zwirzitz, B and Al Hakeem, WG and Oladeinde, A and Guard, JY and Li, X}, title = {16S amplicon-based microbiome biomapping of a commercial broiler hatchery.}, journal = {Animal microbiome}, volume = {6}, number = {1}, pages = {46}, pmid = {39123264}, issn = {2524-4671}, abstract = {Hatcheries, where eggs from multiple breeder farms are incubated and hatched before being sent to different broiler farms, represent a nexus point in the commercial production of broilers in the United States. Considering all downstream microbial quality and safety aspects of broiler production (live production, processing, consumer use) can be potentially affected by the hatchery, a better understanding of microbial ecology within commercial hatcheries is essential. Therefore, a commercial broiler hatchery was biomapped using 16S rRNA amplicon-based microbiome analyses of four sample type categories (Air, Egg, Water, Facility) across five different places in the pre-hatch, hatch, and post-hatch areas. While distinct microbiota were found for each sample type category and hatchery area, microbial community analyses revealed that Egg microbiota trended towards clustering with the facility-related samples when moving from the prehatch to post-hatch areas, highlighting the potential effect of the hatchery environment in shaping the pre-harvest broiler-related microbiota. Prevalence analyses revealed 20 ASVs (Core20) present in the core microbiota of all sample types and areas, with each ASV possessing a unique distribution throughout the hatchery. Interestingly, three Enterobacteriaceae ASVs were in the Core20, including Salmonella. Subsequent analyses showed that Salmonella, while a minor prehatch and hatch Core20ASV, dominated the Enterobacteriaceae niche and total microbiota in the chick pad feces in the post-hatch area of the hatchery, and the presence of this Salmonella ASV in the post-hatch feces was associated with swabs of breakroom tables. These findings highlight the complexity of commercial hatchery microbiota, including identifying chick pad feces and breakroom tables as potentially important sampling or disinfection targets for hatchery managers to focus their Salmonella mitigation efforts to reduce loads entering live production farms.}, }
@article {pmid39122657, year = {2024}, author = {Brenzinger, K and Glatter, T and Hakobyan, A and Meima-Franke, M and Zweers, H and Liesack, W and Bodelier, PLE}, title = {Exploring modes of microbial interactions with implications for methane cycling.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {9}, pages = {}, pmid = {39122657}, issn = {1574-6941}, support = {5535/1-1//DFG/ ; 870.15.073/NWO_/Dutch Research Council/Netherlands ; }, mesh = {*Methane/metabolism ; *Microbial Interactions ; *Volatile Organic Compounds/metabolism ; *Carbon Dioxide/metabolism ; Methylomonas/metabolism/genetics ; Proteomics ; Proteome ; Heterotrophic Processes ; Oxygenases/metabolism/genetics ; }, abstract = {Methanotrophs are the sole biological sink of methane. Volatile organic compounds (VOCs) produced by heterotrophic bacteria have been demonstrated to be a potential modulating factor of methane consumption. Here, we identify and disentangle the impact of the volatolome of heterotrophic bacteria on the methanotroph activity and proteome, using Methylomonas as model organism. Our study unambiguously shows how methanotrophy can be influenced by other organisms without direct physical contact. This influence is mediated by VOCs (e.g. dimethyl-polysulphides) or/and CO2 emitted during respiration, which can inhibit growth and methane uptake of the methanotroph, while other VOCs had a stimulating effect on methanotroph activity. Depending on whether the methanotroph was exposed to the volatolome of the heterotroph or to CO2, proteomics revealed differential protein expression patterns with the soluble methane monooxygenase being the most affected enzyme. The interaction between methanotrophs and heterotrophs can have strong positive or negative effects on methane consumption, depending on the species interacting with the methanotroph. We identified potential VOCs involved in the inhibition while positive effects may be triggered by CO2 released by heterotrophic respiration. Our experimental proof of methanotroph-heterotroph interactions clearly calls for detailed research into strategies on how to mitigate methane emissions.}, }
@article {pmid39122033, year = {2024}, author = {de Menezes, AB and Gashchak, S and Wood, MD and Beresford, NA}, title = {Relationships between radiation, wildfire and the soil microbial communities in the Chornobyl Exclusion Zone.}, journal = {The Science of the total environment}, volume = {950}, number = {}, pages = {175381}, doi = {10.1016/j.scitotenv.2024.175381}, pmid = {39122033}, issn = {1879-1026}, mesh = {*Wildfires ; *Chernobyl Nuclear Accident ; *Soil Microbiology ; *Microbiota ; *Soil Pollutants, Radioactive/analysis ; Radiation Monitoring ; Soil/chemistry ; Bacteria/classification ; Ukraine ; Forests ; }, abstract = {There is considerable uncertainty regarding radiation's effects on biodiversity in natural complex ecosystems typically subjected to multiple environmental disturbances and stresses. In this study we characterised the relationships between soil microbial communities and estimated total absorbed dose rates to bacteria, grassy vegetation and trees in the Red Forest region of the Chornobyl Exclusion Zone. Samples were taken from sites of contrasting ecological histories and along burn and no burn areas following a wildfire. Estimated total absorbed dose rates to bacteria reached levels one order of magnitude higher than those known to affect bacteria in laboratory studies. Sites with harsher ecological conditions, notably acidic pH and low soil moisture, tended to have higher radiation contamination levels. No relationship between the effects of fire and radiation were observed. Microbial groups that correlated with high radiation sites were mostly classified to taxa associated with high environmental stress habitats or stress resistance traits. Distance-based linear models and co-occurrence analysis revealed that the effects of radiation on the soil microbiome were minimal. Hence, the association between high radiation sites and specific microbial groups is more likely a result of the harsher ecological conditions in these sites, rather than due to radiation itself. In this study, we provide a starting point for understanding the relationship between soil microbial communities and estimated total absorbed radiation dose rates to different components of an ecosystem highly contaminated with radiation. Our results suggest that soil microbiomes adapted to natural soil conditions are more likely to be resistant to ionising radiation than expected from laboratory studies, which demonstrates the importance of assessing the impact of ionising radiation on soil microbial communities under field conditions.}, }
@article {pmid39119822, year = {2024}, author = {West, NJ and Landa, M and Obernosterer, I}, title = {Differential association of key bacterial groups with diatoms and Phaeocystis spp. during spring blooms in the Southern Ocean.}, journal = {MicrobiologyOpen}, volume = {13}, number = {4}, pages = {e1428}, pmid = {39119822}, issn = {2045-8827}, support = {LEFE-CYBER//Centre National de la Recherche Scientifique/ ; //Institut Polaire Fran&#xe7;ais Paul Emile Victor/ ; 10-BLAN-0614//Agence Nationale de la Recherche/ ; }, mesh = {*Diatoms/classification ; *Bacteria/classification/genetics/isolation &amp; purification ; *RNA, Ribosomal, 16S/genetics ; *Seawater/microbiology ; *Oceans and Seas ; Haptophyta/classification/growth &amp; development ; Phytoplankton/classification/growth &amp; development ; Phylogeny ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; Seasons ; }, abstract = {Interactions between phytoplankton and heterotrophic bacteria significantly influence the cycling of organic carbon in the ocean, with many of these interactions occurring at the micrometer scale. We explored potential associations between specific phytoplankton and bacteria in two size fractions, 0.8-3 µm and larger than 3 µm, at three naturally iron-fertilized stations and one high nutrient low chlorophyll station in the Southern Ocean. The composition of phytoplankton and bacterial communities was determined by sequencing the rbcL gene and 16S rRNA gene from DNA and RNA extracts, which represent presence and potential activity, respectively. Diatoms, particularly Thalassiosira, contributed significantly to the DNA sequences in the larger size fractions, while haptophytes were dominant in the smaller size fraction. Correlation analysis between the most abundant phytoplankton and bacterial operational taxonomic units revealed strong correlations between Phaeocystis and picoeukaryotes with SAR11, SAR116, Magnetospira, and Planktomarina. In contrast, most Thalassiosira operational taxonomic units showed the highest correlations with Polaribacter, Sulfitobacteria, Erythrobacter, and Sphingobium, while Fragilariopsis, Haslea, and Thalassionema were correlated with OM60, Fluviicola, and Ulvibacter. Our in-situ observations suggest distinct associations between phytoplankton and bacterial taxa, which could play crucial roles in nutrient cycling in the Southern Ocean.}, }
@article {pmid39118147, year = {2024}, author = {Xiong, Y and Mueller, RS and Feng, S and Guo, X and Pan, C}, title = {Proteomic stable isotope probing with an upgraded Sipros algorithm for improved identification and quantification of isotopically labeled proteins.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {148}, pmid = {39118147}, issn = {2049-2618}, support = {R01 AT011618/AT/NCCIH NIH HHS/United States ; R01AT011618/NH/NIH HHS/United States ; }, mesh = {*Proteomics/methods ; *Isotope Labeling ; *Algorithms ; Escherichia coli/metabolism ; Carbon Isotopes/metabolism ; Tandem Mass Spectrometry/methods ; Proteome ; }, abstract = {BACKGROUND: Proteomic stable isotope probing (SIP) is used in microbial ecology to trace a non-radioactive isotope from a labeled substrate into de novo synthesized proteins in specific populations that are actively assimilating and metabolizing the substrate in a complex microbial community. The Sipros algorithm is used in proteomic SIP to identify variably labeled proteins and quantify their isotopic enrichment levels (atom%) by performing enrichment-resolved database searching.<br><br>RESULTS: In this study, Sipros was upgraded to improve the labeled protein identification, isotopic enrichment quantification, and database searching speed. The new Sipros 4 was compared with the existing Sipros 3, Calisp, and MetaProSIP in terms of the number of identifications and the accuracy and precision of atom% quantification on both the peptide and protein levels using standard E. coli cultures with 1.07 atom%, 2 atom%, 5 atom%, 25 atom%, 50 atom%, and 99 atom% [13]C enrichment. Sipros 4 outperformed Calisp and MetaProSIP across all samples, especially in samples with&#x2009;&#x2265;&#x2009;5 atom% [13]C labeling. The computational speed on Sipros 4 was&#x2009;>&#x2009;20 times higher than Sipros 3 and was on par with the overall speed of Calisp- and MetaProSIP-based pipelines. Sipros 4 also demonstrated higher sensitivity for the detection of labeled proteins in two [13]C-SIP experiments on a real-world soil community. The labeled proteins were used to trace [13]C from [13]C-methanol and [13]C-labeled plant exudates to the consuming soil microorganisms and their newly synthesized proteins.<br><br>CONCLUSION: Overall, Sipros 4 improved the quality of the proteomic SIP results and reduced the computational cost of SIP database searching, which will make proteomic SIP more useful and accessible to the border community. Video Abstract.}, }
@article {pmid39113789, year = {2024}, author = {Strik, DPBTB and Ganigue, R}, title = {Editorial: Microbial chain elongation-carbon recovering biorefineries for the circular economy.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {12}, number = {}, pages = {1448975}, pmid = {39113789}, issn = {2296-4185}, }
@article {pmid39113100, year = {2024}, author = {Nieto, EE and Jurburg, SD and Steinbach, N and Festa, S and Morelli, IS and Coppotelli, BM and Chatzinotas, A}, title = {DNA stable isotope probing reveals the impact of trophic interactions on bioaugmentation of soils with different pollution histories.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {146}, pmid = {39113100}, issn = {2049-2618}, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Soil Pollutants/metabolism ; *Biodegradation, Environmental ; *RNA, Ribosomal, 16S/genetics ; *RNA, Ribosomal, 18S/genetics ; *Bacteria/metabolism/classification/genetics ; Biomass ; Carbon Isotopes/metabolism ; Food Chain ; Polycyclic Aromatic Hydrocarbons/metabolism ; Isotope Labeling ; }, abstract = {BACKGROUND: Bioaugmentation is considered a sustainable and cost-effective methodology to recover contaminated environments, but its outcome is highly variable. Predation is a key top-down control mechanism affecting inoculum establishment, however, its effects on this process have received little attention. This study focused on the impact of trophic interactions on bioaugmentation success in two soils with different pollution exposure histories. We inoculated a [13]C-labelled pollutant-degrading consortium in these soils and tracked the fate of the labelled biomass through stable isotope probing (SIP) of DNA. We identified active bacterial and eukaryotic inoculum-biomass consumers through amplicon sequencing of 16S rRNA and 18S rRNA genes coupled to a novel enrichment factor calculation.<br><br>RESULTS: Inoculation effectively increased PAH removal in the&#xa0;short-term, but not in&#xa0;the long-term polluted soil. A decrease in the relative abundance of the inoculated genera was observed already on day 15 in the long-term polluted soil, while growth of these genera was observed in the short-term polluted soil, indicating establishment of the inoculum. In both soils, eukaryotic genera dominated as early incorporators of [13]C-labelled biomass, while bacteria incorporated the labelled biomass at the end of the incubation period, probably through cross-feeding. We also found different successional patterns between the two soils. In the short-term polluted soil, Cercozoa and Fungi genera predominated as early incorporators, whereas Ciliophora, Ochrophyta and Amoebozoa were the predominant genera in the long-term polluted soil.<br><br>CONCLUSION: Our results showed differences in the inoculum establishment and predator community responses, affecting bioaugmentation efficiency. This highlights the need to further study predation effects on inoculum survival to increase the applicability of inoculation-based technologies. Video Abstract.}, }
@article {pmid39110233, year = {2024}, author = {Wei, L and Wang, Y and Li, N and Zhao, N and Xu, S}, title = {Bacteria-Like Gaiella Accelerate Soil Carbon Loss by Decomposing Organic Matter of Grazing Soils in Alpine Meadows on the Qinghai-Tibet Plateau.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {104}, pmid = {39110233}, issn = {1432-184X}, support = {2023-ZJ-767//Qinghai Province Applied Basic Research Program/ ; 2023-ZJ-767//Qinghai Province Applied Basic Research Program/ ; LHZX-2020-02//Joint Special Project of Sanjiangyuan National Park/ ; LHZX-2020-02//Joint Special Project of Sanjiangyuan National Park/ ; }, mesh = {*Soil Microbiology ; Tibet ; *Carbon/metabolism/analysis ; *Soil/chemistry ; *Grassland ; Animals ; Carbon Sequestration ; Herbivory ; Bacteria/metabolism/classification ; }, abstract = {The alpine meadows of the Qinghai-Tibet Plateau have significant potential for storing soil carbon, which is important to global carbon sequestration. Grazing is a major threat to its potential for carbon sequestration. However, grazing poses a major threat to this potential by speeding up the breakdown of organic matter in the soil and releasing carbon, which may further lead to positive carbon-climate change feedback and threaten ecological security. Therefore, in order to accurately explore the driving mechanism and regulatory factors of soil organic matter decomposition in grazing alpine meadows on the Qinghai-Tibet Plateau, we took the grazing sample plots of typical alpine meadows as the research object and set up grazing intensities of different life cycles, aiming to explore the relationship and main regulatory factors of grazing on soil organic matter decomposition and soil microorganisms. The results show the following: (1) soil microorganisms, especially Acidobacteria and Acidobacteria, drove the decomposition of organic matter in the soil, thereby accelerating the release of soil carbon, which was not conducive to soil carbon sequestration in grassland; (2) the grazing triggering effect formed a positive feedback with soil microbial carbon release, accelerating the decomposition of organic matter and soil carbon loss; and (3) the grazing ban and light grazing were more conducive to slowing down soil organic matter decomposition and increasing soil carbon sequestration.}, }
@article {pmid39109653, year = {2024}, author = {Corich, L and Losasso, C and Meneghel, A and Blarasin, FI and Basaglia, G and Corich, MA}, title = {The first case of urosepsis caused by Corynebacterium aurimucosum in an immunocompetent patient.}, journal = {Future microbiology}, volume = {19}, number = {11}, pages = {963-970}, pmid = {39109653}, issn = {1746-0921}, mesh = {Humans ; *Corynebacterium/isolation &amp; purification/genetics/pathogenicity/classification ; Aged ; Female ; *Corynebacterium Infections/microbiology/diagnosis/drug therapy ; *Sepsis/microbiology/drug therapy ; *Urinary Tract Infections/microbiology/drug therapy/diagnosis ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {Non-diphtheroid Corynebacterium sepsis is rare and has affected only immunocompromised or particularly predisposed patients so far. We present the first case of urosepsis caused by Corynebacterium aurimucosum in a 67-year-old woman, without any known immunodeficiencies and in absence of any immunosuppressive therapy, admitted to the hospital for fever and acute dyspnea. This work suggests a new approach in evaluating the isolation of Corynebacteria, especially if isolated from blood. In particular, it highlights the potential infectious role of C. aurimucosum (often considered a contaminant and only rarely identified as an etiological agent of infections) and its clinical consequences, detailing also interesting aspects about its microbiological diagnosis and relative therapy and clarifying contrasting data of literature.}, }
@article {pmid39109421, year = {2024}, author = {Alfahl, Z and Biggins, S and Higgins, O and Chueiri, A and Smith, TJ and Morris, D and O'Dwyer, J and Hynds, PD and Burke, LP and O'Connor, L}, title = {A rapid on-site loop-mediated isothermal amplification technology as an early warning system for the detection of Shiga toxin-producing Escherichia coli in water.}, journal = {Microbiology (Reading, England)}, volume = {170}, number = {8}, pages = {}, pmid = {39109421}, issn = {1465-2080}, mesh = {*Nucleic Acid Amplification Techniques/methods ; *Shiga-Toxigenic Escherichia coli/genetics/isolation &amp; purification ; *Water Microbiology ; Molecular Diagnostic Techniques/methods/instrumentation ; Sensitivity and Specificity ; Rivers/microbiology ; Shiga Toxin 1/genetics ; Groundwater/microbiology ; }, abstract = {Shiga toxin-producing Escherichia coli (STEC) is an important waterborne pathogen capable of causing serious gastrointestinal infections with potentially fatal complications, including haemolytic-uremic syndrome. All STEC serogroups harbour genes that encode at least one Shiga toxin (stx1 and/or stx2), which constitute the primary virulence factors of STEC. Loop-mediated isothermal amplification (LAMP) enables rapid real-time pathogen detection with a high degree of specificity and sensitivity. The aim of this study was to develop and validate an on-site portable diagnostics workstation employing LAMP technology to permit rapid real-time STEC detection in environmental water samples. Water samples (n=28) were collected from groundwater wells (n=13), rivers (n=12), a turlough (n=2) and an agricultural drain (n=1) from the Corrib catchment in Galway. Water samples (100 ml) were passed through a 0.22 µm filter, and buffer was added to elute captured cells. Following filtration, eluates were tested directly using LAMP assays targeting stx1, stx2 and E. coli phoA genes. The portable diagnostics workstation was used in field studies to demonstrate the on-site testing capabilities of the instrument. Real-time PCR assays targeting stx1 and stx2 genes were used to confirm the results. The limit of detection for stx1, stx2 and phoA LAMP assays were 2, 2 and 6 copies, respectively. Overall, stx1, stx2 and phoA genes were detected by LAMP in 15/28 (53.6 %), 9/28 (32.2 %) and 24/28 (85.7 %) samples, respectively. For confirmation, the LAMP results for stx1 and stx2 correlated perfectly (100 %) with those obtained using PCR. The portable diagnostics workstation exhibited high sensitivity throughout the on-site operation, and the average time from sample collection to final result was 40 min. We describe a simple, transferable and efficient diagnostic technology for on-site molecular analysis of various water sources. This method allows on-site testing of drinking water, enabling evidence-based decision-making by public health and water management authorities.}, }
@article {pmid39109205, year = {2024}, author = {Zhu, L and Chen, L and Lin, B and Xu, Y and Dong, W and Lv, Y and Tang, J and Zhang, G and Zhang, L and Yang, S and Yang, Q and Chen, S}, title = {Deciphering the microbial succession and color formation mechanism of "green-covering and red-heart" Guanyin Tuqu.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1412503}, pmid = {39109205}, issn = {1664-302X}, abstract = {"Green-covering and red-heart" Guanyin Tuqu (GRTQ), as a type of special fermentation starter, is characterized by the "green-covering" formed on the surface of Guanyin Tuqu (SQ) and the "red-heart" in the center of Guanyin Tuqu (CQ). However, the mechanisms that promote temporal succession in the GRTQ microbial ecology and the formation of "green-covering and red-heart" characteristics remain unclear. Herein, we correlated the temporal profiles of microbial community succession with the main environmental variables (temperature, moisture, and acidity) and spatial position (center and surface) in GRTQ throughout fermentation. According to the results of high-throughput sequencing and culture-dependent methods, the microbial communities in the CQ and SQ demonstrated functional complementarity. For instance, the bacterial richness index of the CQ was greater than that of SQ, and the fungal richness index of the SQ was greater than that of CQ at the later stage of fermentation. Furthermore, Saccharomycopsis, Saccharomyces, Aspergillus, Monascus, Lactobacillus, Bacillus, Rhodanobacter, and Chitinophaga were identified as the dominant microorganisms in the center, while the surface was represented by Saccharomycopsis, Aspergillus, Monascus, Lactobacillus, Acetobacter, and Weissella. By revealing the physiological characteristics of core microorganisms at different spatial positions of GRTQ, such as Aspergillus clavatus and Monascus purpureus, as well as their interactions with environmental factors, we elucidated the color formation mechanism behind the phenomenon of "green" outside and "red" inside. This study provides fundamental information support for optimizing the production process of GRTQ.}, }
@article {pmid39107417, year = {2024}, author = {Cordovez, V and Carrión, VJ and Rivas Torres, G and Ortiz, DA and Cabrera, W and Balian, H and Vivanco, AK and Pérez-Jaramillo, JE and Chaves, J and Pazmiño, DA and van 't Hof, P and Raaijmakers, JM}, title = {Darwin's expedition revisited to reveal the evolution of plant-microbe interactions on Galápagos.}, journal = {Nature microbiology}, volume = {9}, number = {8}, pages = {1903-1905}, pmid = {39107417}, issn = {2058-5276}, support = {GSC fund 17150//Universidad San Francisco de Quito (USFQ)/ ; }, mesh = {*Plants/microbiology ; Ecuador ; *Biological Evolution ; Host-Pathogen Interactions ; Plant Diseases/microbiology ; }, }
@article {pmid39106714, year = {2024}, author = {Qing, J and Li, C and Zhi, H and Zhang, L and Wu, J and Li, Y}, title = {Exploring macrophage heterogeneity in IgA nephropathy: Mechanisms of renal impairment and current therapeutic targets.}, journal = {International immunopharmacology}, volume = {140}, number = {}, pages = {112748}, doi = {10.1016/j.intimp.2024.112748}, pmid = {39106714}, issn = {1878-1705}, mesh = {*Glomerulonephritis, IGA/metabolism/immunology ; Humans ; *Macrophages/immunology/metabolism ; Kidney/pathology/metabolism/immunology ; Male ; Female ; Glomerular Filtration Rate ; Adult ; Single-Cell Analysis ; }, abstract = {The lack of understanding of the mechanism of renal injury in IgA nephropathy (IgAN) hinders the development of personalized treatment plans and targeted therapies. Improved insight into the cause of renal dysfunction in IgAN is necessary to enhance the effectiveness of strategies for slowing the progression of the disease. This study examined single cell RNA sequencing (scRNA seq) and bulk-RNA seq data and found that the gene expression of renal intrinsic cells (RIC) was significantly changed in patients with renal impairment, with a primary focus on energy metabolism. We discovered a clear metabolic reprogramming of RIC during renal function impairment (RF) using the 'scMetabolism' package, which manifested as a weakening of oxidative phosphorylation, alterations in fatty acid metabolism, and changes in glycolysis. Cellular communication analysis revealed that communication between macrophages (Ma) and RIC became more active and impacted cell function through the ligand-receptor-transcription factor (L-R-TF) axis in patients with RF. Our studies showed a notable upsurge in the expression of gene CLU and the infiltration of CLU[+] Ma in patients with RF. CLU is a multifunctional protein, extensively involved in processes such as cell apoptosis and immune responses. Data obtained from the Nephroseq V5 database and multiplex immunohistochemistry (mIHC) were used to validate the findings, which were found to be robustly correlated with estimated glomerular filtration rate (eGFR) of the IgAN patients, as demonstrated by linear regression (LR). This study provides new insights into the cellular and molecular changes that occur in IgAN during renal impairment, revealing that elevated expression of CLU and CLU[+] Ma percolation are common features in patients with RF. These findings offer potential targets and strategies for personalized management and targeted therapy of IgAN.}, }
@article {pmid39106212, year = {2024}, author = {Pottie, I and Vázquez Fernández, R and Van de Wiele, T and Briers, Y}, title = {Phage lysins for intestinal microbiome modulation: current challenges and enabling techniques.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2387144}, pmid = {39106212}, issn = {1949-0984}, mesh = {*Gastrointestinal Microbiome ; Humans ; *Bacteriophages/physiology ; Animals ; *Endopeptidases/metabolism ; Bacteria/genetics/metabolism/virology/classification ; Probiotics ; Anti-Bacterial Agents/pharmacology ; Bacterial Infections/microbiology/drug therapy/therapy ; Viral Proteins/metabolism/genetics ; Peptidoglycan/metabolism ; }, abstract = {The importance of the microbiota in the intestinal tract for human health has been increasingly recognized. In this perspective, microbiome modulation, a targeted alteration of the microbial composition, has gained interest. Phage lysins, peptidoglycan-degrading enzymes encoded by bacteriophages, are a promising new class of antibiotics currently under clinical development for treating bacterial infections. Due to their high specificity, lysins are considered microbiome-friendly. This review explores the opportunities and challenges of using lysins as microbiome modulators. First, the high specificity of endolysins, which can be further modulated using protein engineering or targeted delivery methods, is discussed. Next, obstacles and possible solutions to assess the microbiome-friendliness of lysins are considered. Finally, lysin delivery to the intestinal tract is discussed, including possible delivery methods such as particle-based and probiotic vehicles. Mapping the hurdles to developing lysins as microbiome modulators and identifying possible ways to overcome these hurdles can help in their development. In this way, the application of these innovative antimicrobial agents can be expanded, thereby taking full advantage of their characteristics.}, }
@article {pmid39105581, year = {2024}, author = {Zhu, Y-X and Yang, T-Y and Deng, J-H and Yin, Y and Song, Z-R and Du, Y-Z}, title = {Stochastic processes drive divergence of bacterial and fungal communities in sympatric wild insect species despite sharing a common diet.}, journal = {mSphere}, volume = {9}, number = {8}, pages = {e0038624}, pmid = {39105581}, issn = {2379-5042}, support = {BK20231330//JST | Natural Science Foundation of Jiangsu Province (Jiangsu Natural Science Foundation)/ ; }, mesh = {Animals ; *Insecta/microbiology ; *Fungi/classification/genetics ; *Microbiota ; *Sympatry ; *Bacteria/classification/genetics/isolation &amp; purification ; *Stochastic Processes ; *Diet ; Mycobiome ; Citrus/microbiology ; }, abstract = {UNLABELLED: Arthropods harbor complex microbiota that play a pivotal role in host fitness. While multiple factors, like host species and diet, shape microbiota in arthropods, their impact on community assembly in wild insects remains largely unknown. In this study, we surveyed bacterial and fungal community assembly in nine sympatric wild insect species that share a common citrus fruit diet. Source tracking analysis suggested that these insects acquire some bacteria and fungi from the citrus fruit with varying degrees. Although sharing a common diet led to microbiota convergence, the diversity, composition, and network of both bacterial and fungal communities varied significantly among surveyed insect groups. Null model analysis indicated that stochastic processes, particularly dispersal limitation and drift, are primary drivers of structuring insect bacterial and fungal communities. Importantly, the influence of each community assembly process varied strongly depending on the host species. Thus, we proposed a speculative view that the host specificity of the microbiome and mycobiome assembly is widespread in wild insects despite sharing the same regional species pool. Overall, this research solidifies the importance of host species in shaping microbiomes and mycobiomes, providing novel insights into their assembly mechanisms in wild insects.<br><br>IMPORTANCE: Since the microbiome has been shown to impact insect fitness, a mechanistic understanding of community assembly has potentially significant applications but remains largely unexplored. In this paper, we investigate bacterial and fungal community assembly in nine sympatric wild insect species that share a common diet. The main findings indicate that stochastic processes drive the divergence of microbiomes and mycobiomes in nine sympatric wild insect species. These findings offer novel insights into the assembly mechanisms of microbiomes and mycobiomes in wild insects.}, }
@article {pmid39103310, year = {2024}, author = {Liu, J and Xu, G and Zhao, S and He, J}, title = {Plastisphere Microbiomes Respiring Persistent Organohalide Pollutants.}, journal = {Environmental science &amp; technology}, volume = {58}, number = {33}, pages = {14740-14752}, doi = {10.1021/acs.est.4c02251}, pmid = {39103310}, issn = {1520-5851}, mesh = {*Microbiota ; Plastics ; Persistent Organic Pollutants/metabolism ; Bacteria/metabolism ; Halogenated Diphenyl Ethers/metabolism ; Biodegradation, Environmental ; }, abstract = {Plastics are invading nearly all ecosystems on earth, acting as emerging repositories for toxic organic pollutants and thereby imposing substantial threats to ecological integrity. The colonization of plastics by microorganisms, forming the plastisphere, has garnered attention due to its potential influence on biogeochemical cycles. However, the capability of plastisphere microorganisms to attenuate organohalide pollutants remains to be evaluated. This study revealed that the plastisphere, collected from coastal ecosystems, harbors unique microbiomes, while the natural accumulation of organohalide pollutants on plastics may favor the proliferation of organohalide-respiring bacteria (OHRB). Laboratory tests further elucidated the high potential of plastisphere microbiota to reductively dehalogenate a variety of organohalide pollutants. Notably, over 70% tested plastisphere completely debrominated tetrabromobisphenol A (TBBPA) and polybrominated diphenyl ethers (PBDEs) to nonhalogenated products, whereas polychlorinated biphenyls (PCBs) were converted to lower congeners under anaerobic conditions. Dehalococcoides, Dehalogenimonas, and novel Dehalococcoidia populations might contribute to the observed dehalogenation based on their growth during incubation and positive correlations with the quantity of halogens removed. Intriguingly, large fractions of these OHRB populations were identified in a lack of the currently known TBBPA/PBDEs/PCBs reductive dehalogenase (RDase) genes, suggesting the presence of novel RDase genes. Microbial community analyses identified organohalides as a crucial factor in determining the composition, diversity, interaction, and assembly of microbes derived from the plastisphere. Collectively, this study underscores the overlooked roles of the plastisphere in the natural attenuation of persistent organohalide pollutants and sheds light on the unignorable impacts of organohalide compounds on the microbial ecology of the plastisphere.}, }
@article {pmid39101559, year = {2024}, author = {Brar, NK and Dhariwal, A and Shekhar, S and Junges, R and Hakansson, AP and Petersen, FC}, title = {HAMLET, a human milk protein-lipid complex, modulates amoxicillin induced changes in an ex vivo biofilm model of the oral microbiome.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1406190}, pmid = {39101559}, issn = {1664-302X}, abstract = {Challenges from infections caused by biofilms and antimicrobial resistance highlight the need for novel antimicrobials that work in conjunction with antibiotics and minimize resistance risk. In this study we investigated the composite effect of HAMLET (human alpha-lactalbumin made lethal to tumor cells), a human milk protein-lipid complex and amoxicillin on microbial ecology using an ex vivo oral biofilm model with pooled saliva samples. HAMLET was chosen due to its multi-targeted antimicrobial mechanism, together with its synergistic effect with antibiotics on single species pathogens, and low risk of resistance development. The combination of HAMLET and low concentrations of amoxicillin significantly reduced biofilm viability, while each of them alone had little or no impact. Using a whole metagenomics approach, we found that the combination promoted a remarkable shift in overall microbial composition compared to the untreated samples. A large proportion of the bacterial species in the combined treatment were Lactobacillus crispatus, a species with probiotic effects, whereas it was only detected in a minor fraction in untreated samples. Although resistome analysis indicated no major shifts in alpha-diversity, the results showed the presence of TEM beta-lactamase genes in low proportions in all treated samples but absence in untreated samples. Our study illustrates HAMLET's capability to alter the effects of amoxicillin on the oral microbiome and potentially favor the growth of selected probiotic bacteria when in combination. The findings extend previous knowledge on the combined effects of HAMLET and antibiotics against target pathogens to include potential modulatory effects on polymicrobial biofilms of human origin.}, }
@article {pmid39101364, year = {2024}, author = {Elias Masiques, N and Vossen, E and De Vrieze, J and De Smet, S and Van Hecke, T}, title = {The formation of sulfur metabolites during in vitro gastrointestinal digestion of fish, white meat and red meat is affected by the addition of fructo-oligosaccharides.}, journal = {Food &amp; function}, volume = {15}, number = {17}, pages = {8729-8739}, doi = {10.1039/d4fo00928b}, pmid = {39101364}, issn = {2042-650X}, mesh = {Animals ; *Fermentation ; *Oligosaccharides/metabolism ; *Red Meat/analysis ; Cattle ; *Digestion ; Swine ; *Chickens ; Fishes/metabolism ; Gastrointestinal Tract/metabolism ; Sulfur/metabolism ; Meat/analysis ; Humans ; Fatty Acids, Volatile/metabolism ; Ammonia/metabolism ; }, abstract = {The formation of sulfur metabolites during large intestinal fermentation of red meat may affect intestinal health. In this study, four muscle sources with varying heme-Fe content (beef, pork, chicken and salmon), with or without fructo-oligosaccharides (FOS), were exposed to an in vitro gastrointestinal digestion and fermentation model, after which the formation of sulfur metabolites, protein fermentation metabolites, and short (SCFA) and branched (BCFA) chain fatty acids was assessed. When FOS were present during muscle fermentation, levels of SCFA (+54%) and H2S (+36%) increased, whereas levels of CS2 (-37%), ammonia (-60%) and indole (-30%) decreased, and the formation of dimethyl sulfides and phenol was suppressed. Red meat fermentation was not accompanied by higher H2S formation, but beef ferments tended to contain 33 to 49% higher CS2 levels compared to the ferments of other muscle sources. In conclusion, there is a greater effect on sulfur fermentation by the addition of FOS to the meats, than the intrinsic heme-Fe content of meat.}, }
@article {pmid39098418, year = {2024}, author = {Zhang, M and Duan, T and Luo, Y and Zhang, H and Li, W and Wang, X and Han, J}, title = {Impact mechanisms of various surfactants on the biodegradation of phenanthrene in soil: Bioavailability and microbial community responses.}, journal = {The Science of the total environment}, volume = {950}, number = {}, pages = {175225}, doi = {10.1016/j.scitotenv.2024.175225}, pmid = {39098418}, issn = {1879-1026}, mesh = {*Phenanthrenes/metabolism ; *Surface-Active Agents/metabolism ; *Biodegradation, Environmental ; *Soil Pollutants/metabolism ; *Soil Microbiology ; Soil/chemistry ; Biological Availability ; Microbiota/drug effects ; Polysorbates ; Glycolipids ; }, abstract = {The present study was conducted to systematically explore the mechanisms underlying the impact of various surfactants (CTAB, SDBS, Tween 80 and rhamnolipid) at different doses (10, 100 and 1000 mg/kg) on the biodegradation of a model polycyclic aromatic hydrocarbon (PAH) by indigenous soil microorganisms, focusing on bioavailability and community responses. The cationic surfactant CTAB inhibited the biodegradation of phenanthrene within the whole tested dosage range by decreasing its bioavailability and adversely affecting soil microbial communities. Appropriate doses of SDBS (1000 mg/kg), Tween 80 (100, 1000 mg/kg) and rhamnolipid at all amendment levels promoted the transformation of phenanthrene from the very slow desorption fraction (Fvslow) to bioavailable fractions (rapid and slow desorption fractions, Frapid and Fslow), assessed via Tenax extraction. However, only Tween 80 and rhamnolipid at these doses significantly improved both the rates and extents of phenanthrene biodegradation by 22.1-204.3 and 38.4-76.7 %, respectively, while 1000 mg/kg SDBS had little effect on phenanthrene removal. This was because the inhibitory effects of anionic surfactant SDBS, especially at high doses, on the abundance, diversity and activity of soil microbial communities surpassed the bioavailability enhancement in dominating biodegradation. In contrast, the nonionic surfactant Tween 80 and biosurfactant rhamnolipid enhanced the bioavailability of phenanthrene for degradation and also that to specific degrading bacterial genera, which stimulated their growth and increased the abundance of the related nidA degradation gene. Moreover, they promoted the total microbial/bacterial biomass, community diversity and polyphenol oxidase activity by providing available substrates and nutrients. These findings contribute to the design of suitable surfactant types and dosages for mitigating the environmental risk of PAHs and simultaneously benefiting microbial ecology in soil through bioremediation.}, }
@article {pmid39095861, year = {2024}, author = {Anthony, WE and Allison, SD and Broderick, CM and Chavez Rodriguez, L and Clum, A and Cross, H and Eloe-Fadrosh, E and Evans, S and Fairbanks, D and Gallery, R and Gontijo, JB and Jones, J and McDermott, J and Pett-Ridge, J and Record, S and Rodrigues, JLM and Rodriguez-Reillo, W and Shek, KL and Takacs-Vesbach, T and Blanchard, JL}, title = {From soil to sequence: filling the critical gap in genome-resolved metagenomics is essential to the future of soil microbial ecology.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {56}, pmid = {39095861}, issn = {2524-6372}, support = {DE-AC05-76RL01830//U.S. Department of Energy/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; 89233218CNA000001//U.S. Department of Energy/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; }, abstract = {Soil microbiomes are heterogeneous, complex microbial communities. Metagenomic analysis is generating vast amounts of data, creating immense challenges in sequence assembly and analysis. Although advances in technology have resulted in the ability to easily collect large amounts of sequence data, soil samples containing thousands of unique taxa are often poorly characterized. These challenges reduce the usefulness of genome-resolved metagenomic (GRM) analysis seen in other fields of microbiology, such as the creation of high quality metagenomic assembled genomes and the adoption of genome scale modeling approaches. The absence of these resources restricts the scale of future research, limiting hypothesis generation and the predictive modeling of microbial communities. Creating publicly available databases of soil MAGs, similar to databases produced for other microbiomes, has the potential to transform scientific insights about soil microbiomes without requiring the computational resources and domain expertise for assembly and binning.}, }
@article {pmid39095500, year = {2024}, author = {}, title = {Bringing microbial ecology into focus.}, journal = {Nature microbiology}, volume = {9}, number = {8}, pages = {1901-1902}, pmid = {39095500}, issn = {2058-5276}, mesh = {*Ecology ; Microbiota ; Humans ; Bacteria/genetics/classification/metabolism ; }, }
@article {pmid39095499, year = {2024}, author = {Carreira, C and Lønborg, C and Acharya, B and Aryal, L and Buivydaite, Z and Borim Corrêa, F and Chen, T and Lorenzen Elberg, C and Emerson, JB and Hillary, L and Khadka, RB and Langlois, V and Mason-Jones, K and Netherway, T and Sutela, S and Trubl, G and Wa Kang'eri, A and Wang, R and White, RA and Winding, A and Zhao, T and Sapkota, R}, title = {Integrating viruses into soil food web biogeochemistry.}, journal = {Nature microbiology}, volume = {9}, number = {8}, pages = {1918-1928}, pmid = {39095499}, issn = {2058-5276}, support = {NNF21OC0072586//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; 36223//Villum Fonden (Villum Foundation)/ ; 1127-00033B//Danmarks Grundforskningsfond (Danish National Research Foundation)/ ; }, mesh = {*Soil Microbiology ; *Food Chain ; *Viruses/genetics/classification/isolation &amp; purification ; *Soil/chemistry ; *Microbiota ; Animals ; Plants/virology/microbiology ; Ecosystem ; Bacteria/virology/metabolism/genetics ; }, abstract = {The soil microbiome is recognized as an essential component of healthy soils. Viruses are also diverse and abundant in soils, but their roles in soil systems remain unclear. Here we argue for the consideration of viruses in soil microbial food webs and describe the impact of viruses on soil biogeochemistry. The soil food web is an intricate series of trophic levels that span from autotrophic microorganisms to plants and animals. Each soil system encompasses contrasting and dynamic physicochemical conditions, with labyrinthine habitats composed of particles. Conditions are prone to shifts in space and time, and this variability can obstruct or facilitate interactions of microorganisms and viruses. Because viruses can infect all domains of life, they must be considered as key regulators of soil food web dynamics and biogeochemical cycling. We highlight future research avenues that will enable a more robust understanding of the roles of viruses in soil function and health.}, }
@article {pmid39094415, year = {2024}, author = {Song, Y and Cao, X and Li, SA and Li, Z and Grossart, HP and Ma, H}, title = {Human activities-impacted lake dissolved organic matter (DOM) affects phycosphere microbial diversity and DOM diversification via carbon metabolism.}, journal = {Journal of environmental management}, volume = {367}, number = {}, pages = {122011}, doi = {10.1016/j.jenvman.2024.122011}, pmid = {39094415}, issn = {1095-8630}, mesh = {*Lakes/microbiology ; *Carbon/metabolism ; Humans ; Benzopyrans ; Bacteria/metabolism ; }, abstract = {Photosynthetic carbon sequestration and microbial carbon metabolism are major processes of algae-bacteria interactions, affecting pollutant degradation as well as fundamental biogeochemical cycles in aquatic systems. Human-induced land-use changes greatly alter the molecular composition and input of terrestrial dissolved organic matter (DOM) in inland lakes. However, how the origin of DOM leads to varying effects on phycosphere microbial communities or molecular composition of DOM, e.g., via carbon metabolism, has been little studied in freshwater. Here, we incubated the cyanobacterium Microcystis aeruginosa and a bacterial community from natural lakes to establish an alga-bacteria model system. This allowed us to investigate how DOM from different sources affects phycosphere microbial diversity and DOM diversification. We showed that Suwannee River fulvic acid (SRFA), Suwannee River natural organic matter (SRNOM) and cropland lake DOM promote algal growth, whereas DOM from an urban lake inhibits algal growth. Algal metabolites and DOM together shaped the chemotaxis response of phycosphere communities. High-resolution mass spectrometry analysis demonstrated that DOM chemo-diversity tended to become uniform after interactions of diverse DOM sources with the algae-bacteria symbiosis system. Molecular thermodynamic analysis of DOM based on a substrate-explicit model further verified that microbial interactions render DOM less bioavailable and thus increase recalcitrant DOM formation. Metabolome analysis uncovered that DOM addition intensifies metabolic pathways related to labile and recalcitrant DOM utilization (mainly lignin/carboxyl-rich alicyclic molecule (CRAM)-like DOM, unsaturated hydrocarbon), whereby cofactor and vitamin metabolism represented an extremely strong activity in all metabolic pathways. Our results highlight covariation and interactions of DOM with microbial metabolism at the molecular level and expands our understanding of microbially mediated DOM shaping aquatic carbon cycling.}, }
@article {pmid39088119, year = {2024}, author = {Ferreira, P and Benabderrahim, MA and Hamza, H and Marchesini, A and Rejili, M and Castro, J and Tavares, RM and Costa, D and Sebastiani, F and Lino-Neto, T}, title = {Exploring the Influence of Date Palm Cultivars on Soil Microbiota.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {103}, pmid = {39088119}, issn = {1432-184X}, support = {2019-SECTION2-15; PRIMA/0001/2019//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2019-SECTION2-15; PRIMA/0001/2019//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2019-SECTION2-15; PRIMA/0001/2019//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2019-SECTION2-15; PRIMA/0001/2019//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; }, mesh = {*Soil Microbiology ; *Phoeniceae/microbiology/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; *Fungi/genetics/classification/isolation &amp; purification/physiology ; Genotype ; Plant Roots/microbiology ; Soil/chemistry ; }, abstract = {Plants thrive in diverse environments, where root-microbe interactions play a pivotal role. Date palm (Phoenix dactylifera L.), with its genetic diversity and resilience, is an ideal model for studying microbial adaptation to different genotypes and stresses. This study aimed to analyze the bacterial and fungal communities associated with traditional date palm cultivars and the widely cultivated "Deglet Nour" were explored using metabarcoding approaches. The microbial diversity analysis identified a rich community with 13,189 bacterial and 6442 fungal Amplicon Sequence Variants (ASVs). Actinobacteriota, Proteobacteria, and Bacteroidota dominated bacterial communities, while Ascomycota dominated fungal communities. Analysis of the microbial community revealed the emergence of two distinct clusters correlating with specific date palm cultivars, but fungal communities showed higher sensitivity to date palm genotype variations compared to bacterial communities. The commercial cultivar "Deglet Nour" exhibited a unique microbial composition enriched in pathogenic fungal taxa, which was correlated with its genetic distance. Overall, our study contributes to understanding the complex interactions between date palm genotypes and soil microbiota, highlighting the genotype role in microbial community structure, particularly among fungi. These findings suggest correlations between date palm genotype, stress tolerance, and microbial assembly, with implications for plant health and resilience. Further research is needed to elucidate genotype-specific microbial interactions and their role in enhancing plant resilience to environmental stresses.}, }
@article {pmid39087852, year = {2024}, author = {Wu, T and Bafort, Q and Mortier, F and Almeida-Silva, F and Natran, A and Van de Peer, Y}, title = {The immediate metabolomic effects of whole-genome duplication in the greater duckweed, Spirodela polyrhiza.}, journal = {American journal of botany}, volume = {111}, number = {8}, pages = {e16383}, pmid = {39087852}, issn = {1537-2197}, support = {833522/ERC_/European Research Council/International ; }, mesh = {*Araceae/genetics/metabolism ; *Genome, Plant ; *Metabolomics ; *Gene Duplication ; Metabolome ; Polyploidy ; Biomass ; }, abstract = {PREMISE: In plants, whole-genome duplication (WGD) is a common mutation with profound evolutionary potential. Given the costs associated with a superfluous genome copy, polyploid establishment is enigmatic. However, in the right environment, immediate phenotypic changes following WGD can facilitate establishment. Metabolite abundances are the direct output of the cell's regulatory network and determine much of the impact of environmental and genetic change on the phenotype. While it is well known that an increase in the bulk amount of genetic material can increase cell size, the impact of gene dosage multiplication on the metabolome remains largely unknown.<br><br>METHODS: We used untargeted metabolomics on four genetically distinct diploid-neoautotetraploid pairs of the greater duckweed, Spirodela polyrhiza, to investigate how WGD affects metabolite abundances per cell and per biomass.<br><br>RESULTS: Autopolyploidy increased metabolite levels per cell, but the response of individual metabolites varied considerably. However, the impact on metabolite level per biomass was restricted because the increased cell size reduced the metabolite concentration per cell. Nevertheless, we detected both quantitative and qualitative effects of WGD on the metabolome. Many effects were strain-specific, but some were shared by all four strains.<br><br>CONCLUSIONS: The nature and impact of metabolic changes after WGD depended strongly on the genotype. Dosage effects have the potential to alter the plant metabolome qualitatively and quantitatively, but were largely balanced out by the reduction in metabolite concentration due to an increase in cell size in this species.}, }
@article {pmid39085652, year = {2024}, author = {Brinch, C and Otani, S and Munk, P and van den Beld, M and Franz, E and Aarestrup, FM}, title = {Discovery of Vibrio cholerae in Urban Sewage in Copenhagen, Denmark.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {102}, pmid = {39085652}, issn = {1432-184X}, support = {NNF16OC0021856//Novo Nordisk Fonden/ ; NNF16OC0021856//Novo Nordisk Fonden/ ; NNF16OC0021856//Novo Nordisk Fonden/ ; NNF16OC0021856//Novo Nordisk Fonden/ ; VEO 874735//Horizon 2020 Framework Programme/ ; VEO 874735//Horizon 2020 Framework Programme/ ; VEO 874735//Horizon 2020 Framework Programme/ ; VEO 874735//Horizon 2020 Framework Programme/ ; VEO 874735//Horizon 2020 Framework Programme/ ; VEO 874735//Horizon 2020 Framework Programme/ ; }, mesh = {Denmark ; *Sewage/microbiology ; *Vibrio cholerae/genetics/isolation &amp; purification/classification ; Genome, Bacterial ; Wastewater/microbiology ; Cholera/microbiology/epidemiology ; }, abstract = {We report the discovery of a persistent presence of Vibrio cholerae at very low abundance in the inlet of a single wastewater treatment plant in Copenhagen, Denmark at least since 2015. Remarkably, no environmental or locally transmitted clinical case of V. cholerae has been reported in Denmark for more than 100 years. We, however, have recovered a near-complete genome out of 115 metagenomic sewage samples taken over the past 8 years, despite the extremely low relative abundance of one V. cholerae read out of 500,000 sequenced reads. Due to the very low relative abundance, routine screening of the individual samples did not reveal V. cholerae. The recovered genome lacks the gene responsible for cholerae toxin production, but although this strain may not pose an immediate public health risk, our finding illustrates the importance, challenges, and effectiveness of wastewater-based pathogen surveillance.}, }
@article {pmid39085298, year = {2024}, author = {Vidal-Verdú, &#xc0; and Torrent, D and Iglesias, A and Latorre-Pérez, A and Abendroth, C and Corbín-Agustí, P and Peretó, J and Porcar, M}, title = {The highly differentiated gut of Pachnoda marginata hosts sequential microbiomes: microbial ecology and potential applications.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {65}, pmid = {39085298}, issn = {2055-5008}, support = {ACIF/2021/110//Generalitat Valenciana (Regional Government of Valencia)/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation &amp; purification ; *Archaea/classification/genetics/isolation &amp; purification ; *Fungi/classification/genetics/isolation &amp; purification ; *Coleoptera/microbiology ; Metagenomics/methods ; Phylogeny ; Gastrointestinal Tract/microbiology ; Sequence Analysis, DNA/methods ; }, abstract = {Insect gut microbiomes play a crucial role in the insect development and are shaped, among other factors, by the specialized insect diet habits as well as the morphological structure of the gut. Rose chafers (Pachnoda spp.; Coleoptera: Scarabaeidae) have a highly differentiated gut characterized by a pronounced hindgut dilation which resembles a miniaturized rumen. Specifically, the species Pachnoda marginata has not been previously studied in detail in terms of microbial ecology. Here, we show a fine scale study of the highly compartmentalized gut of P. marginata by using amplicon and metagenomic sequencing to shed light on the bacterial, archaeal and fungal communities thriving in each section of the gut. We found a microbial gradient along the gut from aerobic (foregut) to strictly anaerobic communities (hindgut). In addition, we have characterized interesting biological activities and metabolic pathways of gut microbial communities related to cellulose degradation, methane production and sulfate reduction. Taken together, our results reveal the highly diverse microbial community and the potential of P. marginata gut as a source of industrially relevant microbial diversity.}, }
@article {pmid39083238, year = {2024}, author = {Romano, I and Ventorino, V and Schettino, M and Magaraci, G and Pepe, O}, title = {Changes in Soil Microbial Communities Induced by Biodegradable and Polyethylene Mulch Residues Under Three Different Temperatures.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {101}, pmid = {39083238}, issn = {1432-184X}, mesh = {*Soil Microbiology ; *Biodegradation, Environmental ; *Temperature ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *Fungi/genetics/metabolism/classification ; *Polyethylene ; *Microbiota ; *Soil/chemistry ; Biodegradable Plastics/metabolism ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Mulching is a common method increasing crop yield and achieving out-of-season production; nevertheless, their removal poses a significant environmental danger. In this scenario, the use of biodegradable plastic mulches comes up as a solution to increase the sustainability of this practice, as they can be tilled in soil without risk for the environment. In this context, it is important to study the microbial response to this practice, considering their direct involvement in plastic biodegradation. This study evaluated the biodegradation of three commercial mulch residues: one conventional non-biodegradable mulch versus two biodegradable ones (white and black compostable Mater-Bi mulches). The experiment was conducted under three incubation temperatures (room temperature 20-25 °C, 30 °C, and 45 °C) for a 6-month trial using fallow agricultural soil. Soil without plastic mulch residues was used as a control. White mater-bi biodegradable mulch residues showed higher degradation rates up to 88.90% at 30 °C, and up to 69.15% at room temperature. Furthermore, incubation at 45 °C determines the absence of degradation for all types of mulch considered. Moreover, bacterial alpha diversity was primarily influenced by plastic type and temperature, while fungal populations were mainly affected by temperature. Beta diversity was impacted by all experimental variables. Predicted functional genes crucial for degrading complex substrates, including those encoding hydrolases, cutinases, cellobiosidases, and lipases, were derived from 16S rRNA gene sequencing data. Cluster analysis based on predicted enzyme-encoding gene abundance revealed two clusters, mainly linked to sampling time. Finally, core microbiome analysis identified dominant bacterial and fungal taxa in various soil-plastic ecosystems during degradation, pinpointing species potentially involved in plastic breakdown. The present study allows an assessment of how different temperatures affect the degradation of mulch residues in soil, providing important insights for different climatic growing zones. It also fills a gap in the literature by directly comparing the effects of biodegradable and polyethylene mulches on soil microbial communities.}, }
@article {pmid39081364, year = {2024}, author = {Schmitz, DA and Wechsler, T and Mignot, I and Kümmerli, R}, title = {Predicting bacterial interaction outcomes from monoculture growth and supernatant assays.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae045}, pmid = {39081364}, issn = {2730-6151}, abstract = {How to derive principles of community dynamics and stability is a central question in microbial ecology. Bottom-up experiments, in which a small number of bacterial species are mixed, have become popular to address it. However, experimental setups are typically limited because co-culture experiments are labor-intensive and species are difficult to distinguish. Here, we use a four-species bacterial community to show that information from monoculture growth and inhibitory effects induced by secreted compounds can be combined to predict the competitive rank order in the community. Specifically, integrative monoculture growth parameters allow building a preliminary competitive rank order, which is then adjusted using inhibitory effects from supernatant assays. While our procedure worked for two different media, we observed differences in species rank orders between media. We then parameterized computer simulations with our empirical data to show that higher order species interactions largely follow the dynamics predicted from pairwise interactions with one important exception. The impact of inhibitory compounds was reduced in higher order communities because their negative effects were spread across multiple target species. Altogether, we formulated three simple rules of how monoculture growth and supernatant assay data can be combined to establish a competitive species rank order in an experimental four-species community.}, }
@article {pmid39081075, year = {2024}, author = {Bontemps, Z and Paranjape, K and Guy, L}, title = {Host-bacteria interactions: ecological and evolutionary insights from ancient, professional endosymbionts.}, journal = {FEMS microbiology reviews}, volume = {48}, number = {4}, pages = {}, pmid = {39081075}, issn = {1574-6976}, support = {F23-0260//Helge Ax:son Johnsons Foundation/ ; //NSERC/ ; }, mesh = {*Symbiosis ; *Host Microbial Interactions/physiology ; *Biological Evolution ; Gammaproteobacteria/genetics/physiology/classification ; Animals ; Bacteria/genetics/classification ; Ecosystem ; }, abstract = {Interactions between eukaryotic hosts and their bacterial symbionts drive key ecological and evolutionary processes, from regulating ecosystems to the evolution of complex molecular machines and processes. Over time, endosymbionts generally evolve reduced genomes, and their relationship with their host tends to stabilize. However, host-bacteria relationships may be heavily influenced by environmental changes. Here, we review these effects on one of the most ancient and diverse endosymbiotic groups, formed by-among others-Legionellales, Francisellaceae, and Piscirickettsiaceae. This group is referred to as Deep-branching Intracellular Gammaproteobacteria (DIG), whose last common ancestor presumably emerged about 2 Ga ago. We show that DIGs are globally distributed, but generally at very low abundance, and are mainly identified in aquatic biomes. Most DIGs harbour a type IVB secretion system, critical for host-adaptation, but its structure and composition vary. Finally, we review the different types of microbial interactions that can occur in diverse environments, with direct or indirect effects on DIG populations. The increased use of omics technologies on environmental samples will allow a better understanding of host-bacterial interactions and help unravel the definition of DIGs as a group from an ecological, molecular, and evolutionary perspective.}, }
@article {pmid39080099, year = {2024}, author = {Tiusanen, M and Becker-Scarpitta, A and Wirta, H}, title = {Distinct Communities and Differing Dispersal Routes in Bacteria and Fungi of Honey Bees, Honey, and Flowers.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {100}, pmid = {39080099}, issn = {1432-184X}, support = {201801360//Koneen S&#xe4;&#xe4;ti&#xf6;/ ; }, mesh = {Bees/microbiology ; Animals ; *Flowers/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Fungi/classification/isolation &amp; purification/genetics ; *Honey/microbiology/analysis ; *Microbiota ; Finland ; Pollination ; DNA Barcoding, Taxonomic ; Seasons ; }, abstract = {Microbiota, the communities of microbes on and in organisms or organic matter, are essential for the functioning of ecosystems. How microbes are shared and transmitted delineates the formation of a microbiota. As pollinators forage, they offer a route to transfer microbes among the flowering plants, themselves, and their nests. To assess how the two components of the microbiota, bacteria and fungi, in pollination communities are shared and transferred, we focused on the honey bee Apis mellifera and collected honey bee, honey (representing the hive microbiota), and flower samples three times during the summer in Finland. We identified the bacteria and fungi by DNA metabarcoding. To determine the impact of honey bees' flower choices on the honey bee and hive microbiota, we identified also plant DNA in honey. The bacterial communities of honey bees, honey, and flowers all differ greatly from each other, while the fungal communities of honey bees and honey are very similar, yet different from flowers. The time of the summer and the sampling area influence all these microbiota. For flowers, the plant identity impacts both bacterial and fungal communities' composition the most. For the dispersal pathways of bacteria to honey bees, they are acquired directly from the honey and indirectly from flowers through the honey, while fungi are directly transmitted to honey bees from flowers. Overall, the distinctiveness of the microbiota of honey bees, honey, and the surrounding flowers suggests the sharing of microbes among them occurs but plays a minor role for the established microbiota.}, }
@article {pmid39079336, year = {2024}, author = {Zhang, Y and Li, X and Ren, A and Yao, M and Chen, C and Zhang, H and van der Meer, W and Liu, G}, title = {Impacts of water treatments on bacterial communities of biofilm and loose deposits in drinking water distribution systems.}, journal = {Environment international}, volume = {190}, number = {}, pages = {108893}, doi = {10.1016/j.envint.2024.108893}, pmid = {39079336}, issn = {1873-6750}, mesh = {*Biofilms/growth &amp; development/drug effects ; *Drinking Water/microbiology ; *Water Purification/methods ; *Water Supply ; *Bacteria ; Water Microbiology ; }, abstract = {Treated drinking water is delivered to customers through drinking water distribution systems (DWDSs). Although studies have focused on exploring the microbial ecology of DWDSs, knowledge about the effects of different water treatments on the bacterial community of biofilm and loose deposits in DWDS is limited. This study assessed the effects of additional treatments on the bacterial communities developed in 10 months' old pilot DWDSs. The results showed a similar bacterial community in the pipe-wall biofilm, which was dominated by Novosphingobium spp. (20-82 %) and Sphingomonas spp. (11-53 %), regardless of the treatment applied. The bacterial communities that were retained in the distribution systems (including pipe-wall biofilm and loose deposits) were similar to the particle-associated bacteria (PAB) in the corresponding supply water. The additional treatments showed clear effects of the removal and/or introduction of particles. The genera Aeromonas spp., Clostridium spp., Legionella spp., and Pseudomonas spp., which contain opportunistic pathogenic species, were only detected among the PAB in ion exchange system. Our study demonstrated that the biofilm community is consistent across treatments, and the contribution from bacteria in loose deposits is important but can be controlled by removing particles. These findings offer more insight into the origin and development of microbial ecology in DWDSs and suggest paths for further research on the possibility of managing the microbial ecology in distribution systems.}, }
@article {pmid39079302, year = {2024}, author = {Zhou, W and Huang, D and Chen, S and Wang, G and Li, R and Xu, W and Lei, Y and Xiao, R and Yin, L and Chen, H and Li, F}, title = {Microplastic dilemma: Assessing the unexpected trade-offs between biodegradable and non-biodegradable forms on plant health, cadmium uptake, and sediment microbial ecology.}, journal = {Journal of hazardous materials}, volume = {477}, number = {}, pages = {135240}, doi = {10.1016/j.jhazmat.2024.135240}, pmid = {39079302}, issn = {1873-3336}, mesh = {*Cadmium/metabolism/toxicity ; *Microplastics/toxicity/metabolism ; *Soil Microbiology ; *Geologic Sediments/microbiology/chemistry ; *Soil Pollutants/metabolism ; Biodegradation, Environmental ; Plant Roots/metabolism/microbiology ; Biodegradable Plastics/metabolism ; Plants/metabolism ; Plant Development/drug effects ; }, abstract = {Despite extensive substitution of biodegradable plastics (BPs) for conventional plastics (CPs), research on their environmental ecological consequences as microplastics (MPs) is scarce. This study aimed to fill this gap by investigating the impacts of six prototypical MPs (categorized into BMPs and CMPs) on plant growth, cadmium (Cd) translocation, and bacterial communities in contaminated sediments. Results showed both BMPs and CMPs hindered plant development; yet interestingly, BMPs provoked more pronounced physiological and biochemical changes alongside increased oxidative stress due to reactive oxygen species accumulation. Notably, most MP types promoted the absorption of Cd by plant roots potentially via a "dilution effect". BMPs also induced larger shifts in soil microbial metabolic functions compared to CMPs. Ramlibacter was identified as a key biomarker distinguishing BMPs from CMPs, with link to multiple N metabolic pathways and N assimilation. This study offers novel insights into intricate biochemical mechanisms and environmental chemistry behaviors underpinning MP-Cd interactions within the plant-microbe-sediment system, emphasizing BMPs' higher potential ecological risks based on their significant effects on plant health and microbial ecology. This work contributes to enhancing the comprehensive understanding of their ecological implications and potential threats to environmental security.}, }
@article {pmid39077993, year = {2024}, author = {Jirsová, D and Wideman, JG}, title = {Integrated overview of stramenopile ecology, taxonomy, and heterotrophic origin.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39077993}, issn = {1751-7370}, support = {2119963//National Science Foundation/ ; GBMF9201//Gordon and Betty Moore Foundation/ ; CZ.02.01.01/00/22_010/0008117//VEDA FELLOWSHIPS within the Operational program Jan Amos Komensky/ ; }, mesh = {Biological Evolution ; *Heterotrophic Processes ; Phylogeny ; Plastids/genetics ; *Stramenopiles/classification/genetics ; }, abstract = {Stramenopiles represent a significant proportion of aquatic and terrestrial biota. Most biologists can name a few, but these are limited to the phototrophic (e.g. diatoms and kelp) or parasitic species (e.g. oomycetes, Blastocystis), with free-living heterotrophs largely overlooked. Though our attention is slowly turning towards heterotrophs, we have only a limited understanding of their biology due to a lack of cultured models. Recent metagenomic and single-cell investigations have revealed the species richness and ecological importance of stramenopiles-especially heterotrophs. However, our lack of knowledge of the cell biology and behaviour of these organisms leads to our inability to match species to their particular ecological functions. Because photosynthetic stramenopiles are studied independently of their heterotrophic relatives, they are often treated separately in the literature. Here, we present stramenopiles as a unified group with shared synapomorphies and evolutionary history. We introduce the main lineages, describe their important biological and ecological traits, and provide a concise update on the origin of the ochrophyte plastid. We highlight the crucial role of heterotrophs and mixotrophs in our understanding of stramenopiles with the goal of inspiring future investigations in taxonomy and life history. To understand each of the many diversifications within stramenopiles-towards autotrophy, osmotrophy, or parasitism-we must understand the ancestral heterotrophic flagellate from which they each evolved. We hope the following will serve as a primer for new stramenopile researchers or as an integrative refresher to those already in the field.}, }
@article {pmid39074063, year = {2024}, author = {Nyathi, M and Dhlamini, Z and Ncube, T}, title = {Cloning Cellulase Genes from Victoria Falls Rainforest Decaying Logs Metagenome.}, journal = {Polish journal of microbiology}, volume = {73}, number = {3}, pages = {343-348}, pmid = {39074063}, issn = {2544-4646}, mesh = {*Cellulase/genetics/metabolism ; *Metagenome ; *Rainforest ; Soil Microbiology ; Cloning, Molecular ; Hydrogen-Ion Concentration ; Escherichia coli/genetics ; Temperature ; Metagenomics ; Bacteria/genetics/classification/enzymology/isolation &amp; purification ; }, abstract = {The Victoria Falls rainforest is a protected site whose forest floors harbor a host of cellulolytic microorganisms involved in biomass degradation. This study collected decaying logs and soil from the rainforest for bioprospecting cellulases from their metagenomes. Metagenomic DNA was isolated from the compound sample. Degenerate cellulase primers were used to amplify cellulase genes in the metagenome. The resulting amplicons cloned into Z-competent Escherichia coli DH5α were analyzed by functional screening for the production of cellulase extracellularly. Functional screening of the clones resulted in one clone (Clone-i) testing positive for extracellular cellulase production. Submerged fermentation of Clone-i was carried out for cellulase production. The cellulases were characterized to determine their activity's optimum pH and temperature. The diversity of the cellulases produced by Clone-i was determined. Clone-i's optimum enzyme activity was observed after 72 hours of incubation at 50°C and pH 5. Clone-i produced 80% more exoglucanases as compared to endoglucanases. The cellulolytic Clone-i' isolate shows Victoria Falls rainforest's potential as an enzyme bioprospecting site, reflecting that metagenomics is a valuable tool in microbial ecology.}, }
@article {pmid39073401, year = {2024}, author = {Williams, SE and Varliero, G and Lurgi, M and Stach, JEM and Race, PR and Curnow, P}, title = {Diversity and structure of the deep-sea sponge microbiome in the equatorial Atlantic Ocean.}, journal = {Microbiology (Reading, England)}, volume = {170}, number = {7}, pages = {}, pmid = {39073401}, issn = {1465-2080}, mesh = {*Porifera/microbiology ; *Microbiota ; *Archaea/classification/genetics/isolation &amp; purification ; Animals ; Atlantic Ocean ; *Bacteria/classification/genetics/isolation &amp; purification ; *Phylogeny ; Seawater/microbiology ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; }, abstract = {Sponges (phylum Porifera) harbour specific microbial communities that drive the ecology and evolution of the host. Understanding the structure and dynamics of these communities is emerging as a primary focus in marine microbial ecology research. Much of the work to date has focused on sponges from warm and shallow coastal waters, while sponges from the deep ocean remain less well studied. Here, we present a metataxonomic analysis of the microbial consortia associated with 23 individual deep-sea sponges. We identify a high abundance of archaea relative to bacteria across these communities, with certain sponge microbiomes comprising more than 90 % archaea. Specifically, the archaeal family Nitrosopumilaceae is prolific, comprising over 99 % of all archaeal reads. Our analysis revealed that sponge microbial communities reflect the host sponge phylogeny, indicating a key role for host taxonomy in defining microbiome composition. Our work confirms the contribution of both evolutionary and environmental processes to the composition of microbial communities in deep-sea sponges.}, }
@article {pmid39073317, year = {2024}, author = {Bahri, S and Bouazizi, S and Nahdi, A and Mlika, M and Hamdi, M and Jameleddine, S}, title = {Insights on the Tunisian Prickly Pear Molasses as a Potential Antifibrotic and Antioxidant Candidate against Lung Fibrosis.}, journal = {Chemistry &amp; biodiversity}, volume = {21}, number = {11}, pages = {e202401030}, doi = {10.1002/cbdv.202401030}, pmid = {39073317}, issn = {1612-1880}, support = {//Tunisian Ministry of Higher Education/ ; //Scientific Research/ ; }, mesh = {Animals ; *Antioxidants/pharmacology/chemistry ; *Rats, Wistar ; Rats ; *Pulmonary Fibrosis/drug therapy/chemically induced/metabolism/pathology ; *Molasses ; Male ; Bleomycin ; Oxidative Stress/drug effects ; Pyrus/chemistry ; Tunisia ; Antifibrotic Agents/pharmacology/chemistry ; Disease Models, Animal ; Lung/drug effects/pathology/metabolism ; }, abstract = {Idiopathic pulmonary fibrosis (IPF) is a chronic and progressive interstitial disease leading to pulmonary damage and respiratory failure. We aimed to investigate the effect of prickly pear molasses (PPM) on an experimental model of pulmonary fibrosis induced by bleomycin (BLM) in Wistar rat. Animals were divided into 5 groups: the control group (G1), the BLM group (G2) and three groups (G3, G4, G5) receiving a single intra-tracheal injection of BLM (4 mg/kg) and PPM (at 2, 4.5 and10 %) that was introduced into the diet one week before BLM injection and continued for 3 weeks. Our phytochemical results revealed significant polyphenol and flavonoid content. LCMS analysis revealed the presence of Sinapinic acid, t-ferulic acid, t-cinnamic acid, Caffeic acid, gallic acid and vallinic acid among others. Our histological study revealed significant decrease in collagen deposition in the groups of rats treated with 4.5 % and 10 % molasses compared to BLM group. Oxidative stress in pulmonary tissues was investigated using catalase (CAT), superoxide dismutase (SOD), and malondialdehyde (MDA) assays. Treatment with PPM normalized the disturbance in the level of these oxidative markers in G3,G4, G5 compared to G2. In conclusion, PPM exhibit antifibrotic and antioxidant activities in BLM model of lung fibrosis.}, }
@article {pmid39073180, year = {2024}, author = {Bielčik, M and Schlägel, UE and Schäfer, M and Aguilar-Trigueros, CA and Lakovic, M and Sosa-Hernández, MA and Hammer, EC and Jeltsch, F and Rillig, MC}, title = {Aligning spatial ecological theory with the study of clonal organisms: the case of fungal coexistence.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {99}, number = {6}, pages = {2211-2233}, doi = {10.1111/brv.13119}, pmid = {39073180}, issn = {1469-185X}, support = {GRK 2118//Deutsche Forschungsgemeinschaft/ ; SCHL 2259/1-1.//Deutsche Forschungsgemeinschaft/ ; 100619639//Fachagentur Nachwachsende Rohstoffe/ ; }, mesh = {*Fungi/physiology ; *Ecosystem ; Models, Biological ; }, abstract = {Established ecological theory has focused on unitary organisms, and thus its concepts have matured into a form that often hinders rather than facilitates the ecological study of modular organisms. Here, we use the example of filamentous fungi to develop concepts that enable integration of non-unitary (modular) organisms into the established community ecology theory, with particular focus on its spatial aspects. In doing so, we provide a link between fungal community ecology and modern coexistence theory (MCT). We first show how community processes and predictions made by MCT can be used to define meaningful scales in fungal ecology. This leads to the novel concept of the unit of community interactions (UCI), a promising conceptual tool for applying MCT to communities of modular organisms with indeterminate clonal growth and hierarchical individuality. We outline plausible coexistence mechanisms structuring fungal communities, and show at what spatial scales and in what habitats they are most likely to act. We end by describing challenges and opportunities for empirical and theoretical research in fungal competitive coexistence.}, }
@article {pmid39071402, year = {2024}, author = {Dieppa-Colón, E and Martin, C and Anantharaman, K}, title = {Prophage-DB: A comprehensive database to explore diversity, distribution, and ecology of prophages.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39071402}, issn = {2692-8205}, support = {R35 GM143024/GM/NIGMS NIH HHS/United States ; T32 GM135066/GM/NIGMS NIH HHS/United States ; }, abstract = {BACKGROUND: Viruses that infect prokaryotes (phages) constitute the most abundant group of biological agents, playing pivotal roles in microbial systems. They are known to impact microbial community dynamics, microbial ecology, and evolution. Efforts to document the diversity, host range, infection dynamics, and effects of bacteriophage infection on host cell metabolism are extremely underexplored. Phages are classified as virulent or temperate based on their life cycles. Temperate phages adopt the lysogenic mode of infection, where the genome integrates into the host cell genome forming a prophage. Prophages enable viral genome replication without host cell lysis, and often contribute novel and beneficial traits to the host genome. Current phage research predominantly focuses on lytic phages, leaving a significant gap in knowledge regarding prophages, including their biology, diversity, and ecological roles.<br><br>RESULTS: Here we develop and describe Prophage-DB, a database of prophages, their proteins, and associated metadata that will serve as a resource for viral genomics and microbial ecology. To create the database, we identified and characterized prophages from genomes in three of the largest publicly available databases. We applied several state-of-the-art tools in our pipeline to annotate these viruses, cluster and taxonomically classify them, and detect their respective auxiliary metabolic genes. In total, we identify and characterize over 350,000 prophages and 35,000 auxiliary metabolic genes. Our prophage database is highly representative based on statistical results and contains prophages from a diverse set of archaeal and bacterial hosts which show a wide environmental distribution.<br><br>CONCLUSION: Prophages are particularly overlooked in viral ecology and merit increased attention due to their vital implications for microbiomes and their hosts. Here, we created Prophage-DB to advance our comprehension of prophages in microbiomes through a comprehensive characterization of prophages in publicly available genomes. We propose that Prophage-DB will serve as a valuable resource for advancing phage research, offering insights into viral taxonomy, host relationships, auxiliary metabolic genes, and environmental distribution.}, }
@article {pmid39066818, year = {2024}, author = {Castellano-Hinojosa, A and Tortosa, G and Fernández-Zambrano, A and Correa-Galeote, D and Bedmar, EJ and Medina-Sánchez, JM}, title = {Strong Saharan Dust Deposition Events Alter Microbial Diversity and Composition in Sediments of High-Mountain Lakes of Sierra Nevada (Spain).}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {99}, pmid = {39066818}, issn = {1432-184X}, support = {A-RNM-237-UGR18//FEDER/Junta de Andaluc&#xed;a-Consejer&#xed;a de Econom&#xed;a y Conocimiento/Proyecto/ ; A-RNM-237-UGR18//FEDER/Junta de Andaluc&#xed;a-Consejer&#xed;a de Econom&#xed;a y Conocimiento/Proyecto/ ; A-RNM-237-UGR18//FEDER/Junta de Andaluc&#xed;a-Consejer&#xed;a de Econom&#xed;a y Conocimiento/Proyecto/ ; A-RNM-237-UGR18//FEDER/Junta de Andaluc&#xed;a-Consejer&#xed;a de Econom&#xed;a y Conocimiento/Proyecto/ ; A-RNM-237-UGR18//FEDER/Junta de Andaluc&#xed;a-Consejer&#xed;a de Econom&#xed;a y Conocimiento/Proyecto/ ; A-RNM-237-UGR18//FEDER/Junta de Andaluc&#xed;a-Consejer&#xed;a de Econom&#xed;a y Conocimiento/Proyecto/ ; PID2020-118872RB-I00//MICIN/AEI/10.13039/501100011033/ ; LifeWatch-2019-10-UGR-01//Ministry of Science and Innovation through the FEDER funds from the Spanish Pluriregional Operational Program 2014-2020 (POPE), LifeWatch-ERIC action line/ ; }, mesh = {*Geologic Sediments/microbiology/chemistry ; *Lakes/microbiology/chemistry ; *Dust/analysis ; Spain ; *Biodiversity ; *Bacteria/classification/genetics/isolation &amp; purification ; Microbiota ; Africa, Northern ; }, abstract = {Mediterranean high-mountain lakes are being increasingly affected by strong Saharan dust deposition events. However, the ecological impacts of these severe atmospheric episodes remain largely unknown. We examined the effects of a strong Saharan dust intrusion to the Iberian Peninsula in 2022 on the physicochemical parameters and prokaryotic communities in sediments of nine high-mountain lakes of Sierra Nevada (Spain) located above 2800 m.a.s.l and in different orientations (north vs. south). A previous year (2021), with lower Saharan dust deposition with respect to 2022, was used for interannual comparisons. The strong dust deposition to the high-mountain lakes resulted in a significant increase in sediment nutrient availability which was linked to changes in the composition of prokaryotic communities. Decreases in alpha diversity and changes in beta diversity of prokaryotic communities were mainly observed in lakes located in the south compared to the north orientation likely because the former was more affected by the atmospheric dust deposition episode. Dust intrusion to the high-mountain lakes resulted in significant changes in the relative abundance of specific genera involved in important nutrient cycling processes such as phosphate solubilization, nitrogen fixation, nitrification, and denitrification. Saharan dust deposition also increased predicted microbial functionality in all lakes. Our findings show that severe atmospheric dust inputs to remote high-mountain lakes of Sierra Nevada can have significant biogeochemical and biodiversity consequences through changes in nutrient availability and prokaryotic communities in sediments of these freshwater ecosystems. This information contributes to understanding how Mediterranean high-mountain lakes of Sierra Nevada face strong intrusions of Saharan dust and their ecological consequences.}, }
@article {pmid39065051, year = {2024}, author = {Du, W and Li, J and Zhang, G and Yu, K and Liu, S}, title = {Spatiotemporal Variations in Co-Occurrence Patterns of Planktonic Prokaryotic Microorganisms along the Yangtze River.}, journal = {Microorganisms}, volume = {12}, number = {7}, pages = {}, pmid = {39065051}, issn = {2076-2607}, support = {52100171//National Natural Science Foundation of China/ ; BYESS2023103//Young Elite Scientist Sponsorship Program by Beijing Association for Science and Technology/ ; }, abstract = {Bacteria and archaea are foundational life forms on Earth and play crucial roles in the development of our planet's biological hierarchy. Their interactions influence various aspects of life, including eukaryotic cell biology, molecular biology, and ecological dynamics. However, the coexistence network patterns of these microorganisms within natural river ecosystems, vital for nutrient cycling and environmental health, are not well understood. To address this knowledge gap, we systematically explored the non-random coexistence patterns of planktonic bacteria and archaea in the 6000-km stretch of the Yangtze River by using high-throughput sequencing technology. By analyzing the O/R ratio, representing the divergence between observed (O%) and random (R%) co-existence incidences, and the module composition, we found a preference of both bacteria and archaea for intradomain associations over interdomain associations. Seasons notably influenced the co-existence of bacteria and archaea, and archaea played a more crucial role in spring as evidenced by their predominant presence of interphyla co-existence and more species as keystone ones. The autumn network was characterized by a higher node or edge number, greater graph density, node degree, degree centralization, and nearest neighbor degree, indicating a more complex and interconnected structure. Landforms markedly affected microbial associations, with more complex networks and more core species found in plain and non-source areas. Distance-decay analysis suggested the importance of geographical distance in shaping bacteria and archaea co-existence patterns (more pronounced in spring). Natural, nutrient, and metal factors, including water temperature, NH4[+]-N, Fe, Al, and Ni were identified as crucial determinants shaping the co-occurrence patterns. Overall, these findings revealed the dynamics of prokaryotic taxa coexistence patterns in response to varying environmental conditions and further contributed to a broader understanding of microbial ecology in freshwater biogeochemical cycling.}, }
@article {pmid39065031, year = {2024}, author = {Sapp, PA and Townsend, JR and Kirby, TO and Govaert, M and Duysburgh, C and Verstrepen, L and Marzorati, M and Marshall, TM and Esposito, R}, title = {AG1[®], a Novel Synbiotic, Maintains Gut Barrier Function following Inflammatory Challenge in a Caco-2/THP1-Blue™ Co-Culture Model.}, journal = {Microorganisms}, volume = {12}, number = {7}, pages = {}, pmid = {39065031}, issn = {2076-2607}, support = {n/a//Athletic Greens International (Carson City, NV 89701)/ ; }, abstract = {Nutritional interventions to reduce gastrointestinal (GI) permeability are of significant interest to physically active adults and those experiencing chronic health conditions. This in vitro study was designed to assess the impact of AG1, a novel synbiotic, on GI permeability following an inflammatory challenge. Interventions [AG1 (vitamins/minerals, pre-/probiotics, and phytonutrients) and control (control medium)] were fed separately into a human GI tract model (stomach, small intestine, and colon). In the colonic phase, the GI contents were combined with fecal inocula from three healthy human donors. GI permeability was evaluated with transepithelial electrical resistance (TEER) in a Caco-2 (apical)/THP1-Blue™ (basolateral) co-culture model. The apical side received sodium butyrate (positive control) or Caco-2 complete medium (negative control) during baseline testing. In the 24 h experiment, the apical side received colonic simulation isolates from the GI model, and the basolateral side was treated with Caco-2 complete medium, then 6 h treatment with lipopolysaccharide. TEER was assessed at 0 h and 24 h, and inflammatory markers were measured at 30 h in triplicate. Paired samples t-tests were used to evaluate endpoint mean difference (MD) for AG1 vs. control. TEER was higher for AG1 (mean ± SD: 99.89 ± 1.32%) vs. control (mean ± SD: 92.87 ± 1.22%) following activated THP1-induced damage [MD: 7.0% (p < 0.05)]. AG1 maintained TEER similar to the level of the negative control [-0.1% (p = 0.02)]. No differences in inflammatory markers were observed. These in vitro data suggest that acute supplementation with AG1 might stimulate protective effects on GI permeability. These changes may be driven by SCFA production due to the pre-/probiotic properties of AG1, but more research is needed.}, }
@article {pmid39062734, year = {2024}, author = {Zhang, H and Li, S and Zhou, S and Guo, W and Chen, P and Li, Y and Wu, W}, title = {Divergence of Phyllosphere Microbial Community Assemblies and Components of Volatile Organic Compounds between the Invasive Sphagneticola trilobata, the Native Sphagneticola calendulacea and Their Hybrids, and Its Implications for Invasiveness.}, journal = {Genes}, volume = {15}, number = {7}, pages = {}, pmid = {39062734}, issn = {2073-4425}, support = {2023KCXTD017//Guangdong Province University Innovative Team Project: Innovation and Development Application of Ornamental Plant Germplasm with Lingnan Characteristics/ ; }, mesh = {*Volatile Organic Compounds/metabolism ; *Microbiota ; *Introduced Species ; Brassicaceae/microbiology/genetics ; China ; }, abstract = {Closely-related plant groups with distinct microbiomes, chemistries and ecological characteristics represent tractable models to explore mechanisms shaping species spread, competitive dynamics and community assembly at the interface of native and introduced ranges. We investigated phyllosphere microbial communities, volatile organic compound (VOC) compositions, and potential interactions among introduced S. trilobata, native S. calendulacea and their hybrid in South China. S. trilobata exhibited higher α diversity but significantly different community composition compared to the native and hybrid groups. However, S. calendulacea and the hybrid shared certain microbial taxa, suggesting potential gene flow or co-existence. The potent antimicrobial VOC profile of S. trilobata, including unique compounds like p-cymene (13.33%), likely contributes to its invasion success. The hybrid's intermediate microbial and VOC profiles suggest possible consequences for species distribution, genetic exchange, and community assembly in heterogeneous environments. This hybrid deserves further study as both an opportunity for and threat to diversity maintenance. These differentiating yet connected plant groups provide insight into ecological and evolutionary dynamics shaping microbiome structure, species co-occurrence and competitive outcomes during biological exchange and habitat transformation. An interdisciplinary approach combining chemical and microbial ecology may reveal mechanisms underlying community stability and change, informing management of species spread in a globalized world.}, }
@article {pmid39061809, year = {2024}, author = {Hriňová, K and Dlapová, J and Kubala, B and Kormanová, &#x13d; and Levarski, Z and Struhárňanská, E and Turňa, J and Stuchlík, S}, title = {Production of Reverse Transcriptase and DNA Polymerase in Bacterial Expression Systems.}, journal = {Bioengineering (Basel, Switzerland)}, volume = {11}, number = {7}, pages = {}, pmid = {39061809}, issn = {2306-5354}, support = {APVV-17-0333//Slovak Research and Development Agency/ ; APVV-21-0215//Slovak Research and Development Agency/ ; APVV-21-0227//Slovak Research and Development Agency/ ; APVV-22-0161//Slovak Research and Development Agency/ ; }, abstract = {DNA amplification and reverse transcription enzymes have proven to be invaluable in fast and reliable diagnostics and research applications because of their processivity, specificity, and robustness. Our study focused on the production of mutant Taq DNA polymerase and mutant M-MLV reverse transcriptase in the expression hosts Vibrio natriegens and Escherichia coli under various expression conditions. We also examined nonspecific extracellular production in V. natriegens. Intracellularly, M-MLV was produced in V. natriegens at the level of 11% of the total cell proteins (TCPs) compared with 16% of TCPs in E. coli. We obtained a soluble protein that accounted for 11% of the enzyme produced in V. natriegens and 22% of the enzyme produced in E. coli. Taq pol was produced intracellularly in V. natriegens at the level of 30% of TCPs compared with 26% of TCPs in E. coli. However, Taq pol was almost non-soluble in E. coli, whereas in V. natriegens, we obtained a soluble protein that accounted for 23% of the produced enzyme. We detected substantial extracellular production of Taq pol. Thus, V. natriegens is a suitable alternative host with the potential for production of recombinant proteins.}, }
@article {pmid39060935, year = {2024}, author = {Baptista, MS and Lee, CK and Monteiro, MR and Torgo, L and Cary, SC and Magalhães, C}, title = {Soils of two Antarctic Dry Valleys exhibit unique microbial community structures in response to similar environmental disturbances.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {52}, pmid = {39060935}, issn = {2524-6372}, abstract = {BACKGROUND: Isolating the effects of deterministic variables (e.g., physicochemical conditions) on soil microbial communities from those of neutral processes (e.g., dispersal) remains a major challenge in microbial ecology. In this study, we disturbed soil microbial communities of two McMurdo Dry Valleys of Antarctica exhibiting distinct microbial biogeographic patterns, both devoid of aboveground biota and different in macro- and micro-physicochemical conditions. We modified the availability of water, nitrogen, carbon, copper ions, and sodium chloride salts in a laboratory-based experiment and monitored the microbial communities for up to two months. Our aim was to mimic a likely scenario in the near future, in which similar selective pressures will be applied to both valleys. We hypothesized that, given their unique microbial communities, the two valleys would select for different microbial populations when subjected to the same disturbances.<br><br>RESULTS: The two soil microbial communities, subjected to the same disturbances, did not respond similarly as reflected in both 16S rRNA genes and transcripts. Turnover of the two microbial communities showed a contrasting response to the same environmental disturbances and revealed different potentials for adaptation to change. These results suggest that the heterogeneity between these microbial communities, reflected in their strong biogeographic patterns, was maintained even when subjected to the same selective pressure and that the 'rare biosphere', at least in these samples, were deeply divergent and did not act as a reservoir for microbiota that enabled convergent responses to change in environmental conditions.<br><br>CONCLUSIONS: Our findings strongly support the occurrence of endemic microbial communities that show a structural resilience to environmental disturbances, spanning a wide range of physicochemical conditions. In the highly arid and nutrient-limited environment of the Dry Valleys, these results provide direct evidence of microbial biogeographic patterns that can shape the communities' response in the face of future environmental changes.}, }
@article {pmid39059201, year = {2024}, author = {Bai, X and Samari-Kermani, M and Schijven, J and Raoof, A and Dinkla, IJT and Muyzer, G}, title = {Enhancing slow sand filtration for safe drinking water production: interdisciplinary insights into Schmutzdecke characteristics and filtration performance in mini-scale filters.}, journal = {Water research}, volume = {262}, number = {}, pages = {122059}, doi = {10.1016/j.watres.2024.122059}, pmid = {39059201}, issn = {1879-2448}, mesh = {*Filtration ; *Drinking Water/microbiology ; *Water Purification/methods ; *Sand ; *Escherichia coli ; Silicon Dioxide/chemistry ; Biofilms ; }, abstract = {The demand for safe drinking water is constantly challenged by increasing biohazards. One widely used solution is implementing indoor-operated slow sand filtration (SSF) as one of the final barriers in water production. SSF has gained popularity due to its low energy consumption and efficient removal of biohazards, especially microorganisms, without using chemicals. SSF involves both physical-chemical and biological removal, particularly in the "Schmutzdecke", which is a biofilm-like layer on the sand bed surface. To achieve the optimal performance of SSF, a systematic understanding of the influence of SSF operating parameters on the Schmutzdecke development and filter filtration performance is required. Our study focused on three operational parameters, i.e., sand material, sand size, and the addition of an inoculum (suspension of matured Schmutzdecke), on the mini-scale filters. The effects of these parameters on the Schmutzdecke development and SSF removal performance were studied by biochemical analyses and 16S amplicon sequencing, together with spiking experiments with Escherichia coli (E. coli) in the mini-scale filters. Our results indicate that the mini-scale filters successfully developed Schmutzdeckes and generated bacterial breakthrough curves efficiently. The sand size and material were found to have an impact on Schmutzdecke's development. The addition of inoculum to new filters did not induce significant changes in the microbial community composition of the Schmutzdecke, but we observed positive effects of faster Schmutzdecke development and better removal performance in some inoculated filters. Our study highlights the value of mini-scale filters for SSF studies, which provide insights into Schmutzdecke microbial ecology and bacterial removal with significantly reduced requirements of materials and effort as compared to larger-scale filters. We found that operational parameters have a greater impact on the Schmutzdecke biochemical characteristics and removal performances than on the microbial community composition. This suggests that Schmutzdecke characteristics may provide more reliable predictors of SSF removal performance, which could help to improve safe drinking water production.}, }
@article {pmid39055957, year = {2024}, author = {Zhang, Y and Gan, G and Li, Y and Li, W and Jiang, Y and Wang, P and Hu, J and Wang, N and Quan, X and Liu, J and Raza, W and Xu, Y and Hohmann, P and Jousset, A and Wang, Y and Shen, Q and Jiang, G and Wei, Z}, title = {Exploring the temporal dynamics of a disease suppressive rhizo-microbiome in eggplants.}, journal = {iScience}, volume = {27}, number = {7}, pages = {110319}, pmid = {39055957}, issn = {2589-0042}, abstract = {The rhizosphere microbiome is important for plant health, yet their contributions to disease resistance and assembly dynamics remain unclear. This study employed rhizosphere microbiome transplantation (RMT) to delineate the impact of the rhizosphere microbiome and the immune response of eggplant (Solanum melongena) on resistance to bacterial wilt caused by Ralstonia solanacearum. We first identified disease-suppressive and disease-conducive rhizosphere microbiome in a susceptible tomato recipient. Using a non-destructive rhizobox and 16S rRNA amplicon sequencing, we monitored the dynamics of both microbiome types during the eggplant development. Most differences were observed at the early stage and then diminished over time. The suppressive microbiome maintained a higher proportion of initial community members throughout eggplant development and exhibited stronger deterministic processes in the early stage, underscoring the importance of plant selection in recruiting protective microbes for rhizosphere immunity. Our study sheds light on the development of microbiome-based strategies for plant disease management and resistance breeding.}, }
@article {pmid39052866, year = {2024}, author = {}, title = {Correction to: Alpine soil microbial ecology in a changing world.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {8}, pages = {}, doi = {10.1093/femsec/fiae085}, pmid = {39052866}, issn = {1574-6941}, }
@article {pmid39052865, year = {2024}, author = {Vuilleumier, S and Barthelmebs, L and Corcoll, N and Hery, M and G Karpouzas, D and Wick, LY}, title = {Editorial: thematic issue on microbial ecotoxicology.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {8}, pages = {}, pmid = {39052865}, issn = {1574-6941}, mesh = {*Ecotoxicology ; }, }
@article {pmid39051617, year = {2024}, author = {Pluym, T and Waegenaar, F and De Gusseme, B and Boon, N}, title = {Microbial drinking water monitoring now and in the future.}, journal = {Microbial biotechnology}, volume = {17}, number = {7}, pages = {e14532}, pmid = {39051617}, issn = {1751-7915}, support = {1S02022N//Fonds Wetenschappelijk Onderzoek/ ; 1S26823N//Fonds Wetenschappelijk Onderzoek/ ; S006221N//Fonds Wetenschappelijk Onderzoek/ ; }, mesh = {*Drinking Water/microbiology ; *Bacteria/genetics/isolation &amp; purification/classification ; Humans ; Water Microbiology ; Environmental Monitoring/methods ; }, abstract = {Over time, humanity has addressed microbial water contamination in various ways. Historically, individuals resorted to producing beer to combat the issue. Fast forward to the 19th century, and we witnessed a scientific approach by Robert Koch. His groundbreaking gelatine plating method aimed to identify and quantify bacteria, with a proposed limit of 100 colony-forming units per millilitre (CFU/mL) to avoid Cholera outbreaks. Despite considerable advancements in plating techniques through experimentation with media compositions and growth temperatures, the reliance on a century-old method for water safety remains the state-of-the-art. Even though most countries succeed in producing qualitative water at the end of the production centres, it is difficult to control, and guarantee, the same quality during distribution. Rather than focusing solely on specific sampling points, we propose a holistic examination of the entire water network to ensure comprehensive safety. Current practices leave room for uncertainties, especially given the low concentrations of pathogens. Innovative methods like flow cytometry and flow cytometric fingerprinting offer the ability to detect changes in the microbiome of drinking water. Additionally, molecular techniques and emerging sequencing technologies, such as third-generation sequencing (MinION), mark a significant leap forward, enhancing detection limits and emphasizing the identification of unwanted genes rather than the unwanted bacteria/microorganisms itself. Over the last decades, there has been the realization that the drinking water distribution networks are complex ecosystems that, beside bacteria, comprise of viruses, protozoans and even isopods. Sequencing techniques to find eukaryotic DNA are necessary to monitor the entire microbiome of the drinking water distribution network. Or will artificial intelligence, big data and machine learning prove to be the way to go for (microbial) drinking water monitoring? In essence, it is time to transcend century-old practices and embrace modern technologies to ensure the safety of our drinking water from production to consumption.}, }
@article {pmid39047455, year = {2024}, author = {Blair, MF and Vaidya, R and Salazar-Benites, G and Bott, CB and Pruden, A}, title = {Relating microbial community composition to treatment performance in an ozone-biologically active carbon filtration potable reuse treatment train.}, journal = {Water research}, volume = {262}, number = {}, pages = {122091}, doi = {10.1016/j.watres.2024.122091}, pmid = {39047455}, issn = {1879-2448}, mesh = {*Ozone ; *Water Purification/methods ; *Filtration ; Microbiota ; Charcoal/chemistry ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Treatment trains that couple ozone (O3) with biologically active carbon (BAC) filtration are of interest as a lower cost, more sustainable, membrane-free approach to water reuse. However, little is known about the microbial communities that are the fundamental drivers of O3-BAC treatment. The objective of this study was to demonstrate microbial community profiling as a diagnostic tool for assessing the functionality, biological stability, and resilience of coupled physical, chemical, advanced oxidative and biological processes employed in water reuse treatment. We utilized 16S rRNA gene amplicon sequencing to profile the bacterial microbiota over time throughout a potable reuse train employing coagulation, flocculation, sedimentation, ozonation, BAC filtration, granular activated carbon (GAC) adsorption, and UV disinfection. A distinct baseline microbiota was associated with each stage of treatment (ANOSIM, p < 0.05, r-stat = 0.52), each undergoing succession with time and operational shifts. Ozonation resulted in the sharpest shifts (i.e., 83.3 % average change in Genus level relative abundances, when adjusted O3:TOC ratio > 1), and also variance, in microbial community composition. Adjustment in O3:TOC ratios, temperature, filter-aid polymer, monochloramine quenching agent, and empty-bed contact time also resulted in measurable changes in the baseline microbial community composition of individual processes, but to a lesser degree. Of these, supplementation of nitrogen and phosphorus resulted in the strongest bifurcation, especially in the microbial communities inhabiting the BAC (ANOSIM: p < 0.05, BAC5 r-stat = 0.32; BAC10 r-stat = 0.54) and GAC (ANOSIM: p < 0.05, GAC10 r-stat = 0.54; GAC20 r-stat = 0.63) units. Additionally, we found that the BAC microbial community was responsive to an inoculation of microbially active media, which resulted in improved TOC removal. The findings of this study improve understanding of bacterial dynamics occurring in advanced water treatment trains and can inform improved system design and operation.}, }
@article {pmid39046569, year = {2024}, author = {Chen, X and Zhang, W and Geng, M and Shen, J and Wang, J}, title = {Carbon and Nutrient Limitations of Microbial Metabolism in Xingkai Lake, China: Abiotic and Biotic Drivers.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {97}, pmid = {39046569}, issn = {1432-184X}, support = {42230507//National Natural Science Foundation of China/ ; 42225708//National Natural Science Foundation of China/ ; }, mesh = {*Lakes/microbiology/chemistry ; China ; *Carbon/metabolism ; *Phosphorus/metabolism/analysis ; *Bacteria/metabolism/classification/genetics/isolation &amp; purification ; *Fungi/metabolism/classification ; *Nitrogen/metabolism ; *Geologic Sediments/microbiology ; *Microbiota ; Nutrients/metabolism/analysis ; }, abstract = {Microbial communities are crucial for water quality and biogeochemical cycling in freshwaters. Microbes secrete extracellular enzymes to decompose organic matter for their needs of nutrients and scarce elements. Yet, there is a lack of knowledge on microbial metabolic limitations in freshwaters, especially in lake sediments. Here, we examined the carbon, nitrogen, and phosphorus-acquiring extracellular enzyme activities and the bacterial and fungal communities of 30 sediments across Xingkai Lake, the largest freshwater lake in Northeast Asia. We further analyzed the microbial metabolic limitations via extracellular enzyme stoichiometry and explored the direct and indirect effects of abiotic and biotic factors on the limitations. We found that microbial metabolisms were primarily limited by phosphorus in Xingkai Lake. For instance, microbial carbon and phosphorus limitations were closely correlated to abiotic factors like water depth, total dissolved solids, sediment total carbon, and conductivity. The metabolic limitations were also affected by biotic factors, such as showing positive relationships with the alpha and beta diversity of bacteria, and with the beta diversity of fungi. In addition, community compositions of bacteria and fungi were mainly correlated to abiotic factors such as total carbon and dissolved organic carbon, respectively. Collectively, microbial metabolic limitations were affected directly or indirectly by abiotic factors and microbial communities. Our findings indicate that microbial metabolic limitations are not only driven by bacteria and fungi but also by abiotic factors such as water depth and total nitrogen, and thus provide empirical evidence for effective management of freshwater lakes under climate warming and intensified human activities.}, }
@article {pmid39046558, year = {2024}, author = {Xie, G and Sun, C and Gong, Y and Luo, W and Tang, X}, title = {Beyond the Bloom: Unraveling the Diversity, Overlap, and Stability of Free-Living and Particle-Attached Bacterial Communities in a Cyanobacteria-Dominated Hypereutrophic Lake.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {96}, pmid = {39046558}, issn = {1432-184X}, support = {WGKQ2022032//West Anhui University/ ; 41971062//National Natural Science Foundation of China/ ; }, mesh = {*Lakes/microbiology ; *Cyanobacteria/genetics/classification ; *Eutrophication ; *Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; *Biodiversity ; RNA, Ribosomal, 16S/genetics ; Seasons ; Ecosystem ; China ; }, abstract = {In aquatic ecosystems with low nutrient levels, organic aggregates (OAs) act as nutrient hotspots, hosting a diverse range of microbial species compared to those in the water column. Lake eutrophication, marked by intensified and prolonged cyanobacterial blooms, significantly impacts material and energy cycling processes, potentially altering the ecological traits of both free-living (FL) and particle-attached (PA) bacteria. However, the extent to which observed patterns of FL and PA bacterial diversity, community assembly, and stability extend to hypereutrophic lakes remains understudied. To address this gap, we investigated bacterial diversity, composition, assembly processes, and stability within hypereutrophic Lake Xingyun. Our results revealed that FL bacterial communities exhibited higher α-diversity than PA counterparts, coupled with discernible taxonomic compositions. Both bacterial communities showed distinct seasonality, influenced by cyanobacterial bloom intensity. Environmental factors accounted for 71.1% and 54.2% of the variation among FL and PA bacteria, respectively. The assembly of the PA bacterial community was predominantly stochastic, while FL assembly was more deterministic. The FL network demonstrated greater stability, complexity, and negative interactions, indicative of competitive relationships, while the PA network showed a prevalence of positive correlations, suggesting mutualistic interactions. Importantly, these findings differ from observations in oligotrophic, mesotrophic, and eutrophic lakes. Overall, this research provides valuable insights into the interplay among bacterial fractions, enhancing our understanding of nutrient status and cyanobacterial blooms in shaping bacterial communities.}, }
@article {pmid39046491, year = {2024}, author = {Soto-Cortés, E and Marroquín-Rodríguez, M and Basanta, MD and Maldonado-López, Y and Parra-Olea, G and Rebollar, EA}, title = {Host Species and Environment Shape the Skin Microbiota of Mexican Axolotls.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {98}, pmid = {39046491}, issn = {1432-184X}, support = {CF-2019/373914//CONAHCYT/ ; CF-2019/373914//CONAHCYT/ ; CF-2019/373914//CONAHCYT/ ; CF-2019/373914//CONAHCYT/ ; CF-2019/373914//CONAHCYT/ ; CF-2019/373914//CONAHCYT/ ; IN205521//PAPIIT/UNAM/ ; }, mesh = {Animals ; *Skin/microbiology ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; Mexico ; *Fungi/classification/isolation &amp; purification/genetics ; Ambystoma mexicanum/microbiology ; Host Specificity ; Environment ; Biodiversity ; }, abstract = {Skin microbiomes in amphibians are complex systems that can be influenced by biotic and abiotic factors. In this study, we examined the effect of host species and environmental conditions on the skin bacterial and fungal microbiota of four obligate paedomorphic salamander species, commonly known as axolotls (Ambystoma andersoni, A. dumerilii, A. mexicanum, and A. taylori), all of them endemic to the Trans-Mexican Volcanic Belt. We found that despite their permanent aquatic lifestyle, these species present a host-specific skin microbiota that is distinct from aquatic communities. We identified skin-associated taxa that were unique to each host species and that differentiated axolotl species based on alpha and beta diversity metrics. Moreover, we identified a set of microbial taxa that were shared across hosts with high relative abundances across skin samples. Specifically, bacterial communities were dominated by Burkholderiales and Pseudomonadales bacterial orders and Capnodiales and Pleosporales fungal orders. Host species and environmental variables collectively explained more microbial composition variation in bacteria (R2 = 0.46) in comparison to fungi (R2 = 0.2). Our results contribute to a better understanding of the factors shaping the diversity and composition of skin microbial communities in Ambystoma. Additional studies are needed to disentangle the effects of specific host associated and environmental factors that could influence the skin microbiome of these endangered species.}, }
@article {pmid39043275, year = {2024}, author = {Fernández-Blanco, C and Pereira, A and Veiga, MC and Kennes, C and Ganigué, R}, title = {Comprehensive comparative study on n-caproate production by Clostridium kluyveri: batch vs. continuous operation modes.}, journal = {Bioresource technology}, volume = {408}, number = {}, pages = {131138}, doi = {10.1016/j.biortech.2024.131138}, pmid = {39043275}, issn = {1873-2976}, mesh = {*Ethanol/metabolism ; *Clostridium kluyveri/metabolism ; *Caproates/metabolism ; Batch Cell Culture Techniques ; Bioreactors ; Fermentation ; Acetates/metabolism ; Oxidation-Reduction ; }, abstract = {Recently, there has been notable interest in researching and industrially producing medium-chain carboxylic acids (MCCAs) like n-caproate and n-caprylate via chain elongation process. This study presents a comprehensive assessment of the behavior and MCCA production profiles of Clostridium kluyveri in batch and continuous modes, at different ethanol:acetate molar ratios (1.5:1, 3.5:1 and 5.5:1). The highest n-caproate concentration, 12.9 ± 0.67 g/L (92.9 ± 1.39 % MCCA selectivity), was achieved in batch mode at a 3.5:1 ratio. Interestingly, higher ratios favored batch mode selectivity over continuous mode when this was equal or higher to 3.5:1. Steady state operation yielded the highest n-caproate (9.5 ± 0.13 g/L) and n-caprylate (0.35 ± 0.020 g/L) concentrations at the 3.5:1 ratio. Increased ethanol:acetate ratios led to a higher excessive ethanol oxidation (EEO) in both operational modes, potentially limiting n-caproate production and selectivity, especially at the 5.5:1 ratio. Overall, this study reports the efficient MCCA production of both batch and continuous modes by C. kluyveri.}, }
@article {pmid39043163, year = {2024}, author = {DeWitt, ME and Sanders, JW}, title = {Tropical Diseases in the United States: Beyond Poverty - Advancing an Ecological Framework in Tropical Medicine.}, journal = {The American journal of tropical medicine and hygiene}, volume = {111}, number = {3}, pages = {449-451}, pmid = {39043163}, issn = {1476-1645}, mesh = {*Tropical Medicine ; Humans ; *Poverty ; United States/epidemiology ; }, }
@article {pmid39039555, year = {2024}, author = {Wang, D and Liu, L and Xu, X and Wang, C and Wang, Y and Deng, Y and Zhang, T}, title = {Distributions, interactions, and dynamics of prokaryotes and phages in a hybrid biological wastewater treatment system.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {134}, pmid = {39039555}, issn = {2049-2618}, mesh = {*Bacteriophages/genetics/classification/physiology/isolation &amp; purification ; *Sewage/virology/microbiology ; *Wastewater/virology/microbiology ; *Bacteria/virology/genetics/classification ; Biofilms ; Metagenomics ; Water Purification/methods ; Microbiota ; }, abstract = {BACKGROUND: Understanding the interactions and dynamics of microbiotas within biological wastewater treatment systems is essential for ensuring their stability and long-term sustainability. In this study, we developed a systematic framework employing multi-omics and Hi-C sequencing to extensively investigate prokaryotic and phage communities within a hybrid biofilm and activated sludge system.<br><br>RESULTS: We uncovered distinct distribution&#xa0;patterns, metabolic capabilities, and activities of functional prokaryotes through the analysis of 454 reconstructed prokaryotic genomes. Additionally, we reconstructed a phage catalog comprising 18,645 viral operational taxonomic units (vOTUs) with high length and contiguity using hybrid assembly, and a distinct distribution of phages was depicted between activated sludge (AS) and biofilm. Importantly, 1340 host-phage pairs were established using Hi-C and conventional in silico methods, unveiling the host-determined phage prevalence. The majority of predicted hosts were found to be involved in various crucial metabolic processes, highlighting the potential vital roles of phages in influencing substance metabolism within this system. Moreover, auxiliary metabolic genes (AMGs) related to various categories (e.g., carbohydrate degradation, sulfur metabolism, transporter) were predicted. Subsequent activity analysis emphasized their potential ability to mediate host metabolism during infection. We also profiled the temporal dynamics of phages and their associated hosts using 13-month time-series metagenomic data, further demonstrating their tight interactions. Notably, we observed lineage-specific infection patterns, such as&#xa0;potentially host abundance- or phage/host ratio-driven phage population changes.<br><br>CONCLUSIONS: The insights gained from this research contribute to the growing body of knowledge surrounding interactions and dynamics of host-phage and pave the way for further exploration and potential applications in the field of microbial ecology. Video Abstract.}, }
@article {pmid39039015, year = {2024}, author = {Vanharanta, M and Santoro, M and Villena-Alemany, C and Piiparinen, J and Piwosz, K and Grossart, HP and Labrenz, M and Spilling, K}, title = {Microbial remineralization processes during postspring-bloom with excess phosphate available in the northern Baltic Sea.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {8}, pages = {}, pmid = {39039015}, issn = {1574-6941}, support = {731065//European Commission/ ; 2021/03/Y/NZ8/00076//National Science Centre, Poland/ ; GR1540/37-1//DFG/ ; }, mesh = {*Seawater/microbiology/chemistry ; *Phosphates/metabolism ; *Bacteria/metabolism/genetics/growth &amp; development ; *Phosphorus/metabolism ; *Carbon/metabolism ; *Nitrogen/metabolism ; Finland ; Oceans and Seas ; Eutrophication ; Heterotrophic Processes ; }, abstract = {The phosphorus (P) concentration is increasing in parts of the Baltic Sea following the spring bloom. The fate of this excess P-pool is an open question, and here we investigate the role of microbial degradation processes in the excess P assimilation phase. During a 17-day-long mesocosm experiment in the southwest Finnish archipelago, we examined nitrogen, phosphorus, and carbon acquiring extracellular enzyme activities in three size fractions (<0.2, 0.2-3, and >3 µm), bacterial abundance, production, community composition, and its predicted metabolic functions. The mesocosms received carbon (C) and nitrogen (N) amendments individually and in combination (NC) to distinguish between heterotrophic and autotrophic processes. Alkaline phosphatase activity occurred mainly in the dissolved form and likely contributed to the excess phosphate conditions together with grazing. At the beginning of the experiment, peptidolytic and glycolytic enzymes were mostly produced by free-living bacteria. However, by the end of the experiment, the NC-treatment induced a shift in peptidolytic and glycolytic activities and degradation of phosphomonoesters toward the particle-associated fraction, likely as a consequence of higher substrate availability. This would potentially promote retention of nutrients in the surface as opposed to sedimentation, but direct sedimentation measurements are needed to verify this hypothesis.}, }
@article {pmid39030648, year = {2024}, author = {Moretti, LG and Crusciol, CAC and Leite, MFA and Momesso, L and Bossolani, JW and Costa, OYA and Hungria, M and Kuramae, EE}, title = {Diverse bacterial consortia: key drivers of rhizosoil fertility modulating microbiome functions, plant physiology, nutrition, and soybean grain yield.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {50}, pmid = {39030648}, issn = {2524-6372}, support = {2016/23699-8; 2018/14892-4//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 151120/2020-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, abstract = {Soybean cultivation in tropical regions relies on symbioses with nitrogen-fixing Bradyrhizobium and plant growth-promoting bacteria (PGPBs), reducing environmental impacts of N fertilizers and pesticides. We evaluate the effects of soybean inoculation with different bacterial consortia combined with PGPBs or microbial secondary metabolites (MSMs) on rhizosoil chemistry, plant physiology, plant nutrition, grain yield, and rhizosphere microbial functions under field conditions over three growing seasons with four treatments: standard inoculation of Bradyrhizobium japonicum and Bradyrhizobium diazoefficiens consortium (SI); SI plus foliar spraying with Bacillus subtilis (SI + Bs); SI plus foliar spraying with Azospirillum brasilense (SI + Az); and SI plus seed application of MSMs enriched in lipo-chitooligosaccharides extracted from B. diazoefficiens and Rhizobium tropici (SI + MSM). Rhizosphere microbial composition, diversity, and function was assessed by metagenomics. The relationships between rhizosoil chemistry, plant nutrition, grain yield, and the abundance of microbial taxa and functions were determined by generalized joint attribute modeling. The bacterial consortia had the most significant impact on rhizosphere soil fertility, which in turn affected the bacterial community, plant physiology, nutrient availability, and production. Cluster analysis identified microbial groups and functions correlated with shifts in rhizosoil chemistry and plant nutrition. Bacterial consortia positively modulated specific genera and functional pathways involved in biosynthesis of plant secondary metabolites, amino acids, lipopolysaccharides, photosynthesis, bacterial secretion systems, and sulfur metabolism. The effects of the bacterial consortia on the soybean holobiont, particularly the rhizomicrobiome and rhizosoil fertility, highlight the importance of selecting appropriate consortia for desired outcomes. These findings have implications for microbial-based agricultural practices that enhance crop productivity, quality, and sustainability.}, }
@article {pmid39030520, year = {2024}, author = {Joo, M and Nam, S}, title = {Adolescent gut microbiome imbalance and its association with immune response in inflammatory bowel diseases and obesity.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {268}, pmid = {39030520}, issn = {1471-2180}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Adolescent ; *RNA, Ribosomal, 16S/genetics ; *Obesity/microbiology/immunology ; Female ; Male ; *Bacteria/classification/genetics/isolation &amp; purification ; *Phylogeny ; Inflammatory Bowel Diseases/microbiology/immunology ; Crohn Disease/microbiology/immunology ; Colitis, Ulcerative/microbiology/immunology ; Dysbiosis/microbiology ; Prevotella/genetics/classification/isolation &amp; purification ; Faecalibacterium prausnitzii/genetics ; Feces/microbiology ; }, abstract = {BACKGROUND: Recently, there has been an increase in the number of studies focusing on the association between the gut microbiome and obesity or inflammatory diseases, especially in adults. However, there is a lack of studies investigating the association between gut microbiome and gastrointestinal (GI) diseases in adolescents.<br><br>METHOD: We obtained 16S rRNA-seq datasets for gut microbiome analysis from 202 adolescents, comprising ulcerative colitis (UC), Crohn's disease (CD), obesity (Ob), and healthy controls (HC). We utilized Quantitative Insights Into Microbial Ecology (QIIME) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) to acquire Operational Taxonomic Units (OTUs). Subsequently, we analyzed Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology (KO) terms and pathway enrichment for the identified OTUs.<br><br>RESULTS: In this study, we investigated the difference between the gut microbiomes in adolescents with GI diseases and those in healthy adolescents using 202 samples of 16S rRNA sequencing data. The distribution of the six main gut microbiota (i.e., unclassified Dorea, unclassified Lachnospiraceae, unclassified Ruminococcus, Faecalibacterium prausnitzii, Prevotella copri, unclassified Sutterella) was different based on the status of obesity and inflammatory diseases. Dysbiosis was observed within Lachnospiraceae in adolescents with inflammatory diseases (i.e., UC and CD), and in adolescents with obesity within Prevotella and Sutterella. More specifically, our results showed that the relative abundance of Faecalibacterium prausnitzii and unclassified Lachnospiraceae was more than 10% and 8% higher, respectively, in the UC group compared to the CD, Ob, and HC groups. Additionally, the Ob group had over 20% and over 3% higher levels of Prevotella copri and unclassified Sutterella, respectively, compared to the UC, CD, and HC groups. Also, inspecting associations between the six specific microbiota and KO terms, we found that the six microbiota -relating KO terms were associated with NOD-like receptor signaling. These six taxa differences may affect the immune system and inflammatory response by affecting NOD-like receptor signaling in the host during critical adolescence.<br><br>CONCLUSION: In this study, we discovered that dysbiosis of the microbial community had varying degrees of influence on the inflammatory and immune response pathways in adolescents with inflammatory diseases and obesity.}, }
@article {pmid39030408, year = {2024}, author = {Gilbert, JA and Hartmann, EM}, title = {The indoors microbiome and human health.}, journal = {Nature reviews. Microbiology}, volume = {22}, number = {12}, pages = {742-755}, pmid = {39030408}, issn = {1740-1534}, mesh = {Humans ; *Microbiota ; Air Microbiology ; Air Pollution, Indoor ; Built Environment ; }, abstract = {Indoor environments serve as habitat for humans and are replete with various reservoirs and niches for microo