@article {pmid40610473,
year = {2025},
author = {Ivanova, EA and Suleymanov, AR and Nikitin, DA and Semenov, MV and Abakumov, EV},
title = {Machine learning-based mapping of Acidobacteriota and Planctomycetota using 16 S rRNA gene metabarcoding data across soils in Russia.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {23763},
pmid = {40610473},
issn = {2045-2322},
support = {24-44-00006//Russian Science Support Foundation/ ; 24-44-00006//Russian Science Support Foundation/ ; },
mesh = {*Machine Learning ; *Soil Microbiology ; *RNA, Ribosomal, 16S/genetics ; Russia ; *DNA Barcoding, Taxonomic/methods ; Soil/chemistry ; Microbiota/genetics ; *Acidobacteria/genetics/classification ; Ecosystem ; },
abstract = {The soil microbiome plays a crucial role in maintaining healthy ecosystems and supporting sustainable agriculture. Studying its biogeographical structure and distribution is essential for understanding the rates and mechanisms of microbially mediated soil ecosystem services. This study aimed to investigate the spatial distribution patterns of Acidobacteriota and Planctomycetota across soils in Russia, summarizing data from 16S rRNA gene metabarcoding of topsoils. A machine learning approach (Random Forest) was employed to generate digital distribution maps using climatic, topographic, vegetation, geological, and soil variables. Model interpration was performed using variable importance assessment and Shapley values. According to the error metrics, the Acidobacteriota model achieved a root mean squared error (RMSE) of 6.67% and an R[2] of 0.41, while the Planctomycetota model achieved an RMSE of 2.04% and an R[2] of 0.46. Both phyla exhibited similar spatial distribution patterns, with relative abundance decreasing from North to South. For Acidobacteriota, vegetation cover, surface temperature, and soil pH were significant predictors, whereas the relative abundance of Planctomycetota was mainly influenced by climatic variables. Specifically, Acidobacteriota were more abundant in areas with dense vegetation, stable surface temperatures, and acidic soils. In contrast, Planctomycetota showed reduced abundance in regions with higher levels of precipitable water vapor. These results highlight the potential of machine learning techniques to visualize predictive biogeographic patterns in soil microbial taxa abundance at the phylum level. Despite limitations related to the heterogeneous nature of source data, focusing on higher taxonomic ranks less sensitive to methodological variation enabled to identify preliminary large-scale distribution trends of microbial phyla in soils.},
}

*Machine Learning
*Soil Microbiology
*RNA, Ribosomal, 16S/genetics
Russia
*DNA Barcoding, Taxonomic/methods
Soil/chemistry
Microbiota/genetics
*Acidobacteria/genetics/classification
Ecosystem

@article {pmid40607773,
year = {2025},
author = {Tao, Y and Liu, D and Shi, Q and Sun, Q and Liu, C and Zeng, X},
title = {Lead exposure in relation to gut homeostasis, microbiota, and metabolites.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0037225},
doi = {10.1128/aem.00372-25},
pmid = {40607773},
issn = {1098-5336},
abstract = {Lead (Pb) is a hazardous heavy metal with no known safe threshold for exposure or consumption, posing significant risks to human health. Pb exposure can cause multiple system damage, depending on exposure levels, duration, and its high bioavailability and bioaccumulative potential. Gastrointestinal tract serves as a primary site for Pb absorption, making it particularly vulnerable to Pb-induced damage, including disruption of gut microbiota composition and metabolic function. This study briefly summarizes the detrimental effects of Pb gut homeostasis, microbial ecology, and host metabolism, which, in turn, further contribute to systemic toxicity. Notably, Pb exposure compromises intestinal barrier integrity, increasing gut permeability and facilitating the translocation of harmful biomolecules into systemic circulation, thereby exacerbating organ dysfunction. Importantly, we underscore that dietary and nutritional interventions such as fiber, probiotic, and vitamin C supplementation is a practicable and effective strategy for mitigating or preventing Pb toxicity.},
}

@article {pmid40606160,
year = {2025},
author = {Al-Khlifeh, E and Khadem, S and Hausmann, B and Berry, D},
title = {Corrigendum: Microclimate shapes the phylosymbiosis of rodent gut microbiota in Jordan's Great Rift Valley.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1639190},
doi = {10.3389/fmicb.2025.1639190},
pmid = {40606160},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2023.1258775.].},
}

@article {pmid40605266,
year = {2025},
author = {Herman, C and Barker, BM and Bartelli, TF and Chandra, V and Krajmalnik-Brown, R and Jewell, M and Li, L and Liao, C and McAllister, F and Nirmalkar, K and Xavier, JB and Caporaso, JG},
title = {A review of engraftment assessments following fecal microbiota transplant.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2525478},
doi = {10.1080/19490976.2025.2525478},
pmid = {40605266},
issn = {1949-0984},
mesh = {*Fecal Microbiota Transplantation ; Humans ; *Gastrointestinal Microbiome ; *Clostridium Infections/therapy/microbiology ; Clostridioides difficile/physiology ; Animals ; Feces/microbiology ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Fecal Microbiota Transplant (FMT) is a treatment for recurrent Clostridium difficile infections and is being explored for other clinical applications, from alleviating digestive and neurological disorders, to restoring microbiomes impacted by cancer treatment. Quantifying the extent of engraftment following an FMT is important in understanding a recipient's response to treatment. Engraftment and clinical response need to be investigated independently to evaluate an FMT's role (or lack thereof) in achieving a clinical response. Standardized bioinformatics methodologies for quantifying engraftment extent would not only improve assessment and understanding of FMT outcomes, but also facilitate comparison of FMT results and protocols across studies. Here we review FMT studies, integrating three concepts from microbial ecology as framework to discuss how these studies approached assessing engraftment extent: 1) Community Coalescence investigates microbiome shifts following FMT engraftment, 2) Indicator Features tracks specific microbiome features as a signal of engraftment, and 3) Resilience examines how resistant post-FMT recipients' microbiomes are to reverting back to baseline. These concepts explore subtly different questions about the microbiome following FMT. Taken together, they provide holistic insight into how an FMT alters a recipient's microbiome composition and provide a clear framework for quantifying and communicating about microbiome engraftment.},
}

*Fecal Microbiota Transplantation
Humans
*Gastrointestinal Microbiome
*Clostridium Infections/therapy/microbiology
Clostridioides difficile/physiology
Animals
Feces/microbiology
Bacteria/classification/genetics/isolation & purification

@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 {pmid40602916,
year = {2025},
author = {Puche, E and Roger, B and Vargas-Sánchez, M and Sánchez-Carrillo, S and Rodrigo, MA},
title = {Freshwater macrophyte type (macroalgae versus phanerogams) mainly determines detritus-derived greenhouse gases production: A microcosm experiment.},
journal = {Journal of environmental sciences (China)},
volume = {157},
number = {},
pages = {674-689},
doi = {10.1016/j.jes.2025.01.015},
pmid = {40602916},
issn = {1001-0742},
mesh = {*Greenhouse Gases/analysis/metabolism ; *Seaweed ; Ecosystem ; Methane/analysis ; Fresh Water ; Carbon Dioxide/analysis ; Eutrophication ; *Environmental Monitoring ; *Air Pollutants/analysis ; },
abstract = {Freshwater ecosystems are crucial in the global emissions of greenhouse gases (GHGs) such as CH4. Macrophytes are the main organic matter (i.e., detritus) supplier to the sediment of these systems, thus controlling CH4 production. However, species-specific differences (structure and composition) may determine contrasting patterns of detritus transformation into CH4. Furthermore, eutrophication can affect the degradation and, consequently, CH4 production. We performed a 64-day microcosm experiment with anoxic incubations of detritus from seven phylogenetically different macrophytes (two charophytes, filamentous algae -Spirogyra, Cladophora-, three submerged plants and an amphibious one), under two trophic conditions (oligo- versus eutrophic) and with/without sediment. We assessed the CH4 and CO2 production and the changes in the detritus quality at the end of the experiment. The ranking in the mean cumulative CH4 production was: Chara hispida > Nitella hyalina > Najas marina ≈ Teucrium scordium > Stuckenia pectinata ≈ Myriophyllum spicatum > filamentous algae, and it was related to the detritus quality. GHGs maximum production rates were 1.6 (N. marina)-1.2 (C. hispida) mmol CH4/(g OC·day) and 1.7 (N. marina)-1.5 (C. hispida) mmol CO2/(g OC·day). The CO2:CH4 ratio was biased towards CO2 during the first 10 days (average ratio of 200) and fell afterwards to about 1 for all macrophyte species and treatments. The sediment favored detritus decomposition (probably due to the "positive priming effect"), increasing GHGs production. The influence of nutrient enrichment was not evident. Delving into the macrophyte detritus quality-GHGs production relationship is needed to forecast the GHGs emissions in macrophyte-dominated systems.},
}

*Greenhouse Gases/analysis/metabolism
*Seaweed
Ecosystem
Methane/analysis
Fresh Water
Carbon Dioxide/analysis
Eutrophication
*Environmental Monitoring
*Air Pollutants/analysis

@article {pmid40602642,
year = {2025},
author = {Pieńkowska, A and Fleischmann, J and Drabesch, S and Merbach, I and Wang, G and Rocha, U and Reitz, T and Marie Muehe, E},
title = {Long-term organic fertilization shields soil prokaryotes from metal stress while mineral fertilization exacerbates it.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {382},
number = {},
pages = {126747},
doi = {10.1016/j.envpol.2025.126747},
pmid = {40602642},
issn = {1873-6424},
abstract = {Metal contamination in agricultural soils threatens prokaryote dynamics essential for soil health and crop productivity. Yet, whether fertilization in the long-run affects their resilience to metals remains unclear. This study examined the biogeochemical impacts of realistically low-dose applications of cadmium, zinc, and lead in soils subjected to 119 years of non-fertilization, mineral-fertilization (NPK), organic-fertilization (manure), or combined mineral-organic fertilization. Amended metals remained in the mobile fraction with the order: mineral < unfertilized < mineral + organic < organic, mirroring the effects on soil prokaryotes. In both unfertilized and mineral-fertilized soils, 16S rRNA gene copy numbers declined by 30 % upon metal addition, but recovery timing differed: in unfertilized soil, recovery began after three days, whereas in mineral-fertilized soil, numbers declined until day seven before recovering. This coincided with an increase in metal-resistant taxa, particularly in mineral-fertilized soil, with 10 significantly affected OTUs, and to a lesser extent in unfertilized soil, with 5 affected OTUs. Carbon-, nitrogen-, and phosphorus-mining enzyme activities increased 50-100 % in mineral-fertilized soils, suggesting enhanced nutrient acquisition to mitigate metal toxicity. In contrast, organic-fertilized soil hosted stable enzymatic activities and microbial copy numbers with minimal community shifts (1 affected OTU), indicating greater resistance to metal amendment. Combined mineral-organic fertilization stabilized copy numbers and enzymatic activity upon metal amendment, but 8 OTUs were affected, including specialized nutrient cyclers, suggesting increased availability of previously adsorbed NPK cations. Our findings indicate that organic fertilization shields prokaryotes from metal stress, while mineral fertilization exacerbates it, highlighting the benefits of organic practices for maintaining soil health and productivity.},
}

@article {pmid40602621,
year = {2025},
author = {Zhang, Z and Yuan, G and Turgun, X and Turgun, Z and Hou, L and Ye, M and Wang, Y and Xu, X},
title = {Biogeographic Patterns and Ecological Roles of Microorganisms in Sediments Along an Estuarine Salinity Gradient.},
journal = {Environmental microbiology reports},
volume = {17},
number = {4},
pages = {e70139},
doi = {10.1111/1758-2229.70139},
pmid = {40602621},
issn = {1758-2229},
support = {2023A1515110368//Guangdong Basic and Applied Basic Research Foundation/ ; XJNUZBS2423//Doctoral Research Foundation of Xinjiang Normal University/ ; 42361144846 and 42461006//National Natural Science Foundation of China/ ; //Tianchi Talents (Xinjiang) Plan Project (Young Doctor)/ ; },
mesh = {*Geologic Sediments/microbiology/chemistry ; *Salinity ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Estuaries ; China ; Biodiversity ; Microbiota ; Ecosystem ; Metagenome ; Phylogeny ; },
abstract = {The distribution patterns and driving mechanisms of microbial biogeographic patterns are fundamental questions in microbiology. This study analysed and compared the bacterial biogeographic patterns in the coastal environment, focusing on the Yangtze Estuary and its adjacent coastal zone. The purpose is to explore the driving mechanisms under spatial distribution, the community assembly processes and potential functions. Our results revealed that the sediment bacterial community structure exhibited a distinct geographical pattern and was significantly influenced by environmental factors. The microbial community displayed a non-random co-occurrence pattern, and the biogeographic patterns were shaped not only by environmental constraints (deterministic processes) but also by stochastic processes resulting from dispersal limitation. The metagenome sequencing analysis revealed a pronounced salinity gradient in the nitrogen-cycling function of the bacterial community. This functional difference appears to be driven by microbial diversity changes from the estuarine region to the ocean, highlighting the key role of microbial ecological characteristics. The findings of this study contribute to a deeper understanding of microbial ecology in estuarine environments, emphasizing the complex interplay between environmental factors and microbial community dynamics in shaping the function of estuarine sediment bacterial communities.},
}

*Geologic Sediments/microbiology/chemistry
*Salinity
*Bacteria/classification/genetics/isolation & purification/metabolism
Estuaries
China
Biodiversity
Microbiota
Ecosystem
Metagenome
Phylogeny

@article {pmid40602574,
year = {2025},
author = {Mu, D and Chen, Q and Gao, B and Xu, H and Chen, W and Wang, K and Wu, X and Yan, C and Zhang, S and Ke, S},
title = {Oxidized chitosan: Combining an "Adhesion-and-Kill" antibacterial strategy with immunoregulation and angiogenesis to enhance methicillin-resistant Staphylococcus Aureus-infected wound healing.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {145664},
doi = {10.1016/j.ijbiomac.2025.145664},
pmid = {40602574},
issn = {1879-0003},
abstract = {The emergence of antibiotic-resistant bacteria, particularly methicillin-resistant Staphylococcus aureus (MRSA), presents a significant challenge in clinical wound management due to their resistance to conventional antibiotics and ability to form persistent biofilms. This study explores the antibacterial properties and wound-healing potential of oxidized chitosan (OCTS), fabricated by oxidizing chitosan with hydrogen peroxide (H2O2), which introduces carboxyl groups to enhance its solubility, adhesion, and antibacterial activity. In vitro experiments demonstrate that OCTS exhibits lower MIC concentration (20 mg/mL vs. 80 mg/mL), superior bactericidal efficiency, stronger adhesion to MRSA, and greater biofilm inhibition than conventional chitosan (CTS), while retaining excellent biocompatibility and hemocompatibility. Multi-omics analyses (proteomics and metabolomics) reveal that OCTS disrupts key metabolic, structural, and redox pathways in MRSA. In a MRSA infection model on mouse skin, OCTS effectively eradicated MRSA in wound sites, reduced inflammation, promoted M2 macrophage polarization, and enhanced angiogenesis, culminating in a rapid wound healing rate of 89.2 ± 3.0 % by day 7. Its low cytotoxicity and excellent biosafety in mice further support its clinical translation. These findings highlight OCTS as a promising multifunctional biomaterial for MRSA-infected wound management, integrating antibacterial, immunoregulatory, and regenerative functions through a unique adhesion-and-kill mechanism.},
}

@article {pmid40602118,
year = {2025},
author = {Liu, Z and Wen, J and Liu, Z and Su, Z and Wu, Z and Shen, H and Wei, H and Zhang, J},
title = {Tire microplastics rather than polystyrene microplastics reduce soil microbial diversity and network complexity and stability, and induce microbial homogenization.},
journal = {Journal of hazardous materials},
volume = {495},
number = {},
pages = {138945},
doi = {10.1016/j.jhazmat.2025.138945},
pmid = {40602118},
issn = {1873-3336},
abstract = {Microplastics (MPs) pollution poses escalating threats to soil biodiversity, yet its impacts on microbial community structure, stability, and assembly are far from fully understood, limiting the comprehensive assessment of MPs risks. This study investigated effects of polystyrene (PS) and tire particle (TP) MPs (0, 1 %, 5 %; w/w) on soil microbial communities in a maize-planted system, evaluating shifts in diversity, network architecture, and assembly processes. Our results demonstrated that high-concentration (5 %) PS MPs significantly enhanced bacterial α-diversity by promoting some taxa (e.g., Planctomycetes, Betaproteobacteria), and increased bacterial network complexity. In contrast, 5 % TP MPs reduced bacterial and fungal diversity, destabilized bacterial networks, and induced taxonomic homogenization. TP MPs amplified deterministic assembly processes by elevating homogeneous selection contribution while reducing stochastic drift, thereby driving microbial community convergence. Bacterial and fungal community structure shifts under TP MPs correlated with soil stoichiometric alterations, including depleted nitrate nitrogen and available phosphorus, and elevated pH, contents of dissolved organic carbon, ammonium nitrogen, and total carbon. These findings highlight the divergent ecological risks posed by PS and TP MPs, and underscore the urgent need for prioritized mitigation of TP MPs pollution in agroecosystems to preserve microbial functional integrity.},
}

@article {pmid40601059,
year = {2025},
author = {Chao, LL and Shih, CM},
title = {Molecular Survey and Genetic Identification of Wolbachia Endosymbionts in Dwelling-Caught Culex quinquefasciatus (Diptera: Culicidae) Mosquitoes from Taiwan.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {69},
pmid = {40601059},
issn = {1432-184X},
support = {NSTC 113-2320-B-037-010; NSTC 114-2923-B-037-001//National Science and Technology Council/ ; },
mesh = {Animals ; *Wolbachia/genetics/classification/isolation & purification/physiology ; *Culex/microbiology ; Taiwan ; *Symbiosis ; Phylogeny ; Female ; Male ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics ; },
abstract = {The genetic identity of Wolbachia endosymbionts was determined in dwelling-caught Culex quinquefasciatus from Taiwan. A total of 370 Cx. quinquefasciatus (245 females and 125 males) was initially screened for Wolbachia infection targeting the universal 16S gene, and the positive samples were further identified their genogroup by a nested-polymerase chain reaction assay to amplify the group-specific Wolbachia surface protein (wsp) gene. In general, 44.59% of Cx. quinquefasciatus was detected with Wolbachia endosymbionts, and 43.2% (54/125) in male and 45.31% (111/245) in female. The group-specific detection was observed in 2.16% (8/370), 41.35% (153/370), and 1.08% (4/370) with groups A, B, and co-infection (A&B), respectively. Phylogenetic analysis revealed that the genetic identities of these Taiwan strains were genetically similar to the groups A and B of Wolbachia with the high sequence homogeneity of 98.7-100% and 96.5-99.8%, respectively. Genetic relatedness is clearly discriminated using both methods of maximum likelihood (ML) and unweighted pair group with arithmetic mean (UPGMA). This study demonstrates the initial genetic identity of Wolbachia endosymbionts with a low prevalence (2.16%) of group A and a high prevalence (41.35%) of group B in dwelling-caught Cx. quinquefasciatus of Taiwan. Because the Cx. quinquefasciatus had been known as a vector for various viral pathogens, the possible impacts of Wolbachia endosymbionts on vector competence of Cx. quinquefasciatus in Taiwan need to be further identified.},
}

Animals
*Wolbachia/genetics/classification/isolation & purification/physiology
*Culex/microbiology
Taiwan
*Symbiosis
Phylogeny
Female
Male
RNA, Ribosomal, 16S/genetics
DNA, Bacterial/genetics

@article {pmid40601038,
year = {2025},
author = {He, T and Chen, Y and Wang, Y and Peng, Z and Mou, Y and Wang, L},
title = {Responses of Microbial Community to Heterogeneous Dissolved Organic Nitrogen Constituents in the Hyporheic Zones of Treated Sewage-Dominated Rivers.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {71},
pmid = {40601038},
issn = {1432-184X},
support = {2021YFB2600200//National Key Research and Development Project of China/ ; grant number 52170159//National Natural Science Foundation of China/ ; No. BE2022601//Key Research and Development Program of Jiangsu Province/ ; 2016-JNHB-007//the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), and the Six Talent Peaks Project in Jiangsu Province/ ; },
mesh = {*Sewage/microbiology/chemistry ; *Nitrogen/metabolism/analysis ; China ; *Rivers/microbiology/chemistry ; *Microbiota ; *Bacteria/classification/metabolism/genetics/isolation & purification ; *Microbial Consortia ; },
abstract = {The hyporheic zone (HZ) of treated sewage-dominated rivers serves as a critical biogeochemical hotspot for dissolved organic nitrogen (DON) transformation, yet the mechanisms linking DON chemodiversity to microbial community dynamics remain poorly resolved. This study integrated spectroscopic fingerprinting, machine learning, and partial least squares path modeling (PLS-PM) to unravel the interactions between redox-stratified DON fractions and microbial consortia in two effluent-impacted rivers (Xi'an, China). The results revealed that DOM spectral parameters associated with distinct DON characteristics posed distinct effects on microbial communities, with the communities in oxic zones largely impacted by autobiogenic, aromatic, and protein-like DON, while the communities in suboxic zones were more intensely impacted by the humification degree of DON. Microbial communities exhibited redox-dependent niche differentiation; i.e., keystone taxa in oxic zones (e.g., Gamma-Proteobacteria) drove nitrogen assimilation, while suboxic taxa (e.g., Verrucomicrobia) prioritized stress-resistant D-amino acid metabolism. PLS-PM demonstrated that biomarkers exerted stronger control on nitrogen cycling (|path coefficients|> 0.6, P < 0.05) than keystone taxa, with summer communities showing higher model fit. Treated sewage-derived DON fostered specialized consortia through biochemical trade-offs, i.e., methionine recycling in oxic zones versus peptidoglycan modification in suboxic zones, thus highlighting the critical role of HZ in mitigating nitrogen pollution. These findings advance predictive modeling of DON-microbe interactions in anthropogenically perturbed aquatic ecosystems.},
}

*Sewage/microbiology/chemistry
*Nitrogen/metabolism/analysis
China
*Rivers/microbiology/chemistry
*Microbiota
*Bacteria/classification/metabolism/genetics/isolation & purification
*Microbial Consortia

@article {pmid40601033,
year = {2025},
author = {Nariman, N and Entling, MH and Krehenwinkel, H and Kennedy, S},
title = {The Microbiome of an Invasive Spider: Reduced Bacterial Richness, but no Indication of Microbial-Mediated Dispersal Behaviour.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {70},
pmid = {40601033},
issn = {1432-184X},
mesh = {Animals ; *Spiders/microbiology/physiology ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; Introduced Species ; Symbiosis ; Europe ; Animal Distribution ; },
abstract = {Mermessus trilobatus, an invasive North American linyphiid spider, has expanded its invasion range up to 1400 km in Europe, accelerating its dispersal speed in less than 40 years. The high heritability of dispersal behaviour and the spatial sorting of high and low dispersers indicate a genetic basis of dispersal behaviour. However, microbial endosymbionts can moderate dispersal behaviour in related species (Rickettsia in Erigone atra). Hence, dispersal behaviour in M. trilobatus might also be dictated by the activity of dispersal-mediating endosymbionts. Here, we investigated the microbiome of invasive M. trilobatus spiders extracted from (1) high- and low-dispersive individuals and (2) spiders originating from locations close to the edge and core of the expansion. We examine the microbiomes for the presence of potential dispersal- and reproduction-mediating bacterial strains and compare the microbial assemblages of spiders based on their dispersal behaviour and locations of origin. The composition of microbial assemblages was similar among spiders of different geographic origins and dispersal behaviour. However, microbial richness was lower in high- than in low-dispersive individuals. Surprisingly, none of the known dispersal- or reproduction-altering endosymbionts of arthropods was identified in any tested spider. This contrasts with published results from North America, where M. trilobatus is a known host of Rickettsia and Wolbachia. Thus, the invasive European population appears to have lost its associated endosymbionts. As endosymbionts can reduce spider mobility, it is possible that their absence facilitates the spread of the invasive spider population. The absence of endosymbionts among the analysed individuals substantiates the role of genetic mechanisms behind the variable dispersal behaviour of invasive M. trilobatus in Europe.},
}

Animals
*Spiders/microbiology/physiology
*Microbiota
*Bacteria/classification/genetics/isolation & purification
Introduced Species
Symbiosis
Europe
Animal Distribution

@article {pmid40600875,
year = {2025},
author = {Yao, J and Wang, H and Fang, J and Shan, S and Joseph, SD and van Zwieten, L and Zhu, K and Chen, D and Jia, H},
title = {Distribution Hotspots, Formation Mechanisms, and Ecological Effects of Reactive Oxygen Species in Soil and Sediment: A Critical Review.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c00581},
pmid = {40600875},
issn = {1520-5851},
abstract = {Reactive oxygen species (ROS), including superoxide radical (O2[•-]), hydrogen peroxide (H2O2), hydroxyl radical ([•]OH), and singlet oxygen ([1]O2), are commonly present in soil and sediment, playing a crucial role in the nutrient biogeochemical cycle, pollutant transformation, and microbial ecology. Previous reviews mainly emphasized ROS toxicity and Fenton chemistry-related reactions, neglecting a comprehensive understanding of ROS distribution and hotspots, formation mechanisms, and ecological effects. Here, the most advanced in situ and ex situ detection methods of ROS in soil and sediment are first summarized to address these gaps. ROS hotspots are identified as active microinterfaces and oxic-anoxic fluctuation zones by graphing the distribution of ROS in soil and sediment. Second, ROS formation processes and mechanisms are outlined, which involve natural organic matter (NOM) and biochar (acting as electron shuttle, geobattery, geoconductor, and photosensitizer), transition metals (mainly via Fenton and Fenton-like reactions), and microbes (producing extracellular ROS and mediating NOM decomposition or metal oxides reduction). Further, as for the ecological effects of ROS, they impact the microbial community, nutrient cycle, and the transformation of organic pollutants and multivalence heavy metals. Finally, we call for more future research that focuses on developing rapid and in situ ROS detection techniques, elucidating the interactive ROS formation mechanisms by trace environmental components, analyzing ecological consequences in ROS hotspots, and practically applying ROS in soil and sediment. A comprehensive understanding of the ROS formation process in soil and sediment is crucial for the study of soil carbon sequestration and natural remediation processes in the context of global green and low-carbon development.},
}

@article {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 = {},
number = {},
pages = {e0016825},
doi = {10.1128/spectrum.00168-25},
pmid = {40600721},
issn = {2165-0497},
abstract = {Bacterial strains that are genetically engineered to constitutively produce fluorescent proteins have aided our study of bacterial physiology, biofilm formation, and interspecies interactions. Here, we report on the construction and utilization of new strains that produce the blue fluorescent protein mTagBFP2, the green fluorescent protein sfGFP, and the red fluorescent protein mScarlet-I3 in species Streptococcus gordonii, Streptococcus mutans, and Streptococcus sanguinis. Gene fragments, developed to contain the constitutive promoter Pveg, the fluorescent gene of interest, as well as aad9, providing resistance to the antibiotic spectinomycin, were inserted into selected open reading frames on the chromosome that were both transcriptionally silent and whose loss caused no measurable changes in fitness. All strains, except for sfGFP in S. sanguinis, were validated to produce a detectable and specific fluorescent signal. Individual stains, along with extracellular polymeric substances (EPS) within biofilms, were visualized and quantified through either widefield or super-resolution confocal microscopy approaches. Finally, to validate the ability to perform single-cell-level analysis using the strains, we imaged and analyzed a triculture mixed-species biofilm of S. gordonii, S. mutans, and S. sanguinis grown with and without the addition of human saliva. Quantification of the loss in membrane integrity using a SYTOX dye revealed that all strains had increased loss of membrane integrity with water or human saliva added to the growth media, but the proportion of the population stained by the SYTOX dye varied by species. In all, these fluorescent strains will be a valuable resource for the continued study of oral microbial ecology.IMPORTANCEStreptococci are among the earliest colonizers of the soft and hard tissues of the oral cavity and are contributors to the oral health status of the host, with involvement in dental caries, endodontic infections, periodontal disease, and the development of oral cancer. Strains genetically modified to produce fluorescent proteins that can be either visualized through microscopy imaging or quantified by their specific fluorescent intensity signal are critical tools toward the study of individual or mixed-species cultures. Our report here details the development and testing of several new strains of fluorescent oral streptococci that can be utilized in the study of microbial ecology, increasing both the availability of tools and documenting experimental approaches toward in vitro assay applications such as the study of intermicrobial interactions.},
}

@article {pmid40600175,
year = {2025},
author = {Etesami, H},
title = {The dual nature of plant growth-promoting bacteria: Benefits, risks, and pathways to sustainable deployment.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100421},
pmid = {40600175},
issn = {2666-5174},
abstract = {Plant growth-promoting bacteria (PGPB) are pivotal in sustainable agriculture, enhancing crop productivity and reducing reliance on chemical inputs. However, their dual role as beneficial agents and potential stressors remains underexplored. This review examines the paradoxical adverse effects of PGPB, challenging the predominantly optimistic narrative surrounding their use. At the plant level, unintended consequences include hormonal imbalances (e.g., auxin-induced root inhibition), phytotoxic metabolite production (e.g., hydrogen cyanide), and trade-offs between growth and defense mechanisms. At the soil level, risks encompass disrupted microbial diversity, altered nutrient cycling, and horizontal gene transfer that may foster pathogenicity. These outcomes are driven by environmental factors (soil pH and moisture), host-specific interactions, and application practices. Mitigation strategies emphasize rigorous strain selection, optimized dosing, and integrated soil management to balance efficacy with ecological safety. Advances in multi-omics technologies and synthetic consortia design offer predictive insights into strain behavior, while long-term ecological assessments are critical to address legacy impacts. The review underscores the necessity of a nuanced, evidence-based approach to PGPB deployment, harmonizing agricultural benefits with environmental stewardship. By addressing knowledge gaps in microbial ecology and risk assessment, this work supports strategies prioritizing both agricultural resilience and soil biodiversity to ensure PGPB contribute sustainably to global food security.},
}

@article {pmid40600142,
year = {2025},
author = {Xia, Y and Lu, L and Wang, L and Qiu, Y and Liu, X and Ge, W},
title = {Multi-omics analyses reveal altered gut microbial thiamine production in obesity.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1516393},
pmid = {40600142},
issn = {1664-302X},
abstract = {OBJECTIVE: Accumulating evidence highlights the important role of B vitamins in maintaining the balance of gut microbial ecology and metabolism, however, few studies have focused on changes in B vitamins homeostasis in the gut and their associations with disease. This study aims to investigate the potential interplay between B vitamins, gut microbiota, and obesity.

METHODS: We conducted an integrated analysis of fecal shotgun metagenomics, fecal metabolome concerning B vitamins and short chain fatty acids (SCFAs), and obese phenotypes in a cohort of 63 participants, including 31 healthy controls and 32 individuals with obesity.

RESULTS: Metabolomic analysis identified significantly lower levels of fecal thiamine in individuals with obesity (P Wilcoxon < 0.001). Fecal thiamine levels exhibited a positive correlation with HDL-C and a negative correlation with BMI, DBP, fasting serum insulin, HOMA-IR, triglycerides, and propionic acid. Binary logistics regression suggested that fecal thiamine deficiency may be a potential contributor to the onset of obesity (Odds ratio: 0.295). Metagenomic analysis indicated that the microbial composition in individuals with obesity was characterized by a predominance of potential opportunistic pathogens, a loss of complexity, and a decrease in thiamine-producing bacteria. Integrated analysis indicated that thiamine deficiency was positively associated with the depletion of thiamine auxotrophic bacteria in the obese microbiome. Functional analysis revealed that KOs content for enzymes involved in the microbial production of thiamine were significantly lower in obesity, including tRNA uracil 4-sulfurtransferase (ThiI, P Wilcoxon = 0.001) and nucleoside-triphosphatase (NTPCR, P Wilcoxon = 0.006), both of which were positively associated with fecal thiamine.

CONCLUSION: Our study highlights the impairment of microbial thiamine production and its broad associations with gut microbiota dysbiosis and obesity-related phenotypes. Our findings provide a rationale for developing treatments that utilize thiamine to prevent obesity by modulating gut microbiota.},
}

@article {pmid40600059,
year = {2025},
author = {Liu, J and Yao, P and Liu, J and Ren, G and Zhang, XH and Liu, J},
title = {Habitat and lifestyle affect the spatial dynamics of prokaryotic communities along a river-estuary-sea continuum.},
journal = {mLife},
volume = {4},
number = {3},
pages = {305-318},
pmid = {40600059},
issn = {2770-100X},
abstract = {Microbial biogeography and its controlling mechanisms are central themes in microbial ecology. However, we still lack a comprehensive understanding of how habitats and lifestyles affect microbial biogeography across complex environmental gradients. In this study, we investigated the planktonic (including free-living [FL] and particle-associated [PA] lifestyles) and benthic prokaryotic communities along a river-estuary-sea continuum of the Changjiang River to explore their distinct spatial dynamics. We observed greater community variability across spatial distances than between habitat and lifestyle types. Spatial variations were evident in FL, PA, and benthic communities, with the highest turnover rates observed in benthic communities, followed by PA, and the lowest turnover rates observed in FL. The replacement effect dominated PA and benthic community variations, whereas the richness effect was more significant in FL communities. Microbial assembly was primarily governed by homogeneous selection and dispersal limitation regardless of habitats/lifestyles, with their ratios decreasing as the spatial distance increased, particularly in the FL fraction. Dispersal limitation had a stronger effect on benthic communities compared to planktonic communities. While heterogeneous selection generally played a minor role, its influence became more pronounced over larger spatial distances and with increasing salinity differences. Finally, we showed that abiotic and biotic factors individually exerted a greater influence on PA communities, whereas their interactions had a stronger effect on FL communities. Our results revealed complex spatial dynamics and assembly mechanisms among microorganisms across different habitats and lifestyles, providing insights into the spatial scaling of community assembly across complex environmental gradients.},
}

@article {pmid40598447,
year = {2025},
author = {Bulzu, PA and Henriques Vieira, H and Ghai, R},
title = {Lineage-specific expansions of polinton-like viruses in photosynthetic cryptophytes.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {154},
pmid = {40598447},
issn = {2049-2618},
support = {25-15920S//Grantová Agentura České Republiky/ ; 24-11998S//Grantová Agentura České Republiky/ ; 20-12496X//Grantová Agentura České Republiky/ ; },
mesh = {*Cryptophyta/virology/genetics ; Metagenomics ; Phylogeny ; Genome, Viral ; Photosynthesis ; *Giant Viruses/genetics/classification ; *DNA Viruses/genetics/classification ; },
abstract = {BACKGROUND: Polinton-like viruses (PLVs) are diverse eukaryotic DNA viral elements (14-40 kb) that often undergo significant expansion within protist genomes through repeated insertion events. Emerging evidence indicates they function as antiviral defense systems in protists, reducing the progeny yield of their infecting giant viruses (phylum Nucleocytoviricota) and influencing the population dynamics and evolution of both viruses and their hosts. While many PLVs have been identified within the genomes of sequenced protists, most were recovered from metagenomic data. Even with the large number of PLVs identified from metagenomic data, their host-virus linkages remain unknown owing to the scarcity of ecologically relevant protist genomes. Additionally, the extent of PLV diversification within abundant freshwater taxa remains undetermined. In order to tackle these questions, high-quality genomes of abundant and representative taxa that bridge genomic and metagenomic PLVs are necessary. In this regard, cryptophytes, which are among the most widely distributed, abundant organisms in freshwaters and have remained largely out of bounds of genomic and metagenomic approaches, are ideal candidates for investigating the diversification of such viral elements both in cellular and environmental context.

RESULTS: We leveraged long-read sequencing to recover large (200-600 Mb), high-quality, and highly repetitive (> 60%) genomes of representative freshwater and marine photosynthetic cryptophytes. We uncovered over a thousand complete PLVs within these genomes, revealing vast lineage-specific expansions, particularly in the common freshwater cryptophyte Rhodomonas lacustris. By combining deep sequence homology annotation with biological network analyses, we discern well-defined PLV groups defined by characteristic gene-sharing patterns and the use of distinct strategies for replication and integration within host genomes. Finally, the PLVs recovered from these cryptophyte genomes also allow us to assign host-virus linkages in environmental sequencing data.

CONCLUSIONS: Our findings provide a primer for understanding the evolutionary history, gene content, modes of replication and infection strategies of cryptophyte PLVs, with special emphasis on their expansion as endogenous viral elements (EVEs) in freshwater bloom-forming R. lacustris. Video Abstract.},
}

*Cryptophyta/virology/genetics
Metagenomics
Phylogeny
Genome, Viral
Photosynthesis
*Giant Viruses/genetics/classification
*DNA Viruses/genetics/classification

@article {pmid40594354,
year = {2025},
author = {Flores, SS and Cordovez, V and Arias Giraldo, LM and Leon-Reyes, A and van 't Hof, P and Raaijmakers, JM and Oyserman, BO},
title = {Unveiling diversity and adaptations of the wild tomato Microbiome in their center of origin in the Ecuadorian Andes.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {22448},
pmid = {40594354},
issn = {2045-2322},
support = {CZ07-000440-2018//SENESCYT scholarship/ ; 10093//Chancellor Grant and COCIBA-USFQ/ ; 10093//Chancellor Grant and COCIBA-USFQ/ ; 024.004.014/NWO_/Dutch Research Council/Netherlands ; 024.004.014/NWO_/Dutch Research Council/Netherlands ; },
mesh = {*Solanum lycopersicum/microbiology/genetics ; *Microbiota/genetics ; Soil Microbiology ; Rhizosphere ; Ecuador ; Plant Roots/microbiology ; Biodiversity ; *Adaptation, Physiological ; Phylogeny ; },
abstract = {Microbiome assembly has been studied for many plant species and is recognized as a key driver of plant growth and plant tolerance to (a)biotic stresses. To date, assembly of the tomato rhizosphere microbiome has been investigated primarily for commercial varieties and field soils subjected to agricultural management practices, whereas the microbiome of wild tomato genotypes in their native habitats remains largely unexplored. This research focused on distinct populations of Solanum pimpinellifolium in three natural habitats in the Ecuadorian Andes to identify the taxonomic and functional diversity of their rhizosphere microbiome. The results showed that, despite genotypic differences among the wild tomato populations, different soil types and soil microbiome compositions, the rhizosphere microbiome showed strikingly compositional similarity across the three habitats. Proteobacteria, in particular taxa classified as Enterobacteriaceae, and specific unclassified fungal taxa were highly represented in the rhizosphere of S. pimpinellifolum. Metagenomic analyses suggested that the prevalence of Enterobacteriaceae on wild tomato roots may be explained by several traits, in particular nutrient competition, motility, iron acquisition, membrane transport, stress response, and plant hormone biosynthesis. These results reveal a conserved microbiome signature associated with wild tomato rhizosphere in their center of origin. Just as the genomes of wild crop ancestors provide a valuable source of beneficial traits for breeding cultivated varieties, exploring their microbiome in native environments could uncover microbial taxa and traits that similarly contribute to crop growth and health.},
}

*Solanum lycopersicum/microbiology/genetics
*Microbiota/genetics
Soil Microbiology
Rhizosphere
Ecuador
Plant Roots/microbiology
Biodiversity
*Adaptation, Physiological
Phylogeny

@article {pmid40594086,
year = {2025},
author = {Leifels, M and Cheng, D and Cai, J and Nadhirah, N and Mohidin, AF and Santillan, E and Woo, Y and Hill, E and Wu, SW and Boon, N and Favere, J and Whittle, AJ and Wuertz, S},
title = {Biofilm detachment significantly affects biological stability of drinking water during intermittent water supply in a pilot scale water distribution system.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {22408},
pmid = {40594086},
issn = {2045-2322},
support = {3S85419//the FWO Flanders/ ; 3S85419//the FWO Flanders/ ; S006221N//FWO-SBO Biostable project/ ; S006221N//FWO-SBO Biostable project/ ; },
mesh = {*Biofilms/growth & development ; *Drinking Water/microbiology ; *Water Supply ; *Water Microbiology ; RNA, Ribosomal, 16S/genetics ; Pilot Projects ; Flow Cytometry ; Water Quality ; Bacteria/genetics/classification ; Water Purification ; },
abstract = {Intermittent service provision (IWS) in piped drinking water distribution systems is practiced in countries with limited water resources; it leads to stagnant periods during which water drains completely from de-pressurized pipes, increasing the likelihood of biofilm detachment upon reconnection when water is supplied to the consumer and thus affecting water quality. Our study examines the impact of uninterrupted or continuous water supply (CWS) and IWS on microbial communities and biofilm detachment, using data from three 30-day experiments conducted in an above-ground drinking water testbed with 90-m long PVC pipes containing residual monochloramine. Flow cytometry (FCM) revealed a significant increase in total and intact cell concentrations when water was supplied intermittently compared to CWS, and the microbial alpha-diversity was significantly higher in CWS sections by both 16S rRNA gene metabarcoding and phenotypic fingerprinting of flow cytometry data. Nitrate levels in the water were significantly higher during initial intermittent flow due to the activity of nitrifying bacteria in biofilms exposed to stagnant water in pipes. Overall, biofilm detachment significantly affects the biological stability of drinking water delivered through IWS compared to CWS. We developed a novel biofilm detachment potential index derived from FCM data to estimate the minimum amount of water needed to be discarded before microbial cell counts and community composition return to baseline levels.},
}

*Biofilms/growth & development
*Drinking Water/microbiology
*Water Supply
*Water Microbiology
RNA, Ribosomal, 16S/genetics
Pilot Projects
Flow Cytometry
Water Quality
Bacteria/genetics/classification
Water Purification

@article {pmid40591097,
year = {2025},
author = {Gisriel, CJ and Schluchter, WM and Gan, F and Golbeck, JH and Ho, MY and Shen, G and Soulier, NT and Thiel, V and Ward, DM and Zhao, J and Zhang, S},
title = {Remembering Don Bryant (1950-2024).},
journal = {Photosynthesis research},
volume = {163},
number = {4},
pages = {37},
pmid = {40591097},
issn = {1573-5079},
}

@article {pmid40589459,
year = {2025},
author = {Ametefe, EN and Thorsen, L and Danwonno, H and Agoha, RK and Glover, RLK and Dzogbefia, VP and Jespersen, L},
title = {Molecular Characterization of Culturable Yeasts and Nonspore-Forming Bacteria Associated With Fermented Kapok Seeds (Kantong), a Traditional Food Condiment in Ghana.},
journal = {International journal of food science},
volume = {2025},
number = {},
pages = {6452183},
pmid = {40589459},
issn = {2314-5765},
abstract = {Fermented kapok seeds, known as kantong in northern Ghana, serve as a traditional food condiment which provides flavor and improves the protein content of soups. In this study, the occurrence of yeasts, lactic acid bacteria (LAB), and other nonspore-forming bacteria in kantong was investigated. Microbial enumeration and phenotypic characterizations on isolated strains were performed. Molecular methods were also employed for grouping and identification of strains, and these included random amplification of polymorphic DNA (RAPD) using Escherichia coli phage-derived M13 primer (M13-PCR typing), repetitive element PCR typing (rep-PCR), and 16S rRNA gene sequencing. After a 48-h fermentation period, microbial load ranged from 4.77 ± 0.11 to 8.9 ± 0.1 log10 CFU/g. The pH of the fermenting condiment decreased from 6.5 to 4.7 during the fermentation period. A total of 190 LAB, 53 enterobacteria, and 39 yeasts were identified at species levels using both phenotypic and molecular methods. The LAB included Pediococcus acidilactici, Weissella paramesenteroides, Pediococcus pentosaceus, Weissella confusa, and Lactiplantibacillus plantarum; the enterobacteria isolated were Acinetobacter baumannii, Klebsiella pneumoniae, Enterococcus faecium, Escherichia coli, and Enterobacter cloacae; and the yeasts identified were Nakaseomyces glabratus, Cyberlindnera fabianii, Pichia kudriavzevii, and Saccharomyces cerevisiae. This work presents fermented kapok seeds as a reservoir of microorganisms, some of which could possess some technological properties which could be harnessed to enhance the nutritional value of Ghanaian foods as well as improve gut health as probiotics. It also reveals the presence of enterobacteria in this spontaneous fermentation, thus impacting the safety of the product and the need for starter culture development.},
}

@article {pmid40589000,
year = {2025},
author = {Sharma, H and Al Noman, A and Ahmad, I and Tonni, SD and Mim, TJ and Afrose, F and Sharma, PD and Parvez, A and Tamanna, S and Al Azad, M and Pathak, R},
title = {Bridging Mind and Gut: The Molecular Mechanisms of microRNA, Microbiota, and Cytokine Interactions in Depression.},
journal = {Current gene therapy},
volume = {},
number = {},
pages = {},
doi = {10.2174/0115665232361169250617192348},
pmid = {40589000},
issn = {1875-5631},
abstract = {Depression is a complex psychiatric disorder that arises from various underlying biological mechanisms. In this review, the role of microRNAs (miRNAs) in modulating gut microbiotacytokine communication and their potential to unravel the pathophysiology of depression and develop novel therapeutic strategies are discussed. MiRNAs are small non-coding RNA molecules that have emerged as key regulators in the bidirectional signaling of the gut-brain axis by modulating gene expression and fine-tuning an intricate dialogue between the microbiota, immune system, and central nervous system. Results show how gut microbiota can shape miRNA expression in brain regions involved in mood regulation; conversely, evidence is accumulating, elucidating how miRNA perturbations can shape microbial ecology. Gut bacteria-derived short-chain fatty acids (SCFAs) fuel this nexus by exerting effects on neurogenesis, neurotransmitter synthesis, neuroinflammation, affective behavior alterations, and depressive-like phenotypes. Pro-inflammatory cytokines such as IL-6, TNF-α, and IL-1β are also known to be associated with depressive symptoms related to altered expression patterns of specific miRNAs across these disorders. This review exposes the novel potential biomarkers and therapeutic targets/strategies to develop innovative methods in the diagnosis and treatment of depression by exploring bidirectional relations among miRNAs, gut microbiota, and cytokines. The knowledge of these molecular networks and pathways has provided the opportunity for designing new-generation therapeutics such as phytobiotics, probiotics, psychobiotics, diet therapies, and nanomedicine based on miRNAs from a future perspective, which will revolutionize the management of mental disorders.},
}

@article {pmid40586542,
year = {2025},
author = {Bruno, JS and Heidrich, V and Restini, FCF and Alves, TMMT and Miranda-Silva, W and Knebel, FH and Cóser, EM and Inoue, LT and Asprino, PF and Camargo, AA and Fregnani, ER},
title = {Dental biofilm serves as an ecological reservoir of acidogenic pathobionts in head and neck cancer patients with radiotherapy-related caries.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0025725},
doi = {10.1128/msphere.00257-25},
pmid = {40586542},
issn = {2379-5042},
abstract = {UNLABELLED: Radiotherapy-related caries (RRC) is an aggressive and debilitating oral toxicity that affects half of the patients who undergo radiotherapy for head and neck cancer. However, the etiology of RRC is not fully established, and there are no clinically validated methods for preventing it. To gain a better understanding of the risk factors and the microbiome's role in causing RRC, we compared clinicopathological characteristics, oncological treatment regimens, oral health condition, and the oral microbiota at three different oral sites of radiotherapy-treated patients with (RRC+) and without radiotherapy-related caries (RRC-). We observed no significant differences between these groups in the clinicopathological characteristics and treatment regimens. However, RRC+ patients were older and had poorer oral health conditions at the start of the radiotherapy treatment, with a lower number of teeth and a higher proportion of rehabilitated teeth. RRC+ patients had lower microbiota diversity and the dental biofilm of RRC+ patients displayed striking alterations in microbiome composition compared to RRC- patients, including enrichment of acidogenic species and altered metabolic potential, with a higher abundance of genes linked to energy-related pathways associated with the synthesis of amino acids and sugars. We also compared the microbiota of RRC+ tissue with conventional caries tissue, revealing lower bacterial diversity and enrichment of Lactobacillaceae members in RRC+. The insights into the irradiated oral microbiota enhance the understanding of RRC etiology and highlight the potential for microbial-targeted therapies in its prevention and treatment.

IMPORTANCE: This study focuses on a dedicated collection of diverse oral sites to comprehensively investigate microbial differences between patients who develop RRC and those who do not. RRC is a severe oral disease that profoundly impacts on the oral health and overall quality of life of cancer survivors. Leveraging shotgun metagenomics, we characterize the unique microbial variations in in vivo irradiated dental biofilms, unveiling novel insights into the microbial ecology of radiotherapy-treated patients. Furthermore, this research integrates extensive data on oral health and oncological profiles, providing a comprehensive understanding of the intricate relationship between oral microbial communities and the outcomes of radiotherapy-induced toxicity.},
}

@article {pmid40586525,
year = {2025},
author = {Taylor, CC and Parks, ST},
title = {There and back again: navigating the return to in-person lab work post-pandemic for the Hybrid Microbial Ecology Course-based Undergraduate Research Experience (H-ME-CURE).},
journal = {Journal of microbiology & biology education},
volume = {},
number = {},
pages = {e0024924},
doi = {10.1128/jmbe.00249-24},
pmid = {40586525},
issn = {1935-7877},
abstract = {The Microbial Ecology Course-based Undergraduate Research Experience (ME-CURE) has evolved over time to accommodate student needs and experiences. Prior to the COVID-19 pandemic, the lab was fully in-person, with a shift to in silico, remote learning from 2020 to 2023. In 2024, the ME-CURE was further adapted to return to in-person learning while maintaining some of the remote learning pedagogy. Significantly, the 2024 Hybrid ME-CURE (H-ME-CURE) built upon the findings of prior iterations of the lab such that students in the 2024 cohort entered with lab isolates, primers, and pathways that were ready for testing. This novel version of the ME-CURE synthesized years of in-person and remote, in silico learning to yield a deeper understanding of microbial pathways and improved molecular data including novel gene sequences for further testing. The goal of this work is to provide the tools that were used to help build the H-ME-CURE by combining past in-person and in silico learning methods of the ME-CURE.},
}

@article {pmid40585502,
year = {2025},
author = {Zhu, M and Zhang, F and Qiu, Z and Zhao, S and Gao, S},
title = {White Light Orchestrates Mycoparasitic and Infection Activities by Regulating Expression of Effectors in Trichothecium roseum.},
journal = {Food science & nutrition},
volume = {13},
number = {7},
pages = {e70396},
pmid = {40585502},
issn = {2048-7177},
abstract = {The fungal developmental processes are orchestrated by white light. Despite the genome assembly of Trichothecium roseum being available, the underlying molecular mechanisms of the white light-mediated developments of T. roseum remain obscure. It was found that white light impaired mycoparasitic activities against the wheat powdery mildew fungus and infection processes on tomato fruits in T. roseum. In vitro and in vivo, white light significantly impaired colony expansion and dramatically increased conidiation of T. roseum. RNA-seq analysis of T. roseum conidia was profiled to illustrate the light-mediated expression of genes. A total of 153 and 666 differentially expressed genes were identified between conidia treated with or without white light at 48- and 96-h post inoculation (hpi). Among genome-wide identified effectors, 8 and 36 effectors were differentially regulated by white light at 48 and 96 hpi, respectively. The core effectors, Tro004101, Tro006854, Tro008316, and Tro004104 were commonly downregulated by white light. Notably, white light regulated gene expression in key metabolic pathways including tryptophan metabolism (3 genes) and tyrosine metabolism (5 genes), as well as the HOG-MAPK signaling cascade. These results demonstrated that white light-compromised T. roseum mycoparasitic and infection activities might be achieved by regulating specific effector expression and differentially modulating metabolism and HOG-MAPK pathways. The genes detected by our transcriptome analysis may be crucial for mycoparasitism and infection by T. roseum and thus serve as targets for future functional analysis. Our findings provide new insights into the white light-orchestrated developments of an important agricultural and economical fungus and will potentially support efforts for the study of fungal effectors.},
}

@article {pmid40584121,
year = {2025},
author = {Barrero, MAO and Varón-López, M and Peñuela-Sierra, LM},
title = {Competing microorganisms with exclusion effects against multidrug-resistant Salmonella Infantis in chicken litter supplemented with growth-promoting antimicrobials.},
journal = {Veterinary world},
volume = {18},
number = {5},
pages = {1127-1136},
pmid = {40584121},
issn = {0972-8988},
abstract = {BACKGROUND AND AIM: The widespread use of antibiotic growth promoters (AGPs) in poultry production has been implicated in altering gut microbiota and promoting the excretion of multidrug-resistant (MDR) bacteria into the environment. Salmonella enterica serovar Infantis (Salmonella Infantis [S.I]), a prevalent zoonotic pathogen, has demonstrated increasing resistance in poultry systems. This study aimed to evaluate the efficacy of natural control microorganisms (NCM), Bacillus subtilis and Lactobacillus plantarum, in reducing the abundance of MDR S.I in fresh chicken litter from birds raised with or without AGP supplementation. It also examined how physicochemical properties and microbial dynamics influence pathogen persistence.

MATERIALS AND METHODS: Microcosms were constructed using litter from broilers raised under two dietary regimes (with and without avilamycin). Treatments included combinations of AGP, S.I, and NCM. Bacterial enumeration was performed using selective media, and whole-genome sequencing of S.I was conducted to characterize antimicrobial resistance and virulence genes. Physicochemical parameters (pH, humidity, temperature, and ammonia) were measured and correlated with microbial loads. Antagonistic activity of NCM strains was assessed using agar diffusion assays.

RESULTS: Genome analysis revealed that S.I carried multiple resistance genes (e.g., blaCTX-M-65, tet(A), and sul1) and efflux systems conferring MDR. In vitro assays showed strong antagonism by L. plantarum and moderate activity by B. subtilis. In microcosms, S.I counts significantly decreased in the presence of both AGP and NCM, indicating synergistic inhibition. Conversely, in the absence of AGP, NCM had a limited effect. Statistical analyses showed strong correlations between microbial groups and physicochemical variables, particularly during later production stages.

CONCLUSION: The application of B. subtilis and L. plantarum in chicken litter significantly reduced S.I colonization under AGP supplementation, suggesting their potential as biocontrol agents. These findings support the development of integrated litter management strategies to mitigate zoonotic and resistant pathogen dissemination, particularly in AGP-using systems. However, the effectiveness of such interventions may vary across farms due to differences in microbial ecology and environmental conditions.},
}

@article {pmid40583496,
year = {2025},
author = {Crull, S and Hammer, E and Mann, AE and O'Connell, LM and Soule, A and Griffith, E and Blouin, T and Brigmon, RL and Richards, VP},
title = {Seasonal Host Shifts for Legionella Within an Industrial Water-Cooling System.},
journal = {Environmental microbiology reports},
volume = {17},
number = {4},
pages = {e70132},
doi = {10.1111/1758-2229.70132},
pmid = {40583496},
issn = {1758-2229},
support = {89303321CEM000080//Office of Environmental Management/ ; //The Laboratory Directed Research and Development (LDRD) program within the Savannah River National Laboratory (SRNL)/ ; },
mesh = {Seasons ; *Legionella/genetics/isolation & purification/physiology/classification ; RNA, Ribosomal, 16S/genetics ; *Water Microbiology ; RNA, Ribosomal, 18S/genetics ; Acanthamoeba ; Phylogeny ; },
abstract = {Legionella is a genus of environmental bacteria containing pathogenic species such as Legionella pneumophila that are responsible for Legionnaires' disease, a potentially fatal respiratory infection. Disease aetiology can involve Legionella replication intracellularly within protists and this study aimed to characterise the Legionella-protist relationship to develop novel outbreak prevention targets. Water and sediment samples were collected from a water-cooling tower in South Carolina over a 6-month period. Concomitantly, multiple environmental parameters were recorded. Bacterial and eukaryotic communities were characterised using 16S rRNA gene V4 region and a 252 bp fragment of 18S rRNA gene, respectively. Co-occurrence network analyses were performed to elucidate Legionella-protist correlations through time. We found that Legionella correlated with different protists as the seasons progressed. Acanthamoeba correlated with Legionella in early spring followed by Vannella and Korotnevella in late spring and early summer, and were joined by Echinamoeba in mid-summer. Vannella and Acanthamoeba are known potential hosts for Legionella, while Korotnevella is a potential undocumented host. Of the environmental parameters, temperature showed strong correlation with protists genera, suggesting that Legionella abundance was driven by temperature-dependent protist availability. Our results highlight ecological shifts that are associated with elevated Legionella levels, which offers potential targets to help predict and prevent disease outbreaks.},
}

Seasons
*Legionella/genetics/isolation & purification/physiology/classification
RNA, Ribosomal, 16S/genetics
*Water Microbiology
RNA, Ribosomal, 18S/genetics
Acanthamoeba
Phylogeny

@article {pmid40583058,
year = {2025},
author = {Cornet, L and Zaidi, SS and Li, J and Ngapout, Y and Shakir, S and Meunier, L and Callot, C and Marande, W and Hanikenne, M and Rombauts, S and Van de Peer, Y and Vanderschuren, H},
title = {A BAC-guided haplotype assembly pipeline increases the resolution of the virus resistance locus CMD2 in cassava.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {185},
pmid = {40583058},
issn = {1474-760X},
support = {F.4515.17//Fonds De La Recherche Scientifique - FNRS/ ; 1.B456.20//Fonds De La Recherche Scientifique - FNRS/ ; 833522/ERC_/European Research Council/International ; BOF.MET.2021.0005.01//Universitair Ziekenhuis Gent/ ; },
mesh = {*Manihot/genetics/virology ; *Disease Resistance/genetics ; *Plant Diseases/genetics/virology ; *Haplotypes ; *Chromosomes, Artificial, Bacterial/genetics ; Genome, Plant ; Chromosome Mapping ; },
abstract = {BACKGROUND: Cassava is an important crop for food security in the tropics where its production is jeopardized by several viral diseases, including the cassava mosaic disease (CMD) which is endemic in Sub-Saharan Africa and the Indian subcontinent. Resistance to CMD is linked to a single dominant locus, namely CMD2. The cassava genome contains highly repetitive regions making the accurate assembly of a reference genome challenging.

RESULTS: In the present study, we generate BAC libraries of the CMD-susceptible cassava cultivar (cv.) 60444 and the CMD-resistant landrace TME3. We subsequently identify and sequence BACs belonging to the CMD2 region in both cultivars using high-accuracy long-read PacBio circular consensus sequencing (ccs) reads. We then sequence and assemble the complete genomes of cv. 60444 and TME3 using a combination of ONT ultra-long reads and optical mapping. Anchoring the assemblies on cassava genetic maps reveals discrepancies in our, as well as in previously released, CMD2 regions of the cv. 60444 and TME3 genomes. A BAC-guided approach to assess cassava genome assemblies significantly improves the synteny between the assembled CMD2 regions of cv. 60444 and TME3 and the CMD2 genetic maps. We then performed repeat-unmasked gene annotation on CMD2 assemblies and identify 81 stress resistance proteins present in the CMD2 region, among which 31 were previously not reported in publicly available CMD2 sequences.

CONCLUSIONS: The BAC-assessed approach improved CMD2 region accuracy and revealed new sequences linked to virus resistance, advancing our understanding of cassava mosaic disease resistance.},
}

*Manihot/genetics/virology
*Disease Resistance/genetics
*Plant Diseases/genetics/virology
*Haplotypes
*Chromosomes, Artificial, Bacterial/genetics
Genome, Plant
Chromosome Mapping

@article {pmid40581745,
year = {2025},
author = {Richter, I and Büttner, H and Hertweck, C},
title = {Endofungal Bacteria as Hidden Facilitators of Biotic Interactions.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf128},
pmid = {40581745},
issn = {1751-7370},
abstract = {Fungi play pivotal roles in ecology and human health, driving nutrient cycling, supporting antibiotic production, and posing threats through toxin production. Less well-recognized, however, is their ability to harbour endosymbiotic bacteria. Advances in genomics and microscopy have revealed the prevalence of endofungal bacteria across diverse fungal phyla, though their functions are primarily inferred from genomic and transcriptomic studies. Recent functional research has begun to shed light on their influence on fungal pathogenicity, physiology, and ecology. These findings raise fundamental questions about the establishment and benefits of bacterial-fungal endosymbiosis, as well as the role of endosymbionts in mediating fungal interactions with other organisms. This review provides an in-depth analysis of the molecular mechanisms involved in the establishment and persistence of these symbioses. It also summarizes the current understanding of how endofungal bacteria impact fungal interactions with other organisms. For instance, endofungal bacteria contribute to the beneficial effects of fungi on plant health and fitness, protect fungal hosts from fungivorous predators, and enhance fungal virulence against plants, animals, and humans. These discoveries highlight the need for holistic investigations into bacterial-fungal endosymbiosis to fully understand their role in natural ecosystems. A deeper understanding of these multipartite partnerships offers exciting opportunities to improve ecosystem management, food safety, disease control, and crop productivity.},
}

@article {pmid40580837,
year = {2025},
author = {Zhou, B and Niu, C and Mao, W and Wang, X and Wu, Z and Wang, Z},
title = {An electrochemical anaerobic dynamic membrane bioreactor for enhanced sludge digestion: Unveiling molecular interactions and microbial mechanisms.},
journal = {Water research},
volume = {285},
number = {},
pages = {124080},
doi = {10.1016/j.watres.2025.124080},
pmid = {40580837},
issn = {1879-2448},
abstract = {This study investigated the effects of stepwise external voltages on an electrochemical anaerobic dynamic membrane bioreactor (EC-AnDMBR) for anaerobic digestion of waste activated sludge. Increasing the applied voltage greatly mitigated membrane fouling, reduced the transmembrane pressure increase rate and enhanced both volatile solids digestion and biogas production. The dynamic membrane structure became looser with fewer biofouling substances, attributed to a 42.6 % increase in the sludge-membrane interaction energy barrier at higher voltages. Electrochemical analysis revealed improved electroactivity of the anaerobic sludge, as evidenced by increased conductivity and reduced internal resistance. The proton-coupled electron transfer (PCET) pathway was promoted, indicated by a significant increase in the hydrogen/deuterium kinetic isotope effect from 616 to 25,990. Molecular simulations of dissolved organic matter (DOM) showed an enrichment of amide and quinone groups, along with stronger hydrogen-bonding and π-cation interactions, which may contribute to the PCET process. Moreover, elevated voltages promoted more deterministic microbial community assembly and reduced upstream microbial immigration. Gene upregulation in organic metabolism, electron/proton transport, and methanogenesis further supported enhanced digestion performance via PCET pathway. These findings offer valuable insights into the molecular mechanisms and microbial ecology of EC-AnDMBR systems, advancing the development of more efficient and sustainable sludge treatment technologies.},
}

@article {pmid40578101,
year = {2025},
author = {Liu, B and Jia, M and Nauwynck, W and Wang, J and Kundu, K and Springael, D and Boon, N},
title = {Hydrogen-powered bacteria enhance organic micropollutant degradation under starvation conditions.},
journal = {Water research},
volume = {285},
number = {},
pages = {124052},
doi = {10.1016/j.watres.2025.124052},
pmid = {40578101},
issn = {1879-2448},
abstract = {Organic micropollutants (OMPs) occur in natural aquatic environments at trace concentrations with suspected adverse effects on the ecosystem and human health. Microbial biodegradation plays a crucial role in OMP-elimination from drinking water resources. However, long-term OMP-biodegradation remains challenging since the metabolic activity of degrading strains is restricted by energy-limited conditions in treatment systems. Molecular hydrogen (H2) has been identified as a universally available energy source utilized by various bacteria under nutrient-starved conditions, and it can be hypothesized that H2 might also support OMP-degrading microbes when other energy carriers are scarce. The potential of H2 as a supporting energy source for OMP-degradation was tested by examining its effect on the biodegradation of 2,6-dichlorobenzamide (BAM) by Aminobacter niigataensis MSH1 and on the physiological status of the MSH1 cells during both nongrowth-linked (500 μg BAM/L) and growth-linked (10,000 μg BAM/L) regimes. MSH1 cells used as inoculum were either not or pre-exposed to H2 and were harvested at different growth phases. During the nongrowth-linked BAM biodegradation, MSH1 pre-exposed to H2 exhibited a 1.2 to 1.5-fold higher initial specific BAM biodegradation rate, resulting in more rapid BAM removal, likely due to the retention of more metabolically active cells, as suggested by a cell vitality assay. During the growth-linked biodegradation, MSH1 pre-exposed to H2 demonstrated accelerated growth with a 1.5-fold higher maximum specific growth rate, which coincided with an improved BAM removal. The positive effects of H2 were only evident for MSH1 cells harvested either at the stationary and/or starvation phase. Evidence of H2 metabolism was supported by H2 consumption measurements. Collectively, this study reveals that microbial H2 metabolism enables OMP-degrading bacteria to sustain metabolic activity under starvation conditions, offering a novel strategy to enhance long-term OMP-biodegradation.},
}

@article {pmid40577691,
year = {2025},
author = {Quellhorst, HE and Ponce, MA and Holguin Rocha, AF and Sakka, MK and Tsintzou, G and Maille, JM and Vagelas, I and Madesis, P and Athanassiou, CG and Scully, ED and Zhu, KY and Morrison, WR},
title = {The capacity of 3 stored product insect species to vector microbes after increasing dispersal periods.},
journal = {Journal of economic entomology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jee/toaf123},
pmid = {40577691},
issn = {1938-291X},
support = {2024-67012-42439//USDA-NIFA/ ; },
abstract = {Prostephanus truncatus (Horn) (Coleoptera: Bostrichidae), Rhyzopertha dominica (F.) (Coleoptera: Bostrichidae), and Sitophilus zeamais Motschulsky (Coleoptera: Curculionidae) are 3 important stored product pests of maize, but there has been little work evaluating how they vector microbes. While there has been some work assessing the microbial ecology of S. zeamais, none has directly assessed whether they transfer microbes to new food patches. Thus, we evaluated the ability of both species to vector microbes when given the opportunity to forage on sterilized potato dextrose agar dishes after a 0, 24, or 72 h dispersal period in a sterilized container. We subsequently photographed the dishes at 3 and 5 d after introduction and quantified the microbial growth using ImageJ. In addition, we isolated unique morphotypes of fungi, extracted DNA and amplified the internal transcribed spacer 5/4 intergenic spacer region, then sequenced to determine fungal identity. We found that 3 species readily vectored several plant pathogenic microbes, including 21 taxa from more than 11 genera, notably Aspergillus spp. Increasing dispersal period (0, 24, 72 h) resulted in a third less microbial growth (mean microbial growth or mean greyscale value from 0 to 255) by S. zeamais after 72 h, while for P. truncatus it resulted in a 2.7-fold increase in microbial growth. Dispersal by S. zeamais (0, 24, 72 h) resulted in 6.6-fold more microbial growth than dispersal by P. truncatus. There was 1.5- to 3.7-fold more microbial growth after 5 d than 3 d by each species. This research has important implications for food safety in the postharvest environment, especially for maize production, storage, and processing.},
}

@article {pmid40577531,
year = {2025},
author = {Duxbury, SJN and Raguideau, S and Cremin, K and Richards, L and Medvecky, M and Rosko, J and Coates, M and Randall, K and Chen, J and Quince, C and Soyer, OS},
title = {Niche formation and metabolic interactions contribute to stable diversity in a spatially structured cyanobacterial community.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf126},
pmid = {40577531},
issn = {1751-7370},
abstract = {Understanding how microbial communities maintain stable compositional diversity is a key question in microbial ecology. Studies from pairwise interactions and synthetic communities indicate that metabolic interactions and spatial organisation can influence diversity, but the relevance of these factors in more complex communities is unclear. Here we used a cyanobacterial enrichment community that consistently forms millimetre-scale granular structures, to investigate compositional diversity and its stability. Over a year of passaging in media without significant carbon source, we found stable co-existence of 17 species belonging to diverse bacterial phyla. Metagenomic analysis revealed polysaccharide breakdown genes and complementary vitamin biosynthesis pathways in these species. Supporting these findings, we show growth of several isolated species on cyanobacterial slime components and experimentally verify vitamin exchanges between two members of the community. Several species had genes for (an)oxygenic photosynthesis and sulfur cycling, the expression of which we verified via meta transcriptomics. Consistent with this, we found that the granular structures displayed oxygen gradients with anoxic interiors. Cyanobacteria and other bacteria were distributed on the periphery and insides of these structures, respectively. Perturbation of the community via glucose addition resulted in fold increases of the heterotrophs, whereas disturbing the community by continual shaking led to fold reductions in several heterotrophs, including anoxygenic phototrophs. In contrast, removal of vitamins supplementation did not consistently alter species coverages, due to predicted vitamin sharing amongst community members. Taken together, these findings indicate that spatial organisation, microenvironment niche formation and metabolic interactions contribute to community compositional diversity and stability.},
}

@article {pmid40577477,
year = {2025},
author = {Li, B and Jiang, L and Johnson, T and Wang, G and Sun, W and Wei, G and Jiao, S and Gu, J and Tiedje, J and Qian, X},
title = {Global health risks lurking in livestock resistome.},
journal = {Science advances},
volume = {11},
number = {26},
pages = {eadt8073},
pmid = {40577477},
issn = {2375-2548},
mesh = {*Livestock/microbiology ; Animals ; *Global Health ; Humans ; Manure/microbiology ; Anti-Bacterial Agents/pharmacology ; Risk Assessment ; *Metagenome ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; },
abstract = {Livestock farming consumes more than 70% of global antibiotics annually, making livestock manures an important vector of anthropogenically influenced antibiotic resistance genes (ARGs). The global pattern of the livestock resistome, its driving mechanisms, and transmission potential to the clinic are not well assessed. We analyzed 4017 livestock manure metagenomes from 26 countries and constructed a comprehensive catalog of livestock ARGs and metagenome-assembled genomes. Livestock resistome is a substantial reservoir of known (2291 subtypes) and latent ARGs (3166 subtypes) and is highly connectable to human resistomes. We depicted the global pattern of livestock resistome and prevalence of clinically critical ARGs, highlighting the role of farm and human antibiotic stewardship in shaping livestock resistome. We developed a risk-assessment framework by integrating mobility potential, clinical significance, and host pathogenic relevance, and prioritized higher risk livestock ARGs, producing a predictive global map of livestock resistome risks that can help guide research and policy.},
}

*Livestock/microbiology
Animals
*Global Health
Humans
Manure/microbiology
Anti-Bacterial Agents/pharmacology
Risk Assessment
*Metagenome
*Drug Resistance, Microbial/genetics
*Drug Resistance, Bacterial/genetics

@article {pmid40501655,
year = {2025},
author = {Chen, J and Pfeifer, K and Steensen, K and Crooke, AM and Wolfram, M and Bobonis, J and Lopatina, A and Bartlau, N and Hussain, FA and Balskus, EP and Polz, MF and Blainey, PC},
title = {Bacterial peptide deformylase inhibitors induce prophages in competitors.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40501655},
issn = {2692-8205},
support = {R01 GM132564/GM/NIGMS NIH HHS/United States ; },
abstract = {While antibiotics mediate chemical warfare among microbes, their roles in the wild extend beyond direct growth inhibition(1). Some antibiotics have the potential to mediate interference competition by triggering a bacterial stress response that subsequently activates endogenous viruses integrated in bacterial genomes (prophages). Canonically, this activation is regulated by the SOS response upon DNA damage. Here we show that a metabolite produced by natural isolates of Vibrio ordalii circumvents the SOS response by directly triggering prophage induction in other Vibrio species, co-occurring in the same environment. While the metabolite was previously classified as a broad-spectrum antibiotic, we observe how it acts as a peptide deformylase inhibitor that specifically induces certain prophages, even when target bacterial cells carry multiple other prophages. Its biosynthetic gene cluster, or ord cluster, also encodes its own peptide deformylase (OrdE) which provides self-immunity to producer strains. Likewise, among natural Vibrio isolates that carry similar prophages, resistance against the ord metabolite was found in those that had acquired a divergent second peptide deformylase. Finally, we show that prophage induction by the ord cluster prevents slower-growing producer strains from being outcompeted by their otherwise fast-growing competitors if they carry an inducible prophage. Thus, we demonstrate how natural products play additional impactful roles in communities beyond antibiotic activity and that prophage induction serves as an interference competition strategy, sustaining community diversity.},
}

@article {pmid40576334,
year = {2025},
author = {Lee, EM and Srinivasan, S and Purvine, SO and Fiedler, TL and Leiser, OP and Proll, SC and Minot, SS and Djukovic, D and Raftery, D and Johnston, C and Fredricks, DN and Deatherage Kaiser, BL},
title = {Syntrophic bacterial and host-microbe interactions in bacterial vaginosis.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf055},
pmid = {40576334},
issn = {1751-7370},
abstract = {Bacterial vaginosis (BV) is a common, polymicrobial condition of the vaginal microbiota that is associated with symptoms such as malodor and excessive discharge, along with increased risk of various adverse sequelae. Host-bacteria and bacteria-bacteria interactions are thought to contribute to the condition, but many of these functions have yet to be elucidated. Using untargeted metaproteomics, we identified 1068 host and 1418 bacterial proteins in a set of cervicovaginal lavage samples collected from 20 participants with BV and 9 who were negative for the condition. We identified Dialister micraerophilus as a major producer of malodorous polyamines and identified a syntrophic interaction between this organism and Fannyhessea vaginae that leads to increased production of putrescine, a metabolite characteristic of BV. Although formate synthesis has not previously been noted in BV, we discovered diverse bacteria associated with the condition express pyruvate formate-lyase enzymes in vivo and confirm these organisms secrete formic acid in vitro. Sodium hypophosphite efficiently inhibited this function in multiple taxa. We also found that the fastidious organism Coriobacteriales bacterium DNF00809 can metabolize formic acid secreted by Gardnerella vaginalis, representing another syntrophic interaction. We noted an increased abundance of the host epithelial repair protein transglutaminase 3 in the metaproteomic data, which we confirmed by enzyme-linked immunosorbent assay. Other proteins identified in our samples implicate Finegoldia magna and Parvimonas micra in the production of malodorous trimethylamine. Some bacterial proteins identified represent novel targets for future therapeutics to disrupt BV communities and promote vaginal colonization by commensal lactobacilli.},
}

@article {pmid40573780,
year = {2025},
author = {Zhang, S and Luo, Z and Peng, J and Wu, X and Meng, X and Qin, Y and Zhu, F},
title = {Analysis of Cadmium Accumulation Characteristics Affected by Rhizosphere Bacterial Community of Two High-Quality Rice Varieties.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/plants14121790},
pmid = {40573780},
issn = {2223-7747},
support = {2024YFD2301400//the National Key Research and Development Program of China/ ; 2024CX09//the Agricultural Science and Technology Innovation Project of Hunan Province, China/ ; },
abstract = {Cadmium-contaminated rice poses serious health risks through the bioaccumulation of Cd (cadmium) from soil to edible grains. Cd contamination disrupts soil microbial ecology and alters microbial diversity. However, the role of cultivar-specific rhizosphere microbial communities in modulating Cd uptake remains unclear. In this study, we aimed to elucidate the mechanism underlying variety-dependent rhizosphere microecological remodeling and Cd accumulation in two independently selected late rice varieties, Yuzhenxiang (YZX) and Xiangwanxian 12 (XWX12). Combining physiological and metagenomic analyses, we revealed variety-specific correlations between root Cd accumulation and dynamic changes in soil pH, soil available phosphorus, and rhizosphere bacteria. The key bacterial genera (Variibacter, Nitrospira) showed differential enrichment patterns under Cd stress. In contrast, Galella and Anaeromyxobacter likely reduce Cd bioavailability by modulating phosphorus availability. Overall, this study elucidates that rice cultivars indirectly shape Cd accumulation patterns via rhizosphere microbial remodeling, providing novel insights for microbial remediation strategies in Cd-contaminated farmland.},
}

@article {pmid40572127,
year = {2025},
author = {Mohammadi, T and Ely, B},
title = {Dolichocephalovirinae Phages Exist as Episomal Pseudolysogens Across Diverse Soil Bacteria.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572127},
issn = {2076-2607},
abstract = {Interactions between bacteria and bacteriophages are important for the maintenance of soil communities. In this study, we characterized the giant bacteriophages found within diverse soil bacteria and 14 additional phages isolated directly from soil samples. Based on their genome sizes and genetic composition, we concluded that these phages belong to the Dolichocephalovirinae subfamily. In addition, we used pulsed-field gel electrophoresis to show that the genomes of these phages were present as episomal pseudolysogens in the cytoplasm of their host cells. These findings suggest that episomal phages are important components of soil microbial ecosystems. Understanding the interactions between bacteriophages and bacteria is essential for microbial ecology, as they influence nutrient cycling, community composition, and host evolution. Furthermore, these phage-bacteria dynamics offer potential applications in plant disease control, as bacteriophages could serve as biocontrol agents against soilborne pathogens, promoting sustainable agricultural practices.},
}

@article {pmid40569388,
year = {2025},
author = {Dellicour, S and Gámbaro, F and Jacquot, M and Lequime, S and Baele, G and Gilbert, M and Pybus, OG and Suchard, MA and Lemey, P},
title = {Comparative performance of viral landscape phylogeography approaches.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {26},
pages = {e2506743122},
doi = {10.1073/pnas.2506743122},
pmid = {40569388},
issn = {1091-6490},
mesh = {Phylogeography/methods ; *RNA Viruses/genetics ; Phylogeny ; Genome, Viral ; Computer Simulation ; },
abstract = {The rapid evolution of RNA viruses implies that their evolutionary and ecological processes occur on the same time scale. Genome sequences of these pathogens therefore can contain information about the processes that govern their transmission and dispersal. Landscape phylogeographic approaches use phylogeographic reconstructions to investigate the impact of environmental factors and variables on the spatial spread of viruses. Here, we extend and improve existing approaches and develop three novel landscape phylogeographic methods that can test the impact of continuous environmental factors on the diffusion velocity of viral lineages. In order to evaluate the different methods, we also implemented two simulation frameworks to test and compare their statistical performance. The results enable us to formulate clear guidelines for the use of three complementary landscape phylogeographic approaches that have sufficient statistical power and low rates of false positives. Our open-source methods are available to the cientific community and can be used to investigate the drivers of viral spread, with potential benefits for understanding virus epidemiology and designing tailored intervention strategies.},
}

Phylogeography/methods
*RNA Viruses/genetics
Phylogeny
Genome, Viral
Computer Simulation

@article {pmid40569073,
year = {2025},
author = {Kobiałka, M and Świerczewski, D and Walczak, M and Urbańczyk, W},
title = {Extremely distinct microbial communities in closely related leafhopper subfamilies: Typhlocybinae and Eurymelinae (Cicadellidae, Hemiptera).},
journal = {mSystems},
volume = {},
number = {},
pages = {e0060325},
doi = {10.1128/msystems.00603-25},
pmid = {40569073},
issn = {2379-5077},
abstract = {UNLABELLED: Among the Hemiptera insects, a widespread way of feeding is sucking sap from host plants. Due to their nutrient-poor diet, these insects enter into obligate symbiosis with their microorganisms involved in the synthesis of components essential for host survival. However, within the Cicadellidae family, there is a relatively large group of mesophyll feeders-Typhlocybinae-that is considered to be devoid of obligate symbiotic companions. In this work, we examine the composition of microorganisms in this subfamily and compare the results with their close relatives-the Eurymelinae subfamily. To study the microbiome, we used high-throughput next-generation sequencing (NGS, Illumina) and advanced microscopic techniques, such as transmission electron microscopy (TEM) and fluorescence in situ hybridization (FISH), in a confocal microscope. In the bodies of Typhlocybinae insects, we did not detect the presence of microorganisms deemed to be obligate symbionts. Their microbial communities consist of facultative symbionts, mainly alphaproteobacteria such as Wolbachia or Rickettsia as well as others that can be considered as facultative, including Spiroplasma, Acidocella, Arsenophonus, Sodalis, Lariskella, Serratia, Cardinium, and Asaia. On the other hand, the Eurymelinae group is characterized by a high diversity of microbial communities, both obligate and facultative, similar to other Cicadomorpha. We find co-symbionts involved in the synthesis of essential amino acids such as Karelsulcia, betaproteobacteria Nasuia, or gammaproteobacteria Sodalis. In other representatives, we observed symbiotic yeast-like fungi from the family Ophiocordycipitaceae or Arsenophonus bacteria inhabiting the interior of Karelsulcia bacteria. Additionally, we investigated some aspects of symbiont transmission and the phylogeny of symbiotic organisms and their hosts.

IMPORTANCE: The Typhlocybinae and Eurymelinae leafhoppers differ significantly in their symbiotic communities. They have different diets, as Typhlocybinae insects feed on parenchyma, which is richer in nutrients, while Eurymelinae, like most representatives of Auchenorrhyncha, consume sap from the phloem fibers of plants. Our work presents comprehensive studies of 42 species belonging to the two above-mentioned, and so far poorly known, Cicadomorpha subfamilies. Phylogenetic studies indicate that the insects from the studied groups have a common ancestor. The diet shift in the Typhlocybinae leafhoppers contributed to major changes in the composition of microorganisms inhabiting the body of these insects. Research on the impact of diet on the microbiome and the subsequent consequences on the evolution and adaptation of organisms plays an important role in the era of climate change.},
}

@article {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 = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf129},
pmid = {40568985},
issn = {1751-7370},
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 (PS index) from macroecology to identify generalists. We applied these concepts to time-series (field) metagenomes from the Piver's Island Coastal Observatory (PICO) to establish that coastal microbial communities are resilient to major perturbations such as tropical cyclones and (uncommon) cold or warm temperature events, in part due to the response of rare populations. Therefore, these results provide support for the insurance hypothesis [i.e., the rare biosphere has the buffering capacity to mitigate the effects of disturbance]. Additionally, generalists appear to contribute proportionally more than specialists to community adaptation to perturbations like warming, supporting the disturbance-specialization hypothesis [i.e., disturbance favors generalists]. Several of these findings were also observed in replicated laboratory mesocosms that aimed to simulate disturbances such as a rain-driven washout of microbial cells and a labile organic matter release from a phytoplankton bloom. Taken together, our results advance understanding of the mechanisms governing microbial population dynamics under changing environmental conditions and have implications for ecosystem modeling.},
}

@article {pmid40567269,
year = {2025},
author = {Mohamadi Nasrabadi, A and Eckstein, D and Mettke, P and Ghanem, N and Kallies, R and Schmidt, M and Mothes, F and Schaefer, T and Graefe, R and Bandara, CD and Maier, M and Liebert, UG and Richnow, H and Herrmann, H},
title = {A Virus Aerosol Chamber Study: The Impact of UVA, UVC, and H2O2 on Airborne Viral Transmission.},
journal = {Environment & health (Washington, D.C.)},
volume = {3},
number = {6},
pages = {648-658},
pmid = {40567269},
issn = {2833-8278},
abstract = {The COVID-19 pandemic highlighted the urgent need to control airborne virus transmission, particularly in indoor environments with limited ventilation. This study evaluates the effectiveness of UVA and UVC irradiation, along with hydrogen peroxide (H2O2), in inactivating aerosolized viruses. A 19 m[3] virus aerosol simulation chamber, replicating indoor conditions, was used to simulate human respiratory emissions by aerosolizing Escherichia phage T4 (T4 phages) embedded in a pig mucin medium that mimics respiratory aerosols. Results showed a clear, dose-dependent reduction in viral genome copies with UVC exposure, where a dose of 129.9 mJ/cm[2] reduced over 99% of the viral genome copies. Although less efficient, UVA still contributed to virus inactivation, reducing detectable phages to 20% at 513.30 J/cm[2]. Mucin provided a protective effect, making virus removal more challenging. Hydrogen peroxide enhanced disinfection, with 1.6 ppm reducing viral genome copies by 78%, and higher concentrations (up to 16 ppm) achieving over 99% reduction in the dark condition. The combination of UVA/UVC with H2O2 further enhanced disinfection, eliminating detectable virus genome copies entirely. These findings underscore the potential for using combined UV light and chemical treatments to effectively mitigate airborne viral transmission in enclosed spaces.},
}

@article {pmid40566942,
year = {2025},
author = {Kara, K and Yilmaz Öztaş, S and Baytok, E},
title = {In Vitro Ruminal Metagenomic Profiles and Ruminal Fermentation Variables of Aromatic Plant Pulps.},
journal = {Veterinary medicine and science},
volume = {11},
number = {4},
pages = {e70447},
doi = {10.1002/vms3.70447},
pmid = {40566942},
issn = {2053-1095},
support = {TSA-2023-13007//Erciyes University Scientific Research Projects Unit/ ; },
mesh = {*Fermentation ; *Rumen/microbiology/metabolism/physiology ; Animals ; Cattle ; Metagenomics ; Animal Feed/analysis ; *Metagenome ; Gastrointestinal Microbiome ; Digestion ; },
abstract = {BACKGROUND: Aromatic plant residues remaining after aromatic oil extraction represent a promising alternative feed source due to their rich bioactive compound content and fibrous structure. However, their fermentative behaviour and microbial degradability in the rumen require evaluation.

OBJECTIVE: This study aimed to determine the nutrient composition, in vitro ruminal gas production, digestibility characteristics and fermentation end-products of aromatic plant pulps (sage, thyme, lavender and yarrow) obtained via hydrodistillation.

METHODS: Dried pulps were analysed for nutrient contents and subjected to in vitro ruminal fermentation for 24 h. Gas production estimated metabolizable energy (ME), net energy for lactation (NEL), organic matter digestibility (OMd), ammonia nitrogen (NH3-N) and short-chain fatty acid (SCFA) profiles were evaluated. Microbial community composition was assessed via 16S rRNA-based metagenomics.

RESULTS: Yarrow pulp had the highest gas production, ME, NEL, OMd and SCFA concentrations (AA, BA, IVA, T-SCFA) (p < 0.05). Thyme pulp exhibited the highest NH3-N levels (75.14 mg/L), suggesting high rumen-degradable protein content. Sage pulp had the lowest NH3-N levels (60.93 mg/L). Microbial composition shifted with fibre content; higher lignin (in lavender) was associated with lower Bacteroidota and higher Firmicutes abundance. Methanogenic archaea (Methanobrevibacter) were least abundant in thyme pulp (p < 0.05).

CONCLUSION: Due to their fermentability and favourable microbial responses, aromatic plant pulps, particularly yarrow, show promise as functional ruminant feed ingredients. These byproducts may enhance ruminal fibre utilization while modulating microbial ecology and reducing methane-associated archaea.},
}

*Fermentation
*Rumen/microbiology/metabolism/physiology
Animals
Cattle
Metagenomics
Animal Feed/analysis
*Metagenome
Gastrointestinal Microbiome
Digestion

@article {pmid40564363,
year = {2025},
author = {Luo, G and Cheng, Y and Xu, Y and Liu, J and Yang, W and Liu, J and Guo, B and Zhu, H},
title = {Monochromatic Light Impacts the Growth Performance, Intestinal Morphology, Barrier Function, Antioxidant Status, and Microflora of Yangzhou Geese.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {12},
pages = {},
doi = {10.3390/ani15121815},
pmid = {40564363},
issn = {2076-2615},
support = {32202622//National Natural Science Foundation of China/ ; 32102542//National Natural Science Foundation of China/ ; CX(24)1012//Jiangsu Agricultural Science and Technology Innovation Fund/ ; 2025SKLAB6-17//Open project of State Key Laboratory of Animal Biotech Breeding/ ; },
abstract = {This study investigates the effect of monochromatic light on the body weight (BW), melatonin concentration and its receptors expression levels, intestinal health, and gut microorganisms of Yangzhou geese. Green light (GL) significantly increased BW, melatonin and its receptor expression levels, villus height (VH) and villus height/crypt depth (VH/CD) ratio, superoxide dismutase (SOD), catalase (CAT), and total antioxidant capacity (T-AOC) activities, as well as the abundance of Synergistota and Prevotellaceae_UCG-001, compared with white light (WL). Blue light (BL) significantly increased the mRNA expression of melatonin membrane receptor 1a (Mel1a) and nuclear receptor 1α (RORα), VH and VH/CD ratio, CAT activity, cecal microbes diversity, and decreased malondialdehyde (MDA) levels. Red light (RL) significantly decreased average daily feed intake, reduced the abundances of Synergistota and Prevotellaceae_UCG-001, and increased Mel1a and RORα mRNA expression levels, MDA content, and cecum microbial diversity. Moreover, melatonin levels were significantly higher in the GL and BL groups compared to RL. Furthermore, the mRNA expression levels of Claudin-10, Occludin, and occludens-1 (ZO-1) were significantly upregulated under GL or BL exposures compared to the WL group, whereas RL only enhanced the expression levels of ZO-1. Spearman's correlation analysis revealed that the relative abundance of Prevotellaceae_UCG-001 exhibited positive correlations with BW, melatonin and its receptors expression, gut health, and antioxidant capacity. Overall, these findings suggested that GL exposure enhanced melatonin synthesis and its receptors expression, modulated intestinal homeostasis and microbial ecology, and ultimately increased goose BW.},
}

@article {pmid40562244,
year = {2025},
author = {Costa, BF and Sawaya, C and Buren, JV and Smith, AL},
title = {Investigating anaerobic digestion microbiome resilience to high PFOA and PFOS mixtures during cometabolism.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132877},
doi = {10.1016/j.biortech.2025.132877},
pmid = {40562244},
issn = {1873-2976},
abstract = {Anaerobic digestion (AD) is a reducing environment with high microbial diversity and potential for biotransformation of PFAS. Yet, their fate and impact on the microbial community remains poorly understood. This study evaluated the long-term impact (100 d) of perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS) spiked at10 mg/L (low) and 100 mg/L (high), respectively. Although resilient to complete system failure, high PFAS concentrations disrupted AD, evidenced by 25-50 % reduction in methane content, 45 %-48 % reduction in cumulative biogas production, and accumulation of butyric acid. No significant decrease in PFAS concentration was observed in the liquid fraction after 100 d relative to the kill controls, indicating PFAS adsorption behavior. However, PFAS concentrations were temporally variable. Microbial community analysis revealed enrichment of notable AD groups, such as Firmicutes, Synergistetes, and Methanomassillicoccus phyla in high PFAS reactors, which underscores the potential for the microbiome adaptation and informs future strategies for PFAS-contaminated sludge treatment.},
}

@article {pmid40561955,
year = {2025},
author = {Yasin, MU and Muhammad, S and Chen, N and Hannan, F and Afzal, M and Haider, Z and Ali, B and Ahmad, I and Rehman, M and Gan, Y},
title = {Nano-engineered biochar enhances soil microbial interactions and maize transcriptomic pathways for cadmium detoxification.},
journal = {Journal of hazardous materials},
volume = {495},
number = {},
pages = {139029},
doi = {10.1016/j.jhazmat.2025.139029},
pmid = {40561955},
issn = {1873-3336},
abstract = {Cadmium (Cd) contamination threatens agroecosystems and food security by degrading soil health, inducing plant oxidative stress, and reducing crop yields. Sustainable strategies integrating biochar (BC) with nanoparticles (NPs) for Cd immobilization and soil-plant-microbe restoration remain underexplored. Here, we demonstrate the efficacy of BC, nano-silicon (nSi), and nano-iron (nFe) to immobilize Cd, improve soil health and reprogram maize stress responses in Cd-contaminated soil. Soil Cd bioavailability, microbial networks, and maize transcriptomes were analyzed under varying BC-nSi-nFe formulations. Among these formulations, the BC + 25 % nSi + 75 % nFe + Cd (T6) composite reduced bioavailable Cd by 21 %, raised soil pH from 6.21 to 6.98, and enhanced soil enzyme activities (118-139 %). T6 improved maize biomass (115-119 %), reduced shoot Cd accumulation (78 %), and suppressed oxidative stress (67-75 % ROS reduction). This study presents transcriptomic evidence showing that BC-NPs composites mitigate Cd stress and modulate maize antioxidant defense and phytohormone signaling pathways, offering new insights into the molecular mechanisms underlying improved plant resilience. Soil microbial networks shifted toward metal-resistant taxa, with enriched glutathione metabolism and nitrogen fixation. BC-NPs composites offer a multidimensional remediation strategy, integrating nanomaterial science, microbial ecology, and plant molecular biology to mitigate Cd toxicity. This approach enhances soil-plant resilience, supporting sustainable agriculture in contaminated ecosystems.},
}

@article {pmid40561631,
year = {2025},
author = {Ma, X and Li, Y and Niu, L and Grossart, HP and Shang, J and Zheng, J and Wu, J},
title = {Salinity regulates nutrient cycling via top-down and bottom-up forces in artificial cut-off tidal channels: Insights from multitrophic microbiota.},
journal = {Water research},
volume = {285},
number = {},
pages = {124037},
doi = {10.1016/j.watres.2025.124037},
pmid = {40561631},
issn = {1879-2448},
abstract = {Artificial cut-off of natural tidal meanders for flood control has substantially altered microbial communities and their role in nutrient cycling, yet the lack of comprehensive investigations into these specific anthropogenic impacts introduces greater uncertainty regarding the resultant water quality of nutrient-enriched estuaries. Here, we investigated how planktonic multitrophic microbiota and their mediated nutrient cycling respond to artificial meander cut-off using the environmental DNA (eDNA) approach. Results showed that despite the decline in α diversity of multitrophic microbiota, the nutrient cycling potential of the water column was enhanced 2.91-fold in the straight tidal channel. The artificial cut-off restructured the microbial food web, with trophic transfer efficiency from basal species to protozoa increasing. Salinity was identified to be the key environmental driver, mitigating the negative impact of decreased biodiversity on estuarine nutrient cycling potential by intensifying protozoan predation on heterotrophic bacteria (top-down forces). Additionally, salinity further enhanced environmental selection (bottom-up forces), reducing heterotrophic bacterial diversity while promoting the proliferation of functional microbial taxa, such as Comamonadaceae, Chitinophagaceae, and Rhodocyclaceae. This study offers novel insights into nutrient cycling in artificial straight tidal channels and provides critical foundations for optimizing restoration and management strategies in anthropogenically modified tidal river.},
}

@article {pmid40560449,
year = {2025},
author = {de Meireles, DA and Souza, T and de A A Carneiro, K and da S Fraga, V and de O Dias, B and da S Batista, D and Martins, EL and de Lima, AFL and Dos Santos Nascimento, G and Campos, MCC},
title = {Treated Wastewater Irrigation Enhances Plant Biomass, Soil Fertility, and Rhizosphere Microbial Activity in C4 and CAM species Grown on a Degraded Planosol.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {7},
pages = {804},
pmid = {40560449},
issn = {1573-2959},
mesh = {*Wastewater/chemistry ; *Agricultural Irrigation/methods ; *Soil Microbiology ; *Soil/chemistry ; *Rhizosphere ; Biomass ; *Waste Disposal, Fluid/methods ; Brazil ; },
abstract = {The Brazilian semi-arid region, marked by erratic rainfall and severely degraded soils, presents critical challenges for sustainable agriculture. In this context, the reuse of treated domestic wastewater-collected from a septic tank and anaerobic filter system-offers a promising strategy to enhance plant productivity and rehabilitate soil conditions, particularly within the Caatinga biome. This study evaluated the long-term (four-year) effects of irrigation with pure water versus treated domestic wastewater on plant dry biomass, soil fertility, and rhizospheric microbial activity in a degraded Planosol. Two plant types were assessed: a C4 species (Mimosa caesalpiniifolia) and a CAM species (Opuntia atropes). Results demonstrated that treated wastewater irrigation significantly increased dry biomass, with a 12.18% increase in the C4 species and a 29.33% increase in the CAM species. Soil chemical fertility improved notably, with wastewater application raising soil pH by 5.0%, increasing soil organic carbon by 87.9%, and enhancing nutrient availability, including nitrogen, potassium, magnesium, and sodium. A 37.5% reduction in exchangeable aluminum further indicated mitigation of soil acidity. Microbial responses varied between species: while soil respiration increased in both rhizospheres-more prominently in CAM species-microbial biomass carbon rose significantly in the C4 rhizosphere but declined in CAM, suggesting species-specific microbial interactions. These findings support the potential of treated domestic wastewater as a nutrient-rich, low-cost irrigation alternative for improving plant performance and soil quality in semi-arid degraded lands. Nevertheless, potential risks-including salinity build-up and pathogen persistence-necessitate long-term monitoring and further environmental safety assessments. By integrating plant physiology, soil chemistry, and microbial ecology, this study offers a comprehensive approach to evaluating wastewater reuse as a sustainable agricultural and ecological restoration practice in the Caatinga biome.},
}

*Wastewater/chemistry
*Agricultural Irrigation/methods
*Soil Microbiology
*Soil/chemistry
*Rhizosphere
Biomass
*Waste Disposal, Fluid/methods
Brazil

@article {pmid28732554,
year = {2017},
author = {De Vuyst, L and Van Kerrebroeck, S and Leroy, F},
title = {Microbial Ecology and Process Technology of Sourdough Fermentation.},
journal = {Advances in applied microbiology},
volume = {100},
number = {},
pages = {49-160},
doi = {10.1016/bs.aambs.2017.02.003},
pmid = {28732554},
issn = {0065-2164},
mesh = {Bread/analysis/*microbiology ; Fermentation ; Food Handling ; Lactobacillus/genetics/*metabolism ; *Microbiota ; Triticum/*metabolism/microbiology ; Yeasts/genetics/*metabolism ; },
abstract = {From a microbiological perspective, sourdough is to be considered as a specific and stressful ecosystem, harboring yeasts and lactic acid bacteria (LAB), that is used for the production of baked goods. With respect to the metabolic impact of the sourdough microbiota, acidification (LAB), flavor formation (LAB and yeasts), and leavening (yeasts and heterofermentative LAB species) are most noticeable. Three distinct types of sourdough fermentation processes can be discerned based on the inocula applied, namely backslopped ones (type 1), those initiated with starter cultures (type 2), and those initiated with a starter culture followed by backslopping (type 3). A sourdough-characteristic LAB species is Lactobacillus sanfranciscensis. A sourdough-characteristic yeast species is Candida humilis. Although it has been suggested that the microbiota of a specific sourdough may be influenced by its geographical origin, region specificity often seems to be an artefact resulting from interpretation of the research data, as those are dependent on sampling, isolation, and identification procedures. It is however clear that sourdough-adapted microorganisms are able to withstand stress conditions encountered during their growth. Based on the technological setup, type 0 (predoughs), type I (artisan bakery firm sourdoughs), type II (industrial liquid sourdoughs), and type III sourdoughs (industrial dried sourdoughs) can be distinguished. The production of all sourdoughs, independent of their classification, depends on several intrinsic and extrinsic factors. Both the flour (type, quality status, etc.) and the process parameters (fermentation temperature, pH and pH evolution, dough yield, water activity, oxygen tension, backslopping procedure and fermentation duration, etc.) determine the dynamics and outcome of (backslopped) sourdough fermentation processes.},
}

Bread/analysis/*microbiology
Fermentation
Food Handling
Lactobacillus/genetics/*metabolism
*Microbiota
Triticum/*metabolism/microbiology
Yeasts/genetics/*metabolism

@article {pmid40559796,
year = {2025},
author = {Popov, IV and Peshkova, DA and Lukbanova, EA and Tsurkova, IS and Emelyantsev, SA and Krikunova, AA and Malinovkin, AV and Chikindas, ML and Ermakov, AM and Popov, IV},
title = {Gut Microbiota Dynamics in Hibernating and Active Nyctalus noctula: Hibernation-Associated Loss of Diversity and Anaerobe Enrichment.},
journal = {Veterinary sciences},
volume = {12},
number = {6},
pages = {},
doi = {10.3390/vetsci12060559},
pmid = {40559796},
issn = {2306-7381},
support = {23-14-00316//Russian Science Foundation/ ; 075-10-2025-017//Ministry of Science and Higher Education of the Russian Federation/ ; },
abstract = {Hibernation in mammals entails profound physiological changes that are known to impact host-associated microbial communities, yet its effects on the gut microbiota of synanthropic bats remain underexplored. In this study, we investigated the gut bacterial composition and diversity of Nyctalus noctula before and during hibernation using high-throughput 16S rRNA amplicon sequencing. Fecal samples from individually banded bats were collected under controlled conditions at a rehabilitation center and analyzed for alpha and beta diversity, as well as differential taxonomic abundance. Hibernation was associated with a marked reduction in microbial diversity according to the Shannon and Simpson indices and a distinct restructuring of gut communities based on the Bray-Curtis dissimilarity index. Active bats exhibited a diverse microbiota enriched in facultative anaerobes, including Lactococcus, Enterococcus, and Escherichia-Shigella, while hibernating individuals were dominated by obligate anaerobes, such as Romboutsia and Paeniclostridium. These findings suggest a contraction and functional specialization of the gut microbiota during torpor, potentially reflecting adaptations to fasting, hypothermia, and reduced gut motility. Our results demonstrate that the bat's gut microbiome is highly responsive to physiological status and underscore the importance of microbial ecology for understanding the host's energy balance and health under seasonal contexts.},
}

@article {pmid40559651,
year = {2025},
author = {Wimmer, BC and Dwan, C and De Medts, J and Duysburgh, C and Rotsaert, C and Marzorati, M},
title = {Undaria pinnatifida Fucoidan Enhances Gut Microbiome, Butyrate Production, and Exerts Anti-Inflammatory Effects in an In Vitro Short-Term SHIME[®] Coupled to a Caco-2/THP-1 Co-Culture Model.},
journal = {Marine drugs},
volume = {23},
number = {6},
pages = {},
doi = {10.3390/md23060242},
pmid = {40559651},
issn = {1660-3397},
support = {n.a.//Marinova Pty Ltd., 249 Kennedy Drive, Cambridge, TAS 7170, Australia/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Polysaccharides/pharmacology/isolation & purification ; *Undaria/chemistry ; *Anti-Inflammatory Agents/pharmacology ; Caco-2 Cells ; Coculture Techniques ; *Butyrates/metabolism ; THP-1 Cells ; Colon/microbiology/drug effects ; Feces/microbiology ; Cytokines/metabolism ; Adult ; Fatty Acids, Volatile/metabolism ; Edible Seaweeds ; },
abstract = {Fucoidans have demonstrated a wide range of bioactivities including immune modulation and benefits in gut health. To gain a deeper understanding on the effects of fucoidan from Undaria pinnatifida (UPF) on the colonic microbiome, the short-term Simulator of the Human Intestinal Microbial Ecosystem[®], a validated in vitro gut model, was applied. Following a three-week intervention period on adult faecal samples from three healthy donors, microbial community activity of the colonic microbiota was assessed by quantifying short-chain fatty acids while composition was analysed utilising 16S-targeted Illumina sequencing. Metagenomic data were used to describe changes in community structure. To assess the secretion of cytokines, co-culture experiments using Caco-2 and THP1-Blue™ cells were performed. UPF supplementation over a three-week period had a profound butyrogenic effect while also enriching colonic microbial diversity, consistently stimulating saccharolytic genera, and reducing genera linked with potentially negative health effects in both regions of the colon. Mild immune modulatory effects of UPF were also observed. Colonic fermentation of UPF showed anti-inflammatory properties by inducing the secretion of the anti-inflammatory cytokines IL-6 and IL-10 in two out of three donors in the proximal and distal colon. In conclusion, UPF supplementation may provide significant gut health benefits.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Polysaccharides/pharmacology/isolation & purification
*Undaria/chemistry
*Anti-Inflammatory Agents/pharmacology
Caco-2 Cells
Coculture Techniques
*Butyrates/metabolism
THP-1 Cells
Colon/microbiology/drug effects
Feces/microbiology
Cytokines/metabolism
Adult
Fatty Acids, Volatile/metabolism
Edible Seaweeds

@article {pmid40558970,
year = {2025},
author = {Vieira, RIM and Peixoto, ADS and Monclaro, AV and Ricart, CAO and Filho, EXF and Miller, RNG and Gomes, TG},
title = {Fungal Coculture: Unlocking the Potential for Efficient Bioconversion of Lignocellulosic Biomass.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {6},
pages = {},
doi = {10.3390/jof11060458},
pmid = {40558970},
issn = {2309-608X},
support = {00193-00002388/2023-21//Foundation for Research Support of the Federal District/ ; },
abstract = {Microbial decomposition of persistent natural compounds such as phenolic lignin and polysaccharides in plant cell walls plays a crucial role in the global carbon cycle and underpins diverse biotechnological applications. Among microbial decomposers, fungi from the Ascomycota and Basidiomycota phyla have evolved specialized mechanisms for efficient lignocellulosic biomass degradation, employing extracellular enzymes and synergistic fungal consortia. Fungal coculture, defined as the controlled, axenic cultivation of multiple fungal species or strains in a single culture medium, is a promising strategy for industrial processes. This approach to biomass conversion offers potential for enhancing production of enzymes, biofuels, and other high-value bioproducts, while enabling investigation of ecological dynamics and metabolic pathways relevant to biorefinery operations. Lignocellulosic biomass conversion into fuels, energy, and biochemicals is central to the bioeconomy, integrating advanced biotechnology with sustainable resource use. Recent advancements in -omics technologies, including genomics, transcriptomics, and proteomics, have facilitated detailed analysis of fungal metabolism, uncovering novel secondary metabolites and enzymatic pathways activated under specific growth conditions. This review highlights the potential of fungal coculture systems to advance sustainable biomass conversion in alignment with circular bioeconomy goals.},
}

@article {pmid40557448,
year = {2025},
author = {Lingua, MS and Sabatino, ME and Cuatrin, A and Salvucci, E and Blajman, JE and Páez, RB and Wunderlin, DA and Baroni, MV},
title = {From waste to worth: stability, bioaccessibility, and cellular antioxidant activity of microencapsulated red grape pomace phenolics.},
journal = {Journal of the science of food and agriculture},
volume = {},
number = {},
pages = {},
doi = {10.1002/jsfa.70010},
pmid = {40557448},
issn = {1097-0010},
support = {//This work was supported by the National Institute of Agricultural Technology (INTA, Argentina) (Projects 2019-PD-I152-A537 and 2019-PE-I150-A5) and the National Agency of Scientific and Technological Promotion (FONCyT, Argentina), and Argentine Wine Corporation (COVIAR) (Project PICTO-COVIAR-2017-0123)./ ; },
abstract = {BACKGROUND: Red grape pomace (RGP) is a recognized winery by-product due to its phenolic profile with valuable antioxidant power and beneficial health properties. Following the latest trends in food science and technology, this study valorizes the use of RGP to obtain a food ingredient rich in antioxidant phenolics. An integrated approach was proposed, investigating the production by spray drying of easy-to-handle microparticles, rich in stable compounds with antioxidant properties demonstrated after simulated digestion using in vitro assays and Caco-2 cells. The changes in microbiota composition after fermentation were also studied.

RESULTS: Among investigated wall materials, maltodextrin/skimmed milk powder (1:1) 300 g L[-1] offered the highest drying yield, appropriate moisture, solubility, and adequate microparticle morphology, as well as the best stability of polyphenols. Encapsulation improved the protection of phenolic compounds and the in vitro antioxidant capacity during 120 days of storage at 4 and 25 °C, as compared to those unencapsulated. Microencapsulated polyphenols bioaccessibility was evident in 15 out of 22 compounds initially quantified, with 6.6% potentially absorbed. The polyphenols from microcapsules modulated positively the microbial ecology after colonic fermentation. Those derived from intestinal digestion demonstrated the highest capacity to reduce the reactive oxygen species under oxidative stress conditions in Caco-2 cells.

CONCLUSION: RGP could be used in the development of new food ingredients as a potential candidate for health promotion. This represents the first report on the benefits of RGP microcapsules as a food ingredient, validating its final biological effects in a cellular model considering the processing and digestion effects. © 2025 Society of Chemical Industry.},
}

@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},
doi = {10.3389/fmicb.2025.1570127},
pmid = {40556886},
issn = {1664-302X},
abstract = {Tannins are plant secondary metabolites that bind organic carbon (C) and nitrogen (N), potentially altering substrate bioavailability for enteric fermentation in ruminants. This interaction may reduce greenhouse gas (GHG) emissions and influence nitrogen partitioning. Given tannins' resistance to ruminal degradation and persistence through the gastrointestinal tract, this study investigated the effects of a tannin-based feed additive on fecal microbial diversity, fecal chemical composition, and GHG emissions. Twenty-four early- to mid-lactation dairy cows were randomized to receive either a tannin-based feed additive (TRT; containing condensed and hydrolyzable tannins from Schinopsis quebracho-colorado [Schltdl.]) or a control diet (CON) for 64 days. Cows were blocked by parity, dry matter intake, milk yield, body weight, and days in milk. Fecal samples were collected on days 0, 16, 32, and 64 and analyzed using 16S rRNA gene amplicon sequencing. Fecal C, N, and indole-3-lactate were measured, and GHG emissions (N2O, CH4, CO2) were assessed via 14-day laboratory incubation. A total of 1,538 amplicon sequence variants were identified, with Firmicutes as the dominant phylum. Fecal phylogenetic diversity showed a significant treatment × day interaction (p < 0.01), with TRT cows exhibiting reduced microbial diversity from day 16 to 64. Fecal C and N concentrations were significantly lower (p < 0.01) in TRT cows on day 16, while indole-3-lactate levels were higher on day 64 (p = 0.02). GHG emissions did not differ significantly between treatments. The tannin-based feed additive influenced fecal microbial community structure and select chemical parameters but did not significantly affect GHG emissions from feces. These findings suggest that dietary tannins may modulate gut microbial ecology with minimal impact on downstream manure-related emissions.},
}

@article {pmid40556136,
year = {2025},
author = {Long, Y and Li, Y and Zhang, J and Liu, J and Han, Q and Cao, Y and Jiang, Y and Liu, C and Hu, Y and Wang, G and Zhang, X and Jin, J and Semenov, M and Han, G and Liu, X and Yu, Z},
title = {Unconventional Nitrogen Fixation and Adaptive Genomics of a New Neorhizobium glycines sp. nov., A Promising Soybean Symbiont.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70046},
pmid = {40556136},
issn = {1365-3040},
support = {//This study was funded by the National Key R & D Program of China (2021YFD1500400), Strategic Priority Research Program of Chinese Academy of Sciences (XDA28020201), National Natural Science Foundation of China (32172123, 42207399)./ ; },
}

@article {pmid40555367,
year = {2025},
author = {McGrath, AH and Steinberg, PD and Egan, S and Kjelleberg, S and Marzinelli, EM},
title = {Disruption of host-associated and benthic microbiota affects reproductive output and settlement of a habitat-forming macroalga.},
journal = {Proceedings. Biological sciences},
volume = {292},
number = {2049},
pages = {20250729},
doi = {10.1098/rspb.2025.0729},
pmid = {40555367},
issn = {1471-2954},
support = {//University of Sydney/ ; //Australian Research Council/ ; //Ecological Society of Australia/ ; },
mesh = {*Microbiota/drug effects ; Reproduction ; Ecosystem ; *Rhodophyta/microbiology/physiology ; Anti-Bacterial Agents/pharmacology ; },
abstract = {The reproduction and establishment of habitat-forming species are key processes affecting their persistence and associated biodiversity. In marine systems, microbial communities associated with habitat-forming macroalgae can influence various aspects of host performance; however, the role of these microorganisms in influencing macroalgal reproduction and settlement is poorly understood. Using a dominant habitat-forming macroalga on Australian rocky shores, Hormosira banksii, we manipulated host- and benthic-associated microbiota to determine the relative importance of microorganisms to reproductive output (number of viable eggs released) and settlement (settlement and morphogenesis of algal zygotes). Disruption of the host microbiota using antibiotics decreased reproductive output after 2 weeks, with the effect dependent on the type of antibiotic used. Disruption of host- and benthic-associated microbiota, in combination, caused a significant decrease in settlement of H. banksii zygotes, with the combined disruption having the greatest impact on settlement success. Our results demonstrate the importance of host-associated microbiota in macroalgal reproduction and an interactive effect of host- and benthic-associated microbiota on settlement-a key ecological process with important implications for host fitness and potentially ecosystem persistence.},
}

*Microbiota/drug effects
Reproduction
Ecosystem
*Rhodophyta/microbiology/physiology
Anti-Bacterial Agents/pharmacology

@article {pmid40553410,
year = {2025},
author = {Bota, JL and Baum, C and Gawronski, S and Grafe, TU and Kerth, G and Schöner, MG and Schöner, CR},
title = {UV treatment of the digestive fluid of Nepenthes hemsleyana pitcher plants affects their digestive process, possibly via reducing microbial inquilines.},
journal = {Oecologia},
volume = {207},
number = {7},
pages = {108},
pmid = {40553410},
issn = {1432-1939},
support = {SCHO1740/1-1//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Ultraviolet Rays ; Animals ; Digestion/radiation effects ; },
abstract = {Interactions with microbes are ubiquitous, and many of them are essential for the survival and success of plants. In Nepenthes pitcher plants, they occur as part of a diverse community of organisms, so-called inquilines, that live inside the digestive fluid of the pitcher traps. However, evidence is ambiguous regarding the role of microbial inquilines: they may complement the plants' prey digestion, fix atmospheric N, act as competitors that reduce plant-available nutrients or affect the plants in other ways unrelated to the breakdown of prey. In a field experiment on Borneo, we investigated the effect of UV disinfection of the digestive fluid on prey digestion of N. hemsleyana that captures and digests insects as well as bat faeces in its pitchers. We show that in the short term, the photosynthetic performance of plants with UV-treated digestive fluids decreases compared to untreated plants, likely due to lower abundances of microbial inquilines. However, at the end of 2 months, responses of pitcher plants with UV-treated and untreated digestive fluids tend to equalise. Nutrient source, whether from insects or bat faeces, does not influence prey digestion. We expect our findings to be a starting point for unveiling the ecological role of microbial inquilines in pitcher plants and how they interact with other inquiline groups of higher trophic levels. Ultimately, this will also help to improve understanding of the functioning and evolution of convergent interactions in other carnivorous plants.},
}

*Ultraviolet Rays
Animals
Digestion/radiation effects

@article {pmid40553254,
year = {2025},
author = {Wu, BX and Ma, JY and Huang, XC and Liang, XS and Ning, BL and Wu, Q and Wang, SZ and Zhou, JH and Fu, WB},
title = {Acupuncture as A Potential Therapeutic Approach for Tourette Syndrome: Modulation of Neurotransmitter Levels and Gut Microbiota.},
journal = {Chinese journal of integrative medicine},
volume = {},
number = {},
pages = {},
pmid = {40553254},
issn = {1993-0402},
abstract = {OBJECTIVE: To investigate the effects of acupuncture on the neurotransmitter levels and gut microbiota in a mouse model of Tourette syndrome (TS).

METHODS: Thirty-six male C57/BL6 mice were randomly divided into 4 groups using a random number table method: 3,3'-iminodipropionitrile (IDPN) group, control group, acupuncture group, and tiapride group, with 9 mice in each group. In the IDPN group, acupuncture group, and tiapride group, mice received daily intraperitoneal injections of IDPN (300 mg/kg body weight) for 7 consecutive days to induce stereotyped behaviors. Subsequently, in the acupuncture intervention group, standardized acupuncture treatment was administered for 14 consecutive days to IDPN-induced TS model mice. The selected acupoints included Baihui (DU 20), Yintang (DU 29), Waiguan (SJ 5), and Zulinqi (GB 41). In the tiapride group, mice were administered tiapride (50 mg/kg body weight) via oral gavage daily for 14 consecutive days. The control group, IDPN group, and acupuncture group received the same volume of saline orally for 14 consecutive days. Stereotypic behaviors were quantified through behavioral assessments. Neurotransmitter levels, including dopamine (DA), glutamate (Glu), and aspartate (ASP) in striatal tissue were measured using enzyme-linked immunosorbent assay. Dopamine transporter (DAT) expression levels were additionally quantified through quantitative polymerase chain reaction (qPCR). Gut microbial composition was analyzed through 16S ribosomal RNA gene sequencing, while metabolic profiling was conducted using liquid chromatography-mass spectrometry (LC-MS).

RESULTS: Acupuncture administration significantly attenuated stereotypic behaviors, concurrently reducing striatal levels of DA, Glu and ASP concentrations while upregulating DAT expression compared with untreated TS controls (P<0.05 or P<0.01). Comparative analysis identified significant differences in Muribaculaceae (P=0.001), Oscillospiraceae (P=0.049), Desulfovibrionaceae (P=0.001), and Marinifilaceae (P=0.014) following acupuncture intervention. Metabolomic profiling revealed alterations in 7 metabolites and 18 metabolic pathways when compared to the TS mice, which involved various amino acid metabolisms associated with DA, Glu, and ASP.

CONCLUSIONS: Acupuncture demonstrates significant modulatory effects on both central neurotransmitter systems and gut microbial ecology, thereby highlighting its dual therapeutic potential for TS management through gut-brain axis regulation.},
}

@article {pmid40548738,
year = {2025},
author = {Mattelin, V and Van Landuyt, J and Kerkhof, F-M and Minnebo, Y and Boon, N},
title = {Integrating taxonomic and phenotypic information through FISH-enhanced flow cytometry for microbial community dynamics analysis.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0197324},
doi = {10.1128/spectrum.01973-24},
pmid = {40548738},
issn = {2165-0497},
abstract = {UNLABELLED: Flow cytometry is a powerful tool to monitor microbial communities, as it allows tracking both changes in the subpopulations and cell numbers at high throughput and a low sample cost. This information can be combined in a phenotypic fingerprint that can be leveraged for diversity analysis. However, as isogenic individuals can manifest phenotypic diversity, for example, due to differing physiological state and phenotypic plasticity, combining the phenotypic information with taxonomic information adds an extra dimension for describing the dynamics of a microbial community. In this research, taxonomic information was incorporated in the microbial fingerprint through fluorescent in situ hybridization (FISH) at a single-cell level. To validate this concept and explore its versatility, two ecosystems with different micro-biodiversity were considered. In the first environment, marine bacteria were monitored for plastic biodegradation in a trickling filter, and in the second, an in vitro simulated human gut microbiome was followed over time. Samples were prepared using different (staining) methods, including FISH, and beta diversity analysis was used to evaluate the level of distinction between differently treated groups in both environments. As a reference to correlate increased distinction with the incorporation of taxonomic information, 16S rRNA gene sequencing was used. Finally, a predictive algorithm was trained to correctly classify samples in the differently treated groups. The results showed that the implementation of FISH in flow cytometry provides more information on a single-cell level to answer specific scientific questions, like distinguishing between phenotypically similar communities or following a specific taxonomic group over time.

IMPORTANCE: Understanding microbial communities is crucial for elucidating their role in maintaining ecosystem health and stability. Researchers are increasingly interested in studying microbial communities by looking at not just their genetic makeup but also their physical traits and functions. In our study, we used common techniques like fluorescence in situ hybridization and flow cytometry, along with advanced data analysis, to better understand these communities. This combination allowed us to gather and use data more effectively, demonstrating that these easy-to-use methods, when paired with proper analysis, can enhance our understanding of changing microbial ecosystems.},
}

@article {pmid40545777,
year = {2025},
author = {VanWallendael, A and Wijewardana, C and Bonnette, J and Vormwald, L and Fritschi, FB and Boe, A and Chambers, S and Mitchell, RB and Rouquette, FM and Wu, Y and Fay, PA and Jastrow, JD and Lovell, JT and Juenger, TE and Lowry, DB},
title = {Local adaptation of both plant and pathogen: an arms-race compromise in switchgrass rust.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70313},
pmid = {40545777},
issn = {1469-8137},
support = {DE-AC02-06CH11357//Biological and Environmental Research/ ; DE-SC0014156//Biological and Environmental Research/ ; DE-SC0017883//Biological and Environmental Research/ ; DE-SC0018409//Biological and Environmental Research/ ; 1832042//Division of Environmental Biology/ ; DE-AC02-05CH11231//Joint Genome Institute/ ; },
abstract = {In coevolving species, parasites locally adapt to host populations as hosts locally adapt to resist parasites. Parasites often outpace host local adaptation since they have rapid life cycles, but host diversity, the strength of selection, and external environmental influence can result in complex outcomes. To better understand local adaptation in host-parasite systems, we examined locally adapted switchgrass (Panicum virgatum), and its leaf rust pathogen (Puccinia novopanici) across a latitudinal range in North America. We grew switchgrass genotypes in 10 replicated multiyear common gardens, measuring rust severity from natural infection in a 'host reciprocal transplant' framework for testing local adaptation. We conducted genome-wide association mapping to identify genetic loci associated with rust severity. Genetically differentiated rust populations were locally adapted to northern and southern switchgrass, despite host local adaptation to environmental conditions in the same regions. Rust resistance was polygenic, and distinct loci were associated with rust severity in the north and south. We narrowed a previously identified large-effect quantitative trait locus for rust severity to a candidate YELLOW STRIPE-LIKE gene and linked numerous other loci to defense-related genes. Overall, our results suggest that both hosts and parasites can be simultaneously locally adapted, especially when parasites impose less selection than other environmental factors.},
}

@article {pmid40542918,
year = {2025},
author = {Zhang, W and Li, XJ and Liu, F and Zhang, J and Tian, J and Gao, Y},
title = {Fungen: clustering and correcting long-read metatranscriptomic data for exploring eukaryotic microorganisms.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {40542918},
issn = {1869-1889},
abstract = {Long-read metatranscriptomics is a powerful and cost-effective technology for elucidating the genetic diversity and expression dynamics of active eukaryotic microorganisms by characterizing full-length transcripts. However, its potential has been limited by the lack of high-quality reference genomes and high sequencing error rates. We present Fungen, a reference-free tool that constructs accurate transcripts from long-read metatranscriptomic data through read clustering and error correction. Fungen achieves superior accuracy in transcript determination while significantly reducing memory usage and offering a 22 to 56-fold speed improvement over existing methods. This novel approach overcomes the challenges posed by sequence similarity among closely related species, enabling the analysis of deeply sequenced metatranscriptomes by generating reliable gene clusters and accurate sequences. Two applications showcase Fungen's capabilities to perform high-resolution taxonomic assignments and gene profiling in marine direct RNA datasets, as well as resolving reliable annotation identities in full-length rRNA targeted sequencing datasets. When applied to soil metatranscriptomic data, Fungen offers valuable insights into the in situ fungal composition and gene expression dynamics, revealing specialized life strategies of plant-pathogenic fungi in soil environments. Overall, Fungen provides a fast, scalable, and accurate solution for analyzing complex metatranscriptomic datasets, paving the way for a comprehensive understanding of eukaryotic diversity and function from long-read sequencing data.},
}

@article {pmid40542710,
year = {2025},
author = {Susukida, S and Miyazawa, K and Ichikawa, H and Muto, K and Yoshimi, A and Kumagai, T and Kato, Y and Abe, K},
title = {Improved Mixing Properties of Stirred Fermentation of an Aspergillus oryzae Hyphal Dispersion Mutant.},
journal = {Biotechnology and bioengineering},
volume = {},
number = {},
pages = {},
doi = {10.1002/bit.70004},
pmid = {40542710},
issn = {1097-0290},
support = {//This study was supported by the Institute for Fermentation, Grant/Award Number: L-2018-2-014; Japan Science and Technology Agency-Adaptable and Seamless Technology Transfer Program through target-driven R&D, Grant/Award Number: JPMJTM19Y4; JSPS KAKENHI, Grant/Award Number: JP20H02895; and New Energy and Industrial Technology Development Organization, Grant/Award Number: JPNP20011./ ; },
abstract = {The complexity of mechanical and biological processes in filamentous fungal fermentation remains a major obstacle to improving product yield. We previously demonstrated that the AGΔ-GAGΔ strain of Aspergillus oryzae, lacking both α-1,3-glucan (AG) and galactosaminogalactan (GAG), had improved hyphal dispersion, reduced culture viscosity, and increased recombinant protein production. Here, we applied computational fluid dynamics (CFD) and multi-omics analysis to characterize the AGΔ-GAGΔ strain during fermentation in a stirred-tank bioreactor. CFD simulations revealed large gas cavities behind the impeller blades and severe compartmentalization in both wild-type and AGΔ-GAGΔ cultures. However, shear stress distribution was broader and gas cavity formation was lower in the AGΔ-GAGΔ strain than in the wild type. The simulation results were consistent with measurements of volumetric oxygen mass transfer coefficients (KLa) and mixing times. Transcriptome analysis revealed upregulation of TCA-cycle genes in AGΔ-GAGΔ relative to the wild type. Analysis of intracellular and extracellular metabolites indicated distinct metabolic profiles associated with oxygen availability. Our findings highlight the critical role of hydrodynamics in fungal fermentation and demonstrate the potential of strain engineering for improving mixing characteristics.},
}

@article {pmid40540980,
year = {2025},
author = {Noviello, D and Amoroso, C and Vecchi, M and Facciotti, F and Caprioli, F},
title = {Curing inflammatory bowel diseases: breaking the barriers of current therapies- emerging strategies for a definitive treatment.},
journal = {Current opinion in immunology},
volume = {95},
number = {},
pages = {102593},
doi = {10.1016/j.coi.2025.102593},
pmid = {40540980},
issn = {1879-0372},
abstract = {Chronic intestinal inflammation in inflammatory bowel diseases (IBD) reflects the interplay of genetic predisposition, immune dysregulation, microbial imbalance, and epithelial barrier defects. Current therapies for IBD primarily focus on controlling inflammation necessitating lifelong treatment and face a 'therapeutic ceiling' due to primary and secondary loss of efficacy over time. Immune-mediated approaches do not address additional pathogenic mechanisms, such as impairment of epithelial barrier and gut microbial ecology. Thus, innovative strategies are required to foster the field closer to a definitive cure. This review discusses novel strategies to overcome current therapeutic limitations, including immune reset via hematopoietic stem cell transplantation and B cell-targeted therapies, antigen-specific interventions such as chimeric antigen receptor T cells and tolerogenic vaccines, and intestinal epithelial barrier restoration. We also explore microbiota-based strategies - ranging from fecal microbiota transplantation to engineered consortia and bacteriophages - and discuss the adjunctive role of diet. Together, we outline a potential research roadmap toward a potential cure for IBD.},
}

@article {pmid40540566,
year = {2025},
author = {Woods, PH and Speth, DR and Laso-Pérez, R and Utter, DR and Ruff, SE and Orphan, VJ},
title = {Identification of key steps in the evolution of anaerobic methanotrophy in Candidatus Methanovorans (ANME-3) archaea.},
journal = {Science advances},
volume = {11},
number = {25},
pages = {eadq5232},
pmid = {40540566},
issn = {2375-2548},
mesh = {*Methane/metabolism ; Anaerobiosis ; Phylogeny ; *Evolution, Molecular ; Genome, Archaeal ; *Archaea/genetics/metabolism ; Metagenomics ; Gene Transfer, Horizontal ; },
abstract = {Despite their large environmental impact and multiple independent emergences, the processes leading to the evolution of anaerobic methanotrophic archaea (ANME) remain unclear. This work uses comparative metagenomics of a recently evolved but understudied ANME group, "Candidatus Methanovorans" (ANME-3), to identify evolutionary processes and innovations at work in ANME, which may be obscured in earlier evolved lineages. We identified horizontal transfer of hdrA homologs and convergent evolution in carbon and energy metabolic genes as potential early steps in Methanovorans evolution. We also identified the erosion of genes required for methylotrophic methanogenesis along with horizontal acquisition of multiheme cytochromes and other loci uniquely associated with ANME. The assembly and comparative analysis of multiple Methanovorans genomes offers important functional context for understanding the niche-defining metabolic differences between methane-oxidizing ANME and their methanogen relatives. Furthermore, this work illustrates the multiple evolutionary modes at play in the transition to a globally important metabolic niche.},
}

*Methane/metabolism
Anaerobiosis
Phylogeny
*Evolution, Molecular
Genome, Archaeal
*Archaea/genetics/metabolism
Metagenomics
Gene Transfer, Horizontal

@article {pmid40539105,
year = {2025},
author = {Zhang, Z and Shi, Z and Zheng, L and Zhang, H},
title = {Remediation of acetochlor-contaminated maize field soil using Serratia odorifera AC-1 fertilizer: effects on soil microbial communities.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1510157},
pmid = {40539105},
issn = {1664-302X},
abstract = {Acetochlor is a chloroacetamide herbicide that is widely applied in corn fields. Nevertheless, the long-term usage of acetochlor in the soil leads to residues, which severely affect the germination of corn seeds and the growth of seedlings, and even exert an influence on the soil microbial community. Microbial degradation of acetochlor is the principal approach for restoring the soil microbial ecology. In this study, the Serratia odorifera AC-1 strain was isolated and identified from the soil for the degradation of residual acetochlor in the soil. To enhance the degradation efficiency, a solid microbial agent was prepared by using activated carbon as a carrier and the AC-1 strain at a 1:1 ratio and applied to the soil for degradation and remediation experiments. The content of the microbial cells in the solid microbial agent was 1.49 × 106 CFU/g after 120 days of preparation. The application of the AC-1 solid microbial agent significantly influenced the relative abundance of soil microbial communities (Actinobacteria, Firmicutes, and Proteobacteria), increasing the diversity of bacterial populations in the soil. The experimental results indicated that after the application of the AC-1 solid microbial agent, the plant height, stem diameter, and photosynthetic efficiency of corn seedlings under acetochlor stress were significantly elevated. When the application rate of the AC-1 solid microbial agent was 5.00 mg/kg, the stem diameter of corn increased by 56.4% compared with the control group. When the acetochlor concentration in the soil was 6.65 mg/kg, the DT50 value of the AC-1 solid microbial agent was 2.28 days. This study clarified the degradation mechanism and remediation capacity of the Serratia odorifera AC-1 strain in acetochlor-contaminated soil and proposed a new strategy to improve the stability and degradation efficiency of the microbial strain by optimizing the immobilization technology of the strain on activated carbon. This research provides a scientific basis and technical guidance for the future application of bioremediation technology in the field environment to remove pesticide residues, restore soil health, and enhance crop productivity.},
}

@article {pmid40537563,
year = {2025},
author = {Embury, EL and Romero-Olivares, AL},
title = {Fungi Follow Flora, Bacteria Track the Seasons: A Tale of a Changing Landscape.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {68},
pmid = {40537563},
issn = {1432-184X},
support = {R16 GM146585/GM/NIGMS NIH HHS/United States ; 1R16GM146585//National Institute of General Medical Sciences of the National Institutes of Health/ ; 2312226//National Science Foundation Building Research Capacity in Biology/ ; },
mesh = {Seasons ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Fungi/classification/genetics/isolation & purification ; Desert Climate ; *Microbiota ; Ecosystem ; Grassland ; Soil/chemistry ; Biomass ; Biodiversity ; },
abstract = {Microbes play critical roles in dryland ecosystems, driving nutrient cycling, soil stability, and plant interactions. Despite their ecological importance, few studies have examined how microbial communities respond to vegetation changes in arid landscapes. In the northern extent of the Chihuahuan Desert, the encroachment of woody shrubs into grasslands has been occurring since the 1800s, largely driven by extensive livestock grazing and increased drought levels. In this study, we investigated how microbial communities respond to both biotic (i.e., vegetation) and abiotic (i.e., seasonality) factors, how they assemble in a changing landscape, and which taxa may be particularly responsive to shrub encroachment or even facilitating this transformation. We assessed microbial communities using soil surface samples across five distinct seasonal periods in a grassland-to-shrubland gradient in the Jornada Experimental Range in the Chihuahuan Desert through the use of phospholipid fatty-acid analysis and DNA metabarcoding techniques. Our findings reveal that bacterial and fungal biomass are significantly influenced by seasonal changes, with strong correlations to humidity and temperature fluctuations. We also found that fungal community assembly and diversity were highly impacted by vegetation whereas seasons were more impactful on bacteria. Our results support the idea that microbes may be playing a crucial role in facilitating the grassland-to-shrubland transition. Overall, our study highlights the complex interactions between microbial communities and biotic and abiotic factors in dryland systems. These findings are essential for understanding the future of dryland ecosystems undergoing shrub encroachment and provide a critical foundation for guiding restoration efforts, particularly those looking to incorporate microbial-mediated solutions.},
}

Seasons
*Soil Microbiology
*Bacteria/classification/genetics/isolation & purification
*Fungi/classification/genetics/isolation & purification
Desert Climate
*Microbiota
Ecosystem
Grassland
Soil/chemistry
Biomass
Biodiversity

@article {pmid40536564,
year = {2025},
author = {Parret, L and Simoens, K and Horemans, B and De Vrieze, J and Smets, I},
title = {Establishing a co-culture aggregate of N-cycle bacteria to elucidate flocculation in biological wastewater treatment.},
journal = {Applied microbiology and biotechnology},
volume = {109},
number = {1},
pages = {149},
pmid = {40536564},
issn = {1432-0614},
support = {C24/18/043//KU Leuven/ ; FWO-G032321N//Fonds Wetenschappelijk Onderzoek/ ; FWO- 1191022N//Fonds Wetenschappelijk Onderzoek/ ; },
mesh = {Flocculation ; *Wastewater/microbiology ; Coculture Techniques/methods ; Sewage/microbiology ; *Bacteria/metabolism/growth & development ; Bioreactors/microbiology ; Alginates ; *Water Purification/methods ; *Nitrogen/metabolism ; Nitrification ; Microbial Consortia ; },
abstract = {Biological flocculation is a complex phenomenon that is often treated as a black box. As a result, flocculation problems are usually remediated without knowledge of the exact causes. We show that it is feasible to exploit a model (N-cycle) consortium with reduced complexity to fundamentally study bioflocculation. Strong nitrifier microcolonies were formed during oxic/anoxic cycles in sequencing batch reactors, using alginate entrapment as a cell retention system. After the release of these aggregates into suspension, macroclusters with flocs of the denitrifier were observed. These results suggest that a living model of a full-scale activated sludge floc can be built through the use of this bottom-up approach. By eliminating shifts in the microbial community, the applied experimental conditions have a more direct effect on the observations. Key Points ∙ Studying flocculation with a model consortium is feasible ∙ Alginate entrapment leads to strong microcolony formation of nitrifiers ∙ FISH by itself is not suitable to study aggregation of a coculture.},
}

Flocculation
*Wastewater/microbiology
Coculture Techniques/methods
Sewage/microbiology
*Bacteria/metabolism/growth & development
Bioreactors/microbiology
Alginates
*Water Purification/methods
*Nitrogen/metabolism
Nitrification
Microbial Consortia

@article {pmid40536143,
year = {2025},
author = {Timmis, K and Williams, P and Karahan, ZC and López-García, P and Rainey, P and Chavarria, M and Greening, C and Steward, K and Hallsworth, JE and Pereira, CS and Giraldo, R and Verstraete, W and Jonjić, S and Ramos, JL and Nunes, O and Ventosa, A and Armstrong, R and Sessitsch, A and Ron, E and Wang, H},
title = {Journals Operating Predatory Practices Are Systematically Eroding the Science Ethos: A Gate and Code Strategy to Minimise Their Operating Space and Restore Research Best Practice.},
journal = {Microbial biotechnology},
volume = {18},
number = {6},
pages = {e70180},
pmid = {40536143},
issn = {1751-7915},
mesh = {*Periodicals as Topic/standards ; Peer Review, Research/standards ; Humans ; },
abstract = {Scientific research seeks to extend knowledge and understanding, an activity that perhaps more than any other advances society and humanity. In essence, it is the search for truth. But, because it seeks new knowledge, there is little or no benchmark for appraisal of the plausibility or validity of the immediate conclusions drawn from new information gained, no instant confirmation. For this and other reasons, the science ethos requires the highest level of rigour to ensure the highest level of probability that new findings are true, or at least the most plausible under the prevailing circumstances and state of knowledge. Research is only as good as its degree of rigour. Rigour comes through intensive and comprehensive scientific training and mentoring that teaches critical and agnostic evaluation of new results, self-scrutiny and self-criticism. Additional rigour comes via independent scrutiny and validation: peer review of results and interpretations submitted as publications, and peer repetition of key experiments. However, the current proliferation of publication vehicles whose business model is based on maximisation of papers published, and the revenue stream of article processing charges (APCs) they generate, is promoting an insidious degradation of rigour and quality standards of reviewing-editing practices. Such predatory practices result in the systematic degradation of research quality and its "truthfulness". Moreover, they undermine the science ethos and threaten to create a new generation of scientists that lack this ethos. These trends will inevitably progressively erode public trust in scientists and the research ecosystem. This Editorial is a call for action to all actors, in particular leaders, in scientific research to oppose predatory practices in science dissemination-to restrict the operational space of those responsible for such practices-in order to restore and maintain research rigour and the science ethos and to prevent a downward spiral of research quality. It proposes two linked actionable solutions to the problem, one for the "pull" element of predatory practices and one for the "push" element of research ecosystem management practices, especially those promoting the publish or perish mentality, that drive authors to publish in journals with predatory practices. To counter the "pull", we propose a solution based on the principle of prevention, rather than cure, and list a number of essential policy decisions and actions that should be taken at all levels of the science chain/cloud to achieve this. A central plank of the concept is journal accreditation, without which a journal would be ineligible for payment of APCs from public funds. For accreditation, a journal would need to convincingly demonstrate adoption of a prescribed journal code of conduct. Ideally, accreditation would also be required for inclusion in journal indexing and ranking services and bibliographic databases. To counter the "push", we propose a top-down imposition of a cultural change in science management that ensures merit-based success of scientists and their careers, research best practice, improved education and mentoring of younger scientists in the science ethos and greater support of them in their careers. This must include explicit recognition of the crucial role of peer reviewing for the good health of the research enterprise, its incentivisation and appropriate appreciation of the time and effort involved. To orchestrate this change, we propose the creation of a multi-stakeholder alliance whose brief is to develop the framework and implementation strategy for changes in the research ecosystem. This Editorial also exhorts all actors to embrace the principle of publish less, publish better and to use public funding provided by tax revenues more effectively to perpetually raise the bar of science quality, dissemination and potential to advance humanity.},
}

*Periodicals as Topic/standards
Peer Review, Research/standards
Humans

@article {pmid40534981,
year = {2025},
author = {Hodgson, RJ and Cando-Dumancela, C and Liddicoat, C and Ramesh, SA and Edwards, RA and Breed, MF},
title = {Strong Host Modulation of Rhizosphere-to-Endosphere Microbial Colonisation in Natural Populations of the Pan-Palaeotropical Keystone Grass Species, Themeda triandra.},
journal = {Ecology and evolution},
volume = {15},
number = {6},
pages = {e71595},
pmid = {40534981},
issn = {2045-7758},
abstract = {Soil microbiota can colonise plant roots through a two-step selection process, involving recruitment of microbiota first from bulk soil into plant rhizospheres, then into root endospheres. This process is poorly understood in all but a few model species (e.g., Arabidopsis), which is surprising given its fundamental role in plant and soil ecology. Here, we examined the microbial community assembly processes across the rhizospheres and root endospheres in eight natural populations of the pan-palaeotropical C4 grass, Themeda triandra, in southern Australia. Using a space-for-time substitution approach, we assessed whether bacterial root colonisation patterns conformed to the two-step model and tested whether community assembly was driven more by deterministic or stochastic processes. Our results show that the two-step selection process shaped bacterial recruitment dynamics across these natural T. triandra populations, and we provide clear evidence that host plants influence microbial assembly via deterministic pressures that produce strong community convergence within endospheres. These findings highlight the central role of host filtering in shaping a conserved 'core' endosphere microbiome. However, limited understanding of these endosphere communities constrains efforts to harness these important relationships to, for example, improve plant propagation and revegetation practices.},
}

@article {pmid40533683,
year = {2025},
author = {Rios-Reyes, A and Gonzalez-Lozano, KJ and Cabral-Miramontes, JP and Hernandez-Gonzalez, JJ and Rios-Sosa, A and Alvarez-Gutierrez, PE and Mireles-Torres, SP and Batista-García, RA and Arechiga-Carvajal, ET},
title = {Exploration of Plant and Microbial Life at "El Chichonal" Volcano with a Sustainable Agriculture Prospection.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {67},
pmid = {40533683},
issn = {1432-184X},
support = {700634//Consejo Nacional de Humanidades, Ciencias y Tecnologías/ ; 2055419//Consejo Nacional de Humanidades, Ciencias y Tecnologías/ ; 1081508//Consejo Nacional de Humanidades, Ciencias y Tecnologías/ ; 315114//Consejo Nacional de Humanidades, Ciencias y Tecnologías/ ; 252373/SEP-CONACYT//Consejo Nacional de Humanidades, Ciencias y Tecnologías/ ; CBF2023-2024-3120//Consejo Nacional de Humanidades, Ciencias y Tecnologías/ ; },
mesh = {*Soil Microbiology ; *Bacteria/classification/isolation & purification/genetics/metabolism ; *Fungi/isolation & purification/classification/genetics ; Agriculture ; Soil/chemistry ; *Volcanic Eruptions ; Bacillus cereus/isolation & purification/genetics ; Plant Roots/microbiology ; Microbiota ; },
abstract = {Active volcanic environments represent extreme habitats with underexplored potential for microbial bioprospecting. This study aimed to characterize pioneer vegetation and associated microbial diversity in the crater of "El Chichonal" volcano, with an emphasis on their potential applications in sustainable agriculture. A physicochemical analysis of the soil was performed, identifying acidic and nutrient-poor conditions. Three pioneer plant species were described: Tibouchina longifolia (dominant) and Poaceae spp. (co-dominant), and Palhinhaea cernua (non-dominant). A total of 311 microorganisms were predominantly bacteria, were isolated from soil, root, stem, and water samples. Bacillus cereus and Priestia megaterium were molecularly identified, and in vitro assays demonstrated their ability to fix nitrogen, produce auxins, and antagonize fungal pathogens (Alternaria solani, Botrytis cinerea, and Colletotrichum gloeosporioides). These results suggest that microorganisms adapted to extreme volcanic environments could be promising sources of plant growth-promoting bacteria (PGPB) with application in biological control.},
}

*Soil Microbiology
*Bacteria/classification/isolation & purification/genetics/metabolism
*Fungi/isolation & purification/classification/genetics
Agriculture
Soil/chemistry
*Volcanic Eruptions
Bacillus cereus/isolation & purification/genetics
Plant Roots/microbiology
Microbiota

@article {pmid40533475,
year = {2025},
author = {Wollrab, S and Schmidt, SR and Woodhouse, J and Kasprzak, P and Berger, SA and Beyer, U and Bodenlos, M and Dalchow, J and Degebrodt, M and Ganzert, L and Gonsiorczyk, T and Huth, E and Kiel, C and Küchler, L and Krienitz, L and Lentz, M and Mach, E and Mallok, U and Nejstgaard, JC and Papke, M and Penske, A and Pinnow, S and Roßberg, R and Ronneberger, D and Sachtleben, M and Scheffler, A and Grossart, HP and Casper, P and Gessner, MO and Koschel, R},
title = {Fifty years of limnological data on Lake Stechlin, a temperate clearwater lake.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1028},
pmid = {40533475},
issn = {2052-4463},
abstract = {We present 50 years of monitoring data on water quality of Lake Stechlin, a deep, dimictic hardwater lake in northeastern Germany known for its exceptionally clear water. Although located in a forested catchment, the lake has undergone major changes in recent decades, including a period of massive heating of surface water when receiving cooling water from a nearby nuclear power plant (1966-1990), accompanied by a greatly shortened water residence time from more than 40 years to less than 300 days. These changes are superimposed by a long-term trend of surface water warming and a concomitant decrease in winter ice cover. Total phosphorus concentrations have quadrupled since 2010 and zones of deep-water oxygen depletion have greatly expanded. The presented dataset covers basic water-chemical and physical records taken at monthly to fortnightly intervals from 1970 to 2020, documenting limnological changes during that period. Furthermore, it serves as a valuable basis to assess and project potential consequences of climate change and other types of environmental change on deep clearwater lakes in temperate climates.},
}

@article {pmid40531665,
year = {2025},
author = {Phithakrotchanakoon, C and Kitikhun, S and Siriarchawatana, P and Charoenyingcharoen, P and Jeennor, S and Nilsakha, T and Chanpet, A and Vorajinda, T and Mayteeworakoon, S and Yukphan, P and Ingsriswang, S},
title = {Flavobacterium mekongense sp. nov., isolated from the Mekong River in Thailand.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {75},
number = {6},
pages = {},
doi = {10.1099/ijsem.0.006815},
pmid = {40531665},
issn = {1466-5034},
mesh = {Thailand ; *Flavobacterium/classification/genetics/isolation & purification ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Rivers/microbiology ; Fatty Acids/chemistry/analysis ; DNA, Bacterial/genetics ; Base Composition ; Bacterial Typing Techniques ; Sequence Analysis, DNA ; Vitamin K 2/analogs & derivatives/chemistry/analysis ; Nucleic Acid Hybridization ; Genome, Bacterial ; Phospholipids/analysis/chemistry ; *Water Microbiology ; },
abstract = {Two Gram-stain-negative, aerobic, non-motile, non-gliding, rod-shaped bacterial strains, designated as TBRC 19031[T] and TBRC 19032, were isolated from water samples collected from the Mekong River, Thailand. Strain TBRC 19031[T] was obtained from Chiang Saen in the upstream section near the borders with China and Myanmar, while TBRC 19032 originated from Khong Chiam, in the downstream section where the river exits Thailand. Colonies of both strains were circular, smooth and deep yellow on Reasoner's 2A agar and did not produce flexirubin-type pigments. Phylogenetic analysis with 16S rRNA gene sequences placed both strains within the genus Flavobacterium, showing the highest sequence similarity to Flavobacterium cheonhonense ARSA-15[T] (98.29% for TBRC 19031[T] and 98.22% for TBRC 19032). However, whole-genome comparisons between the strains and F. cheonhonense ARSA-15[T] revealed average nt identity (89.39% and 89.29%), average aa identity (92.84% and 92.95%) and digital DNA-DNA hybridization (35.00% and 34.70%). The predominant fatty acids were iso-C15:1, iso-C15:0 and iso-C15:0 3-OH, and menaquinone MK-6 was the major respiratory quinone. The major polar lipids of both strains included phosphatidylethanolamine, steryl ester and diacylglycerol. The genome sizes were 3.02 and 3.04 Mbp, with G+C contents of 38.3% and 38.2% for TBRC 19031[T] and TBRC 19032, respectively. Comparative genomic analyses revealed the absence of genes involved in sulphate reduction and denitrification pathways and the presence of a gene encoding phosphatidylinositol synthase, distinguishing them from other Flavobacterium within the clade. Ecological profiling using public metagenomic datasets showed that both strains were associated with lotic freshwater environments. This study not only introduces Flavobacterium mekongense sp. nov. as a new species but also provides broader insights into the ecology, metabolism and environmental distribution of freshwater Flavobacterium. The genomic features identified here offer promising leads for future studies in microbial ecology, comparative genomics and functional gene mining in aquatic ecosystems. The type strain is TBRC 19031[T] (TBRC 19031[T]=NBRC 117006[T]).},
}

Thailand
*Flavobacterium/classification/genetics/isolation & purification
*Phylogeny
RNA, Ribosomal, 16S/genetics
*Rivers/microbiology
Fatty Acids/chemistry/analysis
DNA, Bacterial/genetics
Base Composition
Bacterial Typing Techniques
Sequence Analysis, DNA
Vitamin K 2/analogs & derivatives/chemistry/analysis
Nucleic Acid Hybridization
Genome, Bacterial
Phospholipids/analysis/chemistry
*Water Microbiology

@article {pmid40531656,
year = {2025},
author = {Bou Orm, E and Mukherjee, S and Rifa, E and Créach, A and Grec, S and Bayle, S and Benezet, JC and Bergeret, A and Malhautier, L},
title = {Enhancing Biodiversity-Function Relationships in Field Retting: Towards Key Microbial Indicators for Retting Control.},
journal = {Environmental microbiology reports},
volume = {17},
number = {3},
pages = {e70102},
pmid = {40531656},
issn = {1758-2229},
mesh = {*Biodiversity ; *Fungi/classification/genetics/enzymology/isolation & purification/metabolism ; *Bacteria/classification/genetics/enzymology/isolation & purification/metabolism ; *Cannabis/microbiology/metabolism ; Pectins/metabolism ; Glycoside Hydrolases/metabolism ; Microbiota ; },
abstract = {Hemp field retting is a bioprocess that facilitates fibre extraction by degrading pectin and other matrix components surrounding fibre bundles. However, traditional methods rely on empirical practices, often resulting in inconsistent fibre quality. This study investigates the biodiversity-function relationship in the hemp retting ecosystem to identify microbial and enzymatic indicators for improved process control. Over six weeks of field retting, we monitored bacterial and fungal community dynamics using high-throughput sequencing and assessed enzymatic activity profiles. Our results revealed a sequential enzymatic pattern: pectinases (e.g., polygalacturonase) dominated early stages, followed by hemicellulases (β-xylosidase, β-galactosidase), and later cellulases. These enzymatic shifts were reflected in the changes in microbial community composition, with pectinolytic bacteria (e.g., Proteobacteria) dominating the initial phases and cellulolytic fungi (e.g., Ascomycota) becoming more prevalent later. Our results identified specific microbial taxa correlated with optimal retting, suggesting their potential as bioindicators for monitoring retting. Specifically, key bacterial genera such as Pseudomonas and Sphingomonas, and fungal genera like Cladosporium, were associated with distinct enzymatic profiles. Our findings offer new insights into the microbial ecology of retting, providing both microbial and enzymatic indicators that could inform the development of monitoring strategies for process control, ultimately contributing to more consistent hemp fibre production.},
}

*Biodiversity
*Fungi/classification/genetics/enzymology/isolation & purification/metabolism
*Bacteria/classification/genetics/enzymology/isolation & purification/metabolism
*Cannabis/microbiology/metabolism
Pectins/metabolism
Glycoside Hydrolases/metabolism
Microbiota

@article {pmid40530365,
year = {2025},
author = {Akdur Öztürk, E and Guadano-Procesi, I and Figueiredo, AM and Godfrey, A and Gentekaki, E and Tsaousis, AD and Carmena, D and Dogruman-Al, F},
title = {A protocol for mapping Blastocystis epidemiology and diagnostics from One Health perspective.},
journal = {Open research Europe},
volume = {5},
number = {},
pages = {133},
pmid = {40530365},
issn = {2732-5121},
abstract = {Blastocystis is a globally prevalent gut protist colonising over a billion people worldwide, yet its epidemiology, transmission dynamics, and clinical significance remain underexplored. This protocol represents the first step of a large-scale effort to map Blastocystis epidemiology and diagnostic practices across Europe through the COST Action CA21105: Blastocystis under One Health. By assessing diagnostic methodologies across clinical, veterinary, and environmental sectors, this work sets the foundation for future research and standardisation. Here, we highlight key findings, challenges, and a roadmap for improving Blastocystis detection, ultimately influencing global health policies and microbial ecology studies.},
}

@article {pmid40530126,
year = {2025},
author = {Wu, WJ and Wang, K and Yang, YV and Yang, X},
title = {Identification of neuronal synapse-related signatures and potential therapeutic drugs in colorectal cancer based on machine learning algorithms and molecular docking.},
journal = {Translational cancer research},
volume = {14},
number = {5},
pages = {2737-2757},
pmid = {40530126},
issn = {2219-6803},
abstract = {BACKGROUND: Nervous system-cancer interactions can regulate tumorigenesis, invasion, and metastasis. However, specific biomarkers for targeting neuron synapse in colorectal cancer (CRC) remain unexplored. This study aims to develop a neuronal synapse-related signature (NSRS) to predict survival in CRC patients, identify potential therapeutic drugs, and explore its clinical applications.

METHODS: We collected neuronal synapse genes (NSGs) from the Molecular Signatures Database (MSigDB) and published mass spectrometry data. Using weighted gene co-expression network analysis (WGCNA) and least absolute shrinkage and selection operator Cox regression (LASSO-Cox), we identified prognostic NSGs and constructed a NSRS through multivariate Cox regression. Functional enrichment analysis revealed the molecular characteristics of NSRS subgroups. Additionally, xCell and ESTIMATE algorithms quantified the abundance of 54 cell subtypes and assessed the tumor immune microenvironment (TIME) of the two NSRS subgroups. Finally, drug prediction and molecular docking identified candidate drugs with therapeutic potential.

RESULTS: Seven key prognostic NSGs were identified, and an independent, stable NSRS model was constructed. Kaplan-Meier survival curves indicated that the high NSRS group had poorer outcomes (log-rank test, P<0.05). Functional enrichment analysis revealed significant enrichment of epithelial-mesenchymal transition, hypoxia, and inflammation features in the high NSRS group. xCell and ESTIMATE analyses showed a more complex TIME and lower tumor purity in the high NSRS group, highlighting the role of neuro-tumor interactions in CRC. Drug prediction and molecular docking suggested alprostadil, dihydroergocristine, and nocodazole as candidate drugs for CRC treatment.

CONCLUSIONS: This is the first study to develop neuron synapse-related biomarkers from the perspective of neuron-cancer interactions using machine learning. We constructed a robust NSRS model and identified candidate drugs targeting prognostic NSGs, providing new insights into CRC prognosis and treatment.},
}

@article {pmid40529576,
year = {2025},
author = {Sanz-López, C and Amato, M and Torrent, D and Borrego, M and Anza, M and Bibiso, M and Grijalva-Vallejos, N and Vilanova, C and Porcar, M and Pascual, J},
title = {Microbial ecology of selected traditional Ethiopian fermented products.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1570914},
pmid = {40529576},
issn = {1664-302X},
abstract = {The consumption of traditional fermented foods and beverages plays an important role in the diet of Ethiopia, providing significant nutritional and health benefits to the local population. The present study aimed to investigate the microbial ecology and diversity of nine types of fermented products. These include two foods (Kotcho and Injera), one food condiment (Datta), and six beverages (Tej, Tella, Cheka, Kinito, Borde, and Shamita). A combination of metataxonomic and culturomic approaches was used to achieve a comprehensive characterization of the bacterial communities, together with a thorough physicochemical characterization of the fermented products. This study provides one of the most comprehensive microbial characterizations of a wide selection of Ethiopian fermented products, highlighting that some bacterial species involved in the fermentation processes could contribute to the safety and nutritional quality of fermented foods and, based on previous studies, could also play a key role in enhancing their potential probiotic properties.},
}

@article {pmid40529573,
year = {2025},
author = {Ma, R and Zhang, Z and Wang, J and Han, Y and Li, K and Hou, M and Lei, Y and Xiong, S and Yang, B and Zhi, X and Jiao, Y and Lin, T and Zhang, S and Li, Y},
title = {Mitigating gaseous nitrogen emissions in cotton fields through green manure and reduced nitrogen fertilization.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1615142},
pmid = {40529573},
issn = {1664-302X},
abstract = {Integrating green manure with reduced nitrogen (N) fertilization is a promising strategy to mitigate N emissions in intensive cotton cultivation, however, the underlying mechanisms remain poorly understood. This study investigated the effects of three green manure incorporation patterns-no green manure (NG), Orychophragmus violaceus (OVG), and Vicia villosa (VVG)-combined with four N reduction levels (100, 50, 25%, and conventional) on gaseous N emissions (NH3 and N2O), soil physicochemical properties, and bacterial community characteristics using a cotton field experiment in the Yellow River Basin. Results showed that OVG incorporation with 25% N reduction (N2 treatment) significantly reduced total gaseous N emissions by 36.07% on average during the cotton growth period, reducing NH3 and N2O emissions by 13.31-54.11% and 32.25-68.77%, respectively, compared with N2 application without OVG. OVG application also increased the relative abundance of Proteobacteria (28.10%), enhanced heterogeneous selection in bacterial community assembly (200%), and increased the complexity of co-occurrence networks, compared with NG. Compared with conventional N fertilization (N3 treatment), ≥50% N reduction significantly lowered NH3 (>25.51%) and N2O (>32.76%) emissions, reduced the relative abundance of Acidobacteria (-20.23%), simplified co-occurrence networks, and increased homogeneous selection in bacterial assembly (50.00%). Integrating green manure with 25% N reduction substantially reduced gaseous N emissions, which was associated with the enhanced microbial biomass carbon (MBC) and facilitated recruitment of key bacterial taxa (e.g., Sphingosinicella, Azohydromonas, Phototrophicus) within the microbial co-occurrence network. These findings provide insight into how green manure application coupled with N reduction can mitigate gaseous N losses and reshape soil microbial ecology, offering a theoretical basis for sustainable nutrient management during cotton production.},
}

@article {pmid40528722,
year = {2025},
author = {Gao, D and Guo, X and Yang, Z and Li, H and Chen, Y and Yang, X and Song, L and Yang, X and Yang, J and Zhou, C},
title = {Effects of Sibiraea laevigate maxim polysaccharides on intestinal flora in immunosuppressed mice.},
journal = {Journal of the science of food and agriculture},
volume = {},
number = {},
pages = {},
doi = {10.1002/jsfa.14433},
pmid = {40528722},
issn = {1097-0010},
support = {//The program of Science and Technology Department of Gansu Province (2024ZDPC001, 24YFFA026, 23CXGP0002)/ ; //The innovation Drive assistance project of Gansu for Science and Technology Association (GXH20240328-3)/ ; 2023QB-001//The Young Doctor Fund of Gansu Province/ ; //The youth science and technology talent innovation project of Lanzhou (2023-QN-69)./ ; //The Fundamental Research Funds for the Central Universities of Northwest Minzu University (31920240125-01)./ ; 2024RCXM45//The key talent project of Gansu Province (2024)/ ; },
abstract = {BACKGROUND: The intestinal microbial ecology plays a significant role in maintaining normal physiological function processes and significantly influences the immune system. However, research regarding its effects on gut flora and in vivo immunomodulation is insufficient.

RESULTS: In this study, cyclophosphamide was administered to mice to establish an immunosuppressed mouse model. The regulatory effects of Sibiraea laevigata maxim polysaccharides (SLMPs) on immunity and intestinal microbiota in the immunosuppressed mouse model were investigated. The results indicated that SLMPs could mitigate spleen and thymus damage, protect immune organs, increase the levels of leukocytes, lymphocytes, neutrophils and monocytes in mouse blood and upregulate the levels of IL-2, IFN-γ, TNF-α and IgA in mouse serum. Furthermore, SLMPs can restore intestinal microbial imbalance and enhance the diversity of gut microorganisms in immunosuppressed mice.

CONCLUSION: The findings from this study indicated that SLMPs could enhance immunity and improve the structure and abundance of intestinal flora in mice. These results provide a theoretical basis for the further development and utilization of SLMPs in immunomodulatory adjuvants and functional foods, thereby promoting their application in these fields. © 2025 Society of Chemical Industry.},
}

@article {pmid40528265,
year = {2025},
author = {Selak, L and Meier, DV and Marinović, M and Čačković, A and Kajan, K and Pjevac, P and Orlić, S},
title = {Salinization alters microbial methane cycling in freshwater sediments.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {73},
pmid = {40528265},
issn = {2524-6372},
support = {DOK-2018-09-1550//Hrvatska Zaklada za Znanost/ ; IP-2020-02-9021//Hrvatska Zaklada za Znanost/ ; },
abstract = {Climate change-induced salinization poses a global threat to freshwater ecosystems and challenges microbial communities driving crucial biogeochemical processes, particularly methane cycling. This study examined the impact of salinization and the accompanying sulfate concentration increases on microbial community dynamics and methane cycling in coastal freshwater lake sediments. We show that sulfate enrichment in sediment profiles enables the proliferation of distinct sulfate-reducing bacteria (SRB) that reshape microbial niches by competing with methanogens and promoting sulfate-dependent anaerobic oxidation of methane (AOM). Freshwater SRB clusters, which compete with some methanogens for substrates but also degrade organic compounds into methanogenesis precursors, are replaced by the SEEP-SRB groups that form syntrophic relationships with ANME-1 in salinized sediments. As seawater intrudes and reshapes microbial communities, a methane pocket forms that escapes both aerobic and anaerobic oxidation. Underneath this methane pocket, SRB play a key role in enabling sulfate-dependent AOM, facilitating methane consumption at higher sediment depths. While all microorganisms demonstrated some physiological adaptability potential to elevated osmotic stress, SRB exhibited the highest resilience to increased salinity. These findings highlight how salinization-induced geochemical shifts, particularly sulfate enrichment, directly affect microbial community assembly and impact methane cycling in coastal freshwater ecosystems.},
}

@article {pmid40528093,
year = {2025},
author = {Goswami, R and Sarkar, A and Bandyopadhyay, B and Sadhukhan, S},
title = {Exploring microbial diversity in the Kharasinpur hot spring of West Bengal, India.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {608},
pmid = {40528093},
issn = {1573-4978},
mesh = {*Hot Springs/microbiology ; India ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/isolation & purification/classification ; Phylogeny ; Biodiversity ; Water Microbiology ; Microbiota/genetics ; Hydrogen-Ion Concentration ; Iron/analysis ; },
abstract = {BACKGROUND: Hot springs are natural geothermal environments that harbour thermophilic microorganisms with significant biotechnological potential. Despite extensive studies on many Indian hot springs, Kharasinpur Hot Spring in West Bengal remains totally unexplored in terms of microbial diversity and physicochemical properties.

METHODS: A total of seven bacterial isolates were obtained from water samples collected at the Kharasinpur Hot Spring. These isolates underwent morphological, physiological, biochemical, and molecular characterization through 16S rRNA gene sequencing. Water samples were analyzed for physicochemical parameters such as temperature, pH, total hardness, iron concentration, salt content, and total dissolved solids (TDS).

RESULTS: The water temperature was recorded at 65 °C with a slightly alkaline pH (7.24). The 16S rRNA analysis identified isolates belonging to the phyla Pseudomonadota (e.g., Pseudomonas sp., Hydrogenophaga sp.) and Bacillota (e.g., Staphylococcus sp., Neobacillus sp.). The high iron content in the hot spring water was notable and rendered it unsafe for direct human consumption.

CONCLUSION: This study provides novel insights into the microbial diversity and physicochemical characteristics of a relatively unstudied Indian hot spring. The findings contribute to broader research efforts on hot spring ecosystems in India, enhancing our understanding of their microbial ecology and potential health implications.},
}

*Hot Springs/microbiology
India
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/isolation & purification/classification
Phylogeny
Biodiversity
Water Microbiology
Microbiota/genetics
Hydrogen-Ion Concentration
Iron/analysis

@article {pmid40528049,
year = {2025},
author = {Blair, EM and Margalith, NJ and O'Malley, MA},
title = {Microbial Enrichments Contribute to Characterization Of Desert Tortoise Gut Microbiota.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {66},
pmid = {40528049},
issn = {1432-184X},
support = {DE-SC0020420//U.S. Department of Energy/ ; DE-SC0020420//U.S. Department of Energy/ ; DE-SC0020420//U.S. Department of Energy/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Turtles/microbiology ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Desert Climate ; Fatty Acids, Volatile/metabolism ; Lignin/metabolism ; DNA, Bacterial/genetics ; Biomass ; },
abstract = {Desert tortoises play ecologically significant roles, including plant seed dispersal and mineral cycling, and yet little is known about microbial members that are critical to their gut and overall health. Tortoises consume recalcitrant plant material, which their gut microbiota degrades and converts into usable metabolites and nutrients for the tortoise. Findings from tortoise gut microbiomes may translate well into biotechnological applications as these microbes have evolved to efficiently degrade recalcitrant substrates and generate useful products. In this study, we cultivated microbial communities from desert tortoise fecal samples following a targeted anaerobic enrichment for microbes involved in deconstruction and utilization of plant biomass. We employed 16S rRNA amplicon sequencing to compare cultivated communities to initial fecal source material and found high abundances of Firmicutes and Bacteroidota typically associated with biomass deconstruction in all cultivated samples. Significantly decreased microbial diversity was observed in the cultivated microbial communities, yet several key taxa thrived in lignocellulose enrichments, including Lachnospiraceae and Enterococcus. Additionally, cultivated communities produced short-chain fatty acids under anaerobic conditions, and their growth and metabolic output provide evidence of their viability in the initial fecal communities. Overall, this study adds to the limited understanding of reptilian herbivore microbiota, and offers a path towards biotechnological translation based on the ability of the cultivated communities to convert lignocellulose directly to acetate, propionate, and butyrate.},
}

Animals
*Gastrointestinal Microbiome
*Turtles/microbiology
Feces/microbiology
RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/isolation & purification/metabolism
Desert Climate
Fatty Acids, Volatile/metabolism
Lignin/metabolism
DNA, Bacterial/genetics
Biomass

@article {pmid40527958,
year = {2025},
author = {Jendrusch, MA and Yang, ALJ and Cacace, E and Bobonis, J and Voogdt, CGP and Kaspar, S and Schweimer, K and Perez-Borrajero, C and Lapouge, K and Scheurich, J and Remans, K and Hennig, J and Typas, A and Korbel, JO and Sadiq, SK},
title = {AlphaDesign: a de novo protein design framework based on AlphaFold.},
journal = {Molecular systems biology},
volume = {},
number = {},
pages = {},
pmid = {40527958},
issn = {1744-4292},
support = {de.NBI project: 031A537B//Bundesministerium für Bildung und Forschung (BMBF)/ ; contract 95826//Volkswagen Foundation (VolkswagenStiftung)/ ; 93874-1//Volkswagen Foundation (VolkswagenStiftung)/ ; COFUND grant nr. 847543//EC | Horizon Europe | Excellent Science | HORIZON EUROPE Marie Sklodowska-Curie Actions (MSCA)/ ; },
abstract = {De novo protein design is of fundamental interest to synthetic biology, with a plethora of computational methods of various degrees of generality developed in recent years. Here, we introduce AlphaDesign, a hallucination-based computational framework for de novo protein design developed with maximum generality and usability in mind, which combines AlphaFold with autoregressive diffusion models to enable rapid generation and computational validation of proteins with controllable interactions, conformations and oligomeric state without the requirement for class-dependent model re-training or fine-tuning. We apply our framework to design and systematically validate in vivo active inhibitors of a family of bacterial phage defense systems with toxic effectors called retrons, paving the way towards efficient, rational design of novel proteins as biologics.},
}

@article {pmid40525968,
year = {2025},
author = {Lopez-Echartea, E and Dusek, N and Misialek, M and Mahmud-Un-Nabi, MA and Williamson, R and Marathe, K and Geddes, BA},
title = {Culturomics from field-grown crop plants using dilution to extinction, two-step library preparation and amplicon sequencing.},
journal = {Microbiology (Reading, England)},
volume = {171},
number = {6},
pages = {},
pmid = {40525968},
issn = {1465-2080},
mesh = {RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification/growth & development ; *Zea mays/microbiology ; *Microbiota/genetics ; Phylogeny ; DNA, Bacterial/genetics ; Plant Roots/microbiology ; *Pisum sativum/microbiology ; *Crops, Agricultural/microbiology ; High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA ; Gene Library ; Soil Microbiology ; },
abstract = {Culturomics approaches have advanced microbial research by enabling the high-throughput isolation and characterization of a broader range of bacterial taxa, including some previously considered unculturable. Here, we present the testing and optimization of a protocol for isolating and identifying hundreds of cultivable microbes from field-grown plants. This protocol was tested and optimized using the root microbiomes of field-grown corn and pea plants under varying environmental conditions in ND, USA. By employing dilution-to-extinction culturing and a two-step barcoding PCR strategy targeting the V4 region of the 16S rRNA gene, we identified over 200 unique bacterial isolates. The optimized bioinformatic pipeline, built around the DADA2 package, ensured accurate amplicon sequence variant detection and taxonomy assignment. The resulting bacterial isolates span diverse phylogenetic groups, including plant-associated taxa known for promoting plant growth and mitigating stress. Our findings highlight the value of culturomics in generating microbial collections for synthetic community design and advancing plant-microbe interaction research. The protocol's scalability, cost-effectiveness and robust performance demonstrate its potential for widespread application in agricultural microbiome studies.},
}

RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/isolation & purification/growth & development
*Zea mays/microbiology
*Microbiota/genetics
Phylogeny
DNA, Bacterial/genetics
Plant Roots/microbiology
*Pisum sativum/microbiology
*Crops, Agricultural/microbiology
High-Throughput Nucleotide Sequencing
Sequence Analysis, DNA
Gene Library
Soil Microbiology

@article {pmid40525847,
year = {2025},
author = {Kroos, L and Wall, D and Islam, ST and Whitworth, DE and Muñoz-Dorado, J and Higgs, PI and Singer, M and Mauriello, EM and Treuner-Lange, A and Søgaard-Andersen, L and Kaimer, C and Elías-Arnanz, M and Stojković, EA and Müller, R and Volz, C and Velicer, GJ and Nan, B},
title = {Milestones in the development of Myxococcus xanthus as a model multicellular bacterium.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0007125},
doi = {10.1128/jb.00071-25},
pmid = {40525847},
issn = {1098-5530},
abstract = {From the humblest of beginnings (i.e. a pile of dry cow dung) over 80 years ago, the Gram-negative bacterium Myxococcus xanthus has emerged as a premier model system for studying diverse fields of bacteriology, including multicellular development, sporulation, motility, cell-envelope biogenesis, spatiotemporal regulation, signaling, photoreception, kin recognition, social evolution, and predation. As the flagship representative of myxobacteria found in varied terrestrial and aquatic environments, M. xanthus research has evolved into a collaborative global effort, as reflected by the contributions to this article. In celebration of the upcoming 50th anniversary of the International Conference on the Biology of Myxobacteria, this review highlights the historical and ongoing contributions of M. xanthus as a multifaceted model bacterium.},
}

@article {pmid40524759,
year = {2025},
author = {Lacerda, AL and Proietti, MC and Kessler, F and Mendes, CR and Secchi, ER and Taylor, JD},
title = {Oceanic regions shape the composition of the Antarctic plastisphere.},
journal = {Communications earth & environment},
volume = {6},
number = {1},
pages = {462},
pmid = {40524759},
issn = {2662-4435},
abstract = {Antarctica, once considered pristine, is increasingly threatened by plastic pollution, with debris found in its waters, sediments, sea ice, and biota. Here, we provide a comprehensive molecular survey of both prokaryotic and eukaryotic diversity on plastics around the Antarctic Peninsula, addressing a gap in existing research. Using eDNA metabarcoding, we identified diverse communities, with Pseudomonadota and Bacteroidota dominating prokaryotic communities, while Gyrista (mostly diatoms), Fungi and Arthropods were prevalent among eukaryotes. Geographic location significantly influenced community composition, with differences between the Bransfield Strait and the Gerlache Strait/Bellingshausen Sea. Polymer type and plastic shape did not impact species richness or community structure. These findings offer new insights into the complexity of the Antarctic plastisphere, highlighting potential impacts on biodiversity, ecosystem functions, and the broader implications of marine plastic pollution.},
}

@article {pmid40524188,
year = {2025},
author = {Perillo, VL and Nute, M and Sapoval, N and Curry, KD and Golia, L and Yin, Y and Ogilvie, HA and Nakhleh, L and Segarra, S and Bhaya, D and Cuadrado, DG and Treangen, TJ},
title = {A survey of computational approaches for characterizing microbial interactions in microbial mats.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {168},
pmid = {40524188},
issn = {1474-760X},
support = {EF-2126387//National Science Foundation/ ; BBSRC-NSF/BIO #1921429//National Science Foundation/ ; NSF#2125965//National Science Foundation/ ; PICT 2020-302//Fondo para la Investigación Científica y Tecnológica/ ; Pampa Azul A8 Programa "Investigación//Ministerio de Ciencia, Tecnología e Innovación/ ; Desarrollo e Innovación en Ciencias del Mar"//Ministerio de Ciencia, Tecnología e Innovación/ ; Proposal 503441//Joint Genome Institute/ ; proposal: 10.46936/10.25585/60001132//Joint Genome Institute/ ; },
mesh = {*Microbial Interactions ; *Computational Biology/methods ; *Microbiota ; Ecosystem ; Bacteria/genetics/metabolism ; },
abstract = {In this review, we use microbial mat communities as a general model system to highlight the strengths and limitations of current computational methods for analyzing interactions between members of microbial ecosystems. We describe the factors that make this environment have such a high degree of interaction, and we explore different categories of both laboratory and computational tools for studying these interactions. For each tool, we describe efforts to apply them to microbial mats in the past and, in the process, argue that genome-scale metabolic models have breakthrough potential for modeling microbial interactions in microbial mats.},
}

*Microbial Interactions
*Computational Biology/methods
*Microbiota
Ecosystem
Bacteria/genetics/metabolism

@article {pmid40523669,
year = {2025},
author = {Prakash, O and Chauhan, A and Green, SJ},
title = {The Study of Microbial Physiology Under Microoxic Conditions Is Critical but Neglected.},
journal = {Environmental microbiology reports},
volume = {17},
number = {3},
pages = {e70108},
pmid = {40523669},
issn = {1758-2229},
support = {2200615//BioXFEL Science and Technology Center/ ; DE-FE0032198//DOE's University Training & Research Program University Coal Research (UCR)/ ; 0000602538//The Department of Energy/ ; //Major Research Project (MJRP) intramural grant from Symbiosis International (Deemed University)/ ; 1901371//National Science Foundation/ ; 2200615//National Science Foundation/ ; W911NF2210145//Department of Defence contract/ ; },
mesh = {Anaerobiosis ; Aerobiosis ; *Oxygen/metabolism ; *Bacteria/metabolism/genetics/growth & development ; Ecosystem ; *Bacterial Physiological Phenomena ; Humans ; },
abstract = {During the early evolution of life on Earth, the environment was largely free of molecular oxygen, and only anaerobic life existed. With the subsequent oxidation of oceans and the atmosphere, a wide range of environmental niches, ranging from anoxic to microoxic/hypoxic and oxic, developed. Despite this broad range of natural environments, microbiology as a field has focused on the physiology, metabolism, and genetics of aerobic microorganisms, with less attention paid to anaerobes and much less attention paid to microaerophiles. The disparity in studies between aerobic and anaerobic conditions is rampant in host-associated systems, particularly in human health, and studies of microorganisms in intermediate oxygen conditions between fully aerobic and fully anoxic conditions are exceedingly rare. Studies on the physiological behaviour, metabolism, growth response, and drug susceptibility patterns of commensal and pathogenic organisms are almost totally neglected in microoxic conditions. Furthermore, microorganisms from microaerobic and microoxic ecosystems have been less robustly explored in terms of physiology, growth, and metabolism. In this work, we highlight the importance of understanding the physiological and metabolic behaviours of microorganisms under hypoxic or microoxic conditions.},
}

Anaerobiosis
Aerobiosis
*Oxygen/metabolism
*Bacteria/metabolism/genetics/growth & development
Ecosystem
*Bacterial Physiological Phenomena
Humans

@article {pmid40522148,
year = {2025},
author = {Fejes, R and Séneca, J and Pjevac, P and Lutnik, M and Weisshaar, S and Pilat, N and Steiner, R and Wagner, KH and Woodman, RJ and Bondonno, CP and Hodgson, JM and Berry, D and Wolzt, M and Neubauer, O},
title = {Increased Nitrate Intake From Beetroot Juice Over 4 Weeks Changes the Composition of the Oral, But Not the Intestinal Microbiome.},
journal = {Molecular nutrition & food research},
volume = {},
number = {},
pages = {e70156},
doi = {10.1002/mnfr.70156},
pmid = {40522148},
issn = {1613-4133},
support = {//Austrian Science Fund (FWF)/ ; KLI 858//Clinical Research (KLIF) program/ ; },
abstract = {Inorganic dietary nitrate, metabolized through an endogenous pathway involving nitrate reducing bacteria, improves cardiovascular health, but its effects on the oral and intestinal microbiomes of older adults with treated hypertension are unknown. Our study investigated the effects of nitrate from beetroot juice on the oral and intestinal microbiomes of this population. A randomized, double-blind, placebo-controlled crossover trial was conducted with 15 participants (age range: 56-71 years), who consumed nitrate-rich or nitrate-depleted (placebo) beetroot juice for 4 weeks. The oral microbiome analysis revealed an increase in Neisseria and a decrease in Veillonella relative abundance (for both, PERMANOVA p < 0.001), with no significant changes in the intestinal microbiome composition. Our findings suggest that an increased dietary nitrate intake from a vegetable source may selectively modulate the oral microbiome and promote an increased abundance of nitrate-reducing species, which was previously associated with improved cardiovascular health outcomes.},
}

@article {pmid40521244,
year = {2025},
author = {Addo, M and Apaame, S and Ghanney, MA and Adu, HK and DeWitt, ME and Addo, SO},
title = {Hepatitis B Infection in Outpatients and Pregnant Women Visiting a Mission Hospital in Ghana.},
journal = {Public health challenges..},
volume = {4},
number = {2},
pages = {e70071},
pmid = {40521244},
issn = {2769-2450},
abstract = {Millions of individuals worldwide suffer from hepatitis B, a serious, potentially fatal liver infection brought on by the hepatitis B virus (HBV). Although vaccines are available for HBV, infections continue to persist in Ghana. This study reports the prevalence of HBV infections in outpatients and pregnant women attending antenatal care at the Seventh-day Adventist (SDA) Hospital in Gbawe, Ghana. This retrospective cohort study involved the review of de-identified medical records of outpatients and pregnant women who visited the hospital between 2022 and 2024. Data on their HBV infection status, sex and age were analysed using R version 4.4.1. A total of 531 outpatients and 768 pregnant women visited the hospital during the study period. The prevalence of HBV infection was 7.5% in outpatients and 3.9% in pregnant women. It was observed that outpatients were more likely to be hepatitis B surface antigen (HBsAg) positive (OR = 2.0, 95%CI = 1.24-3.28, p = 0.005). It was also seen that HBV prevalence increased from 2022 to 2023 and decreased in 2024. There is a need for more educational campaigns to raise awareness of HBV infections, especially in pregnant women due to the risk of mother-to-child transmission. Furthermore, vaccinations need to be made affordable and easily accessible to the general population to ensure maximum coverage within the country.},
}

@article {pmid40518732,
year = {2025},
author = {Mota de Almeida, FJ and Rakhimova, O and Romani Vestman, N and Lee, NM and Brundin, M},
title = {In situ imaging and microbiome analysis of calculus-like deposits at the root apex: A case report of refractory apical periodontitis.},
journal = {International endodontic journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/iej.14268},
pmid = {40518732},
issn = {1365-2591},
support = {7003589//Region of Västerbotten (Sweden)/ ; 977100//Region of Västerbotten (Sweden)/ ; RV-967705//Region of Västerbotten (Sweden)/ ; },
abstract = {AIM: This case report explored the application of next-generation sequencing (NGS) and fluorescence in situ hybridization (FISH) to visualize and characterize microbial populations in a refractory endodontic infection with apical calculus-like deposits, a rarely reported phenomenon.

SUMMARY: Histopathologic analysis revealed bacterial biofilms and calcifications on the root surface, with Gram-positive bacteria predominant in both hard and soft tissues. Microbial sequencing showed Pseudomonadota dominated hard tissues, whereas Bacillota were prevalent in soft tissues, with distinct genera like Lactibacterium and Streptococcus identified. FISH imaging confirmed spatially distributed bacterial taxa, including Actinomycetota and Chloroflexota, within the biofilm, aligning with NGS findings. Notably, Bacteroidota was exclusive to soft tissues, whereas Chloroflexota was detected only in hard tissues. The presence of extensive calculus-like deposits on the root surface provided new insights into the microbial complexity of persistent endodontic infections and their management.

KEY LEARNING POINTS: The combination of NGS and FISH provided unprecedented insights into the microbial composition of refractory endodontic infections, revealing a diverse and spatially organized ecosystem. Distinct microbial compositions in hard and soft tissues emphasize the importance of targeted therapeutic strategies for endodontic infections. The presence of unique bacterial taxa and biofilms in calculus-like deposits offers new avenues for research into the pathogenesis and persistence of endodontic infections.},
}

@article {pmid40511921,
year = {2025},
author = {Mayer, L and Nikolov, G and Kunert, M and Horn, M and Willemsen, A},
title = {Mimivirus transcription and translation occur at well-defined locations within amoeba host cells.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {e0055425},
doi = {10.1128/jvi.00554-25},
pmid = {40511921},
issn = {1098-5514},
abstract = {Many giant viruses replicate in the cytoplasm in viral factories. How exactly these viral factories are established and where the different steps of the replication cycle occur remain largely obscure. We have developed a single-molecule messenger RNA fluorescence in situ hybridization (smFISH) protocol for giant viruses in an Acanthamoeba host. Combined with other labeling techniques (FUNCAT, DiD, rRNA FISH, and DAPI), we show the Mimivirus transcription and translation sites during an infection cycle in the amoeba host cell. Although viral mRNA localization changes depend on the infection stage, transcription occurs at well-defined spots within the viral factory. The original viral cores released within the cytoplasm most likely define these spots. When transported outside of the viral factory, the translation of viral mRNA takes place in a well-defined ring surrounding it. With this study, we obtained novel insights into giant virus replication, of which the methods are widely applicable to other viruses for the visualization and quantification of RNA molecules.IMPORTANCEGiant viruses have massive particle and genome sizes, which are known to infect unicellular eukaryotes. Although most viruses replicate in the host cell's nucleus, the giant Mimivirus replicates in viral factories established in the host cell's cytoplasm. Before this study, the location of the various steps in the Mimivirus replication cycle was largely unknown. By developing new protocols to label giant virus mRNA, protein synthesis, host cell membranes and rRNA, we demonstrate that Mimivirus transcription occurs at well-defined sites within the viral factory. In contrast, translation takes place directly outside of it. This is different from other viruses known to have a cytoplasmic life cycle. These results bring us a step closer to understanding how the genome complexity of viruses influences the virus-host interactions and viral replication strategies.},
}

@article {pmid40510670,
year = {2025},
author = {Barnhart, EP and Douterelo, I and Morgan, MJ and Puzon, GJ},
title = {Editorial: Microbial ecology supporting growth of free-living amoebae in natural and engineered water systems.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1620877},
doi = {10.3389/fmicb.2025.1620877},
pmid = {40510670},
issn = {1664-302X},
}

@article {pmid40509663,
year = {2025},
author = {van Dijk, JR and Geelhoed, JS and Geerlings, N and Choyikutty, JA and Boschker, HTS and Verbruggen, E and Meysman, FJR},
title = {Inactive "Ghost" Cells Do Not Affect Motility and Long-Range Electron Transport in Filamentous Cable Bacteria.},
journal = {Environmental microbiology},
volume = {27},
number = {6},
pages = {e70117},
pmid = {40509663},
issn = {1462-2920},
support = {G038819N//Fonds Wetenschappelijk Onderzoek/ ; S004523N//Fonds Wetenschappelijk Onderzoek/ ; //Universiteit Antwerpen/ ; PRINGLE 101046719//HORIZON EUROPE European Innovation Council/ ; EMBO ALTF 102-2023//European Molecular Biology Organization/ ; },
mesh = {Electron Transport ; *Bacteria/metabolism/cytology ; Oxidation-Reduction ; Sulfur/metabolism ; *Bacterial Physiological Phenomena ; },
abstract = {Cable bacteria are multicellular filamentous microorganisms that perform electrogenic sulphur oxidation over centimetre-long distances. These filaments contain so-called "ghost cells", which display a highly reduced cytoplasmic content and a lack of metabolic activity. However, the origin and abundance of these ghost cells are not well understood, raising questions about their formation and potential impact on the functioning of the entire filaments. Here, we quantified the abundance of ghost cells in cable bacteria via a targeted propidium iodide staining technique and investigated their morphology and possible origin. Microscopy revealed that ghost cells are present in filaments under in situ conditions, and hence, they are not an artefact from filament sampling. Interestingly, filaments containing ghost cells retained gliding motility, as well as the capacity for long-distance electron transport, thus suggesting that the functionality of the filament as a whole remains largely unaffected by the presence of these ghost cells. Noteworthy is the higher frequency of ghost cells near the ends of filaments, and within filament fragments retrieved from oxic environments. Our findings provide new insights into the adaptive strategies of filamentous bacteria, highlighting their ability to maintain functionality at the organism level despite the fact that some individual cells are no longer metabolically active.},
}

Electron Transport
*Bacteria/metabolism/cytology
Oxidation-Reduction
Sulfur/metabolism
*Bacterial Physiological Phenomena

@article {pmid40509476,
year = {2025},
author = {Bemis, DH and Camphausen, CE and Liu, E and Dantus, JJ and Navarro, JA and Dykstra, KL and Paltrowitz, LA and Dzhelmach, M and Joerg, M and Tamelessio, P and Belenky, P},
title = {Nutrient Availability and Pathogen Clearance Impact Microbiome Composition in a Gnotobiotic Kimchi Model.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {11},
pages = {},
pmid = {40509476},
issn = {2304-8158},
abstract = {Kimchi is a fermented Korean food typically made with napa cabbage, garlic, radish, ginger, and chili pepper. It is becoming increasingly popular due to its flavor, high fiber content, and purported probiotic benefits. The microbial ecology of the fermentation community has been extensively studied, though what's less understood is how its microbial community changes when nutrients or pathogens are introduced. To study this, we used gnotobiotic cabbage media inoculated with a kimchi starter culture as a model system. These inoculated samples were exposed to E. coli or Bacillus cereus, with or without added nutrients in the form of tryptic soy broth (TSB). We tracked pH, colony-forming units (CFUs), and community composition over time. We also used Oxford Nanopore sequencing to analyze the 16S rRNA gene (V4-V9), followed by use of the Emu algorithm for taxonomic assignments. As expected, LABs suppressed pathogens, but this effect was weaker early on in the nutrient-rich condition. Pathogen exposure changed the overall community-Lactobacillus species became more common, and Leuconostoc mesenteroides less so. Interestingly, adding nutrients alone caused similar microbial shifts to those seen with pathogen exposure. This could suggest that nutrient levels have a larger impact on the final microbiome structure than direct microbial competition. Together, these findings suggest that monitoring total microbial composition, and not just the presence of pathogens, may be important for ensuring kimchi fermentation reproducibility.},
}

@article {pmid40507003,
year = {2025},
author = {Karkala, A and Kotoulas, SC and Tzinas, A and Massa, E and Mouloudi, E and Gkakou, F and Pataka, A},
title = {The Lung Microbiome and Its Impact on Obstructive Sleep Apnea: A Diagnostic Frontier.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {15},
number = {11},
pages = {},
pmid = {40507003},
issn = {2075-4418},
abstract = {Obstructive sleep apnea (OSA), a prevalent disorder characterized by recurrent upper airway collapse, is increasingly recognized as a systemic inflammatory condition influenced by microbial dysregulation. Emerging evidence underscores the lung microbiome as a mediator in OSA pathophysiology, where dysbiotic shifts driven by intermittent hypoxia, oxidative stress and mechanical airway trauma amplify inflammatory cascades and perpetuate respiratory instability. This review synthesizes current knowledge on the bidirectional interplay between OSA and lung microbial communities. It aims to highlight how hypoxia-induced alterations in microbial ecology disrupt immune homeostasis, while inflammation-driven mucosal injury fosters pathogenic colonization. Clinical correlations between specific taxa like Streptococcus and Prevotella, and disease severity, suggest microbial signatures as novel biomarkers for OSA progression and treatment response. Furthermore, oxidative stress markers and pro-inflammatory cytokines emerge as potential diagnostic tools that bridge microbial dysbiosis with sleep-related outcomes. However, challenges persist in sampling standardization of the low-biomass lower airways, as well as in causative mechanisms linking microbial dysbiosis to OSA pathophysiology. By integrating microbial ecology with precision sleep medicine, this paradigm shift promises to transform OSA management from mechanical stabilization to holistic ecosystem restoration.},
}

@article {pmid40504771,
year = {2025},
author = {Augustijn, HE and Reitz, ZL and Zhang, L and Boot, JA and Elsayed, SS and Challis, GL and Medema, MH and van Wezel, GP},
title = {Genome mining based on transcriptional regulatory networks uncovers a novel locus involved in desferrioxamine biosynthesis.},
journal = {PLoS biology},
volume = {23},
number = {6},
pages = {e3003183},
pmid = {40504771},
issn = {1545-7885},
mesh = {*Deferoxamine ; *Gene Regulatory Networks ; Gene Expression Regulation, Bacterial ; *Streptomyces coelicolor/genetics/metabolism ; *Genome, Bacterial ; Multigene Family ; Bacterial Proteins/genetics/metabolism ; Operon ; Computational Biology ; Iron/metabolism ; Data Mining ; },
abstract = {Bacteria produce a plethora of natural products that are in clinical, agricultural and biotechnological use. Genome mining has uncovered millions of biosynthetic gene clusters (BGCs) that encode their biosynthesis, the vast majority of them lacking a clear product or function. Thus, a major challenge is to predict the bioactivities of the molecules these BGCs specify, and how to elicit their expression. Here, we present an innovative strategy whereby we harness the power of regulatory networks combined with global gene expression patterns to predict BGC functions. Bioinformatic analysis of all genes predicted to be controlled by the iron master regulator DmdR1 combined with co-expression data, led to identification of the novel operon desJGH that plays a key role in the biosynthesis of the iron overload drug desferrioxamine (DFO) B in Streptomyces coelicolor. Deletion of either desG or desH strongly reduces the biosynthesis of DFO B, while that of DFO E is enhanced. DesJGH most likely act by changing the balance between the DFO precursors. Our work shows the power of harnessing regulation-based genome mining to functionally prioritize BGCs, accelerating the discovery of novel bioactive molecules.},
}

*Deferoxamine
*Gene Regulatory Networks
Gene Expression Regulation, Bacterial
*Streptomyces coelicolor/genetics/metabolism
*Genome, Bacterial
Multigene Family
Bacterial Proteins/genetics/metabolism
Operon
Computational Biology
Iron/metabolism
Data Mining

@article {pmid40504377,
year = {2025},
author = {Zhang, J and Zhao, Z and Zhu, C and Wang, E and Brunel, B and Li, S and Zheng, Q and Feng, Z and Zhang, H},
title = {Diverse Peanut Bradyrhizobial Communities in Chinese Soils: Insights from Eastern, Central, and Northern Henan Province.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {65},
pmid = {40504377},
issn = {1432-184X},
support = {2024M761756//China Postdoctoral Science Foundation/ ; Yuzutong[2023]No.11//Central Plains Youth Top Talent Project/ ; Sabbatical Year SIP20200726//IPN, Mexico/ ; },
mesh = {*Arachis/microbiology ; China ; *Bradyrhizobium/genetics/classification/isolation & purification ; Phylogeny ; *Soil Microbiology ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics ; Polymorphism, Restriction Fragment Length ; Symbiosis ; Soil/chemistry ; Root Nodules, Plant/microbiology ; Bacterial Proteins/genetics ; },
abstract = {Henan province is a major peanut-producing area in China, but research on rhizobia nodulating peanut have been limited to southern Henan, which accounts for only less than half of the province. A collection of 212 strains of peanut rhizobia was obtained from six field sites in eastern, central, and northern Henan, Central China, by using peanut as a trap host under glasshouse conditions. PCR-RFLP analysis of ribosomal IGS sequences classified the 212 strains into 28 distinct types. Phylogenetic analyses of the 16S rRNA, atpD, gyrB, dnaK, and rpoB genes from 30 representative strains of the 28 IGS types identified revealed the presence of Bradyrhizobium. liaoningense, B. yuanmingense, B. zhengyangense, and two novel Bradyrhizobium genospecies. This composition differs from the peanut rhizobia community found in southern Henan. B. liaoningense was the dominant species, covering 49% of the total isolates across the field sites, while B. zhengyangense accounting for 27%, B. yuanmingense for 7% and the two novel Bradyrhizobium genospecies for 17%. Phylogenetic analysis showed that the symbiosis-related nodC and nifH gene sequences clustered into six groups: three associated exclusively with the peanut host (symbiovar arachidis and two unnamed group), three originating from other legume hosts (sv. glycinearum, cajani and retamae). Through the principal component analysis (PCA) between IGS types or species and soil physicochemical properties and environmental factors, it showed that IGS types 1, 3, 5, 8, 9, 12, 14, 15, 18, and 21 positively correlated with AveTmax, AveTmin, AN and AP. IGS types 4, 11, 16, 17, 20, 25, and 26 were positively associated with Alt, AvePrecp, and pH. IGS types 2, 7, 10, 22, 24, and 27 correlated with AP, while remaining types exhibited correlations with OM. In addition, B. yuanmingense, B. liaoningense, and Bradyrhizobium genosp. I positively affected by AveTmax, AP, AN, and AK. Bradyrhizobium genosp. II positively correlated with AK, AN, and OM while B. zhengyangense mainly affected by AvePrecp and pH. The alkaline soil pH in this study differs greatly from the acid soils in southern Henan, explaining the inconsistency between the species of peanut rhizobia detected in southern Henan and the rest of the province. The symbiotic effect assay demonstrated that all representative strains successfully formed nodules and exhibited a significant increase in symbiotic efficiency. Representative strains revealed diverse abiotic stress tolerance to NaCl, acidity, alkalinity, temperature and drought. It conducted a comprehensive collection of peanut rhizobia in eastern, central, and northern Henan province, identifying two putative novel Bradyrhizobium species and isolating rhizobial strains with high symbiotic efficiency and robust stress tolerance. This study is a necessary basic for the producing and application of peanut rhizobial inoculant in this main agricultural province.},
}

*Arachis/microbiology
China
*Bradyrhizobium/genetics/classification/isolation & purification
Phylogeny
*Soil Microbiology
RNA, Ribosomal, 16S/genetics
DNA, Bacterial/genetics
Polymorphism, Restriction Fragment Length
Symbiosis
Soil/chemistry
Root Nodules, Plant/microbiology
Bacterial Proteins/genetics

@article {pmid40504009,
year = {2025},
author = {Schroer, HW and Markland, K and Ling, F and Just, CL},
title = {Hydraulic Connectivity and Hydrochemistry Influence Microbial Community Structure in Agriculturally Affected Alluvial Aquifers in the Midwestern United States.},
journal = {Environmental science & technology},
volume = {59},
number = {24},
pages = {12279-12291},
doi = {10.1021/acs.est.5c03155},
pmid = {40504009},
issn = {1520-5851},
mesh = {*Groundwater/microbiology ; *Microbiota ; Midwestern United States ; Drinking Water ; },
abstract = {Alluvial aquifers can provide ecosystem services and drinking water, but much remains unknown about human effects on aquifer microbiomes. Therefore, we used amplicon sequencing and hydrochemical characterization to pair microbial communities with environmental conditions across 37 alluvial aquifer wells. The study region spanned eastern Iowa and southern Minnesota (USA) and contained a combination of drinking water and monitoring wells. In terms of microbial ecology, dominant phyla across the wells included Proteobacteria, Bacteroidota, Patescibacteria, Planctomycetota, and Nitrospirota. Tritium, an indicator of infiltration and surface water influence, was the highest correlated variable with the Shannon index (α-diversity) by the Spearman rank sum (ρ = 0.60) and one of only four significant environmental variables in the constrained correspondence analysis. We built random forest regression models to predict tritium concentrations from microbial family relative abundance (held-out testing coefficient of determination (R[2]) = 0.77 and mean absolute percentage error = 7%) and interpreted the models with Shapley additive explanation values. The most important families for predicting tritium concentrations were Nitrosopumilaceae and Methylomirabilaceae. Upwelling methane could contribute to the unusual coupling of ammonia oxidation by Nitrosopumilaceae with simultaneous nitrite-dependent methane oxidation by Methylomirabilaceae. Taken together, we illuminate the relationship among hydrochemistry, hydraulic connectivity, and alluvial aquifer microbiomes.},
}

*Groundwater/microbiology
*Microbiota
Midwestern United States
Drinking Water