@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 & 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.},
}

*Selenium/metabolism/toxicity
*Bacteria/metabolism/drug effects/growth & development
*Stress, Physiological
*Microbial Interactions
Oxidative Stress
Metals, Heavy/metabolism/toxicity
*Bacterial Physiological Phenomena

@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.},
}

*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

@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.},
}

*Surface-Active Agents/metabolism/chemistry
*Fungi/metabolism/genetics
*Bacteria/metabolism/genetics
Biosynthetic Pathways
Yeasts/metabolism
Biosurfactants

@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 & 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.},
}

*Gastrointestinal Microbiome/physiology
Humans
*Dyslipidemias/microbiology/therapy/metabolism/etiology
Homeostasis
*Lipid Metabolism
Animals
Fecal Microbiota Transplantation
Probiotics/therapeutic use
Prebiotics/administration & dosage
Dysbiosis/microbiology/therapy

@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'.},
}

*Pseudomonas aeruginosa/virology/genetics
*CRISPR-Cas Systems
*Pseudomonas Phages/physiology/genetics
*Nutrients/metabolism
*Bacteriophages/physiology

@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'.},
}

*Bacteriophages/physiology/genetics
*Vibrio/virology/immunology/genetics
*Biological Evolution
Host Specificity
Interspersed Repetitive Sequences
Animals

@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 & 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'.},
}

*Pseudomonas aeruginosa/virology/growth & development/genetics
*CRISPR-Cas Systems
*Pseudomonas Phages/physiology
*SOS Response, Genetics
*Bacteriophages/physiology

@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.},
}

Animals
Colombia
*Virome/genetics
*Culicidae/virology
*Metagenomics/methods
*Metagenome
Phylogeny
*Insect Viruses/genetics/classification

@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 & purification ; *Fungi/genetics/classification/isolation & 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.

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.

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.

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.},
}

*Rivers/microbiology
*Geologic Sediments/microbiology
*Bacteria/genetics/classification/isolation & purification
*Fungi/genetics/classification/isolation & purification
Biodiversity
RNA, Ribosomal, 16S/genetics
*Water Microbiology
*Microbiota

@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.},
}

*Type VI Secretion Systems/genetics/metabolism/physiology
*Plants/microbiology
*Bacteria/genetics/metabolism/pathogenicity
Biological Evolution
*Plant Diseases/microbiology
Virulence
Bacterial Proteins/metabolism/genetics

@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 & development/physiology ; *Seaweed/chemistry ; *Fruit/drug effects/growth & development/physiology ; Ascophyllum/chemistry ; Plant Leaves/drug effects/growth & 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.},
}

*Vitis/drug effects/growth & development/physiology
*Seaweed/chemistry
*Fruit/drug effects/growth & development/physiology
Ascophyllum/chemistry
Plant Leaves/drug effects/growth & development
Climate

@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 & purification ; *Eukaryota/classification/genetics/isolation & 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.},
}

Ohio
*Fagus/microbiology
Fungi/genetics/classification/isolation & purification
*Eukaryota/classification/genetics/isolation & purification
*Rain
RNA, Ribosomal, 18S/genetics
Seasons
Trees/microbiology
Biodiversity
Forests
*Microbiota

@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 & 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.},
}

*Sewage/microbiology/chemistry
*Bacteria/genetics/classification/isolation & purification/metabolism
Metagenomics
*Water Pollutants, Chemical/analysis
Microbiota
Metals, Heavy/analysis
Industrial Waste/analysis

@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.

METHODS: We systematically evaluated SCP's impact on neuromotor function and cognitive performance in physiologically aged C57BL/6 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&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.

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.

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 & control ; Rhizosphere ; Soil Microbiology ; *Lysobacter/physiology ; *Microbial Consortia/physiology ; Microbial Interactions ; Biofilms/growth & 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.},
}

*Cucumis sativus/microbiology
*Fusarium/physiology
*Bacillus/physiology
*Plant Diseases/microbiology/prevention & control
Rhizosphere
Soil Microbiology
*Lysobacter/physiology
*Microbial Consortia/physiology
Microbial Interactions
Biofilms/growth & development

@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 & 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.},
}

*beta-Lactamases/genetics
*Methyltransferases/genetics
*Interspersed Repetitive Sequences
*Enterobacteriaceae/genetics/drug effects/isolation & 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

@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 & development/metabolism/classification ; *Eutrophication ; *Bays/microbiology/chemistry ; *Carbon/metabolism ; Diatoms/growth & development/metabolism ; Ecosystem ; Seasons ; *Carbon Cycle ; Dinoflagellida/growth & 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.},
}

*Phytoplankton/growth & development/metabolism/classification
*Eutrophication
*Bays/microbiology/chemistry
*Carbon/metabolism
Diatoms/growth & development/metabolism
Ecosystem
Seasons
*Carbon Cycle
Dinoflagellida/growth & development
Seawater/chemistry

@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, Í 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.},
}

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

@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.

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.

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.

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, Š 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, Á 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//Universität 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//Grantová Agentura České Republiky (Grant Agency of the Czech Republic)/ ; 22-03662S//Grantová Agentura České Republiky (Grant Agency of the Czech Republic)/ ; 25-15813S//Grantová Agentura České Republiky (Grant Agency of the Czech Republic)/ ; 20-12496X//Grantová Agentura České Republiky (Grant Agency of the Czech Republic)/ ; 21-21990S//Grantová Agentura České Republiky (Grant Agency of the Czech Republic)/ ; 022/2019/P//Jihočeská Univerzita v Českých Budějovicích (University of South Bohemia in České Budějovice)/ ; 017/2022/P//Jihočeská Univerzita v Českých Budějovicích (University of South Bohemia in České Budějovice)/ ; },
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.},
}

Animals
*Pollination
Bees/physiology
*Pollen/chemistry
*Nutrients
Feeding Behavior
Seasons

@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 & purification/physiology ; *Fungi/genetics/classification/isolation & 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.},
}

Arctic Regions
*Hepatophyta/microbiology
*Cyanobacteria/genetics/classification/isolation & purification/physiology
*Fungi/genetics/classification/isolation & purification
*Genetic Variation
Symbiosis
Soil Microbiology
Phylogeny
Nitrogen Fixation

@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.

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&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.},
}

Animals
*Manure
*Drug Resistance, Microbial/genetics
*Snails/microbiology
Humans
Introduced Species
Gastrointestinal Microbiome
Soil Microbiology
Environmental Monitoring
RNA, Ribosomal, 16S
Feces/microbiology

@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.},
}

*Gastrointestinal Microbiome/physiology
Humans
*Precision Medicine
Diet
Dietary Fiber
Animals
Metabolic Diseases/microbiology
Inflammation

@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, Á 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/ ; EKÖP- 24- VI/MATE-3//Ministry for Culture and Innovation from the source of the National Research, Development and Innovation Fund/ ; EKÖP-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.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Soil Microbiology
*Plants/microbiology
Soil/chemistry
Ecosystem
Animals

@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 & development ; *Fusarium/growth & development/drug effects/physiology ; *Bacillus subtilis/physiology/metabolism ; *Rhizosphere ; *Plant Diseases/microbiology/prevention & 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.},
}

*Triticum/microbiology/growth & development
*Fusarium/growth & development/drug effects/physiology
*Bacillus subtilis/physiology/metabolism
*Rhizosphere
*Plant Diseases/microbiology/prevention & control
*Microbiota
Soil Microbiology
Plant Roots/microbiology
Endophytes/physiology
Fungicides, Industrial/pharmacology

@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 & 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 & 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 & 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).

METHODS: Participants aged an average of 72.3 years underwent the profiling of cognitive function, amyloid-β (Aβ) deposition, apolipoprotein E (APOE) genetic variants, depression status, nutrition, and lifestyles. Human fecal bacterial FASTA/Q data (SCD, n = 24; MCI, n = 246; AD, n = 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.

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, Aβ deposition, APOE status, and cognitive scores.

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.

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 & 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.},
}

Humans
*Bacteriophages/physiology
*Phage Therapy/methods
*Mouth/microbiology/virology
*Oral Health
Biofilms/growth & development
Microbiota
*Bacteria/virology
*Periodontal Diseases/therapy/microbiology

@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.},
}

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

@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.},
}

*Graft vs Host Disease/microbiology/therapy
Humans
*Microbiota
Hematopoietic Stem Cell Transplantation
Animals
*Ecosystem
Fecal Microbiota Transplantation
Dysbiosis

@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.

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.},
}

*Biotechnology/methods
*Microalgae/metabolism
*Carbon Sequestration
*Bacteria/metabolism
Carbon Dioxide/metabolism
Photosynthesis
Carbon/metabolism

@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 & 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 & 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.},
}

Biofilms/growth & 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

@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.},
}

Metagenome
*Ecosystem
*Microbiota

@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.},
}