@article {pmid42176434,
year = {2026},
author = {Li, J and Zuo, J and Yang, J and Hu, Y and Li, C and Wang, H},
title = {Elevated temperature enhances rpoE/degP-dependent bacterial membrane vesicle biogenesis and blaNDM-5 dissemination in pig-derived carbapenem-resistant Escherichia coli.},
journal = {Veterinary microbiology},
volume = {318},
number = {},
pages = {111076},
doi = {10.1016/j.vetmic.2026.111076},
pmid = {42176434},
issn = {1873-2542},
mesh = {Animals ; *Escherichia coli/genetics/drug effects ; Swine/microbiology ; Carbapenems/pharmacology ; *Hot Temperature ; Anti-Bacterial Agents/pharmacology ; *beta-Lactamases/genetics ; *Carbapenem-Resistant Enterobacteriaceae/genetics ; *Escherichia coli Proteins/genetics/metabolism ; Temperature ; *Escherichia coli Infections/veterinary/microbiology ; Gene Transfer, Horizontal ; },
abstract = {The emergence and dissemination of carbapenem-resistant Enterobacteriaceae in livestock production systems pose a serious threat to animal health and food safety. Bacterial membrane vesicles (BMVs) have recently been recognized as effective vehicles for the horizontal dissemination of antimicrobial resistance genes. However, beyond antibiotic exposure, the contribution of host-derived physiological cues associated with infection, particularly elevated temperature, modeled here as an in vitro high-temperature condition, to BMV biogenesis and vesicle-mediated resistance dissemination remains poorly understood. Here, using a pig-derived carbapenem-resistant Escherichia coli (E. coli) strain, we investigated the effects of elevated temperature conditions (37 ℃ and 42 ℃) on BMV production, vesicular DNA cargo loading, and resistance gene transfer efficiency. Exposure to elevated temperature (42 ℃) significantly increased BMV release by approximately 1.47-fold (P < 0.001) without affecting bacterial growth or vesicle size distribution. BMVs produced under elevated-temperature conditions exhibited a pronounced enrichment of the carbapenem resistance gene blaNDM-5, with vesicular gene copy numbers increasing over two-fold and vesicle-mediated transfer frequency enhanced by approximately 4-5 fold. Transcriptomic profiling revealed that elevated temperature induced a coordinated transcriptional response characterized by remodeling of cell envelope-associated functions and enhanced energy metabolism. Functional genetic analyses further identified the rpoE/degP envelope regulatory axis as a critical determinant linking elevated temperature to increased vesiculation and amplified resistance dissemination. Collectively, these findings demonstrate that elevated temperature can act as a potent non-antibiotic driver of BMV-mediated antimicrobial resistance spread in livestock-associated bacteria under in vitro conditions. These results provide new mechanistic insight into resistance dissemination under disease-relevant physiological conditions.},
}

Animals
*Escherichia coli/genetics/drug effects
Swine/microbiology
Carbapenems/pharmacology
*Hot Temperature
Anti-Bacterial Agents/pharmacology
*beta-Lactamases/genetics
*Carbapenem-Resistant Enterobacteriaceae/genetics
*Escherichia coli Proteins/genetics/metabolism
Temperature
*Escherichia coli Infections/veterinary/microbiology
Gene Transfer, Horizontal

@article {pmid42203451,
year = {2026},
author = {Ichige, R and Urabe, J},
title = {Host Genetic Constraints on the Horizontal Transmission of Daphnia-associated Microbiota.},
journal = {Microbes and environments},
volume = {41},
number = {2},
pages = {},
doi = {10.1264/jsme2.ME26003},
pmid = {42203451},
issn = {1347-4405},
mesh = {Animals ; *Microbiota ; *Daphnia/microbiology/genetics ; *Bacteria/classification/genetics/isolation & purification ; Genotype ; Symbiosis ; *Host Microbial Interactions ; *Daphnia pulex/microbiology/genetics ; Gene Transfer, Horizontal ; },
abstract = {The taxonomic composition of Daphnia microbiota is affected not only by external environmental conditions, but also by the host's internal physiological state, which is partly governed by genetic factors. However, the extent to which host genetics constrain the composition of associated bacterial communities remains unclear. In the present study, we conducted mixed-culture experiments using obligately parthenogenetic Daphnia cf. pulex individuals from genetically distinct lineages. The results obtained showed that the taxonomic composition of host-associated microbiota significantly differed between genotypes, both within and across lineages, with certain bacterial taxa being exclusive to specific genotypes. When genetically distinct hosts were co-cultured, some bacterial taxa initially exclusive to one genotype appeared in the microbiota of another, indicating the horizontal transmission of microbiota between hosts. Nevertheless, the overall taxonomic composition of microbiota was largely unaffected by the presence of genetically different hosts. These results suggest that although the horizontal transfer of microbiota occurs between different Daphnia genotypes, it is not extensive enough to override genotype-specific microbiota compositions. Therefore, in D. cf. pulex, host genetics play a major role in shaping the composition of the associated microbiota.},
}

Animals
*Microbiota
*Daphnia/microbiology/genetics
*Bacteria/classification/genetics/isolation & purification
Genotype
Symbiosis
*Host Microbial Interactions
*Daphnia pulex/microbiology/genetics
Gene Transfer, Horizontal

@article {pmid42206066,
year = {2026},
author = {Zhang, Q and Li, S and Wang, X and Sun, Y and Liu, J and Gao, J and Deng, C and Zhao, W and Ma, Y and Quan, J and Yin, Q and Jian, D and Zhang, R and Qi, R},
title = {Multi-metal contamination shapes abundance, co-occurrence, and mobility potential of resistance and virulence genes in mining-impacted soils.},
journal = {Infectious medicine},
volume = {5},
number = {2},
pages = {100260},
pmid = {42206066},
issn = {2772-431X},
abstract = {BACKGROUND: Antimicrobial resistance is a growing global public health concern, posing a serious threat to human health. This study aimed to characterize the composition and distribution of microbial communities, metal resistance genes (MRGs), antibiotic resistance genes (ARGs), and virulence factor genes (VFGs) under multi-metal stress and assess the impacts of metal and soil properties on the diversity, abundance, carrying rate (proportion of gene carriers), co-occurrence rate (proportion of microorganisms co-carrying multiple gene types), and mobility potential (MP, likelihood of horizontal gene transfer) of these genes.

METHODS: Soil samples were collected from eight sampling sites within a metal mining area (metal-contaminated soil group, MS) and four sites located more than 3 km away from the mining area (control group). Metal concentrations and physicochemical properties of the soils were measured using standard methods. Metagenomic sequencing was performed to characterize the composition and distribution of the microbiome, resistome, and virulome. Statistical modeling was applied to examine the effects of heavy metal content and soil properties on the relative abundance, co-occurrence, and mobilome potential of the three gene types.

RESULTS: Fe, V, Cr, and Cu primarily promoted the diversity, carrying rate, and co-occurrence rate of microbial communities, MRGs, ARGs, and VFGs. In contrast, Ni and Zn exhibited overall inhibitory effects. For every unit increase in Fe and V, the MP of MRGs and VFGs was associated with an increase of 3.0 × 10⁻⁵ and 1.2 × 10⁻⁵, respectively. A per 1 mg/kg increase in Cr and Cu was correlated with a decrease of 4.3 × 10⁻⁵ and 1.1 × 10⁻⁴ in the MP of ARGs and of MRGs, respectively. Positive correlations were found between the MP of plasmid‑mediated ARGs and Cr, and between transposon‑mediated ARGs and Cr/V. The MP of transposon‑mediated MRGs correlated positively with Fe, while Cu correlated negatively with plasmid‑mediated ARGs but positively with insertion sequence‑mediated ARGs. Ni concentration was positively associated with the MP of IS‑mediated VFGs.

CONCLUSIONS: Metals alter the composition and distribution of microbial communities, MRGs, ARGs, and VFGs. A key mechanism underlying this regulation is the modulation of their mobile potential, which either facilitates or restricts horizontal gene transfer.},
}

@article {pmid42207421,
year = {2026},
author = {Wang, X and Shaukat, A and Al-Rasheed, M and Ujjan, NA and Buzdar, JA and Yuan, T},
title = {Paraprobiotics in Modern Broiler Production: Stability, Safety, and Multifunctional Benefits - a Comprehensive Review.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {42207421},
issn = {1867-1314},
abstract = {The growing restrictions on in-feed antibiotics and the global rise of antimicrobial resistance have intensified the demand for safe and sustainable alternatives to support animal health and productivity. Paraprobiotics, defined as non-viable or inactivated bacterial cells, have recently emerged as a promising class of functional bioactives capable of conferring health benefits without the risks associated with live probiotics. Unlike conventional probiotics, paraprobiotics mediate their effects through intact cell structures and microbial metabolites that engage host pattern-recognition receptors, thereby modulating both innate and adaptive immune responses. This review critically examines the antimicrobial efficacy of paraprobiotics in poultry, emphasizing their mechanistic role in maintaining gut barrier integrity, regulating microbial ecology, and mitigating inflammation-induced oxidative stress. Evidence indicates that paraprobiotics suppress pathogenic colonization enhance epithelial function, stimulating antimicrobial peptide production, and improve nutrient utilization and growth performance. Moreover, their stability during feed processing, prolonged shelf-life, and minimal risk of horizontal gene transfer further enhance their suitability for large-scale, intensive production systems. Additionally, emerging inactivation technologies, optimized dosing strategies, and synergistic applications with prebiotics and phytobiotics offer avenues to maximize their functional potential. Collectively, paraprobiotics exemplify a paradigm shift in antimicrobial nutrition providing "dead cells with living functions" that combine safety, efficacy, and sustainability. Their integration into antibiotic-free poultry system hold significant promise for enhancing disease resilience, productive performance and overall sustainability of modern poultry production.},
}

@article {pmid42207801,
year = {2026},
author = {Abed, S and Beig, M and Soltani, S and Pahlevani, M and Speck, P and Shafiei, M and Shahraki, AH and Ghorbani, A},
title = {Genomic and functional characterization of a novel halophilic bacteriophage targeting carbapenem-resistant Klebsiella pneumoniae.},
journal = {PloS one},
volume = {21},
number = {5},
pages = {e0348054},
doi = {10.1371/journal.pone.0348054},
pmid = {42207801},
issn = {1932-6203},
mesh = {*Klebsiella pneumoniae/virology/drug effects ; Animals ; *Bacteriophages/genetics/isolation & purification/physiology ; Genome, Viral ; *Carbapenems/pharmacology ; Mice, Inbred BALB C ; Mice ; *Klebsiella Infections/therapy/microbiology ; Genomics ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a multidrug-resistant (MDR) pathogen causing severe infections in immunocompromised patients, prompting the exploration of alternative therapies like bacteriophage therapy. In this study, we isolated and characterized a novel halophilic lytic bacteriophage, Halo KS-7, targeting K. pneumoniae, and used an AI-driven annotation pipeline in Python to analyze its genome and therapeutic potential. Bacteriophages were isolated from Hospital wastewater, purified through plaque isolation, and confirmed using the double-layer agar method. Morphological analysis via transmission electron microscopy (TEM) and plaque assays assessed lytic activity. In vitro assays, including one‑step growth curve and MOI determination, were performed to evaluate the replication kinetics and lytic activity of bacteriophage Halo KS‑7 against carbapenem‑resistant Klebsiella pneumoniae. In vivo efficacy was assessed using a BALB/c mouse wound infection model by monitoring wound contraction and performing blinded histopathological analysis following phage treatment. DNA sequencing was done using Illumina HiSeq 2000, followed by genome assembly, AI-guided annotation, gene prediction, protein function classification, and comparative genomics using CLC Genomics Workbench. We also evaluated host range, temperature stability, pH sensitivity, and salt stress tolerance to assess therapeutic potential. Halo KS-7 exhibited strong lytic activity against CRKP and was classified as a Myoviridae bacteriophage by TEM. Phenotypic assays demonstrated optimal activity at 37 °C and neutral pH, effective activity from pH 4-10, and enhanced performance in high-salinity conditions. Bacteriophage Halo KS-7 exhibited a short latent period (~20 min), a modest burst size (5.73 PFU/cell), and optimal antibacterial activity at MOI 0.1, resulting in sustained suppression of K. pneumoniae growth in vitro. In vivo, Halo KS-7 treatment significantly enhanced wound healing in infected BALB/c mice, achieving near-complete wound closure, effective infection control, and improved histopathological regeneration comparable to uninfected controls. Halo KS-7 have 58.716 kb linear dsDNA genome (44.4% G + C), contains 49 predicted ORFs, lacks integrase, lysogeny, or antibiotic-resistance genes, and includes three tRNA genes (tRNATyr, tRNAPro, and tRNAAsn). It also includes a toxin gene and auxiliary factors like MazG, pyrophosphatase, and HNH endonucleases that enhance bacterial killing without promoting horizontal gene transfer or resistance. Functional annotation assigned ~65% of ORFs to structural, replication, and packaging roles. Comparative genomics showed moderate similarity to other Myoviridae but with distinct accessory features, emphasizing its novelty and therapeutic value. Halo KS-7 is a novel, strictly lytic bacteriophage with strong antibacterial activity and stress resilience, supporting its use as a promising biocontrol agent against CRKP and its potential for clinical development in managing MDR infections.},
}

*Klebsiella pneumoniae/virology/drug effects
Animals
*Bacteriophages/genetics/isolation & purification/physiology
Genome, Viral
*Carbapenems/pharmacology
Mice, Inbred BALB C
Mice
*Klebsiella Infections/therapy/microbiology
Genomics
Anti-Bacterial Agents/pharmacology

@article {pmid42208292,
year = {2026},
author = {Majumdar, A and Bagchi, D and Kotta-Loizou, I and Buck, M},
title = {The One Health resistome: Integrating environmental, microbial, and human antimicrobial resistance surveillance and risk analysis in the digital age.},
journal = {Journal of hazardous materials},
volume = {513},
number = {},
pages = {142431},
doi = {10.1016/j.jhazmat.2026.142431},
pmid = {42208292},
issn = {1873-3336},
abstract = {Antimicrobial resistance (AMR) and antibiotic resistance (ABR) represent one of the most pressing global health threats, driven by the complex interplay between human, animal, and environmental factors. The One Health resistome framework recognises that resistance genes circulate continuously across clinical, agricultural, and environmental compartments through horizontal gene transfer, co-selection mechanisms, and anthropogenic contamination. This comprehensive review synthesises current evidence on integrated AMR surveillance, examining how digital technologies are transforming our capacity to monitor, predict, and respond to resistance emergence. Key advances include whole-genome sequencing enabling high-resolution pathogen tracking, metagenomics revealing environmental resistome diversity, machine learning algorithms predicting resistance phenotypes with > 85% accuracy, and point-of-care diagnostics extending sophisticated testing to resource-limited settings. Geographic information systems facilitate spatial hotspot identification, while wastewater-based surveillance provides early warning capabilities, detecting resistance genes before clinical manifestation. Despite technological progress, substantial challenges persist: fragmented data streams across sectors, lack of standardised environmental monitoring methods, limited laboratory capacity in low- and middle-income countries, and chronic underfunding. Emerging technologies, portable nanopore sequencing, CRISPR-based diagnostics, artificial intelligence, and blockchain-enabled data governance promise to address these gaps. Realising comprehensive One Health resistome surveillance requires sustained investment in interoperable digital infrastructure, international standardisation, capacity building, and political commitment to cross-sectoral coordination, prioritising equitable global implementation.},
}

@article {pmid42209562,
year = {2026},
author = {Wijaya, AJ and Anžel, A and Hattab, G},
title = {Evaluating ensemble learning approaches for horizontal gene transfer detection.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42209562},
issn = {2045-2322},
mesh = {*Gene Transfer, Horizontal ; Ensemble Learning ; *Genomic Islands/genetics ; *Machine Learning ; Genomics/methods ; Computational Biology/methods ; Classification Algorithms ; },
abstract = {Horizontal gene transfer (HGT) is widely recognized as a major driver of antimicrobial resistance (AMR) dissemination, with genomic islands (GIs) as one of the drivers facilitating the spread. Detecting GIs is essential for improving AMR surveillance. Numerous computational approaches have been developed for GIs detection, including recent advances in machine learning (ML). Several studies in other fields have shown that ML model performance depends on data representations. Combining multiple data representations in ensemble learning has been shown to improve performance in other genomics tasks. However, this approach has not yet been evaluated for GIs detection. To this end, we investigate the efficacy of integrating diverse data representations in ensemble learning for GIs detection, particularly for classification task. Then, we assess its applicability to localizing GIs, which are clusters of genes acquired through HGT, in a genomic sequence. We implemented a two-stage ensemble selection strategy to determine the optimal combination of data representations. Our ensemble selection strategy reveals that combining low-correlated data representations in an ensemble classifier yields a slightly higher Recall than individual representation for the classification task, but the improvement is not statistically significant. Nevertheless, the ensemble classifier could not localize GIs better, suggesting that the cross-task generalizability remains constrained. This finding presents an opportunity for future research to advance the field by redefining the problem formulation of GIs detection.},
}

*Gene Transfer, Horizontal
Ensemble Learning
*Genomic Islands/genetics
*Machine Learning
Genomics/methods
Computational Biology/methods
Classification Algorithms

@article {pmid42213201,
year = {2026},
author = {Pal, A and Chaki, MG},
title = {Operonic architecture of bacterial metal response: envelope constraints, evolutionary mobility, and bioremediation design rules.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {6},
pages = {},
pmid = {42213201},
issn = {1573-0972},
mesh = {*Metals/metabolism ; *Bacteria/genetics/metabolism ; Biodegradation, Environmental ; *Operon/genetics ; Gene Expression Regulation, Bacterial ; Cell Membrane/metabolism ; Homeostasis ; Gram-Negative Bacteria/genetics/metabolism ; Evolution, Molecular ; Bacterial Proteins/genetics/metabolism ; Cell Wall/metabolism ; },
abstract = {Bacteria encounter metals as both essential micronutrients and persistent toxins. These conflicting requirements are managed by genetic components, often organized as operons or coordinated regulons, which link sensing to trafficking, buffering, export, detoxification, biotransformation, and, in certain instances, storage. This review develops a gene-organization-focused perspective on bacterial metal responses, emphasizing metallostasis, resistance, envelope topology, evolutionary mobility, and bioremediation relevance, highlighting two key principles. Firstly, metallostasis maintains homeostatic set-points for essential metals by regulating uptake, allocation, and overflow. Secondly, the cell envelope's topology serves as a primary constraint. In contrast, resistance mechanisms for toxic metals and metalloids strive to achieve near-zero intracellular concentrations by facilitating rapid clearance. Gram-negative bacteria often employ compartmental "handoff" strategies that connect cytosolic relief to high-capacity envelope clearance. Conversely, Gram-positive envelopes tend to favor responses that involve inner-membrane export, along with cytosolic or cell wall buffering. This review structures the components into a modular toolkit, encompassing sensors and regulators, uptake control, exporters and clearance pumps, periplasmic partners, detoxification enzymes, and the dichotomy between sequestration and storage. It further seeks to link recurring architectures to evolutionary mobility and co-selection with antibiotic resistance. Ultimately, these insights are applied to bioremediation.},
}

*Metals/metabolism
*Bacteria/genetics/metabolism
Biodegradation, Environmental
*Operon/genetics
Gene Expression Regulation, Bacterial
Cell Membrane/metabolism
Homeostasis
Gram-Negative Bacteria/genetics/metabolism
Evolution, Molecular
Bacterial Proteins/genetics/metabolism
Cell Wall/metabolism

@article {pmid41975425,
year = {2026},
author = {Di Pierro, F and Thacharodi, A and Kumaraswami, M and Suvorov, A and Zupet, J and Zerbinati, N},
title = {From lab to law: emerging applications, potential benefits, evolving regulatory framework and challenges for engineered probiotics.},
journal = {Microbial cell factories},
volume = {25},
number = {1},
pages = {},
pmid = {41975425},
issn = {1475-2859},
abstract = {UNLABELLED: Engineered probiotics are emerging as versatile biological platforms capable of delivering therapeutic functions, modulating host–microbiota interactions, and enabling innovative strategies for preventing or treating metabolic, infectious, and inflammatory conditions. Advances in synthetic biology have expanded microbial engineering along a continuum ranging from self-cloned or intragenic modifications—based on deletions or recombination events that recapitulate naturally plausible genomic changes—to fully transgenic constructs expressing heterologous bacterial, viral, or human genes. This technological diversity demands proportionate and mechanistically informed safety evaluation, with particular emphasis on genetic stability, ecological compatibility, and the potential for horizontal gene transfer (HGT). This review examines the principal applications of engineered probiotics in human health, including strains designed to enhance endogenous functions, eliminate detrimental activities, neutralize toxins, interfere with pathogen signaling, degrade biofilms, express therapeutic proteins, act as mucosal vaccine platforms, serve as tumor-targeted immunotherapeutic vectors, or enable emerging systemic and brain-directed delivery strategies. We also highlight the current regulatory heterogeneity across international frameworks and discuss the relevance of recent EFSA guidance, which clarifies that modifications involving only deletions or the reinsertion of native sequences may entail markedly different regulatory obligations compared with constructs carrying truly novel genetic traits. To promote regulatory convergence, we propose a unified safety-assessment framework that integrates classical toxicological testing with a construct-specific evaluation of HGT potential. This approach combines whole-genome sequencing to define the engineered locus, validated qPCR assays for highly specific detection, and controlled exposure experiments using competent microbiota and environmental recipient strains to quantify the extremely low probability of gene transfer under worst-case conditions. Such a structured methodology provides a scalable, evidence-driven basis for evaluating engineered probiotics according to the biological nature of the modification rather than a one-size-fits-all model. Engineered probiotics hold substantial translational promise, provided that safety assessments remain adaptive, risk-proportionate, and aligned with mechanistic understanding of microbial genetics and ecology.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12934-026-02997-w.},
}

@article {pmid42198949,
year = {2026},
author = {Durão, P and Cardoso, LL and Martins, LO},
title = {Ecological Context Shapes Resistance Selection Under Antibiotic Pollution.},
journal = {Environmental microbiology},
volume = {28},
number = {6},
pages = {e70333},
doi = {10.1111/1462-2920.70333},
pmid = {42198949},
issn = {1462-2920},
support = {2021.00778.CEECIND/CP1657/CT0009//Fundação para a Ciência e a Tecnologia/ ; UIDB/04612/2020//Fundação para a Ciência e a Tecnologia/ ; UIDP/04612/2020//Fundação para a Ciência e a Tecnologia/ ; },
mesh = {*Anti-Bacterial Agents/pharmacology ; *Selection, Genetic ; *Drug Resistance, Bacterial ; *Bacteria/drug effects/genetics ; *Environmental Pollution ; *Drug Resistance, Microbial ; Microbial Interactions ; Gene Transfer, Horizontal ; },
abstract = {Anthropogenic activities such as pharmaceutical manufacturing, antibiotic use, and waste disposal have increased environmental antibiotic contamination, exposing natural microbial communities to concentrations ranging from sub-inhibitory to strongly selective levels. While antibiotic pollution is widely assumed to promote antimicrobial resistance (AMR), the ecological conditions under which environmental exposure leads to measurable community-level selection remain poorly understood. Here, we integrate eco-evolutionary principles with measured environmental antibiotic concentrations to examine how ecological context shapes the emergence, maintenance, and spread of resistance across environments. We discuss how environmental conditions modulate mutation, horizontal gene transfer, fitness costs, epistasis, and compensatory evolution under antibiotic exposure, and how microbial interactions can either buffer or amplify resistance selection within communities. We further examine how co-selection, environmental heterogeneity, antibiotic degradation products, and alternative ecological functions of antibiotics influence resistance dynamics. Together, these observations support the view that resistance selection thresholds are not fixed concentrations, but ecologically dependent properties shaped by environmental conditions, community composition, and microbial interactions.},
}

*Anti-Bacterial Agents/pharmacology
*Selection, Genetic
*Drug Resistance, Bacterial
*Bacteria/drug effects/genetics
*Environmental Pollution
*Drug Resistance, Microbial
Microbial Interactions
Gene Transfer, Horizontal

@article {pmid42200512,
year = {2026},
author = {Vergara, E and Khaleque, HN and Neira, G and Watkin, ELJ and Valdés, JH and Holmes, DS},
title = {Sulphur metabolism as a key factor in the evolution of environmental adaptation of Acidihalobacter.},
journal = {Microbial genomics},
volume = {12},
number = {5},
pages = {},
doi = {10.1099/mgen.0.001732},
pmid = {42200512},
issn = {2057-5858},
mesh = {Phylogeny ; *Sulfur/metabolism ; *Adaptation, Physiological/genetics ; *Rhodobacteraceae/genetics/metabolism/classification ; Genome, Bacterial ; Evolution, Molecular ; Hydrothermal Vents/microbiology ; Australia ; Oxidation-Reduction ; Italy ; Metagenome ; Pacific Ocean ; Bacterial Proteins/genetics/metabolism ; },
abstract = {This study compares predicted sulphur metabolism genes across four Acidihalobacter type strains and two metagenome-assembled genomes (MAGs), revealing genomic differences that appear to correspond to ecological specialization. Phylogenomic analysis separates the species into two clades: clade I includes Acidihalobacter ferrooxydans from a geothermal region in Italy and the two MAGs derived from deep-sea hydrothermal vents in the Pacific Ocean, while clade II comprises Acidihalobacter aeolianus and Acidihalobacter prosperus from a geothermal region in Italy and Acidihalobacter yilgarnensis from a saline and acidic drainage in Australia. Variations in sulphide/quinone oxidoreductases (SQRs) across the species, in particular in Ah. ferrooxydans and Ah. yilgarnensis, likely relate to the availability and speciation of sulphur substrates, which are strictly governed by local redox potential (Eh) and metal redox cycling in their respective habitats. Notably, only Ah. ferrooxydans (clade I) lacks the canonical sulphur/thiosulphate oxidation (Sox) system for thiosulphate oxidation found in clade II and instead encodes components of an alternative S4I pathway. We hypothesize that this difference reflects an adaptation to dynamic microniches going from highly reduced (sulphide-rich) to oxidized metastable sulphur intermediates. In contrast, the retention of the Sox system in clade II suggests a distinct strategy permitting greater metabolic versatility under fluctuating Eh-pH conditions.Differences in clade I terminal oxidases (cbb3-type cytochrome, bc1 complex) and regulatory elements appear to support further adaptation to environments with elevated H2S, setting this clade apart from clade II members. These adaptations, mainly evidenced by gene redundancy, gene loss and horizontal gene transfer, seem to reflect a unique ecological microniche and evolutionary trajectory for Ah. ferrooxydans distinct from other members of the genus, particularly from a sulphur-based energy metabolism perspective.},
}

Phylogeny
*Sulfur/metabolism
*Adaptation, Physiological/genetics
*Rhodobacteraceae/genetics/metabolism/classification
Genome, Bacterial
Evolution, Molecular
Hydrothermal Vents/microbiology
Australia
Oxidation-Reduction
Italy
Metagenome
Pacific Ocean
Bacterial Proteins/genetics/metabolism

@article {pmid42186200,
year = {2026},
author = {Diaz-Amigo, C and Bartolomé Del Pino, LE and Lejeune, J and Pinto Ferreira, J and Bessy, C},
title = {Antimicrobial resistance and the human gut microbiome-a food safety perspective.},
journal = {Critical reviews in food science and nutrition},
volume = {},
number = {},
pages = {1-29},
doi = {10.1080/10408398.2026.2629533},
pmid = {42186200},
issn = {1549-7852},
abstract = {The gastrointestinal environment is where the resident gut microbiome encounters foodborne microorganisms, antimicrobial resistance genes (ARGs), and bioactive substances from food, all of which may influence the acquisition and dissemination of antimicrobial resistance (AMR). Although resistant bacteria and ARGs are frequently detected in food and food production environments, their contribution to the gut resistome remains unclear. Most ingested microbes are transient and constrained by ecological barriers; however, the conditions that enable horizontal gene transfer in vivo are not well characterized. Multiple factors (e.g., microbial composition and density, the presence of mobile genetic elements, antimicrobial residues, and host physiology) can modulate ARG persistence and mobility, but their relative impact within the gut ecosystem and its associated resistome needs to be better understood. Resistance acquisition also depends on fitness costs and adaptive responses within complex microbial communities. Methodological variability and limited in vivo data further limit comparability and interpretation. This review summarizes current knowledge of AMR dynamics in the gut following dietary exposure and highlights significant knowledge gaps that limit our understanding of factors influencing ARG transfer and persistence in the gastrointestinal environment. Reducing these uncertainties is crucial for strengthening AMR risk assessment and designing more effective mitigation strategies.},
}

@article {pmid42186476,
year = {2026},
author = {Shao, L and Li, S and Yang, L and Wei, S and Shen, G and Shi, L and Zhu, J and Ding, B and Liu, Y and Shi, Y and Liu, Y},
title = {Analysis of microbial structure and function in fermented grains during the fermentation process of Congjiang WeiJiu based on high-throughput sequencing.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e21180},
pmid = {42186476},
issn = {2167-8359},
mesh = {*Fermentation ; High-Throughput Nucleotide Sequencing ; China ; *Microbiota ; *Alcoholic Beverages/microbiology ; *Edible Grain/microbiology ; },
abstract = {BACKGROUND: WeiJiu was a traditional specialty liquor from the Zhuang ethnic villages in Congjiang County, Qiandongnan Miao and Dong Autonomous Prefecture, Guizhou Province. It was brewed using glutinous Xianghe rice, mountain spring water, and ancestral koji as raw materials. Its core production processes consist of five stages: (1) raw material preparation; (2) spreading, cooling and yeast mixing; (3) fermentation and liquor extraction; (4) simmering treatment; (5) sealing and aging. WeiJiu had a dark brown color, a mellow, soft, and sweet taste, and featured the characteristic of becoming more aromatic as it ages. As an intangible cultural heritage item of Qiandongnan Prefecture, its craftsmanship inheritance had long been confined to an empirical paradigm. Due to the lack of research on the composition and function of the microbial community in Congjiang WeiJiu, the microbial changes and metabolite changes during the fermentation process, its quality characteristics and brewing mechanism remain unclear. Therefore, in-depth understanding of the brewing mechanism and essentially improving its quality and production was an urgent priority for research related to Congjiang WeiJiu.

METHOD: In this study, the fermented grains of Congjiang WeiJiu at various fermentation stages: CQ: early fermentation stage (7 d), ZQ: middle fermentation stage (11 d) and WQ: late fermentation stage (15 d) were used as the research objects. High-throughput sequencing technology was employed to analyze microbial community structure and diversity. Functional annotations were performed against KEGG and CAZys databases to explore metabolic pathways and carbohydrate-active enzyme (CAZys) characteristics.

RESULTS: The microbial community exhibited significant stage-specific succession synchronized with fermentation processes. At the phylum level, Bacillota and Pseudomonadota dominated in CQ, Bacillota became predominant in ZQ, and Actinomycetota increased significantly in WQ. At the genus level, Aspergillus, Saccharomyces, and Hyphopichia served as core functional genera in respective stages. Functional annotations showed stage-specific expression of metabolic pathways: KEGG pathways focused on energy and amino acid metabolism (in CQ), carbohydrate metabolism (in ZQ), and stress adaptation (in WQ). CAZys families corresponded to fermentation substrates degradation (GH28, AA1 in CQ), macromolecule conversion (GH13, CBM50 in ZQ), and metabolite modification (GH18, GH16 in WQ). Core functional bacteria enhanced adaptability through evolutionary mechanisms such as horizontal gene transfer, genome streamlining, and plasmid-mediated gene acquisition. The unique simmering process and smoked cellar storage shaped the distinct microbial community and flavor, differing from traditional Luzhou-flavor liquor in yeast succession, lactic acid bacteria metabolism, and mold survival period.},
}

*Fermentation
High-Throughput Nucleotide Sequencing
China
*Microbiota
*Alcoholic Beverages/microbiology
*Edible Grain/microbiology

@article {pmid42186547,
year = {2026},
author = {Zhang, Q and Gentekaki, E and Leger, MM and Zou, S and Zhang, GA and Omar, A and Fu, Y and Gong, J},
title = {Single-cell transcriptomics reveals lateral transfers of multiple functional genes from prokaryotes to free-living ciliated protists in detrital food webs.},
journal = {Marine life science & technology},
volume = {8},
number = {2},
pages = {352-370},
pmid = {42186547},
issn = {2662-1746},
abstract = {UNLABELLED: Lateral gene transfer (LGT) is a key driver of evolutionary innovation, underlying protists' lifestyles and interactions in anaerobic environments. Yet, its significance in free-living protists remains underexplored. Here, we address this gap by presenting the first single-cell transcriptomes of Metopus yantaiensis and genome-wide LGT screens across 36 omics datasets from nine anaerobic APM ciliates (classes Armophorea, Muranotrichea, and Parablepharismea)-a group in soil/sediment environments. Through phylogenetic analyses and validation testing, we identified 63 candidate prokaryotic LGT genes preferentially enriched in APM ciliates. Among these, 19 form interconnected pathways for degrading complex organics (polysaccharides, amino sugars); their high diversity and completeness are rarely seen in reported protist LGTs. A rare fused gene (arcC-OTC) and two novel genes (acs, ME2) were exclusively identified in APM ciliates, with their potential as the first evidence of LGT-mediated carbon metabolite retention and ammonia assimilation in phagotrophic protists inferred. Notably, 27 LGTs (including arcC-OTC, acs, and ME2) trace to candidate phyla radiation (CPR) bacteria or described prokaryotes, marking the first CPR-to-eukaryote LGT documentation. Collectively, these 63 LGTs are predicted to enhance nutrient utilization (complex organics, other carbon metabolites, inorganic elements), bioenergetic efficiency, and stress resistance (heavy metals, oxygen), facilitating soil/sediment adaptation. Overall, our results highlight lateral prokaryotic gene acquisition may be key for free-living anaerobic ciliates' adaptation to new environments, shedding light on protists' evolutionary dynamics and ecological roles.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-026-00382-5.},
}

@article {pmid42192676,
year = {2026},
author = {Hassen, KA and Fafetine, J and Augusto, L and Mandomando, I and Garrine, M and Marcos, R and Sileshi, GW},
title = {Mobile Genetic Elements Associated with Antimicrobial Resistance Across One Health Interfaces in Africa: A Systematic Review and Meta-Analysis.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {5},
pages = {},
doi = {10.3390/antibiotics15050456},
pmid = {42192676},
issn = {2079-6382},
support = {500003545//Centre of Excellence in Agri-Food Systems and Nutrition (CE-AFSN), Eduardo Mondlane Univer-sity/ ; },
abstract = {Background: High infectious disease burden and uncontrolled antibiotic usage across human, animal, and environmental contaminants make antimicrobial resistance (AMR) a growing public health problem in Africa. Mobile genetic elements (MGEs) such plasmids, transposons, integrons, conjugative elements, and phages help spread AMR via horizontal gene transfer (HGT) across human, animal, food, and environmental sources. Despite growing evidence for antibiotic resistance genes (ARGs), Africa lacks a one-health-focused synthesis of mobile genetic element-mediated AMR. Objective: This systematic review and meta-analysis aimed to consolidate information on MGEs and ARGs in AMR dissemination throughout Africa's one health interface. Methods: The literature was searched using PubMed, Scopus, and ScienceDirect. Observational. molecular epidemiology, whole genome sequencing (WGS), and metagenomic investigations of MGE-associated AMR in Africa were eligible. The study selection, data extraction, and quality assessment were performed by two independent reviewer and quality was graded using ROBVIS 2 utilizing Rayyan software. Narrative synthesis, random-effect meta-analysis, subgroup analysis, and meta-regression were utilized. Results: A total of 109 studies were included, with 91 studies contributing to the meta-analysis. MGEs reported were plasmids (71.7%) and integrons (54.8%). ARGs carried by MGEs were blaCTMX-M-15 (78.6%), Sul2 (69.6%), blaTEM (59.1%), and tetA (49.9%). Horizontal gene transfer was seen in 259 instances; however, transmission was unclear. In 442 observations, transmission pathways across human, animal, and environmental interfaces showed AMR prevalence of 75.1% in human, 98.0% in human-animal, and 61.3% in one health interface. Whole-genome sequencing was the most frequently used method for detecting MGEsThe pooled pathogen and AMR prevalence rates were 73.3% (95% CI: 60.5-83.7%) and 94% (95% CI: 85-98%), with significant heterogeneity (I[2] = 97.8% and 97.4%, respectively). The prevalence of Escherichia coli was 93% and Salmonella enterica 85% in subgroup analysis. Fluoroquinolones, aminoglycosides, and beta-lactams were prevalent in humans (89.7%) and human-animal interactions (98.0%) according to AMR Class. Conclusions: Horizontal gene transfer has propagated MGE-mediated antimicrobial resistance across human, animal, and environmental interfaces in Africa. To combat AMR in Africa, coordinated, genomics-informed One Health surveillance and antibiotic stewardship are needed. Due to variability and publication bias, these data should be considered cautiously. Pooled data may only show descriptive patterns, and not necessarily precise continent-wide prevalence estimates.},
}

@article {pmid42192724,
year = {2026},
author = {Skotareva, AE and Sokolova, EA and Voronina, EN},
title = {West Siberian Soil Resistome: Mobile Antibiotic Resistance in Agricultural Microbiomes.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {5},
pages = {},
doi = {10.3390/antibiotics15050502},
pmid = {42192724},
issn = {2079-6382},
support = {125012300671-8//Russian state-funded project/ ; },
abstract = {Background/Objectives: Soil microbiomes in agroecosystems are natural reservoirs of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), creating conditions for horizontal gene transfer (HGT) to clinically relevant bacteria. Southern West Siberia-a globally significant grain-producing region-lacks metagenomic characterization of its soil resistome. This study aimed to establish the first baseline profile of resistome and mobilome composition for West Siberian agricultural soils. Methods: Twelve composite soil samples were collected from agroecosystems under seven crop types across diverse soil types in southern West Siberia (September 2022). Shotgun metagenomics was performed on an Illumina NovaSeq 6000 platform. Taxonomic profiling used Kraken2/Bracken; ARG annotation used Prokka/DeepARG (identity ≥ 70%, probability score ≥ 0.8); while MGE characterization used Platon, HMMER v3.3.2, and Prokka-based integrase annotation. Resistome load was normalized to the single-copy housekeeping gene rpoB; ARG-MGE associations were defined as co-localization within 10 kb on the same contig. Results: Microbial communities were dominated by Pseudomonadota and Bacillota, with a stable core of Streptomycetaceae, Nitrobacteraceae, and Sphingomonadaceae. Normalized resistome load (N/rpoB 2.30-5.37) indicated moderate anthropogenic pressure. Dominant ARGs included efflux pumps (emrA, drrA, tetA, bcr, fsr), target modification (lnrL), and lipid A modification (arnA) genes. Class 1 integron integrase (intI1/rpoB 0.64-1.59) was detected in all 12 samples, exceeding unity in 9 of 12. ARG-MGE co-localizations were found in 11 of 12 samples. In sample Mg_155, genes emrA-emrB and bcr (NODE_16) and arnA and lnrL (NODE_6) were each independently associated with distinct prophage IntA integrase copies within Pseudomonas contigs, documenting multiple parallel horizontal transfer events encompassing resistance to five antibiotic classes. Conclusions: This work establishes the first metagenomic baseline of resistome and mobilome for West Siberian agroecosystems. The obtained data indicate moderate anthropogenic pressure on soil microbiomes, consistent with temperate agricultural systems with limited organic fertilizer input. The detected ARG-MGE co-localizations and evidence of prophage-mediated transfer of resistance determinants beyond their natural hosts suggest that mobilization potential in the region warrants consideration in future AMR monitoring programs.},
}

@article {pmid42192737,
year = {2026},
author = {Balasubramanian, B and Shanmugam, S and Kim, IH},
title = {Companion Dogs and Cats as Key Reservoirs of Antimicrobial Resistance: Evidence and One Health Implications.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {5},
pages = {},
doi = {10.3390/antibiotics15050515},
pmid = {42192737},
issn = {2079-6382},
abstract = {Antimicrobial resistance (AMR) in companion animals is an escalating concern at the interface of veterinary medicine and public health. Dogs and cats, the most commonly treated companion species, are frequently prescribed antimicrobials for dermatological, otic, urinary, and respiratory infections-often involving drug classes that are critically important in human medicine. This overlap underscores the need for judicious use and integrated stewardship within a One Health framework. This narrative review synthesizes current evidence on AMR in companion animals and its implications for One Health. Studies were included if they reported AMR in dogs and cats and addressed zoonotic aspects. Staphylococcus pseudintermedius, S. aureus, Escherichia coli, Pseudomonas aeruginosa, and Enterococcus sp. are examples of clinically significant organisms that are becoming more resistant to several antibiotic classes, which can result in treatment failures and extended illness. Horizontal gene transfer facilitates the spread of resistance determinants across bacterial populations. Improved surveillance systems, prudent antibiotic use, regular culture and susceptibility testing, and enhanced antimicrobial stewardship in veterinary practice are just a few of the many strategies needed to address AMR in companion animals. The integration of companion animals into AMR surveillance, stewardship programs, and infection control strategies is essential. Coordinated One Health interventions are urgently required to mitigate the spread of AMR.},
}

@article {pmid42197392,
year = {2026},
author = {Jiang, RH and Liu, ZK and Han, B and Liao, DN and Li, JY and Wu, Y},
title = {Molecular Epidemiology of the blaCTX-M Gene in Escherichia coli from a Pig Farm: Antimicrobial Resistance Profiles, Genetic Background, and Its Horizontal Transfer and Environmental Dissemination.},
journal = {Microorganisms},
volume = {14},
number = {5},
pages = {},
doi = {10.3390/microorganisms14051007},
pmid = {42197392},
issn = {2076-2607},
support = {Project No.: S202410537038//Hunan Provincial College Student Innovation Training Program/ ; Grant No.QL20230182//Hunan Province graduate scientific research innovation project/ ; },
abstract = {This study investigated the epidemiology, antimicrobial resistance, and transmission risks of β-lactamase, cefotaxime-hydrolyzing, Munich (blaCTX-M)-positive Escherichia coli (CTX-M-EC) in large-scale pig farms in Jiangxi Province (China). In total, 278 samples (manure, wastewater, drinking water, and flies) were collected. CTX-M-EC strains were isolated and analyzed using antimicrobial susceptibility testing, resistance gene profiling, multilocus sequence typing, and genetic environment analysis with gene transfer assessed by transduction experiments. Twenty-seven CTX-M-EC strains (9.71%) were isolated, all exhibiting multi-drug resistance with 100% resistance to cefotaxime, ciprofloxacin, and tetracycline, and >90% resistance to ceftazidime, florfenicol, and trimethoprim-sulfamethoxazole. Four blaCTX-M subtypes were identified. blaCTX-M-55 was the predominant subtype (70.37%) and was distributed across diverse sequence types and serotypes. Each strain harbored multiple antibiotic resistance genes, plasmids, and virulence genes. Mobile elements such as ISEcp1 and IS26 were detected surrounding the blaCTX-M gene, and 96.29% of strains successfully transferred the blaCTX-M gene via transduction. Clones highly homologous to pig manure strains were detected in flies and sewage, suggesting that this resistance gene can spread between animals, the environment, and vectors. These findings highlight the high transmission risk of blaCTX-M and underscore the need for rational antibiotic use, waste management, and vector control within a One Health framework.},
}

@article {pmid42197441,
year = {2026},
author = {Zhou, Y and Xi, R and Wang, S and Li, B and Wu, Y and Wen, C and Zhang, D},
title = {Antimicrobial Susceptibility and Characterization of Extended-Spectrum β-Lactamases in Escherichia coli Isolated from Buffalo Mastitis Milk in Guangdong Province, China.},
journal = {Microorganisms},
volume = {14},
number = {5},
pages = {},
doi = {10.3390/microorganisms14051055},
pmid = {42197441},
issn = {2076-2607},
support = {31772795//National Natural Science Foundation of China/ ; },
abstract = {Antimicrobial resistance (AMR) in Escherichia coli (E. coli) from food-producing animals constitutes a substantial public health concern. This study characterized antimicrobial resistance profiles, phylogenetic diversity, virulence-gene distribution, and plasmid-borne extended-spectrum β-lactamase (ESBL) determinants of E. coli isolates recovered from water buffaloes with subclinical mastitis. Among the 54 ESBL-producing E. coli isolates, all were resistant to ampicillin and cefotaxime. High resistance rates were also observed for cephalothin (75.9%), trimethoprim-sulfamethoxazole (74.0%), ceftiofur (70.4%), florfenicol (68.5%), and cefazolin (63.0%). Lower resistance was recorded for colistin sulfate (40.7%), enrofloxacin (33.3%), and gentamicin (25.9%). Phylogenetic analysis of ESBL producers identified phylogroup B1 (42.6%) as predominant, followed by groups A (29.6%) and D (25.9%). Multilocus sequence typing (MLST) revealed that ST50 (20.4%) was the most common sequence type, and serogroup O150 was dominant (70.4%). Virulence genes, such as iss (81.5%), astA (59.3%), and espP (38.9%), were frequently detected among ESBL isolates. ESBL genes were predominantly blaCTX-M-1 (27.8%) in all isolates, while the narrow-spectrum β-lactamase genes blaTEM-1 (55.6%) and blaOXA-10 (14.8%) were also commonly co-detected. Bioinformatic analysis predicted that all ESBL genes were associated with plasmid-derived contigs, with the predicted plasmid size ranging from approximately 32 to 187 kb and belonging to IncFIB, IncFIA, IncI1, IncFIA + I1, and IncFII replicon types. Conjugation frequencies ranged from 4.8 × 10[-7] to 4.1 × 10[-2], and plasmids were predicted to carry additional resistance genes mediating resistance to chloramphenicol (floR), sulfonamides (sul1, sul3), tetracyclines (tet(A) and tet(B)), and trimethoprim (dfrA1, dfrA12). The co-carriage of ESBL genes with additional antimicrobial resistance and virulence determinants suggests the potential role of water buffaloes as reservoirs of clinically relevant resistance traits that may disseminate through horizontal gene transfer.},
}

@article {pmid42198651,
year = {2026},
author = {Popa, I and Iancu, I and Popa, SA and Gligor, A and Imre, K and Tîrziu, E and Bochiș, T and Pop, C and Degi, J and Ivan, AA and Dahma, M and Plotuna, AM and Pentea, M and Herman, V and Nichita, I},
title = {Antimicrobial Resistance in Veterinary Bacterial Pathogens: Resistance Patterns, Zoonotic Risks and One Health Implications.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {5},
pages = {},
doi = {10.3390/pathogens15050525},
pmid = {42198651},
issn = {2076-0817},
mesh = {Animals ; Humans ; *One Health ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; *Zoonoses/microbiology ; *Bacterial Zoonoses/microbiology/transmission ; *Bacteria/drug effects/genetics ; *Drug Resistance, Bacterial ; *Drug Resistance, Multiple, Bacterial ; *Bacterial Infections/microbiology/veterinary ; Gene Transfer, Horizontal ; Livestock/microbiology ; },
abstract = {Antimicrobial resistance (AMR) has emerged as one of the most significant global health challenges affecting both human and veterinary medicine. The growing prevalence of resistant bacterial strains in livestock and companion animals not only compromises treatment efficacy but also poses serious public health risks through potential zoonotic transmission. Recent molecular and genomic studies have shown the widespread dissemination of resistance genes across different ecological compartments, emphasizing the need for integrated monitoring systems. Antimicrobial stewardship programs and evidence-based interventions are therefore essential in veterinary medicine to mitigate these trends. This is particularly important because the emergence of multidrug-resistant (MDR) pathogens is increasingly associated with mobile genetic elements, such as plasmids, transposons, and integrons, which facilitate horizontal gene transfer within and across bacterial species.},
}

Animals
Humans
*One Health
*Anti-Bacterial Agents/pharmacology/therapeutic use
*Zoonoses/microbiology
*Bacterial Zoonoses/microbiology/transmission
*Bacteria/drug effects/genetics
*Drug Resistance, Bacterial
*Drug Resistance, Multiple, Bacterial
*Bacterial Infections/microbiology/veterinary
Gene Transfer, Horizontal
Livestock/microbiology

@article {pmid42184326,
year = {2026},
author = {Goncharov, ID and Alekseev, AA and Morozova, NE and Sadova, AI and Khodorkovskii, MA},
title = {[Functional and Structural Features of RecA and RAD51 Recombinases in the Contexts of Antibiotic Resistance of Pathogenic Bacteria and Therapy of Cancer].},
journal = {Molekuliarnaia biologiia},
volume = {60},
number = {1},
pages = {144-167},
doi = {10.7868/S3034555326010096},
pmid = {42184326},
issn = {0026-8984},
mesh = {*Rec A Recombinases/genetics/metabolism/antagonists & inhibitors/chemistry ; *Rad51 Recombinase/genetics/metabolism/antagonists & inhibitors/chemistry ; Humans ; *Neoplasms/genetics/drug therapy/enzymology ; *Drug Resistance, Bacterial/genetics ; *Bacterial Proteins/genetics/metabolism/antagonists & inhibitors/chemistry ; SOS Response, Genetics ; *Bacteria/genetics/enzymology/drug effects/pathogenicity ; },
abstract = {The RecA and RAD51 proteins are pivotal enzymes in homologous recombination in bacteria and eukaryotic cells. The proteins, organized into nucleoprotein filaments, mediate precise repair of severe DNA damage, and this repair is essential for maintaining genome stability. Investigating the structures, functions, and regulatory mechanisms of RecA and RAD51 holds significant practical importance. Dysregulation of human recombinase RAD51 has been implicated in various oncological diseases. RAD51 overexpression is frequently observed in malignant tumors and correlates with their drug resistance, underscoring the urgent need for the development of RAD51 inhibitors. In bacteria, RecA activates the SOS response and SOS-induced mutagenesis and participates in horizontal gene transfer, that is, processes directly linked to the emergence and dissemination of antibiotic resistance genes. The global spread of bacterial resistance poses a major challenge worldwide. A potential strategy to address this issue is identifying and developing RecA inhibitors for use in adjuvant therapies aimed at suppressing the mechanisms of bacterial adaptation to antibiotics. This review explores the structural and functional characteristics of the RecA and RAD51 proteins and the nucleoprotein filaments they form. Their roles in recombination repair are considered along with the mechanisms governing their regulation. Furthermore, approaches to inhibition of RecA and RAD51 activities are discussed with a focus on their practical applications.},
}

*Rec A Recombinases/genetics/metabolism/antagonists & inhibitors/chemistry
*Rad51 Recombinase/genetics/metabolism/antagonists & inhibitors/chemistry
Humans
*Neoplasms/genetics/drug therapy/enzymology
*Drug Resistance, Bacterial/genetics
*Bacterial Proteins/genetics/metabolism/antagonists & inhibitors/chemistry
SOS Response, Genetics
*Bacteria/genetics/enzymology/drug effects/pathogenicity

@article {pmid42184816,
year = {2026},
author = {Miao, J and Zhang, C and Jiang, Q and Yao, Z and Cao, K and Chen, J and Wang, H and Liu, N},
title = {Complete Genome of an Alkali-Resistant Rhizobium anhuiense Symbiont of Pea Reveals Species-Specific Plasmid Fusion and Genomic Plasticity.},
journal = {Environmental microbiology reports},
volume = {18},
number = {3},
pages = {e70366},
doi = {10.1111/1758-2229.70366},
pmid = {42184816},
issn = {1758-2229},
support = {//Team development funding from Xianghu Laboratory, the Xiaoshan District Government and the Zhejiang Provincial Government/ ; //2025 Special Cooperation Program between Xianghu Laboratory and Chinese Academy of Agricultural Science/ ; },
mesh = {*Plasmids/genetics ; *Genome, Bacterial ; *Pisum sativum/microbiology/growth & development ; Symbiosis ; Phylogeny ; *Rhizobium/genetics/isolation & purification/classification/physiology/drug effects ; *Alkalies/pharmacology ; Root Nodules, Plant/microbiology ; Gene Transfer, Horizontal ; },
abstract = {The rhizosphere microbiome is crucial for plant growth and stress resilience in sustainable horticulture. Here, we report the complete genome assembly and functional characterisation of Rhizobium anhuiense Xianghu001, a nitrogen-fixing symbiont isolated from pea (Pisum sativum) root nodules. A hybrid assembly strategy combining PacBio reads and Illumina reads yielded a 7.36 Mb high-quality assembly comprising one chromosome, one megaplasmid and four accessory plasmids, encoding 6899 protein-coding genes, of which 66.64% are located on the chromosome. Phylogenomics and synteny confirmed its placement within R. anhuiense. We detected a lineage-specific plasmid fusion forming the megaplasmid, while three accessory plasmids appear to be strain-specific and potentially acquired via horizontal gene transfer. Insertion sequence profiling suggests genome rearrangement shaping plasmid structure. To explore intraspecies diversity, we sequenced six additional local R. anhuiense isolates from pea. Despite their close geographic origin, genomic comparison revealed extensive divergence. Phenotypic assays demonstrated that Xianghu001 significantly promotes pea growth under nitrogen-deficient conditions, increasing chlorophyll content and nitrogen accumulation. It synthesises high levels of IAA (~184 mg/L), tolerates mild salinity (≤ 0.15% NaCl) and grows optimally at alkaline pH (8.0-10.0). Our findings provide a comprehensive genomic and functional framework for R. anhuiense Xianghu001 and underscore its potential as a biofertiliser.},
}

*Plasmids/genetics
*Genome, Bacterial
*Pisum sativum/microbiology/growth & development
Symbiosis
Phylogeny
*Rhizobium/genetics/isolation & purification/classification/physiology/drug effects
*Alkalies/pharmacology
Root Nodules, Plant/microbiology
Gene Transfer, Horizontal

@article {pmid42185652,
year = {2026},
author = {Ocaña-Pallarès, E and Richards, TA and Gabaldón, T and Szöllősi, GJ},
title = {Signatures of gene transfer in the parallel evolution of osmotrophic specialization in eukaryotes.},
journal = {Nature ecology & evolution},
volume = {},
number = {},
pages = {},
pmid = {42185652},
issn = {2397-334X},
abstract = {Recurrent transitions in feeding strategies have shaped the eukaryotic tree of life, as unrelated groups independently evolved similar solutions to common ecological challenges. One of the most interesting yet poorly studied of these shifts is the transition towards osmotrophy. We reconstructed the evolution of four eukaryotic groups that specialized in osmotrophy through convergent evolution. Here we show that these groups arose most likely during the Tonian period (1,000-720 million years ago) or slightly before, and possess a genetic toolkit enriched in shared metabolic functions. We report signatures that are compatible with horizontal gene transfer encompassing at least 20% of this toolkit. Phylogenetic reconciliation analyses show that this fraction of the toolkit ranks in the upper percentiles for inferred horizontal gene transfers, particularly in the period in which the osmotrophic groups originated. Moreover, analyses of the total gene content using supervised phylogenetic screening identified 166 gene tree topologies that are supportive of transfer events involving distantly related eukaryotic osmotrophs. These data include transfer highways between Fungi and Pseudofungi and between Labyrinthulea and Teretosporea. Our work thus unravels the evolutionary history of four independent transitions towards specialization in osmotrophy within the eukaryotes, supporting a role of gene transfer in the evolution of these groups.},
}

@article {pmid42177575,
year = {2026},
author = {Gaddafi, MS and Saeed, SI and Eltai, NO and Lawal, H and Ibrahim, DD and Musawa, IA and Garba, B and Goni, MD and Yakubu, Y},
title = {Climate change and the global spread of antimicrobial resistance in livestock systems: a comprehensive review.},
journal = {One health outlook},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42522-026-00219-2},
pmid = {42177575},
issn = {2524-4655},
abstract = {Climate change and antimicrobial resistance (AMR) are converging threats to livestock systems, food security, and public health. This review synthesizes mechanistic evidence linking climate variables to the proliferation of AMR in livestock and proposes integrated mitigation strategies. Elevated temperatures compromise livestock immunity, increase disease susceptibility, and drive antimicrobial use, while enhancing horizontal gene transfer (HGT) through increased plasmid stability, integrase activity, and bacterial stress responses. Altered precipitation and humidity influence biofilm formation, pathogen survival, and the mobilization of resistant bacteria and antimicrobial residues from manure into soil and water. Floods and droughts further concentrate or disperse resistance determinants across environmental reservoirs, creating transmission bridges between livestock, wildlife, and humans. Key evidence gaps include understudied climate variables (humidity, soil temperature), geographic blind spots (Sub-Saharan Africa, South Asia, Southeast Asia), and a scarcity of field data validating laboratory-based HGT mechanisms. Addressing these challenges requires climate-smart livestock practices (improved housing, adaptive breeding), enhanced antimicrobial stewardship (vaccination, probiotics, biosecurity), and sustainable waste management (anaerobic digestion, composting). Global coordination under a One Health framework, supported by robust policy mechanisms and targeted research funding, is essential to safeguard animal and public health from AMR in a changing climate.},
}

@article {pmid42177952,
year = {2026},
author = {Nieto, ÁVA and Diaz, AH and Millán, MH and Sagredo, D and Gacitua, JA},
title = {Molecular Pathways and Clinical Applications of Probiotics as Effective Supporters of Intestinal, Neurologic, and Cardiovascular Health: a Narrative Review.},
journal = {The Journal of nutritional biochemistry},
volume = {},
number = {},
pages = {110424},
doi = {10.1016/j.jnutbio.2026.110424},
pmid = {42177952},
issn = {1873-4847},
abstract = {PURPOSE OF REVIEW: This narrative review aims to synthesize current knowledge on the molecular mechanisms and clinical applications of probiotics across three major health domains: intestinal, neurologic, and cardiovascular.

RECENT FINDINGS: •Intestinal health: Probiotics such as Lactobacillus rhamnosus GG and Bifidobacterium lactis BB-12 reinforce epithelial integrity via upregulation of tight-junction proteins (occludin, claudin-1), attenuate inflammation through cytokine modulation (↑IL-10, ↓TNF-α, IL-6), and restore eubiosis in conditions including IBS, constipation, and antibiotic-associated diarrhea. • Neurologic health: "Psychobiotic" strains (e.g., L. rhamnosus JB-1, B. longum 1714, L. helveticus R0052 + B. longum R0175) modulate neurotransmitter synthesis (GABA, serotonin), dampen HPA-axis hyperactivity, and reduce neuroinflammation, yielding improvements in anxiety, stress resilience, cognitive function, and slowing brain-atrophy progression in MCI and Alzheimer's disease. • Cardiovascular health: Meta-analyses of 30+ RCTs demonstrate that probiotic supplementation (notably L. acidophilus, L. plantarum, B. longum) lowers total and LDL cholesterol (-7 to -10 mg/dL) via bile-salt hydrolase activity, SCFA-mediated GPR signaling, direct cholesterol assimilation, and modestly reduces systolic (-2 to -4 mmHg) and diastolic blood pressure through anti-inflammatory pathways and improved endothelial function. • Safety: While generally safe in healthy populations, rare adverse events (bacteremia, D-lactic acidosis, horizontal gene transfer) have been reported in immunocompromised or critically ill individuals, underscoring the need for individualized risk-benefit assessments and rigorous adverse-event surveillance.

SUMMARY: Probiotics exert strain-specific, multi-mechanistic benefits on gut barrier integrity, neuroendocrine signaling, and cardiometabolic regulation. To fully realize their therapeutic promise, future research must pursue large-scale, head-to-head clinical trials, integrate multi-omics and precision-design approaches, and establish standardized frameworks for safety monitoring and personalized formulation.},
}

@article {pmid42178378,
year = {2026},
author = {Fueangbangluang, P and Matsutani, M and Kataoka, N and Yakushi, T and Matsushita, K and Trakulnaleamsai, S},
title = {Draft genome and physiological characterization of a newly isolated L-arabinose-utilizing Corynebacterium glutamicum CS176.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-54441-z},
pmid = {42178378},
issn = {2045-2322},
support = {JPMJAL1106//the Advanced Low Carbon Technology Research and Development Program (ALCA) of the Japan Science and Technology Agency (JST)/ ; },
abstract = {This study reports the physiological and genomic characterization of Corynebacterium glutamicum CS176, a newly isolated strain exhibiting a rare combination of traits: efficient L-arabinose utilization and L-glutamate production without chemical induction, even under excess biotin conditions. Genome analysis of the 3.10 Mb draft sequence (54.20% GC) revealed a 7.8 kb L-arabinose utilization gene cluster highly similar to those of arabinose-assimilating strains, suggesting acquisition via horizontal gene transfer. To link genotype with phenotype, the effects of temperature, oxygen availability, carbon sources, and biotin concentration on bacterial growth and L-glutamate production were systematically evaluated under controlled conditions. Optimal growth was observed at 30-37 °C under high oxygen conditions, whereas maximal L-glutamate production (up to 2.5 g/L in mixed substrates) occurred at 37-39.5 °C under medium-low oxygen conditions. Notably, CS176 maintained L-glutamate production across a wide range of biotin concentrations (0-200 µg/L), in contrast to the typical biotin-dependent regulation observed in C. glutamicum. Furthermore, glucose-arabinose co-utilization enhanced both growth and L-glutamate production, highlighting metabolic flexibility. Together, these findings identify CS176 as a promising strain that overcomes key limitations in conventional glutamate fermentation and provides insights for metabolic engineering and sustainable bioprocess development.},
}

@article {pmid42178922,
year = {2026},
author = {Hu, Y and Yang, Y and Hu, X and Mahillon, J and Chen, Z and Xia, H},
title = {Identification of the Integration/Excision Module and Regulatory Elements Involved in the Mobility of IME8, an Integrative and Mobilizable Element From Mosquitocidal Lysinibacillus sphaericus.},
journal = {Microbial biotechnology},
volume = {19},
number = {5},
pages = {e70387},
doi = {10.1111/1751-7915.70387},
pmid = {42178922},
issn = {1751-7915},
support = {32170008//National Natural Science Foundation of China/ ; 32211530564//National Natural Science Foundation of China/ ; JXBS014//key R&D Program of Hubei Jiangxia Laboratory/ ; CZZ26003//Fundamental Research Fund for the Central Universities of South-Central Minzu University/ ; },
mesh = {*Bacillaceae/genetics ; *Recombination, Genetic ; Plasmids ; Bacterial Proteins/genetics/metabolism ; },
abstract = {Lysinibacillus sphaericus, a bacterium successfully used in the control of mosquitoes, bears its insecticidal traits in GI8, a recently identified mosquitocidal genomic island. GI8 is renamed IME8 in the present work, as it displays a typical genetic organization of an Integrative and Mobilizable Element (IME) and its circularized form is not self-conjugative but mobilizable by the pBsph-like plasmid p1593. The IME8 integration module (int-operon) encodes two integrase-like proteins (Int1 and Int2) belonging to the family of tyrosine recombinases, and a hypothetical protein (Hp3). All three ORFs are necessary and function as an essential excision unit of IME8. The chimeric construct "attL-int1-int2-hp3-kan-attR" (hereafter named mini-IME8 cassette) displays integrating property. The integration is specific to an acnL-yolD(attB)-uvrX operon target region, which is not only distributed in various L. sphaericus isolates but is also present among other Lysinibacillus species. The regulation module, reg-operon, encodes an HTH-domain-carrying protein (Reg16) and a putative lytic polysaccharide monooxygenase (LPMO17). Knockout of the reg-operon remarkably increases IME8 excision and transcription levels of int1/int2/hp3 compared to the wild-type situation. However, expression of reg16 or the complete reg-operon both increase the int-operon promoter (Pint) activity in β-galactosidase activity assays, suggesting a complex regulation of the int-operon.},
}

*Bacillaceae/genetics
*Recombination, Genetic
Plasmids
Bacterial Proteins/genetics/metabolism

@article {pmid42181995,
year = {2026},
author = {Mahanta, U and Waßmuth, R and Brighty, S and Treuner-Lange, A and Sharma, G},
title = {Diversity, classification, and evolution of myxobacterial PilY1 proteins.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1826482},
pmid = {42181995},
issn = {1664-302X},
abstract = {Type IVa pili (T4aP) mediate one of the most widespread forms of bacterial surface motility through coordinated cycles of extension, attachment, and retraction that generate pulling forces to propel cells forward. This process is well characterized in diverse Gram-negative bacteria such as Pseudomonas, Myxococcus, and Neisseria, where T4aP filaments are composed of thousands of major pilin subunits and a tip complex formed by minor pilins and the PilY1 adhesin proteins. PilY1 is a multifunctional protein localized at the T4aP machine and pilus tip, playing critical roles in pilus priming, surface adhesion, motility, and virulence. Myxococcus xanthus possesses three distinct PilY1 adhesins with conserved C-terminal but different N-terminal, where each is encoded within separate minor pilin/pilY1 gene clusters, suggesting functional specialization. This study investigates the extent of PilY1 diversity and domain architecture conservation across the phylum Myxococcota using genomic, phylogenetic, and structural approaches, suggesting a remarkable evolutionary strategy for tailoring T4aP tip complexes to diverse environmental and physiological demands. Our analysis of sixty-seven representative genomes reveals that PilY1 proteins are widely distributed and typically occur in multiple copies, with an average of two homologs per genome. Phylogenetic reconstruction identifies several well-supported clades supported by myxobacterial taxonomy, domain architecture, protein length, and cysteine content. Notably, M. xanthus paralogs PilY1.1 and PilY1.2 form a conserved lineage characterized by a DUF4114 domain and appear to have evolved primarily through vertical inheritance, whereas PilY1.3 clusters with homologs from diverse bacterial phyla, suggesting acquisition via horizontal gene transfer. We reconfirmed that pilY1 genes frequently occur in conserved operons with minor pilins (pilX, pilW, pilV, and fimU), supporting their role in forming priming complexes initiating pilus assembly. Structural modeling predicts conserved interaction patterns within minor pilins and PilY1 via β-strand complementation between PilX and PilY1, highlighting a potentially conserved structural feature of T4aP tip complexes. Together, our findings reveal extensive diversification of PilY1 proteins within Myxococcota and suggest that variation in their N-terminal domains contributes to functional specialization of T4aP systems. Future experimental studies will be essential to determine how this diversity shapes mechanosensing, adhesion, and environmental adaptation in myxobacteria and other bacteria.},
}

@article {pmid42183934,
year = {2026},
author = {Halema, AA and Elarabi, NI and Henawy, AR and Almutairi, HH and El-Beltagi, H and Al-Dossary, O and Alsubaie, B and Rezk, AA and Abdelhadi, AA and Abdelhaleem, HAR},
title = {Genome-based characterization of a multifunctional plant growth-promoting and heavy metal-resistant Escherichia coli FACU2024 isolated from Jatropha rhizosphere.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {6},
pages = {},
pmid = {42183934},
issn = {1573-0972},
support = {KFU251835//Deanship of Scientific Research, Vice Presidency for Graduate Studies and Scientific Research, King Faisal University, Saudi Arabia/ ; },
mesh = {*Rhizosphere ; *Escherichia coli/genetics/isolation & purification/drug effects/classification/metabolism ; *Jatropha/microbiology/growth & development ; Soil Microbiology ; *Genome, Bacterial ; *Metals, Heavy/toxicity/metabolism ; Indoleacetic Acids/metabolism ; Plant Roots/microbiology ; Whole Genome Sequencing ; Phosphates/metabolism ; Phylogeny ; Plant Growth Regulators/metabolism ; Plant Development ; },
abstract = {Whole-genome sequencing (WGS) of microbial isolates is a valuable tool for mapping the genomes of novel organisms and is helpful for understanding plant-bacteria interactions. The close relationships between bacteria and plants are essential for maintaining healthy ecosystems, whether the bacteria reside the plant or in the rhizosphere surrounding its roots. In this study, isolation, characterization, and WGS were performed to identify promising plant growth-promoting rhizobacteria (PGPR) using the rhizospheric soil sample of jatropha tree roots. Out of 100 isolates, six (FACU 2024, 2, 3, 4, 5, and 6) exhibited phosphate-solubilizing bacteria (PSB) traits, including solubilizing phosphate and producing indole acetic acid (IAA), and the ability of other plant growth-promoting (PGP) traits was tested. Isolate FACU 2024 exhibited the highest values for IAA production (12.1 µg/ml), soluble phosphate release (300 µg/ml), and phosphate solubilization index (6.7). Therefore, FACU 2024 was molecularly identified as Escherichia coli. The WGS analysis revealed that E. coli FACU 2024 possesses one chromosome and one plasmid with a total length of 4.8 Mb and were submitted on GenBank under accession numbers CP147009 and CP147010. The bacterial genome contained about 142 PGP genes, ranging from 258 to 3744 bp and associated with phosphate solubilization, siderophore production, indole acetic acid (IAA) production, nitrogen metabolism, nitrogen fixation, and nitrite/nitrate reduction. Moreover, genomic islands (GIs) were enriched with genes associated with horizontal gene transfer (HGT), stress response, and environmental adaptation, and prophage analyses were carried out. In addition, 15 heavy metal resistance genes were annotated, such as those for As, Cd, Zn, Pb, Cu, Fe, and Co, ranging from 426 to 2505 bp. This study provides the first comprehensive genetic evidence linking E. coli to key PGPR traits alongside genes conferring resistance to multiple heavy metals. This strain demonstrates potential as a PGPR in addition to heavy metal bioremediation.},
}

*Rhizosphere
*Escherichia coli/genetics/isolation & purification/drug effects/classification/metabolism
*Jatropha/microbiology/growth & development
Soil Microbiology
*Genome, Bacterial
*Metals, Heavy/toxicity/metabolism
Indoleacetic Acids/metabolism
Plant Roots/microbiology
Whole Genome Sequencing
Phosphates/metabolism
Phylogeny
Plant Growth Regulators/metabolism
Plant Development

@article {pmid42172112,
year = {2026},
author = {Deng, K and Guo, R and Lv, S and Zhang, Y and Zhang, C and Xiao, L},
title = {Dual-Track Genome Evolution in Curvularia muehlenbeckiae Suggests Host Jump to Pecan via Putative Mini-Chromosome Acquisition and Zn2Cys6-Centric Co-adaptation.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-04-26-0660-RE},
pmid = {42172112},
issn = {0191-2917},
abstract = {Curvularia muehlenbeckiae (P-6) is an emerging fungal pathogens responsible for severe leaf spot disease in pecan (Carya illinoinensis), however, the genomic mechanisms underlying its host jump remain elusive. Here, we present the first near complete genome assembly of P-6 (33.77 Mb), revealing a karyotype of 14 chromosomes, including two putative mini-chromosomes (Chr13/Chr14) that harbor 17% and 22% of the pathogen's candidate virulence factors, respectively. Notably, Chr14 contains a transposase-flanked secondary metabolite biosynthetic gene cluster (SM_BGC), a configuration often associated with horizontal gene transfer in fungi. Pan-genome analysis exposed a conserved Curvularia virulome (99.55% of P-6 virulence orthogroups) alongside lineage-specific expansions of Major Facilitator Superfamily (MFS) transporters (299 genes) and Zn2Cys6 transcription factors (126 genes) that facilitate adaptation to woody hosts - a signature distinct from graminaceous-infecting Curvularia species. Time-resolved transcriptomics revealed a Zn2Cys6-centric biphasic infection strategy: an early phase (0.5 h post-inoculation [hpi]) governed by Zn2Cys6 hubs regulating MFS transporters and reactive oxygen species (ROS) detoxification genes, and a late necrotrophic phase (72 hpi) mediated by distinct Zn2Cys6 factors inducing carbohydrate metabolism (AMY1, INV2) and toxin production (PKS7, NRPS3). Weighted Gene Co-expression Network Analysis (WGCNA) confirmed stage-specific modules associated with these Zn2Cys6 transcription factors. Ecological profiling indicated optimal growth at 28°C and pH 5.0-6.0, consistent with subtropical disease epidemiology. Our findings support a dual-track evolutionary model where putative mini-chromosomes may facilitate virulence gene acquisition, while correlated expansions of Zn2Cys6 transcription factors and MFS transporters forms a co-regulated network associated with a biphasic infection strategy, identification of these hubs will provide promising targets for eco-friendly management of pecan leaf spot.},
}

@article {pmid42172586,
year = {2026},
author = {Singh, R and Gupta, P and Singh, R and Basant, N},
title = {Environmental Antibiotic Contamination and AMR: Integrating Pathways, Impacts, and AI-Driven Mitigation.},
journal = {Environmental toxicology and chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1093/etojnl/vgag115},
pmid = {42172586},
issn = {1552-8618},
abstract = {The widespread contamination of the environment with antibiotic residues is a significant factor contributing to the global crisis of antimicrobial resistance. Antibiotics from various sources, such as effluents from municipal and hospital wastewater treatment plants, agricultural runoffs, discharges from pharmaceutical manufacturing and improper disposal of expired or unused medicines, create selective pressures in the spread of antibiotic resistance genes. These environmental reservoirs act as hotspots for horizontal gene transfer, facilitating the emergence of multidrug-resistant pathogens. Conventional detection methods including culture-based assays, chromatographic quantification, and molecular diagnostics, provide essential insights but are limited by low throughput, reduced sensitivity to new Antibiotic Resistance Genes, and challenges in real-time monitoring across complex environments. Recent advances, such as whole-genome sequencing, metagenomics, and biosensor-based detection, help to address these gaps by enabling more comprehensive surveillance of the resistome. Artificial intelligence further enhances these approaches by improving data interpretation and pattern recognition, thus complementing traditional and molecular methods rather than replacing them. This review examines the pathways of environmental antibiotic contamination, ecological and health impacts of Antimicrobial Resistance (AMR), and limitations of conventional detection methods. It aims to clarify how these pathways contribute to the AMR crisis, assess the effectiveness of existing surveillance techniques, and identify gaps in current research.},
}

@article {pmid42175760,
year = {2026},
author = {Sudianto, E and Baurain, D and Cornet, L},
title = {Horizontal Gene Transfers Underpin Ribose Heterotrophy and Central Carbon Metabolism Remodeling in Gloeobacteraceae.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evag127},
pmid = {42175760},
issn = {1759-6653},
abstract = {Gloeobacterales occupy a key phylogenetic position among cyanobacteria and are distinguished by the absence of thylakoid membranes. Using comparative genomics and phylogenetic analyses, we show that horizontal gene transfer has played a major role in shaping the central carbon metabolism of this lineage. In Gloeobacteraceae-one of the two families within the order-we identify a complete ribose ATP synthase binding cassette (ABC) importer and associated metabolic enzymes that enable ribose uptake and assimilation into central carbon metabolism alongside photosynthesis, indicative of a photomixotrophic lifestyle. Beyond ribose utilization, their central carbon metabolism exhibits a mosaic architecture shaped by the integration of foreign genes into the Calvin-Benson-Bassham cycle, the pentose phosphate pathway, and the Embden-Meyerhof-Parnas pathway. Uniquely, these genes appear to have been acquired through multiple independent transfer events, as reflected by their dispersed genomic locations and diverse bacterial donors, including other cyanobacteria and Pseudomonadota. These findings highlight Gloeobacterales as a dynamic lineage that continues to adapt and evolve through metabolic innovation and the assimilation of foreign genes into its genomes.},
}

@article {pmid42176173,
year = {2026},
author = {Khan, SA and Siddiqui, SA and Samreen, and Ahmad, I and Neyaz, LA and Abulreesh, HH},
title = {ESBL and carbapenemase-producing enteric pathogens in animal-origin foods: a one health perspective.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {42176173},
issn = {1874-9356},
abstract = {The frequent detection of extended-spectrum β-lactamase (ESBL-E) and carbapenemase-producing Enterobacteriaceae (CPE) in foods of animal origin raises concerns regarding the dissemination of antimicrobial resistance (AMR). Dairy products, poultry, beef, and pork are considered key reservoirs. Multiple studies have indicated a correlation between isolates of food, animal, and human origin. Animal food chains often encompass high ESBL prevalence, whereas comparatively less prevalent CPE are also globally emerging in retail meat and poultry. Antibiotic resistance genes (blaOXA-48, blaNDM, and blaCTX-M) encoded by mobile genetic elements are known to contribute to dissemination across bacterial species as well as in the ecological niche. Horizontal gene transfer of plasmid-mediated genes further contaminates other environmental reservoirs, which complicates control points. Several studies depict a significant variation between low- and middle-income countries, often having high prevalence due to limited food safety controls and antibiotic stewardship. Such food-borne pathogens colonize human systems through food intake, occupational exposure, or handling, leading to serious public health implications. The current review summarizes global evidence on the prevalence and transmission of ESBL-E and CPE in animal food origin with particular emphasis on resistance mechanisms, reservoir and regional occurrence patterns within a One Health framework, and the need for integrated cross-sectoral surveillance and antimicrobial stewardship strategies to mitigate their spread.},
}

@article {pmid42176632,
year = {2026},
author = {Cai, Y and Liu, Y and Li, G and Wong, PK and An, T and Zhao, H},
title = {Dynamic shifts and molecular regulatory mechanisms of three predominant horizontal antibiotic resistance gene transfer modes during photocatalytic disinfection.},
journal = {Journal of hazardous materials},
volume = {513},
number = {},
pages = {142480},
doi = {10.1016/j.jhazmat.2026.142480},
pmid = {42176632},
issn = {1873-3336},
abstract = {The spread of antibiotic resistance genes (ARGs) through horizontal gene transfer (HGT) during disinfection processes poses a significant challenge to water safety. However, the pathway-specific dynamics and regulatory mechanisms remain insufficiently elucidated. This study employed engineered strains harboring plasmids carrying six different ARGs targeting distinct cellular processes to demonstrate photocatalytic disinfection exhibiting unique and time-resolved effects on HGT. The results demonstrate that, although conjugation initially dominated HGT (37.7% - 98.3%), prolonged photocatalytic disinfection triggered a marked shift toward transduction (70% - 92% after 40 min), revealing a critical transduction-associated residual risk. The conjugation of various ARGs was transiently and heterogeneously enhanced (1.6 - 11.6 folds) during early photocatalysis (10 - 20 min), with strains carrying protein-targeting ARG exhibiting the greatest and most sustained promotion due to their higher tolerance to photocatalytic stress. This finding elucidates the role of resistance targets in modulating conjugation during disinfection. Transformation exhibited a sustained enhancement (1.4 - 2.6 folds), whereas transduction maintained remarkably stable throughout the treatment. Mechanistically, photocatalytic disinfection elevated intracellular reactive oxygen species (ROS) levels, total antioxidant capacity, and membrane permeability. These changes synergistically regulated key functional genes, characterized by an initial up-regulation of conjugation-related genes (ftsY, tesB), followed by the sustained activation of SOS response genes (lexA, umuD) and stringent response genes (sspA, rpoS), providing a mechanistic explanation for the dynamic shifts among the three HGT modes. These findings highlight the inadequacy of relying solely on bacterial inactivation as an efficacy metric for disinfection and elucidate the differential regulation of HGT among ARGs with distinct resistance targets.},
}

@article {pmid42177136,
year = {2026},
author = {Ali, I and Xu, X},
title = {Soil carbon regulates antibiotic resistance gene dynamics.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2026.05.002},
pmid = {42177136},
issn = {1878-4380},
abstract = {Antibiotic resistance genes (ARGs) are widespread in soils, yet their persistence is often viewed only through the lens of chemical selection. Here, we propose soil carbon as an integrative ecological driver structuring ARG dynamics in terrestrial systems. By shaping microbial growth, community assembly, colonization resistance, and horizontal gene transfer, soil carbon can either constrain ARG persistence or, under certain conditions, facilitate ARG spread.},
}

@article {pmid42171474,
year = {2026},
author = {Kant, P and Petersen, B and Sicheritz-Pontén, T and Kondabagil, K},
title = {On the Low Abundance of Antibiotic Resistance Genes in Bacteriophage Genomes and Their Random Acquisition via Specialized Transduction.},
journal = {Genome biology and evolution},
volume = {18},
number = {5},
pages = {},
pmid = {42171474},
issn = {1759-6653},
mesh = {*Bacteriophages/genetics ; *Genome, Viral ; *Drug Resistance, Microbial/genetics ; *Transduction, Genetic ; *Drug Resistance, Bacterial/genetics ; Prophages/genetics ; Gene Transfer, Horizontal ; },
abstract = {The role of bacteriophages in spreading antimicrobial resistance genes (ARGs) has been debated for over a decade. Several questions regarding the ARG dissemination potential of bacteriophages remain. For example, do phages frequently carry ARGs? Besides generalized transduction (GT), could specialized transduction (ST) play an essential role in the spread of ARGs? To address these questions, we thoroughly analyzed the available phage genomes, viromes, temperate phages, and prophage sequences for the presence of all known ARGs and their genomic context. Out of the 38,861 phage genome sequences we analyzed, 82 phages were found to possess 141 ARGs in their genomes. Interestingly, a few of the Streptococcus phages were found to carry an entire ARG cluster with four or more genes. An uncharacterized Caudoviricetes phage was found to possess the complete vancomycin operon. In literature, the role of ST in phage-based ARG dissemination is often overlooked. Based on the presence of lysogenic markers, the terminal location of ARGs on phage genomes, and ARG clusters transferred to phages, we suggest that ARGs are predominantly acquired from pathogenic hosts by temperate phages via ST. These findings indicate that, in addition to GT, ST can also play a crucial role in phage-based ARG dissemination. Our study also suggests that the acquisition of ARGs by phages is sporadic. Overall, we propose that phage-mediated gene transfer is governed by a complex interplay of gene transfer bottlenecks and microenvironmental parameters, such as microbial density, diversity, and external stress, in addition to phage properties.},
}

*Bacteriophages/genetics
*Genome, Viral
*Drug Resistance, Microbial/genetics
*Transduction, Genetic
*Drug Resistance, Bacterial/genetics
Prophages/genetics
Gene Transfer, Horizontal

@article {pmid42158020,
year = {2026},
author = {Jaber, R and Mattei, C and Accary, C and Roufayel, R and Abi Khattar, Z and Fajloun, Z},
title = {Animal Venom Pharmacological Resources: Exploiting Bioactive Peptides to Target Multi-Drug-Resistant Bacteria.},
journal = {Biochemistry research international},
volume = {2026},
number = {},
pages = {5088674},
pmid = {42158020},
issn = {2090-2247},
abstract = {BACKGROUND: The escalating rise of multi-drug-resistant (MDR) bacterial strains significantly threatens global health, creating a "silent pandemic" prompted by natural selection, gene mutation, and horizontal gene transfer. This crisis is worsened by the deficit in the development of new treatments, necessitating the innovative discovery of new potent antibacterial agents.

OBJECTIVE: This review examines animal venom, a complex mixture of an evolutionary array of bioactive molecules, as an important emergent source of broad-spectrum antimicrobial peptides (AMPs), creating potential drug templates for next-generation therapeutics.

RESULTS: We highlight numerous identified AMPs from various venomous taxa, including scorpions, snakes, spiders, frogs, bees, and wasps, characterized by their bactericidal activity against both Gram-positive and Gram-negative bacteria. They exhibit diverse mechanisms of action, characterized by rapid membrane disruption models, biofilm inhibition, bacterial enzyme dysregulation, immunomodulatory effects, and the control of intracellular targets. These bioresources serve as a structural base for the development of analogs with enhanced potency, higher selectivity, and less systemic toxicity. We also discuss repurposing strategies applied to the native AMPs, the potential application of nanoparticle technologies and the usage of computational methods.

CONCLUSION: These advanced approaches accelerate the examination of large databases to optimize structure-function characteristics, providing a roadmap for the development of future potential antimicrobial treatments derived from the rich reservoir of animal venom bioactive molecules.},
}

@article {pmid42161273,
year = {2026},
author = {Maurais, EG and Mazzagatti, A and Lin, YF and Narozna, M and Hu, Q and Dahiya, R and Santiago-Ferrer, D and Herlihy, CP and Krebs, M and Pateraki, N and Parcharidou, E and Papathanasiou, S and Beliveau, BJ and Gorbsky, GJ and Cortés-Ciriano, I and Ly, P},
title = {Genome instability triggers intercellular DNA transfer between human cells.},
journal = {Cell},
volume = {},
number = {},
pages = {},
pmid = {42161273},
issn = {1097-4172},
support = {R01 CA289435/CA/NCI NIH HHS/United States ; R35 GM146610/GM/NIGMS NIH HHS/United States ; },
abstract = {The mammalian genome is safeguarded within the confines of the interphase nucleus. However, genomic instability can trigger the mislocalization of nuclear DNA to the cytoplasm within micronuclei or as fragmented chromosomes. Beyond activating cell-autonomous signaling programs, whether such cytoplasmic DNA can elicit non-cell-autonomous consequences to nearby cells remains unclear. Here, we show that cytoplasmic DNAs undergo intercellular transfer through contact-dependent, cytoskeleton-based nanotube structures connecting adjacent human cells. Diverse sources of genomic instability-including exposure to mitotic spindle poisons, ionizing radiation, and Cas9-induced chromosome breakage-promote nanotube-mediated DNA transfer in both cancerous and non-cancerous cells. Transferred DNA fragments are stably inherited as functional extrachromosomal genetic elements in the recipient host genome, thereby conferring heritable phenotypic traits to the recipient cell. Our findings uncover a horizontal gene transfer-like mechanism through which direct cell-cell contact can propagate genomic instability and reshape mammalian genomes.},
}

@article {pmid42164320,
year = {2026},
author = {Ren, Z and Zhao, M and Chen, R and Zhang, X},
title = {Vertical stratification and functional coupling of antibiotic resistance and carbon metabolism in thermokarst lake sediments.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag107},
pmid = {42164320},
issn = {2730-6151},
abstract = {Thermokarst lakes are biogeochemical hotspots and reservoirs of antibiotic resistance genes (ARGs), yet their vertical organization remains poorly understood. Here, we investigated the vertical stratification of ARGs in sediment cores from thermokarst lakes on the Qinghai-Xizang Plateau, quantifying their distribution and associations with mobile genetic elements (MGEs) and carbohydrate-active enzymes (CAZymes). The results revealed pronounced vertical differentiation, with ARG richness decreasing but β-diversity increasing with depth. A total of 386 ARGs were identified, of which 39% increased and 22% decreased significantly along the depth gradient. Multidrug and glycopeptide resistance genes dominated the profiles, while macrolide, tetracycline, and fluoroquinolone resistance were most abundant overall. MGEs, primarily transposase and recombinase genes, were strongly correlated with ARGs, underscoring horizontal gene transfer as a key mechanism for their persistence and dispersal. Co-occurrence analyses further revealed both positive and negative associations between ARGs and CAZymes, indicating synergistic and antagonistic couplings between antibiotic resistance and microbial carbon metabolism. Genes involved in energy-efficient carbon degradation (e.g. glycoside hydrolases and glycosyltransferases) were positively correlated with resistance genes enhancing stress tolerance, whereas negative interactions reflected trade-offs between carbon utilization and resistance maintenance. These findings demonstrate that ARGs are vertically structured and functionally integrated within microbial metabolic networks, providing new insights into their ecological roles in thermokarst lakes.},
}

@article {pmid42168873,
year = {2026},
author = {Zhao, K and Wang, W and Ma, M and Feng, J and Qi, T and Wang, J and He, J},
title = {Genomic characterization of an extensively drug-resistant Klebsiella pneumoniae co-harboring mcr-3.11, blaNDM-5 and blaCTX-M-27 isolated from pelvic effusion in a colon cancer patient.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05193-3},
pmid = {42168873},
issn = {1471-2180},
support = {20260521//Medical Science Research Project of Hebei/ ; USIP2025389//Undergraduate Students' Innovative Pilot Project of Hebei Medical University/ ; },
abstract = {OBJECTIVE: This study aimed to characterize the genomic features and possible transmission mechanisms of an extensively drug-resistant (XDR) Klebsiella pneumoniae (KP2024). The isolate was recovered from pelvic effusion of a postoperative colon cancer patient in Hebei, China, with a focus on the rare mcr-3.11 gene as well as blaNDM-5 and blaCTX-M-27.

RESULTS: Genetic analysis of key resistance determinants identified three epidemiologically important plasmids: an IncFIB plasmid carrying blaCTX-M-27 (pKP2024-1), an IncFII plasmid carrying mcr-3.11 (pKP2024-3), and an IncX3 plasmid carrying blaNDM-5 (pKP2024-4). Comparative genomic analysis indicated that blaCTX-M-27 was located within a highly conserved transposition unit mediated by ISEcp1. Additionally, mcr-3.11 and diacylglycerol kinase (dgkA) formed a conserved mobile genetic element, while blaNDM-5 was located within a typical Tn3-IS3000-IS5-blaNDM-5-bleMBL-trpF-IS26-ISKox3 structure on the IncX3 plasmid. All these plasmids harbored complete conjugative transfer systems or mobile genetic elements, indicating a high potential for horizontal gene transfer.

CONCLUSION: This study reports an XDR K. pneumoniae co-harboring mcr-3.11, blaNDM-5, and blaCTX-M-27, isolated from the postoperative pelvic effusion of a colon cancer patient. Multiple key resistance genes are distributed on different types of plasmids, conferring resistance to "last-line" clinical agents such as carbapenems and colistin. The co-existence of multiple plasmids and the co-evolution of resistance genes may further increase the risk of resistance transmission, highlighting the importance of enhancing clinical surveillance for such highly resistant clones.},
}

@article {pmid42169756,
year = {2026},
author = {Chen, Y and Yu, K and Sun, Y and Yan, Y and Yin, G and Wang, J and Li, X and Tang, S and Pronyk, P and Xia, Y},
title = {Plastic leachates drive conjugative transfer of antibiotic resistance genes.},
journal = {Environmental science and ecotechnology},
volume = {31},
number = {},
pages = {100705},
pmid = {42169756},
issn = {2666-4984},
abstract = {Plastic pollution pervades aquatic ecosystems worldwide, releasing leachates that interact intimately with microbial communities. Antibiotic resistance genes (ARGs) disseminate rapidly through horizontal gene transfer via plasmid conjugation, posing a severe and accelerating threat to public health and environmental stability. While microplastic particles are known to promote ARG exchange within biofilms, the influence of soluble chemical leachates derived from degrading plastics has remained unclear. Here we show that photodegraded leachate from polyvinyl chloride (PVC)-a widely used material in water infrastructure-substantially enhances conjugative transfer of ARGs in both laboratory model systems and natural aquatic microbiomes. Exposure increased transconjugant abundance up to 26.4-fold and conjugation efficiency up to 44.6-fold, with non-monotonic responses modulated by leachate concentration and microbial community diversity. Characterization of the leachate revealed high proportions of biolabile dissolved organic matter alongside additives; mechanistic assays demonstrated that these effects arise through elevated intracellular reactive oxygen species (21% increase), activation of the SOS response and DNA-repair pathways, increased extracellular protein production facilitating cell-cell contact, and compensatory adjustments in the electron transport chain that maintain ATP homeostasis. These results demonstrate that plastic leachates act as potent but previously overlooked facilitators of ARG dissemination beyond the physical effects of microplastics. Our findings reveal a critical synergy between plastic pollution and the global antimicrobial-resistance crisis, underscoring the urgent need for targeted regulations on plastic additives and degradation products in aquatic systems.},
}

@article {pmid42171365,
year = {2026},
author = {Song, Z and Zhou, L and Xu, W and Tian, M and Yu, L and Zhang, X and Song, R and Li, J and Ma, L},
title = {Genomic epidemiology and molecular characterization of Streptococcus pyogenes isolates from pediatric infections in Beijing, China.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0391425},
doi = {10.1128/spectrum.03914-25},
pmid = {42171365},
issn = {2165-0497},
abstract = {Streptococcus pyogenes (Group A Streptococcus, GAS) remains a formidable global public health challenge. In this study, we conducted a high-resolution genomic epidemiology study on 176 non-invasive throat GAS isolates collected from pediatric patients in Beijing, China, between June 2024 and March 2025. Whole-genome sequencing was employed to characterize population structure, phylogenetic relationships, virulence genes, and antimicrobial resistance (AMR) determinants. The results showed that the population of GAS isolates in this study was dominated by emm12/ST36 (77.8%) and emm1 (22.2%) types. The emm1 isolates primarily belonged to ST1274 and ST28, with ST1274 being a single-locus variant of ST28. Crucially, the global M1UK lineage was not detected. Phylogenomic analysis revealed that the emm12 population is structured into a dominant, conserved monophyletic clone (Clade A) co-circulating with diverse ancestral lineages. Pan-genome analysis further demonstrated an open genomic architecture characterized by a vast reservoir of accessory genes, indicating high evolutionary plasticity. While emm1 and emm12 exhibited distinct virulence signatures, a core virulence genome, including the the capsule-encoding hasABC operon, was universally conserved. Notably, we identified one emm12 isolate that acquired the emm1-associated superantigen speA gene via the ΦMGAS5005.1-like prophage. Furthermore, resistance to macrolides (97.7%) and tetracyclines (96.6%) was pervasive across both lineages, underscoring the severity of antimicrobial resistance in circulating GAS isolates. In conclusion, this study illuminates a distinct GAS epidemiological landscape in Beijing characterized by the local expansion of multidrug-resistant emm12 and emm1 clones. These findings emphasize the urgent need for continuous genomic surveillance to monitor the emergence of novel, hypervirulent recombinant variants within this distinct epidemiological context.IMPORTANCEGroup A Streptococcus poses a persistent global health challenge, capable of causing life-threatening invasive infections; thus, monitoring its evolving epidemiology is critical. Global surveillance activities have recently identified an upsurge of the hypervirulent M1UK lineage, and our study of pediatric infections in Beijing identifies a distinct local trajectory dominated by multidrug-resistant emm12 and emm1 lineages. Notably, we documented a horizontal gene transfer event where a multidrug-resistant emm12 isolate acquired the speA superantigen gene-a virulence factor typically associated with the emm1 lineage. This finding illustrates that endemic clones possess the genomic plasticity to combine high virulence potential with existing antimicrobial resistance. Our work highlights that beyond monitoring global high-risk clones like M1UK, observing local evolutionary dynamics is essential to anticipate emerging regional threats.},
}

@article {pmid42156565,
year = {2026},
author = {Ballaben, AS and Cabrera, JM and Moreira, LM and Chandler, M and Varani, AM},
title = {One Health Genomic Perspective on Pseudescherichia vulneris: A Neglected Reservoir of Last-Resort Resistance Genes.},
journal = {Current microbiology},
volume = {83},
number = {7},
pages = {},
pmid = {42156565},
issn = {1432-0991},
mesh = {*Genome, Bacterial ; Humans ; Anti-Bacterial Agents/pharmacology ; Plasmids/genetics ; Animals ; One Health ; Gene Transfer, Horizontal ; *Drug Resistance, Multiple, Bacterial/genetics ; *Enterobacteriaceae/genetics/drug effects ; Genomics ; Interspersed Repetitive Sequences ; *Drug Resistance, Bacterial/genetics ; Enterobacteriaceae Infections/microbiology/veterinary ; },
abstract = {Antimicrobial resistance (AMR) is a critical global threat, often driven by horizontal gene transfer mediated by mobile genetic elements (MGEs) such as plasmids, transposons, and integrons. Among Enterobacterales, IncHI2/IncHI2A plasmids are of particular concern, as they combine broad host range, conjugative potential, and mosaic architecture enriched with antimicrobial resistance genes (ARGs), biocide tolerance, and heavy-metal resistance. This study provides the first systematic comparative genomics of Pseudescherichia vulneris, an underrecognized yet genomically versatile species at the human-animal-environment interface. All 30 publicly available genomes were analyzed to reconstruct the pangenome, resistome, virulome, and associated MGEs. The pangenome was open, reflecting ongoing diversification and strong potential for horizontal gene acquisition. Resistomes were highly heterogeneous, ranging from minimal repertoires in most animal and environmental isolates to multidrug-resistance profiles in hospital-associated and occasional animal genomes. Clinically significant determinants, including blaKPC-2, blaKPC-3, blaCTX-M-9, and mcr-9, were frequently linked to MGEs. blaKPC alleles were mobilized by Tn4401-like elements, while mcr-9 occurred either within IncHI2/IncHI2A plasmids or integrated into chromosomal contexts, underscoring diverse mobilization routes. In contrast, the virulome was comparatively conserved, dominated by motility, chemotaxis, and siderophore systems, unlike pathogenic Enterobacterales that carry broad MGE-associated virulence factors. Co-occurrence analyses showed modular independence between resistance and virulence, with limited overlaps shaped by ecological origins, suggesting that resistome content may adapt to distinctive environments. Collectively, these findings establish P. vulneris as a reservoir and conduit of last-resort resistance genes, reinforcing its relevance for One Health surveillance and highlighting the urgent need for its systematic inclusion in global antimicrobial resistance monitoring frameworks.},
}

*Genome, Bacterial
Humans
Anti-Bacterial Agents/pharmacology
Plasmids/genetics
Animals
One Health
Gene Transfer, Horizontal
*Drug Resistance, Multiple, Bacterial/genetics
*Enterobacteriaceae/genetics/drug effects
Genomics
Interspersed Repetitive Sequences
*Drug Resistance, Bacterial/genetics
Enterobacteriaceae Infections/microbiology/veterinary

@article {pmid42156749,
year = {2026},
author = {Sommer, MOA and Munck, C},
title = {Reply to: Genome contamination may lead to an overestimation of horizontal gene transfer inferences.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42156749},
issn = {2041-1723},
support = {R140-2013-13496//Lundbeckfonden (Lundbeck Foundation)/ ; },
}

@article {pmid42155923,
year = {2026},
author = {Chao, S and Wen, P and Wang, XN and Liang, JL and Fang, Y and Qin, Y and Liao, JW and Shu, WS and Yi, X and Li, JT},
title = {Genomic expansion of efflux pumps is associated with metal-antibiotic super-resistance in bacteria from mining environments.},
journal = {Journal of hazardous materials},
volume = {512},
number = {},
pages = {142417},
doi = {10.1016/j.jhazmat.2026.142417},
pmid = {42155923},
issn = {1873-3336},
abstract = {The synergistic selective pressure of metals on antibiotic resistance can drive the emergence of metal-antibiotic super-resistance in bacteria, representing a critical yet understudied environmental health risk. Moreover, the genetic mechanisms underpinning this risk remain unclear. To address these knowledge gaps, we comprehensively profiled the phenotypic and genotypic metal-antibiotic co-resistance of bacteria from mine tailings and acid mine drainage sediments, which are widespread reservoirs of metal pollution. Our cultivation yielded 48 bacterial strains spanning four phyla and 29 genera. Remarkably, all 22 strains used for resistance test exhibited exceptional multi-drug and multi-metal co-resistance, with minimal inhibitory concentrations exceeding the established breakpoints for pathogens by 10- to 1000-fold. Whole-genome sequencing of two representative resistant strains (WK.6 and WK.16) revealed that they harbored 74 and 48 putative antibiotic resistance genes (ARGs), respectively. Strikingly, the majority of these putative ARGs (62 in WK.6 and 31 in WK.16) were identified as efflux pump genes, accounting for 82% and 65% of their respective antibiotic resistomes. Comparative genomic analysis against reference genomes from public datasets further indicated a significant enrichment of these efflux pump genes in the two strains. Additionally, 14.7% of the putative ARGs in WK.6 and 35% in WK.16 were found to be located within the active range of a specific mobile genetic element, suggesting a potential for horizontal gene transfer. Collectively, our findings suggest that the genomic expansion of efflux pumps may serve as a key genetic foundation for metal-antibiotic super-resistance, highlighting a potentially prevalent adaptive mechanism that may exacerbate the environmental dissemination of such super-resistance.},
}

@article {pmid42146701,
year = {2026},
author = {Hambücken, L and Baurain, D and Cornet, L},
title = {Exploring Thylakoid Emergence: Evolution of Membrane Biogenesis and Photosystem II assembly in early-diverging Cyanobacteria.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.06.686923},
pmid = {42146701},
issn = {2692-8205},
abstract = {Thylakoid membranes (TM) in cyanobacteria and chloroplasts host the light-dependent reactions of oxygenic photosynthesis. Gloeobacterales, the earliest-diverging cyanobacterial lineage, lack TM and perform photosynthesis in the cytoplasmic membrane, representing an ancestral state relative to other cyanobacteria (Phycobacteria). This study investigates the evolutionary origin of TM.Phylogenomic analyses were performed across a phylogenetically diverse set of cyanobacteria, including extensive representation of basal lineages (Gloeobacterales, Thermostichales, Gloeomargaritales and Pseudanabaenales), as well as micro- and macrocyanobacteria, using orthologous proteins involved in membrane dynamics and Photosystem II (PSII) assembly, together with structural modelling using AlphaFold3.We identified two candidate proteins associated with membrane trafficking that may contribute to TM biogenesis, including the SPFH family member Slr1106, proposed to have been acquired by lateral gene transfer. Analysis of 36 PSII assembly factors revealed modifications in late-stage assembly, notably in manganese homeostasis. Structural changes in the YidC translocase may have facilitated relocation of linear electron transfer components from the cytoplasmic membrane to TM.Altogether, these phylogenetic and functional prediction analyses provide new insight into the molecular innovations that led to TM emergence, including membrane trafficking systems, PSII assembly changes, and protein targeting adaptations.},
}

@article {pmid42149652,
year = {2026},
author = {Holtappels, D and Rickus, GEJ and Morgan, T and de Rezende, RR and Koskella, B and Alfenas-Zerbini, P},
title = {Comparative genomics reveals high prophage diversity and horizontal gene transfer of effectors and phage defence systems in the Pseudomonas syringae complex.},
journal = {Microbial genomics},
volume = {12},
number = {5},
pages = {},
pmid = {42149652},
issn = {2057-5858},
mesh = {*Pseudomonas syringae/genetics/virology ; *Prophages/genetics ; *Gene Transfer, Horizontal ; *Genomics/methods ; Bacteriophages/genetics ; Genome, Bacterial ; Genetic Variation ; Phylogeny ; },
abstract = {The mobilome, defined as the collection of mobile genetic elements within a bacterial genome, plays a role in the adaptation of bacteria to abiotic and biotic drivers. In particular, prophages have been reported to contribute to bacterial resistance to virulent bacteriophages, to competitive interactions among bacterial hosts within microbial communities and to pathogenicity and virulence. It is, therefore, critical to better understand the role of prophages in distributing genes and functions within and among bacterial species to predict how bacteria adapt to their biotic environment. Pseudomonas syringae offers an ideal study system to ask these questions, both because of its broad range of lifestyles (spanning from environmental growth to plant pathogens) and its high intraspecies diversity. To examine the role of prophages in this species complex, we compared 587 genomes available from public databases and annotated the defence mechanisms, effectors and prophages in the genomes. We found that this species complex has an elaborate phage pandefensome consisting of 139 defence mechanisms. Assessing taxonomical signatures of the observed prophages uncovered broad differences in the types and numbers of genes encoded by different phage families, emphasizing how the evolutionary advantages conferred to hosts can depend on the prophage composition and offering insight into how these genes might disperse within a community. Our study highlights the intimate association of specific phage families with their hosts and their potential role in shaping key ecological traits of these important species.},
}

*Pseudomonas syringae/genetics/virology
*Prophages/genetics
*Gene Transfer, Horizontal
*Genomics/methods
Bacteriophages/genetics
Genome, Bacterial
Genetic Variation
Phylogeny

@article {pmid42151510,
year = {2026},
author = {de Souza Pereira, LF and Tavares, TCS and Martins, DT and Dias Dantas, CW and de Souza, FOR and Prazeres, MCC and Faturi, C and Rogez, HLG and Ramos, RTJ and Cardenas Alegria, OV and Ribeiro Carneiro Nunes, A},
title = {Characterization of defensome genes and mobile genetic Elements in different types of pasture soil agroecosystems from the Brazilian Amazon.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {42151510},
issn = {1618-1905},
abstract = {The Amazon rainforest represents nearly 40% of the world's tropical forests and has undergone extensive conversion to pasture, profoundly altering soil microbial communities. Given that bacteriophage-driven selective pressure shapes bacterial defense systems (the defensome) as well as mobile genetic elements (MGEs), we examined the diversity and distribution of these genetic components in native forest soils and in pasture soils under two management regimes (with and without fertilization) in the Brazilian Amazon. Metagenomic sequencing revealed pronounced differences in bacterial community structure between forest and pasture sites (R = 0.942), whereas phages communities exhibited no significant variation. Pasture soils-particularly those under fertilization-showed higher abundances of functional genes and mobile genetic elements, including conjugative plasmid-associated genes and insertion sequences. Defensome analyses indicated an increased prevalence of retrons and Pycsar systems in managed soils, while a greater diversity of defense genes was observed in non-fertilized pastures. A strong positive correlation was observed between defensome diversity and MGE diversity, suggesting coordinated dynamics between viral selective pressure and horizontal gene transfer. These findings indicate that forest-to-pasture conversion reshapes microbial functional potential and amplifies genetic mechanisms linked to phage defense and gene mobility, with potential consequences for ecosystem functioning and the dissemination of antimicrobial resistance.},
}

@article {pmid42152762,
year = {2026},
author = {Yang, W and Guo, J},
title = {Unveiling the Hidden Resistome: A Comprehensive Risk Assessment of Latent Antibiotic Resistance Genes in China's Wastewater.},
journal = {Environmental microbiology},
volume = {28},
number = {5},
pages = {e70330},
doi = {10.1111/1462-2920.70330},
pmid = {42152762},
issn = {1462-2920},
support = {2021YFD1600400//National Key Research and Development Program of China/ ; },
mesh = {*Wastewater/microbiology ; China ; Risk Assessment ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; *Bacteria/genetics/drug effects ; Metagenome ; Genes, Bacterial ; Escherichia coli/genetics/drug effects ; *Drug Resistance, Microbial/genetics ; },
abstract = {Wastewater systems are important reservoirs of antibiotic resistance genes (ARGs), but the ecological and health risks of numerous latent ARGs (LARGs) remain unclear. In this study, we analysed 636 wastewater metagenomic samples from China and constructed a database containing 1587 LARGs. Across all environments, LARGs encoding serine-β-lactamases were the most abundant and prevalent. A comprehensive risk assessment, integrating host pathogenicity, gene mobility and environmental prevalence, was performed on 561 LARGs identified in metagenome-assembled genomes. Most LARGs exhibited low levels across all three dimensions, suggesting limited transmission risk. Nevertheless, 37 high-risk LARGs were identified, indicating non-negligible threats. Functional validation showed that the top three extremely high-risk LARGs significantly enhanced host resistance to ampicillin and ciprofloxacin when expressed in Escherichia coli, while AlphaFold3 revealed typical resistance protein folding, further supporting their functional activity. Horizontal gene transfer analysis indicated that these high-risk genes have disseminated from wastewater to natural water bodies such as rivers via plasmid-mediated mechanisms. Collectively, wastewater acts not only as an 'accumulation pool' for LARGs but also as a potential source releasing 'super-risky' resistance gene into the environment. Therefore, urgent efforts are needed to monitor and control these high-risk LARGs and their mobile genetic elements to block their environmental spread.},
}

*Wastewater/microbiology
China
Risk Assessment
Gene Transfer, Horizontal
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Bacterial/genetics
*Bacteria/genetics/drug effects
Metagenome
Genes, Bacterial
Escherichia coli/genetics/drug effects
*Drug Resistance, Microbial/genetics

@article {pmid42155712,
year = {2026},
author = {Geng, R and Huang, B and Duan, Z and Zhao, F and Lü, X and Jiang, Z and Yi, Y},
title = {Antimicrobial Efficacy and Food Application Potential of Bacteriocins LL3 and LL4 from Traditional Dairy-Derived Lactococcus lactis.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2026-28309},
pmid = {42155712},
issn = {1525-3198},
abstract = {To combat foodborne pathogens like Salmonella, this study employed an activity-based screening followed by metagenomic mining of the active isolates to discover and characterize bacteriocins from Inner Mongolian dairy products. From the 15 active isolates, Lactococcus lactis D63 and D64 were identified as harboring a putative biosynthetic gene cluster (BGC) encoding 2 bacteriocins, LL3 and LL4. Both peptides form amphipathic α-helical structures that disrupt bacterial membranes, leading to intracellular leakage and cell death. They exhibited effective antimicrobial activity, particularly against Salmonella Typhimurium. Crucially, when applied in a simulated milk model under standard refrigeration (4°C), synthesized LL4 demonstrated robust preservative efficacy by effectively controlling S. Typhimurium, showing comparable performance to the commercial preservative Nisin. Genetic analysis revealed that this BGC exhibits low basal transcription under standard laboratory growth conditions and shares high homology with plasmid elements, suggesting it is a mobile genetic element acquired via horizontal gene transfer. This study presents LL3 and LL4 as promising natural preservatives and validates metagenomic mining as an efficient strategy for uncovering antimicrobial genes.},
}

@article {pmid42142566,
year = {2026},
author = {Huang, H and Huang, D and Wang, G and Du, L and Chen, H and Zhou, W and Xu, W and Lei, Y},
title = {Microplastic-mediated antimicrobial resistance in aquatic environments: plastisphere dynamics, ecological risks, and mitigation strategies.},
journal = {Environmental research},
volume = {},
number = {},
pages = {124779},
doi = {10.1016/j.envres.2026.124779},
pmid = {42142566},
issn = {1096-0953},
abstract = {The plastisphere, formed by microbial colonization on microplastics (MPs) surfaces, is widely recognized as a key reservoir for antibiotic resistance genes (ARGs). The persistence of MP-associated biofilms further exacerbates the spread of antimicrobial resistance (AMR). How to mitigate MPs and ARGs becomes an emerging issue under the context of One Health. However, given the increasingly fragmented focus of current research, there is a lack of comprehensive reviews on the removal of MPs and ARGs. With this in mind, this paper discusses the mechanisms by which MPs promote AMR production and transfer, as well as the multi-level ecological risks of MPs-ARGs combined pollution. More importantly, we systematically summarize the mechanisms of various wastewater treatment technologies for the simultaneous elimination of ARGs and MPs, including comprehensive biological processes (wastewater treatment plants, constructed wetlands and membrane bioreactors) and physical/chemical processes (adsorption and advanced oxidation processes). Besides, the efficiency and disadvantages of these methods in removing MPs and ARGs from wastewater and future prospects are discussed. In summary, this article offers valid information to reveal the tip of the iceberg of the severity of MPs and ARGs combined pollution. And it promotes the progress of novel and viable methods for the simultaneous removal of MPs and ARGs.},
}

@article {pmid42143575,
year = {2026},
author = {Zhang, P and Zhao, M and Cheng, Z and Ding, Y and Xia, S and Guo, J},
title = {Bile acid metabolism dysregulation following Helicobacter pylori eradication promotes plasmid-mediated antimicrobial resistance in the gut microbiome.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag126},
pmid = {42143575},
issn = {1751-7370},
abstract = {Antimicrobial resistance (AMR) transmission within the gut microbiome poses a major health risk during antibiotic exposure, primarily via horizontal gene transfer (HGT). However, how antibiotic-induced metabolic remodeling of the intestinal environment modulates plasmid-mediated AMR dissemination remains unclear. Herein, integrating metagenomics, metabolomics, in vitro conjugation assays, and in vivo mouse models, we show that Helicobacter pylori eradication therapy reshapes gut metabolism in ways that enhance transfer of antibiotic resistance genes (ARGs). Metagenomic analysis revealed the expansion of Escherichia populations and the enrichment of plasmid-borne ARGs after H. pylori eradication. Fecal filtrates from treated individuals significantly increased conjugation frequencies of the broad-host-range plasmid RP4 in E. coli. Metabolomic profiling identified a pronounced accumulation of primary bile acids, including glycocholic acid, taurocholic acid, glycochenodeoxycholic acid, and taurochenodeoxycholic acids, which could increase bacterial membrane permeability, induce the SOS response, and upregulate conjugation and pilus assembly genes, thereby accelerating ARG transfer. Molecular docking further suggested these bile acids may likely participates in interacting with global plasmid repressors KorA/KorB, derepressing conjugation operons. In mice, H. pylori eradication therapy elevated fecal primary bile acid levels and significantly promoted in vivo plasmid transfer, with the critical role of bile acids further confirmed through interventions using the bile acid sequestrant cholestyramine or glycocholic acid. Together, these findings demonstrate that dysregulation of bile acid metabolism due to H. pylori eradication creates a permissive gut niche for plasmid-mediated ARG dissemination, providing mechanistic insight into how clinical antibiotic regimens can unintentionally promote microbiome-associated AMR risk.},
}

@article {pmid42143834,
year = {2026},
author = {Zheng, B and Qi, J and Ma, L and Hao, C and Zheng, X and Li, Y and Cheng, Y and Yue, C and Liu, Y},
title = {A risk assessment of the environmental and clinical implications of aquaculture-associated, multidrug-resistant Aeromonas veronii.},
journal = {Water research},
volume = {301},
number = {},
pages = {126007},
doi = {10.1016/j.watres.2026.126007},
pmid = {42143834},
issn = {1879-2448},
abstract = {The emergence and spread of antibiotic resistance genes (ARGs) mediated by mobile genetic elements (MGEs) pose a significant threat to public and environmental health. While aquaculture ecosystems are recognised as critical reservoirs for ARGs, the genomic architecture of MGEs that facilitate resistance dissemination in aquatic pathogens - particularly Aeromonas veronii (A. veronii) - remains underexplored. This study isolated a highly virulent, multidrug-resistant strain of A. veronii (Y6) from diseased largemouth bass, underscoring its potential dual threat to aquaculture and public health. Whole-genome sequencing revealed that strain Y6 harbours a chromosomal genomic island, GI22, containing a integron 1, which encodes 15 ARGs. Embedded within this island is a novel composite transposon, TnY6-1, which carries five of these ARGs and has the potential to facilitate horizontal gene transfer. Phylogenetic analysis revealed that strain Y6 clusters closely with human clinical isolates, underscoring its zoonotic potential. Comparative genomic analysis revealed that the resistance gene cassettes in integron 1 of strain Y6 are highly conserved across fish, human, and environmental isolates, suggesting the possibility of ARG transmission between different ecosystems. To quantify the environmental threat posed by TnY6-1, we applied a multidimensional risk assessment framework adapted from the PIPdb database. This marks the first classification of TnY6-1 as a Level IV high-risk MGE. These findings highlight the importance of implementing risk-based surveillance systems targeting hazardous MGEs in aquaculture to reduce the environmental-to-clinical spillover of antimicrobial resistance.},
}

@article {pmid42145856,
year = {2026},
author = {Lopes, IDS and Moreira, AJS and de Barros, M and Bueno, LMS and da Silva, GC and Rosa, JN and Caldeira, JLA and Barros, RA and Bazzolli, DMS and Moreira, MAS},
title = {Fingerprinting PCR Reveals Potential Dissemination of Multidrug Efflux System Genes and Antimicrobial Resistance in Staphylococcus aureus Across Primary Healthcare Units in Brazil.},
journal = {International journal of microbiology},
volume = {2026},
number = {},
pages = {9287240},
pmid = {42145856},
issn = {1687-918X},
abstract = {Multidrug efflux systems (MESs) are major contributors to antimicrobial resistance (AMR) in Staphylococcus aureus, yet their role in primary healthcare settings is poorly understood. Under a One Health framework, we investigated MES-mediated resistance in 38 S. aureus isolates (27 from humans, 11 from dogs) from three Basic Health Units (BHUs) in Viçosa, Brazil. Isolates were characterized by antimicrobial susceptibility testing, PCR for six key efflux genes, and (GTG)5-PCR fingerprinting. Phenotypic efflux activity was evaluated using ethidium bromide fluorescence assays. Thirty-seven isolates were resistant to at least one antimicrobial, most commonly penicillin (57.9%) and erythromycin (55.3%), while all remained susceptible to chloramphenicol, trimethoprim, and linezolid. While the msrA gene was rare (10.5%), other efflux genes like norA/B/C, lmrS, and tet38 were nearly ubiquitous (> 94%). This high genetic prevalence contrasted with low phenotypic resistance, indicating that most MES genes were not expressed. Fingerprinting revealed seven genetic clusters, demonstrating the circulation of closely related strains between human and animal hosts across different health units. Eight isolates showed clear genotype-phenotype concordance, with MES activity confirmed phenotypically. The four msrA-positive, erythromycin-intermediate isolates formed two clonal groups (100% similarity): one shared between two users from different BHUs and another shared between a healthcare worker and a dog from different BHUs, providing direct evidence of interhost and cross-geographic AMR dissemination. Moreover, co-colonization of a single individual with two genetically distinct tetracycline-resistant strains (60% similarity) suggests possible horizontal gene transfer. Although phenotypic MES-mediated resistance was limited (21%), we demonstrate the potential AMR spread across hosts and geographic boundaries, as primary healthcare settings harbor a significant reservoir of MES genes in S. aureus even if they are silent. These results highlight the critical need for integrated One Health surveillance in community settings to mitigate AMR dissemination.},
}

@article {pmid42139776,
year = {2026},
author = {Majumdar, A and Kotta-Loizou, I and Buck, M and Roychowdhury, T},
title = {Temperature-dependent biofilm and sublancin production arrest soil arsenic and antibiotic resistance gene mobility.},
journal = {Journal of hazardous materials},
volume = {512},
number = {},
pages = {142339},
doi = {10.1016/j.jhazmat.2026.142339},
pmid = {42139776},
issn = {1873-3336},
abstract = {Climate change-induced warming and arsenic soil contamination synergistically threaten agricultural sustainability by restructuring microbial communities and accelerating antimicrobial resistance dissemination. Here, through integrated greenhouse and field trials, we demonstrate that Bacillus subtilis 168-derived biofilm and sublancin, a glycosylated antimicrobial peptide, simultaneously immobilise rhizospheric arsenic and suppress horizontal transfer of antibiotic resistance genes (ARGs). Temperature-dependent biofilm formation (25-35°C) enhanced arsenic sequestration within the extracellular polymeric substance matrix, with SEM-EDX revealing a 74% increase in arsenic weight percentage at 35°C and ToF-SIMS confirming ∼14-fold and ∼9-fold increases in root-associated arsenic on biofilm-colonised surfaces in greenhouse and field trials, respectively. Sublancin production peaked at 30°C (129.72 mg L[-1]), selectively suppressing all 12 tested pathogenic Gram-positive species by 74-86% while preserving Gram-negative communities. Bio-amendment reduced horizontal gene transfer frequency by 74.7% (p < 0.001) across all temperature regimes. Transcriptomic profiling revealed coordinated upregulation of exopolysaccharide biosynthesis (FDR ∼1.0 × 10[-27]) and sublancin machinery (sunA: +3.5 log2), alongside downregulation of conventional ARGs (vanA, blaTEM: -2.5 to -4.0 log2). These findings establish sublancin as a dual-function, climate-adaptive soil bio-amendment simultaneously addressing arsenic bioaccumulation and antibiotic resistance gene dissemination under warming scenarios.},
}

@article {pmid42140123,
year = {2026},
author = {Chen, SY and Tang, YM and Zhu, D and Huang, K and Zhao, FJ},
title = {Exposure to arsenic and cadmium promotes conjugative transfer of plasmid-borne antibiotic resistance genes among soil microbiota.},
journal = {Ecotoxicology and environmental safety},
volume = {318},
number = {},
pages = {120269},
doi = {10.1016/j.ecoenv.2026.120269},
pmid = {42140123},
issn = {1090-2414},
abstract = {The spread of antibiotic resistance genes (ARGs) via horizontal gene transfer (HGT) poses a major global health threat. While cadmium (Cd) is known to influence ARG transfer in pure cultures, the effects of arsenic (As) and As-Cd co-exposure on plasmid-mediated conjugation, especially in soil, remain unclear. Here, we show that individual As (100-250 µM) or Cd (100-1000 µM) promoted the conjugative transfer of ARGs carried by plasmids R388 and RP4 in liquid medium, increasing frequency by 1.4- to 3.5-fold. In contrast, the As-Cd combination achieved similar promotion at only 25-50 µM each for the RP4 plasmid. In soil, the As-Cd mixture at concentrations slightly above or equal to environmentally relevant levels enhanced RP4 plasmid transfer to soil bacteria by 1.7- to 3.0-fold over 10 days, whereas individual metal(loid)s at the same concentrations had no significant effect. Metal(loid) exposure altered the composition of the soil transconjugant community, with some enriched taxa exhibiting potential metal(loid) resistance and pathogenic traits. Mechanistically, As exposure induced oxidative stress, SOS response, membrane damage, and viability reduction primarily in the donor (Escherichia coli SM10λπ), while Cd triggered the same four mechanisms mainly in the recipient (Pseudomonas putida KT2440). Their combination synergistically affected both strains at lower concentrations, eliciting a coordinated stress response encompassing all four pathways. Our findings demonstrate that both individual and combined As and Cd stress promote ARG dissemination, but their co-exposure achieves this promotion at substantially lower concentrations, highlighting a heightened risk in co-contaminated soils.},
}

@article {pmid42141512,
year = {2026},
author = {Li, Y and Sun, J and Dai, Z and Jin, LN and Chen, Z and Lin, D and Zhu, L},
title = {Antibiotic Metabolites Are an Overlooked Driver of Resistance Dissemination in Plant Systems.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c04146},
pmid = {42141512},
issn = {1520-5851},
abstract = {Antibiotic pollution in agroecosystems is widely recognized, yet the risks posed by their metabolites remain insufficiently addressed. Using lettuce as a model, we investigated how tetracycline (TC) and its metabolites, anhydrotetracycline (ATC) and epitetracycline (ETC), contribute to the dissemination of antibiotic resistance genes (ARGs). TC primarily accumulated in roots and declined during translocation, whereas ATC exhibited greater persistence and became the predominant residue through in planta transformation. At environmentally relevant concentrations (≤0.1 mg·L[-1]), ATC more effectively expanded the mobilizable resistome than the parent compound by inducing reactive oxygen species, activating the SOS response, increasing membrane permeability, and promoting RP4 plasmid conjugative transfer. These processes facilitated the acquisition of multidrug resistance and the colonization of plant tissues by human pathogens, including Stenotrophomonas maltophilia and Pseudomonas aeruginosa, thereby increasing ARG burdens in both rhizosphere and phyllosphere compartments. Metagenomic analysis further confirmed the coselection of nontetracycline ARGs, such as aph3'-I and catB, and the enrichment of efflux systems (acr/emr) in pathogenic bacteria. Our findings challenge the parent-compound-centered paradigm of antibiotic risk assessment by identifying ATC as a key high-risk driver of ARG dissemination in food plants and highlighting the need to incorporate transformation products into future management strategies.},
}

@article {pmid42142453,
year = {2026},
author = {Pan, Z and Ngoc, MN and Xie, Z and Wang, Q and Wang, J and Chen, X and Chen, C and Lin, Q},
title = {Persistence and dynamics of antibiotic resistance genes in livestock manure during anaerobic digestion.},
journal = {Waste management (New York, N.Y.)},
volume = {220},
number = {},
pages = {115590},
doi = {10.1016/j.wasman.2026.115590},
pmid = {42142453},
issn = {1879-2456},
abstract = {Livestock manure is a primary reservoir of antibiotic resistance genes, and anaerobic digestion is widely employed for its treatment. However, the reduction efficiencies of antibiotic resistance genes during anaerobic digestion vary drastically across studies, and the underlying mechanisms remain obscured by microbial complexity. This work systematically reviews the persistence and dynamics of antibiotic resistance genes in livestock manure anaerobic digestion through the lens of ecological community assembly, specifically examining the tradeoff between deterministic processes (e.g., temperature and pH filtering) andstochastic processes(e.g., microbial immigration and drift). We identify that microbial community diversity and interspecies interactions (cooperation vs. competition) play dual roles: high diversity can act as a barrier to antibiotic resistance gene invasion but also increases the range of potential horizontal gene transfer recipients. Furthermore, the role of viruses is re-evaluated, suggesting that their contribution to host lysis likely outweighs transduction in stable anaerobic digestion systems. By synthesizing evidence from manure-specific studies and bridging mechanistic gaps with fundamental anaerobic digestion microbiology, this review proposes that effective antibiotic resistance gene control requires shifting from simple parameter adjustment to the precise regulation of ecological niches, thereby minimizing environmental dissemination risks.},
}

@article {pmid42138983,
year = {2026},
author = {Touceda-Suárez, M and Ponsero, AJ and Barberán, A},
title = {Urban greenspaces harbour distinct plasmid communities enriched in heavy metal resistance and competitive traits in arid soils.},
journal = {Microbiology (Reading, England)},
volume = {172},
number = {5},
pages = {},
doi = {10.1099/mic.0.001705},
pmid = {42138983},
issn = {1465-2080},
mesh = {*Plasmids/genetics ; *Soil Microbiology ; *Metals, Heavy/pharmacology ; Soil/chemistry ; *Bacteria/genetics/drug effects/classification/isolation & purification ; Gene Transfer, Horizontal ; Metagenome ; Microbiota/genetics ; Cities ; Humans ; *Drug Resistance, Bacterial/genetics ; },
abstract = {Plasmids drive horizontal gene transfer, a fundamental mechanism for soil bacterial evolution and antibiotic resistance emergence. In arid regions, the transformation of natural soils into urban greenspaces introduces dramatic environmental changes that influence the adaptive strategies of soil micro-organisms. Additionally, urban greenspaces can act as interfaces of antibiotic resistance spread between environmental and human microbiomes. Here, we inferred plasmids from soil metagenomes of urban greenspaces in Tucson, AZ, USA, and nearby natural arid habitats. We found urban greenspaces to select for plasmids that carried genes that confer competitive advantages, including motility, prokaryotic defence and resistance to heavy metals. Notably, urban greenspace plasmids exhibited reduced diversity (genetic and functional variants), which could in turn constrain their adaptability to rapid environmental changes. These findings underscore the importance of plasmids as agents mediating soil microbial adaptation to human activities.},
}

*Plasmids/genetics
*Soil Microbiology
*Metals, Heavy/pharmacology
Soil/chemistry
*Bacteria/genetics/drug effects/classification/isolation & purification
Gene Transfer, Horizontal
Metagenome
Microbiota/genetics
Cities
Humans
*Drug Resistance, Bacterial/genetics

@article {pmid42127834,
year = {2026},
author = {Zhu, L and Huang, T and Wang, B and Zhou, L and Sun, Q and Chen, K},
title = {Antibiotics and antibiotic resistance genes increase cyanobacterial blooms by altering microbial nitrogen transformations in water and sediment.},
journal = {Water research},
volume = {301},
number = {},
pages = {126081},
doi = {10.1016/j.watres.2026.126081},
pmid = {42127834},
issn = {1879-2448},
abstract = {The effects of antibiotics and antibiotic resistance genes (ARGs) on endogenous nitrogen (N) biogeochemistry, particularly in relation to cyanobacterial bloom dynamics, remain poorly understood. Therefore, laboratory microcosms simulating the full life cycle of cyanobacteria were established to investigate the effects of clindamycin (CLIN), tetracycline (TC), sulfamethoxazole (SMX), and their mixture (MIX) on N cycling across the sediment-water interface. Antibiotics accelerated ammonia oxidation and thus nitrification in overlying water during cyanobacterial bloom and decline. ARGs may influence N-cycling functional microbiota and the associated N transformation processes indirectly through mechanisms such as MGEs-mediated horizontal gene transfer or modulation of microbial community structure. Antibiotics increased the ammonia supply in overlying water, thereby supporting cyanobacterial blooms, by increasing N-fixing genes and cyanobacteria and associated N fixation. In sediments, N-cycling genes and ARGs were core regulators of NO2[-]-N and NH3-N, suppressing organic N mineralization while promoting denitrification. At low ambient concentrations, CLIN and MIX stimulated cyanobacterial growth and bloom formation by increasing photosynthesis, strengthening N fixation capacity, and alleviating pressure from competing bacteria. By contrast, high concentrations caused toxic, inhibitory effects. Tetracycline increased cyanobacterial growth by reducing nutrient competition and increasing NH3-N uptake at all concentrations. Sulfamethoxazole at 1000 ng/L sustained a longer duration of cyanobacterial bloom, possibly because it alleviates bacterial competition via folate synthesis inhibition. Therefore, by mediating bacterial communities and functional genes, antibiotics and their ARGs regulate endogenous N cycling and consequently influence cyanobacterial blooms. These findings provide novel insights into the mechanisms behind cyanobacterial bloom outbreaks in eutrophic lakes and thus have important implications for managing endogenous pollution.},
}

@article {pmid42130746,
year = {2026},
author = {Wang, Y and Ni, J and Pan, J and Feng, R and Li, W and Zhang, X and Gao, C and Liao, L and Zhang, Z and Yue, H and Zhang, K and Zhang, L and Feng, C and Yao, D and Han, Y and Li, X and Zhou, X and Deng, Z and Zhang, J and Zhou, P and Jing, G and Zhang, Y and Chen, L and Pan, X and Chen, X and Bai, Y and Yan, Y and Huang, J and Ye, Z and Shen, X and Tian, M and Zufall, RA and Wang, P and Lynch, M and Long, H},
title = {Cross-domain transfer of trehalose biosynthesis genes contributes to adaptation in high-altitude environments.},
journal = {National science review},
volume = {13},
number = {8},
pages = {nwag117},
pmid = {42130746},
issn = {2053-714X},
abstract = {High altitudes pose extreme survival challenges for organisms, yet the origins and molecular strategies underlying their resilience remain poorly understood. Here, we report the molecular and evolutionary mechanisms underlying stress resilience in Apourosomoida sp. LHA081A01, a ciliate isolated from a high-altitude Tibetan salt lake that endures high salinity, low temperature, and hypoxia. We identified TreT glycosyltransferases, acquired through horizontal gene transfer from an anaerobic and halophilic Desulfobacteraceae bacterium, to be involved in the synthesis of α,α-trehalose-a universal protein stabilizer absent in most other ciliates but essential for counteracting multiple environmental stressors. Additional strategies include β-carotene accumulation to mitigate oxidative stress from hypoxia, along with numerous others common to many eukaryotes. Extensive gene family expansions and rapid divergence of stress‑responsive genes underscore their evolutionary significance and critical role in surviving harsh habitats. Intolerance to low salinity may render this ciliate, and other protists, vulnerable to climate‑driven salinity declines in Tibetan salt lakes. Together, these extraordinary features-shaped by horizontal gene transfer, natural selection, and regulatory plasticity-position high-altitude microbial eukaryotes as powerful extremophile models for uncovering the molecular mechanisms of stress resilience and adaptive evolution across life.},
}

@article {pmid42135638,
year = {2026},
author = {Yang, Y and Liu, JH and Li, CR and Guo, YB and Li, X},
title = {Global distribution, antimicrobial resistance, and virulence factors of Staphylococcus epidermidis revealed through population genomics.},
journal = {BMC genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12864-026-12922-5},
pmid = {42135638},
issn = {1471-2164},
support = {No. 2025033//Medical Research Project of Chengdu/ ; },
abstract = {BACKGROUND: Staphylococcus epidermidis, typically regarded as a harmless commensal, has become one of the major causes of nosocomial infections, including ocular, skin, medical device-associated and bloodstream infections. Therefore, we analyze its population structure through genomic analysis integrated with metadata.

RESULTS: We performed whole-genome sequencing-based population genomic analyses by integrating 1742 publicly available S. epidermidis genomes (accessed by August 2025) with 94 newly sequenced isolates. Our analyses revealed that S. epidermidis represents a species complex composed of four phylogenetic lineages (phylogroups 1-4) with diverse clonal backgrounds and a broad global distribution. The species harbors an open pan-genome and demonstrates a strong capacity to acquire novel genetic traits through mobile genetic elements. Extensive antimicrobial resistance and substantial virulence potential were observed across lineages. Notably, phylogroup 1, dominated by ST 2, exhibited a 97.8% detection rate of the methicillin resistance gene mecA, likely driven by clonal expansion and horizontal gene transfer, identifying it as a high-risk lineage. The analysis of enriched genes in blood-derived strains showed that the adaptability of S. epidermidis in bloodstream-associated environments is controlled by multiple genes, involving antimicrobial resistance, cell wall remodeling, environmental adaptation, and core metabolism.

CONCLUSIONS: This study provides a comprehensive population genomic framework for S. epidermidis, elucidating its population structure, genomic diversity, antimicrobial resistance, and virulence-associated genetic features. These findings offer valuable insights into the evolutionary dynamics and pathogenic potential of S. epidermidis and provide an important genomic resource to inform infection control strategies and clinical management.},
}

@article {pmid42136995,
year = {2026},
author = {He, Y and Xiang, G and Zhong, G and Zeng, J and Chen, C and Huang, B},
title = {The Adaptations of E. coli SM10λpir (pUCP24T) Under Constant Sub-MIC Gentamicin Treatment.},
journal = {The Canadian journal of infectious diseases & medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale},
volume = {2026},
number = {},
pages = {6978370},
pmid = {42136995},
issn = {1712-9532},
abstract = {BACKGROUND: Antibiotics, as a selection stress, could trigger specific responses in bacterial pathogens. This study aimed to investigate adaptive changes of E. coli SM10λpir (pUCP24T) under constant treatment of sub-MIC Gm (gentamicin).

METHODS: E. coli SM10λpir (pUCP24T) underwent continuous passage culture by serial transfer for 50 days on agar plates containing 30 μg/mL Gm to obtain E. coli SM10λpir (pUCP24T)-E. Two strains were compared for the horizontal gene transfer ability, stability of plasmid pUCP24T, fitness cost, and expression of conjugation-related genes. Based on whole genome and RNA sequencing data, functional enrichment analysis (GO and KEGG) was conducted, along with analyses of plasmid sequencing depth, SNPs, and differentially expressed genes (DEGs).

RESULTS: The conjugation frequency of E. coli SM10λpir (pUCP24T)-E with recipient PAO1 was higher, and its traI expression was significantly upregulated (p < 0.05). In the same strain, the growth rate and competition index were lower (p < 0.05); the sequencing depth of plasmid pUCP24T and the relative expression of the rep gene were much higher (p < 0.05), but the plasmid showed reduced stability. Functional enrichment analysis suggested a possible enhancement of certain physiological processes and metabolic pathways. A total of 1294 DEGs were detected, with obvious upregulation of hycB, hycD, nikE, cspA, and nanA, and obvious downregulation of gadB, gadC, yeiQ, and yjiH, transcription factors (appY, gadE), and sRNAs (arrS, isrC). Additionally, the expression of aerobic respiratory pathway genes (cyoABCDE) in E. coli SM10λpir (pUCP24T)-E increased significantly (p < 0.05).

CONCLUSIONS: The enhanced conjugation frequency during adaptation may be attributed to increased expression of the transfer gene traI and an elevated copy number of plasmid pUCP24T. A heavier fitness cost was imposed on the host during this process. Aerobic respiration and metabolic efficiency were likely potentiated. sRNA isrC was hypothesized to inhibit aerobic respiration by targeting the cytochrome bo oxidase subunit cyoD.},
}

@article {pmid42126071,
year = {2026},
author = {Pardeshi, LA and Kupczok, A and de Ridder, D and Smit, S and van der Lee, TAJ},
title = {Genus-wide homologous recombination of tail fibers maintains tailocin diversity in Pectobacterium.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evag106},
pmid = {42126071},
issn = {1759-6653},
abstract = {Due to their ability to kill closely related strains, phage tail-like bacteriocins, also called tailocins, play an important role in shaping bacterial communities. One such tailocin, called carotovoricin, is also known to be present in the Pectobacterium genus. However, little is known about its evolutionary dynamics and the scope of impact on species interactions in this genus. To investigate the diversity and evolution of carotovoricin, we performed a genus-wide, phylogenetically-structured pangenome study. This analysis inferred that the gene cluster responsible for carotovoricin biosynthesis is conserved across the genus and is located in the same gene neighborhood in all the species. Within the carotovoricin cluster, the tail fiber genes, which determine the host range specificity, exhibit high variability and discordance with the species phylogeny. We show evidence for an evolutionary mechanism involving recombination-mediated exchange of these tail fiber loci across the entire Pectobacterium genus, which complements the previously known mechanism for DNA sequence inversion to maintain tailocin polymorphism at the population level. In addition, the ability to exchange tail-fiber loci in a highly targeted and genus-wide manner could influence the community dynamics in nutrient rich environments such as infected plant tissues. In conclusion, the strong signal for carotovoricin retention and ability to exchange tail fibers indicates that it significantly contributes to the community interactions of the Pectobacterium phytopathogens.},
}

@article {pmid42127424,
year = {2026},
author = {Guo, B and Kong, L},
title = {Chromosome-level genome assembly of the sacoglossan sea slug Elysia atroviridis.},
journal = {The Journal of heredity},
volume = {},
number = {},
pages = {},
doi = {10.1093/jhered/esag037},
pmid = {42127424},
issn = {1465-7333},
abstract = {Some sacoglossan sea slugs (Gastropoda:Heterobranchia) possess the remarkable ability to sequester functional chloroplasts into digestive cells. Elysia atroviridis harvests chloroplasts from its algal prey, which are maintained for a relative long period in cells of the digestive tract. We successfully assembled a high-quality chromosome-level genome of E. atroviridis using PacBio and Hi-C sequencing technologies. The final assembly spans 829.0 Mb with contig and scaffold N50 length of 2.0 Mb and 43.9 Mb, respectively, 89.3% of the assembled sequences were anchored to 15 pseudochromosomes. We found no evidence for horizontal gene transfer (HGT), specifically, no photosynthetic genes encoded in the E. atroviridis nucleus genome. A total of 16,472 protein-coding genes were predicted, of which 96.0% were functionally annotated. Phylogenetic analysis indicated E. atroviridis and E. timida formed a clade and their divergence time was estimated approximately 33 million years ago (Mya). Collinearity analysis revealed a high level of synteny with the genome of both species. This genome provides a valuable resource for further investigation into the evolution and mechanisms of kleptoplasty in sacoglossa.},
}

@article {pmid42114082,
year = {2026},
author = {Kolbow, N and Kong, S and Chafin, T and Justison, J and Ané, C and Solís-Lemus, C},
title = {SNaQ.jl: Improved Scalability for Level-1 Phylogenetic Network Inference.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btag289},
pmid = {42114082},
issn = {1367-4811},
abstract = {MOTIVATION: Phylogenetic networks represent complex biological scenarios that are overlooked in trees, such as hybridization and horizontal gene transfer. Although numerous methods have been developed for phylogenetic network inference, their scalability is severely limited by the computational demands of likelihood optimization and the vastness of network space. Composite (or pseudo-) likelihood approaches like SNaQ have improved computational tractability for network inference, but they remain inadequate for datasets of sizes routinely handled by tree inference methods.

RESULTS: Here, we introduce SNaQ.jl, a new standalone Julia package with the composite likelihood inference originally implemented within PhyloNetworks.jl as well as new scalability features that enhance computational efficiency through (1) parallelization of quartet likelihood calculations during composite likelihood computation, (2) weighted random selection of quartets, and (3) probabilistic decision-making during network search. Through a simulation study and empirical data analysis, we show that this new version of SNaQ.jl (version 1.1) improves average runtimes by up to 499% on average with no change in function parameters or method accuracy.

SNaQ.jl is a new open source Julia package available at https://github.com/JuliaPhylo/SNaQ.jl.},
}

@article {pmid42114669,
year = {2026},
author = {Tolibov, M and Khasanov, S and Mirzabekova, O and Ismatova, M and Proshad, R},
title = {Extracellular vesicle crosstalk in urinary tract infections: Integrating host exosomes and pathogen-derived membrane vesicles for antimicrobial resistance monitoring and diagnostic innovation.},
journal = {Clinica chimica acta; international journal of clinical chemistry},
volume = {590},
number = {},
pages = {121064},
doi = {10.1016/j.cca.2026.121064},
pmid = {42114669},
issn = {1873-3492},
abstract = {Urinary tract infections (UTIs) remain a major global health burden, with rising antimicrobial resistance (AMR) posing severe challenges to diagnosis and treatment. While host-derived urinary exosomes have been recognized as promising noninvasive biomarkers for UTI, the role of pathogen-derived outer membrane vesicles (OMVs) in UTI pathogenesis and AMR has been comparatively underexplored. No comprehensive framework currently integrates both host extracellular vesicles (EVs) and pathogen-derived EVs in the context of UTI diagnosis and antimicrobial resistance monitoring. This review addresses this gap by synthesizing current evidence on the bidirectional EV crosstalk between uropathogens and host cells during UTI. We examine how host exosomes carry antimicrobial effectors and inflammatory signals, while pathogen OMVs serve as vehicles for horizontal gene transfer of antibiotic resistance genes, enzymatic degradation of antibiotics, and immune evasion. We evaluate the diagnostic potential of dual EV profiling, integrating host exosomal markers such as Akt, CD9, and miR-18a-5p with pathogen OMV markers including beta-lactamases and antibiotic resistance genes, to enable simultaneous UTI diagnosis and AMR prediction. We further discuss emerging microfluidic technologies for rapid EV isolation and characterization, the Target Product Profile and Target Specimen Profile frameworks essential for clinical translation, the role of fit-for-purpose specimen panels from professional biobanks in analytical and clinical validation, and the challenges in translating these findings into clinical practice. By bridging the host-pathogen EV divide, this review proposes a paradigm shift toward integrated extracellular vesicle-based diagnostics that could transform UTI management in the era of antimicrobial resistance.},
}

@article {pmid42119140,
year = {2026},
author = {Bao, Y and Ho, YW and Shen, Z and Lam, EY and Fang, JKH and Leung, KMY and Lee, PKH},
title = {Seasonal Divergence between Microbiomes on Microplastics and Natural Particles Increases with Rising Water Temperatures in Urban Rivers.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c13903},
pmid = {42119140},
issn = {1520-5851},
abstract = {The "plastisphere," which comprises microplastics (MPs)-associated microbial communities, is an emerging component of urban river ecosystems. However, its seasonal dynamics remain poorly understood, especially compared with microbiomes on natural particles (NPs). We therefore conducted a year-long metagenomic study at 15 sites across 10 major urban rivers in Hong Kong to compare MP- and NP-associated microbiomes across four seasons. Representative high-quality metagenome-assembled genomes revealed significant seasonal variations in both taxonomic and functional compositions across particle types, with water temperature identified as the primary environmental driver. As temperatures increased, both MP and NP microbiomes exhibited increased taxonomic and functional diversity but reduced functional redundancy and network stability. Compared to NPs, MP microbiomes exhibited higher taxonomic and functional turnover, more complex and connected cooccurrence networks, and distinct taxonomic and functional traits along the temperature gradient. In MP microbiomes, warmer conditions were associated with a higher abundance of pollutant-degrading and putatively virulent taxa (particularly from Firmicutes and Actinobacteria), along with enhanced biosynthetic functions and increased potential microbial sharing and horizontal gene transfer with surrounding aquatic microbiomes. These findings highlight the temperature-dependent ecological impacts of MP microbiomes and underscore the need to consider climatic factors when assessing the long-term ecological risks of MPs in urban riverine ecosystems.},
}

@article {pmid42123350,
year = {2026},
author = {Vacca, M and Calabrese, FM and Filannino, P and De Angelis, M},
title = {Genetically Modified Lactic Acid Bacteria in the EU Food Chain: Applications, Benefits, and Risk Assessment.},
journal = {International journal of molecular sciences},
volume = {27},
number = {9},
pages = {},
doi = {10.3390/ijms27093759},
pmid = {42123350},
issn = {1422-0067},
mesh = {Risk Assessment ; *Lactobacillales/genetics ; Humans ; European Union ; Gene Editing ; *Food Microbiology ; Lactococcus lactis/genetics ; *Microorganisms, Genetically-Modified/genetics ; Probiotics ; },
abstract = {Genetically modified (GM) lactic acid bacteria (LAB) are gaining attention as tools for innovation in the food sector, health applications, and industrial processes. LAB have long been used safely due to their GRAS/QPS status, making them suitable for improving fermentation and synthesizing specific and beneficial metabolites. Advances in genomics and gene editing have significantly expanded the available tools, ranging from classical mutagenesis to site-specific recombination, homologous recombination in non-coding regions, CRISPR-based systems, and food-grade chromosomal integration. These approaches enable the insertion of desired genes and the development of engineered strains with tailored functionalities. GM-LAB are also being studied as live delivery systems for therapeutic molecules, including cytokines, hormones, antimicrobial peptides, and vaccine antigens. Engineered strains of Lactococcus lactis and Lactobacillus spp. have yielded promising outcomes in applications such as mucosal immunization, modulation of inflammatory and metabolic responses, and inhibition of pathogenic microorganisms, including multidrug-resistant bacteria. From an industrial perspective, several studies highlight their potential for cost-effective recombinant protein production and the synthesis of high-value metabolites through fermentation. However, within the European Union, their use is subject to stringent regulatory oversight, requiring comprehensive molecular and environmental risk assessments, careful evaluation of horizontal gene transfer, and a preference for markerless chromosomal integrations. Despite these constraints, GM-LAB offer significant potential to improve food quality, sustainability, and human health.},
}

Risk Assessment
*Lactobacillales/genetics
Humans
European Union
Gene Editing
*Food Microbiology
Lactococcus lactis/genetics
*Microorganisms, Genetically-Modified/genetics
Probiotics

@article {pmid42124328,
year = {2026},
author = {Bonilla, M and El-Amrani, S and Galindo-Moreno, P and Mesa, F},
title = {Oral Phageome as Potential Modulators of Periodontal Dysbiosis. A Systematic Review.},
journal = {Oral diseases},
volume = {},
number = {},
pages = {},
doi = {10.1111/odi.70327},
pmid = {42124328},
issn = {1601-0825},
abstract = {INTRODUCTION: The oral phageome, comprising bacteriophages inhabiting the oral cavity, has been proposed as a potential modulator of periodontal health and disease. This systematic review synthesizes current evidence on interactions between bacteriophages, key periodontal bacteria, and the host in periodontitis.

METHODS: The review followed PRISMA guidelines and was registered in PROSPERO (CRD420250653631). A systematic search of the literature was conducted from January 2025 up to March 2025. Two independent PECOS strategies were applied to include clinical/observational and ex vivo studies. Risk of bias was assessed using the Newcastle-Ottawa Scale, Joanna Briggs Institute Checklist, and a modified SYRCLE's tool.

RESULTS: Of 965 records identified, 17 studies, comprising 623 patients, met the inclusion criteria. Clinical studies suggest alterations in the oral phageome in periodontitis, with increased abundance and activity of lytic phages, whereas temperate phages appear more prevalent in periodontal health. Ex vivo studies demonstrate that bacteriophages can interact with major periodontopathogens, influencing bacterial virulence, biofilm behavior, and horizontal gene transfer.

CONCLUSION: Current evidence does not establish a causal role for bacteriophages in periodontitis. Nevertheless, phages may function as contextual modulators of periodontal dysbiosis, particularly in A. actinomycetemcomitans-associated disease. Further longitudinal and functional multi-omics studies are needed to clarify their clinical relevance.

TRAIL REGISTRATION: PROSPERO ID: CRD420250653631.},
}

@article {pmid42125369,
year = {2014},
author = {, },
title = {Scientific Opinion on application (EFSA-GMO-UK-2009-76) for the placing on the market of soybean MON 87769 genetically modified to contain stearidonic acid, for food and feed uses, import and processing under Regulation (EC) No 1829/2003 from Monsanto.},
journal = {EFSA journal. European Food Safety Authority},
volume = {12},
number = {5},
pages = {3644},
pmid = {42125369},
issn = {1831-4732},
abstract = {Soybean MON 87769 was developed using Agrobacterium tumefaciens transformation and was intended to modify the lipid profile of the extracted oil. Soybean MON 87769 contains a single insert consisting of the Pj.D6D gene encoding the Δ6 desaturase protein from Primula juliae and the Nc.Fad3 gene encoding the Δ15 desaturase protein from Neurospora crassa, both involved in the desaturation of endogenous fatty acids into stearidonic acid. The molecular characterisation of soybean MON 87769 does not raise safety issues. Soybean MON 87769 differs from the conventional counterpart in its fatty acid profile. The safety assessment of the newly expressed desaturases identified no concerns regarding potential toxicity and allergenicity. Nutritional assessment of soybean MON 87769 and derived food products did not identify concerns about human health and nutrition. Consumption of MON 87769 soybean oil replacing other oils in food is not expected to result in adverse effects from increased SDA intake as shown in different exposure scenarios. There are no indications of an increased likelihood of establishment and spread of feral soybean plants. Considering the scope of the application, potential interactions of soybean MON 87769 with the biotic and abiotic environment were not considered a relevant issue. Environmental risks associated with a theoretically possible horizontal gene transfer from soybean MON 87769 to bacteria have not been identified. The post-market environmental monitoring plan and reporting intervals are in line with the intended uses of soybean MON 87769. Since the use of oil derived from the soybean MON 87769 will result in a higher intake of SDA, a post-market monitoring plan is recommended to confirm the exposure assessment using realistic consumption data for the European population.},
}

@article {pmid42125398,
year = {2014},
author = {, },
title = {Scientific Opinion on application (EFSA-GMO-NL-2010-77) for the placing on the market of herbicide-tolerant genetically modified cotton GHB614 × LLCotton25 for food and feed uses, import and processing under Regulation (EC) No 1829/2003 from Bayer CropScience.},
journal = {EFSA journal. European Food Safety Authority},
volume = {12},
number = {5},
pages = {3680},
pmid = {42125398},
issn = {1831-4732},
abstract = {Cotton GHB614 × LLCotton25 was produced by conventional crossing. The EFSA GMO Panel previously assessed the two single cotton events GHB614 and LLCotton25 and did not identify safety concerns. Integrity of the inserts was retained in the two-event stack cotton. No differences requiring further food and feed safety assessment were identified in the compositional analysis of cotton GHB614 × LLCotton25 except for a higher level of gossypol. The EFSA GMO Panel further assessed this difference and considers that it is of no safety relevance for animals and humans. Expression analysis and safety assessment of the newly expressed proteins identified no concerns regarding their potential toxicity and allergenicity. No indications of safety issues regarding the overall allergenicity of cotton GHB614 × LLCotton25 were identified. There are no indications of an increased likelihood of establishment and spread of feral cotton plants. Considering the scope of the application, potential interactions of cotton GHB614 × LLCotton25 with the biotic and abiotic environment were not considered a relevant issue. Environmental risks associated with an unlikely but theoretically possible horizontal gene transfer from cotton GHB614 × LLCotton25 to bacteria have not been identified. The post-market environmental monitoring plan and reporting intervals are in line with the intended uses of cotton GHB614 × LLCotton25.},
}

@article {pmid42113401,
year = {2026},
author = {Bhattacharjee, A and Singh, AK},
title = {Ecological and genomic insights into Bacillus altitudinis as a potential indicator of resistance genes in soil antimicrobial resistance pools.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {42113401},
issn = {1614-7499},
support = {OLP-2035//CSIR/ ; OLP-2081//CSIR/ ; OLP-2503A//CSIR/ ; GPP-0423//DST-ANRF/ ; },
abstract = {Soil associated with intensive poultry farming serves as a seminal reservoir of antimicrobial resistance genes. This study employed an integrated approach that combined metagenomics, phenotypic analysis, and whole-genome sequencing to investigate the soil resistome of poultry farms in the Jorhat district, Northeast India, and to evaluate Bacillus altitudinis as an environmental potential indicator for antimicrobial resistance. Metagenomic analysis of poultry-affected soil revealed a diverse array of resistance genes, including 753 unique resistance ontologies related to β-lactam, glycopeptide, macrolide, aminoglycoside, chloramphenicol, and colistin resistance. Culture-based testing of soil and fecal isolates (400 isolates) showed high resistance rates to colistin and ciprofloxacin (~60%), as well as notable resistance to erythromycin and kanamycin, indicating strong antibiotic selection pressures in these ecosystems. Among multidrug-resistant strains, B. altitudinis S2 was particularly notable, exhibiting high minimum inhibitory concentrations for last-line antibiotics such as vancomycin (>50 µg/mL), colistin (>50 µg/mL), and fourth-generation cephalosporins. It also demonstrated multidrug β-lactam resistance supported by synergistic inhibitors. Whole-genome sequencing (3.7 Mb) uncovered a complex antimicrobial resistance gene (ARG) profile, including vanZ, mcr-1, catA, mph, aph, and oxa-type β-lactamase genes, alongside multiple SMR, MATE, and RND efflux mechanisms. Many of these genes were located within genomic islands, prophage traces, and mobile genetic elements, strongly indicating horizontal gene transfer from various bacteria, including gut-associated enterococci. The genome also contained genes for resistance to heavy metals and oxidative stress, suggesting co-selection processes that sustain ARGs in soil. The study tries to show B. altitudinis as a crucial environmental indicator for ARGs, serving a genetic bridge between poultry gut microbiota and soil antimicrobial resistance pools, highlighting its significance for One Health antimicrobial resistance surveillance.},
}

@article {pmid42106898,
year = {2026},
author = {Shang, J and Zhao, J and Cai, Y and Chen, J and Sun, Z and Wei, Z},
title = {Molecular interface of plant-insect warfare: functions and applications of salivary effectors in piercing-sucking pests.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.70891},
pmid = {42106898},
issn = {1526-4998},
support = {32372633//National Natural Science Foundation of China/ ; 2023YFD1401000//National Key Research and Development Program of China/ ; },
abstract = {Piercing-sucking insects are a significant threat to global crop production, causing direct damage and transmitting pathogens. Conventional strategies like broad-spectrum insecticides face challenges such as pest resistance and environmental sustainability. Salivary proteins secreted during feeding are vital molecular effectors in mediating plant-insect interactions. Understanding their diverse functions is essential for developing novel, sustainable pest management strategies. This review highlights the multifaceted roles of salivary proteins in piercing-sucking insects. They are crucial for feeding (facilitating sheath formation and digestion), regulating growth and reproduction, and maintaining homeostasis. Notably, salivary proteins also modulate plant immunity, functioning as elicitors to trigger defenses or effectors to suppress them. Their functional diversity is further enhanced by evolutionary processes, including horizontal gene transfer, driving co-evolutionary dynamics between insects and plants. Salivary proteins show substantial agricultural potential as targets for RNA interference (RNAi)-based biopesticides and sources of resistance genes for engineering insect-resistant crops. Salivary proteins are critical regulators of plant-insect interactions and promising targets for next-generation pest control strategies. Future research should focus on elucidating less-explored functions, clarifying effector-receptor interactions, and employ multi-omics approaches to identify conserved targets. Translating these insights into applications, such as precision biopesticides and durable resistance in crops, will be crucial for establishing sustainable and effective crop protection systems. © 2026 Society of Chemical Industry.},
}

@article {pmid42106916,
year = {2026},
author = {Fleischhacker, D and Chen, YC and Gordo, NS and Cosic, A and Kalwong, R and Eberl, L and Schild, S},
title = {Host Factor Induced Bacterial Extracellular Vesicles Promote Horizontal Gene Transfer in Vibrio cholerae.},
journal = {Journal of extracellular vesicles},
volume = {15},
number = {5},
pages = {e70301},
pmid = {42106916},
issn = {2001-3078},
support = {10.55776//Austrian Science Fund/ ; P33073//Austrian Science Fund/ ; 32577//Austrian Science Fund/ ; //University of Graz/ ; },
mesh = {*Extracellular Vesicles/metabolism/genetics ; *Vibrio cholerae/genetics/metabolism ; *Gene Transfer, Horizontal ; Humans ; Mitomycin/pharmacology ; Bile ; },
abstract = {Like other Gram-negative bacteria, Vibrio cholerae, releases bacterial extracellular vesicles (BEVs), which have documented roles along the facultative human-pathogen's lifecycle. Most studies have focused on BEVs released its outermost surface under non-stressed conditions, which are mainly composed of outer membrane and periplasmic components. Herein, we comprehensively characterise stress-induced BEVs released upon exposure to the SOS response-inducing genotoxin mitomycin C or the antimicrobial emulsifier bile, which V. cholerae faces during intestinal colonisation. Compared to control BEVs from non-stressed V. cholerae cultures, MMC and bile trigger the release of a high number of enlarged, nucleic acid-rich BEVs with increased cytoplasmic content, a hallmark of cell lysis-derived BEVs. Despite similarities between stress-induced BEVs, our results indicate stressor-specific BEV compositions and divergent SOS response activation, suggesting different biogenesis routes and subtypes of stress-induced BEVs. Stress-induced BEVs promote horizontal gene transfer (HGT) of a chromosomal antibiotic resistance cassette during laboratory cultivation and intestinal colonisation. We provide novel insights in BEV-mediated HGT, which is independent of the PilA-pilus of the competence machinery, but requires the periplasmic ComEA complex and downstream components. BEV-mediated HGT is facilitated under intestinal conditions, that is, exposure to bile and proteases, which highlights the potential of genetic exchange via BEVs during host colonisation.},
}

*Extracellular Vesicles/metabolism/genetics
*Vibrio cholerae/genetics/metabolism
*Gene Transfer, Horizontal
Humans
Mitomycin/pharmacology
Bile

@article {pmid42107727,
year = {2026},
author = {Ramesh, K and Chellam, PV},
title = {Comparative genomic surveillance of fluoroquinolone resistance markers across major riverine hotspots by leveraging public metagenomes.},
journal = {International journal of antimicrobial agents},
volume = {},
number = {},
pages = {107839},
doi = {10.1016/j.ijantimicag.2026.107839},
pmid = {42107727},
issn = {1872-7913},
abstract = {The global surge in fluoroquinolone resistance (FQR) underscores the urgent need for robust environmental surveillance. From a One Health perspective, rivers serve as critical conduits and hotspots for antimicrobial resistance (AMR) dissemination. To address this, we conducted a systematic metagenomic surveillance of FQR across spatially prioritized freshwater ecosystems using distribution data of five major markers (gyr, par, qnr, aac, qep) retrieved from the National Center for Biotechnology Information (NCBI) Pathogen Detection Isolate Browser. Among 164 riverine metagenomic datasets, 31 high-quality datasets from the Mississippi, Yukon, Saint Lawrence, Yangtze, and Pearl rivers were analyzed. FQR genes were detected in 12 datasets, with normalized abundances ranging from 0.01 to 1.22 copies per bacterial cell. Plasmid-mediated qnrS2 and efflux pump genes (qepA2, AbaQ) emerged as the most prevalent determinants. Multivariate analyses revealed river-specific clustering patterns and strong correlations with metal resistance genes, highlighting co-selection pressures. The predominance of conjugative mobile genetic elements indicated an elevated potential for horizontal gene transfer. Taxonomic profiling further revealed enrichment of clinically important and World Health Organization (WHO) priority pathogens. Community structure analyses (Permutational Multivariate Analysis, R[2] = 0.7598, p = 0.003) confirmed significant microbial variations across rivers. Collectively, this integrative approach identifies environmental reservoirs of FQR genes, supporting river-based AMR surveillance. These insights are pivotal for shaping evidence-driven mitigation strategies and informing both national and global AMR policies.},
}

@article {pmid42108537,
year = {2026},
author = {Wajima, T and Kubota, T and Tanaka, E and Hirata, A and Uchiya, KI},
title = {Highly transformable Haemophilus influenzae as a potential amplifier of quinolone resistance dissemination.},
journal = {The Journal of antimicrobial chemotherapy},
volume = {81},
number = {6},
pages = {},
doi = {10.1093/jac/dkag160},
pmid = {42108537},
issn = {1460-2091},
support = {//JSPS/ ; 24K09785//KAKENHI/ ; //Takeda Science Foundation/ ; //Meijo University/ ; },
mesh = {*Quinolones/pharmacology ; *Gene Transfer, Horizontal ; *Haemophilus influenzae/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; Humans ; Haemophilus Infections/microbiology ; *Haemophilus/genetics/drug effects ; *Transformation, Bacterial ; DNA, Bacterial/genetics ; },
abstract = {BACKGROUND: Horizontal gene transfer in Haemophilus spp. is associated with antimicrobial resistance development. Recently, a relationship between quinolone resistance and this transfer has been reported. This study aimed to investigate the mechanisms underlying quinolone resistance spread by focusing on both homogeneous and heterogeneous transfer to H. influenzae.

METHODS: Quinolone-resistant strains of three Haemophilus spp., H. influenzae, H. haemolyticus, and H. parainfluenzae, were used as resistant donors. The H. influenzae laboratory strain Rd and the highly transformable strains 2017-22B and 2018-Y41 were used as recipients. Horizontal transfer assays were performed using genomic DNA from resistant donors or resulting transformants.

RESULTS: Horizontal transfer assays demonstrated that quinolone resistance was transferred from the genomic DNA of H. influenzae and H. haemolyticus to all recipient strains. In contrast, resistance from H. parainfluenzae genomic DNA was transferred only to the strains with higher transformability. In all cases, transfer efficiency was higher when DNA from the transformants was used than when DNA from the original strain was used. Notably, genomic DNA from transformants obtained by transferring resistance from H. parainfluenzae to highly transformable H. influenzae strains transformed Rd into a quinolone-resistant variant. Furthermore, no significant differences in growth were observed between the parent strains and transformants.

CONCLUSIONS: Our findings suggest that highly transformable strains, owing to their enhanced transformation capacity and retained fitness, may facilitate or amplify the dissemination of quinolone resistance under experimental conditions.},
}

*Quinolones/pharmacology
*Gene Transfer, Horizontal
*Haemophilus influenzae/genetics/drug effects
*Drug Resistance, Bacterial/genetics
*Anti-Bacterial Agents/pharmacology
Microbial Sensitivity Tests
Humans
Haemophilus Infections/microbiology
*Haemophilus/genetics/drug effects
*Transformation, Bacterial
DNA, Bacterial/genetics

@article {pmid42109805,
year = {2015},
author = {, },
title = {Scientific Opinion on an application (EFSA-GMO-BE-2011-98) for the placing on the market of herbicide-tolerant genetically modified soybean FG72 for food and feed uses, import and processing under Regulation (EC) No 1829/2003 from Bayer CropScience.},
journal = {EFSA journal. European Food Safety Authority},
volume = {13},
number = {7},
pages = {4167},
pmid = {42109805},
issn = {1831-4732},
abstract = {Soybean FG72 was developed by biolistic transformation to express the HPPD W336 and 2mEPSPS proteins, which confer tolerance to isoxaflutole- and glyphosate-based herbicides. The molecular characterisation of soybean FG72 did not give rise to safety issues. The agronomic and phenotypic characteristics of soybean FG72 tested under field conditions revealed no biologically relevant differences between soybean FG72 and its conventional counterpart that would give rise to any food and feed or environmental safety concerns. No differences in the compositional data requiring further safety assessment were identified. There were no concerns regarding the potential toxicity and allergenicity of the newly expressed proteins HPPD W336 and 2mEPSPS, and no evidence that the genetic modification might significantly change the overall allergenicity of soybean FG72. The nutritional characteristics of soybean FG72 is not expected to differ from that of non-GM soybean varieties. There are no indications of an increased likelihood of establishment and spread of feral soybean plants. Considering the scope of this application, interactions with the biotic and abiotic environment were not considered to be an issue. Risks associated with an unlikely but theoretically possible horizontal gene transfer from soybean FG72 to bacteria have not been identified. The monitoring plan and reporting intervals are in line with the scope of the application. In conclusion, the EFSA GMO Panel considers that the information available for soybean FG72 addresses the scientific comments raised by Member States and that soybean FG72, as described in this application, is as safe as its conventional counterpart and non-GM soybean reference varieties with respect to potential effects on human and animal health and the environment in the context of the scope of this application.},
}

@article {pmid42110713,
year = {2026},
author = {Larnyoh, MD and Amponsah, SK and Offei, A and Ofori, EK and Adi-Dako, O and Kwapong, AA},
title = {The Effect of Antibiotic and Nonantibiotic Drugs on Plasmid-Mediated Bacterial Conjugation.},
journal = {International journal of microbiology},
volume = {2026},
number = {},
pages = {3323758},
pmid = {42110713},
issn = {1687-918X},
abstract = {BACKGROUND: The clinical utility of antibiotics has been eroded by the emergence of antibiotic resistance. One major mechanism by which microorganisms develop resistance to antibiotics and nonantibiotics is by horizontal gene transfer (HGT) via plasmid-mediated conjugation.

AIM: To investigate the impact of specific antibiotics and nonantibiotics on plasmid-mediated bacterial conjugation and elimination.

METHODS: The minimum inhibitory concentration (MIC) of the selected antibiotics and nonantibiotics was determined for Escherichia coli (ATCC 25922) using the broth microdilution method. The anticonjugant activities of the test drugs were assessed using the liquid conjugation assay on plasmids IncN plasmid pKM101, IncP plasmid pUB307, and IncW plasmid R7K in E. coli. Additionally, the ability of the test drugs to eliminate and/or cure plasmids was determined.

RESULTS: At subinhibitory concentrations, several antibiotics-including azithromycin, doxycycline, and ceftriaxone-and nonantibiotic pharmaceuticals, such as amlodipine and propranolol, facilitated the horizontal transfer of plasmid-borne antibiotic-resistant genes in a plasmid-specific manner. Amlodipine notably enhanced the conjugative transfer of IncN plasmid pKM101 by 2.52-fold and the IncP plasmid pUB307 by 4.23-fold. Propranolol also increased the transfer of IncN plasmid pKM101, albeit modestly (1.14-fold). Plasmid curing activity was broad and nonselective in the case of amlodipine, doxycycline, glibenclamide, and levofloxacin, whereas propranolol exhibited plasmid-specificity curing activity, particularly against IncW plasmid R7K.

CONCLUSION: These findings demonstrate that antibiotics and nonantibiotic drugs can exert dual, context-dependent effects, simultaneously promoting plasmid transfer while eliminating specific plasmids. This plasmid-specific interplay highlights the complexity of drug-microbe interactions and underscores the need for careful evaluation of their roles in antimicrobial resistance dynamics.},
}

@article {pmid42112429,
year = {2026},
author = {Mbaraka, A and Meena, RR and Menghani, E and Verma, N},
title = {Targeting biofilm-driven antibiotic resistance: emerging mechanisms and next-generation therapeutic interventions.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1823476},
pmid = {42112429},
issn = {1664-302X},
abstract = {Biofilm mediated antimicrobial resistance (AMR) has become a critical global health and economic challenge, affecting both community and healthcare settings. Microbial Biofilms significantly enhance the antibiotic tolerance and cause the persistent and device-associated infections via limited drug penetration, degradation of antibiotics, and assist horizontal gene transfer. Biofilm-mediated antimicrobial resistance remains a major obstacle to treating infectious diseases today. Biofilms can boost antibiotic tolerance by up to 1,000 times and lead to chronic, persistent, and device-associated infections. The lack of FDA-approved anti-biofilm drugs highlights the urgent need for new therapeutic strategies and mechanistic insights. Redefining the treatment landscape and improving outcomes for resistant infections could be achieved through a multi-platform therapeutic approach. This review summarizes recent developments in our knowledge of how biofilms contribute to antibiotic resistance and highlights new therapeutic strategies, such as nanotechnology, antimicrobial peptides, bacteriophage-derived enzymes, quorum-sensing inhibitors, CRISPR-based tools, microbiome engineering, and AI-driven drug discovery.},
}

@article {pmid42112440,
year = {2026},
author = {Wang, J and Liang, Q},
title = {Beyond bactericidal: targeting plasmid-mediated antibiotic resistance with natural product-based plasmid curing agents.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1802582},
pmid = {42112440},
issn = {1664-302X},
abstract = {Antimicrobial resistance (AMR) has evolved into a severe global public health crisis, with plasmid-mediated horizontal gene transfer (HGT) serving as a core driver for the rapid dissemination of multidrug resistance (MDR). Traditional "bactericidal" antibiotic strategies impose strong selective pressure, failing to eradicate the root cause of resistance while accelerating the enrichment of resistant clones. "Plasmid curing"-a strategy that specifically eliminates resistance plasmids to restore antibiotic susceptibility-has emerged as a promising paradigm shift. While early synthetic curing agents suffered from severe cytotoxicity, natural products (e.g., alkaloids, quinones, terpenoids) exhibit unique potential owing to their structural diversity and multi-target profiles. This review systematically elucidates the molecular mechanisms by which natural products achieve plasmid eradication, including the disruption of Rep-ori replication initiation, interference with ParA-ParB partitioning dynamics, and the blockade of conjugation via type IV secretion system (T4SS) and quorum sensing (QS) inhibition. Crucially, we critically evaluate the methodological workflows-from high-throughput screening to absolute quantitative PCR-necessary to strictly differentiate true in vivo plasmid curing from mere selective bactericidal artifacts. Furthermore, we address current translational bottlenecks, particularly the "therapeutic window paradox," and highlight how integrating advanced nanotechnology, artificial intelligence (AI)-guided drug discovery, and CRISPR-Cas9 synergies will propel the field forward. By shifting the therapeutic paradigm from violent "bacterial killing" to ecologically intelligent "genetic disarmament," natural plasmid-curing agents offer a vital, adjunctive solution for safeguarding the lifespan of legacy antibiotics.},
}

@article {pmid41967492,
year = {2026},
author = {Meza-Padilla, I and Avrani, S and Müller, KM and Nissimov, JI},
title = {A jumbo cyanophage encodes the most comprehensive ribosomal protein set in the known virosphere.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
doi = {10.1093/ismejo/wrag084},
pmid = {41967492},
issn = {1751-7370},
support = {//Secretaría de Ciencia, Humanidades, Tecnología e Innovación (SECIHTI) Becas de Posgrado para Maestrías y Doctorados en Ciencias y Humanidades en el Extranjero scholarship/ ; RGPIN-2022-03350//Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; DGECR-2022-00329//Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; },
mesh = {*Ribosomal Proteins/genetics ; Genome, Viral ; *Bacteriophages/genetics ; *Microcystis/virology ; *Viral Proteins/genetics ; Phylogeny ; Gene Transfer, Horizontal ; Evolution, Molecular ; },
abstract = {It has been proposed that a defining distinction between viruses and cells lies in the absence or presence of ribosomal genes, respectively. Recent studies revealing that viruses occasionally encode ribosomal proteins (RPs) have challenged this view. However, so far, only viral genomes with up to three RPs have been discovered. Here, we perform a functional genome analysis of the Microcystis jumbo phage PhiMa05 and show that it encodes six RPs, an RP acetyltransferase, and a ribosome biogenesis protein. To our knowledge, this makes PhiMa05 the first cyanophage reported to encode RPs, as well as the virus with the most comprehensive RP-coding set of the known virosphere. Evolutionary analyses suggest that these viral RP-coding genes may have been horizontally transferred from a temperate ancestor of PhiMa05 to certain members of the Vampirovibrionia, a non-photosynthetic basal lineage of Cyanobacteriota, via the integration of the viral genome. We find that four RPs, the RP acetyltransferase, and the ribosome biogenesis protein of the PhiMa05-like prophages are the only copies of those proteins that the near-complete genomes of some Vampirovibrio hosts possess. We hypothesize that such cellular organisms may depend on the PhiMa05-like prophage for protein synthesis, and hence life itself. Collectively, our results provide evidence for the existence of viruses with particularly enriched sets of RP-coding genes and indicate that, in some cases, such viral genes have been transferred to cells, potentially becoming essential for the survival of the host.},
}

*Ribosomal Proteins/genetics
Genome, Viral
*Bacteriophages/genetics
*Microcystis/virology
*Viral Proteins/genetics
Phylogeny
Gene Transfer, Horizontal
Evolution, Molecular

@article {pmid42103022,
year = {2026},
author = {de Souza Teixeira Campos, ME and da Costa Custódio, DA and Pereira, CR and Moreira, JLF and Silva, BB and de Carvalho Azevedo, VA and Brenig, B and Silva, ROS and Wouters, ATB and Dorneles, EMS},
title = {Genotypic diversity and zoonotic potential of Salmonella enterica from multiple hosts: implications for One Health.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108513},
doi = {10.1016/j.micpath.2026.108513},
pmid = {42103022},
issn = {1096-1208},
abstract = {Salmonella enterica is a major zoonotic pathogen with significant impact on human and animal health. In this study, 28 isolates obtained from 20 domestic and wild animals in Brazil were characterized using phenotypic antimicrobial susceptibility testing, epidemiological profiling, and whole-genome sequencing (WGS). The isolates were obtained from a diversity of host species and included globally relevant serotypes such as Newport, Typhimurium, and Dublin, as well as three strains classified as subsp. houtenae, two of which were associated with fatal septicemic disease in dogs. Pangenome, mobilome, and multilocus sequence typing (MLST) analyses revealed pronounced genomic plasticity, with only one-third of genes classified as core and the majority comprising accessory or strain-specific repertoires, reflecting a high adaptive potential. Plasmid analysis identified a diverse set of replicon types, including conjugative elements associated with horizontal gene transfer, indicating a central role of mobile genetic elements in shaping the accessory genome. High levels of resistance to clinically important antimicrobials, notably tetracycline, ciprofloxacin, and ampicillin, were observed, together with a substantial proportion of multidrug-resistant and extensively drug-resistant isolates. Genomic analyses detected 58 resistance-associated genes (including both intrinsic and acquired determinants) and 127 virulence-associated genes, with associations observed between key determinants (e.g., tetA and blaTEM-1) and corresponding phenotypic resistance, supporting the potential utility of WGS-based resistance prediction. The frequent co-occurrence of resistance and virulence determinants, often linked to mobile genetic elements, may enhanced capacity of these strains to persist, disseminate, and cause disease across different host species. Although limited by sample size and geographic scope, this study provides insights into the genetic diversity and potential epidemiological relevance of S. enterica within the studied context circulating among domestic and wild animals in Brazil. The findings highlight the circulation of genetically diverse and potentially high-risk strains, including non-enterica subspecies associated with severe systemic infection, and emphasize the value of integrated phenotypic and genomic surveillance to support risk assessment and inform prevention and control strategies.},
}

@article {pmid42103262,
year = {2026},
author = {Kannan, EP and Venkatachalam, P and Raja, G and Sarkaraisamy, P and Gopal, J and Muthu, M},
title = {Detoxification of antibiotic pollution using nanoparticle systems: Introspecting the mechanisms, current status and emerging trends.},
journal = {Environmental research},
volume = {},
number = {},
pages = {124683},
doi = {10.1016/j.envres.2026.124683},
pmid = {42103262},
issn = {1096-0953},
abstract = {The irrational usage and improper disposal of antibiotics in healthcare facilities, households, animal husbandry and agriculture had resulted in widespread accumulation of antibiotic residues in environment. The antibiotic residues play a critical role in accelerating the onset antimicrobial resistance (AMR), by selective pressure on the ecological niche which in turn gets disseminated through vertical and horizontal gene transfer mechanisms among bacteria. This AMR when gets transmitted across environments and to humans causes catastrophic threat to one health. In addition, the antibiotic accumulation disrupts microbial community structure, impairs soil fertility by altering nutrient cycling processes and bioaccumulates in food chains also posing significant ecological imbalances and long-term risk to human and one health. In recent years nanomaterials have emerged as promising candidates for antibiotic detoxification due to their unique physiochemical properties such as tuneable surface properties, higher surface area and enhanced reactivity at nanoscale. By degrading antibiotics from environment nanomaterials reduces the antibiotic exposure and hence reduced the emergence of AMR pathogens and AMR genes (ARGs). Despite the rapid progress, the existing studies remain fragmented lacking a consolidative framework to assess the application of nanoparticle systems for antibiotic degradation. Hence this review bridges the gap by critically comparing and analysing the existing nanomaterials for antibiotic degradation in colloidal system. Further it addresses the knowledge gap and future research directions essential for adapting newer solutions to mitigate antibiotic pollution and their diverse ecological effects.},
}

@article {pmid42103887,
year = {2026},
author = {Brito, PH and Gil, V and Pontes, A and Silva, M and Gonçalves, C and Gonçalves, P},
title = {Regions of low gene expression promote maintenance and adaptation of horizontally acquired genes in yeasts.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-026-10153-8},
pmid = {42103887},
issn = {2399-3642},
abstract = {We showed previously that yeasts in Starmerella and Wickerhamiella genera (W/S clade) exhibit numbers of horizontal gene transfer (HGT) events much larger than found in any other yeast species, with bacteria and other fungi (Pezizomycotina) as donors. Here we shed light on HGT in the W/S clade by carrying out the characterization of xenologous genes present in three species harboring together close to 600 xenologous genes. Metabolic genes were strongly overrepresented and either introduced functions new to yeasts or restored functions that were likely absent in the W/S clade ancestor. RNA-sequencing revealed lower global levels of expression of xenologous vs native yeast genes in two species. This difference is associated with the preferential accumulation of xenologous genes in large, AT-enriched chromosome terminal regions, dubbed "End" domains, characterized by overall lower gene expression. In one species, "End" domains were shown to be more permissive for protein diversification, but only for xenologous genes. We posit that "End" domains may generate favorable conditions for the adaptation and retention of xenologous genes, helping explain the exceptional numbers of HGT events in the W/S clade.},
}

@article {pmid42092757,
year = {2026},
author = {Assis, RAB and Varani, AM and Shands, AC and Sagawa, CHD and Patané, JSL and Setubal, JC and Zaini, PA and Almeida, NF and de Souza, RF and Garcia, CCM and Orellano, EG and Adaskaveg, JE and Dandekar, AM and Moreira, LM},
title = {Unlocking the genetic arsenal of Xanthomonas arboricola: new insights into taxonomic classification, pathogenicity and adaptation beyond the effectorome.},
journal = {BMC genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12864-026-12916-3},
pmid = {42092757},
issn = {1471-2164},
support = {LMM, AMV, NFA, JCS//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; LMM, AMV, NFA, JCS//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; LMM, AMV, NFA, JCS//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; LMM, AMV, NFA, JCS//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
abstract = {BACKGROUND: Xanthomonas arboricola (Xar) is a phytopathogenic bacterial species responsible for economically significant diseases in a wide range of plants, including agricultural, ornamental, and forest species. This study aimed to investigate the genomic basis of host specificity, adaptation, and virulence in Xar through comprehensive comparative genomics.

RESULTS: A total of 177 genomes from nine Xar pathovars were analyzed for evolutionary relationships and effector repertoires. From these, 30 genetically diverse genomes were selected for in-depth comparison. Core, unique, and shared genes were identified and functionally annotated, focusing on their potential roles in adaptation and pathogenicity. Nineteen of the genomes were originally misclassified and did not belong to the Xar species. The remaining 158 genomes clustered into three major clades: I (Xar. pv. juglandis), II (Xar. pv. pruni + Xar. pv. corylina), and III (miscellaneous Xar). Clades I and II exhibited high effector diversity, ranging from 38 to 54 genes, with Xar. pv. corylina harboring the most. In contrast, Clade III genomes had significantly fewer effectors, with subclade IIIa containing only 5 and IIIb up to 15. Only one TAL effector was found in nine Xar. pv. corylina strains (with no conserved RVD patterns) and in both Xar. pv. guizotiae strains (up to 31 RVDs identified). Phylogenomic and effectorome analyses revealed potential genomic islands acquired via horizontal gene transfer, encoding metal metabolism genes, type II/IV secretion systems, and DNA modification enzymes. Additionally, several gene losses were observed: 19 genomes lacked flagellar assembly genes, 15 lacked nitrate metabolism genes, and 9 lacked cellulose biosynthesis and secretion genes. In contrast, all genomes possessed a lasso peptide biosynthetic cluster, highlighting recurrent genomic rearrangements through insertions and deletions.

CONCLUSIONS: This study provides a refined understanding of the genetic diversity and adaptive mechanisms in X. arboricola, emphasizing gene gain/loss events as central to pathovar-specific metabolic and virulence traits. These findings identify novel molecular markers with potential applications in diagnostics and targeted disease control strategies. In particular, the characterization of conserved and lineage-specific effector repertoires provides a framework to inform strategies for breeding resistance through the identification of candidate targets for durable host immunity.},
}

@article {pmid42094579,
year = {2026},
author = {Malaluan, RPP and Dy, RLV},
title = {Acquisition of novel arrays via horizontal gene transfer rewire CRISPR-mediated defense in Pseudomonas aeruginosa.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.27.721218},
pmid = {42094579},
issn = {2692-8205},
abstract = {CRISPR-Cas systems form the adaptive immunity of prokaryotes, conferring sequence-specific protection against genetic parasites. Here, we functionally characterized the CRISPR-Cas system of Pseudomonas aeruginosa ATCC 10145 (PA10145), which led us to discover the existence of an isolated CRISPR array, unique to this system. PA10145 possesses a type I-F CRISPR-Cas composed of a cas operon flanked by two divergently organized CRISPRs. The isolated CRISPR array, CRISPR3, is located ∼1.3 million bp away from the cas loci. The cas and three CRISPR arrays are active. Plasmids with an engineered protospacer matching any of the three arrays were targeted and stimulated hyperactive adaptation in all CRISPR arrays of PA10145 if the plasmids possessed an intact protospacer adjacent motif (PAM), whereas minimal to no adaptation was observed when PAM was mutated. Spacer acquisition via interference-driven adaptation proceeds through strand-biased priming in PA10145. Interestingly, the isolated CRISPR3 and the cas -adjacent CRISPR2 have nearly identical leader sequences with only 3 bp mismatches. From a survey of CRISPR loci in 1,198 P. aeruginosa genomes, isolated arrays only occur as type I-F with similarly matching leaders to CRISPR2. Highly-transmissible mobile genetic elements (MGEs) associate with CRISPR2 and CRISPR3, suggesting that isolated arrays might have originated from recombination events involving CRISPR2 as facilitated by these MGEs. Tracing evolutionary trajectories of the isolated CRISPR3 relative to cas -adjacent arrays revealed that CRISPR3 is laterally transferred across P. aeruginosa genomes. Taken together, these results implicate the role of horizontally-acquired isolated arrays in CRISPR-mediated pan-immunity as gateways to mobilize genetic memories.},
}

@article {pmid42097142,
year = {2026},
author = {El Mouali, Y and Tawk, C and Huang, KD and Sivapornnukul, P and Mengoni, C and Segata, N and Strowig, T},
title = {Biogeography-associated emergence of enhanced oxygen tolerance in the abundant human gut commensal Segatella copri.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.04.006},
pmid = {42097142},
issn = {1934-6069},
abstract = {In the human gut, oxygen levels decrease with increasing distance from the epithelium, creating a gradient that dictates the spatial distribution of commensal bacteria based on varying oxygen tolerance. However, dietary and lifestyle changes can disrupt this ecosystem. Segatella copri, a prevalent ancestral commensal, typically displays greater oxygen sensitivity than Bacteroides species. Here, we find that the transcriptional regulator PerR controls a genetic network underlying S. copri's oxygen response that is critical for gut colonization. Notably, a subset of S. copri strains have acquired an additional oxygen response regulator, OxyR, likely through horizontal gene transfer from other Bacteroidales, conferring enhanced oxygen tolerance. Interestingly, OxyR-positive strains are more prevalent in industrialized countries yet absent in contemporary humans with traditional lifestyles and in ancient human samples. These findings point to recent evolutionary pressures on Segatella, potentially driven by lifestyle changes, which may impact the spatial distribution of the human gut microbiome.},
}

@article {pmid42100691,
year = {2026},
author = {Janelidze, D and Kobakhidze, S and Elbakidze, T and Kotetishvili, M},
title = {Evolution and transmission landscape of the staphylococcal msrA gene mediating resistance to 14-membered macrolides and type B streptogramins.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1815688},
pmid = {42100691},
issn = {1664-302X},
abstract = {INTRODUCTION: Staphylococcus species, particularly Staphylococcus aureus, are leading opportunistic pathogens responsible for a wide range of infections, with antimicrobial resistance-including high rates of macrolide resistance-severely limiting treatment options. The msrA gene encodes the ABC-F protein MsrA, which mediates inducible resistance to 14-membered macrolides and type B streptogramins. Despite its clinical and epidemiological relevance, the evolutionary forces, selective pressures, and transmission routes shaping msrA in staphylococci remain insufficiently understood.

METHODS: Six hundred and one complete staphylococcal msrA coding sequences (CDSs) were retrieved from GenBank. Evolutionary analyses of msrA included nucleotide diversity (π), selection metrics (dN-dS , πa/πs, Tajima's D, Fu's Fs, FUBAR, MEME, and aBSREL), and conservation mapping using DnaSP in relation to MsrA functional domains (UniProt P23212). Linkage disequilibrium (LD) was assessed using ZnS, Za, ZZ, and Wall's statistics. Recombination and transmission pathways were inferred using GARD, RDP4-embedded algorithms, SplitsTree network analysis, and the PHI test.

RESULTS: Forty-one msrA allelic variants were determined, with five predominant alleles accounting for approximately 90% of CDSs; allele 19 was almost exclusive to S. aureus. Nucleotide diversity was moderate (π ≈ 0.039-0.042), and strong purifying selection predominated (πa/πs ≈ 0.169; dN-dS  = -0.138 ± 0.016; strongly negative Fu's Fs), with only four codons showing evidence of episodic positive selection. Three highly conserved regions were identified, mainly overlapping the inter-domain linker and the second nucleotide-binding domain across MsrA. Moderate-to-high LD with minimal decay indicated the persistence of only a limited number of successful allelic variants. Predominant msrA alleles were largely plasmid-associated. Recombination analyses revealed frequent interspecies transfer within Staphylococcus, with S. aureus acting as a central donor to Staphylococcus chromogenes and Staphylococcus saprophyticus, as well as rare intergeneric transfers involving Citrobacter, Enterococcus, Corynebacterium, and Pseudomonas.

CONCLUSION: These findings support a dual evolutionary strategy for msrA: strong purifying selection preserves its essential ribosomal-protection function, while plasmid-mediated dissemination promotes the spread of fit alleles. S. aureus appears to be a key reservoir and vector, facilitating both interspecies and intergeneric transmission. Clinically, this underscores the need for surveillance of plasmid-borne msrA and targeted control of S. aureus reservoirs to limit resistance to macrolides and type B streptogramins.},
}

@article {pmid42101992,
year = {2026},
author = {Csűrös, M},
title = {Reconstructing ancient genomes from gene counts: A robust likelihood framework with sampling bias correction.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {19},
pages = {e2537812123},
doi = {10.1073/pnas.2537812123},
pmid = {42101992},
issn = {1091-6490},
mesh = {Phylogeny ; *Evolution, Molecular ; Likelihood Functions ; Models, Genetic ; *Genome, Archaeal/genetics ; Archaea/genetics ; Gene Transfer, Horizontal ; },
abstract = {Deducing the makeup of ancient genomes is a fundamental challenge in evolutionary biology. While vast genomic datasets exist that span the entire tree of life, current methods for ancestral reconstructions struggle to resolve the inherent ambiguities of gene-sequence evolution at scale. Here, we present a numerically robust computational framework that overcomes the topological uncertainty of gene trees. Instead of tracking every single event, our phylogenetic gain-loss-duplication (GLD) model is based on birth-death processes over gene copies along the species tree. We show that the likelihood and its gradient can be computed efficiently under an adjustable observation bias of minimum gene family size. The framework facilitates unconstrained numerical likelihood maximization and ancestral inference by posterior probabilities. We apply this framework to kingdom-level reconstructions over a 269-genome archaeal dataset and demonstrate that GLD recovers ancestral states with high accuracy. We compare GLD inference with phylogenetic reconciliation from gene sequences (ALE method) and show that implausibly frequent horizontal gene transfer inferred by ALE are often statistical artifacts of collapsing phylogenetic signals in large alignments. In contrast, GLD inferences reveal how two layers of opposing evolutionary mechanics shape microbial genomes: a high-frequency tension between genome streamlining and the pervasive influx of transient genes, complemented by an adaptive counterbalance of recurrent, modular losses, and punctuated massive gains. The GLD framework provides a statistically sound foundation for hypothesizing about gene content evolution across the diversity of entire kingdoms.},
}

Phylogeny
*Evolution, Molecular
Likelihood Functions
Models, Genetic
*Genome, Archaeal/genetics
Archaea/genetics
Gene Transfer, Horizontal

@article {pmid42102165,
year = {2026},
author = {Brann, T and Souza de Oliveira, F and Iriarte, A and Protasio, AV},
title = {Host-Parasite Interactions Revisited: Evidence of Horizontal Transfer of a Transposable Element Between a Snail and Its Parasite.},
journal = {Genome biology and evolution},
volume = {18},
number = {5},
pages = {},
doi = {10.1093/gbe/evag107},
pmid = {42102165},
issn = {1759-6653},
support = {//Department of Pathology, University of Cambridge/ ; 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; //Institutional Internationalization Program (CAPES/PRINT) from Universidade Federal do Paraná (UFPR)/ ; //Christ's College Cambridge/ ; },
mesh = {Animals ; *Gene Transfer, Horizontal ; *DNA Transposable Elements ; *Host-Parasite Interactions/genetics ; *Schistosoma mansoni/genetics ; *Snails/parasitology/genetics ; Phylogeny ; Evolution, Molecular ; },
abstract = {In eukaryotes, horizontal gene transfer (HGT) often involves transposable elements (TEs), host-parasite relationships, aquatic environments, or any of them combined. Horizontal transfer of transposable elements is both impactful, owing to the subsequent transposition burst, and insightful, providing information on organisms' evolutionary history. The flatworm Schistosoma mansoni is a human parasite with two free-living aquatic stages (intercalated between a definitive human host and intermediate snail host) and has a sizable TE content. We aimed to identify and characterize potential instances of HGT leveraging new genomic resources available. Using the latest chromosome-scale genome assembly and available TE sequences for the S. mansoni genome, we identify that two TEs, named Perere-3 and Sr3, are putatively horizontally transferred. We demonstrate the presence of these TEs in the genomes of Schistosoma spp. intermediate hosts, most likely explained by HGT. Perere-3/Sr3 were also found across a wide range of additional organisms not susceptible to schistosome infection, including turtles, fish, and other mollusks. We propose that the patchy distribution of Perere-3/Sr3 across the phylogenetic tree is best explained by HGT. Our synonymous substitution calculations further support HGT, as divergence between schistosome and snail TE sequences is markedly lower than that observed for conserved orthologous genes. We propose that HGT is likely linked to schistosomes' parasitic nature as several snail species sharing the elements are susceptible to infection. However, the rationale for the presence of Perere-3/Sr3 in species beyond this relationship is unknown.},
}

Animals
*Gene Transfer, Horizontal
*DNA Transposable Elements
*Host-Parasite Interactions/genetics
*Schistosoma mansoni/genetics
*Snails/parasitology/genetics
Phylogeny
Evolution, Molecular

@article {pmid42102708,
year = {2026},
author = {Deng, WK and Deng, YH and Xie, SY and Chen, JY and Xing, SC and Liao, XD},
title = {Doxycycline-induced toxic perturbations on manure GHG potential: Phage-microbe interactions and BSF pretreatment mitigation.},
journal = {Ecotoxicology and environmental safety},
volume = {318},
number = {},
pages = {120204},
doi = {10.1016/j.ecoenv.2026.120204},
pmid = {42102708},
issn = {1090-2414},
abstract = {The large-scale production of poultry manure poses significant environmental safety challenges, and Black Soldier Fly (BSF) has emerged as a potential resource utilization solution. However, the toxicological effects of doxycycline (DOX) contamination in poultry feces on methane (CH4) and nitrous oxide (N2O) emission potential throughout the BSF manure recycling process remains unclear, especially from a phage-microbe interaction perspective. This study investigates the roles of bacterial and phage-related functional genes associated with CH4 and N2O metabolism in the "chicken manure-organic fertilizer" and "chicken manure-BSF-chicken" pathways. The results reveal that DOX in poultry manure causes toxicological perturbations of the microbial community, significantly elevating the levels of key functional genes (mcrA/pmoA and (nirS+nirK)/nosZ) linked to GHG emission potential. These DOX-induced elevated gene levels persisted in BSF-derived organic fertilizer and in the feces of laying hens fed BSF reared on contaminated manure. However, 24-hour starvation pretreatment combined with 8-hour drying at 65 °C can effectively alleviate the negative toxicological effects induced by DOX, and the emission potentials of CH4 and N2O in the feces of laying hens fed BSF treated in this way were reduced by 91.1% and 82.4%, respectively. Importantly, phage-mediated horizontal gene transfer (HGT) plays a significant regulatory role in these gene changes, further amplifying the DOX-induced GHG emission risk. This study highlights the potential of BSF pretreatment to reduce the environmental risk of antibiotic-contaminated poultry manure while addressing climate concerns from an environmental toxicology perspective. It also provides a scalable toxicological risk mitigation strategy to reduce greenhouse gas emission potential in poultry farming systems, which is of great significance for the environmental safety of intensive poultry production.},
}

@article {pmid42090264,
year = {2026},
author = {Dubinkina, V and Smith, BJ and Zhao, C and Pino, C and Pollard, KS},
title = {Linkage of nucleotide and functional diversity varies across gut bacteria.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {19},
pages = {e2521012123},
doi = {10.1073/pnas.2521012123},
pmid = {42090264},
issn = {1091-6490},
support = {R01HL160862//HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; //San Simeon fund/ ; //Chan Zuckerberg Biohub/ ; predoctoral fellowship//NSF (NSF)/ ; PHY-2309135//NSF (NSF)/ ; 2919.02//Gordon and Betty Moore Foundation (GBMF)/ ; },
mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; Polymorphism, Single Nucleotide ; *Bacteria/genetics/classification ; Genome, Bacterial ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genetic Linkage ; Genetic Variation ; },
abstract = {Understanding the forces shaping genomic diversity within bacterial species is essential for interpreting microbiome evolution, ecology, and host associations. Here, we analyze over one hundred prevalent gut bacterial species using the Unified Human Gut Genome collection to characterize patterns of intraspecific genomic variability. Gene content divergence scales predictably with divergence in core genome single nucleotide polymorphisms (SNPs), though there is substantial variability in evolutionary dynamics across species. Overall, accessory genes exhibit consistently faster linkage decay compared to core SNPs, highlighting the fluidity of functional repertoires within species boundaries. This signal is strongest for mobile genetic elements, which show minimal linkage to core genome SNPs. Together, our findings reveal species-specific recombination regimes in the gut microbiome, underscoring the importance of accounting for horizontal gene transfer and genome plasticity in microbiome-wide association studies and evolutionary models.},
}

*Gastrointestinal Microbiome/genetics
Humans
Polymorphism, Single Nucleotide
*Bacteria/genetics/classification
Genome, Bacterial
Evolution, Molecular
Gene Transfer, Horizontal
*Genetic Linkage
Genetic Variation

@article {pmid42090770,
year = {2026},
author = {Zhou, L and Xie, J and Zhang, L and Sui, X and Wang, W and Huang, J and Wu, S and Cui, N and He, S and Cheng, S},
title = {Decoding the effect of intermittent feeding strategy on the performances of modular moving bed constructed wetland: Nitrogen removal and antimicrobial resistance dissemination.},
journal = {Journal of hazardous materials},
volume = {511},
number = {},
pages = {142288},
doi = {10.1016/j.jhazmat.2026.142288},
pmid = {42090770},
issn = {1873-3336},
abstract = {Constructed wetlands (CWs) are widely applied for advanced treatment of wastewater treatment plant effluents, and their pollutant removal performance are closely related to the internal oxygen conditions. This study investigated the effect of intermittent feeding strategy (an oxygen regulation strategy) on nitrogen removal performance under antibiotic stress and the fate of antibiotic resistance genes (ARGs) in a newly designed modular moving bed constructed wetland (MMB-CW). The results showed that the intermittent feeding strategy significantly increased ammonium removal by 17.0% (p < 0.05) and maintaining a stable nitrate removal efficiency of 96.4%. The improved performance was primarily attributed to the enrichment of the aerobic denitrifier Thauera and genes napAB, which restructured nitrogen metabolic pathways and alleviated the antibiotic inhibition. However, compared with continuous feeding, intermittent feeding drove a significant absolute increase of 1324.6 TPM in total ARG abundance (p < 0.05). The increased abundance of mobile genetic elements (MGEs) and their positive correlation with that of ARGs indicated enhanced horizontal gene transfer (HGT) driven by MGEs. Intermittent feeding further increased the abundance of genes encoding key functional profiles involved in antioxidative system, SOS repair, membrane permeability, adenosine triphosphate synthesis, extracellular polymeric substance secretion, and signal transduction. These changes in cellular behavior together with the increased abundance of genes related to the competence pseudopilus of bacteria, collectively formed the physiological basis driving HGT of ARGs through bacterial transformation. This study systematically revealed the dual-edged effect of intermittent feeding strategy on the MMB-CW, providing critical performance- and ecological risk-based insights for oxygen regulation strategies in CWs.},
}

@article {pmid42092050,
year = {2026},
author = {Minton, K},
title = {T cell-derived extracellular vesicles promote antitumour immunity through horizontal gene transfer.},
journal = {Nature reviews. Immunology},
volume = {},
number = {},
pages = {},
pmid = {42092050},
issn = {1474-1741},
}

@article {pmid42092359,
year = {2026},
author = {Gluth, A and Zmasek, C and Chiu, S and Moon, TS},
title = {Resilience of recombinant antibiotic resistance gene-containing plasmids against common cell culture disposal methods.},
journal = {Cell reports methods},
volume = {},
number = {},
pages = {101430},
doi = {10.1016/j.crmeth.2026.101430},
pmid = {42092359},
issn = {2667-2375},
abstract = {Antibiotics have saved an untold number of people and animals since penicillin's miraculous discovery in 1928. In the following half-century, progressive discoveries involving antibiotic resistance genes (ARGs), the microorganisms responsible, and their transferrable genetic material have yielded the tools necessary for genetic engineering, birthing the biotechnologies that continue to revolutionize healthcare. After half a century of antibiotic use in the biological sciences, we are, however, faced with an inconvenient question: what happens to residual antibiotics and ARG-containing recombinant DNA after experiments? According to sequencing, we demonstrate that neither severe bleach treatments nor autoclaving completely destroys plasmid-encoded ARGs in bacterial cultures. Furthermore, we show that various bacteria can be transformed using the isolated DNA, confirming that intact plasmids survived these common cell culture disposal methods. This work will catalyze future policy discussions, the development of antibiotic-free selection systems, and continued support for research into the underexplored anthropogenic sources of engineered DNA.},
}

@article {pmid42092531,
year = {2026},
author = {Merlo Kava, V and Ferreira, PC and Galli, LV and Ordonez, J and Mariano, AB and Vargas, JVC},
title = {A Constructal Law interpretation of species variability: Insights from microalgae.},
journal = {Bio Systems},
volume = {},
number = {},
pages = {105809},
doi = {10.1016/j.biosystems.2026.105809},
pmid = {42092531},
issn = {1872-8324},
abstract = {The Constructal Law provides a physical perspective for interpreting evolutionary change as a continuous reorganization of structures that facilitate the flow of energy, matter, and information. In living systems, these flows are inherently coupled, as cellular responses to environmental change depend on the integration of metabolic processes with regulatory and informational networks. Microalgae, with short generation times and diverse evolutionary lineages, are ideal models to explore this principle. This study reanalyzes three previously published experimental investigations on eukaryotic microalgae: the diatom Phaeodactylum tricornutum (Stramenopiles), the coccolithophore Emiliania huxleyi (Haptophytes), and Picochlorum species (Archaeplastida). Their reported evolutionary, physiological, metabolic, morphological, and genomic responses are interpreted through the lens of constructal design. In P. tricornutum, adaptation to elevated CO2 and warming involved coordinated reorganization of metabolic pathways, including respiration, the tricarboxylic acid cycle, lipid metabolism, and protein ubiquitination, reflecting internal configurations that enhance the flow of carbon, energy, electrons, and the regulatory information that coordinates these processes. E. huxleyi displayed complex, sometimes reversible, changes in cell size and calcification under long-term acidification, illustrating trade-offs in energy and material flow. In Picochlorum, genomic plasticity, gene gain and loss, allelic diversity, and horizontal gene transfer provided alternative routes for metabolic flux, demonstrating the genome as a flow-oriented network. Across these phylogenetically distant taxa, adaptive responses show that evolutionary processes can be understood as the reorganization of internal and external flows, consistent with the Constructal Law. This integrative perspective links biological natural selection to physical principles, offering a novel framework for interpreting species variability and adaptive potential in microalgae and beyond.},
}

@article {pmid41851125,
year = {2026},
author = {Zhu, D and Zhang, W and Balcazar, JL and Wang, D and Sun, M and Hu, F and Penuelas, J and Zhu, YG},
title = {The hidden role of rhizospheric viruses in promoting nitrogen fixation in soils.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {41851125},
issn = {2041-1723},
support = {42277115//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Nitrogen Fixation/genetics ; *Soil Microbiology ; *Rhizosphere ; Soil/chemistry ; Gene Transfer, Horizontal ; Nitrogenase/metabolism/genetics ; Azotobacter/genetics/virology/metabolism ; Azospirillum/virology/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; },
abstract = {Biological nitrogen fixation is a cornerstone of terrestrial nitrogen cycling, traditionally attributed to bacterial nitrogenase activity. However, the potential contribution of rhizospheric viruses remains largely unexplored. Here, we reveal the global distribution of nitrogen-fixing genes, with widespread detection of nifA, nifL, nifU, and nifH in both bacteria and viruses, and identify nifU as a viral auxiliary metabolic gene (AMG). Analysis of viral communities in rhizosphere and bulk soils cultivated with cowpea showed that viral nifU expression was significantly upregulated in rhizosphere soils. Using [15]N2 stable-isotope tracing and virus transplantation experiments, we demonstrate that virus-encoded nitrogen-fixing AMGs, horizontally transferred from bacteria such as Azospirillum thermophilum (70-99% homology), increased nitrogenase activity from 1.79 to 3.14 nmol C2H4 g[-1] dry soil h[-1]. This enhancement was accompanied by shifts in bacterial community composition, with the relative abundance of the nitrogen-fixing genus Azotobacter reaching 90.8%. These results uncover a previously hidden role of rhizospheric viruses in promoting bacterial nitrogen fixation, suggesting that viral-mediated gene transfer could be leveraged to enhance nitrogen cycling in soils and inform sustainable soil management strategies.},
}

*Nitrogen Fixation/genetics
*Soil Microbiology
*Rhizosphere
Soil/chemistry
Gene Transfer, Horizontal
Nitrogenase/metabolism/genetics
Azotobacter/genetics/virology/metabolism
Azospirillum/virology/genetics/metabolism
Bacterial Proteins/genetics/metabolism

@article {pmid42084611,
year = {2026},
author = {Wada, T and Inoue, H and Yoshida, S and Murase, Y and Igarashi, Y and Fukushima, Y and Nakajima, C and Suzuki, Y and Mitarai, S},
title = {Genomic comparison of clinical strains of Mycobacterium shinjukuense in Japan reveals low diversity and stable genome structures.},
journal = {Microbial genomics},
volume = {12},
number = {5},
pages = {},
pmid = {42084611},
issn = {2057-5858},
mesh = {Japan ; Phylogeny ; Humans ; *Genome, Bacterial ; Whole Genome Sequencing ; *Genetic Variation ; Mycobacterium tuberculosis/genetics ; *Mycobacterium Infections, Nontuberculous/microbiology ; *Nontuberculous Mycobacteria/genetics/classification/isolation & purification ; Gene Transfer, Horizontal ; Genomics ; Evolution, Molecular ; Polymorphism, Single Nucleotide ; *Mycobacterium/genetics/classification ; },
abstract = {Mycobacterium shinjukuense, a rare non-tuberculous mycobacterial species closely related to Mycobacterium tuberculosis, remains poorly characterized at the genomic level. To obtain insights into its intraspecies genomic diversity and structure variation, we performed whole-genome sequencing on 18 clinical strains of M. shinjukuense collected from Japan between 2010 and 2017. Phylogenetic analysis revealed limited overall genetic diversity, with several clonal clusters likely representing identical strains. The phylogeny exhibited a largely star-like topology with few single nucleotide variations accumulated over time, suggesting a clonal expansion. Complete genome sequencing of five representative strains revealed high synteny, with no large-scale rearrangements, suggesting stable genomic structures. One strain, MSJ-01, harboured a unique 30 kb insertion region, possibly acquired via horizontal gene transfer. These findings provide insights into the genomic diversity and structure of M. shinjukuense, suggesting both its evolutionary stability and its potential to incorporate foreign DNA. This work expands upon available genomic resources and supports the utility of M. shinjukuense as a model for understanding genome evolution in the M. tuberculosis-associated phylotype lineage.},
}

Japan
Phylogeny
Humans
*Genome, Bacterial
Whole Genome Sequencing
*Genetic Variation
Mycobacterium tuberculosis/genetics
*Mycobacterium Infections, Nontuberculous/microbiology
*Nontuberculous Mycobacteria/genetics/classification/isolation & purification
Gene Transfer, Horizontal
Genomics
Evolution, Molecular
Polymorphism, Single Nucleotide
*Mycobacterium/genetics/classification

@article {pmid42086631,
year = {2026},
author = {Moon, K and Kang, I and Cho, JC},
title = {Virome datasets and viral metagenome-assembled genomes from aquaculture-impacted freshwater environments.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-07383-0},
pmid = {42086631},
issn = {2052-4463},
support = {NRF-2022R1A2C3008502//National Research Foundation of Korea (NRF)/ ; NA//Hankuk University of Foreign Studies (HUFS)/ ; },
abstract = {Bacteriophages in natural environments play a critical role in microbial ecology by regulating bacterial populations, mediating nutrient cycling, and facilitating horizontal gene transfer. Aquaculture operations, particularly inland fish farms, are major sources of anthropogenic influence on freshwater ecosystems. Here, we present three viral metagenomic datasets derived from freshwater samples collected at an inland aquaculture effluent site and adjacent upstream and downstream locations along the Sung-am River in Jincheon County, South Korea. The datasets were generated using the Illumina HiSeq X sequencing platform, yielding approximately 10.0-11.2 Gbp per sample. Quality assessments confirmed minimal bacterial contamination, with negligible proportions of rRNA and bacterial marker genes. Assembly using metaSPAdes and MEGAHIT, application of Phables to resolve high-quality phage genomes (viral metagenome-assembled genomes; vMAGs), viral identification with VirSorter2, and clustering using Vclust, resulted in 2,837-3,156 virus operational taxonomic units (vOTUs; ≥10 kb) per sample. Each vOTU sequence is analyzed for taxonomic assignment and putative host prediction. These datasets provide a valuable resource for further studies on viral diversity and microbial ecology in freshwater ecosystems affected by aquaculture.},
}