@article {pmid41175318,
year = {2025},
author = {Peyser, AV and Gonçalves, A and Haisi, A and Araújo, JP and Raimondo, RFS and Heinemann, MB and Cortez, A and Gaeta, NC},
title = {First Pandemic blaCTX-M-8-Producing ST224 E. coli in Brazilian Sheep: Resistance and Genomic Traits.},
journal = {EcoHealth},
volume = {},
number = {},
pages = {},
pmid = {41175318},
issn = {1612-9210},
abstract = {Shiga toxin-producing E. coli (STEC) strains are particularly concerning due to their zoonotic potential and environmental persistence. Ruminants, especially sheep and cattle, serve as primary reservoirs, often shedding pathogenic strains asymptomatically and contributing to foodborne outbreaks through contamination of animal-derived products. This study aimed to characterize antimicrobial-resistant E. coli strains isolated from dairy sheep in Brazil, focusing on phylogenetic backgrounds, resistance profiles, and genomic features. From 65 rectal swab samples collected across five herds in two Brazilian states, 65 E. coli isolates were recovered. Of these, 27.7% showed antimicrobial resistance to at least one drug tested, and 32.3% were identified as STEC. Resistance was most frequently observed against sulfamethoxazole-trimethoprim, tetracycline, and gentamicin. Notably, one isolate (LZB-RS-110) exhibited an extended-spectrum β-lactamase (ESBL) phenotype and a multidrug-resistant profile. Whole-genome sequencing identified clinically relevant resistance genes (e.g., blaCTX-M-8, tetB, sul2), virulence genes (stx1, stx2), and metal tolerance operons. The blaCTX-M-8 gene, harbored on a predicted conjugative IncI1 plasmid, was flanked by mobile genetic elements, suggesting a high potential for horizontal gene transfer. Phylogenomic analysis revealed that LZB-RS-110 is closely related to international isolates from wild and domestic animals, highlighting the global dissemination of high-risk E. coli lineages. These findings underscore the critical role of sheep in the ecology of zoonotic and resistant E. coli, and the broader implications for food safety and One Health. Enhanced surveillance and rational antimicrobial use in livestock are urgently needed to mitigate the spread of resistance and safeguard public health.},
}

@article {pmid41174878,
year = {2025},
author = {Zou, R and Huang, J and Xie, H and Wu, J and Su, J and Yong, Y and Xu, J and Deng, Y and Huang, W},
title = {A chromosome-level genome assembly of Cistanche deserticola provides insights into its evolution and molecular mechanisms of parasitism.},
journal = {Plant communications},
volume = {},
number = {},
pages = {101581},
doi = {10.1016/j.xplc.2025.101581},
pmid = {41174878},
issn = {2590-3462},
abstract = {Cistanche deserticola is a holoparasitic plant of the Orobanchaceae family, parasitizing the roots of Haloxylon ammodendron. The absence of a high-quality genome has impeded understanding of C. deserticola's parasitic mechanisms. We present a chromosome-level assembly of C. deserticola (6.26 Gb) using PacBio HiFi and Hi-C sequencing, with an 81.25 Mb contig N50 and 92.2% BUSCO completeness, encoding 54,640 protein-coding genes. Evolutionary analysis shows that C. deserticola diverged from related Orobanchaceae species approximately 38.23 million years ago. Key parasitic adaptations include extensive photosynthetic gene loss, compensated by retained transporters and carbon metabolic pathways for host nutrient utilization. Bidirectional genetic exchanges include 34 H. ammodendron-derived horizontally transferred (HGT) genes and 98 mobile mRNAs, alongside 14 C. deserticola-derived HGT genes and 77 mobile mRNAs targeting host defenses. Spatial transcriptomic data reveal haustorium-specific expression specializing in nutrient extraction and chemical defense, particularly phenylethanoid glycosides (PhGs) biosynthesis via dispersed duplication-driven gene expansion. This genomic resource illuminates the evolutionary trajectory of C. deserticola and provides a foundation for conservation strategies and biotechnological development of C. deserticola.},
}

@article {pmid41174429,
year = {2025},
author = {Chen, J and Peng, J and Liu, Y and Fu, L and Duan, X and Xu, Z and Zhang, J and Li, Y and Zhao, Y and Guo, L},
title = {Mobile genetic elements potentially drive adaptive evolution of pork-derived multidrug-resistant Salmonella Derby ST40 lineages: An integrated analysis.},
journal = {Food research international (Ottawa, Ont.)},
volume = {221},
number = {Pt 2},
pages = {117352},
doi = {10.1016/j.foodres.2025.117352},
pmid = {41174429},
issn = {1873-7145},
mesh = {*Drug Resistance, Multiple, Bacterial/genetics ; Animals ; Swine ; Phylogeny ; *Salmonella/genetics/drug effects/classification/isolation & purification ; *Interspersed Repetitive Sequences/genetics ; Humans ; Food Microbiology ; Anti-Bacterial Agents/pharmacology ; *Pork Meat/microbiology ; Evolution, Molecular ; Microbial Sensitivity Tests ; China ; },
abstract = {Salmonella Derby (S. Derby) is transmitted to humans through contaminated pork products. S. Derby ST40, with multidrug resistance (MDR) and extensive drug resistance, poses major food safety and public health challenges. By integrating antimicrobial susceptibility testing, phylogenetic analysis, phylogeographic reconstruction, pan-genomics, and pan-genome-wide association study, we investigated adaptive evolution and transmission dynamics of antibiotic resistance in S. Derby ST40 (71 isolates from livestock and 1572 global isolates from humans, food, and environment). Globally, S. Derby ST40 strains (69.36 % pork-derived) were divided into six clades. blaOXA-1-carrying MDR Clade VI evolved in China from Clade II Clade VI carried about 19 resistance genes; its MDR primarily resulted from combined effects of resistance genes in chromosomal MDR regions and mobile genetic elements (MGEs), accumulating via horizontal gene transfer. S. Derby ST40 accessory genes contained abundant recombinases associated with MGEs and resistance genes. Pork-derived MGEs and chromosomal MDR variable regions may drive Clade VI's evolution. Molecular clock analysis indicated that S. Derby ST40 originated in the United States in 1939, and Clade VI diverged from Clade II in China around 1979. Clade VI engaged in global antimicrobial resistance network via intercontinental transmission; China emerged as a main transmission hub in the 21st century. Globally circulating pork- and poultry-derived strains demonstrate more resistance genes than human-derived strains, indicating that animal husbandry and animal food production chains are resistance gene reservoirs. Strengthening antibiotic regulation in livestock farming may curb resistance gene dissemination within food chains, and a One Health governance framework may prevent and control cross-border MDR bacterial transmission.},
}

*Drug Resistance, Multiple, Bacterial/genetics
Animals
Swine
Phylogeny
*Salmonella/genetics/drug effects/classification/isolation & purification
*Interspersed Repetitive Sequences/genetics
Humans
Food Microbiology
Anti-Bacterial Agents/pharmacology
*Pork Meat/microbiology
Evolution, Molecular
Microbial Sensitivity Tests
China

@article {pmid41171917,
year = {2025},
author = {Kato, K and Nakajima, Y and Sakamoto, R and Kumazawa, M and Ifuku, K and Ishikawa, T and Shen, JR and Takabayashi, A and Nagao, R},
title = {Structural insights into the divergent evolution of a photosystem I supercomplex in Euglena gracilis.},
journal = {Science advances},
volume = {11},
number = {44},
pages = {eaea6241},
pmid = {41171917},
issn = {2375-2548},
mesh = {*Euglena gracilis/metabolism/genetics ; *Photosystem I Protein Complex/chemistry/metabolism/genetics ; Phylogeny ; *Evolution, Molecular ; *Light-Harvesting Protein Complexes/chemistry/metabolism/genetics ; Photosynthesis ; Models, Molecular ; Cryoelectron Microscopy ; },
abstract = {Photosystem I (PSI) forms supercomplexes with light-harvesting complexes (LHCs) to perform oxygenic photosynthesis. Here, we report a 2.82-angstrom cryo-electron microscopy structure of the PSI-LHCI supercomplex from Euglena gracilis, a eukaryotic alga with secondary green alga-derived plastids. The structure reveals a PSI monomer core with eight subunits and 13 asymmetrically arranged LHCI proteins. Euglena LHCIs bind diadinoxanthin, which is one of the carotenoids typically associated with red-lineage LHCs and is not present in the canonical LHCI belt found in green-lineage PSI-LHCI structures. Phylogenetic analysis shows that the Euglena LHCIs originated from LHCII-related clades rather than from the green-lineage LHCI group and that the nuclear-encoded PSI subunit PsaD likely originated from cyanobacteria via horizontal gene transfer. These observations indicate a mosaic origin of the Euglena PSI-LHCI. Our findings uncover a noncanonical light-harvesting architecture and highlight the structural and evolutionary plasticity of photosynthetic systems, illustrating how endosymbiotic acquisition and lineage-specific adaptation shape divergent light-harvesting strategies.},
}

*Euglena gracilis/metabolism/genetics
*Photosystem I Protein Complex/chemistry/metabolism/genetics
Phylogeny
*Evolution, Molecular
*Light-Harvesting Protein Complexes/chemistry/metabolism/genetics
Photosynthesis
Models, Molecular
Cryoelectron Microscopy

@article {pmid41171504,
year = {2025},
author = {Karthikeyan, A and Javaid, A and Tabassum, N and Kim, TH and Kim, YM and Jung, WK and Khan, F},
title = {Marine-derived phlorotannins: sustainable inhibitors of multiple virulence factors in Pseudomonas aeruginosa.},
journal = {AMB Express},
volume = {15},
number = {1},
pages = {162},
pmid = {41171504},
issn = {2191-0855},
support = {RS-2021-NR060118//Basic Science Research Program through the National Research Foundation of Korea (NRF), funded by the Ministry of Education/ ; RS-2021-NR060118//Basic Science Research Program through the National Research Foundation of Korea (NRF), funded by the Ministry of Education/ ; RS-2023-00241461//Basic Science Research Program through the National Research Foundation of Korea (NRF), funded by the Ministry of Education/ ; },
abstract = {Pseudomonas aeruginosa is a highly adaptable opportunistic pathogen in diverse environments, causing plant, animal, and human infections. Its remarkable ability to resist antibiotics and deploy multiple virulence strategies is attributed to its large genome, horizontal gene transfer, and complex regulatory networks. In this study, we comprehensively investigated 15 structurally distinct phlorotannins against 18 major virulence-associated proteins, such as quorum-sensing proteins, adhesion proteins, exotoxins, siderophore receptors, secretion system components, proteases, motility, and biofilm formation. Molecular docking and 50-ns molecular dynamics simulations revealed that compounds such as 2-phloroeckol, 7-phloroeckol, phlorofucofuroeckol A, and phlorofucofuroeckol B formed strong and stable interactions with critical targets, type IV pilus biogenesis factor PilY1, ferripyoverdine receptor, and phenazine-1-carboxylate-methyltransferase, with binding free energies as low as - 12.24 kcal/mol. These compounds exhibited a wide range of non-covalent interactions, including hydrogen bonding and π-π stacking, with essential active site residues in target proteins. Drug-likeness and environmental safety assessments utilizing the pkCSM and VEGA (Q)SAR models revealed high oral bioavailability, low toxicity, minimal cytochrome P450 interactions, and mostly non-mutagenic profiles. This study reveals phlorotannins as prospective eco-friendly alternatives for reducing P. aeruginosa infection by addressing a broad spectrum of virulence factors with ecologically benign and biodegradable natural compounds.},
}

@article {pmid41171360,
year = {2025},
author = {van Katwijk, O and Mulder, M and van Alphen, L and Landman, F and Hendrickx, A and Verkerk, A and Sligman, L and Schnabel, R and van der Zwet, W and Smeets, E and Dirks, J and Jamin, C},
title = {Within patient horizontal gene transfer dynamics of a blaNDM-7 plasmid among four different bacterial species.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
pmid = {41171360},
issn = {1435-4373},
abstract = {PURPOSE: We describe the case of a 73-year old male who was found to be a carrier of an blaNDM -producing Citrobacter freundii shortly after admission. During his admission, he developed abdominal abscesses and received multiple courses of piperacillin-tazobactam. In the following months, he was found to carry three other carbapenemase-positive species: Klebsiella oxytoca, Raoultella planticola and Serratia marscescens. RESULTS: Two of these strains had clustering carbapenem-sensitive isolates cultured before. The species all carried an blaNDM-7 encoding incX3 plasmid, which demonstrated horizontal gene transfer within this patient.

CONCLUSION: This case report underlines the importance of mobile genetic elements in infection control, as they serve as transmission vehicles for antimicrobial resistance beyond the spread of identical bacterial strains.},
}

@article {pmid41171056,
year = {2025},
author = {Li, Z and Hu, J and Pan, Y and Xi, Y and Zhang, L},
title = {Bifidobacterium infantis modulates intestinal microecology to inhibit the spread of antimicrobial resistance.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0072825},
doi = {10.1128/msystems.00728-25},
pmid = {41171056},
issn = {2379-5077},
abstract = {UNLABELLED: Early administration of antibiotics in children may heighten the susceptibility to multidrug-resistant bacterial infections. While probiotics are commonly employed for bacterial infection management, their nuanced advantages, particularly in curtailing the spread of antimicrobial resistance (AMR), remain unclear. This study investigated the role and mechanisms of Bifidobacterium infantis in inhibiting the spread of antibiotic resistance genes (ARGs) in the gut. We found that supplementing with B. infantis 15697 significantly enhanced the synthesis of bile acids in mouse feces, particularly tauroursodeoxycholic acid (TUDCA) and taurocholic acid (TCA). Concurrently, the abundance of potential probiotics such as Parabacteroides goldsteinii in the gut significantly increased. Using a mouse infection model, we discovered that B. infantis supplementation inhibited the colonization of antibiotic-resistant Escherichia coli in the gut and the events of horizontal gene transfer, thereby reducing the spread of ARGs. Further analysis revealed that TUDCA and TCA, through their interaction with the OmpC protein, decreased the biofilm formation capability and cell membrane permeability of antibiotic-resistant bacteria, inhibiting the horizontal spread of ARGs. These findings reveal the important role of B. infantis in regulating the gut microbiota and inhibiting the spread of ARGs, providing a theoretical basis for developing new probiotic intervention strategies. This could help reduce the global spread of AMR and protect human health.

IMPORTANCE: The global spread of antimicrobial resistance (AMR) has become a significant threat to public health, particularly in children, where the overuse of antibiotics leads to gut microbiota imbalance and increases the risk of horizontal transfer of antibiotic resistance genes (ARGs). This study supplemented mice with Bifidobacterium infantis 15697, which significantly enhanced the synthesis of bile acids, especially tauroursodeoxycholic acid and taurocholic acid, while promoting the growth of probiotics and inhibiting the colonization of antibiotic-resistant bacteria and the spread of ARGs. This finding not only reveals the important role of B. infantis in regulating the gut microbiota and inhibiting the spread of ARGs but also provides a theoretical basis for developing new probiotic intervention strategies. By modulating the gut microbiota and bile acid metabolism, B. infantis has the potential to become an effective means of reducing the spread of AMR. This is of great significance for protecting the gut health of children and adults, reducing the risk of resistant infections, and also provides scientific evidence for the formulation of global public health policies.},
}

@article {pmid41171004,
year = {2025},
author = {Nguyen, A and Jenkins, GM and Brones, PD and Parrett, GA and Hagen, GM and Bono, JM and Risser, DD},
title = {A new family of bacterial actin-like proteins regulates cell morphology in a filamentous cyanobacterium.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0049925},
doi = {10.1128/msphere.00499-25},
pmid = {41171004},
issn = {2379-5042},
abstract = {Actin proteins are common to all domains of life and exhibit ATP-dependent polymerization to form filaments. In bacteria, four families of bacterial actin-like proteins (BALPs) have been identified and characterized. These BALPs are involved in plasmid partitioning (ParM), cell division (FtsA), magnetosome positioning (MamK), and cell morphology (MreB). Here, we report the identification of a fifth family of BALP, FcmB. Using the model filamentous cyanobacterium Nostoc punctiforme, we demonstrate that FcmB is a BALP that regulates cell morphology in filamentous cyanobacteria. Deletion of fcmB, or fcmC, which encodes an FcmB-interacting protein, resulted in the loss of rod morphology, similar to the phenotype reported for mreB mutants in other bacteria, including cyanobacteria. However, despite the apparent functional similarity, fcmB is not a paralog of mreB, but rather was acquired by horizontal gene transfer of a plasmid partitioning system and subsequent integration into the chromosome. Fluorescent protein fusions and immunofluorescence demonstrate that FcmB forms membrane-bound filaments which wrap around the circumference of the cell, while FcmC is localized to discrete membrane-associated foci and is essential for proper membrane localization of FcmB. Protein-protein interactions were detected between FcmB and FcmC, but not MreB, indicating that FcmB and MreB do not form heterofilaments. It is currently unclear how FcmBC exerts its effect on cell morphology, but both mreB and fcmB are ubiquitous in the developmentally complex heterocyst-forming filamentous cyanobacteria, and the presence of two discrete systems modulating cell morphology may be critical for the remarkable degree of phenotypic plasticity observed in these organisms.IMPORTANCEFilament-forming actin proteins are found in nearly all living organisms. In bacteria, four families of actin proteins have been defined, with biological functions in plasmid partitioning, cell division, magnetosome positioning, and cell morphology. Here, we identify and characterize FcmB, a fifth family of bacterial actin proteins found in filamentous cyanobacteria, and demonstrate that this family evolved from plasmid partitioning actins but influences cell morphology rather than DNA segregation. Filamentous cyanobacteria exhibit substantial phenotypic plasticity and typically contain both FcmB and MreB, the other actin family known to regulate cell morphology. The presence of two distinct families of actin proteins influencing cell morphology may play a critical role in the ability of these organisms to rapidly alter their cell shape.},
}

@article {pmid41170849,
year = {2025},
author = {Yu, T and Xie, J and Huang, X and Huang, J and Bao, G and Yuan, W and Gao, C and Liu, C and Hu, J and Yang, W and Li, G},
title = {BaeR and H-NS control CRISPR-Cas-mediated immunity and virulence in Acinetobacter baumannii.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0106725},
doi = {10.1128/msystems.01067-25},
pmid = {41170849},
issn = {2379-5077},
abstract = {Acinetobacter baumannii balances its remarkable ability to acquire antibiotic resistance genes via horizontal gene transfer (HGT) with the immune defense functions of its CRISPR-Cas system, forming a dynamic equilibrium governed by intricate transcriptional regulation. However, the regulatory mechanisms underlying the I-Fb CRISPR-Cas system in A. baumannii remain poorly understood. This study elucidated a multitiered regulatory axis mediated by BaeR and H-NS that coordinates immune defense and virulence expression in the I-Fb CRISPR-Cas system. Using DNA pull-down and electrophoretic mobility shift assay (EMSA), we demonstrated that H-NS directly binds AT-rich regions within the cas3 promoter, suppressing both interference activity and adaptive immunity of the I-Fb CRISPR-Cas system. Intriguingly, the two-component regulator BaeR controlled this suppression by positively regulating H-NS expression. The results revealed that Δcas3 mutants exhibited increased biofilm thickness, elevated the extracellular matrix component poly N-acetyl glucosamine (PNAG) production, upregulated pilus expression, and significantly enhanced epithelial cell adhesion. Strikingly, Δh-ns-cas3 and ΔbaeR-cas3 double-knockout strains showed no statistically significant differences in virulence phenotypes compared to the Δcas3 single mutants. These findings indicate CRISPR-Cas-mediated inhibition of biofilm formation is abolished upon cas3 deletion, thereby releasing the regulatory constraints imposed by BaeR and H-NS. This dysregulation leads to excessive biofilm and extracellular matrix component accumulation, ultimately amplifying bacterial colonization capacity and pathogenicity in host environments. This discovery reveals the dual regulatory roles of BaeR and H-NS in the A. baumannii I-Fb CRISPR-Cas system, mediating both immune defense and virulence modulation. These insights establish a theoretical foundation for novel antimicrobial strategies targeting CRISPR-Cas regulatory networks.IMPORTANCEA. baumannii, a leading cause of drug-resistant nosocomial infections, evolves antibiotic resistance through horizontal gene transfer (HGT) while employing CRISPR-Cas systems to limit foreign DNA invasion. This study reveals that the I-Fb CRISPR-Cas system, typically a defense mechanism, functions as a repressor of virulence traits in A. baumannii. We demonstrate that the transcriptional regulators H-NS and BaeR form a hierarchical axis suppressing Cas3 expression, thereby constraining biofilm formation and host adhesion. Strikingly, CRISPR-Cas deficiency enhances virulence, thickens biofilms, elevates PNAG production, and enhances epithelial colonization through escape from BaeR-/H-NS-mediated control. This work redefines CRISPR-Cas as a dual-function module balancing immune defense and pathogenicity, exposing the BaeR-H-NS-Cas3 axis as a druggable target for novel anti-infectives aimed at disrupting bacterial adaptive evolution.},
}

@article {pmid41170650,
year = {2025},
author = {Alharbi, MS and Moursi, SA and Alshammari, A and Aboras, R and Rakha, E and Hossain, A and Alshubrumi, S and Alnazha, K and Khaja, ASS and Saleem, M},
title = {Multidrug-resistant Pseudomonas aeruginosa: Pathogenesis, resistance mechanisms, and novel therapeutic strategies.},
journal = {Virulence},
volume = {16},
number = {1},
pages = {2580160},
doi = {10.1080/21505594.2025.2580160},
pmid = {41170650},
issn = {2150-5608},
mesh = {*Pseudomonas aeruginosa/drug effects/pathogenicity/genetics ; *Drug Resistance, Multiple, Bacterial ; Humans ; *Pseudomonas Infections/microbiology/drug therapy ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Biofilms/growth & development/drug effects ; Virulence Factors/genetics ; Virulence ; },
abstract = {Pseudomonas aeruginosa is a highly adaptable Gram-negative opportunistic pathogen and a major contributor to nosocomial infections, particularly in immunocompromised and critically ill patients. Its pathogenicity is mediated through an array of virulence determinants, including lipopolysaccharide (LPS), outer membrane proteins (OMPs), flagella, pili, and exopolysaccharides (alginate, Psl, Pel), which facilitate adhesion, immune evasion, and strong biofilm formation. The bacterium deploys an arsenal of secreted effectors such as exotoxins (ExoS, ExoT, ExoU, ExoY), pyocyanin, and elastases via specialized secretion systems (T1SS - T6SS) to disrupt host defenses and establish persistent infections. Resistance to antibiotics is multifactorial, encompassing restricted membrane permeability, efflux systems (e.g. MexAB-OprM), enzymatic inactivation (e.g. ESBLs, aminoglycoside-modifying enzymes), spontaneous mutations (e.g. gyrA, AmpC), and horizontal gene transfer. Biofilm-associated persister cells further complicate treatment by adopting metabolically dormant states. Innovative therapeutic approaches, including ceftolozane-tazobactam and small molecules with enhanced membrane permeability, are under investigation to circumvent resistance. Concurrently, vaccine development targeting key antigens such as LPS, flagella, T3SS proteins, and OMVs, along with nanoparticle-based platforms and monoclonal antibodies (e.g. IgY, DMAbs), has demonstrated potential in eliciting protective immunity. However, high antigenic variability and serotype diversity hinder broad efficacy. Future strategies must integrate Immunotherapeutics with antivirulence compounds targeting quorum sensing, iron acquisition, and biofilm disruption. A multidisciplinary approach involving translational research and clinical validation is imperative to combat multidrug-resistant P. aeruginosa and improve patient outcomes.},
}

*Pseudomonas aeruginosa/drug effects/pathogenicity/genetics
*Drug Resistance, Multiple, Bacterial
Humans
*Pseudomonas Infections/microbiology/drug therapy
*Anti-Bacterial Agents/pharmacology/therapeutic use
Biofilms/growth & development/drug effects
Virulence Factors/genetics
Virulence

@article {pmid41168882,
year = {2025},
author = {Bowers, RM and Bennett, S and Riley, R and Villada, JC and Da Silva, IR and Woyke, T and Frank, AC},
title = {Host species and geographic location shape microbial diversity and functional potential in the conifer needle microbiome.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {222},
pmid = {41168882},
issn = {2049-2618},
support = {10.46936/10.25585/60000936//U.S. Department of Energy/ ; DEB-1442348//Directorate for Biological Sciences/ ; },
mesh = {*Microbiota/genetics ; *Bacteria/classification/genetics/isolation & purification ; Metagenomics/methods ; *Tracheophyta/microbiology ; Metagenome ; Phylogeny ; *Plant Leaves/microbiology ; Pinus/microbiology ; },
abstract = {BACKGROUND: The aerial surface of plants, known as the phyllosphere, hosts a complex and dynamic microbiome that plays essential roles in plant health and environmental processes. While research has focused on root-associated microbiomes, the phyllosphere remains comparatively understudied, especially in forest ecosystems. Despite the global ecological dominance and importance of conifers, no previous study has applied shotgun metagenomics to their phyllosphere microbiomes.

RESULTS: This study uses metagenomic sequencing to explore the microbial phyllosphere communities of subalpine Western conifer needle surfaces from 67 trees at six sites spanning the Rocky Mountains, including 31 limber pine, 18 Douglas fir, and 18 Engelmann spruce. Sites span ~ 1,075 km and nearly 10° latitude, from Glacier National Park to Rocky Mountain Biological Laboratory, capturing broad environmental variation. Metagenomes were generated for each of the 67 samples, for which we produced individual assemblies, along with three large coassemblies specific to each conifer host. From these datasets, we reconstructed 447 metagenome-assembled genomes (MAGs), 417 of which are non-redundant at the species level. Beyond increasing the total number of extracted MAGs from 153 to 294, the three coassemblies yielded three large MAGs, representing partial sequences of host genomes. Phylogenomics of all microbial MAGs revealed communities predominantly composed of bacteria (n = 327) and fungi (n = 117). We show that both microbial community composition and metabolic potential differ significantly across host tree species and geographic sites, with site exerting a stronger influence than host.

CONCLUSIONS: This dataset offers new insights into the microbial communities inhabiting the conifer needle surface, laying the foundation for future research on needle microbiomes across temporal and spatial scales. Variation in functional capabilities, such as volatile organic compound (VOC) degradation and polysaccharide metabolism, closely tracks shifts in taxonomic composition, indicating that host-specific chemistry, local environmental factors, and regional microbial source pools jointly shape ecological roles. Moreover, the observed patterns of mobile genetic elements and horizontal gene transfer suggest that gene exchange predominantly occurs within microbial lineages, with occasional broader transfers dispersing key functional genes (e.g., those involved in polysaccharide metabolism), which may facilitate microbiome adaptation.},
}

*Microbiota/genetics
*Bacteria/classification/genetics/isolation & purification
Metagenomics/methods
*Tracheophyta/microbiology
Metagenome
Phylogeny
*Plant Leaves/microbiology
Pinus/microbiology

@article {pmid41168025,
year = {2025},
author = {Huang, J and Wang, Q},
title = {Land plant evolution: from microbial interaction to horizontal gene transfer.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2025.10.002},
pmid = {41168025},
issn = {1878-4372},
abstract = {Microbe interaction not only plays an integral role in plant growth and adaptation, but also may lead to genetic integration. Horizontal gene transfer (HGT) from microbes occurs in all major plant groups and appears to be frequent in charophytes and bryophytes. Horizontally acquired microbial genes have contributed to major physiological and structural innovations in land plants. This paper discusses microbial interactions and genetic integration, with a particular focus on recent data regarding the role of horizontally acquired microbial genes in land plant evolution. We suggest that microbes are essential resources for plants, both as an ecological component and as a source of novel genetic material, and that plant colonization of land and further diversification represent a process of exploitation of microbial resources.},
}

@article {pmid41167159,
year = {2025},
author = {Chi, S and Xiao, J and Xu, J and Li, A and Hu, J and Wang, X and Zhang, M and Liu, W and Zhang, Y and Ding, H and Rong, J and Leng, L and Xie, X},
title = {Hydrothermal carbonization: A potent strategy for simultaneously eliminating ARGs-associated pollutants in livestock manure and blocking ARGs horizontal gene transfer.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140256},
doi = {10.1016/j.jhazmat.2025.140256},
pmid = {41167159},
issn = {1873-3336},
abstract = {Antibiotic resistance is a major One Health concern, with livestock manure being a key source of antibiotics, antibiotic resistance genes (ARGs), and pathogens. While conventional treatments such as composting and anaerobic digestion often show incomplete removal and potential ARGs enrichment, hydrothermal carbonization (HTC) offers a promising alternative solution for managing high-moisture swine manure. The effectiveness of HTC was systematically evaluated under varying temperatures (100-240 °C), reaction times (30-240 min), and solid-liquid ratios (1:4-1:8) in this study. Results demonstrated that HTC at 220-240 °C for ≥ 90 min could completely eliminate ARGs and mobile genetic elements (MGEs) from raw pig manure (initial abundance: 10[8]-10 [15] copies/16S rRNA gene), and achieve complete degradation of target antibiotics and pathogens. Furthermore, hydrochar suspensions reduced plasmid RP4 conjugative transfer by 85-98 %, primarily by lowering bioavailable Cu[2 +] /Zn[2+] levels, thus inhibiting horizontal gene transfer. Hydrochar at 240 °C outperformed 220 °C, with 52.2-66.4 % lower bioavailable metal concentrations. These findings establish HTC as an efficient strategy for mitigating ARGs spread and enabling safe manure reuse, with advantages in both treatment efficacy and economic viability over conventional methods.},
}

@article {pmid41166396,
year = {2025},
author = {Corneloup, T and Bellengier, J and Rosinski-Chupin, I and Magnan, M and Chavan, A and Gachet, B and Dixit, Z and Pintard, C and Baron, A and Toko, D and Lambert, A and Choudhury, A and Tenaillon, O},
title = {High-throughput conjugation reveals strain specific recombination patterns enabling precise trait mapping in Escherichia coli.},
journal = {PLoS genetics},
volume = {21},
number = {10},
pages = {e1011636},
doi = {10.1371/journal.pgen.1011636},
pmid = {41166396},
issn = {1553-7404},
abstract = {Genetic exchange is a cornerstone of evolutionary biology and genomics, driving adaptation and enabling the identification of genetic determinants underlying phenotypic traits. In Escherichia coli, horizontal gene transfer via conjugation and transduction not only promotes diversification and adaptation but has also been instrumental in mapping genetic traits. However, the dynamics and variability of bacterial recombination remain poorly understood, particularly concerning the patterns of recombined DNA fragments. To elucidate these patterns and simultaneously develop a tool for trait mapping, we designed a high-throughput conjugation method to generate recombinant libraries. Recombination profiles were inferred through whole-genome sequencing of individual clones and populations after selection of a marker from the donor strain in the recipient. This analysis revealed an extraordinary range of recombined fragment sizes, spanning less than ten kilobases to over a megabase-a pattern that varied across the three tested strains. Mathematical modelling indicated that this diversity in recombined fragment size enables precise identification of selected loci following genetic crosses. Consistently, population sequencing pinpointed a selected marker at kilobase-scale accuracy, offering a robust tool for identifying subtle genetic determinants that could include point mutations in core genes. These findings challenge the conventional view that conjugation always transfers large fragments, suggesting that even short recombined segments, traditionally attributed to transduction, may originate from conjugation.},
}

@article {pmid41160566,
year = {2025},
author = {Banerjee, G and Banerjee, P},
title = {Whole genome sequence of multidrug-resistant Staphylococcus haemolyticus and Enterococcus faecalis isolates from public gymnasium equipment reveals evolving infection potential and resistance.},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0324894},
pmid = {41160566},
issn = {1932-6203},
mesh = {*Enterococcus faecalis/genetics/isolation & purification/drug effects ; *Drug Resistance, Multiple, Bacterial/genetics ; Whole Genome Sequencing ; *Genome, Bacterial ; *Staphylococcus haemolyticus/genetics/isolation & purification/drug effects ; Multilocus Sequence Typing ; Anti-Bacterial Agents/pharmacology ; Humans ; Phylogeny ; Microbial Sensitivity Tests ; },
abstract = {Whole genome sequences (WGSs) of Enterococcus faecalis S3 and Staphylococcus haemolyticus S5, isolated from gymnasium equipment in Tennessee, USA, were analyzed. The genome sizes of E. faecalis S3 and S. haemolyticus S5 were approximately 3.0 Mb and 2.5 Mb, respectively. Both isolates were found to harbor genes conferring resistance to multiple antibiotics, including tetracycline, fluoroquinolone, and macrolide. Gene cluster analysis revealed a cyclic lactone inducer cluster in both strains, which is critical for quorum sensing-mediated pathogenicity. Multilocus sequence typing (MLST) identified E. faecalis S3 as ST40 and S. haemolyticus S5 as ST52. Notably, evolutionary analysis of gene contraction and expansion in these isolates revealed an expansion of genes associated with horizontal gene transfer. This expansion likely represents an evolutionary strategy to facilitate the spread of antibiotic resistance genes to other isolates. These findings offer valuable insights into the genomic apparatus responsible for antibiotic resistance and potential transmission mechanisms in human-associated environments.},
}

*Enterococcus faecalis/genetics/isolation & purification/drug effects
*Drug Resistance, Multiple, Bacterial/genetics
Whole Genome Sequencing
*Genome, Bacterial
*Staphylococcus haemolyticus/genetics/isolation & purification/drug effects
Multilocus Sequence Typing
Anti-Bacterial Agents/pharmacology
Humans
Phylogeny
Microbial Sensitivity Tests

@article {pmid41160243,
year = {2025},
author = {Peter, S and Zulkiffle, MZ and Thlama, BP and Hanafiah, MHMA and Abdullah, FFJ and Kamaludeen, J and Mustafa, S},
title = {Prevalence and mechanisms of antimicrobial resistance in respiratory bacterial pathogens of ruminants: a systematic review.},
journal = {Veterinary research communications},
volume = {50},
number = {1},
pages = {8},
pmid = {41160243},
issn = {1573-7446},
support = {FRGS/1/2023/WAB04/UPM/02/26//Ministry of Higher Education, Malaysia/ ; FRGS/1/2023/WAB04/UPM/02/26//Ministry of Higher Education, Malaysia/ ; FRGS/1/2023/WAB04/UPM/02/26//Ministry of Higher Education, Malaysia/ ; },
mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial ; *Respiratory Tract Infections/microbiology/veterinary/epidemiology ; Prevalence ; *Ruminants/microbiology ; *Bacteria/drug effects ; Sheep ; Goats ; Cattle ; },
abstract = {Antimicrobial resistance (AMR) in respiratory pathogens of ruminants is a growing threat to animal health, veterinary treatment efficacy, and food production. However, consolidated global data on the prevalence and molecular mechanisms of AMR in these pathogens remain limited, particularly across diverse regions and livestock systems. This systematic review aimed to evaluate the prevalence and molecular mechanisms of AMR in bacterial pathogens responsible for respiratory infections in ruminants. A comprehensive search of PubMed, Scopus, Web of Science, and Google Scholar was conducted to identify English-language, peer-reviewed articles published between January 1, 2020, and May 31, 2025. Eligible studies reported on AMR prevalence and/or mechanisms in respiratory pathogens isolated from cattle, sheep, goats, and buffaloes. Study screening, data extraction, and quality appraisal were performed according to PRISMA guidelines, using the Joanna Briggs Institute (JBI) checklist. Fifty studies met the inclusion criteria, covering bacterial isolates from Africa, Asia, Europe, the Americas, and Oceania. Resistance prevalence ranged from 0.8% to 100%, with Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, and Mycoplasma bovis being the most frequently reported pathogens. Resistance was most common against tetracyclines, macrolides, sulfonamides, and β-lactams. Identified mechanisms included β-lactamase production, such as blaROB-1, blaTEM, efflux pumps msr(E), tet(H), target-site mutations gyrA, parC, 23 S rRNA, and horizontal gene transfer via plasmids and integrative and conjugative elements. This review underscores the global burden of AMR and multidrug resistance in ruminant respiratory pathogens and their potential zoonotic implications. Strengthening molecular surveillance, harmonising diagnostic standards, and integrating antimicrobial usage data, especially in underrepresented regions such as Southeast Asia, are essential to inform targeted interventions.},
}

Animals
*Anti-Bacterial Agents/pharmacology
*Drug Resistance, Bacterial
*Respiratory Tract Infections/microbiology/veterinary/epidemiology
Prevalence
*Ruminants/microbiology
*Bacteria/drug effects
Sheep
Goats
Cattle

@article {pmid41152716,
year = {2025},
author = {Wang, Z and Gao, S and Zhang, Y and Shen, H and Cao, X},
title = {Prophage landscape in Enterococcus faecium: diversity, resistance genes, virulence factors, and endolysin profiling.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {964},
pmid = {41152716},
issn = {1471-2164},
abstract = {BACKGROUND: Enterococcus faecium is a major opportunistic pathogen associated with healthcare-associated infections and increasing antimicrobial resistance. Prophages play critical roles in bacterial evolution by mediating horizontal gene transfer, but a comprehensive analysis of prophages in E. faecium has not been performed.

METHODS: A total of 495 complete E. faecium genomes were retrieved from the NCBI database. Prophages were identified and classified using PHASTEST and PhaGCN2.3 software. The interactions between prophages within host genomes were analyzed using logistic regression. Antimicrobial resistance (AMR), virulence factor (VF), and endolysin genes within intact prophages were characterized using Abricate, the VFDB, and the CARD databases. Comparative analyses were conducted between human- and animal-origin strains.

RESULTS: A total of 2119 prophages were detected, of which 1628 were intact. Nearly all E. faecium strains (99.4%) harbored at least one prophage, with an average of 4.2 prophages per genome. Staphy_SPbeta_like (26.4%) and Lister_2389 (22.1%) were the main types of prophages. Exclusion was most prevalent pattern, and specific prophages exhibiting varying interaction profiles. Classification revealed that most prophages belonged to the Bronfenbrennervirinae subfamily and the Herelleviridae family. Among intact prophages, 20.4% carried AMR genes and 1.4% harbored VF gene, primarily the adhesin-encoding gene ecbA. Endolysin genes, detected in 59.6% of prophages, exhibited high sequence diversity. Prophage distribution and types varied significantly among different ST strains, with prophage types showing distinct patterns in carrying AMR, VF, and endolysin-encoding genes. No significant differences in AMR, VF, or endolysin genes were observed between prophages of human and animal origins.

CONCLUSIONS: This study provides the first comprehensive genomic characterization of prophages in E. faecium, revealing their abundance, diversity, and potential roles in resistance, virulence, and evolution. These findings highlight the importance of prophages in shaping the pathogenicity and adaptability of E. faecium and underscore the need for further functional investigations.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-025-12172-x.},
}

@article {pmid41060240,
year = {2025},
author = {Toro-Delgado, E and Laetsch, DR and Hayward, A and Talavera, G and Lohse, K and Vila, R},
title = {Wolbachia Host Shifts and Widespread Occurrence of Reproductive Manipulation Loci in European Butterflies.},
journal = {Molecular ecology},
volume = {34},
number = {21},
pages = {e70125},
doi = {10.1111/mec.70125},
pmid = {41060240},
issn = {1365-294X},
support = {NE/L011522/1//Natural Environment Research Council/ ; 2021-SGR-00420//Departament de Recerca i Universitats, Generalitat de Catalunya/ ; 2021-SGR-01334//Departament de Recerca i Universitats, Generalitat de Catalunya/ ; FPU22/02358//Ministerio de Ciencia, Innovación y Universidades/ ; PID2022-139689NB-I00//Ministerio de Ciencia, Innovación y Universidades/ ; PID2023-152239NB-I00//Ministerio de Ciencia, Innovación y Universidades/ ; BB/N020146/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; /ERC_/European Research Council/International ; },
mesh = {Animals ; *Wolbachia/genetics/classification ; *Butterflies/microbiology/genetics ; Phylogeny ; Symbiosis/genetics ; Reproduction/genetics ; Gene Transfer, Horizontal ; Male ; Female ; Europe ; Genome, Bacterial ; },
abstract = {Wolbachia is the most frequent bacterial endosymbiont of arthropods and nematodes. Although it is mostly vertically transmitted, from parent to offspring through the egg cytoplasm, horizontal transfer of Wolbachia is thought to be common over evolutionary timescales. However, the relative frequency of each transmission mechanism has not been studied systematically in closely related species. Additionally, while Wolbachia is generally regarded as a reproductive manipulator, it is unclear how frequently the symbiont induces such effects. In this study, we investigated the presence, phenotypes and phylogenetic relationships among Wolbachia strains in whole genome sequence data for 18 European butterfly sister-species pairs. We find that sister-species share Wolbachia strains more often than random species pairs and that the probability of strain sharing is higher for younger pairs of host species, especially those with greater range overlap. We also find that split times between Wolbachia strains that infect the same sister-species pair generally pre-date host divergence, ruling out co-divergence in favour of horizontal transfer. However, some strains are younger than the mitochondrial split times of their hosts, so introgressive transfer cannot be ruled out in some cases. In addition, all newly assembled Wolbachia genomes contained putative homologues of genes associated with cytoplasmic incompatibility and male killing. This supports the potential for reproductive manipulation in Wolbachia strains infecting European butterflies, which until now was only inferred from mitochondrial diversity patterns. Our results show that horizontal and introgressive transfer of Wolbachia are frequent even between recently speciated host taxa, suggesting the symbiont's turnover rate is higher than had been inferred previously from surveys of distantly related hosts.},
}

Animals
*Wolbachia/genetics/classification
*Butterflies/microbiology/genetics
Phylogeny
Symbiosis/genetics
Reproduction/genetics
Gene Transfer, Horizontal
Male
Female
Europe
Genome, Bacterial

@article {pmid41156746,
year = {2025},
author = {Tisalema-Guanopatín, E and Cabezas-Mera, F and Pérez-Meza, ÁA and Palacios, V and Espinosa, F and Ligña, E and Cristina Aguilar, A and Reyes-Chacón, J and Grunauer, M and Garzón-Chavez, D},
title = {Genomic Characterization of Carbapenem-Resistant Klebsiella pneumoniae ST1440 and Serratia marcescens Isolates from a COVID-19 ICU Outbreak in Ecuador.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102286},
pmid = {41156746},
issn = {2076-2607},
support = {17118//Universidad San Francisco de Quito, Medicine Grants/ ; },
abstract = {The global rise of antimicrobial resistance (AMR), exacerbated by the COVID-19 pandemic, has led to a surge in infections caused by multidrug-resistant (MDR) bacteria. A key driver of this phenomenon is co-selection, where exposure to one antimicrobial promotes resistance to others via horizontal gene transfer (HGT) mediated by mobile genetic elements (MGEs). Carbapenem-resistant Enterobacteriaceae, known for their genomic plasticity, are particularly worrisome; yet genomic data from Latin America-especially Ecuador-remain scarce. This study investigated four carbapenem-resistant clinical isolates (two Klebsiella pneumoniae ST1440 and two Serratia marcescens) from tracheal aspirates of three ICU patients during a COVID-19 outbreak at Hospital IESS Quito Sur, Ecuador. Phenotypic profiling and whole-genome sequencing were performed, followed by bioinformatic reconstruction of plasmid content. Nineteen plasmids were identified, carrying 70 resistance-related genes, including antimicrobial resistance genes (ARGs), metal resistance genes (MRGs), integrons, transposons, and insertion sequences. Hierarchical clustering revealed six distinct gene clusters, with several co-localizing ARGs and genes for resistance to disinfectants and heavy metals-suggesting strong co-selective pressure. Conjugative plasmids harboring high-risk elements such as blaKPC-2, qacE, and Tn4401 were found in multiple isolates, indicating potential interspecies dissemination. These findings emphasize the importance of plasmid-mediated resistance during the pandemic and highlight the urgent need to enhance genomic surveillance and infection control, particularly in resource-limited healthcare settings.},
}

@article {pmid41156665,
year = {2025},
author = {Domingues, CPF and Rebelo, JS and Dionisio, F and Nogueira, T},
title = {Plasmid Genomic Dynamics and One Health: Drivers of Antibiotic Resistance and Pathogenicity.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {10},
pages = {},
doi = {10.3390/pathogens14101054},
pmid = {41156665},
issn = {2076-0817},
mesh = {*Plasmids/genetics ; Humans ; *One Health ; Animals ; *Bacteria/genetics/pathogenicity/drug effects ; Virulence/genetics ; *Drug Resistance, Bacterial/genetics ; *Genome, Bacterial ; Microbiota ; Genomics ; *Drug Resistance, Microbial/genetics ; },
abstract = {Seen through a One Health perspective, plasmids act as global links, connecting human, animal, and environmental microbiomes while broadening the ecological scope of resistance and virulence. By combining knowledge about plasmid classification, mobility, resistance, virulence, and data sources, this review emphasizes their key role as drivers of bacterial evolution and worldwide health risks. Recognizing plasmids as connectors across microbiomes highlights both the urgency and opportunity to address plasmid-mediated resistance with integrated strategies. Current plasmid databases, such as NCBI RefSeq, PLSDB, IMG/PR, and PlasmidScope, have already greatly advanced our understanding of these connections, and they are likely to profoundly alter how we see plasmid biology and One Health relationships.},
}

*Plasmids/genetics
Humans
*One Health
Animals
*Bacteria/genetics/pathogenicity/drug effects
Virulence/genetics
*Drug Resistance, Bacterial/genetics
*Genome, Bacterial
Microbiota
Genomics
*Drug Resistance, Microbial/genetics

@article {pmid41155856,
year = {2025},
author = {Caivano, G and Sciarra, FM and Messina, P and Cumbo, EM and Caradonna, L and Di Vita, E and Nigliaccio, S and Fontana, DA and Scardina, A and Scardina, GA},
title = {Antimicrobial Resistance and Causal Relationship: A Complex Approach Between Medicine and Dentistry.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {61},
number = {10},
pages = {},
doi = {10.3390/medicina61101870},
pmid = {41155856},
issn = {1648-9144},
mesh = {Humans ; Anti-Bacterial Agents/therapeutic use/pharmacology ; *Drug Resistance, Bacterial ; Biofilms/drug effects ; *Dentistry/methods/trends ; },
abstract = {Antimicrobial resistance (AMR) is widely recognized as a major global public health threat, yet its origins and implications extend beyond the simple misuse or overuse of antibiotics. This study explores AMR as a complex, multifactorial phenomenon shaped by biological, clinical, dental, environmental, and social dynamics, with particular attention to the emerging role of dentistry. A narrative literature review was performed, drawing from textbooks, peer-reviewed articles, and official World Health Organization (WHO) reports, with emphasis on recent findings on periodontal biofilms as reservoirs of resistance genes. The analysis shows that AMR develops through bacterial mutations, horizontal gene transfer, environmental contamination, healthcare-associated practices, and patient behaviors, all of which interact to sustain its spread. Within dentistry, subgingival microresistances are gaining relevance, complicating treatment strategies and underscoring the need for more conscious clinical decision-making. The findings suggest that reducing antibiotic prescriptions or developing new drugs alone will not suffice; instead, a systemic, interdisciplinary approach is required, integrating microbiology, clinical practice, public health, and institutional responsibility. Such awareness is essential to confront the significant clinical, economic, and social implications of AMR and to foster strategies capable of addressing its complex and evolving nature.},
}

Humans
Anti-Bacterial Agents/therapeutic use/pharmacology
*Drug Resistance, Bacterial
Biofilms/drug effects
*Dentistry/methods/trends

@article {pmid41152242,
year = {2025},
author = {Koh, V and Cabrera, R and Sridatta, PSR and Thevasagayam, NM and Lim, ZQ and Marimuthu, K and Venkatachalam, I and Cherng, BPZ and Fong, RKC and Pada, SK and Ooi, ST and Smitasin, N and Thoon, KC and Hsu, LY and Koh, TH and De, PP and Tan, TY and Chan, D and Deepak, RN and Tee, NWS and Gan, YH and Matlock, W and Eyre, DW and Ang, M and Lin, RTP and Teo, J and Ng, OT and , },
title = {Plasmid dynamics driving carbapenemase gene dissemination in healthcare environments: a nationwide analysis of closed Enterobacterales genomes.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9522},
pmid = {41152242},
issn = {2041-1723},
support = {MOH-001763//MOH | National Medical Research Council (NMRC)/ ; CG21APR2005//MOH | National Medical Research Council (NMRC)/ ; MOH-001326-01//MOH | National Medical Research Council (NMRC)/ ; MOH-001706//MOH | National Medical Research Council (NMRC)/ ; },
mesh = {*Plasmids/genetics ; *beta-Lactamases/genetics ; *Bacterial Proteins/genetics/metabolism ; Singapore/epidemiology ; *Enterobacteriaceae/genetics/isolation & purification ; Humans ; *Enterobacteriaceae Infections/microbiology/epidemiology/transmission ; *Genome, Bacterial/genetics ; Gene Transfer, Horizontal ; Genotype ; Carbapenems/pharmacology ; Carbapenem-Resistant Enterobacteriaceae/genetics ; Microbial Sensitivity Tests ; },
abstract = {Plasmid-mediated transmission can account for half of carbapenem-producing Enterobacterales (CPE) dissemination, underscoring the need to identify genetic determinants of plasmid persistence in the hospital setting. From 1,088 CPE isolates detected through nationwide surveillance in Singapore over five years, 1,115 closed carbapenemase-producing plasmids were identified and clustered, of which 92.5% (n = 1031) were grouped into 48 plasmid clusters (PCs). The most common plasmid genotypes were PC1 and PC2. Of 389 isolates carrying blaKPC-2-positive PC1 plasmids and 283 isolates carrying blaNDM-1-positive PC2 plasmids, 236 (60.7%) and 168 (59.4%) putatively acquired the carbapenemase gene via plasmid-mediated horizontal transmission, whereas 153 (39.3%) and 115 (40.6%) putatively acquired the carbapenemase gene via clonal lineage-dependent vertical transmission, respectively. Less abundant plasmids showed distinct inserted genomic regions encoding genes related to heavy metal and formaldehyde detoxification not found in predominant plasmids. Our data suggest that PC1 and PC2 genotypes are better adapted for stable propagation of blaKPC-2 and blaNDM-1, respectively, during inter-patient clonal spread and across multiple species (and sequence types) compared to other genetic settings. We propose that a crucial factor enabling evolutionarily successful carbapenemase plasmid genotypes to achieve hyperendemicity in the population is the maintenance of conserved genomes, thus minimizing fitness costs to their hosts.},
}

*Plasmids/genetics
*beta-Lactamases/genetics
*Bacterial Proteins/genetics/metabolism
Singapore/epidemiology
*Enterobacteriaceae/genetics/isolation & purification
Humans
*Enterobacteriaceae Infections/microbiology/epidemiology/transmission
*Genome, Bacterial/genetics
Gene Transfer, Horizontal
Genotype
Carbapenems/pharmacology
Carbapenem-Resistant Enterobacteriaceae/genetics
Microbial Sensitivity Tests

@article {pmid41152006,
year = {2025},
author = {McInerney, JO},
title = {Classifying Convergences in the Light of Horizontal Gene Transfer: Epaktovars and Xenotypes.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msaf279},
pmid = {41152006},
issn = {1537-1719},
abstract = {The classification of living systems presents significant challenges due to the prevalence of gene transfer between genomes. Traditional taxonomic systems have been designed to describe tree-like evolution and consequently struggle to accommodate network-like evolutionary patterns. In this perspective, I consolidate and clarify terminology for describing organisms whose evolutionary history has not been strictly tree-like. I introduce two complementary concepts: epaktovars - groups (>=2) of organisms exhibiting convergent phenotypes through independent acquisition of similar functions, whether via horizontal gene transfer or independent evolution of analogous solutions; and xenotypes - organisms that share homologous genes acquired through horizontal gene transfer, regardless of whether these shared genes produce similar or different phenotypes. The epaktovar concept mirrors the previously established concept of epaktologs (independent assembly of similar protein domain architectures), while xenotypes extends the concept of xenologs (horizontally transferred homologous genes) to the genome level. Recent research on homoplastic patterns in pangenome evolution enhances our understanding of these phenomena. These concepts also have important applications in synthetic biology and de-extinction efforts, where genetically modified organisms and reconstructed extinct species can be understood as xenotypes and epaktovars of their genetic donors, providing a framework for classifying organisms whose genetic composition has been shaped by human intervention rather than natural evolutionary processes. These terms collectively provide a framework for describing both phenotypic convergence arising through any evolutionary mechanism and shared genetic material resulting specifically from gene transfer across diverse lineages.},
}

@article {pmid41150720,
year = {2025},
author = {Zhao, Y and Ma, Y and Vasileiou, C and Farr, AD and Rogers, DW and Rainey, PB},
title = {Jumbo phage-mediated transduction of genomic islands.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {44},
pages = {e2512465122},
doi = {10.1073/pnas.2512465122},
pmid = {41150720},
issn = {1091-6490},
mesh = {*Genomic Islands/genetics ; *Bacteriophages/genetics/physiology ; *Pseudomonas fluorescens/genetics/virology ; Gene Transfer, Horizontal ; *Transduction, Genetic ; Interspersed Repetitive Sequences/genetics ; },
abstract = {Bacteria acquire new genes by horizontal gene transfer, typically mediated by mobile genetic elements (MGEs). While plasmids, bacteriophages, and certain integrative and conjugative elements are well characterized, the broader diversity of MGEs remains poorly understood. Here, we cultured the bacterium Pseudomonas fluorescens SBW25 with sterile filtrate obtained from garden compost communities. Genome sequencing of derived colonies revealed acquisition of three different mobile elements, each integrated immediately downstream of tmRNA, each flanked by direct repeats, and each encoding a tyrosine integrase (intY) plus putative phage defense systems. Absent are genes with recognized roles in autonomous transfer. Interrogation of DNA sequence databases showed that similar elements are widespread in the genus Pseudomonas and beyond, with Vibrio Pathogenicity Island-1 from Vibrio cholerae as a notable example. Bioinformatic analyses reveal evidence of extensive horizontal transfer among diverse hosts. Detailed analysis of a single element, I55, showed that it is transferred between cells by jumbo phages, and confers fitness benefits via a type II restriction-modification system.},
}

*Genomic Islands/genetics
*Bacteriophages/genetics/physiology
*Pseudomonas fluorescens/genetics/virology
Gene Transfer, Horizontal
*Transduction, Genetic
Interspersed Repetitive Sequences/genetics

@article {pmid40981469,
year = {2025},
author = {Maree, M and Ushijima, Y and Krama, A and Sasaki, M and Miyata, T and Higashide, M and Nguyen, LTT and Morikawa, K},
title = {Mixed-biofilm natural transformation assay reveals the presence of staphylococci in human environments that can transfer SCCmec to Staphylococcus aureus.},
journal = {mSphere},
volume = {10},
number = {10},
pages = {e0044225},
doi = {10.1128/msphere.00442-25},
pmid = {40981469},
issn = {2379-5042},
support = {JP23fk0108630//Japan Agency for Medical Research and Development/ ; JPJSBP120229908//Japan Society for the Promotion of Science/ ; 22H02863//Japan Society for the Promotion of Science/ ; 23K14515//Japan Society for the Promotion of Science/ ; 24KK0148//Japan Society for the Promotion of Science/ ; na//Takano Foundation for the Promotion of Science/ ; },
mesh = {*Biofilms/growth & development ; Humans ; Animals ; *Staphylococcus aureus/genetics ; *Staphylococcus/genetics/isolation & purification ; *Methicillin-Resistant Staphylococcus aureus/genetics ; *Gene Transfer, Horizontal ; Livestock/microbiology ; Staphylococcal Infections/microbiology ; *Transformation, Bacterial ; Pets/microbiology ; Meat/microbiology ; },
abstract = {Methicillin-resistant Staphylococcus aureus (MRSA) is an important pathogen that causes healthcare-, community-, and livestock-associated infections. The methicillin resistance gene mecA is embedded in the mobile genetic element termed Staphylococcal Cassette Chromosome (SCCmec). SCCmec is shared among staphylococci inhabiting human and animal hosts, which are recognized epidemiologically as the genetic reservoir of SCCmec. However, the ability of diverse methicillin-resistant staphylococci (MRS) to serve as SCCmec donors for S. aureus has not been tested experimentally. Here, we investigated the ability of 157 MRS isolates from pets, meat, livestock, and humans to transfer SCCmec to methicillin-sensitive S. aureus strains using a recently developed natural transformation protocol in mixed biofilms. We found that 25 out of 157 isolates were able to transfer SCCmec to S. aureus. The most effective donor species were S. epidermidis (~33% of the tested isolates), S. felis (40%), and S. capitis (30%). Isolates from meat and livestock (collected in Vietnam and Thailand) had lower transfer rates of SCCmec (5% and 3%, respectively), compared to human and pet isolates from Japan (35% and 25%, respectively). The SCCmec transfer depended on site-specific integration/excision mediated by an intact attB site, which is recognized by the SCC recombinase Ccr. Our study experimentally demonstrates the presence of SCCmec donors in our living environments, highlighting the importance of specific staphylococcal species.IMPORTANCEHow MRSA emerges has long been the pivotal question regarding the ever-increasing burden of antimicrobial resistance (AMR) issues for over half a century. Extensive research efforts in bacteriology, epidemiology, genome biology, and healthcare fields have led to the common understanding that SCCmec is transmitted among distinct staphylococcal species. However, global efforts to provide empirical evidence for intercellular SCCmec transmission have yielded limited results. We recently established the mixed-biofilm transformation assay to evaluate intercellular and interspecies SCCmec transmission. This novel assay system allows us to gain insight into the question "How MRSA emerges," and here, we provide the first experimental results about the potential donor species and habitats. This is the first report to show the ability of staphylococci from distinct sources to transfer SCC to S. aureus. Moreover, the new finding of S. felis as an effective donor that is not commensal to humans reinforces the importance of the One Health concept.},
}

*Biofilms/growth & development
Humans
Animals
*Staphylococcus aureus/genetics
*Staphylococcus/genetics/isolation & purification
*Methicillin-Resistant Staphylococcus aureus/genetics
*Gene Transfer, Horizontal
Livestock/microbiology
Staphylococcal Infections/microbiology
*Transformation, Bacterial
Pets/microbiology
Meat/microbiology

@article {pmid41149912,
year = {2025},
author = {Arbildi, E and Ovsejevi, K and Roldán, D and Durán, R and Portela, M and Garmendia, G and Vero, S},
title = {From Isolation to Genomics: Characterization of Aspergillus uvarum HT4 as a Novel Producer of Extracellular Tannase.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {10},
pages = {},
doi = {10.3390/jof11100722},
pmid = {41149912},
issn = {2309-608X},
support = {POS_NAC_2022_1_174159//agencia nacional de investigación e innovacion Uruguay/ ; },
abstract = {Tannases (tannin acyl hydrolases, EC 3.1.1.20) are enzymes of industrial interest due to their ability to hydrolyze hydrolyzable tannins into bioactive compounds like gallic acid. In this study fungal strains capable of producing extracellular tannase were isolated and identified. From tannin-rich substrates, 24 fungal isolates were obtained, of which 17 showed tannase activity. Molecular identification based on calmodulin gene sequencing identified three species of tannase-producing black aspergilli: Aspergillus luchuensis, A. niger (formerly A. welwitschiae), and A. uvarum. The isolate A. uvarum HT4 exhibited the highest extracellular tannase activity (182 U/mL) and was selected for further study. Whole-genome sequencing of HT4 revealed 15 putative tannase genes, most sharing high identity with A. uvarum CBS 121591. Two divergent genes appeared to be acquired via horizontal gene transfer from Aspergillus brunneoviolaceus and Penicillium angulare. Proteomic analysis of the secretome confirmed the expression of two extracellular tannases. The enzyme showed optimal activity at pH 5.0-6.0 and 40-50 °C. Secretome analysis revealed hydrolytic enzymes typical of saprophytic fungi in lignocellulose-rich environments. Importantly, no biosynthetic gene clusters of major mycotoxins were detected, supporting the biosafety of HT4 for industrial applications.},
}

@article {pmid41148714,
year = {2025},
author = {Lertcanawanichakul, M and Bhoopong, P and Horpet, P},
title = {Mangrove Ecosystems as Reservoirs of Antibiotic Resistance Genes: A Narrative Review.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {10},
pages = {},
doi = {10.3390/antibiotics14101022},
pmid = {41148714},
issn = {2079-6382},
support = {The official grant number has not yet been assigned.//Plant Genetic Conservation Project Undeพ the Royal Initiative of Her Royal Highness Princess Maha Chakri Sirindhorn - RSPG/ ; },
abstract = {Background: Mangrove ecosystems are critical coastal environments providing ecological services and acting as buffers between terrestrial and marine systems. Rising antibiotic use in aquaculture and coastal agriculture has led to the dissemination of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in these habitats. Aim: This narrative review aims to synthesize current knowledge on the prevalence, diversity, and environmental drivers of ARGs in mangrove ecosystems, highlighting their role as reservoirs and the potential for horizontal gene transfer. Methods: Studies published up to September 2024 were identified through PubMed, Scopus, Web of Science, and Google Scholar. Inclusion criteria focused on ARGs and ARB in mangrove sediments, water, and associated biota. Data on ARG prevalence, microbial community composition, detection methods, and environmental factors were extracted and narratively synthesized. Results: Seventeen studies from Asia, South America, and Africa were included. ARGs conferring resistance to tetracyclines, sulfonamides, β-lactams, and multidrug resistance were found to be widespread, particularly near aquaculture and urban-influenced areas. Metagenomic analyses revealed diverse resistomes with frequent mobile genetic elements, indicating high potential for horizontal gene transfer. Environmental factors, including sediment type, organic matter, and salinity, influenced ARG abundance and distribution. Conclusions: Mangrove ecosystems act as both reservoirs and natural buffers for ARGs. Sustainable aquaculture practices, continuous environmental monitoring, and integrated One Health approaches are essential to mitigate ARG dissemination in these sensitive coastal habitats.},
}

@article {pmid41148687,
year = {2025},
author = {Nass, NM and Zaher, KA},
title = {Beyond the Resistome: Molecular Insights, Emerging Therapies, and Environmental Drivers of Antibiotic Resistance.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {10},
pages = {},
doi = {10.3390/antibiotics14100995},
pmid = {41148687},
issn = {2079-6382},
abstract = {Antibiotic resistance remains one of the most formidable challenges to modern medicine, threatening to outpace therapeutic innovation and undermine decades of clinical progress. While resistance was once viewed narrowly as a clinical phenomenon, it is now understood as the outcome of complex ecological and molecular interactions that span soil, water, agriculture, animals, and humans. Environmental reservoirs act as silent incubators of resistance genes, with horizontal gene transfer and stress-induced mutagenesis fueling their evolution and dissemination. At the molecular level, advances in genomics, structural biology, and systems microbiology have revealed intricate networks involving plasmid-mediated resistance, efflux pump regulation, integron dynamics, and CRISPR-Cas interactions, providing new insights into the adaptability of pathogens. Simultaneously, the environmental dimensions of resistance, from wastewater treatment plants and aquaculture to airborne dissemination, highlight the urgency of adopting a One Health framework. Yet, alongside this growing threat, novel therapeutic avenues are emerging. Innovative β-lactamase inhibitors, bacteriophage-based therapies, engineered lysins, antimicrobial peptides, and CRISPR-driven antimicrobials are redefining what constitutes an "antibiotic" in the twenty-first century. Furthermore, artificial intelligence and machine learning now accelerate drug discovery and resistance prediction, raising the possibility of precision-guided antimicrobial stewardship. This review synthesizes molecular insights, environmental drivers, and therapeutic innovations to present a comprehensive landscape of antibiotic resistance. By bridging ecological microbiology, molecular biology, and translational medicine, it outlines a roadmap for surveillance, prevention, and drug development while emphasizing the need for integrative policies to safeguard global health.},
}

@article {pmid41147614,
year = {2025},
author = {Schultz, DL and Stouthamer, CM and Kelly, SE and Mathieson, OL and Kleiner, M and Hunter, MS and Schmitz-Esser, S},
title = {Comparative Genomics of the Endosymbiont Cardinium Causing Reproductive Manipulation in Encarsia Parasitoid Wasps.},
journal = {MicrobiologyOpen},
volume = {14},
number = {6},
pages = {e70084},
doi = {10.1002/mbo3.70084},
pmid = {41147614},
issn = {2045-8827},
support = {//This study was funded by NSF Awards #1256905, #2002934, and #2426306 to M. S. Hunter, #2002987 and #2426304 to S. Schmitz-Esser, and IOS #2426305 and IOS #2003107 to M. Kleiner./ ; },
mesh = {Animals ; *Wasps/microbiology/physiology ; *Symbiosis ; *Genome, Bacterial ; *Bacteroidetes/genetics/classification/physiology/isolation & purification ; Genomics ; Reproduction ; Phylogeny ; Parthenogenesis ; },
abstract = {Many invertebrates harbor the vertically transmitted endosymbiotic bacterium Cardinium hertigii, and some display altered reproductive phenotypes due to manipulation by Cardinium. Despite their host impact, genomic information for reproductive manipulator strains of Cardinium is sparse. Of the three reproductive manipulation phenotypes Cardinium is known to induce in its hosts, only two genomes causing cytoplasmic incompatibility (CI) are available, and genomes inducing other manipulation phenotypes are absent. In this study, we have sequenced and assembled four novel Cardinium genomes, three of which are associated with two different reproductive manipulation phenotypes, parthenogenesis induction and CI. Analysis of the genomes revealed that Cardinium associated with parasitoid wasp hosts in the genus Encarsia are generally more closely related to each other than to other Cardinium, but one strain, cEina2, is very similar to the whitefly-associated Cardinium strain cBtQ1. Further, unique and shared candidate genes for host interaction were identified, including putative zinc finger proteins shared by the parthenogenesis-associated strains cEper2 and cEhis1 and a large protein encoded by the CI Cardinium strain cEina3 with very distant similarity to the Wolbachia CI protein CidB. Finally, we predicted the presence of plasmids in three genomes. Also, despite the limited metabolic capacity of Cardinium, we identified potential horizontally transferred genes involved in central metabolism. These genomes will aid future studies to further our understanding of Cardinium-induced reproductive manipulation.},
}

Animals
*Wasps/microbiology/physiology
*Symbiosis
*Genome, Bacterial
*Bacteroidetes/genetics/classification/physiology/isolation & purification
Genomics
Reproduction
Phylogeny
Parthenogenesis

@article {pmid41145054,
year = {2025},
author = {Pereira, AR and de Moraes, LÂG and Rosse, I and de Aquino, SF and Silva, SQ},
title = {Microbial dynamics in a swine wastewater treatment plant and prediction of potential hosts of antibiotic resistance genes.},
journal = {International journal of hygiene and environmental health},
volume = {271},
number = {},
pages = {114698},
doi = {10.1016/j.ijheh.2025.114698},
pmid = {41145054},
issn = {1618-131X},
abstract = {Using a culture-independent approach, this study aimed to evaluate microbial community changes in a swine wastewater treatment plant (SWWTP) and investigate the presence of bacteria for public health concerns, particularly those harboring antibiotic resistance genes (ARG) with pathogenic potential. Through sequencing of fifteen samples collected across five sampling campaigns - at the influent, biodigester outlet, and final effluent - higher microbial diversity was observed in the untreated waste, reflected by a greater relative abundance of operational taxonomic units (OTUs) linked to the families Streptococcaceae (up to 27 %), unidentified members of the order Clostridiales (up to 33 %), and Moraxellaceae (up to 19 %). A microbial succession was observed across subsequent treatment stages, characterized by an increased relative abundance of OTUs associated with Clostridiaceae (0-68 %) and Peptostreptococcaceae (8-25 %), likely driven by environmental conditions. Sequences related to the order Clostridiales and the family Moraxellaceae showed correlations with the resistance genes blaTEM, ermB, qnrB, sul1, and tetA, suggesting that members of these groups could serve as potential gene hosts. The detection of residual ARGs and OTUs related to potentially pathogenic genera such as Clostridium butyricum and Terrisporobacter glycolicus species in the treated effluent raises concerns about the final disposal of this waste, given the possibility of horizontal gene transfer in the environment.},
}

@article {pmid41144667,
year = {2025},
author = {Xu, JY and Yu, YT and Du, S and Shen, LQ and Zhang, Q and Qian, H and Cai, TG and Wang, YF and Zhao, J and Li, HZ and Zhang, C and Zhu, D},
title = {Discarded cigarette butts as overlooked reservoirs and amplifiers of antibiotic resistance genes and pathogens in urban green spaces.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {44},
pages = {e2525377122},
doi = {10.1073/pnas.2525377122},
pmid = {41144667},
issn = {1091-6490},
support = {42222701//MOST | National Natural Science Foundation of China (NSFC)/ ; 22193062//MOST | National Natural Science Foundation of China (NSFC)/ ; 22193062//MOST | National Natural Science Foundation of China (NSFC)/ ; 22125601//MOST | NSFC | National Science Fund for Distinguished Young Scholars (NSF for Distinguished Young Scholars)/ ; 2023321//Youth Innovation Promotion Association of the Chinese Academy of Sciences (CAS YIPA)/ ; 2022A-163-G//Ningbo Yongjiang Talent Project/ ; },
mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Drug Resistance, Microbial/genetics ; China ; *Tobacco Products/microbiology ; Gene Transfer, Horizontal ; *Bacteria/genetics/drug effects ; Genes, Bacterial ; *Drug Resistance, Bacterial/genetics ; Biofilms/growth & development ; },
abstract = {Cigarette butts are widely discarded in urban green spaces, yet their microbial health risks remain poorly understood. In a nationwide survey across China, we investigated the presence, sources, health risks, and drivers of antibiotic resistance genes (ARGs) and potential pathogens in discarded cigarette butts. Shotgun metagenomic and full-length 16S ribosomal rRNA (rRNA) sequencing revealed that cigarette butts harbored significantly higher abundances of ARGs and bacterial pathogens than plant litter or soil. Health risk assessment further showed that cigarette butts carried ARGs with greater mobility, clinical relevance, and pathogenic potential. Genomic analyses highlighted enrichment of ARG-carrying pathogens, particularly Enterobacteriaceae and Pseudomonas, with mobile genetic elements and oxidative stress responses as key contributors. Functional assays, including plasmid transfer, transcriptomic profiling, and single-cell Raman spectroscopy, demonstrated that cigarette butts promoted horizontal gene transfer and upregulated key ARGs (e.g., mexE, mexF, cfrC) under stress conditions. Scanning electron microscopy confirmed biofilm formation on cigarette fibers, supporting enhanced bacterial persistence. Source-tracking analyses identified both human oral and environmental sources of the enriched ARGs and pathogens in cigarette butts. Finally, socioeconomic factors such as lower gross domestic product (GDP), reduced education, and poor sanitation were strongly associated with elevated ARG and pathogen risks. Collectively, our findings identify cigarette butts as overlooked yet potent vectors of ARG and pathogen dissemination in urban green spaces, underscoring the need for targeted interventions within a One Health framework.},
}

Humans
RNA, Ribosomal, 16S/genetics
*Drug Resistance, Microbial/genetics
China
*Tobacco Products/microbiology
Gene Transfer, Horizontal
*Bacteria/genetics/drug effects
Genes, Bacterial
*Drug Resistance, Bacterial/genetics
Biofilms/growth & development

@article {pmid41144183,
year = {2025},
author = {Abavisani, M and Khoshroo, N and Tafti, P and Karbas Foroushan, S and Ebadpour, N and Karav, S and Kesharwani, P and Sahebkar, A},
title = {Mechanisms, Modulation, and Mitigation: Dietary-Gut Microbiome Strategies Against Antibiotic Resistance.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41144183},
issn = {1867-1314},
abstract = {Antibiotic resistance seriously compromises world health by affecting the effectiveness of therapies and greatly raising morbidity, death, and healthcare expenditures. Particularly in hospital environments, the rapid spread of multidrug-resistant organisms hampers the treatment of bacterial infections and challenges the efficacy of current medicines. Antibiotic resistance has multiple mechanisms: biofilm development, horizontal gene transfer, and genetic alterations. To address this developing issue, studies have focused on alternative strategies, including new antimicrobial medicines, combination treatments, and non-traditional remedies. Additionally, dietary therapies, probiotics (the live microorganisms that, when administered in adequate amounts, confer a health benefit on the host), and phytochemicals have garnered interest due to their ability to alter the gut microbiota, the complex community of microorganisms living in the digestive tracts, thus potentially limiting the dissemination of resistant bacteria. These approaches, meanwhile, have difficulties, including limits in clinical translation and the adaptation of bacterial populations. This study aims to comprehensively review the current understanding of the connections between the gut microbiome and the development of antibiotic resistance by investigating the probable underlying mechanistic effects and also highlights the possibility of targeting host-microbiome interactions as a new intervention option.},
}

@article {pmid41144018,
year = {2025},
author = {Kejnovsky, E and Kubat, Z and Sponer, JE},
title = {Acytota and the evolution of complexity.},
journal = {European biophysics journal : EBJ},
volume = {},
number = {},
pages = {},
pmid = {41144018},
issn = {1432-1017},
support = {22-00364S//Grantová Agentura České Republiky/ ; 21-00580S//Grantová Agentura České Republiky/ ; 24-11400S//Grantová Agentura České Republiky/ ; },
abstract = {The overall complexity of organisms increases during the course of evolution, starting with the first self-replicating molecules, followed by prokaryotes and eukaryotes, first unicellular and later multicellular. We present an opinion that non-cellular genetic entities such as transposable elements, plasmids, viruses and viroids, although originally parasitic, selfish and sometimes destructive elements, may contribute to the increase of complexity. We propose that non-cellular genetic elements impose (parasitic) pressure on the cooperative genes of cellular organisms, driving the sequence of evolutionary transitions from the first cooperative replicators to multicellular life forms, and have suggested that they belong to a separate kingdom of life, the Acytota. The complexity increase is probably caused by the high proliferation capacity of these non-cellular genetic elements, their frequent horizontal gene transfer, participation in parasite-host arms races, formation of epigenetic silencing mechanisms as well as the ability to build genetic regulatory networks. Simultaneously, these elements contribute to complexity by supplying genetic material via domestication, genome rearrangements, and dispersal of regulatory elements. Complexity has not only increased during evolution, there are also examples of simplification, both during chemical evolution (in prebiotic chemistry) and the evolution of parasites. Therefore, we describe the ups and downs of organism complexity and discuss the reasons for the general dominant upward trend, namely coevolution and the interaction of existing modules.},
}

@article {pmid41143557,
year = {2025},
author = {Shi, Z and Liu, Q and Zhou, M and Xu, W and Luo, G},
title = {Persistent Risks in the Effluents of Wastewater Treatment Plants: Mobile Genetic Elements and Viral-Mediated Dissemination of Pathogenic Antibiotic-Resistant Bacteria.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c08352},
pmid = {41143557},
issn = {1520-5851},
abstract = {Wastewater treatment plants (WWTPs) are recognized as reservoirs of pathogenic antibiotic-resistant bacteria (PARB), yet their genomic risk dynamics remain unclear. This study recovered PARB genomes from 102 influent and effluent metagenomes from six countries; their activity and risk potential were then experimentally validated with metatranscriptomics on samples from a Shanghai WWTP. A total of 44 PARB genomes were reconstructed, which carried both antibiotic resistance genes (ARGs) and virulence factor genes (VFGs), and they persisted in the effluent. Mobile genetic elements might mediate ARG transfer in 13 PARB genomes. Moreover, bacteriophages infecting PARB harbored and were transcribing ARGs/VFGs, and antiviral defense systems of PARB correlated with horizontal gene transfer (HGT). Evolutionary analyses indicated that influent PARB maintained high microdiversity via homologous recombination, while effluent populations underwent purifying selection, suggesting that wastewater treatment reduced the genetic diversity of PARB through purifying selection. However, the persistent accumulation of PARB as well as HGT might maintain the dissemination of ARGs. This study emphasized the necessity of selecting the PARB genomes for wastewater monitoring, thereby optimizing treatment strategies and mitigating the potential health risks posed by pathogenic bacteria.},
}

@article {pmid41143419,
year = {2025},
author = {Sharp, ME and Sproch, J and Haldeman, S and Tettelin, H and Ratner, AJ},
title = {Expansion of the Group B Streptococcus serotype repertoire via gene acquisition from other streptococcal species.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0122725},
doi = {10.1128/spectrum.01227-25},
pmid = {41143419},
issn = {2165-0497},
abstract = {UNLABELLED: Group B Streptococcus (GBS) is a major cause of invasive infection in infants. The leading GBS vaccine candidate is a capsular polysaccharide-protein conjugate vaccine based on the six most common disease-causing serotypes (Ia, Ib, II-V). Four more recently discovered, less common serotypes (VI-IX) also circulate in the human population. Serotype VIII was initially described in the 1980s in Japan, where it made up a significant proportion of colonizing isolates in pregnant patients. Serotype VIII continues to be an emerging cause of colonization and disease globally. In addition to the 10 known GBS serotypes, intra- and interspecies horizontal gene transfer (HGT) could create GBS strains with novel capsule structures, potentially leading to vaccine escape. Previous work speculated that serotype VIII might be the result of interspecies HGT of a portion of the cps locus. We investigated the function and potential sources of cpsR, encoding a rhamnosyltransferase, in serotype VIII GBS. In a broad-based search for CpsR orthologs, proteins from streptococcal species that live in niches overlapping with GBS (including S. suis and S. gallolyticus) were closely related to CpsR. An unmarked, in-frame GBS ΔcpsR mutant was no longer recognized by serotype VIII-specific antibodies. Reactivity was restored by expressing wild-type cpsR or orthologs from S. suis and S. gallolyticus. In a murine model of vaginal co-colonization, the ΔcpsR mutant was outcompeted by wild-type serotype VIII, suggesting functional serotype VIII capsule provides a competitive advantage in vivo. Our findings are consistent with interspecies HGT as a mechanism underlying emergence of serotype VIII GBS.

IMPORTANCE: Capsular polysaccharide (CPS) is a key virulence factor that aids group B Streptococcus (GBS) in colonization and pathogenicity in humans. The major human vaccine candidate against GBS is a CPS-based vaccine including six serotypes. In addition to the four non-vaccine serotypes, intra- and interspecies horizontal gene transfer (HGT) could create GBS strains with novel capsule structures, potentially leading to vaccine escape. Here, we describe a key gene, cpsR, in the production of GBS serotype VIII and the complementation of its function by orthologs from other streptococci. Our work demonstrates GBS's ability to utilize genes from other streptococci to produce functional capsular polysaccharide. HGT could generate further capsule diversity beyond the 10 current serotypes, potentially increasing the number of strains capable of vaccine escape. Surveillance for such events is warranted.},
}

@article {pmid41142066,
year = {2025},
author = {Kyrychenko, A},
title = {Molecular architecture of giant viruses infecting microbial eukaryotes (protists).},
journal = {Biotechnologia},
volume = {106},
number = {3},
pages = {361-376},
pmid = {41142066},
issn = {2353-9461},
abstract = {In this review, I describe recent findings on the molecular architecture and genomic characterization of giant viruses that infect microbial eukaryotes (protists) across diverse ecosystems and ecological niches. Giant viruses are distinguished by their large and complex genomes, which encode a wide range of functions, including protein translation, carbohydrate and lipid metabolism, nitrogen cycling, light assimilation, and key metabolic pathways such as glycolysis and the tricarboxylic acid cycle. Additionally, these genomes feature unique genes, often acquired through horizontal gene transfer, that are not found in other viruses and contribute to the viruses' ability to manipulate host metabolism and evade host defenses. A core set of genes conserved across different families of giant viruses is highlighted, serving as essential components for key life-cycle processes and providing valuable phylogenetic markers. The review also discusses the role of ORFans and virophages in contributing to the genetic diversity and evolutionary adaptation of these viruses. These findings are crucial for understanding the diversity, evolutionary mechanisms, and complex virus-host interactions of giant viruses, as well as for developing more advanced classification systems. Furthermore, the potential biotechnological applications of unique viral genes and pathways are explored, underscoring the importance of ongoing research in this field.},
}

@article {pmid41139675,
year = {2025},
author = {Gan, P and Yu, X and Zou, J and Li, C and Yao, Z and Ye, Y and Xiong, S and Zhu, X and Zhu, Z and Zhang, J and Hu, J and Li, J and Wu, J and Zhang, S},
title = {Evolution and Functional Adaptation of Phytoplasma Effectors: A Potential Mobile Unit-Driven Perspective.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70253},
pmid = {41139675},
issn = {1365-3040},
support = {//This study was supported by the National Natural Science Foundation of China (Nos. 32025031, 32072381), the Natural Science Foundation of Fujian Province of China (2024J01378, 2025J010022), Yunnan Provincial Science and Technology Talent and Platform Program (Expert Workstation) (202405AF140083)./ ; },
abstract = {Remarkable phenotypic plasticity of phytoplasma infections stems from the fast evolution and functional divergence of a versatile effector arsenal. We first catalogue more than 50 characterised effectors, highlighting their interference with SPL/GATA, TCP, MADS-box and ARF hubs, and the combined consequences for plant morphogenesis, hormone homoeostasis and vector colonisation. We then explain how drastic genome reduction coexists with extensive repeats and is balanced by PMU-mediated replication and recombination to maintain genetic flexibility. Comparisons at the population level indicate that most effectors are located on PMUs, which promote the evolution of effectors through recombination, replication and horizontal transfer. Purifying selection preserves essential virulence functions and eliminates mutations that compromise effector activity, while diversifying selection fine-tunes host specificity and may aid evasion of host immune responses. Finally, we argue that elucidating the mechanistic link between the dynamics of PMUs and effector evolution may provide deeper insights into the molecular mechanisms of host manipulation.},
}

@article {pmid41139486,
year = {2025},
author = {Tran, T and Duong, DV and Le, TD and Bui, XT},
title = {Metagenomic Characterization of Biofilm and Suspended Microbial Communities in a Hybrid Algal Turf Scrubber-Based Wastewater Treatment System.},
journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica},
volume = {133},
number = {10},
pages = {e70072},
doi = {10.1111/apm.70072},
pmid = {41139486},
issn = {1600-0463},
mesh = {*Biofilms/growth & development ; *Wastewater/microbiology ; Metagenomics ; *Water Purification/methods ; Aquaculture ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation & purification ; Drug Resistance, Microbial/genetics ; Animals ; Nitrogen/metabolism ; Metagenome ; },
abstract = {This study investigates a hybrid wastewater treatment system combining a biofilm-based Algal Turf Scrubber (ATS) with a membrane-coupled High Rate Algal Pond (ATS-MHRAP) for shrimp aquaculture effluents. Shotgun metagenomic sequencing was used to compare microbial composition, functional pathways, and antibiotic resistance genes (ARGs) across attached biofilm (ATS1) and suspended biomass (ATS2, HRAP1) under three nutrient loading stages. Biofilm samples (ATS1) exhibited higher microbial richness and evenness, with Shannon index values up to 9.25, compared to 6.93 in suspended cultures. Functional pathways enriched in ATS1 included nitrogen cycling, amino acid metabolism, and terpenoid biosynthesis, with elevated expression of amoA, nirK, and nirS genes under moderate loading. These traits coincided with higher removal efficiency of COD (up to 88.6%), phosphate (82.1%), and total nitrogen (73.4%). ARGs were more diverse in ATS1, with up to 11 resistance classes detected, including β-lactam and sulfonamide genes co-occurring with intI1, indicating possible horizontal gene transfer. The ATS-MHRAP system offers a robust and biologically enriched platform for nature-based aquaculture wastewater treatment. Our findings reveal microbial and functional differentiation between attached and suspended communities, with implications for optimizing dissolved oxygen, nutrient ratios, and retention time.},
}

*Biofilms/growth & development
*Wastewater/microbiology
Metagenomics
*Water Purification/methods
Aquaculture
*Microbiota/genetics
*Bacteria/genetics/classification/isolation & purification
Drug Resistance, Microbial/genetics
Animals
Nitrogen/metabolism
Metagenome

@article {pmid41138978,
year = {2025},
author = {Wang, H and Han, X and Chen, A and Yan, Z and Zhang, R and Wang, Y},
title = {Prevalence and Molecular Epidemiology of optrA-Positive Enterococcus in Herders and Yaks from High-Altitude Tibet, China.},
journal = {Journal of global antimicrobial resistance},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgar.2025.10.016},
pmid = {41138978},
issn = {2213-7173},
abstract = {BACKGROUND: Antimicrobial resistance (AMR) in high-altitude environments remains understudied despite its growing global concern. This study investigates the molecular epidemiology of the optrA gene, which confers resistance to oxazolidinones and phenicols, in Enterococcus species isolated from herders and yak fecal samples in Nagqu, Tibet, China.

METHODS: A total of 161 fecal samples from herders and 42 from yaks were collected and analyzed for the presence of optrA-positive Enterococcus strains. Antimicrobial susceptibility testing (AST) was performed to determine resistance patterns. Whole-genome sequencing (WGS) and phylogenetic analysis were used to assess genetic relationships and the potential for clonal spread and horizontal gene transfer.

RESULTS: The optrA gene was detected in 6.2% (10/161) of human samples and 9.5% (4/42) of yak samples, indicating a higher prevalence in yaks. Resistance was highest for tetracycline (100%), erythromycin (92.9%), and linezolid (92.9%). Phylogenetic analysis revealed clonal dissemination, with some isolates exhibiting high genetic homology. Notably, one E. faecalis strain belonged to ST16, a sequence type commonly found in low-altitude cities, suggesting potential transmission between regions. The optrA gene was frequently associated with mobile genetic elements, indicating a risk of horizontal gene transfer and further dissemination of resistance.

CONCLUSION: The presence of optrA-positive Enterococcus in both human and animal populations in this high-altitude region underscores the role of human-animal interactions in AMR transmission. The increasing prevalence of resistant strains in yaks, coupled with genetic evidence of clonal expansion, highlights the need for a comprehensive One Health approach to AMR surveillance and mitigation in remote, high-altitude environments.},
}

@article {pmid41138327,
year = {2025},
author = {Luo, T and Dai, X and Zhang, Y and Wei, W and Ni, BJ},
title = {Dual-pathway inhibition of antibiotic resistance genes by ferrate (Fe(VI)): Oxidative inactivation and genetic mobility impairment in anaerobically digested sludge.},
journal = {Water research},
volume = {289},
number = {Pt A},
pages = {124648},
doi = {10.1016/j.watres.2025.124648},
pmid = {41138327},
issn = {1879-2448},
abstract = {Antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB) are emerging environmental contaminants that threaten public health, highlighting the urgent need for effective control strategies. Ferrate (Fe(VI)), a strong and eco-friendly oxidant, shows great potential for this purpose. This study systematically evaluated the efficacy of Fe(VI) in mitigating ARGs and ARB in anaerobically digested sludge, with a particular focus on elucidating the underlying mechanisms by which Fe(VI) effects ARGs dissemination through both vertical gene transfer (VGT) and horizontal gene transfer (HGT). Result shows that Fe(VI) doses of 20 and 60 mg/g-TS reduce ARGs by 9.75 % and 19.12 %, respectively, while inactivating up to 24.7 % of ARB at the higher dose. Pathogenic ARB, such as Escherichia coli and Shigella sonnei, are preferentially removed, with abundances decrease by 63.7 % and 28.0 %. Mechanistically, the structural disruption of bacterial cells caused by Fe(VI) in anaerobically digested sludge, as indicated by a 29 % reduction in extracellular polymeric substances and a 23.7 % increase in cell membrane permeability. Subsequently, a marked release of intracellular ARGs into the extracellular environment is also observed, where they are likely subjected to degradation by Fe(VI). This oxidative killing accounts for the observed ARB decrease, thereby limiting the VGT of ARGs. In addition, Fe(VI) impairs the HGT of ARGs by diminishing their mobility potential, reflected in the reduced co-occurence with mobile genetic elements. Meanwhile, sludge bacterial competence for DNA uptake and recombination is markedly reduced, as evidenced by a 9.8 % decline in the abundance of related functional genes. These findings demonstrate that Fe(VI) effectively inhibits the dissemination of ARGs by targeting both primary transmission pathways. It suppresses VGT, thereby reducing the inheritance of ARB within populations, and limits HGT, curbing the spread of mobile ARGs among competent species. By disrupting these two critical routes, Fe(VI) shows strong potential as an effective strategy for mitigating ARGs propagation in sludge systems.},
}

@article {pmid41136898,
year = {2025},
author = {Junier, T and Palmieri, F and Ubags, ND and Trompette, A and Koutsokera, A and Junier, P and Pagni, M and Neuenschwander, S},
title = {Prevalence of oxalotrophy in the human microbiome.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {954},
pmid = {41136898},
issn = {1471-2164},
support = {40B2-0_194701//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; GRS-064/18//Gebert Rüf Stiftung/ ; },
mesh = {Humans ; *Oxalates/metabolism ; *Microbiota/genetics ; Metagenome ; Gene Transfer, Horizontal ; *Bacteria/genetics/metabolism ; },
abstract = {BACKGROUND: Incomplete degradation of oxalate, a compound commonly found in the diet, can lead to disease in humans, particularly affecting the kidneys. The concentration of oxalate in the body depends on several factors, one of which is intestinal absorption-an aspect influenced by oxalotrophy among enteric bacteria. Despite its potential significance, oxalotrophy in the human microbiome remains poorly understood.

RESULTS: In this study, we conducted a systematic search for the co-occurrence of three key oxalotrophy genes-frc, oxc, and oxlT. We developed and validated specific conservation models for each gene and applied them to genomes and metagenomes associated with the human digestive tract, oral cavity, and lungs. Our analysis revealed that oxalotrophy, defined as the capacity to use oxalate as an energy source, is a rare metabolic trait predominantly confined to the gut. We also found evidence that this capacity can be acquired via horizontal gene transfer.

CONCLUSIONS: While oxalotrophy is relatively uncommon, the broader capacity for oxalate degradation is more widespread. Notably, the genes frc and oxc are frequently found in close proximity within genomes, suggesting a selective advantage for organisms possessing this capability. Incomplete degradation of oxalate, a compound commonly found in the diet, can cause disease in humans, particularly affecting the kidney. Its concentration in the body depends on several factors, one of which is intestinal absorption, which is itself affected by oxalotrophy among enteric bacteria. Oxalotrophy in the human microbiome is poorly known. In this study, we perform a systematic search for the simultaneous presence of the three oxalotrophy genes, namely frc, oxc and oxlT. Thanks to the construction and validation of specific conservation models for all three genes, we were able to search for oxalotrophy in genomes and metagenomes associated with the human digestive tract, oral cavity, and lungs. We report that oxalotrophy-the capacity to use oxalate as an energy source-is a rare metabolic trait, mostly confined to the gut, and also find evidence that it can be acquired by horizontal gene transfer. By contrast, the capacity for oxalate degradation is more widespread, and two genes responsible for it (frc and oxc) are almost always close together in the genome, suggesting selection pressure.},
}

Humans
*Oxalates/metabolism
*Microbiota/genetics
Metagenome
Gene Transfer, Horizontal
*Bacteria/genetics/metabolism

@article {pmid41136156,
year = {2026},
author = {Habib, I and Ibrahim Mohamed, MY and Lakshmi, GB and Ghazawi, A and Khan, M},
title = {Resident or transient? Whole-genome approach to tracking colistin-resistant Escherichia coli in the broiler chicken processing chain.},
journal = {Food microbiology},
volume = {134},
number = {},
pages = {104939},
doi = {10.1016/j.fm.2025.104939},
pmid = {41136156},
issn = {1095-9998},
mesh = {Animals ; *Colistin/pharmacology ; *Escherichia coli/genetics/drug effects/isolation & purification/classification ; *Chickens/microbiology ; *Anti-Bacterial Agents/pharmacology ; Whole Genome Sequencing ; Phylogeny ; *Drug Resistance, Bacterial/genetics ; Genome, Bacterial ; Plasmids/genetics ; *Meat/microbiology ; Escherichia coli Proteins/genetics ; Drug Resistance, Multiple, Bacterial/genetics ; Microbial Sensitivity Tests ; Food Contamination/analysis ; },
abstract = {This study presents a genome-informed surveillance model to investigate the persistence and spread of colistin-resistant Escherichia coli in broiler chicken processing. The study targeted a high-throughput poultry facility-previously linked to retail meat contamination by colistin-resistant E. coli and Salmonella-where 200 carcasses were sampled across ten production batches to assess the prevalence and genomic characteristics of antimicrobial-resistant strains within the processing line. We analyzed one E. coli isolate per carcass to characterize antimicrobial resistance (AMR), and utilized whole-genome sequencing (WGS) to delineate phylogeny, virulence, AMR determinants, and plasmid content. Colistin-resistant E. coli isolates were detected in all production batches and were confirmed in 10.5 % (21/200) of the carcasses, with all isolates carrying the mcr-1.1 gene. Notably, 57.1 % of these isolates also harbored a PmrB Y358N putative colistin resistance mutation. Phylogenetic analysis revealed substantial diversity, with 31 sequence types detected; however, six isolates belonging to ST162 were identified as a resident strains cluster, persisting over four months and from multiple farms and flocks. All colistin-resistant E. coli isolates were phenotypically multidrug-resistant (MDR), carrying 10-25 AMR resistance genes per genome, including ESBL genes such as blaCTX-M-55 (57.1 %). Virulence profiling showed a high prevalence of iron acquisition, serum resistance, and efflux-related genes, with an average of 22.5 putative virulence factors per isolate. Plasmidome analysis (n = 20 plasmids) revealed the dominance of IncI2 (60 %) and IncHI2-type replicons, with 90 % of plasmids predicted to be conjugative. Mobile genetic elements involved in horizontal gene transfer, such as MOBP relaxases and MPF-T systems, were prevalent (70 %), indicating a high potential for plasmid-mediated dissemination of AMR genes within the sampled isolates. This work offers a scalable model for processing facility-level AMR tracking and reinforces the value of WGS for industry-led food safety risk management, particularly for high-priority AMR determinants such as colistin resistance.},
}

Animals
*Colistin/pharmacology
*Escherichia coli/genetics/drug effects/isolation & purification/classification
*Chickens/microbiology
*Anti-Bacterial Agents/pharmacology
Whole Genome Sequencing
Phylogeny
*Drug Resistance, Bacterial/genetics
Genome, Bacterial
Plasmids/genetics
*Meat/microbiology
Escherichia coli Proteins/genetics
Drug Resistance, Multiple, Bacterial/genetics
Microbial Sensitivity Tests
Food Contamination/analysis

@article {pmid41136132,
year = {2026},
author = {Spaans, M and Winkler, LS and van den Broek, MA and Daran, JG},
title = {Diversity of α-acetolactate decarboxylase in the Saccharomycotina yeast subphylum: From discovery to brewing application.},
journal = {Food microbiology},
volume = {134},
number = {},
pages = {104903},
doi = {10.1016/j.fm.2025.104903},
pmid = {41136132},
issn = {1095-9998},
mesh = {Fermentation ; Phylogeny ; *Beer/microbiology/analysis ; *Carboxy-Lyases/genetics/metabolism ; Diacetyl/metabolism/analysis ; *Fungal Proteins/genetics/metabolism ; *Saccharomycetales/enzymology/genetics/classification ; Acetoin/metabolism ; Flavoring Agents/metabolism ; Lactates ; },
abstract = {Diacetyl, a vicinal diketone with a low sensory threshold, is a prominent off-flavour in beer, necessitating extended lagering to allow its reduction to non-flavour-active compounds. In brewing, bacterial α-acetolactate decarboxylases are commonly used to mitigate diacetyl formation by converting its precursor, α-acetolactate, directly into acetoin. Here, we report the first discovery and characterization of functional α-acetolactate decarboxylases enzymes of eukaryotic origin, specifically from yeasts within the Saccharomycotina subphylum. Using a homology-based search against fungal genomic databases, 29 candidate genes were identified across 18 yeast species from only three genera (Lipomyces, Dipodascus and Wickerhamiella) and classified into distinct phylogenetic groups. Phylogenetic analysis revealed both fungal and possible bacterial origins, suggesting evolutionary conservation and horizontal gene transfer events. Seven genes were heterologously expressed in Saccharomyces pastorianus lager brewing strains. Fermentation trials in both lab-scale septum flasks and E.B.C. tall tubes demonstrated that yeast-derived α-acetolactate decarboxylases significantly reduced diacetyl levels, with some performing comparably or superior to the benchmark Brevibacillus brevis enzyme. These strains also showed normal fermentation kinetics and produced beers with diacetyl concentrations below sensory thresholds, effectively eliminating the need for extended lagering. Our findings uncover a previously unrecognized enzymatic activity in budding yeasts and present yeast α-acetolactate decarboxylases as promising non-bacterial alternatives to improve process efficiency and sustainability in lager beer production.},
}

Fermentation
Phylogeny
*Beer/microbiology/analysis
*Carboxy-Lyases/genetics/metabolism
Diacetyl/metabolism/analysis
*Fungal Proteins/genetics/metabolism
*Saccharomycetales/enzymology/genetics/classification
Acetoin/metabolism
Flavoring Agents/metabolism
Lactates

@article {pmid41133644,
year = {2025},
author = {Zhu, X and Zou, A and Xianyu, Y},
title = {Bacterial membrane vesicles: from biogenesis to antibiotic resistance.},
journal = {Biomaterials science},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5bm01218j},
pmid = {41133644},
issn = {2047-4849},
abstract = {Bacterial membrane vesicles (MVs) are a heterogeneous group of lipid-bound structures produced by bacteria. Antibiotic stress aggravates the secretion of MVs that contributes to the development of bacterial antibiotic resistance. This review provides a focused, resistance-oriented perspective on the interplay between MVs and antibiotic resistance. We outline MV biogenesis, emphasizing the distinct formation mechanisms of Gram-negative and Gram-positive bacteria. We further focus on the secretion of MVs under antibiotic stress, highlighting pathways such as bacterial envelope stress, SOS response, and cell wall disruption. The pivotal role of MVs in bacterial antibiotic resistance is also elucidated, including neutralizing antibiotics, absorbing phages, and facilitating drug efflux, biofilm formation, and horizontal gene transfer. Current challenges and future prospects for elucidating MV-mediated mechanisms in antibiotic resistance are discussed.},
}

@article {pmid41130916,
year = {2025},
author = {Wadsworth, CB and Goytia, M and Shafer, WM},
title = {Commensal Neisseria and Antimicrobial-Resistant Gonorrhea.},
journal = {Annual review of microbiology},
volume = {79},
number = {1},
pages = {215-240},
doi = {10.1146/annurev-micro-022024-024306},
pmid = {41130916},
issn = {1545-3251},
mesh = {*Gonorrhea/microbiology/drug therapy ; Humans ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Gene Transfer, Horizontal ; *Neisseria gonorrhoeae/genetics/drug effects/physiology ; *Drug Resistance, Bacterial ; *Neisseria/genetics/drug effects/physiology ; Symbiosis ; },
abstract = {Alongside the crisis of antimicrobial-resistant gonorrhea is the threat of bystander selection on commensal Neisseria. As Neisseria species are permissive to gene flow across lineages, their evolutionary fates are irrevocably intertwined. Horizontal gene transfer (HGT) within the genus occurs through transformation and exchange of plasmids through conjugation. Both mechanisms of HGT threaten the long-term efficacy of antimicrobial treatments, with resistance passed between commensals and pathogens multiple times (e.g., mosaic penA and mtr alleles). Here, we underscore the importance of commensal Neisseria as a bubbling cauldron of adaptive solutions for pathogenic Neisseria, review the mechanisms of resistance harbored by commensals and transferred to the gonococcus, and discuss the impact of contemporary selective pressures on the future evolutionary trajectory of the genus. Ultimately, we believe that predicting the future efficacy of antimicrobials for the treatment of gonorrhea will only be successful if the commensal Neisseria are also considered.},
}

*Gonorrhea/microbiology/drug therapy
Humans
*Anti-Bacterial Agents/pharmacology/therapeutic use
Gene Transfer, Horizontal
*Neisseria gonorrhoeae/genetics/drug effects/physiology
*Drug Resistance, Bacterial
*Neisseria/genetics/drug effects/physiology
Symbiosis

@article {pmid41127838,
year = {2025},
author = {Li, X and Wei, L and Li, L and Huang, H and Chen, Y},
title = {Microbial Metabolites: An Underexploited Arsenal to Combat Antibiotic Resistance Dissemination.},
journal = {Environment & health (Washington, D.C.)},
volume = {3},
number = {10},
pages = {1121-1124},
pmid = {41127838},
issn = {2833-8278},
abstract = {The relentless global proliferation of antibiotic resistance genes (ARGs) poses a profound threat to public health and ecological stability. Unlike static chemical pollutants, ARGs propagate through horizontal gene transfer (HGT)(?)a dynamic biological process that facilitates the cross-taxa dissemination of resistance determinants among environmental, commensal, and pathogenic microbes. This ecological amplification of resistance undermines both clinical therapies and environmental resilience, rendering the understanding and control of ARG dissemination a critical challenge in the fight against antibiotic resistance.},
}

@article {pmid41125819,
year = {2025},
author = {Naseem, H and Haider, Z and Mannan, S and Rehman, SU},
title = {Genomic and physiochemical characterization of two lysogenic bacteriophages, ΦCP5(17) and ΦCP17(i), infecting Clostridium perfringens.},
journal = {Archives of virology},
volume = {170},
number = {11},
pages = {229},
pmid = {41125819},
issn = {1432-8798},
support = {110413//IDRC/ ; },
mesh = {*Clostridium perfringens/virology ; *Genome, Viral ; *Bacteriophages/genetics/isolation & purification/ultrastructure/classification/physiology ; Host Specificity ; Lysogeny ; Podoviridae/genetics/isolation & purification/ultrastructure/classification ; Sewage/virology ; Phylogeny ; Hydrogen-Ion Concentration ; Animals ; Temperature ; },
abstract = {Group A Clostridium perfringens is a major poultry pathogen that causes necrotic enteritis. The molecular similarity of its toxins to those of other bacterial species suggests the involvement of horizontal gene transfer through mobile genetic elements or bacteriophages. Lysogenic bacteriophages play an important role in bacterial evolution through horizontal gene transfer. In the present study, we examined and compared the physiochemical characteristics, genome sequences, and tail fiber proteins of two lysogenic bacteriophages infecting C. perfringens. Bacteriophages ΦCP5(17) and ΦCP17(i) were isolated from a sewage sample and tested for their stability at different temperatures and pH conditions, and in simulated gastric fluids. The genomes of these phages were sequenced, and their morphology was examined by electron microscopy. Both phages produced circular, hazy plaques on their host bacteria and were stable up to 60°C, exhibiting optimal activity at pH 7-8. Both bacteriophages were found to have a very narrow host range, with ΦCP17(i) exhibiting a slightly broader host range than ΦCP5(17). Both phages exhibited podovirus morphology and a genome size of 17.8 kb and 17.9 kb for ΦCP5(17) and ΦCP17(i), respectively. According to the ICTV classification system, ΦCP5(17) and ΦCP17(i) belong to the genus Brucesealvirus, family Guelinviridae, and class Caudoviricetes. These phages share 95.6% genomic nucleotide sequence identity, suggesting that they belong to the same species but differ at the subspecies level. Although ΦCP5(17) and ΦCP17(i) have similar morphological and genomic features, their tail fiber proteins differ in their predicted folding patterns. Nucleotide sequence analysis indicated the absence of toxin and antibiotic resistance genes. Both phages encode a SpoVG protein, whose functional role requires further investigation.},
}

*Clostridium perfringens/virology
*Genome, Viral
*Bacteriophages/genetics/isolation & purification/ultrastructure/classification/physiology
Host Specificity
Lysogeny
Podoviridae/genetics/isolation & purification/ultrastructure/classification
Sewage/virology
Phylogeny
Hydrogen-Ion Concentration
Animals
Temperature

@article {pmid41123117,
year = {2025},
author = {Pu, Q and Hao, Z and Zhang, Q and Zhang, K and Meng, B and Feng, X},
title = {Cadmium Elevates Methylmercury Levels in Rice Paddies via Microbial Adaptation and Biogeochemical Alterations.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c12718},
pmid = {41123117},
issn = {1520-5851},
abstract = {Methylmercury (MeHg) in rice poses significant health risks to populations with rice-based diets. While cadmium (Cd) contamination of paddy soils is widespread, its role in influencing MeHg accumulation in rice remains unclear. We combined a nationwide survey of 103 rice paddies with controlled pot and incubation experiments to examine how Cd affects MeHg in soils and rice grains. Soil geochemical parameters, microbial community composition, and horizontal gene transfer (HGT) of functional genes were analyzed to disentangle biological and geochemical mechanisms. Across field sites, Cd concentrations were positively associated with rice MeHg levels, independent of total Hg. Pot and incubation experiments confirmed that Cd exposure increased MeHg levels in soils and grains. This enhancement was mediated by both microbial and geochemical pathways: Cd reshaped microbial communities, promoted HGT that conferred Cd resistance to Hg-methylating bacteria, and altered soil redox potential and dissolved organic carbon, thereby creating conditions favorable for Hg methylation. Our findings reveal Cd as a previously overlooked driver of MeHg risk in rice agroecosystems. Given the co-occurrence of Cd and Hg pollution in global rice-growing regions, integrated management of multiple metals is needed to mitigate MeHg exposure through rice consumption.},
}

@article {pmid41120846,
year = {2025},
author = {Anik, TA and Islam, F and Uzzaman, R and Begum, SA and Akhter, H and Begum, A},
title = {Whole-genome sequencing and genomic characterization of a novel multi-drug resistant esxA-positive Staphylococcus haemolyticus DUEML1 (ST-184) isolated from a respiratory infection case: insights from panresistome analysis.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {677},
pmid = {41120846},
issn = {1471-2180},
abstract = {BACKGROUND: Staphylococcus haemolyticus is a coagulase-negative staphylococcal species and an opportunistic pathogen associated with hospital-acquired infections. The aim of this study was to use whole-genome sequencing (WGS) to characterize a novel multidrug-resistant (MDR) S. haemolyticus strain, DUEML1 (ST-184), isolated from a respiratory infection case in Bangladesh, and to place its resistome and virulence features in the context of global S. haemolyticus isolates.

METHODS: The isolate was obtained in pure culture from the tracheal aspirate of a 51-year-old male patient with respiratory infection, suggesting it was the primary causative agent. WGS was the primary method to analyze the genome of the isolated strain and subsequent in-silico analyses were performed to identify antimicrobial resistance genes, virulence factors, plasmid-associated genes, mobile genetic elements (MGEs), and prophages. Comparative pan-resistome analysis was conducted using 694 publicly available S. haemolyticus genomes retrieved from NCBI.

RESULTS: The isolate exhibited in vitro resistance to levofloxacin, ciprofloxacin, tetracycline, doxycycline, gentamicin, and trimethoprim-sulfamethoxazole, as determined by the disc diffusion test, and demonstrated the capacity for biofilm formation. Several antimicrobial resistance genes (ARGs) such as fosBx1, mgrA, norC, sdrM, sepA and two virulence genes, including esxA and cap8G were detected. To our knowledge, this is the first report of an esxA-positive S. haemolyticus isolate, recovered from a respiratory infection case in Dhaka, Bangladesh. Two plasmid-associated genes repUS23 and repUS46 were detected. Further analyses predicted 63 horizontal gene transfer (HGT) events and identified 147 MGEs, including integration/excision elements, recombination and repair-associated genes, and prophage-associated regions. With a new variant of arcC allele (arcC-38), the isolate was assigned to a novel ST-184. The PathogenFinder predicted a 93% probability that ST-184 is a human pathogen. A comparative analysis of 694 genome sequences identified a wide variety of ARGs, virulence factors, and plasmids in S. haemolyticus isolates from 35 different countries.

CONCLUSION: This study provides the first genomic characterization of a novel S. haemolyticus ST-184 isolate from Bangladesh, highlighting its multidrug-resistant nature and virulence potential. A limitation of this work is the lack of clinical treatment outcome data. Future research should include large-scale genomic surveillance to strengthen our understanding of the genomic architecture of S. haemolyticus.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-025-04406-5.},
}

@article {pmid41120633,
year = {2025},
author = {Feng, Y and Ding, J and Lin, Y and Cui, D and Li, K and Zheng, D and Cai, Z and Bell, SD and Wu, F},
title = {Serial innovations by Asgard archaea shaped the DNA replication machinery of the early eukaryotic ancestor.},
journal = {Nature ecology & evolution},
volume = {},
number = {},
pages = {},
pmid = {41120633},
issn = {2397-334X},
support = {32370003//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {The last eukaryotic common ancestor primarily inherited its core genetic system from archaea. However, it remains unclear when and how these essential machineries expanded their compositional and regulatory sophistication during eukaryogenesis. Here we combine statistical, phylogenetic, structural and biochemical approaches to examine the compositional diversity of the DNA replication machinery, that is, the replisome, across archaea and eukaryotes. We find that different lineages of Asgard archaea encode distinct replisome components with eukaryotic signatures, including a Baldrarchaeia-encoded DNA polymerase δ-like complex, a Sif/Wukong/Heimdallarchaeia-encoded primase complex and a Lokiarchaeales-encoded RFC clamp-loader complex. Copy number expansions driven by horizontal gene transfer probably contributed to the structural diversification of Asgard archaeal replisomes, including phylogenomic markers RfcS and Fen1, which were previously presumed to be transmitted vertically. Our analyses suggest that these distributed innovations were sequentially acquired by the early eukaryotic ancestor before the burst of gene duplications leading to the last eukaryotic common ancestor. By placing the captured events of gene gain and loss within the context of archaea-eukaryote evolution-as inferred from the phylogeny of concatenated single-copy replisome genes-we propose a hypothetical model for the emergence of the complex eukaryotic replisome.},
}

@article {pmid41117958,
year = {2025},
author = {Koech, N and Muoma, J and Banerjee, A and Okoth, P and Wekesa, C},
title = {Modular evolution and regulatory diversification of nodD-like LysR-type transcriptional regulators in α-Proteobacteria.},
journal = {Archives of microbiology},
volume = {207},
number = {12},
pages = {327},
pmid = {41117958},
issn = {1432-072X},
mesh = {*Bacterial Proteins/genetics/metabolism/chemistry ; *Transcription Factors/genetics/metabolism/chemistry ; *Gene Expression Regulation, Bacterial ; *Evolution, Molecular ; *Alphaproteobacteria/genetics/classification/metabolism ; Phylogeny ; Gene Transfer, Horizontal ; Genome, Bacterial ; Operon ; Symbiosis ; },
abstract = {The nodD gene encodes a LysR-type transcriptional regulator critical for nodulation gene expression in rhizobia, yet its evolutionary origin, structural plasticity, and regulatory reach beyond symbiosis remain incompletely resolved. Here we investigate the genomic organization, structural variation, and functional diversification of nodD and its homologs across α-proteobacteria with selected outgroups. Using orthogroup-based pangenome clustering, dated species trees, and gene-tree-species-tree reconciliation, we reconstruct the evolutionary trajectory of nodD, indicating emergence from ancient LTTRs deep in proteobacterial history. Reconciliation reveals widespread duplication and horizontal gene transfer (HGT), with several rhizobia showing notable duplication and exchange, and marine/non-rhizobial taxa contributing to a mosaic of nodD-like genes. Gene-neighborhood and operon analyses show conserved syntenic tendencies in classical rhizobia but extensive architectural divergence in free-living lineages, including frequent monocistronic anchors with extended upstream regions and, when polycistronic, enrichment for transporters and local metabolic enzymes within compact multi-regulator cassettes. Structural comparisons with AlphaFold and PyMOL confirm the canonical LTTR fold while uncovering species-specific deviations concentrated in effector-binding loops and interfaces. Motif discovery and genome-wide scanning identify targets involved in metabolism, stress responses, and transcriptional control, and network analysis reveals modular connectivity spanning core metabolism and accessory processes such as secondary metabolism, transport, and biofilm-associated functions. These findings portray nodD as a structurally conserved yet functionally flexible regulator repeatedly reshaped by duplication, HGT, and local genome context, extending nodD-like systems beyond symbiosis and broadening the regulatory landscape of bacterial LTTRs.},
}

*Bacterial Proteins/genetics/metabolism/chemistry
*Transcription Factors/genetics/metabolism/chemistry
*Gene Expression Regulation, Bacterial
*Evolution, Molecular
*Alphaproteobacteria/genetics/classification/metabolism
Phylogeny
Gene Transfer, Horizontal
Genome, Bacterial
Operon
Symbiosis

@article {pmid40970725,
year = {2025},
author = {Leng, J and Ferrandis-Vila, M and Oldenkamp, R and Mehat, JW and Fivian-Hughes, AS and Kumar Tiwari, S and Van der Putten, B and Trung Nguyen, V and Bethe, A and Clark, J and Singh, P and Semmler, T and Schwarz, S and Alvarez, J and Hoa, NT and Bootsma, M and Menge, C and Berens, C and Schultsz, C and Ritchie, JM and La Ragione, RM},
title = {Evidence of ESBL plasmid transfer and selective persistence of multiple host-associated Escherichia coli isolates in a chicken cecal fermentation model.},
journal = {Applied and environmental microbiology},
volume = {91},
number = {10},
pages = {e0082225},
doi = {10.1128/aem.00822-25},
pmid = {40970725},
issn = {1098-5336},
mesh = {Animals ; *Escherichia coli/genetics/drug effects/isolation & purification/enzymology ; Chickens/microbiology ; *Cecum/microbiology ; *beta-Lactamases/genetics/metabolism ; *Plasmids/genetics ; Cattle ; Swine ; Fermentation ; *Gene Transfer, Horizontal ; *Escherichia coli Infections/microbiology/veterinary ; Anti-Bacterial Agents/pharmacology ; },
abstract = {The guts of animals and humans harbor diverse microbial communities that are regularly exposed to bacteria originating from food, water, and their surroundings. Species such as Escherichia coli are adept at colonizing multiple hosts, along with surviving in the environment. By encoding pathogenic traits and transmissible forms of antimicrobial resistance (AMR), E. coli can also pose a zoonotic risk. Our understanding of the factors that govern host residency is limited. Here, we used a chicken cecal fermentation model to study survival and the AMR transfer potential of 17 host-associated extended-spectrum β-lactamase (ESBL)-producing E. coli isolates. Vessels containing chicken cecal contents were stabilized for 4 days before the addition of a cocktail comprising ESBL-producing E. coli obtained from human, cattle, pig, and chicken hosts. Consecutive sampling showed that pig and cattle-associated isolates persisted in most vessels, although the recovery of all isolates declined over time. Increasing the inoculum dose or adding ceftiofur helped to stabilize populations of ESBL E. coli within the vessels, although this did not result in outgrowth of resistant populations in all vessels. Sequencing revealed that most new ESBL-producing E. coli recovered during the study acquired a blaCTX-M-1 plasmid from a single ESBL E. coli included in the cocktail that lacked host-specific traits (generalist). Our data highlight that isolate-specific differences in the E. coli genome composition likely explain the persistence of specific clones and efficiency of plasmid transfer, both of which could impact the spread of AMR in complex communities.IMPORTANCEThere are few insights into how host-associated Escherichia coli behave within the gut environment of other hosts. E. coli isolates that are immigrants to the gastrointestinal system of humans and animals have the potential to transfer their resistance to other native bacteria. A better understanding of this process is needed to assess how the gastrointestinal environment could serve as a reservoir and a melting pot of new, multidrug-resistant E. coli isolates.},
}

Animals
*Escherichia coli/genetics/drug effects/isolation & purification/enzymology
Chickens/microbiology
*Cecum/microbiology
*beta-Lactamases/genetics/metabolism
*Plasmids/genetics
Cattle
Swine
Fermentation
*Gene Transfer, Horizontal
*Escherichia coli Infections/microbiology/veterinary
Anti-Bacterial Agents/pharmacology

@article {pmid41114150,
year = {2025},
author = {Chen, Z and Zhou, W and Wang, Z and Chen, Z and You, X and Gong, Y},
title = {Analysis of the mitochondrial genome of the Camellia sinensis cv. 'Zhuyeqi': multichromosomal structure, RNA editing sites, and evolutionary characterization.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1644130},
pmid = {41114150},
issn = {1664-462X},
abstract = {INTRODUCTION: Tea (Camellia sinensis) is a significant economic crop, and investigations into the structure and function of its mitochondrial genome are crucial for understanding the evolutionary history and genetic characteristics of this species. This study presents the first comprehensive analysis of the mitochondrial genome of the tea cultivar 'Zhuyeqi' (Camellia sinensis cv. 'Zhuyeqi'), aiming to elucidate its genomic structural features, gene composition, and evolutionary patterns. The findings provide a theoretical foundation for genetic breeding and molecular biology research in tea plants.

METHODS: High-throughput sequencing was employed to sequence the mitochondrial genome of 'Zhuyeqi'. Bioinformatics approaches were utilized for genome assembly and annotation. Various analytical strategies, including identification of RNA editing sites, codon usage bias analysis, repeat sequence recognition, calculation of non-synonymous substitution rates (Ka) and synonymous substitution rates (Ks), comparative genomics, and collinearity analysis, were applied to comprehensively analyze the structural features and evolutionary dynamics of the mitochondrial genome.

RESULTS AND DISCUSSION: The mitochondrial genome of 'Zhuyeqi' consists of one circular chromosome and six linear chromosomes, with a total length of 911,255 bp and a GC content of 46%. Genome annotation identified 77 functional genes, including 38 protein-coding genes (PCGs). The study revealed heterogeneously distributed introns within genes such as trnM-CAT (5 copies) and nad1/2/5/7. RNA editing analysis identified 556 C-to-U editing sites, notably enriched in ccmFn (38 sites) and ccmB (34 sites). Codon usage bias analysis indicated that leucine (Leu, 10%) and arginine (Arg, 7%) were the most frequently used amino acids. Repeat sequence analysis showed that dispersed repeats (780, 72%) dominated, with satellite DNA exhibiting significant distribution biases on chr1 (11) and chr3 (5). Ka/Ks analysis revealed that 37 PCGs were under varying selective pressures (0.09-2.70), with rps4 (Pi=0.09) and atp8 (Pi=0.09) showing exceptionally high variability, while rps19 (Pi=0) was completely conserved. Comparative genomics uncovered 66 homologous segments (25,656 bp) between the mitochondrial and chloroplast genomes, containing 27 intact genes such as trnA-UGC, confirming horizontal gene transfer events. Collinearity analysis demonstrated a high degree of conservation in genomic structures between 'Zhuyeqi' and closely related Camellia species. This study lays an important theoretical foundation for further elucidating the structural characteristics and evolutionary mechanisms of the tea plant mitochondrial genome.},
}

@article {pmid41112119,
year = {2025},
author = {Pandey, D and Gupta, I and Gupta, D},
title = {AmpC β-lactamases: A key to antibiotic resistance in ESKAPE pathogens.},
journal = {Cell surface (Amsterdam, Netherlands)},
volume = {14},
number = {},
pages = {100154},
pmid = {41112119},
issn = {2468-2330},
abstract = {BACKGROUND: AmpC β-lactamases (blaAmpC) are essential drivers of antimicrobial resistance (AMR) in ESKAPE pathogens, bacteria that cause hospital-acquired infections. Understanding AmpC enzymes is essential for uncovering resistance mechanisms and guiding antimicrobial strategies. We analyzed blaAmpC presence, genomic location, copy number, sequence variability, and evolutionary traits in ESKAPE pathogens.

RESULTS: We identified 1790 AmpC enzymes in 4713 complete genomes, classified into nine enzyme groups. Consistent with known taxonomic profiles, no class C β-lactamases were detected in Gram-positive bacteria (Staphylococcus aureus and Enterococcus faecium). Acinetobacter baumannii exhibited the highest occurrence of class C β-lactamases, with Enterobacter spp. showing the second highest prevalence, followed by Pseudomonas aeruginosa and Klebsiella pneumoniae. The largest enzyme group, ADC was restricted to A. baumannii; similarly, ACC, ACT, CMH, and MIR to Enterobacter spp.; and PDC and PIB to P. aeruginosa. Phylogenetic analysis showed divergence among some groups and closer evolutionary relationships in others. Functional Motif analysis revealed conserved catalytic residues across all groups except PIB. Instead of the canonical YXN and KTG motifs, PIB contains YST and AQG variants, respectively. Because of these variations, PIB's ability to bind cephalosporins decreases while enhancing their activity against carbapenems.

CONCLUSIONS: We identified 1790 AmpC enzymes in nine distinct groups across ESKAPE pathogens, with species-specific distribution patterns and notable absence in Gram-positive bacteria. The PIB enzyme group demonstrated unique motif variants (YST/AQG) conferring carbapenem resistance, while other groups maintained conserved catalytic motifs. Phylogenetic analysis revealed evolutionary divergence and horizontal gene transfer potential, emphasizing the need for targeted therapeutic approaches against AmpC-mediated resistance.},
}

@article {pmid41109624,
year = {2025},
author = {Bu, C and Chen, C and Zhang, W and Zhang, R and Yu, J and Hua, Y and Zeng, H and Han, Y and Jia, R and Zhao, Q and Ruan, Y and Ma, L},
title = {Antibiotics, antibiotic resistance genes, and environmental drivers: Assessment of resistance pollution along the Yangtze River Basin.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {386},
number = {},
pages = {127284},
doi = {10.1016/j.envpol.2025.127284},
pmid = {41109624},
issn = {1873-6424},
abstract = {Antibiotic resistance pollution presents a significant global health challenge. The present study systematically investigated the occurrence of 50 antibiotics in the dissolved, suspended particulate matter phases, and surface sediments at 30 locations across the Yangtze River Basin (YRB). Eleven extracellular and intracellular antibiotic resistance genes (eARGs and iARGs) in surface sediments were quantified using fluorescence-based real-time quantitative polymerase chain reaction. Additionally, key relationships between ARGs, antibiotic concentrations, mobile genetic elements, microbial communities, and environmental factors were explored. Results revealed high levels of antibiotic contamination in the dissolved phase, with the cumulative concentration of the 50 target antibiotics ranging 857-7560 ng/L across various sections of the YRB. While iARGs predominated in absolute abundance, eARGs showed higher relative abundance. Mechanistic of intI1-mediated horizontal gene transfer as the principal pathway for the dissemination of ARGs. Redundancy analysis revealed that antibiotic concentrations, environmental factors, and microbial communities collectively explained 57.69 % of the variation in ARGs distribution. Among these, environmental variables such as conductivity and dissolved oxygen indirectly promote the enrichment of ARGs by influencing microbial communities. This study provided a theoretical basis for developing targeted prevention and control strategies against antibiotic resistance pollution in this extensive and economically critical watershed.},
}

@article {pmid41105518,
year = {2025},
author = {Shaw, S and Pragasam, AK and Chowdhury, G and Samanta, P and Roy, D and Ghosh, D and Ramamurthy, T and Karia, J and Ninama, G and Miyoshi, S-i and Akeda, Y and Koley, H and Mukhopadhyay, AK},
title = {Genomic portrayal of emerging carbapenem-resistant El Tor variant Vibrio cholerae O1.},
journal = {Antimicrobial agents and chemotherapy},
volume = {},
number = {},
pages = {e0074025},
doi = {10.1128/aac.00740-25},
pmid = {41105518},
issn = {1098-6596},
abstract = {The escalating prevalence of carbapenem-resistant (CR) enteric pathogens elicits significant challenges to public health management and effective antimicrobial therapy. While carbapenem resistance is rare in Vibrio cholerae O1 (VC), the recent emergence of CR strains reveals a concerning shift in their antimicrobial resistance (AMR) landscape. This study aims to characterize the resistance mechanisms in newly identified El Tor CRVC isolated from cholera patients in Gujarat, India during 2019. Fifty VC isolates were screened for major virulence-associated genes along with the determination of their antibiotic resistance profiles using Kirby-Bauer disk diffusion and MIC assays. Whole-genome sequencing (WGS) was employed to investigate the underlying mechanisms of CR. All the isolates exhibited hypervirulent Haitian alleles of major virulence genes and AMR profiles of typical multidrug resistance (MDR). Strikingly, 12% (6/50) of them were resistant to carbapenems and other antibiotics. Molecular analysis revealed that these CR isolates were clonally related and harbored a 142 kbp IncA/C type conjugative mega-plasmid with several AMR encoding genes, including blaNDM-1, that can be easily transferred to other bacterial species and confer donor AMR patterns. The plasmid's competence for horizontal gene transfer presents a significant risk of dissemination to other enteric pathogens and thereby may complicate the treatment. This finding emphasizes the urgent need for enhanced genomic surveillance and robust antimicrobial stewardship programs aimed at curbing the spread of CRVC strains and mitigating their impact on cholera treatment and containment strategies.},
}

@article {pmid41104936,
year = {2025},
author = {Hauschild, K and Suzuki, M and Wolters, B and Tokuda, M and Yamazaki, R and Masumoto, M and Moriuchi, R and Dohra, H and Bunk, B and Spröer, C and Shintani, M and Smalla, K},
title = {The transferable resistome of biosolids-plasmid sequencing reveals carriage of clinically relevant antibiotic resistance genes.},
journal = {mBio},
volume = {},
number = {},
pages = {e0206825},
doi = {10.1128/mbio.02068-25},
pmid = {41104936},
issn = {2150-7511},
abstract = {UNLABELLED: Biosolids, widely used as organic fertilizers due to their high nutrient content, are significant reservoirs for antimicrobial-resistant bacteria (ARB) carrying transferable antimicrobial resistance genes (ARGs). This study investigated the transferability of ARG-containing plasmids of bacteria from biosolids originating from 12 German wastewater treatment plants (WWTPs) of varying sizes. Using exogenous plasmid captures with the recipient strain Escherichia coli CV601 gfp+, we collected 103 plasmids from 11 WWTPs. Characterization through DNA-based methods, including real-time PCR and Southern blot hybridization, revealed that the highest proportion of transconjugants harbored IncP (57%) and IncN (20%) plasmids. Complete sequencing of representative plasmids identified IncPβ, IncPε, IncQ2, IncN, and IncU plasmids carrying ARGs linked to mobile genetic elements (MGEs), including class 1 integrons, transposons, and IS elements (e.g., Tn402, IS26, and IS6100). These ARG-MGE complexes were integrated into specific plasmid regions, and similar plasmids were found across WWTPs and diverse geographic locations. The results underscore the role of WWTPs as hotspots for horizontal gene transfer, with biosolids serving as reservoirs for multi-resistant bacteria and resistance plasmids. This highlights the urgent need for improved biosolid management strategies to mitigate the release of ARGs and ARB into agricultural environments.

IMPORTANCE: This study emphasizes the critical role of wastewater treatment plants (WWTPs) in facilitating the horizontal transfer of ARGs through biosolids. As biosolids are routinely applied to agricultural soils, their load of clinically relevant ARG content and transferability pose risks to animal and human health through plant-associated bacteria or surface water. By identifying conserved ARG-MGE associations across diverse plasmid types and WWTPs, this work highlights the global and persistent nature of resistance dissemination. These findings underscore the urgent need for sustainable management practices to limit the spread of antimicrobial-resistant bacteria (ARB) and associated ARGs in agricultural ecosystems. Ensuring safe biosolid use will contribute to combating antimicrobial resistance gene connectivity from environmental to human- or animal-associated bacteria globally.},
}

@article {pmid41005125,
year = {2026},
author = {Cross, BJ and Partridge, SR and Sheppard, AE},
title = {Impacts of mobile genetic elements on antimicrobial resistance genes in gram-negative pathogens: Current insights and genomic approaches.},
journal = {Microbiological research},
volume = {302},
number = {},
pages = {128340},
doi = {10.1016/j.micres.2025.128340},
pmid = {41005125},
issn = {1618-0623},
mesh = {*Interspersed Repetitive Sequences/genetics ; *Gram-Negative Bacteria/genetics/drug effects ; Gene Transfer, Horizontal ; *Drug Resistance, Bacterial/genetics ; Genomics/methods ; Genome, Bacterial ; Anti-Bacterial Agents/pharmacology ; Humans ; *Genes, Bacterial ; Plasmids/genetics ; },
abstract = {Antimicrobial resistance threatens to take 10 million lives per year by 2050. It is a recognised global health crisis and understanding the historic and current spread of resistance determinants is important for informing surveillance and control measures. The 'inheritance' of resistance is difficult to track because horizontal transfer is common. Antimicrobial resistance genes (ARGs) spread rapidly between bacteria, plasmids and chromosomes due to different mobile genetic elements (MGEs). This movement can increase the range of species carrying an ARG, simplify acquisition of multi-resistance, or otherwise alter the selective advantage associated with carriage of the ARG. MGE activity is therefore a significant factor in understanding routes of ARG dissemination. Characterising the combinations of MGEs contributing to the movement of individual ARGs is crucial. Each MGE category has unique genetic characteristics, and distinct impacts on the location and expression of associated ARGs. Here, the ways in which MGEs can meaningfully associate with ARGs are discussed. Approaches for extracting information about MGE associations from bacterial genome sequences are also considered. Accurate and informative annotations of the genetic contexts of relevant ARGs provide crucial insight into the presence of MGEs and their locations relative to ARGs. Combining this genomic information with knowledge about relevant biological processes allows more accurate conclusions to be drawn about transmission and dissemination of ARGs.},
}

*Interspersed Repetitive Sequences/genetics
*Gram-Negative Bacteria/genetics/drug effects
Gene Transfer, Horizontal
*Drug Resistance, Bacterial/genetics
Genomics/methods
Genome, Bacterial
Anti-Bacterial Agents/pharmacology
Humans
*Genes, Bacterial
Plasmids/genetics

@article {pmid41102171,
year = {2025},
author = {Leu, AO and Woodcroft, BJ and McIlroy, SJ and Tyson, GW},
title = {Potential for aerobic hydrocarbon oxidation in archaea.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9188},
pmid = {41102171},
issn = {2041-1723},
mesh = {Oxidation-Reduction ; *Hydrocarbons/metabolism ; *Archaea/metabolism/genetics/classification ; Aerobiosis ; Phylogeny ; Genome, Archaeal ; Metagenome ; Gene Transfer, Horizontal ; Mixed Function Oxygenases/genetics/metabolism ; },
abstract = {Over the last decade, there have been significant advances in our understanding of anaerobic hydrocarbon oxidation in archaea. However, the ability to oxidise hydrocarbons aerobically has been described in bacteria but not yet in archaea. Here, we provide evidence supporting potential aerobic hydrocarbon oxidation ability in archaea belonging to a novel order within the class Syntropharchaeia, which we propose to name Candidatus 'Aerarchaeales'. This order is represented by six metagenome-assembled genomes (MAGs) spanning three genera that are found in terrestrial and marine ecosystems. In particular, MAGs belonging to a newly defined genus, Ca. 'Aerovita', encode a copper monooxygenase complex with homology to bacterial hydrocarbon monooxygenases. The presence of genes encoding other oxygen-dependent enzymes, such as haem-copper oxygen reductase, indicates that Ca. 'Aerovita' may be capable of aerobic respiration. Our findings suggest that horizontal gene transfer between archaeal and bacterial domains facilitated the evolution of aerobic hydrocarbon-oxidizing archaea.},
}

Oxidation-Reduction
*Hydrocarbons/metabolism
*Archaea/metabolism/genetics/classification
Aerobiosis
Phylogeny
Genome, Archaeal
Metagenome
Gene Transfer, Horizontal
Mixed Function Oxygenases/genetics/metabolism

@article {pmid41101560,
year = {2025},
author = {Lu, J and Zhou, A and Wang, D and Wan, S and Yang, Y and Lv, N and Li, J and Wu, G},
title = {Convergence of genetic variants in MCR-1 and O-antigen conferring polymyxin resistance and fitness cost.},
journal = {Journal of global antimicrobial resistance},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgar.2025.10.005},
pmid = {41101560},
issn = {2213-7173},
abstract = {OBJECTIVE: The emergence of multidrug-resistant bacteria threatens public health, alongside the wide spread of opportunistic pathogens with a diversity of their serotypes. The fitness cost and morphological variations might result from O-antigen diversity and lipid A modification, while these reconfiguration in lipopolysaccharide (LPS) confer polymyxin resistance.

METHODS: Herein, a multidrug-resistant Escherichia coli named EcE.CRE.COL was isolated from a patient suffering therapeutic laparoscope for liver cancer. Antibiotic susceptibility was measured by the VITEK 2 system. Whole genome sequencing found a chromosome, three plasmids (namely pEcE.CRE.COL015, pEcE.CRE.COL016 and pEcE.CRE.COL032, respectively). Comparative genomics was conducted to identify genetic determinants accounting for multi-drug resistance.

RESULTS: This isolate exhibited distinguishing resistance to carbapenems and polymyxin. Interestingly, pEcE.CRE.COL015 and pEcE.CRE.COL032 harbors blaNDM-5 and mcr-1, accounting for corresponding antimicrobial resistance, respectively. We consequently proposed an evolutionary pattern on the spread of mcr-1, of which transposon-like architecture could play a key role in the dissemination of polymyxin resistance driven by mcr-1. In addition, a novel serotype gene cluster related to defective O-antigen synthesis was determined, likely resulting from a genetic insertion. As a result, SDS-PGAE indicated LPS defectiveness in this isolate, suggesting a different charge in EcE.CRE.COL membrane surface.

CONCLUSION: Collectively, co-occurrence of plasmid-borne mcr-1 and blaNDM-5 was determined, and genetic variations in LPS biosynthesis genes might contribute to a synergistic change in bacterial surface charge and corresponding electrostatics to polymyxin.},
}

@article {pmid41092706,
year = {2025},
author = {Zhang, X and Yang, B and Zhang, H and Guo, X and Zhang, Y},
title = {Nicosulfuron-driven antibiotic resistance in corn silage: Effect and its mitigation by zinc oxide nanoparticles.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140119},
doi = {10.1016/j.jhazmat.2025.140119},
pmid = {41092706},
issn = {1873-3336},
abstract = {Antibiotic resistance genes (ARGs) present in animal feed represent a significant threat to human health via the food chain, and pesticide application in crop production may further accelerate the ARGs dissemination. Corn silage, a primary forage for herbivorous livestock, has been shown to harbor diverse ARGs; however, the impact of pesticide-induced stress and potential mitigation strategies on ARG proliferation remains poorly understood. This study investigated the mechanistic link between nicosulfuron exposure and ARG dynamics in corn silage, as well as the mitigating effects of zinc oxide nanoparticles (ZnO NPs) on ARG under nicosulfuron exposure using metagenomic sequencing and high-throughput quantitative PCR. Nicosulfuron exposure increased (P < 0.05) ARG diversity and abundance, enriched (P < 0.05) ARG-hosting genera such as Pantoea, Escherichia, and Klebsiella, and intensified (P < 0.05) the correlation between ARGs and mobile genetic elements (MGEs). Additionally, it disrupted microbial metabolic pathways and elevated (P < 0.05) the ARG-associated risk index in corn silage. Conversely, ZnO NPs alleviated (P < 0.05) these effects by reducing the abundance of key ARGs-bacA, tetM, and ermB, enhancing microbial diversity, promoting beneficial genera such as Levilactobacillus and Companilactobacillus, and decreasing the complexity of ARG-MGE-microbe co-occurrence networks in corn silage under nicosulfuron exposure. Structural equation modeling indicated that there was a significant association between bacterial community and ARGs proliferation, and it had the strongest explanatory power for the variation in ARGs abundance, followed by MGEs. These findings underscore the ecological risks associated with nicosulfuron and demonstrate that ZnO NPs have the potential to mitigate ARGs dissemination in pesticide-contaminated silage. However, this potential does not qualify ZnO NPs as an effective strategy, and their role in promoting safer forage production still requires further evaluation.},
}

@article {pmid41088812,
year = {2025},
author = {Wang, YX and Hu, JJ and Hou, JJ and Yuan, XJ and Chen, WJ and Li, YJ and Gao, QL and Pan, Y and Lu, SP and Chen, Q and Hu, SR and Shao, ZJ and Xiong, CL},
title = {(Meta)transcriptomic Insights into the Role of Ticks in Poxvirus Evolution and Transmission: A Multicontinental Analysis.},
journal = {Biomedical and environmental sciences : BES},
volume = {38},
number = {9},
pages = {1058-1070},
doi = {10.3967/bes2025.062},
pmid = {41088812},
issn = {2214-0190},
mesh = {Animals ; *Poxviridae/genetics/physiology ; *Ticks/virology ; Phylogeny ; *Transcriptome ; *Evolution, Molecular ; *Poxviridae Infections/transmission/virology ; Genome, Viral ; },
abstract = {OBJECTIVE: Poxviruses are zoonotic pathogens that infect humans, mammals, vertebrates, and arthropods. However, the specific role of ticks in transmission and evolution of these viruses remains unclear.

METHODS: Transcriptomic and metatranscriptomic raw data from 329 sampling pools of seven tick species across five continents were mined to assess the diversity and abundance of poxviruses. Chordopoxviral sequences were assembled and subjected to phylogenetic analysis to trace the origins of the unblasted fragments within these sequences.

RESULTS: Fifty-eight poxvirus species, representing two subfamilies and 20 genera, were identified, with 212 poxviral sequences assembled. A substantial proportion of AT-rich fragments were detected in the assembled poxviral genomes. These genomic sequences contained fragments originating from rodents, archaea, and arthropods.

CONCLUSION: Our findings indicate that ticks play a significant role in the transmission and evolution of poxviruses. These viruses demonstrate the capacity to modulate virulence and adaptability through horizontal gene transfer, gene recombination, and gene mutations, thereby promoting co-existence and co-evolution with their hosts. This study advances understanding of the ecological dynamics of poxvirus transmission and evolution and highlights the potential role of ticks as vectors and vessels in these processes.},
}

Animals
*Poxviridae/genetics/physiology
*Ticks/virology
Phylogeny
*Transcriptome
*Evolution, Molecular
*Poxviridae Infections/transmission/virology
Genome, Viral

@article {pmid41086969,
year = {2025},
author = {Min, B and Xie, J and He, Y and Lin, R and Azari, M and Xie, L},
title = {Role of biofilm carriers in sulfamethoxazole removal and microbial adaptation strategies in integrated fixed-film activated sludge system.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133481},
doi = {10.1016/j.biortech.2025.133481},
pmid = {41086969},
issn = {1873-2976},
abstract = {Attached-growth biofilm processes using specific biofilm carriers are widely employed to enhance antibiotic removal. However, the relationship between antibiotic degradation, resistance risks and microbial adaptation strategies across different carriers is not yet fully understood. Hence, four common biofilm systems, including iron-carbon (Fe@C), granular activated carbon (GAC), ceramic (CE), and polyurethane (PU), were evaluated for sulfamethoxazole (SMX) removal and antibiotic resistance genes (ARGs) risks. GAC and Fe@C systems exhibited higher SMX removal performance, achieving removal efficiency > 99.0 % and 63.8 %, respectively, compared to other carriers (17.4-49.8 %). Moreover, GAC reduced ARGs by 34.8-47.7 % via inhibiting horizontal gene transfer, as demonstrated by a 50.6-74.5 % decrease in core MGEs (intI1_337old, IS6100, and tnpA-2). Conversely, Fe@C exacerbated ARGs accumulation. The high specific surface area and rich pore structure of GAC promoted the colonization of potential SMX-degrading bacteria, notably Thauera, and shaped a multifunctional biofilm system. GAC biofilms exhibited distinct advantages in signal transduction and biofilm formation pathways. Meanwhile, the adsorption capacity of the GAC carrier created a hotspot for SMX biodegradation. This study provides a comprehensive understanding of antibiotic removal and spread of ARGs through the biofilm process.},
}

@article {pmid41086015,
year = {2025},
author = {Sünderhauf, D and Winter, M and Ramshaw, J and Stevenson, EM and Vos, M},
title = {Seaweed exposure modulates Escherichia coli plasmid conjugation rate.},
journal = {Microbiology (Reading, England)},
volume = {171},
number = {10},
pages = {},
doi = {10.1099/mic.0.001622},
pmid = {41086015},
issn = {1465-2080},
mesh = {*Escherichia coli/genetics/physiology ; *Plasmids/genetics ; *Conjugation, Genetic ; *Seaweed/microbiology ; Ulva ; Gene Transfer, Horizontal ; Fucus ; },
abstract = {Seaweeds are a common and diverse component of coastal ecosystems and are known to be associated with Escherichia coli due to faecal pollution. As a biotic substrate, beach-cast seaweed may affect bacterial physiology and thereby horizontal gene transfer (HGT). Here, we test how the presence of three distinct senescing seaweed species affects E. coli plasmid conjugation. We allow the IncP plasmid pKJK5 to conjugate while supplying a substrate of Palmaria palmata (dulse), Ulva lactuca (sea lettuce) or Fucus serratus (serrated wrack). The three seaweed species induce distinct conjugative behaviours in E. coli: U. lactuca has no significant impact relative to a plastic control, the presence of F. serratus results in undetectable levels of conjugation and P. palmata promotes conjugation in a density-independent manner. This study highlights how biotic interactions can influence survival, HGT and antibiotic resistance in a human pathogen.},
}

*Escherichia coli/genetics/physiology
*Plasmids/genetics
*Conjugation, Genetic
*Seaweed/microbiology
Ulva
Gene Transfer, Horizontal
Fucus

@article {pmid40939716,
year = {2025},
author = {Zhang, H and Shao, Y and Li, T and Liu, W and Huang, Y and Jiang, Y and Wang, Z and Xiao, X},
title = {UV-aged biodegradable and non-biodegradable microplastics further enhance horizontal transfer of antibiotic resistance plasmids both in vitro and in intestinal flora.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {385},
number = {},
pages = {127111},
doi = {10.1016/j.envpol.2025.127111},
pmid = {40939716},
issn = {1873-6424},
mesh = {*Microplastics/toxicity ; *Plasmids ; Ultraviolet Rays ; *Gastrointestinal Microbiome/drug effects ; *Gene Transfer, Horizontal ; *Drug Resistance, Microbial/genetics ; },
abstract = {Microplastics is a well-known environmental contaminant that have raised concerns regarding their role in spreading antibiotic resistance genes (ARGs). This study investigates the effect of ultraviolet (UV) aging of 100 nm petroleum-based (polystyrene, PS) and bio-based (polylactic acid, PLA) microplastics on the horizontal transfer of multidrug resistance plasmids. Both PS and PLA significantly increase the frequency of horizontal spread of ARGs, and UV aging of both PS and PLA microplastics further enhance this frequency by 4- to 20-fold, implying that environmental elements, including UV radiation, may increase the ecological danger caused by microplastics. UV aging significantly alters the surface properties of both PS and PLA microplastics and disrupted the integrity of bacterial cell membranes. Moreover, UV-aged microplastics increased cellular uptakes and exacerbated oxidative stress in bacteria by elevating ROS levels and SOD activity. In addition, UV-aged microplastics improved bacterial energy metabolism, providing additional ATP for conjugation process. Finally, UV-aged microplastics aggravated oxidative stress and intestinal inflammation in gut which further promoted the plasmid conjugation rate in vivo by 3.5-fold. The findings not only draw attention to the important role of UV-aged microplastics in permitting ARG spread but also urge thorough risk assessments of degradation of microplastics on public health and ecosystems.},
}

*Microplastics/toxicity
*Plasmids
Ultraviolet Rays
*Gastrointestinal Microbiome/drug effects
*Gene Transfer, Horizontal
*Drug Resistance, Microbial/genetics

@article {pmid41082848,
year = {2025},
author = {Chu, W and Li, X and Li, P and Li, J and Wang, Z and Zhou, H and Yang, X and Chen, S and Zhou, M and Wang, S and Zheng, J and Chen, Y and Yu, Y and Tan, Z},
title = {Enhanced treatment of low C/N domestic wastewater in a membrane photobioreactor: Operational control of microalgal-bacterial symbiosis for synergistic pollutant and antibiotic resistance genes removal.},
journal = {Journal of environmental management},
volume = {394},
number = {},
pages = {127398},
doi = {10.1016/j.jenvman.2025.127398},
pmid = {41082848},
issn = {1095-8630},
abstract = {Conventional wastewater treatment technologies face significant limitations, including high CO2 emissions, poor resource recovery, and growing challenges from emerging contaminants such as antibiotics and their associated antibiotic resistance genes (ARGs), which pose serious risks to aquatic ecosystems and public health. In response to these challenges and within the framework of China's carbon neutrality goals, this study developed a microalgae-activated sludge membrane photobioreactor (MPBR) to enable synergistic pollutant removal and resource recovery from low carbon-to-nitrogen (C/N) domestic wastewater. Under the optimized internal circulation flow rate of 13.5 m[3]/d, the MPBR system achieved high removal efficiencies for ammonia nitrogen (NH4[+]-N, 99.48 %), total nitrogen (TN, 72.89 %), chemical oxygen demand (COD, 63.20 %), and total phosphorus (TP, 80.37 %). Simultaneously, ARGs and mobile genetic elements (MGEs) were reduced by approximately one log, attributed to two primary mechanisms: (1) suppression of ARGs in the sludge zone through the regulation of drug-resistant bacterial populations, and (2) inhibition of horizontal gene transfer in the microalgal zone via nitrogen-driven suppression of ARGs host bacteria, as well as enhanced microalgae-bacteria co-metabolism and community optimization. Furthermore, the optimization of microalgae photosynthesis and nitrogen cycling, along with microbial cooperation under anoxic conditions, supported efficient nutrient recovery while maintaining low-carbon operation. This study offers a novel, carbon-efficient strategy for integrating wastewater purification with ARGs risk mitigation, contributing to sustainable water management aligned with the circular economy and carbon neutrality objectives.},
}

@article {pmid41081360,
year = {2025},
author = {Shin, NR and Duncan, M and Adams, R and McKenna, DD},
title = {250 Million Years of Convergent Evolution and Functional Divergence of Glycoside Hydrolase Family 28 Genes in Xylophagous Beetles (Cerambycidae and Buprestidae): Insights Into Horizontal Gene Transfer, Gene Dynamics, Synteny and Adaptive Divergence.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e70131},
doi = {10.1111/mec.70131},
pmid = {41081360},
issn = {1365-294X},
support = {DEB1355169//National Science Foundation/ ; DEB2110053//National Science Foundation/ ; },
abstract = {Wood-feeding beetles harbour diverse gene families involved in plant cell wall degradation, including glycoside hydrolase family 28 (GH28) genes, which function as polygalacturonases. These genes are believed to have originated from microbial donors via horizontal gene transfers (HGT), followed by gene duplications. However, the evolutionary history of GH28 genes across independently evolved wood-feeding beetle lineages remains unclear. Here, we investigate the distribution, origin and diversification of GH28 genes in two xylophagous beetle groups, Cerambycidae: Lamiinae and Buprestidae: Agrilinae, which diverged over 250 million years ago. Phylogenetic analyses reveal that both groups possess GH28 genes most likely derived from ascomycete fungi, which are distinct from the 'ancestral-type' GH28 genes found in other Cerambycidae. Thus, Lamiinae and Agrilinae acquired similar 'new-type' GH28 genes via convergent HGT events. Comparative genomic analyses show conserved synteny around GH28 loci within each beetle subfamily, but not between them, consistent with independent acquisitions and endogenous retention. Subsequent lineage-specific duplications resulted in the expansion of GH28 gene copies, with protein structural modelling revealing divergent active sites and substrate-binding regions, suggesting functional differentiation and adaptation to distinct ecological contexts. Signatures of positive selection further support adaptive evolution of GH28 enzymes in both groups. Our findings demonstrate convergent acquisition and diversification of GH28 genes in distantly related xylophagous beetles, highlighting the roles of HGT, gene duplication and structural divergence in driving functional innovation. These results underscore how plant cell wall-degrading enzymes have contributed to trophic specialisation and the evolutionary success of specialised phytophagous beetles.},
}

@article {pmid40960772,
year = {2025},
author = {Li, Q and Zhang, LY and Zhou, YJ and Cui, HL and Ren, YJ and Gao, SH and Wang, AJ and Liang, B},
title = {Positive Contribution of Antimicrobial Biodegradation in Mitigating Conjugative Transfer of Antibiotic Resistance Genes.},
journal = {Environmental science & technology},
volume = {59},
number = {40},
pages = {21645-21656},
doi = {10.1021/acs.est.5c06928},
pmid = {40960772},
issn = {1520-5851},
mesh = {Biodegradation, Environmental ; *Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Anti-Bacterial Agents ; Plasmids ; Drug Resistance, Bacterial/genetics ; Anti-Infective Agents ; },
abstract = {The evolution and spread of antimicrobial resistance (AMR) are common global challenge. However, little is known about the regulatory role and mechanisms of antimicrobial biodegradation processes in the transmission of antibiotic resistance genes (ARGs) in the environment. Here, we explored the effects of commonly used antimicrobials (chloramphenicol, sulfamethoxazole, triclocarban, trimethoprim, and parachlorometa-xylenol), their mixtures, and biodegradation processes on the conjugative transfer of plasmid-mediated ARGs from simple populations to complex communities. The findings show that antimicrobials can induce a series of reactions, including increased levels of reactive oxygen species, enhanced cell membrane permeability, and accelerated ATP synthesis, which in turn promote the horizontal transfer of ARGs. Importantly, antimicrobial biodegradation treatments significantly reduce the selective stress of antimicrobials, diminishing the transcription of key relevant genes and controlling the ARG conjugative transfer. Moreover, our findings emphasize the crucial role of antimicrobial biodegradation in reducing the abundance of high-risk pathogen microorganisms in actual community conjugative transference, thereby mitigating the negative health risks posed by antimicrobials. Our results highlight the positive contribution of antimicrobial biodegradation to impede the horizontal transfer of ARGs and provide a scientific basis for developing intervention strategies to manage and mitigate AMR development.},
}

Biodegradation, Environmental
*Drug Resistance, Microbial/genetics
Gene Transfer, Horizontal
Anti-Bacterial Agents
Plasmids
Drug Resistance, Bacterial/genetics
Anti-Infective Agents

@article {pmid41080529,
year = {2025},
author = {Stark, GF and Smith, LE and Truchon, AR and Martin, RM and Denison, ER and Wilhelm, SW},
title = {Microcystis plasmids: the unexplored portion of the mobilome and the presence of potential phage-like plasmids.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf154},
pmid = {41080529},
issn = {2730-6151},
abstract = {While resequencing Microcystis aeruginosa (PCC7806) and its nontoxigenic mutant (PCC7806 ΔmcyB), we discovered identical unreported plasmids in both strains. These strains were separated in culture over 25 years ago, resulting in sequence divergence among their chromosomes. RNA-seq data demonstrated these plasmids were transcriptionally active during chemostat growth. Moreover, in situ metatranscriptomes from Lake Erie revealed genes like those on the PCC7806 plasmid were expressed in the environment. As we investigated plasmids in Microcystis, we found that M. aeruginosa NIES-298 also had a putatively conserved plasmid, but with phage-like features. To gain an understanding of the ecological relevance of these plasmids, we examined Lake Erie metatranscriptomes and found that transcript abundance for predicted plasmid-like contigs was significantly higher than predicted virus-like contigs across the microbial community: this trend was also present when metatranscriptomic reads were mapped to Microcystis-infecting phage and Microcystis-specific plasmid genomes. Our observations demonstrate a potential ecological importance and stability of these extrachromosomal elements in Microcystis. Additionally, this work draws attention to the potential overlap between Microcystis plasmid and phage genomes, and how this may complicate molecular investigations.},
}

@article {pmid41080486,
year = {2025},
author = {Huang, YX and Lv, JM and Ding, CY and Zheng, XY and Liu, XJ and Chen, XN and Yu, SH and Meng, YF and Hu, HY and Wang, X},
title = {Genomic Evolution and Patterns of Horizontal Gene Transfer in Coccomorpha Species.},
journal = {Ecology and evolution},
volume = {15},
number = {10},
pages = {e72158},
pmid = {41080486},
issn = {2045-7758},
abstract = {As a significant group of agricultural and forestry pests, Coccomorpha warrants in-depth investigation into their environmental adaptation mechanisms. This study conducted a comparative genomic analysis using five published chromosome-level genomes of Coccomorpha species. Phylogenetic analysis revealed that the divergence times of these five species ranged from 333.18 to 84.22 million years ago (mya), with each having undergone two whole-genome duplication (WGD) events. The significantly expanded gene families in these species were predominantly enriched in antioxidant-related processes such as oxoacid metabolic process, organic acid metabolic process, and carboxylic acid metabolic process. Furthermore, 260 horizontal gene transfer (HGT) acquired genes were identified across these species, primarily originating from bacteria and archaea. These HGT-acquired genes were mainly involved in nutrient metabolism, suggesting their role in enhancing nutritional acquisition and metabolic flexibility. Through systematic identification of detoxification-related genes, ATP-binding cassette (ABC), carboxylesterases (COE), cytochrome P450, and UDP-glucuronosyltransferases (UGT) were identified as the major detoxification gene families in Coccomorpha, with significant variations in gene number and composition among different species. This study provides comprehensive insights into the genomic adaptations of Coccomorpha species, highlighting the roles of gene family dynamics, HGT, and detoxification mechanisms in their evolutionary success. These findings offer resources for understanding the molecular basis of Coccomorpha adaptation and provide references for developing targeted pest management strategies.},
}

@article {pmid41076908,
year = {2025},
author = {Chen, H and Yi, J and Li, Y and Li, X and Zhang, H and Yang, X and Zhong, H and Yu, G and Qiu, R and Chong, Y},
title = {Accumulation and translocation of antibiotic resistance genes in plants cultivated in hydroponic systems with nitrified biogas slurry.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140092},
doi = {10.1016/j.jhazmat.2025.140092},
pmid = {41076908},
issn = {1873-3336},
abstract = {Hydroponic cultivation with biogas slurry supports nutrient recycling but raises biosafety concerns due to the dissemination of antibiotic resistance genes (ARGs). This study established a hydroponic system using nitrified biogas slurry to grow lettuce and cherry radish, and systematically investigated the accumulation of ARGs, mobile genetic elements (MGEs), high-priority human pathogenic bacteria (HPBs), and virulence factors (VFs) in plant tissues. ARGs predominantly accumulated in roots (0.16 ∼ 0.23 copies/16S rRNA), significantly higher than in leaves (0.01 ∼ 0.11 copies/16S rRNA), with sul1 consistently enriched in the rhizosphere. Filtration pretreatment significantly reduced ARG and MGE levels in cherry radish roots by 30.78 % and 39.43 %, respectively (p < 0.05). ARGs strongly correlated with MGEs (R[2] = 0.97, p < 0.0001), indicating horizontal gene transfer as the key dissemination pathway. Co-occurrence network analysis revealed synergistic enrichment of ARGs and MGEs with HPBs and VFs, highlighting Acinetobacter baumannii and Streptococcus pneumoniae as potential core hosts. These findings demonstrate that ARG accumulation and spread in plants are affected by slurry treatment, plant species, and tissue specificity. While filtration mitigates risks, persistent ARGs in roots necessitate further monitoring. This study informs safe reuse strategies for biogas slurry in agriculture.},
}

@article {pmid41076761,
year = {2025},
author = {Jin, Y and Ping, J and Huang, X and Dai, J and Wang, X and Wang, S},
title = {Nanoscale zero-valent iron coupled with microorganisms enhances the removal of organochlorine pesticides in groundwater: Insights from the role of cascading effects and horizontal gene transfer.},
journal = {Water research},
volume = {288},
number = {Pt B},
pages = {124745},
doi = {10.1016/j.watres.2025.124745},
pmid = {41076761},
issn = {1879-2448},
abstract = {Nanoscale zero-valent iron (nZVIs) represent a promising approach for the remediation of organic chlorine-contaminated groundwater. However, the interaction between nZVIs and indigenous dechlorinating microorganisms is complex, which may have unpredictable effects on the dechlorination of organic chlorine, necessitating further investigation. In this study, we investigated an abandoned pesticide factory in southwest China, combined with microcosm experiment to reconstruct the metabolic pathway of biological dechlorination, and quantified the functional contribution of dechlorination genes and microorganisms. The results showed that the combined treatment of nZVIs and microorganisms significantly enhanced the degradation efficiency of HCHs, DDTs, and their six isomers, achieving removal rates of up to 99 % for HCHs and 87.73 % for DDTs. The concentrations of Cl[-] and Fe[2+] had a direct positive effect on the enrichment of microbial communities harboring HCHs degradation genes. Haloalkane dehalogenase encoded by the dhaA gene was identified as a key enzyme in the degradation of β-HCH precursors, which not only promoted the growth of facultative dehalogenators (particularly Acidovorax and Methyloversatilis) but also enhanced overall dechlorination activity. Importantly, we successfully reconstructed 7 near-complete bacterial metagenome-assembled genomes (MAGs) carrying the dhaA gene, representing taxonomically diverse novel dechlorinating microorganisms. Additionally, nZVIs significantly increased the abundance of mobile genetic elements (MGEs), with 17 MGEs detected within scaffolds harboring dhaA in the 7 MAGs. Integrases and transposases were identified as key drivers facilitating the spread of dhaA. This finding was supported by the shift of dhaA-harboring hosts, and by the incongruent evolutionary patterns observed between the genome-based tree and the dhaA protein phylogenetic tree. To be specific, cascading effects and horizontal gene transfer synergistically promoted the proliferation of dechlorinating microbes, providing novel strategies for managing and remediating organic chlorine-contaminated ecosystems.},
}

@article {pmid41075842,
year = {2025},
author = {da Silva, ES and Martins, AS and Ribeiro, LFS and Cordeiro-Moura, JR and Rodrigues, DAS and Picão, RC and Starling, MCVM and Amorim, CC},
title = {Tackling CECs and antimicrobial resistant bacteria in hospital wastewater using biological and AOP hybrid technologies.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133462},
doi = {10.1016/j.biortech.2025.133462},
pmid = {41075842},
issn = {1873-2976},
abstract = {This study investigated the disinfection, and removal of contaminants of emerging concern (CECs) and antibiotic-resistant bacteria (ARB) from hospital wastewater (HWW) using biological treatment followed by the LED photo-Fenton (BIO + LED-PF) and LED photo-Fenton followed by biological treatment (LED-PF + BIO). BIO was conducted by the Zahn Wellens method, while the LED-PF was applied in a pulse width modulation reactor (20 mg L[-1] Fe[2+], 50 mg L[-1] H2O2, pH 2.8, 70 % duty cycle, 60 min). CECs removal exceeded 90 % using BIO + LED-PF and 71 % using LED-PF + BIO. Both treatments were efficient in removing targets CECs from non-spiked raw HWW achieving concentrations < 1 µg L[-1], except for trimethoprim (BIO + LED-PF). LED-PF + BIO removed 5 and 6 log10 units of total coliforms (TC) and Escherichia coli (MPN/100 mL), respectively, while BIO + LED-PF achieved 5 log10 units of removal of TC and E. coli (MPN/100 mL) elimination. Pathogens considered as "critical" priority by the World Health Organization detected in HWW by MALDI-TOF/MS (cephalosporin-resistant Enterococcus faecalis and E. coli and carbapenem-resistant Klebsiella pneumoniae) were eliminated by both strategies. Approximately 3 logs10 units of ARB were removed for both treatment strategies, yet bacterial regrowth was observed after the LED-PF + BIO (Staphylococcus warneri resistant to ciprofloxacin) and BIO (Citrobacter freundii resistant to ciprofloxacin with 2 log10 units), emphasizing antimicrobial resistance risks. This regrowth was attributed to biomass proliferation and horizontal gene transfer in organic-rich environments. BIO + LED-PF also suppressed ARB, yet regrowth was detected for ARB resistant to SME + TRI. Overall, BIO + LED-PF was the most effective treatment, showing the feasibility of application in-situ in hospitals.},
}

@article {pmid41075480,
year = {2025},
author = {Zhu, Y and Li, D and Zeng, H and Zhang, J and Li, B and Tang, X and Luo, Y and Li, S and Ding, F},
title = {Decoding anammox granulation: Microbial interactions promote granule formation and indirectly shape antibiotic resistance gene dissemination.},
journal = {Water research},
volume = {288},
number = {Pt B},
pages = {124746},
doi = {10.1016/j.watres.2025.124746},
pmid = {41075480},
issn = {1879-2448},
abstract = {The formation of anaerobic ammonium oxidation (anammox) granules plays a crucial role in biomass retention. However, the microbial interaction, metabolic regulation, and risks associated with the dissemination of antibiotic resistance gene (ARG) during granulation remain insufficiently understood. In this study, an anammox granulation reactor was established and analyzed through integrated physicochemical characterization and multi-omics approaches to investigate changes in sludge properties, microbial communities, metabolic gene expression, and ARG profiles throughout granulation process. The results showed that granule size was closely associated with sludge surface free energy and extracellular polymeric substance (EPS) content, particularly the protein content of tightly bound EPS, which exhibited a significantly positive correlation with granule mechanical strength in the stable phase. Members of Proteobacteria exhibited the most significant shifts during granulation and occupied multiple core nodes in the microbial interaction network, indicating their essential roles in sustaining system stability and functional coordination. Metabolic functional analysis revealed selective regulation of carbon metabolism gene expression, which preferentially provides precursors for amino acid and cofactor biosynthesis. Different microbial taxa displayed significant metabolic complementarity in the synthesis of amino acids and cofactors. ARG analyses revealed that granulation was accompanied by an enhanced potential for mobile genetic element mediated horizontal gene transfer of ARG, with antibiotic target replacement and antibiotic efflux as primary resistance mechanisms. These findings deepen the ecological understanding of anammox granulation and offer theoretical support for managing ARG propagation in engineered systems.},
}

@article {pmid41072318,
year = {2025},
author = {Hou, G and Zhou, W and Han, L and Qiao, M and Chen, G and Lou, Q and Shao, S and Chi, S and Zhuo, H and Zhai, W and He, T and Liu, M and Zhang, L and Ding, H},
title = {Ecotoxicological effects of rare earth mining drainage: Unraveling dual antibiotic resistance gene regulation and risk-abundance decoupling through microbial community restructuring.},
journal = {Ecotoxicology and environmental safety},
volume = {305},
number = {},
pages = {119198},
doi = {10.1016/j.ecoenv.2025.119198},
pmid = {41072318},
issn = {1090-2414},
abstract = {Large-scale mining of ion-adsorption rare earth elements (REEs) generates acidic mine drainage (AMD) laden with REEs and heavy metals (HMs), yet its cascading impacts on microbial community assembly and antibiotic resistance genes (ARGs) dissemination across multi-matrices remain poorly characterized. By integrating high-throughput sequencing, co-occurrence network analysis, and partial least squares path modeling (PLS-PM), we unraveled that mining-induced geochemical divergence between mining-impacted areas and adjacent watersheds acts as a dominant environmental filter, reshaping the microbial community assembly and ARGs endowment. Key findings were in three areas: (1) Pollution-driven microbial adaptation. Significant shifts in microbial composition fostered "alternative steady states" without altering richness and induced network polarization-simplification in mining water (degree/density reduced by about 50 %) versus complexification in mining soil (degree/connections increased by about 3-fold), with enhanced mutualistic interactions and a 3-fold reduction in keystone species complexity. (2) ARGs risk-abundance decoupling. Mining areas exhibited 2.6-fold higher ARGs health risks than watersheds (p = 0.019), despite comparable abundance levels (p > 0.05), necessitating a paradigm shift from quantitative surveillance to health risks monitoring. (3) Dual ARGs regulation. While acidic REEs co-contamination directly promoted ARGs proliferation via co-selection (pathway coefficient = 0.254), it concurrently mitigated overall ecological risks through host community restructuring and potential horizontal gene transfer suppression (total effects = -0.186). These findings elucidate the ecological trade-offs between microbial adaptive resilience and ARGs dissemination in mining-impacted ecosystems, while establishing a mechanistic framework for optimizing targeted remediation strategies and sustainable resource extraction protocols.},
}

@article {pmid41070998,
year = {2025},
author = {Akiti, BT and Kaya, G and Kennedy, SP and DasSarma, P and Vincze, T and Fomenkov, A and Roberts, RJ and DasSarma, S},
title = {Genome sequence and methylome of the extremely halophilic bacterium Salinibacter ruber strain M31[T] isolated from a crystallizer pond in Mallorca, Spain.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0085625},
doi = {10.1128/mra.00856-25},
pmid = {41070998},
issn = {2576-098X},
abstract = {Salinibacter ruber strain M31[T], an extremely halophilic bacterium, was isolated from a saltern crystallizer pond in Spain. Single-molecule real-time sequencing revealed a 3.6-Mbp genome with a single 3.55-Mbp circular chromosome and a 35.5-kbp plasmid. The highly acidic proteome includes a total of 2,962 proteins, some of which are archaeal-like.},
}

@article {pmid40983756,
year = {2025},
author = {Dong, S and Wang, S and Li, L and Yu, J and Zhang, Y and Xue, JY and Chen, H and Ma, J and Zeng, Y and Cai, Y and Huang, W and Zhou, X and Wu, J and Li, J and Yao, Y and Hu, R and Zhao, T and Villarreal A, JC and Dirick, L and Liu, L and Ignatov, M and Jin, M and Ruan, J and He, Y and Wang, H and Xu, B and Rozzi, R and Wegrzyn, J and Stevenson, DW and Renzaglia, KS and Chen, H and Zhang, L and Zhang, S and Mackenzie, R and Moreno, JE and Melkonian, M and Wei, T and Gu, Y and Xu, X and Rensing, SA and Huang, J and Long, M and Goffinet, B and Bowman, JL and Van de Peer, Y and Liu, H and Liu, Y},
title = {Bryophytes hold a larger gene family space than vascular plants.},
journal = {Nature genetics},
volume = {57},
number = {10},
pages = {2562-2569},
pmid = {40983756},
issn = {1546-1718},
mesh = {*Bryophyta/genetics/classification ; Phylogeny ; *Multigene Family ; *Genome, Plant/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genes, Plant ; *Plants/genetics ; },
abstract = {After 500 million years of evolution, extant land plants compose the following two sister groups: the bryophytes and the vascular plants. Despite their small size and simple structure, bryophytes thrive in a wide variety of habitats, including extreme conditions. However, the genetic basis for their ecological adaptability and long-term survival is not well understood. A comprehensive super-pangenome analysis, incorporating 123 newly sequenced bryophyte genomes, reveals that bryophytes possess a substantially greater diversity of gene families than vascular plants. This includes a higher number of unique and lineage-specific gene families, originating from extensive new gene formation and continuous horizontal transfer of microbial genes over their long evolutionary history. The evolution of bryophytes' rich and diverse genetic toolkit, which includes new physiological innovations like unique immune receptors, likely facilitated their spread across different biomes. These newly sequenced bryophyte genomes offer a valuable resource for exploring alternative evolutionary strategies for terrestrial success.},
}

*Bryophyta/genetics/classification
Phylogeny
*Multigene Family
*Genome, Plant/genetics
Evolution, Molecular
Gene Transfer, Horizontal
*Genes, Plant
*Plants/genetics

@article {pmid41070122,
year = {2025},
author = {Ruiz, SE and Morandini, FN and Panzetta, ME and Lipari, FG and Irrazábal, MG and Toselli, R and Der Ohannesian, M and Amieva, C and Valdes, ME and Giraudo, FJ and Rollán, MDR and Amé, V and Sola, C and Saka, HA},
title = {Urban wastewater overflows as hotspots for dissemination of bacteria producing extended-spectrum β-lactamases and carbapenemases in the Suquía River, Argentina.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1669531},
pmid = {41070122},
issn = {1664-302X},
abstract = {Antimicrobial resistance (AMR) is a critical global challenge, yet the role of environmental dissemination of antibiotic-resistant bacteria remains underexplored, particularly in developing regions. This study investigated urban wastewater overflows from public streets as vectors for extended-spectrum-β-lactamase (ESBL)- and carbapenemase-producing Enterobacterales and Aeromonas in the Suquía River (Córdoba, Argentina). Sixty-two water samples were analyzed for coliform counts, antimicrobial susceptibility, and resistance genes. Horizontal gene transfer was assessed by conjugation. Sixty-five ESBL- and/or carbapenemase-producing isolates were recovered, including six carbapenemase producers subjected to whole-genome sequencing (WGS). Urban wastewater exhibited coliform levels >10[8] MPN/100 mL, while river counts increased 2-5 logs at urban and downstream sites compared to upstream, where no resistant strains were detected. ESBL- and/or carbapenemase-producers occurred in ~70% of wastewater and river samples, mainly Escherichia coli harboring blaCTX-M . Carbapenemase producers carried blaKPC-2 or blaNDM-1 in Enterobacter, Klebsiella, Citrobacter, and Aeromonas caviae. WGS revealed extensive resistomes, virulence genes, and plasmid replicons, including IncU and IncA/C2 linked to carbapenemases. Conjugation confirmed plasmid-mediated transfer of β-lactamase genes, and genetic context analysis identified clinically recognized transposons. Notably, Enterobacter kobei and Aeromonas caviae from the river carried blaKPC-2 on plasmidic contigs combining clinical and environmental elements, consistent with genetic exchange within aquatic ecosystems and transfer of clinically significant resistance determinants to species adapted for riverine survival. These findings identify urban wastewater overflows as AMR hotspots that facilitate the dissemination of multidrug-resistant bacteria and mobile resistance elements into urban and peri-urban aquatic environments, underscoring the need for integrated environmental AMR surveillance.},
}

@article {pmid41068737,
year = {2025},
author = {Debnath, PP and Chokmangmeepisarn, P and Papadopoulou, A and Coyle, NM and Baker-Austin, C and van Aerle, R and Bass, D and Tyler, CR and Rodkhum, C},
title = {Diversity and antimicrobial resistance among bacterial isolates from finfish aquaculture in Thailand.},
journal = {BMC veterinary research},
volume = {21},
number = {1},
pages = {595},
pmid = {41068737},
issn = {1746-6148},
support = {Second Century Fund (C2F) for postdoctoral fellowships//Chulalongkorn University/ ; FOOD_FF_68_201_3100_017//Chulalongkorn University, Bangkok, Thailand/ ; },
mesh = {Animals ; Thailand ; Aquaculture ; *Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; *Drug Resistance, Bacterial ; *Fishes/microbiology ; *Fish Diseases/microbiology/epidemiology ; *Bacteria/drug effects/isolation & purification ; Drug Resistance, Multiple, Bacterial ; Gram-Negative Bacteria/drug effects ; },
abstract = {BACKGROUND: Global aquaculture, has expanded rapidly, especially in Southeast Asia, with Thailand emerging as a leading producer. However, the sector faces economic losses from disease outbreaks and has problems with escalating antimicrobial resistance (AMR).

RESULTS: This study examined bacterial diversity and AMR in 695 moribund fish samples collected from regions across Thailand between 2018 and 2024, and spanning eight key finfish aquaculture species such as tilapia, Asian sea bass, snakeskin gourami, snakehead, walking catfish and carp species. Gram-negative bacteria (86.62% of isolates) were dominated by Vibrionaceae and Aeromonadaceae, while Gram-positive bacteria were primarily from Streptococcaceae, with notable species including A. veronii, V. vulnificus, S. agalactiae and S. suis. Antibiotic susceptibility testing was conducted with 29 antibiotics across nine different classes and the isolates were classified as wild-type (WT) or non-wild-type (NWT) based on their inhibition zone diameters. The results indicated high resistance levels, particularly against metronidazole, streptomycin, clindamycin, sulfonamide, and kanamycin. Multidrug resistance (MDR) was notably high in Aeromonas and Vibrio species. Antimicrobial resistance gene (ARG) analysis showed a high prevalence of beta-lactam, tetracycline, and fluoroquinolone resistance in Gram-negative bacteria, and resistance to beta-lactams, macrolides, fluoroquinolones, and peptides in Gram-positive bacteria. Antibiotic efflux was the predominant putatively detected resistance mechanism, accounting for 50-60% of ARGs. Identification of unique resistance gene families in Aeromonas spp. and V. vulnificus, including the SMR efflux pump and OXA beta-lactamase, emphasizes the adaptive strategies of these bacteria and the discovery of host-specific resistance mechanisms in S. suis, such as nutrient acquisition pathways, underscores the challenges of controlling and managing AMR in aquaculture systems. Mobile genetic elements (MGEs), particularly IS elements, were found to be widespread in all species, underscoring the significant role of horizontal gene transfer in the dissemination of resistance.

CONCLUSIONS: This study advocates for enhanced AMR surveillance, responsible antibiotic use, and species-specific monitoring to safeguard aquaculture and public health utilizing the one health approach.},
}

Animals
Thailand
Aquaculture
*Anti-Bacterial Agents/pharmacology
Microbial Sensitivity Tests
*Drug Resistance, Bacterial
*Fishes/microbiology
*Fish Diseases/microbiology/epidemiology
*Bacteria/drug effects/isolation & purification
Drug Resistance, Multiple, Bacterial
Gram-Negative Bacteria/drug effects

@article {pmid41068356,
year = {2025},
author = {Paillard, P and Rouger, Q and Thomet, M and Macé, K},
title = {Type IV secretion systems: from structures to mechanisms.},
journal = {The EMBO journal},
volume = {},
number = {},
pages = {},
pmid = {41068356},
issn = {1460-2075},
support = {ANR-22-PAMR-0005//Association Nationale de la Recherche et de la Technologie (ANRT)/ ; Tremplin-ERC VIRULENSSE//Association Nationale de la Recherche et de la Technologie (ANRT)/ ; },
abstract = {Bacterial conjugation is the fundamental process of unidirectional transfer of DNA from a "donor" cell to a "recipient" cell. It is the primary means by which antibiotic resistance genes spread among bacterial populations. Conjugation is mediated by a large molecular machinery termed Type IV secretion system (T4SS), embedded within the donor cell wall. In addition, some bacteria utilise T4SS to inject effector proteins into eukaryotic cells, modulating host functions to their advantage. In this review, we highlight how recent structural studies have substantially advanced our understanding of T4SS molecular mechanisms. We detail these mechanisms across four main sub-processes: assembly of the machinery, pilus biogenesis, donor-recipient cell contact, and substrate recruitment and secretion. By understanding the intricate workings of T4SS, we can gain valuable insights into bacterial evolution, virulence, and horizontal gene transfer, offering potential avenues for developing novel antibacterial strategies.},
}

@article {pmid41062968,
year = {2025},
author = {Han, S and Chen, Z and Liu, Q and Ding, Y and Wang, J and Liu, H and Zou, J and Hong, Z and Zhang, H and Yang, W and Zhang, L and Liu, H and Yuan, M},
title = {Identification and evolution of the plant sulfotransferase family.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {895},
pmid = {41062968},
issn = {1471-2164},
support = {C2024209006//the Natural Science Foundation of Hebei Province/ ; ZD-YG-202313-23//the Key research project of North China University of Science and Technology/ ; },
abstract = {UNLABELLED: Sulfotransferases (SOTs, EC 2.8.2.-), which catalyze sulfate conjugation reactions, are widespread across prokaryotes and eukaryotes. However, the origin, classification and evolution history of SOTs in plants are not as well understood as those in animals and bacteria. In this study, a systematic analysis of an array of sequenced genomes revealed that SOTs were ubiquitously distributed in green plants (Viridiplantae). Phylogenetic analysis classified plant SOTs into three subfamilies, including SULTs (soluble sulfotransferases), TPSTs (tyrosylprotein sulfotransferases), and NFSTs (nodulation factor sulfotransferase). Notably, CHSTs (carbohydrate sulfotransferases), abundant in animals, algae and bacteria, were not found in land plants. High-throughput screening algorithms, phylogenetic and gene structure analyses indicated that land plants might acquire NFSTs through horizontal gene transfer (HGT) from bacteria to green algae. In contrast to the low gene number of TPSTs and NFSTs in land plants, the number of SULTs varied greatly among species. The absence of SULTs resulted in a significantly reduced gene number of SOTs in Cucurbitaceae, whereas the recent expansion of SULTs, mainly driven by tandem duplication (TD), caused a significant increase in SOT gene number in Begoniaceae. The significant variation in the gene number of SULTs across species, along with their evolutionary branching patterns, indicated lineage-specific duplication or contraction of SULTs, which profoundly influenced the production of sulfated metabolites during the diversification of monocots and core eudicots. This study provided the first comprehensive phylogenetic, classification and evolutionary analysis of SOTs in green plants across a broad taxonomic range.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-025-12117-4.},
}

@article {pmid41068170,
year = {2025},
author = {Tsiklauri, R and Kobakhidze, S and Kotetishvili, M},
title = {Interactive networks of donors and recipients of the TetM gene and its evolutionary dynamics across the bacterial domain.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {35312},
pmid = {41068170},
issn = {2045-2322},
mesh = {*Evolution, Molecular ; *Bacteria/genetics ; Phylogeny ; Recombination, Genetic ; Humans ; *Bacterial Proteins/genetics ; Selection, Genetic ; },
abstract = {Identifying primary donors and recipients of the tetM gene is crucial for gaining a deeper understanding of the dynamics underlying the dissemination of resistance to tetracyclines in natural bacterial populations, including those of human and animal pathogens. This study modeled the major donor-recipient network of tetM, also providing important insights into the primary evolutionary mechanisms of this gene. The RDP4- and SplitsTree-embedded algorithms were used to detect genetic recombination events of tetM loci from different bacterial species and genera. FUBAR, MEME, and MEGA11 were employed to determine the evolutionary dynamics of this gene. A large tetM donor-recipient species network, exhibiting different bacterial genera, was determined based on the RDP4- and SplitsTree-generated inferences (P ≤ 3.75E-02; bootstrap and fit values ≥ 90 and ≥ 94.9 respectively). 3 sites were identified as undergoing episodic diversifying selection, while 42 sites were under pervasive negative selection for this gene, with a discrete Gamma distribution value of 0.0500. Notably, Streptococcus agalactiae, Streptococcus equinus, Streptococcus pyogenes, Streptococcus pneumoniae, Enterococcus faecalis, Enterococcus faecium, and Gardnerella vaginalis were suggested to be the predominant donors of tetM involved in inter-species and/or intergeneric recombination. Genetic recombination and pervasive negative selection were suggested to be the primary driving forces underlying the evolution of tetM.},
}

*Evolution, Molecular
*Bacteria/genetics
Phylogeny
Recombination, Genetic
Humans
*Bacterial Proteins/genetics
Selection, Genetic

@article {pmid41067449,
year = {2025},
author = {Yang, H and Cui, B and Zhou, D},
title = {Signaling role of 6-benzylaminopurine in enhanced biotreatment of saline wastewater: performance and mechanisms.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133455},
doi = {10.1016/j.biortech.2025.133455},
pmid = {41067449},
issn = {1873-2976},
abstract = {This study introduced the phytohormone 6-benzylaminopurine (6-BA) as a novel, economical, and eco-friendly bacterial signal molecule (SM), which overcame the cost and instability limitations of acyl-homoserine lactones (AHLs) in high-salinity wastewater treatment. 6-BA bound to histidine kinases in two-component systems (TCS) through hydrogen bonding, triggering downstream signal transduction and metabolic regulation. Under high-salinity stress, 6-BA promoted cellular integrity and ionic homeostasis, increasing live-cell counts by 113.7%. To mitigate phenol toxicity, 6-BA enhanced extracellular polymeric substance (EPS) functions and antioxidant systems, reducing reactive oxygen species (ROS) by 19.8%. 6-BA upregulated genes related to DNA replication, the TCA cycle, and fatty acid synthesis, thereby repairing membrane integrity. 6-BA also enriched degrading enzymes and improved phenol degradation, leading to approximately 20% increases in COD, TN, and TP removal. Crucially, 6-BA restructured the microbial community, reducing antibiotic resistance gene (ARG) host abundance by 27.9% and ARG-encoding plasmids by 32.8, which curtailed horizontal gene transfer risks. Additionally, 6-BA exhibited no observable ecotoxicity. This work proposed 6-BA signaling as a novel bioaugmentation strategy for enhanced remediation of high-salinity wastewater.},
}

@article {pmid41067299,
year = {2025},
author = {Feng, Y and Yuan, Q and Kang, Y and Zheng, M and Li, Z},
title = {Deciphering the mobility, pathogenic hosts, and co-selection of antibiotic resistance genes in untreated wastewater from three different hospitals.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {105840},
doi = {10.1016/j.meegid.2025.105840},
pmid = {41067299},
issn = {1567-7257},
abstract = {OBJECTIVE: Antibiotic resistance genes (ARGs) in hospital wastewater pose significant environmental and public health risks, yet the co-selection mechanisms involving metal/biocide resistance genes (MRGs/BRGs) and the role of mobile genetic elements (MGEs) remain poorly characterized. This study aimed to comprehensively assess the abundance, mobility, pathogenic hosts, and co-selection patterns of ARGs, MRGs, and BRGs in untreated wastewater from three types of hospitals.

METHODS: Untreated wastewater samples from nine sources across three hospital types (general, traditional Chinese medicine, and dental) were analyzed using metagenomic sequencing and assembly. ARGs, MRGs, and BRGs were identified via the SARG and BacMet databases. ARG hosts, mobility, and MGE co-occurrence were analyzed using PlasFlow and MOB-suite, with risk levels evaluated alongside pathogenic bacteria databases.

RESULTS: A total of 1911 ARGs (222 subtypes), 1662 MRGs (167 subtypes), and 916 BRGs (139 subtypes) were detected. Tetracycline, multidrug, and β-lactam resistance genes were predominant, with 46.43 % of ARGs being plasmid-associated. Key pathogens including Klebsiella pneumoniae and Enterococcus spp. harbored high-risk ARGs such as KPC-2 and NDM-1. Notably, 76.2 % of ARGs in traditional Chinese medicine hospital wastewater were classified as high-risk. Significant co-occurrence of ARGs with MGEs (e.g., DDE recombinases) and MRGs/BRGs was observed, underscoring the role of horizontal gene transfer and co-selection.

CONCLUSION: Untreated hospital wastewater represents a significant reservoir of ARGs, with risks exacerbated by pathogenic hosts, MGE-mediated HGT, and metal/biocide co-selection. These findings underscore the urgent need for optimized wastewater treatment strategies to curb the spread of antibiotic resistance and inform future intervention efforts.},
}

@article {pmid41067103,
year = {2025},
author = {Wang, M and Liu, X and Wang, J and Hao, S and Sun, X},
title = {Three-dimensional synergistic mechanism ofphysical injury, microbiota dysbiosis, and gene transfer in the gut of Cipangopaludina cathayensisunder microplastics and roxithromycin exposure.},
journal = {Journal of environmental management},
volume = {394},
number = {},
pages = {127514},
doi = {10.1016/j.jenvman.2025.127514},
pmid = {41067103},
issn = {1095-8630},
abstract = {Microplastics (MPs) and antibiotics pose a combined threat to aquatic organisms by impairing gut health and promoting the spread of antibiotic resistance genes (ARGs). In this study, Cipangopaludina cathayensis was exposed for 28 days to polystyrene MPs, roxithromycin (ROX), and their combination to assess impacts on intestinal barrier integrity, microbiota composition, and ARG proliferation. MPs alone caused significant mucosal damage, villus atrophy, epithelial shedding, and reduced digestive enzyme activities. ROX exposure altered microbiota structure by increasing Bacteroidetes and reducing Firmicutes. Co-exposure (CM group) exacerbated epithelial injury and enzyme inhibition but partially restored balance through enrichment of SCFA-producing, anti-inflammatory bacteria. ARG levels in the CM group rose by over 1000 %, with notable increases in multidrug resistance genes (e.g., blaOXA10) and integrons (e.g., cIntI-1), mainly linked to Bacteroides and Proteobacteria. Transcriptomic data indicated oxidative stress and epithelial disruption under MPs, and upregulation of efflux and integron genes with ROX. Combined exposure triggered DNA repair and SOS pathways, facilitating horizontal gene transfer. These findings highlight a three-dimensional synergistic mechanism-physical damage, microbial dysbiosis, and gene transfer-that amplifies ARG dissemination and intestinal toxicity, underscoring the need to assess ecological risks of composite pollutants in freshwater systems.These processes form a self-reinforcing loop in which physical epithelial damage promotes microbial dysbiosis, which in turn facilitates ARG proliferation through increased permeability and immune disruption.},
}

@article {pmid41066873,
year = {2025},
author = {Hou, J and Liu, M and Li, Y and Li, L and Yao, Y and Xu, H and An, Y},
title = {Seed-borne and environmental transmission mechanisms drive diverse heavy metal-resistant plant growth-promoting bacteria (PGPB) in rice.},
journal = {Environment international},
volume = {204},
number = {},
pages = {109840},
doi = {10.1016/j.envint.2025.109840},
pmid = {41066873},
issn = {1873-6750},
abstract = {Heavy metal-resistant plant growth-promoting bacteria (PGPB) play a crucial role in mitigating heavy metal stress and reducing heavy metal accumulation in plants. However, the origins and transmission mechanisms of PGPB and their associated heavy metal resistance genes (MRGs) in plants remain unclear. To fill this knowledge gap, we collected rice and related environmental samples from heavy metal-contaminated paddy fields. The microbial DNA was recovered from these rice and environmental samples and then analyzed using shotgun metagenomics at the metagenome-assembled genomes (MAGs) level. As a result, 805 MRG-PGPB combinations were detected in rice tissues and related environments under heavy metal contamination conditions. Core MRG-PGPB combinations shared across seed-rice (42.46%) and environment-rice (13.34%) interfaces collectively constituted 55.80% of the detected combinations, demonstrating that environmental translocation and seed-borne vertical transmission jointly drive over half of MRG-PGPB colonization in rice systems. Subsequent source-tracking analysis indicated that PGPBs present in rice primarily originated from seeds, with a substantial proportion also attributed to translocation within rice tissues. Phylogenetic analysis of dominant MRGs further demonstrated the seed-borne vertical transmission of MRGs-PGPB, while simultaneously elucidating that MRGs harbored by PGPB in rice could also be acquired via horizontal gene transfer (HGT) from environmental or seed-borne MRG-PGPB, particularly from atmospheric microbes such as Methylophilus and Serratia. These findings provide valuable insights into harnessing PGPB to enhance rice resilience against heavy metal contamination, thereby contributing to improved food security and sustainable agricultural practices.},
}

@article {pmid41066555,
year = {2025},
author = {Macadangdang, BR and Wang, Y and Woodward, CL and Revilla, JI and Shaw, BM and Sasaninia, K and Varnum, GE and Makanani, SK and Berruto, C and Ahuja, U and Miller, JF},
title = {Targeted protein evolution in the gut microbiome by diversity-generating retroelements.},
journal = {Science (New York, N.Y.)},
volume = {390},
number = {6769},
pages = {eadv2111},
doi = {10.1126/science.adv2111},
pmid = {41066555},
issn = {1095-9203},
mesh = {*Gastrointestinal Microbiome/genetics ; *Retroelements/genetics ; Animals ; *Bacteroides/genetics/classification ; Mice ; Humans ; Female ; *Evolution, Molecular ; Germ-Free Life ; Gene Transfer, Horizontal ; *Bacterial Proteins/genetics ; Genetic Variation ; *Fimbriae Proteins/genetics ; },
abstract = {Diversity-generating retroelements (DGRs) accelerate evolution by rapidly diversifying variable proteins. The human gastrointestinal microbiota harbors the greatest density of DGRs known in nature, suggesting that they play adaptive roles in this environment. We identified >1100 distinct DGRs among human-associated Bacteroides species and discovered a subset that diversify adhesive components of type V pili and related proteins. We show that Bacteroides DGRs are horizontally transferred across species, display activity levels ranging from high to low, and preferentially alter the functional characteristics of ligand-binding residues on adhesive organelles. Specific variable protein sequences are enriched when Bacteroides strains compete with other commensal bacteria in gnotobiotic mice. Analysis of >2700 DGRs from diverse phyla in mother-infant pairs shows that Bacteroides DGRs are disproportionately transferred to vaginally delivered infants where they actively diversify. Our observations provide a foundation for understanding the potential roles of targeted genome plasticity in shaping host-associated microbial communities.},
}

*Gastrointestinal Microbiome/genetics
*Retroelements/genetics
Animals
*Bacteroides/genetics/classification
Mice
Humans
Female
*Evolution, Molecular
Germ-Free Life
Gene Transfer, Horizontal
*Bacterial Proteins/genetics
Genetic Variation
*Fimbriae Proteins/genetics

@article {pmid41065996,
year = {2025},
author = {Zhang, Y and Lin, Y and Ruan, Y and Yang, J and Holden, E and Felgate, H and Solsona, M and Liu, H and Liang, G and Jiang, H and Webber, MA and Zhuo, C},
title = {Pivotal plasmids drive the global spread of CTX-M-27 in Escherichia coli.},
journal = {Infection},
volume = {},
number = {},
pages = {},
pmid = {41065996},
issn = {1439-0973},
support = {82172318//the National Natural Science Foundation of China/ ; },
abstract = {The detection rate of CTX-M-27-producing E. coli has increased worldwide in recent years although relatively little is known about the strains and vectors responsible for this increased isolation.To explore the evolution of CTX-M-27-producing E. coli in the past 20 years at three levels; genetic structure of the blaCTX-M-27 locus, nature of carrying plasmids and types of host bacteria, we analysed 543 genomes of blaCTX-M-27-positive E. coli isolated globally from 2003 to 2020.Results indicated that hospitalised patients are a major reservoir of blaCTX-M-27 carrying isolates but there are a wide variety of other resistance genes, plasmid replicons and virulence factors carried by CTX-M-27-producing E. coli strains. There was a strong positive correlation between carriage of the blaCTX-M-27 gene and the highly virulent clone-ST131 E. coli. IncF-type plasmids were the most common vector of blaCTX-M-27 transmission with a subtype of F plasmids showing a tropism for specific sequence types of E. coli. The DNA transfer and replicon-stability regions of host plasmids showed evidence for significant evolution over time with deletion and truncation events associated with blaCTX-M-27-carrying plasmids being stably maintained in specific host sequence types. Moreover, recently isolated blaCTX-M-27-carrying plasmids were found to contribute to growth of host bacteria suggesting they have evolved to provide benefits to their host. IncF plasmids and the blaCTX-M-27 locus also showed evidence for co-evolution, in particular, "Bridge" co-integrate structures flanked by IS26 were found in this study in IncF plasmids.Together, our results illustrate that blaCTX-M-27 is present on various plasmids which are associated with epidemic host E. coli and it appears carriage of prevalent IncF blaCTX-M-27-carrying plasmids are beneficial for the host. Complex genetic structures are under evolutionary pressure which promote the wide spread of blaCTX-M-27 which is a global health threat.},
}

@article {pmid41065715,
year = {2025},
author = {Feng, Y and Wicke, S},
title = {Systemic organellar genome reconfiguration along the parasitic continuum in the broomrape family (Orobanchaceae).},
journal = {Plant & cell physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/pcp/pcaf131},
pmid = {41065715},
issn = {1471-9053},
abstract = {The transition from autotrophy to heterotrophy in parasitic plants disrupts organellar coordination and presents a unique opportunity to examine the coevolution of cellular genomes. Using the Broomrape family (Orobanchaceae) as a model, we analyzed mitochondrial and plastid genome evolution across 30 species representing the full spectrum of parasitic lifestyles. We show that plastid genome reduction is correlated with mitogenomic expansion, revealing a striking inverse relationship between genome compaction and inflation. Mitogenome enlargement in parasitic taxa is driven by the accumulation of horizontally and intracellularly transferred DNA, proliferation of short repeats, and integration of unique sequences with no detectable homology. Across the family, plastid-derived mitochondrial sequences (MTPTs) are consistently more similar in GC content to plastomes than to mitogenomes, and in several holoparasites, 'ghost' MTPTs preserve regions now lost from plastomes, indicating integration before plastome reduction. Relaxed selection in ATP synthase and ribosomal genes contrasts with intensified selection on components of electron transport and cytochrome c maturation, reflecting functional reconfiguration of mitochondrial respiration in parasitic plants. RNA editing, intron loss, and frameshift insertions further reshape gene structure, particularly in obligate parasites. Together, our findings suggest that parasitism initiates a systemic genomic feedback loop in which relaxed selection and disrupted maintenance mechanisms affect even distant genomic compartments. This study provides a comprehensive evolutionary framework for multi-compartment genome remodeling in parasitic plants and highlights the dynamic interplay between lifestyle specialization and organelle genome evolution.},
}

@article {pmid41065417,
year = {2025},
author = {Lamoureux, A and Elvira-Matelot, E and Porteu, F and Laplane, L},
title = {Revisiting Clonal Evolution Through the Light of Retrotransposons.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {},
number = {},
pages = {e70078},
doi = {10.1002/bies.70078},
pmid = {41065417},
issn = {1521-1878},
support = {//CNRS MITI, 80 Prime/ ; //CNRS 80 Prime program/ ; 2021-1-EMERG-54-CNRS DR 5-1//Cancéropôle IDF/ ; INCa-DGOS-Inserm-ITMO Cancer_18002//SIRIC/ ; //McDonnell Foundation/ ; Equipe labellisée EL2020//Ligue Nationale Contre le Cancer/ ; },
abstract = {The clonal evolution model provides a framework for understanding the evolution of cancer cells. According to this model, cancer cells accumulate genetic mutations over time, and these mutations are passed down to their descendants, leading to genetic diversity within the tumor. Some of these mutations confer selective advantages, causing certain lineages of cancer cells (clones) to dominate and expand. However, this model is rooted in certain conceptual assumptions, which we propose to revisit by considering the potential involvement of retrotransposons in cancer initiation and progression. In recent years, it has become evident that transposable elements, particularly retrotransposons, play a significant role in driving cancer transformation and progression. We first review how current knowledge about retrotransposon activity aligns with the clonal evolution model by highlighting its ability to modulate cancer cell fitness. We then take a forward-looking perspective to explore additional ways retrotransposons may also influence clonal dynamics beyond the current model.},
}

@article {pmid41064843,
year = {2025},
author = {Herawati, O and Bejo, SK and Zakaria, Z and Zubaidah Ramanoon, S},
title = {Impact of antibiotic use on Escherichia coli resistance in goats: A longitudinal cohort study in Selangor, Malaysia.},
journal = {Veterinary world},
volume = {18},
number = {8},
pages = {2479-2486},
pmid = {41064843},
issn = {0972-8988},
abstract = {BACKGROUND AND AIM: Antibiotic resistance (ABR) in food animals poses a significant threat to public health under the One Health framework. In Malaysia, Escherichia coli is a key indicator organism for antimicrobial resistance (AMR) surveillance. However, limited data exist on the resistance profiles of E. coli in goats, particularly in relation to antibiotic usage. This study aimed to evaluate the effect of antibiotic use on the temporal development of ABR in E. coli isolated from goat farms in Selangor.

MATERIALS AND METHODS: A prospective cohort study was conducted on two goat farms: one with a documented history of antibiotic use (Farm 2) and one without (Farm 1). A total of 60 goats (30/farm) were followed for 3 months, with fecal samples collected monthly. E. coli isolates were identified and subjected to antimicrobial susceptibility testing using the Kirby-Bauer disk diffusion method. Data were analyzed using Chi-square tests, logistic regression, and Cox proportional hazards modeling.

RESULTS: A significant association was found between antibiotic use and the presence of ABR E. coli (odds ratio = 5.82; 95% confidence interval [CI]: 1.12-30.20; p < 0.05). The highest resistance was observed in Farm 2 (96.74%) compared to Farm 1 (57.14%). A hazard ratio of 1.74 (95% CI: 1.03-2.94) indicated increased risk over time. Resistance was detected against critically important human antibiotics, including ciprofloxacin, ampicillin, chloramphenicol, and tetracycline. Notably, resistance to meropenem, an antibiotic not approved for veterinary use, was detected in both farms, suggesting possible environmental or interspecies transmission.

CONCLUSION: This study confirms that antibiotic use in goat farming significantly influences the development of ABR in E. coli. The detection of resistance in farms without antibiotic use underscores the need to investigate other contributing factors, such as environmental residues and horizontal gene transfer. These findings support policy recommendations to restrict antibiotic use in livestock and highlight the urgency for comprehensive AMR surveillance and intervention strategies.},
}

@article {pmid41064643,
year = {2025},
author = {de Oliveira, AM and de Castro, CP},
title = {Perspectives in clinical microbiology for combating multi-drug resistant bacterial infections.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1695284},
pmid = {41064643},
issn = {2235-2988},
mesh = {Humans ; *Drug Resistance, Multiple, Bacterial ; *Bacterial Infections/diagnosis/microbiology/drug therapy/therapy ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; *Bacteria/drug effects ; Bacteriophages ; Phage Therapy ; Antimicrobial Peptides/therapeutic use ; },
abstract = {Multidrug-resistant bacterial infections are a major global threat, exacerbated by globalization and poor sanitation. Bacteria develop resistance through mechanisms like enzymatic degradation, efflux pumps, and horizontal gene transfer. Rapid diagnostics and artificial intelligence are crucial for overcoming the limitations of traditional culture methods. Combating this issue requires novel therapeutic strategies, such as bacteriophages, antimicrobial peptides, and microbiome-based therapies. Ultimately, proper antibiotic use, increased research, and global multidisciplinary cooperation are essential to address this complex challenge.},
}

Humans
*Drug Resistance, Multiple, Bacterial
*Bacterial Infections/diagnosis/microbiology/drug therapy/therapy
*Anti-Bacterial Agents/therapeutic use/pharmacology
*Bacteria/drug effects
Bacteriophages
Phage Therapy
Antimicrobial Peptides/therapeutic use

@article {pmid41064044,
year = {2025},
author = {Herold, L and Fitzgerald, BG and Leclercq, GME and Sorbara, MT},
title = {Strain-level variation controls nutrient niche occupancy by health-associated Anaerostipes hadrus.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf163},
pmid = {41064044},
issn = {2730-6151},
abstract = {Nutrient niche access by the gut microbiota impacts community assembly and dynamics, the production of host-benefiting short-chain fatty acids (SCFAs), and pathogen inhibition through colonization resistance. Furthermore, deciphering if and how niche access varies on a strain level will be important as individual strains of gut microbes are selected for inclusion in new live biotherapeutic products. Despite this, for many gut anaerobes, nutrient niche occupancy and impacts of strain variation remain unknown. Here, we examined nutrient niches of Anaerostipes hadrus (AH), a butyrate-producing member of the Lachnospiraceae family. We found that AH isolates encode a carbohydrate metabolism gene repertoire that is distinct from other Lachnospiraceae. Furthermore, tested AH isolates show variation in carbohydrate-related genes between strains and large numbers of genes associated with horizontal gene transfer events. Functionally, we demonstrate that AH isolates exhibit strain-specific patterns of nutrient niche access that can be associated with the gain, loss, and disruption of gene clusters enabling specific carbohydrate metabolism. This strain-specific carbohydrate use drives variable SCFA production. Unexpectedly, strains exhibit differential preferences for carbohydrates, which alter SCFA profiles in environments with multiple possible nutrient niches available. Furthermore, when strains of AH interact in an environment with multiple nutrient niches available, strain-strain interactions result in varying SCFA profiles that extend beyond the additive effects of individual strain behavior. Altogether, these results demonstrate the importance of evaluating strain-level variation in the design of future live biotherapeutic products.},
}

@article {pmid41063607,
year = {2025},
author = {Bernabeu, M and Manzano-Morales, S and Gabaldón, T},
title = {Phylogeny-aware simulations suggest a low impact of unsampled lineages in the inference of gene flow during eukaryogenesis.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evaf190},
pmid = {41063607},
issn = {1759-6653},
abstract = {The topologies of gene trees are broadly used to infer horizontal gene transfer events and characterize the potential donor and acceptor partners. Additionally, ratios between branch lengths in the gene tree can inform about the timing of transfers relative to each other. Using this approach, recent studies have proposed a relative chronology of gene acquisitions in the lineage leading to the last eukaryotic common ancestor (LECA). However, a recognised caveat of the branch-length ratio method are potential biases due to incomplete taxon sampling resulting in so-called "ghost" lineages. Here, we assessed the effect of ghost lineages on the inference of the relative ordering of gene acquisition events during eukaryogenesis. For this, we used a novel simulation framework that populates a dated Tree of Life with plausible "ghost" lineages and simulates their gene transfers to the lineage leading to LECA. Our simulations suggest that a substantial majority of gene acquisitions from distinct ghost donors are inferred with the correct relative order. However, we identify phylogenetic placements where ghost lineages would be more likely to produce misleading results. Overall, our approach offers valuable guidance for the interpretation of future work on eukaryogenesis, and can be readily adapted to other evolutionary scenarios.},
}

@article {pmid41061540,
year = {2025},
author = {Zhang, L and Gao, X and Li, G and Xu, Z and Luo, W},
title = {Metagenomic insights to effective elimination of resistomes in food waste composting by lime addition.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140065},
doi = {10.1016/j.jhazmat.2025.140065},
pmid = {41061540},
issn = {1873-3336},
abstract = {Food waste contains abundant resistomes, including antibiotic and heavy metal resistance genes (ARGs and MRGs), which pose risks to the environment and human health. Composting can be used for food waste treatment, but it fails to effectively eliminate these resistomes. Thus, this study investigated the performance of lime to regulate the dynamics and mobility of ARGs and MRGs in food waste composting by metagenomics. Genome-resolved analysis was further conducted to identify the ARGs and MRGs hosts and their horizontal gene transfer (HGT) events. Results showed that lime addition at 1 % (wet weight) could significantly promote temperature and pH increase to sterilize hosts, particularly pathogen bacteria (e.g. Acinetobacter johnsonii and Enterobacter cloacae), thus reducing the abundance of resistomes by more than 57.1 %. This sterilization notably reduced the number of mobile ARGs and MRGs driven by mobile genetic elements (MGEs). The contribution of MGEs located on chromosomal sequences to horizontally transfer ARGs and MRGs was significantly higher than that on mobilizable plasmids. Further analysis indicated that the reduced resistomes by lime was mainly attributed to effective sterilization of hosts rather than decreased HGT diversity. Thus, this study provides valuable insights into use lime as a low-cost control of resistomes in waste recycling.},
}

@article {pmid41060691,
year = {2025},
author = {Gao, F and Colles, FM and Ko, S and Luo, J and Sheppard, SK and Chen, M},
title = {Genomic epidemiology and the evolution of erm(B)-mediated macrolide resistance in Campylobacter.},
journal = {Microbial genomics},
volume = {11},
number = {10},
pages = {},
doi = {10.1099/mgen.0.001528},
pmid = {41060691},
issn = {2057-5858},
mesh = {*Campylobacter/genetics/drug effects/isolation & purification/classification ; *Macrolides/pharmacology ; Humans ; *Anti-Bacterial Agents/pharmacology ; Phylogeny ; Animals ; *Campylobacter Infections/epidemiology/microbiology ; *Drug Resistance, Bacterial/genetics ; China/epidemiology ; *Methyltransferases/genetics ; Genome, Bacterial ; Microbial Sensitivity Tests ; *Bacterial Proteins/genetics ; Gene Transfer, Horizontal ; Poultry/microbiology ; Evolution, Molecular ; },
abstract = {Campylobacter is a major foodborne bacterial pathogen that has become increasingly resistant to clinically important antimicrobials. Of particular concern is the emergence of erm(B)-mediated macrolide resistance, which has been increasingly documented across Campylobacter isolates from diverse ecological reservoirs. In this study, we investigated the genomic characteristics and epidemiology of erm(B)-carrying clinical Campylobacter isolates from Shanghai, alongside a globally representative dataset of all publicly available strains. Among clinical isolates obtained from a diarrhoeal outpatient surveillance programme between 2020 and 2023 in Shanghai, China, 16% (80/500) were erythromycin-resistant, with 23.8% (19/80) testing positive for erm(B). The genomes of these isolates were sequenced to identify erm(B) gene alleles. Phylogenetic analyses, pairwise comparisons of core and accessory genomes and examination of shared alleles revealed horizontal gene transfer as the predominant mechanism driving the transmission of erm(B) between isolates from various sources. Poultry was identified as a key reservoir for human infections caused by erm(B)-positive Campylobacter isolates. Comparative pangenome analyses of erm(B)-positive and negative isolates identified multiple accessory elements associated with erm(B) acquisition, among which the IS607 family transposon-associated tnpB gene exhibited sequence and structural homology to functional progenitors of CRISPR-Cas nucleases. These findings expand our understanding of the epidemiology of erm(B)-mediated macrolide resistance in Campylobacter and underscore the urgent need for enhanced antimicrobial stewardship in poultry production and targeted surveillance programmes to curb the spread of resistance.},
}

*Campylobacter/genetics/drug effects/isolation & purification/classification
*Macrolides/pharmacology
Humans
*Anti-Bacterial Agents/pharmacology
Phylogeny
Animals
*Campylobacter Infections/epidemiology/microbiology
*Drug Resistance, Bacterial/genetics
China/epidemiology
*Methyltransferases/genetics
Genome, Bacterial
Microbial Sensitivity Tests
*Bacterial Proteins/genetics
Gene Transfer, Horizontal
Poultry/microbiology
Evolution, Molecular

@article {pmid41060684,
year = {2025},
author = {Luque-Jiménez, E and Moreno-Rodríguez, A and Garzón, A and Rubio, A and Pérez-Pulido, AJ},
title = {Discovery of a bacteriophage sequence in a mite genome assembly reveals bacterial contamination and opens new possibilities for exploring arthropod symbionts.},
journal = {Microbial genomics},
volume = {11},
number = {10},
pages = {},
doi = {10.1099/mgen.0.001520},
pmid = {41060684},
issn = {2057-5858},
mesh = {Animals ; *Bacteriophages/genetics ; Symbiosis ; *Mites/microbiology/virology/genetics ; *Acinetobacter baumannii/virology/genetics ; *Acinetobacter/genetics/virology ; Genome, Viral ; Gene Transfer, Horizontal ; },
abstract = {While studying the integration site of a bacteriophage associated with the bacterium Acinetobacter baumannii, we found a genome assembly of the mite Oppiella nova that contained a homologous sequence of this locus. We initially thought of horizontal gene transfer, but it actually uncovered the contamination of 41 genome fragments with a total of 2.28 Mb. This has allowed us to assemble a new genome of the species Acinetobacter guillouiae, which could be a symbiont of the mite, based on the identification of genes potentially related to the diet of this arthropod. This contamination has been unknowingly spread, at least in another article in which authors studied a gene associated with antibiotic resistance. These results recommend the re-assembly of the O. nova genome and show how current sequencing databases have information to study microbial symbionts without the need for new experimentation.},
}

Animals
*Bacteriophages/genetics
Symbiosis
*Mites/microbiology/virology/genetics
*Acinetobacter baumannii/virology/genetics
*Acinetobacter/genetics/virology
Genome, Viral
Gene Transfer, Horizontal

@article {pmid41060308,
year = {2025},
author = {Yang, T and Zhang, M and Yi, Y and Wang, Y and Wang, Z and Zhang, R and Xiao, X and Jian, H},
title = {Diversity and Evolution of Prokaryotic Viral Lytic Proteins.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf200},
pmid = {41060308},
issn = {1751-7370},
abstract = {Lytic proteins, essential for viral life cycles, mediate cell lysis, driving nutrient and gene flow in ecosystems. Despite advances in understanding viral lysis mechanisms, the lytic proteins of prokaryotic viruses remain poorly understood at the macroevolutionary scale. Here, we constructed the Prokaryotic DNA Virus Lytic Protein Dataset, revealing the diversity, distribution patterns, and evolutionary drivers of lytic proteins across viral genomes. Our results demonstrate sequence and structural variation, suggesting that the composition of the lysis system is closely linked to viral genome size, host cell wall structure, and lifestyle, reflecting ecological adaptation. We observed that viral lytic proteins exhibit extensive sequence variation but retain structural conservation, suggesting a stronger selective pressure on structure that may be driven by the need to adapt and conform with specific cell envelope architectures. Phylogenetic analyses identified a significant co-evolutionary signal among lytic proteins, alongside extensive horizontal gene transfer of endolysin and holin encoding genes between bacteriophages and bacteria. These analyses also support that viral lytic proteins likely originated from bacterial sources, with different functional types having multiple independent origins. Moreover, comparative analysis of DNA and RNA virus lytic proteins demonstrates their diversity and differences across viral lineages. Revealing vast unexplored lytic proteins diversity, this study highlights their biotechnological potential against multidrug-resistant pathogens.},
}

@article {pmid41060007,
year = {2025},
author = {Gong, L and Yang, H and Wang, X and Wang, K and Yin, B and Yang, X and Ye, H and Lou, Z and Hu, T and Zhu, W and Zheng, B},
title = {Emergence of ST11 Klebsiella pneumoniae co-carrying blaKPC-2 and blaIMP-8 on conjugative plasmids.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0334524},
doi = {10.1128/spectrum.03345-24},
pmid = {41060007},
issn = {2165-0497},
abstract = {UNLABELLED: Klebsiella pneumoniae is a major pathogen with substantial antimicrobial resistance driven by β-lactamase production. The co-existence of carbapenemase genes blaKPC-2 and blaIMP-8 in the prevalent K. pneumoniae clone is rare and poses significant clinical challenges in China. In this study, we report the first identification of a clinical ST11 K. pneumoniae strain Kp4874, isolated from a hospitalized patient in China, co-carrying blaKPC-2 on a ~134 kb IncFII/IncR hybrid plasmid and blaIMP-8 on a ~75 kb untypable plasmid. Whole-genome sequencing revealed key insertion sequences, including TnAs1 and IS26, facilitating horizontal transfer of these resistance genes. Conjugation experiments confirmed the high transferability of both plasmids, particularly the blaKPC-2 plasmid. Despite harboring multiple virulence genes, the strain's clinical threat stems primarily from its multidrug-resistant profile. This study highlights the potential for rapid dissemination of such strains in healthcare settings and underscores the critical need for robust surveillance and infection control measures.

IMPORTANCE: This study is the first to report the co-existence of blaKPC-2 and blaIMP-8 in an ST11 Klebsiella pneumoniae strain, underscoring the clinical threat posed by these carbapenemase genes. The identification of blaKPC-2 on an IncFII/IncR hybrid plasmid, coupled with the successful conjugation of both resistance genes, highlights the significant potential for horizontal gene transfer and multidrug-resistant dissemination. These findings advance our understanding of plasmid-mediated resistance and emphasize the urgent need for enhanced monitoring and infection control strategies to mitigate the spread of such high-risk strains.},
}

@article {pmid41059698,
year = {2025},
author = {Cuevas-Espelid, W and Uzuegbunam, CU and Carag, JH and Hargita, MN and Page, AM and Stallworth, TC and Makkaoui, N and Satola, SW and Rouphael, NG and Sanchez, S and Dretler, AW},
title = {No evidence of multidrug-resistant Enterobacterales transmission between healthy companion animals and pet owners in the greater Atlanta area: a pilot study.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0050325},
doi = {10.1128/spectrum.00503-25},
pmid = {41059698},
issn = {2165-0497},
abstract = {Antimicrobial resistance (AMR) is a global concern affecting both animals and humans. Pets share a close bond with humans and are exposed to human-related conditions that can, in many cases, facilitate the transmission of bacteria and mobile genetic elements. This prospective observational cohort pilot study aimed to determine the prevalence of multidrug-resistant Gram-negative bacteria (MDR-GNB) colonization in healthy individuals and their companion animals (dogs and cats) in the greater Atlanta area, as well as to understand the prevalence of enteric MDR-GNB. Serial fecal samples from paired humans and their pets were collected and analyzed over a 6-month period (at 0, 2, and 6 months). Thirty-four pet owners participated, with 26 providing stool samples at all three time points. A total of 226 fecal samples were collected from owners and their pets. Seven of 26 humans and 12 of 43 animals were found to carry MDR-GNB, specifically species such as Escherichia coli, Enterobacter ludwigii, Enterobacter hormaechei, and Citrobacter pasteurii. Whole-genome sequencing revealed nine different resistance genes in E. coli isolates from pets and eight from humans, six different plasmid replicons, and all were located in four different phylogroups. Phylogenetic analysis indicates species-specific clustering based on host. Our results demonstrate that while MDR Enterobacterales were present in both humans and their pets in this Atlanta population, there was no evidence of bacterial transmission between pets and their owners during the study period. This finding contradicts previous similar studies that have shown transfer of MDR bacteria. However, it aligns with research that suggests bacterial colonization depends on the strain and the host.IMPORTANCEAntimicrobial resistance in animals, particularly pets, may serve as a potential source of antimicrobial resistance. However, a definitive pathway for the transmission of clonal bacteria or horizontal gene transfer between humans and their pets has not yet been identified. This pilot study aimed to assess the risk of multidrug-resistant (MDR) Enterobacterales transmission between healthy humans and their companion animals (dogs and cats) in the greater Atlanta area. Additionally, it sought to explore any association between MDR bacterial colonization and transmission within participating households. Despite the lack of a fully defined method of transmission, our findings demonstrated that while MDR Enterobacterales were present in both humans and their pets in this Atlanta population, there was no evidence of bacterial transmission between pets and their owners during the study period.},
}