@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 = {},
doi = {10.3390/foods14111948},
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 = {},
doi = {10.3390/diagnostics15111431},
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 = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c03155},
pmid = {40504009},
issn = {1520-5851},
abstract = {Alluvial aquifers can provide ecosystem services and drinking water, but much remains unknown about human effects on aquifer microbiomes. Therefore, we used amplicon sequencing and hydrochemical characterization to pair microbial communities with environmental conditions across 37 alluvial aquifer wells. The study region spanned eastern Iowa and southern Minnesota (USA) and contained a combination of drinking water and monitoring wells. In terms of microbial ecology, dominant phyla across the wells included Proteobacteria, Bacteroidota, Patescibacteria, Planctomycetota, and Nitrospirota. Tritium, an indicator of infiltration and surface water influence, was the highest correlated variable with the Shannon index (α-diversity) by the Spearman rank sum (ρ = 0.60) and one of only four significant environmental variables in the constrained correspondence analysis. We built random forest regression models to predict tritium concentrations from microbial family relative abundance (held-out testing coefficient of determination (R[2]) = 0.77 and mean absolute percentage error = 7%) and interpreted the models with Shapley additive explanation values. The most important families for predicting tritium concentrations were Nitrosopumilaceae and Methylomirabilaceae. Upwelling methane could contribute to the unusual coupling of ammonia oxidation by Nitrosopumilaceae with simultaneous nitrite-dependent methane oxidation by Methylomirabilaceae. Taken together, we illuminate the relationship among hydrochemistry, hydraulic connectivity, and alluvial aquifer microbiomes.},
}

@article {pmid40502102,
year = {2025},
author = {Baty, JJ and Drozdick, AK and Pfeiffer, JK},
title = {P. aeruginosa rhamnolipids stabilize human rhinovirus 14 virions.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.04.657910},
pmid = {40502102},
issn = {2692-8205},
abstract = {UNLABELLED: Many mammalian viruses encounter bacteria and bacterial molecules over the course of infection. Previous work has shown that the microbial ecology of the gut plays an integral role in poliovirus and coxsackievirus infection, where bacterial glycans can facilitate virus-receptor interactions, enhance viral replication, and stabilize viral particles. However, how airway bacteria alter respiratory viral infection is less understood. Therefore, we investigated whether a panel of airway bacteria affect rhinovirus stability. We found that Pseudomonas aeruginosa , an opportunistic airway pathogen, protects human rhinovirus 14 from acid or heat inactivation. Further investigation revealed that P. aeruginosa rhamnolipids, glycolipids with surfactant properties, are necessary and sufficient for stabilization of rhinovirus virions. Taken together, this work demonstrates that specific molecules produced by an opportunistic airway pathogen can influence a respiratory virus.

IMPORTANCE: Bacteria can enhance viral stability and infection for enteric members of the Picornaviridae such as poliovirus and coxsackievirus; however, whether bacteria influence respiratory picornaviruses is unknown. In this study, we examined impacts of airway bacteria on rhinovirus, a major etiological agent of the common cold. We found that P. aeruginosa protects human rhinovirus 14 from both acid and heat inactivation through rhamnolipids. Overall, this work demonstrates bacterial effects on respiratory virus through specific bacterial molecules.},
}

@article {pmid40500964,
year = {2025},
author = {Li, S and Wang, T and Liu, M and Ma, T and Li, Y and Liu, J and Liu, Y and Shen, W and Ma, J and Wang, X and Han, X and Wang, H and Zhang, X},
title = {α-Linolenic Acid-Rich Flaxseed Oil Improves Polycystic Ovary Syndrome via Regulating Lipid Metabolism by GPR120-cAMP Pathway and Restoring Gut Microecology.},
journal = {Molecular nutrition & food research},
volume = {},
number = {},
pages = {e70136},
doi = {10.1002/mnfr.70136},
pmid = {40500964},
issn = {1613-4133},
support = {82460793//National Natural Science Foundation of China/ ; 82160691//National Natural Science Foundation of China/ ; 2023AAC03216//Ningxia Natural Science Foundation, China/ ; 2023BEG02011//Key Research and Development Program of Ningxia/ ; 2022BSB03112//Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; XZ2021003//Key Laboratory of Fertility Preservation and Maintainance of Ministry of Education of Ningxia Medical University/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; },
abstract = {Polycystic ovary syndrome (PCOS) is a common endocrine disorder that affects metabolic and reproductive health in women. α-Linolenic acid (ALA)-rich flaxseed oil as a dietary food has been suggested to offer potential therapeutic benefits in managing metabolic disturbances associated with PCOS. This study investigates the effects of ALA-rich flaxseed oil on lipid metabolism and gut microecology in a PCOS rat model. The PCOS model was induced in rats using letrozole, and the animals were then administered ALA-rich flaxseed oil. Metabolomics, transcriptomics, 16S rRNA sequencing, hormonal levels, and markers of metabolic health were assessed. Results showed that ALA-rich flaxseed oil significantly improved lipid metabolism by reducing serum cholesterol and triglycerides. In addition, we found that the improvement in lipid metabolism may be associated with the activation of the GPR120-cAMP pathway. Furthermore, gut microbiota analysis revealed a restoration of gut microbial ecology, with a shift toward a more balanced and healthy microbial composition. ALA-rich flaxseed oil shows promising potential as a dietary intervention for managing metabolic disturbances in PCOS. Its effects on lipid metabolism and gut microecology highlight its nutritional relevance, offering new insights into the dietary management of PCOS and its associated metabolic disorders.},
}

@article {pmid40500753,
year = {2025},
author = {Bograd, A and Oppenheimer-Shaanan, Y and Levy, A},
title = {Plasmids, prophages, and defense systems are depleted from plant microbiota genomes.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {163},
pmid = {40500753},
issn = {1474-760X},
support = {1535/20//Israeli Science Foundation/ ; 1535/20//Israeli Science Foundation/ ; 1535/20//Israeli Science Foundation/ ; 1001695377//Israeli Ministry of Innovation, Science, and Technology/ ; 1001695377//Israeli Ministry of Innovation, Science, and Technology/ ; 1001695377//Israeli Ministry of Innovation, Science, and Technology/ ; 81259//Israel Innovation Authority/ ; 81259//Israel Innovation Authority/ ; 81259//Israel Innovation Authority/ ; 12-12-0008//Ministry of Agriculture and Rural Development/ ; 12-12-0008//Ministry of Agriculture and Rural Development/ ; 12-12-0008//Ministry of Agriculture and Rural Development/ ; ZN4041//Volkswagen Stiftung/ ; ZN4041//Volkswagen Stiftung/ ; ZN4041//Volkswagen Stiftung/ ; },
mesh = {*Prophages/genetics ; *Plasmids/genetics ; *Plants/microbiology ; *Genome, Bacterial ; *Microbiota/genetics ; Metagenome ; *Bacteria/genetics/virology ; },
abstract = {Plant-associated bacteria significantly impact plant growth and health. Understanding how bacterial genomes adapt to plants can provide insights into their growth promotion and virulence functions. Here, we compare 38,912 bacterial genomes and 6073 metagenomes to explore the distribution of mobile genetic elements and defense systems in plant-associated bacteria. We reveal a consistent taxon-independent depletion of prophages, plasmids, and defense systems in plant-associated bacteria, particularly in the phyllosphere, compared to other ecosystems. The mobilome depletion suggests the presence of unique ecological constraints or molecular mechanisms exerted by plants to control the bacterial mobilomes independently of bacterial immunity.},
}

*Prophages/genetics
*Plasmids/genetics
*Plants/microbiology
*Genome, Bacterial
*Microbiota/genetics
Metagenome
*Bacteria/genetics/virology

@article {pmid40500405,
year = {2025},
author = {Chen, TK and Shiau, YJ},
title = {Effects of Soil Properties and Seasonal Variations on Microbial Communities in Constructed Wetlands.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {64},
pmid = {40500405},
issn = {1432-184X},
support = {110-2313-B-002-033-MY3//National Science and Technology Council/ ; },
mesh = {*Wetlands ; Seasons ; *Soil Microbiology ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Soil/chemistry ; Denitrification ; *Microbiota ; Biodiversity ; Nitrates/analysis ; Sulfates/analysis ; Nitrification ; },
abstract = {Constructed wetlands (CWs) are important ecosystems with numerous benefits such as wastewater treatment, wildlife habitat protection, and stormwater remediation. However, the development of soil microbial communities in CWs over time remains understudied. This study comprehensively investigates microbial diversity and community composition in three constructed wetlands, focusing on the influence of wetland age, soil depth, and environmental factors. The results indicate that both soil depth and seasonal variations significantly affect alpha diversity, particularly in surface soils. The predominant microbial communities, including nitrifying and denitrifying communities, were identified across the studied wetlands. Moreover, sulfate-rich conditions may promote sulfur autotrophic denitrification. Redundancy analysis and multiple linear regression highlighted the distinction between autotrophic and heterotrophic denitrifiers. Soluble organic carbon was identified as a major factor influencing heterotrophic denitrifying bacteria, while sulfate and nitrate levels were more closely associated with autotrophic denitrifying bacteria. Overall, these findings provide valuable insights into microbial community dynamics in CWs and can help optimize wetland management strategies for improved nutrient removal efficiency.},
}

*Wetlands
Seasons
*Soil Microbiology
*Bacteria/classification/genetics/metabolism/isolation & purification
*Soil/chemistry
Denitrification
*Microbiota
Biodiversity
Nitrates/analysis
Sulfates/analysis
Nitrification

@article {pmid40499249,
year = {2025},
author = {McDonagh, F and Murray, EK and Hallahan, B and Miliotis, G},
title = {Systematic examination of off-target effects of antipsychotic medications associated with microbiome disruption and heightened bacterial infection risks.},
journal = {Journal of psychiatric research},
volume = {189},
number = {},
pages = {171-183},
doi = {10.1016/j.jpsychires.2025.05.046},
pmid = {40499249},
issn = {1879-1379},
abstract = {OBJECTIVE: This systematic review aims to critically evaluate the link between antipsychotic drugs and bacterial infection risk, emphasising antimicrobial properties of antipsychotics, and microbiome changes that might heighten susceptibility to bacterial infections.

METHODS: A systematic literature search was conducted across PubMed, Scopus, and Google Scholar, up to March 2024. Peer-reviewed articles that investigated the relationship between antipsychotics, their antimicrobial effects, microbiome alterations, and bacterial infection risk were included. Data extracted included antipsychotic type, infection risks, patient demographics, and study methodologies. Risk-of-bias assessments were performed using tools such as the Newcastle-Ottawa Scale and the SYRCLE risk-of-bias tool.

RESULTS: The review analysed twenty-six studies detailing antimicrobial properties of antipsychotics, four studies on antipsychotic-induced microbiome alterations, and thirty-one studies assessing bacterial infection risk associated with antipsychotics. First-generation antipsychotics were observed to have broad antimicrobial properties, whereas second-generation antipsychotics primarily affected commensal bacteria. At least four antipsychotics were observed to disrupt the gut microbiota. A heightened risk of infection was observed among psychiatric cohorts as well as off-label antipsychotics use, with clozapine linked to a substantial increase in respiratory infection risk.

DISCUSSION: Although antipsychotics remain indispensable in psychiatric care, their association with an increased risk of bacterial infections underscores the need for judicious prescribing and vigilant monitoring. The review identifies significant knowledge gaps attributable to inconsistent research methodologies, small study cohorts, lack of controls, and focus on a limited range of antipsychotics. Further standardised research is essential to deepen our understanding of these associations and to inform improved prescribing practices and risk mitigation strategies.},
}

@article {pmid40498465,
year = {2025},
author = {Samimi, A and Hengoju, S and Martin, K and Rosenbaum, MA},
title = {Advancing droplet-based microbiological assays: optofluidic detection meets multiplexed droplet generation.},
journal = {The Analyst},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5an00130g},
pmid = {40498465},
issn = {1364-5528},
abstract = {Microbiological assays are crucial in understanding microbial ecology and developing new bioproducts. Given the significance of these assays, there is a growing interest in developing high throughput experimentation methods capable of assay multiplexing to enhance the accuracy and efficiency. In this study, we integrate a multiplexed droplet generation set-up into an optofluidic detection chip to facilitate rapid and high throughput analysis of microbiological assays. The optofluidic detection set-up at the same time enables fast and sensitive assessment of droplet condition and content, providing analysis scalability in a high throughput manner. Employing the integration, we produced unique fluorescence barcoded droplets containing defined concentrations of various carbon sources, allowing the simultaneous investigation of microbial growth and metabolic capacity under different experimental conditions. We successfully validated the robustness of the established setup in analyzing and distinguishing different fluorescence barcodes. Our findings highlight the potential of the integrated platform for a broader range of applications in high throughput drug screening, environmental monitoring, and microbiology research.},
}

@article {pmid40498364,
year = {2025},
author = {Castledine, M and Esom, C and Van Nieuwenhuyse, B and Djebara, S and Merabishvili, M and Pirnay, JP and Buckling, A},
title = {Predicting clinical phage therapy outcomes in vitro: results using mixed versus single isolates from an MRSA case study.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf144},
pmid = {40498364},
issn = {1365-2672},
abstract = {AIMS: In phage therapy case studies, 1-3 bacteria isolates are typically tested against phages (phagogram). However, as bacteria populations differ in their susceptibility to phages and antibiotics, the strains selected may not represent how the infecting population will respond to treatment. Our aim was to assess whether the effects of phage on single or a mix of isolates in vitro show more comparable results to that observed during a clinical case study.

METHODS AND RESULTS: The patient presented with a methicillin resistant Staphylococcus aureus infection (MRSA). In this previously published case study, phage therapy alongside antibiotics rapidly cleared blood cultures of bacteria while localised regions, including the lungs, took longer to clear of bacteria. In this follow-up study, mixed isolates were more likely to persist than single isolates in vitro, more closely representing the lung, but not blood, infections. These results may reflect the different degrees of genetic diversity of the infecting bacteria in these sites.

CONCLUSIONS: For this patient, phage therapy predictions were significantly affected by whether we used mixed versus single isolates, but the predictive precision depended on the site of in vivo infection.},
}

@article {pmid40495815,
year = {2025},
author = {Abiriga, D and Odong, R and Bakyayita, GK and Semyalo, R and Okello, W and Grossart, HP},
title = {The microbiology of Uganda's large freshwater lakes experiencing anthropogenic and climatic perturbations: why it matters-a review.},
journal = {Proceedings. Biological sciences},
volume = {292},
number = {2048},
pages = {20243072},
doi = {10.1098/rspb.2024.3072},
pmid = {40495815},
issn = {1471-2954},
mesh = {Uganda ; *Lakes/microbiology ; *Climate Change ; *Anthropogenic Effects ; *Water Microbiology ; Biodiversity ; Bacteria ; },
abstract = {Intensification of pollution of African water resources due to human activities together with climate change has serious implications for Africa's blue economy, biodiversity and human health. Despite these overwhelming threats, there is limited research as evidenced by the underrepresentation of Africa-based data in global ecological and biochemical models. This review, therefore, aims to highlight key challenges and existing research gaps, particularly in Ugandan freshwater ecosystems. We focus on lake microbiology as this scientific field has been greatly underrepresented. Aquatic microorganisms are situated at the base of lake food webs and thus play crucial roles in the evolution and maintenance of water quality, attenuation of pollutants, and control of biogeochemical cycling through the microbial loop. Until now, the microbiology of Ugandan lakes has not been systematically studied. Thus, many open fundamental microbial ecology questions need to be urgently addressed to generate valuable information to advance future research, education, management and policy in Uganda and beyond. These include, but are not limited to: identification of microbial taxa and functional genes in relation to anthropogenic and climatic influence; seasonal and spatial variation in species diversity and functions; diversity and functions of planktonic, sediment, biofilm and mat communities; antimicrobial resistance burden; plastisphere communities; and geomicrobiology.},
}

Uganda
*Lakes/microbiology
*Climate Change
*Anthropogenic Effects
*Water Microbiology
Biodiversity
Bacteria

@article {pmid40493213,
year = {2025},
author = {Vila Duplá, M},
title = {Advancements in Algal Microbiome Research: A Game-Changer for Climate Resilience and Invasion Success?.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {63},
pmid = {40493213},
issn = {1432-184X},
mesh = {*Microbiota ; *Climate Change ; *Seaweed/microbiology ; *Introduced Species ; },
abstract = {While marine microbiomes have been getting more attention in recent years, they remain understudied compared to those of terrestrial systems. With the refinement of molecular methods, microbiome research has extended to other key marine organisms such as macroalgae. The microbiome plays a key role in macroalgal health, adaptation to environmental conditions, and resilience to climate stressors. The main factors affecting the algal microbiome are host specificity (genetics, functional profile, phylum and species identity), life stage, morphology, thallus region, and tissue age. Other significant drivers of microbiome community structure include spatiotemporal distribution and environmental conditions, especially as global stressors intensify with climate change. The mechanisms through which the microbiome of invasive seaweeds might enhance their competitiveness over native species are still unclear. However, there is evidence that, like climate resilience, invasive potential is linked to the functional flexibility of associated microbiota, allowing the host to adapt to the new environmental conditions. The main objective of this review was to synthesize the current understanding of the macroalgal microbiome and propose future directions in microbiome research based on identified shortcomings. Based on the knowledge gaps detected, there is an urgent need for multi-factorial experimental studies that link host and microbiome gene expression through chemical signals under future climate change scenarios, standardization of analytical methods, and a focus on underrepresented geographical regions and species. While algal microbiome research holds great promise for predicting and mitigating the effects of climate change and invasive species, embracing new tools and tackling ecologically relevant mechanistic and applied questions will be essential to advancing this field.},
}

*Microbiota
*Climate Change
*Seaweed/microbiology
*Introduced Species

@article {pmid40492114,
year = {2025},
author = {Zhang, Y and Fan, J and Zhao, J and Zhu, H and Xia, Y and Xu, H},
title = {A telomere-associated molecular landscape reveals immunological, microbial, and therapeutic heterogeneity in colorectal cancer.},
journal = {Frontiers in molecular biosciences},
volume = {12},
number = {},
pages = {1615533},
pmid = {40492114},
issn = {2296-889X},
abstract = {BACKGROUND: Colorectal cancer (CRC) ranks among the most prevalent malignancies of the gastrointestinal tract and remains a leading cause of cancer-related mortality worldwide. Although telomere biology has been increasingly implicated in immune modulation and tumor progression, its clinical significance in CRC remains poorly understood.

METHODS: We developed a telomere score, termed TELscore, by integrating transcriptomic and intratumoral microbiome profiles from publicly available colorectal cancer (CRC) cohorts. To comprehensively characterize TELscore subgroups, we performed pathway enrichment analysis, tumor immune microenvironment (TIME) profiling, and microbiome niche assessment. Whole-slide histopathological images (WSIs) and immunohistochemical (IHC) staining were utilized to visualize immune features, including tertiary lymphoid structures (TLSs), across subgroups. Patients were stratified into high and low TELscore categories, and the predictive robustness was validated across multiple independent training and validation cohorts. Chemotherapeutic drug sensitivity was evaluated using pharmacogenomic data from the Genomics of Drug Sensitivity in Cancer (GDSC) database. Furthermore, the predictive capacity of TELscore for immunotherapy response was independently assessed in an external cohort. Finally, single-cell RNA sequencing (scRNA-seq) analysis was conducted to further dissect the cellular landscape and immunological heterogeneity within the TME.

RESULTS: TELscore stratified patients into two biologically and clinically distinct subgroups. The high TELscore group, which exhibited significantly shorter DFS, showed marked enrichment of tumorigenic pathways such as EMT, along with a distinctly immunosuppressive TME. This was reflected by elevated ESTIMATE/TIDE scores and corroborated by CIBERSORT, which revealed increased infiltration of M0 macrophages and upregulation of immunosuppressive signatures. In contrast, the low TELscore group was enriched for cell cycle related pathways, including E2F targets and the G2/M checkpoint, and demonstrated higher infiltration of pro-inflammatory M1 macrophages. 16S rRNA sequencing further revealed a divergent intratumoral microbiome between subgroups, the high TELscore group harbored significantly greater relative abundance of Selenomonas and Lachnoclostridium, two pathogenic genera previously associated with colorectal tumorigenesis. Complementary histopathological assessment via WSI demonstrated a marked absence of intraTLSs in high TELscore tumors. From a therapeutic standpoint, high TELscore tumors exhibited reduced sensitivity to standard chemotherapeutic agents-including Fluorouracil, Irinotecan, Oxaliplatin, and Docetaxel-as reflected by elevated IC50 values. Conversely, these tumors demonstrated increased susceptibility to MAPK pathway inhibitors, such as Selumetinib and Trametinib. Notably, TELscore also served as a robust predictor of immunotherapy response, which was validated in the IMvigor210 cohort. Finally, scRNA analysis highlighted profound cellular and functional divergence between TELscore subgroups. We identified intensified intercellular communication between inflammatory macrophages and fibroblasts, reinforcing the presence of an immunosuppressive niche.

CONCLUSION: TELscore is a robust stratification tool that captures the interplay between tumor biology, immune characteristics, and microbial ecology in colorectal cancer. By identifying clinically relevant subtypes with distinct therapeutic vulnerabilities, TELscore offers a powerful framework to advance personalized treatment and precision oncology.},
}

@article {pmid40488407,
year = {2025},
author = {Grossman, AS and Lei, L and Botting, JM and Liu, J and Nahar, N and Liu, J and McLean, JS and He, X and Bor, B},
title = {Saccharibacteria deploy two distinct type IV pili, driving episymbiosis, host competition, and twitching motility.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf119},
pmid = {40488407},
issn = {1751-7370},
abstract = {All cultivated Patescibacteria, also known as the candidate phyla radiation, are obligate episymbionts residing on other microbes. Despite being ubiquitous in many diverse environments, including mammalian microbiomes, molecular mechanisms of host identification and binding amongst ultrasmall bacterial episymbionts remain largely unknown. Type 4 pili are well conserved in this group and could potentially facilitate these symbiotic interactions. To test this hypothesis, we genetically targeted pili genes in Saccharibacteria Nanosynbacter lyticus strain TM7x to assess their essentiality and roles in symbiosis. Our results revealed that Nanosynbacter lyticus assembles two distinct type 4 pili: a non-essential thin pilus that has the smallest diameter of any type 4 pili and contributes to host-binding and episymbiont growth; and an essential thick pilus involved in twitching motility. To understand the role of these pili in vivo we developed Saccharibacteria competition assays and species specific Fluorescence in situ hybridization probes. Competition between different Saccharibacteria within mock communities demonstrated consistent competitive outcomes that were not driven by priority effects but were dependent on the thin pilus. Collectively our findings demonstrate that Saccharibacteria encode unique extracellular pili that enable their underexplored episymbiotic lifestyle and competitive fitness within a community.},
}

@article {pmid40487916,
year = {2025},
author = {Okazaki, Y and Nishikawa, Y and Wagatsuma, R and Takeyama, H and Nakano, SI},
title = {Contrasting defense strategies of oligotrophs and copiotrophs revealed by single-cell-resolved virus-host pairing of freshwater bacteria.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf086},
pmid = {40487916},
issn = {2730-6151},
abstract = {Characterizing virus-host pairs and the infection state of individual cells is the major technical challenge in microbial ecology. We addressed these challenges using state-of-the-art single-cell genome technology (SAG-gel) combined with extensive metagenomic datasets targeting the bacterial and viral communities in Lake Biwa. From two water layers and two seasons, we obtained 862 single-cell amplified genomes (SAGs), including 176 viral (double-stranded DNA phage) contigs, which identified novel virus-host pairs involving dominant freshwater lineages. The viral infection rate, estimated by mapping the individual SAG's raw reads to viral contigs, showed little variation among samples (12.1%-18.1%) but significant variation in host taxonomy (4.2%-65.3%), with copiotrophs showing higher values than oligotrophs. The high infection rates of copiotrophs were attributed to collective infection by diverse viruses, suggesting weak density-dependent virus-host selection, presumably due to their nonpersistent interactions with viruses resulting from fluctuating abundance. In contrast, the low infection rates of oligotrophs supported the idea that their codominance with viruses is achieved by genomic microdiversification, which diversifies the virus-host specificity, sustained by their large population size and persistent density-dependent fluctuating selection. Notably, we discovered viruses infecting CL500-11, the dominant bacterioplankton lineage in deep freshwater lakes worldwide. These viruses showed extremely high read coverages in cellular and virion metagenomes but were detected in <1% of host cells, suggesting a low infection rate and high burst size. Overall, we revealed highly diverse virus-host interactions within and between host lineages that were overlooked at the metagenomic resolution.},
}

@article {pmid40487326,
year = {2025},
author = {Bornbusch, SL and Dami, KA},
title = {Connecting microbial ecology to human fertility and reproduction: perspectives from the reproductive microbiomes of animals.},
journal = {F&S reports},
volume = {6},
number = {Suppl 1},
pages = {45-49},
pmid = {40487326},
issn = {2666-3341},
abstract = {In all vertebrates, reproduction occurs in the context of host-associated microbiomes, which are increasingly recognized for their contributions to reproductive success. Although host-associated microbiomes are species specific, synthesizing patterns in microbial ecology across human and animal taxa provides perspectives for understanding the factors that shape microbial communities and their contributions to reproduction. Additionally, the fertility and reproductive physiology of animals under human care-particularly endangered species-is often meticulously monitored to maximize reproductive opportunities. In this mini-review, we examine current knowledge on reproductive microbiomes in animals, focusing, when available, on the sparse literature for wildlife species. We suggest ways in which studying animal microbial ecology may advance human fertility and reproduction by focusing on 3 microbial communities-vaginal, milk, and seminal microbiomes-which represent a large portion of literature and have clear implications for reproductive health. We identify avenues of future research that will further strengthen the linkages between reproductive research in wildlife species and humans and provide potential guidelines for practical applications of microbiome science to human reproductive health.},
}

@article {pmid40483289,
year = {2025},
author = {Swain, PP and Subudhi, E and Sahoo, RK},
title = {Heavy Metals and Carbapenem-Resistant Klebsiella pneumoniae in a River System of Odisha, India: Correlation and Integrated Risk Assessment.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {62},
pmid = {40483289},
issn = {1432-184X},
support = {523/2020(BSR)//University Grants Commission/ ; },
mesh = {*Metals, Heavy/analysis ; *Rivers/microbiology/chemistry ; India ; *Klebsiella pneumoniae/drug effects/genetics/isolation & purification ; Risk Assessment ; *Water Pollutants, Chemical/analysis ; *Carbapenems/pharmacology ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Wastewater/microbiology ; Environmental Monitoring ; Humans ; Microbial Sensitivity Tests ; },
abstract = {The unregulated release of heavy metals and antibiotics into rivers has the potential to significantly impact human health. Infections caused by healthcare-associated pathogen, carbapenem-resistant Klebsiella pneumoniae (CRKP), present a critical challenge to clinical practitioners due to its resistance to last-line antibiotics. In this study, we investigated co-contamination of heavy metals (As, Cd, Cr, Mn, and Pb) and CRKP isolates in water samples from multiple sites along the river receiving wastewater discharge from urban areas of twin-city, Odisha. We used a composite risk scoring framework integrating chemical risks (based on hazard indices (HI) of heavy metals) and biological risks (based on the proportion of CRKP isolates exhibiting multidrug-resistant phenotypes and their multiple antibiotic resistance (MAR) index. Furthermore, Spearman's correlations and redundancy analysis (RDA) were employed to assess the association between heavy metals and antibiotic resistance genes (ARGs). From the total CRKP isolates identified (n = 91), 90.1% and 9.89% exhibited multidrug resistant (MDR) and extensively drug-resistant (XDR) phenotypes, respectively. Sites D2 and C2 were flagged as high-risk sites based on their composite risk scores of 0.735 and 0.699, respectively. Positive correlations were observed between heavy metals and ARGs (blaOXA-48, blaTEM, and blaSHV). The findings raise concern regarding the potential threat of CRKP and heavy metal pollution in river water while also emphasizing the need for integrated assessment to control their release into the environment.},
}

*Metals, Heavy/analysis
*Rivers/microbiology/chemistry
India
*Klebsiella pneumoniae/drug effects/genetics/isolation & purification
Risk Assessment
*Water Pollutants, Chemical/analysis
*Carbapenems/pharmacology
*Anti-Bacterial Agents/pharmacology
Drug Resistance, Multiple, Bacterial/genetics
Wastewater/microbiology
Environmental Monitoring
Humans
Microbial Sensitivity Tests

@article {pmid40482721,
year = {2025},
author = {Araujo, ASF and Pereira, APA and de Medeiros, EV and Mendes, LW},
title = {Root architecture and the rhizosphere microbiome: shaping sustainable agriculture.},
journal = {Plant science : an international journal of experimental plant biology},
volume = {},
number = {},
pages = {112599},
doi = {10.1016/j.plantsci.2025.112599},
pmid = {40482721},
issn = {1873-2259},
abstract = {Understanding root architecture and exudation is fundamental for enhancing crop productivity and promoting sustainable agriculture. Historically, plant researchers have focused on above-ground traits to increase yield and reduce input dependence. However, below-ground traits, especially those related to the root system, are equally critical yet often overlooked due to phenotyping challenges. Root architecture, including some root traits, i.e., lateral root density, root hair abundance, and root tip number, plays central roles in plant establishment, stress tolerance, and the recruitment of beneficial microbes in the rhizosphere. Root exudates, a complex array of chemical compounds released by roots, vary with plant species, developmental stage, and environmental conditions. These compounds act as signals and nutrients, shaping the composition and function of rhizosphere microbial communities. In turn, the microbiome of rhizosphere contributes to plant health by facilitating nutrient uptake, enhancing stress resilience, and providing defense against pathogens. Integrating root traits into breeding programs offers promising opportunities to select for genotypes that are more efficient in recruiting beneficial microbes. Heritable root traits, such as increased branching, finer roots, and higher exudation capacity, can enhance microbiome assembly and stability. The assessment of genes can also regulate of these traits and represent targets for genomics-assisted selection. Some strategies, such as microbiome engineering, particularly through the design of synthetic microbial communities (SynComs), can be used to modulate root architecture and optimize plant-microbe interactions. Despite these promising outcomes, challenges remain in translating SynCom applications to the field due to environmental variability, native microbial competition, and limited understanding of host genetic controls. This review discusses how root architecture shapes the rhizosphere microbiome and explores strategies, such as trait-based breeding and microbiome engineering, for advancing sustainable crop production.},
}

@article {pmid40481550,
year = {2025},
author = {Zhu, F and Ying, H and Siadat, SD and Fateh, A},
title = {The gut-lung axis and microbiome dysbiosis in non-tuberculous mycobacterial infections: immune mechanisms, clinical implications, and therapeutic frontiers.},
journal = {Gut pathogens},
volume = {17},
number = {1},
pages = {40},
pmid = {40481550},
issn = {1757-4749},
abstract = {Non-tuberculous mycobacteria (NTM) are emerging pathogens of global concern, particularly in regions with declining tuberculosis rates. This review synthesizes current evidence on the epidemiology, immune pathogenesis, and microbiome interactions underlying NTM infections. The rising incidence of NTM is driven by environmental factors, immunocompromised populations, and advanced diagnostics. Clinically, NTM manifests as pulmonary, lymphatic, skin/soft tissue, or disseminated disease, with Mycobacterium avium complex (MAC) and M. abscessus being predominant pathogens. Host immunity, particularly Th1 responses mediated by IL-12/IFN-γ and TLR2 signaling, is critical for controlling NTM, while dysregulated immunity (e.g., elevated Th2 cytokines, PD-1/IL-10 pathways) exacerbates susceptibility. Emerging research highlights the gut-lung axis as a pivotal mediator of disease, where microbiome dysbiosis-marked by reduced Prevotella and Bifidobacterium-impairs systemic immunity and promotes NTM progression. Short-chain fatty acids (SCFAs) and microbial metabolites like inosine modulate macrophage and T-cell responses, offering therapeutic potential. Studies reveal distinct airway microbiome signatures in NTM patients, characterized by enriched Streptococcus and Prevotella, and reduced diversity linked to worse outcomes. Despite advances, treatment remains challenging due to biofilm formation, antibiotic resistance, and relapse rates. This review underscores the need for microbiome-targeted therapies, personalized medicine, and longitudinal studies to unravel causal relationships between microbial ecology and NTM pathogenesis.},
}

@article {pmid40481438,
year = {2025},
author = {Babalola, OO and Osuji, IE and Akanmu, AO},
title = {Amplicon-based metagenomic survey of microbes associated with the organic and inorganic rhizosphere soil of Glycine max L.},
journal = {BMC genomic data},
volume = {26},
number = {1},
pages = {40},
pmid = {40481438},
issn = {2730-6844},
abstract = {OBJECTIVES: The metagenomic dataset of 16S rRNA and ITS gene amplicons of DNA were obtained from the cultivated soybean rhizosphere of organic and inorganic treatments. The organic treatments consisted of poultry waste, and cow dung treatments while the inorganic consisted of samples from untreated soybean plots and the bulk. Amplicon sequencing was performed on the Illumina platform, and the raw sequence data were processed and analyzed using Quantitative Insights Into Microbial Ecology (QIIME 2 version 2019.1.).

DATA DESCRIPTION: The analysis revealed a metagenomic library from soybean rhizospheric soils, providing insights into diversity and distribution of the bacterial and fungal community diversities. The most predominant bacteria phylum taxa across the treatments were Proteobacteria, Firmicutes, Actinobacteriota and Bacteriodota, while those for fungi were Ascomycota, Basidiomycota and Glomeromycota. The dataset provides insights into how different organic fertilization sources affect the structure, composition, and diversity of the microbiome in the soybean rhizosphere. The sequences have been deposited in the Sequence Read Archive (SRA) of the National Center for Biotechnology Information (NCBI) with assigned bioproject accession numbers; 16S rRNA (SRP540791) and ITS (SRP541849).},
}

@article {pmid40403739,
year = {2025},
author = {Kramer, SJ and Jones, EL and Estapa, ML and Paul, NL and Rynearson, TA and Santoro, AE and Sudek, S and Durkin, CA},
title = {Sinking particles exporting diatoms and Hacrobia predict the magnitude of oceanic POC flux.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
doi = {10.1093/ismejo/wraf105},
pmid = {40403739},
issn = {1751-7370},
support = {#986836//Simons Foundation Postdoctoral Fellowship in Marine Microbial Ecology/ ; 80NSSC21K0015//NASA Ocean Biology and Biogeochemistry/ ; 80NSSC18K1431//NASA Ocean Biology and Biogeochemistry/ ; 80NSSC17K0716//NASA Ocean Biology and Biogeochemistry/ ; },
mesh = {*Seawater/microbiology/chemistry ; *Phytoplankton/genetics/metabolism/classification ; *Diatoms/metabolism/genetics/classification ; RNA, Ribosomal, 18S/genetics ; Pacific Ocean ; Atlantic Ocean ; *Carbon/metabolism/analysis ; Ecosystem ; Sequence Analysis, DNA ; },
abstract = {Carbon flux to the deep sea can be dictated by surface ocean phytoplankton community composition, but translating surface ocean observations into quantitative predictions of carbon export requires additional consideration of the underlying ecosystem drivers. Here, we used genetic tracers of phytoplankton detected in surface seawater and within sinking particles collected in the mesopelagic ocean to identify mechanistic links between surface communities and carbon export in the North Pacific and North Atlantic Oceans. Phytoplankton 18S rRNA gene sequences were sampled over a 1-month period in surface seawater and within bulk-collected and individually isolated sinking particles using mesopelagic sediment traps (100-500 m). Nearly all phytoplankton amplicon sequence variants exported from the surface were packaged in large (>300 μm) particles. Individually, each of these particles contained only a few distinct phytoplankton amplicon sequence variants, but collectively, large particles transported about half of the surface taxonomic diversity into the mesopelagic. The relative sequence abundances of the surface community detected within particles were quantitatively related to measured carbon fluxes: a linear model based on the relative sequence abundance of just two pigment-based phytoplankton taxa, diatoms and photosynthetic Hacrobia, was predictive of carbon flux magnitude. These two taxa were also enriched in the ecologically distinct particle classes that had the greatest influence on carbon export magnitude. As global, hyperspectral ocean color satellites begin to quantify these taxonomic groups in the surface ocean, the relationship of these taxa to carbon fluxes demonstrated here may help in developing more accurate algorithms to estimate global carbon export in the ocean.},
}

*Seawater/microbiology/chemistry
*Phytoplankton/genetics/metabolism/classification
*Diatoms/metabolism/genetics/classification
RNA, Ribosomal, 18S/genetics
Pacific Ocean
Atlantic Ocean
*Carbon/metabolism/analysis
Ecosystem
Sequence Analysis, DNA

@article {pmid40480043,
year = {2025},
author = {Keating, C and Trego, A and O'Flaherty, V and Ijaz, UZ},
title = {Microbiomes of high-rate anaerobic digestors reveal 'Study'-specific factors and limitations of synthetic wastewater.},
journal = {Water research},
volume = {282},
number = {},
pages = {123931},
doi = {10.1016/j.watres.2025.123931},
pmid = {40480043},
issn = {1879-2448},
abstract = {Anaerobic digestion (AD) is a key technology for the treatment of organic wastes and the production of renewable energy. The stability of the process hinges on the underlying microbial populations. Amplicon sequencing is increasingly used to characterise AD microbiomes, yet sequencing efforts have not translated to process engineering of the microbiome or prediction of failure using microbial tools. Using high-rate biofilm wastewater bioreactors as a study system, we aimed to i) discern trends in archaeal and bacterial diversity, ii) identify a core AD microbiome, iii) determine the functional stability of AD microbiomes, and iv) correlate taxa to experimental conditions. We analysed amplicon sequencing data from 32 high-rate anaerobic digestor studies (> 1258 samples) at various operational conditions and applied a suite of statistical microbiome tools. We found that taxonomic archaeal diversity was highly study dependent, while functional diversity was highly shared across studies. A core AD microbiome was identified with > 100 bacterial genera and 6 archaeal genera which were present at > 1 % relative abundance in at least 50 % of samples. Interestingly, we observed that microbiome stability was significantly impacted by the choice of real or synthetic wastewater, with synthetic wastewaters yielding a more stable and less complex microbiome. This was correlated to the abundances of 37 taxa in the synthetic wastewater, including 3 key methanogens (Methanothrix, Methanobacterium, and Methanosphaerula). This suggests that when synthetic wastewater is used in experimental studies, it may not result in an AD microbiome representative of real wastewater treatment systems.},
}

@article {pmid40476717,
year = {2025},
author = {Baer, J and Little, M and Aquino, J and van der Geer, A and Sánchez-Quinto, A and Ballard, A and Lawrence, C and Carilli, J and Hartmann, A and Rohwer, F},
title = {Viralization as a microbial approach for enhancing coral reef restoration.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf110},
pmid = {40476717},
issn = {1751-7370},
abstract = {Coral reef ecosystems rely on microorganisms to carry out biogeochemical processes essential to the survival of corals and the reef food web. However, widespread shifts from coral to algal dominance as a result of anthropogenic pressures have promoted microbial communities that compromise reef health through deoxygenation and disease. These degraded reefs become locked in a "microbialized" state characterized by high microbial biomass, low oxygen, and heightened pathogenic activity that stymie efforts to outplant corals onto the reef, a common approach applied to restore these ecosystems. Over 18 months, we compared viral and microbial dynamics alongside physical and chemical parameters ("water quality") between two coral outplanting sites and two midwater reef mesocosms called Coral Arks. Seafloor sites exhibited microbialization, whereas Arks maintained conditions with higher viral abundances and virus-to-microbe ratios, smaller and less abundant microorganisms, and consistently higher dissolved oxygen, water flow, and light availability. These conditions, which we term "viralized", supported enhanced coral growth and survival, greater benthic diversity, increased coral recruitment, reduced turf and macroalgae, and higher fish abundance compared to outplanting sites. Despite these benefits, analysis of microbial carbon metabolism genes revealed an underlying trend towards microbialization at both sites, reflecting larger-scale regional decline. These findings emphasize that microbial and physicochemical conditions are drivers of reef restoration outcomes; to be successful, restoration strategies must target the underlying environmental factors that support coral survival and resilience. We identify key microbial and physical variables-such as oxygen levels, flow, and viral activity-associated with viralized reef states, which should serve as focal points for developing new interventions and technologies aimed at creating conditions conducive to reef recovery.},
}

@article {pmid40474779,
year = {2025},
author = {Green, N and Norwood, A and Sidhe, C and Mutlow, A and Aymen, J and Stiles, R and Bushell, J and Lim, T and Culver, E and Reeder, N and Timmer, M and Connelly, F and Charbonneau, J and McCall, W and Koenig, L and Stein, M and Geist, N and Lambert, MR and Hernández-Gómez, O},
title = {Shell Lesion Prevalence and Bacteriome Associations in Threatened Western Pond Turtles (Actinemys marmorata and Actinemys pallida) in California, USA.},
journal = {Journal of wildlife diseases},
volume = {},
number = {},
pages = {},
pmid = {40474779},
issn = {1943-3700},
abstract = {Bacteriome characterization studies can provide insights into the microbial ecology associated with disease. We collected western pond turtles (Actinemys marmorata and Actinemys pallida) from six San Francisco Bay Area, California, US, ponds; assessed their shells for lesions; and collected shell swabs and keratin scrape samples to evaluate bacteriome differences between the whole shell (swabs) and the affected tissues (scrapes). We quantified shell lesion type and prevalence by using visual inspections of photographs collected of the plastron and carapace and then applied 16S rRNA amplicon sequencing to characterize the associated bacteriomes of shells that observed pits, ulcerations, or no lesions. We observed shell lesions at high frequencies throughout our sites, with larger individuals (>100-mm plastron length) more likely to possess injuries. We saw no differences in alpha diversities between shells presenting with lesions and those on which we did not observe lesions; however, swab samples showed higher bacterial richness than keratin scrapes. The bacterial composition within the scrapes was influenced by pond location and then lesion presence. We observed a higher relative abundance of Actinobacteriota, Bacteroidota, Cyanobacteria, and Deinococcota in the shell keratin microflora of turtles with shell lesions. Because western pond turtles are under consideration for listing under the Endangered Species Act of 1973 in the US, understanding patterns of shell disease pathologies and the bacteria associated with disease is imperative for the management of current populations.},
}

@article {pmid40474000,
year = {2025},
author = {Cottam, DE and Cosgrove, DW and Megía-Palma, R and Žagar, A and Blázquez-Castro, S and Faria, JF and Turner, AE and Silva, DO and Pie, MR},
title = {Does the Gut Microbiome of the Insular Lizard Gallotia galloti Reflect Variation in Sex, Environment, and Population Genetic Differentiation?.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {61},
pmid = {40474000},
issn = {1432-184X},
mesh = {Animals ; *Lizards/microbiology/genetics ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Male ; Female ; Spain ; *Bacteria/classification/genetics/isolation & purification ; Environment ; Genetic Variation ; Genetics, Population ; Sex Factors ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Despite their critical role in maintaining organismal health, the factors driving intraspecific variation in gut microbiotas in the wild are poorly understood. Gallotia galloti is a lizard endemic to the Canary Islands characterized by substantial phenotypic and genetic differentiation across populations, as well as by its ability to occur across considerably different environmental conditions. However, the extent to which such diversity is reflected in their gut microbiota is still unknown. Here, we use metabarcoding of fecal samples to explore how the gut microbiome of G. galloti reflects variation in sex, environment, human footprint, and subspecies identity. Fecal samples of 47 individuals were obtained across 13 locations to reflect the extent of intraspecific variation in the species. We found no evidence for consistent differences in microbiota richness across the studied groups, regardless of whether analyses were carried out at the genus, family, or phylum levels. Moreover, neither the richness nor composition of the microbiota was associated with variation in mean annual temperature, annual precipitation, and human footprint. Our results suggest that the generalist diet of G. galloti exposes them to a broad range of food items that provide a common template across the island, despite ecological and historical differences between populations.},
}

Animals
*Lizards/microbiology/genetics
*Gastrointestinal Microbiome/genetics
Feces/microbiology
Male
Female
Spain
*Bacteria/classification/genetics/isolation & purification
Environment
Genetic Variation
Genetics, Population
Sex Factors
RNA, Ribosomal, 16S/genetics

@article {pmid40473091,
year = {2025},
author = {Santos, FSA and Corgosinho, PHC and de Abreu, FVS and Vaca-Sánchez, MS and Corgosinho, PCHC and de Faria, ML and Valério, HM and Borges, MAZ},
title = {Assessing the Impact of Different Scale Removal Methods on the Geometric Morphometrics of Aedes aegypti Wings.},
journal = {Acta tropica},
volume = {},
number = {},
pages = {107686},
doi = {10.1016/j.actatropica.2025.107686},
pmid = {40473091},
issn = {1873-6254},
abstract = {This work aimed to test different treatments for removing wing scales from Aedes aegypti, and evaluate through geometric morphometrics, if these treatments can modify the wing venation morphometric pattern. The treatments were wing agitation in mineral water and NaOH (sodium hydroxide) saline solution using a mini-ultrasound, and manual wing scales removal using a size zero (0) tip brush. We propose an alternative method for mounting wings on slides using glycerin. We conclude that glycerin use for slide mounting provides better optics and translucency, and that treatments with NaOH saline solution and water can impair morphometric analysis of wings. The size zero (0) tip brush treatment efficiently removed wing scales, improving wing structure visualization without causing significant modifications to the specimens.},
}

@article {pmid40471139,
year = {2025},
author = {Gawish, R and Varada, R and Deckert, F and Hladik, A and Steinbichl, L and Cimatti, L and Milanovic, K and Jain, M and Torgasheva, N and Tanzer, A and De Paepe, K and Van de Wiele, T and Hausmann, B and Lang, M and Pechhacker, M and Ibrahim, N and De Vries, I and Brostjan, C and Sixt, M and Gasche, C and Boon, L and Berry, D and Jantsch, MF and Pereira, FC and Vesely, C},
title = {Filamin A editing in myeloid cells reduces intestinal inflammation and protects from colitis.},
journal = {The Journal of experimental medicine},
volume = {222},
number = {9},
pages = {},
pmid = {40471139},
issn = {1540-9538},
support = {57-B28//Austrian Science Fund/ ; V 1025-B//Austrian Science Fund/ ; DOC32-B28//Austrian Science Fund/ ; F8007//Austrian Science Fund/ ; P32678//Austrian Science Fund/ ; //Medical University of Vienna/ ; },
mesh = {*Filamins/genetics/metabolism ; Animals ; *Myeloid Cells/metabolism/pathology ; Humans ; *Colitis/genetics/pathology/prevention & control ; *Inflammation/pathology/genetics ; Mice ; Mice, Inbred C57BL ; Neutrophils/metabolism ; *RNA Editing ; Macrophages/metabolism ; Male ; },
abstract = {Patho-mechanistic origins of ulcerative colitis are still poorly understood. The actin cross-linker filamin A (FLNA) impacts cellular responses through interaction with cytosolic proteins. Posttranscriptional A-to-I editing generates two forms of FLNA: genome-encoded FLNAQ and FLNAR. FLNA is edited in colon fibroblasts, smooth muscle cells, and endothelial cells. We found that the FLNA editing status determines colitis severity. Editing was highest in healthy colons and reduced during murine and human colitis. Mice that exclusively express FLNAR were highly resistant to DSS-induced colitis, whereas fully FLNAQ animals developed severe inflammation. While the genetic induction of FLNA editing influenced transcriptional states of structural cells and microbiome composition, we found that FLNAR exerts protection specifically via myeloid cells, which are physiologically unedited. Introducing fixed FLNAR did not hamper cell migration but reduced macrophage inflammation and rendered neutrophils less prone to NETosis. Thus, loss of FLNA editing correlates with colitis severity, and targeted editing of myeloid cells serves as a novel therapeutic approach in intestinal inflammation.},
}

*Filamins/genetics/metabolism
Animals
*Myeloid Cells/metabolism/pathology
Humans
*Colitis/genetics/pathology/prevention & control
*Inflammation/pathology/genetics
Mice
Mice, Inbred C57BL
Neutrophils/metabolism
*RNA Editing
Macrophages/metabolism
Male

@article {pmid40469738,
year = {2025},
author = {Amen, R and Ganzert, L and Friedl, T and Rybalka, N and Wagner, D},
title = {From single pioneers to complex pro- and eukaryotic microbial networks in soils along a glacier forefield chronosequence in continental Antarctica.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1576898},
pmid = {40469738},
issn = {1664-302X},
abstract = {INTRODUCTION: In the extremely dry and oligotrophic soils of East Antarctica, where low temperatures and humidity result in minimal biological turnover rates, extracellular DNA (eDNA) can persist over extended timescales. Differentiating between sequences from living, potentially active cells (intracellular DNA, or iDNA) and those from ancient, non-living organisms (eDNA) is crucial for accurately assessing the current microbial community and understanding historical microbial dynamics.

METHODS: This study was conducted along a chronosequence in the Larsemann Hills, East Antarctica, where soil samples were collected from sites at varying distances from the glacier. By employing DNA separation methods, we distinguished iDNA, which represents living cells, from eDNA derived from dead organisms. High-throughput sequencing was used to characterize bacterial and eukaryotic communities across different successional stages.

RESULTS: The DNA separation approach revealed distinct bacterial and eukaryotic community structures along the glacier transect. Actinobacteria were consistently abundant across all sites, while other phyla such as Chloroflexi, Gemmatimonadetes, and Proteobacteria thrived in extreme, nutrient-poor environments. Early successional stages were characterized by the simultaneous colonization of green algae Trebouxiophyceae and cryophilic fungi, alongside nitrogen-fixing bacteria, which contributed to initial soil development. The study also identified three distinct modes of microbial distribution, reflecting varying degrees of activity and adaptability.

DISCUSSION: Our findings provide new insights into microbial dynamics in extreme habitats and propose new hypotheses for microbial colonization in newly exposed soils. Moreover, they contribute to the ongoing debate in microbial ecology regarding the viability of dormant or dead cells and emphasize the need for refining DNA-based methods and exploring functional pathways to deepen our understanding of microbial succession in polar regions.},
}

@article {pmid40469504,
year = {2025},
author = {Van Den Bossche, T and Armengaud, J and Benndorf, D and Blakeley-Ruiz, JA and Brauer, M and Cheng, K and Creskey, M and Figeys, D and Grenga, L and Griffin, TJ and Henry, C and Hettich, RL and Holstein, T and Jagtap, PD and Jehmlich, N and Kim, J and Kleiner, M and Kunath, BJ and Malliet, X and Martens, L and Mehta, S and Mesuere, B and Ning, Z and Tanca, A and Uzzau, S and Verschaffelt, P and Wang, J and Wilmes, P and Zhang, X and Zhang, X and Li, L and , },
title = {The microbiologist's guide to metaproteomics.},
journal = {iMeta},
volume = {4},
number = {3},
pages = {e70031},
pmid = {40469504},
issn = {2770-596X},
abstract = {Metaproteomics is an emerging approach for studying microbiomes, offering the ability to characterize proteins that underpin microbial functionality within diverse ecosystems. As the primary catalytic and structural components of microbiomes, proteins provide unique insights into the active processes and ecological roles of microbial communities. By integrating metaproteomics with other omics disciplines, researchers can gain a comprehensive understanding of microbial ecology, interactions, and functional dynamics. This review, developed by the Metaproteomics Initiative (www.metaproteomics.org), serves as a practical guide for both microbiome and proteomics researchers, presenting key principles, state-of-the-art methodologies, and analytical workflows essential to metaproteomics. Topics covered include experimental design, sample preparation, mass spectrometry techniques, data analysis strategies, and statistical approaches.},
}

@article {pmid40468430,
year = {2025},
author = {Khoiri, AN and Costa, NR and Crusciol, CAC and Pariz, CM and Costa, C and Calonego, JC and de Castilhos, AM and de Souza, DM and de Lima Meirelles, PR and Cru, IV and Moretti, LG and Bossolani, JW and Kuramae, EE},
title = {Pigeon pea-mediated soil microbial shifts improve agroecosystem multifunctionality in long-term maize-palisade grass intercropping.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {60},
pmid = {40468430},
issn = {2524-6372},
support = {#2014/21772-4 and #2014/14935-4//São Paulo Research Foundation (FAPESP)/ ; #458225/2014-2//National Council for Scientific and Technological Development (CNPq)/ ; 1378/14//Fundação Agrisus/ ; },
abstract = {BACKGROUND: Intercropping systems enhance agricultural sustainability by promoting ecosystem multifunctionality (EMF). This study examined the impact of adding pigeon pea (M + PG + PP) into a maize-palisade grass (M + PG) intercropping system under a no-till system (NTS) on soil microbial communities and ecosystem services. After five consecutive growing seasons, bulk soil samples from a soybean-based crop-livestock system were analyzed using metagenomics.

RESULTS: The inclusion of pigeon pea significantly improved the EMF index, with higher plant productivity and slightly enhanced outcomes in soil health, lamb meat productivity, and climate protection. The M + PG + PP treatment enriched Bradyrhizobium spp., which were positively correlated with soil health, plant productivity, and EMF index. Functional analysis indicated that M + PG + PP treatment enhanced nitrogen metabolism, biofilm formation, and exopolysaccharide (EPS) biosynthesis, improving soil fertility and microbial activity. Similarly, functional analysis of microbial plant growth-promoting traits revealed that the M + PG + PP treatment promoted microbial functions related to nitrogen and iron acquisition, sulfur assimilation, and plant colonization, all essential for plant growth and nutrient cycling. In contrast, the M + PG treatment primarily enhanced pathways related to competitive exclusion and phytohormone production.

CONCLUSIONS: These findings highlight the importance of incorporating legumes such as pigeon pea into intercropping systems to optimize ecosystem services, enhance soil health, and promote long-term agricultural productivity and sustainability.},
}

@article {pmid40467851,
year = {2025},
author = {Rakotonindrina, V and Andriamananjara, A and Razafimbelo, T and Okamoto, T and Sarr, PS},
title = {Land Cover and Seasonal Variations Shape Soil Microbial Communities and Nutrient Cycling in Madagascar Tropical Forests.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {60},
pmid = {40467851},
issn = {1432-184X},
mesh = {*Soil Microbiology ; Seasons ; Madagascar ; *Forests ; Soil/chemistry ; Tropical Climate ; Nitrogen/analysis/metabolism ; Carbon/analysis ; *Microbiota ; Bacteria/classification/genetics/isolation & purification/metabolism ; Fungi/genetics/classification/isolation & purification/metabolism ; RNA, Ribosomal, 16S/genetics ; Phosphorus/analysis/metabolism ; Trees ; Ecosystem ; },
abstract = {Understanding how land cover and seasonal variations influence soil microbial communities and nutrient cycling is crucial for sustainable land management in tropical forests. However, such investigations are limited in Madagascar's tropical ecosystems. This study investigated the impacts of land cover types and seasonal variations on soil properties and microbial communities in the tropical forest region of Andasibe, Madagascar. Soil samples were collected from four land cover types-tree fallow (TSA), shrub fallow (SSA), eucalyptus forest (EUC), and degraded land (TM)-across three seasonal periods: the dry season, the start of the rainy season, and the end of the rainy season. Both land cover and sampling season affected soil pH and available P, whereas total nitrogen, soil organic carbon, and the C/N ratio were affected only by land cover. The soil organic carbon and total nitrogen concentrations were greater in TM. NextSeq sequencing of the 16S rRNA gene and ITS regions of the nuclear rRNA operon revealed distinct microbial community compositions across land covers, with greater diversity in the TSA and SSA. Bacteria are more sensitive to seasonal changes than are fungi, with phosphate-solubilizing (gcd) and phosphate-mineralizing (phoD) genes being more abundant in the rainy season, emphasizing the role of microbes in nutrient availability under different climatic conditions. Principal component analysis highlighted SSA as a hotspot for microbial activity, reinforcing the potential of shrub ecosystems in soil restoration. These findings reveal strong land cover and seasonal effects on soil microbial functions, with implications for nutrient cycling, ecosystem resilience, and sustainable land management in tropical forest landscapes.},
}

*Soil Microbiology
Seasons
Madagascar
*Forests
Soil/chemistry
Tropical Climate
Nitrogen/analysis/metabolism
Carbon/analysis
*Microbiota
Bacteria/classification/genetics/isolation & purification/metabolism
Fungi/genetics/classification/isolation & purification/metabolism
RNA, Ribosomal, 16S/genetics
Phosphorus/analysis/metabolism
Trees
Ecosystem

@article {pmid40467767,
year = {2025},
author = {Yan, Z and Yao, Y and Xu, Q and He, X and Zhou, X and Wang, H},
title = {Dietary microbiota-mediated shifts in gut microbial ecology and pathogen interactions in giant pandas (Ailuropoda melanoleuca).},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {864},
pmid = {40467767},
issn = {2399-3642},
mesh = {Animals ; *Ursidae/microbiology ; *Gastrointestinal Microbiome ; *Diet/veterinary ; Feces/microbiology ; *Bacteria/genetics/classification ; },
abstract = {The impact of dietary microorganisms on host microbiota is recognized, but the underlying mechanisms remain unclear. This study examined the effects of bamboo surface microbiota, including virulence factors, antibiotic resistance genes (ARGs), and mobile genetic elements from different bamboo parts (leaves, shoots, and culms), on giant panda gut microbiota using three pairs of twins. Results showed that bamboo and fecal samples shared 1670 microbial species, with shoot surface microbiota contributing the highest proportion (21%, Bayesian source tracking) of contemporaneous gut microbiota, primarily by increasing abundances of Escherichia coli and ARGs. Klebsiella pneumoniae and Salmonella enterica also showed high co-occurrence in both bamboo and fecal samples, indicating potential colonization. Additionally, Streptococcus suis, Acinetobacter, and Mycobacterium progressively declined in fecal samples as bamboo shoot intake increased, suggesting these microbes are likely transient. The findings emphasize the impact of foodborne microorganisms on the host and the importance of conservation management.},
}

Animals
*Ursidae/microbiology
*Gastrointestinal Microbiome
*Diet/veterinary
Feces/microbiology
*Bacteria/genetics/classification

@article {pmid40467587,
year = {2025},
author = {Xiong, S and Xie, B and Yin, N and Zhu, H and Gao, H and Xu, X and Xiao, K and Cai, X and Sun, G and Sun, X and Cui, Y and Van de Wiele, T and Zhu, Y},
title = {Prenatal exposure to trace elements impacts mother-infant gut microbiome, metabolome and resistome during the first year of life.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {5186},
pmid = {40467587},
issn = {2041-1723},
support = {No. L232076//Natural Science Foundation of Beijing Municipality (Beijing Natural Science Foundation)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; Female ; Pregnancy ; Infant ; *Trace Elements/adverse effects ; *Metabolome/drug effects ; Feces/microbiology ; *Prenatal Exposure Delayed Effects/microbiology/metabolism ; Adult ; Male ; Metagenomics ; Hair/chemistry ; *Maternal Exposure/adverse effects ; Infant, Newborn ; Bacteria/genetics/classification/drug effects ; Copper ; },
abstract = {Infancy is a critical window for the colonization of gut microbiome. However, xenobiotic impacts on gut microbiome development in early life remain poorly understood. Here, we recruit 146 mother-infant pairs and collect stool samples at 3, 6, and 12 months after delivery for amplicon sequencing (N = 353), metagenomics (N = 65), and metabolomics (N = 198). Trace elements in maternal hair samples (N = 119) affect diversity and composition of the infant gut microbiome. Shannon diversity in 3 month-old infants is correlated positively with selenium and negatively with copper, and relative abundance of Bifidobacterium increases under high exposure to aluminum and manganese. During the first year of life, infants and their paired mothers have distinct microbial diversity and composition, and their bacterial community structures gradually approach. here are 56 differential metabolites between the first and second visit and 515 differential metabolites between the second and third visit. The typical profile of antibiotic resistance genes (ARGs) significantly differs between infants and their mothers. High levels of copper and arsenic exposure may induce the enrichment of ARGs in the infant gut. Our findings highlight the dynamics of the gut microbiome, metabolites, and ARG profiles of mother-infant pairs after delivery, associated with prenatal exposure to trace elements.},
}

Humans
*Gastrointestinal Microbiome/drug effects/genetics
Female
Pregnancy
Infant
*Trace Elements/adverse effects
*Metabolome/drug effects
Feces/microbiology
*Prenatal Exposure Delayed Effects/microbiology/metabolism
Adult
Male
Metagenomics
Hair/chemistry
*Maternal Exposure/adverse effects
Infant, Newborn
Bacteria/genetics/classification/drug effects
Copper

@article {pmid40467261,
year = {2025},
author = {Cabezas-Terán, K and Grootaert, C and Van Camp, J and Ortiz, J and Ruales, J and Donoso, S and Van de Wiele, T},
title = {Bioaccessibility of β-carotene during in vitro co-digestion of encapsulated mango peel carotenoids with milk.},
journal = {Food research international (Ottawa, Ont.)},
volume = {214},
number = {},
pages = {116576},
doi = {10.1016/j.foodres.2025.116576},
pmid = {40467261},
issn = {1873-7145},
mesh = {*Mangifera/chemistry ; *beta Carotene/pharmacokinetics/metabolism ; *Milk/chemistry/metabolism ; *Digestion ; Animals ; Biological Availability ; *Fruit/chemistry ; *Carotenoids ; Particle Size ; },
abstract = {β-carotene is a carotenoid with provitamin A activity whose digestive stability and bioaccessibility prior to intestinal absorption are important to fully exploit its health benefits. Microencapsulation protects carotenoids, but there is a lack of information on the extent to which its characteristics and interactions with complex food matrices could impact the carotenoid micellization during digestion. We evaluated the effect of milk fat content on the in vitro bioaccessibility of β-carotene from microparticles containing carotenoids from mango peel. The microparticles tested contained solvent-extracted carotenoids and supercritical fluid-extracted carotenoids, and were separately co-digested with whole, semi-skimmed and skimmed milks. Bioaccessibility was assessed using an in vitro digestion method adapted to carotenoids. β-carotene recoveries after in vitro digestions ranged from 79.6 to 102.2 %, with the highest values corresponding mainly to microparticles with the lowest initial β-carotene concentration. β-carotene bioaccessibilities ranged from 8.8 to 75.5 %, the highest values being obtained mainly when the microparticles were co-digested with whole milk, especially when those containing supercritical fluid-extracted carotenoids were used. The bioaccessibility-enhancing effect of the milk fat was explained by the higher concentration of free fatty acids in the micellar phase, while the better results in the microparticles containing supercritical-fluid-extract was attributed to the lower initial concentration of β-carotene. In conclusion, increasing the milk fat content increased the bioaccessibility of encapsulated β-carotene from mango peel, further determining that, a lower initial concentration of β-carotene in the microparticles resulted in higher bioaccessibility.},
}

*Mangifera/chemistry
*beta Carotene/pharmacokinetics/metabolism
*Milk/chemistry/metabolism
*Digestion
Animals
Biological Availability
*Fruit/chemistry
*Carotenoids
Particle Size

@article {pmid40467013,
year = {2025},
author = {Valmas, MI and Kormas, K and Karpouzas, DG and Konstantinidis, KT and Rozman, SD and Udiković-Kolić, N and Remus-Emsermann, MNP and Vasileiadis, S},
title = {Targeted analysis of metagenomes: divide and conquer.},
journal = {Biotechnology advances},
volume = {},
number = {},
pages = {108619},
doi = {10.1016/j.biotechadv.2025.108619},
pmid = {40467013},
issn = {1873-1899},
abstract = {The rapidly developing field of targeted analysis of metagenomes focuses on retrieving information about specific genes and/or genome(s) from environmental DNA. The traditional shotgun sequencing methods overemphasise dominant microorganisms and often fail to confidently assign the entirety of the analysed genetic material to specific species, genomovars, or strains. The ultimate goal of the targete methods is to overcome this limitation of throughput and precision of current shotgun metagenomics when analysing complex microbial communities in the quest of refined information. Here, we discuss recent technological advances that are designed to focus the analytical power of diagnostic tools like sequencing, towards phylogenetically or functionally distinct and rare microbial groups and enhance e.g. the confidence in the assignment of genetic elements to their respective owning organisms. We specifically showcase the capabilities of these technological advances for targeted analysis of metagenomes, identify suitable related applications, discuss methodological limitations, and propose solutions for addressing these limitations. This review aspires to inspire highly relevant experimental designs in the future that will unlock unknown and important aspects of microbial ecology, and the yet-uncultivated microbial majority.},
}

@article {pmid40465274,
year = {2025},
author = {Hassen, B and Hammami, S},
title = {Environmental Phages: Ecosystem Dynamics, Biotechnological Applications and their limits, and Future Directions.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf136},
pmid = {40465274},
issn = {1365-2672},
abstract = {Phages, the most abundant biological entities on Earth, play a crucial role in various microbial ecosystems, significantly impacting biogeochemical cycles and bacterial evolution. They inhabit diverse environments, including soil, water, and extreme conditions, where they contribute to the contribute to regulating microbial populations, facilitate genetic exchange and aid in nutrient cycling. Recent research has highlighted their potential in addressing antibiotic resistance, enhancing wastewater treatment, promoting agricultural sustainability, and tackling environmental issues. However, their ability to disseminate antibiotic resistance genes through horizontal gene transfer raises important concerns, warranting a thorough assessment of their ecological and biotechnological applications. This review synthesizes current knowledge on the diversity, ecological roles, and practical uses of environmental phages, emphasizing both their benefits and limitations. By analyzing recent findings and real-world applications, it provides insights into the challenges encountered and future directions for leveraging phages in environmental management, biotechnology, and healthcare.},
}

@article {pmid40464990,
year = {2025},
author = {Peng, Z and Kang, C and Xu, Y and Zhang, C and Zhang, Y and Yan, B and Wang, S and Guo, X and Wan, X and Lv, C and Huang, L and Guo, L and Wang, H},
title = {Effects of Wild and Domesticated Seeds on the Colonization of Rhizosphere Microorganisms in Atractylodes lancea.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {59},
pmid = {40464990},
issn = {1432-184X},
support = {2023YFC3503804//National Key Research and Development Program of China/ ; 2023YFC3503804//National Key Research and Development Program of China/ ; 2023YFC3503804//National Key Research and Development Program of China/ ; 2023YFC3503804//National Key Research and Development Program of China/ ; ZZ18-YO-051, ZZ13-YQ-096//Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; ZZ18-YO-051, ZZ13-YQ-096//Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; ZZ18-YO-051, ZZ13-YQ-096//Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; ZZ18-YO-051, ZZ13-YQ-096//Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; CI2021A03903, CI2021A03905, CI2021B013//Scientific and technological innovation project of China Academy of Chinese Medical Sciences/ ; CI2021A03903, CI2021A03905, CI2021B013//Scientific and technological innovation project of China Academy of Chinese Medical Sciences/ ; CI2021A03903, CI2021A03905, CI2021B013//Scientific and technological innovation project of China Academy of Chinese Medical Sciences/ ; CI2021A03903, CI2021A03905, CI2021B013//Scientific and technological innovation project of China Academy of Chinese Medical Sciences/ ; No: ZYYCXTD-D-202005//Innovation Team and Talents Cultivation Program of National Administration of Traditional Chinese Medicine/ ; No: ZYYCXTD-D-202005//Innovation Team and Talents Cultivation Program of National Administration of Traditional Chinese Medicine/ ; No: ZYYCXTD-D-202005//Innovation Team and Talents Cultivation Program of National Administration of Traditional Chinese Medicine/ ; No: ZYYCXTD-D-202005//Innovation Team and Talents Cultivation Program of National Administration of Traditional Chinese Medicine/ ; },
mesh = {*Rhizosphere ; *Seeds/microbiology/growth & development ; *Soil Microbiology ; *Atractylodes/microbiology/growth & development ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; Seedlings/microbiology/growth & development ; Plant Roots/microbiology ; Domestication ; Endophytes/classification/isolation & purification/genetics ; Plant Leaves/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The domestication of plant species has played a pivotal role in shaping human civilization, yet it has also contributed to a significant reduction in the genetic diversity of crop varieties. This reduction may have profound implications for the formation and establishment of rhizosphere microbial communities in plants. This study systematically investigates microbiome dynamics during seed development in wild and domesticated Atractylodes lancea. The seeds from both wild and domesticated A. lancea exhibited shared microbial genera, while their communities were changed significantly. However, when A. lancea seeds from wild and domesticated germinated into seedlings under identical microbiological conditions, the leaves and root endophytic microbial and rhizosphere microbiome displayed similar genus. Remarkably, the rhizosphere microbial communities of the seedlings consistently enriched Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Paenibacillus, Variovorax, Conexibacter, and norank_f__Micropepsaceae. And this convergence likely arises from the shared chemotype of A. lancea and exposure to identical environmental microbiomes. In summary, this study delineates the transmission processes of A. lancea seed endophytes and identifies the dynamic patterns of microbial shifts during its development from seed to seedling. These findings contribute to a broader understanding of plant-microbe interactions and the role of microbial ecology in crop improvement.},
}

*Rhizosphere
*Seeds/microbiology/growth & development
*Soil Microbiology
*Atractylodes/microbiology/growth & development
*Microbiota
*Bacteria/classification/genetics/isolation & purification
Seedlings/microbiology/growth & development
Plant Roots/microbiology
Domestication
Endophytes/classification/isolation & purification/genetics
Plant Leaves/microbiology
RNA, Ribosomal, 16S/genetics

@article {pmid40463892,
year = {2025},
author = {Shepherd, RM and Oliverio, AM},
title = {The Biogeography of Apicomplexan Parasites in Tropical Soils.},
journal = {Ecology and evolution},
volume = {15},
number = {6},
pages = {e71478},
pmid = {40463892},
issn = {2045-7758},
abstract = {Parasitic protists such as Apicomplexa, an abundant group of soil protists, contribute to ecosystem processes and nutrient cycling in belowground soil systems through their obligate symbioses with soil Metazoa. Yet despite the importance of soil parasites, the biodiversity and biogeography of Apicomplexa in belowground systems remain poorly characterized. Leveraging 205 soils collected across a rainfall gradient spanning the isthmus of Panama, we sought to understand the distribution of soil Apicomplexa lineages and how abiotic (e.g., soil and climatic) and biotic (e.g., soil Metazoa) factors relate to their diversity and structure. Apicomplexa were highly heterogeneous across the samples and comprised 30% of the soil protist community on average. Soil pH, along with phosphorus and magnesium, best explained the overall distribution of Apicomplexa. Soil Metazoa distributions also corresponded to Apicomplexa distributions, and many Metazoan taxa co-occurred with particular Apicomplexa, which may reflect ecological interactions (such as parasitism) or shared habitat preferences. These results highlight the potential roles of both soil and climatic variables and putative hosts in structuring parasite distributions in belowground tropical systems. Our work builds a broader understanding of Apicomplexa biodiversity in tropical soils and sheds light on environmental factors that may contribute to shaping their distribution in belowground systems. These results help inform our understanding of the importance of parasites in tropical forest soils.},
}

@article {pmid40463148,
year = {2025},
author = {Usman, H and Molaei, M and House, S and Haase, MF and Dennis, CL and Niepa, THR},
title = {Magnetically Responsive Nanocultures for Direct Microbial Assessment in Soil Environments.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.17.654660},
pmid = {40463148},
issn = {2692-8205},
abstract = {UNLABELLED: Cultivating microorganisms in native-like conditions is vital for bioprospecting and accessing currently unculturable species. However, there remains a gap in scalable tools that can both mimic native microenvironments and enable targeted recovery of microbes from complex settings. Such approaches are essential to advance our understanding of microbial ecology, predict community functions, and discover novel biotherapeutics. We present magnetic nanocultures-a high-throughput microsystem for isolating and growing environmental microbes under near-native conditions. These nanoliter-scale bioreactors are encapsulated in semi-permeable membranes that form magnetic polymeric microcapsules using iron oxide nanoparticles within polydimethylsiloxane-based shells. This design offers mechanical stability and magnetic actuation, enabling efficient retrieval from soil-like environments. The nanocultures are optimized for optical and biological properties to support microbial encapsulation, growth, and sorting. Our study demonstrates the feasibility of using magnetically responsive microenvironments to cultivate elusive microbes, offering a promising platform for discovering previously uncultured or unknown microbial species.

TEASER: Engineered magnetic nanocultures support microbial growth and magnetic separation from complex environments.},
}

@article {pmid40462960,
year = {2025},
author = {Wheeler, KM and Oh, MW and Fusco, J and Mershon, A and Kim, E and Oliveira, A and Rahme, LG},
title = {MvfR shapes Pseudomonas aeruginosa Interactions in Polymicrobial Contexts: Implications for Targeted Quorum Sensing Inhibition.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.16.654325},
pmid = {40462960},
issn = {2692-8205},
abstract = {Infections often occur in complex niches consisting of multiple bacteria. Despite the in-creasing awareness, there is a fundamental gap in understanding which interactions govern mi-crobial community composition. Pseudomonas aeruginosa is frequently isolated from monomicrobi-al and polymicrobial human infections. This pathogen forms polymicrobial infections with other ESKAPEE pathogens and defies eradication by conventional therapies. By analyzing the competi-tion within cocultures of P. aeruginosa and representative secondary pathogens that commonly co-infect patients, we demonstrate the antagonism of P. aeruginosa against other ESKAPEE pathogens and the contribution of this pathogen's multiple quorum sensing (QS) systems in these interac-tions. QS is a highly conserved bacterial cell-to-cell communication mechanism that coordinates collective gene expressions at the population level, and it is also involved in P. aeruginosa virulence. Using a collection of P. aeruginosa QS mutants of the three major systems, LasR/LasI, MvfR/PqsABCDE, and RhlR/RhlI and mutants of several QS-regulated functions, we reveal that MvfR and, to a lesser extent, LasR and RhlR control competition between P. aeruginosa and other microbes, possibly through their positive impact on pyoverdine, pyochelin, and phenazine genes. We show that MvfR inhibition alters competitive interspecies interactions and preserves the coex- istence of P. aeruginosa with ESKAPEE pathogens tested while disarming the pathogens' ability to form biofilm and adhere to lung epithelial cells. Our results highlight the role of MvfR inhibition in modulating microbial competitive interactions across multiple species, while simultaneously atten-uating virulence traits. These findings reveal the complexity and importance of QS in interspecies interactions and underscore the impact of the anti-virulence approach in microbial ecology and its importance for treating polymicrobial infections.},
}

@article {pmid40462143,
year = {2025},
author = {Kindtler, NL and Sheikh, S and Zervas, A and Ellegaard-Jensen, L and Feld, L and Scheel, M and Jiménez, FC and da Fonseca, RR and Laursen, KH and Jacobsen, CS and Ekelund, F},
title = {Small sample amounts from rhizosphere of barley maintain microbial community structure and diversity revealed by total RNA sequencing.},
journal = {Plant methods},
volume = {21},
number = {1},
pages = {79},
pmid = {40462143},
issn = {1746-4811},
abstract = {Total RNA sequencing is a crucial technique in microbial ecology for profiling active microbial communities in various environments, including the rhizosphere. Since total RNA sequencing yields both 16 S and 18 S ribosomal RNA (rRNA), it is effective for taxonomic profiling of the full microbial community in a sample. However, the effectiveness of this approach with limited initial sample amounts remains unclear. In this study, we grew barley in a growth system designed for highly controlled plant experiments using an inert growth medium inoculated with a soil microbiome. Our objectives were two-fold: firstly, to test the feasibility of extracting total RNA from the rhizosphere of barley grown in an inert growth medium consisting of sand and perlite. Secondly, we aimed to address the challenge of extracting comprehensive taxonomic information from minimal amounts of rhizosphere samples from barley plants, using three different amounts of freeze-dried rhizosphere material: 10, 40, and 200 mg. We showed that although smaller sample amounts yielded lower concentrations of extracted RNA, this did not significantly influence the diversity or composition of the rhizosphere microbiome as indicated by SSU rRNA. Our results demonstrate that total RNA sequencing, focusing on SSU rRNA, robustly captures the taxonomic diversity of active rhizosphere microbial communities, even in small initial sample amounts. Effective use of smaller samples opens new possibilities for detailed studies in environments where sample quantity is limited. We also conclude that the growth system applied in this experiment is suitable for highly controlled plant experiments focusing on total RNA extraction from the rhizosphere.},
}

@article {pmid40461733,
year = {2025},
author = {Ruiz-Blas, F and Friese, A and Bartholomäus, A and Henny, C and Russell, JM and Kallmeyer, J and Vuillemin, A},
title = {The Deep Subsurface Biosphere and its Substrates Along a One-Million-Year Ferruginous Lake Archive.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {58},
pmid = {40461733},
issn = {1432-184X},
support = {KA 2293/8-1//Deutsche Forschungsgemeinschaft/ ; VU 94/1-1//Deutsche Forschungsgemeinschaft/ ; P2GEP2_148621//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; },
mesh = {*Lakes/microbiology/chemistry ; *Geologic Sediments/microbiology/chemistry ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification/metabolism ; Indonesia ; *Archaea/genetics/classification/isolation & purification ; Phylogeny ; Iron/analysis/metabolism ; Biodiversity ; },
abstract = {Lake Towuti, Indonesia, is an ancient stratified lake with ferruginous (iron-rich, sulfate-poor) anoxic bottom water conditions and a long depositional record affected by redox changes in the water column and sediments. As modern analogue of Earth's early ferruginous oceans, it enables the study of an active microbial subsurface biosphere and its role in organic matter and iron mineralization. Combining 16S rRNA genes, cell counts, pore water geochemistry, and bulk sediment profiles from a 100-m-long core, we present the first comprehensive characterization of the deep subsurface biosphere along a one-million-year lacustrine archive. Electron acceptors in the pore water became depleted at shallow depths, resulting in a drastic decrease in cell densities in the fermentative zone, where Bathyarchaeia dominate the microbial community composition. Although alpha and beta diversity reflected initial depletion of substrates during burial, they also varied across successive lithologies, indicating that sediment composition subsequent to deposition also affects diversity. The upper sediments (0-20 mblf) sheltered a dense and diverse microbial community involved in organic matter remineralization, actively producing and converting volatile fatty acids into carbon dioxide and methane. Deeper sediments (20-70 mblf) contained low-diversity microbial communities adapted to nutrient scarcity. In contrast, deepest lacustrine sediments (70-100 mblf) contained an increased microbial diversity reflecting greater availability of organic matter of terrestrial origin. Despite Bathyarchaeia being prime constituents of the deep subsurface biosphere, increased diversity in 16S rRNA gene composition was observed in discrete sediment layers (tephra, diatom ooze, peat). This demonstrated that depositional conditions remained traceable, while stratified microbial communities drove reductive diagenesis.},
}

*Lakes/microbiology/chemistry
*Geologic Sediments/microbiology/chemistry
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/isolation & purification/metabolism
Indonesia
*Archaea/genetics/classification/isolation & purification
Phylogeny
Iron/analysis/metabolism
Biodiversity

@article {pmid40461630,
year = {2025},
author = {Koch, M and Lado, S and Bodner-Adler, B and Carlin, G and Pacífico, C and Bauer, C and Cartwright, R and Seki, D and Steininger, C and Makristathis, A and Umek, W},
title = {Women suffering from overactive bladder syndrome exhibit a higher urethral viral abundance compared to healthy controls: a pilot study.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {19484},
pmid = {40461630},
issn = {2045-2322},
support = {1815//OeNB Jubiläumsfonds/ ; },
mesh = {Humans ; Female ; *Urinary Bladder, Overactive/virology/microbiology ; Pilot Projects ; Middle Aged ; *Urethra/virology/microbiology ; Microbiota ; Case-Control Studies ; Prospective Studies ; Adult ; Phylogeny ; Aged ; Bacteria/genetics ; Virome ; *Viruses/genetics/isolation & purification/classification ; High-Throughput Nucleotide Sequencing ; },
abstract = {The interactions between the human bacterial microbiome and essential bodily functions are well established for organ systems such as the oral cavity, gut, and female reproductive tract. However, the urinary microbiome, particularly its viral component, remains largely unexplored. Emerging evidence suggests that the urinary microbiome may play a significant role in the development of overactive bladder syndrome (OAB). This study aims to fill this knowledge gap by investigating the potential link between the urethral virome and female overactive bladder syndrome, and by aligning these findings with the bacterial microbiome. Prospective pilot study including 15 patients with overactive bladder syndrome and five controls. Current urinary tract infection and antibiotic therapy within the last two months were ruled out and controls were matched to cases by age and body mass index. Urethral swabs (Copan eSwab[®] urethra) were taken from each participant at one single time point. Subsequent viral isolation, purification, and enrichment were conducted using the ViPEP method. Next-generation sequencing was performed on pooled samples, followed by bioinformatic analysis to identify and classify viral contigs. Phylogenetic analysis was conducted to assess genetic relationships among identified viral sequences. The bacterial microbiome was analyzed by sequencing of the variable V3-4 region of the eubacterial 16 S rDNA gene on the Illumina MiSeq platform. We identified twenty-one viruses and bacteriophages only in pooled urethral swab samples of the OAB group, but no valid detections were retained in the control group after analysis. The most abundant human virus in urethral swab samples was human papilloma virus, whereas the most abundant bacteriophages belong to the family of Siphoviridae. In the bacterial microbiome analysis, we identified statistically higher levels of Veillonella and Bacteroides in OAB samples. Results of this pilot study suggest a difference in the urethral virome between women with OAB and healthy controls. When looking deeper into the detected virus families and species, we might postulate a unique microbial pattern of OAB patients. This pattern suggests an interplay of immunosuppression, autoimmune processes and a larger diversity of bacterial and viral microbes. Current evidence strongly suggests a disturbance of the healthy microbiome of the urogenital tract in patients with OAB, leading to subclinical chronic inflammation and thus typical OAB symptoms. Further research should focus on interventions aimed at restoring a healthy microbiome in OAB patients to mitigate inflammation and improve symptom control.},
}

Humans
Female
*Urinary Bladder, Overactive/virology/microbiology
Pilot Projects
Middle Aged
*Urethra/virology/microbiology
Microbiota
Case-Control Studies
Prospective Studies
Adult
Phylogeny
Aged
Bacteria/genetics
Virome
*Viruses/genetics/isolation & purification/classification
High-Throughput Nucleotide Sequencing

@article {pmid40459550,
year = {2025},
author = {Wu, Y and Zhang, F and Zhang, S and Zhang, J and Zhao, S and Qiu, Z and Zhu 朱, M墨},
title = {Curvularia spicifera causing black rot on Ipomoea batatas in China.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-03-25-0477-PDN},
pmid = {40459550},
issn = {0191-2917},
abstract = {Ipomoea batatas (sweet potato) is an annual herb originating from South America and the large and small Antilles. It is widely cultivated in tropical and subtropical regions around the world and is widely grown in most parts of China. As an edible plant with rich nutrition, I. batatas has high economic and medicinal value (Suhendy et al. 2023). In September 2023, black rot-like disease signs and symptoms were observed on the roots of I. batatas in a farmland (about 6667 m2) located in Kaifeng city, Henan Province, China. The roots showed irregular brown or dark spots on the surface, extending to the internal center, and brown to black necrosis. Additionally, above-ground parts of infected plants showed symptoms such as yellowing and wilting of leaves, brown spots on stems, and stunted growth. Around 80 % of monitored plant roots (n = 200) exhibited the symptoms. Infected roots were cut into pieces and then placed on potato dextrose agar (PDA) (light/dark, 16 h/8 h; temperature, 18°C). After a period of 3-10 days, single hyphal tips of each fungal colony were placed on PDA and incubated for another 5-10 days (Paul et al. 2021). Colonies of the fungal pathogen on PDA reached 50 mm in diameter within 7 days, dark gray on the inner side, dark brown extending to the edge, irregular round edge, with abundant aerial mycelium, cotton-like, irregularly convex upward, undulating. The conidia were brown, ellipsoid to oval, 8 to 19 × 3 to 6 μm (n = 50). Morphologically similar isolates with characteristics consistent with those of Curvularia spicifera (Cui et al. 2020) were recovered from 87% of symptomatic root tissues (n=100). The internal transcribed spacer (ITS) region and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene from three independent isolates (CSZM202101, CSZM202102, and CSZM202103) of the fungus were amplified and sequenced with primers ITS1/ITS4 (Seliger et al. 1990) and GAPDH1/GAPDH3R (Bradshaw et al. 2022) according to a previously reported method (Zhu et al. 2022). The resulting sequences were deposited in GenBank (Accession No. OR885691, PV056889, PV056568, PQ839726, PV072835 and PV02836). BLASTn analysis showed that the ITS and GAPDH sequences had 100% (ITS, 516/516; GAPDH, 508/508) identity with C. spicifera (OQ845826 and CBS 274.52 JN192387) from maize (Ram et al. 2024) and pearl millet (S. et al. 2024), respectively. The phylogenetic analysis clearly illustrated that these isolates clustered with the sequences of a representative reference strain of C. spicifera(CBS 274.52, GenBank accession number JN192387). Therefore, the morphological, molecular and phylogenetic analysis indicated that the pathogen was C. spicifera. To complete Koch's postulates, pathogenicity experiments were carried out by inoculating spore suspension (106 spores mL-1) into the wounded roots (n=10) of I. batatas plants. Sterile distilled water treated wounded roots (n=10) served as control. One to two days after inoculation, visible mycelia were produced at the inoculation sites of I. batatas. Inoculated roots showed black rot signs 21 days post-inoculation; controls were unaffected. This was confirmed in three repeated pathogenicity tests. To our knowledge, this is the first report of black rot caused by C. spicifera on I. batatas in China. The emergence of the black rot pathogen could harm valuable food crops and reduce agricultural productivity in China. Accurate identification of the black rot fungus is essential for devising effective disease management strategies and supporting future control of C. spicifera in China.},
}

@article {pmid40459301,
year = {2025},
author = {Zhang, J and Guo, Z and Liu, J and Pan, X and Huang, Y and Cui, X and Wang, Y and Jin, Y and Sheng, J},
title = {Capabilities and Limitations of Air-Dried Soils in Microbial Biogeography: A Regional-Scale Comparative Analysis.},
journal = {Environmental microbiology},
volume = {27},
number = {6},
pages = {e70111},
doi = {10.1111/1462-2920.70111},
pmid = {40459301},
issn = {1462-2920},
support = {KFJ-SW-YW043-2//Field Station Basic Research Project of the Chinese Academy of Sciences/ ; 42107145//National Natural Science Foundation of China/ ; 42407410//National Natural Science Foundation of China/ ; 0270756100ZX//Jiangsu Agricultural Biodiversity Cultivation and Utilization Research Center/ ; CX (22) 2002//Jiangsu Agricultural Science and Technology Innovation Fund/ ; CX (23) 3105//Jiangsu Agricultural Science and Technology Innovation Fund/ ; 3220220039//Pilot Project for Mineral-Land Integration of Jiangsu Province/ ; //Jiangsu Provincial Territorial Ecological Monitoring/ ; },
mesh = {*Soil Microbiology ; *Soil/chemistry ; China ; *Bacteria/classification/genetics/isolation & purification ; *Desiccation ; Biodiversity ; *Microbiota ; },
abstract = {Air-dried soil archives offer valuable potential for studying long-term microbial dynamics, yet systematic evaluations across large spatial scales with paired fresh-soil comparisons remain limited. Here, we systematically evaluated the effects of 1-month air-drying on microbial biogeography across 244 paddy fields in eastern China. Results showed that air-drying significantly altered communities by reducing diversity through the elimination of rare taxa while enriching desiccation-resistant phyla like Firmicutes, Chloroflexi and Actinobacteria. These compositional shifts further triggered functional bias, enhancing fermentation/methanogenesis pathways while suppressing nitrogen cycling processes. Despite these alterations, air-dried samples maintained remarkable fidelity to key ecological patterns observed in fresh soils. Multivariate analyses demonstrated strong structural concordance between paired samples, with soil pH consistently emerging as the primary environmental driver in both data sets. This preservation of biogeographical relationships occurred despite significant changes in underlying ecological mechanisms. Air-dried soil communities exhibited increased stochastic assembly, reduced niche breadth and simplified co-occurrence networks with altered keystone taxa, indicative of a two-phase process: deterministic filtering of drought-sensitive taxa followed by stochastic reorganisation among survivors. Overall, our findings provide a framework for utilising soil archives in microbial ecology, showing that while air-drying introduces predictable distortions, samples retain essential ecological information for reconstructing historical microbial-environmental relationships at large scales.},
}

*Soil Microbiology
*Soil/chemistry
China
*Bacteria/classification/genetics/isolation & purification
*Desiccation
Biodiversity
*Microbiota

@article {pmid40456365,
year = {2025},
author = {Zhao, X and Overbeek, LV and Burgess, CM and Holden, N and Brennan, F and Johannessen, GS and Allende, A and Höfte, M and Cottyn, B and Pothier, JF and Schikora, A and Uyttendaele, M},
title = {Human Pathogenic Microorganisms in Fresh Produce Production: Lessons Learned When Plant Science Meets Food Safety.},
journal = {Journal of food protection},
volume = {},
number = {},
pages = {100551},
doi = {10.1016/j.jfp.2025.100551},
pmid = {40456365},
issn = {1944-9097},
abstract = {To enhance control of human pathogenic microorganisms in plant production systems, an EU COST Action (HUPLANTcontrol CA16110) was initiated, bringing together microbiologists in food, environmental and plant microbial ecology. This article summarizes the outcomes of multiple workshops and the four main lessons learned: (i) many terminologies need further explanation to facilitate multidisciplinary communication on the behavior of human pathogens from pre-harvest plant production to post-harvest food storage, (ii) the complexity of bacterial taxonomy pushes microbial hazard identification for greater resolution of characterisation (to subspecies, or even strain level) needing a multi-method approach, (iii) hazard characterisation should consider a range of factors to evaluate the weight of evidence for adverse health effects in humans, including strain pathogenicity, host susceptibility, and the impact of the plant, food, or human gut microbiome, (iv) a wide diversity of microorganisms in varying numbers and behaviours co-exist in the plant microbiome, including good (beneficial for plant or human health), bad (established human or plant pathogens) or ugly (causing spoilage or opportunistic disease). In conclusion, active listening in communication and a multi-perspective approach are the foundation for every successful conversation when plant science meets food safety.},
}

@article {pmid40456197,
year = {2025},
author = {Song, W and Lin, L and Oh, S and Grossart, HP and Yang, Y},
title = {Tire wear particles in aquatic environments: From biota to ecosystem impacts.},
journal = {Journal of environmental management},
volume = {388},
number = {},
pages = {126059},
doi = {10.1016/j.jenvman.2025.126059},
pmid = {40456197},
issn = {1095-8630},
abstract = {Tire wear particles (TWPs), mainly generated through friction between tires and road surfaces, represent a major source of traffic-related microplastic pollution, posing threats to biota and ecosystem functions. These particles are a complex mixture of toxic compounds, including heavy metals (e.g., zinc) and organic compounds (e.g., 6-PPD), and their diverse leachates exacerbate their ecological impacts. This review collates current knowledge on the occurrence of TWPs and their leachates in aquatic systems, emphasizing their toxicological effects on species and cascading ecological consequences at the community and ecosystem levels. TWP concentrations in aquatic environments span several orders of magnitude, ranging from 10[-5] to 10[4] mg/L in water via pyrolysis-GC/MS. TWPs and their leachates induce oxidative stress, DNA damage, and alter immune responses of aquatic biota, while disrupting feeding behavior, reproduction, and survival. At the ecosystem level, TWPs and their leachates cause shifts in species composition, reduce biodiversity, and alter trophic interactions, destabilizing natural food web dynamics through selective pressure that promotes tolerant taxa and triggers cascading ecological effects. Their presence significantly influences carbon and nitrogen cycling, with environmentally relevant concentrations could promote primary producers, while higher concentrations inhibit photosynthetic nitrogen-fixing biota, disrupt microbial communities, and impair processes such as denitrification and carbon mineralization. Their toxicological and ecological impacts are likely to be intensified by global environmental change, highlighting the need for long-term studies under realistic environmental conditions to better understand underlying mechanisms and develop effective mitigation strategies.},
}

@article {pmid40453667,
year = {2025},
author = {Yang, H and Shao, C and Liu, Z and Zhang, X and Liu, Y and Xiao, J and Tang, L},
title = {Cold- and hot-classified botanical drugs differentially modulate gut microbiota: linking TCM emic classification to microbial ecology.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1545619},
pmid = {40453667},
issn = {1663-9812},
abstract = {INTRODUCTION: Traditional Chinese Medicine (TCM) classifies botanical drugs based on their thermal properties (an emic classification system), categorizing them as "cold" (e.g., "clearing heat" for anti-inflammatory effects) or "hot" (e.g., "warming the middle" for metabolic enhancement). However, the specific roles of these botanical drugs in restoring gut microbiota dysbiosis remain unclear. This study aimed to explore whether TCM-classified cold and hot botanical drugs differentially restore gut microbiota dysbiosis and host physiology in antibiotic-treated mice.

METHODS: Mice with antibiotic-induced dysbiosis were treated with eight TCM-classified botanical drugs (four cold: Rheum palmatum L., Scutellaria baicalensis Georgi, Senna alexandrina Mill., Coptis chinensis Franch.; four hot: Codonopsis pilosula (Franch.) Nannf., Astragalus membranaceus (Fisch.) Bunge, Angelica sinensis (Oliv.) Diels, Panax ginseng C.A.Mey.) for 20 days. Gut microbiota were analyzed via 16S rRNA sequencing on days 5, 10, 15, and 20, alongside physiological parameters including blood glucose, serum lipids, TNF-α, adiponectin, and intestinal histomorphology.

RESULTS: By day 20, all botanical drugs restored the diversity and ranking of dominant genera (those with >10% abundance, such as Lactobacillus and unclassified Muribaculaceae). However, cold-classified drugs, traditionally associated with anti-inflammatory effects, selectively enriched anti-inflammatory taxa, including Akkermansia and Bifidobacterium. In contrast, hot-classified drugs, linked to metabolic enhancement, promoted metabolic-modulating genera such as Clostridia and Eubacterium coprostanoligenes. These differential enrichments corresponded with the therapeutic principles defined by TCM: cold-classified drugs reduced serum TNF-α levels (P < 0.01), demonstrating anti-inflammatory effects, whereas hot-classified drugs improved lipid profiles (TG: P < 0.001), thereby promoting metabolic modulation.

DISCUSSION: TCM-classified cold and hot botanical drugs universally stabilize dominant microbiota while differentially modulating low-abundance taxa. The enrichment of Akkermansia (cold) and Clostridia (hot) offers a microbiota-driven validation of TCM's empirical classification framework. These findings connect traditional knowledge with microbial ecology, underscoring the potential of TCM-guided microbiota modulation for precision therapies.},
}

@article {pmid40450024,
year = {2025},
author = {Masigol, H and Solbach, MD and Pourmoghaddam, MJ and Ahadi, R and Mostowfizadeh-Ghalamfarsa, R and Taheri, SR and Tobias-Hünefeldt, SP and Bonkowski, M and Grossart, HP},
title = {A glimpse into Oomycota diversity in freshwater lakes and adjacent forests using a metabarcoding approach.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {19124},
pmid = {40450024},
issn = {2045-2322},
mesh = {*Lakes/microbiology ; *DNA Barcoding, Taxonomic/methods ; *Biodiversity ; *Forests ; *Oomycetes/genetics/classification/isolation & purification ; Ecosystem ; Germany ; Phylogeny ; Fresh Water/microbiology ; },
abstract = {Oomycota, a diverse group of fungus-like protists, play key ecological roles in aquatic and terrestrial ecosystems, yet their habitat-specific diversity and distribution remain poorly understood. This study investigates the diversity of two major Oomycota classes, Saprolegniomycetes and Peronosporomycetes, in two freshwater lakes and their adjacent forests in northeastern Germany. Using a combination of targeted metabarcoding and traditional isolation techniques, we analyzed samples from six habitats, including soil (forest), rotten leaves (forest and shoreline), sediments (shoreline), and surface waters (littoral and pelagic zones). Metabarcoding revealed 401 Oomycota OTUs, with Pythium, Globisporangium, and Saprolegnia as dominant genera. Culture-based methods identified 110 strains, predominantly from surface water and sediment, with Pythium sensu lato and Saprolegnia as the most frequent taxa. Alpha and beta diversity analyses highlighted distinct community structures influenced by lake and habitat type, with significant co-occurrence of Saprolegniomycetes and Peronosporomycetes across habitats. This study provides the first comprehensive metabarcoding-based exploration of Oomycota biodiversity in interconnected freshwater and terrestrial ecotones, uncovering previously unrecognized patterns of habitat-specific diversity.},
}

*Lakes/microbiology
*DNA Barcoding, Taxonomic/methods
*Biodiversity
*Forests
*Oomycetes/genetics/classification/isolation & purification
Ecosystem
Germany
Phylogeny
Fresh Water/microbiology

@article {pmid40448709,
year = {2025},
author = {Samaniego, T and La Torre, R and Orjeda, G and Ramirez, JL},
title = {Lima Megacity's Influence on Aquatic Microbial Communities in the Rímac River: Dominance Over Spatial and Seasonal Variations.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {57},
pmid = {40448709},
issn = {1432-184X},
support = {B2110006i//Universidad Nacional Mayor de San Marcos/ ; B2110006i//Universidad Nacional Mayor de San Marcos/ ; B2110006i//Universidad Nacional Mayor de San Marcos/ ; },
mesh = {*Rivers/microbiology ; Seasons ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Peru ; *Microbiota ; *Water Microbiology ; Environmental Monitoring ; DNA, Bacterial/genetics ; Biodiversity ; },
abstract = {The Rímac River, a vital watershed on the Peruvian coast, is confronted with substantial environmental challenges stemming from intensive exploitation and widespread contamination. As the primary source of water for Lima, supplying approximately 80% of the city's needs, the river is heavily impacted by pollutants from domestic, hospital, industrial, and mining effluents. These contaminants introduce microbiota that pose significant public health risks. This study utilizes 16S rRNA gene metabarcoding to characterize the bacterial communities along the Rímac River, examining both spatial (upper, middle, and lower basins) and temporal (dry and rainy seasons) variations. Over a year-long sampling period, DNA sequencing revealed pronounced microbiological differences between the Metropolitan and Regional zones, primarily driven by anthropogenic activities. Key findings include a significant reduction in microbial diversity and an increase in pathogenic bacteria within the Metropolitan zone, while the influence of seasonal variations and altitudinal gradients was comparatively minor. Betaproteobacteria emerged as the most abundant class across most samples. Notably, Aliarcobacter cryaerophilus, an indicator of fecal contamination and a potential public health hazard, was predominantly detected in the Metropolitan zone. These results underscore the necessity for comprehensive monitoring of the Rímac River's microbiota, incorporating advanced molecular techniques to effectively track and mitigate pollution. The study emphasizes the urgent need for robust water quality management strategies to protect this critical resource, ensuring the health and sustainability of Lima and its surrounding regions.},
}

*Rivers/microbiology
Seasons
*Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Peru
*Microbiota
*Water Microbiology
Environmental Monitoring
DNA, Bacterial/genetics
Biodiversity

@article {pmid40446899,
year = {2025},
author = {Fang, P and Ye, S and Luo, Z and Guo, R and Jiang, Y and Liu, L and Li, S and Xiao, F},
title = {Nanoplastics under the charge effect: Unveiling the potential threats to amphibian (Rana nigromaculata) growth, intestinal damage, and microbial ecology.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126566},
doi = {10.1016/j.envpol.2025.126566},
pmid = {40446899},
issn = {1873-6424},
abstract = {Nanoplastics (NPs) are a contaminant that may be found in charged forms in the environment, capable of accumulating in aquatic organisms and affecting their health. This study compared the effects of positively charged NPs (PS-NH2, 30nm) and negatively charged NPs (PS-COOH, 30nm) at 6 and 60 mg/L on the growth and development of black-spotted frog tadpoles (Rana nigromaculata), as well as on intestinal damage, and microbial ecology. The results indicated that exposure to both types of NPs significantly reduced the survival rate of tadpoles, while significantly increasing their body weight and body length (p <0.05). Compared to PS-COOH, exposure to PS-NH2 resulted in more adverse intestinal tissue damage and induced more severe intestinal oxidative stress. Furthermore, exposure to PS-NH2 significantly reduced the abundance and diversity of the microbiome associated with gut function and nutrient absorption, indirectly leading to more severe intestinal damage and growth changes. In addition, functional prediction and gene transcription analysis showed that exposure to charged PS-NPs caused changes in genes associated with glycolysis and lipid metabolism, indicating that the glucose-lipid metabolism of tadpoles is impacted. This study demonstrated the growth differences and intestinal toxicity of NPs exposure in tadpoles, explores the potential connections between gut microbiota and glucose-lipid metabolism, and provides new perspectives on the health risks of NPs in amphibians.},
}

@article {pmid40446767,
year = {2025},
author = {Adyari, B and Liao, X and Yan, X and Qiu, Y and Grossart, HP and Li, L and Yu, T and Mao, G and Liu, K and Su, J and Liu, Y and Hu, A},
title = {Anthropogenic gene dissemination in Tibetan Plateau rivers: sewage-driven spread, environmental selection, and microeukaryotic inter-trophic driving factors.},
journal = {Water research},
volume = {284},
number = {},
pages = {123887},
doi = {10.1016/j.watres.2025.123887},
pmid = {40446767},
issn = {1879-2448},
abstract = {The spread of anthropogenic genes, such as antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), virulence factor genes (VFGs), and antibiotic-resistant bacteria (ARBs), is a growing public health concern. However, the role of anthropogenic activities in the dissemination of these genes and bacteria in Tibetan Plateau rivers is still unclear. In this study, we analyzed 138 metagenomic samples from water and sediment across nine Tibetan rivers, along with sewage samples from 21 wastewater treatment plants (WWTPs), at both the gene and contig levels, to investigate the spread of the sewage-enriched genes and their bacterial hosts (contigs) in Tibetan rivers. Overall, sewage input was positively correlated with increased the abundance of an average 56 % and 17 % of detected genes in water and sediment, respectively. However, FEAST source tracking analysis revealed that the overall contribution of sewage across all rivers was significantly lower than that of water and sediment. Additionally, sewage's impact varied across rivers, with the Yarlung Zangbo, the largest river, exhibiting limited influence despite receiving inputs from smaller rivers and WWTPs. Neutral community model (NCM) suggested that neutral processes and negative selection predominantly governed the spread of majority of highly abundant sewage-enriched genes and contigs, suggesting restricted environmental spread. In contrast, a subset of genes over-represented relative to neutral expectations (above-neutral prediction) showed lower overall abundance but higher richness, potentially reflecting selection that favor their retention in certain downstream environments. Furthermore, sewage-enriched genes and contigs in water, regardless of their community assembly processes, were linked to microbial interaction modules dominated by microeukaryotic groups associated with sewage, including consumer protists (ciliate), human parasites (e.g., Naegleria), algae, and fungi. These interactions may facilitate the dissemination of antimicrobial resistance in aquatic environments, though this pattern was less pronounced in sediment.},
}

@article {pmid40446743,
year = {2025},
author = {Jansriphibul, K and Krohn, C and Ball, AS},
title = {Sources of variability for viability PCR using propidium monoazide.},
journal = {Microbiological research},
volume = {298},
number = {},
pages = {128224},
doi = {10.1016/j.micres.2025.128224},
pmid = {40446743},
issn = {1618-0623},
abstract = {The molecular detection of microorganisms in environmental samples relies on PCR-associated molecular workflows that typically cannot differentiate live from dead microbes. Understanding the microbial functions of complex communities can be significantly hindered by presence of the dead microbes. Using propidium monoazide (PMA), PMA-based viability PCR, is arguably the most convenient method to differentiate viability status apart. Errors from variabilities of non-standardized practices and a lack of understanding of the PMA mechanism deter the viability PCR approach. This review discusses the sources of variability in each of four key sequential steps: pre-analysis, PMA activation, DNA extraction and PCR. An analysis of previous literature on optimization of PMA-based viability PCR indicates that often only one source of variability is considered. However, all steps are interrelated and should be considered together when understanding and mitigating unwanted variability, especially in the PMA activation and PCR steps. Research gaps in PMA are addressed, such as the chemical mechanisms of PMA and possible by-products interferences, internal standard spiking and recommendations for future research.},
}

@article {pmid40446651,
year = {2025},
author = {O'Connor, L and Minogue, E and Carolan, S and Darcy, G and Chueiri, A and Faherty, M and Morton, J and Mc Donagh, F and Singh, NK and Venkateswaran, K and Miliotis, G and Smith, TJ},
title = {Rapid detection of the novel human pathogen Pantoea piersonii: advancements in methodology.},
journal = {Diagnostic microbiology and infectious disease},
volume = {113},
number = {2},
pages = {116905},
doi = {10.1016/j.diagmicrobio.2025.116905},
pmid = {40446651},
issn = {1879-0070},
abstract = {Pantoea piersonii a novel bacterium isolated from the International Space Station (ISS) presents a unique challenge for microbial monitoring in spaceflight and more recently in clinical environments. Identification of the organism currently involves culture, followed by whole genome sequencing and analysis of generated sequences. Since the MALDI-TOF profile of this pathogen is absent from the database and 16S rRNA sequencing fails to resolve its identity to the nearest neighbour, a definitive genetic marker is required for unambiguous identification of the organism. Given the increase in the number of reported clinical cases, there exists a need for a rapid method for identification of the organism which could be utilised in a range of environments including the clinical setting. This study describes the design, development and validation of a specific and sensitive real-time PCR assay for the specific detection of P. piersonii. The assay targets a unique region of the malate dehydrogenase gene, confirmed through comparative genomic analysis. We demonstrate the performance of the assay in terms of analytical specificity, sensitivity, and robustness, ensuring its suitability for both space microbiology applications and clinical use.},
}

@article {pmid40445193,
year = {2025},
author = {Cisneros, M and Blanco-Fuertes, M and Lluansí, A and Brotons, P and Henares, D and Pérez-Argüello, A and González-Comino, G and Ciruela, P and Mira, A and Muñoz-Almagro, C},
title = {Synergistic inhibition of pneumococcal growth by Dolosigranulum pigrum and Corynebacterium pseudodiphtheriticum: insights into nasopharyngeal microbial interactions.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0013825},
doi = {10.1128/spectrum.00138-25},
pmid = {40445193},
issn = {2165-0497},
abstract = {Streptococcus pneumoniae is a nasopharynx colonizer that can invade sterile tissues, causing invasive pneumococcal disease (IPD). Dolosigranulum pigrum and Corynebacterium pseudodiphtheriticum are commensal bacteria commonly isolated from the nasopharynx of healthy children, potentially playing a protective role. This study aims to analyze the effects of D. pigrum and C. pseudodiphtheriticum on S. pneumoniae in vitro growth. Pneumococcal strains were collected from IPD patients and healthy carriers in Catalonia (2016-2023). D. pigrum and C. pseudodiphtheriticum strains were isolated from a healthy child's nasopharynx. S. pneumoniae was co-cultured with each commensal bacterium in triplicate experiments. Pneumococcal growth was quantified using a real-time PCR assay targeting the lytA gene. The effect of commensal bacteria on pneumococcal growth was evaluated using a linear mixed-effect regression model. Twenty-eight pneumococcal strains expressing 24 different serotypes and 27 clonal types were analyzed (18 isolated in blood and 10 in nasopharyngeal aspirate). Pneumococcal growth was decreased by D. pigrum (β = -0.763, 95% confidence interval [CI]: -0.94 to -0.59, P < 0.0001) and C. pseudodiphtheriticum (β = -0.583, 95% CI: -0.76 to -0.41, P < 0.0001). The combined presence of both had a stronger inhibitory effect (β = -0.971, 95% CI: -1.15 to -0.79, P < 0.0001). No association was found between isolation site or serotype with pneumococcal growth. D. pigrum and C. pseudodiphtheriticum significantly reduced pneumococcal growth, with a synergistic effect when combined. This antagonistic effect supports the potential protective factor of healthy nasopharyngeal microbiota against IPD and the development of these microorganisms as probiotics.IMPORTANCEInvasive pneumococcal disease (IPD) is a significant worldwide health challenge. The present study highlights the significant inhibitory effect of two commensal bacteria, Dolosigranulum pigrum and Corynebacterium pseudodiphtheriticum, on pneumococcal growth, with a stronger effect observed when both bacteria are present together. Through testing different strains of S. pneumoniae and the implementation of a robust statistical model, this research advances in the knowledge of microbial ecology and provides evidence to support the development of the use of these commensal bacteria as probiotics. These results emphasize the possibility of using the nasopharyngeal microbiota's natural interactions to mitigate the risk of IPD.},
}

@article {pmid40444437,
year = {2025},
author = {Pan, Y and Tao, Y and Yang, X and Du, S and Ding, H and Li, J and Jia, H and Chen, H},
title = {Underlying mechanisms of spatial distribution of prokaryotic community in surface seawater from Arctic Ocean to the Sea of Japan.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0051725},
doi = {10.1128/spectrum.00517-25},
pmid = {40444437},
issn = {2165-0497},
abstract = {Microorganisms play critical roles in marine ecosystems, so understanding the factors shaping microbial communities across various oceanic regions is essential for predicting ecosystem resilience and biogeochemical cycles. This study investigated the marine prokaryotic communities across 22 stations spanning the Arctic Ocean, the Chukchi Sea, the Bering Sea, and the Sea of Japan, with an emphasis on how environmental factors shape these communities. Results showed that the microbial alpha diversity generally declines with increasing latitude, though Arctic Ocean stations exhibited higher Chao 1 indices compared to the Bering Sea. Beta diversity analyses revealed that temperature and salinity were key factors associated with community composition variation across latitudes. Proteobacteria and Cyanobacteria were the dominant phyla showing opposite distribution trends across sampling stations. Cold-adapted oligotrophs such as Planktomarina and the SAR11 clade thrived in Arctic waters, while Sphingomonas, known for pollutant degradation, was more abundant in the Sea of Japan. Temperature was positively correlated to the relative abundance of Sphingomonas. At broad spatial scales, stochastic processes dominated community assembly of microbial phylogenetic diversity, while in specific regions like the Arctic Ocean, deterministic homogeneous selection appeared to shape microbial communities; and temperature showed a pronounced influence on phylogenetic turnover across all samples. Co-occurrence networks identified several key taxa, such as Polaribacter_1, Candidatus_Aquiluna, and NS5_marine_group. Overall, the study underscores temperature's role in shaping microbial community diversity, composition, and assembly processes across latitudinal gradients, highlighting unique community adaptations to extreme environments.IMPORTANCEMicrobes are the invisible engines of ocean health, recycling nutrients and sustaining marine life. This research helps us understand how climate factors like temperature shape these microscopic communities, which differ starkly between icy Arctic waters and warmer seas. As oceans warm due to climate change, microbial populations and their critical roles in cleaning pollutants or supporting food webs could shift dramatically. The study suggests Arctic microbes are uniquely adapted to cold, low-nutrient conditions, making them vulnerable to warming. By linking temperature to microbial diversity, this work provides clues to predict how marine ecosystems might respond to climate shifts, informing efforts to protect ocean biodiversity and processes vital to Earth's carbon and nutrient cycles.},
}

@article {pmid40442489,
year = {2025},
author = {Ostap-Chec, M and Antoł, W and Bajorek, D and Berbeć, E and Moroń, D and Rapacz, M and Miler, K},
title = {Meta-Analysis and Experimental Evidence Reveal No Impact of Nosema ceranae Infection on Honeybee Carbohydrate Consumption.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {56},
pmid = {40442489},
issn = {1432-184X},
support = {Preludium 2021/41/N/NZ8/02917//Narodowe Centrum Nauki/ ; },
mesh = {Animals ; Bees/microbiology/physiology/metabolism ; *Nosema/physiology ; Hemolymph/chemistry/metabolism ; Feeding Behavior ; Trehalose/metabolism/analysis ; *Carbohydrate Metabolism ; },
abstract = {Honeybees (Apis mellifera) are indispensable pollinators for ecosystem stability and agricultural productivity. However, they face numerous challenges, including pathogens threatening their survival and ecosystem services. Among these pathogens, Nosema ceranae, a microsporidian parasite, causes significant damage to the intestinal tract and induces energetic imbalances in the organism, posing a major threat to both individual bees and entire colonies. In response to infections, bees often engage in behavioral defenses, such as self-medicating with antimicrobial substances available in their environment. We hypothesized that bees infected with N. ceranae might compensate behaviorally by increasing their carbohydrate consumption. To test this hypothesis, we conducted a meta-analysis of existing studies comparing sugar consumption in healthy and infected bees, complemented by an experimental study. In our experiment, we measured sugar intake and quantified trehalose levels in the hemolymph, a key indicator of energy reserves. Both the meta-analysis and experimental results consistently showed no significant differences in sugar consumption between healthy and infected bees. Similarly, trehalose levels in the hemolymph remained comparable between the two groups. Our findings suggest that the infection caused by N. ceranae does not elicit compensatory feeding behavior in honeybees. Moreover, the meta-analysis revealed significant gaps in current research, particularly a lack of studies focusing on forager bees, which face the highest energetic demands among colony members. Our findings call for future studies on the energetic effects of nosemosis and studies conducted under natural or semi-natural conditions.},
}

Animals
Bees/microbiology/physiology/metabolism
*Nosema/physiology
Hemolymph/chemistry/metabolism
Feeding Behavior
Trehalose/metabolism/analysis
*Carbohydrate Metabolism

@article {pmid40440849,
year = {2025},
author = {Ramadoss, R and Nishad, AK and Moovarkumudalvan, B and Shomar, B},
title = {Bacterial composition of dust deposited in Qatar: A seasonal study.},
journal = {The Science of the total environment},
volume = {985},
number = {},
pages = {179766},
doi = {10.1016/j.scitotenv.2025.179766},
pmid = {40440849},
issn = {1879-1026},
abstract = {Dust storms in the Middle East threaten public health by deteriorating air quality and transporting microorganisms over vast distances. This study analyzes seasonal variations in dust-borne bacterial diversity on photovoltaic (PV) panels using 16S rRNA gene sequencing and bioinformatics to assess community composition and metabolic potential. Our findings suggest that seasonal ecological factors have potential effects on the composition of the airborne bacterial community. In Qatar, the high atmospheric CO2 levels associated with hydrocarbon refining had promoted the growth of hydrocarbon-degrading bacteria belonging to the phyla Campilobacterota, Proteobacteria, and Bacteroidota. High temperatures and photothermal reactions of summer conditions have favored sulfur-metabolizing bacteria. Conversely, milder temperatures, increased humidity, reduced wind speed, and a decline in summer-favoring bacteria had contributed to the increased abundance of the phyla Patescibacteria, Firmicutes, and Actinobacteriota during other seasons. This study had also identified dust borne pathogenic bacteria associated with human and plant diseases, highlighting the need for environmental surveillance to monitor microbial diversity and its shifts driven by ecological factors. This knowledge is crucial for public health, environmental protection, sustainable farming and advancing our understanding of microbial ecology.},
}

@article {pmid40439420,
year = {2025},
author = {Park, J and Kohn, E and Schenk, S and Davis, KM and Clark, JS and Parfrey, LW},
title = {An experimental test of the influence of microbial manipulation on sugar kelp (Saccharina latissima) supports the core influences host function hypothesis.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0030125},
doi = {10.1128/aem.00301-25},
pmid = {40439420},
issn = {1098-5336},
abstract = {UNLABELLED: Kelp are valued for a wide range of commercial products and their role in kelp forest ecosystems, making kelp cultivation a rapidly expanding economic sector. Microbes associated with kelp and other macroalgae play a critical role in processes such as nutrient exchange, chemical signaling, and defense against pathogens. Thus, manipulating the microbiome to enhance macroalgal growth and resilience is a promising yet underexplored approach for sustainable kelp cultivation. The core microbiome hypothesis suggests that the bacteria that are consistently found on a host (the core microbes) are likely to have a disproportionate impact on host biology, making them an attractive target for microbiome manipulation. In this study, we surveyed wild Saccharina latissima and their surrounding environment to identify core bacterial taxa, compared them to cultivated kelp, and experimentally tested how cultured bacterial isolates affect kelp development. We found that core bacteria are nearly absent in cultivated juvenile sporophytes in nurseries, but eventually colonize them after outplanting to ocean farm sites. Bacterial inoculants had both positive and negative effects on kelp development. Notably, the strength of association of a bacterial genus with kelp in the wild positively correlated with its impact on gametophyte settlement and sporophyte development in kelp co-culture experiments, aligning with predictions from the core microbiome influences host function hypothesis. These findings affirm the feasibility of using microbial manipulations to improve current kelp aquaculture practices and provide a framework for developing these techniques.

IMPORTANCE: Microorganisms consistently associated with hosts are widely thought to be more likely to impact host biology and health. However, this intuitive concept has not been experimentally evaluated. This study formalizes this concept as the Core Microbiome Influences Host Function hypothesis and experimentally tests this hypothesis in sugar kelp (Saccharina). The distribution of bacteria on wild kelp and core microbes was first identified by compiling a broad dataset of the kelp microbiome sampled across space and time. Bacterial cultures were isolated from the surface of sugar kelp and individually grown in laboratory co-culture with sugar kelp spores to assess the ability of bacterial isolates to influence kelp growth and development. In support of the core influences host function hypothesis, isolates belonging to bacterial genera that are more strongly associated with wild sugar kelp are more likely to influence development in laboratory experiments.},
}

@article {pmid40437905,
year = {2025},
author = {Ni, J and Yang, Z and Sun, X and Cui, Q and Zhang, R and Lu, H and Wu, Z and Zhu, J and Mao, H and Liu, K and Tang, C and Wang, C and Xing, C and Zhu, J},
title = {Probiotic Akkermansia muciniphila alleviates acute kidney injury by protecting the intestinal barrier and modulating gut microbiota and metabolites.},
journal = {Journal of biomedical research},
volume = {},
number = {},
pages = {1-12},
doi = {10.7555/JBR.39.20250162},
pmid = {40437905},
issn = {1674-8301},
abstract = {Acute kidney injury (AKI) is a critical condition with limited effective therapies. Akkermansia muciniphila (A. muciniphila) is a probiotic with multiple beneficial effects, including epithelial cell tight junctions regulation. Since renal pathophysiology is associated with gut barrier integrity, we hypothesized that A. muciniphila may have potential preventive effects on AKI. We established a lipopolysaccharide (LPS)-induced AKI mouse model to evaluate the effects of A. muciniphila. Our findings showed that pretreatment with A. muciniphila significantly attenuated kidney injury, as evidenced by reduced serum creatinine and urea nitrogen levels, alongside diminished tubular necrosis and apoptosis. A. muciniphila preserved the intestinal barrier integrity and induced marked shifts in gut microbial ecology and the metabolome. A. muciniphila induced notably an increase in the relative abundance of phylum Proteobacteria while a decrease of Bacteroidetes. At the genus level, Prevotella, Faecalibaculum, Moraxella and Lactobacillus were more abundant in A. muciniphila-pretreated mice. Metabolomic analysis revealed that A. muciniphila altered the gut metabolome affecting modulation of pathways, including tyrosine metabolism, alanine/aspartate/glutamate homeostasis, cancer-related carbon flux, and GABAergic synaptic signaling. In conclusion, our findings demonstrate A. muciniphila's renoprotective effects through gut-kidney axis modulation, laying the foundation for subsequent studies to verify the connection between gut microbiota and AKI.},
}

@article {pmid40436193,
year = {2025},
author = {Lacerda, AL and Casotti, R and Briand, JF and Lenoble, V and Muniategui-Lorenzo, S and Kessler, F and Barre, A and Moscoso-Pérez, CM and Fernández-González, V and Andrade-Garda, JM and Murano, C and Donnarumma, V and Oreste, E and Joyce, H and Hannon, C and Nash, R and Orange, F and Frias, J and Pedrotti, ML},
title = {The plastisphere: a comprehensive description of geographic and temporal community patterns across the Mediterranean Sea and the Atlantic Ocean.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121929},
doi = {10.1016/j.envres.2025.121929},
pmid = {40436193},
issn = {1096-0953},
abstract = {Plastic pollution is a global ecological threat, not only as physical debris but also as a novel substrate hosting microbial communities, known as "plastisphere". Polymer type (virgin vs. recycled), combined with environmental variations, may influence both early and mature colonisation stages. While biogeography has been identified as a key driver of the plastisphere community structure, prior research often relied on isolated studies with no methodological standardization or on opportunistic sampling. Here, this study stands out by conducting a simultaneous and harmonized investigation across environmentally distinct sites in the Mediterranean Sea and the Atlantic Ocean. Three polymers (LDPE, PP-PC, PLA) were incubated in situ, across six locations. Using standardized protocols and eDNA metabarcoding (16S and 18S rRNA), we assessed how biogeography, environmental variables, polymer type, and exposure time shape the diversity and composition of prokaryotic and eukaryotic communities colonizing plastics. Incubations lasted up to one year, with sampling at 7, 30 and 90 days, covering all four seasons. Microbial colonization in all plastics occurred within 7 days, but community richness and maturity fluctuated across sites and seasons. Proteobacteria, Bacteroidia and Planctomycetes were the dominant prokaryotes, while Ciliates, Cercozoa and Dinoflagellata dominated eukaryotes. Taxa with potential for plastic biodegradation (e.g., Oleibacter, Alcanivorax) and pathogenicity (e.g., Pseudomonas, Candida), were identified, highlighting the plastisphere's ecological role. This dataset represents the most comprehensive assessment of marine plastisphere diversity to date, allowing the understanding of species occurrence and their interaction, influence on ecological processes and the emerging health risks, which should be considered when developing global strategies to mitigate ocean plastic pollution.},
}

@article {pmid40435560,
year = {2025},
author = {Fazio, NA and Albertin, W and Masneuf-Pomarede, I and Randazzo, CL and Caggia, C},
title = {Structure of culturable indigenous yeast population and genetic diversity of Saccharomyces cerevisiae and non-Saccharomyces yeasts during spontaneous fermentation of Etna vineyards grapes.},
journal = {International journal of food microbiology},
volume = {440},
number = {},
pages = {111282},
doi = {10.1016/j.ijfoodmicro.2025.111282},
pmid = {40435560},
issn = {1879-3460},
abstract = {The microbial diversity of indigenous yeasts plays a fundamental role in the spontaneous fermentation of wines, contributing to the concept of microbial terroir and potentially influencing the sensory profile of the final product. This study explores the yeast ecology and genetic diversity of Saccharomyces cerevisiae and non-Saccharomyces yeasts in four wineries located on two different sides of Mount Etna, a region of unique viticultural significance due to its volcanic soils and diverse microclimatic conditions. A total of 454 yeast isolates were obtained from spontaneous fermentations of different grape varieties, and identified as belonging to 18 distinct species. The spontaneous fermentation was characterized by an initial dominance of non-Saccharomyces yeasts, especially Hanseniaspora uvarum and Metschnikowia pulcherrima, followed by a gradual dominance of S. cerevisiae at later stages. Microsatellite genotyping revealed significant genetic diversity among S. cerevisiae strains, with some distinct genetic patterns associated with Italian winery environments. Additionally, H. uvarum exhibited significant genetic variation but lacked clear geographic clustering, suggesting complex ecological and enological interactions. Statistical analyses of microbial diversity indices indicated that vineyard-specific factors, including altitude, soil composition, and agronomic practices, may influence yeast community structure among the four wineries. These findings provide new insights into the microbial ecology of Etna wines and highlight the potential of indigenous yeast populations for maintaining and enhancing regional wine identity.},
}

@article {pmid40432969,
year = {2025},
author = {Wang, JQ and Yu, T and Qiu, HY and Ji, SW and Xu, ZQ and Cui, QC and Li, HF and Liang, WF and Feng, S and Fu, CT and Gao, X and Han, ZZ and Tian, WN and Li, JX and Xue, SJ},
title = {Differential impact of spotted fever group rickettsia and anaplasmosis on tick microbial ecology: evidence from multi-species comparative microbiome analysis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1589263},
pmid = {40432969},
issn = {1664-302X},
abstract = {Tick-borne diseases (TBDs) pose a significant public health challenge, as their incidence is increasing due to the effects of climate change and ecological shifts. The interplay between tick-borne pathogens and the host microbiome is an emerging area of research that may elucidate the mechanisms underlying disease susceptibility and severity. To investigate the diversity of microbial communities in ticks infected with vertebrate pathogens, we analyzed the microbiomes of 142 tick specimens. The presence of Rickettsia and Anaplasma pathogens in individual samples was detected through PCR. Our study aimed to elucidate the composition and variation of microbial communities associated with three tick species, which are known vectors for various pathogens affecting both wildlife and humans. We employed high-throughput sequencing techniques to characterize the microbial diversity and conducted statistical analyses to assess the correlation between the presence of specific pathogens and the overall microbial community structure. Pathogen screening revealed an overall positivity rate of 51.9% for Anaplasma and 44.6% for spotted fever group rickettsia (SFGR). Among the three tick species (Dermacentor silvarum, Haemaphysalis concinna, and Haemaphysalis japonica) analyzed, D. silvarum (the predominant species) exhibited the highest pathogen prevalence. The results indicate significant variation in microbial diversity between tick samples, with the presence of Anaplasma and SFGR associated with distinct changes in the microbial community composition. These findings underscore the complex interactions between ticks and their microbial inhabitants, enriching our understanding of tick-borne diseases.},
}

@article {pmid40431577,
year = {2025},
author = {Jia, J and Bao, P and Yu, Q and Li, N and Ren, H and Chen, Q and Yan, P},
title = {Lactobacillus Re-Engineers Gut Microbiota to Overcome E. coli Colonization Resistance in Mice.},
journal = {Veterinary sciences},
volume = {12},
number = {5},
pages = {},
doi = {10.3390/vetsci12050484},
pmid = {40431577},
issn = {2306-7381},
support = {KCXF20201221173205015//the Shenzhen Science and Technology Program/ ; TCYC-TP2023//Xinjiang Tianchi introduction of talent research Program/ ; },
abstract = {The intestinal health and functionality of animals play pivotal roles in nutrient digestion and absorption, as well as in maintaining defense against pathogenic invasions. These biological processes are modulated by various determinants, including husbandry conditions, dietary composition, and gut microbial ecology. The excessive use of anthropogenic antibiotics may disrupt intestinal microbiota composition, potentially leading to dysbiosis that directly compromises host homeostasis. While Lactobacillus species are recognized for their immunomodulatory properties, their precise mechanisms in regulating host anti-inflammatory gene expression and influencing mucosal layer maturation, particularly regarding E. coli colonization resistance, require further elucidation. To investigate the regulatory mechanisms of Lactobacillus in relation to intestinal architecture and function during E. coli infection, we established a colonic infection model using Bal b/c mice, conducting systematic analyses of intestinal morphology, inflammatory mediator profiles, and microbial community dynamics. Our results demonstrate that Lactobacillus supplementation (Pediococcus acidilactici) effectively mitigated E. coli O78-induced enteritis, with co-administration during infection facilitating the restoration of physiological parameters, including body mass, intestinal histoarchitecture, and microbial metabolic functions. Microbiome profiling revealed that the Lactobacillus intervention significantly elevated Lactococcus abundance while reducing Weissella populations (p < 0.05), concurrently enhancing metabolic pathways related to nutrient assimilation and environmental signal processing (including translation mechanisms, ribosomal biogenesis, amino acid transport metabolism, and energy transduction systems; p < 0.05). Mechanistically, Lactobacillus administration attenuated E. coli-induced intestinal pathology through multiple pathways: downregulating pro-inflammatory cytokine expression (IL-1β, IL-1α, and TNF-α), upregulating epithelial junctional complexes (Occludin, Claudin-1, and ZO-1), and stimulating mucin biosynthesis (MUC1 and MUC2; p < 0.05). These modifications collectively enhanced mucosal barrier integrity and promoted epithelial maturation. This investigation advances our comprehension of microbiota-host crosstalk during enteropathogenic infections under probiotic intervention, offering valuable insights for developing novel nutritional strategies and microbial management protocols in animal husbandry.},
}

@article {pmid40431542,
year = {2025},
author = {Karukayil Gopalakrishnan, N and Pappuswamy, M and Meganathan, G and Shanmugam, S and Pushparaj, K and Balasubramanian, B and Kim, IH},
title = {Influence of Probiotic Administration in Canine Feed: A Comprehensive Review.},
journal = {Veterinary sciences},
volume = {12},
number = {5},
pages = {},
doi = {10.3390/vetsci12050449},
pmid = {40431542},
issn = {2306-7381},
abstract = {Dogs are cherished companions, and in today's world, pets are increasingly regarded as family members. Pet owners are placing growing emphasis on their animals' health, particularly for dogs. Probiotics, which are living bacteria that benefit the host when given in sufficient quantities, have drawn a lot of interest in the veterinary nutrition community due to their beneficial effects on companion animals, including dogs. This study emphasizes the advantages of adding probiotics to canine diets in order to enhance the health of the gut flora and the technologies used to incorporate probiotics into canine feed. It looks at the best ways to deal with common dog health problems, highlighting probiotics as a helpful substitute for antibiotics, which can have serious adverse effects, encourage bacterial resistance, and disturb the gut's microbial ecology, which is necessary for digesting. Such disruptions are linked to chronic inflammatory enteropathy and obesity in dogs. This paper also examines biotechnological advancements in probiotic incorporation methods in dog feed, aiming to optimize their health benefits. Probiotic feed supplements may thus represent a promising approach to advancing canine health care, providing a natural adjunct to conventional treatments and preventive measures.},
}

@article {pmid40431287,
year = {2025},
author = {Zhong, J and Ran, Q and Han, Y and Gan, L and Dong, C},
title = {Biosynthetic Mechanisms of Plant Chlorogenic Acid from a Microbiological Perspective.},
journal = {Microorganisms},
volume = {13},
number = {5},
pages = {},
doi = {10.3390/microorganisms13051114},
pmid = {40431287},
issn = {2076-2607},
support = {32360029//the National Science Foundation of China/ ; 32400111//the National Science Foundation of China/ ; Qiankehe Foundation-ZK (2024) General 091//he Guizhou Provincial Basic Research Program (Natural Science)/ ; },
abstract = {Chlorogenic acid (CGA), a phenolic compound with diverse bioactivities, plays a crucial role in plant defense mechanisms and has significant therapeutic potential in human inflammatory and cardiovascular diseases. The biosynthesis and accumulation of CGA in plants result from a complex interplay between internal factors (e.g., hormones, enzymes, and genes) and external factors (e.g., microbial interactions, drought, and temperature fluctuations). This review systematically investigates the influence of microbes on internal regulatory factors governing CGA biosynthesis in plants. CGA is synthesized through four distinct metabolic pathways, with hormones, enzymes, and genes as key regulators. Notably, microbes enhance CGA biosynthesis by improving plant nutrient uptake, supplying essential hormones, regulating the expression of related enzymes and genes, and the interaction between bacteria and fungi. In addition, our review summarizes the challenges currently present in the research and proposes a series of innovative strategies. These include in-depth investigations into the molecular mechanisms of microbial regulation of plant gene expression, gene editing, development of microbial inoculants, construction of synthetic microbial communities, and exogenous application of plant hormones.},
}

@article {pmid40431158,
year = {2025},
author = {Mirete, S and Sánchez-Costa, M and Díaz-Rullo, J and González de Figueras, C and Martínez-Rodríguez, P and González-Pastor, JE},
title = {Metagenome-Assembled Genomes (MAGs): Advances, Challenges, and Ecological Insights.},
journal = {Microorganisms},
volume = {13},
number = {5},
pages = {},
doi = {10.3390/microorganisms13050985},
pmid = {40431158},
issn = {2076-2607},
support = {PID2021-126114NB-C43//Spanish Ministry of Science and Innovation which also included European Regional Development Fund (FEDER)/ ; },
abstract = {Metagenome-assembled genomes (MAGs) have revolutionized microbial ecology by enabling the genome-resolved study of uncultured microorganisms directly from environmental samples. By leveraging high-throughput sequencing, advanced assembly algorithms, and genome binning techniques, researchers can reconstruct microbial genomes without the need for cultivation. These methodological advances have expanded the known microbial diversity, revealing novel taxa and metabolic pathways involved in key biogeochemical cycles, including carbon, nitrogen, and sulfur transformations. MAG-based studies have identified microbial lineages form Archaea and Bacteria responsible for methane oxidation, carbon sequestration in marine sediments, ammonia oxidation, and sulfur metabolism, highlighting their critical roles in ecosystem stability. From a sustainability perspective, MAGs provide essential insights for climate change mitigation, sustainable agriculture, and bioremediation. The ability to characterize microbial communities in diverse environments, including soil, aquatic ecosystems, and extreme habitats, enhances biodiversity conservation and supports the development of microbial-based environmental management strategies. Despite these advancements, challenges such as assembly biases, incomplete metabolic reconstructions, and taxonomic uncertainties persist. Continued improvements in sequencing technologies, hybrid assembly approaches, and multi-omics integration will further refine MAG-based analyses. As methodologies advance, MAGs will remain a cornerstone for understanding microbial contributions to global biogeochemical processes and developing sustainable interventions for environmental resilience.},
}

@article {pmid40427685,
year = {2025},
author = {Chen, Z and Zhong, Y and Chen, L and Liu, W and Lin, C and Chen, Y and Wang, X},
title = {HGF Aggravated Periodontitis-Associated Gut Barrier and Microbial Dysfunction: Implications for Oral-Gut Axis Regulation.},
journal = {Biology},
volume = {14},
number = {5},
pages = {},
doi = {10.3390/biology14050496},
pmid = {40427685},
issn = {2079-7737},
support = {81700985//National Natural Science Foundation of China/ ; 2024A03J0138//Guangzhou Municipal Science and Technology Bureau/ ; 02-408-2304-05037XM and 02-408-240603131063//Plan on Enhancing Scientific Research in Guangzhou Medical University/ ; 202201020203//Guangzhou Science and Technology Program/ ; },
abstract = {While periodontitis is increasingly linked to systemic disorders through the oral-gut axis, the molecular mediators driving gut microbiota dysbiosis and barrier disruption remain elusive. Hepatocyte growth factor (HGF), a novel regulator of inflammatory bone loss in periodontitis, may serve as a critical communicator between oral infection and distal intestinal pathology. This study investigates how HGF overexpression modulates the gut microbial ecosystem and intestinal barrier integrity in a transgenic periodontitis model. In this study, we combined 16S rRNA sequencing of fecal microbiota with comprehensive gut barrier assessments, including systemic markers (D-lactate, LPS, and DAO ELISA), structural integrity (villous morphology), and molecular analysis (ZO-1, occludin, and NOD2 immunohistochemistry), using HGF-overexpressing transgenic (HGF-Tg) mice with periodontitis. The results demonstrated that HGF increased gut permeability in the context of periodontitis, as evidenced by elevated serum levels of D-lactate and LPS compared to wild type (WT) mice. In addition, gut villous morphology disorder was observed in HGF-Tg mice with periodontitis. HGF also diminished the protein level of occludin and upregulated NOD2 expression in mice with periodontitis. Moreover, HGF-Tg mice with periodontitis exhibited significant dysbiosis of gut microbiota, with reduced levels of probiotics (e.g., Faecalibaculum). Notably, HGF also increased the enrichment of the periodontitis-associated pathogens (e.g., Desulfovibrio and Streptococcus) in the gut. Microbial functions, particularly metabolic pathways, were significantly altered by HGF when periodontitis occurred. Some microorganisms like g_Desulfovibrio may play a role in gut barrier disorder in HGF-Tg mice with periodontitis. Overall, our findings position HGF as a novel orchestrator of oral-gut crosstalk, where its overexpression reshapes gut microbial ecology toward a "leaky gut" phenotype to compromise intestinal barrier integrity, further deepening our understanding of the oral-gut axis.},
}

@article {pmid40427319,
year = {2025},
author = {Xu, C and Guo, X and Li, L},
title = {Metagenomic Comparison of Gut Microbes of Lemur catta in Captive and Semi-Free-Range Environments.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {10},
pages = {},
doi = {10.3390/ani15101442},
pmid = {40427319},
issn = {2076-2615},
abstract = {In order to protect endangered species, many zoos adopt diverse rearing models to achieve optimal conservation outcomes. This study employed metagenomic approaches to assess differences in the fecal microbiome of captive and semi-free-ranging ring-tailed lemurs (Lemur catta). The results show that captivity significantly altered the microbial community structure. The inter-individual variability in the microbial community within the captive-bred (CB) group was lower than that in the semi-free-ranging (FR) group, yet these individuals harbored a higher abundance of potential pathogens (Treponema_D). In contrast, microbial genera associated with fiber degradation and short-chain fatty acid production in the FR group were significantly elevated (Faecalibacterium, Roseburia, and Megamonas) as compared to the CB group. Environmental variations between the two rearing systems led to distinct profiles in microbial functions and carbohydrate-active enzyme gene composition. Notably, the FR group of lemurs exhibited an increased abundance of enzyme genes associated with the degradation of complex polysaccharides (cellulose, hemicellulose, and pectin), suggesting that their diet, rich in natural plant fibers, enhances the capacity of their gut microbiota to extract essential energy and nutrients. Conversely, the CB group displayed a more homogeneous microbial community with a higher prevalence of potential pathogens, implying that a captive lifestyle may negatively impact gastrointestinal health. These findings offer valuable insights into the influence of rearing conditions on gut microbial ecology and its potential implications for the health management of ring-tailed lemurs.},
}

@article {pmid40426572,
year = {2025},
author = {Touati, A and Ibrahim, NA and Mairi, A and Kirat, H and Basher, NS and Idres, T},
title = {One Health at Risk: Plasmid-Mediated Spread of mcr-1 Across Clinical, Agricultural, and Environmental Ecosystems.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {5},
pages = {},
doi = {10.3390/antibiotics14050506},
pmid = {40426572},
issn = {2079-6382},
support = {IMSIU-DDRSP2501//Deanship of Scientific Research at Imam Mohammad Ibn Saud Islamic University (IMSIU)/ ; },
abstract = {The global dissemination of plasmid-mediated mcr genes, which confer resistance to the last-resort antibiotic colistin, represents a critical public health challenge driven by the interplay of clinical, agricultural, and environmental factors. This review examines the genetic and ecological dynamics of mcr-bearing plasmids, focusing on their role in disseminating colistin resistance across diverse bacterial hosts and ecosystems. Key plasmid families demonstrate distinct evolutionary strategies, including IncI2, IncHI2, and IncX4. IncI2 plasmids favor stability in livestock and clinical settings. IncHI2 plasmids, on the other hand, leverage transposons to co-select for multidrug resistance, while IncX4 plasmids achieve global dissemination through streamlined, conjugation-efficient architectures. The pervasive spread of mcr genes is exacerbated by their integration into chromosomes via mobile genetic elements and co-selection with resistance to other antibiotic classes, amplifying multidrug-resistant phenotypes. Environmental reservoirs, food chains, and anthropogenic practices further facilitate cross-niche transmission, underscoring the interconnectedness of resistance under the One Health framework. Addressing this crisis requires coordinated strategies, including reducing colistin misuse in agriculture, enhancing surveillance of high-risk plasmid types, and fostering international collaboration to preserve antimicrobial efficacy and mitigate the threat of untreatable infections.},
}

@article {pmid40423845,
year = {2025},
author = {Pérez-Gómez, O and Domínguez-Maqueda, M and García-Márquez, J and Moriñigo, MÁ and Tapia-Paniagua, ST},
title = {Metabolite-Driven Modulation of Biofilm Formation in Shewanella: Insights from Shewanella sp. Pdp11 Extracellular Products.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {55},
pmid = {40423845},
issn = {1432-184X},
support = {PID2020-113637RB-C21//Ministerio de Ciencia e Innovación/ ; PID2020-113637RB-C21//Ministerio de Ciencia e Innovación/ ; PID2020-113637RB-C21//Ministerio de Ciencia e Innovación/ ; PID2020-113637RB-C21//Ministerio de Ciencia e Innovación/ ; PID2020-113637RB-C21//Ministerio de Ciencia e Innovación/ ; },
mesh = {*Shewanella/metabolism/physiology/genetics ; *Biofilms/growth & development/drug effects ; Glycogen/metabolism ; },
abstract = {Biofilm formation is a survival strategy for bacteria, contributing to their persistence in natural and industrial environments. In this study, we investigated the ability of extracellular products (ECPs) produced by the probiotic strain Shewanella sp. Pdp11 under different culture conditions to inhibit biofilm formation in pathogenic and environmental Shewanella strains. ECPs from specific culture conditions altered biofilm formation in several Shewanella strains, with Shewanella hafniensis P14 displaying the highest sensitivity. Metabolomic analysis of the ECPs identified glycogen as a key metabolite associated with biofilm inhibition. Further genomic analysis of S. hafniensis P14 revealed an interruption in its glycogen synthesis pathway, suggesting a dependency on external glycogen-related metabolites for biofilm development. These findings demonstrate that Shewanella sp. Pdp11 ECPs can modify biofilm formation across multiple Shewanella strains, particularly in S. hafniensis P14 through glycogen-associated mechanisms.},
}

*Shewanella/metabolism/physiology/genetics
*Biofilms/growth & development/drug effects
Glycogen/metabolism

@article {pmid40423805,
year = {2025},
author = {Meehan, DE and O'Toole, PW},
title = {A Review of Diet and Foraged Pollen Interactions with the Honeybee Gut Microbiome.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {54},
pmid = {40423805},
issn = {1432-184X},
support = {GOIPG/2024/5035//Taighde Éireann/ ; 12/RC/2273_P2/SFI_/Science Foundation Ireland/Ireland ; },
mesh = {Bees/microbiology/physiology ; Animals ; *Gastrointestinal Microbiome ; *Pollen/metabolism ; *Diet ; },
abstract = {The honeybee Apis mellifera is a globally vital pollinator for flowering plants and crops, but it is currently facing mounting threats to survival due to habitat anthropization, emerging pathogens, and climate change. Over the past decade, increasing research efforts to understand and combat these challenges have led to an exploration of the honeybee gut microbiome-a relatively simple and highly conserved community of commensals which has a range of effects on the host. Researchers have now unravelled the main functional roles of this microbiome which include innate immune system stimulation, metabolism of dietary compounds, and mediation of host development and behaviour. Key amongst these is its role in aiding nutrition through the metabolism of complex carbohydrates and by degradation of otherwise indigestible pollen compounds. Increasingly, research is indicating that a diverse and high-quality pollen diet is key to maintaining healthy colonies and a stable microbiome. However, colonies can struggle to meet these dietary needs, particularly if they are located in anthropized ecosystems. Disruptions to honeybee diets or a reduction in the availability of diverse foraging options can significantly alter the composition of the microbiome, shifting it towards an abnormal state that leaves the honeybee more vulnerable to infection. Seasonal changes, primarily the overwintering period, also induce shifts in microbiome composition and are periods of time when a colony is particularly vulnerable to pathogenic infection. A comprehensive understanding of the effect these variables have on both microbiome composition and colony health is key to tackling the unprecedented environmental challenges that honeybees now face. This review summarises recent research which has elucidated the functional role of the gut microbiome in metabolism and how the composition of this bacterial community can alter due to seasonal change, anthropized landscapes, and dietary shifts. Finally, we also discuss recent studies investigating the effect that dietary supplementation has on the gut microbiome and the application of probiotic candidates for improving colony resilience and strength.},
}

Bees/microbiology/physiology
Animals
*Gastrointestinal Microbiome
*Pollen/metabolism
*Diet

@article {pmid40423261,
year = {2025},
author = {Rotsaert, C and Minnebo, Y and Duysburgh, C and Liu, LS and Mahalak, KK and Firman, J and Mattei, LM and Moustafa, AM and Bittinger, K and Hu, W and Marzorati, M and Michiels, J and Van de Wiele, T},
title = {Digestive parameters and gut microbiota load and composition along the in vivo piglet gastrointestinal tract.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skaf107},
pmid = {40423261},
issn = {1525-3163},
abstract = {The increased attention towards the role of the gut microbiome in health and disease for both animals and humans has fuelled the demand for more relevant and accurate research models. In this study, we present an overview of biochemical and microbial parameters measured throughout the digestive tract of ten TopigsNorsvin x German Piétrain piglets to better understand the in vivo dynamics of digestive and fermentative processes in different gastrointestinal segments, as pigs are suggested to be a representative animal model for the human gastrointestinal tract. Our key findings include region-specific and significantly differing (P < 0.001) pH profiles, with the stomach having the lowest pH (3.36 ± 0.72) and the ileum the highest (7.24 ± 0.18). Dry matter content also varied significantly (P < 0.001), with the stomach having the highest (27.8 ± 2.4%) and the duodenum the lowest (10.6 ± 0.7%). The average total transit time was 12 hours and 45 minutes ± 1 hour and 42 minutes. Enzyme activities (pepsin, trypsin, amylase) showed interindividual differences. Amino acid levels varied among piglets, with total concentrations averaging 7.04 x 102 ± 2.29 x 102 µg mL-1 in the duodenum, 1.19 x 103 ± 2.69 x 102 µg mL-1 in the jejunum and 9.39 x 102 ± 2.54 x 102 µg mL-1 in the ileum. Bile acid concentrations varied strongly between piglets, with high levels in the gall bladder and varying levels throughout the digestive tract. Short-chain fatty acid concentrations increased significantly (P < 0.001) along the digestive tract, with the highest levels in the large intestine. The microbial load increased consistently (P < 0.001) along the digestive tract, with the highest loads in the rectum (6.82 x 1010 ± 2.88 x 1010 cells mL-1). The highest microbial diversity was observed in the lower intestine (i.e. caecum, colon and rectum), with significant shifts in microbial community composition, especially from the ileum to the caecum. This study provides valuable insights into the digestive and microbiological parameters of the porcine gut, confirming the pig's relevance as a model for gastrointestinal research. The findings can inform the development of in vitro or ex vivo models, reducing ethical constraints of animal studies and aiding in the assessment of dietary interventions on gut health.},
}

@article {pmid40422247,
year = {2025},
author = {Wheeler, KM and Oh, MW and Fusco, J and Mershon, A and Kim, E and De Oliveira, A and Rahme, LG},
title = {MvfR Shapes Pseudomonas aeruginosa Interactions in Polymicrobial Contexts: Implications for Targeted Quorum-Sensing Inhibition.},
journal = {Cells},
volume = {14},
number = {10},
pages = {},
doi = {10.3390/cells14100744},
pmid = {40422247},
issn = {2073-4409},
support = {5R01AI177555-02/GF/NIH HHS/United States ; N/A//Massachusetts General Hospital Research Scholar Award/ ; },
mesh = {*Quorum Sensing/genetics ; *Pseudomonas aeruginosa/pathogenicity/physiology/genetics/metabolism ; Humans ; *Bacterial Proteins/metabolism/genetics ; Biofilms/growth & development ; Virulence ; Gene Expression Regulation, Bacterial ; Microbial Interactions ; Pseudomonas Infections/microbiology ; },
abstract = {Infections often occur in complex niches consisting of multiple bacteria. Despite the increasing awareness, there is a fundamental gap in understanding which interactions govern microbial community composition. Pseudomonas aeruginosa is frequently isolated from monomicrobial and polymicrobial human infections. This pathogen forms polymicrobial infections with other ESKAPEE pathogens and defies eradication by conventional therapies. By analyzing the competition within co-cultures of P. aeruginosa and representative secondary pathogens that commonly co-infect patients, we demonstrate the antagonism of P. aeruginosa against other ESKAPEE pathogens and the contribution of this pathogen's multiple quorum-sensing (QS) systems in these interactions. QS is a highly conserved bacterial cell-to-cell communication mechanism that coordinates collective gene expressions at the population level, and it is also involved in P. aeruginosa virulence. Using a collection of P. aeruginosa QS mutants of the three major systems, LasR/LasI, MvfR/PqsABCDE, and RhlR/RhlI, and mutants of several QS-regulated functions, we reveal that MvfR and, to a lesser extent, LasR and RhlR, control competition between P. aeruginosa and other microbes, possibly through their positive impact on pyoverdine, pyochelin, and phenazine genes. We show that MvfR inhibition alters competitive interspecies interactions and preserves the coexistence of P. aeruginosa with the ESKAPEE pathogens tested while disarming the pathogens' ability to form biofilm and adhere to lung epithelial cells. Our results highlight the role of MvfR inhibition in modulating microbial competitive interactions across multiple species, while simultaneously attenuating virulence traits. These findings reveal the complexity and importance of QS in interspecies interactions and underscore the impact of the anti-virulence approach in microbial ecology and its importance for treating polymicrobial infections.},
}

*Quorum Sensing/genetics
*Pseudomonas aeruginosa/pathogenicity/physiology/genetics/metabolism
Humans
*Bacterial Proteins/metabolism/genetics
Biofilms/growth & development
Virulence
Gene Expression Regulation, Bacterial
Microbial Interactions
Pseudomonas Infections/microbiology

@article {pmid40421462,
year = {2025},
author = {Liu, RZ and Zhao, XY and Feng, B and Zhao, WS and Li, MY and Yu, XF and Hu, SP and Li, RP and Gao, JL and Borjigin, Q},
title = {Research on soil bacterial community assembly and function under different straw returning practices in arid and semi-arid agricultural ecosystems over multiple years.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1590686},
pmid = {40421462},
issn = {1664-302X},
abstract = {INTRODUCTION: Straw return has gained attention for its potential to improve soil quality and crop yields, particularly in semi-arid regions like the Tumu Chuan Plain Irrigation Area. Soil bacteria play a crucial role in regulating soil biological processes, and understanding how straw return affects bacterial populations can guide better agricultural management practices.

METHODS: We investigated the impact of continuous straw return on soil bacterial communities using 16S rRNA gene sequencing. Four treatments were applied: Farmers' shallow rotation (CK), straw incorporated with deep tillage (DPR), straw incorporated with subsoiling (SSR), and no-tillage mulching straw return (NTR). Bacterial community structure, metabolic pathways, and assembly mechanisms were analyzed using Bugbase and PICRUSt2 for phenotypic and metabolic pathway predictions.

RESULTS: The study found that straw return practices significantly altered the relative abundance and life history strategies of bacterial phyla, mainly influenced by soil organic matter (SOM) and enzyme activity. The K-strategist to r-strategist ratio was highest in CK (2.06) and lowest in SSR (1.89). DPR and NTR treatments significantly changed bacterial community structure compared to CK (p < 0.05), resembling SSR. Predictions showed that DPR and NTR enhanced carbohydrate and amino acid metabolism and promoted more stable bacterial networks, with homogenous selection and drift effects. Bacterial aggregation in all treatments was driven by random processes, with varying aggregation levels: CK (20%), DPR (38.6%), SSR (16.5%), and NTR (30.7%).

DISCUSSION: The study demonstrates that continuous straw return practices significantly impact soil bacterial communities. DPR and NTR notably improved microbial diversity, bacterial cooperation, and ecosystem stability. These findings provide valuable insights for sustainable agricultural practices in semi-arid regions, enhancing soil microbial ecology and soil health through strategic straw return.},
}

@article {pmid40419814,
year = {2025},
author = {Srivastava, AK and Riaz, A and Jiang, J and Li, X and Uzair, M and Mishra, P and Zeb, A and Zhang, J and Singh, RP and Luo, L and Chen, S and Yang, S and Zhao, Y and Xie, X},
title = {Advancing Climate-Resilient Sorghum: the Synergistic Role of Plant Biotechnology and Microbial Interactions.},
journal = {Rice (New York, N.Y.)},
volume = {18},
number = {1},
pages = {41},
pmid = {40419814},
issn = {1939-8425},
support = {[2022]091//Guizhou Provincial Youth Science and Technology Talents Growth Project/ ; },
abstract = {Climate-related problems such as drought stress, extreme temperature, erratic rainfall patterns, soil degradation, heatwaves, flooding, water logging, pests and diseases afflict the production and sustainability of sorghum. These challenges may be addressed by adopting climate-resilient practices and using advanced agronomic techniques. These challenges are being addressed through innovative applications of plant biotechnology and microbiology, which offer targeted solutions to enhance sorghum's resilience. For instance, biotechnological tools like CRISPR/Cas9 enable precise genetic modifications to improve drought and heat tolerance, while microbial inoculants, such as plant growth-promoting rhizobacteria (PGPR) and arbuscular mycorrhizal fungi (AMF), enhance nutrient uptake and stress tolerance through symbiotic interactions. However, biotechnological tools lead to the development of sorghum varieties with heat, drought and salinity tolerance, while marker-assisted selection significantly accelerates breeding for stress-resilient traits. When genetic engineering is introduced, genes encoding heat shock proteins, Osmo protectants and antioxidant pathways are introduced to increase plant resistance to abiotic stress. These compounds stabilise cellular structures, protect enzymes, and maintain osmotic balance, enhancing the plant's ability to survive and function in adverse environmental conditions. At the same time, it is reported that microbiology offers beneficial microbes, nitrogen-fixing bacteria, phosphate-solubilizing microorganisms, and arbuscular mycorrhizal fungi that help enhance nutrient availability, soil health and water uptake. Combinations of endophytes and microbial inoculants enhance plant immunity to pests and diseases while increasing tolerance to stress. Biocontrol agents such as Bacillus and Trichoderma contain suppression of pathogens and need less dependence on the use of chemical pesticides. On top of that, genetic modification increases the nutritional quality of sorghum biofortified. This is where biotechnology and microbiology work together to deliver sustainable farming systems reducing environmental impacts, boosting yields and securing food supply under environmental stresses. This review aims to examine the synergistic integration of plant biotechnology and microbial interactions as a strategy to enhance sorghum's resilience to climate-induced stresses, including drought, elevated temperatures, and nutrient-deficient soils. It highlights recent advancements in biotechnological tools such as gene editing, marker-assisted selection, and tissue culture, alongside the emerging role of plant-beneficial microbes in promoting stress tolerance and improving soil health. By synthesizing current knowledge across these disciplines, this review seeks to outline a framework for future research that harnesses the intersection of biotechnology and microbial ecology to support the sustainable improvement of sorghum resilience.},
}

@article {pmid40419768,
year = {2025},
author = {Keegstra, JM and Landry, ZC and Zweifel, ST and Roller, BRK and Baumgartner, DA and Carrara, F and Martínez-Pérez, C and Clerc, EE and Ackermann, M and Stocker, R},
title = {Risk-reward trade-off during carbon starvation generates dichotomy in motility endurance among marine bacteria.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40419768},
issn = {2058-5276},
support = {542395FY22//Simons Foundation/ ; 542379FY22//Simons Foundation/ ; GBMF9197//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 205321 207488//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 51NF40 225148//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; },
abstract = {Copiotrophic marine bacteria contribute to the control of carbon storage in the ocean by remineralizing organic matter. Motility presents copiotrophs with a risk-reward trade-off: it is highly beneficial in seeking out sparse nutrient hotspots, but energetically costly. Here we studied the motility endurance of 26 marine isolates, representing 18 species, using video microscopy and cell tracking over 2 days of carbon starvation. We found that the trade-off results in a dichotomy among marine bacteria, in which risk-averse copiotrophs ceased motility within hours ('limostatic'), whereas risk-prone copiotrophs converted ~9% of their biomass per day into energy to retain motility for the 2 days of observation ('limokinetic'). Using machine learning classifiers, we identified a genomic component associated with both strategies, sufficiently robust to predict the response of additional species with 86% accuracy. This dichotomy can help predict the prevalence of foraging strategies in marine microbes and inform models of ocean carbon cycles.},
}

@article {pmid40417422,
year = {2025},
author = {Roothans, N and Pabst, M and van Diemen, M and Herrera Mexicano, C and Zandvoort, M and Abeel, T and van Loosdrecht, MCM and Laureni, M},
title = {Long-term multi-meta-omics resolves the ecophysiological controls of seasonal N2O emissions during wastewater treatment.},
journal = {Nature water},
volume = {3},
number = {5},
pages = {590-604},
pmid = {40417422},
issn = {2731-6084},
abstract = {Nitrous oxide (N2O) is the third most important greenhouse gas and originates primarily from natural and engineered microbiomes. Effective emission mitigations are currently hindered by the largely unresolved ecophysiological controls of coexisting N2O-converting metabolisms in complex communities. To address this, we used biological wastewater treatment as a model ecosystem and combined long-term metagenome-resolved metaproteomics with ex situ kinetic and full-scale operational characterization over nearly 2 years. By leveraging the evidence independently obtained at multiple ecophysiological levels, from individual genetic potential to actual metabolism and emergent community phenotype, the cascade of environmental and operational triggers driving seasonal N2O emissions has ultimately been resolved. We identified nitrifier denitrification as the dominant N2O-producing pathway and dissolved O2 as the prime operational parameter, paving the way to the design and fostering of robust emission control strategies. This work exemplifies the untapped potential of multi-meta-omics in the mechanistic understanding and ecological engineering of microbiomes towards reducing anthropogenic impacts and advancing sustainable biotechnological developments.},
}

@article {pmid40413948,
year = {2025},
author = {Pholtaisong, J and Kongsinkaew, C and On-Mee, T and Chittapun, S and Pornpukdeewattana, S and Todhanakasem, T and Kunyanee, K and Panya, A and Phonsatta, N and Yingcharoen, P and Charoenrat, T},
title = {Natural versus Saccharomyces boulardii self-induced anaerobic coffee fermentation: Effects on physicochemical properties and microbial ecology, and their influence on volatile profiles and sensory attributes across roast levels.},
journal = {Food chemistry},
volume = {488},
number = {},
pages = {144871},
doi = {10.1016/j.foodchem.2025.144871},
pmid = {40413948},
issn = {1873-7072},
abstract = {This study investigates the effects of natural self-induced anaerobic fermentation (NSIAF) and Saccharomyces boulardii self-induced anaerobic fermentation (SSIAF) on Arabica coffee during wet processing. Over 24 h of fermentation, NSIAF exhibited greater microbial diversity, higher titratable acidity, and increased reducing sugar consumption, while SSIAF provided a more controlled microbial environment dominated by S. boulardii. Volatile compound analysis identified 207 compounds, with lighter roasts showing the greatest number of significantly different compounds between NSIAF and SSIAF treatments. Sensory evaluation revealed a higher cupping score for NSIAF at a light roast (82.08 ± 0.14) compared to SSIAF (81.58 ± 0.14), reflecting distinct flavor characteristics imparted by each fermentation process. Both methods achieved specialty coffee standards (≥80 points), highlighting the potential of NSIAF for complex and diverse profiles and the suitability of SSIAF for consistency and controlled fermentation.},
}

@article {pmid40413198,
year = {2025},
author = {Brandão Gontijo, J and Huang, L and Levintal, E and Prieto García, C and Erikson, CB and Coyotl, A and Horwath, WR and Dahlke, HE and Mazza Rodrigues, JL},
title = {Depth-dependent Metagenome-Assembled Genomes of Agricultural Soils under Managed Aquifer Recharge.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {858},
pmid = {40413198},
issn = {2052-4463},
support = {7975//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 2021-38420-34070//United States Department of Agriculture | National Institute of Food and Agriculture (NIFA)/ ; },
mesh = {*Soil Microbiology ; *Groundwater ; Agriculture ; *Metagenome ; Microbiota ; Bacteria/genetics/classification ; Metagenomics ; California ; Archaea/genetics ; Soil ; },
abstract = {Managed Aquifer Recharge (MAR) systems, which intentionally replenish groundwater aquifers with excess water, are critical for addressing water scarcity exacerbated by demographic shifts and climate variability. To date, little is known about the functional diversity of the soil microbiome at different soil depth inhabiting agricultural soils used for MAR. Knowing the functional diversity is pivotal in regulating nutrient cycling and maintaining soil health. Metagenomics, particularly Metagenome-Assembled Genomes (MAGs), provide a powerful tool to explore the diversity of uncultivated soil microbes, facilitating in-depth investigations into microbial functions. In a field experiment conducted in a California vineyard, we sequenced soil DNA before and after water application of MAR. Through this process, we assembled 146 medium and 14 high-quality MAGs, uncovering a wide array of archaeal and bacterial taxa across different soil depths. These findings advance our understanding of the microbial ecology and functional diversity of soils used for MAR, contributing to the development of more informed and sustainable land management strategies.},
}

*Soil Microbiology
*Groundwater
Agriculture
*Metagenome
Microbiota
Bacteria/genetics/classification
Metagenomics
California
Archaea/genetics
Soil

@article {pmid40412969,
year = {2025},
author = {Yan, W and Gu, L and Yue, X and Zhong, H and Wang, D},
title = {Vertical distribution of intracellular protoporphyrin IX in coastal sediment cores: Implications for sedimentology and microbial community composition.},
journal = {Journal of environmental sciences (China)},
volume = {156},
number = {},
pages = {712-724},
doi = {10.1016/j.jes.2024.11.014},
pmid = {40412969},
issn = {1001-0742},
mesh = {*Geologic Sediments/chemistry/microbiology ; *Protoporphyrins/analysis ; *Microbiota ; RNA, Ribosomal, 16S ; *Environmental Monitoring ; },
abstract = {Protoporphyrin IX (PPIX), a basic porphyrin system found in nature, all "porphyrin-type" tetrapyrroles with a biological function are biosynthetically derived thereof. PPIX is a metalloprosthetic group of numerous proteins involved in diverse metabolic and respiratory processes across all domains of life, and is thus considered essential for respiring organisms. Determining the biotic and abiotic factors that influence marine microbial growth and community structure is critical for understanding global biogeochemical cycles. Here, we present vertical profiles of intracellular PPIX and four derivative products (Chlorophyll-a/b and Pheophytin-a/b) from two coastal sediment cores, alongside ancillary geochemical and 16S rRNA microbial community data. Our findings indicated that PPIX is present in the natural sediment environment and displays a decreasing trend with depth, revealing a significant positive correlation with both organic matter and microbial abundance. Co-occurrence networks revealed that the environmental distribution of PPIX was positively correlated with the microbial porphyrin producer (high genetic completeness), but negatively correlated with auxotrophs (absence or low genetic completeness). It emphasized the critical role of PPIX as a biological molecule involved in key physiological processes. These results suggest that PPIX is a prominent component of the shared extracellular metabolite pool, especially in anoxic marine sediments where it exists at physiologically relevant concentrations for microbial metabolism. This study highlighted the significance of PPIX in microbial ecology and its potential impact on biogeochemical cycles in marine sedimentary environments.},
}

*Geologic Sediments/chemistry/microbiology
*Protoporphyrins/analysis
*Microbiota
RNA, Ribosomal, 16S
*Environmental Monitoring

@article {pmid40412391,
year = {2025},
author = {Breyer, E and Stix, C and Kilker, S and Roller, BRK and Panagou, F and Doebke, C and Amano, C and Saavedra, DEM and Coll-García, G and Steger-Mähnert, B and Dachs, J and Berrojalbiz, N and Vila-Costa, M and Sobrino, C and Fuentes-Lema, A and Berthiller, F and Polz, MF and Baltar, F},
title = {The contribution of pelagic fungi to ocean biomass.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.05.004},
pmid = {40412391},
issn = {1097-4172},
abstract = {Metagenomic analysis has recently unveiled the widespread presence of pelagic fungi in the global ocean, yet their quantitative contribution to carbon stocks remains elusive, hindering their incorporation into biogeochemical models. Here, we revealed the biomass of pelagic fungi in the open-ocean water column by combining ergosterol extraction, Calcofluor-White staining, catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH), and microfluidic mass sensor techniques. We compared fungal biomass with the biomass of other more studied microbial groups in the ocean such as archaea and bacteria. Globally, fungi contributed 0.32 Gt C (CI: 0.19-0.46), refining previous uncertainty estimates from two orders of magnitude to less than one. While fungal biomass was lower than that of bacteria, it exceeded that of the archaea (archaea:fungi:bacteria biomass ratio of 1:9:44). Collectively, our findings reveal the important contribution of fungi to open-ocean biomass and, consequently, the marine carbon cycle, emphasizing the need for their inclusion in biogeochemical models.},
}

@article {pmid40411587,
year = {2025},
author = {Kelleher, LA and Anderson, Z and Stratford, JA and Fortunato, CS},
title = {Deciphering Soil Microbial Dynamics in Northeastern American Grasslands with Goldenrods (Solidago sp.).},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {53},
pmid = {40411587},
issn = {1432-184X},
mesh = {*Soil Microbiology ; *Grassland ; Rhizosphere ; *Bacteria/classification/genetics/isolation & purification ; Soil/chemistry ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Pennsylvania ; *Solidago/microbiology ; Plant Roots/microbiology ; Biodiversity ; Hydrogen-Ion Concentration ; },
abstract = {Grasslands are important centers of biodiversity; however, these ecosystems have been in decline. Although many methods for grassland restoration have been developed, the abundant microbial communities in these regions are understudied and could be used to assist in these efforts. In this study, we aimed to understand how microbial communities varied by soil type, grassland site, and environmental conditions. Samples were taken from rhizosphere soil (attached to plant roots), proximal soil (close to the plant roots), and from bulk cores at Ricketts Glen State Park and Nescopeck State Park in northeastern Pennsylvania, USA, during June and August of 2021 and 2022. Rhizosphere soil samples were taken from the native common grassland plant, Solidago rugosa. 16S rRNA gene sequencing revealed that pH as well as soil type (bulk, proximal, or rhizosphere) significantly influenced the microbial community composition of each soil. Each soil type had its own distinct microbial communities, and proximal soil was identified as a transition zone between rhizosphere and bulk microbial communities. We also observed that the rhizosphere communities were dependent upon geography, as these communities were significantly different between grasslands even though the plant species remained the same. Our results highlight the complex nature of soil microbial communities and how many factors, including pH, soil type, and geography, can be overlayed to impact soil microbes. Results suggest future avenues of conservation research through modification and regulation of specific soil microbial communities in order to aid in the rehabilitation of these diminished regions.},
}

*Soil Microbiology
*Grassland
Rhizosphere
*Bacteria/classification/genetics/isolation & purification
Soil/chemistry
RNA, Ribosomal, 16S/genetics
*Microbiota
Pennsylvania
*Solidago/microbiology
Plant Roots/microbiology
Biodiversity
Hydrogen-Ion Concentration

@article {pmid40410028,
year = {2025},
author = {Vareschi, S and Jaut, V and Vijay, S and Allen, RJ and Schreiber, F},
title = {Antimicrobial efflux and biofilms: an interplay leading to emergent resistance evolution.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.04.012},
pmid = {40410028},
issn = {1878-4380},
abstract = {The biofilm mode of growth and drug efflux are both important factors that impede the treatment of bacterial infections with antimicrobials. Decades of work have uncovered the mechanisms involved in both efflux and biofilm-mediated antimicrobial tolerance, but links between these phenomena have only recently been discovered. Novel findings show how efflux impacts global cellular physiology and antibiotic tolerance, underpinned by phenotypic heterogeneity. In addition efflux can mediate cell-to-cell interactions, relevant in biofilms, via mechanisms including efflux of signaling molecules and metabolites, signaling using pump components and the establishment of local antibiotic gradients via pumping. These recent findings suggest that biofilm antibiotic tolerance and efflux are closely coupled, with synergistic effects leading to the evolution of antimicrobial resistance in the biofilm environment.},
}

@article {pmid40408931,
year = {2025},
author = {Conall Holohan, B and Trego, A and Keating, C and Bressani-Ribeiro, T and Chernicharo, CL and Daigger, G and Galdi, SM and Knörle, U and Paissoni, E and Robles, A and Rogalla, F and Shin, C and Soares, A and Smith, AL and Szczuka, A and Hughes, D and O'Flaherty, V},
title = {Anaerobic microbial core for municipal wastewater treatment - the sustainable platform for resource recovery.},
journal = {Current opinion in biotechnology},
volume = {94},
number = {},
pages = {103317},
doi = {10.1016/j.copbio.2025.103317},
pmid = {40408931},
issn = {1879-0429},
abstract = {The requirement for carbon neutrality and bioresource recovery has shifted our views on water treatment from health and pollution avoidance to one of sustainability with water and nutrient circularity. Despite progress, the current process of wastewater treatment is linear, based on core aerobic microbiology, which is unlikely to be carbon neutral due to its large use of energy and production of waste sludge. Here, we outline a shift from aerobic to anaerobic microbiology at the core of wastewater treatment and resource recovery, illustrating the state-of-the-art technologies available for this paradigm shift. Anaerobic metabolism primarily offers the benefit of minimal energy input (up to 50% reduction) and minimal biomass production, resulting in up to 95% less waste sludge compared with aerobic treatment, which is increasingly attractive, given dialogue surrounding emerging contaminants in biosolids. Recent innovative research solutions have made ambient (mainstream) anaerobic treatment a ready substitute for the aerobic processes for municipal wastewater in temperate regions. Moreover, utilising anaerobic treatment as the core carbon removal step allows for more biological downstream resource recovery with several opportunities to couple the process with (anaerobic) nitrogen and phosphorus recovery, namely, potential mainstream anaerobic ammonium oxidation (anammox) and methane oxidation (N-DAMO). Furthermore, these technologies can be mixed and matched with membranes and ion-exchange systems, high-value biochemical production, and/or water reuse installations. As such, we propose the reconfiguration of the wastewater treatment plant of the futurewith anaerobic microbiology. Mainstream anaerobic treatment at the core of a truly sustainable platform for modern municipal wastewater treatment, facilitating circular economy and net-zero carbon goals.},
}

@article {pmid40408805,
year = {2025},
author = {Bi, W and Butardo, V and Sha, G and Zhang, H and Wu, X and Wang, L},
title = {Microbial degradation and pollutant control in aerobic composting and anaerobic digestion of organic wastes: A review.},
journal = {Waste management (New York, N.Y.)},
volume = {204},
number = {},
pages = {114894},
doi = {10.1016/j.wasman.2025.114894},
pmid = {40408805},
issn = {1879-2456},
abstract = {Aerobic composting (AC) and anaerobic digestion (AD) are promising technologies for organic waste treatment, but their efficiency and safety are influenced by complex waste composition and persistent contaminants. This review identifies the advances in understanding microbial community dynamics, enzymatic degradation pathways, and the fate of contaminants during AC and AD processes. The findings indicate that substrate composition shapes dominant microbial populations and their degradative enzymes, with this correlation potentially useful for predicting functional microbial communities. Additionally, AC shows advantages in antibiotic elimination while AD excels in heavy metal immobilization, with both contributing to removing certain antibiotic resistance genes (ARGs). The strategic manipulation of environmental conditions, particularly temperature and oxygen levels, can drive microbial succession to optimize organic matter decomposition while minimizing ARG proliferation. Economic analyses reveal that AC offers lower operational costs and AD generates valuable by-products with potential energy recovery from organic waste. Case studies indicate that integrating both technologies can overcome individual limitations and enhance degradation efficiency compared to conventional single-technology approaches. This work proposes a comprehensive framework for developing coupled AC-AD systems to achieve more efficient and safer organic waste valorization than conventional single-technology approaches. This review has important implications for advancing sustainable waste management practices and mitigating the spread of antibiotic resistance in the environment.},
}

@article {pmid40408146,
year = {2025},
author = {Fontanarrosa, P and Clare, C and Fedorec, AJH and Barnes, CP},
title = {MIMIC: A Python Package for Simulating, Inferring, and Predicting Microbial Community Interactions and Dynamics.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf174},
pmid = {40408146},
issn = {1367-4811},
abstract = {SUMMARY: The study of microbial communities is vital for understanding their impact on environmental, health, and technological domains. The Modelling and Inference of MICrobiomes Project (MIMIC) introduces a Python package designed to advance the simulation, inference, and prediction of microbial community interactions and dynamics. Addressing the complex nature of microbial ecosystems, MIMIC integrates a suite of mathematical models, including previously used approaches such as Generalized Lotka-Volterra (gLV), Gaussian Processes (GP), and Vector Autoregression (VAR) plus newly developed models for integrating multi-omic data, to offer a versatile framework for analysing microbial dynamics. By leveraging Bayesian inference and machine learning techniques, MIMIC provides the ability to infer the dynamics of microbial communities from empirical data, facilitating a deeper understanding of their complex biological processes, unveiling possible unknown ecological interactions, and enabling the design of microbial communities. Such insights could help to advance microbial ecology research, optimizing biotechnological applications, and contribute to environmental sustainability and public health strategies. MIMIC is designed for flexibility and ease of use, aiming to support researchers and practitioners in microbial ecology and microbiome research.

MIMIC is freely available under the MIT License at https://github.com/ucl-cssb/MIMIC. It is implemented in Python (version 3.7 or higher) and is compatible with Windows, macOS, and Linux operating systems. MIMIC depends on standard Python libraries including NumPy, SciPy, and PyMC. Comprehensive examples and tutorials (including the main text demonstrations) are provided as Jupyter notebooks in the examples/directory and at the MIMIC Docs website, along with detailed installation instructions and real-world data use cases. The software will remain freely available for at least two years following publication. A code snapshot for this publication is also available at Zenodo: https://doi.org/10.5281/zenodo.15149003.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}

@article {pmid40407874,
year = {2025},
author = {Velthuis, M and Zoccarato, L and Veraart, AJ and Monaghan, MT and Funke, E and Verdonschot, P and Grossart, HP and Hilt, S},
title = {Light-Driven Changes in Macrophyte Tissue Quality Affect the Composition of Associated Microbial Communities.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {52},
pmid = {40407874},
issn = {1432-184X},
support = {Veni.202.053//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; },
mesh = {Biofilms/growth & development/radiation effects ; *Fungi/classification/genetics/radiation effects/isolation & purification ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Microbiota/radiation effects ; *Light ; *Hydrocharitaceae/microbiology/radiation effects/chemistry/metabolism ; Nitrogen/metabolism/analysis ; Carbon/metabolism/analysis ; Phosphorus/metabolism/analysis ; Biodiversity ; Plant Leaves/microbiology ; Phenols/analysis/metabolism ; },
abstract = {Microbial biofilms are important components in macrophyte decomposition, and their composition depends on the decomposition stage and host plant quality. Here, we investigated how macrophyte tissue quality (i.e., C:N:P stoichiometry and phenolic contents) influences epiphytic microbial biofilms during litter decomposition. Consecutive experiments were conducted to (1) modify the C:N:P stoichiometry and phenolic content of the freshwater macrophyte Elodea nuttallii by manipulating light and nutrient availability and (2) test how the modified tissue quality affected epiphytic microbial biofilm diversity and community composition before and during macrophyte decomposition. Our results showed that shading led to lower C:N ratios (28.6 to 12.6) and higher phenolic content (10.8 to 19.2 µg/mg dry weight). Simultaneously, shading affected the epiphytic bacterial and fungal community composition, and these shifts correlated with the macrophyte C:N ratio. While no effects of macrophyte tissue quality on decomposition rates were observed, the epiphytic bacterial community composition on the litter was significantly affected by light treatment, time, and their interaction. Bacterial community composition shifted from a high abundance of Comamonadaceae to a more diverse community over time. Overall bacterial diversity was lower on the litter grown in the shaded mesocosms. Fungal diversity and community composition during litter decomposition were not affected by litter quality. Overall, our results reveal a structuring role of macrophyte tissue quality on its associated microbial biofilm and uniquely show a continuation of light-driven changes in epiphytic bacterial community composition after exposure. We conclude that light-driven changes in C:N stoichiometry are a crucial factor in shaping epiphytic microbial communities during macrophyte decomposition.},
}

Biofilms/growth & development/radiation effects
*Fungi/classification/genetics/radiation effects/isolation & purification
*Bacteria/classification/genetics/isolation & purification/metabolism
*Microbiota/radiation effects
*Light
*Hydrocharitaceae/microbiology/radiation effects/chemistry/metabolism
Nitrogen/metabolism/analysis
Carbon/metabolism/analysis
Phosphorus/metabolism/analysis
Biodiversity
Plant Leaves/microbiology
Phenols/analysis/metabolism

@article {pmid40407873,
year = {2025},
author = {Van Heurck, B and Cardenas, DV and Hylén, A and Jankowska, E and Cole, DB and Montserrat, F and Kreuzburg, M and Romaniello, SJ and Meysman, FJR},
title = {Microbial Community Structure in Contrasting Hawaiian Coastal Sediments.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {51},
pmid = {40407873},
issn = {1432-184X},
mesh = {*Geologic Sediments/microbiology/chemistry ; Hawaii ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation & purification ; *Seawater/microbiology/chemistry ; Bays/microbiology/chemistry ; Biodiversity ; },
abstract = {Microbe-mineral interactions play a fundamental role in marine sediments and global biogeochemical cycles. Here, we investigated the sediment microbial communities in two contrasting field sites on Big Island, Hawaii (USA), that differ in their bay morphology and sediment grain size distributions: Papakōlea Beach (exposed, finer sediment) and Richardson Ocean Park (sheltered, coarser sediment). We selected three stations within each bay and characterized the mineral and chemical composition of the sediment and porewater, and used 16S rRNA amplicon sequencing of the V4V5 hypervariable region to investigate the naturally occurring microbial communities. Microbial community structure differed significantly between the two bays, rather than within each bay, whereby microbial diversity was markedly lower at Papakōlea compared to Richardson. We correlated environmental variables to microbial community structure in order to identify the key drivers of community differences between and within the two bays. Our study suggests that differing physico-chemical properties of the sediment and porewater, resulting from the contrasting bay morphologies and geophysical drivers, are the main factors influencing microbial community structure in these two bays. Papakōlea Beach is a naturally occurring "green sand" beach, due to its high olivine content. This site was selected in the broader context of a field campaign investigating olivine as a source mineral for ocean alkalinity enhancement (OAE), a carbon dioxide removal technology. Our results highlight the complexity of marine sediment environments, with implications for the monitoring, reporting and verification of future field trials involving olivine addition for ocean alkalinity enhancement.},
}

*Geologic Sediments/microbiology/chemistry
Hawaii
*Microbiota
RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/isolation & purification
*Seawater/microbiology/chemistry
Bays/microbiology/chemistry
Biodiversity

@article {pmid40406230,
year = {2025},
author = {Li, M and Meng, Z and Li, J and Zhang, X and Wang, Y and Li, X and Yang, Y and Li, Y and Yang, X and Chen, X and Fan, Y},
title = {Stochastic processes dominate the community assembly of ectomycorrhizal fungi associated with Betula platyphylla in Inner Mongolia, China.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19364},
pmid = {40406230},
issn = {2167-8359},
mesh = {*Mycorrhizae/genetics/classification/isolation & purification ; China ; *Soil Microbiology ; *Betula/microbiology ; Stochastic Processes ; Biodiversity ; Rhizosphere ; DNA, Fungal/genetics ; Mycobiome ; },
abstract = {The maintenance and driving mechanisms of microbial community structure have become important research focuses in microbial ecology. Therefore, clarifying the assembly of ectomycorrhizal (EM) fungal communities can provide a relevant basis for studying forest diversity, ecological diversity, and ecological evolution. Betula platyphylla is a typical EM dependent tree species with characteristics such as renewal ability and strong competitive adaptability, and it plays a crucial ecological function in Inner Mongolia. However, the research on EM fungi's diversity and community assembly is very limited. We investigated EM fungal communities associated with B. platyphylla from 15 rhizosphere soil samples across five sites in Inner Mongolia. The fungal rDNA ITS2 region was sequenced using Illumina Miseq sequencing. A total of 295 EM fungal OTUs belonging to two phyla, three classes, nine orders, 20 families, and 31 genera were identified, of which Russula, Cortinarius, and Sebacina were the most dominant taxa. Significant differences existed in the composition of dominant genera of EM fungi across the five sites, and the relative abundances of dominant genera also showed significant differences among the sites. The β NTI and NCM fitting analyses suggest that stochastic processes mainly determine the EM fungal community assembly. Our study indicates that B. platyphylla harbors a high EM fungal diversity and highlights the important role of the stochastic process in driving community assembly of mutualistic fungi associated with B. platyphylla in north China.},
}

*Mycorrhizae/genetics/classification/isolation & purification
China
*Soil Microbiology
*Betula/microbiology
Stochastic Processes
Biodiversity
Rhizosphere
DNA, Fungal/genetics
Mycobiome

@article {pmid40405772,
year = {2025},
author = {Onghena, L and Heldens, A and De Paepe, K and Antwi, M and Van Vlierberghe, H and Raevens, S and Verhelst, X and Hoorens, A and Devisscher, L and van Nieuwenhove, Y and Van de Wiele, T and Geerts, A and Lefere, S},
title = {The double-edged sword of metabolic and bariatric surgery: extending the biliary limb can trigger bacterial translocation, sepsis, and liver inflammation - an experimental study.},
journal = {International journal of surgery (London, England)},
volume = {},
number = {},
pages = {},
doi = {10.1097/JS9.0000000000002502},
pmid = {40405772},
issn = {1743-9159},
abstract = {BACKGROUND: Metabolic and bariatric surgery (MBS) procedures with extended biliary limb length are gaining popularity to expedite weight loss but can induce liver failure. We aimed to investigate the underlying pathophysiology for this potentially fatal complication.

MATERIALS AND METHODS: We compared mouse models of vertical sleeve plication, sleeve gastrectomy, Roux-en-Y gastric bypass (RYGB), and one-anastomosis gastric bypass with three biliary limb lengths (25% = Ω1, 50% = Ω2, 75% = Ω3) by analyzing mortality, weight loss, metabolic and liver health, bacterial translocation, inflammation, and biliary and fecal microbiome. Gut decontamination with oral antibiotics (amoxicillin, vancomycin, neomycin, and metronidazole) was performed in a subset of Ω3 mice. Liver histology from mice with different biliary limb lengths was compared to samples from human patients who developed liver failure following biliopancreatic diversion or RYGB.

RESULTS: RYGB and Ω1&2 significantly improved glucose intolerance and liver steatosis compared to sham surgery. However, extending the biliary limb (Ω3) resulted in 100% mortality. The Ω3 procedure induced bacterial translocation of enterococcus genus to the spleen and biliary fluid, consistent with increased serum lipopolysaccharide levels and terminal ileum, biliary limb, and hepatic inflammation. Liver histology in Ω3 mice was characterized by mediovesicular steatosis, closely resembling the histological picture observed in patients with liver failure after MBS. Oral gut decontamination significantly improved Ω3 one-week-survival from 31.3% to 80.0%, prevented bacterial overgrowth in biliary fluid and spleen, and decreased liver damage.

CONCLUSION: Mortality in longer biliary limb MBS surgery is caused by bacterial overgrowth, translocation, and gut-liver axis inflammation, which were reversed by oral gut decontamination with antibiotics.},
}

@article {pmid40405300,
year = {2025},
author = {He, T and Moukarzel, R and Fu, M and Yang, M and Du, R and Zhao, J and Liu, J and Wu, J and Deng, W and Zhu, Y and Yang, M and Zhu, S and Du, F},
title = {Rain-shelter cultivation promotes grapevine health by altering phyllosphere microecology in rainy areas.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {56},
pmid = {40405300},
issn = {2524-6372},
support = {32360712//National Natural Science Foundation of China/ ; 32360712//National Natural Science Foundation of China/ ; 32360712//National Natural Science Foundation of China/ ; 32360712//National Natural Science Foundation of China/ ; 32360712//National Natural Science Foundation of China/ ; 32360712//National Natural Science Foundation of China/ ; 32360712//National Natural Science Foundation of China/ ; 32360712//National Natural Science Foundation of China/ ; 202101BD070001-125//Yunnan Province Agricultural Joint Special Project/ ; 202101BD070001-125//Yunnan Province Agricultural Joint Special Project/ ; 202101BD070001-125//Yunnan Province Agricultural Joint Special Project/ ; 202101BD070001-125//Yunnan Province Agricultural Joint Special Project/ ; 202101BD070001-125//Yunnan Province Agricultural Joint Special Project/ ; 202101BD070001-125//Yunnan Province Agricultural Joint Special Project/ ; 202101BD070001-125//Yunnan Province Agricultural Joint Special Project/ ; 202101BD070001-125//Yunnan Province Agricultural Joint Special Project/ ; 202101BD070001-125//Yunnan Province Agricultural Joint Special Project/ ; 2018HA009//Yunnan Provincial Academician Exploration Funding Project/ ; },
abstract = {Grapes are a globally significant fruit crop, but their cultivation is often challenged by leaf diseases, which limit industrial productivity. Rain-shelter cultivation has emerged as a sustainable agricultural strategy to mitigate these challenges. This study examines the effects of rain-shelter cultivation, compared to open-air cultivation, on the microclimate within the grape canopy and the microbial ecology of the grape phyllosphere. The research focused on two cultivation methods: rain-shelter and open-air cultivation. Key environmental factors such as temperature, relative humidity, and light intensity within the grape canopy were measured during the growing season. The study also explored how these conditions influence the biodiversity, stability, and functional roles of phyllosphere microbiota, particularly focusing on the community assembly processes of bacteria and oomycetes, and the efficacy of culturable microorganisms in combating grape leaf diseases. The results showed that rain-shelter cultivation signifcantly reduced leaf humidity, increased canopy temperature, and decreased light intensity, regardless of weather conditions. This approach led to a significant decrease in the incidence of grape downy mildew without affecting the overall Shannon diversity index of phyllosphere microbes. At the Class level, there was a reduction in Cystobasidiomycetes, Bacteroidia, Brocadiae, and Phycisphaerae, while Oligoflexia levels are significantly increased under rain-shelter conditions. Genus-level analysis revealed significant reductions in plant pathogens such as Erysiphe, Alternaria, and Cercospora. The study found that rain-shelter cultivation shifts fungal community assembly from stochastic to deterministic processes, while bacterial networks showed increased stability. Additionally, the beneficial microorganism Pseudomonas aeruginosa exhibited a preventive effect against grape leaf diseases, enhancing grape berry quality by increasing puncture resistance and leaf internode length. These findings provide understanding of the complex relationship between grape canopy microclimate, disease management, and microbial dynamics suggesting rain-shelter cultivation as a viable strategy for sustainable grape production, it offers insights into the research and development of future biological control agents.},
}

@article {pmid40404904,
year = {2025},
author = {Scheelings, TF and Kodikara, S and Beale, DJ and Van, TTH and Moore, RJ and Skerratt, LF},
title = {Pondering Ponds: Exploring Correlations Between Cloacal Microbiota and Blood Metabolome in Freshwater Turtles.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {50},
pmid = {40404904},
issn = {1432-184X},
mesh = {Animals ; *Turtles/microbiology/blood ; *Metabolome ; *Bacteria/classification/genetics/isolation & purification/metabolism ; RNA, Ribosomal, 16S/genetics ; *Cloaca/microbiology ; *Ponds/microbiology ; *Microbiota ; Gastrointestinal Microbiome ; Fresh Water ; },
abstract = {The gut microbiota of vertebrates significantly influences host physiology, yet little is known about how habitat factors shape microbiotas in non-human species, especially freshwater turtles. This study explores the relationship between cloacal microbiota and serum metabolome in eastern longneck turtles (Chelodina longicollis), marking the first such investigation in chelonians. By comparing microbiotas from two distinct pond environments, we applied a multi-omics approach combining 16S rRNA sequencing and metabolomic profiling. Results showed that location influenced microbial composition and metabolic profiles, with dominant bacterial phyla Pseudomonadota, Actinomycetota, and Bacillota, and distinct families linked to differences in microbial diversity. Notably, turtles from one pond displayed an unusually high proportion of Actinomycetota. We also found a clear connection between microbiota diversity and metabolome, suggesting certain bacterial combinations impact host physiology. These findings offer important insights into the complex interaction between microbial communities and metabolism in freshwater turtles, a highly threatened group. This research emphasises the value of integrating microbiota and metabolomic data in conservation strategies and highlights the need for further longitudinal studies to explore the dynamic host-microbiota relationship in these understudied species.},
}

Animals
*Turtles/microbiology/blood
*Metabolome
*Bacteria/classification/genetics/isolation & purification/metabolism
RNA, Ribosomal, 16S/genetics
*Cloaca/microbiology
*Ponds/microbiology
*Microbiota
Gastrointestinal Microbiome
Fresh Water

@article {pmid40402470,
year = {2025},
author = {Moukarzel, R and Waller, LP and Jones, EE and Ridgway, HJ},
title = {Arbuscular mycorrhizal fungal symbiosis in New Zealand ecosystems: challenges and opportunities.},
journal = {Letters in applied microbiology},
volume = {78},
number = {5},
pages = {},
doi = {10.1093/lambio/ovaf070},
pmid = {40402470},
issn = {1472-765X},
mesh = {*Mycorrhizae/physiology/genetics/classification ; New Zealand ; *Symbiosis ; *Ecosystem ; *Plants/microbiology ; Soil Microbiology ; },
abstract = {Arbuscular mycorrhizal fungi (AMF) are obligate biotrophs that form a symbiotic and mutualistic relationship with most terrestrial plants, playing an important role in plant growth, nutrient acquisition, and ecosystem stability. This review synthesizes current knowledge on AMF colonization in plants within New Zealand ecosystems, including the challenges and opportunities of molecular identification techniques used in characterizing AMF communities in natural and managed systems. The ecosystem services provided by AMF, such as improved growth parameters, enhanced nutrition, and disease control, are discussed in detail, highlighting their significance in sustainable agriculture and natural ecosystems. Additionally, the role of AMF in invasion ecology was examined, revealing their dual potential to either facilitate or hinder invasive plant species. Despite significant advances in understanding AMF biology, future research is needed to explore the underlying mechanisms of AMF-plant interactions and to address the challenges caused by changing environmental conditions. This review focused on the importance of AMF in promoting ecosystem resilience and suggests avenues for future research to harness their full potential in agricultural and ecological contexts.},
}

*Mycorrhizae/physiology/genetics/classification
New Zealand
*Symbiosis
*Ecosystem
*Plants/microbiology
Soil Microbiology

@article {pmid40402324,
year = {2025},
author = {Mizeriene, G and Lygis, V and Prospero, S},
title = {Oomycete Diversity and Ecology in Declining Alder Stands in Switzerland.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {49},
pmid = {40402324},
issn = {1432-184X},
support = {Project Code 14.035//Sciex-NMSch Fellowship/ ; },
mesh = {Switzerland ; *Alnus/microbiology/parasitology ; *Oomycetes/classification/isolation & purification/genetics ; *Biodiversity ; *Soil Microbiology ; Plant Diseases/microbiology ; Rhizosphere ; Phytophthora/isolation & purification/classification/genetics ; Phylogeny ; Pythium/isolation & purification/genetics/classification ; },
abstract = {In this study, we assessed the occurrence and diversity of four oomycete genera (Phytophthora, Phytopythium, Pythium, and Globisporangium) in 13 declining alder (Alnus glutinosa and A. incana) stands in Switzerland. For this, we sampled and analyzed soil from tree rhizosphere, water from streams and rivers along which the stands were located, and symptomatic alder bark. The overall isolation rate was 47.2%, with a total of 400 oomycete isolates recovered at all 13 sites. The highest incidence of oomycete isolates was in soil samples (baiting, 82.5% isolation rate), followed by water (baiting, 14.7%), and bark (direct isolation, 2.7%). Of all recovered oomycete isolates, 90.3% could be successfully assigned to a known species, for a total of 23 species identified, including both preferential saprotrophs and pathogens. Among all genera, Phytophthora was the most abundant with 273 isolates (75.6%), followed by Phytopythium, Pythium, and Globisporangium. Oomycete species diversity showed a significant variation among substrates. Only one species-Phytophthora lacustris-was abundant in all substrates, while 16 species were restricted to a specific substrate, mainly soil. The rhizosphere of symptomatic alder trees harbored the most diverse oomycete community, highlighting once again the importance of soil as a reservoir for these microorganisms. Only two Phytophthora species were isolated from alder bark lesions, namely, P. × alni, the known causal agent of alder decline, and P. lacustris. The low recovery rate of P. × alni might be due to attempts to isolate it from old, inactive lesions, but may also suggest that alder decline might be caused by other oomycetes infecting the root system of the trees.},
}

Switzerland
*Alnus/microbiology/parasitology
*Oomycetes/classification/isolation & purification/genetics
*Biodiversity
*Soil Microbiology
Plant Diseases/microbiology
Rhizosphere
Phytophthora/isolation & purification/classification/genetics
Phylogeny
Pythium/isolation & purification/genetics/classification

@article {pmid40402315,
year = {2025},
author = {Mitchell, JK and Matthee, S and Ndhlovu, A and Miller, M and Buss, P and Matthee, CA},
title = {The Microbiome and Coxiella Diversity Found in Amblyomma hebraeum and Dermacentor rhinocerinus Ticks Sampled from White Rhinoceros.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {48},
pmid = {40402315},
issn = {1432-184X},
mesh = {Animals ; *Microbiota ; *Perissodactyla/parasitology/microbiology ; *Amblyomma/microbiology ; *Coxiella/genetics/classification/isolation & purification ; *Dermacentor/microbiology ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; South Africa ; Coxiella burnetii/genetics/isolation & purification ; DNA, Bacterial/genetics ; Bacteria/classification/genetics/isolation & purification ; Female ; Male ; },
abstract = {The microbiome and the prevalence of the pathogenic bacterium Coxiella burnetii in ticks associated with white rhinoceros, Ceratotherium simum, is unknown. Targeted Illumina 16S rRNA amplicon sequencing was used to characterize the bacterial microbiome diversity found within 40 Amblyomma hebraeum and 40 Dermacentor rhinocerinus ticks collected from 40 white rhinoceros individuals in the Kruger National Park, South Africa. Specific emphasis was also given to further investigate the prevalence of the pathogenic C. burnetti in these tick species. At the phylum level, Proteobacteria dominated both tick microbiomes, followed by Actinobacteria and Firmicutes; Coxiella was the most abundant genus within A. hebraeum and Rickettsia within D. rhinocerinus. While alpha diversity did not differ significantly between the two tick species, beta diversity revealed significant species-specific differences in bacterial community composition. Additionally, there was no correlation between sampling region and microbiome diversity or composition for either tick species. Twenty-five Coxiella amplicon sequence variants (ASVs) were identified, forming three distinct monophyletic Coxiella clades and a fourth single ASV lineage. The Coxiella clades showed a correlation to tick species identity with D. rhinocerinus harboring significantly greater Coxiella diversity than A. hebraeum-potentially indicative of different coevolutionary pathways between the bacteria and their respective hosts. PCR of the IS1111 transposase gene for 238 ticks detected a 66.1% (56.7-74.4%) prevalence for C. burnetii in D. rhinocerinus compared to 55.8% in A. hebraeum (46.5-64.8%). These findings support a notion that each tick species is characterized by its own microbiome community composition and that both A. hebraeum and D. rhinocerinus may act as reservoirs and potential vectors of C. burnetii to white rhinoceros.},
}

Animals
*Microbiota
*Perissodactyla/parasitology/microbiology
*Amblyomma/microbiology
*Coxiella/genetics/classification/isolation & purification
*Dermacentor/microbiology
RNA, Ribosomal, 16S/genetics
Phylogeny
South Africa
Coxiella burnetii/genetics/isolation & purification
DNA, Bacterial/genetics
Bacteria/classification/genetics/isolation & purification
Female
Male

@article {pmid40402178,
year = {2025},
author = {Salazar, J and González, J and Riofrío, R and Siavichay, F and Carrera, M and Mogrovejo, A and Barrera-Galicia, G and Valdez-Tenezaca, A},
title = {MALDI-TOF Mass Spectrometry Characterization of Culturable Microbiota Associated with the Skin of Amphibians from the Southern Andes Mountains of Ecuador.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {47},
pmid = {40402178},
issn = {1432-184X},
support = {PICCIITT19-11//Universidad Católica de Cuenca/ ; PICCIITT19-11//Universidad Católica de Cuenca/ ; PICCIITT19-11//Universidad Católica de Cuenca/ ; },
mesh = {Ecuador ; Animals ; *Skin/microbiology ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; *Microbiota ; *Bacteria/classification/isolation & purification/genetics ; *Fungi/classification/isolation & purification/genetics ; *Anura/microbiology ; Biodiversity ; },
abstract = {Ecuador is recognized for having a high diversity of anuran species, which are distributed mainly south of the Andes mountains. However, due to their geographic location and accessibility, there are few studies related to the culturable microbiota of these amphibians in this region. The objective of this study was to explore the bacterial and fungal biodiversity present on the skin of wild anuran species in the southern Andes of Ecuador and to observe whether geographical barriers in the region could increase the variability of the culturable microbiota through MALDI-TOF mass spectrometry. This analysis revealed the presence of 29 bacterial taxa and 9 fungal taxa, consisting mainly of: Pseudomonas chlororaphis (28%), Acinetobacter iwoffii (14%), Pseudomonas fluorescens (14%), and Hortaea werneckii (26.4%), Fusarium solani (20.5%), Syncephalastrum spp. (20.5%), respectively. Diversity varied across the five sampling locations, with geographic location proving to be a significant driver of diversity. Some of the most abundant bacterial and fungal genera have important associations with skin diseases in wildlife and humans. This work represents a glimpse into the complex biodiversity of bacteria and fungi that inhabit the skin substrate, and further studies will be needed to better understand bacterial and fungal biodiversity with potential implications for establishing conservation strategies, along with the development of necessary animal protection measures.},
}

Ecuador
Animals
*Skin/microbiology
Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
*Microbiota
*Bacteria/classification/isolation & purification/genetics
*Fungi/classification/isolation & purification/genetics
*Anura/microbiology
Biodiversity

@article {pmid40401940,
year = {2025},
author = {Nieves-Morales, R and Paez-Diaz, JA and Rivera-Lopez, EO and Pérez-Santos, N and Borrero-Villabol, SJ and Rodríguez-Ramos, J and Nieves-Rivera, AM and Rios-Velazquez, C},
title = {Characterization of fungal communities in Puerto Rican caves using internal transcribed spacer sequencing.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0002225},
doi = {10.1128/mra.00022-25},
pmid = {40401940},
issn = {2576-098X},
abstract = {Cave ecosystems harbor unique and diverse microbial ecology, with fungal communities playing important roles. This study utilizes internal transcribed spacer across seven caves in the northern limestone karst belt area of Puerto Rico to investigate fungal composition. This enhances scientific understanding of subterranean microbial dynamics and supports conservation efforts.},
}