@article {pmid41313007,
year = {2025},
author = {Fletcher, JR and Hansen, LA and Hoyser, JR and Hanna, AE and Martinez, R and Freeman, CD and Thorns, NT and Penningroth, MR and Villarreal, AR and Vogt, GA and Tyler, MA and Hines, KM and Hunter, RC},
title = {Commensal-derived short-chain fatty acids disrupt lipid membrane homeostasis in Staphylococcus aureus.},
journal = {mBio},
volume = {},
number = {},
pages = {e0139225},
doi = {10.1128/mbio.01392-25},
pmid = {41313007},
issn = {2150-7511},
abstract = {The role of commensal anaerobic bacteria in chronic respiratory infections is unclear, yet they can exist in abundances comparable to canonical pathogens in vivo. Their contributions to the metabolic landscape of the host environment may influence pathogen behavior by competing for nutrients and creating inhospitable conditions via toxic metabolites. Here, we show that the anaerobe-derived short-chain fatty acids (SCFAs) propionate and butyrate negatively affect Staphylococcus aureus physiology by disrupting branched-chain fatty acid (BCFA) metabolism. In turn, alterations to BCFA abundance impair S. aureus growth, compromise membrane integrity, diminish expression of the accessory gene regulator quorum-sensing system, and increase sensitivity to membrane-targeting antimicrobials. Disrupted BCFA metabolism also reduced S. aureus fitness in competition with Pseudomonas aeruginosa, suggesting that airway microbiome composition and the metabolites they exchange can directly impact pathogen succession over time. The pleiotropic effects of SCFAs on S. aureus fitness and their ubiquity as metabolites in the human host also suggest that they may be effective as adjuvants to traditional antimicrobial agents when used in combination.IMPORTANCEStaphylococcus aureus is a primary pathogen of chronic airway disease yet is also found in the upper airways of 30%-50% of the population to no obvious detriment. Thus, identifying the host and/or microbial factors that tip the balance between its commensal and pathogenic states may be key to its control. Here, we reveal that short-chain fatty acids produced by commensal microbiota promote a marked remodeling of the S. aureus lipid membrane that, in turn, sensitizes the pathogen to antimicrobials, disrupts accessory gene regulator quorum signaling, and reduces its competitive fitness. Altogether, these data suggest that co-colonizing microbiota and the metabolites they exchange with S. aureus may be key players in the microbial ecology of airway disease.},
}

@article {pmid41311479,
year = {2025},
author = {Gao, Y and Zhang, L and Zhang, Y and Huang, J and Wu, C and Zhou, R},
title = {Synthetic microbial community SMC-L1 optimizes flavor chemistry in reduced salt soy sauce via targeted metabolic reprogramming.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1701479},
pmid = {41311479},
issn = {1664-302X},
abstract = {The high sodium content in traditional soy sauce presents significant public health concerns, particularly related to hypertension and cardiovascular diseases. However, reducing salt content often disrupts microbial ecology and impairs flavor formation during fermentation. To overcome this challenge, we developed synthetic microbial communities (SynMCs) for reduced-salt (13% NaCl) moromi fermentation under traditional sun-brewing conditions. Using integrated multi-omics analyses, we identified an optimal consortium (SMC-L1) incorporating Tetragenococcus halophilus T10 as a key lactic acid bacterium alongside functional yeast strains. This defined community maintained fermentation stability while significantly enhancing flavor-relevant biochemical profiles. SMC-L1 inoculation markedly improved key quality parameters, increasing total nitrogen by 40.8% and amino acid nitrogen by 56.7%. Furthermore, it elevated critical metabolites including organic acids, particularly succinate, free amino acids, and short-chain esters. Network analysis revealed robust ecology-metabolite relationships: Tetragenococcus abundance correlated with succinate production and ester synthesis, while Aspergillus dynamics corresponded with free amino acid accumulation. These findings highlight how targeted microbial consortia can reprogram metabolic networks under salt-reduced conditions. From a food microbiology perspective, this study demonstrates that rational design of microbial communities can effectively decouple salt reduction from flavor deterioration in fermented foods. The metabolic pathways observed, particularly the anaerobic TCA cycle activity connecting Tetragenococcus to succinate accumulation, provides mechanistic insights into microbial adaptation to reduced-salt environments. This approach offers a viable strategy for developing healthier fermented products without compromising their sensory characteristics, advancing both fundamental knowledge and practical applications in food biotechnology.},
}

@article {pmid41307726,
year = {2025},
author = {Ferreira, CM and de Affonseca, DB and Barbosa, FAS and Campos, AB and Menezes, R and Brait, L and Viana, PAB and Trindade-Silva, AE and Loiola, M and Azevedo, AR and Coutinho, FH and Assis, APA and Bruce, T and Ramos, PIP and Ara, A and Brouns, R and Andrade, RFS and Guimarães, PR and Meirelles, PM},
title = {Rare Phyla, Such as CPR and DPANN, Shape Ecosystem-Level Microbial Community Structure Dissimilarities.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {135},
pmid = {41307726},
issn = {1432-184X},
support = {88887-468244-2019-00//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 114693/2022-6//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; RYC2022-037094-I//Ministerio de Ciencia e Innovación/ ; Serra-1709-17818//Instituto Serrapilheira/ ; },
mesh = {*Bacteria/classification/genetics/isolation & purification ; *Archaea/classification/genetics/isolation & purification ; *Microbiota ; *Ecosystem ; Metagenome ; Biodiversity ; Phylogeny ; Soil Microbiology ; },
abstract = {Rare microbial lineages, such as members of the candidate phyla radiation (CPR) bacteria and Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) archaea, are increasingly recognized as key components of microbial communities in natural systems. Yet, their global distribution, biogeographic patterns, and broader role in shaping microbial community structure across diverse ecosystems remain poorly characterized. Here, we analyzed 2860 metagenomes spanning nine ecosystems using a curated reference database and a bias-aware taxonomic filtering approach to quantify the richness, relative abundance, and structural influence of low-abundance microbial taxa on community structure across a wide range of ecosystems. Our findings reveal that rare taxa, primarily CPR and DPANN, disproportionately shape microbial community dissimilarities across global ecosystems. We observed that the richness of these two groups, that drives community structure variation, increases with latitude, peaking in temperate regions, thereby contrasting classical latitudinal diversity patterns and suggesting unique biogeographic drivers. CPR and DPANN were predominantly enriched in free-living environments, particularly groundwater and soil, then in host-associated habitats, consistent with niche specialization shaped by environmental filtering and dispersal constraints. These findings challenge abundance-centric assumptions in microbial ecology and highlight the need to integrate low-abundance taxa into macroecological frameworks. Fully resolving their ecological functions, however, will require targeted experimental and multi-omics investigations.},
}

*Bacteria/classification/genetics/isolation & purification
*Archaea/classification/genetics/isolation & purification
*Microbiota
*Ecosystem
Metagenome
Biodiversity
Phylogeny
Soil Microbiology

@article {pmid41304320,
year = {2025},
author = {Tawidian, P and Tucker, BJ and Zembsch, TE and Ip, HS and Bartholomay, LC},
title = {Infection-Mediated Shifts in the Microbial Communities of Deer-Fed Ixodes scapularis Ticks.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
pmid = {41304320},
issn = {2076-2607},
support = {cooperative agreement U01CK000505/CC/CDC HHS/United States ; G21AC10134//United States Department of Agriculture/ ; },
abstract = {The holobiont of the blacklegged tick (Ixodes scapularis) includes maternally inherited rickettsial endosymbionts and environmentally acquired microbes that may influence tick fitness and vector competence. While previous studies have focused on characterizing the microbiota of I. scapularis ticks, less is known about the influence of tick infection status on microbial assemblages. Here, we collected engorged female I. scapularis ticks from hunter-harvested white-tailed deer (Odocoileus virginianus) across 11 counties in Wisconsin during fall 2022. The ticks were maintained in laboratory conditions for oviposition and then frozen for nucleic acid extraction. The infection status of each tick was determined using qPCR, targeting Borrelia spp., Babesia spp., and Powassan virus. Bacterial and fungal communities were characterized through amplicon-based sequencing targeting the 16S rRNA gene and ITS2 region, respectively. Our targeted pathogen testing revealed that 14.1% of the collected ticks were infected with Babesia odocoilei and 23.3% with Borrelia burgdorferi. The microbial community composition of ticks was significantly influenced by infection status and pathogen identity. Notably, Borrelia-infected ticks exhibited distinct microbiota profiles and increased microbial network connectivity. These findings provide new insights into the microbial ecology of deer-fed I. scapularis ticks and highlight the role of infection in shaping both microbiota and mycobiota communities.},
}

@article {pmid41304309,
year = {2025},
author = {Paoli, JE and Thongthum, T and Bassett, M and Beardsley, J and Tagliamonte, MS and Cash, MN and Spertus Newman, J and Smith, LM and Anderson, BD and Salemi, M and Subramaniam, K and von Fricken, ME and Braun de Torrez, E and Mathis, V and Mavian, CN},
title = {Virome and Microbiome of Florida Bats Illuminate Viral Co-Infections, Dietary Viral Signals, and Gut Microbiome Shifts.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112625},
pmid = {41304309},
issn = {2076-2607},
support = {Department of Pathology EPIG RAS 2021-2022//University of Florida/ ; Florida Informatics Institute SEED 2022-2023//University of Florida/ ; Biodiversity Institute SEED 2022-2023//University of Florida/ ; },
abstract = {Florida's bat virome remains poorly characterized despite the state's high bat species diversity and conservation importance. We characterized viral metagenomes from rectal tissues, anal swabs, and feces of Myotis austroriparius and Tadarida brasiliensis sampled across north Florida. We recovered a near-complete Hubei virga-like virus 2 (HVLV2) genome from T. brasiliensis feces, a finding consistent with an arthropod-derived dietary signal rather than active bat infection. An Alphacoronavirus (AlphaCoV) was detected in two M. austroriparius specimens, including one with a putative co-infection involving an Astrovirus (AstV), the first detection of AstV in Florida bats to date. Parallel profiling of the M. austroriparius gut microbiome highlighted compositional differences in the co-infected individual relative to AlphaCoV-only and virus-negative bats, suggestive of potential associations between viral detection and gut microbial shifts. Our study expands the known viral diversity in Florida bat populations, and demonstrates how metagenomics can simultaneously illuminate host diet, viral exposure, and gut microbial ecology. This approach provides a scalable framework for monitoring how diet, microbiome composition, and environmental pressures shape the bat virome, and inform conservation and zoonotic risk assessments.},
}

@article {pmid41304257,
year = {2025},
author = {Ma, R and Chen, Y and Chen, X and Zhang, J and Liu, C and Yang, L and Song, Y and Sun, Z and Lin, X and Ai, T and Ren, D and Chen, S},
title = {The Dominant Role of Dietary Differences in Shaping the Intestinal Microbial Communities of Grass Carp, Carp, and Crucian Carp in a Saline-Alkali Lake in Xinjiang During Winter.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112572},
pmid = {41304257},
issn = {2076-2607},
support = {Grant No. 2023YFD2401000;Grant No.2023TSYCCX0128;2024AB019;Grant No. XJARS-08-14//The Key R & D plan of Ministry of Science and Technology;The Tianshan Talent Training Project of Xinjiang;The Key Scientific and Technological Research Projects of Xinjiang Production and Construction Corps;Xinjiang Agriculture Research System/ ; },
abstract = {In this study, gut microorganisms of herbivorous grass carp, omnivorous carp, crucian carp, and aquatic microorganisms were collected from natural salt-alkali lakes and ponds in Xinjiang in winter to analyze their community structures. We sequenced 16S rRNA amplicons to investigate the composition and function of the microorganisms in the gut. PCoA analysis revealed that the gut microbiota of herbivorous and omnivorous fish formed two distinct clusters. Proteobacteria, Actinobacteria, Desulfobacterota, Firmicutes, and Chloroflexia are the dominant bacteria in the gut of fish. Proteobacteria, Bacteroidetes, Actinobacteria, Cyanobacteria, and Gram-negative bacteria are the dominant bacteria in the water. Carbohydrate- and protein-degrading bacteria, such as Desulfofustis, Lactiplantibacillus, and Vibrio, were predominant in omnivorous fish (CC and GRC), while cold-resistant bacteria, such as Shewanella and Psychromonas, were colonized in grass carp. This suggests that the same environment does not lead to similar gut bacteria, and that specific endogenous factors play a far more important role in shaping the microbiota composition than environmental factors.},
}

@article {pmid41304168,
year = {2025},
author = {Ouyang, H and Grześkowiak, Ł and Vahjen, W and Zentek, J and Martínez-Vallespín, B},
title = {Effects of Fibrous By-Products on Growth Performance, Ileal Nutrient Digestibility, Intestinal Morphology, and Microbiota Composition in Weaned Piglets.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112482},
pmid = {41304168},
issn = {2076-2607},
abstract = {Three fibrous by-products were evaluated over a 35-day feeding period in 64 weaned piglets, randomly assigned to four groups: a control without by-products (CON) and three others with diets containing 8% carrot pomace (CRT), 8% brewers' spent grain (BSG), or 8% carob pods (CRB). The growth performance, feed intake, feed conversion ratio, and apparent ileal digestibility of protein and amino acids were not affected. The jejunal and colonic morphology showed no statistical differences, although small numerical increases in the villus height and villus height-to-crypt ratio were noted with the by-products. Total short-chain fatty acid concentrations were stable, but their profile shifted: acetate increased in CRT and CRB (p < 0.001) mainly at the expense of propionate (p = 0.005). The microbiota composition in the proximal colon showed modest changes, with the highest Bifidobacterium spp. abundance in CRT and lowest in CRB (p = 0.042), reduced Ruminococcaceae UCG 005 with all the by-products (p = 0.008), and greater microbial richness in CRB (p = 0.009). These results suggest that a moderate inclusion of fibrous by-products may influence intestinal microbial ecology and fermentation patterns without negatively affecting performance or nutrient digestibility in weaned piglets, with no source appearing superior, thereby highlighting their potential as sustainable feed ingredients.},
}

@article {pmid41304165,
year = {2025},
author = {Tong, F and Feng, X and Yuan, H and Chen, Y and Chen, P},
title = {Oyster Aquaculture Impacts on Environment and Microbial Taxa in Dapeng Cove.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112480},
pmid = {41304165},
issn = {2076-2607},
support = {SML2023SP237//Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai)/ ; 2023TD06//Central Public-interest Scientific Institution Basal, Research Fund, CAFS/ ; 2024YFD2401405; 2024YFB4206600//National Key Research and Development Program of China/ ; },
abstract = {Environmental physicochemical factors and microorganisms play critical roles in the health of oysters. However, the impact of high-density oyster farming-a highly efficient filter-feeding bivalve system-on environmental conditions and microbial community structure and function remains poorly understood. This study conducted four-season monitoring of the water and sediment parameters in a semi-enclosed bay commercial oyster aquaculture (OA) system and a control area (CT), coupled with 16S rRNA amplicon sequencing of the environmental microbiota. Oyster aquaculture caused negligible disruption to water column parameters but significantly increased the concentrations of total organic carbon (TOC, annual mean OA vs. CT:1.15% vs. 0.56%), sulfides (annual mean OA vs. CT:67.72 vs. 24.99 mg·kg[-1]), and heavy metals (Cd, Pb, Cu, Zn, and Cr) in the sediment. α-diversity (Shannon and Chao indices) exhibited minimal overall perturbation, with significant inter-regional differences observed only in winter for both water and sediment. The bacterial community structure of the water column was significantly altered only in winter, whereas sediment communities showed structural shifts in spring, summer, and autumn. Water microbiota were primarily influenced by turbidity, dissolved oxygen, salinity, the Si/N ratio, and silicates. Sediment microbiota were correlated with Pb, Cu, Zn, TOC, Cr, and sediment particle size. Water bacterial functions displayed only four significantly divergent biogeochemical processes annually (sulfur compound respiration; OA vs. CT). In contrast, sediment bacteria exhibited 29 significantly disrupted functions annually, with the greatest seasonal divergence in winter (11/67 functions). Spring, summer, and autumn sediment functions showed distinct patterns. Understanding these environmental-microbial interactions is essential for sustainable oyster aquaculture and ecological optimization.},
}

@article {pmid41304129,
year = {2025},
author = {Zhong, Y and Wu, C and E, J and Gu, Y and Chi, H and Du, X},
title = {Bioavailability, Ecological Risk, and Microbial Response of Rare Earth Elements in Sediments of the Remediated Yitong River: An Integrated DGT and Multi-Parameter Assessment.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112443},
pmid = {41304129},
issn = {2076-2607},
abstract = {The expanding use of rare earth elements (REEs) in high-tech industrials has increased their environmental release, raising concerns about their ecological risks. This study employed the Diffusive Gradients in Thin Films (DGT) technique to assess REE bioavailability, spatial distribution, and ecological risks of REEs in sediments of the Yitong River, a historically polluted urban river in Changchun, China. Sediment characteristics (organic matter, pH, salinity), nutrient dynamics (N, P), and metal concentrations (Fe, Mn, As, etc.) were analyzed alongside REEs to evaluate their interactions and environmental drivers. Results revealed that REE concentrations (0.453-1.687 μg L[-1]) were dominated by light REEs (50.1%), with levels an order of magnitude lower than heavily industrialized regions. Ecological risk quotients (RQ) for individual REEs were below thresholds (RQ < 1), indicating negligible immediate risks, though spatial trends suggested urban runoff influences. Probabilistic risk assessment integrating DGT data and species sensitivity distributions (SSD) estimated a low combined toxic probability (2.26%) for REEs and nutrients. Microbial community analysis revealed correlations between specific bacterial (e.g., Clostridium, Dechloromonas) and fungal genera (e.g., Pseudeurotium) with metals and REEs, highlighting microbial sensitivity to pollutant shifts. This study provides a multidimensional framework linking REE bioavailability, sediment geochemistry, and microbial ecology, offering insights for managing REE contamination in urban riverine systems.},
}

@article {pmid41304117,
year = {2025},
author = {Guo, M and Liu, D and Xia, Z and Xie, T and Su, L and Pérez-Moreno, J and Yu, F},
title = {Geographic Provenances Outweigh Tissue Compartments in Bacteriome Assembly of the Ectomycorrhizal, Edible, and Hallucinogenic if Undercooked, Lanmoa asiatica (Boletaceae, Boletales) Mushroom from Yunnan China.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112431},
pmid = {41304117},
issn = {2076-2607},
support = {KCXFZJ-DDBF-202403//Designated Support Project of Chinese Academy of Sciences/ ; Guike AB22080097//the Key Research and Development Program of GuangXi/ ; 202205AD160036//the Yunnan Technology Innovation Program/ ; },
abstract = {Ectomycorrhizal fungal sporomes represent complex microuniverses harboring structurally and functionally eclectic microbiomes with significant ecological roles and potential anthropogenic applications. Nevertheless, the factors governing the assembly of these microbial communities remain poorly understood, and numerous fungal taxa, including many ectomycorrhizal species, remain uninvestigated. This study characterizes the bacteriome of the socioculturally and economically important yet hallucinogenic-if-raw ectomycorrhizal bolete Lanmoa asiatica. We analyzed 36 basidiomata from four geographic locations within China, partitioning each into pileus, stipe, and hymenophore tissues, and sequenced the V5-V7 region of the bacterial 16S rRNA gene. Proteobacteria dominated (>85%), with Pantoea, Sphingomonas, and the Burkholderia complex identified as core genera. Contrary to expectations, α-diversity was highest in the stipe (Chao1 index up to 1934) rather than the exposed hymenophore. PERMANOVA indicated that geographic origin (R[2] = 0.46, p < 0.001) was a stronger structuring force than tissue type (R[2] = 0.28, p < 0.01). Functional prediction via PICRUSt2 revealed enrichments in lipid metabolism, antimicrobial resistance, and apoptosis pathways across sites, while tissue-specific functions involved carbohydrate and nitrogen metabolism. These findings support a hierarchical model of bacteriome assembly where broad-scale environmental filters override micro-niche differentiation, providing a biogeographic framework for the conservation of this highly valued edible mushroom.},
}

@article {pmid41301533,
year = {2025},
author = {Sabharwal, A and Haase, EM and Scannapieco, FA},
title = {Amylase Binding to Oral Streptococci: A Key Interaction for Human Oral Microbial Ecology, Adaptation and Fitness.},
journal = {Biomolecules},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/biom15111616},
pmid = {41301533},
issn = {2218-273X},
support = {1R01DE022673-01/NH/NIH HHS/United States ; 1C06DC022673-18/NH/NIH HHS/United States ; },
mesh = {Humans ; *Mouth/microbiology ; *Streptococcus/metabolism/enzymology ; Biofilms/growth & development ; *Amylases/metabolism ; Bacterial Adhesion ; Adaptation, Physiological ; Microbiota ; },
abstract = {The interaction between human salivary alpha-amylase (HSAmy) and amylase-binding oral streptococci (ABS) helps determine the bacteria that colonize the oral cavity by establishing dental biofilms. Streptococci are important pioneer species of the oral cavity and influence oral health as well as common diseases such as dental caries. Various oral streptococcal species express distinct amylase-binding proteins, among which amylase-binding protein A (AbpA), encoded by the abpA gene in Streptococcus gordonii and several other species, which is the most extensively studied. Amylase binding facilitates microbial adhesion to host surfaces and biofilm formation and enables bacteria to harness the host's amylase enzymatic activity at their cell surface, enhancing their capacity to metabolize dietary starch for nutritional gain. Additionally, amylase binding may also influence bacterial cell division and stress tolerance by engaging novel bacterial signaling pathways. From an evolutionary perspective, both Neanderthals and modern humans exhibit functional adaptations in nutrient metabolism, including selection for salivary amylase-binding oral streptococci, highlighting the importance of microbial co-adaptation in response to host diet. Further research is warranted to elucidate the broader roles of amylase binding to bacteria in host-bacterial signaling, bacterial cell division and fitness and the evolutionary trajectory of the oral microbiome.},
}

Humans
*Mouth/microbiology
*Streptococcus/metabolism/enzymology
Biofilms/growth & development
*Amylases/metabolism
Bacterial Adhesion
Adaptation, Physiological
Microbiota

@article {pmid41301495,
year = {2025},
author = {Teslya, AV and Stepanov, AA and Poshvina, DV and Petrushin, IS and Vasilchenko, AS},
title = {From Lab to Field: Context-Dependent Impacts of Pseudomonas-Produced 2,4-Diacetylphloroglucinol on Soil Microbial Ecology.},
journal = {Biomolecules},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/biom15111578},
pmid = {41301495},
issn = {2218-273X},
support = {19-76-30005//Russian Science Foundation/ ; FEVZ-2024-0005//The Ministry of Science and Higher Education of the Russian Federation/ ; },
mesh = {*Soil Microbiology ; *Phloroglucinol/analogs & derivatives/pharmacology/metabolism ; *Pseudomonas/metabolism ; Fungi/drug effects/genetics ; Bacteria/drug effects/genetics ; Microbiota/drug effects ; },
abstract = {The secondary metabolite 2,4-diacetylphloroglucinol (2,4-DAPG), which is produced by Pseudomonas bacteria, is a potent antimicrobial agent with well-documented properties that suppress phytopathogens. However, its broader ecological impact on soil microbial communities is not understood. Through a combination of controlled microcosm and field trials, we have demonstrated that the effects of 2,4-DAPG are highly context-dependent. Laboratory exposure (10 mg kg[-1]) altered the abundance of 8.53% of bacterial and 6.91% of fungal amplicon sequence variants, and simplified the bacterial co-occurrence networks (reduced number of nodes and links). In contrast, field conditions amplified bacterial sensitivity (the Shannon index decreased from 4.77 to 4.17, p < 0.05) but maintained fungal stability (Shannon index varied from 3.93 to 3.97, p > 0.05); these conditions affected a smaller proportion of fungal ASVs (4.23%). Taxonomic analysis revealed consistent suppression of fungi of the Mucoromycota (e.g., Mortierella) and context-dependent shifts in bacteria, with an enrichment of Bacillota (e.g., Bacillus, Paenibacillus) in the laboratory but not in the field. Enzymatic responses revealed a dose-dependent activation of the C-cycle, with up to 7.4-fold increases in the laboratory and up to a 10.5-fold increase in the field. P- and N- cycles showed more complex dynamics, with acid phosphatase activity increasing 3.8-fold in laboratory conditions and recovering from initial suppression to an increase of 144% in field conditions, while N-acetylglucosaminidase activity increased and L-leucine aminopeptidase decreased under laboratory conditions. Our results suggest that the response of microorganisms to 2,4-DAPG in natural soils is reduced, probably due to functional redundancy and pre-adaptation to abiotic stresses. This difference between laboratory and field studies warns against extrapolating data from controlled experiments to predict outcomes in agricultural ecosystems, and emphasizes the need for a context-specific evaluation of biocontrol agents.},
}

*Soil Microbiology
*Phloroglucinol/analogs & derivatives/pharmacology/metabolism
*Pseudomonas/metabolism
Fungi/drug effects/genetics
Bacteria/drug effects/genetics
Microbiota/drug effects

@article {pmid41301464,
year = {2025},
author = {Cai, Y and Zhao, F and Cheng, X},
title = {Gut Microbiota and Ferroptosis in Colorectal Cancer: A Comprehensive Review of Mechanisms and Therapeutic Strategies to Overcome Immune Checkpoint Resistance.},
journal = {Biomolecules},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/biom15111546},
pmid = {41301464},
issn = {2218-273X},
mesh = {Humans ; *Ferroptosis/drug effects ; *Gastrointestinal Microbiome/drug effects ; *Colorectal Neoplasms/microbiology/immunology/therapy/drug therapy/pathology/metabolism ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; Animals ; *Drug Resistance, Neoplasm ; },
abstract = {Colorectal cancer (CRC) remains a leading cause of cancer-related mortality worldwide. Although immune checkpoint inhibitors (ICIs) have achieved striking clinical efficacy in the subset of CRCs with mismatch repair deficiency/high microsatellite instability (dMMR/MSI-H), the vast majority of patients-those with proficient mismatch repair/microsatellite-stable (pMMR/MSS) tumors-derive little benefit from current immunotherapies. Ferroptosis, an iron-dependent form of regulated cell death driven by lethal accumulation of lipid peroxides, has emerged as a promising antitumor mechanism that can interact with and modulate antitumor immunity. Concurrently, the gut microbiota exerts powerful control over host metabolism and immune tone through microbial community structure and metabolite production; accumulating evidence indicates that microbiota-derived factors can either sensitize tumors to ferroptosis (for example, via short-chain fatty acids) or confer resistance (for example, indole-3-acrylic acid produced by Peptostreptococcus anaerobius acting through the AHR→ALDH1A3→FSP1/CoQ axis). In this review we synthesize mechanistic data linking microbial ecology, iron and lipid metabolism, and immune regulation to ferroptotic vulnerability in CRC. We discuss translational strategies to exploit this "microbiota-ferroptosis" axis-including precision microbiome modulation, dietary interventions, pharmacologic ferroptosis inducers, and tumor-targeted delivery systems-and we outline biomarker frameworks and trial designs to evaluate combinations with ICIs. We also highlight major challenges, such as interindividual microbiome variability, potential collateral harm to ferroptosis-sensitive immune cells, adaptive antioxidant compensation (e.g., NRF2/FSP1 activation), and safety/regulatory issues for live biotherapeutics. In summary, this review highlights that targeting the microbiota-ferroptosis axis may represent a rational and potentially transformative approach to reprogramming the tumor microenvironment and overcoming immune checkpoint resistance in pMMR/MSS colorectal cancer; however, further research is essential to validate this concept and address existing challenges.},
}

Humans
*Ferroptosis/drug effects
*Gastrointestinal Microbiome/drug effects
*Colorectal Neoplasms/microbiology/immunology/therapy/drug therapy/pathology/metabolism
*Immune Checkpoint Inhibitors/therapeutic use/pharmacology
Animals
*Drug Resistance, Neoplasm

@article {pmid41300079,
year = {2025},
author = {Guo, X and Lin, M and Le, TN and Zhou, Z and Zhao, M and Cai, H},
title = {Impact of Aspergillus Species on Microbial Community Dynamics and Their Associations with Fermentation Properties in Fermented Walnut-Based Soy Sauce.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {22},
pages = {},
doi = {10.3390/foods14223921},
pmid = {41300079},
issn = {2304-8158},
support = {32172214, 31972079//National Natural Science Foundation of China/ ; },
abstract = {This study investigated microbial community dynamics and their links to fermentation traits in solid-state fermentation of walnut -based soy sauce (WSS) using walnut meal-soybean meal mixtures. Via 16S rRNA sequencing and molecular docking, it analyzed the effects of three distinct starter culture treatments-Aspergillus oryzae (AO), Aspergillus niger (AN), and mixed starter culture (A. oryzae + A. niger, ON)-as well as fermentation duration on microbial diversity and physicochemical properties, aiming to clarify microbial-driven quality mechanisms. Physicochemical analysis demonstrated superior fermentation performance in the AO group, showing significantly higher amino nitrogen (NH3-N) accumulation (0.23 g/100 mL) and protease activity (30.5 U/mL) compared to the AN group, with the mixed inoculation group (ON) exhibiting intermediate results, indicating A. oryzae's dominant role in mixed fermentation. Via PCA and Shannon index, microbial diversity analyses revealed starter cultures shaped microbial community structure: Enterococcus and Staphylococcaceae were enriched by AO starter, and Klebsiella dominated in AN group. Additionally, temporal succession of the microbiota occurred during post-fermentation of WSS, with Lactobacillales, Staphylococcus, and special flavor-producing functional flora dominating early, middle, and later stages, respectively. Staphylococcus positively correlated with protease activity and amino nitrogen, critical for quality. Molecular docking showed major walnut polyphenols significantly affected protease activity, aiding process optimization. This research provides theoretical foundations for improving WSS production and enriches understanding of solid-state fermentation microbial ecology.},
}

@article {pmid41299791,
year = {2025},
author = {Cheng, Q and Ma, J and Yang, Y and Ma, J and Grossart, HP and Xu, L and Lin, H},
title = {Enrichment of vitamin B12-producing Porphyrobacter in the phycosphere microbiome promotes microalgal stress adaptation to antibiotic exposure.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {240},
pmid = {41299791},
issn = {2049-2618},
support = {42207285//National Natural Science Foundation of China/ ; 42177002//National Natural Science Foundation of China/ ; LMS25C150001//Natural Science Foundation of Zhejiang Province/ ; 2021R52045//Leading talents in scientific and technological innovation, high-level Talents of Zhejiang Special Support Program/ ; 202204T14//Key Scientific Research and Development Program of Hangzhou/ ; },
mesh = {*Vitamin B 12/biosynthesis/metabolism ; *Microalgae/drug effects/microbiology/growth & development/physiology ; *Anti-Bacterial Agents/pharmacology ; *Microbiota ; Stress, Physiological ; Adaptation, Physiological ; },
abstract = {BACKGROUND: Planktonic microalgae deploy multifaceted responsive and adaptive strategies against anthropogenic pollutants; however, current understanding of antibiotic resistance mechanisms remains predominantly focused on intrinsic physiological adaptations. While microalgae maintain intimate relationships with the phycosphere microbiome, the ecological roles of these associated microbes in mediating host adaptation to polluted environments are inadequately characterized.

RESULTS: We identified a phycosphere microbiome-involved antibiotic resistance mechanism in Dictyosphaerium sp., a pollution-tolerant Chlorophyta microalgae exhibiting remarkable enrofloxacin (ENR) tolerance. Microalgal growth displayed initial inhibition followed by significant promotion under 5 mg/L ENR exposure. This resilience was associated with the restructuring of phycosphere microbiome, characterized by Porphyrobacter enrichment and functional enhancement of algal fitness-promoting pathways, including upregulation of cobalamin biosynthesis genes (log2FC = 7.76) and a 33.3-fold increase in extracellular B12 accumulation. Consequently, we isolated the ENR-selected microbial taxa to elucidate their roles in microalgal stress adaptation. Co-culturing axenic Dictyosphaerium sp. with Porphyrobacter enhanced microalgal growth by 36.5% after 8-day ENR exposure, whereas non-dominant bacteria exhibited negligible effects. Based on the transcriptomic and metabolomic analyses of the algal system when Porphyrobacter was dominant, we subsequently compared the growth of axenic microalgae with and without B vitamin (B1, B6, B7, B12) supplementation. Experimental validation demonstrated the pivotal role of B12-producing Porphyrobacter in enhancing microalgal ENR adaptation through (i) stimulating extracellular polymeric substances production and subsequently enhancing ENR removal via EPS-mediated adsorption and (ii) alleviating intracellular oxidative stress via elevating superoxide dismutase and peroxidase activities and reducing malondialdehyde levels. Additionally, this B12-producing bacteria/B12-mediated adaptability exhibited cross-species conservation, improving ENR resistance in Chlorella vulgaris and Scenedesmus quadricauda, with analogous protection observed under ciprofloxacin and norfloxacin exposures.

CONCLUSION: Collectively, our findings establish stress-induced enrichment of B12-producing Porphyrobacter within the phycosphere microbiome as a pivotal mechanism underlying microalgal antibiotic adaptation. This insight facilitates the rational development of microalgae-microbiome systems for enhanced wastewater treatment and sustainable bioproduction, with applications in aquatic feed supplementation, biofuel production, and biofertilizer development. Video Abstract.},
}

*Vitamin B 12/biosynthesis/metabolism
*Microalgae/drug effects/microbiology/growth & development/physiology
*Anti-Bacterial Agents/pharmacology
*Microbiota
Stress, Physiological
Adaptation, Physiological

@article {pmid41299662,
year = {2025},
author = {Jiménez, DJ and Jamil, T and Miliotis, G and Schultz, J and Patel, N and Aldakheel, L and Kontis, N and García, FC and Villela, HDM and Duarte, GAS and Barno, AR and Farran, A and Alsaggaf, A and Santoro, ÉP and Tumeo, A and Page, A and Wong, S and Kabza, A and Putra, A and Park, C and Angelov, A and Driguez, P and Peixoto, RS and Green, SJ and Tighe, S and Rosado, AS and Venkateswaran, K},
title = {Microbial community characterization in Red Sea-derived samples using a field-deployable DNA extraction system and nanopore sequencing.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-025-00819-x},
pmid = {41299662},
issn = {2524-6372},
support = {BAS/1/1096-01-0//King Abdullah University of Science and Technology/ ; },
abstract = {BACKGROUND: In this study, xTitan, a field-deployable, automated, and versatile nucleic acid extraction system was employed to characterize microbial communities in Red Sea-derived samples, including coral colonies, mangrove sediments, and seawater. The use of the xTitan in the field was intended to minimize sample transport bias, obtaining data that may be closer to "ground truth" for microbial diversity. The observed microbial communities from DNA extracted in the field using the xTitan system were compared to DNA extractions performed in a laboratory setting using both xTitan and a standard commercial kit (Qiagen) after approximately 24 h of sample transfer and storage.

RESULTS: Microbial community analyses conducted on DNA extracted using the xTitan system and the Qiagen kit yielded similar alpha diversity metric values, with a trend toward higher diversity observed in most samples extracted with the xTitan. The microbial community structure in samples from a Pocillopora verrucosa colony, mangrove sediments, and seawater was affected by the DNA extraction system. In the P. verrucosa colony, 16S rRNA gene sequences affiliated to Endozoicomonas acroporae were preferentially abundant when DNA was extracted in the field with the xTitan system rather than in the lab. In mangrove sediments, significant differences (P-value < 0.05) in beta diversity and functional gene profiles were observed when comparing in-field to in-lab xTitan DNA extracts. In seawater, a pronounced decrease in the relative abundance of cyanobacterial populations was observed when DNA was extracted with both methods after samples were transported to the lab on ice. In addition, hundreds of species in mangrove-associated samples were differentially abundant when DNA was extracted on-site with the xTitan system compared to in-lab extractions. Balneolaceae was one of the most abundant taxa in mangrove sediments and several genera from this family were detected in all replicates across all DNA extraction systems.

CONCLUSIONS: The usability of different field-deployable instruments for microbial community characterization in marine-derived samples was demonstrated. Moreover, differences in beta diversity were observed when DNA was extracted in-field versus in-lab using the xTitan system, particularly for mangrove-associated samples. These results highlight the value of on-site nucleic acid extraction for enhancing the detection of microbial taxa that can be sensitive to cold storage. This study enabled the testing of the xTitan on Red Sea-derived samples, generating comprehensive information on the effects of DNA extraction systems and transportation of samples on coral and mangrove-associated microbiomes.},
}

@article {pmid41299176,
year = {2025},
author = {Wirbel, J and Hickey, AS and Chang, D and Enright, NJ and Dvorak, M and Chanin, RB and Schmidtke, DT and Bhatt, AS},
title = {Long-read metagenomics reveals phage dynamics in the human gut microbiome.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {41299176},
issn = {1476-4687},
abstract = {Gut bacteriophages profoundly impact microbial ecology and health[1-3]; yet, they are understudied. Using deep long-read bulk metagenomic sequencing, we tracked prophage integration dynamics in stool samples from six healthy individuals, spanning a 2-year timescale. Although most prophages remained stably integrated into their hosts, approximately 5% of phages were dynamically gained or lost from persistent bacterial hosts. Within a sample, we found that bacterial hosts with and without a given prophage coexisted simultaneously. Furthermore, phage induction, when detected, occurred predominantly at low levels (1-3× coverage compared to the host region), in line with theoretical expectations[4]. We identified multiple instances of integration of the same phage into bacteria of different taxonomic families, challenging the dogma that phages are specific to a host of a given species or strain[5]. Finally, we describe a new class of 'IScream phages', which co-opt bacterial IS30 transposases to mediate their mobilization, representing a previously unrecognized form of phage domestication of selfish bacterial elements. Taken together, these findings illuminate fundamental aspects of phage-bacterial dynamics in the human gut microbiome and expand our understanding of the evolutionary mechanisms that drive horizontal gene transfer and microbial genome plasticity.},
}

@article {pmid41299132,
year = {2025},
author = {Zhang, J and Zhou, X and Rong, X and Salem, H and Zhang, J and Yin, B and Guo, X and Zhang, Y},
title = {Effects of Plant Phylogeny and Traits on the Composition of Phyllosphere Microbial Communities in a Typical Temperate Desert in Central Asia.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02635-9},
pmid = {41299132},
issn = {1432-184X},
support = {2022D01A351//The Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; Non//The Tianchi Talent Introduction Project of Xinjiang Uygur Autonomous Region/ ; 2022D01D083//The Key Project of Xinjiang Uygur Autonomous Region Natural Science Foundation/ ; 2022TSYCLJ0058//The Leading Talents in Sci-Technological Innovation Project of "Tianshan Talent" Training Plan of Xinjiang Uygur Autonomous Region/ ; },
abstract = {Phyllosphere microorganisms play a vital role in supporting host plant health and adaptability. Although previous research on the effects of host performance and their phylogenetic associations on phyllosphere microbial communities has predominantly focused on tropical, subtropical, and temperate forestry ecosystems, the responses of these microbial communities to plant phylogeny and functional traits in temperate desert environments remains poorly understood. In this study, we conducted a quantitative analysis of bacterial and fungal community structures in the phyllosphere of 39 plant species from the Gurbantunggut Desert, a typical temperate desert in Central Asia. Variation partitioning analysis revealed that plant phylogeny, leaf physicochemical properties, and leaf morphological characteristics collectively explained the variation in phyllosphere microbial communities. Specifically, these factors accounted for 19.26%, 14.53%, and 2.32% of the variance in bacterial communities, and 11.55%, 8.36%, and 2.19% of the variance in fungal communities, respectively. A significant hierarchical pattern emerged: plant phylogeny > leaf physicochemical properties > leaf morphological characteristics, highlighting the dominant role of plant filtering effects in community assembly. Linear mixed-effects model analysis further confirmed the significant influence of multiple plant attributes, including phylogeny and functional traits, on microbial community structure. Plant-microbe interaction analysis revealed distinct host preferences of microbial taxa across different plant taxonomic levels. Co-evolutionary analysis also indicated a significant phylogenetic association between host plants and their phyllosphere amplicon sequence variants (ASVs). Overall, our findings demonstrate that plant attributes, particularly plant phylogeny and functional traits, are key factors driving the assembly of phyllosphere microbial communities in deserts. This study provides new insights into species coexistence mechanisms in fragile habitats and enhances our understanding of plant-microbe interactions in global desert ecosystem.},
}

@article {pmid41297120,
year = {2025},
author = {Rajbhandari, RM and Shrestha, S and Manandhar, P and Napit, R and Sadaula, A and Chaudhary, A and Raut, R and Gortázar, C and Alves, PC and de la Fuente, J and Queirós, J and Forcina, G and Karmacharya, D},
title = {Comparing the respiratory tract microbiome in captive elephants and humans in Chitwan National Park: Implications for conservation medicine.},
journal = {Comparative immunology, microbiology and infectious diseases},
volume = {125},
number = {},
pages = {102422},
doi = {10.1016/j.cimid.2025.102422},
pmid = {41297120},
issn = {1878-1667},
abstract = {The study of gut microbiome in both animals and humans living in proximity has proven crucial in understanding their coevolution, the potential for microbial transfer and the dynamics behind various diseases. Similarly, the investigation of respiratory microbiomes has been gaining popularity due to its significance and impact on respiratory health. Here, we use 16S rRNA metabarcoding to explore the respiratory microbiome of captive Asian elephants (Elephas maximus) and their mahouts (i.e., trainers and handlers) in Chitwan National Park (Nepal), with local villagers residing out of the protected area acting as control. Sputum samples were collected to characterize their bacterial composition, while its functional profile was inferred with PICRUSt2. Additionally, the occurrence of genera hosting potentially pathogenic ESKAPE-E species was evaluated. Our findings revealed high similarity in the bacterial and functional composition of the respiratory microbiome of elephants and mahouts, with Bacillota and Pseudomonadota emerging as the most abundant phyla across all host categories and the controls displaying the highest diversity. A striking difference was observed in relation to the family Bacillaceae that dominated the microbial composition of both mahouts and elephants but not controls. Genera hosting potentially pathogenic ESKAPE-E bacteria were found in all host categories, which underscores the need for in-depth analyses to identify the species involved. Our study delivers valuable insights in the respiratory microbial community of both Asian elephants and humans, thus laying the basis for further investigations on their diversity and function, unveiling their role in respiratory health of both host species.},
}

@article {pmid41296916,
year = {2025},
author = {Rettura, F and Lambiase, C and Bottari, A and Filippini, F and Giacomelli, L and Pistello, M and Bellini, M},
title = {Gut Virome: What's the Role in Irritable Bowel Syndrome?.},
journal = {Reviews in medical virology},
volume = {35},
number = {6},
pages = {e70080},
doi = {10.1002/rmv.70080},
pmid = {41296916},
issn = {1099-1654},
support = {2022FRE3RH//Italian Ministry of University and Research/ ; CUP I53D23000480006//National Recovery and Resilience Plan/ ; },
mesh = {Humans ; *Irritable Bowel Syndrome/virology/microbiology/therapy ; *Virome ; *Gastrointestinal Microbiome ; Bacteriophages/physiology ; Dysbiosis/virology ; Animals ; },
abstract = {The gut virome, an integral but still poorly understood component of the gut microbiota, is emerging as an important player in the pathophysiology of irritable bowel syndrome (IBS). Recent evidence suggests that alterations in virome diversity and phage-bacteria interactions contribute to gut dysbiosis, immune modulation and gut barrier dysfunction in IBS. This review summarises current knowledge on virome alterations in IBS and emphasises the role of bacteriophages in shaping microbial ecology and host responses. Different virome signatures in the different subtypes of IBS highlight the potential of the virome for disease stratification and personalised therapeutic strategies. In addition, we discuss the analytical challenges in virome research and explore novel virome-targeted interventions, including phage therapy and dietary modulation. A deeper understanding of virome dynamics in the gut could open new avenues for precision medicine approaches to treat IBS.},
}

Humans
*Irritable Bowel Syndrome/virology/microbiology/therapy
*Virome
*Gastrointestinal Microbiome
Bacteriophages/physiology
Dysbiosis/virology
Animals

@article {pmid41296063,
year = {2025},
author = {Guo, M and Zhou, Z and Zheng, Y and Fu, D and Hou, L and Zhu, R},
title = {Ubiquity and Dominance of Comammox Over AOB and AOA and their Links To ARGs in Antarctic Lake Sediments.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02664-4},
pmid = {41296063},
issn = {1432-184X},
support = {2022YFF0801101//National Key Research and Development Program of China/ ; 42576267//National Natural Science Foundation of China/ ; },
abstract = {Complete ammonia oxidizers (comammox), oxidizing ammonia to nitrate directly, have been found to exist widely in multiple environments, but their distribution patterns are still under-explored in Antarctic environments. For the first time, the sediments were collected from West Antarctic lakes to investigate distribution patterns and community structure for comammox, ammonia oxidizing archaea (AOA) and bacteria (AOB), and nitrite-oxidizing bacteria (NOB), as well as the associations between ammonia oxidizers and antibiotic resistance genes (ARGs). Comammox clade B and AOB were dominant ammonia oxidizers, with the abundances of (1.62 ± 0.10) × 10[2] - (5.21 ± 0.74) × 10[6] and (0.17 ± 0.05) × 10[5] - (4.79 ± 0.65) × 10[5] copies g[- 1] sediment, respectively. Comammox clade B, instead of clade A, occurred in all sediments, exhibiting higher abundances than AOB and AOA in most of the sediments. The abundances for comammox clade B demonstrated significant positive correlation (p < 0.01) with NH4[+]-N levels, but negative correlation (p < 0.05) with C: N ratios. The coexistence of ammonia oxidizers in lake sediments was jointly structured by niche differentiation and environmental variables, and pH, modulated by penguin guano input, was found to be the most crucial factor in shaping their community structure. Co-occurrence network analyses revealed strong synergistic interactions between comammox and AOB, AOA, NOB, which played a critical role in nitrification processes. Our results further confirmed that comammox could act as important hosts for ARGs, hence stimulated their transmission and proliferation in the sediments. This study presented novel insights into the distribution patterns for ammonia oxidizers, their niche differentiation and the associations with ARGs in natural lake sediments of West Antarctica.},
}

@article {pmid41295040,
year = {2025},
author = {Abdul Rahiman, S and Qiblawey, H},
title = {Anammox-MBR Technology: Breakthroughs and Challenges in Sustainable Nitrogen Removal from Wastewater.},
journal = {Membranes},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/membranes15110337},
pmid = {41295040},
issn = {2077-0375},
support = {QUHI-CENG-25/26-747//Qatar University/ ; },
abstract = {Wastewater nitrogen pollution is a serious environmental problem, and traditional treatment techniques are frequently constrained by their high energy requirements and operational complexity. The anaerobic ammonium oxidation (anammox) process combined with membrane bioreactor (MBR) technology (anammox-MBR) offers a practical and energy-efficient solution for the sustainable removal of nitrogen, further enhanced by its potential to minimize emissions of nitrous oxide (N2O), a potent greenhouse gas with a global warming potential nearly 300 times that of carbon dioxide. This review outlines the most recent advancements in anammox-MBR systems, highlighting their ability to achieve nitrogen removal efficiencies of more than 70-90% and, in integrated systems with reverse osmosis, to recover up to 75% of the inflow as high-quality reusable water. Significant advancements such as high-rate activated sludge coupling, reverse osmosis integration, microaeration methods, and membrane surface modifications have decreased membrane fouling, accelerated startup times, and enhanced system stability. Despite these achievements, there are still issues that hinder widespread use, such as membrane fouling exacerbated by hydrophobic anammox metabolites, sensitivity to low temperatures (≤10 °C), and the persistent challenge of suppressing nitrite-oxidizing bacteria (NOB), which compete for the essential nitrite substrate. To enable cost-effective, energy-efficient, and environmentally sustainable large-scale applications, future research directions will focus on creating cold-tolerant anammox strains, advanced anti-fouling membranes, and AI-driven process optimization.},
}

@article {pmid41294522,
year = {2025},
author = {Špiljak, B and Andabak Rogulj, A and Lončar Brzak, B and Brailo, V and Škrinjar, I and Ozretić, P and Vidović Juras, D},
title = {Desquamative Gingivitis and the Oral Microbiome: Insights into Immune-Microbial Interactions in Mucosal Inflammation.},
journal = {Dentistry journal},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/dj13110541},
pmid = {41294522},
issn = {2304-6767},
abstract = {Desquamative gingivitis (DG) is a clinical presentation characterized by erythema, epithelial desquamation, and mucosal fragility, commonly associated with immune-mediated diseases such as oral lichen planus (OLP), mucous membrane pemphigoid (MMP), and pemphigus vulgaris (PV). While traditionally viewed as a manifestation of immune dysregulation, growing evidence suggests that the oral microbiome may modulate disease onset, persistence, and severity. This review summarizes current knowledge on the oral microbiota in DG and its underlying diseases, explores mechanistic links between dysbiosis and immune activation, and discusses clinical and research implications. A narrative literature review was conducted using PubMed and Scopus, focusing on studies analyzing the oral microbiome in OLP, MMP, and PV. Emphasis was placed on molecular microbiology techniques, immune profiling, and functional or longitudinal approaches. In OLP, microbial dysbiosis is consistently reported, including reduced diversity and increased abundance of pro-inflammatory genera such as Fusobacterium, Prevotella, and Capnocytophaga. These shifts correlate with epithelial barrier disruption and inflammatory cytokine production. Although data on MMP and PV are limited, early findings suggest microbial involvement in sustaining inflammation, delaying healing, and possibly amplifying autoimmune responses. Dysbiosis may activate Toll-like receptors, skew T cell responses, and contribute to the breakdown of immune tolerance. DG may reflect a dynamic interplay between immune mechanisms and microbial ecology. While evidence is strongest for OLP, preliminary data suggest broader microbial contributions across DG-associated diseases. Microbiome-informed approaches could enhance diagnostic accuracy and support the development of adjunctive therapies.},
}

@article {pmid41293856,
year = {2025},
author = {Schäfer, RB and Baikova, D and Bayat, HS and Beermann, AJ and Berger, SA and Boenigk, J and Brauns, M and Burfeid-Castellanos, A and Cardinale, BJ and David, GM and Feckler, A and Feld, CK and Fink, P and Gessner, MO and Hadziomerovic, U and Hering, D and Le, TTY and Macaulay, SJ and Madariaga, GM and Serge Mayombo, NA and Pimentel, IM and Orr, JA and Osakpolor, S and Schlenker, A and Sures, B and Vermiert, AM and Vos, M and Weitere, M and Schürings, C},
title = {Effects of Biodiversity Loss on Freshwater Ecosystem Functions Increase With the Number of Stressors.},
journal = {Global change biology},
volume = {31},
number = {11},
pages = {e70617},
doi = {10.1111/gcb.70617},
pmid = {41293856},
issn = {1365-2486},
support = {426547801//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Biodiversity ; *Fresh Water ; *Ecosystem ; *Stress, Physiological ; Biomass ; },
abstract = {A multitude of anthropogenic stressors drive biodiversity loss and alter ecosystem functioning. Freshwaters, which contribute disproportionally to global biodiversity and biogeochemical cycles, are particularly threatened. Although the relationship between biodiversity and ecosystem functions (BEF) is generally well-established, especially in terrestrial ecosystems, the role of multiple, co-occurring stressors in modulating the relationship remains unclear. We conducted a meta-analysis to address this knowledge gap by assessing the effect of multiple stressors on the relationship between taxon richness and four measures of ecosystem function. The relationship was generally positive, with the slope becoming steeper as the number of stressors increased, suggesting that exposure to multiple stressors exacerbates impacts of biodiversity loss on ecosystem function. Multiple stressor effects on both taxon richness and ecosystem functions were largely predictable from individual stressor effects, although antagonistic effects on ecosystem functions emerged in 14% of the considered cases. The type of stressor and ecosystem function, along with taxonomic group, exerted no influence on the BEF relationship, contrary to our expectations. Microbial production and biomass declined most strongly in response to stressors, despite notable variability. Overall, our findings imply that functional consequences of freshwater biodiversity loss are more severe under multifaceted environmental change than previously assumed.},
}

*Biodiversity
*Fresh Water
*Ecosystem
*Stress, Physiological
Biomass

@article {pmid41292685,
year = {2025},
author = {O'Brien, JM and Blais, ND and Holland-Moritz, H and Shek, KL and Douglas, TA and Barbato, RA and Ernakovich, JG},
title = {Consistent microbial responses during the aerobic thaw of Alaskan permafrost soils.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1654065},
pmid = {41292685},
issn = {1664-302X},
abstract = {Arctic systems are warming at four times the global average, causing permafrost-permanently frozen soil, ice, organic matter, and bedrock-to thaw. Permafrost thaw exposes previously unavailable soil carbon and nutrients to decomposition-a process mediated by microbes-which releases greenhouse gases such as carbon dioxide and methane into the atmosphere. While it is well established that thaw alters the composition and function of the permafrost microbiome, patterns revealing common responses to thaw across different permafrost soil types have not yet emerged. In this study, we address how permafrost thaw impacts microbiome diversity, alters species abundance, and contributes to carbon flux in the Arctic. We sampled peat-like, mineral, and organic-mineral permafrost from three locations in central and northern Alaska. We assessed their abiotic soil properties and microbiome characteristics before and after a 3-month laboratory microcosm incubation. Across all sites, prokaryotic biomass increased following thaw, measured as 16S rRNA gene copy number. This change in biomass was positively correlated with cumulative respiration, indicating an increase in microbial activity post-thaw. We evaluated the thaw response of microbial taxa across three sites, identifying taxa that significantly increased in abundance post-thaw. Common responders shared across all sites belonged to the families Beijerinckiaceae, Burkholderiaceae, Clostridiaceae, Oxalobacteraceae, Pseudomonadaceae, and Sporichthyaceae, indicating a common set of taxa that consistently respond to thaw regardless of site-specific conditions. Alpha diversity decreased with thaw across all sites, likely reflecting the increased dominance of specific thaw-responsive taxa that may be driving post-thaw biogeochemistry and increased respiration. Taken together, we deepen the understanding of different permafrost microbiomes and their response to thaw, which has implications for the permafrost-climate feedback and enables more accurate predictions of how Arctic ecosystem structure and function respond to change.},
}

@article {pmid41291355,
year = {2025},
author = {Han, H and Luo, Z and Pei, X and Xie, Y and Zhu, Y and Li, J and Zou, T and Wang, Z and Su, C},
title = {Microbial-Plant Interaction: Bacillus subtilis-Driven Gravel Soil Improvement and Growth Promotion of Festuca arundinacea.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02634-w},
pmid = {41291355},
issn = {1432-184X},
abstract = {The rapid expansion of tunnel engineering in China has led to extensive excavation of gravelly soils, resulting in significant land occupation that threatens the ecological environment and surrounding biota. As a result, there is an increasing need for effective ecological restoration of nutrient-poor gravelly soils, where challenges in vegetation establishment and sustainable soil management persist. This study evaluates the potential of Bacillus subtilis to promote the growth of Festuca arundinacea in engineered gravel soils through a controlled greenhouse experiment, examining its effects on plant growth, soil nutrient dynamics, and microbial community structure. The results showed that, compared to the control group (CK), neither the Bacillus subtilis treatment group (Bs) nor the nutrient application treatment group (LB) significantly altered the soil bacterial species composition at the phylum level. However, at the genus level, Azotobacter dominated the LB group, while Sphingomonas was the predominant genus in both the CK and Bs groups. Additionally, Bacillus subtilis significantly increased bacterial diversity relative to the nutrient application treatment, leading to substantial changes in microbial community composition. Furthermore, Bacillus subtilis notably enhanced both aboveground and belowground biomass, improved nutrient uptake, and increased the availability of phosphorus and potassium. It also stimulated soil enzymatic activities involved in carbon, nitrogen, and phosphorus cycling, emphasizing its critical role in nutrient cycling. Thus, Bacillus subtilis-driven soil enhancement offers a promising solution for ecological restoration in nutrient-poor gravelly soils, where conventional amendments are often ineffective. These findings underscore the potential of microbial-plant synergies to improve soil fertility and support sustainable vegetation restoration.},
}

@article {pmid41291216,
year = {2025},
author = {Jurado, J and Garcia-Vega, A and Vasquez, Y and Villegas-Plazas, M and Roldan, F},
title = {Field-Scale AMD Remediation: Microbial Community Dynamics and Functional Insights in Biochemical Passive Reactors.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02628-8},
pmid = {41291216},
issn = {1432-184X},
abstract = {Acid mine drainage (AMD) generated during coal mining activities is characterized by low pH, high concentrations of dissolved metals and metalloids, and elevated sulfate levels, all of which significantly impact surrounding ecosystems. Scaling up biochemical passive reactor (BPR) systems represents a promising approach for the in situ bioremediation of AMD. While numerous laboratory-scale studies have described the taxonomic and functional composition of microbial communities in BPRs, typically dominated by (ligno)cellulolytic organisms and sulfate-reducing bacteria (SRB), it remains unclear whether this composition is maintained at the field-pilot scale under environmental conditions. To address this gap, 16S rRNA gene metabarcoding and shotgun metagenomics analyses were performed to characterize the taxonomic and functional diversity of microbial communities in the BPRs within a multi-unit field-pilot system. The results revealed that bioremediation effectiveness was driven by syntrophic interactions among hydrolytic, fermentative, and sulfate-reducing bacteria, aligning with laboratory-scale observations. While community composition shifts altered specific taxa, core operational dynamics remained preserved.},
}

@article {pmid41291200,
year = {2025},
author = {Zha, Y and Fan, L and Shen, T and Zhang, Y and Ren, H},
title = {Triptolide ameliorates LPS-induced acute lung injury in Balb/c mice through gut-lung axis-mediated regulation of bile acid metabolism and gut microbiota.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-29758-w},
pmid = {41291200},
issn = {2045-2322},
support = {PW2022A-21//the Scientific Research Program of Shanghai Pudong New Area Health Commission/ ; },
abstract = {Acute lung injury (ALI) associated with pulmonary edema is a severe clinical condition characterized by acute inflammation, disrupted lung barrier function, and high mortality. Current therapeutic strategies remain limited, highlighting the need for exploring novel agents and their underlying mechanisms. Triptolide (TP), an active component derived from Tripterygium wilfordii, has shown anti-inflammatory and tissue-protective properties[1,2], but its specific role in alleviating ALI and the involvement of the lung-gut axis in metabolic regulation remain poorly understood. This study aims to investigate the therapeutic effects of TP on LPS-induced ALI, focusing on its impact on pulmonary edema and inflammatory injury. By analyzing the lung-gut axis using multi-omics approaches, we seek to clarify the metabolic network regulatory mechanisms through which TP exerts its effects. LPS-induced ALI model was established in Balb/c mice, with TP administered as the therapeutic intervention. Histopathological examination of lung tissues and detection of pro-inflammatory cytokines were performed to assess lung injury. Untargeted metabolomics via LC-MS/MS was used to identify differential metabolites in lung tissues and serum, while metagenomic sequencing analyzed changes in gut microbiota composition. Integrated multi-omics analysis was applied to explore associations between gut microbiota alterations, serum metabolites, and pulmonary bile acid levels. TP administration significantly reduced histopathological damage in lung tissues of ALI mice and decreased pro-inflammatory cytokine levels. Metabolomics profiling revealed distinct changes in key metabolites, including bile acids, amino acid derivatives, and energy metabolism intermediates, in both lung tissues and serum after TP treatment. Metagenomic analysis showed that TP restructured gut microbiota composition, with functional enrichment in glycolysis and thiamine metabolism pathways. Integrated analysis confirmed strong correlations between dynamic microbiota changes, serum metabolite profiles, and pulmonary bile acid levels, indicating a regulatory role of the lung-gut axis. This study demonstrates that TP alleviates pulmonary edema and inflammatory injury in ALI by modulating gut microbial ecology and function, which drives bile acid metabolic reprogramming and regulates metabolite interactions within the lung-gut axis. These findings provide novel insights into TP's therapeutic mechanism and support its potential application in ALI treatment.},
}

@article {pmid41291153,
year = {2025},
author = {Joshi, H and Caprio, M and Reon, L and Fan, P},
title = {Rumen Microbiota-Based Machine Learning Approach for Predicting Heat Stress and Identifying Associated Microbes.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02656-4},
pmid = {41291153},
issn = {1432-184X},
abstract = {Heat stress poses a significant global challenge to sustainable livestock production, leading to detrimental impacts on animal production and welfare. Reduced appetite and increased body temperature further disrupt the gastrointestinal microbial ecosystem of heat-stressed animals, altering nutrient digestion and affecting host production. However, reported heat-stress-associated microbes have varied across studies, partly due to inconsistencies in microbiota analysis pipelines and taxonomic levels reported. In this study, to identify consistent rumen microbial taxa influenced by heat stress and evaluate potential of rumen microbiota in heat stress prediction, we collected publicly available raw 16S rRNA gene amplicon sequencing data of rumen fluid samples from lactating Holstein cattle housed in thermoneutral or heat stress condition from eight studies, analyzed their microbial composition using a consistent bioinformatic pipeline, and built machine learning models with the rumen microbiota profile to predict heat stress. Important rumen microbial taxa were selected using Boruta (a feature selection algorithm to identify important features) as potential biomarkers to predict heat stress, such as lactate-producing bacteria Lactobacillales, fiber-degrading bacteria Ruminococcaceae UCG-001, and methanogenic archaea Methanomicrobium. Additionally, the random forest model using the available animal factors and relative abundance of rumen microbial taxa showed a much higher performance for heat stress prediction, compared to the model without rumen microbiota profile (Area Under the Curve: 0.851 vs. 0.440). This study confirmed a distinct rumen microbiota signature in heat-stressed lactating Holstein cattle and identified specific rumen microbial taxa as potential biomarkers that could be targeted to mitigate heat-stress responses in dairy cows.},
}

@article {pmid41291109,
year = {2025},
author = {Cohen, DD and Faigenboim, A and Elingold, I and Sher, Y and Galpaz, N and Minz, D},
title = {Dynamics in Microbial Communities Associated with the Development of Soil Fatigue in Banana.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02637-7},
pmid = {41291109},
issn = {1432-184X},
abstract = {Soil fatigue, well documented in various crops, presents a significant challenge to banana production by causing fast and then gradual declines in plant growth and yield over years of cultivation. Despite its impact on profitability, the underlying mechanisms driving soil fatigue remain poorly understood; however, a strong link to shifts in the soil microbiome has been suggested. We investigated the dynamics of microbial communities in relation to soil fatigue, using a novel semi-controlled outdoor experimental system. Soil at different stages of fatigue (0 to 42 months of banana cultivation) was generated in large containers filled with initially healthy soil. Banana plants grown in these soils were replaced with new plants which showed soil age-dependent growth. Three months postplanting, soil and root samples were collected for analyses of soil parameters and microbial community composition using bacterial (16S) and fungal (ITS) amplicon sequencing. We identified minor age-related shifts in mainly pH, potassium, and organic matter in the soil. While alpha diversity remained unchanged, significant shifts in bacterial and fungal community composition were observed in fatigued soils. Notably, the relative abundance of bacterial families such as Flavobacteriaceae, Pseudomonaceae, and Acidibacter increased, as did some fungal taxa (many from groups with known pathogens)-Ceratobasidiaceae (including Rhizoctonia), Dothideomycetes, and Stachybotryaceae. Simultaneously, the relative abundance of bacterial families with known beneficial members, including Gemmatimonadaceae, Moraxellaceae, Sphingomonadaceae, and Azospirillaceae, as well as symbiotic fungal taxa such as Glomeraceae and Lasiosphaeriaceae, declined. Thus, soil fatigue may be correlated to the proliferation of pathogenic populations and a loss of beneficial microorganisms.},
}

@article {pmid41291103,
year = {2025},
author = {Katanić, Z and Ćurković-Perica, M and Idžojtić, M and Boljevac, K and Krstin, L},
title = {Status of Dutch Elm Disease Fungus Ophiostoma novo-ulmi and Assessment of Its Temporal Variability in Croatia.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02601-5},
pmid = {41291103},
issn = {1432-184X},
abstract = {Dutch elm disease (DED) was originally caused by the ascomycete Ophiostoma ulmi, which has been replaced by a more virulent species, O. novo-ulmi, divided into subsp. novo-ulmi and subsp. americana. Permeable reproductive barriers, a period of co-occurrence of O. ulmi and O. novo-ulmi, and the current overlap of O. novo-ulmi subspecies have been important in shaping the present O. novo-ulmi populations in Europe, which were initially clonal, predominantly of the MAT-2 type. This study confirmed the persistence of O. novo-ulmi in Croatia over the years, although at some forest sites, the diseased elms were not detected. The methodology used to assess changes in O. novo-ulmi populations was based on the col1 and cu genes, which have subspecies-specific nucleotide differences, analysis of MAT idiomorphs, and temperature-growth responses. The col1 and cu gene sequencing did not reveal a change in the number of isolates with the recombinant col1/cu genotype over 10 years (2012-2022). At both sampling times, approximately one-fourth of all analyzed isolates had recombinant col1/cu genotypes. However, the frequency of MAT-1 isolates, which all have MAT-1 genes originating from O. ulmi, increased during this period. Differences in growth rate at 20, 26, and 30 °C revealed variations in the temperature response of isolates, which were affected by sampling time and mating type. The MAT-1 isolates were shown to grow more slowly than MAT-2 at the three temperatures tested. The advantage of MAT-2 was reflected in temporal differences in growth rate at resampled sites, particularly at lower temperatures. These results suggest that changes in the frequency of mating types in Croatia occurred between 2012 and 2022, accompanied by modifications in the pathogen's response to temperature at the population level.},
}

@article {pmid41291089,
year = {2025},
author = {Calbet, A},
title = {Pelagic Shuttles of Antibiotic Resistance Genes: Zooplankton as Overlooked Vectors Across Space and Food Webs.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02669-z},
pmid = {41291089},
issn = {1432-184X},
abstract = {Antibiotic resistance genes (ARGs) accumulate in aquatic environments, where they create reservoirs and transmission pathways that can undermine antimicrobial treatments and alter the microbial community structure in ways that ultimately affect human and animal health. However, the contribution of zooplankton in these pathways remains critically overlooked. Emerging evidence shows that compared with surrounding water, copepods and cladocerans accumulate ARG loads that are one to two orders of magnitude greater, acting as microbial hotspots that disperse resistant bacteria across seasons and depths. Inside protistan vacuoles, densely packed prey cells undergo conjugation, rapidly accelerating horizontal ARG transfer. Long-term archives reveal persistent ocean-wide dissemination of the class-1 integron integrase (intI1) and sul2 genes since at least the 1970s. Here, I synthesize mechanistic and field evidence, pinpoint knowledge gaps, and recommend priorities: integrate zooplankton into routine ARG surveillance, quantify biofilm-mediated exchanges, and mitigate contamination from coselective pollutants to curb zooplankton-driven ARG propagation. By framing zooplankton-associated ARG dynamics within the broader community ecology of antimicrobial resistance, this mini-review highlights how aquatic food-web processes feed back into the emergence, evolution, and transmission of resistance that concerns for One Health outcomes beyond the clinic.},
}

@article {pmid41290433,
year = {2025},
author = {Ishibashi, S and Susukida, S and Muto, K and Miyazawa, K and Zhang, S and Yoshimi, A and Tabata, E and Abe, K},
title = {Using pure oxygen aeration to increase recombinant protein production by an Aspergillus oryzae hyphal dispersion strain.},
journal = {Journal of bioscience and bioengineering},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jbiosc.2025.10.011},
pmid = {41290433},
issn = {1347-4421},
abstract = {A high growth rate is essential for increasing protein production efficiency in liquid fermentation of filamentous fungi, such as Aspergillus oryzae. However, the increase in culture viscosity due to fungal growth constrains the overall yield. We have demonstrated that culture viscosity is lower in A. oryzae AGΔ-GAGΔ strains, which are deficient in the cell surface polysaccharides α-1,3-glucan (AG) and galactosaminogalactan (GAG), than in the wild-type (WT) strains. Nevertheless, even in aerated fermentation, an increase in AGΔ-GAGΔ viscosity results in oxygen depletion, which limits fungal growth and enzyme production. In this study, we investigated viscosity dynamics and protein production during high-cell-density fermentation of AGΔ-GAGΔ under pure oxygen aeration. Fed-batch cultivation of the WT and AGΔ-GAGΔ strains, expressing recombinant xylanase (XynF1), was used to compare the effects of air and pure oxygen aeration at the same flow rate. At 60 h, AGΔ-GAGΔ under pure oxygen aeration showed higher cell density (1.2× WT under pure oxygen aeration, 2.1× AGΔ-GAGΔ under air aeration) and XynF1 activity (1.8× WT under pure oxygen aeration, 2.3× AGΔ-GAGΔ under air aeration). Under pure oxygen aeration, AGΔ-GAGΔ showed lower viscosity (0.32×) and mixing time (0.50×) than WT. At 60 h, fine mycelial pellets (micropellets; 200-700 μm) were clearly observed in AGΔ-GAGΔ under pure oxygen but not under air aeration. These findings suggest that oxygen enrichment during AGΔ-GAGΔ cultivation mitigated the increase in viscosity, thereby promoting higher cell density and protein production. The formation of micropellets in AGΔ-GAGΔ likely contributed to a reduction in culture viscosity.},
}

@article {pmid41289323,
year = {2025},
author = {Li, C and Urem, M and Kotsogianni, I and Lau, J and Du, C and Elsayed, SS and Martin, NI and McNae, IW and Voskamp, P and Mayer, C and Rigali, S and Pannu, N and Abrahams, JP and Schada von Borzyskowski, L and van Wezel, GP},
title = {The novel GlcNAc 6-phosphate dehydratase NagS governs a metabolic checkpoint that controls nutrient signaling in Streptomyces.},
journal = {PLoS biology},
volume = {23},
number = {11},
pages = {e3003514},
doi = {10.1371/journal.pbio.3003514},
pmid = {41289323},
issn = {1545-7885},
abstract = {Streptomyces bacteria are renowned for their multicellular lifestyle and as Nature's medicine makers, producing the majority of the clinical antibiotics. A landmark event during early development is the lytic dismantling of the substrate mycelium. Degradation of the hyphal cell-wall leads to the accumulation of N-acetylglucosamine (GlcNAc) in the colonies, which is a metabolic checkpoint during the onset of development and antibiotic production. Here, we show that GlcNAc sensing requires a toxicity pathway dependent on the enzyme GlcNAc-6P dehydratase (NagS). Dehydration of GlcNAc-6P by NagS to 6P-chromogen I is an unprecedented reaction in central metabolism that is highly conserved in - and limited to - the Streptomycetaceae. 6P-chromogen I is metabolized into a structural analogue of ribose by a promiscuous activity of GlcNAc-6P deacetylase NagA. Toxicity is relieved by supplementing the growth media with ribose. Structure-function analysis of NagS not only highlighted key residues in the active site of the enzyme in interaction with its substrate GlcNAc-6P, but also revealed 6-phosphogluconate as its catalytic inhibitor. Our work uncovers a conserved metabolic toxicity pathway in Streptomyces that revolves around a novel enzyme that plays a key role in nutrient signaling.},
}

@article {pmid41288749,
year = {2025},
author = {Ndabankulu, KP and Zama, N and Suinyuy, TN and Magadlela, A},
title = {Soil Microbe Interaction and Extracellular Enzyme Activity Mediated by Encephalartos villosus in KwaZulu-Natal Scarp Forest Ecosystems.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {132},
pmid = {41288749},
issn = {1432-184X},
support = {129403//National Research Foundation, South Africa/ ; 138091//National Research Foundation/ ; },
mesh = {*Soil Microbiology ; South Africa ; Soil/chemistry ; Forests ; *Bacteria/classification/enzymology/genetics/isolation & purification/metabolism ; Rhizosphere ; Symbiosis ; Ecosystem ; Microbiota ; },
abstract = {Cycads are ancient gymnosperms that play a crucial role in the soil health of scarp forests through their symbiotic associations with nutrient-cycling bacteria. However, the abundance of cycads in scarp forests has been decreasing at an alarming rate, highlighting the importance of determining the role of these species in nutrient cycling, microbial dynamics, and soil health. This study examined soil nutrient and microbial dynamics associated with Encephalartos villosus across four scarp forest sites in KwaZulu-Natal, South Africa. Soil samples were collected from the rhizosphere and non-rhizosphere zones (3-5 m away from the canopy) of mature plants. Results show that collection point did not influence soil nutrient and properties statistically; however, site-level variation was evident, with Hlathikhulu showing higher pH and nutrient concentrations, while Vernon Crookes exhibited lower pH and nutrient availability. Rhizosphere soils supported a greater diversity of nutrient-cycling bacteria, particularly taxa from the genera Bacillus, Burkholderia, Enterobacter, Luteibacter, and Pseudomonas with N-fixing, P-solubilizing, and N-cycling functions. Non-metric multidimensional scaling (NMDS) revealed that site differences, mainly driven by Mg, Ca, K, Zn, pH, and total cations, were stronger predictors of soil nutrient and microbial community variation than collection point alone. Enzyme assays showed that glucosaminidase and acid phosphatase were associated with community differences. These findings indicate that E. villosus enhances soil nutrient enrichment and microbial functional diversity in scarp forests, although the strength of these effects depends on local site conditions. Conservation of E. villosus is therefore critical, not only for species survival but also for sustaining soil fertility and ecosystem functioning in nutrient-limited scarp forest habitats.},
}

*Soil Microbiology
South Africa
Soil/chemistry
Forests
*Bacteria/classification/enzymology/genetics/isolation & purification/metabolism
Rhizosphere
Symbiosis
Ecosystem
Microbiota

@article {pmid41288747,
year = {2025},
author = {Kim, J and Cui, Y and Nam, KH and Lee, JW and Kim, JG and Chun, SJ},
title = {Effects of CP4-EPSPS-Containing Brassica juncea Hybrids on the Gut and Fecal Microbiota of the Terrestrial Decomposer Armadillidium vulgare.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {131},
pmid = {41288747},
issn = {1432-184X},
support = {NIE-A-2025-04; NIE-A-2025-06//Ministry of Environment (MOE) of the South Korea/ ; },
mesh = {*Mustard Plant/genetics ; *Feces/microbiology ; *Gastrointestinal Microbiome ; *Plants, Genetically Modified/genetics ; Animals ; Bacteria/classification/genetics/isolation & purification ; Fungi/classification/genetics/isolation & purification ; Republic of Korea ; Plant Leaves ; },
abstract = {The unintended spread of genetically modified (GM) crops and introgression into wild relatives raises concerns about ecological impacts. In South Korea, CP4-EPSPS-containing Brassica juncea hybrids (GM-hybrid B. juncea) have been detected in natural ecosystems. However, the impact of these GM crops on ecology remains unclear. In this study, we aimed to investigate the potential effects of GM-hybrid B. juncea on the gut and fecal microbiomes of Armadillidium vulgare, a dominant decomposer in natural habitats and an ideal model organism for assessing the ecological impact of GM plant material. Leaf litter from wild-type and GM-hybrid B. juncea was collected from the field, and feeding experiments were conducted using A. vulgare under controlled conditions. Although no significant differences in survival rates or growth were observed between groups, microbiome analysis revealed significant changes in both bacterial and fungal community composition and functional profiles in the gut and feces of the GM-hybrid-fed group. Specifically, in the GM-hybrid-fed group, the proportion of intestinal Plectosphaerella (Glomerellales) increased. Additionally, the bacterial Shannon index decreased, whereas the fungal Shannon index increased. Microbial network analysis revealed distinct interaction patterns and GM-hybrid-specific modules. GM-hybrids may influence decomposer-associated microbiomes through indirect pathways. Such influences could affect ecosystem-level processes such as decomposition and nutrient cycling. This experimental framework can be extended to other crop-derived hybrids or applied to different ecological contexts, providing a valuable basis for future assessments of transgene impacts on ecosystem functions.},
}

*Mustard Plant/genetics
*Feces/microbiology
*Gastrointestinal Microbiome
*Plants, Genetically Modified/genetics
Animals
Bacteria/classification/genetics/isolation & purification
Fungi/classification/genetics/isolation & purification
Republic of Korea
Plant Leaves

@article {pmid41288715,
year = {2025},
author = {Yang, W and Deng, Z and Blair, D and Hu, W and Yin, M},
title = {Heavy-metal Pollution Affects Daphnia Fitness by Altering Diversity of the Gut Microbiota.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {130},
pmid = {41288715},
issn = {1432-184X},
support = {32271690//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Daphnia/drug effects/microbiology/genetics/physiology ; *Gastrointestinal Microbiome/drug effects ; *Nickel/toxicity ; *Metals, Heavy/toxicity ; *Water Pollutants, Chemical/toxicity ; Bacteria/classification/genetics/drug effects ; Germ-Free Life ; *Genetic Fitness/drug effects ; },
abstract = {The role of gut microbiota in shaping host fitness is already well established. However, it remains unclear to what extent the gut microbiota influences host fitness in the presence of environmental stressors. Here, we tested the hypothesis that responses of water flea Daphnia to the heavy metal nickel are mediated by gut microbiota. Germ-free D. magna exhibited somewhat lower fitness than did those with gut microbiota transplant. Among germ-free Daphnia, those that were exposed to heavy metals did not differ in fitness from unexposed Daphnia. In contrast, when incubated with their donors' gut microbiota, initially germ-free D. magna continuously exposed to nickel for 21 days showed a significantly lower survival rate than those not exposed to nickel. We detected a reduced set of microbes in the formerly germ-free Daphnia in the presence of nickel. Transcriptomic analysis of Daphnia showed that expression/regulation of genes related to oxygen transport, chitin metabolism, and detoxification changed in response to the reduced gut microbiomes acquired in the presence of nickel. Our findings show that the toxic effects of heavy metal led to a reduced diversity of gut microbiota in Daphnia and can thus affect host fitness.},
}

Animals
*Daphnia/drug effects/microbiology/genetics/physiology
*Gastrointestinal Microbiome/drug effects
*Nickel/toxicity
*Metals, Heavy/toxicity
*Water Pollutants, Chemical/toxicity
Bacteria/classification/genetics/drug effects
Germ-Free Life
*Genetic Fitness/drug effects

@article {pmid41288688,
year = {2025},
author = {Wardhani, R and Shin, J and Lee, S and Lee, J and Nam, YH and Lee, MH and Han, KL and Ahn, H},
title = {Evaluation of Aquamicrobium lusatiense NLF 2-7 as a Biocontrol Agent in Manure Composting: Effects on Odorous Compounds and Microbial Community Under Mesophilic Conditions.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {129},
pmid = {41288688},
issn = {1432-184X},
support = {NNIBR20253108//Nakdonggang National Institute of Biological Resources/ ; RS-2021-IP321088//Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry/ ; },
mesh = {*Composting/methods ; *Manure/microbiology ; *Odorants/prevention & control/analysis ; Hydrogen Sulfide/metabolism/analysis ; *Soil Microbiology ; *Bacteria/classification/metabolism/genetics ; Biodegradation, Environmental ; Sulfides/metabolism/analysis ; Soil/chemistry ; *Biological Control Agents ; Microbiota ; },
abstract = {Microbial inoculation is a commonly applied approach in composting to enhance organic matter biodegradation and reduce odor emissions. However, the different characteristics of bacteria in terms of temperature can be considered to optimize their effect during different phases of composting. A mesophilic bacterium, namely Aquamicrobium lusatiense NLF 2-7, was evaluated to mitigate odor emissions and enhance the bacterial community under mesophilic composting. Two different treatments were designed: treatment 1 with a single inoculation on the initial day and treatment 2 with split inoculation at the initial and after 2 weeks. Results show that the treatments improve organic matter decomposition by 17.7-28.6% and significantly reduce volatile sulfur compound emissions, especially dimethyl sulfide (DMS) and hydrogen sulfide (H2S) during the initial phase of composting. DMS emissions were mostly emitted in the first week, with reduction rates of 60.3% and 61.5% in both treatments, respectively. Additionally, mean phenol emissions were reduced by 7.9% in treatment 1 and 11.7% in treatment 2. The dominant bacterial phyla during composting were Bacillota, Pseudomonadota, Bacteroidota, and Actinomycetota, comprising 74 to 95% of the total population. This experiment suggests that A. lusatiense NLF 2-7, which is known for reducing sulfur emissions, can also enhance organic matter decomposition. Split inoculation appears more beneficial, with an initial inoculation managing sulfur emissions early on, followed by a second inoculation after the thermophilic phase to control phenol emissions throughout the composting process.},
}

*Composting/methods
*Manure/microbiology
*Odorants/prevention & control/analysis
Hydrogen Sulfide/metabolism/analysis
*Soil Microbiology
*Bacteria/classification/metabolism/genetics
Biodegradation, Environmental
Sulfides/metabolism/analysis
Soil/chemistry
*Biological Control Agents
Microbiota

@article {pmid41288389,
year = {2025},
author = {Taheri, S and Schwarzkopf, E and Berman, HL and Brandt, N and McNeill, J and Sevier, N and Ruffieux, M and Dunn, RR and Smukowski Heil, C},
title = {The role of flour type and feeding schedule on the sourdough microbiome.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0238025},
doi = {10.1128/spectrum.02380-25},
pmid = {41288389},
issn = {2165-0497},
abstract = {Sourdough starters are fermentations of various grains by bacteria and yeast and are of worldwide economic and cultural importance. Sourdoughs are sometimes spontaneously inoculated, and their resident microbial communities are in part shaped by environmental factors, potentially including flour, water, air, human microbiota, equipment, geography, and temperature. The number of different genera of bacteria and yeast found in sourdoughs is large; however, only a handful of species typically dominate an individual sourdough starter. Understanding how and why certain species form a mature climax community in a particular environment is a key question in microbial ecology. To investigate this question, we used a meta-barcoding approach and tested whether different baking flours (all-purpose, bread, and whole wheat) and frequency of feeding, also known as backslopping, shape the sourdough starter microbial community over the course of one month. We found that the yeast genus Kazachstania rapidly rose in frequency and became the most abundant yeast in all starters, regardless of flour type or feeding schedule. In contrast, flour type did affect the bacterial community. Mature sourdoughs all contained the bacterial genera Companilactobacillus, Levilactobacillus, Lactiplantibacillus, Furfurilactobacillus, and Acetobacter, with Companilactobacillus detected at higher relative abundance in whole wheat flour and Levilactobacillus detected at higher relative abundance in bread flour. We conclude that flour can shape the microbial community of sourdough and has potential implications for functional traits.IMPORTANCEHow organisms disperse and colonize new environments is central to our understanding of biodiversity. Sourdough, the often spontaneously inoculated fermentation of grains by bacteria and yeast, represents a great system to test and observe how microorganisms come to inhabit a particular niche. In our study, we investigate how environmental parameters such as flour type and feeding frequency influence the microbial community. We find that the common sourdough yeast genus Kazachstania is most abundant in all starters regardless of treatment, but we also find a significant effect of flour type on the lactic acid bacteria composition of the sourdough starters. This work shows how the environment can impact the presence and abundance of particular microorganisms and prompts future studies to test how particular lactic acid bacteria species can specialize on certain resources.},
}

@article {pmid41286473,
year = {2025},
author = {Wang, H and Yang, Y and Zhang, H and Chen, X and Zhang, R and Hou, W and Zhang, G},
title = {Symbiotic N-Fixing Bacteria in the Root and Leaf of Typical Alpine Grassland Plants.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {127},
pmid = {41286473},
issn = {1432-184X},
mesh = {Grassland ; *Plant Roots/microbiology ; *Symbiosis ; *Plant Leaves/microbiology ; RNA, Ribosomal, 16S/genetics ; Tibet ; *Nitrogen-Fixing Bacteria/classification/genetics/isolation & purification/physiology ; Nitrogen Fixation ; Phylogeny ; DNA, Bacterial/genetics ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Soil Microbiology ; },
abstract = {Alpine plants in nitrogen-deficient environments can acquire nitrogen by associating with endophytic nitrogen-fixing microorganisms that inhabit their roots and leaves to form symbiotic relationships. However, research is limited on nitrogen-fixing bacterial communities in the roots and leaves of alpine grassland plants, especially regarding the differences between various plant parts. In this study, we compared the root and leaf bacterial communities of four alpine plant families (Asteraceae, Leguminosae, Poaceae, and Rosaceae) in the alpine meadow ecosystem of Naqu, Tibet, using culture-based methods, 16S rRNA, and nifH gene pyrosequencing. The results showed greater bacterial diversity in the root compared to the leaf, and Fabaceae plants harbored a higher abundance of nitrogen-fixing bacteria. Interestingly, the roots and leaves of non-Fabaceae plants (Kobresia, Festuca ovina, and Leontopodium) also harbored abundant nitrogen-fixing communities such as Microbacterium, Curtobacterium, and Rhodococcus. Compared with subtropical environments, Cyanobacteria are important symbiotic nitrogen-fixing bacteria in plants of alpine ecosystems. These findings indicate that plant species and plant parts strongly influence the selection of bacterial populations. Understanding these microbial ecological functions in alpine grasslands provides scientific insights for optimizing agricultural practices and ecosystem management.},
}

Grassland
*Plant Roots/microbiology
*Symbiosis
*Plant Leaves/microbiology
RNA, Ribosomal, 16S/genetics
Tibet
*Nitrogen-Fixing Bacteria/classification/genetics/isolation & purification/physiology
Nitrogen Fixation
Phylogeny
DNA, Bacterial/genetics
*Bacteria/classification/genetics/isolation & purification/metabolism
Soil Microbiology

@article {pmid41286374,
year = {2025},
author = {Jones, AK and Jordan, HR and Wolff, CL and Lashley, MA and Barton, BT},
title = {Lasting Effects of Different Scaled Mass Mortality Events on Soil Microbial Communities.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02625-x},
pmid = {41286374},
issn = {1432-184X},
abstract = {Death is a natural process present in all ecosystems; however, mass mortality events are instances of larger than average numbers of animals dying in a relatively short period of time. These events are increasing in frequency and magnitude, and the effects of mass mortalities - especially their long-term effects - are understudied. To better understand the long-term effects of mass mortalities in terrestrial ecosystems, we conducted experimental mass mortality events to determine if key ecosystem properties remained affected after 4 years. The experiment crossed three types of input treatments (control, carrion, and nutrient additive) with scavenger access (open plots versus fenced plots). To evaluate how increasing carrion biomass affected the ecosystem, sites were randomly assigned biomass (25, 59, 182, 363, 726 kg total (20m[2] plots)). Biomasses consisted of feral swine carcasses or the equivalent amount of N, phosphorus, and K nutrients. After 4 years, we found that while soil N did not differ among treatments, soil K and Ca significantly increased with biomass. Microbial communities significantly differed at the 182 kg biomass treatments compared to others and indicated significant effects between carrion and nutrient additive treatments. These results demonstrate that large die-offs, such as mass mortality events, can have long-lasting effects on soil composition through increased soil nutrients and alter soil microbial community (i.e., reduced Bacilliaceae, etc.). These long-lasting impacts can permanently alter the soil community, which can lead to cascading bottom-up effects that can alter the entire ecosystem structure.},
}

@article {pmid41286365,
year = {2025},
author = {Bondarenko, S and Obiol, A and Casamayor, EO and Massana, R},
title = {Non-Dikarya Fungal Clades Are Everywhere: What 18S rRNA Gene Metabarcoding Reveals About Cross-System Distribution of Fungi.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02642-w},
pmid = {41286365},
issn = {1432-184X},
support = {2020 BP 00293//Agència de Gestió d'Ajuts Universitaris i de Recerca (AGAUR), Generalitat de Catalunya/ ; PID2021-127701NB-I00//Ministerio de Ciencia e Innovación/ ; PID2019-108457RB-I00//Ministerio de Ciencia e Innovación/ ; },
abstract = {Non-Dikarya fungi remain poorly characterized due to their cryptic morphology, cultivation difficulties, and limited representation in reference databases. To investigate their diversity and environmental distribution at a global scale, we reanalyzed over 6000 environmental samples using metabarcoding targeting the V4 region of the 18S rRNA gene, encompassing marine, freshwater, soil, hypersaline, polar, and other habitats. We constructed reference phylogenetic trees based on near full-length 18S rRNA gene sequences to enable accurate placement of short-read amplicon sequence variants (ASVs). This approach yielded robust classification at the phylum level and provided finer-scale clade resolution within major non-Dikarya groups. We delineated precise clades within Chytridiomycota, Microsporidia, Rozellida, and Aphelidea, and unveiled several novel ones. Our results show strong ecological structuring of fungal communities across habitats, with inland systems harboring greater fungal abundance and broader phylogenetic diversity than marine systems. Non-Dikarya fungi were consistently detected across diverse environments, including extreme habitats such as hypersaline lakes, deep sediments, and polar regions, where they were often the dominant fungal taxa. Although most ASVs tended to occur in a limited number of ecologically related habitats, phylogenetically related ASVs within the same clade were often adapted to different environments, indicating ecological diversity within clades. Our findings underscore both the ecological relevance and the cryptic diversity of non-Dikarya fungi in globally distributed environments, including extreme ones. Improved taxonomic resolution and broader reference dataset coverage are required to fully integrate these newly characterized lineages into fungal systematics and environmental surveys.},
}

@article {pmid41286193,
year = {2025},
author = {García-Gutiérrez, L and Mellado, E and Martin-Sanchez, PM},
title = {Contribution of DNA Metabarcoding to the Environmental Fungal Assessments in Hospitals.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02626-w},
pmid = {41286193},
issn = {1432-184X},
support = {PID2021-123184OA-I00//Agencia Estatal de Investigación/ ; },
abstract = {Hospitals are particularly sensitive environments where immunosuppressed patients might acquire invasive fungal infections. Therefore, it is necessary to carry out periodical environmental microbiological assessments that evaluate the fungal bioburden in air and surfaces from different hospital zones. Current microbiological monitoring protocols at healthcare settings are mostly based on cultivation, while environmental DNA (eDNA) assessments are still scarce and should be further evaluated. To fill this gap, this study combines a large sampling scheme, comprising > 200 samples (air, surface, dust and soil) collected from four zones at three Spanish hospitals in two campaigns (winter and autumn), with two eDNA approaches (DNA metabarcoding and quantitative PCR) to characterize the hospital mycobiomes (diversity, community composition and airborne load), compared to a parallel culture-dependent study. DNA metabarcoding revealed a much more comprehensive inventory of hospital fungi compared to culturing; however, both approaches found similar dominant taxa including a variety of potentially opportunistic human pathogens. Hospital mycobiomes were affiliated to 4 phyla (mostly Ascomycota and Basidiomycota), 35 classes, 114 orders, 305 families, 643 genera and 535 species. The dominant genera, in both air and surfaces from the three hospitals, were Cladosporium, Alternaria, Aureobasidium, Penicillium, Neodidymelliopsis, Aspergillus, Pseudopithomyces and Stemphylium. The yeasts Candida and Clavispora were particularly abundant on high-touch surfaces indoors. The most important explanatory factors for the variance in community composition were the hospital and zone where samples were collected, the type of sample and the sampling campaign. DNA metabarcoding can assist hospital managers by providing an in-depth characterization of the baseline hospital mycobiome during normal operating conditions, as well as identifying and controlling community imbalances and associated health risks under demanding situations such as construction works or reported clinical outbreaks.},
}

@article {pmid41286179,
year = {2025},
author = {Sultanova, Z and Dönertaş, HM and Hita, A and Aguilar, P and Dag, B and Lucas-Lledo, JI and Latorre, A and Carazo, P},
title = {Age-Dependent Gut Microbiota Dynamics and Their Association with Male Life-History Traits in Drosophila melanogaster.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02640-y},
pmid = {41286179},
issn = {1432-184X},
support = {ECF-2022-214//Leverhulme Trust/ ; P2021-00-007//Carl-Zeiss-Stiftung/ ; CGL2014-58722-P//Spanish Ministry of Economy and Competitivity/ ; PGC2018-099344-B-I00//Spanish Ministry of Economy and Competitivity/ ; },
abstract = {Growing evidence suggests that the gut microbiota is closely intertwined with life-history evolution in a wide range of species, including well-studied model organisms like Drosophila melanogaster. Although recent studies have explored the relationship between gut microbiota and female life-history, the link between gut microbiota and male life-history remains relatively unexplored. In this study, we investigated how gut microbiota changes with male age as well as the associations between gut microbiota composition and male life-history traits in D. melanogaster. Using 22 isolines from the Drosophila melanogaster Genetic Reference Panel (DGRP), we measured lifespan, early/late-life reproduction, and early/late-life physiological performance. We characterized the gut microbiota composition in young (5 days old) and old (26 days old) flies using 16S rDNA sequencing. We observed substantial variation in both male life-history traits and gut microbiota composition across isolines and age groups. Using machine learning, we show that gut microbiota composition could predict the chronological age of the organisms with high accuracy. The most important species contributing to machine learning prediction belonged to the Acetobacter and Ralstonia genera. Associations between gut microbiota and life-history traits were also notable, particularly involving different species from the Acetobacter genus. Our findings suggest that taxa such as Acetobacter may be relevant to the evolutionary ecology of host-microbe interactions in male fruit flies.},
}

@article {pmid41286138,
year = {2025},
author = {Liu, XQ and An, XP and He, WX and Xu, XH and Hashem, A and Abd-Allah, EF and Wu, QS},
title = {Hairy Vetch Intercropping Attenuates Mycorrhizal Benefits to Walnut Growth and Soil Organic Carbon Sequestration via Glomalin.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {128},
pmid = {41286138},
issn = {1432-184X},
support = {SCXX-XZCG-22016//Hubei Province '14th Five-Year' Major Science and Technology Aid Tibet Project/ ; ORF-2025-356//Ongoing Research Funding program, King Saud University, Riyadh, Saudi Arabia/ ; },
mesh = {*Juglans/growth & development/microbiology ; *Mycorrhizae/physiology/growth & development ; *Soil/chemistry ; Soil Microbiology ; *Carbon Sequestration ; Plant Roots/microbiology/growth & development ; Carbon/metabolism/analysis ; Biomass ; *Agriculture/methods ; *Fungal Proteins/metabolism ; *Glycoproteins/metabolism ; },
abstract = {Intercropping is a prevalent soil management strategy within walnut orchards, while its impacts on the functionality of arbuscular mycorrhizal fungi (AMF) in walnuts (Juglans regia) remain unclear, especially concerning soil carbon (C) sequestration via glomalin-related soil protein (GRSP). This study aimed to explore the effects of inoculation with the AMF species Diversispora spurca and intercropping with hairy vetch (Vicia villosa) on walnut biomass accumulation, soil water-stable aggregate (WSA) stability, leaf and root C (Cleaf and Croot) content, soil organic carbon (SOC), GRSP, and GRSP-contained C (CGRSP), in addition to the contribution rate of CGRSP to SOC. The intercropping treatment significantly inhibited root mycorrhizal colonization rate, soil hyphal length, and spore density in AMF-inoculated walnut plants. Individual AMF inoculation, rather than individual intercropping, significantly promoted shoot and root biomass accumulation, WSA stability, SOC, Cleaf and Croot, the levels of purified easily extractable (EEG), difficultly extractable (DEG), and total GRSP (TG), as well as their C contents. The combination treatment (AMF inoculation + intercropping) displayed limited benefits, improving just WSA stability without yielding synergistic advantages over individual treatments. Arbuscular mycorrhizal fungal inoculation significantly increased CGRSP, especially CDEG, while individual intercropping resulted in a reduction of CDEG. The combination treatment elevated both CDEG and CTG, albeit to a lesser extent than AMF alone. The contribution rates of CEEG, CDEG, and CTG to SOC were 0.33% - 0.53%, 1.16% - 1.78%, and 1.49% - 2.31%, respectively. Although AMF inoculation significantly increased the contribution rates of CDEG and CTG to SOC, this effect was diminished when combined with intercropping. Notably, CDEG, rather than CEEG, exhibited a significantly positive correlation with SOC and WSA stability. The findings provide new insights into the mechanisms of SOC sequestration in walnuts grown in controlled environments and offer a theoretical basis for the application of AMF in walnut cultivation.},
}

*Juglans/growth & development/microbiology
*Mycorrhizae/physiology/growth & development
*Soil/chemistry
Soil Microbiology
*Carbon Sequestration
Plant Roots/microbiology/growth & development
Carbon/metabolism/analysis
Biomass
*Agriculture/methods
*Fungal Proteins/metabolism
*Glycoproteins/metabolism

@article {pmid41284260,
year = {2025},
author = {Song, H and Dowdell, K and Delafont, V and Skerlos, S and Raskin, L},
title = {The Neglected Role of Heterotrophic Protists in Engineered Water Systems.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c04958},
pmid = {41284260},
issn = {1520-5851},
abstract = {Heterotrophic protists can be considered the dark matter of microbial communities in engineered water systems. They are ubiquitous and ecologically significant yet remain largely overlooked. Although a growing body of research demonstrates their pivotal roles (e.g., predation, symbiosis, and nutrient cycling) in microbial communities in natural ecosystems, their functions in engineered water systems are poorly characterized, and heterotrophic protists are frequently excluded from microbial analyses. This is largely due to methodological constraints that have only recently been overcome. Recent advances in imaging, high-throughput sequencing, and meta-omics approaches, combined with expanding reference databases, have revolutionized studies of protist diversity and functions in a wide range of natural environments. Drawing on research from the fields of protistology, microbial ecology, and environmental microbiology, this review explores how the well-documented ecological roles of heterotrophic protists in natural environments translate to engineered ecosystems, offering insights into their functions in water treatment. We critically evaluate recent literature to synthesize both beneficial roles and potential risks of heterotrophic protists in various water treatment systems, while identifying key knowledge gaps and proposing directions for future research. We advocate for a shift in perspective that recognizes heterotrophic protists as important players and call for their integration into microbial community characterization and ecological frameworks in microbial ecology studies of engineered water systems. This integration will transform our understanding of microbial communities in engineered water systems, ultimately enabling novel, mechanistic, and ecologically informed management strategies.},
}

@article {pmid41280504,
year = {2025},
author = {Ganguly, D and Roy, R and Mondal, P and Chakraborty, P and Paul, P and Das, S and Mallik, M and Maity, A and Trivedi, S and Tribedi, P and Sarkar, S},
title = {Nisin, a promising antimicrobial peptide, forestalls the methicillin-resistant Staphylococcus aureus biofilm network via reactive oxygen species generation.},
journal = {3 Biotech},
volume = {15},
number = {12},
pages = {428},
pmid = {41280504},
issn = {2190-572X},
abstract = {UNLABELLED: Staphylococcal infections have been reported to be a significant global threat to the effective management of public healthcare due to their drug resistance property. This attribute has further been complicated by their robust biofilm-forming potential. This escalating threat of biofilm-associated infections necessitates innovative and promising therapeutic strategies. Hence, in the present study, the biofilm threat of methicillin-resistant Staphylococcus aureus (MRSA) has been challenged by Nisin, a natural lantibiotic produced by Lactococcus lactis. This compound showed a promising antibacterial effect with minimum inhibitory concentrations (MICs) of 150 µg/ml against MRSA. Furthermore, a series of experiments has been conducted to confirm the antibiofilm potential of Nisin against MRSA. Towards this direction, the sub-MIC dose of Nisin (40 µg/mL) was found to inhibit biofilm formation by ~ 51% for MRSA. To support this finding, extracellular polymeric substance (EPS) was measured under the Nisin-treated and untreated conditions of MRSA. It was observed that Nisin could destabilise the MRSA biofilm by reducing the EPS production to an extent of ~ 55%. Mechanistic studies further demonstrated that Nisin was found to increase the intracellular accumulation of reactive oxygen species (ROS), which could lead to the alteration of cell membrane permeability. Additionally, Nisin attenuated staphyloxanthin production (~ 54%), hemolytic ability (~ 26%), and fibrinogen clumping ability (~ 27%) of MRSA, suggesting its interference in the virulence profile of MRSA. Collectively, these findings suggest Nisin's dual role as a promising Staphylococcal biofilm inhibitor and virulence factor suppressor, making it a viable option for the treatment of MRSA-linked infections.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-025-04597-8.},
}

@article {pmid41278148,
year = {2025},
author = {Dely, A and Racicot, R and Samples, R and Giddings, LA},
title = {Draft genome sequence and metabolomics data for Streptomyces sp. ADLamb9 isolated from the rhizosphere of Lavandula dentata.},
journal = {Data in brief},
volume = {63},
number = {},
pages = {112199},
pmid = {41278148},
issn = {2352-3409},
abstract = {Iron-chelating molecules or siderophores play pivotal roles in soil ecosystems, particularly in facilitating plant iron uptake as well as the phytoremediation of metal-polluted environments. Lavandula dentata, commonly referred to as French Lavender, is a valuable species for siderophore production due to its ability to thrive in iron-deficient Mediterranean soils by forming symbiotic relationships with siderophore-producing rhizosphere microbes. Here, we used a Chrome Azurol S (CAS) overlay assay to isolate a yellow-pigmented L. dentata rhizosphere siderophore-producing bacterium. This isolate also demonstrated antibacterial and antifungal activities against Bacillus subtilis and Aspergillus flavus, respectively. Genomic sequencing revealed that the isolate was Streptomyces sp. ADLamb9 with a genome size of 8.2 Mb and 71.77% GC content. antiSMASH analysis of the Streptomyces sp. ADLamb9 genome identified four putative siderophore biosynthetic gene clusters as well as the catecholate siderophore mirubactin. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) masses consistent with desferrioxamine B (561.3604 m/z), IC202C (517.3342 m/z), mirubactin (605.2207 m/z), as well as previously unreported desferrioxamine A1C. Notably, the presence of the rare earth element cerium differentially affected the accumulation of catecholate and hydroxamate siderophores, highlighting our incomplete understanding of the complex regulation and relationship between siderophore biosynthesis genes. These datasets, deposited at NCBI under the BioProject accession number PRJNA1224804, contribute to the broader scientific understanding of metabolite diversity and genomic features of Streptomyces sp. ADLamb9, providing insight into its use in bioremediation, especially in the presence of rare earth elements.},
}

@article {pmid41277839,
year = {2025},
author = {Qian, M and Zhu, D and Yao, K-y and Liu, S-y and Li, M-k and Ye, M and Zhu, Y-g},
title = {Coexistence of virome-encoded health-associated genes and pathogenic genes in global habitats.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0150125},
doi = {10.1128/aem.01501-25},
pmid = {41277839},
issn = {1098-5336},
abstract = {UNLABELLED: Viral remnants constitute approximately 8% of the human genome, reflecting extensive historical gene exchange between viruses and their hosts. Some viral genomes harbor genes acquired through horizontal gene transfer that are associated with potential benefits to human health, alongside genes associated with pathogenicity. However, their global distribution, functional characteristics, and coexistence patterns remain poorly understood. Here, using the Integrated Microbial Genomes and Virome (IMG/VR v4) database, we identified 4,556 viruses carrying gene segments associated with human health across eight habitat types spanning 13 regions and 76 countries worldwide. Among viruses with identifiable hosts, those distributed in humans (478) accounted for the highest proportion. The viral genes associated with human health included BCO1 (beta-carotene oxygenase 1), bioB (biotin synthase), COQ2 (4-hydroxybenzoate polyprenyltransferase), GPX1 (glutathione peroxidase 1), GSTs (glutathione transferases), GSTT1 (glutathione S-transferase theta 1), GULO (L-gulonolactone oxidase), and menA (1,4-dihydroxy-2-naphthoate polyprenyltransferase). These genes not only associate with human health but also function as auxiliary metabolic genes in viral genomes. Notably, four pathogenic genes were found in viral sequences carrying health-associated genes, with potential for transcription and expression, indicating functional interactions. Experimental transduction of the viral bioB gene into Escherichia coli altered the expression of host pathogenic genes GCH1 (GTP cyclohydrolase IA) and UGDH (UDP-glucose 6-dehydrogenase), supporting potential cross-regulatory interactions. Overall, this study incorporates health-associated genes into viral genomics, highlighting their coexistence with pathogenic genes, and provides new insights into virus-host coevolution and potential biotechnological applications.

IMPORTANCE: Viruses are the most abundant biological entities on Earth and key drivers of microbial evolution through horizontal gene transfer. While often studied for their pathogenic effects, viruses can also carry genes that influence host metabolism and health. Genes associated with human health have been identified in viral genomes, yet their global distribution, functions, and coexistence with pathogenic genes remain largely unexplored. This study integrates datasets of health-associated genes into viral genomic analyses, revealing for the first time the coexistence of viral health-associated genes with those linked to pathogenicity. This dual genetic potential is observed across diverse habitats, highlighting viruses as multifaceted reservoirs of both beneficial and harmful genes. The study findings advance understanding of viral functional diversity and open new avenues for exploring viral roles in microbial ecology, biotechnology, and human health.},
}

@article {pmid41277251,
year = {2025},
author = {Bron, A and Beltramo, C and Durif, C and Arora, T and Deschamps, C and Couturier, I and Domingo-Almenara, X and Otero, YF and Denis, S and Van de Wiele, T and Blanquet-Diot, S},
title = {Small intestine is not colon: a new in vitro model of the human ileum microbiome integrating the mucosal microenvironment and feeding status.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2579353},
doi = {10.1080/19490976.2025.2579353},
pmid = {41277251},
issn = {1949-0984},
mesh = {Humans ; *Ileum/microbiology ; *Gastrointestinal Microbiome/physiology ; *Colon/microbiology ; Adult ; *Intestinal Mucosa/microbiology ; Fatty Acids, Volatile/metabolism ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Fermentation ; Male ; Feces/microbiology ; Models, Biological ; Female ; Bile Acids and Salts/metabolism ; },
abstract = {The small intestinal microbiota plays a key role in human health but is understudied due to the invasiveness of sampling. There is no available model of the human ileal microbiome simulating the key nutritional and physicochemical parameters shaping this ecosystem, which has been fully validated based on in vivo data. Here, the Mucosal Artificial Ileum (M-ARILE) was set up to reproduce the pH, transit time, anoxic conditions, dynamics of feeding and microenvironments (luminal versus mucosal) found in a healthy human mid-ileum. To validate the newly developed in vitro system, nine-day fermentations were performed under either ileal or colonic conditions using the same fecal inoculum (n = 3 adult volunteers). The gut microbiota composition and metabolic activities were monitored daily. Distinct microbial signatures and metabolite profiles were obtained between in vitro ileum and colon conditions. In accordance with in vivo data, Peptostreptococcaceae, Clostridiaceae and Enterococcaceae were enriched in the ileum and associated with lower short-chain fatty acid production but higher O2 percentages. Interestingly, the abundances of key populations, such as Akkermansiaceae, and bile acid profiles were dependent on the feeding status of the M-ARILE. This new model provides a powerful platform for mechanistic studies on the role of ileal microbes in human nutrition and health considering inter-individual variabilities.},
}

Humans
*Ileum/microbiology
*Gastrointestinal Microbiome/physiology
*Colon/microbiology
Adult
*Intestinal Mucosa/microbiology
Fatty Acids, Volatile/metabolism
*Bacteria/classification/metabolism/genetics/isolation & purification
Fermentation
Male
Feces/microbiology
Models, Biological
Female
Bile Acids and Salts/metabolism

@article {pmid41275375,
year = {2025},
author = {Su, Z and Zhang, X and Wang, Q and Tang, Q and Yang, D and Liu, Y},
title = {amplysis: an R package for microbial composition and diversity analysis using 16S rRNA amplicon data.},
journal = {Briefings in functional genomics},
volume = {24},
number = {},
pages = {},
pmid = {41275375},
issn = {2041-2657},
support = {//Guangxi Education Agency/ ; //Guangxi Province Talent Project/ ; 42377012//National Natural Science Foundation of China/ ; },
mesh = {*RNA, Ribosomal, 16S/genetics ; *Software ; *Microbiota/genetics ; *Computational Biology/methods ; Biodiversity ; Bacteria/genetics/classification ; },
abstract = {The downstream analysis of 16S rRNA sequencing data remains a significant challenge for researchers lacking extensive bioinformatics expertise, often requiring proficiency in diverse tools and methodologies. To address this, we present amplysis, an R package designed to streamline the analysis and visualization of 16S rRNA amplicon sequencing data through an intuitive, code-light workflow. amplysis integrates data importing, processing, statistical analysis, and visualization into a unified framework. Key features include data normalization, microbial composition profiling, alpha/beta diversity analysis, ordination methods (e.g. Principal Component Analysis), and publication-ready visualization tools. The package's utility was demonstrated through three case studies, one of which analyzed microbial community responses to hexachlorocyclohexane (HCH) degradation in groundwater environments. Using amplysis, we efficiently generated phylum/genus-level abundance plots, alpha-diversity indices, and Principal Coordinates Analysis ordination, revealing significant shifts in community structure and diversity under HCH stress. The other case studies utilized publicly available data from published studies by other researchers. These results underscore the package's ability to simplify complex analyses while ensuring reproducibility and high-quality output. By integrating modular, user-friendly functions, amplysis lowers the barrier to robust microbiome data exploration. The package is available on GitHub (https://github.com/min-perilla/amplysis), offering a valuable resource for researchers in microbial ecology and environmental genomics.},
}

*RNA, Ribosomal, 16S/genetics
*Software
*Microbiota/genetics
*Computational Biology/methods
Biodiversity
Bacteria/genetics/classification

@article {pmid41275050,
year = {2025},
author = {Naziębło, A and Pytlak, A and Furtak, A and Dobrzyński, J},
title = {Advances and Hotspots in Research on Verrucomicrobiota: Focus on Agroecosystems.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02657-3},
pmid = {41275050},
issn = {1432-184X},
support = {2021/41/B/NZ9/03130//Narodowe Centrum Nauki/ ; 2021/41/B/NZ9/03130//Narodowe Centrum Nauki/ ; },
abstract = {Members of the phylum Verrucomicrobiota are abundant yet relatively understudied soil bacteria that play key roles in biogeochemical cycling and plant-microbe interactions. They participate in the carbon (C) and nitrogen (N) cycles through the degradation of complex organic polymers such as cellulose, pectin, and starch - via the production of hydrolytic enzymes (e.g., cellulases, xylanases, chitinases), and through nitrogen transformations including denitrification, ammonification, and nitrogen fixation. Methanotrophic representatives (Methylacidiphilum, Methylacidimicrobium) oxidise methane under acidic or thermophilic conditions, thereby contributing to greenhouse gas mitigation. The ecological distribution and activity of Verrucomicrobiota are strongly influenced by nutrient availability, particularly of C, N, phosphorus (P), and potassium (K). Their variable responses to these elements reflect diverse life-history strategies, encompassing both copiotrophic (r-strategist) and oligotrophic (K-strategist) taxa. While Spartobacteria (e.g., Ca. Udaeobacter) are typically oligotrophic, classes such as Opitutia and Verrucomicrobiae exhibit mixed strategies. Beyond nutrient cycling, several members of the phylum function as plant growth-promoting and stress mitigating bacteria. They produce phytohormones (e.g., indole-3-acetic acid) and siderophores, increase the availability of nitrogen and solubilise phosphate. Some taxa exhibit antioxidant activity and can suppress phytopathogens such as Fusarium oxysporum through secondary metabolite production. These traits suggest a significant potential in soil health improvement. Overall, Verrucomicrobiota represent a functionally diverse and ecologically significant bacterial phylum whose metabolic versatility, adaptive life strategies, and plant-associated traits underscore their central role in sustainable agricultural ecosystems.},
}

@article {pmid41274594,
year = {2025},
author = {Zou, H and Ying, W and Mafla Endara, PM and Klinghammer, F and Bai, J and Kang, H and Hammer, EC},
title = {Deep learning-driven investigation of nanoplastic impacts on soil protist behavior in soil chips.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {127414},
doi = {10.1016/j.envpol.2025.127414},
pmid = {41274594},
issn = {1873-6424},
abstract = {Nanoplastics are emerging environmental contaminants that increasingly threaten soil ecosystems, yet their effects on microbial behavior remain poorly understood. This is mainly due to the lack of experimental tools capable of directly observing microbial dynamics in situ under realistic soil-like conditions. Here, we present a proof-of-concept system that enables real-time, high-throughput monitoring of soil protists within microfluidic soil chips under nanoplastic exposure. Using microscopy video analysis integrated with a deep learning-based detection model and a transformer-based trajectory reconstruction algorithm, we quantitatively measured the movement of morpho-/locomotion type groups flagellates, ciliates, and amoebae across a gradient of nanoplastic concentrations (0, 2, and 10 mg/L). Our results showed reduced movement velocities for the groups of flagellates and ciliates under high nanoplastic conditions with a 24%-30% reduction in speed, while affect on amoebae was not detected. The trajectory data also provides novel insights into how protists navigate soil-like structures. Beyond these specific findings, our approach establishes a transformative framework for observing microbial life directly in its microenvironment, comparable to how animal behavior is monitored in ecological studies. By bridging real-time imaging and artificial intelligence, this method offers a new angle to study protist-environment interactions without the need for culture extraction. It opens the door to rethinking how microbial ecology, soil contamination, and biotic responses to environmental stressors are investigated, advancing opportunities from static, population-level measurements to dynamic, behavioral-level understanding within realistic habitats.},
}

@article {pmid41273983,
year = {2025},
author = {Wu, YX and Wang, HY and Chu, WC and Gao, YY and Xia, MQ and Liu, FF},
title = {Ecological implications of biodegradable and conventional microplastics: Dissolved organic matter bioavailability and microbial response in marine systems.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140526},
doi = {10.1016/j.jhazmat.2025.140526},
pmid = {41273983},
issn = {1873-3336},
abstract = {The increasing accumulation of microplastics (MPs) in marine environments raises concerns about their ecological impacts, particularly through the release of dissolved organic matter (DOM). However, the bioavailability and ecological effects of MPs-derived DOM (MPs-DOM) remain poorly understood. In this study, we systematically investigated the leaching characteristics and microbial bioavailability of DOM derived from three biodegradable MPs (BMPs) including polylactic acid (PLA), polycaprolactone (PCL), polybutylene adipate terephthalate (PBAT) and two conventional MPs (CMPs, PE: polyethylene, PET: polyethylene terephthalate) under simulated photoaging. Our results demonstrated that BMPs released significantly more dissolved organic carbon (DOC) than CMPs, with PBAT showing the highest yield (40.77 vs. PE: 11.63 mg-DOC g-C[-1]). Optical analyses revealed that BMPs-DOM contained more protein-like fluorescent components, with higher fluorescence index and biological index, indicating greater lability. BMPs-DOM stimulated microbial growth more efficiently, with PBAT supporting the highest bacterial concentrations (∼52 ×10[3] cells mL[-1]) and DOC utilization (76.39 %). 16S rRNA sequencing revealed that MPs-DOM exposure reduced community richness, reshaped microbial communities through selective enrichment of copiotrophic and plastic-degrading taxa (e.g., Pseudomonas, Bacteroidota), and promoted stochastically driven assembly with specialized functional modules. Our study highlights that while BMPs may alleviate particulate plastic accumulation, their labile DOM release warrants careful evaluation for potential impacts on marine microbial ecology.},
}

@article {pmid41273632,
year = {2025},
author = {Bi, J and Li, J and Rahman, SU and Long, Y and Hui, N and Romantschuk, M and Zheng, J and Zhang, X and Hou, D and Tan, J and Bi, Q and Xia, H and Yu, X and Luo, L and Liu, X},
title = {Balancing water efficiency and crop productivity: rhizosphere microbiome shifts in drought-resistant rice.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {12},
pages = {469},
pmid = {41273632},
issn = {1573-0972},
}

@article {pmid41272024,
year = {2025},
author = {Khatbane, M and Mangavel, C and Borges, F and Aridhi, S and Toussaint, Y},
title = {Knowledge graph embedding for predicting and analyzing microbial interactions.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-27591-9},
pmid = {41272024},
issn = {2045-2322},
support = {R31PNCVX//ML4Community Project/ ; R31PNCVX//ML4Community Project/ ; R31PNCVX//ML4Community Project/ ; R31PNCVX//ML4Community Project/ ; R31PNCVX//ML4Community Project/ ; },
abstract = {Interactions between microorganisms play a major role in shaping the structure and function of microbial communities, yet their prediction remains a challenge in microbial ecology. While currently available machine learning methods have shown promising performance, they often rely on extensive input features that are obtained from labor-intensive experiments. Here, we propose a new framework to predict pairwise interactions that minimizes the need for in vitro experimentation. Our approach is based on knowledge graph embedding, which learns the representation of microorganisms and their interactions in an embedding space. Using a dataset of interactions between 20 soil bacterial strains cocultured in 40 different carbon source environments, we demonstrate the effectiveness of our framework in accurately predicting pairwise interactions. Notably, we show that our model can predict interactions involving strains with missing culture data. We additionally show that the obtained embeddings can reveal similarities between carbon source environments, enabling the prediction of interactions in one environment based on the outcomes in a similar environment between the same pair of microorganisms. Furthermore, our approach allows the design of a recommendation system that can be used to guide microbial community engineering. These findings demonstrate that knowledge graph embedding is a promising modeling strategy in microbial ecology.},
}

@article {pmid41271578,
year = {2025},
author = {Man, M and Castañeda-Gómez, L and Moisan, MA and Gagné, P and Martineau, C and Ghosh Biswas, R and Knorr, MA and Frey, SD and Cadotte, MW and Nadelhoffer, KJ and Lajtha, K and Simpson, AJ and Simpson, MJ},
title = {Deciphering the Complex Interactions between Litter Inputs and Microbial Responses in Modulating Long-Term Soil Organic Matter Dynamics.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c08706},
pmid = {41271578},
issn = {1520-5851},
abstract = {Natural climate solutions that focus on increasing carbon in forests rely on the potential for additional carbon that may be incorporated into soil organic matter (SOM). The fate of soil carbon in temperate forests remains uncertain due to the complex role of microbes and their regulation of carbon flows in soils, especially with the addition of extra litter. We identified comprehensive molecular-level evidence that revealed shifts in SOM composition and microbial communities after 30 years of added litter in a temperate deciduous forest. Chronic litter addition failed to add new soil carbon after 30 years and correlated with reorganization in microbial community composition and altered carbon use. Excluding detrital inputs decreased soil carbon content, resulting in enhanced SOM decomposition and shifts toward specific bacterial groups (such as oligotrophs) that can utilize less energetically favorable carbon substrates that are typically more recalcitrant. Collectively, we found that microbial communities shifted in composition and altered carbon use strategies and traits, which aligned with changes to the molecular composition of SOM. Finally, this work demonstrates that in mesic temperate forests, decadal increases in litterfall, resulting from increased ecosystem productivity or management, may not offset soil carbon losses from climate change nor enhance carbon sequestration.},
}

@article {pmid41270014,
year = {2025},
author = {Madsusan, A and Krainara, S and Suksong, W and Sudchoo, K and Tohmoh, N and Jonggrijug, P and Maipunklang, C and Chadaram, C and Samaeng, K and Kurdthongmee, P and Noosab, U and Nakapong, A and Udomsri, Y and Kanaso, S and Sakorn, N and Guan, NY and Sangkhano, S},
title = {Impact of a tropical monsoon climate on formaldehyde exposure and microbial contamination in anatomy dissection hall.},
journal = {PloS one},
volume = {20},
number = {11},
pages = {e0337238},
doi = {10.1371/journal.pone.0337238},
pmid = {41270014},
issn = {1932-6203},
mesh = {*Formaldehyde/analysis/adverse effects ; Humans ; *Occupational Exposure/analysis ; *Tropical Climate ; *Dissection ; Thailand ; *Air Pollution, Indoor/analysis ; *Anatomy/education ; Microbiota ; },
abstract = {Gross anatomy dissection is an essential component of medical and health science education, yet it presents notable occupational hazards, particularly from formaldehyde (FA) exposure and microbial contamination. These risks may be intensified in anatomy dissection halls located in tropical monsoon (Am) climates, where elevated humidity and temperature promote both chemical volatility and microbial persistence. This study assessed the combined effects of such climatic conditions on FA concentrations and microbial ecology within a naturally ventilated dissection hall in southern Thailand. FA levels were measured through personal and area air sampling across seven anatomical regions, while microbial contamination on cadaver-contact surfaces was evaluated using culture-based methods and high-throughput sequencing. Functional prediction of microbial communities was performed using PICRUSt2 to assess their metabolic adaptation to environmental stressors. The results revealed that both personal and indoor FA concentrations (mean 1.17 ± 0.39 ppm and 1.09 ± 0.45 ppm, respectively) exceeded several international occupational exposure limits, with the highest levels observed during dissections involving deep or adipose-rich anatomical regions. Microbial analyses identified stress-tolerant and potentially pathogenic genera, including Bdellovibrio, Aequorivita, and Aspergillus spp., along with enriched pathways involved in aromatic compound degradation and environmental resilience. These findings highlight the limitations of natural ventilation in controlling occupational exposures and microbial contamination in Am climate anatomy laboratories. The study supports the implementation of climate-responsive engineering controls and laboratory management strategies that address chemical safety, thermal regulation, and biosafety to promote healthier and more sustainable dissection environments in similar high-risk settings.},
}

*Formaldehyde/analysis/adverse effects
Humans
*Occupational Exposure/analysis
*Tropical Climate
*Dissection
Thailand
*Air Pollution, Indoor/analysis
*Anatomy/education
Microbiota

@article {pmid41269303,
year = {2025},
author = {Xin, H and He, L and Zhu, B},
title = {Ecological Insights into Gut Microbiota Networks Across Cognitive States in Alzheimer's Disease.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02662-6},
pmid = {41269303},
issn = {1432-184X},
support = {No. 202212691//Jiangxi Provincial Health Commission/ ; },
abstract = {The ecological mechanisms governing gut microbial community stability during Alzheimer's disease (AD) progression remain poorly understood. This study employed an ecological network to investigate microbial interactions and stability across cognitively normal controls (CK), individuals with mild cognitive impairment (MCI), and AD patients. We observed a stepwise decline in network complexity across groups, characterized by reduced clustering coefficients and average degree, from CK to AD. While the MCI group exhibited intermediate structural complexity, it displayed the highest vulnerability and lowest robustness, indicating a critical transitional state. Keystone taxa analysis revealed a significant shift in microbial community, with the CK network was enriched with diverse, potentially beneficial keystone taxa, whereas the AD network retained only connector species, and the MCI network showed a complete absence of keystone taxa. Cohesion analysis revealed a non-linear trajectory of microbial interactions, with negative cohesion peaking in MCI. Our findings demonstrate that cognitive decline is associated with a fundamental reorganization of the gut microbial ecosystem. This reorganization pattern reveals a resilient state in health, a vulnerable phase in MCI, and a stable yet dysbiotic configuration in AD, with keystone taxa serving as pivotal regulators of community stability. Community assembly analysis showed a shift from deterministic to stochastic processes during cognitive decline, with weakened host regulatory mechanisms. These findings advance our understanding of the gut microbial ecology in neurodegenerative disease and reveal the mechanism by which microbial communities reorganize network to maintain stability in different cognitive states.},
}

@article {pmid41268901,
year = {2025},
author = {Zhao, Y and Zhao, Y and Dong, Y and Sun, X and Zhang, W and Zhao, L and Grégori, G},
title = {Biogeography of Virioplankton Abundance and Subcluster Patterns in the Northwest Pacific: A Large-Scale Perspective.},
journal = {MicrobiologyOpen},
volume = {14},
number = {6},
pages = {e70161},
doi = {10.1002/mbo3.70161},
pmid = {41268901},
issn = {2045-8827},
support = {//This study was financially supported by the National Natural Science Foundation of China (No. 42076139), National Key Research and Development Program of China (No. 2024YFE0114300), and the Sino-French International Research Project (CNRS-CAS) Dynamics and Function of Marine Microorganisms (IRP-DYF2M): insight from physics and remote sensing./ ; },
mesh = {Pacific Ocean ; *Seawater/virology ; *Plankton/virology/classification ; *Viruses/classification/isolation & purification/genetics ; Flow Cytometry ; Phylogeography ; Biodiversity ; },
abstract = {Marine virioplankton, the most abundant biological entities in the ocean, play essential roles in microbial ecology and biogeochemical cycling. This study investigates their biogeography in the Northwest Pacific using enhanced-resolution flow cytometry and phenotypic diversity analyses. By resolving four consistent viral subclusters across oceanic and coastal waters and detecting a fifth subcluster in the Yellow Sea, we revealed previously unrecognized patterns of viral community structures. Viral abundances ranged from 3.69 × 10[6] to 17.09 × 10[6] particles/mL, showing clear coastal-oceanic differentiation. Environmental gradients, particularly temperature, chlorophyll, and picoplankton abundance, emerged as the primary drivers of virioplankton community structure. These findings underscored the tight coupling between viral populations and their microbial hosts across contrasting marine environments. Phenotypic diversity analysis revealed distinct viral communities in the Luzon Strait, despite comparable abundance patterns to adjacent regions, demonstrating the method's sensitivity in detecting subtle community shifts. This study advances understanding of marine viral biogeography and introduces a robust framework for investigating viral community dynamics. The approach enables high-throughput screening across large spatial scales while maintaining sensitivity to fine-scale community variations, offering new possibilities for monitoring viral responses to environmental change in marine ecosystems.},
}

Pacific Ocean
*Seawater/virology
*Plankton/virology/classification
*Viruses/classification/isolation & purification/genetics
Flow Cytometry
Phylogeography
Biodiversity

@article {pmid41268888,
year = {2025},
author = {Trivedi, S and Roy, R and Naskar, A and Das, B and Chakraborty, P and Paul, P and Das, S and Malik, M and Tribedi, P},
title = {Cuminaldehyde Potentiates the Antimicrobial and Antibiofilm Activity of Vancomycin: A Biochemical Study to Manage the Threats of Methicillin Resistant Staphylococcus aureus (MRSA).},
journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica},
volume = {133},
number = {11},
pages = {e70087},
doi = {10.1111/apm.70087},
pmid = {41268888},
issn = {1600-0463},
support = {TNU/R&D/MG/24/02//The Neotia University/ ; TNU/R&D/MG/24/04//The Neotia University/ ; },
mesh = {*Methicillin-Resistant Staphylococcus aureus/drug effects/physiology ; *Vancomycin/pharmacology ; *Biofilms/drug effects ; *Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; Drug Synergism ; Humans ; Oxidative Stress/drug effects ; Bacterial Adhesion/drug effects ; Reactive Oxygen Species/metabolism ; *Benzaldehydes/pharmacology ; Staphylococcal Infections/microbiology/drug therapy ; Virulence Factors/metabolism ; },
abstract = {Methicillin-resistant Staphylococcus aureus (MRSA) is reported to cause serious health issues in humans by exploiting its biofilm network. To combat this global concern, the combined efficacy of cuminaldehyde (a bioactive phytochemical) and vancomycin (an antibiotic) was tested against MRSA strains. While both compounds exhibited independent antibacterial activity, their combination revealed improved efficacy against MRSA through additive interactions. Response surface methodology (RSM)-generated quadratic models optimized the combinatorial doses, revealing significant microbial growth inhibition of the MRSA strains (p < 0.05). Furthermore, the combined application of cuminaldehyde and vancomycin at sub-MIC doses could inhibit biofilm formation by lowering bacterial adhesion, extracellular polysaccharide (EP) synthesis and the extent of biofilm-associated proteins. Additionally, the mechanistic studies revealed that the said combination (cuminaldehyde and vancomycin) was found to accumulate oxidative stress with a ~2.5-fold increase in intracellular reactive oxygen species (ROS) and a ~2.3-fold reduction in membrane integrity. In view of the same, this combination attenuated key virulence factors (protease, hemolysin, and coagulase) and metabolic activity of MRSA. Hence, the combinations involving cuminaldehyde and vancomycin could potentially enhance the antimicrobial and antibiofilm efficacy, presenting a promising approach to combat the escalating crisis linked with MRSA-associated threats.},
}

*Methicillin-Resistant Staphylococcus aureus/drug effects/physiology
*Vancomycin/pharmacology
*Biofilms/drug effects
*Anti-Bacterial Agents/pharmacology
Microbial Sensitivity Tests
Drug Synergism
Humans
Oxidative Stress/drug effects
Bacterial Adhesion/drug effects
Reactive Oxygen Species/metabolism
*Benzaldehydes/pharmacology
Staphylococcal Infections/microbiology/drug therapy
Virulence Factors/metabolism

@article {pmid41268502,
year = {2025},
author = {Fu, Y and Dou, Q and Wang, F and Virta, M and Zhang, T and Elsner, M and Amelung, W and Jiang, X and Tiedje, JM},
title = {A flowing database: Harnessing sewage-based surveillance for antimicrobial resistance.},
journal = {Innovation (Cambridge (Mass.))},
volume = {6},
number = {11},
pages = {100977},
pmid = {41268502},
issn = {2666-6758},
}

@article {pmid41267490,
year = {2025},
author = {Sharma, P and Dagariya, S and Sharma, S and Singh, M},
title = {Uncovering the nexus of human health hazards of nanoplastics, gut-dysbiosis and antibiotic-resistance.},
journal = {Journal of environmental science and health. Part C, Toxicology and carcinogenesis},
volume = {},
number = {},
pages = {1-60},
doi = {10.1080/26896583.2025.2578871},
pmid = {41267490},
issn = {2689-6591},
abstract = {Nanoplastics (1-1000 nm) (NPs) represent a novel and insidious class of emerging contaminants with the potential to profoundly disrupt gut microbial ecology and accelerate the spread of antibiotic resistance two critical and converging threats to global health. While prior studies have examined the toxicokinetics of NPs and their general microbial interactions, this review provides the first comprehensive synthesis specifically focused on the nexus between NPs, gut dysbiosis, and the propagation of antibiotic resistance genes (ARGs). This review highlights how NPs alter gut microbiota composition, suppressing beneficial microbes while fostering opportunistic pathogens and how such imbalances may contribute to human health issues. Importantly, emerging evidence also suggests that NPs may serve as unrecognized vectors for horizontal gene transfer (HGT), enabling the rapid dissemination of ARGs via conjugation, transformation, transduction, and extracellular vesicles within the gastrointestinal tract. In addition, this review also identifies urgent methodological gaps in detecting NPs in biological matrices and the environment, as well as assessing their mechanistic impacts, calling for innovation in analytical approaches. By presenting an interdisciplinary perspective that bridges nanotoxicology, microbiome science, and antimicrobial resistance, this article sheds light on an underexplored yet urgent frontier in environmental health, offering novel insights to guide future research, risk assessment, and policy development.},
}

@article {pmid41266882,
year = {2025},
author = {Hu, H and Zhang, Y and Liu, Z and Han, Y and Luo, Y and Zhang, C and Yu, Y and Wang, J and Li, B and Su, S},
title = {Microbial Diversity Affects the Cold Tolerance of Red Swamp Crayfish (Procambarus clarkii) by Regulating Histamine Metabolism.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02659-1},
pmid = {41266882},
issn = {1432-184X},
support = {No. 2025JBFR03//Central Public-interest Scientific Institution Basal Research Fund, Freshwater Fisheries Research Center, CAFS/ ; No. 2025JBFR03//Central Public-interest Scientific Institution Basal Research Fund, Freshwater Fisheries Research Center, CAFS/ ; No. 2025JBFR03//Central Public-interest Scientific Institution Basal Research Fund, Freshwater Fisheries Research Center, CAFS/ ; No. 2025JBFR03//Central Public-interest Scientific Institution Basal Research Fund, Freshwater Fisheries Research Center, CAFS/ ; No. 2025JBFR03//Central Public-interest Scientific Institution Basal Research Fund, Freshwater Fisheries Research Center, CAFS/ ; DTYZ2024003//"Soil Transplantation" Team Project of Panjin Talent Program/ ; DTYZ2024003//"Soil Transplantation" Team Project of Panjin Talent Program/ ; DTYZ2024003//"Soil Transplantation" Team Project of Panjin Talent Program/ ; DTYZ2024003//"Soil Transplantation" Team Project of Panjin Talent Program/ ; DTYZ2024003//"Soil Transplantation" Team Project of Panjin Talent Program/ ; DTYZ2024003//"Soil Transplantation" Team Project of Panjin Talent Program/ ; JBGS [2021]123//"JBGS" Project of Seed Industry Revitalization in Jiangsu Province/ ; JBGS [2021]123//"JBGS" Project of Seed Industry Revitalization in Jiangsu Province/ ; JBGS [2021]123//"JBGS" Project of Seed Industry Revitalization in Jiangsu Province/ ; 2023TD39//Central Public-Interest Scientific Institution Basal Research Fund, CAFS/ ; 2023TD39//Central Public-Interest Scientific Institution Basal Research Fund, CAFS/ ; },
abstract = {The red swamp crayfish (Procambarus clarkii) is one of the important freshwater aquaculture species in China, but its growth and development are greatly affected by temperature, which makes it difficult to expand its aquaculture range to the northern regions of China. The composition of gut microbes plays a vital role in resisting environmental pressure, and is also an important driving factor for amino acid metabolism in the body. However, little is known about the relationship between microorganisms, metabolism, and cold-resistance ability of P. clarkii. In this study, we performed the cold-resistance and antioxidant ability test, gut microbiota diversity analysis, quantitative analysis of histamine, and bioinformatics analysis of histamine receptor (HR) family on P. clarkii. The results showed that the cold-resistance crayfish exhibited high antioxidant ability and low gut microbiota diversity after acute cold stress. Next, we also found that there was significant correlation between the Lactobacilli genus and histamine abundance, indicating that the excellent cold tolerance ability of crayfish may stem from the degradation of histamine by Lactobacilli. Finally, it was revealed that HR genes had considerable quantity of gene copies, conservative evolution in crustacean lineages and expression differences in low-temperature tolerant populations. These results suggested that the diversity of Lactobacillus mediated changes in histamine metabolism affect antioxidant capacity, which is one of the reasons why P. clarkii exhibits cold resistance ability. This finding provided a theoretical basis for understanding the microorganism-histamine regulation mechanism of red swamp crayfish under cold stress, promoting the breeding and healthy culture of cold-resistance strain.},
}

@article {pmid41266660,
year = {2025},
author = {Caroppo, C and Caruso, G and Bergamasco, A and Decembrini, F},
title = {Phytoplankton diversity and size structure in the Central-Southern Tyrrhenian Sea: implications for microbial functioning.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02650-w},
pmid = {41266660},
issn = {1432-184X},
abstract = {Microbial community dynamics in relation to mesoscale hydrographical features are almost unknown particularly in the pelagic Central-Southern Tyrrhenian Sea. To get a more comprehensive view of phytoplankton community structure and microbial community functioning, datasets of phytoplankton abundance, composition and some microbial enzyme activities (leucine aminopeptidase, LAP, beta-glucosidase, GLU and alkaline phosphatase, AP) from six cruises carried out twenty years ago were analyzed. Hydrographic characteristics identified the presence of both Atlantic Waters (AW) and Tyrrhenian Intermediate Waters (TIW). Size structure of phytoplankton biomass showed an unexpected high contribution of the pico-phytoplankton to the total primary production (> 60%) determining a predominant microbial food web. Phytoplankton distribution patterns varied more significantly on a seasonal rather than spatial scale. Autumn assemblages were characterized by the highest abundance and carbon content, with species mainly belonging to dinoflagellates whose growth was supported by intense microbial activities. In contrast, in the summer diatoms developed in unstable TIW where microbial activity was declining. Enzymatic activities varied in the different water masses and seasons, with high LAP activity in summer AW (s-AW) as well as in deep TIW (d-TIW), while AP and GLU reached their maximum in autumn AW (a-AW), suggesting quick organic matter recycling. Coupled primary production and hydrolysis in mixed AW (m-AW) and in a-AW indicated synchronized autotrophic and heterotrophic processes, while in TIW organic matter was only partially recycled. Overall, microbial metabolism was closely shaped by hydrographic and seasonal dynamics, confirming its key role in biogeochemical cycles. Our data could provide a baseline study for future research dealing with the microbial functioning in this Mediterranean region.},
}

@article {pmid41074769,
year = {2025},
author = {Tucker, SJ and Freel, KC and Eren, AM and Rappé, MS},
title = {Habitat-specificity in SAR11 is associated with a few genes under high selection.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
doi = {10.1093/ismejo/wraf216},
pmid = {41074769},
issn = {1751-7370},
support = {#989028//Simons Postdoctoral Fellowship in Marine Microbial Ecology/ ; NA20NOS4200123//National Science Foundation Graduate Research/ ; 1842402//National Science Foundation Graduate Research/ ; #687269//Simons Foundation/ ; },
mesh = {*Ecosystem ; Phylogeny ; *Selection, Genetic ; *Seawater/microbiology ; Metagenome ; *Alphaproteobacteria/genetics/classification/isolation & purification ; Metagenomics ; Genome, Bacterial ; Pacific Ocean ; Genetic Variation ; },
abstract = {The order Pelagibacterales (SAR11) is the most abundant group of heterotrophic bacteria in the global surface ocean, where individual sublineages likely play distinct roles in oceanic biogeochemical cycles. Yet, understanding the determinants of niche-partitioning within SAR11 has been a formidable challenge due to the high genetic diversity within individual SAR11 sublineages and the limited availability of high-quality genomes from both cultivation and metagenomic reconstruction. Through an integrated metapangenomic analysis of 71 new SAR11 isolate genomes and a time-series of metagenomes from the prominent source of isolation, we reveal an ecological and phylogenetic partitioning of metabolic traits across SAR11 genera. We resolve distinct habitat-preferences among genera for coastal or offshore environments of the tropical Pacific and identify a handful of genes involved in carbon and nitrogen metabolisms that appear to contribute to these contrasting lifestyles. Furthermore, we find that some habitat-specific genes experience high selective pressures, indicating that they are critical determinants of SAR11 fitness and niche differentiation. Together, these insights reveal the underlying evolutionary processes shaping niche-partitioning within sympatric and parapatric populations of SAR11 and demonstrate that the immense genomic diversity of SAR11 bacteria naturally segregates into ecologically and genetically cohesive units, or ecotypes, that vary in spatial distributions in the tropical Pacific.},
}

*Ecosystem
Phylogeny
*Selection, Genetic
*Seawater/microbiology
Metagenome
*Alphaproteobacteria/genetics/classification/isolation & purification
Metagenomics
Genome, Bacterial
Pacific Ocean
Genetic Variation

@article {pmid41265332,
year = {2025},
author = {Mol, Z and Segers, L and Van Langenhove, H and Vandermarliere, T and De Gusseme, B and Walgraeve, C and Demeestere, K},
title = {Pressure-induced taste and odour deviations within the high-pressure drinking water distribution system.},
journal = {Water research},
volume = {289},
number = {Pt B},
pages = {124965},
doi = {10.1016/j.watres.2025.124965},
pmid = {41265332},
issn = {1879-2448},
abstract = {Taste and odour (T&O) issues in tap water decrease the willingness of consumers to drink it. Production and/or release of odour compounds during drinking water distribution should be avoided as the water is directly delivered to consumers without further treatment. Odours can be caused by leaching of compounds from pipe materials, microbial metabolism, disinfection reactions, or diffusion of odour compounds or precursors from external sources. Increasing knowledge of T&O origins is needed to better solve future problems. Therefore, this research focuses on odour linked to changes in pressure because of maintenance work at the high-pressure (HP) drinking water distribution system. A trace analytical method targeting 45 T&O compounds is further optimized by including derivatisation to improve halophenol detection. Next, in a field section of a real HP pipe (± 3 km), three scenarios were systematically investigated. Lowering the overpressure in the HP pipe from 10 to 5 bar resulted in an observed bitumen/asphalt odour, that further increased in intensity after a subsequent sudden pressure drop to 2 bar. Based on the odour threshold and profile, two halophenols were detected that may have contributed to this odour observation. When the section was partially emptied, 6 halophenols and 5 other T&O compounds were identified. Our results indicate that pressure changes induce the leaching of T&O compounds from sealing materials connecting the 6m-pipe sections. This is further supported by the detection of similar T&O compounds in a water extract of the sealing materials and in an odorous household sample collected after maintenance work in the HP-network.},
}

@article {pmid41264968,
year = {2025},
author = {Yang, C and Bao, L and Shi, Z and Xv, X and Li, J and Jiang, D and You, L},
title = {Jingning formula alleviates ADHD by restoring gut microbiota dysbiosis and tryptophan metabolic dysfunction.},
journal = {Journal of pharmaceutical and biomedical analysis},
volume = {269},
number = {},
pages = {117256},
doi = {10.1016/j.jpba.2025.117256},
pmid = {41264968},
issn = {1873-264X},
abstract = {Jingning Fang (JNF), a clinically used herbal medicine for attention deficit hyperactivity disorder (ADHD), demonstrates significant efficacy in alleviating core symptoms such as hyperactivity and impulsivity in pediatric patients. To systematically investigate its therapeutic mechanisms, we implemented an integrated approach encompassing UPLC-Q-TOF/MS-based untargeted metabolomics profiling of brain, serum, and fecal specimens, targeted quantification of tryptophan pathway metabolites across these biological compartments, and gut microbiome characterization via 16S rRNA sequencing. Our analysis revealed a prominently dysregulated metabolic pathway in ADHD, characterized by perturbations in tryptophan metabolism that were particularly pronounced in feces (P < 0.05). Notably, the kynurenic acid (KYNA)/quinolinic acid (QUINA) ratio, a pivotal indicator of kynurenine pathway homeostasis, exhibited robust correlations with both behavioral manifestations and gut microbial ecology. These findings provide a mechanistic basis for JNF's clinical efficacy in ADHD management by highlighting its role in restoring gut microbiome balance and tryptophan metabolic homeostasis.},
}

@article {pmid41264852,
year = {2025},
author = {Kosmopoulos, JC and Anantharaman, K},
title = {Viral Dark Matter: Illuminating Protein Function, Ecology, and Biotechnological Promises.},
journal = {Biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.biochem.5c00349},
pmid = {41264852},
issn = {1520-4995},
abstract = {Viruses are the most abundant biological entities on Earth and play central roles in shaping microbiomes and influencing ecosystem functions. Yet, most viral genes remain uncharacterized, comprising what is commonly referred to as "viral dark matter." Metagenomic studies across diverse environments consistently show that 40-90% of viral genes lack known homologues or annotated functions. This persistent knowledge gap limits our ability to interpret viral sequence data, understand virus-host interactions, and assess the ecological or applied significance of viral genes. Among the most intriguing components of viral dark matter are auxiliary viral genes (AVGs), including auxiliary metabolic genes (AMGs), regulatory genes (AReGs), and host-physiology-modifying genes (APGs), which may alter host function during infection and contribute to microbial metabolism, stress tolerance, or resistance. In this Review, we explore recent advances in the discovery and functional characterization of viral dark matter. We highlight representative examples of novel viral proteins across diverse ecosystems, including human microbiomes, soil, oceans, and extreme environments, and discuss what is known and still unknown about their roles. We then examine the bioinformatic and experimental challenges that hinder functional characterization and present emerging strategies to overcome these barriers. Finally, we highlight both the fundamental and applied benefits that multidisciplinary efforts to characterize viral proteins can bring. By integrating computational predictions with experimental validation and fostering collaboration across disciplines, we emphasize that illuminating viral dark matter is both feasible and essential for advancing microbial ecology and unlocking new tools for biotechnology.},
}

@article {pmid41264018,
year = {2025},
author = {Villalón, A and Rodríguez Alonso, Á and Carballo, J and Rodríguez López, LA and Pérez, MJ},
title = {Diversity of Bacteria and Yeasts Present in an Automobile Treatment System.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02651-9},
pmid = {41264018},
issn = {1432-184X},
abstract = {The formation of biofilms in industrial environments poses a significant challenge because of their ability to degrade materials, contaminate products, and harbour pathogenic microorganisms. In the automotive industry, surface treatment systems (STS) used to prepare car bodies can provide a favourable environment for microbial development, driven by the presence of water, organic matter, and variable physicochemical conditions. In this context, the microbial diversity present in the different STS baths of an automotive plant, as well as in the process water, was analysed. Through culture-based methods and molecular analysis, 33 bacterial and 6 yeast species were identified. The results revealed a constant presence of bacteria at all sampling points, whereas yeasts were detected less frequently and in more localized areas (Industrial and Dechromatized Water, E2, Conversion stage, E4 and Passivation stage). This study underscores the importance to enhance cleaning and disinfection protocols in STS, as high bacterial counts persisted even after rinsing stages, in order to prevent economic losses, product degradation and health risks. Furthermore, it highlights the potential use of certain microorganisms in biotechnology and bioremediation applications.},
}

@article {pmid41263569,
year = {2025},
author = {Ding, W and Ling, Z and Liu, X and Zhang, J and Cheng, Y and Zhu, Z and Wu, L and Xu, X and Gao, Y and Hu, X},
title = {Impact of carbapenem-resistant Klebsiella pneumoniae infection on gut microbiota and host immunity: a case-control study.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0297525},
doi = {10.1128/spectrum.02975-25},
pmid = {41263569},
issn = {2165-0497},
abstract = {Carbapenem-resistant Klebsiella pneumoniae (CRKP) represents a critical global health threat with limited treatment options. While the gut microbiota is a reservoir for opportunistic pathogens and a regulator of host immunity, the reciprocal impact of systemic CRKP infection on gut microbial ecology and immune responses remains poorly defined. In a prospective case-control study, 38 patients with confirmed CRKP infection and 38 matched hospitalized controls without CRKP were enrolled. Fecal samples underwent 16S rRNA gene sequencing to characterize microbial profiles, and serum cytokine levels were quantified using multiplex immunoassays. CRKP infection was associated with significantly reduced microbial diversity and a distinct shift in community structure, characterized by depletion of beneficial commensals (Bacteroides, Faecalibacterium, Roseburia) and enrichment of pathobionts (Klebsiella, Enterococcus). Enterotype analysis revealed a predominance of a Klebsiella/Enterococcus-dominated enterotype in CRKP patients. Functional predictions indicated impaired carbohydrate and butyrate metabolism alongside increased virulence- and resistance-associated pathways. Systemically, patients exhibited elevated pro-inflammatory cytokines (IL-6, TNF-α, IFN-γ) and chemokines (IP-10, MCP-1, RANTES). Correlation analyses linked opportunistic taxa with heightened inflammatory markers, while beneficial short-chain fatty acid producers showed inverse associations. Systemic CRKP infection is associated with profound gut dysbiosis and a hyper-inflammatory immune response. The strong microbiota-immune correlations suggest that the gut microbiota may serve as a biomarker and a potential therapeutic target for mitigating CRKP-associated immune dysfunction, though the directional relationship (cause vs. consequence) between dysbiosis and CRKP infection remains to be elucidated.IMPORTANCECarbapenem-resistant Klebsiella pneumoniae (CRKP) is a critical global threat with limited therapeutic options. This study reveals that systemic CRKP infection is associated with profound gut dysbiosis-characterized by loss of beneficial commensals (e.g., Faecalibacterium) and expansion of pathobionts (e.g., Klebsiella, Enterococcus)-as well as a hyperinflammatory immune response. We demonstrate strong correlations between specific microbial taxa and host cytokines, suggesting that the gut microbiome may hold potential as a biomarker and therapeutic target. These findings enhance our understanding of host-microbe interactions in CRKP infection and support the exploration of microbiota-based therapies. However, further studies, including longitudinal and animal models, are needed to clarify whether gut dysbiosis directly influences CRKP outcomes or is a secondary consequence.},
}

@article {pmid41263391,
year = {2025},
author = {Gilbert, JA and Scholz, AH and Dominguez Bello, MG and Korsten, L and Berg, G and Singh, BK and Boetius, A and Wang, F and Greening, C and Wrighton, K and Bordenstein, SR and Jansson, J and Lennon, JT and Souza, V and Allard, SM and Thomas, T and Cowan, D and Crowther, TW and Nguyen, N and Harper, L and Haraoui, LP and Ishaq, SL and McFall-Ngai, M and Redford, KH and Peixoto, R},
title = {Safeguarding microbial biodiversity: microbial conservation specialist group within the species survival commission of the International Union for Conservation of Nature.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
doi = {10.1093/ismejo/wraf239},
pmid = {41263391},
issn = {1751-7370},
}

@article {pmid41263344,
year = {2025},
author = {Gilbert, JA and Scholz, AH and Dominguez Bello, MG and Korsten, L and Berg, G and Singh, BK and Boetius, A and Wang, F and Greening, C and Wrighton, K and Bordenstein, SR and Jansson, J and Lennon, JT and Souza, V and Allard, SM and Thomas, T and Cowan, D and Crowther, TW and Nguyen, N and Harper, L and Haraoui, LP and Ishaq, SL and McFall-Ngai, M and Redford, KH and Peixoto, R},
title = {Safeguarding microbial biodiversity: microbial conservation specialist group within the species survival commission of the International Union for Conservation of Nature.},
journal = {FEMS microbiology ecology},
volume = {101},
number = {12},
pages = {},
doi = {10.1093/femsec/fiaf107},
pmid = {41263344},
issn = {1574-6941},
support = {//Gordon and Betty Moore Foundation/ ; },
}

@article {pmid41263324,
year = {2025},
author = {Gilbert, JA and Scholz, AH and Dominguez Bello, MG and Korsten, L and Berg, G and Singh, BK and Boetius, A and Wang, F and Greening, C and Wrighton, K and Bordenstein, SR and Jansson, J and Lennon, JT and Souza, V and Allard, SM and Thomas, T and Cowan, D and Crowther, TW and Nguyen, N and Harper, L and Haraoui, L-P and Ishaq, SL and McFall-Ngai, M and Redford, KH and Peixoto, R},
title = {Safeguarding microbial biodiversity: microbial conservation specialist group within the species survival commission of the International Union for Conservation of Nature.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0150525},
doi = {10.1128/msystems.01505-25},
pmid = {41263324},
issn = {2379-5077},
}

@article {pmid41262936,
year = {2025},
author = {Postec, A and Yumoto, I and Morales-Barrera, L and Gessesse, A and McMillan, DGG},
title = {Editorial: Microbial ecology and biotechnological potential of alkaline environments.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1726999},
pmid = {41262936},
issn = {1664-302X},
}

@article {pmid41262263,
year = {2025},
author = {Bautista, J and López-Cortés, A},
title = {Chronobiome medicine: circadian regulation of host-microbiota crosstalk in systemic physiology.},
journal = {Frontiers in endocrinology},
volume = {16},
number = {},
pages = {1691172},
pmid = {41262263},
issn = {1664-2392},
mesh = {Humans ; *Circadian Rhythm/physiology ; *Gastrointestinal Microbiome/physiology ; Animals ; },
abstract = {Circadian rhythms, governed by central and peripheral clocks, orchestrate nearly all aspects of human physiology, including metabolism, endocrine function, neuroimmune activity, and behavior. Emerging evidence reveals that these oscillations are closely intertwined with the gut microbiota, which itself displays diurnal fluctuations in composition and metabolite production. This bidirectional regulation establishes a dynamic circadian-microbiota axis that synchronizes nutrient processing, hormonal secretion, immune surveillance, and neural signaling. Disruption of this temporal alignment, through genetic, environmental, or lifestyle factors, precipitates systemic dysregulation, fostering metabolic syndrome, endocrine imbalance, immune dysfunction, neuropsychiatric vulnerability, cardiovascular alterations, and carcinogenesis. Mechanistic studies highlight that microbial-derived metabolites such as short-chain fatty acids, bile acids, and indoles act as circadian cues, while host clock genes modulate microbial ecology and intestinal barrier integrity. These insights underscore the translational potential of circadian precision medicine, in which time-restricted feeding, probiotics, prebiotics, and chronotherapy restore synchrony between microbial and host clocks. This review synthesizes current knowledge on circadian modulation of microbiota-mediated crosstalk across metabolic, neural, immune, and endocrine pathways, emphasizing its implications for health, disease, and novel therapeutic strategies.},
}

Humans
*Circadian Rhythm/physiology
*Gastrointestinal Microbiome/physiology
Animals

@article {pmid41260033,
year = {2025},
author = {Zhang, Q and Zhang, S and Cao, X and Zhi, Y and Guo, Y},
title = {The gut microbiota in post-stroke depression: A systematic review of microbial mechanisms and therapeutic targeting of neuroinflammation.},
journal = {Microbiological research},
volume = {303},
number = {},
pages = {128391},
doi = {10.1016/j.micres.2025.128391},
pmid = {41260033},
issn = {1618-0623},
abstract = {Post-stroke depression (PSD), a frequent and debilitating complication after stroke, severely hinders rehabilitation. Emerging evidence underscores the role of neuroinflammation and the gut microbiota in PSD pathogenesis. This review systematically elaborates the mechanisms by which gut dysbiosis contributes to PSD-related neuroinflammation via immune cell regulation (e.g., Treg/Th17 balance), microbial metabolites (e.g., SCFAs, tryptophan derivatives), and neural pathways (vagus nerve, HPA axis). A key focus is the comparative analysis of the gut microbiota in PSD against major depressive disorder (MDD) and Alzheimer's disease (AD), revealing a unique, stroke-induced microbial signature characterized by a loss of protective symbionts and a bloom of pro-inflammatory taxa. We further discuss the translational potential of microbiota-targeted interventions (e.g., probiotics, prebiotics) for PSD. By integrating clinical microbial ecology with mechanistic insights, this review synthesizes evidence suggesting that the gut microbiome may represent a promising diagnostic and therapeutic target for PSD, offering a distinct perspective from previous literature.},
}

@article {pmid41259914,
year = {2025},
author = {Yang, W and Wang, X},
title = {Transmission mechanisms and risk tracing of antibiotic resistance genes in rivers driven by wastewater inputs.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140523},
doi = {10.1016/j.jhazmat.2025.140523},
pmid = {41259914},
issn = {1873-3336},
abstract = {Aquatic environments are critical for ARG dissemination, yet contributions from different wastewater sources, dominant HGT mechanisms, and residual risks in natural waters remain unclear. Based on 863 metagenomic samples across China, we systematically analyzed wastewater inputs, HGT mechanisms, and risks of riverine ARGs. Wastewater treatment plants were the primary source, contributing about 50 % of riverine ARGs. Conjugation dominated ARG transfer, primarily via F-type type IV secretion systems. High-transmission plasmids were widespread. Although phage-mediated transduction represented only 3 % of HGT, it facilitated cross-environmental spread of clinically significant blaGES-18. Metagenome-assembled genomes revealed 78 % of resistant bacteria belonged to Pseudomonadota; 42 % co-harbored virulence factors. Phylogenetic analysis showed high inter-generic mobility of sul1/sul2, explaining their environmental persistence. Overall risk in rivers decreased by 44 % - 93 % compared to wastewaters. However, Acinetobacter carrying blaOXA and Cellvibrio sp002483145 carrying blaKHM-1 were phylogenetically close to Acinetobacter baumannii and Pseudomonas aeruginosa, indicating potential pathways toward key pathogens. Our study identifies wastewater as the main source of riverine ARGs, reveals conjugation as the primary transmission mechanism with transduction playing a secondary role, and demonstrates that high-risk ARGs can still spread to pathogenic bacteria in rivers. These findings are crucial for developing effective strategies to mitigate ARG risks.},
}

@article {pmid41259520,
year = {2025},
author = {Usman, H and Molaei, M and House, SD and Haase, MF and Dennis, CL and Niepa, THR},
title = {Magnetically responsive nanocultures for direct microbial assessment in soil environments.},
journal = {Science advances},
volume = {11},
number = {47},
pages = {eady2654},
doi = {10.1126/sciadv.ady2654},
pmid = {41259520},
issn = {2375-2548},
mesh = {*Soil Microbiology ; *Soil/chemistry ; Bioreactors ; Magnetic Iron Oxide Nanoparticles/chemistry ; },
abstract = {Cultivating microorganisms in native-like conditions is vital for bioprospecting and accessing now unculturable species. However, there remains a gap in scalable tools that can both mimic native microenvironments and enable targeted recovery of microbes from complex settings. Such approaches are essential to advance our understanding of microbial ecology, predict community functions, and discover previously unidentified biotherapeutics. We present magnetic nanocultures-a high-throughput microsystem for isolating and growing environmental microbes under near-native conditions. These nanoliter-scale bioreactors are encapsulated in semipermeable membranes that form magnetic polymeric microcapsules using iron oxide nanoparticles within polydimethylsiloxane-based shells. This design offers mechanical stability and magnetic actuation, enabling efficient retrieval from soil-like environments. The nanocultures are optimized for optical and biological properties to support microbial encapsulation, growth, and sorting. Our study demonstrates the feasibility of using magnetically responsive microenvironments to cultivate elusive microbes, offering a promising platform for bioprospecting previously uncultured or unknown microbial species.},
}

*Soil Microbiology
*Soil/chemistry
Bioreactors
Magnetic Iron Oxide Nanoparticles/chemistry

@article {pmid41258716,
year = {2025},
author = {Marsh, CC and Nel Van Zyl, K and Babalola, OO and Böhmer, R and Cowan, DA and Moganedi, KLM and Moroenyane, I and Naidoo, J and Nieves Delgado, A and Posma, JM and Segal, LN and Setati, ME},
title = {From description to implementation: key takeaways from the 3rd African Microbiome Symposium.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0068325},
doi = {10.1128/msphere.00683-25},
pmid = {41258716},
issn = {2379-5042},
abstract = {The 3rd African Microbiome Symposium was held in Cape Town, South Africa, from 20 to 22 November 2024. The symposium featured a diverse range of local and international microbiome research and provided a platform for 79 researchers, students, and industry members to engage in discussions on the microbiome within an African context and focusing on translational research. This meeting review shares highlights, findings, and recommendations derived from the event. Insights from two panel discussions revealed key barriers to microbiome research in Africa, including limited funding, infrastructure gaps, and a shortage of trained local scientists. Recommendations centered on increased investment, institutional training, adherence to ethical guidelines, and the fostering of equitable global partnerships.},
}

@article {pmid41258518,
year = {2025},
author = {Cong, D and Liu, J and Yu, S and Wu, P and Qin, M},
title = {Assessment of Anthropogenic Impacts on Water Quality and Microbial Communities in the Heilongjiang Maolan Gou National Nature Reserve.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02645-7},
pmid = {41258518},
issn = {1432-184X},
abstract = {Freshwater ecosystems within protected areas play a vital role in maintaining biodiversity and ecological stability, yet they are increasingly threatened by anthropogenic disturbances such as agriculture and tourism. Understanding the impacts of human activities on water quality and microbial community dynamics is essential for the effective conservation and management. This study investigates the spatial variability of water quality and microbial communities across the core, buffer, and experimental zones of the Heilongjiang Maolan Gou National Nature Reserve. Twelve water samples were collected and analyzed for key physicochemical parameters (turbidity, electrical conductivity (EC), chemical oxygen demand (COD), biochemical oxygen demand (BOD), NH4[+], PO4[3-] and heavy metals). The core zone exhibited excellent water quality with low turbidity (0.4-0.5 NTU), EC (45-130 µS/cm), COD (8-10 mg/L), BOD (1.5-2.2 mg/L). In contrast, the experimental zone showed significant contamination due to agriculture and tourism, with high COD (up to 35 mg/L), BOD (up to 6.5 mg/L), NH4[+] (0.18-0.35 mg/L), and PO4[3-] (0.008-0.035 mg/L). Heavy metal concentrations, particularly Cd (up to 0.24 µg/L), were elevated in the experimental zone, correlating with higher Pollution and Water Quality Indices (HPI up to 96.4, WQI up to 61.28). According to standard classifications, HPI values > 100 indicated heavy pollution and WQI scores between 50 and 100 denoted moderate to poor water quality, highlighting degraded conditions in the experimental zone. Microbial analysis revealed distinct community structures across zones, with enhanced pollutant-degrading taxa such as Pseudomonas (noted for aromatic hydrocarbon degradation) and members of Bacteroidota (associated with organic matter breakdown) in the experimental zone. These findings highlight the need for sustainable management to mitigate human impacts and preserve ecological health within the reserve.},
}

@article {pmid41258495,
year = {2025},
author = {Gutiérrez-Sarmiento, W and Fosado-Mendoza, M and Lozano-Flores, C and Varela-Echavarría, A},
title = {The Body Wall Microbiome of the Terrestrial Slug Deroceras laeve Reveals Potential Endosymbionts and Shares Core Organisms with Other Mollusks.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02652-8},
pmid = {41258495},
issn = {1432-184X},
support = {CBF2023-2024-834//SECIHTI/ ; IN211322//DGAPA-UNAM PAPIIT/ ; },
abstract = {The marsh slug Deroceras laeve is an invasive mollusk found in gardens, field crops, and wetlands. It lacks a protective shell, suggesting that microbial communities are associated with its adaptability to the environment. Here, we used a whole shotgun metagenomic approach to analyse the complex microbiome of D. laeve and compared it to that of other mollusks. This demonstrated the presence in D. laeve of bacteriophages such as Erwinia phage, Certrevirus, and Machinavirus, which target plant pathogen bacteria. In the Archaea domain the halophilics Halovivax and Halobaculum predominated, but also present were the methanogens Methanobacterium, Methanobrevibacter, Methanocaldococcus, Methanococcus, and Methanosarcina, involved in phosphate solubilization and methanogenesis during decomposition of organic matter. The Bacteria domain was dominated by γ-Pseudomonadota such as Buttiauxella, Citrobacter, Enterobacter, Klebsiella, Kluyvera, Leclercia, and Pseudomonas which are producers of enzymes that degrade biomass and complex carbohydrates. Regarding the fungal community, filamentous or yeast ascomycetes predominated such as Debaryomyces, Puccina, and Pyricularia known as plant pathogens or associated with decaying organic matter. Consistent with these findings, functional analysis revealed enrichment in genes involved in fermentation and carbohydrate metabolism. Remarkably, regardless of species, ecosystem, and tissue type, we found that the core microbiome of the mollusks in this study is mainly structured by the Phyla Uroviricota, Euryarchaeaota, Pseudomonadota, and Ascomycota, with diversity at the genus level. This suggests ancient symbiotic interactions of these mollusks with specific types of microbes which may have been critical for adaptability to their environment.},
}

@article {pmid41258437,
year = {2025},
author = {Romaní, AM and Núria, P and Marta, P and Giulia, G},
title = {Drought Drives Extracellular Polymeric Substances Accumulation and Functional Shifts in Streambed Biofilm Communities.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02649-3},
pmid = {41258437},
issn = {1432-184X},
abstract = {This study investigates the adaptive response of streambed microbial biofilms to water scarcity, focusing on the role of extracellular polymeric substances (EPS) production across a gradient of hydrological conditions. Sediment samples from 37 streams in the north-eastern Iberian Peninsula, encompassing both permanent and intermittent flow regimes, were analysed for EPS-polysaccharide content, microbial biomass, chlorophyll-a, and biofilm function (carbon substrate utilization profiles). Drought conditions were characterized based on the number of dry days over the eight months preceding sampling. Results revealed that EPS production increased significantly in intermittent streams, particularly under long-term drought, reaffirming that EPS synthesis is a key microbial strategy to mitigate desiccation stress. Notably, when normalized to prokaryotic density, EPS content exhibited a significant positive correlation with drought duration, emphasizing the dominant role of heterotrophic bacteria over algae in EPS secretion. However, EPS content alone was not a universal indicator of water scarcity, which showed a large variability in permanently flowing streams. Functional profiling showed clear shifts in carbon substrate utilization associated with stream hydrology. Intermittent streams exhibited a broader metabolic range, and particularly a capacity to use phenolic compounds, suggesting an adaptation to terrestrial organic matter inputs. Contrary to expectations, functional diversity increased in drier conditions, challenging assumptions derived from controlled experiments and underscoring the resilience of Mediterranean microbial biofilm communities to drought. These findings provide empirical support for EPS-mediated drought adaptation in natural biofilms and highlight functional diversity as a potential mechanism maintaining ecosystem processes under increasing aridity due to climate change.},
}

@article {pmid41258129,
year = {2025},
author = {Cabrerizo, MJ and González-Olalla, JM and Medina-Sánchez, JM and Vila-Duplá, M and Carrillo, P},
title = {Warming Fluctuations Strengthen the Photo-Phagotrophic Coupling in Mixoplanktonic Protists.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02658-2},
pmid = {41258129},
issn = {1432-184X},
support = {PID2022-136280NA-I00//MICIN/AEI/10.13039/501100011033 and the European Regional Development Fund/ ; RYC2023-042504-I//MICIU/AEI/10.13039/501100011033 and the European Social Fund plus (ESF+)/ ; DGP-POST-2024-00283//Junta de Andalucía/ ; TED2021-131262B-I00//MCIN/AEI/10.13039/501100011033 and by the European Union NextGeneration EU/PRTR/ ; FPU19/05924//Ministerio de Ciencia e Innovación/ ; PID2020-118872RB-I00//MICIN/AEI/10.13039/501100011033 and the European Regional Development Fund (ERDF)/ ; },
abstract = {Mixoplankton, a major trophic group in aquatic ecosystems, are being affected by global warming. However, most studies on temperature effects use constant mean conditions, overlooking how short-term thermal fluctuations could deviate from climate projections and impact this group. We experimentally quantified how increasing amplitudes of warming fluctuation (± 1, 3, and 5 °C) alter carbon-specific electron transport (ETR[c]), net photosynthesis (P[c]), respiration (R[c]), phagotrophy (Ph[c]), carbon use efficiency (CUE), and growth (µ) in four protist species (three mixoplanktonic and one strict phototroph). We observed a consistent positive link between photosynthetic efficiency (P[c]:ETR[c] ratio) and Ph[c], and a shift towards a strengthening of the Ph[c] (P[c]:ETR[c] / Ph[c] ratio) with greater thermal fluctuation. A potential explanation is a selective behavior aimed to increase phagotrophy to obtain inorganic nutrients through ingested prey internal re-cycling rather than relying on the environment, to support an enhanced photosynthetic efficiency and growth. An enhanced, coupled photo-phagotrophy activity could boost mixoplankton competitiveness compared to phytoplankton. Our findings underscore the need to incorporate trophic flexibility and its interaction with environmental variability into trait-based models to better predict community dynamics, biogeochemical cycling, and food web structure in aquatic ecosystems.},
}

@article {pmid41254852,
year = {2025},
author = {Alster, CJ and Schipper, LA and Bååth, E},
title = {Thermal Adaptation of Bacterial and Fungal Growth in a Geothermally Influenced Soil Transect.},
journal = {Global change biology},
volume = {31},
number = {11},
pages = {e70605},
doi = {10.1111/gcb.70605},
pmid = {41254852},
issn = {1365-2486},
support = {MFP-UOW1904//Marsden Fund/ ; },
mesh = {*Soil Microbiology ; New Zealand ; *Fungi/growth & development ; *Bacteria/growth & development ; Temperature ; *Soil/chemistry ; },
abstract = {Numerous studies have investigated microbial adaptation to increasing soil temperature, but limitations in experimental design hinder comprehensive understanding. These include short-term laboratory studies with constant environmental conditions and field studies with few distinct temperature treatments. Here, we utilized a long-term natural soil geothermal gradient in Aotearoa, New Zealand, ranging in mean annual soil temperature (MAT) from 17°C to 42°C to explore thermal adaptation of microbial growth rates. We collected soil from 28 locations along the gradient and measured bacterial growth rate (via leucine incorporation) at eight temperatures (4°C-45°C) and fungal growth rate (via Ac-in-ergosterol) at two temperatures (16°C and 39°C). We then fit Macromolecular Rate Theory and the Ratkowsky equation to estimate the temperature minimum (T min $$ {T}_
{min}
$$), optimum (T opt $$ {T}_
{opt}
$$), and inflection point (T inf $$ {T}_
{inf}
$$) for bacterial growth, and a temperature sensitivity index to compare relative fungal and bacterial growth rates. We found predictable changes in thermal adaptation of bacterial growth along the geothermal gradient with temperature response curves shifting 0.22°C-0.27°C per 1°C increase in MAT regardless of the temperature metric (i.e., T min $$ {T}_
{min}
$$ , T opt $$ {T}_
{opt}
$$ , and T inf $$ {T}_
{inf}
$$) used. Thermal adaptation of bacterial and fungal growth increased roughly in parallel. We also compared the bacterial growth results to published temperature response data of microbial respiration (with added glucose) from this geothermal gradient. Rates of thermal adaptation for bacterial growth and microbial respiration were similar, suggesting synchronicity across microbial processes. The less than 1°C change in all measured temperatures metrics per degree increase in MAT resulted in microbial growth and activity closer to in situ temperatures at high soil temperatures and lower than in situ temperatures under non-elevated soil temperatures. Overall, our results highlight the use of geothermal gradients and appropriate temperature models in studying thermal adaptation of soil microbial processes; the predictability of results also underscores potential for incorporating microbial thermal adaptation into soil carbon modeling efforts.},
}

*Soil Microbiology
New Zealand
*Fungi/growth & development
*Bacteria/growth & development
Temperature
*Soil/chemistry

@article {pmid41254344,
year = {2025},
author = {Distante, A and Garino, D and Cerrato, C and Perez-Ardavin, J and Flores, FQ and Lopetuso, L and Mir, MC},
title = {The role of the human microbiome in prostate cancer: a systematic review from diagnosis to treatment.},
journal = {Prostate cancer and prostatic diseases},
volume = {},
number = {},
pages = {},
pmid = {41254344},
issn = {1476-5608},
abstract = {BACKGROUND: Prostate cancer (PC) heterogeneity and treatment resistance remain major clinical challenges, with emerging evidence implicating the microbiome as a key modulator of disease pathogenesis. While microbial dysbiosis has been linked to PC diagnosis, progression, and therapeutic outcomes, the mechanisms underlying these associations are poorly understood. This review synthesizes current evidence on the diagnostic, prognostic, and therapeutic potential of the microbiome in PC.

METHODS: A systematic search of PubMed, Embase, and Cochrane Central Register of Controlled Trials (through April 2024) was conducted following PRISMA guidelines (PROSPERO: CRD42024534899). Controlled and observational studies investigating microbial roles in PC diagnosis (e.g., ISUP grading group), prognosis, or treatment response were included. Data extraction and quality assessment used the QUIPS tool. From 810 screened records, 42 studies met inclusion criteria.

RESULTS: Distinct microbial profiles differentiated PC from controls, with Mycoplasma genitalium and Staphylococcus spp. enriched in prostate tumors (3.1- and 2.7-fold, respectively) and correlated with inflammation (IL-6: r = 0.38, p = 0.002). Urinary microbiota showed diagnostic potential (sensitivity: 58-82%), though sampling methods influenced variability. Prognostically, Betaproteobacteria gut enrichment predicted earlier castration-resistant progression (5.2 months; HR 1.8, 95% CI 1.3-2.5), while ADT-induced dysbiosis (e.g., Klebsiella overgrowth) accelerated resistance (2.1-fold risk). Therapies altered microbial ecology: radiotherapy depleted Bacteroides (linked to proctitis; OR 3.1), and immunotherapy responders harbored higher Akkermansia muciniphila. Microbial androgen synthesis and endotoxin production emerged as resistance mechanisms.

CONCLUSIONS: The microbiome influences PC detection, aggressiveness, and treatment efficacy through direct (tissue-resident) and indirect (gut-derived) mechanisms. Standardized profiling and microbiome-modulating strategies (e.g., probiotics during ADT) may personalize management. Prospective trials are needed to validate causality and translate microbial biomarkers into clinical practice.},
}

@article {pmid41252854,
year = {2025},
author = {Chen, X and Huang, Y and Zhu, X and Gan, C and An, W and Liu, Y and Zhou, S and Xu, M},
title = {Global biogeographic patterns and assembly processes of landfill leachate microbiomes.},
journal = {Water research},
volume = {289},
number = {Pt B},
pages = {124922},
doi = {10.1016/j.watres.2025.124922},
pmid = {41252854},
issn = {1879-2448},
abstract = {Approximately 95 % of municipal solid waste is disposed of in landfill globally, generating leachate that is known as a complex mixture of biodegradable and persistent toxic compounds. Microbes are main forces for tackling the toxic leachate but the patterns of microbial assembly in such treatments are largely unknown, limiting the proper optimization of leachate treatment efficiency. This study, for the first time, presents a global-scale analysis involving 151 landfill leachate treatment samples for uncovering mechanisms of microbial assembly from an ecological perspective. The information of microbiome from 97 treatments in Asia, 41 treatments in Europe, and 13 treatments in North America were collected. The results revealed pronounced biogeographic divergence, with Asian samples (particularly those from India) exhibiting lower microbial diversity and richness compared to Europe and North America counterparts. Geographical-climatic and socio-economic factors significantly influenced microbial composition, with elevation and per capita GDP being primary drivers. Further, the community assembly was predominantly governed by deterministic processes. Co-occurrence network analyses demonstrated distinct microbial interaction patterns across continents, with Asian networks being more vulnerable to collapse under external disturbances. This study provides critical insights into the global microbial ecology of landfill leachate treatment, offering a foundation for developing targeted bioremediation strategies.},
}

@article {pmid41251823,
year = {2025},
author = {Della Mónica, IF and Godeas, AM and Scervino, JM},
title = {Hyphosphere interactions: P-solubilizing fungi modulate AMF phosphatase activity and mycorrhizal symbiosis via exudate-mediated communication.},
journal = {Mycorrhiza},
volume = {35},
number = {6},
pages = {66},
pmid = {41251823},
issn = {1432-1890},
support = {UBACyT 20020220400300BA//Secretaría de Ciencia y Técnica, Universidad de Buenos Aires/ ; PIBAA 28720210100694CO//Consejo Nacional de Investigaciones Científicas y Técnicas/ ; PICT 01283-2021//Agencia Nacional de Promoción de la Investigación, el Desarrollo Tecnológico y la Innovación/ ; PINI 04/B253//Fundación de la Universidad Nacional del Comahue para el Desarrollo Regional/ ; },
mesh = {*Mycorrhizae/physiology/enzymology ; *Symbiosis ; Plant Roots/microbiology ; *Phosphorus/metabolism ; Acid Phosphatase/metabolism ; *Phosphoric Monoester Hydrolases/metabolism ; Daucus carota/microbiology ; *Glomeromycota/physiology/enzymology ; *Phosphates/metabolism ; },
abstract = {Arbuscular mycorrhizal fungi (AMF) form symbiotic associations with plant roots, enhancing water and nutrient absorption. Phosphate-solubilizing fungi (PSF) can solubilize and mineralize phosphorus, an essential nutrient with low bioavailability, and eventually interact with AMF. However, the understanding of how they interact in the hyphosphere, where root influence is absent, remains limited. Furthermore, the effect of PSF on the phosphatase activity of AMF, related to the P efficiency in acquisition and utilization, within the hyphosphere and mycorrhizosphere zones, remains unclear. Therefore, this study aimed to assess the effect of three different PSF (Talaromyces flavus, T. helicus, and T. diversus) exudates on extracellular acid phosphatases and alkaline phosphatases associated with intra- and extraradical AMF structures in the hyphosphere and mycorrhizosphere, in vitro. To achieve this aim, the AMF Rhizophagus intraradices was cultured with Ri T-DNA transformed carrot roots in a system using Petri dishes that mimicked the hyphosphere (with 2 sections: (a) with roots and AMF, and (b) with only AMF) and the mycorrhizosphere (with roots and AMF in the same place). Different concentrations of PSF exudates were placed in either the hyphosphere or the mycorrhizosphere, and at the end of the experiment (8 weeks), the phosphatase activity of the AMF was measured. This research highlights that the enzymatic activity of AMF is modulated by PSF exudates, depending on whether these exudates are present in the hyphosphere or the mycorrhizosphere. Exudates in the hyphosphere, where PSF are directly associated with AMF hyphae, have a more pronounced effect on AMF extraradical alkaline phosphatases than acid phosphatases, and promote symbiosis efficiency. In contrast, PSF exudates in the mycorrhizosphere had a neutral or negative effect on symbiosis efficiency, improving the extraradical alkaline phosphatases of AMF and the acid phosphatases of the roots. Also, the effect depends on the fungal identity. AMF act as mediators in this context, improving communication between the roots and the hyphosphere microbiome. When exploring the soil, the hyphae encounter compounds produced by microorganisms, thus establishing a complex network of interactions. These interactions enhance the symbiotic efficiency of AMF, modulating the host plant without direct contact. These results show that microbial interactions not only influence the efficiency of phosphorus transfer to plants but also have broader implications for soil health and fertility management.},
}

*Mycorrhizae/physiology/enzymology
*Symbiosis
Plant Roots/microbiology
*Phosphorus/metabolism
Acid Phosphatase/metabolism
*Phosphoric Monoester Hydrolases/metabolism
Daucus carota/microbiology
*Glomeromycota/physiology/enzymology
*Phosphates/metabolism

@article {pmid41251489,
year = {2025},
author = {Ye, H and Šlipogor, V and Hanson, BT and Séneca, J and Hausmann, B and Herbold, CW and Pjevac, P and Bugnyar, T and Loy, A},
title = {Associations between gut microbiota and personality traits: insights from a captive common marmoset (Callithrix jacchus) colony.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0044325},
doi = {10.1128/spectrum.00443-25},
pmid = {41251489},
issn = {2165-0497},
abstract = {Recent studies have suggested associations between consistent inter-individual behavioral variation (i.e., animal personality) and gut microbiota. Non-human primates living under controlled conditions are valuable models to investigate diet-independent microbiome-host interactions. In this study, we investigated associations between specific gut microbiota members and personality traits, as well as group membership, sex, age class, breeding status, and relatedness of 26 captive common marmosets (Callithrix jacchus), maintained under the same diet and housing conditions. Personality was assessed using an established testing battery in repeated tests. Then, we collected a total of 225 fecal samples during the summers of 2017 and 2019 from five marmoset social groups for 16S rRNA gene amplicon sequencing. Within-individual microbiota variance was smaller than that between group members. Group members also exhibited more similar gut microbiota than individuals from different groups in each sampling year. Beta diversity of the gut microbiota was linked with personality traits, age class, sex, and breeding status, but not with genetic relatedness. We identified specific bacterial taxa associated with personality traits. In particular, members of the sulfite-reducing genus Desulfovibrio were enriched in more avoidant marmosets. Amplicon sequencing of the dissimilatory sulfite reductase gene dsrB confirmed this pattern, yet additionally revealed an unknown uncultured bacterium that was the predominant sulfite-reducing bacterium in the fecal samples and was linked to more explorative individuals. These findings highlight specific association patterns between identified microbial taxa and personality traits in captive common marmosets.IMPORTANCEThis study provides valuable insights into the intricate relationship between gut microbiota and host personality traits, using captive common marmosets as a model. By controlling for diet and housing conditions, it probes key host factors such as personality, age, sex, and social group membership, offering a robust framework for understanding microbiome-host interactions. The discovery of specific microbial taxa associated with personality traits, particularly the enrichment of sulfite-reducing genera in more avoidant individuals, underscores the potential of the gut microbiome to reflect or be associated with personality differences. These findings advance our understanding of microbiome-host dynamics and pave the way for future research on the mechanistic links between behavior and gut microbiota in other animal models and across broader ecological contexts.},
}

@article {pmid41251323,
year = {2025},
author = {Ferreira, J and Lievens, B and Rediers, H},
title = {Development of a spore-based confrontation assay to screen for biocontrol organisms with antagonistic activity against oomycete and fungal pathogens.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf286},
pmid = {41251323},
issn = {1365-2672},
abstract = {AIMS: Screenings for biocontrol organisms against fungal and oomycete pathogens are typically performed on mycelium. While this allows for high-throughput screenings, it omits a major actor in pathogenicity, i.e. the spores. This study aims to improve the screening strategy using a spore-based confrontation assay (SBCA), as well as comparing its performance to the traditional mycelium-based confrontation assay (MBCA) and microscopy analyses of spore germination.

METHODS AND RESULTS: The SBCA was used to screen for 38 candidate biocontrol bacteria against two relevant broad-spectrum phytopathogens, Botrytis cinerea and Phytophthora cactorum. The performance of the SBCA was benchmarked to the traditional mycelium-based confrontation assay and microscopy observations for spore germination inhibition. The SBCA demonstrated a higher hit rate and reproducibility than its counterparts. The bacteria tested exhibited diverse traits in vitro such as production of lytic enzymes, biosurfactant, bioactive volatile organic compounds, and cell-free extracts. These characteristics suggest potential biocontrol modes of action, such as antibiosis (via diffusible metabolites and enzymes) or competition for nutrients and space. For two Pseudomonas strains, the biocontrol activity against P. cactorum was confirmed in planta in a detached leaf assay.

CONCLUSIONS: This study showcases a versatile and robust spore-based screening that outperforms conventional screening methods. Through the use of the SBCA, two promising biocontrol strains with antagonistic activity against P. cactorum in strawberry were identified.},
}

@article {pmid41250675,
year = {2025},
author = {Gao, Y and Bai, J and Zhou, F and He, Y and Wang, Y and Huang, X},
title = {ICCTax: a hierarchical taxonomic classifier for metagenomic sequences on a large language model.},
journal = {Bioinformatics advances},
volume = {5},
number = {1},
pages = {vbaf257},
pmid = {41250675},
issn = {2635-0041},
abstract = {MOTIVATION: Metagenomic data increasingly reflect the coexistence of species from Archaea, Bacteria, Eukaryotes, and Viruses in complex environments. Taxonomic classification across the four superkingdoms is essential for understanding microbial communities, exploring genomic evolutionary relationships, and identifying novel species. This task is inherently imbalanced, uneven, and hierarchical. Genomic sequences provide crucial information for taxonomy classification, but many existing methods relying on sequence similarity to reference genomes often leave sequences misclassified due to incomplete or absent reference databases. Large language models offer a novel approach to extract intrinsic characteristics from sequences.

RESULTS: We present ICCTax, a classifier integrating the large language model HyenaDNA with complementary-view-based hierarchical metric learning and hierarchical-level compactness loss to identify taxonomic genomic sequences. ICCTax accurately classifies sequences to 155 genera and 43 phyla across the four superkingdoms, including unseen taxa. Across three datasets built with different strategies, ICCTax outperforms baseline methods, particularly on Out-of-Distribution data. On Simulated Marine Metagenomic Communities datasets from three oceanic sites, DairyDB-16S rRNA, Tara Oceans, and wastewater metagenomic datasets, it demonstrates strong performance, showcasing real-world applicability. ICCTax can further support identification of novel species and functional genes across diverse environments, enhancing understanding of microbial ecology.

Code is available at https://github.com/Ying-Lab/ICCTax.},
}

@article {pmid41249638,
year = {2025},
author = {Tinning, Z and Kaestli, M and Nowland, SJ and Siboni, N and Seymour, JR and Gibb, KS and Padovan, AC},
title = {Dynamics of Bacterial and Vibrio Communities in Blacklip Rock Oysters in the Seasonal Tropics.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {125},
pmid = {41249638},
issn = {1432-184X},
support = {2020-043//Fisheries Research and Development Corporation/ ; Discovery Project DP240100370//Australian Research Council/ ; },
mesh = {Animals ; *Vibrio/isolation & purification/genetics/classification ; *Ostreidae/microbiology ; Seasons ; Aquaculture ; Seawater/microbiology ; *Microbiota ; Australia ; Tropical Climate ; Shellfish/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Humans ; },
abstract = {Cultivation of the tropical Blacklip Rock Oyster (BRO) (Saccostrea spathulata) is an emerging Indigenous-led aquaculture industry in the seasonal tropics of northern Australia. However, little is currently known about the potential for pathogen outbreaks in this species. We conducted a year-long study to establish a microbial baseline to identify potential oyster and human health risks to inform future food safety decision making in this nascent industry. In healthy oysters, we identified both the core microbiome of this oyster species and the presence of potential oyster and human pathogens. The core bacteriome comprised nine bacterial families, while the core vibriome comprised the animal pathogens Vibrio harveyi and V. owensii. The potential human pathogen V. parahaemolyticus was detected in some oysters during the wet season, during periods of increased rainfall, turbidity and total nitrogen. The bacteriome and vibriome of oysters were significantly different to the adjacent seawater and therefore we concluded that seawater is not an appropriate surrogate for pathogen risk surveillance in this developing industry. These results provide new knowledge on the microbiology of a previously understudied oyster species and will inform monitoring methods, harvesting and shellfish quality compliance in this emerging Indigenous-led industry.},
}

Animals
*Vibrio/isolation & purification/genetics/classification
*Ostreidae/microbiology
Seasons
Aquaculture
Seawater/microbiology
*Microbiota
Australia
Tropical Climate
Shellfish/microbiology
*Bacteria/classification/genetics/isolation & purification
Humans

@article {pmid41249586,
year = {2025},
author = {Zhou, S and Bi, J and Zhou, S and Luo, L and Yan, X and Zou, J and Ji, Y and Zhao, S and Qiu, J and Liu, Z and Jiang, J and Wang, B and Liu, X},
title = {Community Assembly Mechanisms Underlying Divergent Responses of Indica and Japonica Rice Rhizosphere Microbiota to Drought Stress.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {126},
pmid = {41249586},
issn = {1432-184X},
support = {2022YFD2300302//National Key Research and Development Program of China/ ; 42277304//National Natural Science Foundation of China/ ; 42407399//National Natural Science Foundation of China/ ; XUEKEN2022003//Fundamental Research Funds for the Central Universities/ ; BX20240168//National Postdoctoral Program for Innovative Talents/ ; BK20241558//Natural Science Foundation of Jiangsu Province/ ; 2024ZB624//Jiangsu Funding Program for Excellent Postdoctoral Talent/ ; },
mesh = {*Oryza/microbiology/growth & development/physiology/genetics/classification ; *Rhizosphere ; *Droughts ; *Microbiota ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation & purification/metabolism ; RNA, Ribosomal, 16S/genetics ; Stress, Physiological ; Agricultural Irrigation ; },
abstract = {Drought stress markedly reduces rice yield, with notable genotypic variation in drought tolerance. While the rhizosphere microbiome is regarded as the second genome of plants, how the indica and japonica rice rhizosphere microbial communities respond to deficit irrigation and their relationship with yield remain to be elucidated. Here, we conducted field experiments using 12 indica and 12 japonica rice varieties under full and deficit irrigation regimes. Yield-related traits, including filled grain number, seed setting rate, two-plant yield, and thousand grain weight, were measured, and the rhizosphere microbial communities were characterized by 16S rRNA gene sequencing. In line with previous studies, japonica varieties showed superior drought resistance in terms of yield performance. Both rice genotype and irrigation regime significantly influenced the composition and functional potential of the rhizosphere microbiome. Compared to indica rice, the japonica rice rhizosphere was enriched with more beneficial microorganisms. Enrichment of nitrogen‑metabolism‑related groups, such as Microvirga and Nitrososphaeraceae, may contribute to rhizosphere nitrogen cycling and support nitrogen availability for the rice. Similarly, higher abundance of Streptomyces in japonica varieties under drought conditions may be associated with improved drought tolerance. These microbial genera were closely associated with rice yield. Moreover, the japonica rhizosphere microbiome was less disturbed by water limitation, showing higher stability. Overall, the rhizosphere microbiome of japonica rice exhibited functional optimization under drought stress by promoting the enrichment of beneficial and nitrogen-cycling microbes, thereby enhancing drought resistance and yield stability. This study demonstrated a significant correlation between rhizosphere microbial communities and rice yield, providing fundamental insights that may contribute to future strategies for optimizing crop productivity through microbiome management in sustainable agriculture.},
}

*Oryza/microbiology/growth & development/physiology/genetics/classification
*Rhizosphere
*Droughts
*Microbiota
*Soil Microbiology
*Bacteria/classification/genetics/isolation & purification/metabolism
RNA, Ribosomal, 16S/genetics
Stress, Physiological
Agricultural Irrigation

@article {pmid41248576,
year = {2025},
author = {Zhou, Y and Chang, L and Sun, H and Li, W and Ao, T and Lin, J},
title = {Evaluation of reclaimed treated wastewater on soil quality, microbial community and function in urban greening irrigation.},
journal = {Journal of environmental management},
volume = {395},
number = {},
pages = {127958},
doi = {10.1016/j.jenvman.2025.127958},
pmid = {41248576},
issn = {1095-8630},
abstract = {Reclaimed treated wastewater (TWW) offers a sustainable irrigation alternative for urban greening amid freshwater scarcity. However, its impact on soil quality and microbial ecology in urban landscapes remains underexplored. This study assessed the effects of three TWW types and one TWW-purified water mixture on soil properties, heavy metal accumulation, enzyme activity and microbial community dynamics in Common Nandina (Nandina domestica Thunb.) systems over three- and five-month in Nanjing, China, using a metagenomic approach. The results showed that TWW irrigation significantly increased soil nitrogen, phosphorus content and pH (P < 0.05), with stronger effects observed at three-month (P < 0.05). Soil heavy metal content varied, with Cr and As exhibiting potential accumulation. Enzyme activity (N-acetyl-glucosaminidase and phosphatase) was positively influenced by TWW irrigation at three-month. Metagenomic analysis revealed significant shifts in microbial community composition, particularly fungi, with Mucoromycota increasing and Ascomycota decreasing under TWW. The Normalized Stochasticity Ratio indicated increased stochasticity in microbial assembly under TWW irrigation (P < 0.05). Functionally, TWW increased abundance of functional genes related to amino acid metabolism and peroxisomes (P < 0.05), but decreased degradation genes for aromatic compounds. TWW also increased the abundance of antibiotic resistance genes (ARGs), particularly those related to triclosan and glycopeptide, and plant pathogenic genera like Aspergillus and Fusarium. The findings suggest that while TWW irrigation improves certain soil properties and microbial functions in the short term, it may pose ecological risks from heavy metal and microbial contamination, offering key insights for sustainable urban irrigation strategies.},
}

@article {pmid41247962,
year = {2025},
author = {Wei, D and Hu, S and Tang, T and Yang, Y and Meng, F and Peng, Y},
title = {Confinement Reduces Surface Accumulation of Swimming Bacteria.},
journal = {Physical review letters},
volume = {135},
number = {18},
pages = {188401},
doi = {10.1103/dvc8-tlh1},
pmid = {41247962},
issn = {1079-7114},
mesh = {*Models, Biological ; Hydrodynamics ; *Bacterial Physiological Phenomena ; Movement ; *Escherichia coli/physiology ; },
abstract = {Many swimming bacteria naturally inhabit confined environments, yet how confinement influences their swimming behaviors remains unclear. Here, we combine experiments, continuum modeling, and particle-based simulations to investigate near-surface bacterial swimming in dilute suspensions under varying confinement. Confinement reduces near-surface accumulation and facilitates bacterial escape. These effects are quantitatively captured by models incorporating the force quadrupole, a higher-order hydrodynamic singularity, that generates a rotational flow reorienting bacteria away from surfaces. Under strong confinement, bacterial trajectories straighten due to the balancing torques exerted by opposing surfaces. These findings highlight the role of hydrodynamic quadrupole interactions in near-surface bacterial motility, with implications for microbial ecology, infection control, and industrial applications.},
}

*Models, Biological
Hydrodynamics
*Bacterial Physiological Phenomena
Movement
*Escherichia coli/physiology

@article {pmid41247508,
year = {2025},
author = {Wenten, IG},
title = {Rethinking Biofilm Engineering and Fouling Resistance in Membrane Bioreactors.},
journal = {Langmuir : the ACS journal of surfaces and colloids},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.langmuir.5c03864},
pmid = {41247508},
issn = {1520-5827},
abstract = {Membrane bioreactors (MBRs) are increasingly recognized as a key technology in sustainable wastewater treatment, offering a high effluent quality through the integration of biological degradation and membrane filtration. Among the critical factors influencing their performance are biofilm dynamics and membrane fouling. This article critically examines recent advances in biofilm engineering and antifouling strategies for MBRs, with an emphasis on microbial community modulation, quorum quenching, and hydrodynamic control to improve biofilm stability. In parallel, the review examines material-based and biological methods to mitigate membrane fouling, emphasizing multifunctional surfaces and emerging biocontrol strategies. Key operational challenges, such as energy consumption, cleaning frequency, and membrane aging, are evaluated alongside future research directions in materials design, microbial ecology, and real-time system optimization. The integration of these innovations is essential for advancing MBR technologies that are robust, resource-efficient, and aligned with circular economy principles.},
}

@article {pmid41247324,
year = {2025},
author = {Weagley, JS and Cárdenas, LAC and Romani, A and Sullender, ME and Aggarwal, S and Makimaa, H and Hogarty, MP and Rodgers, R and Kennedy, EA and Foster, L and Schriefer, LA and Baldridge, MT},
title = {Differential Microbial Community Assembly Following Co-housing versus Microbiota Transplant.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf256},
pmid = {41247324},
issn = {1751-7370},
abstract = {Mouse models are vital tools for discerning the relative contributions of host and microbial genetics to disease, often requiring the transfer of microbiota between different mouse strains. Transfer methods include antibiotic treatment of recipients and colonization using either co-housing with donors or the transplantation of faecal or caecal donor material. However, the efficiency and dynamics of these methods in reconstituting recipients with donor microbes is not well understood. We thus directly compared co-housing, faecal transplantation, and caecal transplantation methods. Donor mice from Taconic Biosciences, possessing distinct microbial communities, served as the microbial source for recipient mice from Jackson Laboratories, which were treated with antibiotics to disrupt their native microbiota. We monitored bacterial and viral populations longitudinally over the course of antibiotics treatment and reconstitution using 16S rRNA gene sequencing, quantitative PCR, and shotgun sequencing of viral-like particles. As expected, antibiotic treatment rapidly depleted microbial biomass and diversity, with slow and incomplete natural recovery of the microbiota in non-transfer-recipient control mice. Although all transfer methods reconstituted recipient mice with donor microbiota, co-housing achieved this more rapidly for both bacterial and viral communities. Overall, faecal and caecal transplant resulted in highly similar colonization processes with some minor variation in enrichment for two specific bacterial families. This study provides valuable insights into microbial ecology, as well as the dynamics underlying experimental microbial transfer methods, enhancing reproducibility and informing best practices for microbiota transfer in mouse models.},
}

@article {pmid41247030,
year = {2025},
author = {Van Beek, JM and Robles, G and Mewalal, R and Blaby, I and Hatzenpichler, R},
title = {A collection of archaeal 16S rRNA Clone-FISH cultures for probe validation in fluorescence in situ hybridization experiments.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0113125},
doi = {10.1128/mra.01131-25},
pmid = {41247030},
issn = {2576-098X},
abstract = {We present a collection of 30 Escherichia coli cultures (Clone-FISH cultures), each carrying a plasmid for the heterologous expression of a (near) full-length 16S rRNA gene from 1 of 30 lineages of archaea, including 17 yet uncultured ones. We make these clones available for use as controls in fluorescence in situ hybridization experiments.},
}

@article {pmid41247018,
year = {2025},
author = {Xiong, M and Kuang, W and Liu, Z and Tong, R and Deng, X and Wang, N and Wan, X and Feng, M and Luo, Y and Zhang, B and Zhang, Z and Zheng, F},
title = {Quercetin alleviates ulcerative colitis via regulating gut microbiota and tryptophan metabolism.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0070325},
doi = {10.1128/msystems.00703-25},
pmid = {41247018},
issn = {2379-5077},
abstract = {UNLABELLED: Quercetin, a natural flavonoid in traditional Chinese medicinal plants, has shown promise in alleviating ulcerative colitis symptoms despite uncertainties about its exact mode of action. This study explored how quercetin influences tryptophan breakdown and gut bacterial populations in mice with chemically induced colitis. The treatment demonstrated measurable improvements-normalizing body weight, reducing spleen enlargement, lowering clinical severity scores, preserving colon structure, and healing tissue damage. Through advanced microbiome profiling and metabolic analysis, researchers observed increased populations of helpful gut microbes alongside higher concentrations of tryptophan byproducts. These biochemical shifts stimulated the aryl hydrocarbon receptor system, which plays a key role in restoring gut lining integrity. The collective evidence points to quercetin's therapeutic potential through its dual action on microbial ecology and tryptophan-derived signaling pathways.

IMPORTANCE: Ulcerative colitis is a chronic inflammatory disease with limited effective therapeutic options. In this study, quercetin-a flavonoid commonly found in traditional Chinese medicinal herbs-was shown to relieve colitis symptoms by reshaping gut microbiota and restoring tryptophan metabolism. Notably, the increase in indolelactic acid, a key microbial metabolite, led to activation of the aryl hydrocarbon receptor, which supports intestinal barrier integrity and dampens inflammation. These findings reveal a gut microbiota-derived metabolite-host signaling axis as a central mechanism of action, highlighting the potential of quercetin as a microbiota-targeted therapeutic approach for UC.},
}

@article {pmid41246320,
year = {2025},
author = {Dey, P},
title = {Genes, guts, and microbes: decoding host-driven microbial regulation using intestine-specific conditional knockouts.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1674913},
doi = {10.3389/fimmu.2025.1674913},
pmid = {41246320},
issn = {1664-3224},
mesh = {Animals ; *Gastrointestinal Microbiome/immunology/genetics ; Humans ; Dysbiosis ; Mice, Knockout ; *Intestines/microbiology/immunology ; *Intestinal Mucosa/metabolism/microbiology/immunology ; *Host Microbial Interactions/genetics ; Mice ; },
abstract = {This narrative review underscores the influence of host genetics in actively regulating gut microbiota composition and function, highlighting the distinctive advantages of intestine-specific conditional knockout (cKO) models in gut microbiome research. In contrast to whole-body knockouts or germ-free animals, these precision models, enabled by Cre-loxP technology, eliminate confounding systemic effects to elucidate how localized host genes within intestinal cells regulate the gut microbial ecology. The review identifies three fundamental host-driven regulatory mechanisms through the analysis of specific gene deletions: (1) barrier integrity (e.g., mucus and junction proteins), (2) immune defenses (e.g., antimicrobial peptides and glycan synthesis), and (3) metabolic signaling (e.g., bile acid receptors and glucose transporter). These pathways jointly impose microbial symbiosis, and their disruption leads to dysbiosis characterized by increased abundance of pathobionts (e.g., Escherichia, Proteobacteria), directly connecting host genetics to inflammatory and metabolic disorders. This host-centric viewpoint emphasizes the gut as an active regulator, rather than a passive microenvironment for the microbiota, providing significant insights for creating tailored therapeutics that focus on host pathways to restore microbial balance in disorders such as inflammatory bowel diseases.},
}

Animals
*Gastrointestinal Microbiome/immunology/genetics
Humans
Dysbiosis
Mice, Knockout
*Intestines/microbiology/immunology
*Intestinal Mucosa/metabolism/microbiology/immunology
*Host Microbial Interactions/genetics
Mice